diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,7 +1,13 @@ Revision history for haskell-igraph =================================== -v0.8.0 -- XXXX-XX-XX +v0.8.5 -- 2025-08-05 +-------------------- + +* Ship igraph C sources v0.8.5 +* Add more functions + +v0.8.0 -- 2020-02-22 -------------------- * Ship igraph C sources v0.8.0 diff --git a/LICENSE b/LICENSE --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright (c) 2016-2020 Kai Zhang +Copyright (c) 2016-2021 Kai Zhang Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the diff --git a/cbits/bytestring.c b/cbits/bytestring.c --- a/cbits/bytestring.c +++ b/cbits/bytestring.c @@ -342,7 +342,7 @@ igraph_strvector_t *str; size_t i; igraph_strvector_init(str, from->len); - for (i = 0; i++; i < from->len) { + for (i = 0; i < from->len; i++) { igraph_strvector_set(str, i, bytestring_to_char(from->data[i])); } return str; @@ -352,7 +352,7 @@ bsvector_t *str; size_t i; bsvector_init(str, from->len); - for (i = 0; i++; i < from->len) { + for (i = 0; i < from->len; i++) { bsvector_set(str, i, char_to_bytestring(from->data[i])); } return str; diff --git a/cbits/bytestring.h b/cbits/bytestring.h new file mode 100644 --- /dev/null +++ b/cbits/bytestring.h @@ -0,0 +1,115 @@ +#ifndef HASKELL_IGRAPH_BYTESTRING +#define HASKELL_IGRAPH_BYTESTRING + +#include "igraph.h" + +__BEGIN_DECLS + +typedef struct bytestring_t { + unsigned long int len; + char *value; +} bytestring_t; + +typedef struct bsvector_t { + bytestring_t **data; + long int len; +} bsvector_t; + +#define BSVECTOR_INIT_FINALLY(v, size) \ + do { IGRAPH_CHECK(bsvector_init(v, size)); \ + IGRAPH_FINALLY(bsvector_destroy, v); } while (0) + +/** + * \define STR + * Indexing string vectors + * + * This is a macro which allows to query the elements of a string vector in + * simpler way than \ref igraph_strvector_get(). Note this macro cannot be + * used to set an element, for that use \ref igraph_strvector_set(). + * \param sv The string vector + * \param i The the index of the element. + * \return The element at position \p i. + * + * Time complexity: O(1). + */ +#define BS(sv,i) ((const bytestring_t *)((sv).data[(i)])) + +int bsvector_init(bsvector_t *sv, long int len); + +DECLDIR void bsvector_destroy(bsvector_t *sv); + +DECLDIR void bsvector_get(const bsvector_t *sv, long int idx, bytestring_t **value); + +DECLDIR int bsvector_set(bsvector_t *sv, long int idx, const bytestring_t *value); + +DECLDIR void bsvector_remove_section(bsvector_t *v, long int from, long int to); + +DECLDIR void bsvector_remove(bsvector_t *v, long int elem); + +/* +void bsvector_move_interval(bsvector_t *v, long int begin, + long int end, long int to) { + long int i; + assert(v != 0); + assert(v->data != 0); + for (i=to; idata[i] != 0) { + destroy_bytestring(v->data[i]); + } + } + for (i=0; idata[begin+i] != 0) { + size_t len=strlen(v->data[begin+i])+1; + v->data[to+i]=igraph_Calloc(len, char); + memcpy(v->data[to+i], v->data[begin+i], sizeof(char)*len); + } + } +} +*/ + +int bsvector_copy(bsvector_t *to, const bsvector_t *from); + +int bsvector_append(bsvector_t *to, const bsvector_t *from); + +void bsvector_clear(bsvector_t *sv); + +int bsvector_resize(bsvector_t* v, long int newsize); + +/** + * \ingroup strvector + * \function igraph_strvector_permdelete + * \brief Removes elements from a string vector (for internal use) + */ + +void bsvector_permdelete(bsvector_t *v, const igraph_vector_t *index, + long int nremove); + +/** + * \ingroup strvector + * \function igraph_strvector_remove_negidx + * \brief Removes elements from a string vector (for internal use) + */ + +void bsvector_remove_negidx(bsvector_t *v, const igraph_vector_t *neg, + long int nremove); + +int bsvector_index(const bsvector_t *v, bsvector_t *newv, + const igraph_vector_t *idx); + +long int bsvector_size(const bsvector_t *sv); + +bytestring_t* new_bytestring(int n); + +void destroy_bytestring(bytestring_t* str); + +char* bytestring_to_char(bytestring_t* from); + +bytestring_t* char_to_bytestring(char* from); + +igraph_strvector_t* bsvector_to_strvector(bsvector_t* from); + +bsvector_t* strvector_to_bsvector(igraph_strvector_t* from); + +__END_DECLS + +#endif diff --git a/cbits/haskell_attributes.c b/cbits/haskell_attributes.c --- a/cbits/haskell_attributes.c +++ b/cbits/haskell_attributes.c @@ -466,8 +466,6 @@ } if (oldrec->type == IGRAPH_ATTRIBUTE_STRING) { if (ne != bsvector_size(newstr)) { - printf("number of edges: %d\n", ne); - printf("number of attributes: %d\n", bsvector_size(newstr)); IGRAPH_ERROR("Invalid string attribute length", IGRAPH_EINVAL); } IGRAPH_CHECK(bsvector_append(oldstr, newstr)); diff --git a/cbits/haskell_attributes.h b/cbits/haskell_attributes.h new file mode 100644 --- /dev/null +++ b/cbits/haskell_attributes.h @@ -0,0 +1,218 @@ +#ifndef HASKELL_IGRAPH_ATTRIBUTE +#define HASKELL_IGRAPH_ATTRIBUTE + +#include "igraph.h" +#include "bytestring.h" + +#include + +igraph_bool_t igraph_haskell_attribute_find(const igraph_vector_ptr_t *ptrvec, + const char *name, long int *idx); + +typedef struct igraph_haskell_attributes_t { + igraph_vector_ptr_t gal; + igraph_vector_ptr_t val; + igraph_vector_ptr_t eal; +} igraph_haskell_attributes_t; + +int igraph_haskell_attributes_copy_attribute_record(igraph_attribute_record_t **newrec, + const igraph_attribute_record_t *rec); + + +int igraph_haskell_attribute_init(igraph_t *graph, igraph_vector_ptr_t *attr); + +void igraph_haskell_attribute_destroy(igraph_t *graph); + +void igraph_haskell_attribute_copy_free(igraph_haskell_attributes_t *attr); + +int igraph_haskell_attribute_copy(igraph_t *to, const igraph_t *from, + igraph_bool_t ga, igraph_bool_t va, igraph_bool_t ea); + +int igraph_haskell_attribute_add_vertices(igraph_t *graph, long int nv, + igraph_vector_ptr_t *nattr); + +void igraph_haskell_attribute_permute_free(igraph_vector_ptr_t *v); + +int igraph_haskell_attribute_permute_vertices(const igraph_t *graph, + igraph_t *newgraph, + const igraph_vector_t *idx); + +int igraph_haskell_attribute_combine_vertices(const igraph_t *graph, + igraph_t *newgraph, + const igraph_vector_ptr_t *merges, + const igraph_attribute_combination_t *comb); + +int igraph_haskell_attribute_add_edges(igraph_t *graph, const igraph_vector_t *edges, + igraph_vector_ptr_t *nattr); + +int igraph_haskell_attribute_permute_edges(const igraph_t *graph, + igraph_t *newgraph, + const igraph_vector_t *idx); + +int igraph_haskell_attribute_combine_edges(const igraph_t *graph, + igraph_t *newgraph, + const igraph_vector_ptr_t *merges, + const igraph_attribute_combination_t *comb); + +int igraph_haskell_attribute_get_info(const igraph_t *graph, + igraph_strvector_t *gnames, + igraph_vector_t *gtypes, + igraph_strvector_t *vnames, + igraph_vector_t *vtypes, + igraph_strvector_t *enames, + igraph_vector_t *etypes); + +igraph_bool_t igraph_haskell_attribute_has_attr(const igraph_t *graph, + igraph_attribute_elemtype_t type, + const char *name); + +int igraph_haskell_attribute_gettype(const igraph_t *graph, + igraph_attribute_type_t *type, + igraph_attribute_elemtype_t elemtype, + const char *name); + +int igraph_haskell_attribute_get_numeric_graph_attr(const igraph_t *graph, + const char *name, + igraph_vector_t *value); + +int igraph_haskell_attribute_get_bool_graph_attr(const igraph_t *graph, + const char *name, + igraph_vector_bool_t *value); + +int igraph_haskell_attribute_get_string_graph_attr(const igraph_t *graph, + const char *name, + igraph_strvector_t *value_); + +int igraph_haskell_attribute_get_numeric_vertex_attr(const igraph_t *graph, + const char *name, + igraph_vs_t vs, + igraph_vector_t *value); + +int igraph_haskell_attribute_get_bool_vertex_attr(const igraph_t *graph, + const char *name, + igraph_vs_t vs, + igraph_vector_bool_t *value); + +int igraph_haskell_attribute_get_string_vertex_attr(const igraph_t *graph, + const char *name, + igraph_vs_t vs, + igraph_strvector_t *value_); + +int igraph_haskell_attribute_get_numeric_edge_attr(const igraph_t *graph, + const char *name, + igraph_es_t es, + igraph_vector_t *value); + +int igraph_haskell_attribute_get_string_edge_attr(const igraph_t *graph, + const char *name, + igraph_es_t es, + igraph_strvector_t *value_); + +int igraph_haskell_attribute_get_bool_edge_attr(const igraph_t *graph, + const char *name, + igraph_es_t es, + igraph_vector_bool_t *value); + +igraph_real_t igraph_haskell_attribute_GAN(const igraph_t *graph, const char *name); + +igraph_bool_t igraph_haskell_attribute_GAB(const igraph_t *graph, const char *name); + +const bytestring_t* igraph_haskell_attribute_GAS(const igraph_t *graph, const char *name); + +igraph_real_t igraph_haskell_attribute_VAN(const igraph_t *graph, const char *name, + igraph_integer_t vid); + +igraph_bool_t igraph_haskell_attribute_VAB(const igraph_t *graph, const char *name, + igraph_integer_t vid); + +const bytestring_t* igraph_haskell_attribute_VAS(const igraph_t *graph, const char *name, + igraph_integer_t vid); + +igraph_real_t igraph_haskell_attribute_EAN(const igraph_t *graph, const char *name, + igraph_integer_t eid); + +igraph_bool_t igraph_haskell_attribute_EAB(const igraph_t *graph, const char *name, + igraph_integer_t eid); + +const bytestring_t* igraph_haskell_attribute_EAS(const igraph_t *graph, const char *name, + igraph_integer_t eid); + +int igraph_haskell_attribute_VANV(const igraph_t *graph, const char *name, + igraph_vs_t vids, igraph_vector_t *result); + +int igraph_haskell_attribute_VABV(const igraph_t *graph, const char *name, + igraph_vs_t vids, igraph_vector_bool_t *result); + +int igraph_haskell_attribute_EANV(const igraph_t *graph, const char *name, + igraph_es_t eids, igraph_vector_t *result); + +int igraph_haskell_attribute_EABV(const igraph_t *graph, const char *name, + igraph_es_t eids, igraph_vector_bool_t *result); + +int igraph_haskell_attribute_VASV(const igraph_t *graph, const char *name, + igraph_vs_t vids, igraph_strvector_t *result); + +int igraph_haskell_attribute_EASV(const igraph_t *graph, const char *name, + igraph_es_t eids, igraph_strvector_t *result); + +int igraph_haskell_attribute_list(const igraph_t *graph, + igraph_strvector_t *gnames, igraph_vector_t *gtypes, + igraph_strvector_t *vnames, igraph_vector_t *vtypes, + igraph_strvector_t *enames, igraph_vector_t *etypes); + +int igraph_haskell_attribute_GAN_set(igraph_t *graph, const char *name, + igraph_real_t value); + +int igraph_haskell_attribute_GAB_set(igraph_t *graph, const char *name, + igraph_bool_t value); + +int igraph_haskell_attribute_GAS_set(igraph_t *graph, const char *name, + const bytestring_t *value); + +int igraph_haskell_attribute_VAN_set(igraph_t *graph, const char *name, + igraph_integer_t vid, igraph_real_t value); + +int igraph_haskell_attribute_VAB_set(igraph_t *graph, const char *name, + igraph_integer_t vid, igraph_bool_t value); + +int igraph_haskell_attribute_VAS_set(igraph_t *graph, const char *name, + igraph_integer_t vid, const bytestring_t *value); + +int igraph_haskell_attribute_EAN_set(igraph_t *graph, const char *name, + igraph_integer_t eid, igraph_real_t value); + +int igraph_haskell_attribute_EAB_set(igraph_t *graph, const char *name, + igraph_integer_t eid, igraph_bool_t value); + +int igraph_haskell_attribute_EAS_set(igraph_t *graph, const char *name, + igraph_integer_t eid, const bytestring_t *value); + +int igraph_haskell_attribute_VAN_setv(igraph_t *graph, const char *name, + const igraph_vector_t *v); + +int igraph_haskell_attribute_VAB_setv(igraph_t *graph, const char *name, + const igraph_vector_bool_t *v); + +int igraph_haskell_attribute_VAS_setv(igraph_t *graph, const char *name, + const bsvector_t *sv); + +int igraph_haskell_attribute_EAN_setv(igraph_t *graph, const char *name, + const igraph_vector_t *v); + +int igraph_haskell_attribute_EAB_setv(igraph_t *graph, const char *name, + const igraph_vector_bool_t *v); + +int igraph_haskell_attribute_EAS_setv(igraph_t *graph, const char *name, + const bsvector_t *sv); + +void igraph_haskell_attribute_free_rec(igraph_attribute_record_t *rec); + +void igraph_haskell_attribute_remove_g(igraph_t *graph, const char *name); + +void igraph_haskell_attribute_remove_v(igraph_t *graph, const char *name); + +void igraph_haskell_attribute_remove_e(igraph_t *graph, const char *name); + +void igraph_haskell_attribute_remove_all(igraph_t *graph, igraph_bool_t g, + igraph_bool_t v, igraph_bool_t e); +#endif diff --git a/cbits/haskell_igraph.h b/cbits/haskell_igraph.h new file mode 100644 --- /dev/null +++ b/cbits/haskell_igraph.h @@ -0,0 +1,8 @@ +#ifndef HASKELL_IGRAPH +#define HASKELL_IGRAPH + +#include "igraph.h" + +void haskelligraph_init(); + +#endif diff --git a/haskell-igraph.cabal b/haskell-igraph.cabal --- a/haskell-igraph.cabal +++ b/haskell-igraph.cabal @@ -1,653 +1,860 @@ -cabal-version: 2.2 -name: haskell-igraph -version: 0.8.0 -synopsis: Bindings to the igraph C library (v0.8.0). -description: igraph<"http://igraph.org/c/"> is a library for creating - and manipulating large graphs. This package provides the Haskell - interface of igraph. -license: MIT -license-file: LICENSE -author: Kai Zhang -maintainer: kai@kzhang.org -copyright: (c) 2016-2020 Kai Zhang -category: Math -build-type: Simple -extra-source-files: - include/*.h - igraph/include/*.h - igraph/include/*.pmt - igraph/include/f2c/*.h - igraph/include/prpack/*.h - igraph/include/cs/*.h - igraph/include/cliquer/*.h - igraph/include/bliss/*.hh - igraph/include/plfit/*.h - igraph/AUTHORS - igraph/COPYING - stack.yaml - README.md - ChangeLog.md - -library - exposed-modules: - IGraph.Internal.Initialization - IGraph.Internal.Constants - IGraph.Internal - IGraph - IGraph.Mutable - IGraph.Random - IGraph.Types - IGraph.Algorithms - IGraph.Algorithms.Structure - IGraph.Algorithms.Community - IGraph.Algorithms.Clique - --IGraph.Algorithms.Layout - IGraph.Algorithms.Motif - IGraph.Algorithms.Generators - IGraph.Algorithms.Isomorphism - IGraph.Algorithms.Centrality - - other-modules: - IGraph.Internal.C2HS - - build-depends: - base >= 4.0 && < 5.0 - , bytestring >= 0.9 - , cereal - , conduit >= 1.3.0 - , containers - , data-ordlist - , primitive - , singletons - - extra-libraries: stdc++ - hs-source-dirs: src - default-language: Haskell2010 - ghc-options: -Wall - build-tool-depends: c2hs:c2hs >=0.25.0 - c-sources: - cbits/haskell_igraph.c - cbits/haskell_attributes.c - cbits/bytestring.c - - -- igraph - igraph/src/abort_.c - igraph/src/adjlist.c - igraph/src/arithchk.c - igraph/src/arpack.c - igraph/src/array.c - igraph/src/atlas.c - igraph/src/attributes.c - igraph/src/backspac.c - igraph/src/basic_query.c - igraph/src/bfgs.c - igraph/src/bigint.c - igraph/src/bignum.c - igraph/src/bipartite.c - igraph/src/blas.c - igraph/src/c_abs.c - igraph/src/cabs.c - igraph/src/cattributes.c - igraph/src/c_cos.c - igraph/src/c_div.c - igraph/src/centrality.c - igraph/src/c_exp.c - igraph/src/cliquer.c - igraph/src/cliquer_graph.c - igraph/src/cliques.c - igraph/src/c_log.c - igraph/src/close.c - igraph/src/cocitation.c - igraph/src/cohesive_blocks.c - igraph/src/coloring.c - igraph/src/community.c - igraph/src/community_leiden.c - igraph/src/complex.c - igraph/src/components.c - igraph/src/conversion.c - igraph/src/cores.c - igraph/src/cs_add.c - igraph/src/cs_amd.c - igraph/src/cs_chol.c - igraph/src/cs_cholsol.c - igraph/src/cs_compress.c - igraph/src/cs_counts.c - igraph/src/cs_cumsum.c - igraph/src/cs_dfs.c - igraph/src/cs_dmperm.c - igraph/src/cs_droptol.c - igraph/src/cs_dropzeros.c - igraph/src/cs_dupl.c - igraph/src/cs_entry.c - igraph/src/cs_ereach.c - igraph/src/cs_etree.c - igraph/src/cs_fkeep.c - igraph/src/cs_gaxpy.c - igraph/src/cs_happly.c - igraph/src/cs_house.c - igraph/src/c_sin.c - igraph/src/cs_ipvec.c - igraph/src/cs_leaf.c - igraph/src/cs_load.c - igraph/src/cs_lsolve.c - igraph/src/cs_ltsolve.c - igraph/src/cs_lu.c - igraph/src/cs_lusol.c - igraph/src/cs_malloc.c - igraph/src/cs_maxtrans.c - igraph/src/cs_multiply.c - igraph/src/cs_norm.c - igraph/src/cs_permute.c - igraph/src/cs_pinv.c - igraph/src/cs_post.c - igraph/src/cs_print.c - igraph/src/cs_pvec.c - igraph/src/cs_qr.c - igraph/src/cs_qrsol.c - igraph/src/c_sqrt.c - igraph/src/cs_randperm.c - igraph/src/cs_reach.c - igraph/src/cs_scatter.c - igraph/src/cs_scc.c - igraph/src/cs_schol.c - igraph/src/cs_spsolve.c - igraph/src/cs_sqr.c - igraph/src/cs_symperm.c - igraph/src/cs_tdfs.c - igraph/src/cs_transpose.c - igraph/src/cs_updown.c - igraph/src/cs_usolve.c - igraph/src/cs_util.c - igraph/src/cs_utsolve.c - igraph/src/ctype.c - igraph/src/d_abs.c - igraph/src/d_acos.c - igraph/src/d_asin.c - igraph/src/dasum.c - igraph/src/d_atan.c - igraph/src/d_atn2.c - igraph/src/daxpy.c - igraph/src/d_cnjg.c - igraph/src/dcopy.c - igraph/src/d_cos.c - igraph/src/d_cosh.c - igraph/src/d_dim.c - igraph/src/ddot.c - igraph/src/decomposition.c - igraph/src/derf_.c - igraph/src/derfc_.c - igraph/src/d_exp.c - igraph/src/dfe.c - igraph/src/dgebak.c - igraph/src/dgebal.c - igraph/src/dgeev.c - igraph/src/dgeevx.c - igraph/src/dgehd2.c - igraph/src/dgehrd.c - igraph/src/dgemm.c - igraph/src/dgemv.c - igraph/src/dgeqr2.c - igraph/src/dger.c - igraph/src/dgesv.c - igraph/src/dgetf2.c - igraph/src/dgetrf.c - igraph/src/dgetrs.c - igraph/src/dgetv0.c - igraph/src/dhseqr.c - igraph/src/d_imag.c - igraph/src/d_int.c - igraph/src/disnan.c - igraph/src/distances.c - igraph/src/dlabad.c - igraph/src/dlacn2.c - igraph/src/dlacpy.c - igraph/src/dladiv.c - igraph/src/dlae2.c - igraph/src/dlaebz.c - igraph/src/dlaev2.c - igraph/src/dlaexc.c - igraph/src/dlagtf.c - igraph/src/dlagts.c - igraph/src/dlahqr.c - igraph/src/dlahr2.c - igraph/src/dlaisnan.c - igraph/src/dlaln2.c - igraph/src/dlamch.c - igraph/src/dlaneg.c - igraph/src/dlange.c - igraph/src/dlanhs.c - igraph/src/dlanst.c - igraph/src/dlansy.c - igraph/src/dlanv2.c - igraph/src/dlapy2.c - igraph/src/dlaqr0.c - igraph/src/dlaqr1.c - igraph/src/dlaqr2.c - igraph/src/dlaqr3.c - igraph/src/dlaqr4.c - igraph/src/dlaqr5.c - igraph/src/dlaqrb.c - igraph/src/dlaqtr.c - igraph/src/dlar1v.c - igraph/src/dlarfb.c - igraph/src/dlarf.c - igraph/src/dlarfg.c - igraph/src/dlarft.c - igraph/src/dlarfx.c - igraph/src/dlarnv.c - igraph/src/dlarra.c - igraph/src/dlarrb.c - igraph/src/dlarrc.c - igraph/src/dlarrd.c - igraph/src/dlarre.c - igraph/src/dlarrf.c - igraph/src/dlarrj.c - igraph/src/dlarrk.c - igraph/src/dlarrr.c - igraph/src/dlarrv.c - igraph/src/dlartg.c - igraph/src/dlaruv.c - igraph/src/dlascl.c - igraph/src/dlaset.c - igraph/src/dlasq2.c - igraph/src/dlasq3.c - igraph/src/dlasq4.c - igraph/src/dlasq5.c - igraph/src/dlasq6.c - igraph/src/dlasr.c - igraph/src/dlasrt.c - igraph/src/dlassq.c - igraph/src/dlaswp.c - igraph/src/dlasy2.c - igraph/src/dlatrd.c - igraph/src/d_lg10.c - igraph/src/d_log.c - igraph/src/d_mod.c - igraph/src/dmout.c - igraph/src/dnaitr.c - igraph/src/dnapps.c - igraph/src/dnaup2.c - igraph/src/dnaupd.c - igraph/src/dnconv.c - igraph/src/dneigh.c - igraph/src/dneupd.c - igraph/src/dngets.c - igraph/src/d_nint.c - igraph/src/dnrm2.c - igraph/src/dolio.c - igraph/src/dorg2r.c - igraph/src/dorghr.c - igraph/src/dorgqr.c - igraph/src/dorm2l.c - igraph/src/dorm2r.c - igraph/src/dormhr.c - igraph/src/dormql.c - igraph/src/dormqr.c - igraph/src/dormtr.c - igraph/src/dotproduct.c - igraph/src/dpotf2.c - igraph/src/dpotrf.c - igraph/src/d_prod.c - igraph/src/dqueue.c - igraph/src/drot.c - igraph/src/dsaitr.c - igraph/src/dsapps.c - igraph/src/dsaup2.c - igraph/src/dsaupd.c - igraph/src/dscal.c - igraph/src/dsconv.c - igraph/src/dseigt.c - igraph/src/dsesrt.c - igraph/src/dseupd.c - igraph/src/dsgets.c - igraph/src/d_sign.c - igraph/src/d_sin.c - igraph/src/d_sinh.c - igraph/src/dsortc.c - igraph/src/dsortr.c - igraph/src/d_sqrt.c - igraph/src/dstatn.c - igraph/src/dstats.c - igraph/src/dstebz.c - igraph/src/dstein.c - igraph/src/dstemr.c - igraph/src/dsteqr.c - igraph/src/dsterf.c - igraph/src/dstqrb.c - igraph/src/dswap.c - igraph/src/dsyevr.c - igraph/src/dsymv.c - igraph/src/dsyr2.c - igraph/src/dsyr2k.c - igraph/src/dsyrk.c - igraph/src/dsytd2.c - igraph/src/dsytrd.c - igraph/src/d_tan.c - igraph/src/d_tanh.c - igraph/src/dtime_.c - igraph/src/dtrevc.c - igraph/src/dtrexc.c - igraph/src/dtrmm.c - igraph/src/dtrmv.c - igraph/src/dtrsen.c - igraph/src/dtrsm.c - igraph/src/dtrsna.c - igraph/src/dtrsv.c - igraph/src/dtrsyl.c - igraph/src/due.c - igraph/src/dummy.c - igraph/src/dvout.c - igraph/src/ef1asc_.c - igraph/src/ef1cmc_.c - igraph/src/eigen.c - igraph/src/embedding.c - igraph/src/endfile.c - igraph/src/erf_.c - igraph/src/erfc_.c - igraph/src/err.c - igraph/src/error.c - igraph/src/etime_.c - igraph/src/exit_.c - igraph/src/f77_aloc.c - igraph/src/f77vers.c - igraph/src/fast_community.c - igraph/src/feedback_arc_set.c - igraph/src/flow.c - igraph/src/fmt.c - igraph/src/fmtlib.c - igraph/src/foreign.c - igraph/src/foreign-dl-lexer.c - igraph/src/foreign-dl-parser.c - igraph/src/foreign-gml-lexer.c - igraph/src/foreign-gml-parser.c - igraph/src/foreign-graphml.c - igraph/src/foreign-lgl-lexer.c - igraph/src/foreign-lgl-parser.c - igraph/src/foreign-ncol-lexer.c - igraph/src/foreign-ncol-parser.c - igraph/src/foreign-pajek-lexer.c - igraph/src/foreign-pajek-parser.c - igraph/src/forestfire.c - igraph/src/fortran_intrinsics.c - igraph/src/ftell_.c - igraph/src/games.c - igraph/src/getenv_.c - igraph/src/glet.c - igraph/src/glpk_support.c - igraph/src/gml_tree.c - igraph/src/gss.c - igraph/src/h_abs.c - igraph/src/hacks.c - igraph/src/h_dim.c - igraph/src/h_dnnt.c - igraph/src/heap.c - igraph/src/h_indx.c - igraph/src/h_len.c - igraph/src/hl_ge.c - igraph/src/hl_gt.c - igraph/src/hl_le.c - igraph/src/hl_lt.c - igraph/src/h_mod.c - igraph/src/h_nint.c - igraph/src/h_sign.c - igraph/src/i77vers.c - igraph/src/i_abs.c - igraph/src/idamax.c - igraph/src/i_dim.c - igraph/src/i_dnnt.c - igraph/src/ieeeck.c - igraph/src/igraph_buckets.c - igraph/src/igraph_cliquer.c - igraph/src/igraph_error.c - igraph/src/igraph_estack.c - igraph/src/igraph_fixed_vectorlist.c - igraph/src/igraph_grid.c - igraph/src/igraph_hashtable.c - igraph/src/igraph_heap.c - igraph/src/igraph_marked_queue.c - igraph/src/igraph_psumtree.c - igraph/src/igraph_set.c - igraph/src/igraph_stack.c - igraph/src/igraph_strvector.c - igraph/src/igraph_trie.c - igraph/src/i_indx.c - igraph/src/iio.c - igraph/src/iladlc.c - igraph/src/iladlr.c - igraph/src/ilaenv.c - igraph/src/i_len.c - igraph/src/ilnw.c - igraph/src/i_mod.c - igraph/src/i_nint.c - igraph/src/inquire.c - igraph/src/interrupt.c - igraph/src/iparmq.c - igraph/src/i_sign.c - igraph/src/iterators.c - igraph/src/ivout.c - igraph/src/kolmogorov.c - igraph/src/lad.c - igraph/src/lapack.c - igraph/src/layout.c - igraph/src/layout_dh.c - igraph/src/layout_fr.c - igraph/src/layout_gem.c - igraph/src/layout_kk.c - igraph/src/lbfgs.c - igraph/src/lbitbits.c - igraph/src/lbitshft.c - igraph/src/len_trim.c - igraph/src/l_ge.c - igraph/src/l_gt.c - igraph/src/l_le.c - igraph/src/l_lt.c - igraph/src/lread.c - igraph/src/lsame.c - igraph/src/lsap.c - igraph/src/lwrite.c - igraph/src/matching.c - igraph/src/math.c - igraph/src/matrix.c - igraph/src/maximal_cliques.c - igraph/src/memory.c - igraph/src/microscopic_update.c - igraph/src/mixing.c - igraph/src/motifs.c - igraph/src/open.c - igraph/src/operators.c - igraph/src/optimal_modularity.c - igraph/src/options.c - igraph/src/other.c - igraph/src/paths.c - igraph/src/plfit.c - igraph/src/pow_ci.c - igraph/src/pow_dd.c - igraph/src/pow_di.c - igraph/src/pow_hh.c - igraph/src/pow_ii.c - igraph/src/pow_ri.c - igraph/src/pow_zi.c - igraph/src/pow_zz.c - igraph/src/progress.c - igraph/src/qsort.c - igraph/src/qsort_r.c - igraph/src/r_abs.c - igraph/src/r_acos.c - igraph/src/random.c - igraph/src/random_walk.c - igraph/src/r_asin.c - igraph/src/r_atan.c - igraph/src/r_atn2.c - igraph/src/r_cnjg.c - igraph/src/r_cos.c - igraph/src/r_cosh.c - igraph/src/rdfmt.c - igraph/src/r_dim.c - igraph/src/reorder.c - igraph/src/rewind.c - igraph/src/r_exp.c - igraph/src/r_imag.c - igraph/src/r_int.c - igraph/src/r_lg10.c - igraph/src/r_log.c - igraph/src/r_mod.c - igraph/src/r_nint.c - igraph/src/rsfe.c - igraph/src/r_sign.c - igraph/src/r_sin.c - igraph/src/r_sinh.c - igraph/src/rsli.c - igraph/src/rsne.c - igraph/src/r_sqrt.c - igraph/src/r_tan.c - igraph/src/r_tanh.c - igraph/src/sbm.c - igraph/src/scan.c - igraph/src/s_cat.c - igraph/src/scg_approximate_methods.c - igraph/src/scg.c - igraph/src/scg_exact_scg.c - igraph/src/scg_kmeans.c - igraph/src/scg_optimal_method.c - igraph/src/scg_utils.c - igraph/src/s_cmp.c - igraph/src/s_copy.c - igraph/src/second.c - igraph/src/separators.c - igraph/src/sfe.c - igraph/src/sig_die.c - igraph/src/signal_.c - igraph/src/signbit.c - igraph/src/sir.c - igraph/src/spanning_trees.c - igraph/src/sparsemat.c - igraph/src/s_paus.c - igraph/src/spectral_properties.c - igraph/src/spmatrix.c - igraph/src/s_rnge.c - igraph/src/s_stop.c - igraph/src/statusbar.c - igraph/src/st-cuts.c - igraph/src/structural_properties.c - igraph/src/structure_generators.c - igraph/src/sue.c - igraph/src/sugiyama.c - igraph/src/system_.c - igraph/src/topology.c - igraph/src/triangles.c - igraph/src/type_indexededgelist.c - igraph/src/types.c - igraph/src/typesize.c - igraph/src/uio.c - igraph/src/uninit.c - igraph/src/util.c - igraph/src/vector.c - igraph/src/vector_ptr.c - igraph/src/version.c - igraph/src/visitors.c - igraph/src/wref.c - igraph/src/wrtfmt.c - igraph/src/wsfe.c - igraph/src/wsle.c - igraph/src/wsne.c - igraph/src/xerbla.c - igraph/src/xwsne.c - igraph/src/z_abs.c - igraph/src/z_cos.c - igraph/src/z_div.c - igraph/src/zeroin.c - igraph/src/zeta.c - igraph/src/z_exp.c - igraph/src/z_log.c - igraph/src/z_sin.c - igraph/src/z_sqrt.c - - cxx-sources: - igraph/src/clustertool.cpp - igraph/src/degree_sequence.cpp - igraph/src/DensityGrid_3d.cpp - igraph/src/DensityGrid.cpp - igraph/src/drl_graph_3d.cpp - igraph/src/drl_graph.cpp - igraph/src/drl_layout_3d.cpp - igraph/src/drl_layout.cpp - igraph/src/drl_parse.cpp - igraph/src/gengraph_box_list.cpp - igraph/src/gengraph_degree_sequence.cpp - igraph/src/gengraph_graph_molloy_hash.cpp - igraph/src/gengraph_graph_molloy_optimized.cpp - igraph/src/gengraph_mr-connected.cpp - igraph/src/gengraph_powerlaw.cpp - igraph/src/gengraph_random.cpp - igraph/src/NetDataTypes.cpp - igraph/src/NetRoutines.cpp - igraph/src/pottsmodel_2.cpp - igraph/src/prpack_base_graph.cpp - igraph/src/prpack.cpp - igraph/src/prpack_igraph_graph.cpp - igraph/src/prpack_preprocessed_ge_graph.cpp - igraph/src/prpack_preprocessed_gs_graph.cpp - igraph/src/prpack_preprocessed_scc_graph.cpp - igraph/src/prpack_preprocessed_schur_graph.cpp - igraph/src/prpack_result.cpp - igraph/src/prpack_solver.cpp - igraph/src/prpack_utils.cpp - igraph/src/walktrap_communities.cpp - igraph/src/walktrap.cpp - igraph/src/walktrap_graph.cpp - igraph/src/walktrap_heap.cpp - igraph/src/bliss.cc - igraph/src/bliss_heap.cc - igraph/src/defs.cc - igraph/src/graph.cc - igraph/src/igraph_hrg.cc - igraph/src/igraph_hrg_types.cc - igraph/src/infomap.cc - igraph/src/infomap_FlowGraph.cc - igraph/src/infomap_Greedy.cc - igraph/src/infomap_Node.cc - igraph/src/orbit.cc - igraph/src/partition.cc - igraph/src/uintseqhash.cc - igraph/src/utils.cc - - include-dirs: - include - igraph/include - igraph/include/f2c - igraph/include/prpack - igraph/include/cs - igraph/include/cliquer - igraph/include/bliss - igraph/include/plfit - - cxx-options: -DPRPACK_IGRAPH_SUPPORT - -test-suite tests - type: exitcode-stdio-1.0 - hs-source-dirs: tests - ghc-options: -Wall - main-is: test.hs - other-modules: - Test.Basic - Test.Attributes - Test.Algorithms - Test.Utils - - default-language: Haskell2010 - build-depends: - base - , haskell-igraph - , cereal - , conduit >= 1.3.0 - , data-ordlist - , matrices - , tasty - , tasty-golden - , tasty-hunit - , random - -source-repository head - type: git - location: https://github.com/kaizhang/haskell-igraph.git - +cabal-version: 2.2 + +-- This file has been generated from package.yaml by hpack version 0.33.0. +-- +-- see: https://github.com/sol/hpack +-- +-- hash: eec35679c2bc2e9790d121f0e5e57bf25eb87dcf0776ae132bba4f4ff0d168b1 + +name: haskell-igraph +version: 0.8.5 +synopsis: Bindings to the igraph C library (v0.8.5). +description: igraph<"http://igraph.org/c/"> is a library for creating and manipulating large graphs. This package provides the Haskell interface of igraph. +category: Math +homepage: https://github.com/jmazon/haskell-igraph#readme +bug-reports: https://github.com/jmazon/haskell-igraph/issues +author: Kai Zhang +maintainer: Jean-Baptiste Mazon +copyright: (c) 2016-2021 Kai Zhang +license: MIT +license-file: LICENSE +build-type: Simple +extra-source-files: + cbits/bytestring.h + cbits/haskell_attributes.h + cbits/haskell_igraph.h + igraph/include/arith.h + igraph/include/atlas-edges.h + igraph/include/bigint.h + igraph/include/bignum.h + igraph/include/config.h + igraph/include/DensityGrid.h + igraph/include/DensityGrid_3d.h + igraph/include/drl_graph.h + igraph/include/drl_graph_3d.h + igraph/include/drl_layout.h + igraph/include/drl_layout_3d.h + igraph/include/drl_Node.h + igraph/include/drl_Node_3d.h + igraph/include/drl_parse.h + igraph/include/f2c.h + igraph/include/foreign-dl-header.h + igraph/include/foreign-dl-parser.h + igraph/include/foreign-gml-header.h + igraph/include/foreign-gml-parser.h + igraph/include/foreign-lgl-header.h + igraph/include/foreign-lgl-parser.h + igraph/include/foreign-ncol-header.h + igraph/include/foreign-ncol-parser.h + igraph/include/foreign-pajek-header.h + igraph/include/foreign-pajek-parser.h + igraph/include/gengraph_box_list.h + igraph/include/gengraph_definitions.h + igraph/include/gengraph_degree_sequence.h + igraph/include/gengraph_graph_molloy_hash.h + igraph/include/gengraph_graph_molloy_optimized.h + igraph/include/gengraph_hash.h + igraph/include/gengraph_header.h + igraph/include/gengraph_powerlaw.h + igraph/include/gengraph_qsort.h + igraph/include/gengraph_random.h + igraph/include/gengraph_vertex_cover.h + igraph/include/hrg_dendro.h + igraph/include/hrg_graph.h + igraph/include/hrg_graph_simp.h + igraph/include/hrg_rbtree.h + igraph/include/hrg_splittree_eq.h + igraph/include/igraph.h + igraph/include/igraph_adjlist.h + igraph/include/igraph_arpack.h + igraph/include/igraph_arpack_internal.h + igraph/include/igraph_array.h + igraph/include/igraph_array_pmt.h + igraph/include/igraph_attributes.h + igraph/include/igraph_bipartite.h + igraph/include/igraph_blas.h + igraph/include/igraph_blas_internal.h + igraph/include/igraph_centrality.h + igraph/include/igraph_cliquer.h + igraph/include/igraph_cliques.h + igraph/include/igraph_cocitation.h + igraph/include/igraph_cohesive_blocks.h + igraph/include/igraph_coloring.h + igraph/include/igraph_community.h + igraph/include/igraph_complex.h + igraph/include/igraph_components.h + igraph/include/igraph_constants.h + igraph/include/igraph_constructors.h + igraph/include/igraph_conversion.h + igraph/include/igraph_datatype.h + igraph/include/igraph_decls.h + igraph/include/igraph_dqueue.h + igraph/include/igraph_dqueue_pmt.h + igraph/include/igraph_eigen.h + igraph/include/igraph_embedding.h + igraph/include/igraph_epidemics.h + igraph/include/igraph_error.h + igraph/include/igraph_estack.h + igraph/include/igraph_flow.h + igraph/include/igraph_flow_internal.h + igraph/include/igraph_foreign.h + igraph/include/igraph_games.h + igraph/include/igraph_glpk_support.h + igraph/include/igraph_gml_tree.h + igraph/include/igraph_graphlets.h + igraph/include/igraph_hacks_internal.h + igraph/include/igraph_handle_exceptions.h + igraph/include/igraph_heap.h + igraph/include/igraph_heap_pmt.h + igraph/include/igraph_hrg.h + igraph/include/igraph_interface.h + igraph/include/igraph_interrupt.h + igraph/include/igraph_interrupt_internal.h + igraph/include/igraph_isoclasses.h + igraph/include/igraph_iterators.h + igraph/include/igraph_lapack.h + igraph/include/igraph_lapack_internal.h + igraph/include/igraph_layout.h + igraph/include/igraph_lsap.h + igraph/include/igraph_marked_queue.h + igraph/include/igraph_matching.h + igraph/include/igraph_math.h + igraph/include/igraph_matrix.h + igraph/include/igraph_matrix_pmt.h + igraph/include/igraph_memory.h + igraph/include/igraph_microscopic_update.h + igraph/include/igraph_mixing.h + igraph/include/igraph_motifs.h + igraph/include/igraph_neighborhood.h + igraph/include/igraph_nongraph.h + igraph/include/igraph_operators.h + igraph/include/igraph_paths.h + igraph/include/igraph_pmt.h + igraph/include/igraph_pmt_off.h + igraph/include/igraph_progress.h + igraph/include/igraph_psumtree.h + igraph/include/igraph_qsort.h + igraph/include/igraph_random.h + igraph/include/igraph_scan.h + igraph/include/igraph_scg.h + igraph/include/igraph_separators.h + igraph/include/igraph_sparsemat.h + igraph/include/igraph_spmatrix.h + igraph/include/igraph_stack.h + igraph/include/igraph_stack_pmt.h + igraph/include/igraph_statusbar.h + igraph/include/igraph_structural.h + igraph/include/igraph_strvector.h + igraph/include/igraph_threading.h + igraph/include/igraph_topology.h + igraph/include/igraph_transitivity.h + igraph/include/igraph_types.h + igraph/include/igraph_types_internal.h + igraph/include/igraph_vector.h + igraph/include/igraph_vector_pmt.h + igraph/include/igraph_vector_ptr.h + igraph/include/igraph_vector_type.h + igraph/include/igraph_version.h + igraph/include/igraph_visitor.h + igraph/include/infomap_FlowGraph.h + igraph/include/infomap_Greedy.h + igraph/include/infomap_Node.h + igraph/include/maximal_cliques_template.h + igraph/include/NetDataTypes.h + igraph/include/NetRoutines.h + igraph/include/pottsmodel_2.h + igraph/include/prpack.h + igraph/include/scg_headers.h + igraph/include/structural_properties_internal.h + igraph/include/triangles_template.h + igraph/include/triangles_template1.h + igraph/include/walktrap_communities.h + igraph/include/walktrap_graph.h + igraph/include/walktrap_heap.h + igraph/include/array.pmt + igraph/include/dqueue.pmt + igraph/include/heap.pmt + igraph/include/matrix.pmt + igraph/include/stack.pmt + igraph/include/vector.pmt + igraph/include/f2c/fio.h + igraph/include/f2c/fmt.h + igraph/include/f2c/fp.h + igraph/include/f2c/lio.h + igraph/include/f2c/signal1.h + igraph/include/f2c/sysdep1.h + igraph/include/prpack/prpack.h + igraph/include/prpack/prpack_base_graph.h + igraph/include/prpack/prpack_csc.h + igraph/include/prpack/prpack_csr.h + igraph/include/prpack/prpack_edge_list.h + igraph/include/prpack/prpack_igraph_graph.h + igraph/include/prpack/prpack_preprocessed_ge_graph.h + igraph/include/prpack/prpack_preprocessed_graph.h + igraph/include/prpack/prpack_preprocessed_gs_graph.h + igraph/include/prpack/prpack_preprocessed_scc_graph.h + igraph/include/prpack/prpack_preprocessed_schur_graph.h + igraph/include/prpack/prpack_result.h + igraph/include/prpack/prpack_solver.h + igraph/include/prpack/prpack_utils.h + igraph/include/cs/cs.h + igraph/include/cs/UFconfig.h + igraph/include/cliquer/cliquer.h + igraph/include/cliquer/cliquerconf.h + igraph/include/cliquer/graph.h + igraph/include/cliquer/misc.h + igraph/include/cliquer/reorder.h + igraph/include/cliquer/set.h + igraph/include/bliss/bignum.hh + igraph/include/bliss/defs.hh + igraph/include/bliss/graph.hh + igraph/include/bliss/heap.hh + igraph/include/bliss/kqueue.hh + igraph/include/bliss/kstack.hh + igraph/include/bliss/orbit.hh + igraph/include/bliss/partition.hh + igraph/include/bliss/uintseqhash.hh + igraph/include/bliss/utils.hh + igraph/include/plfit/arithmetic_ansi.h + igraph/include/plfit/arithmetic_sse_double.h + igraph/include/plfit/arithmetic_sse_float.h + igraph/include/plfit/error.h + igraph/include/plfit/gss.h + igraph/include/plfit/hzeta.h + igraph/include/plfit/kolmogorov.h + igraph/include/plfit/lbfgs.h + igraph/include/plfit/mt.h + igraph/include/plfit/platform.h + igraph/include/plfit/plfit.h + igraph/include/plfit/sampling.h + igraph/AUTHORS + igraph/COPYING + stack.yaml + +extra-doc-files: + README.md + ChangeLog.md + +source-repository head + type: git + location: https://github.com/jmazon/haskell-igraph + +library + exposed-modules: + IGraph.Internal.Initialization + IGraph.Internal.Constants + IGraph.Internal + IGraph + IGraph.Mutable + IGraph.Random + IGraph.Types + IGraph.Algorithms + IGraph.Algorithms.Structure + IGraph.Algorithms.Community + IGraph.Algorithms.Clique + IGraph.Algorithms.Layout + IGraph.Algorithms.Motif + IGraph.Algorithms.Generators + IGraph.Algorithms.Isomorphism + IGraph.Algorithms.Centrality + other-modules: + IGraph.Internal.C2HS + hs-source-dirs: + src + ghc-options: -Wall -fno-warn-unused-matches + cxx-options: -std=c++11 -DPRPACK_IGRAPH_SUPPORT + include-dirs: + cbits + igraph/include + igraph/include/f2c + igraph/include/prpack + igraph/include/cs + igraph/include/cliquer + igraph/include/bliss + igraph/include/plfit + c-sources: + cbits/bytestring.c + cbits/haskell_attributes.c + cbits/haskell_igraph.c + igraph/src/abort_.c + igraph/src/adjlist.c + igraph/src/arithchk.c + igraph/src/arpack.c + igraph/src/array.c + igraph/src/atlas.c + igraph/src/attributes.c + igraph/src/backspac.c + igraph/src/basic_query.c + igraph/src/bfgs.c + igraph/src/bigint.c + igraph/src/bignum.c + igraph/src/bipartite.c + igraph/src/blas.c + igraph/src/c_abs.c + igraph/src/c_cos.c + igraph/src/c_div.c + igraph/src/c_exp.c + igraph/src/c_log.c + igraph/src/c_sin.c + igraph/src/c_sqrt.c + igraph/src/cabs.c + igraph/src/cattributes.c + igraph/src/centrality.c + igraph/src/cliquer.c + igraph/src/cliquer_graph.c + igraph/src/cliques.c + igraph/src/close.c + igraph/src/cocitation.c + igraph/src/cohesive_blocks.c + igraph/src/coloring.c + igraph/src/community.c + igraph/src/community_leiden.c + igraph/src/complex.c + igraph/src/components.c + igraph/src/conversion.c + igraph/src/cores.c + igraph/src/cs_add.c + igraph/src/cs_amd.c + igraph/src/cs_chol.c + igraph/src/cs_cholsol.c + igraph/src/cs_compress.c + igraph/src/cs_counts.c + igraph/src/cs_cumsum.c + igraph/src/cs_dfs.c + igraph/src/cs_dmperm.c + igraph/src/cs_droptol.c + igraph/src/cs_dropzeros.c + igraph/src/cs_dupl.c + igraph/src/cs_entry.c + igraph/src/cs_ereach.c + igraph/src/cs_etree.c + igraph/src/cs_fkeep.c + igraph/src/cs_gaxpy.c + igraph/src/cs_happly.c + igraph/src/cs_house.c + igraph/src/cs_ipvec.c + igraph/src/cs_leaf.c + igraph/src/cs_load.c + igraph/src/cs_lsolve.c + igraph/src/cs_ltsolve.c + igraph/src/cs_lu.c + igraph/src/cs_lusol.c + igraph/src/cs_malloc.c + igraph/src/cs_maxtrans.c + igraph/src/cs_multiply.c + igraph/src/cs_norm.c + igraph/src/cs_permute.c + igraph/src/cs_pinv.c + igraph/src/cs_post.c + igraph/src/cs_print.c + igraph/src/cs_pvec.c + igraph/src/cs_qr.c + igraph/src/cs_qrsol.c + igraph/src/cs_randperm.c + igraph/src/cs_reach.c + igraph/src/cs_scatter.c + igraph/src/cs_scc.c + igraph/src/cs_schol.c + igraph/src/cs_spsolve.c + igraph/src/cs_sqr.c + igraph/src/cs_symperm.c + igraph/src/cs_tdfs.c + igraph/src/cs_transpose.c + igraph/src/cs_updown.c + igraph/src/cs_usolve.c + igraph/src/cs_util.c + igraph/src/cs_utsolve.c + igraph/src/ctype.c + igraph/src/d_abs.c + igraph/src/d_acos.c + igraph/src/d_asin.c + igraph/src/d_atan.c + igraph/src/d_atn2.c + igraph/src/d_cnjg.c + igraph/src/d_cos.c + igraph/src/d_cosh.c + igraph/src/d_dim.c + igraph/src/d_exp.c + igraph/src/d_imag.c + igraph/src/d_int.c + igraph/src/d_lg10.c + igraph/src/d_log.c + igraph/src/d_mod.c + igraph/src/d_nint.c + igraph/src/d_prod.c + igraph/src/d_sign.c + igraph/src/d_sin.c + igraph/src/d_sinh.c + igraph/src/d_sqrt.c + igraph/src/d_tan.c + igraph/src/d_tanh.c + igraph/src/dasum.c + igraph/src/daxpy.c + igraph/src/dcopy.c + igraph/src/ddot.c + igraph/src/decomposition.c + igraph/src/derf_.c + igraph/src/derfc_.c + igraph/src/dfe.c + igraph/src/dgebak.c + igraph/src/dgebal.c + igraph/src/dgeev.c + igraph/src/dgeevx.c + igraph/src/dgehd2.c + igraph/src/dgehrd.c + igraph/src/dgemm.c + igraph/src/dgemv.c + igraph/src/dgeqr2.c + igraph/src/dger.c + igraph/src/dgesv.c + igraph/src/dgetf2.c + igraph/src/dgetrf.c + igraph/src/dgetrs.c + igraph/src/dgetv0.c + igraph/src/dhseqr.c + igraph/src/disnan.c + igraph/src/distances.c + igraph/src/dlabad.c + igraph/src/dlacn2.c + igraph/src/dlacpy.c + igraph/src/dladiv.c + igraph/src/dlae2.c + igraph/src/dlaebz.c + igraph/src/dlaev2.c + igraph/src/dlaexc.c + igraph/src/dlagtf.c + igraph/src/dlagts.c + igraph/src/dlahqr.c + igraph/src/dlahr2.c + igraph/src/dlaisnan.c + igraph/src/dlaln2.c + igraph/src/dlamch.c + igraph/src/dlaneg.c + igraph/src/dlange.c + igraph/src/dlanhs.c + igraph/src/dlanst.c + igraph/src/dlansy.c + igraph/src/dlanv2.c + igraph/src/dlapy2.c + igraph/src/dlaqr0.c + igraph/src/dlaqr1.c + igraph/src/dlaqr2.c + igraph/src/dlaqr3.c + igraph/src/dlaqr4.c + igraph/src/dlaqr5.c + igraph/src/dlaqrb.c + igraph/src/dlaqtr.c + igraph/src/dlar1v.c + igraph/src/dlarf.c + igraph/src/dlarfb.c + igraph/src/dlarfg.c + igraph/src/dlarft.c + igraph/src/dlarfx.c + igraph/src/dlarnv.c + igraph/src/dlarra.c + igraph/src/dlarrb.c + igraph/src/dlarrc.c + igraph/src/dlarrd.c + igraph/src/dlarre.c + igraph/src/dlarrf.c + igraph/src/dlarrj.c + igraph/src/dlarrk.c + igraph/src/dlarrr.c + igraph/src/dlarrv.c + igraph/src/dlartg.c + igraph/src/dlaruv.c + igraph/src/dlascl.c + igraph/src/dlaset.c + igraph/src/dlasq2.c + igraph/src/dlasq3.c + igraph/src/dlasq4.c + igraph/src/dlasq5.c + igraph/src/dlasq6.c + igraph/src/dlasr.c + igraph/src/dlasrt.c + igraph/src/dlassq.c + igraph/src/dlaswp.c + igraph/src/dlasy2.c + igraph/src/dlatrd.c + igraph/src/dmout.c + igraph/src/dnaitr.c + igraph/src/dnapps.c + igraph/src/dnaup2.c + igraph/src/dnaupd.c + igraph/src/dnconv.c + igraph/src/dneigh.c + igraph/src/dneupd.c + igraph/src/dngets.c + igraph/src/dnrm2.c + igraph/src/dolio.c + igraph/src/dorg2r.c + igraph/src/dorghr.c + igraph/src/dorgqr.c + igraph/src/dorm2l.c + igraph/src/dorm2r.c + igraph/src/dormhr.c + igraph/src/dormql.c + igraph/src/dormqr.c + igraph/src/dormtr.c + igraph/src/dotproduct.c + igraph/src/dpotf2.c + igraph/src/dpotrf.c + igraph/src/dqueue.c + igraph/src/drot.c + igraph/src/dsaitr.c + igraph/src/dsapps.c + igraph/src/dsaup2.c + igraph/src/dsaupd.c + igraph/src/dscal.c + igraph/src/dsconv.c + igraph/src/dseigt.c + igraph/src/dsesrt.c + igraph/src/dseupd.c + igraph/src/dsgets.c + igraph/src/dsortc.c + igraph/src/dsortr.c + igraph/src/dstatn.c + igraph/src/dstats.c + igraph/src/dstebz.c + igraph/src/dstein.c + igraph/src/dstemr.c + igraph/src/dsteqr.c + igraph/src/dsterf.c + igraph/src/dstqrb.c + igraph/src/dswap.c + igraph/src/dsyevr.c + igraph/src/dsymv.c + igraph/src/dsyr2.c + igraph/src/dsyr2k.c + igraph/src/dsyrk.c + igraph/src/dsytd2.c + igraph/src/dsytrd.c + igraph/src/dtime_.c + igraph/src/dtrevc.c + igraph/src/dtrexc.c + igraph/src/dtrmm.c + igraph/src/dtrmv.c + igraph/src/dtrsen.c + igraph/src/dtrsm.c + igraph/src/dtrsna.c + igraph/src/dtrsv.c + igraph/src/dtrsyl.c + igraph/src/due.c + igraph/src/dummy.c + igraph/src/dvout.c + igraph/src/ef1asc_.c + igraph/src/ef1cmc_.c + igraph/src/eigen.c + igraph/src/embedding.c + igraph/src/endfile.c + igraph/src/erf_.c + igraph/src/erfc_.c + igraph/src/err.c + igraph/src/error.c + igraph/src/etime_.c + igraph/src/exit_.c + igraph/src/f77_aloc.c + igraph/src/f77vers.c + igraph/src/fast_community.c + igraph/src/feedback_arc_set.c + igraph/src/flow.c + igraph/src/fmt.c + igraph/src/fmtlib.c + igraph/src/foreign-dl-lexer.c + igraph/src/foreign-dl-parser.c + igraph/src/foreign-gml-lexer.c + igraph/src/foreign-gml-parser.c + igraph/src/foreign-graphml.c + igraph/src/foreign-lgl-lexer.c + igraph/src/foreign-lgl-parser.c + igraph/src/foreign-ncol-lexer.c + igraph/src/foreign-ncol-parser.c + igraph/src/foreign-pajek-lexer.c + igraph/src/foreign-pajek-parser.c + igraph/src/foreign.c + igraph/src/forestfire.c + igraph/src/fortran_intrinsics.c + igraph/src/ftell_.c + igraph/src/games.c + igraph/src/getenv_.c + igraph/src/glet.c + igraph/src/glpk_support.c + igraph/src/gml_tree.c + igraph/src/gss.c + igraph/src/h_abs.c + igraph/src/h_dim.c + igraph/src/h_dnnt.c + igraph/src/h_indx.c + igraph/src/h_len.c + igraph/src/h_mod.c + igraph/src/h_nint.c + igraph/src/h_sign.c + igraph/src/hacks.c + igraph/src/heap.c + igraph/src/hl_ge.c + igraph/src/hl_gt.c + igraph/src/hl_le.c + igraph/src/hl_lt.c + igraph/src/hzeta.c + igraph/src/i77vers.c + igraph/src/i_abs.c + igraph/src/i_dim.c + igraph/src/i_dnnt.c + igraph/src/i_indx.c + igraph/src/i_len.c + igraph/src/i_mod.c + igraph/src/i_nint.c + igraph/src/i_sign.c + igraph/src/idamax.c + igraph/src/ieeeck.c + igraph/src/igraph_buckets.c + igraph/src/igraph_cliquer.c + igraph/src/igraph_error.c + igraph/src/igraph_estack.c + igraph/src/igraph_fixed_vectorlist.c + igraph/src/igraph_grid.c + igraph/src/igraph_hashtable.c + igraph/src/igraph_heap.c + igraph/src/igraph_marked_queue.c + igraph/src/igraph_psumtree.c + igraph/src/igraph_set.c + igraph/src/igraph_stack.c + igraph/src/igraph_strvector.c + igraph/src/igraph_trie.c + igraph/src/iio.c + igraph/src/iladlc.c + igraph/src/iladlr.c + igraph/src/ilaenv.c + igraph/src/ilnw.c + igraph/src/inquire.c + igraph/src/interrupt.c + igraph/src/iparmq.c + igraph/src/iterators.c + igraph/src/ivout.c + igraph/src/kolmogorov.c + igraph/src/l_ge.c + igraph/src/l_gt.c + igraph/src/l_le.c + igraph/src/l_lt.c + igraph/src/lad.c + igraph/src/lapack.c + igraph/src/layout.c + igraph/src/layout_dh.c + igraph/src/layout_fr.c + igraph/src/layout_gem.c + igraph/src/layout_kk.c + igraph/src/lbfgs.c + igraph/src/lbitbits.c + igraph/src/lbitshft.c + igraph/src/len_trim.c + igraph/src/lread.c + igraph/src/lsame.c + igraph/src/lsap.c + igraph/src/lwrite.c + igraph/src/matching.c + igraph/src/math.c + igraph/src/matrix.c + igraph/src/maximal_cliques.c + igraph/src/memory.c + igraph/src/microscopic_update.c + igraph/src/mixing.c + igraph/src/motifs.c + igraph/src/mt.c + igraph/src/open.c + igraph/src/operators.c + igraph/src/optimal_modularity.c + igraph/src/options.c + igraph/src/other.c + igraph/src/paths.c + igraph/src/platform.c + igraph/src/plfit.c + igraph/src/pow_ci.c + igraph/src/pow_dd.c + igraph/src/pow_di.c + igraph/src/pow_hh.c + igraph/src/pow_ii.c + igraph/src/pow_ri.c + igraph/src/pow_zi.c + igraph/src/pow_zz.c + igraph/src/progress.c + igraph/src/qsort.c + igraph/src/qsort_r.c + igraph/src/r_abs.c + igraph/src/r_acos.c + igraph/src/r_asin.c + igraph/src/r_atan.c + igraph/src/r_atn2.c + igraph/src/r_cnjg.c + igraph/src/r_cos.c + igraph/src/r_cosh.c + igraph/src/r_dim.c + igraph/src/r_exp.c + igraph/src/r_imag.c + igraph/src/r_int.c + igraph/src/r_lg10.c + igraph/src/r_log.c + igraph/src/r_mod.c + igraph/src/r_nint.c + igraph/src/r_sign.c + igraph/src/r_sin.c + igraph/src/r_sinh.c + igraph/src/r_sqrt.c + igraph/src/r_tan.c + igraph/src/r_tanh.c + igraph/src/random.c + igraph/src/random_walk.c + igraph/src/rbinom.c + igraph/src/rdfmt.c + igraph/src/reorder.c + igraph/src/rewind.c + igraph/src/rsfe.c + igraph/src/rsli.c + igraph/src/rsne.c + igraph/src/s_cat.c + igraph/src/s_cmp.c + igraph/src/s_copy.c + igraph/src/s_paus.c + igraph/src/s_rnge.c + igraph/src/s_stop.c + igraph/src/sampling.c + igraph/src/sbm.c + igraph/src/scan.c + igraph/src/scg.c + igraph/src/scg_approximate_methods.c + igraph/src/scg_exact_scg.c + igraph/src/scg_kmeans.c + igraph/src/scg_optimal_method.c + igraph/src/scg_utils.c + igraph/src/second.c + igraph/src/separators.c + igraph/src/sfe.c + igraph/src/sig_die.c + igraph/src/signal_.c + igraph/src/signbit.c + igraph/src/sir.c + igraph/src/spanning_trees.c + igraph/src/sparsemat.c + igraph/src/spectral_properties.c + igraph/src/spmatrix.c + igraph/src/st-cuts.c + igraph/src/statusbar.c + igraph/src/structural_properties.c + igraph/src/structure_generators.c + igraph/src/sue.c + igraph/src/sugiyama.c + igraph/src/system_.c + igraph/src/topology.c + igraph/src/triangles.c + igraph/src/type_indexededgelist.c + igraph/src/types.c + igraph/src/typesize.c + igraph/src/uio.c + igraph/src/uninit.c + igraph/src/util.c + igraph/src/vector.c + igraph/src/vector_ptr.c + igraph/src/version.c + igraph/src/visitors.c + igraph/src/wref.c + igraph/src/wrtfmt.c + igraph/src/wsfe.c + igraph/src/wsle.c + igraph/src/wsne.c + igraph/src/xerbla.c + igraph/src/xwsne.c + igraph/src/z_abs.c + igraph/src/z_cos.c + igraph/src/z_div.c + igraph/src/z_exp.c + igraph/src/z_log.c + igraph/src/z_sin.c + igraph/src/z_sqrt.c + igraph/src/zeroin.c + cxx-sources: + igraph/src/clustertool.cpp + igraph/src/degree_sequence.cpp + igraph/src/DensityGrid.cpp + igraph/src/DensityGrid_3d.cpp + igraph/src/drl_graph.cpp + igraph/src/drl_graph_3d.cpp + igraph/src/drl_layout.cpp + igraph/src/drl_layout_3d.cpp + igraph/src/drl_parse.cpp + igraph/src/gengraph_box_list.cpp + igraph/src/gengraph_degree_sequence.cpp + igraph/src/gengraph_graph_molloy_hash.cpp + igraph/src/gengraph_graph_molloy_optimized.cpp + igraph/src/gengraph_mr-connected.cpp + igraph/src/gengraph_powerlaw.cpp + igraph/src/gengraph_random.cpp + igraph/src/NetDataTypes.cpp + igraph/src/NetRoutines.cpp + igraph/src/pottsmodel_2.cpp + igraph/src/prpack.cpp + igraph/src/prpack_base_graph.cpp + igraph/src/prpack_igraph_graph.cpp + igraph/src/prpack_preprocessed_ge_graph.cpp + igraph/src/prpack_preprocessed_gs_graph.cpp + igraph/src/prpack_preprocessed_scc_graph.cpp + igraph/src/prpack_preprocessed_schur_graph.cpp + igraph/src/prpack_result.cpp + igraph/src/prpack_solver.cpp + igraph/src/prpack_utils.cpp + igraph/src/walktrap.cpp + igraph/src/walktrap_communities.cpp + igraph/src/walktrap_graph.cpp + igraph/src/walktrap_heap.cpp + igraph/src/bliss.cc + igraph/src/bliss_heap.cc + igraph/src/defs.cc + igraph/src/graph.cc + igraph/src/igraph_hrg.cc + igraph/src/igraph_hrg_types.cc + igraph/src/infomap.cc + igraph/src/infomap_FlowGraph.cc + igraph/src/infomap_Greedy.cc + igraph/src/infomap_Node.cc + igraph/src/orbit.cc + igraph/src/partition.cc + igraph/src/uintseqhash.cc + igraph/src/utils.cc + extra-libraries: + stdc++ + build-tool-depends: + c2hs:c2hs >=0.25.0 + build-depends: + base >=4.10 && <5.0 + , bytestring >=0.9 + , cereal + , conduit >=1.3.0 + , containers + , data-ordlist + , primitive + , singletons >=3.0 + , singletons-base + , singletons-th + default-language: Haskell2010 + +test-suite test + type: exitcode-stdio-1.0 + main-is: test.hs + other-modules: + Test.Basic + Test.Attributes + Test.Algorithms + Test.Utils + hs-source-dirs: + tests + ghc-options: -threaded + build-depends: + base + , cereal + , conduit >=1.3.0 + , data-ordlist + , haskell-igraph + , matrices + , random + , tasty + , tasty-golden + , tasty-hunit + default-language: Haskell2010 diff --git a/igraph/AUTHORS b/igraph/AUTHORS --- a/igraph/AUTHORS +++ b/igraph/AUTHORS @@ -2,3 +2,5 @@ Tamas Nepusz Szabolcs Horvat Vincent Traag +Fabio Zanini + diff --git a/igraph/include/DensityGrid.h b/igraph/include/DensityGrid.h --- a/igraph/include/DensityGrid.h +++ b/igraph/include/DensityGrid.h @@ -36,17 +36,14 @@ // Compile time adjustable parameters - -#include - -using namespace std; - #include "drl_layout.h" #include "drl_Node.h" #ifdef MUSE_MPI #include #endif +#include + namespace drl { class DensityGrid { @@ -74,7 +71,7 @@ // new dynamic variables -- SBM float (*fall_off)[RADIUS * 2 + 1]; float (*Density)[GRID_SIZE]; - deque* Bins; + std::deque* Bins; // old static variables //float fall_off[RADIUS*2+1][RADIUS*2+1]; diff --git a/igraph/include/DensityGrid_3d.h b/igraph/include/DensityGrid_3d.h --- a/igraph/include/DensityGrid_3d.h +++ b/igraph/include/DensityGrid_3d.h @@ -36,17 +36,14 @@ // Compile time adjustable parameters - -#include - -using namespace std; - #include "drl_layout_3d.h" #include "drl_Node_3d.h" #ifdef MUSE_MPI #include #endif +#include + namespace drl3d { class DensityGrid { @@ -74,7 +71,7 @@ // new dynamic variables -- SBM float (*fall_off)[RADIUS * 2 + 1][RADIUS * 2 + 1]; float (*Density)[GRID_SIZE][GRID_SIZE]; - deque* Bins; + std::deque* Bins; // old static variables //float fall_off[RADIUS*2+1][RADIUS*2+1]; diff --git a/igraph/include/NetDataTypes.h b/igraph/include/NetDataTypes.h --- a/igraph/include/NetDataTypes.h +++ b/igraph/include/NetDataTypes.h @@ -43,7 +43,7 @@ #ifndef NETDATATYPES_H #define NETDATATYPES_H -#include +#include //########################################################################################### @@ -449,7 +449,7 @@ template HugeArray::HugeArray(void) { - max_bit_left = 1 << 31; //wir setzen das 31. Bit auf 1 + max_bit_left = 1UL << 31; //wir setzen das 31. Bit auf 1 size = 2; max_index = 0; highest_field_index = 0; @@ -486,7 +486,7 @@ shift_index++; } h_index.field_index = 31 - shift_index; // das hoechste besetzte Bit im Index - help_index = 1 << h_index.field_index; // in help_index wird das hoechste besetzte Bit von Index gesetzt + help_index = 1UL << h_index.field_index; // in help_index wird das hoechste besetzte Bit von Index gesetzt h_index.in_field_index = (index ^ help_index); // index XOR help_index, womit alle bits unter dem hoechsten erhalten bleiben return h_index; } @@ -497,7 +497,7 @@ unsigned long data_size; while (size < index + 1) { highest_field_index++; - data_size = 1 << highest_field_index; + data_size = 1UL << highest_field_index; data = new DATA[data_size]; for (unsigned long i = 0; i < data_size; i++) { data[i] = 0; diff --git a/igraph/include/bliss/bignum.hh b/igraph/include/bliss/bignum.hh --- a/igraph/include/bliss/bignum.hh +++ b/igraph/include/bliss/bignum.hh @@ -21,7 +21,7 @@ */ #include -#include +// #include #include #include #include @@ -111,7 +111,7 @@ /** * Print the number in the file stream \a fp. */ - size_t print(FILE* const fp) const {return fprintf(fp, "%Lg", v); } + // size_t print(FILE* const fp) const {return fprintf(fp, "%Lg", v); } int tostring(char **str) const { int size=static_cast( (std::log(std::abs(v))/std::log(10.0))+4 ); diff --git a/igraph/include/bliss/defs.hh b/igraph/include/bliss/defs.hh --- a/igraph/include/bliss/defs.hh +++ b/igraph/include/bliss/defs.hh @@ -29,11 +29,6 @@ # define BLISS_USE_GMP #endif -#ifdef USING_R -#include -#define fatal_error(...) (error(__VA_ARGS__)) -#endif - namespace bliss { /** @@ -47,9 +42,7 @@ * There should not be a return from this function but exit or * a jump to code that deallocates the AbstractGraph instance that called this. */ -#ifndef USING_R void fatal_error(const char* fmt, ...); -#endif #if defined(BLISS_DEBUG) diff --git a/igraph/include/bliss/graph.hh b/igraph/include/bliss/graph.hh --- a/igraph/include/bliss/graph.hh +++ b/igraph/include/bliss/graph.hh @@ -29,7 +29,7 @@ class AbstractGraph; } -#include +// #include #include #include "kstack.hh" #include "kqueue.hh" @@ -81,6 +81,7 @@ public: Stats() { reset(); } /** Print the statistics. */ + /* size_t print(FILE* const fp) const { size_t r = 0; @@ -94,6 +95,7 @@ fflush(fp); return r; } + */ /** An approximation (due to possible overflows/rounding errors) of * the size of the automorphism group. */ long double get_group_size_approx() const {return group_size_approx;} @@ -241,6 +243,7 @@ const unsigned int* aut), void* hook_user_param); +#if 0 /** * Write the graph to a file in a variant of the DIMACS format. * See the bliss website @@ -264,6 +267,7 @@ * \param file_name the name of the file to which the graph is written */ virtual void write_dot(const char * const file_name) = 0; +#endif /** * Get a hash value for the graph. @@ -294,7 +298,7 @@ unsigned int verbose_level; /** \internal * The output stream for verbose output. */ - FILE *verbstr; + // FILE *verbstr; protected: /** \internal @@ -391,7 +395,7 @@ * Data structures and routines for refining the partition p into equitable */ Heap neighbour_heap; - virtual bool split_neighbourhood_of_unit_cell(Partition::Cell *) = 0; + virtual bool split_neighbourhood_of_unit_cell(Partition::Cell * const) = 0; virtual bool split_neighbourhood_of_cell(Partition::Cell * const) = 0; void refine_to_equitable(); void refine_to_equitable(Partition::Cell * const unit_cell); @@ -658,6 +662,7 @@ */ ~Graph(); +#if 0 /** * Read the graph from the file \a fp in a variant of the DIMACS format. * See the bliss website @@ -690,6 +695,7 @@ * \copydoc AbstractGraph::write_dot(const char * const file_name) */ void write_dot(const char* const file_name); +#endif /** * \copydoc AbstractGraph::is_automorphism(const std::vector& perm) const @@ -898,6 +904,7 @@ */ ~Digraph(); +#if 0 /** * Read the graph from the file \a fp in a variant of the DIMACS format. * See the bliss website @@ -928,6 +935,7 @@ * \copydoc AbstractGraph::write_dot(const char * const file_name) */ void write_dot(const char * const file_name); +#endif /** * \copydoc AbstractGraph::is_automorphism(const std::vector& perm) const diff --git a/igraph/include/bliss/partition.hh b/igraph/include/bliss/partition.hh --- a/igraph/include/bliss/partition.hh +++ b/igraph/include/bliss/partition.hh @@ -25,7 +25,7 @@ } #include -#include +//#include #include #include "kstack.hh" #include "kqueue.hh" @@ -186,12 +186,12 @@ /** * Print the partition into the file stream \a fp. */ - size_t print(FILE* const fp, const bool add_newline = true) const; + // size_t print(FILE* const fp, const bool add_newline = true) const; /** * Print the partition cell sizes into the file stream \a fp. */ - size_t print_signature(FILE* const fp, const bool add_newline = true) const; + // size_t print_signature(FILE* const fp, const bool add_newline = true) const; /* * Splits the Cell \a cell into [cell_1,...,cell_n] diff --git a/igraph/include/bliss/uintseqhash.hh b/igraph/include/bliss/uintseqhash.hh --- a/igraph/include/bliss/uintseqhash.hh +++ b/igraph/include/bliss/uintseqhash.hh @@ -1,7 +1,7 @@ #ifndef BLISS_UINTSEQHASH_HH #define BLISS_UINTSEQHASH_HH -#include +// #include /* Copyright (c) 2003-2015 Tommi Junttila diff --git a/igraph/include/bliss/utils.hh b/igraph/include/bliss/utils.hh --- a/igraph/include/bliss/utils.hh +++ b/igraph/include/bliss/utils.hh @@ -26,11 +26,12 @@ * */ -#include -using namespace std; +//#include +#include namespace bliss { +#if 0 /** * Print the permutation \a perm of {0,...,N-1} in the cycle format * in the file stream \a fp. @@ -51,6 +52,7 @@ void print_permutation(FILE* fp, const std::vector& perm, const unsigned int offset = 0); +#endif /** * Check whether \a perm is a valid permutation on {0,...,N-1}. diff --git a/igraph/include/cliquer/set.h b/igraph/include/cliquer/set.h --- a/igraph/include/cliquer/set.h +++ b/igraph/include/cliquer/set.h diff --git a/igraph/include/config.h b/igraph/include/config.h --- a/igraph/include/config.h +++ b/igraph/include/config.h @@ -11,6 +11,7 @@ #define HAVE_RINTF 1 #define HAVE_ROUND 1 #define HAVE_SNPRINTF 1 +#undef HAVE_ISFINITE /* libraries */ #define HAVE_MEMORY_H 1 @@ -18,8 +19,10 @@ #define HAVE_STRINGS_H 1 #define HAVE_STRING_H 1 +#define HAVE_TLS 1 #define IGRAPH_F77_SAVE static IGRAPH_THREAD_LOCAL -#define IGRAPH_THREAD_LOCAL +#define IGRAPH_THREAD_LOCAL __thread +#define TLS __thread #define INTERNAL_ARPACK 1 #define INTERNAL_BLAS 1 @@ -27,13 +30,15 @@ #define INTERNAL_GLPK 1 #define INTERNAL_LAPACK 1 + #define LT_OBJDIR ".libs/" #define PACKAGE "igraph" #define PACKAGE_BUGREPORT "igraph@igraph.org" #define PACKAGE_NAME "igraph" -#define PACKAGE_STRING "igraph 0.8.0" +#define PACKAGE_STRING "igraph 0.8.5" #define PACKAGE_TARNAME "igraph" #define PACKAGE_URL "" -#define PACKAGE_VERSION "0.8.0" +#define PACKAGE_VERSION "0.8.5" #define STDC_HEADERS 1 -#define VERSION "0.8.0" +#define VERSION "0.8.5" +#undef YYTEXT_POINTER diff --git a/igraph/include/drl_graph.h b/igraph/include/drl_graph.h --- a/igraph/include/drl_graph.h +++ b/igraph/include/drl_graph.h @@ -37,6 +37,10 @@ #include "DensityGrid.h" #include "igraph_layout.h" +#include +#include +#include + namespace drl { // layout schedule information @@ -81,8 +85,8 @@ void update_nodes ( ); float Compute_Node_Energy ( int node_ind ); void Solve_Analytic ( int node_ind, float &pos_x, float &pos_y ); - void get_positions ( vector &node_indices, float return_positions[2 * MAX_PROCS] ); - void update_density ( vector &node_indices, + void get_positions ( std::vector &node_indices, float return_positions[2 * MAX_PROCS] ); + void update_density ( std::vector &node_indices, float old_positions[2 * MAX_PROCS], float new_positions[2 * MAX_PROCS] ); void update_node_pos ( int node_ind, @@ -95,11 +99,11 @@ // graph decomposition information int num_nodes; // number of nodes in graph float highest_sim; // highest sim for normalization - map id_catalog; // id_catalog[file id] = internal id - map > neighbors; // neighbors of nodes on this proc. + std::map id_catalog; // id_catalog[file id] = internal id + std::map > neighbors; // neighbors of nodes on this proc. // graph layout information - vector positions; + std::vector positions; DensityGrid density_server; // original VxOrd information diff --git a/igraph/include/drl_graph_3d.h b/igraph/include/drl_graph_3d.h --- a/igraph/include/drl_graph_3d.h +++ b/igraph/include/drl_graph_3d.h @@ -37,6 +37,10 @@ #include "DensityGrid_3d.h" #include "igraph_layout.h" +#include +#include +#include + namespace drl3d { // layout schedule information @@ -73,8 +77,8 @@ void update_nodes ( ); float Compute_Node_Energy ( int node_ind ); void Solve_Analytic ( int node_ind, float &pos_x, float &pos_y, float &pos_z ); - void get_positions ( vector &node_indices, float return_positions[3 * MAX_PROCS] ); - void update_density ( vector &node_indices, + void get_positions ( std::vector &node_indices, float return_positions[3 * MAX_PROCS] ); + void update_density ( std::vector &node_indices, float old_positions[3 * MAX_PROCS], float new_positions[3 * MAX_PROCS] ); void update_node_pos ( int node_ind, @@ -87,11 +91,11 @@ // graph decomposition information int num_nodes; // number of nodes in graph float highest_sim; // highest sim for normalization - map id_catalog; // id_catalog[file id] = internal id - map > neighbors; // neighbors of nodes on this proc. + std::map id_catalog; // id_catalog[file id] = internal id + std::map > neighbors; // neighbors of nodes on this proc. // graph layout information - vector positions; + std::vector positions; DensityGrid density_server; // original VxOrd information diff --git a/igraph/include/drl_parse.h b/igraph/include/drl_parse.h --- a/igraph/include/drl_parse.h +++ b/igraph/include/drl_parse.h @@ -37,6 +37,8 @@ #include #endif +#include + namespace drl { class parse { @@ -49,10 +51,10 @@ ~parse () {} // user parameters - string sim_file; // .sim file - string coord_file; // .coord file - string parms_file; // .parms file - string real_file; // .real file + std::string sim_file; // .sim file + std::string coord_file; // .coord file + std::string parms_file; // .parms file + std::string real_file; // .real file int rand_seed; // random seed int >= 0 float edge_cut; // edge cutting real [0,1] diff --git a/igraph/include/gengraph_box_list.h b/igraph/include/gengraph_box_list.h --- a/igraph/include/gengraph_box_list.h +++ b/igraph/include/gengraph_box_list.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -27,12 +27,6 @@ #ifndef _BOX_LIST_H #define _BOX_LIST_H - -#ifndef _MSC_VER - #ifndef register - #define register - #endif -#endif namespace gengraph { diff --git a/igraph/include/gengraph_definitions.h b/igraph/include/gengraph_definitions.h --- a/igraph/include/gengraph_definitions.h +++ b/igraph/include/gengraph_definitions.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -21,12 +21,6 @@ #ifndef DEFINITIONS_H #define DEFINITIONS_H -#ifndef _MSC_VER - #ifndef register - #define register - #endif -#endif - #include #include #include @@ -124,7 +118,7 @@ if(fabs(x)<1e-6) return x+0.5*x*x+0.333333333333333*x*x*x; else return log(1.0+x); } -//*/ +*/ //Fast search or replace @@ -197,7 +191,7 @@ static int _random_bits = 0; inline int random_bit() { - register int a = _random_bits; + int a = _random_bits; _random_bits = a >> 1; if (_random_bits_stored--) { return a & 0x1; diff --git a/igraph/include/gengraph_degree_sequence.h b/igraph/include/gengraph_degree_sequence.h --- a/igraph/include/gengraph_degree_sequence.h +++ b/igraph/include/gengraph_degree_sequence.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, diff --git a/igraph/include/gengraph_graph_molloy_hash.h b/igraph/include/gengraph_graph_molloy_hash.h --- a/igraph/include/gengraph_graph_molloy_hash.h +++ b/igraph/include/gengraph_graph_molloy_hash.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -209,7 +209,7 @@ // same, but when multiple shortest path are possible, average the weights. double *vertex_betweenness_asp(bool trivial_path); //___________________________________________________________________________________ - //*/ + */ }; diff --git a/igraph/include/gengraph_graph_molloy_optimized.h b/igraph/include/gengraph_graph_molloy_optimized.h --- a/igraph/include/gengraph_graph_molloy_optimized.h +++ b/igraph/include/gengraph_graph_molloy_optimized.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -265,7 +265,7 @@ bool try_shuffle(int T, int K); //___________________________________________________________________________________ - //*/ + */ /*___________________________________________________________________________________ Not to use anymore : replaced by vertex_betweenness() 22/04/2005 @@ -277,7 +277,7 @@ // same, but when multiple shortest path are possible, average the weights. double *vertex_betweenness_asp(bool trivial_path); //___________________________________________________________________________________ - //*/ + */ }; diff --git a/igraph/include/gengraph_hash.h b/igraph/include/gengraph_hash.h --- a/igraph/include/gengraph_hash.h +++ b/igraph/include/gengraph_hash.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, diff --git a/igraph/include/gengraph_header.h b/igraph/include/gengraph_header.h --- a/igraph/include/gengraph_header.h +++ b/igraph/include/gengraph_header.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -41,17 +41,6 @@ } } - -#ifdef _WIN32 -#include -#include -void set_priority_low() { - HANDLE hProcess = OpenProcess(PROCESS_ALL_ACCESS, TRUE, _getpid()); - SetPriorityClass(hProcess, IDLE_PRIORITY_CLASS); -} -#else -#include -#endif namespace gengraph { diff --git a/igraph/include/gengraph_powerlaw.h b/igraph/include/gengraph_powerlaw.h --- a/igraph/include/gengraph_powerlaw.h +++ b/igraph/include/gengraph_powerlaw.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, diff --git a/igraph/include/gengraph_qsort.h b/igraph/include/gengraph_qsort.h --- a/igraph/include/gengraph_qsort.h +++ b/igraph/include/gengraph_qsort.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -24,10 +24,6 @@ #include #include -#ifndef register - #define register -#endif - namespace gengraph { //___________________________________________________________________________ @@ -63,7 +59,7 @@ return; } for (int i = 1; i < t; i++) { - register int *w = v + i; + int *w = v + i; int tmp = *w; while (w != v && *(w - 1) > tmp) { *w = *(w - 1); @@ -147,7 +143,7 @@ return; } for (int i = 1; i < t; i++) { - register double *w = v + i; + double *w = v + i; double tmp = *w; while (w != v && *(w - 1) > tmp) { *w = *(w - 1); @@ -260,7 +256,7 @@ int mx = mem[0]; int mn = mem[0]; for (yo = mem + n - 1; yo != mem; yo--) { - register int x = *yo; + int x = *yo; if (x > mx) { mx = x; } @@ -399,7 +395,7 @@ return; } for (int i = 1; i < t; i++) { - register int *w = v + i; + int *w = v + i; int tmp = *w; while (w != v && lex_comp(l[tmp], l[*(w - 1)], s) < 0) { *w = *(w - 1); @@ -521,7 +517,7 @@ return; } for (int i = 1; i < t; i++) { - register int *w = v + i; + int *w = v + i; int tmp = *w; while (w != v && mix_comp_indirect(key, tmp, *(w - 1), neigh, degs) < 0) { *w = *(w - 1); diff --git a/igraph/include/gengraph_random.h b/igraph/include/gengraph_random.h --- a/igraph/include/gengraph_random.h +++ b/igraph/include/gengraph_random.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -22,8 +22,6 @@ #define RNG_H #include "igraph_random.h" -#include -using namespace std; namespace KW_RNG { diff --git a/igraph/include/gengraph_vertex_cover.h b/igraph/include/gengraph_vertex_cover.h --- a/igraph/include/gengraph_vertex_cover.h +++ b/igraph/include/gengraph_vertex_cover.h @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -28,10 +28,7 @@ // Moreover, vertex_cover() keeps links[] intact, permuting only the adjacency lists #include "gengraph_box_list.h" - -#ifndef register - #define register -#endif +#include namespace gengraph { @@ -57,9 +54,9 @@ if (!bl.is_empty()) { v = bl.get_max(); int *w = neigh[v]; - register int v2 = *(w++); - register int dm = deg[v2]; - register int k = deg[v] - 1; + int v2 = *(w++); + int dm = deg[v2]; + int k = deg[v] - 1; while (k--) if (deg[*(w++)] > dm) { v2 = *(w - 1); dm = deg[v2]; diff --git a/igraph/include/heap.pmt b/igraph/include/heap.pmt --- a/igraph/include/heap.pmt +++ b/igraph/include/heap.pmt @@ -33,6 +33,12 @@ #define LEFTCHILD(x) (((x)+1)*2-1) #define RIGHTCHILD(x) (((x)+1)*2) +/* Define internal functions */ +void FUNCTION(igraph_heap, i_build)(BASE* arr, long int size, long int head); +void FUNCTION(igraph_heap, i_shift_up)(BASE* arr, long int size, long int elem); +void FUNCTION(igraph_heap, i_sink)(BASE* arr, long int size, long int head); +void FUNCTION(igraph_heap, i_switch)(BASE* arr, long int e1, long int e2); + /** * \ingroup heap * \function igraph_heap_init diff --git a/igraph/include/hrg_dendro.h b/igraph/include/hrg_dendro.h --- a/igraph/include/hrg_dendro.h +++ b/igraph/include/hrg_dendro.h @@ -65,18 +65,15 @@ #ifndef IGRAPH_HRG_DENDRO #define IGRAPH_HRG_DENDRO -#include -#include -#include -#include - #include "hrg_graph.h" #include "hrg_rbtree.h" #include "hrg_splittree_eq.h" #include "igraph_hrg.h" -using namespace std; +#include +#include + using namespace fitHRG; namespace fitHRG { @@ -105,7 +102,7 @@ int x; int y; short int t; - string sp; + std::string sp; }; struct child { int index; @@ -147,7 +144,7 @@ class split { public: - string s; // partition assignment of leaf vertices + std::string s; // partition assignment of leaf vertices split(): s("") { } ~split() { } void initializeSplit(const int n) { @@ -157,7 +154,7 @@ } } bool checkSplit() { - if (s.empty() || s.find("-", 0) != string::npos) { + if (s.empty() || s.find("-", 0) != std::string::npos) { return false; } else { return true; @@ -181,7 +178,7 @@ class interns { private: ipair* edgelist; // list of internal edges represented - string* splitlist; // split representation of the internal edges + std::string* splitlist; // split representation of the internal edges int** indexLUT; // table of indices of internal edges in edgelist int q; // number of internal edges int count; // (for adding edges) edgelist index of new edge to add @@ -196,9 +193,9 @@ // returns a uniformly random internal edge, O(1) ipair* getRandomEdge(); // returns the ith split of the splitlist, O(1) - string getSplit(const int); + std::string getSplit(const int); // replace an existing split, O(1) - bool replaceSplit(const int, const string); + bool replaceSplit(const int, const std::string); // swaps two edges, O(1) bool swapEdges(const int, const int, const short int, const int, const int, const short int); @@ -250,12 +247,12 @@ // return path to root from leaf list* binarySearchFind(const double); // build split for this internal edge - string buildSplit(elementd*); + std::string buildSplit(elementd*); // compute number of edges between two internal subtrees int computeEdgeCount(const int, const short int, const int, const short int); // (consensus tree) counts children - int countChildren(const string); + int countChildren(const std::string); // find internal node of D that is common ancestor of i,j elementd* findCommonAncestor(list**, const int, const int); // return reverse of path to leaf from root diff --git a/igraph/include/hrg_graph.h b/igraph/include/hrg_graph.h --- a/igraph/include/hrg_graph.h +++ b/igraph/include/hrg_graph.h @@ -61,13 +61,11 @@ #ifndef IGRAPH_HRG_GRAPH #define IGRAPH_HRG_GRAPH -#include -#include -#include - #include "hrg_rbtree.h" -using namespace std; +#include +#include +#include namespace fitHRG { @@ -96,7 +94,7 @@ #define IGRAPH_HRG_VERT class vert { public: - string name; // (external) name of vertex + std::string name; // (external) name of vertex int degree; // degree of this vertex vert(): name(""), degree(0) { } @@ -122,7 +120,7 @@ // returns degree of vertex i int getDegree(const int); // returns name of vertex i - string getName(const int); + std::string getName(const int); // returns edge list of vertex i edge* getNeighborList(const int); // return ptr to histogram of edge (i,j) @@ -148,7 +146,7 @@ // allocate edge histograms void setAdjacencyHistograms(const int); // set name of vertex i - bool setName(const int, const string); + bool setName(const int, const std::string); private: bool predict; // do we need prediction? diff --git a/igraph/include/hrg_graph_simp.h b/igraph/include/hrg_graph_simp.h --- a/igraph/include/hrg_graph_simp.h +++ b/igraph/include/hrg_graph_simp.h @@ -60,14 +60,11 @@ #ifndef IGRAPH_HRG_SIMPLEGRAPH #define IGRAPH_HRG_SIMPLEGRAPH -#include -#include -#include - #include "hrg_rbtree.h" #include "hrg_dendro.h" -using namespace std; +#include +#include namespace fitHRG { @@ -89,7 +86,7 @@ #define IGRAPH_HRG_SIMPLEVERT class simpleVert { public: - string name; // (external) name of vertex + std::string name; // (external) name of vertex int degree; // degree of this vertex int group_true; // index of vertex's true group @@ -129,7 +126,7 @@ // returns group label of vertex i int getGroupLabel(const int); // returns name of vertex i - string getName(const int); + std::string getName(const int); // returns edge list of vertex i simpleEdge* getNeighborList(const int); // return pointer to a node @@ -141,7 +138,7 @@ // returns n int getNumNodes(); // set name of vertex i - bool setName(const int, const string); + bool setName(const int, const std::string); private: simpleVert* nodes; // list of nodes diff --git a/igraph/include/hrg_rbtree.h b/igraph/include/hrg_rbtree.h --- a/igraph/include/hrg_rbtree.h +++ b/igraph/include/hrg_rbtree.h @@ -55,10 +55,6 @@ #ifndef IGRAPH_HRG_RBTREE #define IGRAPH_HRG_RBTREE -#include - -using namespace std; - namespace fitHRG { // ******** Basic Structures ********************************************* diff --git a/igraph/include/hrg_splittree_eq.h b/igraph/include/hrg_splittree_eq.h --- a/igraph/include/hrg_splittree_eq.h +++ b/igraph/include/hrg_splittree_eq.h @@ -62,9 +62,7 @@ #ifndef IGRAPH_HRG_SPLITTREE #define IGRAPH_HRG_SPLITTREE -#include - -using namespace std; +#include namespace fitHRG { @@ -74,7 +72,7 @@ #define IGRAPH_HRG_SLIST class slist { public: - string x; // stored elementd in linked-list + std::string x; // stored elementd in linked-list slist* next; // pointer to next elementd slist(): x(""), next(0) { } ~slist() { } @@ -83,7 +81,7 @@ class keyValuePairSplit { public: - string x; // elementsp split (string) + std::string x; // elementsp split (string) double y; // stored weight (double) int c; // stored count (int) keyValuePairSplit* next; // linked-list pointer @@ -95,7 +93,7 @@ class elementsp { public: - string split; // split represented as a string + std::string split; // split represented as a string double weight; // total weight of this split int count; // number of observations of this split @@ -149,21 +147,21 @@ // default constructor/destructor splittree(); ~splittree(); // returns value associated with searchKey - double returnValue(const string); + double returnValue(const std::string); // returns T if searchKey found, and points foundNode at the // corresponding node - elementsp* findItem(const string); + elementsp* findItem(const std::string); // update total_count and total_weight void finishedThisRound(); // insert a new key with stored value - bool insertItem(string, double); + bool insertItem(std::string, double); void clearTree(); // delete a node with given key - void deleteItem(string); + void deleteItem(std::string); // delete the entire tree void deleteTree(); // return array of keys in tree - string* returnArrayOfKeys(); + std::string* returnArrayOfKeys(); // return list of keys in tree slist* returnListOfKeys(); // return the tree as a list of keyValuePairSplits diff --git a/igraph/include/igraph_adjlist.h b/igraph/include/igraph_adjlist.h --- a/igraph/include/igraph_adjlist.h +++ b/igraph/include/igraph_adjlist.h @@ -59,13 +59,12 @@ /* igraph_integer_t no); */ /** * \define igraph_adjlist_get - * Query a vector in an adjlist + * \brief Query a vector in an adjacency list. * * Returns a pointer to an igraph_vector_int_t object from an * adjacency list. The vector can be modified as desired. * \param al The adjacency list object. - * \param no The vertex of which the vertex of adjacent vertices are - * returned. + * \param no The vertex whose adjacent vertices will be returned. * \return Pointer to the igraph_vector_int_t object. * * Time complexity: O(1). @@ -93,7 +92,7 @@ /** * \define igraph_inclist_get - * Query a vector in an incidence list + * \brief Query a vector in an incidence list. * * Returns a pointer to an igraph_vector_int_t object from an * incidence list containing edge ids. The vector can be modified, @@ -124,14 +123,14 @@ /* igraph_integer_t no); */ /** * \define igraph_lazy_adjlist_get - * Query neighbor vertices + * \brief Query neighbor vertices. * * If the function is called for the first time for a vertex then the * result is stored in the adjacency list and no further query * operations are needed when the neighbors of the same vertex are * queried again. * \param al The lazy adjacency list. - * \param no The vertex id to query. + * \param no The vertex ID to query. * \return Pointer to a vector. It is allowed to modify it and * modification does not affect the original graph. * @@ -159,7 +158,7 @@ /** * \define igraph_lazy_inclist_get - * Query incident edges + * \brief Query incident edges. * * If the function is called for the first time for a vertex, then the * result is stored in the incidence list and no further query @@ -195,7 +194,7 @@ /** * \define igraph_adjedgelist_get - * Query a vector in an incidence list + * \brief Query a vector in an incidence list. * * This macro was superseded by \ref igraph_inclist_get() in igraph 0.6. * Please use \ref igraph_inclist_get() instead of this macro. @@ -214,7 +213,7 @@ /** * \define igraph_lazy_adjedgelist_get - * Query a vector in a lazy incidence list + * \brief Query a vector in a lazy incidence list. * * This macro was superseded by \ref igraph_lazy_inclist_get() in igraph 0.6. * Please use \ref igraph_lazy_inclist_get() instead of this macro. diff --git a/igraph/include/igraph_arpack.h b/igraph/include/igraph_arpack.h --- a/igraph/include/igraph_arpack.h +++ b/igraph/include/igraph_arpack.h @@ -25,8 +25,8 @@ #include "igraph_vector.h" #include "igraph_matrix.h" -#ifndef ARPACK_H -#define ARPACK_H +#ifndef IGRAPH_ARPACK_H +#define IGRAPH_ARPACK_H #include "igraph_decls.h" @@ -222,34 +222,34 @@ typedef struct igraph_arpack_options_t { /* INPUT */ - char bmat[1]; /* I-standard problem, G-generalized */ - int n; /* Dimension of the eigenproblem */ - char which[2]; /* LA, SA, LM, SM, BE */ - int nev; /* Number of eigenvalues to be computed */ - igraph_real_t tol; /* Stopping criterion */ - int ncv; /* Number of columns in V */ - int ldv; /* Leading dimension of V */ - int ishift; /* 0-reverse comm., 1-exact with tridiagonal */ - int mxiter; /* Maximum number of update iterations to take */ - int nb; /* Block size on the recurrence, only 1 works */ - int mode; /* The kind of problem to be solved (1-5) - 1: A*x=l*x, A symmetric - 2: A*x=l*M*x, A symm. M pos. def. - 3: K*x = l*M*x, K symm., M pos. semidef. - 4: K*x = l*KG*x, K s. pos. semidef. KG s. indef. - 5: A*x = l*M*x, A symm., M symm. pos. semidef. */ - int start; /* 0: random, 1: use the supplied vector */ - int lworkl; /* Size of temporary storage, default is fine */ - igraph_real_t sigma; /* The shift for modes 3,4,5 */ - igraph_real_t sigmai; /* The imaginary part of shift for rnsolve */ + char bmat[1]; /* I-standard problem, G-generalized */ + int n; /* Dimension of the eigenproblem */ + char which[2]; /* LA, SA, LM, SM, BE */ + int nev; /* Number of eigenvalues to be computed */ + igraph_real_t tol; /* Stopping criterion */ + int ncv; /* Number of columns in V */ + int ldv; /* Leading dimension of V */ + int ishift; /* 0-reverse comm., 1-exact with tridiagonal */ + int mxiter; /* Maximum number of update iterations to take */ + int nb; /* Block size on the recurrence, only 1 works */ + int mode; /* The kind of problem to be solved (1-5) + 1: A*x=l*x, A symmetric + 2: A*x=l*M*x, A symm. M pos. def. + 3: K*x = l*M*x, K symm., M pos. semidef. + 4: K*x = l*KG*x, K s. pos. semidef. KG s. indef. + 5: A*x = l*M*x, A symm., M symm. pos. semidef. */ + int start; /* 0: random, 1: use the supplied vector */ + int lworkl; /* Size of temporary storage, default is fine */ + igraph_real_t sigma; /* The shift for modes 3,4,5 */ + igraph_real_t sigmai; /* The imaginary part of shift for rnsolve */ /* OUTPUT */ - int info; /* What happened, see docs */ - int ierr; /* What happened in the dseupd call */ - int noiter; /* The number of iterations taken */ + int info; /* What happened, see docs */ + int ierr; /* What happened in the dseupd call */ + int noiter; /* The number of iterations taken */ int nconv; - int numop; /* Number of OP*x operations */ - int numopb; /* Number of B*x operations if BMAT='G' */ - int numreo; /* Number of steps of re-orthogonalizations */ + int numop; /* Number of OP*x operations */ + int numopb; /* Number of B*x operations if BMAT='G' */ + int numreo; /* Number of steps of re-orthogonalizations */ /* INTERNAL */ int iparam[11]; int ipntr[14]; diff --git a/igraph/include/igraph_array_pmt.h b/igraph/include/igraph_array_pmt.h --- a/igraph/include/igraph_array_pmt.h +++ b/igraph/include/igraph_array_pmt.h @@ -36,16 +36,16 @@ #define ARRAY3(m,i,j,k) ((m).data.stor_begin[(m).n1n2*(k)+(m).n1*(j)+(i)]) #endif -int FUNCTION(igraph_array3, init)(TYPE(igraph_array3) *a, long int n1, long int n2, +DECLDIR int FUNCTION(igraph_array3, init)(TYPE(igraph_array3) *a, long int n1, long int n2, long int n3); -void FUNCTION(igraph_array3, destroy)(TYPE(igraph_array3) *a); -long int FUNCTION(igraph_array3, size)(const TYPE(igraph_array3) *a); -long int FUNCTION(igraph_array3, n)(const TYPE(igraph_array3) *a, long int idx); -int FUNCTION(igraph_array3, resize)(TYPE(igraph_array3) *a, long int n1, long int n2, +DECLDIR void FUNCTION(igraph_array3, destroy)(TYPE(igraph_array3) *a); +DECLDIR long int FUNCTION(igraph_array3, size)(const TYPE(igraph_array3) *a); +DECLDIR long int FUNCTION(igraph_array3, n)(const TYPE(igraph_array3) *a, long int idx); +DECLDIR int FUNCTION(igraph_array3, resize)(TYPE(igraph_array3) *a, long int n1, long int n2, long int n3); -void FUNCTION(igraph_array3, null)(TYPE(igraph_array3) *a); -BASE FUNCTION(igraph_array3, sum)(const TYPE(igraph_array3) *a); -void FUNCTION(igraph_array3, scale)(TYPE(igraph_array3) *a, BASE by); -void FUNCTION(igraph_array3, fill)(TYPE(igraph_array3) *a, BASE e); -int FUNCTION(igraph_array3, update)(TYPE(igraph_array3) *to, +DECLDIR void FUNCTION(igraph_array3, null)(TYPE(igraph_array3) *a); +DECLDIR BASE FUNCTION(igraph_array3, sum)(const TYPE(igraph_array3) *a); +DECLDIR void FUNCTION(igraph_array3, scale)(TYPE(igraph_array3) *a, BASE by); +DECLDIR void FUNCTION(igraph_array3, fill)(TYPE(igraph_array3) *a, BASE e); +DECLDIR int FUNCTION(igraph_array3, update)(TYPE(igraph_array3) *to, const TYPE(igraph_array3) *from); diff --git a/igraph/include/igraph_attributes.h b/igraph/include/igraph_attributes.h --- a/igraph/include/igraph_attributes.h +++ b/igraph/include/igraph_attributes.h @@ -21,8 +21,8 @@ */ -#ifndef REST_ATTRIBUTES_H -#define REST_ATTRIBUTES_H +#ifndef IGRAPH_ATTRIBUTES_H +#define IGRAPH_ATTRIBUTES_H #include "igraph_decls.h" #include "igraph_datatype.h" @@ -385,7 +385,7 @@ /* Experimental attribute handler in C */ -extern const igraph_attribute_table_t igraph_cattribute_table; +DECLDIR extern const igraph_attribute_table_t igraph_cattribute_table; DECLDIR igraph_real_t igraph_cattribute_GAN(const igraph_t *graph, const char *name); DECLDIR igraph_bool_t igraph_cattribute_GAB(const igraph_t *graph, const char *name); @@ -778,7 +778,7 @@ #define SETVASV(graph,n,v) (igraph_cattribute_VAS_setv((graph),(n),(v))) /** * \define SETEANV - * Set a numeric edge attribute for all vertices + * Set a numeric edge attribute for all edges * * This is a shorthand for \ref igraph_cattribute_EAN_setv(). * \param graph The graph. @@ -788,7 +788,7 @@ #define SETEANV(graph,n,v) (igraph_cattribute_EAN_setv((graph),(n),(v))) /** * \define SETEABV - * Set a boolean edge attribute for all vertices + * Set a boolean edge attribute for all edges * * This is a shorthand for \ref igraph_cattribute_EAB_setv(). * \param graph The graph. @@ -798,7 +798,7 @@ #define SETEABV(graph,n,v) (igraph_cattribute_EAB_setv((graph),(n),(v))) /** * \define SETEASV - * Set a string edge attribute for all vertices + * Set a string edge attribute for all edges * * This is a shorthand for \ref igraph_cattribute_EAS_setv(). * \param graph The graph. diff --git a/igraph/include/igraph_blas.h b/igraph/include/igraph_blas.h --- a/igraph/include/igraph_blas.h +++ b/igraph/include/igraph_blas.h @@ -21,8 +21,8 @@ */ -#ifndef BLAS_H -#define BLAS_H +#ifndef IGRAPH_BLAS_H +#define IGRAPH_BLAS_H #include "igraph_types.h" #include "igraph_vector.h" @@ -59,6 +59,9 @@ igraph_real_t beta, igraph_real_t* y); DECLDIR igraph_real_t igraph_blas_dnrm2(const igraph_vector_t *v); + +DECLDIR int igraph_blas_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2, + igraph_real_t *res); __END_DECLS diff --git a/igraph/include/igraph_blas_internal.h b/igraph/include/igraph_blas_internal.h --- a/igraph/include/igraph_blas_internal.h +++ b/igraph/include/igraph_blas_internal.h @@ -34,13 +34,13 @@ #ifndef INTERNAL_BLAS #define igraphdaxpy_ daxpy_ - #define igraphdger_ dger_ + #define igraphdger_ dger_ #define igraphdcopy_ dcopy_ #define igraphdscal_ dscal_ #define igraphdswap_ dswap_ #define igraphdgemm_ dgemm_ #define igraphdgemv_ dgemv_ - #define igraphddot_ ddot_ + #define igraphddot_ ddot_ #define igraphdnrm2_ dnrm2_ #define igraphlsame_ lsame_ #define igraphdrot_ drot_ @@ -50,6 +50,11 @@ #define igraphdtrsm_ dtrsm_ #define igraphdtrsv_ dtrsv_ #define igraphdnrm2_ dnrm2_ + #define igraphdsymv_ dsymv_ + #define igraphdsyr2_ dsyr2_ + #define igraphdsyr2k_ dsyr2k_ + #define igraphdtrmv_ dtrmv_ + #define igraphdsyrk_ dsyrk_ #endif int igraphdgemv_(char *trans, int *m, int *n, igraph_real_t *alpha, @@ -61,5 +66,7 @@ double *beta, double *c__, int *ldc); double igraphdnrm2_(int *n, double *x, int *incx); + +double igraphddot_(int *n, double *dx, int *incx, double *dy, int *incy); #endif diff --git a/igraph/include/igraph_cliques.h b/igraph/include/igraph_cliques.h --- a/igraph/include/igraph_cliques.h +++ b/igraph/include/igraph_cliques.h @@ -83,7 +83,7 @@ /** * \typedef igraph_clique_handler_t - * \brief Type of clique handler functions + * \brief Type of clique handler functions. * * Callback type, called when a clique was found. * diff --git a/igraph/include/igraph_coloring.h b/igraph/include/igraph_coloring.h --- a/igraph/include/igraph_coloring.h +++ b/igraph/include/igraph_coloring.h @@ -1,3 +1,23 @@ +/* + Heuristic graph coloring algorithms. + Copyright (C) 2017 Szabolcs Horvat + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301 USA +*/ + #ifndef IGRAPH_COLORING_H #define IGRAPH_COLORING_H @@ -7,7 +27,9 @@ /** * \typedef igraph_coloring_greedy_t - * Ordering heuristics for igraph_vertex_coloring_greedy + * \brief Ordering heuristics for greedy graph coloring. + * + * Ordering heuristics for \ref igraph_vertex_coloring_greedy(). * * \enumval IGRAPH_COLORING_GREEDY_COLORED_NEIGHBORS Choose vertex with largest number of already colored neighbors. * diff --git a/igraph/include/igraph_datatype.h b/igraph/include/igraph_datatype.h --- a/igraph/include/igraph_datatype.h +++ b/igraph/include/igraph_datatype.h @@ -57,11 +57,14 @@ * - is This is basically the same as os, but this time * for the incoming edges. * - * For undirected graph, the same edge list is stored, ie. an - * undirected edge is stored only once, and for checking whether there - * is an undirected edge from \c v1 to \c v2 one - * should search for both \c from=v1, \c to=v2 and - * \c from=v2, \c to=v1. + * For undirected graphs, the same edge list is stored, i.e. an + * undirected edge is stored only once. Currently, undirected edges + * are canonicalized so that the index of the 'from' vertex is not greater + * than the index of the 'to' vertex. Thus, if v1 <= v2, only the edge (v1, v2) + * needs to be searched for, not (v2, v1), to determine if v1 and v2 are connected. + * However, this fact is NOT guaranteed by the documented public API, + * and should not be relied upon by the implementation of any functions, + * except those belonging to the minimal API in type_indexededgelist.c. * * The storage requirements for a graph with \c |V| vertices * and \c |E| edges is \c O(|E|+|V|). diff --git a/igraph/include/igraph_decls.h b/igraph/include/igraph_decls.h --- a/igraph/include/igraph_decls.h +++ b/igraph/include/igraph_decls.h @@ -8,18 +8,15 @@ #define __END_DECLS /* empty */ #endif +/* In igraph 0.8, we use DECLDIR only with MSVC, not other compilers on Windows. */ #undef DECLDIR -#if defined (_WIN32) || defined (WIN32) || defined (_WIN64) || defined (WIN64) - #if defined (__MINGW32__) || defined (__CYGWIN32__) +#if defined (_MSC_VER) + #ifdef IGRAPH_EXPORTS + #define DECLDIR __declspec(dllexport) + #elif defined(IGRAPH_STATIC) #define DECLDIR /**/ #else - #ifdef IGRAPH_EXPORTS - #define DECLDIR __declspec(dllexport) - #elif defined(IGRAPH_STATIC) - #define DECLDIR /**/ - #else - #define DECLDIR __declspec(dllimport) - #endif + #define DECLDIR __declspec(dllimport) #endif #else #define DECLDIR /**/ diff --git a/igraph/include/igraph_dqueue_pmt.h b/igraph/include/igraph_dqueue_pmt.h --- a/igraph/include/igraph_dqueue_pmt.h +++ b/igraph/include/igraph_dqueue_pmt.h @@ -44,6 +44,6 @@ DECLDIR BASE FUNCTION(igraph_dqueue, head) (const TYPE(igraph_dqueue)* q); DECLDIR BASE FUNCTION(igraph_dqueue, back) (const TYPE(igraph_dqueue)* q); DECLDIR int FUNCTION(igraph_dqueue, push) (TYPE(igraph_dqueue)* q, BASE elem); -int FUNCTION(igraph_dqueue, print)(const TYPE(igraph_dqueue)* q); -int FUNCTION(igraph_dqueue, fprint)(const TYPE(igraph_dqueue)* q, FILE *file); +DECLDIR int FUNCTION(igraph_dqueue, print)(const TYPE(igraph_dqueue)* q); +DECLDIR int FUNCTION(igraph_dqueue, fprint)(const TYPE(igraph_dqueue)* q, FILE *file); DECLDIR BASE FUNCTION(igraph_dqueue, e)(const TYPE(igraph_dqueue) *q, long int idx); diff --git a/igraph/include/igraph_error.h b/igraph/include/igraph_error.h --- a/igraph/include/igraph_error.h +++ b/igraph/include/igraph_error.h @@ -112,7 +112,7 @@ * function of type \ref igraph_error_handler_t and calling * \ref igraph_set_error_handler(). This feature is useful for interface * writers, as \a igraph will have the chance to - * signal errors the appropriate way, eg. the R interface defines an + * signal errors the appropriate way, e.g. the R interface defines an * error handler which calls the error() * function, as required by R, while the Python interface has an error * handler which raises an exception according to the Python way. @@ -217,7 +217,7 @@ * program. */ -extern igraph_error_handler_t igraph_error_handler_abort; +DECLDIR igraph_error_handler_t igraph_error_handler_abort; /** * \var igraph_error_handler_ignore @@ -227,7 +227,7 @@ * with the error code. */ -extern igraph_error_handler_t igraph_error_handler_ignore; +DECLDIR igraph_error_handler_t igraph_error_handler_ignore; /** * \var igraph_error_handler_printignore @@ -237,7 +237,7 @@ * standard error and returns with the error code. */ -extern igraph_error_handler_t igraph_error_handler_printignore; +DECLDIR igraph_error_handler_t igraph_error_handler_printignore; /** * \function igraph_set_error_handler @@ -268,7 +268,7 @@ * \enumval IGRAPH_ENOMEM There wasn't enough memory to allocate * on the heap. * \enumval IGRAPH_PARSEERROR A parse error was found in a file. - * \enumval IGRAPH_EINVAL A parameter's value is invalid. Eg. negative + * \enumval IGRAPH_EINVAL A parameter's value is invalid. E.g. negative * number was specified as the number of vertices. * \enumval IGRAPH_EXISTS A graph/vertex/edge attribute is already * installed with the given name. @@ -278,7 +278,7 @@ * \enumval IGRAPH_NONSQUARE A non-square matrix was received while a * square matrix was expected. * \enumval IGRAPH_EINVMODE Invalid mode parameter. - * \enumval IGRAPH_EFILE A file operation failed. Eg. a file doesn't exist, + * \enumval IGRAPH_EFILE A file operation failed. E.g. a file doesn't exist, * or the user has no rights to open it. * \enumval IGRAPH_UNIMPLEMENTED Attempted to call an unimplemented or * disabled (at compile-time) function. @@ -330,8 +330,6 @@ * \enumval IGRAPH_ERWSTUCK Random walk got stuck. */ -/* Each enum value below must have a corresponding error string in - * igraph_i_error_strings[] in igraph_error.c */ typedef enum { IGRAPH_SUCCESS = 0, IGRAPH_FAILURE = 1, @@ -394,6 +392,8 @@ IGRAPH_ERWSTUCK = 59, IGRAPH_STOP = 60, /* undocumented, used internally; signals a request to stop in functions like igraph_i_maximal_cliques_bk */ } igraph_error_type_t; +/* Each enum value above must have a corresponding error string in + * igraph_i_error_strings[] in igraph_error.c */ /** * \define IGRAPH_ERROR @@ -408,7 +408,7 @@ * \ref igraph_error() directly. * \param reason Textual description of the error. This should be * something more descriptive than the text associated with the error - * code. Eg. if the error code is \c IGRAPH_EINVAL, + * code. E.g. if the error code is \c IGRAPH_EINVAL, * its associated text (see \ref igraph_strerror()) is "Invalid * value" and this string should explain which parameter was invalid * and maybe why. @@ -448,7 +448,7 @@ * \brief Trigger an error, printf-like version. * * \param reason Textual description of the error, interpreted as - * a printf format string. + * a \c printf format string. * \param file The source file in which the error was noticed. * \param line The line in the source file which triggered the error. * \param igraph_errno The \a igraph error code. @@ -564,7 +564,13 @@ */ #define IGRAPH_FINALLY(func,ptr) \ - IGRAPH_FINALLY_REAL((igraph_finally_func_t*)(func), (ptr)) + { \ + /* the following branch makes the compiler check the compatibility of \ + * func and ptr to detect cases when we are accidentally invoking an \ + * incorrect destructor function with the pointer */ \ + if (0) { func(ptr); } \ + IGRAPH_FINALLY_REAL((igraph_finally_func_t*)(func), (ptr)); \ + } #if !defined(GCC_VERSION_MAJOR) && defined(__GNUC__) #define GCC_VERSION_MAJOR __GNUC__ @@ -578,6 +584,19 @@ #define IGRAPH_LIKELY(a) a #endif +#if IGRAPH_VERIFY_FINALLY_STACK == 1 +#define IGRAPH_CHECK(a) \ + do { \ + int enter_stack_size = IGRAPH_FINALLY_STACK_SIZE(); \ + int igraph_i_ret=(a); \ + if (IGRAPH_UNLIKELY(igraph_i_ret != 0)) {\ + IGRAPH_ERROR("", igraph_i_ret); \ + } \ + if (IGRAPH_UNLIKELY(enter_stack_size != IGRAPH_FINALLY_STACK_SIZE())) { \ + IGRAPH_ERROR("Non-matching number of IGRAPH_FINALLY and IGRAPH_FINALLY_CLEAN", IGRAPH_FAILURE); \ + } \ + } while (0) +#else /** * \define IGRAPH_CHECK * \brief Check the return value of a function call. @@ -596,18 +615,19 @@ * igraph_error_handler_printignore), and the \a igraph function * signalling the error is called from another \a igraph function * then we need to make sure that the error is propagated back to - * the auxiliary (ie. non-igraph) calling function. This is achieved + * the auxiliary (i.e. non-igraph) calling function. This is achieved * by using IGRAPH_CHECK on every \a igraph * call which can return an error code. */ - #define IGRAPH_CHECK(a) do { \ int igraph_i_ret=(a); \ if (IGRAPH_UNLIKELY(igraph_i_ret != 0)) {\ IGRAPH_ERROR("", igraph_i_ret); \ } } while (0) +#endif + /** * \section about_igraph_warnings Warning messages * @@ -658,8 +678,8 @@ DECLDIR igraph_warning_handler_t* igraph_set_warning_handler(igraph_warning_handler_t* new_handler); -extern igraph_warning_handler_t igraph_warning_handler_ignore; -extern igraph_warning_handler_t igraph_warning_handler_print; +DECLDIR igraph_warning_handler_t igraph_warning_handler_ignore; +DECLDIR igraph_warning_handler_t igraph_warning_handler_print; /** * \function igraph_warning diff --git a/igraph/include/igraph_flow.h b/igraph/include/igraph_flow.h --- a/igraph/include/igraph_flow.h +++ b/igraph/include/igraph_flow.h @@ -33,7 +33,7 @@ __BEGIN_DECLS /* -------------------------------------------------- */ -/* MAximum flows, minimum cuts & such */ +/* Maximum flows, minimum cuts & such */ /* -------------------------------------------------- */ /** diff --git a/igraph/include/igraph_handle_exceptions.h b/igraph/include/igraph_handle_exceptions.h new file mode 100644 --- /dev/null +++ b/igraph/include/igraph_handle_exceptions.h @@ -0,0 +1,14 @@ +#ifndef IGRAPH_HANDLE_EXCEPTIONS_H +#define IGRAPH_HANDLE_EXCEPTIONS_H + +#include +#include + +#define IGRAPH_HANDLE_EXCEPTIONS(code) \ + try { code; } \ + catch (const std::bad_alloc &e) { IGRAPH_ERROR(e.what(), IGRAPH_ENOMEM); } \ + catch (const std::exception &e) { IGRAPH_ERROR(e.what(), IGRAPH_FAILURE); } \ + catch (...) { IGRAPH_ERROR("Unknown exception caught", IGRAPH_FAILURE); } + + +#endif // IGRAPH_HANDLE_EXCEPTIONS_H diff --git a/igraph/include/igraph_heap_pmt.h b/igraph/include/igraph_heap_pmt.h --- a/igraph/include/igraph_heap_pmt.h +++ b/igraph/include/igraph_heap_pmt.h @@ -37,9 +37,3 @@ DECLDIR BASE FUNCTION(igraph_heap, delete_top)(TYPE(igraph_heap)* h); DECLDIR long int FUNCTION(igraph_heap, size)(TYPE(igraph_heap)* h); DECLDIR int FUNCTION(igraph_heap, reserve)(TYPE(igraph_heap)* h, long int size); - -void FUNCTION(igraph_heap, i_build)(BASE* arr, long int size, long int head); -void FUNCTION(igraph_heap, i_shift_up)(BASE* arr, long int size, long int elem); -void FUNCTION(igraph_heap, i_sink)(BASE* arr, long int size, long int head); -void FUNCTION(igraph_heap, i_switch)(BASE* arr, long int e1, long int e2); - diff --git a/igraph/include/igraph_hrg.h b/igraph/include/igraph_hrg.h --- a/igraph/include/igraph_hrg.h +++ b/igraph/include/igraph_hrg.h @@ -81,6 +81,7 @@ DECLDIR int igraph_hrg_sample(const igraph_t *graph, igraph_t *sample, igraph_vector_ptr_t *samples, + igraph_integer_t no_samples, igraph_hrg_t *hrg, igraph_bool_t start); diff --git a/igraph/include/igraph_interface.h b/igraph/include/igraph_interface.h --- a/igraph/include/igraph_interface.h +++ b/igraph/include/igraph_interface.h @@ -76,10 +76,49 @@ DECLDIR int igraph_incident(const igraph_t *graph, igraph_vector_t *eids, igraph_integer_t vid, igraph_neimode_t mode); -#define IGRAPH_FROM(g,e) ((igraph_integer_t)(VECTOR((g)->from)[(long int)(e)])) -#define IGRAPH_TO(g,e) ((igraph_integer_t)(VECTOR((g)->to) [(long int)(e)])) -#define IGRAPH_OTHER(g,e,v) \ - ((igraph_integer_t)(IGRAPH_TO(g,(e))==(v) ? IGRAPH_FROM((g),(e)) : IGRAPH_TO((g),(e)))) +/** + * \define IGRAPH_FROM + * \brief The source vertex of an edge. + * + * Faster than \ref igraph_edge(), but no error checking is done: \p eid is assumed to be valid. + * + * \param graph The graph. + * \param eid The edge ID. + * \return The source vertex of the edge. + * \sa \ref igraph_edge() if error checking is desired. + */ +#define IGRAPH_FROM(graph,eid) ((igraph_integer_t)(VECTOR((graph)->from)[(long int)(eid)])) + +/** + * \define IGRAPH_TO + * \brief The target vertex of an edge. + * + * Faster than \ref igraph_edge(), but no error checking is done: \p eid is assumed to be valid. + * + * \param graph The graph object. + * \param eid The edge ID. + * \return The target vertex of the edge. + * \sa \ref igraph_edge() if error checking is desired. + */ +#define IGRAPH_TO(graph,eid) ((igraph_integer_t)(VECTOR((graph)->to) [(long int)(eid)])) + +/** + * \define IGRAPH_OTHER + * \brief The other endpoint of an edge. + * + * Typically used with undirected edges when one endpoint of the edge is known, + * and the other endpoint is needed. No error checking is done: + * \p eid and \p vid are assumed to be valid. + * + * \param graph The graph object. + * \param eid The edge ID. + * \param vid The vertex ID of one endpoint of an edge. + * \return The other endpoint of the edge. + * \sa \ref IGRAPH_TO() and \ref IGRAPH_FROM() to get the source and target + * of directed edges. + */ +#define IGRAPH_OTHER(graph,eid,vid) \ + ((igraph_integer_t)(IGRAPH_TO(graph,(eid))==(vid) ? IGRAPH_FROM((graph),(eid)) : IGRAPH_TO((graph),(eid)))) __END_DECLS diff --git a/igraph/include/igraph_isoclasses.h b/igraph/include/igraph_isoclasses.h new file mode 100644 --- /dev/null +++ b/igraph/include/igraph_isoclasses.h @@ -0,0 +1,54 @@ +/* -*- mode: C -*- */ +/* + IGraph library. + Copyright (C) 2008-2020 The igraph development team + 334 Harvard street, Cambridge, MA 02139 USA + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301 USA + +*/ + +#ifndef IGRAPH_ISOCLASSES_H +#define IGRAPH_ISOCLASSES_H + +#undef __BEGIN_DECLS +#undef __END_DECLS +#ifdef __cplusplus + #define __BEGIN_DECLS extern "C" { + #define __END_DECLS } +#else + #define __BEGIN_DECLS /* empty */ + #define __END_DECLS /* empty */ +#endif + +__BEGIN_DECLS + +extern const unsigned int igraph_i_isoclass_3[]; +extern const unsigned int igraph_i_isoclass_4[]; +extern const unsigned int igraph_i_isoclass_3u[]; +extern const unsigned int igraph_i_isoclass_4u[]; +extern const unsigned int igraph_i_isoclass2_3[]; +extern const unsigned int igraph_i_isoclass2_4[]; +extern const unsigned int igraph_i_isoclass2_3u[]; +extern const unsigned int igraph_i_isoclass2_4u[]; +extern const unsigned int igraph_i_isoclass_3_idx[]; +extern const unsigned int igraph_i_isoclass_4_idx[]; +extern const unsigned int igraph_i_isoclass_3u_idx[]; +extern const unsigned int igraph_i_isoclass_4u_idx[]; + +__END_DECLS + +#endif diff --git a/igraph/include/igraph_lsap.h b/igraph/include/igraph_lsap.h --- a/igraph/include/igraph_lsap.h +++ b/igraph/include/igraph_lsap.h @@ -1,6 +1,6 @@ -#ifndef IGRAPH_LSAP -#define IGRAPH_LSAP +#ifndef IGRAPH_LSAP_H +#define IGRAPH_LSAP_H #include "igraph_types.h" #include "igraph_vector.h" diff --git a/igraph/include/igraph_matrix.h b/igraph/include/igraph_matrix.h --- a/igraph/include/igraph_matrix.h +++ b/igraph/include/igraph_matrix.h @@ -89,11 +89,11 @@ */ #define MATRIX(m,i,j) ((m).data.stor_begin[(m).nrow*(j)+(i)]) -igraph_bool_t igraph_matrix_all_e_tol(const igraph_matrix_t *lhs, +DECLDIR igraph_bool_t igraph_matrix_all_e_tol(const igraph_matrix_t *lhs, const igraph_matrix_t *rhs, igraph_real_t tol); -int igraph_matrix_zapsmall(igraph_matrix_t *m, igraph_real_t tol); +DECLDIR int igraph_matrix_zapsmall(igraph_matrix_t *m, igraph_real_t tol); __END_DECLS diff --git a/igraph/include/igraph_matrix_pmt.h b/igraph/include/igraph_matrix_pmt.h --- a/igraph/include/igraph_matrix_pmt.h +++ b/igraph/include/igraph_matrix_pmt.h @@ -44,7 +44,7 @@ /* MATRIX */ DECLDIR BASE FUNCTION(igraph_matrix, e)(const TYPE(igraph_matrix) *m, long int row, long int col); -BASE* FUNCTION(igraph_matrix, e_ptr)(const TYPE(igraph_matrix) *m, +DECLDIR BASE* FUNCTION(igraph_matrix, e_ptr)(const TYPE(igraph_matrix) *m, long int row, long int col); DECLDIR void FUNCTION(igraph_matrix, set)(TYPE(igraph_matrix)* m, long int row, long int col, BASE value); @@ -60,7 +60,7 @@ /* Matrix views */ /*-----------------------*/ -const TYPE(igraph_matrix) *FUNCTION(igraph_matrix, view)(const TYPE(igraph_matrix) *m, +DECLDIR const TYPE(igraph_matrix) *FUNCTION(igraph_matrix, view)(const TYPE(igraph_matrix) *m, const BASE *data, long int nrow, long int ncol); @@ -207,37 +207,33 @@ /* Print as text */ /*------------------------*/ -int FUNCTION(igraph_matrix, print)(const TYPE(igraph_matrix) *m); -int FUNCTION(igraph_matrix, printf)(const TYPE(igraph_matrix) *m, +DECLDIR int FUNCTION(igraph_matrix, print)(const TYPE(igraph_matrix) *m); +DECLDIR int FUNCTION(igraph_matrix, printf)(const TYPE(igraph_matrix) *m, const char *format); -int FUNCTION(igraph_matrix, fprint)(const TYPE(igraph_matrix) *m, +DECLDIR int FUNCTION(igraph_matrix, fprint)(const TYPE(igraph_matrix) *m, FILE *file); #ifdef BASE_COMPLEX -int igraph_matrix_complex_real(const igraph_matrix_complex_t *v, +DECLDIR int igraph_matrix_complex_real(const igraph_matrix_complex_t *v, igraph_matrix_t *real); -int igraph_matrix_complex_imag(const igraph_matrix_complex_t *v, +DECLDIR int igraph_matrix_complex_imag(const igraph_matrix_complex_t *v, igraph_matrix_t *imag); -int igraph_matrix_complex_realimag(const igraph_matrix_complex_t *v, +DECLDIR int igraph_matrix_complex_realimag(const igraph_matrix_complex_t *v, igraph_matrix_t *real, igraph_matrix_t *imag); -int igraph_matrix_complex_create(igraph_matrix_complex_t *v, +DECLDIR int igraph_matrix_complex_create(igraph_matrix_complex_t *v, const igraph_matrix_t *real, const igraph_matrix_t *imag); -int igraph_matrix_complex_create_polar(igraph_matrix_complex_t *v, +DECLDIR int igraph_matrix_complex_create_polar(igraph_matrix_complex_t *v, const igraph_matrix_t *r, const igraph_matrix_t *theta); #endif -/* ----------------------------------------------------------------------------*/ -/* For internal use only, may be removed, rewritten ... */ -/* ----------------------------------------------------------------------------*/ - -int FUNCTION(igraph_matrix, permdelete_rows)(TYPE(igraph_matrix) *m, +DECLDIR int FUNCTION(igraph_matrix, permdelete_rows)(TYPE(igraph_matrix) *m, long int *index, long int nremove); -int FUNCTION(igraph_matrix, delete_rows_neg)(TYPE(igraph_matrix) *m, +DECLDIR int FUNCTION(igraph_matrix, delete_rows_neg)(TYPE(igraph_matrix) *m, const igraph_vector_t *neg, long int nremove); diff --git a/igraph/include/igraph_memory.h b/igraph/include/igraph_memory.h --- a/igraph/include/igraph_memory.h +++ b/igraph/include/igraph_memory.h @@ -21,8 +21,8 @@ */ -#ifndef REST_MEMORY_H -#define REST_MEMORY_H +#ifndef IGRAPH_MEMORY_H +#define IGRAPH_MEMORY_H #include #include "igraph_decls.h" diff --git a/igraph/include/igraph_nongraph.h b/igraph/include/igraph_nongraph.h --- a/igraph/include/igraph_nongraph.h +++ b/igraph/include/igraph_nongraph.h @@ -72,7 +72,6 @@ DECLDIR int igraph_running_mean(const igraph_vector_t *data, igraph_vector_t *res, igraph_integer_t binwidth); -DECLDIR int igraph_fisher_yates_shuffle(igraph_vector_t *seq); DECLDIR int igraph_random_sample(igraph_vector_t *res, igraph_real_t l, igraph_real_t h, igraph_integer_t length); DECLDIR int igraph_convex_hull(const igraph_matrix_t *data, igraph_vector_t *resverts, diff --git a/igraph/include/igraph_scg.h b/igraph/include/igraph_scg.h --- a/igraph/include/igraph_scg.h +++ b/igraph/include/igraph_scg.h @@ -48,94 +48,94 @@ IGRAPH_SCG_DIRECTION_RIGHT = 3 } igraph_scg_direction_t; -int igraph_scg_grouping(const igraph_matrix_t *V, - igraph_vector_t *groups, - igraph_integer_t nt, - const igraph_vector_t *nt_vec, - igraph_scg_matrix_t mtype, - igraph_scg_algorithm_t algo, - const igraph_vector_t *p, - igraph_integer_t maxiter); +DECLDIR int igraph_scg_grouping(const igraph_matrix_t *V, + igraph_vector_t *groups, + igraph_integer_t nt, + const igraph_vector_t *nt_vec, + igraph_scg_matrix_t mtype, + igraph_scg_algorithm_t algo, + const igraph_vector_t *p, + igraph_integer_t maxiter); -int igraph_scg_semiprojectors(const igraph_vector_t *groups, - igraph_scg_matrix_t mtype, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse, - const igraph_vector_t *p, - igraph_scg_norm_t norm); +DECLDIR int igraph_scg_semiprojectors(const igraph_vector_t *groups, + igraph_scg_matrix_t mtype, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse, + const igraph_vector_t *p, + igraph_scg_norm_t norm); -int igraph_scg_norm_eps(const igraph_matrix_t *V, - const igraph_vector_t *groups, - igraph_vector_t *eps, - igraph_scg_matrix_t mtype, - const igraph_vector_t *p, - igraph_scg_norm_t norm); +DECLDIR int igraph_scg_norm_eps(const igraph_matrix_t *V, + const igraph_vector_t *groups, + igraph_vector_t *eps, + igraph_scg_matrix_t mtype, + const igraph_vector_t *p, + igraph_scg_norm_t norm); -int igraph_scg_adjacency(const igraph_t *graph, - const igraph_matrix_t *matrix, - const igraph_sparsemat_t *sparsemat, - const igraph_vector_t *ev, - igraph_integer_t nt, - const igraph_vector_t *nt_vec, - igraph_scg_algorithm_t algo, - igraph_vector_t *values, - igraph_matrix_t *vectors, - igraph_vector_t *groups, - igraph_bool_t use_arpack, - igraph_integer_t maxiter, - igraph_t *scg_graph, - igraph_matrix_t *scg_matrix, - igraph_sparsemat_t *scg_sparsemat, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse); +DECLDIR int igraph_scg_adjacency(const igraph_t *graph, + const igraph_matrix_t *matrix, + const igraph_sparsemat_t *sparsemat, + const igraph_vector_t *ev, + igraph_integer_t nt, + const igraph_vector_t *nt_vec, + igraph_scg_algorithm_t algo, + igraph_vector_t *values, + igraph_matrix_t *vectors, + igraph_vector_t *groups, + igraph_bool_t use_arpack, + igraph_integer_t maxiter, + igraph_t *scg_graph, + igraph_matrix_t *scg_matrix, + igraph_sparsemat_t *scg_sparsemat, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse); -int igraph_scg_stochastic(const igraph_t *graph, - const igraph_matrix_t *matrix, - const igraph_sparsemat_t *sparsemat, - const igraph_vector_t *ev, - igraph_integer_t nt, - const igraph_vector_t *nt_vec, - igraph_scg_algorithm_t algo, - igraph_scg_norm_t norm, - igraph_vector_complex_t *values, - igraph_matrix_complex_t *vectors, - igraph_vector_t *groups, - igraph_vector_t *p, - igraph_bool_t use_arpack, - igraph_integer_t maxiter, - igraph_t *scg_graph, - igraph_matrix_t *scg_matrix, - igraph_sparsemat_t *scg_sparsemat, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse); +DECLDIR int igraph_scg_stochastic(const igraph_t *graph, + const igraph_matrix_t *matrix, + const igraph_sparsemat_t *sparsemat, + const igraph_vector_t *ev, + igraph_integer_t nt, + const igraph_vector_t *nt_vec, + igraph_scg_algorithm_t algo, + igraph_scg_norm_t norm, + igraph_vector_complex_t *values, + igraph_matrix_complex_t *vectors, + igraph_vector_t *groups, + igraph_vector_t *p, + igraph_bool_t use_arpack, + igraph_integer_t maxiter, + igraph_t *scg_graph, + igraph_matrix_t *scg_matrix, + igraph_sparsemat_t *scg_sparsemat, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse); -int igraph_scg_laplacian(const igraph_t *graph, - const igraph_matrix_t *matrix, - const igraph_sparsemat_t *sparsemat, - const igraph_vector_t *ev, - igraph_integer_t nt, - const igraph_vector_t *nt_vec, - igraph_scg_algorithm_t algo, - igraph_scg_norm_t norm, - igraph_scg_direction_t direction, - igraph_vector_complex_t *values, - igraph_matrix_complex_t *vectors, - igraph_vector_t *groups, - igraph_bool_t use_arpack, - igraph_integer_t maxiter, - igraph_t *scg_graph, - igraph_matrix_t *scg_matrix, - igraph_sparsemat_t *scg_sparsemat, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse); +DECLDIR int igraph_scg_laplacian(const igraph_t *graph, + const igraph_matrix_t *matrix, + const igraph_sparsemat_t *sparsemat, + const igraph_vector_t *ev, + igraph_integer_t nt, + const igraph_vector_t *nt_vec, + igraph_scg_algorithm_t algo, + igraph_scg_norm_t norm, + igraph_scg_direction_t direction, + igraph_vector_complex_t *values, + igraph_matrix_complex_t *vectors, + igraph_vector_t *groups, + igraph_bool_t use_arpack, + igraph_integer_t maxiter, + igraph_t *scg_graph, + igraph_matrix_t *scg_matrix, + igraph_sparsemat_t *scg_sparsemat, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse); __END_DECLS diff --git a/igraph/include/igraph_sparsemat.h b/igraph/include/igraph_sparsemat.h --- a/igraph/include/igraph_sparsemat.h +++ b/igraph/include/igraph_sparsemat.h @@ -59,228 +59,226 @@ int col; } igraph_sparsemat_iterator_t; -int igraph_sparsemat_init(igraph_sparsemat_t *A, int rows, int cols, int nzmax); -int igraph_sparsemat_copy(igraph_sparsemat_t *to, +DECLDIR int igraph_sparsemat_init(igraph_sparsemat_t *A, int rows, int cols, int nzmax); +DECLDIR int igraph_sparsemat_copy(igraph_sparsemat_t *to, const igraph_sparsemat_t *from); -void igraph_sparsemat_destroy(igraph_sparsemat_t *A); -int igraph_sparsemat_realloc(igraph_sparsemat_t *A, int nzmax); +DECLDIR void igraph_sparsemat_destroy(igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_realloc(igraph_sparsemat_t *A, int nzmax); -long int igraph_sparsemat_nrow(const igraph_sparsemat_t *A); -long int igraph_sparsemat_ncol(const igraph_sparsemat_t *B); -igraph_sparsemat_type_t igraph_sparsemat_type(const igraph_sparsemat_t *A); -igraph_bool_t igraph_sparsemat_is_triplet(const igraph_sparsemat_t *A); -igraph_bool_t igraph_sparsemat_is_cc(const igraph_sparsemat_t *A); +DECLDIR long int igraph_sparsemat_nrow(const igraph_sparsemat_t *A); +DECLDIR long int igraph_sparsemat_ncol(const igraph_sparsemat_t *B); +DECLDIR igraph_sparsemat_type_t igraph_sparsemat_type(const igraph_sparsemat_t *A); +DECLDIR igraph_bool_t igraph_sparsemat_is_triplet(const igraph_sparsemat_t *A); +DECLDIR igraph_bool_t igraph_sparsemat_is_cc(const igraph_sparsemat_t *A); -int igraph_sparsemat_permute(const igraph_sparsemat_t *A, - const igraph_vector_int_t *p, - const igraph_vector_int_t *q, - igraph_sparsemat_t *res); +DECLDIR int igraph_sparsemat_permute(const igraph_sparsemat_t *A, + const igraph_vector_int_t *p, + const igraph_vector_int_t *q, + igraph_sparsemat_t *res); -int igraph_sparsemat_index(const igraph_sparsemat_t *A, - const igraph_vector_int_t *p, - const igraph_vector_int_t *q, - igraph_sparsemat_t *res, - igraph_real_t *constres); +DECLDIR int igraph_sparsemat_index(const igraph_sparsemat_t *A, + const igraph_vector_int_t *p, + const igraph_vector_int_t *q, + igraph_sparsemat_t *res, + igraph_real_t *constres); -int igraph_sparsemat_entry(igraph_sparsemat_t *A, int row, int col, - igraph_real_t elem); -int igraph_sparsemat_compress(const igraph_sparsemat_t *A, - igraph_sparsemat_t *res); -int igraph_sparsemat_transpose(const igraph_sparsemat_t *A, - igraph_sparsemat_t *res, int values); -igraph_bool_t igraph_sparsemat_is_symmetric(const igraph_sparsemat_t *A); -int igraph_sparsemat_dupl(igraph_sparsemat_t *A); -int igraph_sparsemat_fkeep(igraph_sparsemat_t *A, - int (*fkeep)(int, int, igraph_real_t, void*), - void *other); -int igraph_sparsemat_dropzeros(igraph_sparsemat_t *A); -int igraph_sparsemat_droptol(igraph_sparsemat_t *A, igraph_real_t tol); -int igraph_sparsemat_multiply(const igraph_sparsemat_t *A, - const igraph_sparsemat_t *B, - igraph_sparsemat_t *res); -int igraph_sparsemat_add(const igraph_sparsemat_t *A, - const igraph_sparsemat_t *B, - igraph_real_t alpha, - igraph_real_t beta, - igraph_sparsemat_t *res); -int igraph_sparsemat_gaxpy(const igraph_sparsemat_t *A, - const igraph_vector_t *x, - igraph_vector_t *res); +DECLDIR int igraph_sparsemat_entry(igraph_sparsemat_t *A, int row, int col, + igraph_real_t elem); +DECLDIR int igraph_sparsemat_compress(const igraph_sparsemat_t *A, + igraph_sparsemat_t *res); +DECLDIR int igraph_sparsemat_transpose(const igraph_sparsemat_t *A, + igraph_sparsemat_t *res, int values); +DECLDIR igraph_bool_t igraph_sparsemat_is_symmetric(const igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_dupl(igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_fkeep(igraph_sparsemat_t *A, + int (*fkeep)(int, int, igraph_real_t, void*), + void *other); +DECLDIR int igraph_sparsemat_dropzeros(igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_droptol(igraph_sparsemat_t *A, igraph_real_t tol); +DECLDIR int igraph_sparsemat_multiply(const igraph_sparsemat_t *A, + const igraph_sparsemat_t *B, + igraph_sparsemat_t *res); +DECLDIR int igraph_sparsemat_add(const igraph_sparsemat_t *A, + const igraph_sparsemat_t *B, + igraph_real_t alpha, + igraph_real_t beta, + igraph_sparsemat_t *res); +DECLDIR int igraph_sparsemat_gaxpy(const igraph_sparsemat_t *A, + const igraph_vector_t *x, + igraph_vector_t *res); -int igraph_sparsemat_lsolve(const igraph_sparsemat_t *A, - const igraph_vector_t *b, - igraph_vector_t *res); -int igraph_sparsemat_ltsolve(const igraph_sparsemat_t *A, - const igraph_vector_t *b, - igraph_vector_t *res); -int igraph_sparsemat_usolve(const igraph_sparsemat_t *A, - const igraph_vector_t *b, - igraph_vector_t *res); -int igraph_sparsemat_utsolve(const igraph_sparsemat_t *A, - const igraph_vector_t *b, - igraph_vector_t *res); +DECLDIR int igraph_sparsemat_lsolve(const igraph_sparsemat_t *A, + const igraph_vector_t *b, + igraph_vector_t *res); +DECLDIR int igraph_sparsemat_ltsolve(const igraph_sparsemat_t *A, + const igraph_vector_t *b, + igraph_vector_t *res); +DECLDIR int igraph_sparsemat_usolve(const igraph_sparsemat_t *A, + const igraph_vector_t *b, + igraph_vector_t *res); +DECLDIR int igraph_sparsemat_utsolve(const igraph_sparsemat_t *A, + const igraph_vector_t *b, + igraph_vector_t *res); -int igraph_sparsemat_cholsol(const igraph_sparsemat_t *A, - const igraph_vector_t *b, - igraph_vector_t *res, - int order); +DECLDIR int igraph_sparsemat_cholsol(const igraph_sparsemat_t *A, + const igraph_vector_t *b, + igraph_vector_t *res, + int order); -int igraph_sparsemat_lusol(const igraph_sparsemat_t *A, - const igraph_vector_t *b, - igraph_vector_t *res, - int order, - igraph_real_t tol); +DECLDIR int igraph_sparsemat_lusol(const igraph_sparsemat_t *A, + const igraph_vector_t *b, + igraph_vector_t *res, + int order, + igraph_real_t tol); -int igraph_sparsemat_print(const igraph_sparsemat_t *A, - FILE *outstream); +DECLDIR int igraph_sparsemat_print(const igraph_sparsemat_t *A, + FILE *outstream); -int igraph_sparsemat_eye(igraph_sparsemat_t *A, int n, int nzmax, - igraph_real_t value, - igraph_bool_t compress); +DECLDIR int igraph_sparsemat_eye(igraph_sparsemat_t *A, int n, int nzmax, + igraph_real_t value, + igraph_bool_t compress); -int igraph_sparsemat_diag(igraph_sparsemat_t *A, int nzmax, - const igraph_vector_t *values, - igraph_bool_t compress); +DECLDIR int igraph_sparsemat_diag(igraph_sparsemat_t *A, int nzmax, + const igraph_vector_t *values, + igraph_bool_t compress); -int igraph_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A, - igraph_bool_t directed); +DECLDIR int igraph_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A, + igraph_bool_t directed); -int igraph_weighted_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A, - igraph_bool_t directed, const char *attr, - igraph_bool_t loops); +DECLDIR int igraph_weighted_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A, + igraph_bool_t directed, const char *attr, + igraph_bool_t loops); -int igraph_get_sparsemat(const igraph_t *graph, igraph_sparsemat_t *res); +DECLDIR int igraph_get_sparsemat(const igraph_t *graph, igraph_sparsemat_t *res); -int igraph_matrix_as_sparsemat(igraph_sparsemat_t *res, - const igraph_matrix_t *mat, - igraph_real_t tol); +DECLDIR int igraph_matrix_as_sparsemat(igraph_sparsemat_t *res, + const igraph_matrix_t *mat, + igraph_real_t tol); -int igraph_sparsemat_as_matrix(igraph_matrix_t *res, - const igraph_sparsemat_t *spmat); +DECLDIR int igraph_sparsemat_as_matrix(igraph_matrix_t *res, + const igraph_sparsemat_t *spmat); typedef enum { IGRAPH_SPARSEMAT_SOLVE_LU, IGRAPH_SPARSEMAT_SOLVE_QR } igraph_sparsemat_solve_t; -int igraph_sparsemat_arpack_rssolve(const igraph_sparsemat_t *A, - igraph_arpack_options_t *options, - igraph_arpack_storage_t *storage, - igraph_vector_t *values, - igraph_matrix_t *vectors, - igraph_sparsemat_solve_t solvemethod); +DECLDIR int igraph_sparsemat_arpack_rssolve(const igraph_sparsemat_t *A, + igraph_arpack_options_t *options, + igraph_arpack_storage_t *storage, + igraph_vector_t *values, + igraph_matrix_t *vectors, + igraph_sparsemat_solve_t solvemethod); -int igraph_sparsemat_arpack_rnsolve(const igraph_sparsemat_t *A, - igraph_arpack_options_t *options, - igraph_arpack_storage_t *storage, - igraph_matrix_t *values, - igraph_matrix_t *vectors); +DECLDIR int igraph_sparsemat_arpack_rnsolve(const igraph_sparsemat_t *A, + igraph_arpack_options_t *options, + igraph_arpack_storage_t *storage, + igraph_matrix_t *values, + igraph_matrix_t *vectors); -int igraph_sparsemat_lu(const igraph_sparsemat_t *A, - const igraph_sparsemat_symbolic_t *dis, - igraph_sparsemat_numeric_t *din, double tol); +DECLDIR int igraph_sparsemat_lu(const igraph_sparsemat_t *A, + const igraph_sparsemat_symbolic_t *dis, + igraph_sparsemat_numeric_t *din, double tol); -int igraph_sparsemat_qr(const igraph_sparsemat_t *A, - const igraph_sparsemat_symbolic_t *dis, - igraph_sparsemat_numeric_t *din); +DECLDIR int igraph_sparsemat_qr(const igraph_sparsemat_t *A, + const igraph_sparsemat_symbolic_t *dis, + igraph_sparsemat_numeric_t *din); -int igraph_sparsemat_luresol(const igraph_sparsemat_symbolic_t *dis, - const igraph_sparsemat_numeric_t *din, - const igraph_vector_t *b, - igraph_vector_t *res); +DECLDIR int igraph_sparsemat_luresol(const igraph_sparsemat_symbolic_t *dis, + const igraph_sparsemat_numeric_t *din, + const igraph_vector_t *b, + igraph_vector_t *res); -int igraph_sparsemat_qrresol(const igraph_sparsemat_symbolic_t *dis, - const igraph_sparsemat_numeric_t *din, - const igraph_vector_t *b, - igraph_vector_t *res); +DECLDIR int igraph_sparsemat_qrresol(const igraph_sparsemat_symbolic_t *dis, + const igraph_sparsemat_numeric_t *din, + const igraph_vector_t *b, + igraph_vector_t *res); -int igraph_sparsemat_symbqr(long int order, const igraph_sparsemat_t *A, - igraph_sparsemat_symbolic_t *dis); +DECLDIR int igraph_sparsemat_symbqr(long int order, const igraph_sparsemat_t *A, + igraph_sparsemat_symbolic_t *dis); -int igraph_sparsemat_symblu(long int order, const igraph_sparsemat_t *A, - igraph_sparsemat_symbolic_t *dis); +DECLDIR int igraph_sparsemat_symblu(long int order, const igraph_sparsemat_t *A, + igraph_sparsemat_symbolic_t *dis); -void igraph_sparsemat_symbolic_destroy(igraph_sparsemat_symbolic_t *dis); -void igraph_sparsemat_numeric_destroy(igraph_sparsemat_numeric_t *din); +DECLDIR void igraph_sparsemat_symbolic_destroy(igraph_sparsemat_symbolic_t *dis); +DECLDIR void igraph_sparsemat_numeric_destroy(igraph_sparsemat_numeric_t *din); -igraph_real_t igraph_sparsemat_max(igraph_sparsemat_t *A); -igraph_real_t igraph_sparsemat_min(igraph_sparsemat_t *A); -int igraph_sparsemat_minmax(igraph_sparsemat_t *A, - igraph_real_t *min, igraph_real_t *max); +DECLDIR igraph_real_t igraph_sparsemat_max(igraph_sparsemat_t *A); +DECLDIR igraph_real_t igraph_sparsemat_min(igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_minmax(igraph_sparsemat_t *A, + igraph_real_t *min, igraph_real_t *max); -long int igraph_sparsemat_count_nonzero(igraph_sparsemat_t *A); -long int igraph_sparsemat_count_nonzerotol(igraph_sparsemat_t *A, - igraph_real_t tol); -int igraph_sparsemat_rowsums(const igraph_sparsemat_t *A, - igraph_vector_t *res); -int igraph_sparsemat_colsums(const igraph_sparsemat_t *A, - igraph_vector_t *res); +DECLDIR long int igraph_sparsemat_count_nonzero(igraph_sparsemat_t *A); +DECLDIR long int igraph_sparsemat_count_nonzerotol(igraph_sparsemat_t *A, + igraph_real_t tol); +DECLDIR int igraph_sparsemat_rowsums(const igraph_sparsemat_t *A, + igraph_vector_t *res); +DECLDIR int igraph_sparsemat_colsums(const igraph_sparsemat_t *A, + igraph_vector_t *res); -int igraph_sparsemat_rowmins(igraph_sparsemat_t *A, - igraph_vector_t *res); -int igraph_sparsemat_colmins(igraph_sparsemat_t *A, - igraph_vector_t *res); +DECLDIR int igraph_sparsemat_rowmins(igraph_sparsemat_t *A, + igraph_vector_t *res); +DECLDIR int igraph_sparsemat_colmins(igraph_sparsemat_t *A, + igraph_vector_t *res); -int igraph_sparsemat_rowmaxs(igraph_sparsemat_t *A, - igraph_vector_t *res); -int igraph_sparsemat_colmaxs(igraph_sparsemat_t *A, - igraph_vector_t *res); +DECLDIR int igraph_sparsemat_rowmaxs(igraph_sparsemat_t *A, + igraph_vector_t *res); +DECLDIR int igraph_sparsemat_colmaxs(igraph_sparsemat_t *A, + igraph_vector_t *res); -int igraph_sparsemat_which_min_rows(igraph_sparsemat_t *A, - igraph_vector_t *res, - igraph_vector_int_t *pos); -int igraph_sparsemat_which_min_cols(igraph_sparsemat_t *A, - igraph_vector_t *res, - igraph_vector_int_t *pos); +DECLDIR int igraph_sparsemat_which_min_rows(igraph_sparsemat_t *A, + igraph_vector_t *res, + igraph_vector_int_t *pos); +DECLDIR int igraph_sparsemat_which_min_cols(igraph_sparsemat_t *A, + igraph_vector_t *res, + igraph_vector_int_t *pos); -int igraph_sparsemat_scale(igraph_sparsemat_t *A, igraph_real_t by); +DECLDIR int igraph_sparsemat_scale(igraph_sparsemat_t *A, igraph_real_t by); -int igraph_sparsemat_add_rows(igraph_sparsemat_t *A, long int n); -int igraph_sparsemat_add_cols(igraph_sparsemat_t *A, long int n); -int igraph_sparsemat_resize(igraph_sparsemat_t *A, long int nrow, - long int ncol, int nzmax); -int igraph_sparsemat_nonzero_storage(const igraph_sparsemat_t *A); -int igraph_sparsemat_getelements(const igraph_sparsemat_t *A, - igraph_vector_int_t *i, - igraph_vector_int_t *j, - igraph_vector_t *x); -int igraph_sparsemat_getelements_sorted(const igraph_sparsemat_t *A, - igraph_vector_int_t *i, - igraph_vector_int_t *j, - igraph_vector_t *x); -int igraph_sparsemat_scale_rows(igraph_sparsemat_t *A, - const igraph_vector_t *fact); -int igraph_sparsemat_scale_cols(igraph_sparsemat_t *A, - const igraph_vector_t *fact); -int igraph_sparsemat_multiply_by_dense(const igraph_sparsemat_t *A, - const igraph_matrix_t *B, - igraph_matrix_t *res); -int igraph_sparsemat_dense_multiply(const igraph_matrix_t *A, - const igraph_sparsemat_t *B, - igraph_matrix_t *res); +DECLDIR int igraph_sparsemat_add_rows(igraph_sparsemat_t *A, long int n); +DECLDIR int igraph_sparsemat_add_cols(igraph_sparsemat_t *A, long int n); +DECLDIR int igraph_sparsemat_resize(igraph_sparsemat_t *A, long int nrow, + long int ncol, int nzmax); +DECLDIR int igraph_sparsemat_nonzero_storage(const igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_getelements(const igraph_sparsemat_t *A, + igraph_vector_int_t *i, + igraph_vector_int_t *j, + igraph_vector_t *x); +DECLDIR int igraph_sparsemat_getelements_sorted(const igraph_sparsemat_t *A, + igraph_vector_int_t *i, + igraph_vector_int_t *j, + igraph_vector_t *x); +DECLDIR int igraph_sparsemat_scale_rows(igraph_sparsemat_t *A, + const igraph_vector_t *fact); +DECLDIR int igraph_sparsemat_scale_cols(igraph_sparsemat_t *A, + const igraph_vector_t *fact); +DECLDIR int igraph_sparsemat_multiply_by_dense(const igraph_sparsemat_t *A, + const igraph_matrix_t *B, + igraph_matrix_t *res); +DECLDIR int igraph_sparsemat_dense_multiply(const igraph_matrix_t *A, + const igraph_sparsemat_t *B, + igraph_matrix_t *res); -int igraph_i_sparsemat_view(igraph_sparsemat_t *A, int nzmax, int m, int n, - int *p, int *i, double *x, int nz); +DECLDIR int igraph_i_sparsemat_view(igraph_sparsemat_t *A, int nzmax, int m, int n, + int *p, int *i, double *x, int nz); -int igraph_sparsemat_sort(const igraph_sparsemat_t *A, - igraph_sparsemat_t *sorted); +DECLDIR int igraph_sparsemat_sort(const igraph_sparsemat_t *A, + igraph_sparsemat_t *sorted); -int igraph_sparsemat_nzmax(const igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_nzmax(const igraph_sparsemat_t *A); -int igraph_sparsemat_neg(igraph_sparsemat_t *A); +DECLDIR int igraph_sparsemat_neg(igraph_sparsemat_t *A); -int igraph_sparsemat_iterator_init(igraph_sparsemat_iterator_t *it, - igraph_sparsemat_t *sparsemat); -int igraph_sparsemat_iterator_reset(igraph_sparsemat_iterator_t *it); -igraph_bool_t -igraph_sparsemat_iterator_end(const igraph_sparsemat_iterator_t *it); -int igraph_sparsemat_iterator_row(const igraph_sparsemat_iterator_t *it); -int igraph_sparsemat_iterator_col(const igraph_sparsemat_iterator_t *it); -int igraph_sparsemat_iterator_idx(const igraph_sparsemat_iterator_t *it); -igraph_real_t -igraph_sparsemat_iterator_get(const igraph_sparsemat_iterator_t *it); -int igraph_sparsemat_iterator_next(igraph_sparsemat_iterator_t *it); +DECLDIR int igraph_sparsemat_iterator_init(igraph_sparsemat_iterator_t *it, + igraph_sparsemat_t *sparsemat); +DECLDIR int igraph_sparsemat_iterator_reset(igraph_sparsemat_iterator_t *it); +DECLDIR igraph_bool_t igraph_sparsemat_iterator_end(const igraph_sparsemat_iterator_t *it); +DECLDIR int igraph_sparsemat_iterator_row(const igraph_sparsemat_iterator_t *it); +DECLDIR int igraph_sparsemat_iterator_col(const igraph_sparsemat_iterator_t *it); +DECLDIR int igraph_sparsemat_iterator_idx(const igraph_sparsemat_iterator_t *it); +DECLDIR igraph_real_t igraph_sparsemat_iterator_get(const igraph_sparsemat_iterator_t *it); +DECLDIR int igraph_sparsemat_iterator_next(igraph_sparsemat_iterator_t *it); __END_DECLS diff --git a/igraph/include/igraph_statusbar.h b/igraph/include/igraph_statusbar.h --- a/igraph/include/igraph_statusbar.h +++ b/igraph/include/igraph_statusbar.h @@ -21,8 +21,8 @@ */ -#ifndef IGRAPH_STATUSBAR -#define IGRAPH_STATUSBAR +#ifndef IGRAPH_STATUSBAR_H +#define IGRAPH_STATUSBAR_H #include "igraph_decls.h" diff --git a/igraph/include/igraph_strvector.h b/igraph/include/igraph_strvector.h --- a/igraph/include/igraph_strvector.h +++ b/igraph/include/igraph_strvector.h @@ -57,7 +57,7 @@ #define IGRAPH_STRVECTOR_NULL { 0,0 } #define IGRAPH_STRVECTOR_INIT_FINALLY(v, size) \ do { IGRAPH_CHECK(igraph_strvector_init(v, size)); \ - IGRAPH_FINALLY( (igraph_finally_func_t*) igraph_strvector_destroy, v); } while (0) + IGRAPH_FINALLY( igraph_strvector_destroy, v); } while (0) DECLDIR int igraph_strvector_init(igraph_strvector_t *sv, long int len); DECLDIR void igraph_strvector_destroy(igraph_strvector_t *sv); diff --git a/igraph/include/igraph_types.h b/igraph/include/igraph_types.h --- a/igraph/include/igraph_types.h +++ b/igraph/include/igraph_types.h @@ -21,8 +21,8 @@ */ -#ifndef REST_TYPES_H -#define REST_TYPES_H +#ifndef IGRAPH_TYPES_H +#define IGRAPH_TYPES_H #include "igraph_decls.h" diff --git a/igraph/include/igraph_vector.h b/igraph/include/igraph_vector.h --- a/igraph/include/igraph_vector.h +++ b/igraph/include/igraph_vector.h @@ -28,14 +28,6 @@ #include "igraph_types.h" #include "igraph_complex.h" -#ifdef HAVE_STDINT_H - #include -#else - #if defined(HAVE_SYS_INT_TYPES_H) && HAVE_SYS_INT_TYPES_H - #include /* for Solaris */ - #endif -#endif - __BEGIN_DECLS /* -------------------------------------------------- */ @@ -144,6 +136,11 @@ do { IGRAPH_CHECK(igraph_vector_bool_init(v, size)); \ IGRAPH_FINALLY(igraph_vector_bool_destroy, v); } while (0) #endif +#ifndef IGRAPH_VECTOR_CHAR_INIT_FINALLY +#define IGRAPH_VECTOR_CHAR_INIT_FINALLY(v, size) \ + do { IGRAPH_CHECK(igraph_vector_char_init(v, size)); \ + IGRAPH_FINALLY(igraph_vector_char_destroy, v); } while (0) +#endif #ifndef IGRAPH_VECTOR_INT_INIT_FINALLY #define IGRAPH_VECTOR_INT_INIT_FINALLY(v, size) \ do { IGRAPH_CHECK(igraph_vector_int_init(v, size)); \ @@ -168,15 +165,14 @@ DECLDIR int igraph_vector_zapsmall(igraph_vector_t *v, igraph_real_t tol); -/* These are for internal use only */ -int igraph_vector_order(const igraph_vector_t* v, const igraph_vector_t *v2, +DECLDIR int igraph_vector_order(const igraph_vector_t* v, const igraph_vector_t *v2, igraph_vector_t* res, igraph_real_t maxval); -int igraph_vector_order1(const igraph_vector_t* v, +DECLDIR int igraph_vector_order1(const igraph_vector_t* v, igraph_vector_t* res, igraph_real_t maxval); -int igraph_vector_order1_int(const igraph_vector_t* v, +DECLDIR int igraph_vector_order1_int(const igraph_vector_t* v, igraph_vector_int_t* res, igraph_real_t maxval); -int igraph_vector_order2(igraph_vector_t *v); -int igraph_vector_rank(const igraph_vector_t *v, igraph_vector_t *res, +DECLDIR int igraph_vector_order2(igraph_vector_t *v); +DECLDIR int igraph_vector_rank(const igraph_vector_t *v, igraph_vector_t *res, long int nodes); __END_DECLS diff --git a/igraph/include/igraph_vector_pmt.h b/igraph/include/igraph_vector_pmt.h --- a/igraph/include/igraph_vector_pmt.h +++ b/igraph/include/igraph_vector_pmt.h @@ -40,29 +40,29 @@ /*--------------------*/ #ifndef VECTOR - /** - * \ingroup vector - * \define VECTOR - * \brief Accessing an element of a vector. - * - * Usage: - * \verbatim VECTOR(v)[0] \endverbatim - * to access the first element of the vector, you can also use this in - * assignments, like: - * \verbatim VECTOR(v)[10]=5; \endverbatim - * - * Note that there are no range checks right now. - * This functionality might be redefined later as a real function - * instead of a #define. - * \param v The vector object. - * - * Time complexity: O(1). - */ - #define VECTOR(v) ((v).stor_begin) +/** + * \ingroup vector + * \define VECTOR + * \brief Accessing an element of a vector. + * + * Usage: + * \verbatim VECTOR(v)[0] \endverbatim + * to access the first element of the vector, you can also use this in + * assignments, like: + * \verbatim VECTOR(v)[10]=5; \endverbatim + * + * Note that there are no range checks right now. + * This functionality might be redefined later as a real function + * instead of a #define. + * \param v The vector object. + * + * Time complexity: O(1). + */ +#define VECTOR(v) ((v).stor_begin) #endif DECLDIR BASE FUNCTION(igraph_vector, e)(const TYPE(igraph_vector)* v, long int pos); -BASE* FUNCTION(igraph_vector, e_ptr)(const TYPE(igraph_vector)* v, long int pos); +DECLDIR BASE* FUNCTION(igraph_vector, e_ptr)(const TYPE(igraph_vector)* v, long int pos); DECLDIR void FUNCTION(igraph_vector, set)(TYPE(igraph_vector)* v, long int pos, BASE value); DECLDIR BASE FUNCTION(igraph_vector, tail)(const TYPE(igraph_vector) *v); @@ -177,6 +177,9 @@ DECLDIR igraph_bool_t FUNCTION(igraph_vector, search)(const TYPE(igraph_vector) *v, long int from, BASE what, long int *pos); +DECLDIR igraph_bool_t FUNCTION(igraph_vector, binsearch_slice)(const TYPE(igraph_vector) *v, + BASE what, long int *pos, + long int start, long int end); DECLDIR igraph_bool_t FUNCTION(igraph_vector, binsearch)(const TYPE(igraph_vector) *v, BASE what, long int *pos); DECLDIR igraph_bool_t FUNCTION(igraph_vector, binsearch2)(const TYPE(igraph_vector) *v, @@ -202,6 +205,7 @@ /*-----------*/ DECLDIR void FUNCTION(igraph_vector, sort)(TYPE(igraph_vector) *v); +DECLDIR void FUNCTION(igraph_vector, reverse_sort)(TYPE(igraph_vector) *v); DECLDIR long int FUNCTION(igraph_vector, qsort_ind)(TYPE(igraph_vector) *v, igraph_vector_t *inds, igraph_bool_t descending); @@ -209,10 +213,10 @@ /* Printing */ /*-----------*/ -int FUNCTION(igraph_vector, print)(const TYPE(igraph_vector) *v); -int FUNCTION(igraph_vector, printf)(const TYPE(igraph_vector) *v, +DECLDIR int FUNCTION(igraph_vector, print)(const TYPE(igraph_vector) *v); +DECLDIR int FUNCTION(igraph_vector, printf)(const TYPE(igraph_vector) *v, const char *format); -int FUNCTION(igraph_vector, fprint)(const TYPE(igraph_vector) *v, FILE *file); +DECLDIR int FUNCTION(igraph_vector, fprint)(const TYPE(igraph_vector) *v, FILE *file); #ifdef BASE_COMPLEX @@ -232,34 +236,30 @@ #endif -/* ----------------------------------------------------------------------------*/ -/* For internal use only, may be removed, rewritten ... */ -/* ----------------------------------------------------------------------------*/ - -int FUNCTION(igraph_vector, init_real)(TYPE(igraph_vector)*v, int no, ...); -int FUNCTION(igraph_vector, init_int)(TYPE(igraph_vector)*v, int no, ...); -int FUNCTION(igraph_vector, init_real_end)(TYPE(igraph_vector)*v, BASE endmark, ...); -int FUNCTION(igraph_vector, init_int_end)(TYPE(igraph_vector)*v, int endmark, ...); +DECLDIR int FUNCTION(igraph_vector, init_real)(TYPE(igraph_vector)*v, int no, ...); +DECLDIR int FUNCTION(igraph_vector, init_int)(TYPE(igraph_vector)*v, int no, ...); +DECLDIR int FUNCTION(igraph_vector, init_real_end)(TYPE(igraph_vector)*v, BASE endmark, ...); +DECLDIR int FUNCTION(igraph_vector, init_int_end)(TYPE(igraph_vector)*v, int endmark, ...); -int FUNCTION(igraph_vector, move_interval)(TYPE(igraph_vector) *v, +DECLDIR int FUNCTION(igraph_vector, move_interval)(TYPE(igraph_vector) *v, long int begin, long int end, long int to); -int FUNCTION(igraph_vector, move_interval2)(TYPE(igraph_vector) *v, +DECLDIR int FUNCTION(igraph_vector, move_interval2)(TYPE(igraph_vector) *v, long int begin, long int end, long int to); -void FUNCTION(igraph_vector, permdelete)(TYPE(igraph_vector) *v, +DECLDIR void FUNCTION(igraph_vector, permdelete)(TYPE(igraph_vector) *v, const igraph_vector_t *index, long int nremove); -int FUNCTION(igraph_vector, filter_smaller)(TYPE(igraph_vector) *v, BASE elem); -int FUNCTION(igraph_vector, get_interval)(const TYPE(igraph_vector) *v, +DECLDIR int FUNCTION(igraph_vector, filter_smaller)(TYPE(igraph_vector) *v, BASE elem); +DECLDIR int FUNCTION(igraph_vector, get_interval)(const TYPE(igraph_vector) *v, TYPE(igraph_vector) *res, long int from, long int to); -int FUNCTION(igraph_vector, difference_sorted)(const TYPE(igraph_vector) *v1, +DECLDIR int FUNCTION(igraph_vector, difference_sorted)(const TYPE(igraph_vector) *v1, const TYPE(igraph_vector) *v2, TYPE(igraph_vector) *result); -int FUNCTION(igraph_vector, intersect_sorted)(const TYPE(igraph_vector) *v1, +DECLDIR int FUNCTION(igraph_vector, intersect_sorted)(const TYPE(igraph_vector) *v1, const TYPE(igraph_vector) *v2, TYPE(igraph_vector) *result); -int FUNCTION(igraph_vector, index)(const TYPE(igraph_vector) *v, +DECLDIR int FUNCTION(igraph_vector, index)(const TYPE(igraph_vector) *v, TYPE(igraph_vector) *newv, const igraph_vector_t *idx); -int FUNCTION(igraph_vector, index_int)(TYPE(igraph_vector) *v, +DECLDIR int FUNCTION(igraph_vector, index_int)(TYPE(igraph_vector) *v, const igraph_vector_int_t *idx); diff --git a/igraph/include/igraph_version.h b/igraph/include/igraph_version.h --- a/igraph/include/igraph_version.h +++ b/igraph/include/igraph_version.h @@ -28,13 +28,13 @@ __BEGIN_DECLS -#define IGRAPH_VERSION "0.8.0" +#define IGRAPH_VERSION "0.8.5" #define IGRAPH_VERSION_MAJOR 0 #define IGRAPH_VERSION_MINOR 8 -#define IGRAPH_VERSION_PATCH 0 +#define IGRAPH_VERSION_PATCH 5 #define IGRAPH_VERSION_PRERELEASE "" -int igraph_version(const char **version_string, +DECLDIR int igraph_version(const char **version_string, int *major, int *minor, int *subminor); diff --git a/igraph/include/igraph_visitor.h b/igraph/include/igraph_visitor.h --- a/igraph/include/igraph_visitor.h +++ b/igraph/include/igraph_visitor.h @@ -62,7 +62,7 @@ * as a request to stop the BFS and return to the caller. If a BFS * is terminated like this, then all elements of the result vectors * that were not yet calculated at the point of the termination - * contain \c IGRAPH_NAN. + * contain NaN. * * \sa \ref igraph_bfs() */ @@ -109,7 +109,7 @@ * as a request to stop the DFS and return to the caller. If a DFS * is terminated like this, then all elements of the result vectors * that were not yet calculated at the point of the termination - * contain \c IGRAPH_NAN. + * contain NaN. * * \sa \ref igraph_dfs() */ diff --git a/igraph/include/infomap_FlowGraph.h b/igraph/include/infomap_FlowGraph.h --- a/igraph/include/infomap_FlowGraph.h +++ b/igraph/include/infomap_FlowGraph.h @@ -62,7 +62,7 @@ double alpha, beta; int Ndanglings; - vector danglings; // id of dangling nodes + std::vector danglings; // id of dangling nodes double exit; // double exitFlow; // diff --git a/igraph/include/infomap_Greedy.h b/igraph/include/infomap_Greedy.h --- a/igraph/include/infomap_Greedy.h +++ b/igraph/include/infomap_Greedy.h @@ -69,16 +69,16 @@ double alpha, beta; // local copy of fgraph alpha, beta (=alpha - Nnode = graph->Nnode;1) - vector node_index; // module number of each node + std::vector node_index; // module number of each node int Nempty; - vector mod_empty; + std::vector mod_empty; - vector mod_exit; // version tmp de node - vector mod_size; - vector mod_danglingSize; - vector mod_teleportWeight; - vector mod_members; + std::vector mod_exit; // version tmp de node + std::vector mod_size; + std::vector mod_danglingSize; + std::vector mod_teleportWeight; + std::vector mod_members; }; void delete_Greedy(Greedy *greedy); diff --git a/igraph/include/infomap_Node.h b/igraph/include/infomap_Node.h --- a/igraph/include/infomap_Node.h +++ b/igraph/include/infomap_Node.h @@ -30,18 +30,15 @@ #include "igraph_interface.h" -class Node; -using namespace std; - class Node { public: Node(); Node(int modulenr, double tpweight); - vector members; - vector< pair > inLinks; - vector< pair > outLinks; + std::vector members; + std::vector< std::pair > inLinks; + std::vector< std::pair > outLinks; double selfLink; double teleportWeight; diff --git a/igraph/include/plfit/error.h b/igraph/include/plfit/error.h --- a/igraph/include/plfit/error.h +++ b/igraph/include/plfit/error.h @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. diff --git a/igraph/include/plfit/gss.h b/igraph/include/plfit/gss.h --- a/igraph/include/plfit/gss.h +++ b/igraph/include/plfit/gss.h @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. @@ -55,7 +55,7 @@ * The gss() function calls this function to obtain the values of the objective * function when needed. A client program must implement this function to evaluate * the value of the objective function, given the location. - * + * * @param instance The user data sent for the gss() function by the client. * @param x The current value of the variable. * @retval double The value of the objective function for the current diff --git a/igraph/include/plfit/hzeta.h b/igraph/include/plfit/hzeta.h new file mode 100644 --- /dev/null +++ b/igraph/include/plfit/hzeta.h @@ -0,0 +1,96 @@ +/* This file was imported from a private scientific library + * based on GSL coined Home Scientific Libray (HSL) by its author + * Jerome Benoit; this very material is itself inspired from the + * material written by G. Jungan and distributed by GSL. + * Ultimately, some modifications were done in order to render the + * imported material independent from the rest of GSL. + */ + +/* `hsl/hsl_sf_zeta.h' C header file +// HSL - Home Scientific Library +// Copyright (C) 2005-2018 Jerome Benoit +// +// HSL is free software; you can redistribute it and/or +// modify it under the terms of the GNU General Public License +// as published by the Free Software Foundation; either version 2 +// of the License, or (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program; if not, write to the Free Software +// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + +/* For futher details, see its source conterpart src/hzeta.c */ + +/* Author: Jerome G. Benoit < jgmbenoit _at_ rezozer _dot_ net > */ + +#ifndef __HZETA_H__ +#define __HZETA_H__ + +#undef __BEGIN_DECLS +#undef __END_DECLS +#ifdef __cplusplus +# define __BEGIN_DECLS extern "C" { +# define __END_DECLS } +#else +# define __BEGIN_DECLS /* empty */ +# define __END_DECLS /* empty */ +#endif + +__BEGIN_DECLS + + +/* Hurwitz Zeta Function + * zeta(s,q) = Sum[ (k+q)^(-s), {k,0,Infinity} ] + * + * s > 1.0, q > 0.0 + */ +double hsl_sf_hzeta(const double s, const double q); + +/* First Derivative of Hurwitz Zeta Function + * zeta'(s,q) = - Sum[ Ln(k+q)/(k+q)^(s), {k,0,Infinity} ] + * + * s > 1.0, q > 0.0 + */ +double hsl_sf_hzeta_deriv(const double s, const double q); + +/* Second Derivative of Hurwitz Zeta Function + * zeta''(s,q) = + Sum[ Ln(k+q)^2/(k+q)^(s), {k,0,Infinity} ] + * + * s > 1.0, q > 0.0 + */ +double hsl_sf_hzeta_deriv2(const double s, const double q); + +/* Logarithm of Hurwitz Zeta Function + * lnzeta(s,q) = ln(zeta(s,q)) + * + * s > 1.0, q > 0.0 (and q >> 1) + */ +double hsl_sf_lnhzeta(const double s, const double q); + +/* Logarithmic Derivative of Hurwitz Zeta Function + * lnzeta'(s,q) = zeta'(s,q)/zeta(s,q) + * + * s > 1.0, q > 0.0 (and q >> 1) + */ +double hsl_sf_lnhzeta_deriv(const double s, const double q); + +/* Logarithm and Logarithmic Derivative of Hurwitz Zeta Function: + * nonredundant computation version: + * - lnzeta(s,q) and lnzeta'(s,q) are stored in *deriv0 and *deriv1, respectively; + * - the return value and the value stored in *deriv0 are the same; + * - deriv0 and deriv1 must be effective pointers, that is, not the NULL pointer. + * + * s > 1.0, q > 0.0 (and q >> 1) + */ +double hsl_sf_lnhzeta_deriv_tuple(const double s, const double q, double * deriv0, double * deriv1); + + +__END_DECLS + +#endif // __HZETA_H__ diff --git a/igraph/include/plfit/kolmogorov.h b/igraph/include/plfit/kolmogorov.h --- a/igraph/include/plfit/kolmogorov.h +++ b/igraph/include/plfit/kolmogorov.h @@ -1,17 +1,17 @@ /* kolmogorov.h - * + * * Copyright (C) 2010-2011 Tamas Nepusz - * + * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. diff --git a/igraph/include/plfit/mt.h b/igraph/include/plfit/mt.h new file mode 100644 --- /dev/null +++ b/igraph/include/plfit/mt.h @@ -0,0 +1,103 @@ +/* mt.h + * + * Mersenne Twister random number generator, based on the implementation of + * Michael Brundage (which has been placed in the public domain). + * + * Author: Tamas Nepusz (original by Michael Brundage) + * + * See the following URL for the original implementation: + * http://www.qbrundage.com/michaelb/pubs/essays/random_number_generation.html + * + * This file has been placed in the public domain. + */ + +#ifndef __MT_H__ +#define __MT_H__ + +/* VS 2010, i.e. _MSC_VER == 1600, already has stdint.h */ +#if defined(_MSC_VER) && _MSC_VER < 1600 +# define uint32_t __int32 +#else +# include +#endif + +#undef __BEGIN_DECLS +#undef __END_DECLS +#ifdef __cplusplus +# define __BEGIN_DECLS extern "C" { +# define __END_DECLS } +#else +# define __BEGIN_DECLS /* empty */ +# define __END_DECLS /* empty */ +#endif + +__BEGIN_DECLS + +#define MT_LEN 624 + +/** + * \def MT_RAND_MAX + * + * The maximum random number that \c mt_random() can generate. + */ +#define MT_RAND_MAX 0xFFFFFFFF + +/** + * Struct that stores the internal state of a Mersenne Twister random number + * generator. + */ +typedef struct { + int mt_index; + uint32_t mt_buffer[MT_LEN]; +} mt_rng_t; + +/** + * \brief Initializes a Mersenne Twister random number generator. + * + * The random number generator is seeded with random 32-bit numbers obtained + * from the \em built-in random number generator using consecutive calls to + * \c rand(). + * + * \param rng the random number generator to initialize + */ +void mt_init(mt_rng_t* rng); + +/** + * \brief Initializes a Mersenne Twister random number generator, seeding it + * from another one. + * + * The random number generator is seeded with random 32-bit numbers obtained + * from another, initialized Mersenne Twister random number generator. + * + * \param rng the random number generator to initialize + * \param seeder the random number generator that will seed the one being + * initialized. When null, the random number generator will + * be initialized from the built-in RNG as if \ref mt_init() + * was called. + */ +void mt_init_from_rng(mt_rng_t* rng, mt_rng_t* seeder); + +/** + * \brief Returns the next 32-bit random number from the given Mersenne Twister + * random number generator. + * + * \param rng the random number generator to use + * \return the next 32-bit random number from the generator + */ +uint32_t mt_random(mt_rng_t* rng); + +/** + * \brief Returns a uniformly distributed double from the interval [0;1) + * based on the next value of the given Mersenne Twister random number + * generator. + * + * \param rng the random number generator to use + * \return a uniformly distributed random number from the interval [0;1) + */ +double mt_uniform_01(mt_rng_t* rng); + +__END_DECLS + +#endif + + diff --git a/igraph/include/plfit/platform.h b/igraph/include/plfit/platform.h --- a/igraph/include/plfit/platform.h +++ b/igraph/include/plfit/platform.h @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. @@ -34,11 +34,22 @@ __BEGIN_DECLS +#if defined(_MSC_VER) && _MSC_VER < 1900 +#include + +#define snprintf igraph_i_snprintf +#define isnan(x) ((x) != (x)) +#define isfinite(x) _finite(x) + +extern double _plfit_fmin(double a, double b); +extern double _plfit_round(double x); + +#define fmin _plfit_fmin +#define round _plfit_round +#endif + #ifdef _MSC_VER -#define snprintf sprintf_s #define inline __inline -#define isnan(x) _isnan(x) -#define isfinite(x) _finite(x) #endif #ifndef INFINITY @@ -46,7 +57,7 @@ #endif #ifndef NAN -# define NAN (INFINITY-INFINITY) +# define NAN ((double)0.0 / (double)DBL_MIN) #endif __END_DECLS diff --git a/igraph/include/plfit/plfit.h b/igraph/include/plfit/plfit.h --- a/igraph/include/plfit/plfit.h +++ b/igraph/include/plfit/plfit.h @@ -1,17 +1,18 @@ +/* vim:set ts=4 sw=4 sts=4 et: */ /* plfit.h - * + * * Copyright (C) 2010-2011 Tamas Nepusz - * + * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. @@ -21,6 +22,7 @@ #define __PLFIT_H__ #include +#include "mt.h" #undef __BEGIN_DECLS #undef __END_DECLS @@ -35,47 +37,61 @@ __BEGIN_DECLS #define PLFIT_VERSION_MAJOR 0 -#define PLFIT_VERSION_MINOR 6 -#define PLFIT_VERSION_STRING "0.6" +#define PLFIT_VERSION_MINOR 8 +#define PLFIT_VERSION_STRING "0.8" typedef unsigned short int plfit_bool_t; typedef enum { - PLFIT_GSS_OR_LINEAR, - PLFIT_LINEAR_ONLY, - PLFIT_DEFAULT_CONTINUOUS_METHOD = PLFIT_GSS_OR_LINEAR + PLFIT_LINEAR_ONLY, + PLFIT_STRATIFIED_SAMPLING, + PLFIT_GSS_OR_LINEAR, + PLFIT_DEFAULT_CONTINUOUS_METHOD = PLFIT_STRATIFIED_SAMPLING } plfit_continuous_method_t; typedef enum { - PLFIT_LBFGS, - PLFIT_LINEAR_SCAN, - PLFIT_PRETEND_CONTINUOUS, - PLFIT_DEFAULT_DISCRETE_METHOD = PLFIT_LBFGS + PLFIT_LBFGS, + PLFIT_LINEAR_SCAN, + PLFIT_PRETEND_CONTINUOUS, + PLFIT_DEFAULT_DISCRETE_METHOD = PLFIT_LBFGS } plfit_discrete_method_t; +typedef enum { + PLFIT_P_VALUE_SKIP, + PLFIT_P_VALUE_APPROXIMATE, + PLFIT_P_VALUE_EXACT, + PLFIT_DEFAULT_P_VALUE_METHOD = PLFIT_P_VALUE_EXACT +} plfit_p_value_method_t; + typedef struct _plfit_result_t { - double alpha; /* fitted power-law exponent */ - double xmin; /* cutoff where the power-law behaviour kicks in */ - double L; /* log-likelihood of the sample */ - double D; /* test statistic for the KS test */ - double p; /* p-value of the KS test */ + double alpha; /* fitted power-law exponent */ + double xmin; /* cutoff where the power-law behaviour kicks in */ + double L; /* log-likelihood of the sample */ + double D; /* test statistic for the KS test */ + double p; /* p-value of the KS test */ } plfit_result_t; /********** structure that holds the options of plfit **********/ typedef struct _plfit_continuous_options_t { - plfit_bool_t finite_size_correction; - plfit_continuous_method_t xmin_method; + plfit_bool_t finite_size_correction; + plfit_continuous_method_t xmin_method; + plfit_p_value_method_t p_value_method; + double p_value_precision; + mt_rng_t* rng; } plfit_continuous_options_t; typedef struct _plfit_discrete_options_t { - plfit_bool_t finite_size_correction; - plfit_discrete_method_t alpha_method; - struct { - double min; - double max; - double step; - } alpha; + plfit_bool_t finite_size_correction; + plfit_discrete_method_t alpha_method; + struct { + double min; + double max; + double step; + } alpha; + plfit_p_value_method_t p_value_method; + double p_value_precision; + mt_rng_t* rng; } plfit_discrete_options_t; int plfit_continuous_options_init(plfit_continuous_options_t* options); @@ -87,23 +103,41 @@ /********** continuous power law distribution fitting **********/ int plfit_log_likelihood_continuous(double* xs, size_t n, double alpha, - double xmin, double* l); + double xmin, double* l); int plfit_estimate_alpha_continuous(double* xs, size_t n, double xmin, const plfit_continuous_options_t* options, plfit_result_t* result); -int plfit_estimate_alpha_continuous_sorted(double* xs, size_t n, double xmin, - const plfit_continuous_options_t* options, plfit_result_t* result); int plfit_continuous(double* xs, size_t n, - const plfit_continuous_options_t* options, plfit_result_t* result); + const plfit_continuous_options_t* options, plfit_result_t* result); -/********** discrete power law distribution fitting **********/ +/*********** discrete power law distribution fitting ***********/ int plfit_estimate_alpha_discrete(double* xs, size_t n, double xmin, const plfit_discrete_options_t* options, plfit_result_t *result); int plfit_log_likelihood_discrete(double* xs, size_t n, double alpha, double xmin, double* l); int plfit_discrete(double* xs, size_t n, const plfit_discrete_options_t* options, - plfit_result_t* result); + plfit_result_t* result); +/***** resampling routines to generate synthetic replicates ****/ + +int plfit_resample_continuous(double* xs, size_t n, double alpha, double xmin, + size_t num_samples, mt_rng_t* rng, double* result); +int plfit_resample_discrete(double* xs, size_t n, double alpha, double xmin, + size_t num_samples, mt_rng_t* rng, double* result); + +/******** calculating the p-value of a fitted model only *******/ + +int plfit_calculate_p_value_continuous(double* xs, size_t n, + const plfit_continuous_options_t* options, plfit_bool_t xmin_fixed, + plfit_result_t *result); +int plfit_calculate_p_value_discrete(double* xs, size_t n, + const plfit_discrete_options_t* options, plfit_bool_t xmin_fixed, + plfit_result_t *result); + +/************* calculating descriptive statistics **************/ + +int plfit_moments(double* data, size_t n, double* mean, double* variance, + double* skewness, double* kurtosis); + __END_DECLS #endif /* __PLFIT_H__ */ - diff --git a/igraph/include/plfit/sampling.h b/igraph/include/plfit/sampling.h new file mode 100644 --- /dev/null +++ b/igraph/include/plfit/sampling.h @@ -0,0 +1,177 @@ +/* sampling.h + * + * Copyright (C) 2012 Tamas Nepusz + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or (at + * your option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + */ + +#ifndef __SAMPLING_H__ +#define __SAMPLING_H__ + +#include +#include "mt.h" + +#undef __BEGIN_DECLS +#undef __END_DECLS +#ifdef __cplusplus +# define __BEGIN_DECLS extern "C" { +# define __END_DECLS } +#else +# define __BEGIN_DECLS /* empty */ +# define __END_DECLS /* empty */ +#endif + +__BEGIN_DECLS + +/** + * Draws a sample from a binomial distribution with the given count and + * probability values. + * + * This function is borrowed from R; see the corresponding license in + * \c rbinom.c. The return value is always an integer. + * + * The function is \em not thread-safe. + * + * \param n the number of trials + * \param p the success probability of each trial + * \param rng the Mersenne Twister random number generator to use + * \return the value drawn from the given binomial distribution. + */ +double plfit_rbinom(double n, double p, mt_rng_t* rng); + +/** + * Draws a sample from a Pareto distribution with the given minimum value and + * power-law exponent. + * + * \param xmin the minimum value of the distribution. Must be positive. + * \param alpha the exponent. Must be positive + * \param rng the Mersenne Twister random number generator to use + * + * \return the sample or NaN if one of the parameters is invalid + */ +extern double plfit_rpareto(double xmin, double alpha, mt_rng_t* rng); + +/** + * Draws a given number of samples from a Pareto distribution with the given + * minimum value and power-law exponent. + * + * \param xmin the minimum value of the distribution. Must be positive. + * \param alpha the exponent. Must be positive + * \param n the number of samples to draw + * \param rng the Mersenne Twister random number generator to use + * \param result the array where the result should be written. It must + * have enough space to store n items + * + * \return \c PLFIT_EINVAL if one of the parameters is invalid, zero otherwise + */ +int plfit_rpareto_array(double xmin, double alpha, size_t n, mt_rng_t* rng, + double* result); + +/** + * Draws a sample from a zeta distribution with the given minimum value and + * power-law exponent. + * + * \param xmin the minimum value of the distribution. Must be positive. + * \param alpha the exponent. Must be positive + * \param rng the Mersenne Twister random number generator to use + * + * \return the sample or NaN if one of the parameters is invalid + */ +extern double plfit_rzeta(long int xmin, double alpha, mt_rng_t* rng); + +/** + * Draws a given number of samples from a zeta distribution with the given + * minimum value and power-law exponent. + * + * \param xmin the minimum value of the distribution. Must be positive. + * \param alpha the exponent. Must be positive + * \param n the number of samples to draw + * \param rng the Mersenne Twister random number generator to use + * \param result the array where the result should be written. It must + * have enough space to store n items + * + * \return \c PLFIT_EINVAL if one of the parameters is invalid, zero otherwise + */ +int plfit_rzeta_array(long int xmin, double alpha, size_t n, mt_rng_t* rng, + double* result); + +/** + * Draws a sample from a uniform distribution with the given lower and + * upper bounds. + * + * The lower bound is inclusive, the uppoer bound is not. + * + * \param lo the lower bound + * \param hi the upper bound + * \param rng the Mersenne Twister random number generator to use + * \return the value drawn from the given uniform distribution. + */ +extern double plfit_runif(double lo, double hi, mt_rng_t* rng); + +/** + * Draws a sample from a uniform distribution over the [0; 1) interval. + * + * The interval is closed from the left and open from the right. + * + * \param rng the Mersenne Twister random number generator to use + * \return the value drawn from the given uniform distribution. + */ +extern double plfit_runif_01(mt_rng_t* rng); + +/** + * Random sampler using Walker's alias method. + */ +typedef struct { + long int num_bins; /**< Number of bins */ + long int* indexes; /**< Index of the "other" element in each bin */ + double* probs; /**< Probability of drawing the "own" element from a bin */ +} plfit_walker_alias_sampler_t; + +/** + * \brief Initializes the sampler with item probabilities. + * + * \param sampler the sampler to initialize + * \param ps pointer to an array containing a value proportional to the + * sampling probability of each item in the set being sampled. + * \param n the number of items in the array + * \return error code + */ +int plfit_walker_alias_sampler_init(plfit_walker_alias_sampler_t* sampler, + double* ps, size_t n); + +/** + * \brief Destroys an initialized sampler and frees the allocated memory. + * + * \param sampler the sampler to destroy + */ +void plfit_walker_alias_sampler_destroy(plfit_walker_alias_sampler_t* sampler); + +/** + * \brief Draws a given number of samples from the sampler and writes them + * to a given array. + * + * \param sampler the sampler to use + * \param xs pointer to an array where the sampled items should be + * written + * \param n the number of samples to draw + * \param rng the Mersenne Twister random number generator to use + * \return error code + */ +int plfit_walker_alias_sampler_sample(const plfit_walker_alias_sampler_t* sampler, + long int* xs, size_t n, mt_rng_t* rng); + +__END_DECLS + +#endif diff --git a/igraph/include/plfit/zeta.h b/igraph/include/plfit/zeta.h deleted file mode 100644 --- a/igraph/include/plfit/zeta.h +++ /dev/null @@ -1,53 +0,0 @@ -/* specfunc/gsl_sf_zeta.h - * - * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2004 Gerard Jungman - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -/* Author: G. Jungman */ - -/* This file was taken from the GNU Scientific Library. Some modifications - * were done in order to make it independent from the rest of GSL - */ - -#ifndef __ZETA_H__ -#define __ZETA_H__ - -#undef __BEGIN_DECLS -#undef __END_DECLS -#ifdef __cplusplus -# define __BEGIN_DECLS extern "C" { -# define __END_DECLS } -#else -# define __BEGIN_DECLS /* empty */ -# define __END_DECLS /* empty */ -#endif - -__BEGIN_DECLS - - -/* Hurwitz Zeta Function - * zeta(s,q) = Sum[ (k+q)^(-s), {k,0,Infinity} ] - * - * s > 1.0, q > 0.0 - */ -double gsl_sf_hzeta(const double s, const double q); - - -__END_DECLS - -#endif /* __ZETA_H__ */ - diff --git a/igraph/include/pottsmodel_2.h b/igraph/include/pottsmodel_2.h --- a/igraph/include/pottsmodel_2.h +++ b/igraph/include/pottsmodel_2.h diff --git a/igraph/include/prpack/prpack_base_graph.h b/igraph/include/prpack/prpack_base_graph.h --- a/igraph/include/prpack/prpack_base_graph.h +++ b/igraph/include/prpack/prpack_base_graph.h @@ -37,6 +37,6 @@ void normalize_weights(); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_csc.h b/igraph/include/prpack/prpack_csc.h --- a/igraph/include/prpack/prpack_csc.h +++ b/igraph/include/prpack/prpack_csc.h @@ -25,6 +25,6 @@ int64_t* heads; int64_t* tails; }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_csr.h b/igraph/include/prpack/prpack_csr.h --- a/igraph/include/prpack/prpack_csr.h +++ b/igraph/include/prpack/prpack_csr.h @@ -11,6 +11,6 @@ int* tails; }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_edge_list.h b/igraph/include/prpack/prpack_edge_list.h --- a/igraph/include/prpack/prpack_edge_list.h +++ b/igraph/include/prpack/prpack_edge_list.h @@ -11,6 +11,6 @@ int* tails; }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_igraph_graph.h b/igraph/include/prpack/prpack_igraph_graph.h --- a/igraph/include/prpack/prpack_igraph_graph.h +++ b/igraph/include/prpack/prpack_igraph_graph.h @@ -17,7 +17,7 @@ igraph_bool_t directed = true); }; -}; +} // PRPACK_IGRAPH_SUPPORT #endif diff --git a/igraph/include/prpack/prpack_preprocessed_ge_graph.h b/igraph/include/prpack/prpack_preprocessed_ge_graph.h --- a/igraph/include/prpack/prpack_preprocessed_ge_graph.h +++ b/igraph/include/prpack/prpack_preprocessed_ge_graph.h @@ -21,6 +21,6 @@ ~prpack_preprocessed_ge_graph(); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_preprocessed_graph.h b/igraph/include/prpack/prpack_preprocessed_graph.h --- a/igraph/include/prpack/prpack_preprocessed_graph.h +++ b/igraph/include/prpack/prpack_preprocessed_graph.h @@ -12,6 +12,6 @@ double* d; }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_preprocessed_gs_graph.h b/igraph/include/prpack/prpack_preprocessed_gs_graph.h --- a/igraph/include/prpack/prpack_preprocessed_gs_graph.h +++ b/igraph/include/prpack/prpack_preprocessed_gs_graph.h @@ -25,6 +25,6 @@ ~prpack_preprocessed_gs_graph(); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_preprocessed_scc_graph.h b/igraph/include/prpack/prpack_preprocessed_scc_graph.h --- a/igraph/include/prpack/prpack_preprocessed_scc_graph.h +++ b/igraph/include/prpack/prpack_preprocessed_scc_graph.h @@ -34,6 +34,6 @@ ~prpack_preprocessed_scc_graph(); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_preprocessed_schur_graph.h b/igraph/include/prpack/prpack_preprocessed_schur_graph.h --- a/igraph/include/prpack/prpack_preprocessed_schur_graph.h +++ b/igraph/include/prpack/prpack_preprocessed_schur_graph.h @@ -28,6 +28,6 @@ ~prpack_preprocessed_schur_graph(); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_result.h b/igraph/include/prpack/prpack_result.h --- a/igraph/include/prpack/prpack_result.h +++ b/igraph/include/prpack/prpack_result.h @@ -1,6 +1,8 @@ #ifndef PRPACK_RESULT #define PRPACK_RESULT +#include + namespace prpack { // Result class. @@ -14,7 +16,7 @@ double preprocess_time; double compute_time; long num_es_touched; - const char* method; + std::string method; int converged; // constructor prpack_result(); @@ -22,6 +24,6 @@ ~prpack_result(); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_solver.h b/igraph/include/prpack/prpack_solver.h --- a/igraph/include/prpack/prpack_solver.h +++ b/igraph/include/prpack/prpack_solver.h @@ -173,6 +173,6 @@ const char* method); }; -}; +} #endif diff --git a/igraph/include/prpack/prpack_utils.h b/igraph/include/prpack/prpack_utils.h --- a/igraph/include/prpack/prpack_utils.h +++ b/igraph/include/prpack/prpack_utils.h @@ -28,7 +28,7 @@ static double* permute(const int length, const double* a, const int* coding); }; -}; +} #endif diff --git a/igraph/include/scg_headers.h b/igraph/include/scg_headers.h --- a/igraph/include/scg_headers.h +++ b/igraph/include/scg_headers.h @@ -55,11 +55,11 @@ #ifndef SCG_HEADERS_H #define SCG_HEADERS_H -#include -#include - #include "igraph_types.h" #include "igraph_vector.h" + +#include +#include typedef struct ind_val { int ind; diff --git a/igraph/include/vector.pmt b/igraph/include/vector.pmt --- a/igraph/include/vector.pmt +++ b/igraph/include/vector.pmt @@ -754,17 +754,27 @@ /** * \ingroup vector + * \function igraph_vector_reverse_sort_cmp + * \brief Internal comparison function of vector elements, used by + * \ref igraph_vector_reverse_sort(). + */ + +int FUNCTION(igraph_vector, reverse_sort_cmp)(const void *a, const void *b) { + const BASE *da = (const BASE *) a; + const BASE *db = (const BASE *) b; + + return (*da < *db) - (*da > *db); +} + +/** + * \ingroup vector * \function igraph_vector_sort * \brief Sorts the elements of the vector into ascending order. * - * - * This function uses the built-in sort function of the C library. * \param v Pointer to an initialized vector object. * - * Time complexity: should be - * O(nlogn) for - * n - * elements. + * Time complexity: + * O(n log n) for n elements. */ void FUNCTION(igraph_vector, sort)(TYPE(igraph_vector) *v) { @@ -775,6 +785,24 @@ } /** + * \ingroup vector + * \function igraph_vector_reverse_sort + * \brief Sorts the elements of the vector into descending order. + * + * \param v Pointer to an initialized vector object. + * + * Time complexity: + * O(n log n) for n elements. + */ + +void FUNCTION(igraph_vector, reverse_sort)(TYPE(igraph_vector) *v) { + assert(v != NULL); + assert(v->stor_begin != NULL); + igraph_qsort(v->stor_begin, (size_t) FUNCTION(igraph_vector, size)(v), + sizeof(BASE), FUNCTION(igraph_vector, reverse_sort_cmp)); +} + +/** * Ascending comparison function passed to qsort from igraph_vector_qsort_ind */ int FUNCTION(igraph_vector, i_qsort_ind_cmp_asc)(const void *p1, const void *p2) { @@ -1710,6 +1738,51 @@ 0, FUNCTION(igraph_vector, size)(v)); } +/** + * \ingroup vector + * \function igraph_vector_binsearch_slice + * \brief Finds an element by binary searching a sorted slice of a vector. + * + * + + * It is assumed that the indicated slice of the vector, from \p start to \p end, + * is sorted. If the specified element (\p what) is not in the slice of the + * vector, then the position of where it should be inserted (to keep the vector + * sorted) is returned. + * \param v The \type igraph_vector_t object. + * \param what The element to search for. + * \param pos Pointer to a \type long int. This is set to the position of an + * instance of \p what in the slice of the vector if it is present. If \p + * v does not contain \p what then \p pos is set to the position to which + * it should be inserted (to keep the the vector sorted). + * \param start The start position of the slice to search (inclusive). + * \param end The end position of the slice to search (exclusive). + * \return Positive integer (true) if \p what is found in the vector, + * zero (false) otherwise. + * + * Time complexity: O(log(n)), + * n is the number of elements in the slice of \p v, i.e. \p end - \p start. + */ + +igraph_bool_t FUNCTION(igraph_vector, binsearch_slice)(const TYPE(igraph_vector) *v, + BASE what, long int *pos, + long int start, long int end) { + long int left = start; + long int right = end - 1; + + if (left < 0) + IGRAPH_ERROR("Invalid start position.", IGRAPH_EINVAL); + + if (right >= FUNCTION(igraph_vector, size)(v)) + IGRAPH_ERROR("Invalid end position.", IGRAPH_EINVAL); + + if (left > right) + IGRAPH_ERROR("Invalid slice, start position must be smaller than end position.", + IGRAPH_EINVAL); + + return FUNCTION(igraph_i_vector, binsearch_slice)(v, what, pos, start, end); +} + igraph_bool_t FUNCTION(igraph_i_vector, binsearch_slice)(const TYPE(igraph_vector) *v, BASE what, long int *pos, long int start, long int end) { @@ -1930,7 +2003,7 @@ * \function igraph_vector_append * \brief Append a vector to another one. * - * The target vector will be resized (except \p from is empty). + * The target vector will be resized (except when \p from is empty). * \param to The vector to append to. * \param from The vector to append, it is kept unchanged. * \return Error code. @@ -2008,8 +2081,8 @@ * \brief Update a vector from another one. * * After this operation the contents of \p to will be exactly the same - * \p from. \p to will be resized if it was originally shorter or - * longer than \p from. + * as that of \p from. The vector \p to will be resized if it was originally + * shorter or longer than \p from. * \param to The vector to update. * \param from The vector to update from. * \return Error code. @@ -2063,8 +2136,8 @@ * Note that currently no range checking is performed. * \param v The input vector. * \param i Index of the first element. - * \param j index of the second element. (Might be the same as the - * first.) + * \param j Index of the second element (may be the same as the + * first one). * \return Error code, currently always \c IGRAPH_SUCCESS. * * Time complexity: O(1). @@ -2110,7 +2183,7 @@ * \brief Shuffles a vector in-place using the Fisher-Yates method * * - * The Fisher-Yates shuffle ensures that every implementation is + * The Fisher-Yates shuffle ensures that every permutation is * equally probable when using a proper randomness source. Of course * this does not apply to pseudo-random generators as the cycle of * these generators is less than the number of possible permutations diff --git a/igraph/include/walktrap_communities.h b/igraph/include/walktrap_communities.h --- a/igraph/include/walktrap_communities.h +++ b/igraph/include/walktrap_communities.h @@ -54,12 +54,11 @@ // see readme.txt for more details -#ifndef COMMUNITIES_H -#define COMMUNITIES_H +#ifndef WALKTRAP_COMMUNITIES_H +#define WALKTRAP_COMMUNITIES_H #include "walktrap_graph.h" #include "walktrap_heap.h" - #include "igraph_community.h" #include "config.h" @@ -173,4 +172,4 @@ } } /* end of namespaces */ -#endif +#endif // WALKTRAP_COMMUNITIES_H diff --git a/igraph/include/walktrap_graph.h b/igraph/include/walktrap_graph.h --- a/igraph/include/walktrap_graph.h +++ b/igraph/include/walktrap_graph.h @@ -55,9 +55,8 @@ /* FSF address above was fixed by Tamas Nepusz */ -#ifndef GRAPH_H -#define GRAPH_H -#include +#ifndef WALKTRAP_GRAPH_H +#define WALKTRAP_GRAPH_H #include "igraph_community.h" @@ -65,8 +64,6 @@ namespace walktrap { -using namespace std; - class Edge { // code an edge of a given vertex public: int neighbor; // the number of the neighbor vertex @@ -104,5 +101,5 @@ } } /* end of namespaces */ -#endif +#endif // WALKTRAP_GRAPH_H diff --git a/igraph/include/walktrap_heap.h b/igraph/include/walktrap_heap.h --- a/igraph/include/walktrap_heap.h +++ b/igraph/include/walktrap_heap.h @@ -53,8 +53,8 @@ //----------------------------------------------------------------------------- // see readme.txt for more details -#ifndef HEAP_H -#define HEAP_H +#ifndef WALKTRAP_HEAP_H +#define WALKTRAP_HEAP_H namespace igraph { @@ -130,5 +130,5 @@ } } /* end of namespaces */ -#endif +#endif // WALKTRAP_HEAP_H diff --git a/igraph/src/DensityGrid.cpp b/igraph/src/DensityGrid.cpp --- a/igraph/src/DensityGrid.cpp +++ b/igraph/src/DensityGrid.cpp @@ -33,17 +33,14 @@ // This file contains the member definitions of the DensityGrid.h class // This code is modified from the original code by B.N. Wylie -#include +#include "drl_Node.h" +#include "DensityGrid.h" +#include "igraph_error.h" + #include -#include #include -#include using namespace std; - -#include "drl_Node.h" -#include "DensityGrid.h" -#include "igraph_error.h" #define GET_BIN(y, x) (Bins[y*GRID_SIZE+x]) diff --git a/igraph/src/DensityGrid_3d.cpp b/igraph/src/DensityGrid_3d.cpp --- a/igraph/src/DensityGrid_3d.cpp +++ b/igraph/src/DensityGrid_3d.cpp @@ -33,17 +33,14 @@ // This file contains the member definitions of the DensityGrid.h class // This code is modified from the original code by B.N. Wylie -#include +#include "drl_Node_3d.h" +#include "DensityGrid_3d.h" +#include "igraph_error.h" + #include -#include #include -#include using namespace std; - -#include "drl_Node_3d.h" -#include "DensityGrid_3d.h" -#include "igraph_error.h" #define GET_BIN(z, y, x) (Bins[(z*GRID_SIZE+y)*GRID_SIZE+x]) diff --git a/igraph/src/NetDataTypes.cpp b/igraph/src/NetDataTypes.cpp --- a/igraph/src/NetDataTypes.cpp +++ b/igraph/src/NetDataTypes.cpp @@ -43,10 +43,9 @@ #ifdef HAVE_CONFIG_H #include #endif -#include -#include -#include + #include "NetDataTypes.h" +#include //################################################################################# //############################################################################### diff --git a/igraph/src/NetRoutines.cpp b/igraph/src/NetRoutines.cpp --- a/igraph/src/NetRoutines.cpp +++ b/igraph/src/NetRoutines.cpp @@ -40,15 +40,15 @@ * (at your option) any later version. * * * ***************************************************************************/ -#include -#include -#include + #include "NetRoutines.h" #include "NetDataTypes.h" #include "igraph_types.h" #include "igraph_interface.h" #include "igraph_conversion.h" + +#include int igraph_i_read_network(const igraph_t *graph, const igraph_vector_t *weights, diff --git a/igraph/src/adjlist.c b/igraph/src/adjlist.c --- a/igraph/src/adjlist.c +++ b/igraph/src/adjlist.c @@ -37,7 +37,7 @@ * neighbor vertices or incident edges of a given vertex. Typically, * this representation is good if we need to iterate over the neighbors * of all vertices many times. E.g. when finding the shortest paths - * between every pairs of vertices or calculating closeness centrality + * between all pairs of vertices or calculating closeness centrality * for all the vertices. * * The igraph_adjlist_t stores the adjacency lists @@ -61,7 +61,7 @@ * the neighbors of v are queried and stored in a vector of the * adjacency list, so they don't need to be queried again. Lazy * adjacency lists are handy if you have an at least linear operation - * (because initialization is generally linear in terms of number of + * (because initialization is generally linear in terms of the number of * vertices), but you don't know how many vertices you will visit * during the computation. * @@ -73,9 +73,9 @@ /** * \function igraph_adjlist_init - * Initialize an adjacency list of vertices from a given graph + * \brief Constructs an adjacency list of vertices from a given graph. * - * Create a list of vectors containing the neighbors of all vertices + * Creates a list of vectors containing the neighbors of all vertices * in a graph. The adjacency list is independent of the graph after * creation, e.g. the graph can be destroyed and modified, the * adjacency list contains the state of the graph at the time of its @@ -133,7 +133,7 @@ /** * \function igraph_adjlist_init_empty - * Initialize an empty adjacency list + * \brief Initializes an empty adjacency list. * * Creates a list of vectors, one for each vertex. This is useful when you * are \em constructing a graph using an adjacency list representation as @@ -165,7 +165,7 @@ /** * \function igraph_adjlist_init_complementer - * Adjacency lists for the complementer graph + * \brief Adjacency lists for the complementer graph. * * This function creates adjacency lists for the complementer * of the input graph. In the complementer graph all edges are present @@ -248,7 +248,7 @@ /** * \function igraph_adjlist_destroy - * Deallocate memory + * \brief Deallocates an adjacency list. * * Free all memory allocated for an adjacency list. * \param al The adjacency list to destroy. @@ -283,7 +283,7 @@ /** * \function igraph_adjlist_size - * Number of vertices in an adjacency list. + * \brief Number of vertices in an adjacency list. * * \param al The adjacency list. * \return The number of elements. @@ -301,7 +301,7 @@ /** * \function igraph_adjlist_sort - * Sort each vector in an adjacency list. + * \brief Sorts each vector in an adjacency list. * * Sorts every vector of the adjacency list. * \param al The adjacency list. @@ -319,9 +319,10 @@ /** * \function igraph_adjlist_simplify - * Simplify + * \brief Simplifies an adjacency list. * - * Simplify an adjacency list, ie. remove loop and multiple edges. + * Simplifies an adjacency list, i.e. removes loop and multiple edges. + * * \param al The adjacency list. * \return Error code. * @@ -359,21 +360,27 @@ int igraph_adjlist_remove_duplicate(const igraph_t *graph, igraph_adjlist_t *al) { - long int i; - long int n = al->length; + long int i, j, l, n, p; + igraph_vector_int_t *v; + IGRAPH_UNUSED(graph); + + n = al->length; for (i = 0; i < n; i++) { - igraph_vector_int_t *v = &al->adjs[i]; - long int j, p = 1, l = igraph_vector_int_size(v); - for (j = 1; j < l; j++) { - long int e = (long int) VECTOR(*v)[j]; - /* Non-loop edges, and one end of loop edges are fine. */ - /* We use here, that the vector is sorted and we also keep it sorted */ - if (e != i || VECTOR(*v)[j - 1] != e) { - VECTOR(*v)[p++] = e; + v = &al->adjs[i]; + l = igraph_vector_int_size(v); + if (l > 0) { + p = 1; + for (j = 1; j < l; j++) { + long int e = (long int) VECTOR(*v)[j]; + /* Non-loop edges, and one end of loop edges are fine. */ + /* We assume that the vector is sorted and we also keep it sorted */ + if (e != i || VECTOR(*v)[j - 1] != e) { + VECTOR(*v)[p++] = e; + } } + igraph_vector_int_resize(v, p); } - igraph_vector_int_resize(v, p); } return 0; @@ -466,7 +473,7 @@ /** * \function igraph_adjedgelist_init - * Initialize an incidence list of edges + * \brief Initializes an incidence list of edges. * * This function was superseded by \ref igraph_inclist_init() in igraph 0.6. * Please use \ref igraph_inclist_init() instead of this function. @@ -484,7 +491,7 @@ /** * \function igraph_adjedgelist_destroy - * Frees all memory allocated for an incidence list. + * \brief Frees all memory allocated for an incidence list. * * This function was superseded by \ref igraph_inclist_destroy() in igraph 0.6. * Please use \ref igraph_inclist_destroy() instead of this function. @@ -500,21 +507,25 @@ int igraph_inclist_remove_duplicate(const igraph_t *graph, igraph_inclist_t *al) { - long int i; - long int n = al->length; + long int i, j, l, n, p; + igraph_vector_int_t* v; + + n = al->length; for (i = 0; i < n; i++) { - igraph_vector_int_t *v = &al->incs[i]; - long int j, p = 1, l = igraph_vector_int_size(v); - for (j = 1; j < l; j++) { - long int e = (long int) VECTOR(*v)[j]; - /* Non-loop edges and one end of loop edges are fine. */ - /* We use here, that the vector is sorted and we also keep it sorted */ - if (IGRAPH_FROM(graph, e) != IGRAPH_TO(graph, e) || - VECTOR(*v)[j - 1] != e) { - VECTOR(*v)[p++] = e; + v = &al->incs[i]; + l = igraph_vector_int_size(v); + if (l > 0) { + p = 1; + for (j = 1; j < l; j++) { + long int e = (long int) VECTOR(*v)[j]; + /* Non-loop edges and one end of loop edges are fine. */ + /* We assume that the vector is sorted and we also keep it sorted */ + if (VECTOR(*v)[j - 1] != e) { + VECTOR(*v)[p++] = e; + } } + igraph_vector_int_resize(v, p); } - igraph_vector_int_resize(v, p); } return 0; @@ -544,13 +555,21 @@ /** * \function igraph_inclist_init - * Initialize an incidence list of edges + * \brief Initializes an incidence list. * - * Create a list of vectors containing the incident edges for all + * Creates a list of vectors containing the incident edges for all * vertices. The incidence list is independent of the graph after * creation, subsequent changes of the graph object do not update the * incidence list, and changes to the incidence list do not update the * graph. + * + * + * When \p mode is \c IGRAPH_IN or \c IGRAPH_OUT, each edge ID will appear + * in the incidence list \em once. When \p mode is \c IGRAPH_ALL, each edge ID + * will appear in the incidence list \em twice, once for the source vertex + * and once for the target edge. It also means that the edge IDs of loop edges + * will appear \em twice for the \em same vertex. + * * \param graph The input graph. * \param il Pointer to an uninitialized incidence list. * \param mode Constant specifying whether incoming edges @@ -605,7 +624,7 @@ /** * \function igraph_inclist_init_empty - * \brief Initialize an incidence list corresponding to an empty graph. + * \brief Initializes an incidence list corresponding to an empty graph. * * This function essentially creates a list of empty vectors that may * be treated as an incidence list for a graph with a given number of @@ -638,7 +657,7 @@ /** * \function igraph_inclist_destroy - * Frees all memory allocated for an incidence list. + * \brief Frees all memory allocated for an incidence list. * * \param eal The incidence list to destroy. * @@ -657,7 +676,7 @@ /** * \function igraph_inclist_clear - * Removes all edges from an incidence list. + * \brief Removes all edges from an incidence list. * * \param il The incidence list. * Time complexity: depends on memory management, typically O(n), where n is @@ -672,7 +691,7 @@ /** * \function igraph_lazy_adjlist_init - * Constructor + * \brief Initialized a lazy adjacency list. * * Create a lazy adjacency list for vertices. This function only * allocates some memory for storing the vectors of an adjacency list, @@ -720,7 +739,7 @@ /** * \function igraph_lazy_adjlist_destroy - * Deallocate memory + * \brief Deallocate a lazt adjacency list. * * Free all allocated memory for a lazy adjacency list. * \param al The adjacency list to deallocate. @@ -735,7 +754,7 @@ /** * \function igraph_lazy_adjlist_clear - * Removes all edges from a lazy adjacency list. + * \brief Removes all edges from a lazy adjacency list. * * \param al The lazy adjacency list. * Time complexity: depends on memory management, typically O(n), where n is @@ -789,7 +808,7 @@ /** * \function igraph_lazy_adjedgelist_init - * Initializes a lazy incidence list of edges + * \brief Initializes a lazy incidence list of edges. * * This function was superseded by \ref igraph_lazy_inclist_init() in igraph 0.6. * Please use \ref igraph_lazy_inclist_init() instead of this function. @@ -807,7 +826,7 @@ /** * \function igraph_lazy_adjedgelist_destroy - * Frees all memory allocated for an incidence list. + * \brief Frees all memory allocated for an incidence list. * * This function was superseded by \ref igraph_lazy_inclist_destroy() in igraph 0.6. * Please use \ref igraph_lazy_inclist_destroy() instead of this function. @@ -830,17 +849,25 @@ /** * \function igraph_lazy_inclist_init - * Initializes a lazy incidence list of edges + * \brief Initializes a lazy incidence list of edges. * * Create a lazy incidence list for edges. This function only * allocates some memory for storing the vectors of an incidence list, * but the incident edges are not queried, only when \ref * igraph_lazy_inclist_get() is called. + * + * + * When \p mode is \c IGRAPH_IN or \c IGRAPH_OUT, each edge ID will appear + * in the incidence list \em once. When \p mode is \c IGRAPH_ALL, each edge ID + * will appear in the incidence list \em twice, once for the source vertex + * and once for the target edge. It also means that the edge IDs of loop edges + * will appear \em twice for the \em same vertex. + * * \param graph The input graph. * \param al Pointer to an uninitialized incidence list. * \param mode Constant, it gives whether incoming edges * (IGRAPH_IN), outgoing edges - * (IGRPAH_OUT) or both types of edges + * (IGRAPH_OUT) or both types of edges * (IGRAPH_ALL) are considered. It is ignored for * undirected graphs. * \return Error code. @@ -876,7 +903,7 @@ /** * \function igraph_lazy_inclist_destroy - * Deallocates memory + * \brief Deallocates a lazy incidence list. * * Frees all allocated memory for a lazy incidence list. * \param al The incidence list to deallocate. @@ -891,9 +918,10 @@ /** * \function igraph_lazy_inclist_clear - * Removes all edges from a lazy incidence list. + * \brief Removes all edges from a lazy incidence list. * * \param il The lazy incidence list. + * * Time complexity: depends on memory management, typically O(n), where n is * the total number of elements in the incidence list. */ diff --git a/igraph/src/arpack.c b/igraph/src/arpack.c --- a/igraph/src/arpack.c +++ b/igraph/src/arpack.c @@ -32,7 +32,7 @@ /* The ARPACK example file dssimp.f is used as a template */ -int igraph_i_arpack_err_dsaupd(int error) { +static int igraph_i_arpack_err_dsaupd(int error) { switch (error) { case 1: return IGRAPH_ARPACK_MAXIT; case 3: return IGRAPH_ARPACK_NOSHIFT; @@ -54,7 +54,7 @@ } } -int igraph_i_arpack_err_dseupd(int error) { +static int igraph_i_arpack_err_dseupd(int error) { switch (error) { case -1: return IGRAPH_ARPACK_NPOS; case -2: return IGRAPH_ARPACK_NEVNPOS; @@ -76,7 +76,7 @@ } -int igraph_i_arpack_err_dnaupd(int error) { +static int igraph_i_arpack_err_dnaupd(int error) { switch (error) { case 1: return IGRAPH_ARPACK_MAXIT; case 3: return IGRAPH_ARPACK_NOSHIFT; @@ -97,7 +97,7 @@ } } -int igraph_i_arpack_err_dneupd(int error) { +static int igraph_i_arpack_err_dneupd(int error) { switch (error) { case 1: return IGRAPH_ARPACK_REORDER; case -1: return IGRAPH_ARPACK_NPOS; @@ -258,9 +258,9 @@ * "Solver" for 1x1 eigenvalue problems since ARPACK sometimes blows up with * these. */ -int igraph_i_arpack_rssolve_1x1(igraph_arpack_function_t *fun, void *extra, - igraph_arpack_options_t* options, - igraph_vector_t* values, igraph_matrix_t* vectors) { +static int igraph_i_arpack_rssolve_1x1(igraph_arpack_function_t *fun, void *extra, + igraph_arpack_options_t* options, + igraph_vector_t* values, igraph_matrix_t* vectors) { igraph_real_t a, b; int nev = options->nev; @@ -294,9 +294,9 @@ * "Solver" for 1x1 eigenvalue problems since ARPACK sometimes blows up with * these. */ -int igraph_i_arpack_rnsolve_1x1(igraph_arpack_function_t *fun, void *extra, - igraph_arpack_options_t* options, - igraph_matrix_t* values, igraph_matrix_t* vectors) { +static int igraph_i_arpack_rnsolve_1x1(igraph_arpack_function_t *fun, void *extra, + igraph_arpack_options_t* options, + igraph_matrix_t* values, igraph_matrix_t* vectors) { igraph_real_t a, b; int nev = options->nev; @@ -330,9 +330,9 @@ * "Solver" for 2x2 nonsymmetric eigenvalue problems since ARPACK sometimes * blows up with these. */ -int igraph_i_arpack_rnsolve_2x2(igraph_arpack_function_t *fun, void *extra, - igraph_arpack_options_t* options, igraph_matrix_t* values, - igraph_matrix_t* vectors) { +static int igraph_i_arpack_rnsolve_2x2(igraph_arpack_function_t *fun, void *extra, + igraph_arpack_options_t* options, igraph_matrix_t* values, + igraph_matrix_t* vectors) { igraph_real_t vec[2], mat[4]; igraph_real_t a, b, c, d; igraph_real_t trace, det, tsq4_minus_d; @@ -484,9 +484,9 @@ * "Solver" for symmetric 2x2 eigenvalue problems since ARPACK sometimes blows * up with these. */ -int igraph_i_arpack_rssolve_2x2(igraph_arpack_function_t *fun, void *extra, - igraph_arpack_options_t* options, igraph_vector_t* values, - igraph_matrix_t* vectors) { +static int igraph_i_arpack_rssolve_2x2(igraph_arpack_function_t *fun, void *extra, + igraph_arpack_options_t* options, igraph_vector_t* values, + igraph_matrix_t* vectors) { igraph_real_t vec[2], mat[4]; igraph_real_t a, b, c, d; igraph_real_t trace, det, tsq4_minus_d; @@ -778,7 +778,7 @@ * \brief Tries to set up the value of \c ncv in an \c igraph_arpack_options_t * automagically. */ -void igraph_i_arpack_auto_ncv(igraph_arpack_options_t* options) { +static void igraph_i_arpack_auto_ncv(igraph_arpack_options_t* options) { /* This is similar to how Octave determines the value of ncv, with some * modifications. */ int min_ncv = options->nev * 2 + 1; @@ -811,7 +811,7 @@ * \brief Prints a warning that informs the user that the ARPACK solver * did not converge. */ -void igraph_i_arpack_report_no_convergence(const igraph_arpack_options_t* options) { +static void igraph_i_arpack_report_no_convergence(const igraph_arpack_options_t* options) { char buf[1024]; snprintf(buf, sizeof(buf), "ARPACK solver failed to converge (%d iterations, " "%d/%d eigenvectors converged)", options->iparam[2], diff --git a/igraph/src/attributes.c b/igraph/src/attributes.c --- a/igraph/src/attributes.c +++ b/igraph/src/attributes.c @@ -422,11 +422,7 @@ type = (igraph_attribute_combination_type_t)va_arg(ap, int); if (type == IGRAPH_ATTRIBUTE_COMBINE_FUNCTION) { -#if defined(__GNUC__) - func = va_arg(ap, void (*)(void)); -#else - func = va_arg(ap, void*); -#endif + func = va_arg(ap, igraph_function_pointer_t); } if (strlen(name) == 0) { diff --git a/igraph/src/bfgs.c b/igraph/src/bfgs.c --- a/igraph/src/bfgs.c +++ b/igraph/src/bfgs.c @@ -24,7 +24,6 @@ #include "igraph_nongraph.h" #include "igraph_interrupt_internal.h" #include "igraph_statusbar.h" -#include "memory.h" #include "config.h" #include diff --git a/igraph/src/bignum.c b/igraph/src/bignum.c --- a/igraph/src/bignum.c +++ b/igraph/src/bignum.c @@ -19,11 +19,10 @@ * * $Id: bignum.c,v 1.17 2005/07/23 02:55:53 pullmoll Exp $ ******************************************************************************/ -#include + #include "bignum.h" -#include "config.h" -#include "math.h" #include "igraph_error.h" +#include "config.h" #ifndef ASM_X86 #ifdef X86 diff --git a/igraph/src/bipartite.c b/igraph/src/bipartite.c --- a/igraph/src/bipartite.c +++ b/igraph/src/bipartite.c @@ -150,11 +150,11 @@ return 0; } -int igraph_i_bipartite_projection(const igraph_t *graph, - const igraph_vector_bool_t *types, - igraph_t *proj, - int which, - igraph_vector_t *multiplicity) { +static int igraph_i_bipartite_projection(const igraph_t *graph, + const igraph_vector_bool_t *types, + igraph_t *proj, + int which, + igraph_vector_t *multiplicity) { long int no_of_nodes = igraph_vcount(graph); long int i, j, k; diff --git a/igraph/src/blas.c b/igraph/src/blas.c --- a/igraph/src/blas.c +++ b/igraph/src/blas.c @@ -108,3 +108,20 @@ int one = 1; return igraphdnrm2_(&n, VECTOR(*v), &one); } + +int igraph_blas_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2, + igraph_real_t *res) { + + int n = igraph_vector_size(v1); + int one = 1; + + if (igraph_vector_size(v2) != n) { + IGRAPH_ERROR("Dot product of vectors with different dimensions", + IGRAPH_EINVAL); + } + + *res = igraphddot_(&n, VECTOR(*v1), &one, VECTOR(*v2), &one); + + return 0; +} + diff --git a/igraph/src/bliss.cc b/igraph/src/bliss.cc --- a/igraph/src/bliss.cc +++ b/igraph/src/bliss.cc @@ -25,6 +25,7 @@ #include "igraph_datatype.h" #include "igraph_interface.h" +#include "igraph_handle_exceptions.h" using namespace bliss; using namespace std; @@ -53,7 +54,7 @@ } -void bliss_free_graph(AbstractGraph *g) { +static void bliss_free_graph(AbstractGraph *g) { delete g; } @@ -118,7 +119,7 @@ // this is the callback function used with AbstractGraph::find_automorphisms() // it collects the group generators into a pointer vector -void collect_generators(void *generators, unsigned int n, const unsigned int *aut) { +static void collect_generators(void *generators, unsigned int n, const unsigned int *aut) { igraph_vector_ptr_t *gen = static_cast(generators); igraph_vector_t *newvector = igraph_Calloc(1, igraph_vector_t); igraph_vector_init(newvector, n); @@ -153,24 +154,27 @@ */ int igraph_canonical_permutation(const igraph_t *graph, const igraph_vector_int_t *colors, igraph_vector_t *labeling, igraph_bliss_sh_t sh, igraph_bliss_info_t *info) { - AbstractGraph *g = bliss_from_igraph(graph); - IGRAPH_FINALLY(bliss_free_graph, g); - const unsigned int N = g->get_nof_vertices(); + IGRAPH_HANDLE_EXCEPTIONS( + AbstractGraph *g = bliss_from_igraph(graph); + IGRAPH_FINALLY(bliss_free_graph, g); + const unsigned int N = g->get_nof_vertices(); - IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph))); - IGRAPH_CHECK(bliss_set_colors(g, colors)); + IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph))); + IGRAPH_CHECK(bliss_set_colors(g, colors)); - Stats stats; - const unsigned int *cl = g->canonical_form(stats, NULL, NULL); - IGRAPH_CHECK(igraph_vector_resize(labeling, N)); - for (unsigned int i = 0; i < N; i++) { - VECTOR(*labeling)[i] = cl[i]; - } + Stats stats; + const unsigned int *cl = g->canonical_form(stats, NULL, NULL); + IGRAPH_CHECK(igraph_vector_resize(labeling, N)); + for (unsigned int i = 0; i < N; i++) { + VECTOR(*labeling)[i] = cl[i]; + } - bliss_info_to_igraph(info, stats); + bliss_info_to_igraph(info, stats); - delete g; - IGRAPH_FINALLY_CLEAN(1); + delete g; + IGRAPH_FINALLY_CLEAN(1); + ); + return IGRAPH_SUCCESS; } @@ -199,19 +203,21 @@ */ int igraph_automorphisms(const igraph_t *graph, const igraph_vector_int_t *colors, igraph_bliss_sh_t sh, igraph_bliss_info_t *info) { - AbstractGraph *g = bliss_from_igraph(graph); - IGRAPH_FINALLY(bliss_free_graph, g); + IGRAPH_HANDLE_EXCEPTIONS( + AbstractGraph *g = bliss_from_igraph(graph); + IGRAPH_FINALLY(bliss_free_graph, g); - IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph))); - IGRAPH_CHECK(bliss_set_colors(g, colors)); + IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph))); + IGRAPH_CHECK(bliss_set_colors(g, colors)); - Stats stats; - g->find_automorphisms(stats, NULL, NULL); + Stats stats; + g->find_automorphisms(stats, NULL, NULL); - bliss_info_to_igraph(info, stats); + bliss_info_to_igraph(info, stats); - delete g; - IGRAPH_FINALLY_CLEAN(1); + delete g; + IGRAPH_FINALLY_CLEAN(1); + ); return IGRAPH_SUCCESS; } @@ -241,20 +247,23 @@ int igraph_automorphism_group( const igraph_t *graph, const igraph_vector_int_t *colors, igraph_vector_ptr_t *generators, igraph_bliss_sh_t sh, igraph_bliss_info_t *info) { - AbstractGraph *g = bliss_from_igraph(graph); - IGRAPH_FINALLY(bliss_free_graph, g); + IGRAPH_HANDLE_EXCEPTIONS( + AbstractGraph *g = bliss_from_igraph(graph); + IGRAPH_FINALLY(bliss_free_graph, g); - IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph))); - IGRAPH_CHECK(bliss_set_colors(g, colors)); + IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph))); + IGRAPH_CHECK(bliss_set_colors(g, colors)); - Stats stats; - igraph_vector_ptr_resize(generators, 0); - g->find_automorphisms(stats, collect_generators, generators); + Stats stats; + igraph_vector_ptr_resize(generators, 0); + g->find_automorphisms(stats, collect_generators, generators); - bliss_info_to_igraph(info, stats); + bliss_info_to_igraph(info, stats); - delete g; - IGRAPH_FINALLY_CLEAN(1); + delete g; + IGRAPH_FINALLY_CLEAN(1); + ); + return IGRAPH_SUCCESS; } diff --git a/igraph/src/bliss_heap.cc b/igraph/src/bliss_heap.cc --- a/igraph/src/bliss_heap.cc +++ b/igraph/src/bliss_heap.cc @@ -1,6 +1,6 @@ -#include -#include -#include +#include +//#include +#include #include "defs.hh" #include "heap.hh" diff --git a/igraph/src/cattributes.c b/igraph/src/cattributes.c --- a/igraph/src/cattributes.c +++ b/igraph/src/cattributes.c @@ -23,10 +23,10 @@ #include "igraph_attributes.h" #include "igraph_memory.h" -#include "config.h" #include "igraph_math.h" #include "igraph_interface.h" #include "igraph_random.h" +#include "config.h" #include @@ -1577,7 +1577,8 @@ igraph_free(funcs); igraph_free(TODO); - IGRAPH_FINALLY_CLEAN(2); + igraph_i_cattribute_permute_free(new_val); + IGRAPH_FINALLY_CLEAN(3); return 0; } @@ -2187,7 +2188,7 @@ igraph_free(funcs); igraph_free(TODO); - IGRAPH_FINALLY_CLEAN(2); + IGRAPH_FINALLY_CLEAN(3); return 0; } @@ -2638,7 +2639,7 @@ * is no attribute handler at all. * * The C attribute handler supports attaching real numbers and - * character strings as attributes. No vectors are allowed, ie. every + * character strings as attributes. No vectors are allowed, i.e. every * vertex might have an attribute called name, but it is * not possible to have a coords graph (or other) * attribute which is a vector of numbers. @@ -3801,7 +3802,7 @@ IGRAPH_FINALLY(igraph_free, log); rec->value = log; IGRAPH_CHECK(igraph_vector_bool_copy(log, v)); - IGRAPH_FINALLY(igraph_vector_destroy, log); + IGRAPH_FINALLY(igraph_vector_bool_destroy, log); IGRAPH_CHECK(igraph_vector_ptr_push_back(val, rec)); IGRAPH_FINALLY_CLEAN(4); } @@ -3878,7 +3879,7 @@ /** * \function igraph_cattribute_EAN_setv - * Set a numeric edge attribute for all vertices. + * Set a numeric edge attribute for all edges. * * The attribute will be added if not present yet. * \param graph The graph. @@ -3944,7 +3945,7 @@ /** * \function igraph_cattribute_EAB_setv - * Set a boolean edge attribute for all vertices. + * Set a boolean edge attribute for all edges. * * The attribute will be added if not present yet. * \param graph The graph. @@ -4010,7 +4011,7 @@ /** * \function igraph_cattribute_EAS_setv - * Set a string edge attribute for all vertices. + * Set a string edge attribute for all edges. * * The attribute will be added if not present yet. * \param graph The graph. diff --git a/igraph/src/centrality.c b/igraph/src/centrality.c --- a/igraph/src/centrality.c +++ b/igraph/src/centrality.c @@ -22,9 +22,6 @@ */ -#include -#include /* memset */ -#include #include "igraph_centrality.h" #include "igraph_math.h" #include "igraph_memory.h" @@ -42,6 +39,9 @@ #include "bigint.h" #include "prpack.h" +#include +#include /* memset */ + int igraph_personalized_pagerank_arpack(const igraph_t *graph, igraph_vector_t *vector, igraph_real_t *value, const igraph_vs_t vids, @@ -50,7 +50,7 @@ const igraph_vector_t *weights, igraph_arpack_options_t *options); -igraph_bool_t igraph_i_vector_mostly_negative(const igraph_vector_t *vector) { +static igraph_bool_t igraph_i_vector_mostly_negative(const igraph_vector_t *vector) { /* Many of the centrality measures correspond to the eigenvector of some * matrix. When v is an eigenvector, c*v is also an eigenvector, therefore * it may happen that all the scores in the eigenvector are negative, in which @@ -89,8 +89,8 @@ return (mi < 1e-5) ? 1 : 0; } -int igraph_i_eigenvector_centrality(igraph_real_t *to, const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_eigenvector_centrality(igraph_real_t *to, const igraph_real_t *from, + int n, void *extra) { igraph_adjlist_t *adjlist = extra; igraph_vector_int_t *neis; long int i, j, nlen; @@ -115,8 +115,8 @@ const igraph_vector_t *weights; } igraph_i_eigenvector_centrality_t; -int igraph_i_eigenvector_centrality2(igraph_real_t *to, const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_eigenvector_centrality2(igraph_real_t *to, const igraph_real_t *from, + int n, void *extra) { igraph_i_eigenvector_centrality_t *data = extra; const igraph_t *graph = data->graph; @@ -140,25 +140,6 @@ return 0; } -int igraph_i_eigenvector_centrality_loop(igraph_adjlist_t *adjlist) { - - long int i, j, k, nlen, n = igraph_adjlist_size(adjlist); - igraph_vector_int_t *neis; - - for (i = 0; i < n; i++) { - neis = igraph_adjlist_get(adjlist, i); - nlen = igraph_vector_int_size(neis); - for (j = 0; j < nlen && VECTOR(*neis)[j] < i; j++) ; - for (k = j; k < nlen && VECTOR(*neis)[k] == i; k++) ; - if (k != j) { - /* First loop edge is 'j', first non-loop edge is 'k' */ - igraph_vector_int_remove_section(neis, j + (k - j) / 2, k); - } - } - - return 0; -} - int igraph_eigenvector_centrality_undirected(const igraph_t *graph, igraph_vector_t *vector, igraph_real_t *value, igraph_bool_t scale, const igraph_vector_t *weights, @@ -236,8 +217,6 @@ IGRAPH_CHECK(igraph_adjlist_init(graph, &adjlist, IGRAPH_ALL)); IGRAPH_FINALLY(igraph_adjlist_destroy, &adjlist); - IGRAPH_CHECK(igraph_i_eigenvector_centrality_loop(&adjlist)); - IGRAPH_CHECK(igraph_arpack_rssolve(igraph_i_eigenvector_centrality, &adjlist, options, 0, &values, &vectors)); @@ -252,8 +231,6 @@ IGRAPH_CHECK(igraph_inclist_init(graph, &inclist, IGRAPH_ALL)); IGRAPH_FINALLY(igraph_inclist_destroy, &inclist); - IGRAPH_CHECK(igraph_inclist_remove_duplicate(graph, &inclist)); - IGRAPH_CHECK(igraph_arpack_rssolve(igraph_i_eigenvector_centrality2, &data, options, 0, &values, &vectors)); @@ -504,21 +481,34 @@ * * Eigenvector centrality is a measure of the importance of a node in a * network. It assigns relative scores to all nodes in the network based - * on the principle that connections to high-scoring nodes contribute - * more to the score of the node in question than equal connections to - * low-scoring nodes. In practice, this is determined by calculating the + * on the principle that connections from high-scoring nodes contribute + * more to the score of the node in question than equal connections from + * low-scoring nodes. Specifically, the eigenvector centrality of each + * vertex is proportional to the sum of eigenvector centralities of its + * neighbors. In practice, the centralities are determined by calculating the * eigenvector corresponding to the largest positive eigenvalue of the - * adjacency matrix. The centrality scores returned by igraph are always - * normalized such that the largest eigenvector centrality score is one - * (with one exception, see below). + * adjacency matrix. In the undirected case, this function considers + * the diagonal entries of the adjacency matrix to be \em twice the number of + * self-loops on the corresponding vertex. * * - * Since the eigenvector centrality scores of nodes in different components - * do not affect each other, it may be beneficial for large graphs to - * decompose it first into weakly connected components and calculate the - * centrality scores individually for each component. + * The centrality scores returned by igraph can be normalized + * (using the \p scale parameter) such that the largest eigenvector centrality + * score is 1 (with one exception, see below). * * + * In the directed case, the left eigenvector of the adjacency matrix is + * calculated. In other words, the centrality of a vertex is proportional + * to the sum of centralities of vertices pointing to it. + * + * + * Eigenvector centrality is meaningful only for connected graphs. + * Graphs that are not connected should be decomposed into connected + * components, and the eigenvector centrality calculated for each separately. + * This function does not verify that the graph is connected. If it is not, + * in the undirected case the scores of all but one component will be zeros. + * + * * Also note that the adjacency matrix of a directed acyclic graph or the * adjacency matrix of an empty graph does not possess positive eigenvalues, * therefore the eigenvector centrality is not defined for these graphs. @@ -529,7 +519,7 @@ * parameter, see below) and checking whether the eigenvalue is very close * to zero. * - * \param graph The input graph. It might be directed. + * \param graph The input graph. It may be directed. * \param vector Pointer to an initialized vector, it will be resized * as needed. The result of the computation is stored here. It can * be a null pointer, then it is ignored. @@ -591,9 +581,9 @@ } igraph_i_kleinberg_data2_t; /* ARPACK auxiliary routine for the unweighted HITS algorithm */ -int igraph_i_kleinberg_unweighted(igraph_real_t *to, - const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_kleinberg_unweighted(igraph_real_t *to, + const igraph_real_t *from, + int n, void *extra) { igraph_i_kleinberg_data_t *data = (igraph_i_kleinberg_data_t*)extra; igraph_adjlist_t *in = data->in; igraph_adjlist_t *out = data->out; @@ -625,9 +615,9 @@ } /* ARPACK auxiliary routine for the weighted HITS algorithm */ -int igraph_i_kleinberg_weighted(igraph_real_t *to, - const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_kleinberg_weighted(igraph_real_t *to, + const igraph_real_t *from, + int n, void *extra) { igraph_i_kleinberg_data2_t *data = (igraph_i_kleinberg_data2_t*)extra; igraph_inclist_t *in = data->in; @@ -663,10 +653,10 @@ return 0; } -int igraph_i_kleinberg(const igraph_t *graph, igraph_vector_t *vector, - igraph_real_t *value, igraph_bool_t scale, - const igraph_vector_t *weights, - igraph_arpack_options_t *options, int inout) { +static int igraph_i_kleinberg(const igraph_t *graph, igraph_vector_t *vector, + igraph_real_t *value, igraph_bool_t scale, + const igraph_vector_t *weights, + igraph_arpack_options_t *options, int inout) { igraph_adjlist_t myinadjlist, myoutadjlist; igraph_inclist_t myininclist, myoutinclist; @@ -934,8 +924,8 @@ igraph_vector_t *reset; } igraph_i_pagerank_data2_t; -int igraph_i_pagerank(igraph_real_t *to, const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_pagerank(igraph_real_t *to, const igraph_real_t *from, + int n, void *extra) { igraph_i_pagerank_data_t *data = extra; igraph_adjlist_t *adjlist = data->adjlist; @@ -996,8 +986,8 @@ return 0; } -int igraph_i_pagerank2(igraph_real_t *to, const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_pagerank2(igraph_real_t *to, const igraph_real_t *from, + int n, void *extra) { igraph_i_pagerank_data2_t *data = extra; const igraph_t *graph = data->graph; @@ -1608,7 +1598,8 @@ nobigint); } -int igraph_i_betweenness_estimate_weighted(const igraph_t *graph, +static int igraph_i_betweenness_estimate_weighted( + const igraph_t *graph, igraph_vector_t *res, const igraph_vs_t vids, igraph_bool_t directed, @@ -1678,11 +1669,18 @@ igraph_vector_int_t *neis; long int nlen; - igraph_stack_push(&S, minnei); - if (cutoff > 0 && VECTOR(dist)[minnei] >= cutoff + 1.0) { + /* Ignore vertices that are more distant than the cutoff */ + if (cutoff >= 0 && mindist > cutoff + 1.0) { + /* Reset variables if node is too distant */ + VECTOR(tmpscore)[minnei] = 0; + VECTOR(dist)[minnei] = 0; + VECTOR(nrgeo)[minnei] = 0; + igraph_vector_int_clear(igraph_adjlist_get(&fathers, minnei)); continue; } + igraph_stack_push(&S, minnei); + /* Now check all neighbors of 'minnei' for a shorter path */ neis = igraph_inclist_get(&inclist, minnei); nlen = igraph_vector_int_size(neis); @@ -1717,7 +1715,9 @@ VECTOR(dist)[to] = altdist; IGRAPH_CHECK(igraph_2wheap_modify(&Q, to, -altdist)); - } else if (cmp_result == 0) { + } else if (cmp_result == 0 && + (altdist <= cutoff + 1.0 || cutoff < 0)) { + /* Only add if the node is not more distant than the cutoff */ igraph_vector_int_t *v = igraph_adjlist_get(&fathers, to); igraph_vector_int_push_back(v, minnei); VECTOR(nrgeo)[to] += VECTOR(nrgeo)[minnei]; @@ -1738,6 +1738,7 @@ VECTOR(*tmpres)[w] += VECTOR(tmpscore)[w]; } + /* Reset variables */ VECTOR(tmpscore)[w] = 0; VECTOR(dist)[w] = 0; VECTOR(nrgeo)[w] = 0; @@ -1784,7 +1785,7 @@ return 0; } -void igraph_i_destroy_biguints(igraph_biguint_t *p) { +static void igraph_i_destroy_biguints(igraph_biguint_t *p) { igraph_biguint_t *p2 = p; while ( *((long int*)(p)) ) { igraph_biguint_destroy(p); @@ -1815,8 +1816,8 @@ * \param directed Logical, if true directed paths will be considered * for directed graphs. It is ignored for undirected graphs. * \param cutoff The maximal length of paths that will be considered. - * If zero or negative, the exact betweenness will be calculated - * (no upper limit on path lengths). + * If negative or zero, the exact betweenness will be calculated, and + * there will be no upper limit on path lengths. * \param weights An optional vector containing edge weights for * calculating weighted betweenness. Supply a null pointer here * for unweighted betweenness. @@ -1866,6 +1867,11 @@ igraph_biguint_t D, R, T; + /* Ensure that 0 is interpreted as infinity in the igraph 0.8 series. TODO: remove for 0.9. */ + if (cutoff == 0) { + cutoff = -1; + } + if (weights) { return igraph_i_betweenness_estimate_weighted(graph, res, vids, directed, cutoff, weights, nobigint); @@ -1956,12 +1962,22 @@ while (!igraph_dqueue_empty(&q)) { long int actnode = (long int) igraph_dqueue_pop(&q); - IGRAPH_CHECK(igraph_stack_push(&stack, actnode)); - if (cutoff > 0 && distance[actnode] >= cutoff + 1) { + /* Ignore vertices that are more distant than the cutoff */ + if (cutoff >= 0 && distance[actnode] > cutoff + 1) { + /* Reset variables if node is too distant */ + distance[actnode] = 0; + if (nobigint) { + nrgeo[actnode] = 0; + } else { + igraph_biguint_set_limb(&big_nrgeo[actnode], 0); + } + tmpscore[actnode] = 0; + igraph_vector_int_clear(igraph_adjlist_get(adjlist_in_p, actnode)); continue; } + IGRAPH_CHECK(igraph_stack_push(&stack, actnode)); neis = igraph_adjlist_get(adjlist_out_p, actnode); nneis = igraph_vector_int_size(neis); for (j = 0; j < nneis; j++) { @@ -1970,7 +1986,9 @@ distance[neighbor] = distance[actnode] + 1; IGRAPH_CHECK(igraph_dqueue_push(&q, neighbor)); } - if (distance[neighbor] == distance[actnode] + 1) { + if (distance[neighbor] == distance[actnode] + 1 && + (distance[neighbor] <= cutoff + 1 || cutoff < 0)) { + /* Only add if the node is not more distant than the cutoff */ igraph_vector_int_t *v = igraph_adjlist_get(adjlist_in_p, neighbor); igraph_vector_int_push_back(v, actnode); @@ -2016,6 +2034,7 @@ VECTOR(*tmpres)[actnode] += tmpscore[actnode]; } + /* Reset variables */ distance[actnode] = 0; if (nobigint) { nrgeo[actnode] = 0; @@ -2079,7 +2098,8 @@ return 0; } -int igraph_i_edge_betweenness_estimate_weighted(const igraph_t *graph, +static int igraph_i_edge_betweenness_estimate_weighted( + const igraph_t *graph, igraph_vector_t *result, igraph_bool_t directed, igraph_real_t cutoff, @@ -2518,8 +2538,7 @@ * \param graph The graph object. * \param res The result of the computation, a vector containing the * closeness centrality scores for the given vertices. - * \param vids Vector giving the vertices for which the closeness - * centrality scores will be computed. + * \param vids The vertices for which the closeness centrality will be computed. * \param mode The type of shortest paths to be used for the * calculation in directed graphs. Possible values: * \clist @@ -2563,13 +2582,13 @@ normalized); } -int igraph_i_closeness_estimate_weighted(const igraph_t *graph, - igraph_vector_t *res, - const igraph_vs_t vids, - igraph_neimode_t mode, - igraph_real_t cutoff, - const igraph_vector_t *weights, - igraph_bool_t normalized) { +static int igraph_i_closeness_estimate_weighted(const igraph_t *graph, + igraph_vector_t *res, + const igraph_vs_t vids, + igraph_neimode_t mode, + igraph_real_t cutoff, + const igraph_vector_t *weights, + igraph_bool_t normalized) { /* See igraph_shortest_paths_dijkstra() for the implementation details and the dirty tricks. */ @@ -2727,8 +2746,7 @@ * \param graph The graph object. * \param res The result of the computation, a vector containing the * closeness centrality scores for the given vertices. - * \param vids Vector giving the vertices for which the closeness - * centrality scores will be computed. + * \param vids The vertices for which the closeness centrality will be estimated. * \param mode The type of shortest paths to be used for the * calculation in directed graphs. Possible values: * \clist diff --git a/igraph/src/cliquer.c b/igraph/src/cliquer.c --- a/igraph/src/cliquer.c +++ b/igraph/src/cliquer.c diff --git a/igraph/src/cliquer_graph.c b/igraph/src/cliquer_graph.c --- a/igraph/src/cliquer_graph.c +++ b/igraph/src/cliquer_graph.c diff --git a/igraph/src/cliques.c b/igraph/src/cliques.c --- a/igraph/src/cliques.c +++ b/igraph/src/cliques.c @@ -23,7 +23,6 @@ #include "igraph_cliques.h" #include "igraph_memory.h" -#include "igraph_random.h" #include "igraph_constants.h" #include "igraph_adjlist.h" #include "igraph_interrupt_internal.h" @@ -37,7 +36,7 @@ #include #include /* memset */ -void igraph_i_cliques_free_res(igraph_vector_ptr_t *res) { +static void igraph_i_cliques_free_res(igraph_vector_ptr_t *res) { long i, n; n = igraph_vector_ptr_size(res); @@ -50,14 +49,15 @@ igraph_vector_ptr_clear(res); } -int igraph_i_find_k_cliques(const igraph_t *graph, - long int size, - const igraph_real_t *member_storage, - igraph_real_t **new_member_storage, - long int old_clique_count, - long int *clique_count, - igraph_vector_t *neis, - igraph_bool_t independent_vertices) { +static int igraph_i_find_k_cliques( + const igraph_t *graph, + long int size, + const igraph_real_t *member_storage, + igraph_real_t **new_member_storage, + long int old_clique_count, + long int *clique_count, + igraph_vector_t *neis, + igraph_bool_t independent_vertices) { long int j, k, l, m, n, new_member_storage_size; const igraph_real_t *c1, *c2; @@ -188,9 +188,9 @@ * They are practically the same except that the complementer of the graph * should be used in the latter case. */ -int igraph_i_cliques(const igraph_t *graph, igraph_vector_ptr_t *res, - igraph_integer_t min_size, igraph_integer_t max_size, - igraph_bool_t independent_vertices) { +static int igraph_i_cliques(const igraph_t *graph, igraph_vector_ptr_t *res, + igraph_integer_t min_size, igraph_integer_t max_size, + igraph_bool_t independent_vertices) { igraph_integer_t no_of_nodes; igraph_vector_t neis; @@ -303,7 +303,7 @@ /** * \function igraph_cliques - * \brief Find all or some cliques in a graph + * \brief Finds all or some cliques in a graph. * * * Cliques are fully connected subgraphs of a graph. @@ -312,17 +312,13 @@ * If you are only interested in the size of the largest clique in the graph, * use \ref igraph_clique_number() instead. * - * The current implementation of this function searches - * for maximal independent vertex sets (see \ref - * igraph_maximal_independent_vertex_sets()) in the complementer graph - * using the algorithm published in: - * S. Tsukiyama, M. Ide, H. Ariyoshi and I. Shirawaka. A new algorithm - * for generating all the maximal independent sets. SIAM J Computing, - * 6:505--517, 1977. + * The current implementation of this function + * uses version 1.21 of the Cliquer library by Sampo Niskanen and + * Patric R. J. Östergård, http://users.aalto.fi/~pat/cliquer.html * * \param graph The input graph. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_vector_t + * here, i.e. \p res will contain pointers to \ref igraph_vector_t * objects which contain the indices of vertices involved in a clique. * The pointer vector will be resized if needed but note that the * objects in the pointer vector will not be freed. @@ -334,7 +330,7 @@ * * \sa \ref igraph_largest_cliques() and \ref igraph_clique_number(). * - * Time complexity: TODO + * Time complexity: Exponential * * \example examples/simple/igraph_cliques.c */ @@ -346,7 +342,7 @@ /** * \function igraph_clique_size_hist - * \brief Count cliques of each size in the graph + * \brief Counts cliques of each size in the graph. * * * Cliques are fully connected subgraphs of a graph. @@ -358,7 +354,7 @@ * \param graph The input graph. * \param hist Pointer to an initialized vector. The result will be stored * here. The first element will store the number of size-1 cliques, the second - * element the number of size-2 cliques, etc. For cliques smaller than \c min_size, + * element the number of size-2 cliques, etc. For cliques smaller than \p min_size, * zero counts will be returned. * \param min_size Integer giving the minimum size of the cliques to be * returned. If negative or zero, no lower bound will be used. @@ -385,7 +381,7 @@ * Cliques are fully connected subgraphs of a graph. This function * enumerates all cliques within the given size range and calls * \p cliquehandler_fn for each of them. The cliques are passed to the - * callback function as an igraph_vector_t *. Destroying and + * callback function as a pointer to an \ref igraph_vector_t. Destroying and * freeing this vector is left up to the user. Use \ref igraph_vector_destroy() * to destroy it first, then free it using \ref igraph_free(). * @@ -399,7 +395,7 @@ * \param max_size Integer giving the maximum size of the cliques to be * returned. If negative or zero, no upper bound will be used. * \param cliquehandler_fn Callback function to be called for each clique. - * See also igraph_clique_handler_t. + * See also \ref igraph_clique_handler_t. * \param arg Extra argument to supply to \p cliquehandler_fn. * \return Error code. * @@ -417,7 +413,7 @@ /** * \function igraph_weighted_cliques - * \brief Find all cliques in a given weight range in a vertex weighted graph + * \brief Finds all cliques in a given weight range in a vertex weighted graph. * * * Cliques are fully connected subgraphs of a graph. @@ -434,7 +430,7 @@ * \param vertex_weights A vector of vertex weights. The current implementation * will truncate all weights to their integer parts. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_vector_t + * here, i.e. \p res will contain pointers to \ref igraph_vector_t * objects which contain the indices of vertices involved in a clique. * The pointer vector will be resized if needed but note that the * objects in the pointer vector will not be freed. @@ -474,7 +470,7 @@ * \param vertex_weights A vector of vertex weights. The current implementation * will truncate all weights to their integer parts. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_vector_t + * here, i.e. \p res will contain pointers to \ref igraph_vector_t * objects which contain the indices of vertices involved in a clique. * The pointer vector will be resized if needed but note that the * objects in the pointer vector will not be freed. @@ -492,7 +488,7 @@ /** * \function igraph_weighted_clique_number - * \brief Find the weight of the largest weight clique in the graph + * \brief Finds the weight of the largest weight clique in the graph. * * The current implementation of this function * uses version 1.21 of the Cliquer library by Sampo Niskanen and @@ -524,9 +520,10 @@ igraph_integer_t max_size; } igraph_i_maximal_clique_data_t; -int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data); +static int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data); -int igraph_i_maximal_or_largest_cliques_or_indsets(const igraph_t *graph, +static int igraph_i_maximal_or_largest_cliques_or_indsets( + const igraph_t *graph, igraph_vector_ptr_t *res, igraph_integer_t *clique_number, igraph_bool_t keep_only_largest, @@ -534,7 +531,7 @@ /** * \function igraph_independent_vertex_sets - * \brief Find all independent vertex sets in a graph + * \brief Finds all independent vertex sets in a graph. * * * A vertex set is considered independent if there are no edges between @@ -553,7 +550,7 @@ * * \param graph The input graph. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_vector_t + * here, i.e. \p res will contain pointers to \ref igraph_vector_t * objects which contain the indices of vertices involved in an independent * vertex set. The pointer vector will be resized if needed but note that the * objects in the pointer vector will not be freed. @@ -619,7 +616,8 @@ igraph_bool_t keep_only_largest; /* True if we keep only the largest sets */ } igraph_i_max_ind_vsets_data_t; -int igraph_i_maximal_independent_vertex_sets_backtrack(const igraph_t *graph, +static int igraph_i_maximal_independent_vertex_sets_backtrack( + const igraph_t *graph, igraph_vector_ptr_t *res, igraph_i_max_ind_vsets_data_t *clqdata, igraph_integer_t level) { @@ -763,7 +761,7 @@ return 0; } -void igraph_i_free_set_array(igraph_set_t* array) { +static void igraph_i_free_set_array(igraph_set_t* array) { long int i = 0; while (igraph_set_inited(array + i)) { igraph_set_destroy(array + i); @@ -774,7 +772,7 @@ /** * \function igraph_maximal_independent_vertex_sets - * \brief Find all maximal independent vertex sets of a graph + * \brief Finds all maximal independent vertex sets of a graph. * * * A maximal independent vertex set is an independent vertex set which @@ -797,7 +795,7 @@ * * \param graph The input graph. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_vector_t + * here, i.e. \p res will contain pointers to \ref igraph_vector_t * objects which contain the indices of vertices involved in an independent * vertex set. The pointer vector will be resized if needed but note that the * objects in the pointer vector will not be freed. @@ -864,7 +862,7 @@ /** * \function igraph_independence_number - * \brief Find the independence number of the graph + * \brief Finds the independence number of the graph. * * * The independence number of a graph is the cardinality of the largest @@ -943,8 +941,8 @@ /* MAXIMAL CLIQUES, LARGEST CLIQUES */ /*************************************************************************/ -int igraph_i_maximal_cliques_store_max_size(const igraph_vector_t* clique, void* data, - igraph_bool_t* cont) { +static int igraph_i_maximal_cliques_store_max_size(const igraph_vector_t* clique, void* data, + igraph_bool_t* cont) { igraph_integer_t* result = (igraph_integer_t*)data; IGRAPH_UNUSED(cont); if (*result < igraph_vector_size(clique)) { @@ -953,7 +951,7 @@ return IGRAPH_SUCCESS; } -int igraph_i_maximal_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) { +static int igraph_i_maximal_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) { igraph_vector_ptr_t* result = (igraph_vector_ptr_t*)data; igraph_vector_t* vec; @@ -969,7 +967,7 @@ return IGRAPH_SUCCESS; } -int igraph_i_maximal_cliques_store_size_check(const igraph_vector_t* clique, void* data_, igraph_bool_t* cont) { +static int igraph_i_maximal_cliques_store_size_check(const igraph_vector_t* clique, void* data_, igraph_bool_t* cont) { igraph_i_maximal_clique_data_t* data = (igraph_i_maximal_clique_data_t*)data_; igraph_vector_t* vec; igraph_integer_t size = (igraph_integer_t) igraph_vector_size(clique); @@ -990,7 +988,7 @@ return IGRAPH_SUCCESS; } -int igraph_i_largest_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) { +static int igraph_i_largest_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) { igraph_vector_ptr_t* result = (igraph_vector_ptr_t*)data; igraph_vector_t* vec; long int i, n; @@ -1033,7 +1031,7 @@ * * * Note that this is not necessarily the same as a maximal clique, - * ie. the largest cliques are always maximal but a maximal clique is + * i.e. the largest cliques are always maximal but a maximal clique is * not always largest. * * The current implementation of this function searches @@ -1066,7 +1064,7 @@ /** * \function igraph_clique_number - * \brief Find the clique number of the graph + * \brief Finds the clique number of the graph. * * * The clique number of a graph is the size of the largest clique. @@ -1091,13 +1089,13 @@ igraph_vector_int_t cand_filtered; } igraph_i_maximal_cliques_stack_frame; -void igraph_i_maximal_cliques_stack_frame_destroy(igraph_i_maximal_cliques_stack_frame *frame) { +static void igraph_i_maximal_cliques_stack_frame_destroy(igraph_i_maximal_cliques_stack_frame *frame) { igraph_vector_int_destroy(&frame->cand); igraph_vector_int_destroy(&frame->fini); igraph_vector_int_destroy(&frame->cand_filtered); } -void igraph_i_maximal_cliques_stack_destroy(igraph_stack_ptr_t *stack) { +static void igraph_i_maximal_cliques_stack_destroy(igraph_stack_ptr_t *stack) { igraph_i_maximal_cliques_stack_frame *frame; while (!igraph_stack_ptr_empty(stack)) { @@ -1109,7 +1107,7 @@ igraph_stack_ptr_destroy(stack); } -int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data) { +static int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data) { int directed = igraph_is_directed(graph); long int i, j, k, l; igraph_integer_t no_of_nodes, nodes_to_check, nodes_done; @@ -1331,7 +1329,7 @@ return IGRAPH_SUCCESS; } -int igraph_i_maximal_or_largest_cliques_or_indsets(const igraph_t *graph, +static int igraph_i_maximal_or_largest_cliques_or_indsets(const igraph_t *graph, igraph_vector_ptr_t *res, igraph_integer_t *clique_number, igraph_bool_t keep_only_largest, diff --git a/igraph/src/clustertool.cpp b/igraph/src/clustertool.cpp --- a/igraph/src/clustertool.cpp +++ b/igraph/src/clustertool.cpp @@ -45,11 +45,6 @@ #include #endif -#include -#include -#include -#include - #include "NetDataTypes.h" #include "NetRoutines.h" #include "pottsmodel_2.h" @@ -61,22 +56,25 @@ #include "igraph_interface.h" #include "igraph_components.h" #include "igraph_interrupt_internal.h" +#include "igraph_handle_exceptions.h" -int igraph_i_community_spinglass_orig(const igraph_t *graph, - const igraph_vector_t *weights, - igraph_real_t *modularity, - igraph_real_t *temperature, - igraph_vector_t *membership, - igraph_vector_t *csize, - igraph_integer_t spins, - igraph_bool_t parupdate, - igraph_real_t starttemp, - igraph_real_t stoptemp, - igraph_real_t coolfact, - igraph_spincomm_update_t update_rule, - igraph_real_t gamma); +static int igraph_i_community_spinglass_orig( + const igraph_t *graph, + const igraph_vector_t *weights, + igraph_real_t *modularity, + igraph_real_t *temperature, + igraph_vector_t *membership, + igraph_vector_t *csize, + igraph_integer_t spins, + igraph_bool_t parupdate, + igraph_real_t starttemp, + igraph_real_t stoptemp, + igraph_real_t coolfact, + igraph_spincomm_update_t update_rule, + igraph_real_t gamma); -int igraph_i_community_spinglass_negative(const igraph_t *graph, +static int igraph_i_community_spinglass_negative( + const igraph_t *graph, const igraph_vector_t *weights, igraph_real_t *modularity, igraph_real_t *temperature, @@ -89,9 +87,9 @@ igraph_real_t coolfact, igraph_spincomm_update_t update_rule, igraph_real_t gamma, - /* igraph_matrix_t *adhesion, */ - /* igraph_matrix_t *normalised_adhesion, */ - /* igraph_real_t *polarization, */ + /* igraph_matrix_t *adhesion, */ + /* igraph_matrix_t *normalised_adhesion, */ + /* igraph_real_t *polarization, */ igraph_real_t gamma_minus); /** @@ -205,45 +203,47 @@ /* igraph_real_t *polarization, */ igraph_real_t gamma_minus) { - switch (implementation) { - case IGRAPH_SPINCOMM_IMP_ORIG: - return igraph_i_community_spinglass_orig(graph, weights, modularity, - temperature, membership, csize, - spins, parupdate, starttemp, - stoptemp, coolfact, update_rule, - gamma); - break; - case IGRAPH_SPINCOMM_IMP_NEG: - return igraph_i_community_spinglass_negative(graph, weights, modularity, - temperature, membership, csize, - spins, parupdate, starttemp, - stoptemp, coolfact, - update_rule, gamma, - /* adhesion, normalised_adhesion, */ - /* polarization, */ - gamma_minus); - break; - default: - IGRAPH_ERROR("Unknown `implementation' in spinglass community finding", - IGRAPH_EINVAL); - } - + IGRAPH_HANDLE_EXCEPTIONS( + switch (implementation) { + case IGRAPH_SPINCOMM_IMP_ORIG: + return igraph_i_community_spinglass_orig(graph, weights, modularity, + temperature, membership, csize, + spins, parupdate, starttemp, + stoptemp, coolfact, update_rule, + gamma); + break; + case IGRAPH_SPINCOMM_IMP_NEG: + return igraph_i_community_spinglass_negative(graph, weights, modularity, + temperature, membership, csize, + spins, parupdate, starttemp, + stoptemp, coolfact, + update_rule, gamma, + /* adhesion, normalised_adhesion, */ + /* polarization, */ + gamma_minus); + break; + default: + IGRAPH_ERROR("Unknown `implementation' in spinglass community finding", + IGRAPH_EINVAL); + } + ); return 0; } -int igraph_i_community_spinglass_orig(const igraph_t *graph, - const igraph_vector_t *weights, - igraph_real_t *modularity, - igraph_real_t *temperature, - igraph_vector_t *membership, - igraph_vector_t *csize, - igraph_integer_t spins, - igraph_bool_t parupdate, - igraph_real_t starttemp, - igraph_real_t stoptemp, - igraph_real_t coolfact, - igraph_spincomm_update_t update_rule, - igraph_real_t gamma) { +static int igraph_i_community_spinglass_orig( + const igraph_t *graph, + const igraph_vector_t *weights, + igraph_real_t *modularity, + igraph_real_t *temperature, + igraph_vector_t *membership, + igraph_vector_t *csize, + igraph_integer_t spins, + igraph_bool_t parupdate, + igraph_real_t starttemp, + igraph_real_t stoptemp, + igraph_real_t coolfact, + igraph_spincomm_update_t update_rule, + igraph_real_t gamma) { unsigned long changes, runs; igraph_bool_t use_weights = 0; @@ -448,94 +448,96 @@ igraph_integer_t spins, igraph_spincomm_update_t update_rule, igraph_real_t gamma) { - - igraph_bool_t use_weights = 0; - double prob; - ClusterList *cl_cur; - network *net; - PottsModel *pm; - char startnode[255]; + IGRAPH_HANDLE_EXCEPTIONS( + igraph_bool_t use_weights = 0; + double prob; + ClusterList *cl_cur; + network *net; + PottsModel *pm; + char startnode[255]; - /* Check arguments */ + /* Check arguments */ - if (spins < 2 || spins > 500) { - IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL); - } - if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE && - update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) { - IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL); - } - if (weights) { - if (igraph_vector_size(weights) != igraph_ecount(graph)) { - IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); + if (spins < 2 || spins > 500) { + IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL); } - use_weights = 1; - } - if (gamma < 0.0) { - IGRAPH_ERROR("Invalid gamme value", IGRAPH_EINVAL); - } - if (vertex < 0 || vertex > igraph_vcount(graph)) { - IGRAPH_ERROR("Invalid vertex id", IGRAPH_EINVAL); - } + if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE && + update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) { + IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL); + } + if (weights) { + if (igraph_vector_size(weights) != igraph_ecount(graph)) { + IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL); + } + use_weights = 1; + } + if (gamma < 0.0) { + IGRAPH_ERROR("Invalid gamme value", IGRAPH_EINVAL); + } + if (vertex < 0 || vertex > igraph_vcount(graph)) { + IGRAPH_ERROR("Invalid vertex id", IGRAPH_EINVAL); + } - /* Check whether we have a single component */ - igraph_bool_t conn; - IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK)); - if (!conn) { - IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL); - } + /* Check whether we have a single component */ + igraph_bool_t conn; + IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK)); + if (!conn) { + IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL); + } - net = new network; - net->node_list = new DL_Indexed_List(); - net->link_list = new DL_Indexed_List(); - net->cluster_list = new DL_Indexed_List*>(); + net = new network; + net->node_list = new DL_Indexed_List(); + net->link_list = new DL_Indexed_List(); + net->cluster_list = new DL_Indexed_List*>(); - /* Transform the igraph_t */ - IGRAPH_CHECK(igraph_i_read_network(graph, weights, - net, use_weights, 0)); + /* Transform the igraph_t */ + IGRAPH_CHECK(igraph_i_read_network(graph, weights, + net, use_weights, 0)); - prob = 2.0 * net->sum_weights / double(net->node_list->Size()) - / double(net->node_list->Size() - 1); + prob = 2.0 * net->sum_weights / double(net->node_list->Size()) + / double(net->node_list->Size() - 1); - pm = new PottsModel(net, (unsigned int)spins, update_rule); + pm = new PottsModel(net, (unsigned int)spins, update_rule); - /* initialize the random number generator */ - RNG_BEGIN(); + /* initialize the random number generator */ + RNG_BEGIN(); - /* to be exected, if we want to find the community around a particular node*/ - /* the initial conf is needed, because otherwise, - the degree of the nodes is not in the weight property, stupid!!! */ - pm->assign_initial_conf(-1); - snprintf(startnode, 255, "%li", (long int)vertex + 1); - pm->FindCommunityFromStart(gamma, prob, startnode, community, - cohesion, adhesion, inner_links, outer_links); + /* to be exected, if we want to find the community around a particular node*/ + /* the initial conf is needed, because otherwise, + the degree of the nodes is not in the weight property, stupid!!! */ + pm->assign_initial_conf(-1); + snprintf(startnode, 255, "%li", (long int)vertex + 1); + pm->FindCommunityFromStart(gamma, prob, startnode, community, + cohesion, adhesion, inner_links, outer_links); - while (net->link_list->Size()) { - delete net->link_list->Pop(); - } - while (net->node_list->Size()) { - delete net->node_list->Pop(); - } - while (net->cluster_list->Size()) { - cl_cur = net->cluster_list->Pop(); - while (cl_cur->Size()) { - cl_cur->Pop(); + while (net->link_list->Size()) { + delete net->link_list->Pop(); } - delete cl_cur; - } - delete net->link_list; - delete net->node_list; - delete net->cluster_list; + while (net->node_list->Size()) { + delete net->node_list->Pop(); + } + while (net->cluster_list->Size()) { + cl_cur = net->cluster_list->Pop(); + while (cl_cur->Size()) { + cl_cur->Pop(); + } + delete cl_cur; + } + delete net->link_list; + delete net->node_list; + delete net->cluster_list; - RNG_END(); + RNG_END(); - delete net; - delete pm; + delete net; + delete pm; + ); return 0; } -int igraph_i_community_spinglass_negative(const igraph_t *graph, +static int igraph_i_community_spinglass_negative( + const igraph_t *graph, const igraph_vector_t *weights, igraph_real_t *modularity, igraph_real_t *temperature, @@ -548,9 +550,9 @@ igraph_real_t coolfact, igraph_spincomm_update_t update_rule, igraph_real_t gamma, - /* igraph_matrix_t *adhesion, */ - /* igraph_matrix_t *normalised_adhesion, */ - /* igraph_real_t *polarization, */ + /* igraph_matrix_t *adhesion, */ + /* igraph_matrix_t *normalised_adhesion, */ + /* igraph_real_t *polarization, */ igraph_real_t gamma_minus) { unsigned long changes, runs; diff --git a/igraph/src/cocitation.c b/igraph/src/cocitation.c --- a/igraph/src/cocitation.c +++ b/igraph/src/cocitation.c @@ -254,13 +254,10 @@ return 0; } -int igraph_i_neisets_intersect(const igraph_vector_t *v1, - const igraph_vector_t *v2, long int *len_union, - long int *len_intersection); -int igraph_i_neisets_intersect(const igraph_vector_t *v1, - const igraph_vector_t *v2, long int *len_union, - long int *len_intersection) { +static int igraph_i_neisets_intersect(const igraph_vector_t *v1, + const igraph_vector_t *v2, long int *len_union, + long int *len_intersection) { /* ASSERT: v1 and v2 are sorted */ long int i, j, i0, jj0; i0 = igraph_vector_size(v1); jj0 = igraph_vector_size(v2); @@ -460,7 +457,7 @@ if (seen == 0) { IGRAPH_ERROR("cannot calculate Jaccard similarity", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, seen); + IGRAPH_FINALLY(igraph_free, seen); for (i = 0; i < k; i++) { j = (long int) VECTOR(*pairs)[i]; @@ -474,7 +471,7 @@ } } - free(seen); + igraph_Free(seen); IGRAPH_FINALLY_CLEAN(1); } diff --git a/igraph/src/cohesive_blocks.c b/igraph/src/cohesive_blocks.c --- a/igraph/src/cohesive_blocks.c +++ b/igraph/src/cohesive_blocks.c @@ -27,13 +27,12 @@ #include "igraph_flow.h" #include "igraph_separators.h" #include "igraph_structural.h" -#include "igraph_components.h" #include "igraph_dqueue.h" #include "igraph_constructors.h" #include "igraph_interrupt_internal.h" #include "igraph_statusbar.h" -void igraph_i_cohesive_blocks_free(igraph_vector_ptr_t *ptr) { +static void igraph_i_cohesive_blocks_free(igraph_vector_ptr_t *ptr) { long int i, n = igraph_vector_ptr_size(ptr); for (i = 0; i < n; i++) { @@ -45,7 +44,7 @@ } } -void igraph_i_cohesive_blocks_free2(igraph_vector_ptr_t *ptr) { +static void igraph_i_cohesive_blocks_free2(igraph_vector_ptr_t *ptr) { long int i, n = igraph_vector_ptr_size(ptr); for (i = 0; i < n; i++) { @@ -57,7 +56,7 @@ } } -void igraph_i_cohesive_blocks_free3(igraph_vector_ptr_t *ptr) { +static void igraph_i_cohesive_blocks_free3(igraph_vector_ptr_t *ptr) { long int i, n = igraph_vector_ptr_size(ptr); for (i = 0; i < n; i++) { @@ -75,14 +74,14 @@ * all neighboring components. */ -int igraph_i_cb_components(igraph_t *graph, - const igraph_vector_bool_t *excluded, - igraph_vector_long_t *components, - long int *no, - /* working area follows */ - igraph_vector_long_t *compid, - igraph_dqueue_t *Q, - igraph_vector_t *neis) { +static int igraph_i_cb_components(igraph_t *graph, + const igraph_vector_bool_t *excluded, + igraph_vector_long_t *components, + long int *no, + /* working area follows */ + igraph_vector_long_t *compid, + igraph_dqueue_t *Q, + igraph_vector_t *neis) { long int no_of_nodes = igraph_vcount(graph); long int i; @@ -137,8 +136,8 @@ return 0; } -igraph_bool_t igraph_i_cb_isin(const igraph_vector_t *needle, - const igraph_vector_t *haystack) { +static igraph_bool_t igraph_i_cb_isin(const igraph_vector_t *needle, + const igraph_vector_t *haystack) { long int nlen = igraph_vector_size(needle); long int hlen = igraph_vector_size(haystack); long int np = 0, hp = 0; diff --git a/igraph/src/coloring.c b/igraph/src/coloring.c --- a/igraph/src/coloring.c +++ b/igraph/src/coloring.c @@ -1,4 +1,23 @@ +/* + Heuristic graph coloring algorithms. + Copyright (C) 2017 Szabolcs Horvat + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301 USA +*/ + #include "igraph_coloring.h" #include "igraph_interface.h" #include "igraph_adjlist.h" @@ -6,7 +25,7 @@ #include "igraph_types_internal.h" -int igraph_i_vertex_coloring_greedy_cn(const igraph_t *graph, igraph_vector_int_t *colors) { +static int igraph_i_vertex_coloring_greedy_cn(const igraph_t *graph, igraph_vector_int_t *colors) { long i, vertex, maxdeg; long vc = igraph_vcount(graph); igraph_2wheap_t cn; /* indexed heap storing number of already coloured neighbours */ @@ -115,7 +134,7 @@ * \brief Computes a vertex coloring using a greedy algorithm. * * - * This function assigns a "color"---represented as a non-negative integer---to + * This function assigns a "color"—represented as a non-negative integer—to * each vertex of the graph in such a way that neighboring vertices never have * the same color. The obtained coloring is not necessarily minimal. * diff --git a/igraph/src/community.c b/igraph/src/community.c --- a/igraph/src/community.c +++ b/igraph/src/community.c @@ -27,7 +27,6 @@ #include "igraph_memory.h" #include "igraph_random.h" #include "igraph_arpack.h" -#include "igraph_arpack_internal.h" #include "igraph_adjlist.h" #include "igraph_interface.h" #include "igraph_interrupt_internal.h" @@ -50,7 +49,7 @@ #include #endif -int igraph_i_rewrite_membership_vector(igraph_vector_t *membership) { +static int igraph_i_rewrite_membership_vector(igraph_vector_t *membership) { long int no = (long int) igraph_vector_max(membership) + 1; igraph_vector_t idx; long int realno = 0; @@ -73,13 +72,13 @@ return 0; } -int igraph_i_community_eb_get_merges2(const igraph_t *graph, - const igraph_vector_t *edges, - const igraph_vector_t *weights, - igraph_matrix_t *res, - igraph_vector_t *bridges, - igraph_vector_t *modularity, - igraph_vector_t *membership) { +static int igraph_i_community_eb_get_merges2(const igraph_t *graph, + const igraph_vector_t *edges, + const igraph_vector_t *weights, + igraph_matrix_t *res, + igraph_vector_t *bridges, + igraph_vector_t *modularity, + igraph_vector_t *membership) { igraph_vector_t mymembership; long int no_of_nodes = igraph_vcount(graph); @@ -177,7 +176,7 @@ /** * \function igraph_community_eb_get_merges - * \brief Calculating the merges, ie. the dendrogram for an edge betweenness community structure + * \brief Calculating the merges, i.e. the dendrogram for an edge betweenness community structure * * * This function is handy if you have a sequence of edge which are @@ -293,8 +292,8 @@ } /* Find the smallest active element in the vector */ -long int igraph_i_vector_which_max_not_null(const igraph_vector_t *v, - const char *passive) { +static long int igraph_i_vector_which_max_not_null(const igraph_vector_t *v, + const char *passive) { long int which, i = 0, size = igraph_vector_size(v); igraph_real_t max; while (passive[i]) { @@ -358,7 +357,7 @@ * \param membership If not a null pointer, then the membership vector, * corresponding to the highest modularity value, is stored here. * \param directed Logical constant, whether to calculate directed - * betweenness (ie. directed paths) for directed graphs. It is + * betweenness (i.e. directed paths) for directed graphs. It is * ignored for undirected graphs. * \param weights An optional vector containing edge weights. If null, * the unweighted edge betweenness scores will be calculated and @@ -482,7 +481,9 @@ IGRAPH_CHECK(igraph_vector_resize(result, no_of_edges)); if (edge_betweenness) { IGRAPH_CHECK(igraph_vector_resize(edge_betweenness, no_of_edges)); - VECTOR(*edge_betweenness)[no_of_edges - 1] = 0; + if (no_of_edges > 0) { + VECTOR(*edge_betweenness)[no_of_edges - 1] = 0; + } } IGRAPH_VECTOR_INIT_FINALLY(&eb, no_of_edges); @@ -719,7 +720,7 @@ if (result_owned) { igraph_vector_destroy(result); - free(result); + igraph_Free(result); IGRAPH_FINALLY_CLEAN(2); } @@ -890,7 +891,7 @@ * \param graph The input graph. It must be undirected; directed graphs are * not supported yet. * \param membership Numeric vector which gives the type of each - * vertex, ie. the component to which it belongs. + * vertex, i.e. the component to which it belongs. * It does not have to be consecutive, i.e. empty communities are * allowed. * \param modularity Pointer to a real number, the result will be @@ -1052,7 +1053,7 @@ * range 0, ..., n - 1. * * \param membership Numeric vector which gives the type of each - * vertex, ie. the component to which it belongs. + * vertex, i.e. the component to which it belongs. * The vector will be altered in-place. * \param new_to_old Pointer to a vector which will contain the * old component ID for each new one, or NULL, @@ -1176,9 +1177,9 @@ igraph_real_t sumweights; } igraph_i_community_leading_eigenvector_data_t; -int igraph_i_community_leading_eigenvector(igraph_real_t *to, - const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_community_leading_eigenvector(igraph_real_t *to, + const igraph_real_t *from, + int n, void *extra) { igraph_i_community_leading_eigenvector_data_t *data = extra; long int j, k, nlen, size = n; @@ -1237,9 +1238,9 @@ return 0; } -int igraph_i_community_leading_eigenvector2(igraph_real_t *to, - const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_community_leading_eigenvector2(igraph_real_t *to, + const igraph_real_t *from, + int n, void *extra) { igraph_i_community_leading_eigenvector_data_t *data = extra; long int j, k, nlen, size = n; @@ -1303,9 +1304,9 @@ return 0; } -int igraph_i_community_leading_eigenvector_weighted(igraph_real_t *to, - const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_community_leading_eigenvector_weighted(igraph_real_t *to, + const igraph_real_t *from, + int n, void *extra) { igraph_i_community_leading_eigenvector_data_t *data = extra; long int j, k, nlen, size = n; @@ -1367,9 +1368,9 @@ return 0; } -int igraph_i_community_leading_eigenvector2_weighted(igraph_real_t *to, - const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_community_leading_eigenvector2_weighted(igraph_real_t *to, + const igraph_real_t *from, + int n, void *extra) { igraph_i_community_leading_eigenvector_data_t *data = extra; long int j, k, nlen, size = n; @@ -1436,7 +1437,7 @@ return 0; } -void igraph_i_levc_free(igraph_vector_ptr_t *ptr) { +static void igraph_i_levc_free(igraph_vector_ptr_t *ptr) { long int i, n = igraph_vector_ptr_size(ptr); for (i = 0; i < n; i++) { igraph_vector_t *v = VECTOR(*ptr)[i]; @@ -1447,8 +1448,8 @@ } } -void igraph_i_error_handler_none(const char *reason, const char *file, - int line, int igraph_errno) { +static void igraph_i_error_handler_none(const char *reason, const char *file, + int line, int igraph_errno) { IGRAPH_UNUSED(reason); IGRAPH_UNUSED(file); IGRAPH_UNUSED(line); @@ -1514,7 +1515,7 @@ * \ref igraph_vector_t object. The user is responsible of * deallocating the memory that belongs to the individual vectors, * by calling first \ref igraph_vector_destroy(), and then - * free() on them. + * \ref igraph_free() on them. * \param history Pointer to an initialized vector or a null pointer. * If not a null pointer, then a trace of the algorithm is stored * here, encoded numerically. The various operations: @@ -2682,7 +2683,7 @@ } igraph_i_multilevel_community_list; /* Computes the modularity of a community partitioning */ -igraph_real_t igraph_i_multilevel_community_modularity( +static igraph_real_t igraph_i_multilevel_community_modularity( const igraph_i_multilevel_community_list *communities) { igraph_real_t result = 0; long int i; @@ -2703,7 +2704,7 @@ long int id; } igraph_i_multilevel_link; -int igraph_i_multilevel_link_cmp(const void *a, const void *b) { +static int igraph_i_multilevel_link_cmp(const void *a, const void *b) { long int r = (((igraph_i_multilevel_link*)a)->from - ((igraph_i_multilevel_link*)b)->from); if (r != 0) { @@ -2715,7 +2716,7 @@ } /* removes multiple edges and returns new edge id's for each edge in |E|log|E| */ -int igraph_i_multilevel_simplify_multiple(igraph_t *graph, igraph_vector_t *eids) { +static int igraph_i_multilevel_simplify_multiple(igraph_t *graph, igraph_vector_t *eids) { long int ecount = igraph_ecount(graph); long int i, l = -1, last_from = -1, last_to = -1; igraph_bool_t directed = igraph_is_directed(graph); @@ -2730,7 +2731,7 @@ if (links == 0) { IGRAPH_ERROR("multi-level community structure detection failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, links); + IGRAPH_FINALLY(igraph_free, links); for (i = 0; i < ecount; i++) { igraph_edge(graph, (igraph_integer_t) i, &from, &to); @@ -2760,7 +2761,7 @@ VECTOR(*eids)[links[i].id] = l; } - free(links); + igraph_Free(links); IGRAPH_FINALLY_CLEAN(1); igraph_destroy(graph); @@ -2777,7 +2778,7 @@ igraph_real_t weight; } igraph_i_multilevel_community_link; -int igraph_i_multilevel_community_link_cmp(const void *a, const void *b) { +static int igraph_i_multilevel_community_link_cmp(const void *a, const void *b) { return (int) (((igraph_i_multilevel_community_link*)a)->community - ((igraph_i_multilevel_community_link*)b)->community); } @@ -2795,11 +2796,12 @@ * communities incident on this vertex and the total weight of edges * pointing to these communities */ -int igraph_i_multilevel_community_links(const igraph_t *graph, - const igraph_i_multilevel_community_list *communities, - igraph_integer_t vertex, igraph_vector_t *edges, - igraph_real_t *weight_all, igraph_real_t *weight_inside, igraph_real_t *weight_loop, - igraph_vector_t *links_community, igraph_vector_t *links_weight) { +static int igraph_i_multilevel_community_links( + const igraph_t *graph, + const igraph_i_multilevel_community_list *communities, + igraph_integer_t vertex, igraph_vector_t *edges, + igraph_real_t *weight_all, igraph_real_t *weight_inside, igraph_real_t *weight_loop, + igraph_vector_t *links_community, igraph_vector_t *links_weight) { long int i, n, last = -1, c = -1; igraph_real_t weight = 1; @@ -2869,10 +2871,10 @@ return 0; } -igraph_real_t igraph_i_multilevel_community_modularity_gain( - const igraph_i_multilevel_community_list *communities, - igraph_integer_t community, igraph_integer_t vertex, - igraph_real_t weight_all, igraph_real_t weight_inside) { +static igraph_real_t igraph_i_multilevel_community_modularity_gain( + const igraph_i_multilevel_community_list *communities, + igraph_integer_t community, igraph_integer_t vertex, + igraph_real_t weight_all, igraph_real_t weight_inside) { IGRAPH_UNUSED(vertex); return weight_inside - communities->item[(long int)community].weight_all * weight_all / communities->weight_sum; @@ -2884,7 +2886,7 @@ * detection where a copy of the original graph is used anyway. * The membership vector will also be rewritten by the underlying * igraph_membership_reindex call */ -int igraph_i_multilevel_shrink(igraph_t *graph, igraph_vector_t *membership) { +static int igraph_i_multilevel_shrink(igraph_t *graph, igraph_vector_t *membership) { igraph_vector_t edges; long int no_of_nodes = igraph_vcount(graph); long int no_of_edges = igraph_ecount(graph); @@ -2955,9 +2957,11 @@ * * Time complexity: in average near linear on sparse graphs. */ -int igraph_i_community_multilevel_step(igraph_t *graph, - igraph_vector_t *weights, igraph_vector_t *membership, - igraph_real_t *modularity) { +static int igraph_i_community_multilevel_step( + igraph_t *graph, + igraph_vector_t *weights, + igraph_vector_t *membership, + igraph_real_t *modularity) { long int i, j; long int vcount = igraph_vcount(graph); @@ -3316,15 +3320,15 @@ } -int igraph_i_compare_communities_vi(const igraph_vector_t *v1, - const igraph_vector_t *v2, igraph_real_t* result); -int igraph_i_compare_communities_nmi(const igraph_vector_t *v1, - const igraph_vector_t *v2, igraph_real_t* result); -int igraph_i_compare_communities_rand(const igraph_vector_t *v1, - const igraph_vector_t *v2, igraph_real_t* result, igraph_bool_t adjust); -int igraph_i_split_join_distance(const igraph_vector_t *v1, - const igraph_vector_t *v2, igraph_integer_t* distance12, - igraph_integer_t* distance21); +static int igraph_i_compare_communities_vi(const igraph_vector_t *v1, + const igraph_vector_t *v2, igraph_real_t* result); +static int igraph_i_compare_communities_nmi(const igraph_vector_t *v1, + const igraph_vector_t *v2, igraph_real_t* result); +static int igraph_i_compare_communities_rand(const igraph_vector_t *v1, + const igraph_vector_t *v2, igraph_real_t* result, igraph_bool_t adjust); +static int igraph_i_split_join_distance(const igraph_vector_t *v1, + const igraph_vector_t *v2, igraph_integer_t* distance12, + igraph_integer_t* distance21); /** * \ingroup communities @@ -3518,7 +3522,7 @@ * membership vectors v1 and v2. This is needed by both Meila's and Danon's * community comparison measure. */ -int igraph_i_entropy_and_mutual_information(const igraph_vector_t* v1, +static int igraph_i_entropy_and_mutual_information(const igraph_vector_t* v1, const igraph_vector_t* v2, double* h1, double* h2, double* mut_inf) { long int i, n = igraph_vector_size(v1); long int k1 = (long int)igraph_vector_max(v1) + 1; @@ -3531,12 +3535,12 @@ if (p1 == 0) { IGRAPH_ERROR("igraph_i_entropy_and_mutual_information failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, p1); + IGRAPH_FINALLY(igraph_free, p1); p2 = igraph_Calloc(k2, double); if (p2 == 0) { IGRAPH_ERROR("igraph_i_entropy_and_mutual_information failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, p2); + IGRAPH_FINALLY(igraph_free, p2); /* Calculate the entropy of v1 */ *h1 = 0.0; @@ -3584,7 +3588,7 @@ igraph_spmatrix_iter_destroy(&mit); igraph_spmatrix_destroy(&m); - free(p1); free(p2); + igraph_Free(p1); igraph_Free(p2); IGRAPH_FINALLY_CLEAN(4); @@ -3603,7 +3607,7 @@ * * Time complexity: O(n log(n)) */ -int igraph_i_compare_communities_nmi(const igraph_vector_t *v1, const igraph_vector_t *v2, +static int igraph_i_compare_communities_nmi(const igraph_vector_t *v1, const igraph_vector_t *v2, igraph_real_t* result) { double h1, h2, mut_inf; @@ -3633,7 +3637,7 @@ * * Time complexity: O(n log(n)) */ -int igraph_i_compare_communities_vi(const igraph_vector_t *v1, const igraph_vector_t *v2, +static int igraph_i_compare_communities_vi(const igraph_vector_t *v1, const igraph_vector_t *v2, igraph_real_t* result) { double h1, h2, mut_inf; @@ -3654,7 +3658,7 @@ * Time complexity: O(n log(max(k1, k2))), where n is the number of vertices, k1 * and k2 are the number of clusters in each of the clusterings. */ -int igraph_i_confusion_matrix(const igraph_vector_t *v1, const igraph_vector_t *v2, +static int igraph_i_confusion_matrix(const igraph_vector_t *v1, const igraph_vector_t *v2, igraph_spmatrix_t *m) { long int k1 = (long int)igraph_vector_max(v1) + 1; long int k2 = (long int)igraph_vector_max(v2) + 1; @@ -3685,7 +3689,7 @@ * Time complexity: O(n log(max(k1, k2))), where n is the number of vertices, k1 * and k2 are the number of clusters in each of the clusterings. */ -int igraph_i_split_join_distance(const igraph_vector_t *v1, const igraph_vector_t *v2, +static int igraph_i_split_join_distance(const igraph_vector_t *v1, const igraph_vector_t *v2, igraph_integer_t* distance12, igraph_integer_t* distance21) { long int n = igraph_vector_size(v1); igraph_vector_t rowmax, colmax; @@ -3750,8 +3754,9 @@ * Time complexity: O(n log(max(k1, k2))), where n is the number of vertices, k1 * and k2 are the number of clusters in each of the clusterings. */ -int igraph_i_compare_communities_rand(const igraph_vector_t *v1, - const igraph_vector_t *v2, igraph_real_t *result, igraph_bool_t adjust) { +static int igraph_i_compare_communities_rand( + const igraph_vector_t *v1, const igraph_vector_t *v2, + igraph_real_t *result, igraph_bool_t adjust) { igraph_spmatrix_t m; igraph_spmatrix_iter_t mit; igraph_vector_t rowsums, colsums; diff --git a/igraph/src/community_leiden.c b/igraph/src/community_leiden.c --- a/igraph/src/community_leiden.c +++ b/igraph/src/community_leiden.c @@ -46,7 +46,8 @@ * and is updated in-place. * */ -int igraph_i_community_leiden_fastmovenodes(const igraph_t *graph, +static int igraph_i_community_leiden_fastmovenodes( + const igraph_t *graph, const igraph_inclist_t *edges_per_node, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights, const igraph_real_t resolution_parameter, @@ -121,7 +122,7 @@ VECTOR(cluster_weights)[current_cluster] -= VECTOR(*node_weights)[v]; VECTOR(nb_nodes_per_cluster)[current_cluster]--; if (VECTOR(nb_nodes_per_cluster)[current_cluster] == 0) { - igraph_stack_push(&empty_clusters, current_cluster); + IGRAPH_CHECK(igraph_stack_push(&empty_clusters, current_cluster)); } /* Find out neighboring clusters */ @@ -136,12 +137,14 @@ for (i = 0; i < degree; i++) { long int e = VECTOR(*edges)[i]; long int u = (long int)IGRAPH_OTHER(graph, e, v); - c = VECTOR(*membership)[u]; - if (!VECTOR(neighbor_cluster_added)[c]) { - VECTOR(neighbor_cluster_added)[c] = 1; - VECTOR(neighbor_clusters)[nb_neigh_clusters++] = c; + if (u != v) { + c = VECTOR(*membership)[u]; + if (!VECTOR(neighbor_cluster_added)[c]) { + VECTOR(neighbor_cluster_added)[c] = 1; + VECTOR(neighbor_clusters)[nb_neigh_clusters++] = c; + } + VECTOR(edge_weights_per_cluster)[c] += VECTOR(*edge_weights)[e]; } - VECTOR(edge_weights_per_cluster)[c] += VECTOR(*edge_weights)[e]; } /* Calculate maximum diff */ @@ -176,7 +179,7 @@ long int e = VECTOR(*edges)[i]; long int u = (long int)IGRAPH_OTHER(graph, e, v); if (VECTOR(node_is_stable)[u] && VECTOR(*membership)[u] != best_cluster) { - igraph_dqueue_push(&unstable_nodes, u); + IGRAPH_CHECK(igraph_dqueue_push(&unstable_nodes, u)); VECTOR(node_is_stable)[u] = 0; } } @@ -215,7 +218,10 @@ * resulting \c nb_refined_clusters, then nodes in \c node_subset are numbered * C, C + 1, ..., C' - 1. */ -int igraph_i_community_leiden_clean_refined_membership(const igraph_vector_t* node_subset, igraph_vector_t *refined_membership, igraph_integer_t* nb_refined_clusters) { +static int igraph_i_community_leiden_clean_refined_membership( + const igraph_vector_t* node_subset, + igraph_vector_t *refined_membership, + igraph_integer_t* nb_refined_clusters) { long int i, n = igraph_vector_size(node_subset); igraph_vector_t new_cluster; @@ -280,7 +286,8 @@ * igraph_i_community_leiden_clean_refined_membership for more information about * this aspect. */ -int igraph_i_community_leiden_mergenodes(const igraph_t *graph, +static int igraph_i_community_leiden_mergenodes( + const igraph_t *graph, const igraph_inclist_t *edges_per_node, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights, const igraph_vector_t *node_subset, @@ -324,7 +331,7 @@ for (j = 0; j < degree; j++) { long int e = VECTOR(*edges)[j]; long int u = (long int)IGRAPH_OTHER(graph, e, v); - if (VECTOR(*membership)[u] == cluster_subset) { + if (u != v && VECTOR(*membership)[u] == cluster_subset) { VECTOR(external_edge_weight_per_cluster_in_subset)[i] += VECTOR(*edge_weights)[e]; } } @@ -378,7 +385,7 @@ for (j = 0; j < degree; j++) { long int e = (long int)VECTOR(*edges)[j]; long int u = (long int)IGRAPH_OTHER(graph, e, v); - if (VECTOR(*membership)[u] == cluster_subset) { + if (u != v && VECTOR(*membership)[u] == cluster_subset) { long int c = VECTOR(*refined_membership)[u]; if (!VECTOR(neighbor_cluster_added)[c]) { VECTOR(neighbor_cluster_added)[c] = 1; @@ -420,7 +427,7 @@ if (total_cum_trans_diff < IGRAPH_INFINITY) { igraph_real_t r = igraph_rng_get_unif(igraph_rng_default(), 0, total_cum_trans_diff); long int chosen_idx; - igraph_i_vector_binsearch_slice(&cum_trans_diff, r, &chosen_idx, 0, nb_neigh_clusters); + igraph_vector_binsearch_slice(&cum_trans_diff, r, &chosen_idx, 0, nb_neigh_clusters); chosen_cluster = VECTOR(neighbor_clusters)[chosen_idx]; } else { chosen_cluster = best_cluster; @@ -479,7 +486,7 @@ * should be ensured that all clusters are always properly empty (or * non-existing) before calling this function. */ -int igraph_i_community_get_clusters(const igraph_vector_t *membership, igraph_vector_ptr_t *clusters) { +static int igraph_i_community_get_clusters(const igraph_vector_t *membership, igraph_vector_ptr_t *clusters) { long int i, c, n = igraph_vector_size(membership); igraph_vector_t *cluster; for (i = 0; i < n; i++) { @@ -498,7 +505,7 @@ } /* Add node i to cluster vector */ - igraph_vector_push_back(cluster, i); + IGRAPH_CHECK(igraph_vector_push_back(cluster, i)); } return IGRAPH_SUCCESS; @@ -518,7 +525,7 @@ * aggregated_membership are all expected to be initialized. * */ -int igraph_i_community_leiden_aggregate( +static int igraph_i_community_leiden_aggregate( const igraph_t *graph, const igraph_inclist_t *edges_per_node, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights, const igraph_vector_t *membership, const igraph_vector_t *refined_membership, const igraph_integer_t nb_refined_clusters, igraph_t *aggregated_graph, igraph_vector_t *aggregated_edge_weights, igraph_vector_t *aggregated_node_weights, igraph_vector_t *aggregated_membership) { @@ -531,7 +538,7 @@ /* Get refined clusters */ IGRAPH_CHECK(igraph_vector_ptr_init(&refined_clusters, nb_refined_clusters)); - igraph_vector_ptr_set_item_destructor(&refined_clusters, igraph_vector_destroy); + IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&refined_clusters, igraph_vector_destroy); IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &refined_clusters); IGRAPH_CHECK(igraph_i_community_get_clusters(refined_membership, &refined_clusters)); @@ -591,10 +598,11 @@ long int c2 = VECTOR(neighbor_clusters)[i]; /* Add edge */ - igraph_vector_push_back(&aggregated_edges, c); igraph_vector_push_back(&aggregated_edges, c2); + IGRAPH_CHECK(igraph_vector_push_back(&aggregated_edges, c)); + IGRAPH_CHECK(igraph_vector_push_back(&aggregated_edges, c2)); /* Add edge weight */ - igraph_vector_push_back(aggregated_edge_weights, VECTOR(edge_weight_to_cluster)[c2]); + IGRAPH_CHECK(igraph_vector_push_back(aggregated_edge_weights, VECTOR(edge_weight_to_cluster)[c2])); VECTOR(edge_weight_to_cluster)[c2] = 0.0; VECTOR(neighbor_cluster_added)[c2] = 0; @@ -604,17 +612,21 @@ } - IGRAPH_CHECK(igraph_create(aggregated_graph, &aggregated_edges, nb_refined_clusters, - IGRAPH_UNDIRECTED)); - igraph_vector_destroy(&neighbor_clusters); igraph_vector_bool_destroy(&neighbor_cluster_added); igraph_vector_destroy(&edge_weight_to_cluster); - igraph_vector_destroy(&aggregated_edges); igraph_vector_ptr_destroy_all(&refined_clusters); - IGRAPH_FINALLY_CLEAN(5); + IGRAPH_FINALLY_CLEAN(4); + igraph_destroy(aggregated_graph); + IGRAPH_CHECK(igraph_create(aggregated_graph, &aggregated_edges, nb_refined_clusters, + IGRAPH_UNDIRECTED)); + + igraph_vector_destroy(&aggregated_edges); + + IGRAPH_FINALLY_CLEAN(1); + return IGRAPH_SUCCESS; } @@ -641,9 +653,10 @@ * weights inside cluster c. This is how the quality is calculated in practice. * */ -int igraph_i_community_leiden_quality(const igraph_t *graph, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights, - const igraph_vector_t *membership, const igraph_integer_t nb_comms, const igraph_real_t resolution_parameter, - igraph_real_t *quality) { +static int igraph_i_community_leiden_quality( + const igraph_t *graph, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights, + const igraph_vector_t *membership, const igraph_integer_t nb_comms, const igraph_real_t resolution_parameter, + igraph_real_t *quality) { igraph_vector_t cluster_weights; igraph_real_t total_edge_weight = 0.0; igraph_eit_t eit; @@ -697,13 +710,14 @@ * partition for the aggregate network. */ int igraph_i_community_leiden(const igraph_t *graph, - const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights, + igraph_vector_t *edge_weights, igraph_vector_t *node_weights, const igraph_real_t resolution_parameter, const igraph_real_t beta, igraph_vector_t *membership, igraph_integer_t *nb_clusters, igraph_real_t *quality) { igraph_integer_t nb_refined_clusters; long int i, c, n = igraph_vcount(graph); - igraph_t *aggregated_graph, *tmp_graph; - igraph_vector_t *aggregated_edge_weights, *aggregated_node_weights, *aggregated_membership; + igraph_t aggregated_graph, *i_graph; + igraph_vector_t aggregated_edge_weights, aggregated_node_weights, aggregated_membership; + igraph_vector_t *i_edge_weights, *i_node_weights, *i_membership; igraph_vector_t tmp_edge_weights, tmp_node_weights, tmp_membership; igraph_vector_t refined_membership; igraph_vector_int_t aggregate_node; @@ -722,8 +736,9 @@ /* Initialize clusters */ IGRAPH_CHECK(igraph_vector_ptr_init(&clusters, n)); - igraph_vector_ptr_set_item_destructor(&clusters, igraph_vector_destroy); + IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&clusters, igraph_vector_destroy); IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &clusters); + /* Initialize aggregate nodes, which initially is identical to simply the * nodes in the graph. */ IGRAPH_CHECK(igraph_vector_int_init(&aggregate_node, n)); @@ -732,18 +747,36 @@ VECTOR(aggregate_node)[i] = i; } + /* Initialize refined membership */ IGRAPH_CHECK(igraph_vector_init(&refined_membership, 0)); IGRAPH_FINALLY(igraph_vector_destroy, &refined_membership); - /* Initialize aggregated graph, weights and membership. */ - aggregated_graph = graph; - aggregated_edge_weights = edge_weights; - aggregated_node_weights = node_weights; - aggregated_membership = membership; + /* Initialize aggregated graph */ + IGRAPH_CHECK(igraph_empty(&aggregated_graph, 0, IGRAPH_UNDIRECTED)); + IGRAPH_FINALLY(igraph_destroy, &aggregated_graph); + /* Initialize aggregated edge weights */ + IGRAPH_CHECK(igraph_vector_init(&aggregated_edge_weights, 0)); + IGRAPH_FINALLY(igraph_vector_destroy, &aggregated_edge_weights); + + /* Initialize aggregated node weights */ + IGRAPH_CHECK(igraph_vector_init(&aggregated_node_weights, 0)); + IGRAPH_FINALLY(igraph_vector_destroy, &aggregated_node_weights); + + /* Initialize aggregated membership */ + IGRAPH_CHECK(igraph_vector_init(&aggregated_membership, 0)); + IGRAPH_FINALLY(igraph_vector_destroy, &aggregated_membership); + + /* Set actual graph, weights and membership to be used. */ + i_graph = (igraph_t*)graph; + i_edge_weights = edge_weights; + i_node_weights = node_weights; + i_membership = membership; + /* Clean membership and count number of *clusters */ - IGRAPH_CHECK(igraph_reindex_membership(aggregated_membership, NULL, nb_clusters)); + IGRAPH_CHECK(igraph_reindex_membership(i_membership, NULL, nb_clusters)); + if (*nb_clusters > n) { IGRAPH_ERROR("Too many communities in membership vector", IGRAPH_EINVAL); } @@ -751,45 +784,45 @@ do { /* Get incidence list for fast iteration */ - IGRAPH_CHECK(igraph_inclist_init(aggregated_graph, &edges_per_node, IGRAPH_ALL)); + IGRAPH_CHECK(igraph_inclist_init( i_graph, &edges_per_node, IGRAPH_ALL)); IGRAPH_FINALLY(igraph_inclist_destroy, &edges_per_node); /* Move around the nodes in order to increase the quality */ - IGRAPH_CHECK(igraph_i_community_leiden_fastmovenodes(aggregated_graph, + IGRAPH_CHECK(igraph_i_community_leiden_fastmovenodes(i_graph, &edges_per_node, - aggregated_edge_weights, aggregated_node_weights, + i_edge_weights, i_node_weights, resolution_parameter, nb_clusters, - aggregated_membership)); + i_membership)); /* We only continue clustering if not all clusters are represented by a * single node yet */ - continue_clustering = (*nb_clusters < igraph_vcount(aggregated_graph)); + continue_clustering = (*nb_clusters < igraph_vcount(i_graph)); if (continue_clustering) { /* Set original membership */ if (level > 0) { for (i = 0; i < n; i++) { long int v_aggregate = VECTOR(aggregate_node)[i]; - VECTOR(*membership)[i] = VECTOR(*aggregated_membership)[v_aggregate]; + VECTOR(*membership)[i] = VECTOR(*i_membership)[v_aggregate]; } } /* Get node sets for each cluster. */ - IGRAPH_CHECK(igraph_i_community_get_clusters(aggregated_membership, &clusters)); + IGRAPH_CHECK(igraph_i_community_get_clusters(i_membership, &clusters)); /* Ensure refined membership is correct size */ - IGRAPH_CHECK(igraph_vector_resize(&refined_membership, igraph_vcount(aggregated_graph))); + IGRAPH_CHECK(igraph_vector_resize(&refined_membership, igraph_vcount(i_graph))); /* Refine each cluster */ nb_refined_clusters = 0; for (c = 0; c < *nb_clusters; c++) { igraph_vector_t* cluster = (igraph_vector_t*)VECTOR(clusters)[c]; - IGRAPH_CHECK(igraph_i_community_leiden_mergenodes(aggregated_graph, + IGRAPH_CHECK(igraph_i_community_leiden_mergenodes(i_graph, &edges_per_node, - aggregated_edge_weights, aggregated_node_weights, - cluster, aggregated_membership, c, + i_edge_weights, i_node_weights, + cluster, i_membership, c, resolution_parameter, beta, &nb_refined_clusters, &refined_membership)); /* Empty cluster */ @@ -798,8 +831,9 @@ /* If refinement didn't aggregate anything, we aggregate on the basis of * the actual clustering */ - if (nb_refined_clusters >= igraph_vcount(aggregated_graph)) { - igraph_vector_update(&refined_membership, aggregated_membership); + if (nb_refined_clusters >= igraph_vcount(i_graph)) { + igraph_vector_update(&refined_membership, i_membership); + nb_refined_clusters = *nb_clusters; } /* Keep track of aggregate node. */ @@ -810,70 +844,27 @@ VECTOR(aggregate_node)[i] = (igraph_integer_t)VECTOR(refined_membership)[v_aggregate]; } - /* Allocate temporary graph */ - tmp_graph = igraph_Calloc(1, igraph_t); - if (tmp_graph == 0) { - IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate graph", IGRAPH_ENOMEM); - } - IGRAPH_FINALLY(free, tmp_graph); - IGRAPH_CHECK(igraph_i_community_leiden_aggregate( - aggregated_graph, &edges_per_node, aggregated_edge_weights, aggregated_node_weights, - aggregated_membership, &refined_membership, nb_refined_clusters, - tmp_graph, &tmp_edge_weights, &tmp_node_weights, &tmp_membership)); - - /* Graph has been created by aggregation, ensure it is properly destroyed if - * an error occurs. */ - IGRAPH_FINALLY(igraph_destroy, tmp_graph); - - if (level >= 1) { - /* Destroy previously allocated graph (note that aggregated_graph points to - * the previously allocated tmp_graph). */ - igraph_destroy(aggregated_graph); - igraph_Free(aggregated_graph); - IGRAPH_FINALLY_CLEAN(2); - } + i_graph, &edges_per_node, i_edge_weights, i_node_weights, + i_membership, &refined_membership, nb_refined_clusters, + &aggregated_graph, &tmp_edge_weights, &tmp_node_weights, &tmp_membership)); /* On the lowest level, the actual graph and node and edge weights and - * membership are used. On higher levels, we will have to use a new graph - * and node and edge weights to represent them. We perform the allocation - * of memory here. We only allocate the memory once, and simply update - * them in any subsequent rounds. + * membership are used. On higher levels, we will use the aggregated graph + * and associated vectors. */ if (level == 0) { - aggregated_edge_weights = igraph_Calloc(1, igraph_vector_t); - if (aggregated_edge_weights == 0) { - IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate edge weights", IGRAPH_ENOMEM); - } - IGRAPH_FINALLY(free, aggregated_edge_weights); - IGRAPH_CHECK(igraph_vector_init(aggregated_edge_weights, 0)); - IGRAPH_FINALLY(igraph_vector_destroy, aggregated_edge_weights); - - aggregated_node_weights = igraph_Calloc(1, igraph_vector_t); - if (aggregated_node_weights == 0) { - IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate node weights", IGRAPH_ENOMEM); - } - IGRAPH_FINALLY(free, aggregated_node_weights); - IGRAPH_CHECK(igraph_vector_init(aggregated_node_weights, 0)); - IGRAPH_FINALLY(igraph_vector_destroy, aggregated_node_weights); - - aggregated_membership = igraph_Calloc(1, igraph_vector_t); - if (aggregated_membership == 0) { - IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate membership", IGRAPH_ENOMEM); - } - IGRAPH_FINALLY(free, aggregated_membership); - IGRAPH_CHECK(igraph_vector_init(aggregated_membership, 0)); - IGRAPH_FINALLY(igraph_vector_destroy, aggregated_membership); + /* Set actual graph, weights and membership to be used. */ + i_graph = &aggregated_graph; + i_edge_weights = &aggregated_edge_weights; + i_node_weights = &aggregated_node_weights; + i_membership = &aggregated_membership; } - /* Set the aggregated graph correctly */ - aggregated_graph = tmp_graph; - - /* Update the aggregated administration. This does not allocate memory, - * it will always fit in existing memory allocated previously. */ - igraph_vector_update(aggregated_edge_weights, &tmp_edge_weights); - igraph_vector_update(aggregated_node_weights, &tmp_node_weights); - igraph_vector_update(aggregated_membership, &tmp_membership); + /* Update the aggregated administration. */ + IGRAPH_CHECK(igraph_vector_update(i_edge_weights, &tmp_edge_weights)); + IGRAPH_CHECK(igraph_vector_update(i_node_weights, &tmp_node_weights)); + IGRAPH_CHECK(igraph_vector_update(i_membership, &tmp_membership)); level += 1; } @@ -883,21 +874,12 @@ IGRAPH_FINALLY_CLEAN(1); } while (continue_clustering); - /* If memory was allocated to represent the aggregated administration we need - * to make sure it is properly freed. This is only done if we have at least - * passed on to the next level of aggregation. - */ - if (level > 0) { - igraph_destroy(aggregated_graph); - igraph_Free(aggregated_graph); - igraph_vector_destroy(aggregated_membership); - igraph_Free(aggregated_membership); - igraph_vector_destroy(aggregated_node_weights); - igraph_Free(aggregated_node_weights); - igraph_vector_destroy(aggregated_edge_weights); - igraph_Free(aggregated_edge_weights); - IGRAPH_FINALLY_CLEAN(8); - } + /* Free aggregated graph and associated vectors */ + igraph_vector_destroy(&aggregated_membership); + igraph_vector_destroy(&aggregated_node_weights); + igraph_vector_destroy(&aggregated_edge_weights); + igraph_destroy(&aggregated_graph); + IGRAPH_FINALLY_CLEAN(4); /* Free remaining memory */ igraph_vector_destroy(&refined_membership); @@ -910,7 +892,7 @@ /* Calculate quality */ if (quality) { - igraph_i_community_leiden_quality(graph, edge_weights, node_weights, membership, *nb_clusters, resolution_parameter, quality); + IGRAPH_CHECK(igraph_i_community_leiden_quality(graph, edge_weights, node_weights, membership, *nb_clusters, resolution_parameter, quality)); } return IGRAPH_SUCCESS; @@ -924,7 +906,7 @@ * This function implements the Leiden algorithm for finding community * structure, see Traag, V. A., Waltman, L., & van Eck, N. J. (2019). From * Louvain to Leiden: guaranteeing well-connected communities. Scientific - * reports, 9(1), 5233. http://dx.doi.org/10.1038/s41598-019-41695-z. + * reports, 9(1), 5233. http://dx.doi.org/10.1038/s41598-019-41695-z * * * It is similar to the multilevel algorithm, often called the Louvain @@ -1002,7 +984,6 @@ const igraph_real_t resolution_parameter, const igraph_real_t beta, const igraph_bool_t start, igraph_vector_t *membership, igraph_integer_t *nb_clusters, igraph_real_t *quality) { igraph_vector_t *i_edge_weights, *i_node_weights; - int ret; igraph_integer_t n = igraph_vcount(graph); if (start) { @@ -1036,12 +1017,12 @@ if (i_edge_weights == 0) { IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for edge weights", IGRAPH_ENOMEM); } + IGRAPH_FINALLY(igraph_free, i_edge_weights); IGRAPH_CHECK(igraph_vector_init(i_edge_weights, igraph_ecount(graph))); - IGRAPH_FINALLY(free, i_edge_weights); IGRAPH_FINALLY(igraph_vector_destroy, i_edge_weights); igraph_vector_fill(i_edge_weights, 1); } else { - i_edge_weights = edge_weights; + i_edge_weights = (igraph_vector_t*)edge_weights; } /* Check edge weights to possibly use default */ @@ -1050,18 +1031,18 @@ if (i_node_weights == 0) { IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for node weights", IGRAPH_ENOMEM); } + IGRAPH_FINALLY(igraph_free, i_node_weights); IGRAPH_CHECK(igraph_vector_init(i_node_weights, n)); - IGRAPH_FINALLY(free, i_node_weights); IGRAPH_FINALLY(igraph_vector_destroy, i_node_weights); igraph_vector_fill(i_node_weights, 1); } else { - i_node_weights = node_weights; + i_node_weights = (igraph_vector_t*)node_weights; } /* Perform actual Leiden algorithm */ - ret = igraph_i_community_leiden(graph, i_edge_weights, i_node_weights, - resolution_parameter, beta, - membership, nb_clusters, quality); + IGRAPH_CHECK(igraph_i_community_leiden(graph, i_edge_weights, i_node_weights, + resolution_parameter, beta, + membership, nb_clusters, quality)); if (!edge_weights) { igraph_vector_destroy(i_edge_weights); @@ -1075,5 +1056,5 @@ IGRAPH_FINALLY_CLEAN(2); } - return ret; + return IGRAPH_SUCCESS; } diff --git a/igraph/src/components.c b/igraph/src/components.c --- a/igraph/src/components.c +++ b/igraph/src/components.c @@ -32,7 +32,6 @@ #include "igraph_stack.h" #include "igraph_vector.h" #include "config.h" -#include #include static int igraph_i_clusters_weak(const igraph_t *graph, igraph_vector_t *membership, @@ -410,7 +409,7 @@ if (already_added == 0) { IGRAPH_ERROR("is connected (weak) failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, already_added); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, already_added); IGRAPH_DQUEUE_INIT_FINALLY(&q, 10); IGRAPH_VECTOR_INIT_FINALLY(&neis, 0); @@ -616,7 +615,7 @@ igraph_vector_destroy(&neis); igraph_vector_destroy(&verts); igraph_dqueue_destroy(&q); - igraph_free(already_added); + igraph_Free(already_added); IGRAPH_FINALLY_CLEAN(5); /* + components */ return 0; @@ -877,7 +876,7 @@ * components. * * - * Somewhat arbitrarily, igraph does not consider comppnents containing + * Somewhat arbitrarily, igraph does not consider components containing * a single vertex only as being biconnected. Isolated vertices will * not be part of any of the biconnected components. * @@ -889,7 +888,7 @@ * a spanning tree of the biconnected component is returned. * Note you'll have to * destroy each vector first by calling \ref igraph_vector_destroy() - * and then free() on it, plus you need to call + * and then \ref igraph_free() on it, plus you need to call * \ref igraph_vector_ptr_destroy() on the list to regain all * allocated memory. * \param component_edges If not a NULL pointer, then the edges of the @@ -1146,9 +1145,15 @@ /* igraph_bridges -- find all bridges in the graph */ -/* based on https://www.geeksforgeeks.org/bridge-in-a-graph/ */ +/* The algorithm is based on https://www.geeksforgeeks.org/bridge-in-a-graph/ + but instead of keeping track of the parent of each vertex in the DFS tree + we keep track of its incoming edge. This is necessary to support multigraphs. */ -static int igraph_i_bridges_rec(const igraph_t *graph, const igraph_inclist_t *il, igraph_integer_t u, igraph_integer_t *time, igraph_vector_t *bridges, igraph_vector_bool_t *visited, igraph_vector_int_t *disc, igraph_vector_int_t *low, igraph_vector_int_t *parent) { +static int igraph_i_bridges_rec( + const igraph_t *graph, const igraph_inclist_t *il, igraph_integer_t u, + igraph_integer_t *time, igraph_vector_t *bridges, igraph_vector_bool_t *visited, + igraph_vector_int_t *disc, igraph_vector_int_t *low, igraph_vector_int_t *incoming_edge) +{ igraph_vector_int_t *incedges; long nc; /* neighbour count */ long i; @@ -1167,15 +1172,15 @@ igraph_integer_t v = IGRAPH_TO(graph, edge) == u ? IGRAPH_FROM(graph, edge) : IGRAPH_TO(graph, edge); if (! VECTOR(*visited)[v]) { - VECTOR(*parent)[v] = u; - IGRAPH_CHECK(igraph_i_bridges_rec(graph, il, v, time, bridges, visited, disc, low, parent)); + VECTOR(*incoming_edge)[v] = edge; + IGRAPH_CHECK(igraph_i_bridges_rec(graph, il, v, time, bridges, visited, disc, low, incoming_edge)); VECTOR(*low)[u] = VECTOR(*low)[u] < VECTOR(*low)[v] ? VECTOR(*low)[u] : VECTOR(*low)[v]; if (VECTOR(*low)[v] > VECTOR(*disc)[u]) { IGRAPH_CHECK(igraph_vector_push_back(bridges, edge)); } - } else if (v != VECTOR(*parent)[u]) { + } else if (edge != VECTOR(*incoming_edge)[u]) { VECTOR(*low)[u] = VECTOR(*low)[u] < VECTOR(*disc)[v] ? VECTOR(*low)[u] : VECTOR(*disc)[v]; } } @@ -1204,7 +1209,7 @@ igraph_inclist_t il; igraph_vector_bool_t visited; igraph_vector_int_t disc, low; - igraph_vector_int_t parent; + igraph_vector_int_t incoming_edge; long n; long i; igraph_integer_t time; @@ -1223,10 +1228,10 @@ IGRAPH_CHECK(igraph_vector_int_init(&low, n)); IGRAPH_FINALLY(igraph_vector_int_destroy, &low); - IGRAPH_CHECK(igraph_vector_int_init(&parent, n)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &parent); + IGRAPH_CHECK(igraph_vector_int_init(&incoming_edge, n)); + IGRAPH_FINALLY(igraph_vector_int_destroy, &incoming_edge); for (i = 0; i < n; ++i) { - VECTOR(parent)[i] = -1; + VECTOR(incoming_edge)[i] = -1; } igraph_vector_clear(bridges); @@ -1234,10 +1239,10 @@ time = 0; for (i = 0; i < n; ++i) if (! VECTOR(visited)[i]) { - IGRAPH_CHECK(igraph_i_bridges_rec(graph, &il, i, &time, bridges, &visited, &disc, &low, &parent)); + IGRAPH_CHECK(igraph_i_bridges_rec(graph, &il, i, &time, bridges, &visited, &disc, &low, &incoming_edge)); } - igraph_vector_int_destroy(&parent); + igraph_vector_int_destroy(&incoming_edge); igraph_vector_int_destroy(&low); igraph_vector_int_destroy(&disc); igraph_vector_bool_destroy(&visited); diff --git a/igraph/src/conversion.c b/igraph/src/conversion.c --- a/igraph/src/conversion.c +++ b/igraph/src/conversion.c @@ -37,8 +37,8 @@ * \brief Returns the adjacency matrix of a graph * * - * The result is an incidence matrix, it contains numbers greater - * than one if there are multiple edges in the graph. + * The result is an adjacency matrix. Entry i, j of the matrix + * contains the number of edges connecting vertex i to vertex j. * \param graph Pointer to the graph to convert * \param res Pointer to an initialized matrix object, it will be * resized if needed. @@ -172,8 +172,8 @@ * \brief Returns the adjacency matrix of a graph in sparse matrix format * * - * The result is an incidence matrix, it contains numbers greater - * than one if there are multiple edges in the graph. + * The result is an adjacency matrix. Entry i, j of the matrix + * contains the number of edges connecting vertex i to vertex j. * \param graph Pointer to the graph to convert * \param res Pointer to an initialized sparse matrix object, it will be * resized if needed. @@ -782,8 +782,6 @@ return 0; } -int igraph_i_normalize_sparsemat(igraph_sparsemat_t *sparsemat, - igraph_bool_t column_wise); int igraph_i_normalize_sparsemat(igraph_sparsemat_t *sparsemat, diff --git a/igraph/src/defs.cc b/igraph/src/defs.cc --- a/igraph/src/defs.cc +++ b/igraph/src/defs.cc @@ -1,5 +1,6 @@ #include #include +#include #include "defs.hh" /* @@ -23,20 +24,17 @@ namespace bliss { -#ifndef USING_R - void fatal_error(const char* fmt, ...) { + char buffer[1024]; va_list ap; va_start(ap, fmt); - fprintf(stderr,"Bliss fatal error: "); - vfprintf(stderr, fmt, ap); - fprintf(stderr, "\nAborting!\n"); + sprintf(buffer, "Bliss fatal error: "); + vsprintf(buffer, fmt, ap); + throw std::runtime_error(buffer); va_end(ap); exit(1); } - -#endif } diff --git a/igraph/src/degree_sequence.cpp b/igraph/src/degree_sequence.cpp --- a/igraph/src/degree_sequence.cpp +++ b/igraph/src/degree_sequence.cpp @@ -1,6 +1,6 @@ /* Constructing realizations of degree sequences and bi-degree sequences. - Copyright (C) 2018 Szabolcs Horvat + Copyright (C) 2018-2020 Szabolcs Horvat This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -82,10 +82,6 @@ vd_pair vd = vertices.back(); vertices.pop_back(); - if (vd.degree < 0) { - IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL); - } - if (vd.degree == 0) { continue; } @@ -148,10 +144,6 @@ vd_pair vd = **pt; vertices.erase(*pt); - if (vd.degree < 0) { - IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL); - } - if (vd.degree == 0) { continue; } @@ -226,12 +218,8 @@ } - if (vdp->degree.first < 0 || vdp->degree.second < 0) { - IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL); - } - // are there a sufficient number of other vertices to connect to? - if (vertices.size() < vdp->degree.second - 1) { + if (vertices.size() - 1 < vdp->degree.second) { goto fail; } @@ -294,10 +282,6 @@ continue; } - if (vd.degree.first < 0 || vd.degree.second < 0) { - IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL); - } - int k = 0; vlist::iterator it; for (it = vertices.begin(); @@ -342,6 +326,10 @@ IGRAPH_ERROR("The sum of degrees must be even for an undirected graph", IGRAPH_EINVAL); } + if (igraph_vector_min(deg) < 0) { + IGRAPH_ERROR("Vertex degrees must be non-negative", IGRAPH_EINVAL); + } + igraph_vector_t edges; IGRAPH_CHECK(igraph_vector_init(&edges, deg_sum)); IGRAPH_FINALLY(igraph_vector_destroy, &edges); @@ -384,6 +372,10 @@ IGRAPH_ERROR("In- and out-degree sequences do not sum to the same value", IGRAPH_EINVAL); } + if (igraph_vector_min(outdeg) < 0 || igraph_vector_min(indeg) < 0) { + IGRAPH_ERROR("Vertex degrees must be non-negative", IGRAPH_EINVAL); + } + igraph_vector_t edges; IGRAPH_CHECK(igraph_vector_init(&edges, 2 * edge_count)); IGRAPH_FINALLY(igraph_vector_destroy, &edges); @@ -426,6 +418,32 @@ * * The \c method parameter controls the order in which the vertices to be connected are chosen. * + * + * References: + * + * + * V. Havel, + * Poznámka o existenci konečných grafů (A remark on the existence of finite graphs), + * Časopis pro pěstování matematiky 80, 477-480 (1955). + * http://eudml.org/doc/19050 + * + * + * S. L. Hakimi, + * On Realizability of a Set of Integers as Degrees of the Vertices of a Linear Graph, + * Journal of the SIAM 10, 3 (1962). + * https://www.jstor.org/stable/2098746 + * + * + * D. J. Kleitman and D. L. Wang, + * Algorithms for Constructing Graphs and Digraphs with Given Valences and Factors, + * Discrete Mathematics 6, 1 (1973). + * https://doi.org/10.1016/0012-365X%2873%2990037-X + * + * + * Sz. Horvát and C. D. Modes, + * Connectivity matters: Construction and exact random sampling of connected graphs (2020). + * https://arxiv.org/abs/2009.03747 + * * \param graph Pointer to an uninitialized graph object. * \param outdeg The degree sequence for a simple undirected graph * (if \p indeg is NULL or of length zero), or the out-degree sequence of @@ -438,8 +456,8 @@ * The vertex with smallest remaining degree is selected first. The result is usually * a graph with high negative degree assortativity. In the undirected case, this method * is guaranteed to generate a connected graph, provided that a connected realization exists. - * See http://szhorvat.net/pelican/hh-connected-graphs.html for a proof. - * In the directed case it tends to generate weakly connected graphs, but this is not + * See Horvát and Modes (2020) as well as http://szhorvat.net/pelican/hh-connected-graphs.html + * for a proof. In the directed case it tends to generate weakly connected graphs, but this is not * guaranteed. * \cli IGRAPH_REALIZE_DEGSEQ_LARGEST * The vertex with the largest remaining degree is selected first. The result diff --git a/igraph/src/distances.c b/igraph/src/distances.c --- a/igraph/src/distances.c +++ b/igraph/src/distances.c @@ -22,6 +22,7 @@ */ +#include "igraph_paths.h" #include "igraph_datatype.h" #include "igraph_dqueue.h" #include "igraph_iterators.h" @@ -30,11 +31,11 @@ #include "igraph_interface.h" #include "igraph_adjlist.h" -int igraph_i_eccentricity(const igraph_t *graph, - igraph_vector_t *res, - igraph_vs_t vids, - igraph_neimode_t mode, - const igraph_adjlist_t *adjlist) { +static int igraph_i_eccentricity(const igraph_t *graph, + igraph_vector_t *res, + igraph_vs_t vids, + igraph_neimode_t mode, + const igraph_adjlist_t *adjlist) { int no_of_nodes = igraph_vcount(graph); igraph_dqueue_long_t q; diff --git a/igraph/src/dotproduct.c b/igraph/src/dotproduct.c --- a/igraph/src/dotproduct.c +++ b/igraph/src/dotproduct.c @@ -24,7 +24,7 @@ #include "igraph_games.h" #include "igraph_random.h" #include "igraph_constructors.h" -#include "igraph_lapack.h" +#include "igraph_blas.h" /** * \function igraph_dot_product_game @@ -80,7 +80,7 @@ continue; } igraph_vector_view(&v2, &MATRIX(*vecs, 0, j), nrow); - igraph_lapack_ddot(&v1, &v2, &prob); + igraph_blas_ddot(&v1, &v2, &prob); if (prob < 0 && ! warned_neg) { warned_neg = 1; IGRAPH_WARNING("Negative connection probability in " diff --git a/igraph/src/drl_graph.cpp b/igraph/src/drl_graph.cpp --- a/igraph/src/drl_graph.cpp +++ b/igraph/src/drl_graph.cpp @@ -32,13 +32,10 @@ */ // This file contains the member definitions of the master class -#include -#include + #include #include -#include #include -#include using namespace std; diff --git a/igraph/src/drl_graph_3d.cpp b/igraph/src/drl_graph_3d.cpp --- a/igraph/src/drl_graph_3d.cpp +++ b/igraph/src/drl_graph_3d.cpp @@ -32,13 +32,9 @@ */ // This file contains the member definitions of the master class -#include -#include #include #include -#include #include -#include using namespace std; diff --git a/igraph/src/drl_layout.cpp b/igraph/src/drl_layout.cpp --- a/igraph/src/drl_layout.cpp +++ b/igraph/src/drl_layout.cpp @@ -45,12 +45,7 @@ // 5/6/2005 // C++ library routines -#include -#include #include -#include -#include -#include #include using namespace std; @@ -70,6 +65,8 @@ #include "igraph_random.h" #include "igraph_interface.h" +#include "igraph_handle_exceptions.h" + namespace drl { // int main(int argc, char **argv) { @@ -460,17 +457,19 @@ const igraph_vector_t *weights, const igraph_vector_bool_t *fixed) { - RNG_BEGIN(); + IGRAPH_HANDLE_EXCEPTIONS( + RNG_BEGIN(); - drl::graph neighbors(graph, options, weights); - neighbors.init_parms(options); - if (use_seed) { - IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 2)); - neighbors.read_real(res, fixed); - } - neighbors.draw_graph(res); + drl::graph neighbors(graph, options, weights); + neighbors.init_parms(options); + if (use_seed) { + IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 2)); + neighbors.read_real(res, fixed); + } + neighbors.draw_graph(res); - RNG_END(); + RNG_END(); + ); return 0; } diff --git a/igraph/src/drl_layout_3d.cpp b/igraph/src/drl_layout_3d.cpp --- a/igraph/src/drl_layout_3d.cpp +++ b/igraph/src/drl_layout_3d.cpp @@ -45,12 +45,7 @@ // 5/6/2005 // C++ library routines -#include -#include #include -#include -#include -#include #include using namespace std; @@ -70,6 +65,8 @@ #include "igraph_random.h" #include "igraph_interface.h" +#include "igraph_handle_exceptions.h" + /** * \function igraph_layout_drl_3d * The DrL layout generator, 3d version. @@ -106,18 +103,19 @@ igraph_layout_drl_options_t *options, const igraph_vector_t *weights, const igraph_vector_bool_t *fixed) { - - RNG_BEGIN(); + IGRAPH_HANDLE_EXCEPTIONS( + RNG_BEGIN(); - drl3d::graph neighbors(graph, options, weights); - neighbors.init_parms(options); - if (use_seed) { - IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 3)); - neighbors.read_real(res, fixed); - } - neighbors.draw_graph(res); + drl3d::graph neighbors(graph, options, weights); + neighbors.init_parms(options); + if (use_seed) { + IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 3)); + neighbors.read_real(res, fixed); + } + neighbors.draw_graph(res); - RNG_END(); + RNG_END(); + ); return 0; } diff --git a/igraph/src/drl_parse.cpp b/igraph/src/drl_parse.cpp --- a/igraph/src/drl_parse.cpp +++ b/igraph/src/drl_parse.cpp @@ -32,14 +32,6 @@ */ // This file contains the methods for the parse.h class -#include -#include -#include -#include -#include - -using namespace std; - #include "drl_layout.h" #include "drl_parse.h" diff --git a/igraph/src/eigen.c b/igraph/src/eigen.c --- a/igraph/src/eigen.c +++ b/igraph/src/eigen.c @@ -30,7 +30,7 @@ #include #include -int igraph_i_eigen_arpackfun_to_mat(igraph_arpack_function_t *fun, +static int igraph_i_eigen_arpackfun_to_mat(igraph_arpack_function_t *fun, int n, void *extra, igraph_matrix_t *res) { @@ -55,7 +55,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_lm(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_lm(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -133,7 +133,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_sm(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_sm(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -209,7 +209,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_la(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_la(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -226,7 +226,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_sa(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_sa(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -242,7 +242,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_be(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_be(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -321,7 +321,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_all(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_all(const igraph_matrix_t *A, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -334,7 +334,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_iv(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_iv(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -349,7 +349,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_sel(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack_sel(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_t *values, igraph_matrix_t *vectors) { @@ -363,7 +363,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_lapack(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_lapack(const igraph_matrix_t *A, const igraph_sparsemat_t *sA, igraph_arpack_function_t *fun, int n, void *extra, @@ -444,7 +444,7 @@ const igraph_sparsemat_t *sA; } igraph_i_eigen_matrix_sym_arpack_data_t; -int igraph_i_eigen_matrix_sym_arpack_cb(igraph_real_t *to, +static int igraph_i_eigen_matrix_sym_arpack_cb(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { @@ -457,14 +457,14 @@ } else { /* data->sA */ igraph_vector_t vto, vfrom; igraph_vector_view(&vto, to, n); - igraph_vector_view(&vfrom, to, n); + igraph_vector_view(&vfrom, from, n); igraph_vector_null(&vto); igraph_sparsemat_gaxpy(data->sA, &vfrom, &vto); } return 0; } -int igraph_i_eigen_matrix_symmetric_arpack_be(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_arpack_be(const igraph_matrix_t *A, const igraph_sparsemat_t *sA, igraph_arpack_function_t *fun, int n, void *extra, @@ -535,7 +535,7 @@ return 0; } -int igraph_i_eigen_matrix_symmetric_arpack(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_symmetric_arpack(const igraph_matrix_t *A, const igraph_sparsemat_t *sA, igraph_arpack_function_t *fun, int n, void *extra, @@ -637,7 +637,7 @@ 3 Larger real part 4 Larger imaginary part */ -int igraph_i_eigen_matrix_lapack_cmp_lm(void *extra, const void *a, +static int igraph_i_eigen_matrix_lapack_cmp_lm(void *extra, const void *a, const void *b) { igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra; int *aa = (int*) a, *bb = (int*) b; @@ -682,7 +682,7 @@ 4 Smaller imaginary part This ensures that lm has exactly the opposite order to sm */ -int igraph_i_eigen_matrix_lapack_cmp_sm(void *extra, const void *a, +static int igraph_i_eigen_matrix_lapack_cmp_sm(void *extra, const void *a, const void *b) { igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra; int *aa = (int*) a, *bb = (int*) b; @@ -725,7 +725,7 @@ 2 Real eigenvalues come before complex ones 3 Larger complex part */ -int igraph_i_eigen_matrix_lapack_cmp_lr(void *extra, const void *a, +static int igraph_i_eigen_matrix_lapack_cmp_lr(void *extra, const void *a, const void *b) { igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra; @@ -764,7 +764,7 @@ This is opposite to LR */ -int igraph_i_eigen_matrix_lapack_cmp_sr(void *extra, const void *a, +static int igraph_i_eigen_matrix_lapack_cmp_sr(void *extra, const void *a, const void *b) { igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra; @@ -801,7 +801,7 @@ 2 Real eigenvalues before complex ones 3 Larger real part */ -int igraph_i_eigen_matrix_lapack_cmp_li(void *extra, const void *a, +static int igraph_i_eigen_matrix_lapack_cmp_li(void *extra, const void *a, const void *b) { igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra; @@ -839,7 +839,7 @@ 3 Smaller real part Order is opposite to LI */ -int igraph_i_eigen_matrix_lapack_cmp_si(void *extra, const void *a, +static int igraph_i_eigen_matrix_lapack_cmp_si(void *extra, const void *a, const void *b) { igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra; @@ -888,7 +888,7 @@ } \ } while (0) -int igraph_i_eigen_matrix_lapack_reorder(const igraph_vector_t *real, +static int igraph_i_eigen_matrix_lapack_reorder(const igraph_vector_t *real, const igraph_vector_t *imag, const igraph_matrix_t *compressed, const igraph_eigen_which_t *which, @@ -1006,7 +1006,7 @@ return 0; } -int igraph_i_eigen_matrix_lapack_common(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_common(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { @@ -1042,21 +1042,21 @@ } -int igraph_i_eigen_matrix_lapack_lm(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_lm(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_sm(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_sm(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_lr(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_lr(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { @@ -1064,42 +1064,42 @@ } -int igraph_i_eigen_matrix_lapack_sr(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_sr(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_li(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_li(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_si(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_si(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_select(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_select(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_all(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack_all(const igraph_matrix_t *A, const igraph_eigen_which_t *which, igraph_vector_complex_t *values, igraph_matrix_complex_t *vectors) { return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack(const igraph_matrix_t *A, +static int igraph_i_eigen_matrix_lapack(const igraph_matrix_t *A, const igraph_sparsemat_t *sA, igraph_arpack_function_t *fun, int n, void *extra, @@ -1172,7 +1172,7 @@ return 0; } -int igraph_i_eigen_checks(const igraph_matrix_t *A, +static int igraph_i_eigen_checks(const igraph_matrix_t *A, const igraph_sparsemat_t *sA, igraph_arpack_function_t *fun, int n) { @@ -1322,7 +1322,7 @@ return 0; } -int igraph_i_eigen_adjacency_arpack_sym_cb(igraph_real_t *to, +static int igraph_i_eigen_adjacency_arpack_sym_cb(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_adjlist_t *adjlist = (igraph_adjlist_t *) extra; @@ -1342,7 +1342,7 @@ return 0; } -int igraph_i_eigen_adjacency_arpack(const igraph_t *graph, +static int igraph_i_eigen_adjacency_arpack(const igraph_t *graph, const igraph_eigen_which_t *which, igraph_arpack_options_t *options, igraph_arpack_storage_t* storage, diff --git a/igraph/src/embedding.c b/igraph/src/embedding.c --- a/igraph/src/embedding.c +++ b/igraph/src/embedding.c @@ -24,7 +24,6 @@ #include "igraph_embedding.h" #include "igraph_interface.h" #include "igraph_adjlist.h" -#include "igraph_random.h" #include "igraph_centrality.h" #include "igraph_blas.h" @@ -40,7 +39,7 @@ /* Adjacency matrix, unweighted, undirected. Eigendecomposition is used */ -int igraph_i_asembeddingu(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_asembeddingu(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_adjlist_t *outlist = data->outlist; @@ -65,7 +64,7 @@ /* Adjacency matrix, weighted, undirected. Eigendecomposition is used. */ -int igraph_i_asembeddinguw(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_asembeddinguw(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_inclist_t *outlist = data->eoutlist; @@ -93,7 +92,7 @@ } /* Adjacency matrix, unweighted, directed. SVD. */ -int igraph_i_asembedding(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_asembedding(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_adjlist_t *outlist = data->outlist; @@ -131,7 +130,7 @@ } /* Adjacency matrix, unweighted, directed. SVD, right eigenvectors */ -int igraph_i_asembedding_right(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_asembedding_right(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_adjlist_t *inlist = data->inlist; @@ -155,7 +154,7 @@ } /* Adjacency matrix, weighted, directed. SVD. */ -int igraph_i_asembeddingw(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_asembeddingw(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_inclist_t *outlist = data->eoutlist; @@ -199,7 +198,7 @@ } /* Adjacency matrix, weighted, directed. SVD, right eigenvectors. */ -int igraph_i_asembeddingw_right(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_asembeddingw_right(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_inclist_t *inlist = data->einlist; @@ -227,7 +226,7 @@ } /* Laplacian D-A, unweighted, undirected. Eigendecomposition. */ -int igraph_i_lsembedding_da(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lsembedding_da(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_adjlist_t *outlist = data->outlist; @@ -251,7 +250,7 @@ } /* Laplacian D-A, weighted, undirected. Eigendecomposition. */ -int igraph_i_lsembedding_daw(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lsembedding_daw(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; igraph_inclist_t *outlist = data->eoutlist; @@ -279,7 +278,7 @@ } /* Laplacian DAD, unweighted, undirected. Eigendecomposition. */ -int igraph_i_lsembedding_dad(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lsembedding_dad(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; @@ -313,7 +312,7 @@ return 0; } -int igraph_i_lsembedding_dadw(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lsembedding_dadw(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; @@ -370,7 +369,7 @@ } /* Laplacian I-DAD, unweighted, undirected. Eigendecomposition. */ -int igraph_i_lsembedding_idad(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lsembedding_idad(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { int i; @@ -383,7 +382,7 @@ return 0; } -int igraph_i_lsembedding_idadw(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lsembedding_idadw(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { int i; @@ -396,7 +395,7 @@ } /* Laplacian OAP, unweighted, directed. SVD. */ -int igraph_i_lseembedding_oap(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lseembedding_oap(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; @@ -454,7 +453,7 @@ } /* Laplacian OAP, unweighted, directed. SVD, right eigenvectors. */ -int igraph_i_lseembedding_oap_right(igraph_real_t *to, +static int igraph_i_lseembedding_oap_right(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; @@ -490,7 +489,7 @@ } /* Laplacian OAP, weighted, directed. SVD. */ -int igraph_i_lseembedding_oapw(igraph_real_t *to, const igraph_real_t *from, +static int igraph_i_lseembedding_oapw(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; @@ -554,7 +553,7 @@ } /* Laplacian OAP, weighted, directed. SVD, right eigenvectors. */ -int igraph_i_lseembedding_oapw_right(igraph_real_t *to, +static int igraph_i_lseembedding_oapw_right(igraph_real_t *to, const igraph_real_t *from, int n, void *extra) { igraph_i_asembedding_data_t *data = extra; @@ -593,7 +592,7 @@ return 0; } -int igraph_i_spectral_embedding(const igraph_t *graph, +static int igraph_i_spectral_embedding(const igraph_t *graph, igraph_integer_t no, const igraph_vector_t *weights, igraph_eigen_which_position_t which, @@ -785,29 +784,29 @@ * Adjacency spectral embedding * * Spectral decomposition of the adjacency matrices of graphs. - * This function computes a \code{no}-dimensional Euclidean + * This function computes an n-dimensional Euclidean * representation of the graph based on its adjacency * matrix, A. This representation is computed via the singular value - * decomposition of the adjacency matrix, A=UDV^T. In the case, + * decomposition of the adjacency matrix, A=U D V^T. In the case, * where the graph is a random dot product graph generated using latent - * position vectors in R^no for each vertex, the embedding will + * position vectors in R^n for each vertex, the embedding will * provide an estimate of these latent vectors. * * - * For undirected graphs the latent positions are calculated as - * X=U^no D^(1/2) where U^no equals to the first no columns of U, and + * For undirected graphs, the latent positions are calculated as + * X = U^n D^(1/2) where U^n equals to the first no columns of U, and * D^(1/2) is a diagonal matrix containing the square root of the selected * singular values on the diagonal. * * - * For directed graphs the embedding is defined as the pair - * X=U^no D^(1/2), Y=V^no D^(1/2). (For undirected graphs U=V, - * so it is enough to keep one of them.) + * For directed graphs, the embedding is defined as the pair + * X = U^n D^(1/2), Y = V^n D^(1/2). + * (For undirected graphs U=V, so it is sufficient to keep one of them.) * * \param graph The input graph, can be directed or undirected. - * \param no An integer scalar. This value is the embedding dimension of + * \param n An integer scalar. This value is the embedding dimension of * the spectral embedding. Should be smaller than the number of - * vertices. The largest no-dimensional non-zero + * vertices. The largest n-dimensional non-zero * singular values are used for the spectral embedding. * \param weights Optional edge weights. Supply a null pointer for * unweighted graphs. @@ -824,7 +823,7 @@ * For directed graphs, IGRAPH_EIGEN_LM and * IGRAPH_EIGEN_LA are the same because singular * values are used for the ordering instead of eigenvalues. - * \param scaled Whether to return X and Y (if scaled is non-zero), or + * \param scaled Whether to return X and Y (if \c scaled is true), or * U and V. * \param X Initialized matrix, the estimated latent positions are * stored here. @@ -847,7 +846,7 @@ */ int igraph_adjacency_spectral_embedding(const igraph_t *graph, - igraph_integer_t no, + igraph_integer_t n, const igraph_vector_t *weights, igraph_eigen_which_position_t which, igraph_bool_t scaled, @@ -869,14 +868,14 @@ callback_right = 0; } - return igraph_i_spectral_embedding(graph, no, weights, which, scaled, + return igraph_i_spectral_embedding(graph, n, weights, which, scaled, X, Y, D, cvec, /* deg2=*/ 0, options, callback, callback_right, /*symmetric=*/ !directed, /*eigen=*/ !directed, /*zapsmall=*/ 1); } -int igraph_i_lse_und(const igraph_t *graph, +static int igraph_i_lse_und(const igraph_t *graph, igraph_integer_t no, const igraph_vector_t *weights, igraph_eigen_which_position_t which, @@ -937,7 +936,7 @@ return 0; } -int igraph_i_lse_dir(const igraph_t *graph, +static int igraph_i_lse_dir(const igraph_t *graph, igraph_integer_t no, const igraph_vector_t *weights, igraph_eigen_which_position_t which, @@ -994,7 +993,7 @@ * \ref igraph_adjacency_spectral_embedding, but works on the Laplacian * of the graph, instead of the adjacency matrix. * \param graph The input graph. - * \param no The number of eigenvectors (or singular vectors if the graph + * \param n The number of eigenvectors (or singular vectors if the graph * is directed) to use for the embedding. * \param weights Optional edge weights. Supply a null pointer for * unweighted graphs. @@ -1025,7 +1024,7 @@ * means I - Di A Di, where I * is the identity matrix. * \endclist - * \param scaled Whether to return X and Y (if scaled is non-zero), or + * \param scaled Whether to return X and Y (if \c scaled is true), or * U and V. * \param X Initialized matrix, the estimated latent positions are * stored here. @@ -1047,7 +1046,7 @@ */ int igraph_laplacian_spectral_embedding(const igraph_t *graph, - igraph_integer_t no, + igraph_integer_t n, const igraph_vector_t *weights, igraph_eigen_which_position_t which, igraph_neimode_t degmode, @@ -1059,10 +1058,10 @@ igraph_arpack_options_t *options) { if (igraph_is_directed(graph)) { - return igraph_i_lse_dir(graph, no, weights, which, degmode, type, scaled, + return igraph_i_lse_dir(graph, n, weights, which, degmode, type, scaled, X, Y, D, options); } else { - return igraph_i_lse_und(graph, no, weights, which, degmode, type, scaled, + return igraph_i_lse_und(graph, n, weights, which, degmode, type, scaled, X, Y, D, options); } } @@ -1090,7 +1089,7 @@ * * This function can also be used for the general separation problem, * where we assume that the left and the right of the vector are coming - * from two Normal distributions, with different means, and we want + * from two normal distributions, with different means, and we want * to know their border. * * \param sv A numeric vector, the ordered singular values. diff --git a/igraph/src/error.c b/igraph/src/error.c --- a/igraph/src/error.c +++ b/igraph/src/error.c @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. @@ -20,6 +20,7 @@ #include #include #include "error.h" +#include "platform.h" static char *plfit_i_error_strings[] = { "No error", @@ -69,6 +70,6 @@ } #endif -void plfit_error_handler_ignore(const char *reason, const char *file, int line, - int plfit_errno) { +void plfit_error_handler_ignore(const char* reason, const char* file, int line, + int plfit_errno) { } diff --git a/igraph/src/fast_community.c b/igraph/src/fast_community.c --- a/igraph/src/fast_community.c +++ b/igraph/src/fast_community.c @@ -109,8 +109,8 @@ /* Scans the community neighborhood list for the new maximal dq value. * Returns 1 if the maximum is different from the previous one, * 0 otherwise. */ -int igraph_i_fastgreedy_community_rescan_max( - igraph_i_fastgreedy_community* comm) { +static int igraph_i_fastgreedy_community_rescan_max( + igraph_i_fastgreedy_community* comm) { long int i, n; igraph_i_fastgreedy_commpair *p, *best; igraph_real_t bestdq, currdq; @@ -141,24 +141,24 @@ } /* Destroys the global community list object */ -void igraph_i_fastgreedy_community_list_destroy( - igraph_i_fastgreedy_community_list* list) { +static void igraph_i_fastgreedy_community_list_destroy( + igraph_i_fastgreedy_community_list* list) { long int i; for (i = 0; i < list->n; i++) { igraph_vector_ptr_destroy(&list->e[i].neis); } - free(list->e); + igraph_Free(list->e); if (list->heapindex != 0) { - free(list->heapindex); + igraph_Free(list->heapindex); } if (list->heap != 0) { - free(list->heap); + igraph_Free(list->heap); } } /* Community list heap maintenance: sift down */ -void igraph_i_fastgreedy_community_list_sift_down( - igraph_i_fastgreedy_community_list* list, long int idx) { +static void igraph_i_fastgreedy_community_list_sift_down( + igraph_i_fastgreedy_community_list* list, long int idx) { long int root, child, c1, c2; igraph_i_fastgreedy_community* dummy; igraph_integer_t dummy2; @@ -192,8 +192,8 @@ } /* Community list heap maintenance: sift up */ -void igraph_i_fastgreedy_community_list_sift_up( - igraph_i_fastgreedy_community_list* list, long int idx) { +static void igraph_i_fastgreedy_community_list_sift_up( + igraph_i_fastgreedy_community_list* list, long int idx) { long int root, parent, c1, c2; igraph_i_fastgreedy_community* dummy; igraph_integer_t dummy2; @@ -223,8 +223,8 @@ } /* Builds the community heap for the first time */ -void igraph_i_fastgreedy_community_list_build_heap( - igraph_i_fastgreedy_community_list* list) { +static void igraph_i_fastgreedy_community_list_build_heap( + igraph_i_fastgreedy_community_list* list) { long int i; for (i = list->no_of_communities / 2 - 1; i >= 0; i--) { igraph_i_fastgreedy_community_list_sift_down(list, i); @@ -236,8 +236,8 @@ #define igraph_i_fastgreedy_community_list_find_in_heap(list, idx) (list)->heapindex[idx] /* Dumps the heap - for debugging purposes */ -void igraph_i_fastgreedy_community_list_dump_heap( - igraph_i_fastgreedy_community_list* list) { +static void igraph_i_fastgreedy_community_list_dump_heap( + igraph_i_fastgreedy_community_list* list) { long int i; debug("Heap:\n"); for (i = 0; i < list->no_of_communities; i++) { @@ -258,8 +258,8 @@ /* Checks if the community heap satisfies the heap property. * Only useful for debugging. */ -void igraph_i_fastgreedy_community_list_check_heap( - igraph_i_fastgreedy_community_list* list) { +static void igraph_i_fastgreedy_community_list_check_heap( + igraph_i_fastgreedy_community_list* list) { long int i; for (i = 0; i < list->no_of_communities / 2; i++) { if ((2 * i + 1 < list->no_of_communities && *list->heap[i]->maxdq->dq < *list->heap[2 * i + 1]->maxdq->dq) || @@ -272,8 +272,8 @@ } /* Removes a given element from the heap */ -void igraph_i_fastgreedy_community_list_remove( - igraph_i_fastgreedy_community_list* list, long int idx) { +static void igraph_i_fastgreedy_community_list_remove( + igraph_i_fastgreedy_community_list* list, long int idx) { igraph_real_t old; long int commidx; @@ -298,8 +298,8 @@ /* Removes a given element from the heap when there are no more neighbors * for it (comm->maxdq is NULL) */ -void igraph_i_fastgreedy_community_list_remove2( - igraph_i_fastgreedy_community_list* list, long int idx, long int comm) { +static void igraph_i_fastgreedy_community_list_remove2( + igraph_i_fastgreedy_community_list* list, long int idx, long int comm) { long int i; if (idx == list->no_of_communities - 1) { @@ -327,8 +327,8 @@ /* Removes the pair belonging to community k from the neighborhood list * of community c (that is, clist[c]) and recalculates maxdq */ -void igraph_i_fastgreedy_community_remove_nei( - igraph_i_fastgreedy_community_list* list, long int c, long int k) { +static void igraph_i_fastgreedy_community_remove_nei( + igraph_i_fastgreedy_community_list* list, long int c, long int k) { long int i, n; igraph_bool_t rescan = 0; igraph_i_fastgreedy_commpair *p; @@ -371,7 +371,7 @@ /* Auxiliary function to sort a community pair list with respect to the * `second` field */ -int igraph_i_fastgreedy_commpair_cmp(const void* p1, const void* p2) { +static int igraph_i_fastgreedy_commpair_cmp(const void* p1, const void* p2) { igraph_i_fastgreedy_commpair *cp1, *cp2; cp1 = *(igraph_i_fastgreedy_commpair**)p1; cp2 = *(igraph_i_fastgreedy_commpair**)p2; @@ -381,9 +381,9 @@ /* Sorts the neighbor list of the community with the given index, optionally * optimizing the process if we know that the list is nearly sorted and only * a given pair is in the wrong place. */ -void igraph_i_fastgreedy_community_sort_neighbors_of( - igraph_i_fastgreedy_community_list* list, long int index, - igraph_i_fastgreedy_commpair* changed_pair) { +static void igraph_i_fastgreedy_community_sort_neighbors_of( + igraph_i_fastgreedy_community_list* list, long int index, + igraph_i_fastgreedy_commpair* changed_pair) { igraph_vector_ptr_t* vec; long int i, n; igraph_bool_t can_skip_sort = 0; @@ -453,9 +453,9 @@ * of the community list clist to newdq and restores the heap property * in community c if necessary. Returns 1 if the maximum in the row had * to be updated, zero otherwise */ -int igraph_i_fastgreedy_community_update_dq( - igraph_i_fastgreedy_community_list* list, - igraph_i_fastgreedy_commpair* p, igraph_real_t newdq) { +static int igraph_i_fastgreedy_community_update_dq( + igraph_i_fastgreedy_community_list* list, + igraph_i_fastgreedy_commpair* p, igraph_real_t newdq) { long int i, j, to, from; igraph_real_t olddq; igraph_i_fastgreedy_community *comm_to, *comm_from; @@ -698,12 +698,12 @@ if (communities.e == 0) { IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, communities.e); + IGRAPH_FINALLY(igraph_free, communities.e); communities.heap = (igraph_i_fastgreedy_community**)calloc((size_t) no_of_nodes, sizeof(igraph_i_fastgreedy_community*)); if (communities.heap == 0) { IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, communities.heap); + IGRAPH_FINALLY(igraph_free, communities.heap); communities.heapindex = (igraph_integer_t*)calloc((size_t)no_of_nodes, sizeof(igraph_integer_t)); if (communities.heapindex == 0) { IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM); @@ -722,7 +722,7 @@ if (dq == 0) { IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, dq); + IGRAPH_FINALLY(igraph_free, dq); debug("Creating community pair list\n"); IGRAPH_CHECK(igraph_eit_create(graph, igraph_ess_all(0), &edgeit)); IGRAPH_FINALLY(igraph_eit_destroy, &edgeit); @@ -730,7 +730,7 @@ if (pairs == 0) { IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, pairs); + IGRAPH_FINALLY(igraph_free, pairs); loop_weight_sum = 0; for (i = 0, j = 0; !IGRAPH_EIT_END(edgeit); i += 2, j++, IGRAPH_EIT_NEXT(edgeit)) { long int eidx = IGRAPH_EIT_GET(edgeit); @@ -1022,12 +1022,12 @@ if (ivec == 0) { IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, ivec); + IGRAPH_FINALLY(igraph_free, ivec); for (i = 0; i < no_of_joins; i++) { ivec[i] = i + 1; } igraph_matrix_permdelete_rows(merges, ivec, total_joins - no_of_joins); - free(ivec); + igraph_Free(ivec); IGRAPH_FINALLY_CLEAN(1); } IGRAPH_PROGRESS("fast greedy community detection", 100.0, 0); @@ -1038,8 +1038,8 @@ } debug("Freeing memory\n"); - free(pairs); - free(dq); + igraph_Free(pairs); + igraph_Free(dq); igraph_i_fastgreedy_community_list_destroy(&communities); igraph_vector_destroy(&a); IGRAPH_FINALLY_CLEAN(4); diff --git a/igraph/src/feedback_arc_set.c b/igraph/src/feedback_arc_set.c --- a/igraph/src/feedback_arc_set.c +++ b/igraph/src/feedback_arc_set.c @@ -475,7 +475,7 @@ if (vptr == 0) { IGRAPH_ERROR("cannot calculate feedback arc set using IP", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, vptr); + IGRAPH_FINALLY(igraph_free, vptr); IGRAPH_CHECK(igraph_vector_init(vptr, 0)); IGRAPH_FINALLY_CLEAN(1); VECTOR(vertices_by_components)[i] = vptr; @@ -487,7 +487,7 @@ if (vptr == 0) { IGRAPH_ERROR("cannot calculate feedback arc set using IP", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, vptr); + IGRAPH_FINALLY(igraph_free, vptr); IGRAPH_CHECK(igraph_vector_init(vptr, 0)); IGRAPH_FINALLY_CLEAN(1); VECTOR(edges_by_components)[i] = vptr; diff --git a/igraph/src/flow.c b/igraph/src/flow.c --- a/igraph/src/flow.c +++ b/igraph/src/flow.c @@ -33,15 +33,12 @@ #include "igraph_structural.h" #include "igraph_components.h" #include "igraph_types_internal.h" -#include "config.h" #include "igraph_math.h" #include "igraph_dqueue.h" -#include "igraph_visitor.h" #include "igraph_interrupt_internal.h" #include "igraph_topology.h" +#include "config.h" -#include -#include /* * Some general remarks about the functions in this file. @@ -156,16 +153,16 @@ * undirected edge. */ -int igraph_i_maxflow_undirected(const igraph_t *graph, - igraph_real_t *value, - igraph_vector_t *flow, - igraph_vector_t *cut, - igraph_vector_t *partition, - igraph_vector_t *partition2, - igraph_integer_t source, - igraph_integer_t target, - const igraph_vector_t *capacity, - igraph_maxflow_stats_t *stats) { +static int igraph_i_maxflow_undirected(const igraph_t *graph, + igraph_real_t *value, + igraph_vector_t *flow, + igraph_vector_t *cut, + igraph_vector_t *partition, + igraph_vector_t *partition2, + igraph_integer_t source, + igraph_integer_t target, + const igraph_vector_t *capacity, + igraph_maxflow_stats_t *stats) { igraph_integer_t no_of_edges = (igraph_integer_t) igraph_ecount(graph); igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph); igraph_vector_t edges; @@ -253,10 +250,10 @@ &first, ¤t, &to, &excess, \ &rescap, &rev)) -void igraph_i_mf_gap(long int b, igraph_maxflow_stats_t *stats, - igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets, - long int no_of_nodes, - igraph_vector_long_t *distance) { +static void igraph_i_mf_gap(long int b, igraph_maxflow_stats_t *stats, + igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets, + long int no_of_nodes, + igraph_vector_long_t *distance) { long int bo; (stats->nogap)++; @@ -269,12 +266,12 @@ } } -void igraph_i_mf_relabel(long int v, long int no_of_nodes, - igraph_vector_long_t *distance, - igraph_vector_long_t *first, - igraph_vector_t *rescap, igraph_vector_long_t *to, - igraph_vector_long_t *current, - igraph_maxflow_stats_t *stats, int *nrelabelsince) { +static void igraph_i_mf_relabel(long int v, long int no_of_nodes, + igraph_vector_long_t *distance, + igraph_vector_long_t *first, + igraph_vector_t *rescap, igraph_vector_long_t *to, + igraph_vector_long_t *current, + igraph_maxflow_stats_t *stats, int *nrelabelsince) { long int min = no_of_nodes; long int k, l, min_edge = 0; @@ -293,14 +290,14 @@ } } -void igraph_i_mf_push(long int v, long int e, long int n, - igraph_vector_long_t *current, - igraph_vector_t *rescap, igraph_vector_t *excess, - long int target, long int source, - igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets, - igraph_vector_long_t *distance, - igraph_vector_long_t *rev, igraph_maxflow_stats_t *stats, - int *npushsince) { +static void igraph_i_mf_push(long int v, long int e, long int n, + igraph_vector_long_t *current, + igraph_vector_t *rescap, igraph_vector_t *excess, + long int target, long int source, + igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets, + igraph_vector_long_t *distance, + igraph_vector_long_t *rev, igraph_maxflow_stats_t *stats, + int *npushsince) { igraph_real_t delta = RESCAP(e) < EXCESS(v) ? RESCAP(e) : EXCESS(v); (stats->nopush)++; (*npushsince)++; @@ -314,19 +311,19 @@ EXCESS(v) -= delta; } -void igraph_i_mf_discharge(long int v, - igraph_vector_long_t *current, - igraph_vector_long_t *first, - igraph_vector_t *rescap, - igraph_vector_long_t *to, - igraph_vector_long_t *distance, - igraph_vector_t *excess, - long int no_of_nodes, long int source, - long int target, igraph_buckets_t *buckets, - igraph_dbuckets_t *ibuckets, - igraph_vector_long_t *rev, - igraph_maxflow_stats_t *stats, - int *npushsince, int *nrelabelsince) { +static void igraph_i_mf_discharge(long int v, + igraph_vector_long_t *current, + igraph_vector_long_t *first, + igraph_vector_t *rescap, + igraph_vector_long_t *to, + igraph_vector_long_t *distance, + igraph_vector_t *excess, + long int no_of_nodes, long int source, + long int target, igraph_buckets_t *buckets, + igraph_dbuckets_t *ibuckets, + igraph_vector_long_t *rev, + igraph_maxflow_stats_t *stats, + int *npushsince, int *nrelabelsince) { do { long int i; long int start = (long int) CURRENT(v); @@ -360,14 +357,14 @@ } while (1); } -void igraph_i_mf_bfs(igraph_dqueue_long_t *bfsq, - long int source, long int target, - long int no_of_nodes, igraph_buckets_t *buckets, - igraph_dbuckets_t *ibuckets, - igraph_vector_long_t *distance, - igraph_vector_long_t *first, igraph_vector_long_t *current, - igraph_vector_long_t *to, igraph_vector_t *excess, - igraph_vector_t *rescap, igraph_vector_long_t *rev) { +static void igraph_i_mf_bfs(igraph_dqueue_long_t *bfsq, + long int source, long int target, + long int no_of_nodes, igraph_buckets_t *buckets, + igraph_dbuckets_t *ibuckets, + igraph_vector_long_t *distance, + igraph_vector_long_t *first, igraph_vector_long_t *current, + igraph_vector_long_t *to, igraph_vector_t *excess, + igraph_vector_t *rescap, igraph_vector_long_t *rev) { long int k, l; @@ -414,8 +411,8 @@ * assigning positive real numbers to the edges and satisfying two * requirements: (1) the flow value is less than the capacity of the * edge and (2) at each vertex except the source and the target, the - * incoming flow (ie. the sum of the flow on the incoming edges) is - * the same as the outgoing flow (ie. the sum of the flow on the + * incoming flow (i.e. the sum of the flow on the incoming edges) is + * the same as the outgoing flow (i.e. the sum of the flow on the * outgoing edges). The value of the flow is the incoming flow at the * target vertex. The maximum flow is the flow with the maximum * value. @@ -745,7 +742,7 @@ IGRAPH_CHECK(igraph_vector_int_init(&added, no_of_nodes)); IGRAPH_FINALLY(igraph_vector_int_destroy, &added); IGRAPH_CHECK(igraph_dqueue_init(&Q, 100)); - IGRAPH_FINALLY(igraph_dqueue_destroy, &added); + IGRAPH_FINALLY(igraph_dqueue_destroy, &Q); igraph_dqueue_push(&Q, source); igraph_dqueue_push(&Q, 0); @@ -1031,8 +1028,8 @@ * assigning positive real numbers to the edges and satisfying two * requirements: (1) the flow value is less than the capacity of the * edge and (2) at each vertex except the source and the target, the - * incoming flow (ie. the sum of the flow on the incoming edges) is - * the same as the outgoing flow (ie. the sum of the flow on the + * incoming flow (i.e. the sum of the flow on the incoming edges) is + * the same as the outgoing flow (i.e. the sum of the flow on the * outgoing edges). The value of the flow is the incoming flow at the * target vertex. The maximum flow is the flow with the maximum * value. @@ -1212,12 +1209,12 @@ * It can also calculate the cut itself, not just the cut value. */ -int igraph_i_mincut_undirected(const igraph_t *graph, - igraph_real_t *res, - igraph_vector_t *partition, - igraph_vector_t *partition2, - igraph_vector_t *cut, - const igraph_vector_t *capacity) { +static int igraph_i_mincut_undirected(const igraph_t *graph, + igraph_real_t *res, + igraph_vector_t *partition, + igraph_vector_t *partition2, + igraph_vector_t *cut, + const igraph_vector_t *capacity) { igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph); igraph_integer_t no_of_edges = (igraph_integer_t) igraph_ecount(graph); @@ -1479,12 +1476,12 @@ return 0; } -int igraph_i_mincut_directed(const igraph_t *graph, - igraph_real_t *value, - igraph_vector_t *partition, - igraph_vector_t *partition2, - igraph_vector_t *cut, - const igraph_vector_t *capacity) { +static int igraph_i_mincut_directed(const igraph_t *graph, + igraph_real_t *value, + igraph_vector_t *partition, + igraph_vector_t *partition2, + igraph_vector_t *cut, + const igraph_vector_t *capacity) { long int i; long int no_of_nodes = igraph_vcount(graph); igraph_real_t flow; @@ -1665,9 +1662,9 @@ } -int igraph_i_mincut_value_undirected(const igraph_t *graph, - igraph_real_t *res, - const igraph_vector_t *capacity) { +static int igraph_i_mincut_value_undirected(const igraph_t *graph, + igraph_real_t *res, + const igraph_vector_t *capacity) { return igraph_i_mincut_undirected(graph, res, 0, 0, 0, capacity); } @@ -1747,11 +1744,11 @@ return 0; } -int igraph_i_st_vertex_connectivity_directed(const igraph_t *graph, - igraph_integer_t *res, - igraph_integer_t source, - igraph_integer_t target, - igraph_vconn_nei_t neighbors) { +static int igraph_i_st_vertex_connectivity_directed(const igraph_t *graph, + igraph_integer_t *res, + igraph_integer_t source, + igraph_integer_t target, + igraph_vconn_nei_t neighbors) { igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph); igraph_integer_t no_of_edges = (igraph_integer_t) igraph_ecount(graph); @@ -1835,11 +1832,11 @@ return 0; } -int igraph_i_st_vertex_connectivity_undirected(const igraph_t *graph, - igraph_integer_t *res, - igraph_integer_t source, - igraph_integer_t target, - igraph_vconn_nei_t neighbors) { +static int igraph_i_st_vertex_connectivity_undirected(const igraph_t *graph, + igraph_integer_t *res, + igraph_integer_t source, + igraph_integer_t target, + igraph_vconn_nei_t neighbors) { igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph); igraph_t newgraph; @@ -1902,7 +1899,7 @@ * target. Directed paths are considered in directed graphs. * * The vertex connectivity of a pair is the same as the number - * of different (ie. node-independent) paths from source to + * of different (i.e. node-independent) paths from source to * target. * * The current implementation uses maximum flow calculations to @@ -1953,8 +1950,8 @@ return 0; } -int igraph_i_vertex_connectivity_directed(const igraph_t *graph, - igraph_integer_t *res) { +static int igraph_i_vertex_connectivity_directed(const igraph_t *graph, + igraph_integer_t *res) { igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph); long int i, j; @@ -1991,8 +1988,8 @@ return 0; } -int igraph_i_vertex_connectivity_undirected(const igraph_t *graph, - igraph_integer_t *res) { +static int igraph_i_vertex_connectivity_undirected(const igraph_t *graph, + igraph_integer_t *res) { igraph_t newgraph; IGRAPH_CHECK(igraph_copy(&newgraph, graph)); @@ -2008,9 +2005,9 @@ } /* Use that vertex.connectivity(G) <= edge.connectivity(G) <= min(degree(G)) */ -int igraph_i_connectivity_checks(const igraph_t *graph, - igraph_integer_t *res, - igraph_bool_t *found) { +static int igraph_i_connectivity_checks(const igraph_t *graph, + igraph_integer_t *res, + igraph_bool_t *found) { igraph_bool_t conn; *found = 0; @@ -2529,4 +2526,3 @@ return IGRAPH_SUCCESS; } - diff --git a/igraph/src/foreign-dl-lexer.c b/igraph/src/foreign-dl-lexer.c --- a/igraph/src/foreign-dl-lexer.c +++ b/igraph/src/foreign-dl-lexer.c @@ -590,16 +590,16 @@ #include "foreign-dl-parser.h" #define YY_EXTRA_TYPE igraph_i_dl_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno; -/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1) -#endif +#define YY_FATAL_ERROR(msg) \ + igraph_error("Fatal error in DL parser: " # msg, __FILE__, \ + __LINE__, IGRAPH_PARSEERROR); #ifdef stdout # undef stdout #endif #define stdout 0 -#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \ - __LINE__, IGRAPH_PARSEERROR); +#endif #define YY_NO_INPUT 1 #line 606 "foreign-dl-lexer.c" diff --git a/igraph/src/foreign-gml-lexer.c b/igraph/src/foreign-gml-lexer.c --- a/igraph/src/foreign-gml-lexer.c +++ b/igraph/src/foreign-gml-lexer.c @@ -499,16 +499,16 @@ #include "foreign-gml-parser.h" #define YY_EXTRA_TYPE igraph_i_gml_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno; -/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1) -#endif +#define YY_FATAL_ERROR(msg) \ + igraph_error("Fatal error in GML parser: " # msg, __FILE__, \ + __LINE__, IGRAPH_PARSEERROR); #ifdef stdout # undef stdout #endif #define stdout 0 -#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \ - __LINE__, IGRAPH_PARSEERROR); +#endif #define YY_NO_INPUT 1 #line 514 "foreign-gml-lexer.c" diff --git a/igraph/src/foreign-graphml.c b/igraph/src/foreign-graphml.c --- a/igraph/src/foreign-graphml.c +++ b/igraph/src/foreign-graphml.c @@ -133,8 +133,8 @@ "attribute specifications", file, line, 0, target); } -igraph_real_t igraph_i_graphml_parse_numeric(const char* char_data, - igraph_real_t default_value) { +static igraph_real_t igraph_i_graphml_parse_numeric(const char* char_data, + igraph_real_t default_value) { double result; if (char_data == 0) { @@ -148,8 +148,8 @@ return result; } -igraph_bool_t igraph_i_graphml_parse_boolean(const char* char_data, - igraph_bool_t default_value) { +static igraph_bool_t igraph_i_graphml_parse_boolean(const char* char_data, + igraph_bool_t default_value) { int value; if (char_data == 0) { return default_value; @@ -172,7 +172,7 @@ return value != 0; } -void igraph_i_graphml_attribute_record_destroy(igraph_i_graphml_attribute_record_t* rec) { +static void igraph_i_graphml_attribute_record_destroy(igraph_i_graphml_attribute_record_t* rec) { if (rec->record.type == IGRAPH_ATTRIBUTE_NUMERIC) { if (rec->record.value != 0) { igraph_vector_destroy((igraph_vector_t*)rec->record.value); @@ -200,7 +200,7 @@ } } -void igraph_i_graphml_destroy_state(struct igraph_i_graphml_parser_state* state) { +static void igraph_i_graphml_destroy_state(struct igraph_i_graphml_parser_state* state) { if (state->destroyed) { return; } @@ -231,7 +231,7 @@ IGRAPH_FINALLY_CLEAN(1); } -void igraph_i_graphml_sax_handler_error(void *state0, const char* msg, ...) { +static void igraph_i_graphml_sax_handler_error(void *state0, const char* msg, ...) { struct igraph_i_graphml_parser_state *state = (struct igraph_i_graphml_parser_state*)state0; va_list ap; @@ -249,7 +249,7 @@ va_end(ap); } -xmlEntityPtr igraph_i_graphml_sax_handler_get_entity(void *state0, +static xmlEntityPtr igraph_i_graphml_sax_handler_get_entity(void *state0, const xmlChar* name) { xmlEntityPtr predef = xmlGetPredefinedEntity(name); IGRAPH_UNUSED(state0); @@ -260,7 +260,7 @@ return blankEntity; } -void igraph_i_graphml_handle_unknown_start_tag(struct igraph_i_graphml_parser_state *state) { +static void igraph_i_graphml_handle_unknown_start_tag(struct igraph_i_graphml_parser_state *state) { if (state->st != UNKNOWN) { igraph_vector_int_push_back(&state->prev_state_stack, state->st); state->st = UNKNOWN; @@ -270,7 +270,7 @@ } } -void igraph_i_graphml_sax_handler_start_document(void *state0) { +static void igraph_i_graphml_sax_handler_start_document(void *state0) { struct igraph_i_graphml_parser_state *state = (struct igraph_i_graphml_parser_state*)state0; int ret; @@ -359,7 +359,7 @@ IGRAPH_FINALLY(igraph_i_graphml_destroy_state, state); } -void igraph_i_graphml_sax_handler_end_document(void *state0) { +static void igraph_i_graphml_sax_handler_end_document(void *state0) { struct igraph_i_graphml_parser_state *state = (struct igraph_i_graphml_parser_state*)state0; long i, l; @@ -559,9 +559,9 @@ #define XML_ATTR_VALUE_END(it) (*(it+4)) #define XML_ATTR_VALUE(it) *(it+3), (*(it+4))-(*(it+3)) -igraph_i_graphml_attribute_record_t* igraph_i_graphml_add_attribute_key( - const xmlChar** attrs, int nb_attrs, - struct igraph_i_graphml_parser_state *state) { +static igraph_i_graphml_attribute_record_t* igraph_i_graphml_add_attribute_key( + const xmlChar** attrs, int nb_attrs, + struct igraph_i_graphml_parser_state *state) { xmlChar **it; xmlChar *localname; igraph_trie_t *trie = 0; @@ -749,10 +749,10 @@ return rec; } -void igraph_i_graphml_attribute_data_setup(struct igraph_i_graphml_parser_state *state, - const xmlChar **attrs, - int nb_attrs, - igraph_attribute_elemtype_t type) { +static void igraph_i_graphml_attribute_data_setup(struct igraph_i_graphml_parser_state *state, + const xmlChar **attrs, + int nb_attrs, + igraph_attribute_elemtype_t type) { xmlChar **it; int i; @@ -782,8 +782,8 @@ } } -void igraph_i_graphml_append_to_data_char(struct igraph_i_graphml_parser_state *state, - const xmlChar *data, int len) { +static void igraph_i_graphml_append_to_data_char(struct igraph_i_graphml_parser_state *state, + const xmlChar *data, int len) { long int data_char_new_start = 0; if (!state->successful) { @@ -805,7 +805,7 @@ state->data_char[data_char_new_start + len] = '\0'; } -void igraph_i_graphml_attribute_data_finish(struct igraph_i_graphml_parser_state *state) { +static void igraph_i_graphml_attribute_data_finish(struct igraph_i_graphml_parser_state *state) { const char *key = fromXmlChar(state->data_key); igraph_attribute_elemtype_t type = state->data_type; igraph_trie_t *trie = 0; @@ -930,8 +930,8 @@ } } -void igraph_i_graphml_attribute_default_value_finish( - struct igraph_i_graphml_parser_state *state) { +static void igraph_i_graphml_attribute_default_value_finish( + struct igraph_i_graphml_parser_state *state) { igraph_i_graphml_attribute_record_t *graphmlrec = state->current_attr_record; if (graphmlrec == 0) { @@ -971,10 +971,10 @@ } } -void igraph_i_graphml_sax_handler_start_element_ns( - void *state0, const xmlChar* localname, const xmlChar* prefix, - const xmlChar* uri, int nb_namespaces, const xmlChar** namespaces, - int nb_attributes, int nb_defaulted, const xmlChar** attributes) { +static void igraph_i_graphml_sax_handler_start_element_ns( + void *state0, const xmlChar* localname, const xmlChar* prefix, + const xmlChar* uri, int nb_namespaces, const xmlChar** namespaces, + int nb_attributes, int nb_defaulted, const xmlChar** attributes) { struct igraph_i_graphml_parser_state *state = (struct igraph_i_graphml_parser_state*)state0; xmlChar** it; @@ -1174,7 +1174,8 @@ } } -void igraph_i_graphml_sax_handler_end_element_ns(void *state0, +static void igraph_i_graphml_sax_handler_end_element_ns( + void *state0, const xmlChar* localname, const xmlChar* prefix, const xmlChar* uri) { struct igraph_i_graphml_parser_state *state = @@ -1232,7 +1233,7 @@ } } -void igraph_i_graphml_sax_handler_chars(void* state0, const xmlChar* ch, int len) { +static void igraph_i_graphml_sax_handler_chars(void* state0, const xmlChar* ch, int len) { struct igraph_i_graphml_parser_state *state = (struct igraph_i_graphml_parser_state*)state0; @@ -1294,7 +1295,7 @@ #define IS_FORBIDDEN_CONTROL_CHAR(x) ((x) < ' ' && (x) != '\t' && (x) != '\r' && (x) != '\n') -int igraph_i_xml_escape(char* src, char** dest) { +static int igraph_i_xml_escape(char* src, char** dest) { long int destlen = 0; char *s, *d; unsigned char ch; @@ -1353,13 +1354,13 @@ * graphs. Currently only the most basic import functionality is implemented * in igraph: it can read GraphML files without nested graphs and hyperedges. * Attributes of the graph are loaded only if an attribute interface - * is attached, ie. if you use igraph from R or Python. + * is attached, i.e. if you use igraph from R or Python. * * - * Graph attribute names are taken from the \c attr.name attributes of the - * \c key tags in the GraphML file. Since \c attr.name is not mandatory, + * Graph attribute names are taken from the attr.name attributes of the + * \c key tags in the GraphML file. Since attr.name is not mandatory, * igraph will fall back to the \c id attribute of the \c key tag if - * \c attr.name is missing. + * attr.name is missing. * * \param graph Pointer to an uninitialized graph object. * \param instream A stream, it should be readable. diff --git a/igraph/src/foreign-lgl-lexer.c b/igraph/src/foreign-lgl-lexer.c --- a/igraph/src/foreign-lgl-lexer.c +++ b/igraph/src/foreign-lgl-lexer.c @@ -485,16 +485,16 @@ #include "foreign-lgl-parser.h" #define YY_EXTRA_TYPE igraph_i_lgl_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno; -/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1) -#endif +#define YY_FATAL_ERROR(msg) \ + igraph_error("Fatal error in LGL parser: " # msg, __FILE__, \ + __LINE__, IGRAPH_PARSEERROR); #ifdef stdout # undef stdout #endif #define stdout 0 -#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \ - __LINE__, IGRAPH_PARSEERROR); +#endif #define YY_NO_INPUT 1 #line 500 "foreign-lgl-lexer.c" diff --git a/igraph/src/foreign-ncol-lexer.c b/igraph/src/foreign-ncol-lexer.c --- a/igraph/src/foreign-ncol-lexer.c +++ b/igraph/src/foreign-ncol-lexer.c @@ -485,16 +485,16 @@ #include "foreign-ncol-parser.h" #define YY_EXTRA_TYPE igraph_i_ncol_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno; -/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1) -#endif +#define YY_FATAL_ERROR(msg) \ + igraph_error("Fatal error in NCOL parser: " # msg, __FILE__, \ + __LINE__, IGRAPH_PARSEERROR); #ifdef stdout # undef stdout #endif #define stdout 0 -#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \ - __LINE__, IGRAPH_PARSEERROR); +#endif #define YY_NO_INPUT 1 #line 500 "foreign-ncol-lexer.c" diff --git a/igraph/src/foreign-pajek-lexer.c b/igraph/src/foreign-pajek-lexer.c --- a/igraph/src/foreign-pajek-lexer.c +++ b/igraph/src/foreign-pajek-lexer.c @@ -604,16 +604,16 @@ #include "foreign-pajek-parser.h" #define YY_EXTRA_TYPE igraph_i_pajek_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno; -/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1) -#endif +#define YY_FATAL_ERROR(msg) \ + igraph_error("Fatal error in PAJEK parser: " # msg, __FILE__, \ + __LINE__, IGRAPH_PARSEERROR); #ifdef stdout # undef stdout #endif #define stdout 0 -#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \ - __LINE__, IGRAPH_PARSEERROR); +#endif #define YY_NO_INPUT 1 #line 619 "foreign-pajek-lexer.c" diff --git a/igraph/src/foreign-pajek-parser.c b/igraph/src/foreign-pajek-parser.c --- a/igraph/src/foreign-pajek-parser.c +++ b/igraph/src/foreign-pajek-parser.c @@ -2690,7 +2690,7 @@ if (tmp==0) { IGRAPH_ERROR("cannot add element to hash table", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp); + IGRAPH_FINALLY(igraph_free, tmp); strncpy(tmp, value, len); tmp[len]='\0'; @@ -2717,7 +2717,7 @@ if (tmp==0) { IGRAPH_ERROR("cannot add element to hash table", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp); + IGRAPH_FINALLY(igraph_free, tmp); strncpy(tmp, value, len); tmp[len]='\0'; diff --git a/igraph/src/foreign.c b/igraph/src/foreign.c --- a/igraph/src/foreign.c +++ b/igraph/src/foreign.c @@ -22,7 +22,6 @@ */ #include "igraph_foreign.h" -#include "config.h" #include "igraph_math.h" #include "igraph_gml_tree.h" #include "igraph_memory.h" @@ -31,6 +30,7 @@ #include "igraph_interrupt_internal.h" #include "igraph_constructors.h" #include "igraph_types_internal.h" +#include "config.h" #include /* isspace */ #include @@ -53,10 +53,10 @@ * \brief Reads an edge list from a file and creates a graph. * * - * This format is simply a series of even number integers separated by - * whitespace. The one edge (ie. two integers) per line format is thus - * not required (but recommended for readability). Edges of directed - * graphs are assumed to be in from, to order. + * This format is simply a series of an even number of non-negative integers separated by + * whitespace. The integers represent vertex IDs. Placing each edge (i.e. pair of integers) + * on a separate line is not required, but it is recommended for readability. + * Edges of directed graphs are assumed to be in "from, to" order. * \param graph Pointer to an uninitialized graph object. * \param instream Pointer to a stream, it should be readable. * \param n The number of vertices in the graph. If smaller than the @@ -485,7 +485,7 @@ * project files (.paj) are not. These might be * supported in the future if there is need for it. * \oli Time events networks are not supported. - * \oli Hypergraphs (ie. graphs with non-binary edges) are not + * \oli Hypergraphs (i.e. graphs with non-binary edges) are not * supported. * \oli Graphs with both directed and non-directed edges are not * supported, are they cannot be represented in @@ -499,35 +499,35 @@ * If there are attribute handlers installed, * igraph also reads the vertex and edge attributes * from the file. Most attributes are renamed to be more informative: - * `\c color' instead of `\c c', `\c xfact' instead of `\c x_fact', - * `\c yfact' instead of `y_fact', `\c labeldist' instead of `\c lr', - * `\c labeldegree2' instead of `\c lphi', `\c framewidth' instead of `\c bw', - * `\c fontsize' - * instead of `\c fos', `\c rotation' instead of `\c phi', `\c radius' instead - * of `\c r', - * `\c diamondratio' instead of `\c q', `\c labeldegree' instead of `\c la', - * `\c vertexsize' - * instead of `\c size', `\c color' instead of `\c ic', `\c framecolor' instead of - * `\c bc', `\c labelcolor' instead of `\c lc', these belong to vertices. + * \c color instead of \c c, \c xfact instead of \c x_fact, + * \c yfact instead of y_fact, \c labeldist instead of \c lr, + * \c labeldegree2 instead of \c lphi, \c framewidth instead of \c bw, + * \c fontsize + * instead of \c fos, \c rotation instead of \c phi, \c radius instead + * of \c r, + * \c diamondratio instead of \c q, \c labeldegree instead of \c la, + * \c vertexsize + * instead of \c size, \c color instead of \c ic, \c framecolor instead of + * \c bc, \c labelcolor instead of \c lc, these belong to vertices. * * - * Edge attributes are also renamed, `\c s' to `\c arrowsize', `\c w' - * to `\c edgewidth', `\c h1' to `\c hook1', `\c h2' to `\c hook2', - * `\c a1' to `\c angle1', `\c a2' to `\c angle2', `\c k1' to - * `\c velocity1', `\c k2' to `\c velocity2', `\c ap' to `\c - * arrowpos', `\c lp' to `\c labelpos', `\c lr' to - * `\c labelangle', `\c lphi' to `\c labelangle2', `\c la' to `\c - * labeldegree', `\c fos' to - * `\c fontsize', `\c a' to `\c arrowtype', `\c p' to `\c - * linepattern', `\c l' to `\c label', `\c lc' to - * `\c labelcolor', `\c c' to `\c color'. + * Edge attributes are also renamed, \c s to \c arrowsize, \c w + * to \c edgewidth, \c h1 to \c hook1, \c h2 to \c hook2, + * \c a1 to \c angle1, \c a2 to \c angle2, \c k1 to + * \c velocity1, \c k2 to \c velocity2, \c ap to \c + * arrowpos, \c lp to \c labelpos, \c lr to + * \c labelangle, \c lphi to \c labelangle2, \c la to \c + * labeldegree, \c fos to + * \c fontsize, \c a to \c arrowtype, \c p to \c + * linepattern, \c l to \c label, \c lc to + * \c labelcolor, \c c to \c color. * * - * In addition the following vertex attributes might be added: `\c id' - * if there are vertex ids in the file, `\c x' and `\c y' or `\c x' - * and `\c y' and `\c z' if there are vertex coordinates in the file. + * In addition the following vertex attributes might be added: \c id + * if there are vertex ids in the file, \c x and \c y or \c x + * and \c y and \c z if there are vertex coordinates in the file. * - * The `\c weight' edge attribute might be + * The \c weight edge attribute might be * added if there are edge weights present. * * @@ -878,7 +878,7 @@ return 0; } -int igraph_i_read_graph_graphdb_getword(FILE *instream) { +static int igraph_i_read_graph_graphdb_getword(FILE *instream) { int b1, b2; unsigned char c1, c2; b1 = fgetc(instream); @@ -977,7 +977,7 @@ int igraph_gml_yyparse (igraph_i_gml_parsedata_t* context); void igraph_gml_yyset_in (FILE * in_str, void* yyscanner ); -void igraph_i_gml_destroy_attrs(igraph_vector_ptr_t **ptr) { +static void igraph_i_gml_destroy_attrs(igraph_vector_ptr_t **ptr) { long int i; igraph_vector_ptr_t *vec; for (i = 0; i < 3; i++) { @@ -1005,7 +1005,7 @@ } } -igraph_real_t igraph_i_gml_toreal(igraph_gml_tree_t *node, long int pos) { +static igraph_real_t igraph_i_gml_toreal(igraph_gml_tree_t *node, long int pos) { igraph_real_t value = 0.0; int type = igraph_gml_tree_type(node, pos); @@ -1025,10 +1025,10 @@ return value; } -const char *igraph_i_gml_tostring(igraph_gml_tree_t *node, long int pos) { +static const char *igraph_i_gml_tostring(igraph_gml_tree_t *node, long int pos) { int type = igraph_gml_tree_type(node, pos); - char tmp[256]; + static char tmp[256]; const char *p = tmp; long int i; igraph_real_t d; @@ -1155,7 +1155,7 @@ } gtree = igraph_gml_tree_get_tree(context.tree, gidx); - IGRAPH_FINALLY(igraph_i_gml_destroy_attrs, &attrs); + IGRAPH_FINALLY(igraph_i_gml_destroy_attrs, attrs); igraph_vector_ptr_init(&gattrs, 0); igraph_vector_ptr_init(&vattrs, 0); igraph_vector_ptr_init(&eattrs, 0); @@ -1942,7 +1942,7 @@ #define E_COLOR 22 #define E_LAST 23 -int igraph_i_pajek_escape(char* src, char** dest) { +static int igraph_i_pajek_escape(char* src, char** dest) { long int destlen = 0; igraph_bool_t need_escape = 0; @@ -2010,18 +2010,30 @@ * the attributes of the vertices and edges, of course this requires * an attribute handler to be installed. The names of the * corresponding vertex and edge attributes are listed at \ref - * igraph_read_graph_pajek(), eg. the `\c color' vertex attributes - * determines the color (`\c c' in Pajek) parameter. + * igraph_read_graph_pajek(), eg. the \c color vertex attributes + * determines the color (\c c in Pajek) parameter. * * * As of version 0.6.1 igraph writes bipartite graphs into Pajek files * correctly, i.e. they will be also bipartite when read into Pajek. - * As Pajek is less flexible for bipartite graphs (the numeric ids of + * As Pajek is less flexible for bipartite graphs (the numeric IDs of * the vertices must be sorted according to vertex type), igraph might * need to reorder the vertices when writing a bipartite Pajek file. - * This effectively means that numeric vertex ids usually change when + * This effectively means that numeric vertex IDs usually change when * a bipartite graph is written to a Pajek file, and then read back * into igraph. + * + * + * Early versions of Pajek supported only Windows-style line endings + * in Pajek files, but recent versions support both Windows and Unix + * line endings. igraph therefore uses the platform-native line endings + * when the input file is opened in text mode, and uses Unix-style + * line endings when the input file is opened in binary mode. If you + * are using an old version of Pajek, you are on Unix and you are having + * problems reading files written by igraph on a Windows machine, convert the + * line endings manually with a text editor or with \c unix2dos or \c iconv + * from the command line). + * * \param graph The graph object to write. * \param outstream The file to write to. It should be opened and * writable. Make sure that you open the file in binary format if you use MS Windows, @@ -2091,7 +2103,10 @@ }; const char *estrnames2[] = { "a", "p", "l", "lc", "c" }; - const char *newline = "\x0d\x0a"; + /* Newer Pajek versions support both Unix and Windows-style line endings, + * so we just use Unix style. This will get converted to CRLF on Windows + * when the file is opened in text mode */ + const char *newline = "\n"; igraph_es_t es; igraph_eit_t eit; @@ -2466,7 +2481,7 @@ return 0; } -int igraph_i_gml_convert_to_key(const char *orig, char **key) { +static int igraph_i_gml_convert_to_key(const char *orig, char **key) { int no = 1; char strno[50]; size_t i, len = strlen(orig), newlen = 0, plen = 0; @@ -2741,7 +2756,7 @@ return 0; } -int igraph_i_dot_escape(const char *orig, char **result) { +static int igraph_i_dot_escape(const char *orig, char **result) { /* do we have to escape the string at all? */ long int i, j, len = (long int) strlen(orig), newlen = 0; igraph_bool_t need_quote = 0, is_number = 1; @@ -3386,5 +3401,3 @@ } #undef CHECK - - diff --git a/igraph/src/forestfire.c b/igraph/src/forestfire.c --- a/igraph/src/forestfire.c +++ b/igraph/src/forestfire.c @@ -38,7 +38,7 @@ } igraph_i_forest_fire_data_t; -void igraph_i_forest_fire_free(igraph_i_forest_fire_data_t *data) { +static void igraph_i_forest_fire_free(igraph_i_forest_fire_data_t *data) { long int i; for (i = 0; i < data->no_of_nodes; i++) { igraph_vector_destroy(data->inneis + i); @@ -117,21 +117,20 @@ igraph_real_t param_geom_out = 1 - fw_prob; igraph_real_t param_geom_in = 1 - fw_prob * bw_factor; - if (fw_prob < 0) { - IGRAPH_ERROR("Forest fire model: 'fw_prob' should be between non-negative", + if (fw_prob < 0 || fw_prob >= 1) { + IGRAPH_ERROR("Forest fire model: 'fw_prob' must satisfy 0 <= fw_prob < 1.", IGRAPH_EINVAL); } - if (bw_factor < 0) { - IGRAPH_ERROR("Forest fire model: 'bw_factor' should be non-negative", + if (bw_factor * fw_prob < 0 || bw_factor * fw_prob >= 1) { + IGRAPH_ERROR("Forest fire model: 'bw_factor' must satisfy 0 <= bw_factor * fw_prob < 1.", IGRAPH_EINVAL); } if (ambs < 0) { - IGRAPH_ERROR("Number of ambassadors ('ambs') should be non-negative", + IGRAPH_ERROR("Forest fire model: Number of ambassadors must not be negative.", IGRAPH_EINVAL); } - if (fw_prob == 0 || ambs == 0) { - IGRAPH_WARNING("'fw_prob or ambs is zero, creating empty graph"); + if (ambs == 0) { IGRAPH_CHECK(igraph_empty(graph, nodes, directed)); return 0; } diff --git a/igraph/src/fortran_intrinsics.c b/igraph/src/fortran_intrinsics.c --- a/igraph/src/fortran_intrinsics.c +++ b/igraph/src/fortran_intrinsics.c @@ -23,31 +23,31 @@ #include -double digitsdbl_(double x) { +double digitsdbl_(double *x) { return (double) DBL_MANT_DIG; } -double epsilondbl_(double x) { +double epsilondbl_(double *x) { return DBL_EPSILON; } -double hugedbl_(double x) { +double hugedbl_(double *x) { return DBL_MAX; } -double tinydbl_(double x) { +double tinydbl_(double *x) { return DBL_MIN; } -int maxexponentdbl_(double x) { +int maxexponentdbl_(double *x) { return DBL_MAX_EXP; } -int minexponentdbl_(double x) { +int minexponentdbl_(double *x) { return DBL_MIN_EXP; } -double radixdbl_(double x) { +double radixdbl_(double *x) { return (double) FLT_RADIX; } diff --git a/igraph/src/games.c b/igraph/src/games.c --- a/igraph/src/games.c +++ b/igraph/src/games.c @@ -47,8 +47,8 @@ igraph_psumtree_t *sumtrees; } igraph_i_citing_cited_type_game_struct_t; -void igraph_i_citing_cited_type_game_free ( - igraph_i_citing_cited_type_game_struct_t *s); +static void igraph_i_citing_cited_type_game_free ( + igraph_i_citing_cited_type_game_struct_t *s); /** * \section about_games * @@ -56,39 +56,39 @@ * they generate a different graph every time you call them. */ -int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n, - igraph_integer_t m, - const igraph_vector_t *outseq, - igraph_bool_t outpref, - igraph_bool_t directed, - const igraph_t *start_from); +static int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n, + igraph_integer_t m, + const igraph_vector_t *outseq, + igraph_bool_t outpref, + igraph_bool_t directed, + const igraph_t *start_from); -int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph, - igraph_integer_t n, - igraph_real_t power, - igraph_integer_t m, - const igraph_vector_t *outseq, - igraph_bool_t outpref, - igraph_real_t A, - igraph_bool_t directed, - const igraph_t *start_from); +static int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph, + igraph_integer_t n, + igraph_real_t power, + igraph_integer_t m, + const igraph_vector_t *outseq, + igraph_bool_t outpref, + igraph_real_t A, + igraph_bool_t directed, + const igraph_t *start_from); -int igraph_i_barabasi_game_psumtree(igraph_t *graph, - igraph_integer_t n, - igraph_real_t power, - igraph_integer_t m, - const igraph_vector_t *outseq, - igraph_bool_t outpref, - igraph_real_t A, - igraph_bool_t directed, - const igraph_t *start_from); +static int igraph_i_barabasi_game_psumtree(igraph_t *graph, + igraph_integer_t n, + igraph_real_t power, + igraph_integer_t m, + const igraph_vector_t *outseq, + igraph_bool_t outpref, + igraph_real_t A, + igraph_bool_t directed, + const igraph_t *start_from); -int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n, - igraph_integer_t m, - const igraph_vector_t *outseq, - igraph_bool_t outpref, - igraph_bool_t directed, - const igraph_t *start_from) { +static int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n, + igraph_integer_t m, + const igraph_vector_t *outseq, + igraph_bool_t outpref, + igraph_bool_t directed, + const igraph_t *start_from) { long int no_of_nodes = n; long int no_of_neighbors = m; @@ -124,7 +124,7 @@ if (bag == 0) { IGRAPH_ERROR("barabasi_game failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, bag); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, bag); /* The first node(s) in the bag */ if (start_from) { @@ -190,15 +190,15 @@ return 0; } -int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph, - igraph_integer_t n, - igraph_real_t power, - igraph_integer_t m, - const igraph_vector_t *outseq, - igraph_bool_t outpref, - igraph_real_t A, - igraph_bool_t directed, - const igraph_t *start_from) { +static int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph, + igraph_integer_t n, + igraph_real_t power, + igraph_integer_t m, + const igraph_vector_t *outseq, + igraph_bool_t outpref, + igraph_real_t A, + igraph_bool_t directed, + const igraph_t *start_from) { long int no_of_nodes = n; long int no_of_neighbors = m; @@ -296,15 +296,15 @@ return 0; } -int igraph_i_barabasi_game_psumtree(igraph_t *graph, - igraph_integer_t n, - igraph_real_t power, - igraph_integer_t m, - const igraph_vector_t *outseq, - igraph_bool_t outpref, - igraph_real_t A, - igraph_bool_t directed, - const igraph_t *start_from) { +static int igraph_i_barabasi_game_psumtree(igraph_t *graph, + igraph_integer_t n, + igraph_real_t power, + igraph_integer_t m, + const igraph_vector_t *outseq, + igraph_bool_t outpref, + igraph_real_t A, + igraph_bool_t directed, + const igraph_t *start_from) { long int no_of_nodes = n; long int no_of_neighbors = m; @@ -437,7 +437,7 @@ * no outgoing edges, so the first number in this vector is * ignored. * \param outpref Boolean, if true not only the in- but also the out-degree - * of a vertex increases its citation probability. Ie. the + * of a vertex increases its citation probability. I.e., the * citation probability is determined by the total degree of * the vertices. Ignored and assumed to be true if the graph * being generated is undirected. @@ -860,7 +860,7 @@ if (bag1 == 0) { IGRAPH_ERROR("degree sequence game (simple)", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, bag1); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, bag1); for (i = 0; i < no_of_nodes; i++) { for (j = 0; j < VECTOR(*out_seq)[i]; j++) { @@ -872,7 +872,7 @@ if (bag2 == 0) { IGRAPH_ERROR("degree sequence game (simple)", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, bag2); + IGRAPH_FINALLY(igraph_free, bag2); for (i = 0; i < no_of_nodes; i++) { for (j = 0; j < VECTOR(*in_seq)[i]; j++) { bag2[bagp2++] = i; @@ -965,6 +965,8 @@ * until it finally succeeds. */ finished = 0; while (!finished) { + IGRAPH_ALLOW_INTERRUPTION(); + /* Be optimistic :) */ failed = 0; @@ -1111,6 +1113,8 @@ * until it finally succeeds. */ finished = 0; while (!finished) { + IGRAPH_ALLOW_INTERRUPTION(); + /* Be optimistic :) */ failed = 0; @@ -1210,15 +1214,24 @@ return IGRAPH_SUCCESS; } +/* swap two elements of a vector_int */ +#define SWAP_INT_ELEM(vec, i, j) \ + { \ + igraph_integer_t temp; \ + temp = VECTOR(vec)[i]; \ + VECTOR(vec)[i] = VECTOR(vec)[j]; \ + VECTOR(vec)[j] = temp; \ + } + int igraph_degree_sequence_game_no_multiple_undirected_uniform(igraph_t *graph, const igraph_vector_t *degseq) { igraph_vector_int_t stubs; igraph_vector_t edges; igraph_bool_t degseq_ok; igraph_vector_ptr_t adjlist; - long i, j, k; + long i, j; long vcount, ecount, stub_count; - IGRAPH_CHECK(igraph_is_graphical_degree_sequence(degseq, 0, °seq_ok)); + IGRAPH_CHECK(igraph_is_graphical_degree_sequence(degseq, NULL, °seq_ok)); if (!degseq_ok) { IGRAPH_ERROR("No simple undirected graph can realize the given degree sequence", IGRAPH_EINVAL); } @@ -1230,16 +1243,21 @@ IGRAPH_VECTOR_INT_INIT_FINALLY(&stubs, stub_count); IGRAPH_VECTOR_INIT_FINALLY(&edges, stub_count); - k = 0; - for (i = 0; i < vcount; ++i) { - long deg = (long) VECTOR(*degseq)[i]; - for (j = 0; j < deg; ++j) { - VECTOR(stubs)[k++] = i; + /* Fill stubs vector. */ + { + long k = 0; + for (i = 0; i < vcount; ++i) { + long deg = (long) VECTOR(*degseq)[i]; + for (j = 0; j < deg; ++j) { + VECTOR(stubs)[k++] = i; + } } } + /* Build an adjacency list in terms of sets; used to check for multi-edges. */ IGRAPH_CHECK(igraph_vector_ptr_init(&adjlist, vcount)); IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&adjlist, igraph_set_destroy); + IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist); for (i = 0; i < vcount; ++i) { igraph_set_t *set = igraph_malloc(sizeof(igraph_set_t)); if (! set) { @@ -1248,21 +1266,28 @@ IGRAPH_CHECK(igraph_set_init(set, 0)); VECTOR(adjlist)[i] = set; IGRAPH_CHECK(igraph_set_reserve(set, (long) VECTOR(*degseq)[i])); - } - IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist); + } RNG_BEGIN(); for (;;) { igraph_bool_t success = 1; - IGRAPH_CHECK(igraph_vector_int_shuffle(&stubs)); + /* Shuffle stubs vector with Fisher-Yates and check for self-loops and multi-edges as we go. */ for (i = 0; i < ecount; ++i) { - igraph_integer_t from = VECTOR(stubs)[2 * i]; - igraph_integer_t to = VECTOR(stubs)[2 * i + 1]; + long k, from, to; - /* loop edge, fail */ - if (to == from) { + k = RNG_INTEGER(2*i, stub_count-1); + SWAP_INT_ELEM(stubs, 2*i, k); + + k = RNG_INTEGER(2*i+1, stub_count-1); + SWAP_INT_ELEM(stubs, 2*i+1, k); + + from = VECTOR(stubs)[2*i]; + to = VECTOR(stubs)[2*i+1]; + + /* self-loop, fail */ + if (from == to) { success = 0; break; } @@ -1286,11 +1311,12 @@ break; } - IGRAPH_ALLOW_INTERRUPTION(); - + /* Clear adjacency list. */ for (j = 0; j < vcount; ++j) { igraph_set_clear((igraph_set_t *) VECTOR(adjlist)[j]); } + + IGRAPH_ALLOW_INTERRUPTION(); } RNG_END(); @@ -1307,13 +1333,14 @@ return IGRAPH_SUCCESS; } + int igraph_degree_sequence_game_no_multiple_directed_uniform( igraph_t *graph, const igraph_vector_t *out_deg, const igraph_vector_t *in_deg) { igraph_vector_int_t out_stubs, in_stubs; igraph_vector_t edges; igraph_bool_t degseq_ok; igraph_vector_ptr_t adjlist; - long i, j, k, l; + long i, j; long vcount, ecount; IGRAPH_CHECK(igraph_is_graphical_degree_sequence(out_deg, in_deg, °seq_ok)); @@ -1328,23 +1355,28 @@ IGRAPH_VECTOR_INT_INIT_FINALLY(&in_stubs, ecount); IGRAPH_VECTOR_INIT_FINALLY(&edges, 2 * ecount); - k = 0; l = 0; - for (i = 0; i < vcount; ++i) { - long dout, din; + /* Fill in- and out-stubs vectors. */ + { + long k = 0, l = 0; + for (i = 0; i < vcount; ++i) { + long dout, din; - dout = (long) VECTOR(*out_deg)[i]; - for (j = 0; j < dout; ++j) { - VECTOR(out_stubs)[k++] = i; - } + dout = (long) VECTOR(*out_deg)[i]; + for (j = 0; j < dout; ++j) { + VECTOR(out_stubs)[k++] = i; + } - din = (long) VECTOR(*in_deg)[i]; - for (j = 0; j < din; ++j) { - VECTOR(in_stubs)[l++] = i; + din = (long) VECTOR(*in_deg)[i]; + for (j = 0; j < din; ++j) { + VECTOR(in_stubs)[l++] = i; + } } } + /* Build an adjacency list in terms of sets; used to check for multi-edges. */ IGRAPH_CHECK(igraph_vector_ptr_init(&adjlist, vcount)); IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&adjlist, igraph_set_destroy); + IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist); for (i = 0; i < vcount; ++i) { igraph_set_t *set = igraph_malloc(sizeof(igraph_set_t)); if (! set) { @@ -1353,21 +1385,25 @@ IGRAPH_CHECK(igraph_set_init(set, 0)); VECTOR(adjlist)[i] = set; IGRAPH_CHECK(igraph_set_reserve(set, (long) VECTOR(*out_deg)[i])); - } - IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist); + } RNG_BEGIN(); for (;;) { igraph_bool_t success = 1; - IGRAPH_CHECK(igraph_vector_int_shuffle(&out_stubs)); + /* Shuffle out-stubs vector with Fisher-Yates and check for self-loops and multi-edges as we go. */ for (i = 0; i < ecount; ++i) { - igraph_integer_t from = VECTOR(out_stubs)[i]; - igraph_integer_t to = VECTOR(in_stubs)[i]; + long k, from, to; igraph_set_t *set; - /* loop edge, fail */ + k = RNG_INTEGER(i, ecount-1); + SWAP_INT_ELEM(out_stubs, i, k); + + from = VECTOR(out_stubs)[i]; + to = VECTOR(in_stubs)[i]; + + /* self-loop, fail */ if (to == from) { success = 0; break; @@ -1392,11 +1428,12 @@ break; } - IGRAPH_ALLOW_INTERRUPTION(); - + /* Clear adjacency list. */ for (j = 0; j < vcount; ++j) { igraph_set_clear((igraph_set_t *) VECTOR(adjlist)[j]); } + + IGRAPH_ALLOW_INTERRUPTION(); } RNG_END(); @@ -1414,6 +1451,9 @@ return IGRAPH_SUCCESS; } +#undef SWAP_INT_ELEM + + /* This is in gengraph_mr-connected.cpp */ int igraph_degree_sequence_game_vl(igraph_t *graph, @@ -1426,9 +1466,9 @@ * * \param graph Pointer to an uninitialized graph object. * \param out_deg The degree sequence for an undirected graph (if - * \p in_seq is of length zero), or the out-degree + * \p in_seq is \c NULL or of length zero), or the out-degree * sequence of a directed graph (if \p in_deq is not - * of length zero. + * of length zero). * \param in_deg It is either a zero-length vector or * \c NULL (if an undirected * graph is generated), or the in-degree sequence. @@ -1439,34 +1479,36 @@ * For undirected graphs, it puts all vertex IDs in a bag * such that the multiplicity of a vertex in the bag is the same as * its degree. Then it draws pairs from the bag until the bag becomes - * empty. This method can generate both loop (self) edges and multiple + * empty. This method may generate both loop (self) edges and multiple * edges. For directed graphs, the algorithm is basically the same, * but two separate bags are used for the in- and out-degrees. * Undirected graphs are generated with probability proportional to * (\prod_{i<j} A_{ij} ! \prod_i A_{ii} !!)^{-1}, * where \c A denotes the adjacency matrix and !! denotes - * the double factorial. - * The corresponding expression for directed ones is + * the double factorial. Here \c A is assumed to have twice the number of + * self-loops on its diagonal. + * The corresponding expression for directed graphs is * (\prod_{i,j} A_{ij}!)^{-1}. * Thus the probability of all simple graphs (which only have 0s and 1s * in the adjacency matrix) is the same, while that of - * non-simple ones depends on their structure. + * non-simple ones depends on their edge and self-loop multiplicities. * \cli IGRAPH_DEGSEQ_SIMPLE_NO_MULTIPLE - * This method is similar to \c IGRAPH_DEGSEQ_SIMPLE + * This method generates simple graphs. + * It is similar to \c IGRAPH_DEGSEQ_SIMPLE * but tries to avoid multiple and loop edges and restarts the - * generation from scratch if it gets stuck. It is not guaranteed - * to sample uniformly from the space of all possible graphs with - * the given sequence, but it is relatively fast and it will + * generation from scratch if it gets stuck. It can generate all simple + * realizations of a degree sequence, but it is not guaranteed + * to sample them uniformly. This method is relatively fast and it will * eventually succeed if the provided degree sequence is graphical, * but there is no upper bound on the number of iterations. * \cli IGRAPH_DEGSEQ_SIMPLE_NO_MULTIPLE_UNIFORM * This method is identical to \c IGRAPH_DEGSEQ_SIMPLE, but if the * generated graph is not simple, it rejects it and re-starts the - * generation. It samples all simple graphs with the same probability. + * generation. It generates all simple graphs with the same probability. * \cli IGRAPH_DEGSEQ_VL - * This method is a much more sophisticated generator than the - * previous ones. It can sample undirected, connected simple graphs - * uniformly and uses Monte-Carlo methods to randomize the graphs. + * This method samples undirected connected graphs approximately + * uniformly. It is a Monte Carlo method based on degree-preserving + * edge swaps. * This generator should be favoured if undirected and connected * graphs are to be generated and execution time is not a concern. * igraph uses the original implementation of Fabien Viger; for the algorithm, @@ -1540,7 +1582,7 @@ * growing) random graphs. * \param graph Uninitialized graph object. * \param n The number of vertices in the graph. - * \param m The number of edges to add in a time step (ie. after + * \param m The number of edges to add in a time step (i.e. after * adding a vertex). * \param directed Boolean, whether to generate a directed graph. * \param citation Boolean, if \c TRUE, the edges always @@ -2268,7 +2310,7 @@ * \param nodes The number of vertices in the graph. * \param radius The radius within which the vertices will be connected. * \param torus Logical constant, if true periodic boundary conditions - * will be used, ie. the vertices are assumed to be on a torus + * will be used, i.e. the vertices are assumed to be on a torus * instead of a square. * \return Error code. * @@ -2382,9 +2424,7 @@ } -void igraph_i_preference_game_free_vids_by_type(igraph_vector_ptr_t *vecs); - -void igraph_i_preference_game_free_vids_by_type(igraph_vector_ptr_t *vecs) { +static void igraph_i_preference_game_free_vids_by_type(igraph_vector_ptr_t *vecs) { int i = 0, n; igraph_vector_t *v; @@ -2926,13 +2966,9 @@ return 0; } -int igraph_i_rewire_edges_no_multiple(igraph_t *graph, igraph_real_t prob, - igraph_bool_t loops, - igraph_vector_t *edges); - -int igraph_i_rewire_edges_no_multiple(igraph_t *graph, igraph_real_t prob, - igraph_bool_t loops, - igraph_vector_t *edges) { +static int igraph_i_rewire_edges_no_multiple(igraph_t *graph, igraph_real_t prob, + igraph_bool_t loops, + igraph_vector_t *edges) { int no_verts = igraph_vcount(graph); int no_edges = igraph_ecount(graph); @@ -3386,7 +3422,7 @@ * * * The \p preference argument specifies the preferences for the - * citation lags, ie. its first elements contains the attractivity + * citation lags, i.e. its first elements contains the attractivity * of the very recently cited vertices, etc. The last element is * special, it contains the attractivity of the vertices which were * never cited. This element should be bigger than zero. @@ -3627,7 +3663,7 @@ return 0; } -void igraph_i_citing_cited_type_game_free(igraph_i_citing_cited_type_game_struct_t *s) { +static void igraph_i_citing_cited_type_game_free(igraph_i_citing_cited_type_game_struct_t *s) { long int i; if (!s->sumtrees) { return; @@ -3651,7 +3687,7 @@ * category of both the citing and the cited vertex and is given in * the \p pref matrix. The categories of the citing vertex correspond * to the rows, the categories of the cited vertex to the columns of - * this matrix. Ie. the element in row \c i and column \c j gives the + * this matrix. I.e. the element in row \c i and column \c j gives the * probability that a \c j vertex is cited, if the category of the * citing vertex is \c i. * @@ -3783,16 +3819,15 @@ * */ int igraph_simple_interconnected_islands_game( - igraph_t *graph, - igraph_integer_t islands_n, - igraph_integer_t islands_size, - igraph_real_t islands_pin, - igraph_integer_t n_inter) { + igraph_t *graph, + igraph_integer_t islands_n, + igraph_integer_t islands_size, + igraph_real_t islands_pin, + igraph_integer_t n_inter) { igraph_vector_t edges = IGRAPH_VECTOR_NULL; igraph_vector_t s = IGRAPH_VECTOR_NULL; - int retval = 0; int nbNodes; double maxpossibleedgesPerIsland; double maxedgesPerIsland; @@ -3816,73 +3851,63 @@ IGRAPH_ERROR("Invalid number of inter-islands links", IGRAPH_EINVAL); } - // how much memory ? + /* how much memory ? */ nbNodes = islands_n * islands_size; maxpossibleedgesPerIsland = ((double)islands_size * ((double)islands_size - (double)1)) / (double)2; maxedgesPerIsland = islands_pin * maxpossibleedgesPerIsland; nbEdgesInterIslands = n_inter * (islands_n * (islands_n - 1)) / 2; - maxedges = maxedgesPerIsland * islands_n + nbEdgesInterIslands; - - // debug&tests : printf("total nodes %d, maxedgesperisland %f, maxedgesinterislands %d, maxedges %f\n", nbNodes, maxedgesPerIsland, nbEdgesInterIslands, maxedges); + maxedges = maxedgesPerIsland * islands_n + nbEdgesInterIslands; - // reserve enough place for all the edges, thanks ! + /* reserve enough space for all the edges */ IGRAPH_VECTOR_INIT_FINALLY(&edges, 0); IGRAPH_CHECK(igraph_vector_reserve(&edges, (long int) maxedges)); RNG_BEGIN(); - // first create all the islands - for (is = 1; is <= islands_n; is++) { // for each island + /* first create all the islands */ + for (is = 1; is <= islands_n; is++) { /* for each island */ - // index for start and end of nodes in this island + /* index for start and end of nodes in this island */ startIsland = islands_size * (is - 1); endIsland = startIsland + islands_size - 1; - - // debug&tests : printf("start %d,end %d\n", startIsland, endIsland); - - // create the random numbers to be used (into s) + /* create the random numbers to be used (into s) */ IGRAPH_VECTOR_INIT_FINALLY(&s, 0); IGRAPH_CHECK(igraph_vector_reserve(&s, (long int) maxedgesPerIsland)); last = RNG_GEOM(islands_pin); - // debug&tests : printf("last=%f \n", last); - while (last < maxpossibleedgesPerIsland) { // maxedgesPerIsland + while (last < maxpossibleedgesPerIsland) { /* maxedgesPerIsland */ IGRAPH_CHECK(igraph_vector_push_back(&s, last)); myrand = RNG_GEOM(islands_pin); - last += myrand; //RNG_GEOM(islands_pin); - //printf("myrand=%f , last=%f \n", myrand, last); + last += myrand; /* RNG_GEOM(islands_pin); */ last += 1; } - // change this to edges ! + /* change this to edges ! */ for (i = 0; i < igraph_vector_size(&s); i++) { - long int to = (long int) floor((sqrt(8 * VECTOR(s)[i] + 1) + 1) / 2); long int from = (long int) (VECTOR(s)[i] - (((igraph_real_t)to) * (to - 1)) / 2); to += startIsland; from += startIsland; - // debug&tests : printf("from %d to %d\n", from, to); + igraph_vector_push_back(&edges, from); igraph_vector_push_back(&edges, to); } - // clear the memory used for random number for this island + /* clear the memory used for random number for this island */ igraph_vector_destroy(&s); IGRAPH_FINALLY_CLEAN(1); - // create the links with other islands - for (i = is + 1; i <= islands_n; i++) { // for each other island (not the previous ones) - - // debug&tests : printf("link islands %d and %d\n", is, i); - for (j = 0; j < n_inter; j++) { // for each link between islands + /* create the links with other islands */ + for (i = is + 1; i <= islands_n; i++) { /* for each other island (not the previous ones) */ + for (j = 0; j < n_inter; j++) { /* for each link between islands */ long int from = (long int) RNG_UNIF(startIsland, endIsland); long int to = (long int) RNG_UNIF((i - 1) * islands_size, i * islands_size); - //printf("from %d to %d\n", from, to); + igraph_vector_push_back(&edges, from); igraph_vector_push_back(&edges, to); } @@ -3892,14 +3917,14 @@ RNG_END(); - // actually fill the graph object - IGRAPH_CHECK(retval = igraph_create(graph, &edges, nbNodes, 0)); + /* actually fill the graph object */ + IGRAPH_CHECK(igraph_create(graph, &edges, nbNodes, 0)); - // an clear remaining things + /* clean remaining things */ igraph_vector_destroy(&edges); IGRAPH_FINALLY_CLEAN(1); - return retval; + return IGRAPH_SUCCESS; } @@ -4318,8 +4343,11 @@ * graphs, at least one of k and the number of vertices must be even. * * - * The game simply uses \ref igraph_degree_sequence_game with appropriately - * constructed degree sequences. + * Currently, this game simply uses \ref igraph_degree_sequence_game with + * the \c SIMPLE_NO_MULTIPLE method and appropriately constructed degree sequences. + * Thefore, it does not sample uniformly: while it can generate all k-regular graphs + * with the given number of vertices, it does not generate each one with the same + * probability. * * \param graph Pointer to an uninitialized graph object. * \param no_of_nodes The number of nodes in the generated graph. @@ -4744,7 +4772,7 @@ * \brief Generates a random tree with the given number of nodes * * This function samples uniformly from the set of labelled trees, - * i.e. it can generate each labelled tree with the same probability. + * i.e. it generates each labelled tree with the same probability. * * \param graph Pointer to an uninitialized graph object. * \param n The number of nodes in the tree. @@ -4752,7 +4780,7 @@ * \param method The algorithm to use to generate the tree. Possible values: * \clist * \cli IGRAPH_RANDOM_TREE_PRUFER - * This algorithm samples Prüfer sequences unformly, then converts them to trees. + * This algorithm samples Prüfer sequences uniformly, then converts them to trees. * Directed trees are not currently supported. * \cli IGRAPH_RANDOM_LERW * This algorithm effectively performs a loop-erased random walk on the complete graph diff --git a/igraph/src/gengraph_box_list.cpp b/igraph/src/gengraph_box_list.cpp --- a/igraph/src/gengraph_box_list.cpp +++ b/igraph/src/gengraph_box_list.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -24,7 +24,7 @@ namespace gengraph { void box_list::insert(int v) { - register int d = deg[v]; + int d = deg[v]; if (d < 1) { return; } @@ -41,10 +41,10 @@ } void box_list::pop(int v) { - register int p = prev[v]; - register int n = next[v]; + int p = prev[v]; + int n = next[v]; if (p < 0) { - register int d = deg[v]; + int d = deg[v]; assert(list[d - 1] == v); list[d - 1] = n; if (d == dmax && n < 0) do { @@ -90,13 +90,13 @@ int *w = neigh[v]; while (k--) { int v2 = *(w++); - register int *w2 = neigh[v2]; + int *w2 = neigh[v2]; while (*w2 != v) { w2++; } - register int *w3 = neigh[v2] + (deg[v2] - 1); + int *w3 = neigh[v2] + (deg[v2] - 1); assert(w2 <= w3); - register int tmp = *w3; + int tmp = *w3; *w3 = *w2; *w2 = tmp; pop(v2); diff --git a/igraph/src/gengraph_degree_sequence.cpp b/igraph/src/gengraph_degree_sequence.cpp --- a/igraph/src/gengraph_degree_sequence.cpp +++ b/igraph/src/gengraph_degree_sequence.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, diff --git a/igraph/src/gengraph_graph_molloy_hash.cpp b/igraph/src/gengraph_graph_molloy_hash.cpp --- a/igraph/src/gengraph_graph_molloy_hash.cpp +++ b/igraph/src/gengraph_graph_molloy_hash.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -132,7 +132,7 @@ int *p = hc + 2 + n; int *l = links; for (int i = 0; i < n; i++) for (int j = HASH_SIZE(deg[i]); j--; l++) { - register int d; + int d; if ((d = *l) != HASH_NONE && d >= i) { *(p++) = d; } @@ -1168,6 +1168,6 @@ } //___________________________________________________________________________________ -//*/ +*/ } // namespace gengraph diff --git a/igraph/src/gengraph_graph_molloy_optimized.cpp b/igraph/src/gengraph_graph_molloy_optimized.cpp --- a/igraph/src/gengraph_graph_molloy_optimized.cpp +++ b/igraph/src/gengraph_graph_molloy_optimized.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -34,9 +34,6 @@ #include "igraph_statusbar.h" #include "igraph_progress.h" -#ifndef register - #define register -#endif using namespace std; @@ -1051,7 +1048,7 @@ int dv = deg[v]; double f = target[v] / paths[v]; // pick ALL fathers - register int father; + int father; for (int k = 0; k < dv; k++) if (dist[father = ww[k]] == pd) { // increase target[] of father target[father] += paths[father] * f; @@ -2081,7 +2078,7 @@ //___________________________________________________________________________________ -//*/ +*/ @@ -2216,6 +2213,6 @@ return b; } -//*/ +*/ } // namespace gengraph diff --git a/igraph/src/gengraph_mr-connected.cpp b/igraph/src/gengraph_mr-connected.cpp --- a/igraph/src/gengraph_mr-connected.cpp +++ b/igraph/src/gengraph_mr-connected.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -28,16 +28,18 @@ #include "igraph_types.h" #include "igraph_error.h" +#include "igraph_handle_exceptions.h" + namespace gengraph { // return negative number if program should exit int parse_options(int &argc, char** &argv); // options -static const bool MONITOR_TIME = false; +// static const bool MONITOR_TIME = false; static const int SHUFFLE_TYPE = FINAL_HEURISTICS; -static const bool RAW_DEGREES = false; -static const FILE *Fdeg = stdin; +// static const bool RAW_DEGREES = false; +// static const FILE *Fdeg = stdin; //_________________________________________________________________________ // int main(int argc, char** argv) { @@ -137,48 +139,50 @@ int igraph_degree_sequence_game_vl(igraph_t *graph, const igraph_vector_t *out_seq, const igraph_vector_t *in_seq) { - long int sum = igraph_vector_sum(out_seq); - if (sum % 2 != 0) { - IGRAPH_ERROR("Sum of degrees should be even", IGRAPH_EINVAL); - } + IGRAPH_HANDLE_EXCEPTIONS( + long int sum = igraph_vector_sum(out_seq); + if (sum % 2 != 0) { + IGRAPH_ERROR("Sum of degrees should be even", IGRAPH_EINVAL); + } - RNG_BEGIN(); + RNG_BEGIN(); - if (in_seq && igraph_vector_size(in_seq) != 0) { - RNG_END(); - IGRAPH_ERROR("This generator works with undirected graphs only", IGRAPH_EINVAL); - } + if (in_seq && igraph_vector_size(in_seq) != 0) { + RNG_END(); + IGRAPH_ERROR("This generator works with undirected graphs only", IGRAPH_EINVAL); + } - degree_sequence *dd = new degree_sequence(out_seq); + degree_sequence *dd = new degree_sequence(out_seq); - graph_molloy_opt *g = new graph_molloy_opt(*dd); - delete dd; + graph_molloy_opt *g = new graph_molloy_opt(*dd); + delete dd; - if (!g->havelhakimi()) { - delete g; - RNG_END(); - IGRAPH_ERROR("Cannot realize the given degree sequence as an undirected, simple graph", - IGRAPH_EINVAL); - } + if (!g->havelhakimi()) { + delete g; + RNG_END(); + IGRAPH_ERROR("Cannot realize the given degree sequence as an undirected, simple graph", + IGRAPH_EINVAL); + } - if (!g->make_connected()) { - delete g; - RNG_END(); - IGRAPH_ERROR("Cannot make a connected graph from the given degree sequence", - IGRAPH_EINVAL); - } + if (!g->make_connected()) { + delete g; + RNG_END(); + IGRAPH_ERROR("Cannot make a connected graph from the given degree sequence", + IGRAPH_EINVAL); + } - int *hc = g->hard_copy(); - delete g; - graph_molloy_hash *gh = new graph_molloy_hash(hc); - delete [] hc; + int *hc = g->hard_copy(); + delete g; + graph_molloy_hash *gh = new graph_molloy_hash(hc); + delete [] hc; - gh->shuffle(5 * gh->nbarcs(), 100 * gh->nbarcs(), SHUFFLE_TYPE); + gh->shuffle(5 * gh->nbarcs(), 100 * gh->nbarcs(), SHUFFLE_TYPE); - IGRAPH_CHECK(gh->print(graph)); - delete gh; + IGRAPH_CHECK(gh->print(graph)); + delete gh; - RNG_END(); + RNG_END(); + ); return 0; } diff --git a/igraph/src/gengraph_powerlaw.cpp b/igraph/src/gengraph_powerlaw.cpp --- a/igraph/src/gengraph_powerlaw.cpp +++ b/igraph/src/gengraph_powerlaw.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, diff --git a/igraph/src/gengraph_random.cpp b/igraph/src/gengraph_random.cpp --- a/igraph/src/gengraph_random.cpp +++ b/igraph/src/gengraph_random.cpp @@ -7,7 +7,7 @@ * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or + * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, @@ -28,8 +28,8 @@ // See the header file random.h for a description of the contents of this // file as well as references and credits. -#include #include "gengraph_random.h" +#include using namespace std; using namespace KW_RNG; diff --git a/igraph/src/glet.c b/igraph/src/glet.c --- a/igraph/src/glet.c +++ b/igraph/src/glet.c @@ -75,7 +75,7 @@ int nc; } igraph_i_subclique_next_free_t; -void igraph_i_subclique_next_free(void *ptr) { +static void igraph_i_subclique_next_free(void *ptr) { igraph_i_subclique_next_free_t *data = ptr; int i; if (data->resultids) { @@ -123,15 +123,15 @@ * */ -int igraph_i_subclique_next(const igraph_t *graph, - const igraph_vector_t *weights, - const igraph_vector_int_t *ids, - const igraph_vector_ptr_t *cliques, - igraph_t **result, - igraph_vector_t **resultweights, - igraph_vector_int_t **resultids, - igraph_vector_t *clique_thr, - igraph_vector_t *next_thr) { +static int igraph_i_subclique_next(const igraph_t *graph, + const igraph_vector_t *weights, + const igraph_vector_int_t *ids, + const igraph_vector_ptr_t *cliques, + igraph_t **result, + igraph_vector_t **resultweights, + igraph_vector_int_t **resultids, + igraph_vector_t *clique_thr, + igraph_vector_t *next_thr) { /* The input is a set of cliques, that were found at a previous level. For each clique, we calculate the next threshold, drop the isolate @@ -173,9 +173,9 @@ igraph_vector_init(&newedges, 100); IGRAPH_FINALLY(igraph_vector_destroy, &newedges); igraph_vector_int_init(&mark, no_of_nodes); - IGRAPH_FINALLY(igraph_vector_destroy, &mark); + IGRAPH_FINALLY(igraph_vector_int_destroy, &mark); igraph_vector_int_init(&map, no_of_nodes); - IGRAPH_FINALLY(igraph_vector_destroy, &map); + IGRAPH_FINALLY(igraph_vector_int_destroy, &map); igraph_vector_int_init(&edges, 100); IGRAPH_FINALLY(igraph_vector_int_destroy, &edges); igraph_vector_init(&neis, 10); @@ -294,7 +294,7 @@ return 0; } -void igraph_i_graphlets_destroy_vectorlist(igraph_vector_ptr_t *vl) { +static void igraph_i_graphlets_destroy_vectorlist(igraph_vector_ptr_t *vl) { int i, n = igraph_vector_ptr_size(vl); for (i = 0; i < n; i++) { igraph_vector_t *v = (igraph_vector_t*) VECTOR(*vl)[i]; @@ -305,12 +305,12 @@ igraph_vector_ptr_destroy(vl); } -int igraph_i_graphlets(const igraph_t *graph, - const igraph_vector_t *weights, - igraph_vector_ptr_t *cliques, - igraph_vector_t *thresholds, - const igraph_vector_int_t *ids, - igraph_real_t startthr) { +static int igraph_i_graphlets(const igraph_t *graph, + const igraph_vector_t *weights, + igraph_vector_ptr_t *cliques, + igraph_vector_t *thresholds, + const igraph_vector_int_t *ids, + igraph_real_t startthr) { /* This version is different from the main function, and is appropriate to use in recursive calls, because it _adds_ the @@ -401,7 +401,7 @@ const igraph_vector_t *thresholds; } igraph_i_graphlets_filter_t; -int igraph_i_graphlets_filter_cmp(void *data, const void *a, const void *b) { +static int igraph_i_graphlets_filter_cmp(void *data, const void *a, const void *b) { igraph_i_graphlets_filter_t *ddata = (igraph_i_graphlets_filter_t *) data; int *aa = (int*) a; int *bb = (int*) b; @@ -430,8 +430,8 @@ } } -int igraph_i_graphlets_filter(igraph_vector_ptr_t *cliques, - igraph_vector_t *thresholds) { +static int igraph_i_graphlets_filter(igraph_vector_ptr_t *cliques, + igraph_vector_t *thresholds) { /* Filter out non-maximal cliques. Every non-maximal clique is part of a maximal clique, at the same threshold. @@ -583,6 +583,7 @@ return 0; } +/* TODO: not made static because it is used by the R interface */ int igraph_i_graphlets_project(const igraph_t *graph, const igraph_vector_t *weights, const igraph_vector_ptr_t *cliques, @@ -794,7 +795,7 @@ const igraph_vector_t *Mu; } igraph_i_graphlets_order_t; -int igraph_i_graphlets_order_cmp(void *data, const void *a, const void *b) { +static int igraph_i_graphlets_order_cmp(void *data, const void *a, const void *b) { igraph_i_graphlets_order_t *ddata = (igraph_i_graphlets_order_t*) data; int *aa = (int*) a; int *bb = (int*) b; diff --git a/igraph/src/glpk_support.c b/igraph/src/glpk_support.c --- a/igraph/src/glpk_support.c +++ b/igraph/src/glpk_support.c @@ -30,7 +30,6 @@ #include "igraph_error.h" #include "igraph_interrupt_internal.h" #include -#include #include void igraph_i_glpk_interruption_hook(glp_tree *tree, void *info) { diff --git a/igraph/src/graph.cc b/igraph/src/graph.cc --- a/igraph/src/graph.cc +++ b/igraph/src/graph.cc @@ -1,4 +1,5 @@ -#include + +// #include #include #include #include @@ -15,11 +16,6 @@ #include #endif -#ifdef USING_R -#undef stdout -#define stdout NULL -#endif - /* Copyright (c) 2003-2015 Tommi Junttila Released under the GNU Lesser General Public License version 3. @@ -62,6 +58,7 @@ first_path_automorphism = 0; best_path_automorphism = 0; in_search = false; + refine_equal_to_first = false; /* Default value for using "long prune" */ opt_use_long_prune = true; @@ -72,7 +69,7 @@ verbose_level = 0; - verbstr = stdout; + // verbstr = stdout; report_hook = 0; report_user_param = 0; @@ -115,7 +112,7 @@ void AbstractGraph::set_verbose_file(FILE* const fp) { - verbstr = fp; + // verbstr = fp; } @@ -811,6 +808,7 @@ root.in_best_path = false; root.cmp_to_best_path = 0; root.long_prune_begin = 0; + root.needs_long_prune = false; root.failure_recording_ival = 0; @@ -1034,15 +1032,6 @@ */ if(index == cell->length and all_same_level == current_level+1) all_same_level = current_level; - if(verbstr and verbose_level >= 2) { - fprintf(verbstr, - "Level %u: orbits=%u, index=%u/%u, all_same_level=%u\n", - current_level, - first_path_orbits.nof_orbits(), - index, cell->length, - all_same_level); - fflush(verbstr); - } } continue; } @@ -2080,6 +2069,7 @@ *-------------------------------------------------------------------------*/ +#if 0 void Digraph::write_dot(const char* const filename) { @@ -2116,6 +2106,7 @@ fprintf(fp, "}\n"); } +#endif void @@ -2185,6 +2176,7 @@ * *-------------------------------------------------------------------------*/ +#if 0 Digraph* Digraph::read_dimacs(FILE* const fp, FILE* const errstr) { @@ -2341,11 +2333,11 @@ delete g; return 0; } - - +#endif +#if 0 void Digraph::write_dimacs(FILE* const fp) { @@ -2387,7 +2379,7 @@ } } } - +#endif @@ -3688,12 +3680,6 @@ cr_component_elements += cell->length; } - if(verbstr and verbose_level > 2) { - fprintf(verbstr, "NU-component with %lu cells and %u vertices\n", - (long unsigned)cr_component.size(), cr_component_elements); - fflush(verbstr); - } - return true; } @@ -3889,12 +3875,6 @@ component_elements += cell->length; } - if(verbstr and verbose_level > 2) { - fprintf(verbstr, "NU-component with %lu cells and %u vertices\n", - (long unsigned)component.size(), component_elements); - fflush(verbstr); - } - return true; } @@ -4034,6 +4014,7 @@ * *-------------------------------------------------------------------------*/ +#if 0 Graph* Graph::read_dimacs(FILE* const fp, FILE* const errstr) { @@ -4249,7 +4230,7 @@ } } } - +#endif void @@ -4370,6 +4351,7 @@ *-------------------------------------------------------------------------*/ +#if 0 void Graph::write_dot(const char* const filename) { @@ -4407,8 +4389,7 @@ fprintf(fp, "}\n"); } - - +#endif @@ -5430,12 +5411,6 @@ cr_component_elements += cell->length; } - if(verbstr and verbose_level > 2) { - fprintf(verbstr, "NU-component with %lu cells and %u vertices\n", - (long unsigned)cr_component.size(), cr_component_elements); - fflush(verbstr); - } - return true; } @@ -5593,12 +5568,6 @@ component.push_back(cell->first); component_elements += cell->length; } - - if(verbstr and verbose_level > 2) { - fprintf(verbstr, "NU-component with %lu cells and %u vertices\n", - (long unsigned)component.size(), component_elements); - fflush(verbstr); - } return true; } diff --git a/igraph/src/gss.c b/igraph/src/gss.c --- a/igraph/src/gss.c +++ b/igraph/src/gss.c @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. @@ -151,4 +151,3 @@ return successful ? PLFIT_SUCCESS : PLFIT_FAILURE; } - diff --git a/igraph/src/heap.c b/igraph/src/heap.c --- a/igraph/src/heap.c +++ b/igraph/src/heap.c @@ -24,10 +24,9 @@ #include "igraph_types.h" #include "igraph_types_internal.h" #include "igraph_memory.h" -#include "igraph_random.h" #include "igraph_error.h" -#include "config.h" #include "igraph_math.h" +#include "config.h" #include #include /* memcpy & co. */ @@ -289,12 +288,12 @@ if (tmp1 == 0) { IGRAPH_ERROR("indheap reserve failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp1); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, tmp1); tmp2 = igraph_Calloc(size, long int); if (tmp2 == 0) { IGRAPH_ERROR("indheap reserve failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp2); + IGRAPH_FINALLY(igraph_free, tmp2); memcpy(tmp1, h->stor_begin, (size_t) actual_size * sizeof(igraph_real_t)); memcpy(tmp2, h->index_begin, (size_t) actual_size * sizeof(long int)); igraph_Free(h->stor_begin); @@ -575,17 +574,17 @@ if (tmp1 == 0) { IGRAPH_ERROR("d_indheap reserve failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp1); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, tmp1); tmp2 = igraph_Calloc(size, long int); if (tmp2 == 0) { IGRAPH_ERROR("d_indheap reserve failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp2); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, tmp2); tmp3 = igraph_Calloc(size, long int); if (tmp3 == 0) { IGRAPH_ERROR("d_indheap reserve failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp3); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, tmp3); memcpy(tmp1, h->stor_begin, (size_t) actual_size * sizeof(igraph_real_t)); memcpy(tmp2, h->index_begin, (size_t) actual_size * sizeof(long int)); diff --git a/igraph/src/hzeta.c b/igraph/src/hzeta.c new file mode 100644 --- /dev/null +++ b/igraph/src/hzeta.c @@ -0,0 +1,651 @@ +/* vim:set ts=4 sw=2 sts=2 et: */ + +/* This file was imported from a private scientific library + * based on GSL coined Home Scientific Libray (HSL) by its author + * Jerome Benoit; this very material is itself inspired from the + * material written by G. Jungan and distributed by GSL. + * Ultimately, some modifications were done in order to render the + * imported material independent from the rest of GSL. + */ + +/* `hsl/specfunc/hzeta.c' C source file +// HSL - Home Scientific Library +// Copyright (C) 2017-2018 Jerome Benoit +// +// HSL is free software; you can redistribute it and/or +// modify it under the terms of the GNU General Public License +// as published by the Free Software Foundation; either version 2 +// of the License, or (at your option) any later version. +// +// This program is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this program; if not, write to the Free Software +// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +*/ + +/* +// The material in this file is mainly inspired by the material written by +// G. Jungan and distributed under GPLv2 by the GNU Scientific Library (GSL) +// ( https://www.gnu.org/software/gsl/ [specfunc/zeta.c]), itself inspired by +// the material written by Moshier and distributed in the Cephes Mathematical +// Library ( http://www.moshier.net/ [zeta.c]). +// +// More specifically, hsl_sf_hzeta_e is a slightly modifed clone of +// gsl_sf_hzeta_e as found in GSL 2.4; the remaining is `inspired by'. +// [Sooner or later a _Working_Note_ may be deposited at ResearchGate +// ( https://www.researchgate.net/profile/Jerome_Benoit )] +*/ + +/* Author: Jerome G. Benoit < jgmbenoit _at_ rezozer _dot_ net > */ + +#ifdef _MSC_VER +#define _USE_MATH_DEFINES +#endif + +#include +#include +#include "hzeta.h" +#include "error.h" +#include "platform.h" + +/* imported from gsl_machine.h */ + +#define GSL_LOG_DBL_MIN (-7.0839641853226408e+02) +#define GSL_LOG_DBL_MAX 7.0978271289338397e+02 +#define GSL_DBL_EPSILON 2.2204460492503131e-16 + +/* imported from gsl_math.h */ + +#ifndef M_LOG2E +#define M_LOG2E 1.44269504088896340735992468100 /* log_2 (e) */ +#endif + +/* imported from gsl_sf_result.h */ + +struct gsl_sf_result_struct { + double val; + double err; +}; +typedef struct gsl_sf_result_struct gsl_sf_result; + +/* imported and adapted from hsl/specfunc/specfunc_def.h */ + +#define HSL_SF_EVAL_RESULT(FnE) \ + gsl_sf_result result; \ + FnE ; \ + return (result.val); + +#define HSL_SF_EVAL_TUPLE_RESULT(FnET) \ + gsl_sf_result result0; \ + gsl_sf_result result1; \ + FnET ; \ + *tuple1=result1.val; \ + *tuple0=result0.val; \ + return (result0.val); + +/* */ + + +#define HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT 10 +#define HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER 32 + +#define HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX 256 + +// B_{2j}/(2j) +static +double hsl_sf_hzeta_eulermaclaurin_series_coeffs[HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={ + +1.0, + +1.0/12.0, + -1.0/720.0, + +1.0/30240.0, + -1.0/1209600.0, + +1.0/47900160.0, + -691.0/1307674368000.0, + +1.0/74724249600.0, + -3.38968029632258286683019539125e-13, + +8.58606205627784456413590545043e-15, + -2.17486869855806187304151642387e-16, + +5.50900282836022951520265260890e-18, + -1.39544646858125233407076862641e-19, + +3.53470703962946747169322997780e-21, + -8.95351742703754685040261131811e-23, + +2.26795245233768306031095073887e-24, + -5.74479066887220244526388198761e-26, + +1.45517247561486490186626486727e-27, + -3.68599494066531017818178247991e-29, + +9.33673425709504467203255515279e-31, + -2.36502241570062993455963519637e-32, + +5.99067176248213430465991239682e-34, + -1.51745488446829026171081313586e-35, + +3.84375812545418823222944529099e-37, + -9.73635307264669103526762127925e-39, + +2.46624704420068095710640028029e-40, + -6.24707674182074369314875679472e-42, + +1.58240302446449142975108170683e-43, + -4.00827368594893596853001219052e-45, + +1.01530758555695563116307139454e-46, + -2.57180415824187174992481940976e-48, + +6.51445603523381493155843485864e-50, + -1.65013099068965245550609878048e-51 + }; // hsl_sf_hzeta_eulermaclaurin_series_coeffs + +// 4\zeta(2j)/(2\pi)^(2j) +static +double hsl_sf_hzeta_eulermaclaurin_series_majorantratios[HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={ + -2.0, + +1.0/6.0, + +1.0/360.0, + +1.0/15120.0, + +1.0/604800.0, + +1.0/23950080.0, + +691.0/653837184000.0, + +1.0/37362124800.0, + +3617.0/5335311421440000.0, + +1.71721241125556891282718109009e-14, + +4.34973739711612374608303284773e-16, + +1.10180056567204590304053052178e-17, + +2.79089293716250466814153725281e-19, + +7.06941407925893494338645995561e-21, + +1.79070348540750937008052226362e-22, + +4.53590490467536612062190147774e-24, + +1.14895813377444048905277639752e-25, + +2.91034495122972980373252973454e-27, + +7.37198988133062035636356495982e-29, + +1.86734685141900893440651103056e-30, + +4.73004483140125986911927039274e-32, + +1.19813435249642686093198247936e-33, + +3.03490976893658052342162627173e-35, + +7.68751625090837646445889058198e-37, + +1.94727061452933820705352425585e-38, + +4.93249408840136191421280056051e-40, + +1.24941534836414873862975135893e-41, + +3.16480604892898285950216341362e-43, + +8.01654737189787193706002438098e-45, + +2.03061517111391126232614278906e-46, + +5.14360831648374349984963881946e-48, + +1.30289120704676298631168697172e-49, + +3.30026198137930491101219756091e-51 + }; // hsl_sf_hzeta_eulermaclaurin_series_majorantratios + + +extern +int hsl_sf_hzeta_e(const double s, const double q, gsl_sf_result * result) { + + /* CHECK_POINTER(result) */ + + if ((s <= 1.0) || (q <= 0.0)) { + PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL); + } + else { + const double max_bits=54.0; // max_bits=\lceil{s}\rceil with \zeta(s,2)=\zeta(s)-1=GSL_DBL_EPSILON + const double ln_term0=-s*log(q); + if (ln_term0 < GSL_LOG_DBL_MIN+1.0) { + PLFIT_ERROR("underflow", PLFIT_UNDRFLOW); + } + else if (GSL_LOG_DBL_MAX-1.0 < ln_term0) { + PLFIT_ERROR("overflow", PLFIT_OVERFLOW); + } +#if 1 + else if (((max_bits < s) && (q < 1.0)) || ((0.5*max_bits < s) && (q < 0.25))) { + result->val=pow(q,-s); + result->err=2.0*GSL_DBL_EPSILON*fabs(result->val); + return (PLFIT_SUCCESS); + } + else if ((0.5*max_bits < s) && (q < 1.0)) { + const double a0=pow(q,-s); + const double p1=pow(q/(1.0+q),s); + const double p2=pow(q/(2.0+q),s); + const double ans=a0*(1.0+p1+p2); + result->val=ans; + result->err=GSL_DBL_EPSILON*(2.0+0.5*s)*fabs(result->val); + return (PLFIT_SUCCESS); + } +#endif + else { // Euler-Maclaurin summation formula + const double qshift=HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+q; + const double inv_qshift=1.0/qshift; + const double sqr_inv_qshift=inv_qshift*inv_qshift; + const double inv_sm1=1.0/(s-1.0); + const double pmax=pow(qshift,-s); + double terms[HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN}; + double delta=NAN; + double tscp=s; + double scp=tscp; + double pcp=pmax*inv_qshift; + double ratio=scp*pcp; + size_t n=0; + size_t j=0; + double ans=0.0; + double mjr=NAN; + + for(j=0;jval=+ans; + result->err=2.0*((HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+1.0)*GSL_DBL_EPSILON*fabs(ans)+mjr); + return (PLFIT_SUCCESS); + } + } + + return (PLFIT_SUCCESS); } + +extern +double hsl_sf_hzeta(const double s, const double q) { + HSL_SF_EVAL_RESULT(hsl_sf_hzeta_e(s,q,&result)); } + +extern +int hsl_sf_hzeta_deriv_e(const double s, const double q, gsl_sf_result * result) { + + /* CHECK_POINTER(result) */ + + if ((s <= 1.0) || (q <= 0.0)) { + PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL); + } + else { + const double ln_hz_term0=-s*log(q); + if (ln_hz_term0 < GSL_LOG_DBL_MIN+1.0) { + PLFIT_ERROR("underflow", PLFIT_UNDRFLOW); + } + else if (GSL_LOG_DBL_MAX-1.0 < ln_hz_term0) { + PLFIT_ERROR("overflow", PLFIT_OVERFLOW); + } + else { // Euler-Maclaurin summation formula + const double qshift=HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+q; + const double inv_qshift=1.0/qshift; + const double sqr_inv_qshift=inv_qshift*inv_qshift; + const double inv_sm1=1.0/(s-1.0); + const double pmax=pow(qshift,-s); + const double lmax=log(qshift); + double terms[HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN}; + double delta=NAN; + double tscp=s; + double scp=tscp; + double pcp=pmax*inv_qshift; + double lcp=lmax-1.0/s; + double ratio=scp*pcp*lcp; + double qs=NAN; + size_t n=0; + size_t j=0; + double ans=0.0; + double mjr=NAN; + + for(j=0,qs=q;jval=-ans; + result->err=2.0*((HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+1.0)*GSL_DBL_EPSILON*fabs(ans)+mjr); + return (PLFIT_SUCCESS); + } + } + + return (PLFIT_SUCCESS); } + +extern +double hsl_sf_hzeta_deriv(const double s, const double q) { + HSL_SF_EVAL_RESULT(hsl_sf_hzeta_deriv_e(s,q,&result)); } + +extern +int hsl_sf_hzeta_deriv2_e(const double s, const double q, gsl_sf_result * result) { + + /* CHECK_POINTER(result) */ + + if ((s <= 1.0) || (q <= 0.0)) { + PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL); + } + else { + const double ln_hz_term0=-s*log(q); + if (ln_hz_term0 < GSL_LOG_DBL_MIN+1.0) { + PLFIT_ERROR("underflow", PLFIT_UNDRFLOW); + } + else if (GSL_LOG_DBL_MAX-1.0 < ln_hz_term0) { + PLFIT_ERROR("overflow", PLFIT_OVERFLOW); + } + else { // Euler-Maclaurin summation formula + const double qshift=HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+q; + const double inv_qshift=1.0/qshift; + const double sqr_inv_qshift=inv_qshift*inv_qshift; + const double inv_sm1=1.0/(s-1.0); + const double pmax=pow(qshift,-s); + const double lmax=log(qshift); + const double lmax_p_inv_sm1=lmax+inv_sm1; + const double sqr_inv_sm1=inv_sm1*inv_sm1; + const double sqr_lmax=lmax*lmax; + const double sqr_lmax_p_inv_sm1=lmax_p_inv_sm1*lmax_p_inv_sm1; + double terms[HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN}; + double delta=NAN; + double tscp=s; + double slcp=NAN; + double plcp=NAN; + double scp=tscp; + double pcp=pmax*inv_qshift; + double lcp=1.0/s-lmax; + double sqr_lcp=lmax*(lmax-2.0/s); + double ratio=scp*pcp*sqr_lcp; + double qs=NAN; + double lqs=NAN; + size_t n=0; + size_t j=0; + double ans=0.0; + double mjr=NAN; + + for(j=0,qs=q;jval=+ans; + result->err=2.0*((HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+1.0)*GSL_DBL_EPSILON*fabs(ans)+mjr); + return (PLFIT_SUCCESS); + } + } + + return (PLFIT_SUCCESS); } + +extern +double hsl_sf_hzeta_deriv2(const double s, const double q) { + HSL_SF_EVAL_RESULT(hsl_sf_hzeta_deriv2_e(s,q,&result)); } + +static inline +double hsl_sf_hZeta0_zed(const double s, const double q) { +#if 1 + const long double ld_q=(long double)(q); + const long double ld_s=(long double)(s); + const long double ld_log1prq=log1pl(1.0L/ld_q); + const long double ld_epsilon=expm1l(-ld_s*ld_log1prq); + const long double ld_z=ld_s+(ld_q+0.5L*ld_s+0.5L)*ld_epsilon; + const double z=(double)(ld_z); +#else + double z=s+(q+0.5*s+0.5)*expm1(-s*log1p(1.0/q)); +#endif + return (z); } + +// Z_{0}(s,a) = a^s \left(\frac{1}{2}+\frac{a}{s-1}\right)^{-1} \zeta(s,a) - 1 +// Z_{0}(s,a) = O\left(\frac{(s-1)s}{6a^{2}}\right) +static +int hsl_sf_hZeta0(const double s, const double q, double * value, double * abserror) { + const double criterion=ceil(10.0*s-q); + const size_t shift=(criterion<0.0)?0: + (criterionval=log1p(ln_hZeta0_value); + result->err=(2.0*GSL_DBL_EPSILON*ln_hz_coeff+hZeta0_abserror)/(1.0+ln_hZeta0_value); + } + + if (result_deriv) { + const double ld_hz_coeff2=1.0+inv_sm1*M_LOG2E; + const double ld_hz_coeff1=1.0+inv_qsm1*ld_hz_coeff2; + double hZeta1_value=NAN; + double hZeta1_abserror=NAN; + hsl_sf_hZeta1(s,2.0,M_LN2,&hZeta1_value,&hZeta1_abserror,NULL); + hZeta0_value*=hz_coeff1; + hZeta0_value+=hz_coeff0; + hZeta1_value+=1.0; + hZeta1_value*=-M_LN2*ld_hz_coeff1; + result_deriv->val=hZeta1_value/hZeta0_value; + result_deriv->err=2.0*GSL_DBL_EPSILON*fabs(result_deriv->val)+(hZeta0_abserror+hZeta1_abserror); + } + } + else { + const double ln_q=log(q); + double hZeta0_value=NAN; + double hZeta0_abserror=NAN; + hsl_sf_hZeta0(s,q,&hZeta0_value,&hZeta0_abserror); + if (result) { + const double ln_hz_term0=-s*ln_q; + const double ln_hz_term1=log(0.5+q/(s-1.0)); + result->val=ln_hz_term0+ln_hz_term1+log1p(hZeta0_value); + result->err=2.0*GSL_DBL_EPSILON*(fabs(ln_hz_term0)+fabs(ln_hz_term1))+hZeta0_abserror/(1.0+hZeta0_value); + } + if (result_deriv) { + double hZeta1_value=NAN; + double hZeta1_abserror=NAN; + double ld_hz_coeff1=NAN; + hsl_sf_hZeta1(s,q,ln_q,&hZeta1_value,&hZeta1_abserror,&ld_hz_coeff1); + result_deriv->val=-ln_q*ld_hz_coeff1*(1.0+hZeta1_value)/(1.0+hZeta0_value); + result_deriv->err=2.0*GSL_DBL_EPSILON*fabs(result_deriv->val)+(hZeta0_abserror+hZeta1_abserror); + } + } + + return (PLFIT_SUCCESS); } + +extern +double hsl_sf_lnhzeta_deriv_tuple(const double s, const double q, double * tuple0, double * tuple1) { + HSL_SF_EVAL_TUPLE_RESULT(hsl_sf_lnhzeta_deriv_tuple_e(s,q,&result0,&result1)); } + +extern +int hsl_sf_lnhzeta_e(const double s, const double q, gsl_sf_result * result) { + return (hsl_sf_lnhzeta_deriv_tuple_e(s,q,result,NULL)); } + +extern +double hsl_sf_lnhzeta(const double s, const double q) { + HSL_SF_EVAL_RESULT(hsl_sf_lnhzeta_e(s,q,&result)); } + +extern +int hsl_sf_lnhzeta_deriv_e(const double s, const double q, gsl_sf_result * result) { + return (hsl_sf_lnhzeta_deriv_tuple_e(s,q,NULL,result)); } + +extern +double hsl_sf_lnhzeta_deriv(const double s, const double q) { + HSL_SF_EVAL_RESULT(hsl_sf_lnhzeta_deriv_e(s,q,&result)); } + +// +// End of file `hsl/specfunc/hzeta.c'. diff --git a/igraph/src/igraph_fixed_vectorlist.c b/igraph/src/igraph_fixed_vectorlist.c --- a/igraph/src/igraph_fixed_vectorlist.c +++ b/igraph/src/igraph_fixed_vectorlist.c @@ -50,7 +50,7 @@ } IGRAPH_FINALLY(igraph_free, l->vecs); IGRAPH_CHECK(igraph_vector_ptr_init(&l->v, size)); - IGRAPH_FINALLY(igraph_fixed_vectorlist_destroy, &l->v); + IGRAPH_FINALLY(igraph_vector_ptr_destroy, &l->v); IGRAPH_VECTOR_INIT_FINALLY(&sizes, size); for (i = 0; i < no; i++) { diff --git a/igraph/src/igraph_hashtable.c b/igraph/src/igraph_hashtable.c --- a/igraph/src/igraph_hashtable.c +++ b/igraph/src/igraph_hashtable.c @@ -32,7 +32,7 @@ IGRAPH_CHECK(igraph_trie_init(&ht->keys, 1)); IGRAPH_FINALLY(igraph_trie_destroy, &ht->keys); IGRAPH_CHECK(igraph_strvector_init(&ht->elements, 0)); - IGRAPH_FINALLY(igraph_trie_destroy, &ht->elements); + IGRAPH_FINALLY(igraph_strvector_destroy, &ht->elements); IGRAPH_CHECK(igraph_strvector_init(&ht->defaults, 0)); IGRAPH_FINALLY_CLEAN(2); @@ -87,7 +87,7 @@ if (tmp == 0) { IGRAPH_ERROR("cannot add element to hash table", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, tmp); + IGRAPH_FINALLY(igraph_free, tmp); strncpy(tmp, elem, elemlen); tmp[elemlen] = '\0'; diff --git a/igraph/src/igraph_hrg.cc b/igraph/src/igraph_hrg.cc --- a/igraph/src/igraph_hrg.cc +++ b/igraph/src/igraph_hrg.cc @@ -82,7 +82,7 @@ }; } -int markovChainMonteCarlo(dendro *d, unsigned int period, +static int markovChainMonteCarlo(dendro *d, unsigned int period, igraph_hrg_t *hrg) { igraph_real_t bestL = d->getLikelihood(); @@ -121,7 +121,7 @@ return 0; } -int markovChainMonteCarlo2(dendro *d, int num_samples) { +static int markovChainMonteCarlo2(dendro *d, int num_samples) { bool flag_taken; double dL, ptest = 1.0 / (50.0 * (double)(d->g->numNodes())); int sample_num = 0, t = 1, thresh = 200 * d->g->numNodes(); @@ -150,7 +150,7 @@ return 0; } -int MCMCEquilibrium_Find(dendro *d, igraph_hrg_t *hrg) { +static int MCMCEquilibrium_Find(dendro *d, igraph_hrg_t *hrg) { // We want to run the MCMC until we've found equilibrium; we // use the heuristic of the average log-likelihood (which is @@ -187,8 +187,8 @@ return 0; } -int igraph_i_hrg_getgraph(const igraph_t *igraph, - dendro *d) { +static int igraph_i_hrg_getgraph(const igraph_t *igraph, + dendro *d) { int no_of_nodes = igraph_vcount(igraph); int no_of_edges = igraph_ecount(igraph); @@ -217,9 +217,9 @@ return 0; } -int igraph_i_hrg_getsimplegraph(const igraph_t *igraph, - dendro *d, simpleGraph **sg, - int num_bins) { +static int igraph_i_hrg_getsimplegraph(const igraph_t *igraph, + dendro *d, simpleGraph **sg, + int num_bins) { int no_of_nodes = igraph_vcount(igraph); int no_of_edges = igraph_ecount(igraph); @@ -448,7 +448,7 @@ int igraph_hrg_sample(const igraph_t *input_graph, igraph_t *sample, igraph_vector_ptr_t *samples, - int no_samples, + igraph_integer_t no_samples, igraph_hrg_t *hrg, igraph_bool_t start) { @@ -693,7 +693,7 @@ return 0; } -int MCMCEquilibrium_Sample(dendro *d, int num_samples) { +static int MCMCEquilibrium_Sample(dendro *d, int num_samples) { // Because moves in the dendrogram space are chosen (Monte // Carlo) so that we sample dendrograms with probability @@ -725,7 +725,7 @@ return 0; } -int QsortPartition (pblock* array, int left, int right, int index) { +static int QsortPartition (pblock* array, int left, int right, int index) { pblock p_value, temp; p_value.L = array[index].L; p_value.i = array[index].i; @@ -772,7 +772,7 @@ return stored; } -void QsortMain (pblock* array, int left, int right) { +static void QsortMain (pblock* array, int left, int right) { if (right > left) { int pivot = left; int part = QsortPartition(array, left, right, pivot); @@ -782,7 +782,7 @@ return; } -int rankCandidatesByProbability(simpleGraph *sg, dendro *d, +static int rankCandidatesByProbability(simpleGraph *sg, dendro *d, pblock *br_list, int mk) { int mkk = 0; int n = sg->getNumNodes(); @@ -804,7 +804,7 @@ return 0; } -int recordPredictions(pblock *br_list, igraph_vector_t *edges, +static int recordPredictions(pblock *br_list, igraph_vector_t *edges, igraph_vector_t *prob, int mk) { IGRAPH_CHECK(igraph_vector_resize(edges, mk * 2)); diff --git a/igraph/src/igraph_hrg_types.cc b/igraph/src/igraph_hrg_types.cc --- a/igraph/src/igraph_hrg_types.cc +++ b/igraph/src/igraph_hrg_types.cc @@ -41,6 +41,7 @@ #include "igraph_constructors.h" #include "igraph_random.h" +using namespace std; using namespace fitHRG; // ******** Red-Black Tree Methods *************************************** diff --git a/igraph/src/igraph_psumtree.c b/igraph/src/igraph_psumtree.c --- a/igraph/src/igraph_psumtree.c +++ b/igraph/src/igraph_psumtree.c @@ -31,7 +31,7 @@ #include #include -double igraph_i_log2(double f) { +static double igraph_i_log2(double f) { return log(f) / log(2.0); } diff --git a/igraph/src/igraph_strvector.c b/igraph/src/igraph_strvector.c --- a/igraph/src/igraph_strvector.c +++ b/igraph/src/igraph_strvector.c @@ -24,7 +24,6 @@ #include "igraph_types.h" #include "igraph_strvector.h" #include "igraph_memory.h" -#include "igraph_random.h" #include "igraph_error.h" #include "config.h" diff --git a/igraph/src/igraph_trie.c b/igraph/src/igraph_trie.c --- a/igraph/src/igraph_trie.c +++ b/igraph/src/igraph_trie.c @@ -39,7 +39,7 @@ * igraph_vector_ptr_init() and igraph_vector_init() might be returned. */ -int igraph_i_trie_init_node(igraph_trie_node_t *t) { +static int igraph_i_trie_init_node(igraph_trie_node_t *t) { IGRAPH_STRVECTOR_INIT_FINALLY(&t->strs, 0); IGRAPH_VECTOR_PTR_INIT_FINALLY(&t->children, 0); IGRAPH_VECTOR_INIT_FINALLY(&t->values, 0); @@ -47,7 +47,7 @@ return 0; } -void igraph_i_trie_destroy_node(igraph_trie_node_t *t, igraph_bool_t sfree); +static void igraph_i_trie_destroy_node(igraph_trie_node_t *t); /** * \ingroup igraphtrie @@ -59,8 +59,8 @@ int igraph_trie_init(igraph_trie_t *t, igraph_bool_t storekeys) { t->maxvalue = -1; t->storekeys = storekeys; - IGRAPH_CHECK(igraph_i_trie_init_node( (igraph_trie_node_t *)t )); - IGRAPH_FINALLY(igraph_i_trie_destroy_node, t); + IGRAPH_CHECK(igraph_i_trie_init_node( (igraph_trie_node_t *) t )); + IGRAPH_FINALLY(igraph_i_trie_destroy_node, (igraph_trie_node_t *) t ); if (storekeys) { IGRAPH_CHECK(igraph_strvector_init(&t->keys, 0)); } @@ -74,13 +74,13 @@ * \brief Destroys a node of a trie (not to be called directly). */ -void igraph_i_trie_destroy_node(igraph_trie_node_t *t, igraph_bool_t sfree) { +static void igraph_i_trie_destroy_node_helper(igraph_trie_node_t *t, igraph_bool_t sfree) { long int i; igraph_strvector_destroy(&t->strs); for (i = 0; i < igraph_vector_ptr_size(&t->children); i++) { igraph_trie_node_t *child = VECTOR(t->children)[i]; if (child != 0) { - igraph_i_trie_destroy_node(child, 1); + igraph_i_trie_destroy_node_helper(child, 1); } } igraph_vector_ptr_destroy(&t->children); @@ -90,6 +90,10 @@ } } +static void igraph_i_trie_destroy_node(igraph_trie_node_t *t) { + igraph_i_trie_destroy_node_helper(t, 0); +} + /** * \ingroup igraphtrie * \brief Destroys a trie (frees allocated memory). @@ -99,7 +103,7 @@ if (t->storekeys) { igraph_strvector_destroy(&t->keys); } - igraph_i_trie_destroy_node( (igraph_trie_node_t*) t, 0); + igraph_i_trie_destroy_node( (igraph_trie_node_t*) t); } @@ -108,7 +112,7 @@ * \brief Internal helping function for igraph_trie_t */ -long int igraph_i_strdiff(const char *str, const char *key) { +static long int igraph_i_strdiff(const char *str, const char *key) { long int diff = 0; while (key[diff] != '\0' && str[diff] != '\0' && str[diff] == key[diff]) { @@ -210,9 +214,9 @@ IGRAPH_ERROR("cannot add to trie", IGRAPH_ENOMEM); } str2[diff] = '\0'; - IGRAPH_FINALLY(free, str2); + IGRAPH_FINALLY(igraph_free, str2); IGRAPH_CHECK(igraph_strvector_set(&t->strs, i, str2)); - free(str2); + igraph_Free(str2); IGRAPH_FINALLY_CLEAN(4); VECTOR(t->values)[i] = newvalue; @@ -246,9 +250,9 @@ IGRAPH_ERROR("cannot add to trie", IGRAPH_ENOMEM); } str2[diff] = '\0'; - IGRAPH_FINALLY(free, str2); + IGRAPH_FINALLY(igraph_free, str2); IGRAPH_CHECK(igraph_strvector_set(&t->strs, i, str2)); - free(str2); + igraph_Free(str2); IGRAPH_FINALLY_CLEAN(4); VECTOR(t->values)[i] = -1; @@ -345,7 +349,7 @@ strncpy(tmp, key, length); tmp[length] = '\0'; - IGRAPH_FINALLY(free, tmp); + IGRAPH_FINALLY(igraph_free, tmp); IGRAPH_CHECK(igraph_trie_get(t, tmp, id)); igraph_Free(tmp); IGRAPH_FINALLY_CLEAN(1); diff --git a/igraph/src/infomap.cc b/igraph/src/infomap.cc --- a/igraph/src/infomap.cc +++ b/igraph/src/infomap.cc @@ -318,5 +318,8 @@ delete fgraph; IGRAPH_FINALLY_CLEAN(1); + + IGRAPH_CHECK(igraph_reindex_membership(membership, 0, 0)); + return IGRAPH_SUCCESS; } diff --git a/igraph/src/infomap_FlowGraph.cc b/igraph/src/infomap_FlowGraph.cc --- a/igraph/src/infomap_FlowGraph.cc +++ b/igraph/src/infomap_FlowGraph.cc @@ -26,6 +26,8 @@ #define plogp( x ) ( (x) > 0.0 ? (x)*log(x) : 0.0 ) +using namespace std; + void FlowGraph::init(int n, const igraph_vector_t *v_weights) { alpha = 0.15; beta = 1.0 - alpha; diff --git a/igraph/src/infomap_Greedy.cc b/igraph/src/infomap_Greedy.cc --- a/igraph/src/infomap_Greedy.cc +++ b/igraph/src/infomap_Greedy.cc @@ -26,6 +26,8 @@ #include #define plogp( x ) ( (x) > 0.0 ? (x)*log(x) : 0.0 ) +using namespace std; + Greedy::Greedy(FlowGraph * fgraph) { graph = fgraph; Nnode = graph->Nnode; diff --git a/igraph/src/infomap_Node.cc b/igraph/src/infomap_Node.cc --- a/igraph/src/infomap_Node.cc +++ b/igraph/src/infomap_Node.cc @@ -24,6 +24,8 @@ #include "infomap_Node.h" +using namespace std; + Node::Node() { exit = 0.0; size = 0.0; diff --git a/igraph/src/interrupt.c b/igraph/src/interrupt.c --- a/igraph/src/interrupt.c +++ b/igraph/src/interrupt.c @@ -24,10 +24,6 @@ #include "igraph_interrupt.h" #include "config.h" -#include -#include -#include - IGRAPH_THREAD_LOCAL igraph_interruption_handler_t *igraph_i_interruption_handler = 0; diff --git a/igraph/src/iterators.c b/igraph/src/iterators.c --- a/igraph/src/iterators.c +++ b/igraph/src/iterators.c @@ -23,7 +23,6 @@ #include "igraph_iterators.h" #include "igraph_memory.h" -#include "igraph_random.h" #include "igraph_interface.h" #include "config.h" @@ -878,7 +877,7 @@ * \function igraph_ess_all * \brief Edge set, all edges (immediate version) * - * The immediate version of the all-vertices selector. + * The immediate version of the all-edges selector. * * \param order Constant giving the order of the edges in the edge * selector. See \ref igraph_es_all() for the possible values. @@ -1430,12 +1429,12 @@ return es->type; } -int igraph_i_es_pairs_size(const igraph_t *graph, - const igraph_es_t *es, igraph_integer_t *result); -int igraph_i_es_path_size(const igraph_t *graph, - const igraph_es_t *es, igraph_integer_t *result); -int igraph_i_es_multipairs_size(const igraph_t *graph, - const igraph_es_t *es, igraph_integer_t *result); +static int igraph_i_es_pairs_size(const igraph_t *graph, + const igraph_es_t *es, igraph_integer_t *result); +static int igraph_i_es_path_size(const igraph_t *graph, + const igraph_es_t *es, igraph_integer_t *result); +static int igraph_i_es_multipairs_size(const igraph_t *graph, + const igraph_es_t *es, igraph_integer_t *result); /** * \function igraph_es_size @@ -1514,8 +1513,8 @@ return 0; } -int igraph_i_es_pairs_size(const igraph_t *graph, - const igraph_es_t *es, igraph_integer_t *result) { +static int igraph_i_es_pairs_size(const igraph_t *graph, + const igraph_es_t *es, igraph_integer_t *result) { long int n = igraph_vector_size(es->data.path.ptr); long int no_of_nodes = igraph_vcount(graph); long int i; @@ -1542,8 +1541,8 @@ return 0; } -int igraph_i_es_path_size(const igraph_t *graph, - const igraph_es_t *es, igraph_integer_t *result) { +static int igraph_i_es_path_size(const igraph_t *graph, + const igraph_es_t *es, igraph_integer_t *result) { long int n = igraph_vector_size(es->data.path.ptr); long int no_of_nodes = igraph_vcount(graph); long int i; @@ -1569,27 +1568,27 @@ return 0; } -int igraph_i_es_multipairs_size(const igraph_t *graph, - const igraph_es_t *es, igraph_integer_t *result) { +static int igraph_i_es_multipairs_size(const igraph_t *graph, + const igraph_es_t *es, igraph_integer_t *result) { IGRAPH_UNUSED(graph); IGRAPH_UNUSED(es); IGRAPH_UNUSED(result); IGRAPH_ERROR("Cannot calculate edge selector length", IGRAPH_UNIMPLEMENTED); } /**************************************************/ -int igraph_i_eit_create_allfromto(const igraph_t *graph, - igraph_eit_t *eit, - igraph_neimode_t mode); -int igraph_i_eit_pairs(const igraph_t *graph, - igraph_es_t es, igraph_eit_t *eit); -int igraph_i_eit_multipairs(const igraph_t *graph, - igraph_es_t es, igraph_eit_t *eit); -int igraph_i_eit_path(const igraph_t *graph, - igraph_es_t es, igraph_eit_t *eit); +static int igraph_i_eit_create_allfromto(const igraph_t *graph, + igraph_eit_t *eit, + igraph_neimode_t mode); +static int igraph_i_eit_pairs(const igraph_t *graph, + igraph_es_t es, igraph_eit_t *eit); +static int igraph_i_eit_multipairs(const igraph_t *graph, + igraph_es_t es, igraph_eit_t *eit); +static int igraph_i_eit_path(const igraph_t *graph, + igraph_es_t es, igraph_eit_t *eit); -int igraph_i_eit_create_allfromto(const igraph_t *graph, - igraph_eit_t *eit, - igraph_neimode_t mode) { +static int igraph_i_eit_create_allfromto(const igraph_t *graph, + igraph_eit_t *eit, + igraph_neimode_t mode) { igraph_vector_t *vec; long int no_of_nodes = igraph_vcount(graph); long int i; @@ -1647,8 +1646,8 @@ return 0; } -int igraph_i_eit_pairs(const igraph_t *graph, - igraph_es_t es, igraph_eit_t *eit) { +static int igraph_i_eit_pairs(const igraph_t *graph, + igraph_es_t es, igraph_eit_t *eit) { long int n = igraph_vector_size(es.data.path.ptr); long int no_of_nodes = igraph_vcount(graph); long int i; @@ -1686,8 +1685,8 @@ return 0; } -int igraph_i_eit_multipairs(const igraph_t *graph, - igraph_es_t es, igraph_eit_t *eit) { +static int igraph_i_eit_multipairs(const igraph_t *graph, + igraph_es_t es, igraph_eit_t *eit) { long int n = igraph_vector_size(es.data.path.ptr); long int no_of_nodes = igraph_vcount(graph); @@ -1718,8 +1717,8 @@ return 0; } -int igraph_i_eit_path(const igraph_t *graph, - igraph_es_t es, igraph_eit_t *eit) { +static int igraph_i_eit_path(const igraph_t *graph, + igraph_es_t es, igraph_eit_t *eit) { long int n = igraph_vector_size(es.data.path.ptr); long int no_of_nodes = igraph_vcount(graph); long int i, len; diff --git a/igraph/src/kolmogorov.c b/igraph/src/kolmogorov.c --- a/igraph/src/kolmogorov.c +++ b/igraph/src/kolmogorov.c @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. diff --git a/igraph/src/lad.c b/igraph/src/lad.c --- a/igraph/src/lad.c +++ b/igraph/src/lad.c @@ -46,13 +46,7 @@ -- Tamas Nepusz, 11 July 2013 */ -#include -#include -#include -#include -#include -#include - +#include "igraph_topology.h" #include "igraph_interface.h" #include "igraph_adjlist.h" #include "igraph_vector.h" @@ -61,6 +55,12 @@ #include "igraph_matrix.h" #include "igraph_interrupt_internal.h" +#include +#include +#include +#include + + /* define boolean type as char */ #define true 1 #define false 0 @@ -99,7 +99,7 @@ igraph_matrix_char_t isEdge; } Tgraph; -int igraph_i_lad_createGraph(const igraph_t *igraph, Tgraph* graph) { +static int igraph_i_lad_createGraph(const igraph_t *igraph, Tgraph* graph) { long int i, j, n; long int no_of_nodes = igraph_vcount(igraph); igraph_vector_int_t *neis; @@ -112,8 +112,7 @@ IGRAPH_CHECK(igraph_adjlist_init(igraph, &graph->succ, IGRAPH_OUT)); IGRAPH_FINALLY(igraph_adjlist_destroy, &graph->succ); - IGRAPH_CHECK(igraph_matrix_char_init(&graph->isEdge, - no_of_nodes, no_of_nodes)); + IGRAPH_CHECK(igraph_matrix_char_init(&graph->isEdge, no_of_nodes, no_of_nodes)); IGRAPH_FINALLY(igraph_matrix_char_destroy, &graph->isEdge); for (i = 0; i < no_of_nodes; i++) { @@ -129,9 +128,18 @@ } } - return 0; + IGRAPH_FINALLY_CLEAN(3); + + return IGRAPH_SUCCESS; } +static void igraph_i_lad_destroyGraph(Tgraph *graph) { + igraph_matrix_char_destroy(&graph->isEdge); + igraph_adjlist_destroy(&graph->succ); + igraph_vector_destroy(&graph->nbSucc); +} + + /* ---------------------------------------------------------*/ /* Coming from domains.c */ /* ---------------------------------------------------------*/ @@ -169,19 +177,19 @@ or -1 if v is not matched */ } Tdomain; -bool igraph_i_lad_toFilterEmpty(Tdomain* D) { +static bool igraph_i_lad_toFilterEmpty(Tdomain* D) { /* return true if there is no more nodes in toFilter */ return (D->nextOutToFilter < 0); } -void igraph_i_lad_resetToFilter(Tdomain *D) { +static void igraph_i_lad_resetToFilter(Tdomain *D) { /* empty to filter and unmark the vertices that are marked to be filtered */ igraph_vector_char_null(&D->markedToFilter); D->nextOutToFilter = -1; } -int igraph_i_lad_nextToFilter(Tdomain* D, int size) { +static int igraph_i_lad_nextToFilter(Tdomain* D, int size) { /* precondition: emptyToFilter = false remove a node from toFilter (FIFO) unmark this node and return it */ @@ -198,7 +206,7 @@ return u; } -void igraph_i_lad_addToFilter(int u, Tdomain* D, int size) { +static void igraph_i_lad_addToFilter(int u, Tdomain* D, int size) { /* if u is not marked, then add it to toFilter and mark it */ if (VECTOR(D->markedToFilter)[u]) { return; @@ -215,13 +223,13 @@ VECTOR(D->toFilter)[D->lastInToFilter] = u; } -bool igraph_i_lad_isInD(int u, int v, Tdomain* D) { +static bool igraph_i_lad_isInD(int u, int v, Tdomain* D) { /* returns true if v belongs to D(u); false otherwise */ return (MATRIX(D->posInVal, u, v) < VECTOR(D->firstVal)[u] + VECTOR(D->nbVal)[u]); } -int igraph_i_lad_augmentingPath(int u, Tdomain* D, int nbV, bool* result) { +static int igraph_i_lad_augmentingPath(int u, Tdomain* D, int nbV, bool* result) { /* return true if there exists an augmenting path starting from u and ending on a free vertex v in the bipartite directed graph G=(U, V, E) such that U=pattern nodes, V=target nodes, and @@ -289,7 +297,7 @@ return 0; } -int igraph_i_lad_removeAllValuesButOne(int u, int v, Tdomain* D, Tgraph* Gp, +static int igraph_i_lad_removeAllValuesButOne(int u, int v, Tdomain* D, Tgraph* Gp, Tgraph* Gt, bool* result) { /* remove all values but v from D(u) and add all successors of u in toFilter return false if an inconsistency is detected wrt to @@ -323,7 +331,7 @@ } -int igraph_i_lad_removeValue(int u, int v, Tdomain* D, Tgraph* Gp, +static int igraph_i_lad_removeValue(int u, int v, Tdomain* D, Tgraph* Gp, Tgraph* Gt, bool* result) { /* remove v from D(u) and add all successors of u in toFilter return false if an inconsistency is detected wrt global all diff */ @@ -358,7 +366,7 @@ } -int igraph_i_lad_matchVertices(int nb, igraph_vector_int_t* toBeMatched, +static int igraph_i_lad_matchVertices(int nb, igraph_vector_int_t* toBeMatched, bool induced, Tdomain* D, Tgraph* Gp, Tgraph* Gt, int *invalid) { /* for each u in toBeMatched[0..nb-1], match u to @@ -439,7 +447,7 @@ } -bool igraph_i_lad_matchVertex(int u, bool induced, Tdomain* D, Tgraph* Gp, +static bool igraph_i_lad_matchVertex(int u, bool induced, Tdomain* D, Tgraph* Gp, Tgraph *Gt) { int invalid; /* match u to D->val[D->firstVal[u]] and filter domains of other non @@ -461,13 +469,13 @@ } -int igraph_i_lad_qcompare (void const *a, void const *b) { +static int igraph_i_lad_qcompare (void const *a, void const *b) { /* function used by the qsort function */ int pa = *((int*)a) - *((int*)b); return pa; } -bool igraph_i_lad_compare(int size_mu, int* mu, int size_mv, int* mv) { +static bool igraph_i_lad_compare(int size_mu, int* mu, int size_mv, int* mv) { /* return true if for every element u of mu there exists a different element v of mv such that u <= v; return false otherwise */ @@ -484,9 +492,9 @@ return true; } -int igraph_i_lad_initDomains(bool initialDomains, - igraph_vector_ptr_t *domains, Tdomain* D, - Tgraph* Gp, Tgraph* Gt, int *empty) { +static int igraph_i_lad_initDomains(bool initialDomains, + const igraph_vector_ptr_t *domains, Tdomain *D, + const Tgraph *Gp, const Tgraph *Gt, int *empty) { /* for every pattern node u, initialize D(u) with every vertex v such that for every neighbor u' of u there exists a different neighbor v' of v such that degree(u) <= degree(v) @@ -498,8 +506,6 @@ int *mu, *mv; int matchingSize, u, v, i, j; igraph_vector_t *vec; - igraph_vector_t *Gp_uneis; - igraph_vector_t *Gt_vneis; val = igraph_Calloc(Gp->nbVertices * Gt->nbVertices, int); if (val == 0) { @@ -512,16 +518,13 @@ IGRAPH_ERROR("cannot allocated 'dom' array in igraph_i_lad_initDomains", IGRAPH_ENOMEM); } - IGRAPH_CHECK(igraph_vector_int_init(&D->globalMatchingP, Gp->nbVertices)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &D->globalMatchingP); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->globalMatchingP, Gp->nbVertices); igraph_vector_int_fill(&D->globalMatchingP, -1L); - IGRAPH_CHECK(igraph_vector_int_init(&D->globalMatchingT, Gt->nbVertices)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &D->globalMatchingT); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->globalMatchingT, Gt->nbVertices); igraph_vector_int_fill(&D->globalMatchingT, -1L); - IGRAPH_CHECK(igraph_vector_int_init(&D->nbVal, Gp->nbVertices)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &D->nbVal); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->nbVal, Gp->nbVertices); IGRAPH_CHECK(igraph_vector_int_init(&D->firstVal, Gp->nbVertices)); IGRAPH_FINALLY(igraph_vector_int_destroy, &D->firstVal); @@ -537,8 +540,7 @@ IGRAPH_CHECK(igraph_vector_char_init(&D->markedToFilter, Gp->nbVertices)); IGRAPH_FINALLY(igraph_vector_char_destroy, &D->markedToFilter); - IGRAPH_CHECK(igraph_vector_int_init(&D->toFilter, Gp->nbVertices)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &D->toFilter); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->toFilter, Gp->nbVertices); D->valSize = 0; matchingSize = 0; @@ -603,30 +605,55 @@ } if (VECTOR(D->nbVal)[u] == 0) { *empty = 1; /* empty domain */ + igraph_free(val); igraph_free(dom); - return 0; + + /* On this branch, 'val' and 'matching' are unused. + * We init them anyway so that we can have a consistent destructor. */ + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->val, 0); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->matching, 0); + IGRAPH_FINALLY_CLEAN(10); + + return IGRAPH_SUCCESS; } } - IGRAPH_CHECK(igraph_vector_int_init(&D->val, D->valSize)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &D->val); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->val, D->valSize); for (i = 0; i < D->valSize; i++) { VECTOR(D->val)[i] = val[i]; } - IGRAPH_CHECK(igraph_vector_int_init(&D->matching, matchingSize)); - IGRAPH_FINALLY(igraph_vector_int_destroy, &D->matching); + IGRAPH_VECTOR_INT_INIT_FINALLY(&D->matching, matchingSize); igraph_vector_int_fill(&D->matching, -1); D->nextOutToFilter = 0; D->lastInToFilter = (int) (Gp->nbVertices - 1); + *empty = 0; igraph_free(val); igraph_free(dom); - return 0; + + IGRAPH_FINALLY_CLEAN(10); + + return IGRAPH_SUCCESS; } +static void igraph_i_lad_destroyDomains(Tdomain *D) { + igraph_vector_int_destroy(&D->globalMatchingP); + igraph_vector_int_destroy(&D->globalMatchingT); + igraph_vector_int_destroy(&D->nbVal); + igraph_vector_int_destroy(&D->firstVal); + igraph_matrix_int_destroy(&D->posInVal); + igraph_matrix_int_destroy(&D->firstMatch); + igraph_vector_char_destroy(&D->markedToFilter); + igraph_vector_int_destroy(&D->toFilter); + + igraph_vector_int_destroy(&D->val); + igraph_vector_int_destroy(&D->matching); +} + + /* ---------------------------------------------------------*/ /* Coming from allDiff.c */ /* ---------------------------------------------------------*/ @@ -637,14 +664,14 @@ #define toBeDeleted 3 #define deleted 4 -void igraph_i_lad_addToDelete(int u, int* list, int* nb, int* marked) { +static void igraph_i_lad_addToDelete(int u, int* list, int* nb, int* marked) { if (marked[u] < toBeDeleted) { list[(*nb)++] = u; marked[u] = toBeDeleted; } } -int igraph_i_lad_updateMatching(int sizeOfU, int sizeOfV, +static int igraph_i_lad_updateMatching(int sizeOfU, int sizeOfV, igraph_vector_int_t *degree, igraph_vector_int_t *firstAdj, igraph_vector_int_t *adj, @@ -897,7 +924,7 @@ return 0; } -void igraph_i_lad_DFS(int nbU, int nbV, int u, bool* marked, int* nbSucc, +static void igraph_i_lad_DFS(int nbU, int nbV, int u, bool* marked, int* nbSucc, int* succ, igraph_vector_int_t * matchedWithU, int* order, int* nb) { /* perform a depth first search, starting from u, in the bipartite @@ -925,7 +952,7 @@ order[*nb] = u; (*nb)--; } -int igraph_i_lad_SCC(int nbU, int nbV, int* numV, int* numU, +static int igraph_i_lad_SCC(int nbU, int nbV, int* numV, int* numU, int* nbSucc, int* succ, int* nbPred, int* pred, igraph_vector_int_t * matchedWithU, @@ -1000,7 +1027,7 @@ } -int igraph_i_lad_ensureGACallDiff(bool induced, Tgraph* Gp, Tgraph* Gt, +static int igraph_i_lad_ensureGACallDiff(bool induced, Tgraph* Gp, Tgraph* Gt, Tdomain* D, int *invalid) { /* precondition: D->globalMatchingP is an all different matching of the pattern vertices @@ -1127,7 +1154,7 @@ /* Coming from lad.c */ /* ---------------------------------------------------------*/ -int igraph_i_lad_checkLAD(int u, int v, Tdomain* D, Tgraph* Gp, Tgraph* Gt, +static int igraph_i_lad_checkLAD(int u, int v, Tdomain* D, Tgraph* Gp, Tgraph* Gt, bool *result) { /* return true if G_(u, v) has a adj(u)-covering matching; false otherwise */ @@ -1278,7 +1305,7 @@ /* Coming from main.c */ /* ---------------------------------------------------------*/ -int igraph_i_lad_filter(bool induced, Tdomain* D, Tgraph* Gp, Tgraph* Gt, +static int igraph_i_lad_filter(bool induced, Tdomain* D, Tgraph* Gp, Tgraph* Gt, bool *result) { /* filter domains of all vertices in D->toFilter wrt LAD and ensure GAC(allDiff) @@ -1327,7 +1354,7 @@ -int igraph_i_lad_solve(int timeLimit, bool firstSol, bool induced, +static int igraph_i_lad_solve(int timeLimit, bool firstSol, bool induced, Tdomain* D, Tgraph* Gp, Tgraph* Gt, int *invalid, igraph_bool_t *iso, igraph_vector_t *map, igraph_vector_ptr_t *maps, @@ -1575,14 +1602,18 @@ } IGRAPH_CHECK(igraph_i_lad_createGraph(pattern, &Gp)); + IGRAPH_FINALLY(igraph_i_lad_destroyGraph, &Gp); + IGRAPH_CHECK(igraph_i_lad_createGraph(target, &Gt)); + IGRAPH_FINALLY(igraph_i_lad_destroyGraph, &Gt); if (Gp.nbVertices > Gt.nbVertices) { goto exit3; } - IGRAPH_CHECK(igraph_i_lad_initDomains(initialDomains, domains, &D, &Gp, - &Gt, &invalidDomain)); + IGRAPH_CHECK(igraph_i_lad_initDomains(initialDomains, domains, &D, &Gp, &Gt, &invalidDomain)); + IGRAPH_FINALLY(igraph_i_lad_destroyDomains, &D); + if (invalidDomain) { goto exit2; } @@ -1634,32 +1665,16 @@ IGRAPH_FINALLY_CLEAN(1); exit: - - igraph_vector_int_destroy(&D.val); - igraph_vector_int_destroy(&D.matching); - IGRAPH_FINALLY_CLEAN(2); - exit2: - igraph_vector_int_destroy(&D.globalMatchingP); - igraph_vector_int_destroy(&D.globalMatchingT); - igraph_vector_int_destroy(&D.nbVal); - igraph_vector_int_destroy(&D.firstVal); - igraph_matrix_int_destroy(&D.posInVal); - igraph_matrix_int_destroy(&D.firstMatch); - igraph_vector_char_destroy(&D.markedToFilter); - igraph_vector_int_destroy(&D.toFilter); - IGRAPH_FINALLY_CLEAN(8); + igraph_i_lad_destroyDomains(&D); + IGRAPH_FINALLY_CLEAN(1); exit3: - igraph_matrix_char_destroy(&Gt.isEdge); - igraph_adjlist_destroy(&Gt.succ); - igraph_vector_destroy(&Gt.nbSucc); - igraph_matrix_char_destroy(&Gp.isEdge); - igraph_adjlist_destroy(&Gp.succ); - igraph_vector_destroy(&Gp.nbSucc); - IGRAPH_FINALLY_CLEAN(6); + igraph_i_lad_destroyGraph(&Gt); + igraph_i_lad_destroyGraph(&Gp); + IGRAPH_FINALLY_CLEAN(2); return 0; } diff --git a/igraph/src/lapack.c b/igraph/src/lapack.c --- a/igraph/src/lapack.c +++ b/igraph/src/lapack.c @@ -21,6 +21,7 @@ */ +#include "igraph_blas.h" #include "igraph_lapack.h" #include "igraph_lapack_internal.h" @@ -615,7 +616,7 @@ * * * Optionally also, it computes a balancing transformation to improve - * the conditioning of the eigenvalues and eigenvectors (\p ilo, \pihi, + * the conditioning of the eigenvalues and eigenvectors (\p ilo, \p ihi, * \p scale, and \p abnrm), reciprocal condition numbers for the * eigenvalues (\p rconde), and reciprocal condition numbers for the * right eigenvectors (\p rcondv). @@ -625,8 +626,8 @@ * A * v(j) = lambda(j) * v(j) * where lambda(j) is its eigenvalue. * The left eigenvector u(j) of A satisfies - * u(j)**H * A = lambda(j) * u(j)**H - * where u(j)**H denotes the conjugate transpose of u(j). + * u(j)^H * A = lambda(j) * u(j)^H + * where u(j)^H denotes the conjugate transpose of u(j). * * * The computed eigenvectors are normalized to have Euclidean norm @@ -635,7 +636,7 @@ * * Balancing a matrix means permuting the rows and columns to make it * more nearly upper triangular, and applying a diagonal similarity - * transformation D * A * D**(-1), where D is a diagonal matrix, to + * transformation D * A * D^(-1), where D is a diagonal matrix, to * make its rows and columns closer in norm and the condition numbers * of its eigenvalues and eigenvectors smaller. The computed * reciprocal condition numbers correspond to the balanced matrix. @@ -654,7 +655,7 @@ * triangular. Do not diagonally scale. * \cli IGRAPH_LAPACK_DGEEVX_BALANCE_SCALE * diagonally scale the matrix, i.e. replace A by - * D*A*D**(-1), where D is a diagonal matrix, chosen to make + * D*A*D^(-1), where D is a diagonal matrix, chosen to make * the rows and columns of A more equal in norm. Do not * permute. * \cli IGRAPH_LAPACK_DGEEVX_BALANCE_BOTH @@ -683,7 +684,7 @@ * J=1,...,ilo-1 or I=ihi+1,...,N. * \param scale Pointer to an initialized vector or a NULL pointer. If * not a NULL pointer, then details of the permutations and scaling - * factors applied when balancing \param A, are stored here. + * factors applied when balancing \p A, are stored here. * If P(j) is the index of the row and column * interchanged with row and column j, and D(j) is the scaling * factor applied to row and column j, then @@ -938,17 +939,10 @@ int igraph_lapack_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2, igraph_real_t *res) { - - int n = igraph_vector_size(v1); - int one = 1; - - if (igraph_vector_size(v2) != n) { - IGRAPH_ERROR("Dot product of vectors with different dimensions", - IGRAPH_EINVAL); - } - - *res = igraphddot_(&n, VECTOR(*v1), &one, VECTOR(*v2), &one); - - return 0; + IGRAPH_WARNING( + "igraph_lapack_ddot() is a misnomer; use igraph_blas_ddot() instead. " + "igraph_lapack_ddot() will be removed in igraph 0.9.0." + ); + return igraph_blas_ddot(v1, v2, res); } diff --git a/igraph/src/layout.c b/igraph/src/layout.c --- a/igraph/src/layout.c +++ b/igraph/src/layout.c @@ -44,7 +44,6 @@ #include "config.h" #include #include "igraph_math.h" -#include /* FIXME */ /** @@ -380,9 +379,7 @@ return 0; } -void igraph_i_norm2d(igraph_real_t *x, igraph_real_t *y); - -void igraph_i_norm2d(igraph_real_t *x, igraph_real_t *y) { +static void igraph_i_norm2d(igraph_real_t *x, igraph_real_t *y) { igraph_real_t len = sqrt((*x) * (*x) + (*y) * (*y)); if (len != 0) { *x /= len; @@ -696,13 +693,7 @@ } -int igraph_i_layout_reingold_tilford_unreachable( - const igraph_t *graph, - igraph_neimode_t mode, - long int real_root, - long int no_of_nodes, - igraph_vector_t *pnewedges); -int igraph_i_layout_reingold_tilford_unreachable( +static int igraph_i_layout_reingold_tilford_unreachable( const igraph_t *graph, igraph_neimode_t mode, long int real_root, @@ -782,24 +773,27 @@ of the subtree rooted at this node */ long int right_contour; /* Next right node of the contour of the subtree rooted at this node */ - igraph_real_t offset_follow_lc; /* X offset when following the left contour */ - igraph_real_t offset_follow_rc; /* X offset when following the right contour */ + igraph_real_t offset_to_left_contour; /* X offset when following the left contour */ + igraph_real_t offset_to_right_contour; /* X offset when following the right contour */ + long int left_extreme; /* Leftmost node on the deepest layer of the subtree rooted at this node */ + long int right_extreme; /* Rightmost node on the deepest layer of the subtree rooted at this node */ + igraph_real_t offset_to_left_extreme; /* X offset when jumping to the left extreme node */ + igraph_real_t offset_to_right_extreme; /* X offset when jumping to the right extreme node */ }; -int igraph_i_layout_reingold_tilford_postorder(struct igraph_i_reingold_tilford_vertex *vdata, - long int node, long int vcount); -int igraph_i_layout_reingold_tilford_calc_coords(struct igraph_i_reingold_tilford_vertex *vdata, - igraph_matrix_t *res, long int node, - long int vcount, igraph_real_t xpos); +static int igraph_i_layout_reingold_tilford_postorder(struct igraph_i_reingold_tilford_vertex *vdata, + long int node, long int vcount); +static int igraph_i_layout_reingold_tilford_calc_coords(struct igraph_i_reingold_tilford_vertex *vdata, + igraph_matrix_t *res, long int node, + long int vcount, igraph_real_t xpos); -int igraph_i_layout_reingold_tilford(const igraph_t *graph, - igraph_matrix_t *res, - igraph_neimode_t mode, - long int root); -int igraph_i_layout_reingold_tilford(const igraph_t *graph, - igraph_matrix_t *res, - igraph_neimode_t mode, - long int root) { +/* uncomment the next line for debugging the Reingold-Tilford layout */ +/* #define LAYOUT_RT_DEBUG 1 */ + +static int igraph_i_layout_reingold_tilford(const igraph_t *graph, + igraph_matrix_t *res, + igraph_neimode_t mode, + long int root) { long int no_of_nodes = igraph_vcount(graph); long int i, n, j; igraph_dqueue_t q = IGRAPH_DQUEUE_NULL; @@ -825,8 +819,12 @@ vdata[i].offset = 0.0; vdata[i].left_contour = -1; vdata[i].right_contour = -1; - vdata[i].offset_follow_lc = 0.0; - vdata[i].offset_follow_rc = 0.0; + vdata[i].offset_to_left_contour = 0.0; + vdata[i].offset_to_right_contour = 0.0; + vdata[i].left_extreme = i; + vdata[i].right_extreme = i; + vdata[i].offset_to_left_extreme = 0.0; + vdata[i].offset_to_right_extreme = 0.0; } vdata[root].parent = root; vdata[root].level = 0; @@ -868,10 +866,29 @@ IGRAPH_PROGRESS("Reingold-Tilford tree layout", 100.0, NULL); +#ifdef LAYOUT_RT_DEBUG + for (i = 0; i < no_of_nodes; i++) { + printf( + "%3ld: offset = %.2f, contours = [%ld, %ld], contour offsets = [%.2f, %.2f]\n", + i, vdata[i].offset, + vdata[i].left_contour, vdata[i].right_contour, + vdata[i].offset_to_left_contour, vdata[i].offset_to_right_contour + ); + if (vdata[i].left_extreme != i || vdata[i].right_extreme != i) { + printf( + " extrema = [%ld, %ld], offsets to extrema = [%.2f, %.2f]\n", + vdata[i].left_extreme, vdata[i].right_extreme, + vdata[i].offset_to_left_extreme, vdata[i].offset_to_right_extreme + ); + } + } +#endif + return 0; } -int igraph_i_layout_reingold_tilford_calc_coords(struct igraph_i_reingold_tilford_vertex *vdata, +static int igraph_i_layout_reingold_tilford_calc_coords( + struct igraph_i_reingold_tilford_vertex *vdata, igraph_matrix_t *res, long int node, long int vcount, igraph_real_t xpos) { long int i; @@ -888,12 +905,16 @@ return 0; } -int igraph_i_layout_reingold_tilford_postorder(struct igraph_i_reingold_tilford_vertex *vdata, +static int igraph_i_layout_reingold_tilford_postorder( + struct igraph_i_reingold_tilford_vertex *vdata, long int node, long int vcount) { long int i, j, childcount, leftroot, leftrootidx; + const igraph_real_t minsep = 1; igraph_real_t avg; - /* printf("Starting visiting node %d\n", node); */ +#ifdef LAYOUT_RT_DEBUG + printf("Starting visiting node %ld\n", node); +#endif /* Check whether this node is a leaf node */ childcount = 0; @@ -922,93 +943,156 @@ * will be checked against the left contour of the next subtree */ leftroot = leftrootidx = -1; avg = 0.0; - /*printf("Visited node %d and arranged its subtrees\n", node);*/ +#ifdef LAYOUT_RT_DEBUG + printf("Visited node %ld and arranged its subtrees\n", node); +#endif for (i = 0, j = 0; i < vcount; i++) { if (i == node) { continue; } if (vdata[i].parent == node) { - /*printf(" Placing child %d on level %d\n", i, vdata[i].level);*/ if (leftroot >= 0) { /* Now we will follow the right contour of leftroot and the * left contour of the subtree rooted at i */ - long lnode, rnode; - igraph_real_t loffset, roffset, minsep, rootsep; + long lnode, rnode, auxnode; + igraph_real_t loffset, roffset, rootsep, newoffset; + +#ifdef LAYOUT_RT_DEBUG + printf(" Placing child %ld on level %ld, to the right of %ld\n", i, vdata[i].level, leftroot); +#endif lnode = leftroot; rnode = i; - minsep = 1; rootsep = vdata[leftroot].offset + minsep; - loffset = 0; roffset = minsep; - /*printf(" Contour: [%d, %d], offsets: [%lf, %lf], rootsep: %lf\n", - lnode, rnode, loffset, roffset, rootsep);*/ + loffset = vdata[leftroot].offset; roffset = loffset + minsep; + + /* Keep on updating the right contour now that we have attached + * a new node to the subtree being built */ + vdata[node].right_contour = i; + vdata[node].offset_to_right_contour = rootsep; + +#ifdef LAYOUT_RT_DEBUG + printf(" Contour: [%ld, %ld], offsets: [%lf, %lf], rootsep: %lf\n", + lnode, rnode, loffset, roffset, rootsep); +#endif while ((lnode >= 0) && (rnode >= 0)) { /* Step to the next level on the right contour of the left subtree */ if (vdata[lnode].right_contour >= 0) { - loffset += vdata[lnode].offset_follow_rc; + loffset += vdata[lnode].offset_to_right_contour; lnode = vdata[lnode].right_contour; } else { - /* Left subtree ended there. The right contour of the left subtree - * will continue to the next step on the right subtree. */ + /* Left subtree ended there. The left and right contour + * of the left subtree will continue to the next step + * on the right subtree. */ if (vdata[rnode].left_contour >= 0) { - /*printf(" Left subtree ended, continuing left subtree's left and right contour on right subtree (node %ld)\n", vdata[rnode].left_contour);*/ - vdata[lnode].left_contour = vdata[rnode].left_contour; - vdata[lnode].right_contour = vdata[rnode].left_contour; - vdata[lnode].offset_follow_lc = vdata[lnode].offset_follow_rc = - (roffset - loffset) + vdata[rnode].offset_follow_lc; - /*printf(" vdata[lnode].offset_follow_* = %.4f\n", vdata[lnode].offset_follow_lc);*/ + auxnode = vdata[node].left_extreme; + + /* this is the "threading" step that the original + * paper is talking about */ + newoffset = (vdata[node].offset_to_right_extreme - vdata[node].offset_to_left_extreme) + minsep + vdata[rnode].offset_to_left_contour; + vdata[auxnode].left_contour = vdata[rnode].left_contour; + vdata[auxnode].right_contour = vdata[rnode].left_contour; + vdata[auxnode].offset_to_left_contour = vdata[auxnode].offset_to_right_contour = newoffset; + + /* since we attached a larger subtree to the + * already placed left subtree, we need to update + * the extrema of the subtree rooted at 'node' */ + vdata[node].left_extreme = vdata[i].left_extreme; + vdata[node].right_extreme = vdata[i].right_extreme; + vdata[node].offset_to_left_extreme = vdata[i].offset_to_left_extreme + rootsep; + vdata[node].offset_to_right_extreme = vdata[i].offset_to_right_extreme + rootsep; +#ifdef LAYOUT_RT_DEBUG + printf(" Left subtree ended earlier, continuing left subtree's left and right contour on right subtree (node %ld gets connected to node %ld)\n", auxnode, vdata[rnode].left_contour); + printf(" New contour following offset for node %ld is %lf\n", auxnode, vdata[auxnode].offset_to_left_contour); +#endif + } else { + /* Both subtrees are ending at the same time; the + * left extreme node of the subtree rooted at + * 'node' remains the same but the right extreme + * will change */ + vdata[node].right_extreme = vdata[i].right_extreme; + vdata[node].offset_to_right_extreme = vdata[i].offset_to_right_extreme + rootsep; } lnode = -1; } /* Step to the next level on the left contour of the right subtree */ if (vdata[rnode].left_contour >= 0) { - roffset += vdata[rnode].offset_follow_lc; + roffset += vdata[rnode].offset_to_left_contour; rnode = vdata[rnode].left_contour; } else { - /* Right subtree ended here. The left contour of the right + /* Right subtree ended here. The right contour of the right * subtree will continue to the next step on the left subtree. * Note that lnode has already been advanced here */ if (lnode >= 0) { - /*printf(" Right subtree ended, continuing right subtree's left and right contour on left subtree (node %ld)\n", lnode);*/ - vdata[rnode].left_contour = lnode; - vdata[rnode].right_contour = lnode; - vdata[rnode].offset_follow_lc = vdata[rnode].offset_follow_rc = - (loffset - roffset); /* loffset has also been increased earlier */ - /*printf(" vdata[rnode].offset_follow_* = %.4f\n", vdata[rnode].offset_follow_lc);*/ + auxnode = vdata[i].right_extreme; + + /* this is the "threading" step that the original + * paper is talking about */ + newoffset = loffset - rootsep - vdata[i].offset_to_right_extreme; + vdata[auxnode].left_contour = lnode; + vdata[auxnode].right_contour = lnode; + vdata[auxnode].offset_to_left_contour = vdata[auxnode].offset_to_right_contour = newoffset; + + /* no need to update the extrema of the subtree + * rooted at 'node' because the right subtree was + * smaller */ +#ifdef LAYOUT_RT_DEBUG + printf(" Right subtree ended earlier, continuing right subtree's left and right contour on left subtree (node %ld gets connected to node %ld)\n", auxnode, lnode); + printf(" New contour following offset for node %ld is %lf\n", auxnode, vdata[auxnode].offset_to_left_contour); +#endif } rnode = -1; } - /*printf(" Contour: [%d, %d], offsets: [%lf, %lf], rootsep: %lf\n", - lnode, rnode, loffset, roffset, rootsep);*/ +#ifdef LAYOUT_RT_DEBUG + printf(" Contour: [%ld, %ld], offsets: [%lf, %lf], rootsep: %lf\n", + lnode, rnode, loffset, roffset, rootsep); +#endif /* Push subtrees away if necessary */ if ((lnode >= 0) && (rnode >= 0) && (roffset - loffset < minsep)) { - /*printf(" Pushing right subtree away by %lf\n", minsep-roffset+loffset);*/ +#ifdef LAYOUT_RT_DEBUG + printf(" Pushing right subtree away by %lf\n", minsep-roffset+loffset); +#endif rootsep += minsep - roffset + loffset; roffset = loffset + minsep; + vdata[node].offset_to_right_contour = rootsep; } } - /*printf(" Offset of subtree with root node %d will be %lf\n", i, rootsep);*/ +#ifdef LAYOUT_RT_DEBUG + printf(" Offset of subtree with root node %ld will be %lf\n", i, rootsep); +#endif vdata[i].offset = rootsep; - vdata[node].right_contour = i; - vdata[node].offset_follow_rc = rootsep; + vdata[node].offset_to_right_contour = rootsep; avg = (avg * j) / (j + 1) + rootsep / (j + 1); leftrootidx = j; leftroot = i; } else { + /* This is the first child of the node being considered so we + * can simply place the subtree on our virtual canvas */ +#ifdef LAYOUT_RT_DEBUG + printf(" Placing child %ld on level %ld as first child\n", i, vdata[i].level); +#endif leftrootidx = j; leftroot = i; vdata[node].left_contour = i; vdata[node].right_contour = i; - vdata[node].offset_follow_lc = 0.0; - vdata[node].offset_follow_rc = 0.0; + vdata[node].offset_to_left_contour = 0.0; + vdata[node].offset_to_right_contour = 0.0; + vdata[node].left_extreme = vdata[i].left_extreme; + vdata[node].right_extreme = vdata[i].right_extreme; + vdata[node].offset_to_left_extreme = vdata[i].offset_to_left_extreme; + vdata[node].offset_to_right_extreme = vdata[i].offset_to_right_extreme; avg = vdata[i].offset; } j++; } } - /*printf("Shifting node to be centered above children. Shift amount: %lf\n", avg);*/ - vdata[node].offset_follow_lc -= avg; - vdata[node].offset_follow_rc -= avg; +#ifdef LAYOUT_RT_DEBUG + printf("Shifting node %ld to be centered above children. Shift amount: %lf\n", node, avg); +#endif + vdata[node].offset_to_left_contour -= avg; + vdata[node].offset_to_right_contour -= avg; + vdata[node].offset_to_left_extreme -= avg; + vdata[node].offset_to_right_extreme -= avg; for (i = 0, j = 0; i < vcount; i++) { if (i == node) { continue; @@ -1419,10 +1503,12 @@ #define COULOMBS_CONSTANT 8987500000.0 -igraph_real_t igraph_i_distance_between(const igraph_matrix_t *c, long int a, - long int b); +static igraph_real_t igraph_i_distance_between( + const igraph_matrix_t *c, + long int a, long int b); -int igraph_i_determine_electric_axal_forces(const igraph_matrix_t *pos, +static int igraph_i_determine_electric_axal_forces( + const igraph_matrix_t *pos, igraph_real_t *x, igraph_real_t *y, igraph_real_t directed_force, @@ -1430,14 +1516,16 @@ long int other_node, long int this_node); -int igraph_i_apply_electrical_force(const igraph_matrix_t *pos, - igraph_vector_t *pending_forces_x, - igraph_vector_t *pending_forces_y, - long int other_node, long int this_node, - igraph_real_t node_charge, - igraph_real_t distance); +static int igraph_i_apply_electrical_force( + const igraph_matrix_t *pos, + igraph_vector_t *pending_forces_x, + igraph_vector_t *pending_forces_y, + long int other_node, long int this_node, + igraph_real_t node_charge, + igraph_real_t distance); -int igraph_i_determine_spring_axal_forces(const igraph_matrix_t *pos, +static int igraph_i_determine_spring_axal_forces( + const igraph_matrix_t *pos, igraph_real_t *x, igraph_real_t *y, igraph_real_t directed_force, igraph_real_t distance, @@ -1445,27 +1533,30 @@ long int other_node, long int this_node); -int igraph_i_apply_spring_force(const igraph_matrix_t *pos, - igraph_vector_t *pending_forces_x, - igraph_vector_t *pending_forces_y, - long int other_node, - long int this_node, int spring_length, - igraph_real_t spring_constant); +static int igraph_i_apply_spring_force( + const igraph_matrix_t *pos, + igraph_vector_t *pending_forces_x, + igraph_vector_t *pending_forces_y, + long int other_node, + long int this_node, int spring_length, + igraph_real_t spring_constant); -int igraph_i_move_nodes(igraph_matrix_t *pos, - const igraph_vector_t *pending_forces_x, - const igraph_vector_t *pending_forces_y, - igraph_real_t node_mass, - igraph_real_t max_sa_movement); +static int igraph_i_move_nodes( + igraph_matrix_t *pos, + const igraph_vector_t *pending_forces_x, + const igraph_vector_t *pending_forces_y, + igraph_real_t node_mass, + igraph_real_t max_sa_movement); -igraph_real_t igraph_i_distance_between(const igraph_matrix_t *c, long int a, - long int b) { +static igraph_real_t igraph_i_distance_between( + const igraph_matrix_t *c, + long int a, long int b) { igraph_real_t diffx = MATRIX(*c, a, 0) - MATRIX(*c, b, 0); igraph_real_t diffy = MATRIX(*c, a, 1) - MATRIX(*c, b, 1); return sqrt( diffx * diffx + diffy * diffy ); } -int igraph_i_determine_electric_axal_forces(const igraph_matrix_t *pos, +static int igraph_i_determine_electric_axal_forces(const igraph_matrix_t *pos, igraph_real_t *x, igraph_real_t *y, igraph_real_t directed_force, @@ -1518,12 +1609,13 @@ return 0; } -int igraph_i_apply_electrical_force(const igraph_matrix_t *pos, - igraph_vector_t *pending_forces_x, - igraph_vector_t *pending_forces_y, - long int other_node, long int this_node, - igraph_real_t node_charge, - igraph_real_t distance) { +static int igraph_i_apply_electrical_force( + const igraph_matrix_t *pos, + igraph_vector_t *pending_forces_x, + igraph_vector_t *pending_forces_y, + long int other_node, long int this_node, + igraph_real_t node_charge, + igraph_real_t distance) { igraph_real_t directed_force = COULOMBS_CONSTANT * ((node_charge * node_charge) / (distance * distance)); @@ -1541,7 +1633,8 @@ return 0; } -int igraph_i_determine_spring_axal_forces(const igraph_matrix_t *pos, +static int igraph_i_determine_spring_axal_forces( + const igraph_matrix_t *pos, igraph_real_t *x, igraph_real_t *y, igraph_real_t directed_force, igraph_real_t distance, @@ -1579,12 +1672,13 @@ return 0; } -int igraph_i_apply_spring_force(const igraph_matrix_t *pos, - igraph_vector_t *pending_forces_x, - igraph_vector_t *pending_forces_y, - long int other_node, - long int this_node, int spring_length, - igraph_real_t spring_constant) { +static int igraph_i_apply_spring_force( + const igraph_matrix_t *pos, + igraph_vector_t *pending_forces_x, + igraph_vector_t *pending_forces_y, + long int other_node, + long int this_node, int spring_length, + igraph_real_t spring_constant) { // determined using Hooke's Law: // force = -kx @@ -1625,11 +1719,12 @@ return 0; } -int igraph_i_move_nodes(igraph_matrix_t *pos, - const igraph_vector_t *pending_forces_x, - const igraph_vector_t *pending_forces_y, - igraph_real_t node_mass, - igraph_real_t max_sa_movement) { +static int igraph_i_move_nodes( + igraph_matrix_t *pos, + const igraph_vector_t *pending_forces_x, + const igraph_vector_t *pending_forces_y, + igraph_real_t node_mass, + igraph_real_t max_sa_movement) { // Since each iteration is isolated, time is constant at 1. // Therefore: @@ -1822,11 +1917,13 @@ return 0; } +/* not 'static', used in tests */ int igraph_i_layout_merge_dla(igraph_i_layout_mergegrid_t *grid, long int actg, igraph_real_t *x, igraph_real_t *y, igraph_real_t r, igraph_real_t cx, igraph_real_t cy, igraph_real_t startr, igraph_real_t killr); +/* TODO: not 'static' because used in tests */ int igraph_i_layout_sphere_2d(igraph_matrix_t *coords, igraph_real_t *x, igraph_real_t *y, igraph_real_t *r); int igraph_i_layout_sphere_3d(igraph_matrix_t *coords, igraph_real_t *x, @@ -1981,7 +2078,8 @@ return 0; } -int igraph_i_layout_sphere_2d(igraph_matrix_t *coords, igraph_real_t *x, igraph_real_t *y, +int igraph_i_layout_sphere_2d(igraph_matrix_t *coords, + igraph_real_t *x, igraph_real_t *y, igraph_real_t *r) { long int nodes = igraph_matrix_nrow(coords); long int i; @@ -2012,7 +2110,8 @@ return 0; } -int igraph_i_layout_sphere_3d(igraph_matrix_t *coords, igraph_real_t *x, igraph_real_t *y, +int igraph_i_layout_sphere_3d(igraph_matrix_t *coords, + igraph_real_t *x, igraph_real_t *y, igraph_real_t *z, igraph_real_t *r) { long int nodes = igraph_matrix_nrow(coords); long int i; @@ -2094,14 +2193,14 @@ return 0; } -int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from, - int n, void *extra); +static int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from, + int n, void *extra); -int igraph_i_layout_mds_single(const igraph_t* graph, igraph_matrix_t *res, - igraph_matrix_t *dist, long int dim); +static int igraph_i_layout_mds_single(const igraph_t* graph, igraph_matrix_t *res, + igraph_matrix_t *dist, long int dim); -int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from, - int n, void *extra) { +static int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from, + int n, void *extra) { igraph_matrix_t* matrix = (igraph_matrix_t*)extra; IGRAPH_UNUSED(n); igraph_blas_dgemv_array(0, 1, matrix, from, 0, to); diff --git a/igraph/src/layout_dh.c b/igraph/src/layout_dh.c --- a/igraph/src/layout_dh.c +++ b/igraph/src/layout_dh.c @@ -26,9 +26,11 @@ #include "igraph_interface.h" #include "igraph_random.h" #include "igraph_math.h" +#include "igraph_interrupt_internal.h" #include +/* not 'static', used in tests */ igraph_bool_t igraph_i_segments_intersect(float p0_x, float p0_y, float p1_x, float p1_y, float p2_x, float p2_y, @@ -52,6 +54,7 @@ return s >= 0 && s <= 1 && t >= 0 && t <= 1 ? 1 : 0; } +/* not 'static', used in tests */ float igraph_i_point_segment_dist2(float v_x, float v_y, float u1_x, float u1_y, float u2_x, float u2_y) { @@ -240,6 +243,8 @@ for (round = 0; round < maxiter + fineiter; round++) { igraph_integer_t p; igraph_vector_int_shuffle(&perm); + + IGRAPH_ALLOW_INTERRUPTION(); fine_tuning = round >= maxiter; if (fine_tuning) { diff --git a/igraph/src/layout_fr.c b/igraph/src/layout_fr.c --- a/igraph/src/layout_fr.c +++ b/igraph/src/layout_fr.c @@ -28,16 +28,16 @@ #include "igraph_components.h" #include "igraph_types_internal.h" -int igraph_layout_i_fr(const igraph_t *graph, - igraph_matrix_t *res, - igraph_bool_t use_seed, - igraph_integer_t niter, - igraph_real_t start_temp, - const igraph_vector_t *weight, - const igraph_vector_t *minx, - const igraph_vector_t *maxx, - const igraph_vector_t *miny, - const igraph_vector_t *maxy) { +static int igraph_layout_i_fr(const igraph_t *graph, + igraph_matrix_t *res, + igraph_bool_t use_seed, + igraph_integer_t niter, + igraph_real_t start_temp, + const igraph_vector_t *weight, + const igraph_vector_t *minx, + const igraph_vector_t *maxx, + const igraph_vector_t *miny, + const igraph_vector_t *maxy) { igraph_integer_t no_nodes = igraph_vcount(graph); igraph_integer_t no_edges = igraph_ecount(graph); @@ -188,12 +188,13 @@ return 0; } -int igraph_layout_i_grid_fr(const igraph_t *graph, - igraph_matrix_t *res, igraph_bool_t use_seed, - igraph_integer_t niter, igraph_real_t start_temp, - const igraph_vector_t *weight, const igraph_vector_t *minx, - const igraph_vector_t *maxx, const igraph_vector_t *miny, - const igraph_vector_t *maxy) { +static int igraph_layout_i_grid_fr( + const igraph_t *graph, + igraph_matrix_t *res, igraph_bool_t use_seed, + igraph_integer_t niter, igraph_real_t start_temp, + const igraph_vector_t *weight, const igraph_vector_t *minx, + const igraph_vector_t *maxx, const igraph_vector_t *miny, + const igraph_vector_t *maxy) { igraph_integer_t no_nodes = igraph_vcount(graph); igraph_integer_t no_edges = igraph_ecount(graph); diff --git a/igraph/src/layout_kk.c b/igraph/src/layout_kk.c --- a/igraph/src/layout_kk.c +++ b/igraph/src/layout_kk.c @@ -41,8 +41,10 @@ * contain the result (x-positions in column zero and * y-positions in column one) and will be resized if needed. * \param use_seed Boolean, whether to use the values supplied in the - * \p res argument as the initial configuration. If zero then a - * random initial configuration is used. + * \p res argument as the initial configuration. If zero and there + * are any limits on the X or Y coordinates, then a random initial + * configuration is used. Otherwise the vertices are placed on a + * circle of radius 1 as the initial configuration. * \param maxiter The maximum number of iterations to perform. A reasonable * default value is at least ten (or more) times the number of * vertices. @@ -285,7 +287,7 @@ /* Update delta, only with/for the affected node */ VECTOR(D1)[m] = VECTOR(D2)[m] = 0.0; for (i = 0; i < no_nodes; i++) { - igraph_real_t old_dx, old_dy, old_mi, new_dx, new_dy, new_mi_dist, old_mi_dist; + igraph_real_t old_dx, old_dy, new_dx, new_dy, new_mi_dist, old_mi_dist; if (i == m) { continue; } @@ -340,8 +342,10 @@ * contain the result (x-positions in column zero and * y-positions in column one) and will be resized if needed. * \param use_seed Boolean, whether to use the values supplied in the - * \p res argument as the initial configuration. If zero then a - * random initial configuration is used. + * \p res argument as the initial configuration. If zero and there + * are any limits on the X, Y or Z coordinates, then a random initial + * configuration is used. Otherwise the vertices are placed uniformly + * on a sphere of radius 1 as the initial configuration. * \param maxiter The maximum number of iterations to perform. A reasonable * default value is at least ten (or more) times the number of * vertices. @@ -577,6 +581,7 @@ dz = old_z - MATRIX(*res, i, 2); dist = sqrt(dx * dx + dy * dy + dz * dz); den = dist * (dx * dx + dy * dy + dz * dz); + k_mi = MATRIX(kij, m, i); l_mi = MATRIX(lij, m, i); Axx += k_mi * (1 - l_mi * (dy * dy + dz * dz) / den); @@ -594,9 +599,16 @@ #define DET(a,b,c,d,e,f,g,h,i) ((a*e*i+b*f*g+c*d*h)-(c*e*g+b*d*i+a*f*h)) detnum = DET(Axx, Axy, Axz, Axy, Ayy, Ayz, Axz, Ayz, Azz); - delta_x = DET(Ax, Ay, Az, Axy, Ayy, Ayz, Axz, Ayz, Azz) / detnum; - delta_y = DET(Axx, Axy, Axz, Ax, Ay, Az, Axz, Ayz, Azz) / detnum; - delta_z = DET(Axx, Axy, Axz, Axy, Ayy, Ayz, Ax, Ay, Az ) / detnum; + if (detnum != 0) { + delta_x = DET(Ax, Ay, Az, Axy, Ayy, Ayz, Axz, Ayz, Azz) / detnum; + delta_y = DET(Axx, Axy, Axz, Ax, Ay, Az, Axz, Ayz, Azz) / detnum; + delta_z = DET(Axx, Axy, Axz, Axy, Ayy, Ayz, Ax, Ay, Az ) / detnum; + } else { + /* No new stable position for node m; this can happen in rare + * cases, e.g., if the graph has two nodes only. It's best to leave + * the node where it is. */ + delta_x = delta_y = delta_z = 0; + } new_x = old_x + delta_x; new_y = old_y + delta_y; diff --git a/igraph/src/lsap.c b/igraph/src/lsap.c --- a/igraph/src/lsap.c +++ b/igraph/src/lsap.c @@ -2,12 +2,11 @@ #include "igraph_lsap.h" #include "igraph_error.h" -#include +/* #include */ #include #include #include /* INT_MAX */ #include /* DBL_MAX */ -#include #include /* constants used for improving readability of code */ @@ -40,30 +39,30 @@ /* public interface */ /* constructors and destructor */ -AP *ap_create_problem(double *t, int n); -AP *ap_create_problem_from_matrix(double **t, int n); -AP *ap_read_problem(char *file); -void ap_free(AP *p); +static AP *ap_create_problem(double *t, int n); +static AP *ap_create_problem_from_matrix(double **t, int n); +static AP *ap_read_problem(char *file); +static void ap_free(AP *p); -int ap_assignment(AP *p, int *res); -int ap_costmatrix(AP *p, double **m); -int ap_datamatrix(AP *p, double **m); -int ap_iterations(AP *p); -int ap_hungarian(AP *p); -double ap_mincost(AP *p); -void ap_print_solution(AP *p); -void ap_show_data(AP *p); -int ap_size(AP *p); -int ap_time(AP *p); +static int ap_assignment(AP *p, int *res); +static int ap_costmatrix(AP *p, double **m); +static int ap_datamatrix(AP *p, double **m); +static int ap_iterations(AP *p); +static int ap_hungarian(AP *p); +static double ap_mincost(AP *p); +/* static void ap_print_solution(AP *p); */ +/* static void ap_show_data(AP *p); */ +static int ap_size(AP *p); +static int ap_time(AP *p); /* error reporting */ -void ap_error(char *message); +/* static void ap_error(char *message); */ /* private functions */ -void preprocess(AP *p); -void preassign(AP *p); -int cover(AP *p, int *ri, int *ci); -void reduce(AP *p, int *ri, int *ci); +static void preprocess(AP *p); +static void preassign(AP *p); +static int cover(AP *p, int *ri, int *ci); +static void reduce(AP *p, int *ri, int *ci); int ap_hungarian(AP *p) { int n; /* size of problem */ diff --git a/igraph/src/matching.c b/igraph/src/matching.c --- a/igraph/src/matching.c +++ b/igraph/src/matching.c @@ -21,17 +21,15 @@ */ -#include -#include -#include "config.h" #include "igraph_adjlist.h" #include "igraph_constructors.h" #include "igraph_conversion.h" #include "igraph_dqueue.h" -#include "igraph_flow.h" #include "igraph_interface.h" #include "igraph_matching.h" #include "igraph_structural.h" +#include "config.h" +#include /* #define MATCHING_DEBUG */ @@ -207,10 +205,12 @@ return IGRAPH_SUCCESS; } -int igraph_i_maximum_bipartite_matching_unweighted(const igraph_t* graph, +static int igraph_i_maximum_bipartite_matching_unweighted( + const igraph_t* graph, const igraph_vector_bool_t* types, igraph_integer_t* matching_size, igraph_vector_long_t* matching); -int igraph_i_maximum_bipartite_matching_weighted(const igraph_t* graph, +static int igraph_i_maximum_bipartite_matching_weighted( + const igraph_t* graph, const igraph_vector_bool_t* types, igraph_integer_t* matching_size, igraph_real_t* matching_weight, igraph_vector_long_t* matching, const igraph_vector_t* weights, igraph_real_t eps); @@ -306,7 +306,8 @@ } } -int igraph_i_maximum_bipartite_matching_unweighted_relabel(const igraph_t* graph, +static int igraph_i_maximum_bipartite_matching_unweighted_relabel( + const igraph_t* graph, const igraph_vector_bool_t* types, igraph_vector_t* labels, igraph_vector_long_t* matching, igraph_bool_t smaller_set); @@ -323,7 +324,8 @@ * Avancée en Calcul Scientifique). * http://www.cerfacs.fr/algor/reports/2011/TR_PA_11_33.pdf */ -int igraph_i_maximum_bipartite_matching_unweighted(const igraph_t* graph, +static int igraph_i_maximum_bipartite_matching_unweighted( + const igraph_t* graph, const igraph_vector_bool_t* types, igraph_integer_t* matching_size, igraph_vector_long_t* matching) { long int i, j, k, n, no_of_nodes = igraph_vcount(graph); @@ -460,7 +462,8 @@ return IGRAPH_SUCCESS; } -int igraph_i_maximum_bipartite_matching_unweighted_relabel(const igraph_t* graph, +static int igraph_i_maximum_bipartite_matching_unweighted_relabel( + const igraph_t* graph, const igraph_vector_bool_t* types, igraph_vector_t* labels, igraph_vector_long_t* match, igraph_bool_t smaller_set) { long int i, j, n, no_of_nodes = igraph_vcount(graph), matched_to; @@ -529,7 +532,8 @@ * an edge falls below \c eps, it will be considered tight. If all your * weights are integers, you can safely set \c eps to zero. */ -int igraph_i_maximum_bipartite_matching_weighted(const igraph_t* graph, +static int igraph_i_maximum_bipartite_matching_weighted( + const igraph_t* graph, const igraph_vector_bool_t* types, igraph_integer_t* matching_size, igraph_real_t* matching_weight, igraph_vector_long_t* matching, const igraph_vector_t* weights, igraph_real_t eps) { diff --git a/igraph/src/math.c b/igraph/src/math.c --- a/igraph/src/math.c +++ b/igraph/src/math.c @@ -33,9 +33,7 @@ #endif int igraph_finite(double x) { -#ifdef isfinite - return isfinite(x); -#elif HAVE_ISFINITE == 1 +#if HAVE_DECL_ISFINITE return isfinite(x); #elif HAVE_FINITE == 1 return finite(x); @@ -79,11 +77,13 @@ int i; if (n < 1 || n > 1000) { - IGRAPH_NAN; + IGRAPH_WARNING("chebyshev_eval: argument out of domain"); + return IGRAPH_NAN; } if (x < -1.1 || x > 1.1) { - IGRAPH_NAN; + IGRAPH_WARNING("chebyshev_eval: argument out of domain"); + return IGRAPH_NAN; } twox = x * 2; @@ -256,11 +256,11 @@ } int igraph_is_posinf(double x) { - return isinf(x) == 1; + return isinf(x) && x > 0; } int igraph_is_neginf(double x) { - return isinf(x) == -1; + return isinf(x) && x < 0; } /** diff --git a/igraph/src/maximal_cliques.c b/igraph/src/maximal_cliques.c --- a/igraph/src/maximal_cliques.c +++ b/igraph/src/maximal_cliques.c @@ -35,13 +35,14 @@ #define CONCAT2(a,b) CONCAT2x(a,b) #define FUNCTION(name,sfx) CONCAT2(name,sfx) -int igraph_i_maximal_cliques_reorder_adjlists( - const igraph_vector_int_t *PX, - int PS, int PE, int XS, int XE, - const igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist); +static int igraph_i_maximal_cliques_reorder_adjlists( + const igraph_vector_int_t *PX, + int PS, int PE, int XS, int XE, + const igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist); -int igraph_i_maximal_cliques_select_pivot(const igraph_vector_int_t *PX, +static int igraph_i_maximal_cliques_select_pivot( + const igraph_vector_int_t *PX, int PS, int PE, int XS, int XE, const igraph_vector_int_t *pos, const igraph_adjlist_t *adjlist, @@ -49,23 +50,26 @@ igraph_vector_int_t *nextv, int oldPS, int oldXE); -int igraph_i_maximal_cliques_down(igraph_vector_int_t *PX, - int PS, int PE, int XS, int XE, - igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist, int mynextv, - igraph_vector_int_t *R, - int *newPS, int *newXE); +static int igraph_i_maximal_cliques_down( + igraph_vector_int_t *PX, + int PS, int PE, int XS, int XE, + igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist, int mynextv, + igraph_vector_int_t *R, + int *newPS, int *newXE); -int igraph_i_maximal_cliques_PX(igraph_vector_int_t *PX, int PS, int *PE, - int *XS, int XE, igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist, int v, - igraph_vector_int_t *H); +static int igraph_i_maximal_cliques_PX( + igraph_vector_int_t *PX, int PS, int *PE, + int *XS, int XE, igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist, int v, + igraph_vector_int_t *H); -int igraph_i_maximal_cliques_up(igraph_vector_int_t *PX, int PS, int PE, - int XS, int XE, igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist, - igraph_vector_int_t *R, - igraph_vector_int_t *H); +static int igraph_i_maximal_cliques_up( + igraph_vector_int_t *PX, int PS, int PE, + int XS, int XE, igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist, + igraph_vector_int_t *R, + igraph_vector_int_t *H); #define PRINT_PX do { \ int j; \ @@ -109,11 +113,11 @@ printf("\n"); \ } while (0) -int igraph_i_maximal_cliques_reorder_adjlists( - const igraph_vector_int_t *PX, - int PS, int PE, int XS, int XE, - const igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist) { +static int igraph_i_maximal_cliques_reorder_adjlists( + const igraph_vector_int_t *PX, + int PS, int PE, int XS, int XE, + const igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist) { int j; int sPS = PS + 1, sPE = PE + 1; @@ -140,7 +144,8 @@ return 0; } -int igraph_i_maximal_cliques_select_pivot(const igraph_vector_int_t *PX, +static int igraph_i_maximal_cliques_select_pivot( + const igraph_vector_int_t *PX, int PS, int PE, int XS, int XE, const igraph_vector_int_t *pos, const igraph_adjlist_t *adjlist, @@ -216,12 +221,12 @@ VECTOR(*pos)[v2] = (p1)+1; \ } while (0) -int igraph_i_maximal_cliques_down(igraph_vector_int_t *PX, - int PS, int PE, int XS, int XE, - igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist, int mynextv, - igraph_vector_int_t *R, - int *newPS, int *newXE) { +static int igraph_i_maximal_cliques_down(igraph_vector_int_t *PX, + int PS, int PE, int XS, int XE, + igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist, int mynextv, + igraph_vector_int_t *R, + int *newPS, int *newXE) { igraph_vector_int_t *vneis = igraph_adjlist_get(adjlist, mynextv); int j, vneislen = igraph_vector_int_size(vneis); @@ -247,10 +252,10 @@ #undef SWAP -int igraph_i_maximal_cliques_PX(igraph_vector_int_t *PX, int PS, int *PE, - int *XS, int XE, igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist, int v, - igraph_vector_int_t *H) { +static int igraph_i_maximal_cliques_PX(igraph_vector_int_t *PX, int PS, int *PE, + int *XS, int XE, igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist, int v, + igraph_vector_int_t *H) { int vpos = VECTOR(*pos)[v] - 1; int tmp = VECTOR(*PX)[*PE]; @@ -264,11 +269,11 @@ return 0; } -int igraph_i_maximal_cliques_up(igraph_vector_int_t *PX, int PS, int PE, - int XS, int XE, igraph_vector_int_t *pos, - igraph_adjlist_t *adjlist, - igraph_vector_int_t *R, - igraph_vector_int_t *H) { +static int igraph_i_maximal_cliques_up(igraph_vector_int_t *PX, int PS, int PE, + int XS, int XE, igraph_vector_int_t *pos, + igraph_adjlist_t *adjlist, + igraph_vector_int_t *R, + igraph_vector_int_t *H) { int vv; igraph_vector_int_pop_back(R); @@ -287,7 +292,7 @@ /** * \function igraph_maximal_cliques - * \brief Find all maximal cliques of a graph + * \brief Finds all maximal cliques in a graph. * * * A maximal clique is a clique which can't be extended any more by @@ -311,7 +316,7 @@ * * \param graph The input graph. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_vector_t + * here, i.e. \p res will contain pointers to \ref igraph_vector_t * objects which contain the indices of vertices involved in a clique. * The pointer vector will be resized if needed but note that the * objects in the pointer vector will not be freed. Note that vertices @@ -415,11 +420,11 @@ /** * \function igraph_maximal_cliques_callback - * \brief Finds maximal cliques in a graph and calls a function for each one + * \brief Finds maximal cliques in a graph and calls a function for each one. * * This function enumerates all maximal cliques within the given size range * and calls \p cliquehandler_fn for each of them. The cliques are passed to the - * callback function as an igraph_vector_t *. Destroying and + * callback function as a pointer to an \ref igraph_vector_t. Destroying and * freeing this vector is left up to the user. Use \ref igraph_vector_destroy() * to destroy it first, then free it using \ref igraph_free(). * @@ -457,7 +462,7 @@ /** * \function igraph_maximal_cliques_hist - * \brief Count the number of maximal cliques of each size in a graph. + * \brief Counts the number of maximal cliques of each size in a graph. * * This function counts how many maximal cliques of each size are present in * the graph. Size-1 maximal cliques are simply isolated vertices. @@ -472,7 +477,7 @@ * \param hist Pointer to an initialized vector. The result will be stored * here. The first element will store the number of size-1 maximal cliques, * the second element the number of size-2 maximal cliques, etc. - * For cliques smaller than \c min_size, zero counts will be returned. + * For cliques smaller than \p min_size, zero counts will be returned. * \param min_size Integer giving the minimum size of the cliques to be * returned. If negative or zero, no lower bound will be used. * \param max_size Integer giving the maximum size of the cliques to be diff --git a/igraph/src/motifs.c b/igraph/src/motifs.c --- a/igraph/src/motifs.c +++ b/igraph/src/motifs.c @@ -27,31 +27,17 @@ #include "igraph_adjlist.h" #include "igraph_interrupt_internal.h" #include "igraph_interface.h" +#include "igraph_isoclasses.h" #include "igraph_nongraph.h" -#include "igraph_structural.h" #include "igraph_stack.h" #include "config.h" -#include - -extern unsigned int igraph_i_isoclass_3[]; -extern unsigned int igraph_i_isoclass_4[]; -extern unsigned int igraph_i_isoclass_3u[]; -extern unsigned int igraph_i_isoclass_4u[]; -extern unsigned int igraph_i_isoclass2_3[]; -extern unsigned int igraph_i_isoclass2_4[]; -extern unsigned int igraph_i_isoclass2_3u[]; -extern unsigned int igraph_i_isoclass2_4u[]; -extern unsigned int igraph_i_isoclass_3_idx[]; -extern unsigned int igraph_i_isoclass_4_idx[]; -extern unsigned int igraph_i_isoclass_3u_idx[]; -extern unsigned int igraph_i_isoclass_4u_idx[]; - /** * Callback function for igraph_motifs_randesu that counts the motifs by * isomorphism class in a histogram. */ -igraph_bool_t igraph_i_motifs_randesu_update_hist(const igraph_t *graph, +static igraph_bool_t igraph_i_motifs_randesu_update_hist( + const igraph_t *graph, igraph_vector_t *vids, int isoclass, void* extra) { igraph_vector_t *hist = (igraph_vector_t*)extra; IGRAPH_UNUSED(graph); IGRAPH_UNUSED(vids); @@ -65,14 +51,14 @@ * * * Motifs are small connected subgraphs of a given structure in a - * graph. It is argued that the motif profile (ie. the number of + * graph. It is argued that the motif profile (i.e. the number of * different motifs in the graph) is characteristic for different * types of networks and network function is related to the motifs in * the graph. * * * This function is able to find the different motifs of size three - * and four (ie. the number of different subgraphs with three and four + * and four (i.e. the number of different subgraphs with three and four * vertices) in the network. * * @@ -108,7 +94,7 @@ * in a graph. * \return Error code. * \sa \ref igraph_motifs_randesu_estimate() for estimating the number - * of motifs in a graph, this can help to set the \c cut_prob + * of motifs in a graph, this can help to set the \p cut_prob * parameter; \ref igraph_motifs_randesu_no() to calculate the total * number of motifs of a given size in a graph; * \ref igraph_motifs_randesu_callback() for calling a callback function @@ -169,14 +155,14 @@ * * * Similarly to \ref igraph_motifs_randesu(), this function is able to find the - * different motifs of size three and four (ie. the number of different + * different motifs of size three and four (i.e. the number of different * subgraphs with three and four vertices) in the network. However, instead of * counting them, the function will call a callback function for each motif * found to allow further tests or post-processing. * * - * The \c cut_prob argument also allows sampling the motifs, just like for - * \ref igraph_motifs_randesu(). Set the \c cut_prob argument to a zero vector + * The \p cut_prob argument also allows sampling the motifs, just like for + * \ref igraph_motifs_randesu(). Set the \p cut_prob argument to a zero vector * for finding all motifs. * * \param graph The graph to find the motifs in. @@ -214,7 +200,7 @@ long int *added; char *subg; - unsigned int *arr_idx, *arr_code; + const unsigned int *arr_idx, *arr_code; int code = 0; unsigned char mul, idx; @@ -447,7 +433,7 @@ * * The total number of motifs is estimated by taking a sample of * vertices and counts all motifs in which these vertices are - * included. (There is also a \c cut_prob parameter which gives the + * included. (There is also a \p cut_prob parameter which gives the * probabilities to cut a branch of the search tree.) * * @@ -658,12 +644,9 @@ * \brief Count the total number of motifs in a graph * * - * This function counts the total number of motifs in a graph without - * assigning isomorphism classes to them. - * - * - * Directed motifs will be counted in directed graphs and undirected - * motifs in undirected graphs. + * This function counts the total number of motifs in a graph, + * i.e. the number of of (weakly) connected triplets or quadruplets, + * without assigning isomorphism classes to them. * * \param graph The graph object to study. * \param no Pointer to an integer type, the result will be stored diff --git a/igraph/src/mt.c b/igraph/src/mt.c new file mode 100644 --- /dev/null +++ b/igraph/src/mt.c @@ -0,0 +1,95 @@ +/* mt.c + * + * Mersenne Twister random number generator, based on the implementation of + * Michael Brundage (which has been placed in the public domain). + * + * Author: Tamas Nepusz (original by Michael Brundage) + * + * See the following URL for the original implementation: + * http://www.qbrundage.com/michaelb/pubs/essays/random_number_generation.html + * + * This file has been placed in the public domain. + */ + +#include + +#include "igraph_random.h" + +#include "mt.h" + +static uint16_t get_random_uint16() { + return RNG_INT31() & 0xFFFF; +} + +void mt_init(mt_rng_t* rng) { + mt_init_from_rng(rng, 0); +} + +void mt_init_from_rng(mt_rng_t* rng, mt_rng_t* seeder) { + int i; + + if (seeder == 0) { + for (i = 0; i < MT_LEN; i++) { + /* RAND_MAX is guaranteed to be at least 32767, so we can use two + * calls to rand() to produce a random 32-bit number */ + rng->mt_buffer[i] = (get_random_uint16() << 16) + get_random_uint16(); + } + } else { + for (i = 0; i < MT_LEN; i++) { + rng->mt_buffer[i] = mt_random(seeder); + } + } + + rng->mt_index = 0; +} + +#define MT_IA 397 +#define MT_IB (MT_LEN - MT_IA) +#define UPPER_MASK 0x80000000 +#define LOWER_MASK 0x7FFFFFFF +#define MATRIX_A 0x9908B0DF +#define TWIST(b,i,j) ((b)[i] & UPPER_MASK) | ((b)[j] & LOWER_MASK) +#define MAGIC(s) (((s)&1)*MATRIX_A) + +uint32_t mt_random(mt_rng_t* rng) { + uint32_t * b = rng->mt_buffer; + int idx = rng->mt_index; + uint32_t s; + int i; + + if (idx == MT_LEN * sizeof(uint32_t)) { + idx = 0; + i = 0; + for (; i < MT_IB; i++) { + s = TWIST(b, i, i+1); + b[i] = b[i + MT_IA] ^ (s >> 1) ^ MAGIC(s); + } + for (; i < MT_LEN-1; i++) { + s = TWIST(b, i, i+1); + b[i] = b[i - MT_IB] ^ (s >> 1) ^ MAGIC(s); + } + + s = TWIST(b, MT_LEN-1, 0); + b[MT_LEN-1] = b[MT_IA-1] ^ (s >> 1) ^ MAGIC(s); + } + + rng->mt_index = idx + sizeof(uint32_t); + return *(uint32_t *)((unsigned char *)b + idx); + /* + Matsumoto and Nishimura additionally confound the bits returned to the caller + but this doesn't increase the randomness, and slows down the generator by + as much as 25%. So I omit these operations here. + + r ^= (r >> 11); + r ^= (r << 7) & 0x9D2C5680; + r ^= (r << 15) & 0xEFC60000; + r ^= (r >> 18); + */ +} + + +double mt_uniform_01(mt_rng_t* rng) { + return ((double)mt_random(rng)) / MT_RAND_MAX; +} + + diff --git a/igraph/src/operators.c b/igraph/src/operators.c --- a/igraph/src/operators.c +++ b/igraph/src/operators.c @@ -31,8 +31,8 @@ #include "igraph_attributes.h" #include "igraph_conversion.h" #include "igraph_qsort.h" -#include #include "config.h" +#include /** * \function igraph_disjoint_union @@ -47,7 +47,7 @@ * and |E1|+|E2| edges. * * - * Both graphs need to have the same directedness, ie. either both + * Both graphs need to have the same directedness, i.e. either both * directed or both undirected. * * @@ -119,7 +119,7 @@ * of vertices and edges in the graphs. * * - * Both graphs need to have the same directedness, ie. either both + * Both graphs need to have the same directedness, i.e. either both * directed or both undirected. * * @@ -183,8 +183,7 @@ return 0; } -int igraph_i_order_edgelist_cmp(void *edges, const void *e1, - const void *e2) { +static int igraph_i_order_edgelist_cmp(void *edges, const void *e1, const void *e2) { igraph_vector_t *edgelist = edges; long int edge1 = (*(const long int*) e1) * 2; long int edge2 = (*(const long int*) e2) * 2; @@ -210,9 +209,9 @@ #define IGRAPH_MODE_UNION 1 #define IGRAPH_MODE_INTERSECTION 2 -int igraph_i_merge(igraph_t *res, int mode, - const igraph_t *left, const igraph_t *right, - igraph_vector_t *edge_map1, igraph_vector_t *edge_map2) { +static int igraph_i_merge(igraph_t *res, int mode, + const igraph_t *left, const igraph_t *right, + igraph_vector_t *edge_map1, igraph_vector_t *edge_map2) { long int no_of_nodes_left = igraph_vcount(left); long int no_of_nodes_right = igraph_vcount(right); @@ -431,7 +430,7 @@ edge_map1, edge_map2); } -void igraph_i_union_many_free(igraph_vector_ptr_t *v) { +static void igraph_i_union_many_free(igraph_vector_ptr_t *v) { long int i, n = igraph_vector_ptr_size(v); for (i = 0; i < n; i++) { if (VECTOR(*v)[i] != 0) { @@ -442,7 +441,7 @@ igraph_vector_ptr_destroy(v); } -void igraph_i_union_many_free2(igraph_vector_ptr_t *v) { +static void igraph_i_union_many_free2(igraph_vector_ptr_t *v) { long int i, n = igraph_vector_ptr_size(v); for (i = 0; i < n; i++) { if (VECTOR(*v)[i] != 0) { @@ -453,7 +452,7 @@ igraph_vector_ptr_destroy(v); } -void igraph_i_union_many_free3(igraph_vector_ptr_t *v) { +static void igraph_i_union_many_free3(igraph_vector_ptr_t *v) { long int i, n = igraph_vector_ptr_size(v); for (i = 0; i < n; i++) { if (VECTOR(*v)[i] != 0) { @@ -469,8 +468,8 @@ * * * This function calculates the intersection of the graphs stored in - * the \c graphs argument. Only those edges will be included in the - * result graph which are part of every graph in \c graphs. + * the \p graphs argument. Only those edges will be included in the + * result graph which are part of every graph in \p graphs. * * * The number of vertices in the result graph will be the maximum @@ -492,7 +491,7 @@ * igraph_difference() for other operators. * * Time complexity: O(|V|+|E|), |V| is the number of vertices, - * |E| is the number of edges in the smallest graph (ie. the graph having + * |E| is the number of edges in the smallest graph (i.e. the graph having * the less vertices). */ @@ -924,9 +923,9 @@ * * * The number of vertices in the result is the number of vertices in - * the original graph, ie. the left, first operand. In the results - * graph only edges will be included from \c orig which are not - * present in \c sub. + * the original graph, i.e. the left, first operand. In the results + * graph only edges will be included from \p orig which are not + * present in \p sub. * * \param res Pointer to an uninitialized graph object, the result * will be stored here. @@ -999,6 +998,10 @@ IGRAPH_CHECK(igraph_vector_push_back(&edges, i)); IGRAPH_CHECK(igraph_vector_push_back(&edges, v1)); n1--; + /* handle loop edges properly in undirected graphs */ + if (!directed && i == v1) { + n1--; + } } else if (v2 > v1) { n2--; } else { @@ -1015,6 +1018,11 @@ IGRAPH_CHECK(igraph_vector_push_back(&edge_ids, e1)); IGRAPH_CHECK(igraph_vector_push_back(&edges, i)); IGRAPH_CHECK(igraph_vector_push_back(&edges, v1)); + + /* handle loop edges properly in undirected graphs */ + if (!directed && v1 == i) { + n1--; + } } n1--; } @@ -1032,6 +1040,11 @@ IGRAPH_CHECK(igraph_vector_push_back(&edge_ids, e1)); IGRAPH_CHECK(igraph_vector_push_back(&edges, i)); IGRAPH_CHECK(igraph_vector_push_back(&edges, v1)); + + /* handle loop edges properly in undirected graphs */ + if (!directed && v1 == i) { + n1--; + } } n1--; } diff --git a/igraph/src/optimal_modularity.c b/igraph/src/optimal_modularity.c --- a/igraph/src/optimal_modularity.c +++ b/igraph/src/optimal_modularity.c @@ -23,7 +23,6 @@ */ #include "igraph_interface.h" -#include "igraph_structural.h" #include "igraph_community.h" #include "igraph_error.h" #include "igraph_glpk_support.h" diff --git a/igraph/src/options.c b/igraph/src/options.c --- a/igraph/src/options.c +++ b/igraph/src/options.c @@ -4,14 +4,14 @@ * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at + * the Free Software Foundation; either version 2 of the License, or (at * your option) any later version. - * + * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. @@ -21,18 +21,24 @@ #include "plfit.h" const plfit_continuous_options_t plfit_continuous_default_options = { - /* .finite_size_correction = */ 0, - /* .xmin_method = */ PLFIT_GSS_OR_LINEAR + /* .finite_size_correction = */ 0, + /* .xmin_method = */ PLFIT_DEFAULT_CONTINUOUS_METHOD, + /* .p_value_method = */ PLFIT_DEFAULT_P_VALUE_METHOD, + /* .p_value_precision = */ 0.01, + /* .rng = */ 0 }; const plfit_discrete_options_t plfit_discrete_default_options = { - /* .finite_size_correction = */ 0, - /* .alpha_method = */ PLFIT_LBFGS, - /* .alpha = */ { - /* .min = */ 1.01, - /* .max = */ 5, - /* .step = */ 0.01 - } + /* .finite_size_correction = */ 0, + /* .alpha_method = */ PLFIT_DEFAULT_DISCRETE_METHOD, + /* .alpha = */ { + /* .min = */ 1.01, + /* .max = */ 5, + /* .step = */ 0.01 + }, + /* .p_value_method = */ PLFIT_DEFAULT_P_VALUE_METHOD, + /* .p_value_precision = */ 0.01, + /* .rng = */ 0 }; int plfit_continuous_options_init(plfit_continuous_options_t* options) { @@ -44,4 +50,3 @@ *options = plfit_discrete_default_options; return PLFIT_SUCCESS; } - diff --git a/igraph/src/orbit.cc b/igraph/src/orbit.cc --- a/igraph/src/orbit.cc +++ b/igraph/src/orbit.cc @@ -1,5 +1,5 @@ -#include -#include +#include +#include #include "defs.hh" #include "orbit.hh" diff --git a/igraph/src/other.c b/igraph/src/other.c --- a/igraph/src/other.c +++ b/igraph/src/other.c @@ -22,16 +22,13 @@ */ #include "igraph_nongraph.h" +#include "igraph_random.h" #include "igraph_types.h" -#include "igraph_memory.h" #include "igraph_interrupt_internal.h" -#include "igraph_types_internal.h" #include "config.h" #include "plfit/error.h" #include "plfit/plfit.h" #include -#include -#include /** * \ingroup nongraph @@ -356,9 +353,13 @@ } } + RNG_BEGIN(); + plfit_stored_error_handler = plfit_set_error_handler(igraph_i_plfit_error_handler_store); if (discrete) { plfit_discrete_options_init(&disc_options); + /* approximation method should be switched to PLFIT_P_VALUE_EXACT in igraph 0.9 */ + disc_options.p_value_method = PLFIT_P_VALUE_APPROXIMATE; disc_options.finite_size_correction = (plfit_bool_t) finite_size_correction; if (xmin >= 0) { @@ -369,6 +370,10 @@ } } else { plfit_continuous_options_init(&cont_options); + /* approximation method should be switched to PLFIT_P_VALUE_EXACT in igraph 0.9 */ + cont_options.p_value_method = PLFIT_P_VALUE_APPROXIMATE; + /* xmin method should be switched to PLFIT_STRATIFIED_SAMPLING in igraph 0.9 */ + cont_options.xmin_method = PLFIT_GSS_OR_LINEAR; cont_options.finite_size_correction = (plfit_bool_t) finite_size_correction; if (xmin >= 0) { @@ -379,6 +384,8 @@ } } plfit_set_error_handler(plfit_stored_error_handler); + + RNG_END(); switch (retval) { case PLFIT_FAILURE: diff --git a/igraph/src/partition.cc b/igraph/src/partition.cc --- a/igraph/src/partition.cc +++ b/igraph/src/partition.cc @@ -1,4 +1,4 @@ -#include +#include #include #include #include "graph.hh" @@ -344,7 +344,7 @@ } - +#if 0 size_t Partition::print(FILE* const fp, const bool add_newline) const { @@ -388,7 +388,7 @@ if(add_newline) r += fprintf(fp, "\n"); return r; } - +#endif void diff --git a/igraph/src/paths.c b/igraph/src/paths.c --- a/igraph/src/paths.c +++ b/igraph/src/paths.c @@ -21,6 +21,7 @@ */ +#include "igraph_paths.h" #include "igraph_interface.h" #include "igraph_interrupt_internal.h" #include "igraph_vector_ptr.h" diff --git a/igraph/src/platform.c b/igraph/src/platform.c new file mode 100644 --- /dev/null +++ b/igraph/src/platform.c @@ -0,0 +1,36 @@ +/* platform.c + * + * Copyright (C) 2014 Tamas Nepusz + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or (at + * your option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + */ + +#include "platform.h" + +#ifdef _MSC_VER + +inline double _plfit_fmin(double a, double b) { + return (a < b) ? a : b; +} + +inline double _plfit_round(double x) { + return floor(x+0.5); +} + +#endif + +/* Dummy function to prevent a warning when compiling with Clang - the file + * would contain no symbols */ +void _plfit_i_unused() {} diff --git a/igraph/src/plfit.c b/igraph/src/plfit.c --- a/igraph/src/plfit.c +++ b/igraph/src/plfit.c @@ -1,778 +1,1309 @@ -/* plfit.c - * - * Copyright (C) 2010-2011 Tamas Nepusz - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -#include -#include -#include -#include -#include -#include "error.h" -#include "gss.h" -#include "lbfgs.h" -#include "platform.h" -#include "plfit.h" -#include "kolmogorov.h" -#include "zeta.h" - -/* #define PLFIT_DEBUG */ - -#define DATA_POINTS_CHECK \ - if (n <= 0) { \ - PLFIT_ERROR("no data points", PLFIT_EINVAL); \ - } - -#define XMIN_CHECK_ZERO \ - if (xmin <= 0) { \ - PLFIT_ERROR("xmin must be greater than zero", PLFIT_EINVAL); \ - } -#define XMIN_CHECK_ONE \ - if (xmin < 1) { \ - PLFIT_ERROR("xmin must be at least 1", PLFIT_EINVAL); \ - } - -static int double_comparator(const void *a, const void *b) { - const double *da = (const double*)a; - const double *db = (const double*)b; - return (*da > *db) - (*da < *db); -} - -/** - * Given a sorted array of doubles, return another array that contains pointers - * into the array for the start of each block of identical elements. - * - * \param begin pointer to the beginning of the array - * \param end pointer to the first element after the end of the array - * \param result_length if not \c NULL, the number of unique elements in the - * given array is returned here - */ -static double** unique_element_pointers(double* begin, double* end, size_t* result_length) { - double* ptr = begin; - double** result; - double prev_x; - size_t num_elts = 15; - size_t used_elts = 0; - - /* Special case: empty array */ - if (begin == end) { - result = calloc(1, sizeof(double*)); - if (result != 0) { - result[0] = 0; - } - return result; - } - - /* Allocate initial result array, including the guard element */ - result = calloc(num_elts+1, sizeof(double*)); - if (result == 0) - return 0; - - prev_x = *begin; - result[used_elts++] = begin; - - /* Process the input array */ - for (ptr = begin+1; ptr < end; ptr++) { - if (*ptr == prev_x) - continue; - - /* New block found */ - if (used_elts >= num_elts) { - /* Array full; allocate a new chunk */ - num_elts = num_elts*2 + 1; - result = realloc(result, sizeof(double*) * (num_elts+1)); - if (result == 0) - return 0; - } - - /* Store the new element */ - result[used_elts++] = ptr; - prev_x = *ptr; - } - - /* Calculate the result length */ - if (result_length != 0) { - *result_length = used_elts; - } - - /* Add the guard entry to the end of the result */ - result[used_elts++] = 0; - - return result; -} - -static void plfit_i_perform_finite_size_correction(plfit_result_t* result, size_t n) { - result->alpha = result->alpha * (n-1) / n + 1.0 / n; -} - -/********** Continuous power law distribution fitting **********/ - -void plfit_i_logsum_less_than_continuous(double* begin, double* end, - double xmin, double* result, size_t* m) { - double logsum = 0.0; - size_t count = 0; - - for (; begin != end; begin++) { - if (*begin >= xmin) { - count++; - logsum += log(*begin / xmin); - } - } - - *m = count; - *result = logsum; -} - -double plfit_i_logsum_continuous(double* begin, double* end, double xmin) { - double logsum = 0.0; - for (; begin != end; begin++) - logsum += log(*begin / xmin); - return logsum; -} - -int plfit_i_estimate_alpha_continuous(double* xs, size_t n, - double xmin, double* alpha) { - double result; - size_t m; - - XMIN_CHECK_ZERO; - - plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &result, &m); - - if (m == 0) { - PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL); - } - - *alpha = 1 + m / result; - - return PLFIT_SUCCESS; -} - -int plfit_i_estimate_alpha_continuous_sorted(double* xs, size_t n, - double xmin, double* alpha) { - double* end = xs+n; - - XMIN_CHECK_ZERO; - - for (; xs != end && *xs < xmin; xs++); - if (xs == end) { - PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL); - } - - *alpha = 1 + (end-xs) / plfit_i_logsum_continuous(xs, end, xmin); - - return PLFIT_SUCCESS; -} - -static int plfit_i_ks_test_continuous(double* xs, double* xs_end, - const double alpha, const double xmin, double* D) { - /* Assumption: xs is sorted and cut off at xmin so the first element is - * always larger than or equal to xmin. */ - double result = 0, n; - int m = 0; - - n = xs_end - xs; - - while (xs < xs_end) { - double d = fabs(1-pow(xmin / *xs, alpha-1) - m / n); - - if (d > result) - result = d; - - xs++; m++; - } - - *D = result; - - return PLFIT_SUCCESS; -} - -int plfit_log_likelihood_continuous(double* xs, size_t n, double alpha, - double xmin, double* L) { - double logsum, c; - size_t m; - - if (alpha <= 1) { - PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL); - } - XMIN_CHECK_ZERO; - - c = (alpha - 1) / xmin; - plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &logsum, &m); - *L = -alpha * logsum + log(c) * m; - - return PLFIT_SUCCESS; -} - -int plfit_estimate_alpha_continuous(double* xs, size_t n, double xmin, - const plfit_continuous_options_t* options, plfit_result_t *result) { - double *xs_copy; - - if (!options) - options = &plfit_continuous_default_options; - - /* Make a copy of xs and sort it */ - xs_copy = (double*)malloc(sizeof(double) * n); - memcpy(xs_copy, xs, sizeof(double) * n); - qsort(xs_copy, n, sizeof(double), double_comparator); - - PLFIT_CHECK(plfit_estimate_alpha_continuous_sorted(xs_copy, n, xmin, - options, result)); - - free(xs_copy); - - return PLFIT_SUCCESS; -} - -int plfit_estimate_alpha_continuous_sorted(double* xs, size_t n, double xmin, - const plfit_continuous_options_t* options, plfit_result_t *result) { - double* end; - - if (!options) - options = &plfit_continuous_default_options; - - end = xs + n; - while (xs < end && *xs < xmin) - xs++; - n = (size_t) (end - xs); - - PLFIT_CHECK(plfit_i_estimate_alpha_continuous_sorted(xs, n, - xmin, &result->alpha)); - PLFIT_CHECK(plfit_i_ks_test_continuous(xs, end, result->alpha, - xmin, &result->D)); - - if (options->finite_size_correction) - plfit_i_perform_finite_size_correction(result, n); - result->xmin = xmin; - result->p = plfit_ks_test_one_sample_p(result->D, n); - plfit_log_likelihood_continuous(xs, n, result->alpha, result->xmin, &result->L); - - return PLFIT_SUCCESS; -} - -typedef struct { - double *begin; /**< Pointer to the beginning of the array holding the data */ - double *end; /**< Pointer to after the end of the array holding the data */ - double **uniques; /**< Pointers to unique elements of the input array */ - plfit_result_t last; /**< Result of the last evaluation */ -} plfit_continuous_xmin_opt_data_t; - -double plfit_i_continuous_xmin_opt_evaluate(void* instance, double x) { - plfit_continuous_xmin_opt_data_t* data = (plfit_continuous_xmin_opt_data_t*)instance; - double* begin = data->uniques[(int)x]; - - data->last.xmin = *begin; - -#ifdef PLFIT_DEBUG - printf("Trying with xmin = %.4f\n", *begin); -#endif - - plfit_i_estimate_alpha_continuous_sorted(begin, (size_t) (data->end-begin), *begin, - &data->last.alpha); - plfit_i_ks_test_continuous(begin, data->end, data->last.alpha, *begin, - &data->last.D); - - return data->last.D; -} - -int plfit_i_continuous_xmin_opt_progress(void* instance, double x, double fx, - double min, double fmin, double left, double right, int k) { -#ifdef PLFIT_DEBUG - printf("Iteration #%d: [%.4f; %.4f), x=%.4f, fx=%.4f, min=%.4f, fmin=%.4f\n", - k, left, right, x, fx, min, fmin); -#endif - - /* Continue only if `left' and `right' point to different integers */ - return (int)left == (int)right; -} - -int plfit_continuous(double* xs, size_t n, const plfit_continuous_options_t* options, - plfit_result_t* result) { - gss_parameter_t gss_param; - plfit_continuous_xmin_opt_data_t opt_data; - plfit_result_t best_result; - int success; - size_t i, best_n, num_uniques; - double x, *px; - - DATA_POINTS_CHECK; - - if (!options) - options = &plfit_continuous_default_options; - - /* Make a copy of xs and sort it */ - opt_data.begin = (double*)malloc(sizeof(double) * n); - memcpy(opt_data.begin, xs, sizeof(double) * n); - qsort(opt_data.begin, n, sizeof(double), double_comparator); - opt_data.end = opt_data.begin + n; - - /* Create an array containing pointers to the unique elements of the input. From - * each block of unique elements, we add the pointer to the first one. */ - opt_data.uniques = unique_element_pointers(opt_data.begin, opt_data.end, - &num_uniques); - if (opt_data.uniques == 0) - return PLFIT_ENOMEM; - - /* We will now determine the best xmin that yields the lowest D-score. - * First we try a golden section search if needed. If that fails, we try - * a linear search. - */ - if (options->xmin_method == PLFIT_GSS_OR_LINEAR && num_uniques > 5) { - gss_parameter_init(&gss_param); - success = (gss(0, num_uniques-5, &x, 0, - plfit_i_continuous_xmin_opt_evaluate, - plfit_i_continuous_xmin_opt_progress, &opt_data, &gss_param) == 0); - best_result = opt_data.last; - /* plfit_i_continuous_xmin_opt_evaluate will set opt_data.last to - * indicate the location of the optimum and the value of D */ - } else { - success = 0; - } - - if (success) { - /* calculate best_n because we'll need it later. Luckily x indicates - * the index in opt_data.uniques that we have to look up in order to - * find the first element in the array that is included */ - px = opt_data.uniques[(int)x]; - best_n = (size_t) (opt_data.end-px+1); - } else { - /* GSS failed or skipped; try linear search */ - - /* Prepare some variables */ - best_n = 0; - best_result.D = DBL_MAX; - best_result.xmin = 0; - best_result.alpha = 0; - - for (i = 0; i < num_uniques-1; i++) { - plfit_i_continuous_xmin_opt_evaluate(&opt_data, i); - if (opt_data.last.D < best_result.D) { - best_result = opt_data.last; - best_n = (size_t) (opt_data.end - - opt_data.uniques[i] + 1); - } - } - } - - /* Get rid of the uniques array, we don't need it any more */ - free(opt_data.uniques); - - /* Sort out the result */ - *result = best_result; - if (options->finite_size_correction) - plfit_i_perform_finite_size_correction(result, best_n); - result->p = plfit_ks_test_one_sample_p(result->D, best_n); - plfit_log_likelihood_continuous(opt_data.begin + n - best_n, best_n, - result->alpha, result->xmin, &result->L); - - /* Get rid of the copied data as well */ - free(opt_data.begin); - - return PLFIT_SUCCESS; -} - -/********** Discrete power law distribution fitting **********/ - -typedef struct { - size_t m; - double logsum; - double xmin; -} plfit_i_estimate_alpha_discrete_data_t; - -double plfit_i_logsum_discrete(double* begin, double* end, double xmin) { - double logsum = 0.0; - for (; begin != end; begin++) - logsum += log(*begin); - return logsum; -} - -void plfit_i_logsum_less_than_discrete(double* begin, double* end, double xmin, - double* logsum, size_t* m) { - double result = 0.0; - size_t count = 0; - - for (; begin != end; begin++) { - if (*begin < xmin) - continue; - - result += log(*begin); - count++; - } - - *logsum = result; - *m = count; -} - -lbfgsfloatval_t plfit_i_estimate_alpha_discrete_lbfgs_evaluate( - void* instance, const lbfgsfloatval_t* x, - lbfgsfloatval_t* g, const int n, - const lbfgsfloatval_t step) { - plfit_i_estimate_alpha_discrete_data_t* data; - lbfgsfloatval_t result; - double dx = step; - double huge = 1e10; /* pseudo-infinity; apparently DBL_MAX does not work */ - - data = (plfit_i_estimate_alpha_discrete_data_t*)instance; - -#ifdef PLFIT_DEBUG - printf("- Evaluating at %.4f (step = %.4f, xmin = %.4f)\n", *x, step, data->xmin); -#endif - - if (isnan(*x)) { - g[0] = huge; - return huge; - } - - /* Find the delta X value to estimate the gradient */ - if (dx > 0.001 || dx == 0) - dx = 0.001; - else if (dx < -0.001) - dx = -0.001; - - /* Is x[0] in its valid range? */ - if (x[0] <= 1.0) { - /* The Hurwitz zeta function is infinite in this case */ - g[0] = (dx > 0) ? -huge : huge; - return huge; - } - if (x[0] + dx <= 1.0) - g[0] = huge; - else - g[0] = data->logsum + data->m * - (log(gsl_sf_hzeta(x[0] + dx, data->xmin)) - log(gsl_sf_hzeta(x[0], data->xmin))) / dx; - - result = x[0] * data->logsum + data->m * log(gsl_sf_hzeta(x[0], data->xmin)); - -#ifdef PLFIT_DEBUG - printf(" - Gradient: %.4f\n", g[0]); - printf(" - Result: %.4f\n", result); -#endif - - return result; -} - -int plfit_i_estimate_alpha_discrete_lbfgs_progress(void* instance, - const lbfgsfloatval_t* x, const lbfgsfloatval_t* g, - const lbfgsfloatval_t fx, const lbfgsfloatval_t xnorm, - const lbfgsfloatval_t gnorm, const lbfgsfloatval_t step, - int n, int k, int ls) { - return 0; -} - -int plfit_i_estimate_alpha_discrete_linear_scan(double* xs, size_t n, double xmin, - double* alpha, const plfit_discrete_options_t* options, - plfit_bool_t sorted) { - double curr_alpha, best_alpha, L, L_max; - double logsum; - size_t m; - - XMIN_CHECK_ONE; - if (options->alpha.min <= 1.0) { - PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL); - } - if (options->alpha.max < options->alpha.min) { - PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL); - } - if (options->alpha.step <= 0) { - PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL); - } - - if (sorted) { - logsum = plfit_i_logsum_discrete(xs, xs+n, xmin); - m = n; - } else { - plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &logsum, &m); - } - - best_alpha = options->alpha.min; L_max = -DBL_MAX; - for (curr_alpha = options->alpha.min; curr_alpha <= options->alpha.max; - curr_alpha += options->alpha.step) { - L = -curr_alpha * logsum - m * log(gsl_sf_hzeta(curr_alpha, xmin)); - if (L > L_max) { - L_max = L; - best_alpha = curr_alpha; - } - } - - *alpha = best_alpha; - - return PLFIT_SUCCESS; -} - -int plfit_i_estimate_alpha_discrete_lbfgs(double* xs, size_t n, double xmin, - double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) { - lbfgs_parameter_t param; - lbfgsfloatval_t* variables; - plfit_i_estimate_alpha_discrete_data_t data; - int ret; - - XMIN_CHECK_ONE; - - /* Initialize algorithm parameters */ - lbfgs_parameter_init(¶m); - param.max_iterations = 0; /* proceed until infinity */ - - /* Set up context for optimization */ - data.xmin = xmin; - if (sorted) { - data.logsum = plfit_i_logsum_discrete(xs, xs+n, xmin); - data.m = n; - } else { - plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &data.logsum, &data.m); - } - - /* Allocate space for the single alpha variable */ - variables = lbfgs_malloc(1); - variables[0] = 3.0; /* initial guess */ - - /* Optimization */ - ret = lbfgs(1, variables, /* ptr_fx = */ 0, - plfit_i_estimate_alpha_discrete_lbfgs_evaluate, - plfit_i_estimate_alpha_discrete_lbfgs_progress, - &data, ¶m); - - if (ret < 0 && - ret != LBFGSERR_ROUNDING_ERROR && - ret != LBFGSERR_MAXIMUMLINESEARCH && - ret != LBFGSERR_CANCELED) { - char buf[4096]; - snprintf(buf, 4096, "L-BFGS optimization signaled an error (error code = %d)", ret); - lbfgs_free(variables); - PLFIT_ERROR(buf, PLFIT_FAILURE); - } - *alpha = variables[0]; - - /* Deallocate the variable array */ - lbfgs_free(variables); - - return PLFIT_SUCCESS; -} - -int plfit_i_estimate_alpha_discrete_fast(double* xs, size_t n, double xmin, - double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) { - plfit_continuous_options_t cont_options; - - if (!options) - options = &plfit_discrete_default_options; - - plfit_continuous_options_init(&cont_options); - cont_options.finite_size_correction = options->finite_size_correction; - - XMIN_CHECK_ONE; - - if (sorted) { - return plfit_i_estimate_alpha_continuous_sorted(xs, n, xmin-0.5, alpha); - } else { - return plfit_i_estimate_alpha_continuous(xs, n, xmin-0.5, alpha); - } -} - -int plfit_i_estimate_alpha_discrete(double* xs, size_t n, double xmin, - double* alpha, const plfit_discrete_options_t* options, - plfit_bool_t sorted) { - switch (options->alpha_method) { - case PLFIT_LBFGS: - PLFIT_CHECK(plfit_i_estimate_alpha_discrete_lbfgs(xs, n, xmin, alpha, - options, sorted)); - break; - - case PLFIT_LINEAR_SCAN: - PLFIT_CHECK(plfit_i_estimate_alpha_discrete_linear_scan(xs, n, xmin, - alpha, options, sorted)); - break; - - case PLFIT_PRETEND_CONTINUOUS: - PLFIT_CHECK(plfit_i_estimate_alpha_discrete_fast(xs, n, xmin, - alpha, options, sorted)); - break; - - default: - PLFIT_ERROR("unknown optimization method specified", PLFIT_EINVAL); - } - - return PLFIT_SUCCESS; -} - -static int plfit_i_ks_test_discrete(double* xs, double* xs_end, const double alpha, - const double xmin, double* D) { - /* Assumption: xs is sorted and cut off at xmin so the first element is - * always larger than or equal to xmin. */ - double result = 0, n, hzeta, x; - int m = 0; - - n = xs_end - xs; - hzeta = gsl_sf_hzeta(alpha, xmin); - - while (xs < xs_end) { - double d; - - x = *xs; - d = fabs(1-(gsl_sf_hzeta(alpha, x) / hzeta) - m / n); - - if (d > result) - result = d; - - do { - xs++; m++; - } while (xs < xs_end && *xs == x); - } - - *D = result; - - return PLFIT_SUCCESS; -} - -int plfit_log_likelihood_discrete(double* xs, size_t n, double alpha, double xmin, double* L) { - double result; - size_t m; - - if (alpha <= 1) { - PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL); - } - XMIN_CHECK_ONE; - - plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &result, &m); - result = - alpha * result - m * log(gsl_sf_hzeta(alpha, xmin)); - - *L = result; - - return PLFIT_SUCCESS; -} - -int plfit_estimate_alpha_discrete(double* xs, size_t n, double xmin, - const plfit_discrete_options_t* options, plfit_result_t *result) { - double *xs_copy, *end; - - if (!options) - options = &plfit_discrete_default_options; - - /* Check the validity of the input parameters */ - DATA_POINTS_CHECK; - if (options->alpha_method == PLFIT_LINEAR_SCAN) { - if (options->alpha.min <= 1.0) { - PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL); - } - if (options->alpha.max < options->alpha.min) { - PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL); - } - if (options->alpha.step <= 0) { - PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL); - } - } - - /* Make a copy of xs and sort it */ - xs_copy = (double*)malloc(sizeof(double) * n); - memcpy(xs_copy, xs, sizeof(double) * n); - qsort(xs_copy, n, sizeof(double), double_comparator); - - xs = xs_copy; end = xs_copy + n; - while (xs < end && *xs < xmin) - xs++; - n = (size_t) (end - xs); - - PLFIT_CHECK(plfit_i_estimate_alpha_discrete(xs, n, xmin, &result->alpha, - options, /* sorted = */ 1)); - PLFIT_CHECK(plfit_i_ks_test_discrete(xs, end, result->alpha, xmin, &result->D)); - - result->xmin = xmin; - if (options->finite_size_correction) - plfit_i_perform_finite_size_correction(result, n); - result->p = plfit_ks_test_one_sample_p(result->D, n); - plfit_log_likelihood_discrete(xs, n, result->alpha, result->xmin, &result->L); - - free(xs_copy); - - return PLFIT_SUCCESS; -} - -int plfit_discrete(double* xs, size_t n, const plfit_discrete_options_t* options, - plfit_result_t* result) { - double curr_D, curr_alpha; - plfit_result_t best_result; - double *xs_copy, *px, *end, *end_xmin, prev_x; - size_t best_n; - size_t m; - - if (!options) - options = &plfit_discrete_default_options; - - /* Check the validity of the input parameters */ - DATA_POINTS_CHECK; - if (options->alpha_method == PLFIT_LINEAR_SCAN) { - if (options->alpha.min <= 1.0) { - PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL); - } - if (options->alpha.max < options->alpha.min) { - PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL); - } - if (options->alpha.step <= 0) { - PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL); - } - } - - /* Make a copy of xs and sort it */ - xs_copy = (double*)malloc(sizeof(double) * n); - memcpy(xs_copy, xs, sizeof(double) * n); - qsort(xs_copy, n, sizeof(double), double_comparator); - - best_result.D = DBL_MAX; - best_result.xmin = 1; - best_result.alpha = 1; - best_n = 0; - - /* Make sure there are at least three distinct values if possible */ - px = xs_copy; end = px + n; end_xmin = end - 1; m = 0; - prev_x = *end_xmin; - while (*end_xmin == prev_x && end_xmin > px) - end_xmin--; - prev_x = *end_xmin; - while (*end_xmin == prev_x && end_xmin > px) - end_xmin--; - - prev_x = 0; - while (px < end_xmin) { - while (px < end_xmin && *px == prev_x) { - px++; m++; - } - - plfit_i_estimate_alpha_discrete(px, n - m, *px, - &curr_alpha, options, /* sorted = */ 1); - plfit_i_ks_test_discrete(px, end, curr_alpha, *px, &curr_D); - - if (curr_D < best_result.D) { - best_result.alpha = curr_alpha; - best_result.xmin = *px; - best_result.D = curr_D; - best_n = n - m; - } - - prev_x = *px; - px++; m++; - } - - *result = best_result; - if (options->finite_size_correction) - plfit_i_perform_finite_size_correction(result, best_n); - result->p = plfit_ks_test_one_sample_p(result->D, best_n); - plfit_log_likelihood_discrete(xs_copy+(n-best_n), best_n, - result->alpha, result->xmin, &result->L); - - free(xs_copy); - - return PLFIT_SUCCESS; -} - +/* vim:set ts=4 sw=4 sts=4 et: */ +/* plfit.c + * + * Copyright (C) 2010-2011 Tamas Nepusz + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or (at + * your option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + */ + +#include +#include +#include +#include +#include +#include "error.h" +#include "gss.h" +#include "lbfgs.h" +#include "platform.h" +#include "plfit.h" +#include "kolmogorov.h" +#include "sampling.h" +#include "hzeta.h" + +/* #define PLFIT_DEBUG */ + +#define DATA_POINTS_CHECK \ + if (n <= 0) { \ + PLFIT_ERROR("no data points", PLFIT_EINVAL); \ + } + +#define XMIN_CHECK_ZERO \ + if (xmin <= 0) { \ + PLFIT_ERROR("xmin must be greater than zero", PLFIT_EINVAL); \ + } +#define XMIN_CHECK_ONE \ + if (xmin < 1) { \ + PLFIT_ERROR("xmin must be at least 1", PLFIT_EINVAL); \ + } + +static int plfit_i_resample_continuous(double* xs_head, size_t num_smaller, + size_t n, double alpha, double xmin, size_t num_samples, mt_rng_t* rng, + double* result); +static int plfit_i_resample_discrete(double* xs_head, size_t num_smaller, + size_t n, double alpha, double xmin, size_t num_samples, mt_rng_t* rng, + double* result); + +static int double_comparator(const void *a, const void *b) { + const double *da = (const double*)a; + const double *db = (const double*)b; + return (*da > *db) - (*da < *db); +} + +static int plfit_i_copy_and_sort(double* xs, size_t n, double** result) { + *result = (double*)malloc(sizeof(double) * n); + if (*result == 0) { + PLFIT_ERROR("cannot create sorted copy of input data", PLFIT_ENOMEM); + } + + memcpy(*result, xs, sizeof(double) * n); + qsort(*result, n, sizeof(double), double_comparator); + + return PLFIT_SUCCESS; +} + +/** + * Given an unsorted array of doubles, counts how many elements there are that + * are smaller than a given value. + * + * \param begin pointer to the beginning of the array + * \param end pointer to the first element after the end of the array + * \param xmin the threshold value + * + * \return the nubmer of elements in the array that are smaller than the given + * value. + */ +static size_t count_smaller(double* begin, double* end, double xmin) { + double* p; + size_t counter = 0; + + for (p = begin; p < end; p++) { + if (*p < xmin) { + counter++; + } + } + + return counter; +} + +/** + * Given an unsorted array of doubles, return another array that contains the + * elements that are smaller than a given value + * + * \param begin pointer to the beginning of the array + * \param end pointer to the first element after the end of the array + * \param xmin the threshold value + * \param result_length if not \c NULL, the number of unique elements in the + * given array is returned here + * + * \return pointer to the head of the new array or 0 if there is not enough + * memory + */ +static double* extract_smaller(double* begin, double* end, double xmin, + size_t* result_length) { + size_t counter = count_smaller(begin, end, xmin); + double *p, *result; + + result = calloc(counter, sizeof(double)); + if (result == 0) + return 0; + + for (p = result; begin < end; begin++) { + if (*begin < xmin) { + *p = *begin; + p++; + } + } + + if (result_length) { + *result_length = counter; + } + + return result; +} + +/** + * Given a sorted array of doubles, return another array that contains pointers + * into the array for the start of each block of identical elements. + * + * \param begin pointer to the beginning of the array + * \param end pointer to the first element after the end of the array + * \param result_length if not \c NULL, the number of unique elements in the + * given array is returned here + * + * \return pointer to the head of the new array or 0 if there is not enough + * memory + */ +static double** unique_element_pointers(double* begin, double* end, size_t* result_length) { + double* ptr = begin; + double** result; + double prev_x; + size_t num_elts = 15; + size_t used_elts = 0; + + /* Special case: empty array */ + if (begin == end) { + result = calloc(1, sizeof(double*)); + if (result != 0) { + result[0] = 0; + } + return result; + } + + /* Allocate initial result array, including the guard element */ + result = calloc(num_elts+1, sizeof(double*)); + if (result == 0) + return 0; + + prev_x = *begin; + result[used_elts++] = begin; + + /* Process the input array */ + for (ptr = begin+1; ptr < end; ptr++) { + if (*ptr == prev_x) + continue; + + /* New block found */ + if (used_elts >= num_elts) { + /* Array full; allocate a new chunk */ + num_elts = num_elts*2 + 1; + result = realloc(result, sizeof(double*) * (num_elts+1)); + if (result == 0) + return 0; + } + + /* Store the new element */ + result[used_elts++] = ptr; + prev_x = *ptr; + } + + /* Calculate the result length */ + if (result_length != 0) { + *result_length = used_elts; + } + + /* Add the guard entry to the end of the result */ + result[used_elts++] = 0; + + return result; +} + +static void plfit_i_perform_finite_size_correction(plfit_result_t* result, size_t n) { + result->alpha = result->alpha * (n-1) / n + 1.0 / n; +} + +/********** Continuous power law distribution fitting **********/ + +static void plfit_i_logsum_less_than_continuous(double* begin, double* end, + double xmin, double* result, size_t* m) { + double logsum = 0.0; + size_t count = 0; + + for (; begin != end; begin++) { + if (*begin >= xmin) { + count++; + logsum += log(*begin / xmin); + } + } + + *m = count; + *result = logsum; +} + +static double plfit_i_logsum_continuous(double* begin, double* end, double xmin) { + double logsum = 0.0; + for (; begin != end; begin++) + logsum += log(*begin / xmin); + return logsum; +} + +static int plfit_i_estimate_alpha_continuous(double* xs, size_t n, + double xmin, double* alpha) { + double result; + size_t m; + + XMIN_CHECK_ZERO; + + plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &result, &m); + + if (m == 0) { + PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL); + } + + *alpha = 1 + m / result; + + return PLFIT_SUCCESS; +} + +static int plfit_i_estimate_alpha_continuous_sorted(double* xs, size_t n, + double xmin, double* alpha) { + double* end = xs+n; + + XMIN_CHECK_ZERO; + + for (; xs != end && *xs < xmin; xs++); + if (xs == end) { + PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL); + } + + *alpha = 1 + (end-xs) / plfit_i_logsum_continuous(xs, end, xmin); + + return PLFIT_SUCCESS; +} + +static int plfit_i_ks_test_continuous(double* xs, double* xs_end, + const double alpha, const double xmin, double* D) { + /* Assumption: xs is sorted and cut off at xmin so the first element is + * always larger than or equal to xmin. */ + double result = 0, n; + int m = 0; + + n = xs_end - xs; + + while (xs < xs_end) { + double d = fabs(1-pow(xmin / *xs, alpha-1) - m / n); + + if (d > result) + result = d; + + xs++; m++; + } + + *D = result; + + return PLFIT_SUCCESS; +} + +static int plfit_i_calculate_p_value_continuous(double* xs, size_t n, + const plfit_continuous_options_t *options, plfit_bool_t xmin_fixed, + plfit_result_t *result) { + long int num_trials; + long int successes = 0; + double *xs_head; + size_t num_smaller; + plfit_continuous_options_t options_no_p_value = *options; + int retval = PLFIT_SUCCESS; + + if (options->p_value_method == PLFIT_P_VALUE_SKIP) { + result->p = NAN; + return PLFIT_SUCCESS; + } + + if (options->p_value_method == PLFIT_P_VALUE_APPROXIMATE) { + num_smaller = count_smaller(xs, xs + n, result->xmin); + result->p = plfit_ks_test_one_sample_p(result->D, n - num_smaller); + return PLFIT_SUCCESS; + } + + options_no_p_value.p_value_method = PLFIT_P_VALUE_SKIP; + num_trials = (long int)(0.25 / options->p_value_precision / options->p_value_precision); + if (num_trials <= 0) { + PLFIT_ERROR("invalid p-value precision", PLFIT_EINVAL); + } + + /* Extract the head of xs that contains elements smaller than xmin */ + xs_head = extract_smaller(xs, xs+n, result->xmin, &num_smaller); + if (xs_head == 0) + PLFIT_ERROR("cannot calculate exact p-value", PLFIT_ENOMEM); + +#ifdef _OPENMP +#pragma omp parallel +#endif + { + /* Parallel section starts here. If we are compiling using OpenMP, each + * thread will use its own RNG that is seeded from the master RNG. If + * we are compiling without OpenMP, there is only one thread and it uses + * the master RNG. This section must be critical to ensure that only one + * thread is using the master RNG at the same time. */ +#ifdef _OPENMP + mt_rng_t private_rng; +#endif + mt_rng_t *p_rng; + double *ys; + long int i; + plfit_result_t result_synthetic; + +#ifdef _OPENMP +#pragma omp critical + { + p_rng = &private_rng; + mt_init_from_rng(p_rng, options->rng); + } +#else + p_rng = options->rng; +#endif + + /* Allocate memory to sample into */ + ys = calloc(n, sizeof(double)); + if (ys == 0) { + retval = PLFIT_ENOMEM; + } else { + /* The main for loop starts here. */ +#ifdef _OPENMP +#pragma omp for reduction(+:successes) +#endif + for (i = 0; i < num_trials; i++) { + plfit_i_resample_continuous(xs_head, num_smaller, n, result->alpha, + result->xmin, n, p_rng, ys); + if (xmin_fixed) { + plfit_estimate_alpha_continuous(ys, n, result->xmin, + &options_no_p_value, &result_synthetic); + } else { + plfit_continuous(ys, n, &options_no_p_value, &result_synthetic); + } + if (result_synthetic.D > result->D) + successes++; + } + free(ys); + } + + /* End of parallelized part */ + } + + free(xs_head); + + if (retval == PLFIT_SUCCESS) { + result->p = successes / ((double)num_trials); + } else { + PLFIT_ERROR("cannot calculate exact p-value", retval); + } + + return retval; +} + +int plfit_log_likelihood_continuous(double* xs, size_t n, double alpha, + double xmin, double* L) { + double logsum, c; + size_t m; + + if (alpha <= 1) { + PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL); + } + XMIN_CHECK_ZERO; + + c = (alpha - 1) / xmin; + plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &logsum, &m); + *L = -alpha * logsum + log(c) * m; + + return PLFIT_SUCCESS; +} + +int plfit_estimate_alpha_continuous_sorted(double* xs, size_t n, double xmin, + const plfit_continuous_options_t* options, plfit_result_t *result) { + double *begin, *end; + + if (!options) + options = &plfit_continuous_default_options; + + begin = xs; + end = xs + n; + while (begin < end && *begin < xmin) + begin++; + + PLFIT_CHECK(plfit_i_estimate_alpha_continuous_sorted(begin, end-begin, + xmin, &result->alpha)); + PLFIT_CHECK(plfit_i_ks_test_continuous(begin, end, result->alpha, + xmin, &result->D)); + + if (options->finite_size_correction) + plfit_i_perform_finite_size_correction(result, end-begin); + result->xmin = xmin; + + PLFIT_CHECK(plfit_log_likelihood_continuous(begin, end-begin, result->alpha, + result->xmin, &result->L)); + PLFIT_CHECK(plfit_i_calculate_p_value_continuous(xs, n, options, 1, result)); + + return PLFIT_SUCCESS; +} + +int plfit_estimate_alpha_continuous(double* xs, size_t n, double xmin, + const plfit_continuous_options_t* options, plfit_result_t *result) { + double *xs_copy; + + if (!options) + options = &plfit_continuous_default_options; + + PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy)); + PLFIT_CHECK(plfit_estimate_alpha_continuous_sorted(xs_copy, n, xmin, + options, result)); + free(xs_copy); + + return PLFIT_SUCCESS; +} + +typedef struct { + double *begin; /**< Pointer to the beginning of the array holding the data */ + double *end; /**< Pointer to after the end of the array holding the data */ + double **probes; /**< Pointers to the elements of the array that will be probed */ + size_t num_probes; /**< Number of probes */ + plfit_result_t last; /**< Result of the last evaluation */ +} plfit_continuous_xmin_opt_data_t; + +static double plfit_i_continuous_xmin_opt_evaluate(void* instance, double x) { + plfit_continuous_xmin_opt_data_t* data = (plfit_continuous_xmin_opt_data_t*)instance; + double* begin = data->probes[(long int)x]; + + data->last.xmin = *begin; + +#ifdef PLFIT_DEBUG + printf("Trying with probes[%ld] = %.4f\n", (long int)x, *begin); +#endif + + plfit_i_estimate_alpha_continuous_sorted(begin, data->end-begin, *begin, + &data->last.alpha); + plfit_i_ks_test_continuous(begin, data->end, data->last.alpha, *begin, + &data->last.D); + + return data->last.D; +} + +static int plfit_i_continuous_xmin_opt_progress(void* instance, double x, double fx, + double min, double fmin, double left, double right, int k) { +#ifdef PLFIT_DEBUG + printf("Iteration #%d: [%.4f; %.4f), x=%.4f, fx=%.4f, min=%.4f, fmin=%.4f\n", + k, left, right, x, fx, min, fmin); +#endif + + /* Continue only if `left' and `right' point to different integers */ + return (int)left == (int)right; +} + +static int plfit_i_continuous_xmin_opt_linear_scan( + plfit_continuous_xmin_opt_data_t* opt_data, plfit_result_t* best_result, + size_t* best_n) { + size_t i; + plfit_result_t global_best_result; + size_t global_best_n; + + /* Prepare some variables */ + global_best_n = 0; + global_best_result.D = DBL_MAX; + global_best_result.xmin = 0; + global_best_result.alpha = 0; + + /* Due to the OpenMP parallelization, we do things as follows. Each + * OpenMP thread will search for the best D-score on its own and store + * the result in a private local_best_result variable. The end of the + * parallel block contains a critical section that threads will enter + * one by one and compare their private local_best_result with a + * global_best that is shared among the threads. + */ +#ifdef _OPENMP +#pragma omp parallel shared(global_best_result, global_best_n) private(i) firstprivate(opt_data) +#endif + { + /* These variables are private since they are declared within the + * parallel block */ + plfit_result_t local_best_result; + plfit_continuous_xmin_opt_data_t local_opt_data = *opt_data; + size_t local_best_n; + + /* Initialize the local_best_result and local_best_n variables */ + local_best_n = 0; + local_best_result.D = DBL_MAX; + local_best_result.xmin = 0; + local_best_result.alpha = 0; + + /* The range of the for loop below is divided among the threads. + * nowait means that there will be no implicit barrier at the end + * of the loop so threads that get there earlier can enter the + * critical section without waiting for the others */ +#ifdef _OPENMP +#pragma omp for nowait schedule(dynamic,10) +#endif + for (i = 0; i < local_opt_data.num_probes-1; i++) { + plfit_i_continuous_xmin_opt_evaluate(&local_opt_data, i); + if (local_opt_data.last.D < local_best_result.D) { +#ifdef PLFIT_DEBUG + printf("Found new local best at %g with D=%g\n", + local_opt_data.last.xmin, local_opt_data.last.D); +#endif + local_best_result = local_opt_data.last; + local_best_n = local_opt_data.end - local_opt_data.probes[i] + 1; + } + } + + /* Critical section that finds the global best result from the + * local ones collected by each thread */ +#ifdef _OPENMP +#pragma omp critical +#endif + if (local_best_result.D < global_best_result.D) { + global_best_result = local_best_result; + global_best_n = local_best_n; +#ifdef PLFIT_DEBUG + printf("Found new global best at %g with D=%g\n", global_best_result.xmin, + global_best_result.D); +#endif + } + } + + *best_result = global_best_result; + *best_n = global_best_n; + +#ifdef PLFIT_DEBUG + printf("Returning global best: %g\n", best_result->xmin); +#endif + + return PLFIT_SUCCESS; +} + +int plfit_continuous(double* xs, size_t n, const plfit_continuous_options_t* options, + plfit_result_t* result) { + gss_parameter_t gss_param; + plfit_continuous_xmin_opt_data_t opt_data; + plfit_result_t best_result = { + /* alpha = */ NAN, + /* xmin = */ NAN, + /* L = */ NAN, + /* D = */ NAN, + /* p = */ NAN + }; + + int success; + size_t i, best_n, num_uniques; + double x, *px, **uniques; + + DATA_POINTS_CHECK; + + /* Sane defaults */ + best_n = n; + if (!options) + options = &plfit_continuous_default_options; + + /* Make a copy of xs and sort it */ + PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &opt_data.begin)); + opt_data.end = opt_data.begin + n; + + /* Create an array containing pointers to the unique elements of the input. From + * each block of unique elements, we add the pointer to the first one. */ + uniques = unique_element_pointers(opt_data.begin, opt_data.end, &num_uniques); + if (uniques == 0) + PLFIT_ERROR("cannot fit continuous power-law", PLFIT_ENOMEM); + + /* We will now determine the best xmin that yields the lowest D-score. The + * 'success' variable will denote whether the search procedure we tried was + * successful. If it is false after having exhausted all options, we fall + * back to a linear search. */ + success = 0; + switch (options->xmin_method) { + case PLFIT_GSS_OR_LINEAR: + /* Try golden section search first. */ + if (num_uniques > 5) { + opt_data.probes = uniques; + opt_data.num_probes = num_uniques; + gss_parameter_init(&gss_param); + success = (gss(0, opt_data.num_probes-5, &x, 0, + plfit_i_continuous_xmin_opt_evaluate, + plfit_i_continuous_xmin_opt_progress, &opt_data, &gss_param) == 0); + if (success) { + px = opt_data.probes[(int)x]; + best_n = opt_data.end-px+1; + best_result = opt_data.last; + } + } + break; + + case PLFIT_STRATIFIED_SAMPLING: + if (num_uniques >= 50) { + /* Try stratified sampling to narrow down the interval where the minimum + * is likely to reside. We check 10% of the unique items, distributed + * evenly, find the one with the lowest D-score, and then check the + * area around it more thoroughly. */ + const size_t subdivision_length = 10; + size_t num_strata = num_uniques / subdivision_length; + double **strata = calloc(num_strata, sizeof(double*)); + + for (i = 0; i < num_strata; i++) { + strata[i] = uniques[i * subdivision_length]; + } + + opt_data.probes = strata; + opt_data.num_probes = num_strata; + plfit_i_continuous_xmin_opt_linear_scan(&opt_data, &best_result, &best_n); + + opt_data.num_probes = 0; + for (i = 0; i < num_strata; i++) { + if (*strata[i] == best_result.xmin) { + /* Okay, scan more thoroughly from strata[i-1] to strata[i+1], + * which is from uniques[(i-1)*subdivision_length] to + * uniques[(i+1)*subdivision_length */ + opt_data.probes = uniques + (i > 0 ? (i-1)*subdivision_length : 0); + opt_data.num_probes = 0; + if (i != 0) + opt_data.num_probes += subdivision_length; + if (i != num_strata-1) + opt_data.num_probes += subdivision_length; + break; + } + } + + free(strata); + if (opt_data.num_probes > 0) { + /* Do a strict linear scan in the subrange determined above */ + plfit_i_continuous_xmin_opt_linear_scan(&opt_data, + &best_result, &best_n); + success = 1; + } else { + /* This should not happen, but we handle it anyway */ + success = 0; + } + } + break; + + default: + /* Just use the linear search */ + break; + } + + if (!success) { + /* More advanced search methods failed or were skipped; try linear search */ + opt_data.probes = uniques; + opt_data.num_probes = num_uniques; + plfit_i_continuous_xmin_opt_linear_scan(&opt_data, &best_result, &best_n); + success = 1; + } + + /* Get rid of the uniques array, we don't need it any more */ + free(uniques); + + /* Sort out the result */ + *result = best_result; + if (options->finite_size_correction) + plfit_i_perform_finite_size_correction(result, best_n); + + PLFIT_CHECK(plfit_log_likelihood_continuous(opt_data.begin + n - best_n, best_n, + result->alpha, result->xmin, &result->L)); + PLFIT_CHECK(plfit_i_calculate_p_value_continuous(opt_data.begin, n, options, 0, result)); + + /* Get rid of the copied data as well */ + free(opt_data.begin); + + return PLFIT_SUCCESS; +} + +/********** Discrete power law distribution fitting **********/ + +typedef struct { + size_t m; + double logsum; + double xmin; +} plfit_i_estimate_alpha_discrete_data_t; + +static double plfit_i_logsum_discrete(double* begin, double* end, double xmin) { + double logsum = 0.0; + for (; begin != end; begin++) + logsum += log(*begin); + return logsum; +} + +static void plfit_i_logsum_less_than_discrete(double* begin, double* end, double xmin, + double* logsum, size_t* m) { + double result = 0.0; + size_t count = 0; + + for (; begin != end; begin++) { + if (*begin < xmin) + continue; + + result += log(*begin); + count++; + } + + *logsum = result; + *m = count; +} + +static lbfgsfloatval_t plfit_i_estimate_alpha_discrete_lbfgs_evaluate( + void* instance, const lbfgsfloatval_t* x, + lbfgsfloatval_t* g, const int n, + const lbfgsfloatval_t step) { + plfit_i_estimate_alpha_discrete_data_t* data; + lbfgsfloatval_t result; + double dx = step; + double huge = 1e10; /* pseudo-infinity; apparently DBL_MAX does not work */ + double lnhzeta_x=NAN; + double lnhzeta_deriv_x=NAN; + + data = (plfit_i_estimate_alpha_discrete_data_t*)instance; + +#ifdef PLFIT_DEBUG + printf("- Evaluating at %.4f (step = %.4f, xmin = %.4f)\n", *x, step, data->xmin); +#endif + + if (isnan(*x)) { + g[0] = huge; + return huge; + } + + /* Find the delta X value to estimate the gradient */ + if (dx > 0.001 || dx == 0) + dx = 0.001; + else if (dx < -0.001) + dx = -0.001; + + /* Is x[0] in its valid range? */ + if (x[0] <= 1.0) { + /* The Hurwitz zeta function is infinite in this case */ + g[0] = (dx > 0) ? -huge : huge; + return huge; + } + if (x[0] + dx <= 1.0) { + g[0] = huge; + result = x[0] * data->logsum + data->m * hsl_sf_lnhzeta(x[0], data->xmin); + } else { + hsl_sf_lnhzeta_deriv_tuple(x[0], data->xmin, &lnhzeta_x, &lnhzeta_deriv_x); + g[0] = data->logsum + data->m * lnhzeta_deriv_x; + result = x[0] * data->logsum + data->m * lnhzeta_x; + } + +#ifdef PLFIT_DEBUG + printf(" - Gradient: %.4f\n", g[0]); + printf(" - Result: %.4f\n", result); +#endif + + return result; +} + +static int plfit_i_estimate_alpha_discrete_lbfgs_progress(void* instance, + const lbfgsfloatval_t* x, const lbfgsfloatval_t* g, + const lbfgsfloatval_t fx, const lbfgsfloatval_t xnorm, + const lbfgsfloatval_t gnorm, const lbfgsfloatval_t step, + int n, int k, int ls) { + return 0; +} + +static int plfit_i_estimate_alpha_discrete_linear_scan(double* xs, size_t n, + double xmin, double* alpha, const plfit_discrete_options_t* options, + plfit_bool_t sorted) { + double curr_alpha, best_alpha, L, L_max; + double logsum; + size_t m; + + XMIN_CHECK_ONE; + if (options->alpha.min <= 1.0) { + PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL); + } + if (options->alpha.max < options->alpha.min) { + PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL); + } + if (options->alpha.step <= 0) { + PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL); + } + + if (sorted) { + logsum = plfit_i_logsum_discrete(xs, xs+n, xmin); + m = n; + } else { + plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &logsum, &m); + } + + best_alpha = options->alpha.min; L_max = -DBL_MAX; + for (curr_alpha = options->alpha.min; curr_alpha <= options->alpha.max; + curr_alpha += options->alpha.step) { + L = -curr_alpha * logsum - m * hsl_sf_lnhzeta(curr_alpha, xmin); + if (L > L_max) { + L_max = L; + best_alpha = curr_alpha; + } + } + + *alpha = best_alpha; + + return PLFIT_SUCCESS; +} + +static int plfit_i_estimate_alpha_discrete_lbfgs(double* xs, size_t n, double xmin, + double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) { + lbfgs_parameter_t param; + lbfgsfloatval_t* variables; + plfit_i_estimate_alpha_discrete_data_t data; + int ret; + + XMIN_CHECK_ONE; + + /* Initialize algorithm parameters */ + lbfgs_parameter_init(¶m); + param.max_iterations = 0; /* proceed until infinity */ + + /* Set up context for optimization */ + data.xmin = xmin; + if (sorted) { + data.logsum = plfit_i_logsum_discrete(xs, xs+n, xmin); + data.m = n; + } else { + plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &data.logsum, &data.m); + } + + /* Allocate space for the single alpha variable */ + variables = lbfgs_malloc(1); + variables[0] = 3.0; /* initial guess */ + + /* Optimization */ + ret = lbfgs(1, variables, /* ptr_fx = */ 0, + plfit_i_estimate_alpha_discrete_lbfgs_evaluate, + plfit_i_estimate_alpha_discrete_lbfgs_progress, + &data, ¶m); + + if (ret < 0 && + ret != LBFGSERR_ROUNDING_ERROR && + ret != LBFGSERR_MAXIMUMLINESEARCH && + ret != LBFGSERR_MINIMUMSTEP && + ret != LBFGSERR_CANCELED) { + char buf[4096]; + snprintf(buf, 4096, "L-BFGS optimization signaled an error (error code = %d)", ret); + lbfgs_free(variables); + PLFIT_ERROR(buf, PLFIT_FAILURE); + } + *alpha = variables[0]; + + /* Deallocate the variable array */ + lbfgs_free(variables); + + return PLFIT_SUCCESS; +} + +static int plfit_i_estimate_alpha_discrete_fast(double* xs, size_t n, double xmin, + double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) { + plfit_continuous_options_t cont_options; + + if (!options) + options = &plfit_discrete_default_options; + + plfit_continuous_options_init(&cont_options); + cont_options.finite_size_correction = options->finite_size_correction; + + XMIN_CHECK_ONE; + + if (sorted) { + return plfit_i_estimate_alpha_continuous_sorted(xs, n, xmin-0.5, alpha); + } else { + return plfit_i_estimate_alpha_continuous(xs, n, xmin-0.5, alpha); + } +} + +static int plfit_i_estimate_alpha_discrete(double* xs, size_t n, double xmin, + double* alpha, const plfit_discrete_options_t* options, + plfit_bool_t sorted) { + switch (options->alpha_method) { + case PLFIT_LBFGS: + PLFIT_CHECK(plfit_i_estimate_alpha_discrete_lbfgs(xs, n, xmin, alpha, + options, sorted)); + break; + + case PLFIT_LINEAR_SCAN: + PLFIT_CHECK(plfit_i_estimate_alpha_discrete_linear_scan(xs, n, xmin, + alpha, options, sorted)); + break; + + case PLFIT_PRETEND_CONTINUOUS: + PLFIT_CHECK(plfit_i_estimate_alpha_discrete_fast(xs, n, xmin, + alpha, options, sorted)); + break; + + default: + PLFIT_ERROR("unknown optimization method specified", PLFIT_EINVAL); + } + + return PLFIT_SUCCESS; +} + +static int plfit_i_ks_test_discrete(double* xs, double* xs_end, const double alpha, + const double xmin, double* D) { + /* Assumption: xs is sorted and cut off at xmin so the first element is + * always larger than or equal to xmin. */ + double result = 0, n, lnhzeta, x; + int m = 0; + + n = xs_end - xs; + lnhzeta = hsl_sf_lnhzeta(alpha, xmin); + + while (xs < xs_end) { + double d; + + x = *xs; + + /* Re the next line: this used to be the following: + * + * fabs( 1 - hzeta(alpha, x) / hzeta(alpha, xmin) - m / n) + * + * However, using the Hurwitz zeta directly sometimes yields + * underflows (see Github pull request #17 and related issues). + * hzeta(alpha, x) / hzeta(alpha, xmin) can be replaced with + * exp(lnhzeta(alpha, x) - lnhzeta(alpha, xmin)), but then + * we have 1 - exp(something), which is better to calculate + * with a dedicated expm1() function. + */ + d = fabs( expm1( hsl_sf_lnhzeta(alpha, x) - lnhzeta ) + m / n); + + if (d > result) + result = d; + + do { + xs++; m++; + } while (xs < xs_end && *xs == x); + } + + *D = result; + + return PLFIT_SUCCESS; +} + +static int plfit_i_calculate_p_value_discrete(double* xs, size_t n, + const plfit_discrete_options_t* options, plfit_bool_t xmin_fixed, + plfit_result_t *result) { + long int num_trials; + long int successes = 0; + double *xs_head; + size_t num_smaller; + plfit_discrete_options_t options_no_p_value = *options; + int retval = PLFIT_SUCCESS; + + if (options->p_value_method == PLFIT_P_VALUE_SKIP) { + /* skipping p-value calculation */ + result->p = NAN; + return PLFIT_SUCCESS; + } + + if (options->p_value_method == PLFIT_P_VALUE_APPROXIMATE) { + /* p-value approximation; most likely an upper bound */ + num_smaller = count_smaller(xs, xs + n, result->xmin); + result->p = plfit_ks_test_one_sample_p(result->D, n - num_smaller); + return PLFIT_SUCCESS; + } + + options_no_p_value.p_value_method = PLFIT_P_VALUE_SKIP; + num_trials = (long int)(0.25 / options->p_value_precision / options->p_value_precision); + if (num_trials <= 0) { + PLFIT_ERROR("invalid p-value precision", PLFIT_EINVAL); + } + + /* Extract the head of xs that contains elements smaller than xmin */ + xs_head = extract_smaller(xs, xs+n, result->xmin, &num_smaller); + if (xs_head == 0) + PLFIT_ERROR("cannot calculate exact p-value", PLFIT_ENOMEM); + +#ifdef _OPENMP +#pragma omp parallel +#endif + { + /* Parallel section starts here. If we are compiling using OpenMP, each + * thread will use its own RNG that is seeded from the master RNG. If + * we are compiling without OpenMP, there is only one thread and it uses + * the master RNG. This section must be critical to ensure that only one + * thread is using the master RNG at the same time. */ +#ifdef _OPENMP + mt_rng_t private_rng; +#endif + mt_rng_t *p_rng; + double *ys; + long int i; + plfit_result_t result_synthetic; + +#ifdef _OPENMP +#pragma omp critical + { + p_rng = &private_rng; + mt_init_from_rng(p_rng, options->rng); + } +#else + p_rng = options->rng; +#endif + + /* Allocate memory to sample into */ + ys = calloc(n, sizeof(double)); + if (ys == 0) { + retval = PLFIT_ENOMEM; + } else { + /* The main for loop starts here. */ +#ifdef _OPENMP +#pragma omp for reduction(+:successes) +#endif + for (i = 0; i < num_trials; i++) { + plfit_i_resample_discrete(xs_head, num_smaller, n, result->alpha, + result->xmin, n, p_rng, ys); + if (xmin_fixed) { + plfit_estimate_alpha_discrete(ys, n, result->xmin, + &options_no_p_value, &result_synthetic); + } else { + plfit_discrete(ys, n, &options_no_p_value, &result_synthetic); + } + if (result_synthetic.D > result->D) + successes++; + } + + free(ys); + } + + /* End of parallelized part */ + } + + free(xs_head); + + if (retval == PLFIT_SUCCESS) { + result->p = successes / ((double)num_trials); + } else { + PLFIT_ERROR("cannot calculate exact p-value", retval); + } + + return retval; +} + +int plfit_log_likelihood_discrete(double* xs, size_t n, double alpha, double xmin, double* L) { + double result; + size_t m; + + if (alpha <= 1) { + PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL); + } + XMIN_CHECK_ONE; + + plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &result, &m); + result = - alpha * result - m * hsl_sf_lnhzeta(alpha, xmin); + + *L = result; + + return PLFIT_SUCCESS; +} + +int plfit_estimate_alpha_discrete(double* xs, size_t n, double xmin, + const plfit_discrete_options_t* options, plfit_result_t *result) { + double *xs_copy, *begin, *end; + + if (!options) + options = &plfit_discrete_default_options; + + /* Check the validity of the input parameters */ + DATA_POINTS_CHECK; + if (options->alpha_method == PLFIT_LINEAR_SCAN) { + if (options->alpha.min <= 1.0) { + PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL); + } + if (options->alpha.max < options->alpha.min) { + PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL); + } + if (options->alpha.step <= 0) { + PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL); + } + } + + PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy)); + + begin = xs_copy; end = xs_copy + n; + while (begin < end && *begin < xmin) + begin++; + + PLFIT_CHECK(plfit_i_estimate_alpha_discrete(begin, end-begin, xmin, &result->alpha, + options, /* sorted = */ 1)); + PLFIT_CHECK(plfit_i_ks_test_discrete(begin, end, result->alpha, xmin, &result->D)); + + result->xmin = xmin; + if (options->finite_size_correction) + plfit_i_perform_finite_size_correction(result, end-begin); + + PLFIT_CHECK(plfit_log_likelihood_discrete(begin, end-begin, result->alpha, + result->xmin, &result->L)); + PLFIT_CHECK(plfit_i_calculate_p_value_discrete(xs, n, options, 1, result)); + + free(xs_copy); + + return PLFIT_SUCCESS; +} + +int plfit_discrete(double* xs, size_t n, const plfit_discrete_options_t* options, + plfit_result_t* result) { + double curr_D, curr_alpha; + plfit_result_t best_result; + double *xs_copy, *px, *end, *end_xmin, prev_x; + size_t best_n; + int m; + + if (!options) + options = &plfit_discrete_default_options; + + /* Check the validity of the input parameters */ + DATA_POINTS_CHECK; + if (options->alpha_method == PLFIT_LINEAR_SCAN) { + if (options->alpha.min <= 1.0) { + PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL); + } + if (options->alpha.max < options->alpha.min) { + PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL); + } + if (options->alpha.step <= 0) { + PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL); + } + } + + PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy)); + + best_result.D = DBL_MAX; + best_result.xmin = 1; + best_result.alpha = 1; + best_n = 0; + + /* Make sure there are at least three distinct values if possible */ + px = xs_copy; end = px + n; end_xmin = end - 1; m = 0; + prev_x = *end_xmin; + while (*end_xmin == prev_x && end_xmin > px) + end_xmin--; + prev_x = *end_xmin; + while (*end_xmin == prev_x && end_xmin > px) + end_xmin--; + + prev_x = 0; + while (px < end_xmin) { + while (px < end_xmin && *px == prev_x) { + px++; m++; + } + + plfit_i_estimate_alpha_discrete(px, n-m, *px, &curr_alpha, options, + /* sorted = */ 1); + plfit_i_ks_test_discrete(px, end, curr_alpha, *px, &curr_D); + + if (curr_D < best_result.D) { + best_result.alpha = curr_alpha; + best_result.xmin = *px; + best_result.D = curr_D; + best_n = n-m; + } + + prev_x = *px; + px++; m++; + } + + *result = best_result; + if (options->finite_size_correction) + plfit_i_perform_finite_size_correction(result, best_n); + + PLFIT_CHECK(plfit_log_likelihood_discrete(xs_copy+(n-best_n), best_n, + result->alpha, result->xmin, &result->L)); + PLFIT_CHECK(plfit_i_calculate_p_value_discrete(xs_copy, n, options, 0, result)); + + free(xs_copy); + + return PLFIT_SUCCESS; +} + +/***** resampling routines to generate synthetic replicates ****/ + +static int plfit_i_resample_continuous(double* xs_head, size_t num_smaller, + size_t n, double alpha, double xmin, size_t num_samples, mt_rng_t* rng, + double* result) +{ + size_t num_orig_samples, i; + + /* Calculate how many samples have to be drawn from xs_head */ + num_orig_samples = (size_t) plfit_rbinom(num_samples, num_smaller / (double)n, rng); + + /* Draw the samples from xs_head */ + for (i = 0; i < num_orig_samples; i++, result++) { + *result = xs_head[(size_t)plfit_runif(0, num_smaller, rng)]; + } + + /* Draw the remaining samples from the fitted distribution */ + PLFIT_CHECK(plfit_rpareto_array(xmin, alpha-1, num_samples-num_orig_samples, rng, + result)); + + return PLFIT_SUCCESS; +} + +int plfit_resample_continuous(double* xs, size_t n, double alpha, double xmin, + size_t num_samples, mt_rng_t* rng, double* result) { + double *xs_head; + size_t num_smaller = 0; + int retval; + + /* Extract the head of xs that contains elements smaller than xmin */ + xs_head = extract_smaller(xs, xs+n, xmin, &num_smaller); + if (xs_head == 0) + PLFIT_ERROR("cannot resample continuous dataset", PLFIT_ENOMEM); + + retval = plfit_i_resample_continuous(xs_head, num_smaller, n, alpha, xmin, + num_samples, rng, result); + + /* Free xs_head; we don't need it any more */ + free(xs_head); + + return retval; +} + +static int plfit_i_resample_discrete(double* xs_head, size_t num_smaller, size_t n, + double alpha, double xmin, size_t num_samples, mt_rng_t* rng, + double* result) +{ + size_t num_orig_samples, i; + + /* Calculate how many samples have to be drawn from xs_head */ + num_orig_samples = (size_t) plfit_rbinom(num_samples, num_smaller / (double)n, rng); + + /* Draw the samples from xs_head */ + for (i = 0; i < num_orig_samples; i++, result++) { + *result = xs_head[(size_t)plfit_runif(0, num_smaller, rng)]; + } + + /* Draw the remaining samples from the fitted distribution */ + PLFIT_CHECK(plfit_rzeta_array((long int)xmin, alpha, + num_samples-num_orig_samples, rng, result)); + + return PLFIT_SUCCESS; +} + +int plfit_resample_discrete(double* xs, size_t n, double alpha, double xmin, + size_t num_samples, mt_rng_t* rng, double* result) { + double *xs_head; + size_t num_smaller = 0; + int retval; + + /* Extract the head of xs that contains elements smaller than xmin */ + xs_head = extract_smaller(xs, xs+n, xmin, &num_smaller); + if (xs_head == 0) + PLFIT_ERROR("cannot resample discrete dataset", PLFIT_ENOMEM); + + retval = plfit_i_resample_discrete(xs_head, num_smaller, n, alpha, xmin, + num_samples, rng, result); + + /* Free xs_head; we don't need it any more */ + free(xs_head); + + return retval; +} + +/******** calculating the p-value of a fitted model only *******/ + +int plfit_calculate_p_value_continuous(double* xs, size_t n, + const plfit_continuous_options_t* options, plfit_bool_t xmin_fixed, + plfit_result_t *result) { + double* xs_copy; + + PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy)); + PLFIT_CHECK(plfit_i_calculate_p_value_continuous(xs_copy, n, options, + xmin_fixed, result)); + free(xs_copy); + + return PLFIT_SUCCESS; +} + +int plfit_calculate_p_value_discrete(double* xs, size_t n, + const plfit_discrete_options_t* options, plfit_bool_t xmin_fixed, + plfit_result_t *result) { + double* xs_copy; + + PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy)); + PLFIT_CHECK(plfit_i_calculate_p_value_discrete(xs_copy, n, options, + xmin_fixed, result)); + free(xs_copy); + + return PLFIT_SUCCESS; +} diff --git a/igraph/src/pottsmodel_2.cpp b/igraph/src/pottsmodel_2.cpp --- a/igraph/src/pottsmodel_2.cpp +++ b/igraph/src/pottsmodel_2.cpp @@ -42,18 +42,17 @@ * * ***************************************************************************/ -#include -#include -#include -#include #include "pottsmodel_2.h" #include "NetRoutines.h" -using namespace std; - #include "igraph_random.h" #include "igraph_interrupt_internal.h" #include "config.h" + +#include +#include + +using namespace std; //################################################################################################# PottsModel::PottsModel(network *n, unsigned int qvalue, int m) : acceptance(0) { diff --git a/igraph/src/prpack_solver.cpp b/igraph/src/prpack_solver.cpp --- a/igraph/src/prpack_solver.cpp +++ b/igraph/src/prpack_solver.cpp @@ -237,7 +237,7 @@ } else { // TODO: throw exception } - ret->method = m.c_str(); + ret->method = m; ret->read_time = read_time; ret->preprocess_time = preprocess_time; ret->compute_time = compute_time; diff --git a/igraph/src/prpack_utils.cpp b/igraph/src/prpack_utils.cpp --- a/igraph/src/prpack_utils.cpp +++ b/igraph/src/prpack_utils.cpp @@ -16,7 +16,7 @@ #include "igraph_error.h" #endif -#if defined(_WIN32) || defined(_WIN64) +#if defined(_WIN32) #ifndef WIN32_LEAN_AND_MEAN #define WIN32_LEAN_AND_MEAN #include diff --git a/igraph/src/qsort.c b/igraph/src/qsort.c --- a/igraph/src/qsort.c +++ b/igraph/src/qsort.c @@ -31,6 +31,8 @@ * SUCH DAMAGE. */ +#include "igraph_qsort.h" + #ifdef _MSC_VER /* MSVC does not have inline when compiling C source files */ #define inline __inline @@ -76,9 +78,7 @@ es % sizeof(long) ? 2 : es == sizeof(long)? 0 : 1; static inline void -swapfunc(a, b, n, swaptype) -char *a, *b; -int n, swaptype; +swapfunc(char *a, char *b, int n, int swaptype) { if (swaptype <= 1) swapcode(long, a, b, n) diff --git a/igraph/src/random.c b/igraph/src/random.c --- a/igraph/src/random.c +++ b/igraph/src/random.c @@ -22,22 +22,20 @@ */ #include "igraph_random.h" +#include "igraph_nongraph.h" #include "igraph_error.h" -#include "config.h" - -#include -#include -#include #include "igraph_math.h" #include "igraph_types.h" #include "igraph_vector.h" #include "igraph_memory.h" -#include "igraph_matrix.h" +#include "config.h" +#include +#include /** * \section about_rngs * - *
+ *
* About random numbers in igraph, use cases * * @@ -54,9 +52,9 @@ /** * \section rng_use_cases * - *
Use cases + *
Use cases * - *
Normal (default) use + *
Normal (default) use * * If the user does not use any of the RNG functions explicitly, but calls * some of the randomized igraph functions, then a default RNG is set @@ -73,7 +71,7 @@ * *
* - *
Reproducible simulations + *
Reproducible simulations * * If reproducible results are needed, then the user should set the * seed of the default random number generator explicitly, using the @@ -84,7 +82,7 @@ * *
* - *
Changing the default generator + *
Changing the default generator * * By default igraph uses the \ref igraph_rng_default() random number * generator. This can be changed any time by calling \ref @@ -94,7 +92,7 @@ * *
* - *
Using multiple generators + *
Using multiple generators * * igraph also provides functions to set up multiple random number * generators, using the \ref igraph_rng_init() function, and then @@ -110,7 +108,7 @@ * *
* - *
Example + *
Example * * \example examples/simple/random_seed.c * @@ -126,8 +124,7 @@ long int x[31]; } igraph_i_rng_glibc2_state_t; -unsigned long int igraph_i_rng_glibc2_get(int *i, int *j, int n, - long int *x) { +static unsigned long int igraph_i_rng_glibc2_get(int *i, int *j, int n, long int *x) { unsigned long int k; x[*i] += x[*j]; @@ -158,8 +155,8 @@ /* this function is independent of the bit size */ -void igraph_i_rng_glibc2_init(long int *x, int n, - unsigned long int s) { +static void igraph_i_rng_glibc2_init(long int *x, int n, + unsigned long int s) { int i; if (s == 0) { @@ -514,7 +511,7 @@ * * \param rng The random number generator to use as default from now * on. Calling \ref igraph_rng_destroy() on it, while it is still - * being used as the default will result craches and/or + * being used as the default will result crashes and/or * unpredictable results. * * Time complexity: O(1). @@ -977,8 +974,9 @@ * result vector. */ -int igraph_i_random_sample_alga(igraph_vector_t *res, igraph_integer_t l, igraph_integer_t h, - igraph_integer_t length) { +static int igraph_i_random_sample_alga(igraph_vector_t *res, + igraph_integer_t l, igraph_integer_t h, + igraph_integer_t length) { igraph_real_t N = h - l + 1; igraph_real_t n = length; @@ -1538,7 +1536,7 @@ return (x < y) ? x : y; } -#if HAVE_WORKING_ISFINITE || HAVE_ISFINITE +#if HAVE_WORKING_ISFINITE || HAVE_DECL_ISFINITE /* isfinite is defined in according to C99 */ #define R_FINITE(x) isfinite(x) #elif HAVE_WORKING_FINITE || HAVE_FINITE @@ -1556,7 +1554,7 @@ #endif int R_finite(double x) { -#if HAVE_WORKING_ISFINITE || HAVE_ISFINITE +#if HAVE_WORKING_ISFINITE || HAVE_DECL_ISFINITE return isfinite(x); #elif HAVE_WORKING_FINITE || HAVE_FINITE return finite(x); diff --git a/igraph/src/random_walk.c b/igraph/src/random_walk.c --- a/igraph/src/random_walk.c +++ b/igraph/src/random_walk.c @@ -43,7 +43,7 @@ * \param start The start vertex for the walk. * \param steps The number of steps to take. If the random walk gets * stuck, then the \p stuck argument specifies what happens. - * \param mode How to walk along the edges in direted graphs. + * \param mode How to walk along the edges in directed graphs. * \c IGRAPH_OUT means following edge directions, \c IGRAPH_IN means * going opposite the edge directions, \c IGRAPH_ALL means ignoring * edge directions. This argument is ignored for undirected graphs. @@ -142,7 +142,7 @@ * \param start The start vertex for the walk. * \param steps The number of steps to take. If the random walk gets * stuck, then the \p stuck argument specifies what happens. - * \param mode How to walk along the edges in direted graphs. + * \param mode How to walk along the edges in directed graphs. * \c IGRAPH_OUT means following edge directions, \c IGRAPH_IN means * going opposite the edge directions, \c IGRAPH_ALL means ignoring * edge directions. This argument is ignored for undirected graphs. diff --git a/igraph/src/rbinom.c b/igraph/src/rbinom.c new file mode 100644 --- /dev/null +++ b/igraph/src/rbinom.c @@ -0,0 +1,209 @@ +/* + * Mathlib : A C Library of Special Functions + * Copyright (C) 1998 Ross Ihaka + * Copyright (C) 2000-2002 The R Core Team + * Copyright (C) 2007 The R Foundation + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * http://www.r-project.org/Licenses/ + * + * SYNOPSIS + * + * #include + * double rbinom(double nin, double pp) + * + * DESCRIPTION + * + * Random variates from the binomial distribution. + * + * REFERENCE + * + * Kachitvichyanukul, V. and Schmeiser, B. W. (1988). + * Binomial random variate generation. + * Communications of the ACM 31, 216-222. + * (Algorithm BTPEC). + */ + +/* + * Modifications for this file were performed by Tamas Nepusz to make it fit + * better with plfit. The license of the original file applies to the + * modifications as well. + */ + +#include +#include +#include +#include "sampling.h" +#include "platform.h" + +#define repeat for(;;) + +double plfit_rbinom(double nin, double pp, mt_rng_t* rng) +{ + /* FIXME: These should become THREAD_specific globals : */ + + static double c, fm, npq, p1, p2, p3, p4, qn; + static double xl, xll, xlr, xm, xr; + + static double psave = -1.0; + static int nsave = -1; + static int m; + + double f, f1, f2, u, v, w, w2, x, x1, x2, z, z2; + double p, q, np, g, r, al, alv, amaxp, ffm, ynorm; + int i, ix, k, n; + + if (!isfinite(nin)) return NAN; + r = floor(nin + 0.5); + if (r != nin) return NAN; + if (!isfinite(pp) || + /* n=0, p=0, p=1 are not errors */ + r < 0 || pp < 0. || pp > 1.) return NAN; + + if (r == 0 || pp == 0.) return 0; + if (pp == 1.) return r; + + n = (int) r; + + p = fmin(pp, 1. - pp); + q = 1. - p; + np = n * p; + r = p / q; + g = r * (n + 1); + + /* Setup, perform only when parameters change [using static (globals): */ + + /* FIXING: Want this thread safe + -- use as little (thread globals) as possible + */ + if (pp != psave || n != nsave) { + psave = pp; + nsave = n; + if (np < 30.0) { + /* inverse cdf logic for mean less than 30 */ + qn = pow(q, (double) n); + goto L_np_small; + } else { + ffm = np + p; + m = (int) ffm; + fm = m; + npq = np * q; + p1 = (int)(2.195 * sqrt(npq) - 4.6 * q) + 0.5; + xm = fm + 0.5; + xl = xm - p1; + xr = xm + p1; + c = 0.134 + 20.5 / (15.3 + fm); + al = (ffm - xl) / (ffm - xl * p); + xll = al * (1.0 + 0.5 * al); + al = (xr - ffm) / (xr * q); + xlr = al * (1.0 + 0.5 * al); + p2 = p1 * (1.0 + c + c); + p3 = p2 + c / xll; + p4 = p3 + c / xlr; + } + } else if (n == nsave) { + if (np < 30.0) + goto L_np_small; + } + + /*-------------------------- np = n*p >= 30 : ------------------- */ + repeat { + u = plfit_runif_01(rng) * p4; + v = plfit_runif_01(rng); + /* triangular region */ + if (u <= p1) { + ix = (int)(xm - p1 * v + u); + goto finis; + } + /* parallelogram region */ + if (u <= p2) { + x = xl + (u - p1) / c; + v = v * c + 1.0 - fabs(xm - x) / p1; + if (v > 1.0 || v <= 0.) + continue; + ix = (int) x; + } else { + if (u > p3) { /* right tail */ + ix = (int)(xr - log(v) / xlr); + if (ix > n) + continue; + v = v * (u - p3) * xlr; + } else {/* left tail */ + ix = (int)(xl + log(v) / xll); + if (ix < 0) + continue; + v = v * (u - p2) * xll; + } + } + /* determine appropriate way to perform accept/reject test */ + k = abs(ix - m); + if (k <= 20 || k >= npq / 2 - 1) { + /* explicit evaluation */ + f = 1.0; + if (m < ix) { + for (i = m + 1; i <= ix; i++) + f *= (g / i - r); + } else if (m != ix) { + for (i = ix + 1; i <= m; i++) + f /= (g / i - r); + } + if (v <= f) + goto finis; + } else { + /* squeezing using upper and lower bounds on log(f(x)) */ + amaxp = (k / npq) * ((k * (k / 3. + 0.625) + 0.1666666666666) / npq + 0.5); + ynorm = -k * k / (2.0 * npq); + alv = log(v); + if (alv < ynorm - amaxp) + goto finis; + if (alv <= ynorm + amaxp) { + /* stirling's formula to machine accuracy */ + /* for the final acceptance/rejection test */ + x1 = ix + 1; + f1 = fm + 1.0; + z = n + 1 - fm; + w = n - ix + 1.0; + z2 = z * z; + x2 = x1 * x1; + f2 = f1 * f1; + w2 = w * w; + if (alv <= xm * log(f1 / x1) + (n - m + 0.5) * log(z / w) + (ix - m) * log(w * p / (x1 * q)) + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / f2) / f2) / f2) / f2) / f1 / 166320.0 + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / z2) / z2) / z2) / z2) / z / 166320.0 + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / x2) / x2) / x2) / x2) / x1 / 166320.0 + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / w2) / w2) / w2) / w2) / w / 166320.) + goto finis; + } + } + } + + L_np_small: + /*---------------------- np = n*p < 30 : ------------------------- */ + + repeat { + ix = 0; + f = qn; + u = plfit_runif_01(rng); + repeat { + if (u < f) + goto finis; + if (ix > 110) + break; + u -= f; + ix++; + f *= (g / ix - r); + } + } + finis: + if (psave > 0.5) + ix = n - ix; + return (double)ix; +} + diff --git a/igraph/src/reorder.c b/igraph/src/reorder.c --- a/igraph/src/reorder.c +++ b/igraph/src/reorder.c diff --git a/igraph/src/sampling.c b/igraph/src/sampling.c new file mode 100644 --- /dev/null +++ b/igraph/src/sampling.c @@ -0,0 +1,304 @@ +/* sampling.c + * + * Copyright (C) 2012 Tamas Nepusz + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or (at + * your option) any later version. + * + * This program is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + */ + +#include + +#include "igraph_random.h" + +#include "error.h" +#include "sampling.h" +#include "platform.h" + +inline double plfit_runif(double lo, double hi, mt_rng_t* rng) { + if (rng == 0) { + return RNG_UNIF(lo, hi); + } + return lo + mt_uniform_01(rng) * (hi-lo); +} + +inline double plfit_runif_01(mt_rng_t* rng) { + if (rng == 0) { + return RNG_UNIF01(); + } + return mt_uniform_01(rng); +} + +inline double plfit_rpareto(double xmin, double alpha, mt_rng_t* rng) { + if (alpha <= 0 || xmin <= 0) + return NAN; + + /* 1-u is used in the base here because we want to avoid the case of + * sampling zero */ + return pow(1-plfit_runif_01(rng), -1.0 / alpha) * xmin; +} + +int plfit_rpareto_array(double xmin, double alpha, size_t n, mt_rng_t* rng, + double* result) { + double gamma; + + if (alpha <= 0 || xmin <= 0) + return PLFIT_EINVAL; + + if (result == 0 || n == 0) + return PLFIT_SUCCESS; + + gamma = -1.0 / alpha; + while (n > 0) { + /* 1-u is used in the base here because we want to avoid the case of + * sampling zero */ + *result = pow(1-plfit_runif_01(rng), gamma) * xmin; + result++; n--; + } + + return PLFIT_SUCCESS; +} + +inline double plfit_rzeta(long int xmin, double alpha, mt_rng_t* rng) { + double u, v, t; + long int x; + double alpha_minus_1 = alpha-1; + double minus_1_over_alpha_minus_1 = -1.0 / (alpha-1); + double b; + double one_over_b_minus_1; + + if (alpha <= 0 || xmin < 1) + return NAN; + + xmin = (long int) round(xmin); + + /* Rejection sampling for the win. We use Y=floor(U^{-1/alpha} * xmin) as the + * envelope distribution, similarly to Chapter X.6 of Luc Devroye's book + * (where xmin is assumed to be 1): http://luc.devroye.org/chapter_ten.pdf + * + * Some notes that should help me recover what I was doing: + * + * p_i = 1/zeta(alpha, xmin) * i^-alpha + * q_i = (xmin/i)^{alpha-1} - (xmin/(i+1))^{alpha-1} + * = (i/xmin)^{1-alpha} - ((i+1)/xmin)^{1-alpha} + * = [i^{1-alpha} - (i+1)^{1-alpha}] / xmin^{1-alpha} + * + * p_i / q_i attains its maximum at xmin=i, so the rejection constant is: + * + * c = p_xmin / q_xmin + * + * We have to accept the sample if V <= (p_i / q_i) * (q_xmin / p_xmin) = + * (i/xmin)^-alpha * [xmin^{1-alpha} - (xmin+1)^{1-alpha}] / [i^{1-alpha} - (i+1)^{1-alpha}] = + * [xmin - xmin^alpha / (xmin+1)^{alpha-1}] / [i - i^alpha / (i+1)^{alpha-1}] = + * xmin/i * [1-(xmin/(xmin+1))^{alpha-1}]/[1-(i/(i+1))^{alpha-1}] + * + * In other words (and substituting i with X, which is the same), + * + * V * (X/xmin) <= [1 - (1+1/xmin)^{1-alpha}] / [1 - (1+1/i)^{1-alpha}] + * + * Let b := (1+1/xmin)^{alpha-1} and let T := (1+1/i)^{alpha-1}. Then: + * + * V * (X/xmin) <= [(b-1)/b] / [(T-1)/T] + * V * (X/xmin) * (T-1) / (b-1) <= T / b + * + * which is the same as in Devroye's book, except for the X/xmin term, and + * the definition of b. + */ + b = pow(1 + 1.0/xmin, alpha_minus_1); + one_over_b_minus_1 = 1.0/(b-1); + do { + do { + u = plfit_runif_01(rng); + v = plfit_runif_01(rng); + /* 1-u is used in the base here because we want to avoid the case of + * having zero in x */ + x = (long int) floor(pow(1-u, minus_1_over_alpha_minus_1) * xmin); + } while (x < xmin); + t = pow((x+1.0)/x, alpha_minus_1); + } while (v*x*(t-1)*one_over_b_minus_1*b > t*xmin); + + return x; +} + +int plfit_rzeta_array(long int xmin, double alpha, size_t n, mt_rng_t* rng, + double* result) { + double u, v, t; + long int x; + double alpha_minus_1 = alpha-1; + double minus_1_over_alpha_minus_1 = -1.0 / (alpha-1); + double b, one_over_b_minus_1; + + if (alpha <= 0 || xmin < 1) + return PLFIT_EINVAL; + + if (result == 0 || n == 0) + return PLFIT_SUCCESS; + + /* See the comments in plfit_rzeta for an explanation of the algorithm + * below. */ + xmin = (long int) round(xmin); + b = pow(1 + 1.0/xmin, alpha_minus_1); + one_over_b_minus_1 = 1.0/(b-1); + + while (n > 0) { + do { + do { + u = plfit_runif_01(rng); + v = plfit_runif_01(rng); + /* 1-u is used in the base here because we want to avoid the case of + * having zero in x */ + x = (long int) floor(pow(1-u, minus_1_over_alpha_minus_1) * xmin); + } while (x < xmin); /* handles overflow as well */ + t = pow((x+1.0)/x, alpha_minus_1); + } while (v*x*(t-1)*one_over_b_minus_1*b > t*xmin); + *result = x; + if (x < 0) return PLFIT_EINVAL; + result++; n--; + } + + return PLFIT_SUCCESS; +} + +int plfit_walker_alias_sampler_init(plfit_walker_alias_sampler_t* sampler, + double* ps, size_t n) { + double *p, *p2, *ps_end; + double sum; + long int *short_sticks, *long_sticks; + long int num_short_sticks, num_long_sticks; + size_t i; + + sampler->num_bins = n; + + ps_end = ps + n; + + /* Initialize indexes and probs */ + sampler->indexes = (long int*)calloc(n, sizeof(long int)); + if (sampler->indexes == 0) { + return PLFIT_ENOMEM; + } + sampler->probs = (double*)calloc(n, sizeof(double)); + if (sampler->probs == 0) { + free(sampler->indexes); + return PLFIT_ENOMEM; + } + + /* Normalize the probability vector; count how many short and long sticks + * are there initially */ + for (sum = 0.0, p = ps; p != ps_end; p++) { + sum += *p; + } + sum = n / sum; + + num_short_sticks = num_long_sticks = 0; + for (p = ps, p2 = sampler->probs; p != ps_end; p++, p2++) { + *p2 = *p * sum; + if (*p2 < 1) { + num_short_sticks++; + } else if (*p2 > 1) { + num_long_sticks++; + } + } + + /* Allocate space for short & long stick indexes */ + long_sticks = (long int*)calloc(num_long_sticks, sizeof(long int)); + if (long_sticks == 0) { + free(sampler->probs); + free(sampler->indexes); + return PLFIT_ENOMEM; + } + short_sticks = (long int*)calloc(num_long_sticks, sizeof(long int)); + if (short_sticks == 0) { + free(sampler->probs); + free(sampler->indexes); + free(long_sticks); + return PLFIT_ENOMEM; + } + + /* Initialize short_sticks and long_sticks */ + num_short_sticks = num_long_sticks = 0; + for (i = 0, p = sampler->probs; i < n; i++, p++) { + if (*p < 1) { + short_sticks[num_short_sticks++] = i; + } else if (*p > 1) { + long_sticks[num_long_sticks++] = i; + } + } + + /* Prepare the index table */ + while (num_short_sticks && num_long_sticks) { + long int short_index, long_index; + short_index = short_sticks[--num_short_sticks]; + long_index = long_sticks[num_long_sticks-1]; + sampler->indexes[short_index] = long_index; + sampler->probs[long_index] = /* numerical stability */ + (sampler->probs[long_index] + sampler->probs[short_index]) - 1; + if (sampler->probs[long_index] < 1) { + short_sticks[num_short_sticks++] = long_index; + num_long_sticks--; + } + } + + /* Fix numerical stability issues */ + while (num_long_sticks) { + i = long_sticks[--num_long_sticks]; + sampler->probs[i] = 1; + } + while (num_short_sticks) { + i = short_sticks[--num_short_sticks]; + sampler->probs[i] = 1; + } + + return PLFIT_SUCCESS; +} + + +void plfit_walker_alias_sampler_destroy(plfit_walker_alias_sampler_t* sampler) { + if (sampler->indexes) { + free(sampler->indexes); + sampler->indexes = 0; + } + if (sampler->probs) { + free(sampler->probs); + sampler->probs = 0; + } +} + + +int plfit_walker_alias_sampler_sample(const plfit_walker_alias_sampler_t* sampler, + long int *xs, size_t n, mt_rng_t* rng) { + double u; + long int j; + long int *x; + + x = xs; + + if (rng == 0) { + /* Using built-in RNG */ + while (n > 0) { + u = RNG_UNIF01(); + j = RNG_INTEGER(0, sampler->num_bins - 1); + *x = (u < sampler->probs[j]) ? j : sampler->indexes[j]; + n--; x++; + } + } else { + /* Using Mersenne Twister */ + while (n > 0) { + u = mt_uniform_01(rng); + j = mt_random(rng) % sampler->num_bins; + *x = (u < sampler->probs[j]) ? j : sampler->indexes[j]; + n--; x++; + } + } + + return PLFIT_SUCCESS; +} diff --git a/igraph/src/sbm.c b/igraph/src/sbm.c --- a/igraph/src/sbm.c +++ b/igraph/src/sbm.c @@ -89,7 +89,7 @@ igraph_matrix_minmax(pref_matrix, &minp, &maxp); if (minp < 0 || maxp > 1) { - IGRAPH_ERROR("Connection probabilities must in [0,1]", IGRAPH_EINVAL); + IGRAPH_ERROR("Connection probabilities must be in [0,1]", IGRAPH_EINVAL); } if (n < 0) { @@ -106,7 +106,7 @@ } if (igraph_vector_int_min(block_sizes) < 0) { - IGRAPH_ERROR("Block size must be non-negative", IGRAPH_EINVAL); + IGRAPH_ERROR("Block sizes must be non-negative", IGRAPH_EINVAL); } if (igraph_vector_int_sum(block_sizes) != n) { diff --git a/igraph/src/scan.c b/igraph/src/scan.c --- a/igraph/src/scan.c +++ b/igraph/src/scan.c @@ -75,7 +75,7 @@ } /* From triangles.c */ - +/* TODO add to private header */ int igraph_i_trans4_al_simplify(igraph_adjlist_t *al, const igraph_vector_int_t *rank); @@ -83,8 +83,8 @@ "backwards" according to the rank vector. It works on edge lists */ -int igraph_i_trans4_il_simplify(const igraph_t *graph, igraph_inclist_t *il, - const igraph_vector_int_t *rank) { +static int igraph_i_trans4_il_simplify(const igraph_t *graph, igraph_inclist_t *il, + const igraph_vector_int_t *rank) { long int i; long int n = il->length; @@ -119,10 +119,10 @@ /* This one handles both weighted and unweighted cases */ -int igraph_i_local_scan_1_directed(const igraph_t *graph, - igraph_vector_t *res, - const igraph_vector_t *weights, - igraph_neimode_t mode) { +static int igraph_i_local_scan_1_directed(const igraph_t *graph, + igraph_vector_t *res, + const igraph_vector_t *weights, + igraph_neimode_t mode) { int no_of_nodes = igraph_vcount(graph); igraph_inclist_t incs; @@ -180,9 +180,9 @@ return 0; } -int igraph_i_local_scan_1_directed_all(const igraph_t *graph, - igraph_vector_t *res, - const igraph_vector_t *weights) { +static int igraph_i_local_scan_1_directed_all(const igraph_t *graph, + igraph_vector_t *res, + const igraph_vector_t *weights) { int no_of_nodes = igraph_vcount(graph); igraph_inclist_t incs; @@ -250,9 +250,9 @@ return 0; } -int igraph_i_local_scan_1_sumweights(const igraph_t *graph, - igraph_vector_t *res, - const igraph_vector_t *weights) { +static int igraph_i_local_scan_1_sumweights(const igraph_t *graph, + igraph_vector_t *res, + const igraph_vector_t *weights) { long int no_of_nodes = igraph_vcount(graph); long int node, i, j, nn; @@ -384,10 +384,10 @@ return 0; } -int igraph_i_local_scan_0_them_w(const igraph_t *us, const igraph_t *them, - igraph_vector_t *res, - const igraph_vector_t *weights_them, - igraph_neimode_t mode) { +static int igraph_i_local_scan_0_them_w(const igraph_t *us, const igraph_t *them, + igraph_vector_t *res, + const igraph_vector_t *weights_them, + igraph_neimode_t mode) { igraph_t is; igraph_vector_t map2; diff --git a/igraph/src/scg.c b/igraph/src/scg.c --- a/igraph/src/scg.c +++ b/igraph/src/scg.c @@ -79,6 +79,7 @@ #include "igraph_eigen.h" #include "igraph_interface.h" #include "igraph_structural.h" +#include "igraph_community.h" #include "igraph_constructors.h" #include "igraph_conversion.h" #include "igraph_memory.h" @@ -121,7 +122,7 @@ * role, as for instance is the case of dynamical processes on networks. * * - *
SCG in brief + *
SCG in brief * * The main idea of SCG is to operate on a matrix a shrinkage operation * specifically designed to preserve some of the matrix eigenpairs while @@ -209,7 +210,7 @@ * *
* - *
Functions for performing SCG + *
Functions for performing SCG * * The main functions are \ref igraph_scg_adjacency(), \ref * igraph_scg_laplacian() and \ref igraph_scg_stochastic(). @@ -240,7 +241,7 @@ * *
* - *
References + *
References * * [1] D. Morton de Lachapelle, D. Gfeller, and P. De Los Rios, * Shrinking Matrices while Preserving their Eigenpairs with Application @@ -468,16 +469,18 @@ igraph_matrix_int_destroy(&gr_mat); IGRAPH_FINALLY_CLEAN(1); + IGRAPH_CHECK(igraph_reindex_membership(groups, 0, 0)); + return 0; } -int igraph_i_scg_semiprojectors_sym(const igraph_vector_t *groups, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse, - int no_of_groups, - int no_of_nodes) { +static int igraph_i_scg_semiprojectors_sym(const igraph_vector_t *groups, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse, + int no_of_groups, + int no_of_nodes) { igraph_vector_t tab; int i; @@ -536,14 +539,14 @@ return 0; } -int igraph_i_scg_semiprojectors_lap(const igraph_vector_t *groups, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse, - int no_of_groups, - int no_of_nodes, - igraph_scg_norm_t norm) { +static int igraph_i_scg_semiprojectors_lap(const igraph_vector_t *groups, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse, + int no_of_groups, + int no_of_nodes, + igraph_scg_norm_t norm) { igraph_vector_t tab; int i; @@ -633,15 +636,15 @@ return 0; } -int igraph_i_scg_semiprojectors_sto(const igraph_vector_t *groups, - igraph_matrix_t *L, - igraph_matrix_t *R, - igraph_sparsemat_t *Lsparse, - igraph_sparsemat_t *Rsparse, - int no_of_groups, - int no_of_nodes, - const igraph_vector_t *p, - igraph_scg_norm_t norm) { +static int igraph_i_scg_semiprojectors_sto(const igraph_vector_t *groups, + igraph_matrix_t *L, + igraph_matrix_t *R, + igraph_sparsemat_t *Lsparse, + igraph_sparsemat_t *Rsparse, + int no_of_groups, + int no_of_nodes, + const igraph_vector_t *p, + igraph_scg_norm_t norm) { igraph_vector_t pgr, pnormed; int i; @@ -974,9 +977,9 @@ return 0; } -int igraph_i_matrix_laplacian(const igraph_matrix_t *matrix, - igraph_matrix_t *mymatrix, - igraph_scg_norm_t norm) { +static int igraph_i_matrix_laplacian(const igraph_matrix_t *matrix, + igraph_matrix_t *mymatrix, + igraph_scg_norm_t norm) { igraph_vector_t degree; int i, j, n = (int) igraph_matrix_nrow(matrix); @@ -1006,9 +1009,9 @@ return 0; } -int igraph_i_sparsemat_laplacian(const igraph_sparsemat_t *sparse, - igraph_sparsemat_t *mysparse, - igraph_scg_norm_t norm) { +static int igraph_i_sparsemat_laplacian(const igraph_sparsemat_t *sparse, + igraph_sparsemat_t *mysparse, + igraph_scg_norm_t norm) { igraph_vector_t degree; int i, n = (int) igraph_sparsemat_nrow(sparse); @@ -1058,9 +1061,9 @@ return 0; } -int igraph_i_matrix_stochastic(const igraph_matrix_t *matrix, - igraph_matrix_t *mymatrix, - igraph_scg_norm_t norm) { +static int igraph_i_matrix_stochastic(const igraph_matrix_t *matrix, + igraph_matrix_t *mymatrix, + igraph_scg_norm_t norm) { int i, j, n = (int) igraph_matrix_nrow(matrix); IGRAPH_CHECK(igraph_matrix_copy(mymatrix, matrix)); @@ -1096,12 +1099,13 @@ return 0; } +/* TODO prototype; function is defined in conversion.c */ int igraph_i_normalize_sparsemat(igraph_sparsemat_t *sparsemat, igraph_bool_t column_wise); -int igraph_i_sparsemat_stochastic(const igraph_sparsemat_t *sparse, - igraph_sparsemat_t *mysparse, - igraph_scg_norm_t norm) { +static int igraph_i_sparsemat_stochastic(const igraph_sparsemat_t *sparse, + igraph_sparsemat_t *mysparse, + igraph_scg_norm_t norm) { IGRAPH_CHECK(igraph_sparsemat_copy(mysparse, sparse)); IGRAPH_FINALLY(igraph_sparsemat_destroy, mysparse); @@ -1112,15 +1116,15 @@ return 0; } -int igraph_i_scg_get_result(igraph_scg_matrix_t type, - const igraph_matrix_t *matrix, - const igraph_sparsemat_t *sparsemat, - const igraph_sparsemat_t *Lsparse, - const igraph_sparsemat_t *Rsparse_t, - igraph_t *scg_graph, - igraph_matrix_t *scg_matrix, - igraph_sparsemat_t *scg_sparsemat, - igraph_bool_t directed) { +static int igraph_i_scg_get_result(igraph_scg_matrix_t type, + const igraph_matrix_t *matrix, + const igraph_sparsemat_t *sparsemat, + const igraph_sparsemat_t *Lsparse, + const igraph_sparsemat_t *Rsparse_t, + igraph_t *scg_graph, + igraph_matrix_t *scg_matrix, + igraph_sparsemat_t *scg_sparsemat, + igraph_bool_t directed) { /* We need to calculate either scg_matrix (if input is dense), or scg_sparsemat (if input is sparse). For the latter we might need @@ -1269,20 +1273,20 @@ return 0; } -int igraph_i_scg_common_checks(const igraph_t *graph, - const igraph_matrix_t *matrix, - const igraph_sparsemat_t *sparsemat, - const igraph_vector_t *ev, - igraph_integer_t nt, - const igraph_vector_t *nt_vec, - const igraph_matrix_t *vectors, - const igraph_matrix_complex_t *vectors_cmplx, - const igraph_vector_t *groups, - const igraph_t *scg_graph, - const igraph_matrix_t *scg_matrix, - const igraph_sparsemat_t *scg_sparsemat, - const igraph_vector_t *p, - igraph_real_t *evmin, igraph_real_t *evmax) { +static int igraph_i_scg_common_checks(const igraph_t *graph, + const igraph_matrix_t *matrix, + const igraph_sparsemat_t *sparsemat, + const igraph_vector_t *ev, + igraph_integer_t nt, + const igraph_vector_t *nt_vec, + const igraph_matrix_t *vectors, + const igraph_matrix_complex_t *vectors_cmplx, + const igraph_vector_t *groups, + const igraph_t *scg_graph, + const igraph_matrix_t *scg_matrix, + const igraph_sparsemat_t *scg_sparsemat, + const igraph_vector_t *p, + igraph_real_t *evmin, igraph_real_t *evmax) { int no_of_nodes = -1; igraph_real_t min, max; diff --git a/igraph/src/scg_approximate_methods.c b/igraph/src/scg_approximate_methods.c --- a/igraph/src/scg_approximate_methods.c +++ b/igraph/src/scg_approximate_methods.c @@ -64,10 +64,9 @@ * centers as used in intervals_plus_kmeans. */ +#include "scg_headers.h" #include "igraph_error.h" #include "igraph_types.h" -#include "scg_headers.h" -#include "igraph_memory.h" #include "igraph_vector.h" int igraph_i_intervals_plus_kmeans(const igraph_vector_t *v, int *gr, diff --git a/igraph/src/scg_exact_scg.c b/igraph/src/scg_exact_scg.c --- a/igraph/src/scg_exact_scg.c +++ b/igraph/src/scg_exact_scg.c @@ -29,8 +29,8 @@ * See also Section 5.4.1 (last paragraph) of the above reference. */ -#include "igraph_memory.h" #include "scg_headers.h" +#include "igraph_memory.h" #include int igraph_i_exact_coarse_graining(const igraph_real_t *v, diff --git a/igraph/src/scg_kmeans.c b/igraph/src/scg_kmeans.c --- a/igraph/src/scg_kmeans.c +++ b/igraph/src/scg_kmeans.c @@ -31,8 +31,6 @@ * See also Section 5.3.3 of the above reference. */ -#include "igraph_memory.h" - #include "scg_headers.h" int igraph_i_kmeans_Lloyd(const igraph_vector_t *x, int n, int p, diff --git a/igraph/src/scg_optimal_method.c b/igraph/src/scg_optimal_method.c --- a/igraph/src/scg_optimal_method.c +++ b/igraph/src/scg_optimal_method.c @@ -35,13 +35,12 @@ * starting from 0. */ +#include "scg_headers.h" #include "igraph_error.h" #include "igraph_memory.h" #include "igraph_matrix.h" #include "igraph_vector.h" -#include "scg_headers.h" - int igraph_i_optimal_partition(const igraph_real_t *v, int *gr, int n, int nt, int matrix, const igraph_real_t *p, igraph_real_t *value) { @@ -114,7 +113,7 @@ IGRAPH_MATRIX_INIT_FINALLY(&F, nt, n); IGRAPH_CHECK(igraph_matrix_int_init(&Q, nt, n)); - IGRAPH_FINALLY(igraph_matrix_destroy, &Q); + IGRAPH_FINALLY(igraph_matrix_int_destroy, &Q); for (i = 0; i < n; i++) { MATRIX(Q, 0, i)++; @@ -238,4 +237,3 @@ return 0; } - diff --git a/igraph/src/scg_utils.c b/igraph/src/scg_utils.c --- a/igraph/src/scg_utils.c +++ b/igraph/src/scg_utils.c @@ -27,10 +27,9 @@ * functions used throughout the SCGlib. */ +#include "scg_headers.h" #include "igraph_error.h" #include "igraph_memory.h" - -#include "scg_headers.h" /*to be used with qsort and struct ind_val arrays */ int igraph_i_compare_ind_val(const void *a, const void *b) { diff --git a/igraph/src/separators.c b/igraph/src/separators.c --- a/igraph/src/separators.c +++ b/igraph/src/separators.c @@ -28,21 +28,18 @@ #include "igraph_vector.h" #include "igraph_interface.h" #include "igraph_flow.h" -#include "igraph_flow_internal.h" #include "igraph_components.h" #include "igraph_structural.h" -#include "igraph_constructors.h" -#include "igraph_stack.h" #include "igraph_interrupt_internal.h" -int igraph_i_is_separator(const igraph_t *graph, - igraph_vit_t *vit, - long int except, - igraph_bool_t *res, - igraph_vector_bool_t *removed, - igraph_dqueue_t *Q, - igraph_vector_t *neis, - long int no_of_nodes) { +static int igraph_i_is_separator(const igraph_t *graph, + igraph_vit_t *vit, + long int except, + igraph_bool_t *res, + igraph_vector_bool_t *removed, + igraph_dqueue_t *Q, + igraph_vector_t *neis, + long int no_of_nodes) { long int start = 0; @@ -266,11 +263,11 @@ } \ } while (0) -int igraph_i_clusters_leaveout(const igraph_adjlist_t *adjlist, - igraph_vector_t *components, - igraph_vector_t *leaveout, - unsigned long int *mark, - igraph_dqueue_t *Q) { +static int igraph_i_clusters_leaveout(const igraph_adjlist_t *adjlist, + igraph_vector_t *components, + igraph_vector_t *leaveout, + unsigned long int *mark, + igraph_dqueue_t *Q) { /* Another trick: we use the same 'leaveout' vector to mark the * vertices that were already found in the BFS @@ -314,8 +311,8 @@ return 0; } -igraph_bool_t igraph_i_separators_newsep(const igraph_vector_ptr_t *comps, - const igraph_vector_t *newc) { +static igraph_bool_t igraph_i_separators_newsep(const igraph_vector_ptr_t *comps, + const igraph_vector_t *newc) { long int co, nocomps = igraph_vector_ptr_size(comps); @@ -330,12 +327,12 @@ return 1; } -int igraph_i_separators_store(igraph_vector_ptr_t *separators, - const igraph_adjlist_t *adjlist, - igraph_vector_t *components, - igraph_vector_t *leaveout, - unsigned long int *mark, - igraph_vector_t *sorter) { +static int igraph_i_separators_store(igraph_vector_ptr_t *separators, + const igraph_adjlist_t *adjlist, + igraph_vector_t *components, + igraph_vector_t *leaveout, + unsigned long int *mark, + igraph_vector_t *sorter) { /* We need to stote N(C), the neighborhood of C, but only if it is * not already stored among the separators. @@ -387,7 +384,7 @@ return 0; } -void igraph_i_separators_free(igraph_vector_ptr_t *separators) { +static void igraph_i_separators_free(igraph_vector_ptr_t *separators) { long int i, n = igraph_vector_ptr_size(separators); for (i = 0; i < n; i++) { igraph_vector_t *vec = VECTOR(*separators)[i]; @@ -557,8 +554,8 @@ #undef UPDATEMARK -int igraph_i_minimum_size_separators_append(igraph_vector_ptr_t *old, - igraph_vector_ptr_t *new) { +static int igraph_i_minimum_size_separators_append(igraph_vector_ptr_t *old, + igraph_vector_ptr_t *new) { long int olen = igraph_vector_ptr_size(old); long int nlen = igraph_vector_ptr_size(new); @@ -587,9 +584,9 @@ return 0; } -int igraph_i_minimum_size_separators_topkdeg(const igraph_t *graph, - igraph_vector_t *res, - long int k) { +static int igraph_i_minimum_size_separators_topkdeg(const igraph_t *graph, + igraph_vector_t *res, + long int k) { long int no_of_nodes = igraph_vcount(graph); igraph_vector_t deg, order; long int i; @@ -612,7 +609,7 @@ return 0; } -void igraph_i_separators_stcuts_free(igraph_vector_ptr_t *p) { +static void igraph_i_separators_stcuts_free(igraph_vector_ptr_t *p) { long int i, n = igraph_vector_ptr_size(p); for (i = 0; i < n; i++) { igraph_vector_t *v = VECTOR(*p)[i]; diff --git a/igraph/src/sir.c b/igraph/src/sir.c --- a/igraph/src/sir.c +++ b/igraph/src/sir.c @@ -28,15 +28,16 @@ #include "igraph_psumtree.h" #include "igraph_memory.h" #include "igraph_structural.h" +#include "igraph_interrupt_internal.h" int igraph_sir_init(igraph_sir_t *sir) { - igraph_vector_init(&sir->times, 1); + IGRAPH_CHECK(igraph_vector_init(&sir->times, 1)); IGRAPH_FINALLY(igraph_vector_destroy, &sir->times); - igraph_vector_int_init(&sir->no_s, 1); + IGRAPH_CHECK(igraph_vector_int_init(&sir->no_s, 1)); IGRAPH_FINALLY(igraph_vector_int_destroy, &sir->no_s); - igraph_vector_int_init(&sir->no_i, 1); + IGRAPH_CHECK(igraph_vector_int_init(&sir->no_i, 1)); IGRAPH_FINALLY(igraph_vector_int_destroy, &sir->no_i); - igraph_vector_int_init(&sir->no_r, 1); + IGRAPH_CHECK(igraph_vector_int_init(&sir->no_r, 1)); IGRAPH_FINALLY_CLEAN(3); return 0; } @@ -55,12 +56,12 @@ igraph_vector_int_destroy(&sir->no_r); } -void igraph_i_sir_destroy(igraph_vector_ptr_t *v) { +static void igraph_i_sir_destroy(igraph_vector_ptr_t *v) { int i, n = igraph_vector_ptr_size(v); for (i = 0; i < n; i++) { - igraph_sir_t *s = VECTOR(*v)[i]; - if (s) { - igraph_sir_destroy(s); + if ( VECTOR(*v)[i] ) { + igraph_sir_destroy( VECTOR(*v)[i]) ; + igraph_Free( VECTOR(*v)[i] ); /* this also sets the vector_ptr element to NULL */ } } } @@ -127,16 +128,17 @@ IGRAPH_WARNING("Edge directions are ignored in SIR model"); } if (beta < 0) { - IGRAPH_ERROR("Beta must be non-negative in SIR model", IGRAPH_EINVAL); + IGRAPH_ERROR("The infection rate beta must be non-negative in SIR model", IGRAPH_EINVAL); } - if (gamma < 0) { - IGRAPH_ERROR("Gamma must be non-negative in SIR model", IGRAPH_EINVAL); + /* With a recovery rate of zero, the simulation would never stop. */ + if (gamma <= 0) { + IGRAPH_ERROR("The recovery rate gamma must be positive in SIR model", IGRAPH_EINVAL); } if (no_sim <= 0) { IGRAPH_ERROR("Number of SIR simulations must be positive", IGRAPH_EINVAL); } - igraph_is_simple(graph, &simple); + IGRAPH_CHECK(igraph_is_simple(graph, &simple)); if (!simple) { IGRAPH_ERROR("SIR model only works with simple graphs", IGRAPH_EINVAL); } @@ -156,7 +158,7 @@ if (!sir) { IGRAPH_ERROR("Cannot run SIR model", IGRAPH_ENOMEM); } - igraph_sir_init(sir); + IGRAPH_CHECK(igraph_sir_init(sir)); VECTOR(*result)[i] = sir; } @@ -202,6 +204,8 @@ igraph_real_t r; long int vchange; + IGRAPH_ALLOW_INTERRUPTION(); + psum = igraph_psumtree_sum(&tree); tt = igraph_rng_get_exp(igraph_rng_default(), psum); r = RNG_UNIF(0, psum); @@ -235,18 +239,10 @@ } } - if (times_v) { - igraph_vector_push_back(times_v, tt + igraph_vector_tail(times_v)); - } - if (no_s_v) { - igraph_vector_int_push_back(no_s_v, ns); - } - if (no_i_v) { - igraph_vector_int_push_back(no_i_v, ni); - } - if (no_r_v) { - igraph_vector_int_push_back(no_r_v, nr); - } + IGRAPH_CHECK(igraph_vector_push_back(times_v, tt + igraph_vector_tail(times_v))); + IGRAPH_CHECK(igraph_vector_int_push_back(no_s_v, ns)); + IGRAPH_CHECK(igraph_vector_int_push_back(no_i_v, ni)); + IGRAPH_CHECK(igraph_vector_int_push_back(no_r_v, nr)); } /* psum > 0 */ diff --git a/igraph/src/spanning_trees.c b/igraph/src/spanning_trees.c --- a/igraph/src/spanning_trees.c +++ b/igraph/src/spanning_trees.c @@ -33,10 +33,10 @@ #include "igraph_progress.h" #include "igraph_types_internal.h" -int igraph_i_minimum_spanning_tree_unweighted(const igraph_t *graph, - igraph_vector_t *result); -int igraph_i_minimum_spanning_tree_prim(const igraph_t *graph, - igraph_vector_t *result, const igraph_vector_t *weights); +static int igraph_i_minimum_spanning_tree_unweighted(const igraph_t *graph, + igraph_vector_t *result); +static int igraph_i_minimum_spanning_tree_prim(const igraph_t *graph, + igraph_vector_t *result, const igraph_vector_t *weights); /** * \ingroup structural @@ -203,8 +203,7 @@ } -int igraph_i_minimum_spanning_tree_unweighted(const igraph_t* graph, - igraph_vector_t* res) { +static int igraph_i_minimum_spanning_tree_unweighted(const igraph_t* graph, igraph_vector_t* res) { long int no_of_nodes = igraph_vcount(graph); long int no_of_edges = igraph_ecount(graph); @@ -271,8 +270,8 @@ return IGRAPH_SUCCESS; } -int igraph_i_minimum_spanning_tree_prim(const igraph_t* graph, - igraph_vector_t* res, const igraph_vector_t *weights) { +static int igraph_i_minimum_spanning_tree_prim( + const igraph_t* graph, igraph_vector_t* res, const igraph_vector_t *weights) { long int no_of_nodes = igraph_vcount(graph); long int no_of_edges = igraph_ecount(graph); diff --git a/igraph/src/sparsemat.c b/igraph/src/sparsemat.c --- a/igraph/src/sparsemat.c +++ b/igraph/src/sparsemat.c @@ -320,10 +320,10 @@ return 0; } -int igraph_i_sparsemat_index_rows(const igraph_sparsemat_t *A, - const igraph_vector_int_t *p, - igraph_sparsemat_t *res, - igraph_real_t *constres) { +static int igraph_i_sparsemat_index_rows(const igraph_sparsemat_t *A, + const igraph_vector_int_t *p, + igraph_sparsemat_t *res, + igraph_real_t *constres) { igraph_sparsemat_t II, II2; long int nrow = A->cs->m; @@ -358,10 +358,10 @@ return 0; } -int igraph_i_sparsemat_index_cols(const igraph_sparsemat_t *A, - const igraph_vector_int_t *q, - igraph_sparsemat_t *res, - igraph_real_t *constres) { +static int igraph_i_sparsemat_index_cols(const igraph_sparsemat_t *A, + const igraph_vector_int_t *q, + igraph_sparsemat_t *res, + igraph_real_t *constres) { igraph_sparsemat_t JJ, JJ2; long int ncol = A->cs->n; @@ -590,6 +590,7 @@ return 0; } +static igraph_bool_t igraph_i_sparsemat_is_symmetric_cc(const igraph_sparsemat_t *A) { igraph_sparsemat_t t, tt; @@ -619,6 +620,7 @@ return res; } +static igraph_bool_t igraph_i_sparsemat_is_symmetric_triplet(const igraph_sparsemat_t *A) { igraph_sparsemat_t tmp; @@ -1048,8 +1050,8 @@ return 0; } -int igraph_i_sparsemat_cc(igraph_t *graph, const igraph_sparsemat_t *A, - igraph_bool_t directed) { +static int igraph_i_sparsemat_cc(igraph_t *graph, const igraph_sparsemat_t *A, + igraph_bool_t directed) { igraph_vector_t edges; long int no_of_nodes = A->cs->m; @@ -1088,8 +1090,8 @@ return 0; } -int igraph_i_sparsemat_triplet(igraph_t *graph, const igraph_sparsemat_t *A, - igraph_bool_t directed) { +static int igraph_i_sparsemat_triplet(igraph_t *graph, const igraph_sparsemat_t *A, + igraph_bool_t directed) { igraph_vector_t edges; long int no_of_nodes = A->cs->m; @@ -1149,11 +1151,11 @@ } } -int igraph_i_weighted_sparsemat_cc(const igraph_sparsemat_t *A, - igraph_bool_t directed, const char *attr, - igraph_bool_t loops, - igraph_vector_t *edges, - igraph_vector_t *weights) { +static int igraph_i_weighted_sparsemat_cc(const igraph_sparsemat_t *A, + igraph_bool_t directed, const char *attr, + igraph_bool_t loops, + igraph_vector_t *edges, + igraph_vector_t *weights) { long int no_of_edges = A->cs->p[A->cs->n]; int *p = A->cs->p; @@ -1189,12 +1191,12 @@ return 0; } -int igraph_i_weighted_sparsemat_triplet(const igraph_sparsemat_t *A, - igraph_bool_t directed, - const char *attr, - igraph_bool_t loops, - igraph_vector_t *edges, - igraph_vector_t *weights) { +static int igraph_i_weighted_sparsemat_triplet(const igraph_sparsemat_t *A, + igraph_bool_t directed, + const char *attr, + igraph_bool_t loops, + igraph_vector_t *edges, + igraph_vector_t *weights) { IGRAPH_UNUSED(A); IGRAPH_UNUSED(directed); IGRAPH_UNUSED(attr); IGRAPH_UNUSED(loops); IGRAPH_UNUSED(edges); IGRAPH_UNUSED(weights); @@ -1338,8 +1340,8 @@ #undef CHECK -int igraph_i_sparsemat_eye_triplet(igraph_sparsemat_t *A, int n, int nzmax, - igraph_real_t value) { +static int igraph_i_sparsemat_eye_triplet(igraph_sparsemat_t *A, int n, int nzmax, + igraph_real_t value) { long int i; IGRAPH_CHECK(igraph_sparsemat_init(A, n, n, nzmax)); @@ -1351,8 +1353,8 @@ return 0; } -int igraph_i_sparsemat_eye_cc(igraph_sparsemat_t *A, int n, - igraph_real_t value) { +static int igraph_i_sparsemat_eye_cc(igraph_sparsemat_t *A, int n, + igraph_real_t value) { long int i; if (! (A->cs = cs_spalloc(n, n, n, /*values=*/ 1, /*triplet=*/ 0)) ) { @@ -1397,8 +1399,8 @@ } } -int igraph_i_sparsemat_diag_triplet(igraph_sparsemat_t *A, int nzmax, - const igraph_vector_t *values) { +static int igraph_i_sparsemat_diag_triplet(igraph_sparsemat_t *A, int nzmax, + const igraph_vector_t *values) { int i, n = (int) igraph_vector_size(values); @@ -1412,8 +1414,8 @@ } -int igraph_i_sparsemat_diag_cc(igraph_sparsemat_t *A, - const igraph_vector_t *values) { +static int igraph_i_sparsemat_diag_cc(igraph_sparsemat_t *A, + const igraph_vector_t *values) { int i, n = (int) igraph_vector_size(values); @@ -1461,10 +1463,10 @@ } } -int igraph_i_sparsemat_arpack_multiply(igraph_real_t *to, - const igraph_real_t *from, - int n, - void *extra) { +static int igraph_i_sparsemat_arpack_multiply(igraph_real_t *to, + const igraph_real_t *from, + int n, + void *extra) { igraph_sparsemat_t *A = extra; igraph_vector_t vto, vfrom; igraph_vector_view(&vto, to, n); @@ -1481,10 +1483,10 @@ igraph_sparsemat_solve_t method; } igraph_i_sparsemat_arpack_rssolve_data_t; -int igraph_i_sparsemat_arpack_solve(igraph_real_t *to, - const igraph_real_t *from, - int n, - void *extra) { +static int igraph_i_sparsemat_arpack_solve(igraph_real_t *to, + const igraph_real_t *from, + int n, + void *extra) { igraph_i_sparsemat_arpack_rssolve_data_t *data = extra; igraph_vector_t vfrom, vto; @@ -1958,8 +1960,8 @@ return 0; } -int igraph_i_sparsemat_as_matrix_cc(igraph_matrix_t *res, - const igraph_sparsemat_t *spmat) { +static int igraph_i_sparsemat_as_matrix_cc(igraph_matrix_t *res, + const igraph_sparsemat_t *spmat) { int nrow = (int) igraph_sparsemat_nrow(spmat); int ncol = (int) igraph_sparsemat_ncol(spmat); @@ -1986,8 +1988,8 @@ return 0; } -int igraph_i_sparsemat_as_matrix_triplet(igraph_matrix_t *res, - const igraph_sparsemat_t *spmat) { +static int igraph_i_sparsemat_as_matrix_triplet(igraph_matrix_t *res, + const igraph_sparsemat_t *spmat) { int nrow = (int) igraph_sparsemat_nrow(spmat); int ncol = (int) igraph_sparsemat_ncol(spmat); int *i = spmat->cs->p; @@ -2201,8 +2203,8 @@ return res; } -int igraph_i_sparsemat_rowsums_triplet(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_rowsums_triplet(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int i; int *pi = A->cs->i; double *px = A->cs->x; @@ -2217,8 +2219,8 @@ return 0; } -int igraph_i_sparsemat_rowsums_cc(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_rowsums_cc(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int ne = A->cs->p[A->cs->n]; double *px = A->cs->x; int *pi = A->cs->i; @@ -2254,8 +2256,8 @@ } } -int igraph_i_sparsemat_rowmins_triplet(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_rowmins_triplet(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int i; int *pi = A->cs->i; double *px = A->cs->x; @@ -2273,8 +2275,8 @@ return 0; } -int igraph_i_sparsemat_rowmins_cc(igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_rowmins_cc(igraph_sparsemat_t *A, + igraph_vector_t *res) { int ne; double *px; int *pi; @@ -2308,8 +2310,8 @@ } -int igraph_i_sparsemat_rowmaxs_triplet(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_rowmaxs_triplet(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int i; int *pi = A->cs->i; double *px = A->cs->x; @@ -2327,8 +2329,8 @@ return 0; } -int igraph_i_sparsemat_rowmaxs_cc(igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_rowmaxs_cc(igraph_sparsemat_t *A, + igraph_vector_t *res) { int ne; double *px; int *pi; @@ -2361,8 +2363,8 @@ } } -int igraph_i_sparsemat_colmins_triplet(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_colmins_triplet(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int i; int *pp = A->cs->p; double *px = A->cs->x; @@ -2380,8 +2382,8 @@ return 0; } -int igraph_i_sparsemat_colmins_cc(igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_colmins_cc(igraph_sparsemat_t *A, + igraph_vector_t *res) { int n; double *px; int *pp; @@ -2419,8 +2421,8 @@ } } -int igraph_i_sparsemat_colmaxs_triplet(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_colmaxs_triplet(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int i; int *pp = A->cs->p; double *px = A->cs->x; @@ -2438,8 +2440,8 @@ return 0; } -int igraph_i_sparsemat_colmaxs_cc(igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_colmaxs_cc(igraph_sparsemat_t *A, + igraph_vector_t *res) { int n; double *px; int *pp; @@ -2477,9 +2479,9 @@ } } -int igraph_i_sparsemat_which_min_rows_triplet(igraph_sparsemat_t *A, - igraph_vector_t *res, - igraph_vector_int_t *pos) { +static int igraph_i_sparsemat_which_min_rows_triplet(igraph_sparsemat_t *A, + igraph_vector_t *res, + igraph_vector_int_t *pos) { int i; int *pi = A->cs->i; int *pp = A->cs->p; @@ -2501,9 +2503,9 @@ return 0; } -int igraph_i_sparsemat_which_min_rows_cc(igraph_sparsemat_t *A, - igraph_vector_t *res, - igraph_vector_int_t *pos) { +static int igraph_i_sparsemat_which_min_rows_cc(igraph_sparsemat_t *A, + igraph_vector_t *res, + igraph_vector_int_t *pos) { int n; double *px; int *pp; @@ -2545,9 +2547,9 @@ } } -int igraph_i_sparsemat_which_min_cols_triplet(igraph_sparsemat_t *A, - igraph_vector_t *res, - igraph_vector_int_t *pos) { +static int igraph_i_sparsemat_which_min_cols_triplet(igraph_sparsemat_t *A, + igraph_vector_t *res, + igraph_vector_int_t *pos) { int i; int *pi = A->cs->i; @@ -2570,9 +2572,9 @@ return 0; } -int igraph_i_sparsemat_which_min_cols_cc(igraph_sparsemat_t *A, - igraph_vector_t *res, - igraph_vector_int_t *pos) { +static int igraph_i_sparsemat_which_min_cols_cc(igraph_sparsemat_t *A, + igraph_vector_t *res, + igraph_vector_int_t *pos) { int n, j, p; double *px; double *pr; @@ -2612,8 +2614,8 @@ } } -int igraph_i_sparsemat_colsums_triplet(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_colsums_triplet(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int i; int *pp = A->cs->p; double *px = A->cs->x; @@ -2628,8 +2630,8 @@ return 0; } -int igraph_i_sparsemat_colsums_cc(const igraph_sparsemat_t *A, - igraph_vector_t *res) { +static int igraph_i_sparsemat_colsums_cc(const igraph_sparsemat_t *A, + igraph_vector_t *res) { int n = A->cs->n; double *px = A->cs->x; int *pp = A->cs->p; @@ -2828,8 +2830,8 @@ return 0; } -int igraph_i_sparsemat_scale_cols_cc(igraph_sparsemat_t *A, - const igraph_vector_t *fact) { +static int igraph_i_sparsemat_scale_cols_cc(igraph_sparsemat_t *A, + const igraph_vector_t *fact) { int *i = A->cs->i; igraph_real_t *x = A->cs->x; int no_of_edges = A->cs->p[A->cs->n]; @@ -2848,8 +2850,8 @@ return 0; } -int igraph_i_sparsemat_scale_cols_triplet(igraph_sparsemat_t *A, - const igraph_vector_t *fact) { +static int igraph_i_sparsemat_scale_cols_triplet(igraph_sparsemat_t *A, + const igraph_vector_t *fact) { int *j = A->cs->p; igraph_real_t *x = A->cs->x; int no_of_edges = A->cs->nz; diff --git a/igraph/src/spectral_properties.c b/igraph/src/spectral_properties.c --- a/igraph/src/spectral_properties.c +++ b/igraph/src/spectral_properties.c @@ -27,10 +27,10 @@ #include "config.h" #include -int igraph_i_weighted_laplacian(const igraph_t *graph, igraph_matrix_t *res, - igraph_sparsemat_t *sparseres, - igraph_bool_t normalized, - const igraph_vector_t *weights) { +static int igraph_i_weighted_laplacian(const igraph_t *graph, igraph_matrix_t *res, + igraph_sparsemat_t *sparseres, + igraph_bool_t normalized, + const igraph_vector_t *weights) { igraph_eit_t edgeit; int no_of_nodes = (int) igraph_vcount(graph); diff --git a/igraph/src/spmatrix.c b/igraph/src/spmatrix.c --- a/igraph/src/spmatrix.c +++ b/igraph/src/spmatrix.c @@ -24,14 +24,11 @@ #include "igraph_types.h" #include "igraph_spmatrix.h" -#include "igraph_memory.h" -#include "igraph_random.h" #include "igraph_error.h" #include "config.h" #include #include /* memcpy & co. */ -#include /** * \section igraph_spmatrix_constructor_and_destructor Sparse matrix constructors diff --git a/igraph/src/st-cuts.c b/igraph/src/st-cuts.c --- a/igraph/src/st-cuts.c +++ b/igraph/src/st-cuts.c @@ -28,18 +28,16 @@ #include "igraph_constants.h" #include "igraph_interface.h" #include "igraph_adjlist.h" -#include "igraph_conversion.h" #include "igraph_constructors.h" #include "igraph_structural.h" #include "igraph_components.h" -#include "igraph_types_internal.h" -#include "config.h" #include "igraph_math.h" #include "igraph_dqueue.h" #include "igraph_visitor.h" #include "igraph_marked_queue.h" #include "igraph_stack.h" #include "igraph_estack.h" +#include "config.h" /* * \function igraph_even_tarjan_reduction @@ -244,7 +242,7 @@ igraph_vector_long_t next; } igraph_i_dbucket_t; -int igraph_i_dbucket_init(igraph_i_dbucket_t *buck, long int size) { +static int igraph_i_dbucket_init(igraph_i_dbucket_t *buck, long int size) { IGRAPH_CHECK(igraph_vector_long_init(&buck->head, size)); IGRAPH_FINALLY(igraph_vector_long_destroy, &buck->head); IGRAPH_CHECK(igraph_vector_long_init(&buck->next, size)); @@ -252,42 +250,42 @@ return 0; } -void igraph_i_dbucket_destroy(igraph_i_dbucket_t *buck) { +static void igraph_i_dbucket_destroy(igraph_i_dbucket_t *buck) { igraph_vector_long_destroy(&buck->head); igraph_vector_long_destroy(&buck->next); } -int igraph_i_dbucket_insert(igraph_i_dbucket_t *buck, long int bid, - long int elem) { +static int igraph_i_dbucket_insert(igraph_i_dbucket_t *buck, long int bid, + long int elem) { /* Note: we can do this, since elem is not in any buckets */ VECTOR(buck->next)[elem] = VECTOR(buck->head)[bid]; VECTOR(buck->head)[bid] = elem + 1; return 0; } -long int igraph_i_dbucket_empty(const igraph_i_dbucket_t *buck, - long int bid) { +static long int igraph_i_dbucket_empty(const igraph_i_dbucket_t *buck, + long int bid) { return VECTOR(buck->head)[bid] == 0; } -long int igraph_i_dbucket_delete(igraph_i_dbucket_t *buck, long int bid) { +static long int igraph_i_dbucket_delete(igraph_i_dbucket_t *buck, long int bid) { long int elem = VECTOR(buck->head)[bid] - 1; VECTOR(buck->head)[bid] = VECTOR(buck->next)[elem]; return elem; } -int igraph_i_dominator_LINK(long int v, long int w, - igraph_vector_long_t *ancestor) { +static int igraph_i_dominator_LINK(long int v, long int w, + igraph_vector_long_t *ancestor) { VECTOR(*ancestor)[w] = v + 1; return 0; } /* TODO: don't always reallocate path */ -int igraph_i_dominator_COMPRESS(long int v, - igraph_vector_long_t *ancestor, - igraph_vector_long_t *label, - igraph_vector_long_t *semi) { +static int igraph_i_dominator_COMPRESS(long int v, + igraph_vector_long_t *ancestor, + igraph_vector_long_t *label, + igraph_vector_long_t *semi) { igraph_stack_long_t path; long int w = v; long int top, pretop; @@ -319,10 +317,10 @@ return 0; } -long int igraph_i_dominator_EVAL(long int v, - igraph_vector_long_t *ancestor, - igraph_vector_long_t *label, - igraph_vector_long_t *semi) { +static long int igraph_i_dominator_EVAL(long int v, + igraph_vector_long_t *ancestor, + igraph_vector_long_t *label, + igraph_vector_long_t *semi) { if (VECTOR(*ancestor)[v] == 0) { return v; } else { @@ -362,7 +360,7 @@ * \param dom Pointer to an initialized vector or a null pointer. If * not a null pointer, then the immediate dominator of each * vertex will be stored here. For vertices that are not - * reachable from the root, \c IGRAPH_NAN is stored here. For + * reachable from the root, NaN is stored here. For * the root vertex itself, -1 is added. * \param domtree Pointer to an uninitialized igraph_t, or NULL. If * not a null pointer, then the dominator tree is returned @@ -579,7 +577,8 @@ const igraph_vector_t *map; } igraph_i_all_st_cuts_minimal_dfs_data_t; -igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_incb(const igraph_t *graph, +static igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_incb( + const igraph_t *graph, igraph_integer_t vid, igraph_integer_t dist, void *extra) { @@ -604,7 +603,8 @@ return 0; } -igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_otcb(const igraph_t *graph, +static igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_otcb( + const igraph_t *graph, igraph_integer_t vid, igraph_integer_t dist, void *extra) { @@ -623,13 +623,13 @@ return 0; } -int igraph_i_all_st_cuts_minimal(const igraph_t *graph, - const igraph_t *domtree, - long int root, - const igraph_marked_queue_t *X, - const igraph_vector_bool_t *GammaX, - const igraph_vector_t *invmap, - igraph_vector_t *minimal) { +static int igraph_i_all_st_cuts_minimal(const igraph_t *graph, + const igraph_t *domtree, + long int root, + const igraph_marked_queue_t *X, + const igraph_vector_bool_t *GammaX, + const igraph_vector_t *invmap, + igraph_vector_t *minimal) { long int no_of_nodes = igraph_vcount(graph); igraph_stack_t stack; @@ -684,6 +684,7 @@ return 0; } +/* not 'static' because used in igraph_all_st_cuts.c test program */ int igraph_i_all_st_cuts_pivot(const igraph_t *graph, const igraph_marked_queue_t *S, const igraph_estack_t *T, @@ -1118,10 +1119,10 @@ zero-indegree vertices. */ -int igraph_i_all_st_mincuts_minimal(const igraph_t *Sbar, - const igraph_vector_bool_t *active, - const igraph_vector_t *invmap, - igraph_vector_t *minimal) { +static int igraph_i_all_st_mincuts_minimal(const igraph_t *Sbar, + const igraph_vector_bool_t *active, + const igraph_vector_t *invmap, + igraph_vector_t *minimal) { long int no_of_nodes = igraph_vcount(Sbar); igraph_vector_t indeg; @@ -1169,7 +1170,7 @@ igraph_vector_destroy(&indeg); igraph_vector_destroy(&neis); - IGRAPH_FINALLY_CLEAN(3); + IGRAPH_FINALLY_CLEAN(2); return 0; } @@ -1178,14 +1179,14 @@ const igraph_vector_bool_t *active; } igraph_i_all_st_mincuts_data_t; -int igraph_i_all_st_mincuts_pivot(const igraph_t *graph, - const igraph_marked_queue_t *S, - const igraph_estack_t *T, - long int source, - long int target, - long int *v, - igraph_vector_t *Isv, - void *arg) { +static int igraph_i_all_st_mincuts_pivot(const igraph_t *graph, + const igraph_marked_queue_t *S, + const igraph_estack_t *T, + long int source, + long int target, + long int *v, + igraph_vector_t *Isv, + void *arg) { igraph_i_all_st_mincuts_data_t *data = arg; const igraph_vector_bool_t *active = data->active; @@ -1283,10 +1284,14 @@ * \function igraph_all_st_mincuts * All minimum s-t cuts of a directed graph * - * This function lists all minimum edge cuts between two vertices, in a - * directed graph. The implemented algorithm - * is described in JS Provan and DR Shier: A Paradigm for listing - * (s,t)-cuts in graphs, Algorithmica 15, 351--372, 1996. + * This function lists all edge cuts between two vertices, in a directed graph, + * with minimum total capacity. Possibly, multiple cuts may have the same total + * capacity, although there is often only one minimum cut in weighted graphs. + * It is recommended to supply integer-values capacities. Otherwise, not all + * minimum cuts may be detected because of numerical roundoff errors. + * The implemented algorithm is described in JS Provan and DR + * Shier: A Paradigm for listing (s,t)-cuts in graphs, Algorithmica 15, + * 351--372, 1996. * * \param graph The input graph, it must be directed. * \param value Pointer to a real number, the value of the minimum cut @@ -1306,8 +1311,9 @@ * ignored if it is a null pointer. * \param source The id of the source vertex. * \param target The id of the target vertex. - * \param capacity Vector of edge capacities. If this is a null - * pointer, then all edges are assumed to have capacity one. + * \param capacity Vector of edge capacities. All capacities must be + * strictly positive. If this is a null pointer, then all edges + * are assumed to have capacity one. * \return Error code. * * Time complexity: O(n(|V|+|E|))+O(F), where |V| is the number of @@ -1358,6 +1364,10 @@ } if (source == target) { IGRAPH_ERROR("`source' and 'target' are the same vertex", IGRAPH_EINVAL); + } + if (capacity != NULL && igraph_vector_min(capacity) <= 0) + { + IGRAPH_ERROR("Not all capacities are strictly positive.", IGRAPH_EINVAL); } if (!partition1s) { diff --git a/igraph/src/statusbar.c b/igraph/src/statusbar.c --- a/igraph/src/statusbar.c +++ b/igraph/src/statusbar.c @@ -21,10 +21,10 @@ */ -#include "config.h" #include "igraph_types.h" #include "igraph_statusbar.h" #include "igraph_error.h" +#include "config.h" #include #include diff --git a/igraph/src/structural_properties.c b/igraph/src/structural_properties.c --- a/igraph/src/structural_properties.c +++ b/igraph/src/structural_properties.c @@ -1554,7 +1554,7 @@ } /* Not declared static so that the testsuite can use it, but not part of the public API. */ -int igraph_rewire_core(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode, igraph_bool_t use_adjlist) { +int igraph_i_rewire(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode, igraph_bool_t use_adjlist) { long int no_of_nodes = igraph_vcount(graph); long int no_of_edges = igraph_ecount(graph); char message[256]; @@ -1785,7 +1785,7 @@ int igraph_rewire(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode) { igraph_bool_t use_adjlist = n >= REWIRE_ADJLIST_THRESHOLD; - return igraph_rewire_core(graph, n, mode, use_adjlist); + return igraph_i_rewire(graph, n, mode, use_adjlist); } @@ -1915,11 +1915,13 @@ for (i = 0; i < no_of_new_nodes; i++) { long int old_vid = (long int) VECTOR(*my_vids_new2old)[i]; long int new_vid = i; + igraph_bool_t skip_loop_edge; IGRAPH_CHECK(igraph_incident(graph, &nei_edges, old_vid, IGRAPH_OUT)); n = igraph_vector_size(&nei_edges); if (directed) { + /* directed graph; this is easier */ for (j = 0; j < n; j++) { eid = (igraph_integer_t) VECTOR(nei_edges)[j]; @@ -1933,10 +1935,15 @@ IGRAPH_CHECK(igraph_vector_push_back(&eids_new2old, eid)); } } else { + /* undirected graph. We need to be careful with loop edges as each + * loop edge will appear twice. We use a boolean flag to skip every + * second loop edge */ + skip_loop_edge = 0; for (j = 0; j < n; j++) { eid = (igraph_integer_t) VECTOR(nei_edges)[j]; - if (IGRAPH_FROM(graph, eid) != old_vid) { /* avoid processing edges twice */ + if (IGRAPH_FROM(graph, eid) != old_vid) { + /* avoid processing edges twice */ continue; } @@ -1944,9 +1951,18 @@ if (!to) { continue; } + to -= 1; + if (new_vid == to) { + /* this is a loop edge; check whether we need to skip it */ + skip_loop_edge = !skip_loop_edge; + if (skip_loop_edge) { + continue; + } + } + IGRAPH_CHECK(igraph_vector_push_back(&new_edges, new_vid)); - IGRAPH_CHECK(igraph_vector_push_back(&new_edges, to - 1)); + IGRAPH_CHECK(igraph_vector_push_back(&new_edges, to)); IGRAPH_CHECK(igraph_vector_push_back(&eids_new2old, eid)); } } @@ -2540,7 +2556,7 @@ * C[i] = sum( sum( (p[i,q] p[q,j])^2, q in V[i], q != i,j ), j in * V[], j != i) * - * for a graph of order (ie. number of vertices) N, where proportional + * for a graph of order (i.e. number of vertices) N, where proportional * tie strengths are defined as *
* p[i,j]=(a[i,j]+a[j,i]) / sum(a[i,k]+a[k,i], k in V[i], k != i), @@ -2948,7 +2964,7 @@ * \brief Calculates the size of the neighborhood of a given vertex. * * The neighborhood of a given order of a vertex includes all vertices - * which are closer to the vertex than the order. Ie. order 0 is + * which are closer to the vertex than the order. I.e., order 0 is * always the vertex itself, order 1 is the vertex plus its immediate * neighbors, order 2 is order 1 plus the immediate neighbors of the * vertices in order 1, etc. @@ -3074,7 +3090,7 @@ * Calculate the neighborhood of vertices. * * The neighborhood of a given order of a vertex includes all vertices - * which are closer to the vertex than the order. Ie. order 0 is + * which are closer to the vertex than the order. I.e., order 0 is * always the vertex itself, order 1 is the vertex plus its immediate * neighbors, order 2 is order 1 plus the immediate neighbors of the * vertices in order 1, etc. @@ -3085,15 +3101,15 @@ * \param res An initialized pointer vector. Note that the objects * (pointers) in the vector will \em not be freed, but the pointer * vector will be resized as needed. The result of the calculation - * will be stored here in \c vector_t objects. + * will be stored here in \ref igraph_vector_t objects. * \param vids The vertices for which the calculation is performed. * \param order Integer giving the order of the neighborhood. * \param mode Specifies how to use the direction of the edges if a * directed graph is analyzed. For \c IGRAPH_OUT only the outgoing * edges are followed, so all vertices reachable from the source - * vertex in at most \c order steps are included. For \c IGRAPH_IN + * vertex in at most \p order steps are included. For \c IGRAPH_IN * all vertices from which the source vertex is reachable in at most - * \c order steps are included. \c IGRAPH_ALL ignores the direction + * \p order steps are included. \c IGRAPH_ALL ignores the direction * of the edges. This argument is ignored for undirected graphs. * \param mindist The minimum distance to include a vertex in the counting. * If this is one, then the starting vertex is not counted. If this is @@ -3228,7 +3244,7 @@ * Vincent Matossian, thanks Vincent. * \param graph The input graph. * \param res Pointer to a pointer vector, the result will be stored - * here, ie. \c res will contain pointers to \c igraph_t + * here, ie. \p res will contain pointers to \c igraph_t * objects. It will be resized if needed but note that the * objects in the pointer vector will not be freed. * \param vids The vertices for which the calculation is performed. @@ -3236,9 +3252,9 @@ * \param mode Specifies how to use the direction of the edges if a * directed graph is analyzed. For \c IGRAPH_OUT only the outgoing * edges are followed, so all vertices reachable from the source - * vertex in at most \c order steps are counted. For \c IGRAPH_IN + * vertex in at most \p order steps are counted. For \c IGRAPH_IN * all vertices from which the source vertex is reachable in at most - * \c order steps are counted. \c IGRAPH_ALL ignores the direction + * \p order steps are counted. \c IGRAPH_ALL ignores the direction * of the edges. This argument is ignored for undirected graphs. * \param mindist The minimum distance to include a vertex in the counting. * If this is one, then the starting vertex is not counted. If this is @@ -3568,7 +3584,7 @@ igraph_bool_t found = 0; IGRAPH_VECTOR_INIT_FINALLY(&neis, 0); for (i = 0; i < vc; i++) { - igraph_neighbors(graph, &neis, (igraph_integer_t) i, IGRAPH_OUT); + IGRAPH_CHECK(igraph_neighbors(graph, &neis, (igraph_integer_t) i, IGRAPH_OUT)); n = igraph_vector_size(&neis); for (j = 0; j < n; j++) { if (VECTOR(neis)[j] == i) { @@ -3781,6 +3797,7 @@ return 0; } + /** * \function igraph_count_multiple * \brief Count the number of appearances of the edges in a graph. @@ -3801,15 +3818,15 @@ * * \sa \ref igraph_is_multiple() and \ref igraph_simplify(). * - * Time complexity: O(e*d), e is the number of edges to check and d is the + * Time complexity: O(E d), E is the number of edges to check and d is the * average degree (out-degree in directed graphs) of the vertices at the * tail of the edges. */ - int igraph_count_multiple(const igraph_t *graph, igraph_vector_t *res, igraph_es_t es) { igraph_eit_t eit; long int i; + igraph_bool_t directed = igraph_is_directed(graph); igraph_lazy_inclist_t inclist; IGRAPH_CHECK(igraph_eit_create(graph, es, &eit)); @@ -3835,7 +3852,7 @@ } } /* for loop edges, divide the result by two */ - if (to == from) { + if (!directed && to == from) { VECTOR(*res)[i] /= 2; } } @@ -3843,9 +3860,11 @@ igraph_lazy_inclist_destroy(&inclist); igraph_eit_destroy(&eit); IGRAPH_FINALLY_CLEAN(2); - return 0; + + return IGRAPH_SUCCESS; } + /** * \function igraph_girth * \brief The girth of a graph is the length of the shortest circle in it. @@ -5968,6 +5987,10 @@ } } + igraph_vector_destroy(&edge_neis); + igraph_vector_destroy(&neis); + IGRAPH_FINALLY_CLEAN(2); + if (knnk) { for (i = 0; i < maxdeg; i++) { igraph_real_t dh = VECTOR(deghist)[i]; @@ -5982,7 +6005,7 @@ IGRAPH_FINALLY_CLEAN(1); } - igraph_vector_destroy(&neis); + igraph_vector_destroy(&strength); igraph_vector_destroy(°); IGRAPH_FINALLY_CLEAN(2); @@ -5999,39 +6022,54 @@ /** * \function igraph_avg_nearest_neighbor_degree - * Average nearest neighbor degree. + * Average neighbor degree. * - * Calculates the average degree of the neighbors for each vertex, and - * optionally, the same quantity in the function of vertex degree. + * Calculates the average degree of the neighbors for each vertex (\p knn), and + * optionally, the same quantity as a function of the vertex degree (\p knnk). * - * For isolate vertices \p knn is set to \c - * IGRAPH_NAN. The same is done in \p knnk for vertex degrees that + * + * For isolated vertices \p knn is set to NaN. + * The same is done in \p knnk for vertex degrees that * don't appear in the graph. * - * \param graph The input graph, it can be directed but the - * directedness of the edges is ignored. + * + * The weighted version computes a weighted average of the neighbor degrees as + * + * k_nn_u = 1/s_u sum_v w_uv k_v, + * + * where s_u = sum_v w_uv is the sum of the incident edge weights + * of vertex \c u, i.e. its strength. + * The sum runs over the neighbors \c v of vertex \c u + * as indicated by \p mode. w_uv denotes the weighted adjacency matrix + * and k_v is the neighbors' degree, specified by \p neighbor_degree_mode. + * + * + * Reference: + * A. Barrat, M. Barthélemy, R. Pastor-Satorras, and A. Vespignani, + * The architecture of complex weighted networks, + * Proc. Natl. Acad. Sci. USA 101, 3747 (2004). + * https://dx.doi.org/10.1073/pnas.0400087101 + * + * \param graph The input graph. It may be directed. * \param vids The vertices for which the calculation is performed. - * \param mode The neighbors over which is averaged. - * \param neighbor_degree_mode The degree of the neighbors which is - * averaged. + * \param mode The type of neighbors to consider in directed graphs. + * \c IGRAPH_OUT considers out-neighbors, \c IGRAPH_IN in-neighbors + * and \c IGRAPH_ALL ignores edge directions. + * \param neighbor_degree_mode The type of degree to average in directed graphs. + * \c IGRAPH_OUT averages out-degrees, \c IGRAPH_IN averages in-degrees + * and \c IGRAPH_ALL ignores edge directions for the degree calculation. * \param vids The vertices for which the calculation is performed. * \param knn Pointer to an initialized vector, the result will be - * stored here. It will be resized as needed. Supply a NULL pointer + * stored here. It will be resized as needed. Supply a \c NULL pointer * here, if you only want to calculate \c knnk. - * \param knnk Pointer to an initialized vector, the average nearest - * neighbor degree in the function of vertex degree is stored + * \param knnk Pointer to an initialized vector, the average + * neighbor degree as a function of the vertex degree is stored * here. The first (zeroth) element is for degree one vertices, - * etc. Supply a NULL pointer here if you don't want to calculate + * etc. Supply a \c NULL pointer here if you don't want to calculate * this. * \param weights Optional edge weights. Supply a null pointer here - * for the non-weighted version. The weighted version computes - * a weighted average of the neighbor degrees, i.e. - * - * k_nn_i = 1/s_i sum_j w_ij k_j + * for the non-weighted version. * - * where s_i is the sum of the weights, the sum runs over - * the neighbors as indicated by \c mode (with appropriate weights) - * and k_j is the degree, specified by \c neighbor_degree_mode. * \return Error code. * * Time complexity: O(|V|+|E|), linear in the number of vertices and @@ -6493,8 +6531,7 @@ int igraph_contract_vertices(igraph_t *graph, const igraph_vector_t *mapping, - const igraph_attribute_combination_t - *vertex_comb) { + const igraph_attribute_combination_t *vertex_comb) { igraph_vector_t edges; long int no_of_nodes = igraph_vcount(graph); long int no_of_edges = igraph_ecount(graph); @@ -6907,15 +6944,22 @@ } } -int igraph_i_is_graphical_degree_sequence_undirected( - const igraph_vector_t *degrees, igraph_bool_t *res) { +int igraph_i_is_graphical_degree_sequence_undirected(const igraph_vector_t *degrees, igraph_bool_t *res) { igraph_vector_t work; long int w, b, s, c, n, k; + n = igraph_vector_size(degrees); + + /* zero-length sequences are considered graphical */ + if (n == 0) { + *res = 1; + return IGRAPH_SUCCESS; + } + IGRAPH_CHECK(igraph_vector_copy(&work, degrees)); IGRAPH_FINALLY(igraph_vector_destroy, &work); - igraph_vector_sort(&work); + igraph_vector_reverse_sort(&work); /* This algorithm is outlined in TR-2011-11 of the Egervary Research Group, * ISSN 1587-4451. The main loop of the algorithm is O(n) but it is dominated @@ -6926,13 +6970,12 @@ * the degrees themselves. w and k are zero-based here; in the technical * report they are 1-based */ *res = 1; - n = igraph_vector_size(&work); w = n - 1; b = 0; s = 0; c = 0; for (k = 0; k < n; k++) { - b += VECTOR(*degrees)[k]; + b += VECTOR(work)[k]; c += w; - while (w > k && VECTOR(*degrees)[w] <= k + 1) { - s += VECTOR(*degrees)[w]; + while (w > k && VECTOR(work)[w] <= k + 1) { + s += VECTOR(work)[w]; c -= (k + 1); w--; } @@ -6948,7 +6991,7 @@ igraph_vector_destroy(&work); IGRAPH_FINALLY_CLEAN(1); - return 0; + return IGRAPH_SUCCESS; } typedef struct { diff --git a/igraph/src/structure_generators.c b/igraph/src/structure_generators.c --- a/igraph/src/structure_generators.c +++ b/igraph/src/structure_generators.c @@ -100,18 +100,18 @@ return 0; } -int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix, - igraph_vector_t *edges); -int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix, - igraph_vector_t *edges); -int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix, - igraph_vector_t *edges); -int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix, - igraph_vector_t *edges); -int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix, - igraph_vector_t *edges); +static int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix, + igraph_vector_t *edges); +static int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix, + igraph_vector_t *edges); +static int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix, + igraph_vector_t *edges); +static int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix, + igraph_vector_t *edges); +static int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix, + igraph_vector_t *edges); -int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { +static int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j, k; @@ -129,7 +129,7 @@ return 0; } -int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { +static int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j, k; @@ -151,7 +151,7 @@ return 0; } -int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { +static int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j, k; @@ -168,7 +168,7 @@ return 0; } -int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { +static int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j, k; @@ -185,7 +185,7 @@ return 0; } -int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { +static int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j, k; @@ -311,32 +311,39 @@ return 0; } -int igraph_i_weighted_adjacency_directed(const igraph_matrix_t *adjmatrix, +static int igraph_i_weighted_adjacency_directed( + const igraph_matrix_t *adjmatrix, igraph_vector_t *edges, igraph_vector_t *weights, igraph_bool_t loops); -int igraph_i_weighted_adjacency_plus(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops); -int igraph_i_weighted_adjacency_max(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops); -int igraph_i_weighted_adjacency_upper(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops); -int igraph_i_weighted_adjacency_lower(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops); -int igraph_i_weighted_adjacency_min(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops); +static int igraph_i_weighted_adjacency_plus( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops); +static int igraph_i_weighted_adjacency_max( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops); +static int igraph_i_weighted_adjacency_upper( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops); +static int igraph_i_weighted_adjacency_lower( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops); +static int igraph_i_weighted_adjacency_min( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops); -int igraph_i_weighted_adjacency_directed(const igraph_matrix_t *adjmatrix, +static int igraph_i_weighted_adjacency_directed( + const igraph_matrix_t *adjmatrix, igraph_vector_t *edges, igraph_vector_t *weights, igraph_bool_t loops) { @@ -362,10 +369,11 @@ return 0; } -int igraph_i_weighted_adjacency_plus(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops) { +static int igraph_i_weighted_adjacency_plus( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j; @@ -391,10 +399,11 @@ return 0; } -int igraph_i_weighted_adjacency_max(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops) { +static int igraph_i_weighted_adjacency_max( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j; @@ -420,10 +429,11 @@ return 0; } -int igraph_i_weighted_adjacency_upper(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops) { +static int igraph_i_weighted_adjacency_upper( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j; @@ -445,10 +455,11 @@ return 0; } -int igraph_i_weighted_adjacency_lower(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops) { +static int igraph_i_weighted_adjacency_lower( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j; @@ -470,10 +481,11 @@ return 0; } -int igraph_i_weighted_adjacency_min(const igraph_matrix_t *adjmatrix, - igraph_vector_t *edges, - igraph_vector_t *weights, - igraph_bool_t loops) { +static int igraph_i_weighted_adjacency_min( + const igraph_matrix_t *adjmatrix, + igraph_vector_t *edges, + igraph_vector_t *weights, + igraph_bool_t loops) { long int no_of_nodes = igraph_matrix_nrow(adjmatrix); long int i, j; @@ -750,18 +762,31 @@ /** * \ingroup generators * \function igraph_lattice - * \brief Creates most kinds of lattices. + * \brief Arbitrary dimensional square lattices. * + * Creates d-dimensional square lattices of the given size. Optionally, + * the lattice can be made periodic, and the neighbors within a given + * graph distance can be connected. + * + * + * In the zero-dimensional case, the singleton graph is returned. + * + * + * The vertices of the resulting graph are ordered such that the + * index of the vertex at position (i_0, i_1, i_2, ..., i_d) + * in a lattice of size (n_0, n_1, ..., n_d) will be + * i_0 + n_0 * i_1 + n_0 * n_1 * i_2 + .... + * * \param graph An uninitialized graph object. * \param dimvector Vector giving the sizes of the lattice in each of - * its dimensions. Ie. the dimension of the lattice will be the + * its dimensions. The dimension of the lattice will be the * same as the length of this vector. * \param nei Integer value giving the distance (number of steps) * within which two vertices will be connected. - * \param directed Boolean, whether to create a directed graph. The - * direction of the edges is determined by the generation - * algorithm and is unlikely to suit you, so this isn't a very - * useful option. + * \param directed Boolean, whether to create a directed graph. + * If the \c mutual and \c circular arguments are not set to true, + * edges will be directed from lower-index vertices towards + * higher-index ones. * \param mutual Boolean, if the graph is directed this gives whether * to create all connections as mutual. * \param circular Boolean, defines whether the generated lattice is @@ -770,10 +795,10 @@ * \c IGRAPH_EINVAL: invalid (negative) * dimension vector. * - * Time complexity: if \p nei is less than two then it is O(|V|+|E|) (as + * Time complexity: If \p nei is less than two then it is O(|V|+|E|) (as * far as I remember), |V| and |E| are the number of vertices - * and edges in the generated graph. Otherwise it is O(|V|*d^o+|E|), d - * is the average degree of the graph, o is the \p nei argument. + * and edges in the generated graph. Otherwise it is O(|V|*d^k+|E|), d + * is the average degree of the graph, k is the \p nei argument. */ int igraph_lattice(igraph_t *graph, const igraph_vector_t *dimvector, igraph_integer_t nei, igraph_bool_t directed, igraph_bool_t mutual, @@ -794,14 +819,14 @@ coords = igraph_Calloc(dims, long int); if (coords == 0) { - IGRAPH_ERROR("lattice failed", IGRAPH_ENOMEM); + IGRAPH_ERROR("Lattice creation failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, coords); /* TODO: hack */ + IGRAPH_FINALLY(igraph_free, coords); weights = igraph_Calloc(dims, long int); if (weights == 0) { - IGRAPH_ERROR("lattice failed", IGRAPH_ENOMEM); + IGRAPH_ERROR("Lattice creation failed", IGRAPH_ENOMEM); } - IGRAPH_FINALLY(free, weights); + IGRAPH_FINALLY(igraph_free, weights); if (dims > 0) { weights[0] = 1; for (i = 1; i < dims; i++) { @@ -1991,9 +2016,7 @@ 32, 33 }; -int igraph_i_famous(igraph_t *graph, const igraph_real_t *data); - -int igraph_i_famous(igraph_t *graph, const igraph_real_t *data) { +static int igraph_i_famous(igraph_t *graph, const igraph_real_t *data) { long int no_of_nodes = (long int) data[0]; long int no_of_edges = (long int) data[1]; igraph_bool_t directed = (igraph_bool_t) data[2]; @@ -2110,11 +2133,11 @@ * vertices and 12 edges. * \cli Petersen * A 3-regular graph with 10 vertices and 15 edges. It is - * the smallest hypohamiltonian graph, ie. it is + * the smallest hypohamiltonian graph, i.e. it is * non-hamiltonian but removing any single vertex from it makes it * Hamiltonian. * \cli Robertson - * The unique (4,5)-cage graph, ie. a 4-regular + * The unique (4,5)-cage graph, i.e. a 4-regular * graph of girth 5. It has 19 vertices and 38 edges. * \cli Smallestcyclicgroup * A smallest nontrivial graph @@ -2370,7 +2393,7 @@ * invalid Prüfer sequence given * \endclist * - * \sa \ref igraph_tree(), \ref igraph_tree_game() + * \sa \ref igraph_to_prufer(), \ref igraph_tree(), \ref igraph_tree_game() * */ diff --git a/igraph/src/sugiyama.c b/igraph/src/sugiyama.c --- a/igraph/src/sugiyama.c +++ b/igraph/src/sugiyama.c @@ -22,7 +22,7 @@ */ -#include "config.h" +#include "igraph_layout.h" #include "igraph_centrality.h" #include "igraph_components.h" #include "igraph_constants.h" @@ -34,6 +34,7 @@ #include "igraph_memory.h" #include "igraph_structural.h" #include "igraph_types.h" +#include "config.h" #include @@ -157,8 +158,8 @@ /** * Initializes a layering. */ -int igraph_i_layering_init(igraph_i_layering_t* layering, - const igraph_vector_t* membership) { +static int igraph_i_layering_init(igraph_i_layering_t* layering, + const igraph_vector_t* membership) { long int i, n, num_layers; if (igraph_vector_size(membership) == 0) { @@ -193,21 +194,21 @@ /** * Destroys a layering. */ -void igraph_i_layering_destroy(igraph_i_layering_t* layering) { +static void igraph_i_layering_destroy(igraph_i_layering_t* layering) { igraph_vector_ptr_destroy_all(&layering->layers); } /** * Returns the number of layers in a layering. */ -int igraph_i_layering_num_layers(const igraph_i_layering_t* layering) { +static int igraph_i_layering_num_layers(const igraph_i_layering_t* layering) { return (int) igraph_vector_ptr_size(&layering->layers); } /** * Returns the list of vertices in a given layer */ -igraph_vector_t* igraph_i_layering_get(const igraph_i_layering_t* layering, +static igraph_vector_t* igraph_i_layering_get(const igraph_i_layering_t* layering, long int index) { return (igraph_vector_t*)VECTOR(layering->layers)[index]; } diff --git a/igraph/src/topology.c b/igraph/src/topology.c --- a/igraph/src/topology.c +++ b/igraph/src/topology.c @@ -31,6 +31,7 @@ #include "igraph_stack.h" #include "igraph_attributes.h" #include "igraph_structural.h" +#include "igraph_isoclasses.h" #include "config.h" const unsigned int igraph_i_isoclass_3[] = { 0, 1, 1, 3, 1, 5, 6, 7, @@ -689,6 +690,9 @@ * (between 0 and 15), for undirected graph it is only 4. For graphs * with four vertices it is 218 (directed) and 11 (undirected). * + * + * Multi-edges and self-loops are ignored by this function. + * * \param graph The graph object. * \param isoclass Pointer to an integer, the isomorphism class will * be stored here. @@ -754,26 +758,31 @@ * \brief Decides whether two graphs are isomorphic * * - * From Wikipedia: The graph isomorphism problem or GI problem is the - * graph theory problem of determining whether, given two graphs G1 - * and G2, it is possible to permute (or relabel) the vertices of one - * graph so that it is equal to the other. Such a permutation is - * called a graph isomorphism. + * In simple terms, two graphs are isomorphic if they become indistinguishable + * from each other once their vertex labels are removed (rendering the vertices + * within each graph indistiguishable). More precisely, two graphs are isomorphic + * if there is a one-to-one mapping from the vertices of the first one + * to the vertices of the second such that it transforms the edge set of the + * first graph into the edge set of the second. This mapping is called + * an \em isomorphism. * - * This function decides which graph isomorphism algorithm to be + * Currently, this function supports simple graphs and graphs + * with self-loops, but does not support multigraphs. + * + * This function decides which graph isomorphism algorithm to be * used based on the input graphs. Right now it does the following: * \olist * \oli If one graph is directed and the other undirected then an * error is triggered. + * \oli If one of the graphs has multi-edges then an error is triggered. * \oli If the two graphs does not have the same number of vertices * and edges it returns with \c FALSE. * \oli Otherwise, if the graphs have three or four vertices then an O(1) * algorithm is used with precomputed data. * \oli Otherwise BLISS is used, see \ref igraph_isomorphic_bliss(). * \endolist - * * - * Please call the VF2 and BLISS functions directly if you need + * Please call the VF2 and BLISS functions directly if you need * something more sophisticated, e.g. you need the isomorphic mapping. * * \param graph1 The first graph. @@ -793,8 +802,15 @@ long int nodes1 = igraph_vcount(graph1), nodes2 = igraph_vcount(graph2); long int edges1 = igraph_ecount(graph1), edges2 = igraph_ecount(graph2); igraph_bool_t dir1 = igraph_is_directed(graph1), dir2 = igraph_is_directed(graph2); - igraph_bool_t loop1, loop2; + igraph_bool_t loop1, loop2, multi1, multi2; + IGRAPH_CHECK(igraph_has_multiple(graph1, &multi1)); + IGRAPH_CHECK(igraph_has_multiple(graph2, &multi2)); + + if (multi1 || multi2) { + IGRAPH_ERROR("Isomorphism testing is not implemented for multigraphs", IGRAPH_UNIMPLEMENTED); + } + if (dir1 != dir2) { IGRAPH_ERROR("Cannot compare directed and undirected graphs", IGRAPH_EINVAL); } else if (nodes1 != nodes2 || edges1 != edges2) { @@ -821,7 +837,8 @@ * Graph isomorphism for 3-4 vertices * * This function uses precomputed indices to decide isomorphism - * problems for graphs with only 3 or 4 vertices. + * problems for graphs with only 3 or 4 vertices. Multi-edges + * and self-loops are ignored by this function. * \param graph1 The first input graph. * \param graph2 The second input graph. Must have the same * directedness as \p graph1. @@ -1640,7 +1657,8 @@ void *arg, *carg; } igraph_i_iso_cb_data_t; -igraph_bool_t igraph_i_isocompat_node_cb(const igraph_t *graph1, +static igraph_bool_t igraph_i_isocompat_node_cb( + const igraph_t *graph1, const igraph_t *graph2, const igraph_integer_t g1_num, const igraph_integer_t g2_num, @@ -1649,7 +1667,8 @@ return data->node_compat_fn(graph1, graph2, g1_num, g2_num, data->carg); } -igraph_bool_t igraph_i_isocompat_edge_cb(const igraph_t *graph1, +static igraph_bool_t igraph_i_isocompat_edge_cb( + const igraph_t *graph1, const igraph_t *graph2, const igraph_integer_t g1_num, const igraph_integer_t g2_num, @@ -1658,9 +1677,9 @@ return data->edge_compat_fn(graph1, graph2, g1_num, g2_num, data->carg); } -igraph_bool_t igraph_i_isomorphic_vf2(igraph_vector_t *map12, - igraph_vector_t *map21, - void *arg) { +static igraph_bool_t igraph_i_isomorphic_vf2(igraph_vector_t *map12, + igraph_vector_t *map21, + void *arg) { igraph_i_iso_cb_data_t *data = arg; igraph_bool_t *iso = data->arg; IGRAPH_UNUSED(map12); IGRAPH_UNUSED(map21); @@ -1699,11 +1718,11 @@ * \param map12 Pointer to an initialized vector or a NULL pointer. If not * a NULL pointer then the mapping from \p graph1 to \p graph2 is * stored here. If the graphs are not isomorphic then the vector is - * cleared (ie. has zero elements). + * cleared (i.e. has zero elements). * \param map21 Pointer to an initialized vector or a NULL pointer. If not * a NULL pointer then the mapping from \p graph2 to \p graph1 is * stored here. If the graphs are not isomorphic then the vector is - * cleared (ie. has zero elements). + * cleared (i.e. has zero elements). * \param node_compat_fn A pointer to a function of type \ref * igraph_isocompat_t. This function will be called by the algorithm to * determine whether two nodes are compatible. @@ -1756,7 +1775,8 @@ return 0; } -igraph_bool_t igraph_i_count_isomorphisms_vf2(const igraph_vector_t *map12, +static igraph_bool_t igraph_i_count_isomorphisms_vf2( + const igraph_vector_t *map12, const igraph_vector_t *map21, void *arg) { igraph_i_iso_cb_data_t *data = arg; @@ -1828,7 +1848,7 @@ return 0; } -void igraph_i_get_isomorphisms_free(igraph_vector_ptr_t *data) { +static void igraph_i_get_isomorphisms_free(igraph_vector_ptr_t *data) { long int i, n = igraph_vector_ptr_size(data); for (i = 0; i < n; i++) { igraph_vector_t *vec = VECTOR(*data)[i]; @@ -1837,7 +1857,8 @@ } } -igraph_bool_t igraph_i_get_isomorphisms_vf2(const igraph_vector_t *map12, +static igraph_bool_t igraph_i_get_isomorphisms_vf2( + const igraph_vector_t *map12, const igraph_vector_t *map21, void *arg) { @@ -1883,11 +1904,11 @@ * \param edge_color2 The edge color vector for the second graph. * \param maps Pointer vector. On return it is empty if the input graphs * are no isomorphic. Otherwise it contains pointers to - * igraph_vector_t objects, each vector is an + * \ref igraph_vector_t objects, each vector is an * isomorphic mapping of \p graph2 to \p graph1. Please note that * you need to 1) Destroy the vectors via \ref * igraph_vector_destroy(), 2) free them via - * free() and then 3) call \ref + * \ref igraph_free() and then 3) call \ref * igraph_vector_ptr_destroy() on the pointer vector to deallocate all * memory when \p maps is no longer needed. * \param node_compat_fn A pointer to a function of type \ref @@ -2473,7 +2494,8 @@ return 0; } -igraph_bool_t igraph_i_subisomorphic_vf2(const igraph_vector_t *map12, +static igraph_bool_t igraph_i_subisomorphic_vf2( + const igraph_vector_t *map12, const igraph_vector_t *map21, void *arg) { igraph_i_iso_cb_data_t *data = arg; @@ -2560,7 +2582,8 @@ return 0; } -igraph_bool_t igraph_i_count_subisomorphisms_vf2(const igraph_vector_t *map12, +static igraph_bool_t igraph_i_count_subisomorphisms_vf2( + const igraph_vector_t *map12, const igraph_vector_t *map21, void *arg) { igraph_i_iso_cb_data_t *data = arg; @@ -2635,7 +2658,7 @@ return 0; } -void igraph_i_get_subisomorphisms_free(igraph_vector_ptr_t *data) { +static void igraph_i_get_subisomorphisms_free(igraph_vector_ptr_t *data) { long int i, n = igraph_vector_ptr_size(data); for (i = 0; i < n; i++) { igraph_vector_t *vec = VECTOR(*data)[i]; @@ -2644,7 +2667,8 @@ } } -igraph_bool_t igraph_i_get_subisomorphisms_vf2(const igraph_vector_t *map12, +static igraph_bool_t igraph_i_get_subisomorphisms_vf2( + const igraph_vector_t *map12, const igraph_vector_t *map21, void *arg) { @@ -2690,11 +2714,11 @@ * edge-colored. * \param edge_color2 The edge color vector for the second graph. * \param maps Pointer vector. On return it contains pointers to - * igraph_vector_t objects, each vector is an + * \ref igraph_vector_t objects, each vector is an * isomorphic mapping of \p graph2 to a subgraph of \p graph1. Please note that * you need to 1) Destroy the vectors via \ref * igraph_vector_destroy(), 2) free them via - * free() and then 3) call \ref + * \ref igraph_free() and then 3) call \ref * igraph_vector_ptr_destroy() on the pointer vector to deallocate all * memory when \p maps is no longer needed. * \param node_compat_fn A pointer to a function of type \ref diff --git a/igraph/src/triangles.c b/igraph/src/triangles.c --- a/igraph/src/triangles.c +++ b/igraph/src/triangles.c @@ -394,7 +394,7 @@ /* This removes loop, multiple edges and edges that point "backwards" according to the rank vector. */ - +/* TODO used in scan.c, add prototype to private header */ int igraph_i_trans4_al_simplify(igraph_adjlist_t *al, const igraph_vector_int_t *rank) { long int i; diff --git a/igraph/src/type_indexededgelist.c b/igraph/src/type_indexededgelist.c --- a/igraph/src/type_indexededgelist.c +++ b/igraph/src/type_indexededgelist.c @@ -25,13 +25,13 @@ #include "igraph_interface.h" #include "igraph_attributes.h" #include "igraph_memory.h" -#include /* memset & co. */ #include "config.h" /* Internal functions */ -int igraph_i_create_start(igraph_vector_t *res, igraph_vector_t *el, igraph_vector_t *index, - igraph_integer_t nodes); +static int igraph_i_create_start( + igraph_vector_t *res, igraph_vector_t *el, + igraph_vector_t *index, igraph_integer_t nodes); /** * \section about_basic_interface @@ -829,8 +829,9 @@ * */ -int igraph_i_create_start(igraph_vector_t *res, igraph_vector_t *el, igraph_vector_t *iindex, - igraph_integer_t nodes) { +static int igraph_i_create_start( + igraph_vector_t *res, igraph_vector_t *el, + igraph_vector_t *iindex, igraph_integer_t nodes) { # define EDGE(i) (VECTOR(*el)[ (long int) VECTOR(*iindex)[(i)] ]) @@ -1018,7 +1019,9 @@ * will be placed here. * \return Error code. The current implementation always returns with * success. - * \sa \ref igraph_get_eid() for the opposite operation. + * \sa \ref igraph_get_eid() for the opposite operation; + * \ref IGRAPH_TO(), \ref IGRAPH_FROM() and \ref IGRAPH_OTHER() for + * a faster but non-error-checked version. * * Added in version 0.2. * diff --git a/igraph/src/uninit.c b/igraph/src/uninit.c --- a/igraph/src/uninit.c +++ b/igraph/src/uninit.c @@ -1,3 +1,8 @@ + +/* Defining _GNU_SOURCE enables the GNU extensions fedisableexcept() and feenableexcept() + * when using glibc. It must be defined before any standard headers are included. */ +#define _GNU_SOURCE 1 +#include #include #include #include @@ -253,9 +258,7 @@ #ifdef __GLIBC__ #define IEEE0_done -#if ((__GLIBC__>=2) && (__GLIBC_MINOR__>=2)) -#define _GNU_SOURCE 1 -#include +#if ((__GLIBC__ > 2) || ((__GLIBC__ == 2) && (__GLIBC_MINOR__ >= 2))) static void ieee0(Void) diff --git a/igraph/src/utils.cc b/igraph/src/utils.cc --- a/igraph/src/utils.cc +++ b/igraph/src/utils.cc @@ -23,6 +23,7 @@ namespace bliss { +#if 0 void print_permutation(FILE* const fp, const unsigned int N, @@ -88,6 +89,7 @@ fprintf(fp, ")"); } } +#endif bool is_permutation(const unsigned int N, const unsigned int* perm) diff --git a/igraph/src/vector_ptr.c b/igraph/src/vector_ptr.c --- a/igraph/src/vector_ptr.c +++ b/igraph/src/vector_ptr.c @@ -37,12 +37,12 @@ * (igraph_vector_ptr_t) * * The \type igraph_vector_ptr_t data type is very similar to - * the \type igraph_vector_t type, but it stores generic pointers instead of + * the \ref igraph_vector_t type, but it stores generic pointers instead of * real numbers. * - * This type has the same space complexity as \type + * This type has the same space complexity as \ref * igraph_vector_t, and most implemented operations work the same way - * as for \type igraph_vector_t. + * as for \ref igraph_vector_t. * * This type is mostly used to pass to or receive from a set of * graphs to some \a igraph functions, such as \ref @@ -160,7 +160,7 @@ * * If an item destructor is set for this pointer vector, this function will * first call the destructor on all elements of the vector and then - * free all the elements using free(). If an item destructor is not set, + * free all the elements using \ref igraph_free(). If an item destructor is not set, * the elements will simply be freed. * * \param v Pointer to the pointer vector whose elements will be freed. @@ -254,7 +254,7 @@ * \brief Gives the number of elements in the pointer vector. * * \param v The pointer vector object. - * \return The size of the object, ie. the number of pointers stored. + * \return The size of the object, i.e. the number of pointers stored. * * Time complexity: O(1). */ @@ -273,7 +273,7 @@ * * This function resizes a pointer to vector to zero length. Note that * the pointed objects are \em not deallocated, you should call - * free() on them, or make sure that their allocated memory is freed + * \ref igraph_free() on them, or make sure that their allocated memory is freed * in some other way, you'll get memory leaks otherwise. If you have * set up an item destructor earlier, the destructor will be called * on every element. @@ -537,7 +537,7 @@ * Sometimes it is necessary to sort the pointers in the vector based on * the property of the element being referenced by the pointer. This * function allows us to sort the vector based on an arbitrary external - * comparison function which accepts two \c void* pointers \c p1 and \c p2 + * comparison function which accepts two void * pointers \c p1 and \c p2 * and returns an integer less than, equal to or greater than zero if the * first argument is considered to be respectively less than, equal to, or * greater than the second. \c p1 and \c p2 will point to the pointer in the diff --git a/igraph/src/walktrap.cpp b/igraph/src/walktrap.cpp --- a/igraph/src/walktrap.cpp +++ b/igraph/src/walktrap.cpp @@ -55,18 +55,12 @@ #include "walktrap_graph.h" #include "walktrap_communities.h" -#include -#include -#include -#include -#include #include "igraph_community.h" #include "igraph_components.h" #include "igraph_interface.h" #include "igraph_interrupt_internal.h" -using namespace std; using namespace igraph::walktrap; /** @@ -75,12 +69,12 @@ * This function is the implementation of the Walktrap community * finding algorithm, see Pascal Pons, Matthieu Latapy: Computing * communities in large networks using random walks, - * http://arxiv.org/abs/physics/0512106 + * https://arxiv.org/abs/physics/0512106 * * * Currently the original C++ implementation is used in igraph, - * see http://www-rp.lip6.fr/~latapy/PP/walktrap.html - * I'm grateful to Matthieu Latapy and Pascal Pons for providing this + * see https://www-complexnetworks.lip6.fr/~latapy/PP/walktrap.html + * We are grateful to Matthieu Latapy and Pascal Pons for providing this * source code. * * diff --git a/igraph/src/walktrap_communities.cpp b/igraph/src/walktrap_communities.cpp --- a/igraph/src/walktrap_communities.cpp +++ b/igraph/src/walktrap_communities.cpp @@ -54,12 +54,11 @@ // see readme.txt for more details #include "walktrap_communities.h" -#include -#include -#include +#include "config.h" #include +#include -#include "config.h" +using namespace std; namespace igraph { diff --git a/igraph/src/walktrap_graph.cpp b/igraph/src/walktrap_graph.cpp --- a/igraph/src/walktrap_graph.cpp +++ b/igraph/src/walktrap_graph.cpp @@ -53,14 +53,10 @@ //----------------------------------------------------------------------------- // see readme.txt for more details -#include -#include -#include -#include -#include // strlen #include "walktrap_graph.h" - #include "igraph_interface.h" +#include +#include // strlen using namespace std; diff --git a/igraph/src/walktrap_heap.cpp b/igraph/src/walktrap_heap.cpp --- a/igraph/src/walktrap_heap.cpp +++ b/igraph/src/walktrap_heap.cpp @@ -54,11 +54,7 @@ // see readme.txt for more details #include "walktrap_heap.h" -#include -#include - -using namespace std; using namespace igraph::walktrap; void Neighbor_heap::move_up(int index) { diff --git a/igraph/src/zeroin.c b/igraph/src/zeroin.c --- a/igraph/src/zeroin.c +++ b/igraph/src/zeroin.c @@ -79,6 +79,7 @@ ************************************************************************ */ +#include "igraph_nongraph.h" #include "igraph_types.h" #include "igraph_interrupt_internal.h" diff --git a/igraph/src/zeta.c b/igraph/src/zeta.c deleted file mode 100644 --- a/igraph/src/zeta.c +++ /dev/null @@ -1,154 +0,0 @@ -/* specfunc/zeta.c - * - * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2004 Gerard Jungman - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -/* Author: G. Jungman */ - -/* This file was taken from the GNU Scientific Library. Some modifications - * were done in order to make it independent from the rest of GSL - */ - -/* -#include -#include -#include -#include -#include -#include -#include -#include - -#include "error.h" - -#include "chebyshev.h" -#include "cheb_eval.c" -*/ - -#include -#include -#include "error.h" - -/*-*-*-*-*-*-*-*-*-*- From gsl_machine.h -*-*-*-*-*-*-*-*-*-*-*-*-*/ - -#define GSL_LOG_DBL_MIN (-7.0839641853226408e+02) -#define GSL_LOG_DBL_MAX 7.0978271289338397e+02 -#define GSL_DBL_EPSILON 2.2204460492503131e-16 - -/*-*-*-*-*-*-*-*-*-* From gsl_sf_result.h *-*-*-*-*-*-*-*-*-*-*-*/ - -struct gsl_sf_result_struct { - double val; - double err; -}; -typedef struct gsl_sf_result_struct gsl_sf_result; - -/*-*-*-*-*-*-*-*-*-*-*-* Private Section *-*-*-*-*-*-*-*-*-*-*-*/ - -/* coefficients for Maclaurin summation in hzeta() - * B_{2j}/(2j)! - */ -static double hzeta_c[15] = { - 1.00000000000000000000000000000, - 0.083333333333333333333333333333, - -0.00138888888888888888888888888889, - 0.000033068783068783068783068783069, - -8.2671957671957671957671957672e-07, - 2.0876756987868098979210090321e-08, - -5.2841901386874931848476822022e-10, - 1.3382536530684678832826980975e-11, - -3.3896802963225828668301953912e-13, - 8.5860620562778445641359054504e-15, - -2.1748686985580618730415164239e-16, - 5.5090028283602295152026526089e-18, - -1.3954464685812523340707686264e-19, - 3.5347070396294674716932299778e-21, - -8.9535174270375468504026113181e-23 -}; - -/*-*-*-*-*-*-*-*-*-*-*-* Functions with Error Codes *-*-*-*-*-*-*-*-*-*-*-*/ - -static int gsl_sf_hzeta_e(const double s, const double q, gsl_sf_result * result) -{ - /* CHECK_POINTER(result) */ - - if(s <= 1.0 || q <= 0.0) { - PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL); - } - else { - const double max_bits = 54.0; - const double ln_term0 = -s * log(q); - - if(ln_term0 < GSL_LOG_DBL_MIN + 1.0) { - PLFIT_ERROR("underflow", PLFIT_UNDRFLOW); - } - else if(ln_term0 > GSL_LOG_DBL_MAX - 1.0) { - PLFIT_ERROR("overflow", PLFIT_OVERFLOW); - } - else if((s > max_bits && q < 1.0) || (s > 0.5*max_bits && q < 0.25)) { - result->val = pow(q, -s); - result->err = 2.0 * GSL_DBL_EPSILON * fabs(result->val); - return PLFIT_SUCCESS; - } - else if(s > 0.5*max_bits && q < 1.0) { - const double p1 = pow(q, -s); - const double p2 = pow(q/(1.0+q), s); - const double p3 = pow(q/(2.0+q), s); - result->val = p1 * (1.0 + p2 + p3); - result->err = GSL_DBL_EPSILON * (0.5*s + 2.0) * fabs(result->val); - return PLFIT_SUCCESS; - } - else { - /* Euler-Maclaurin summation formula - * [Moshier, p. 400, with several typo corrections] - */ - const int jmax = 12; - const int kmax = 10; - int j, k; - const double pmax = pow(kmax + q, -s); - double scp = s; - double pcp = pmax / (kmax + q); - double ans = pmax*((kmax+q)/(s-1.0) + 0.5); - - for(k=0; kval = ans; - result->err = 2.0 * (jmax + 1.0) * GSL_DBL_EPSILON * fabs(ans); - return PLFIT_SUCCESS; - } - } -} - -/*-*-*-*-*-*-*-*-*-* Functions w/ Natural Prototypes *-*-*-*-*-*-*-*-*-*-*/ - -double gsl_sf_hzeta(const double s, const double a) -{ - gsl_sf_result result; - gsl_sf_hzeta_e(s, a, &result); - return result.val; -} - diff --git a/include/bytestring.h b/include/bytestring.h deleted file mode 100644 --- a/include/bytestring.h +++ /dev/null @@ -1,111 +0,0 @@ -#ifndef HASKELL_IGRAPH_BYTESTRING -#define HASKELL_IGRAPH_BYTESTRING - -#include "igraph.h" - -typedef struct bytestring_t { - unsigned long int len; - char *value; -} bytestring_t; - -typedef struct bsvector_t { - bytestring_t **data; - long int len; -} bsvector_t; - -#define BSVECTOR_INIT_FINALLY(v, size) \ - do { IGRAPH_CHECK(bsvector_init(v, size)); \ - IGRAPH_FINALLY( (igraph_finally_func_t*) bsvector_destroy, v); } while (0) - -/** - * \define STR - * Indexing string vectors - * - * This is a macro which allows to query the elements of a string vector in - * simpler way than \ref igraph_strvector_get(). Note this macro cannot be - * used to set an element, for that use \ref igraph_strvector_set(). - * \param sv The string vector - * \param i The the index of the element. - * \return The element at position \p i. - * - * Time complexity: O(1). - */ -#define BS(sv,i) ((const bytestring_t *)((sv).data[(i)])) - -int bsvector_init(bsvector_t *sv, long int len); - -void bsvector_destroy(bsvector_t *sv); - -void bsvector_get(const bsvector_t *sv, long int idx, bytestring_t **value); - -int bsvector_set(bsvector_t *sv, long int idx, const bytestring_t *value); - -void bsvector_remove_section(bsvector_t *v, long int from, long int to); - -void bsvector_remove(bsvector_t *v, long int elem); - -/* -void bsvector_move_interval(bsvector_t *v, long int begin, - long int end, long int to) { - long int i; - assert(v != 0); - assert(v->data != 0); - for (i=to; idata[i] != 0) { - destroy_bytestring(v->data[i]); - } - } - for (i=0; idata[begin+i] != 0) { - size_t len=strlen(v->data[begin+i])+1; - v->data[to+i]=igraph_Calloc(len, char); - memcpy(v->data[to+i], v->data[begin+i], sizeof(char)*len); - } - } -} -*/ - -int bsvector_copy(bsvector_t *to, const bsvector_t *from); - -int bsvector_append(bsvector_t *to, const bsvector_t *from); - -void bsvector_clear(bsvector_t *sv); - -int bsvector_resize(bsvector_t* v, long int newsize); - -/** - * \ingroup strvector - * \function igraph_strvector_permdelete - * \brief Removes elements from a string vector (for internal use) - */ - -void bsvector_permdelete(bsvector_t *v, const igraph_vector_t *index, - long int nremove); - -/** - * \ingroup strvector - * \function igraph_strvector_remove_negidx - * \brief Removes elements from a string vector (for internal use) - */ - -void bsvector_remove_negidx(bsvector_t *v, const igraph_vector_t *neg, - long int nremove); - -int bsvector_index(const bsvector_t *v, bsvector_t *newv, - const igraph_vector_t *idx); - -long int bsvector_size(const bsvector_t *sv); - -bytestring_t* new_bytestring(int n); - -void destroy_bytestring(bytestring_t* str); - -char* bytestring_to_char(bytestring_t* from); - -bytestring_t* char_to_bytestring(char* from); - -igraph_strvector_t* bsvector_to_strvector(bsvector_t* from); - -bsvector_t* strvector_to_bsvector(igraph_strvector_t* from); - -#endif diff --git a/include/haskell_attributes.h b/include/haskell_attributes.h deleted file mode 100644 --- a/include/haskell_attributes.h +++ /dev/null @@ -1,218 +0,0 @@ -#ifndef HASKELL_IGRAPH_ATTRIBUTE -#define HASKELL_IGRAPH_ATTRIBUTE - -#include "igraph.h" -#include "bytestring.h" - -#include - -igraph_bool_t igraph_haskell_attribute_find(const igraph_vector_ptr_t *ptrvec, - const char *name, long int *idx); - -typedef struct igraph_haskell_attributes_t { - igraph_vector_ptr_t gal; - igraph_vector_ptr_t val; - igraph_vector_ptr_t eal; -} igraph_haskell_attributes_t; - -int igraph_haskell_attributes_copy_attribute_record(igraph_attribute_record_t **newrec, - const igraph_attribute_record_t *rec); - - -int igraph_haskell_attribute_init(igraph_t *graph, igraph_vector_ptr_t *attr); - -void igraph_haskell_attribute_destroy(igraph_t *graph); - -void igraph_haskell_attribute_copy_free(igraph_haskell_attributes_t *attr); - -int igraph_haskell_attribute_copy(igraph_t *to, const igraph_t *from, - igraph_bool_t ga, igraph_bool_t va, igraph_bool_t ea); - -int igraph_haskell_attribute_add_vertices(igraph_t *graph, long int nv, - igraph_vector_ptr_t *nattr); - -void igraph_haskell_attribute_permute_free(igraph_vector_ptr_t *v); - -int igraph_haskell_attribute_permute_vertices(const igraph_t *graph, - igraph_t *newgraph, - const igraph_vector_t *idx); - -int igraph_haskell_attribute_combine_vertices(const igraph_t *graph, - igraph_t *newgraph, - const igraph_vector_ptr_t *merges, - const igraph_attribute_combination_t *comb); - -int igraph_haskell_attribute_add_edges(igraph_t *graph, const igraph_vector_t *edges, - igraph_vector_ptr_t *nattr); - -int igraph_haskell_attribute_permute_edges(const igraph_t *graph, - igraph_t *newgraph, - const igraph_vector_t *idx); - -int igraph_haskell_attribute_combine_edges(const igraph_t *graph, - igraph_t *newgraph, - const igraph_vector_ptr_t *merges, - const igraph_attribute_combination_t *comb); - -int igraph_haskell_attribute_get_info(const igraph_t *graph, - igraph_strvector_t *gnames, - igraph_vector_t *gtypes, - igraph_strvector_t *vnames, - igraph_vector_t *vtypes, - igraph_strvector_t *enames, - igraph_vector_t *etypes); - -igraph_bool_t igraph_haskell_attribute_has_attr(const igraph_t *graph, - igraph_attribute_elemtype_t type, - const char *name); - -int igraph_haskell_attribute_gettype(const igraph_t *graph, - igraph_attribute_type_t *type, - igraph_attribute_elemtype_t elemtype, - const char *name); - -int igraph_haskell_attribute_get_numeric_graph_attr(const igraph_t *graph, - const char *name, - igraph_vector_t *value); - -int igraph_haskell_attribute_get_bool_graph_attr(const igraph_t *graph, - const char *name, - igraph_vector_bool_t *value); - -int igraph_haskell_attribute_get_string_graph_attr(const igraph_t *graph, - const char *name, - igraph_strvector_t *value_); - -int igraph_haskell_attribute_get_numeric_vertex_attr(const igraph_t *graph, - const char *name, - igraph_vs_t vs, - igraph_vector_t *value); - -int igraph_haskell_attribute_get_bool_vertex_attr(const igraph_t *graph, - const char *name, - igraph_vs_t vs, - igraph_vector_bool_t *value); - -int igraph_haskell_attribute_get_string_vertex_attr(const igraph_t *graph, - const char *name, - igraph_vs_t vs, - igraph_strvector_t *value_); - -int igraph_haskell_attribute_get_numeric_edge_attr(const igraph_t *graph, - const char *name, - igraph_es_t es, - igraph_vector_t *value); - -int igraph_haskell_attribute_get_string_edge_attr(const igraph_t *graph, - const char *name, - igraph_es_t es, - igraph_strvector_t *value_); - -int igraph_haskell_attribute_get_bool_edge_attr(const igraph_t *graph, - const char *name, - igraph_es_t es, - igraph_vector_bool_t *value); - -igraph_real_t igraph_haskell_attribute_GAN(const igraph_t *graph, const char *name); - -igraph_bool_t igraph_haskell_attribute_GAB(const igraph_t *graph, const char *name); - -const bytestring_t* igraph_haskell_attribute_GAS(const igraph_t *graph, const char *name); - -igraph_real_t igraph_haskell_attribute_VAN(const igraph_t *graph, const char *name, - igraph_integer_t vid); - -igraph_bool_t igraph_haskell_attribute_VAB(const igraph_t *graph, const char *name, - igraph_integer_t vid); - -const bytestring_t* igraph_haskell_attribute_VAS(const igraph_t *graph, const char *name, - igraph_integer_t vid); - -igraph_real_t igraph_haskell_attribute_EAN(const igraph_t *graph, const char *name, - igraph_integer_t eid); - -igraph_bool_t igraph_haskell_attribute_EAB(const igraph_t *graph, const char *name, - igraph_integer_t eid); - -const bytestring_t* igraph_haskell_attribute_EAS(const igraph_t *graph, const char *name, - igraph_integer_t eid); - -int igraph_haskell_attribute_VANV(const igraph_t *graph, const char *name, - igraph_vs_t vids, igraph_vector_t *result); - -int igraph_haskell_attribute_VABV(const igraph_t *graph, const char *name, - igraph_vs_t vids, igraph_vector_bool_t *result); - -int igraph_haskell_attribute_EANV(const igraph_t *graph, const char *name, - igraph_es_t eids, igraph_vector_t *result); - -int igraph_haskell_attribute_EABV(const igraph_t *graph, const char *name, - igraph_es_t eids, igraph_vector_bool_t *result); - -int igraph_haskell_attribute_VASV(const igraph_t *graph, const char *name, - igraph_vs_t vids, igraph_strvector_t *result); - -int igraph_haskell_attribute_EASV(const igraph_t *graph, const char *name, - igraph_es_t eids, igraph_strvector_t *result); - -int igraph_haskell_attribute_list(const igraph_t *graph, - igraph_strvector_t *gnames, igraph_vector_t *gtypes, - igraph_strvector_t *vnames, igraph_vector_t *vtypes, - igraph_strvector_t *enames, igraph_vector_t *etypes); - -int igraph_haskell_attribute_GAN_set(igraph_t *graph, const char *name, - igraph_real_t value); - -int igraph_haskell_attribute_GAB_set(igraph_t *graph, const char *name, - igraph_bool_t value); - -int igraph_haskell_attribute_GAS_set(igraph_t *graph, const char *name, - const bytestring_t *value); - -int igraph_haskell_attribute_VAN_set(igraph_t *graph, const char *name, - igraph_integer_t vid, igraph_real_t value); - -int igraph_haskell_attribute_VAB_set(igraph_t *graph, const char *name, - igraph_integer_t vid, igraph_bool_t value); - -int igraph_haskell_attribute_VAS_set(igraph_t *graph, const char *name, - igraph_integer_t vid, const bytestring_t *value); - -int igraph_haskell_attribute_EAN_set(igraph_t *graph, const char *name, - igraph_integer_t eid, igraph_real_t value); - -int igraph_haskell_attribute_EAB_set(igraph_t *graph, const char *name, - igraph_integer_t eid, igraph_bool_t value); - -int igraph_haskell_attribute_EAS_set(igraph_t *graph, const char *name, - igraph_integer_t eid, const bytestring_t *value); - -int igraph_haskell_attribute_VAN_setv(igraph_t *graph, const char *name, - const igraph_vector_t *v); - -int igraph_haskell_attribute_VAB_setv(igraph_t *graph, const char *name, - const igraph_vector_bool_t *v); - -int igraph_haskell_attribute_VAS_setv(igraph_t *graph, const char *name, - const bsvector_t *sv); - -int igraph_haskell_attribute_EAN_setv(igraph_t *graph, const char *name, - const igraph_vector_t *v); - -int igraph_haskell_attribute_EAB_setv(igraph_t *graph, const char *name, - const igraph_vector_bool_t *v); - -int igraph_haskell_attribute_EAS_setv(igraph_t *graph, const char *name, - const bsvector_t *sv); - -void igraph_haskell_attribute_free_rec(igraph_attribute_record_t *rec); - -void igraph_haskell_attribute_remove_g(igraph_t *graph, const char *name); - -void igraph_haskell_attribute_remove_v(igraph_t *graph, const char *name); - -void igraph_haskell_attribute_remove_e(igraph_t *graph, const char *name); - -void igraph_haskell_attribute_remove_all(igraph_t *graph, igraph_bool_t g, - igraph_bool_t v, igraph_bool_t e); -#endif diff --git a/include/haskell_igraph.h b/include/haskell_igraph.h deleted file mode 100644 --- a/include/haskell_igraph.h +++ /dev/null @@ -1,8 +0,0 @@ -#ifndef HASKELL_IGRAPH -#define HASKELL_IGRAPH - -#include "igraph.h" - -void haskelligraph_init(); - -#endif diff --git a/src/IGraph/Algorithms.hs b/src/IGraph/Algorithms.hs --- a/src/IGraph/Algorithms.hs +++ b/src/IGraph/Algorithms.hs @@ -2,7 +2,7 @@ ( module IGraph.Algorithms.Structure , module IGraph.Algorithms.Community , module IGraph.Algorithms.Clique --- , module IGraph.Algorithms.Layout + , module IGraph.Algorithms.Layout , module IGraph.Algorithms.Motif , module IGraph.Algorithms.Generators , module IGraph.Algorithms.Isomorphism @@ -12,7 +12,7 @@ import IGraph.Algorithms.Structure import IGraph.Algorithms.Community import IGraph.Algorithms.Clique ---import IGraph.Algorithms.Layout +import IGraph.Algorithms.Layout import IGraph.Algorithms.Motif import IGraph.Algorithms.Generators import IGraph.Algorithms.Isomorphism diff --git a/src/IGraph/Algorithms/Centrality.chs b/src/IGraph/Algorithms/Centrality.chs --- a/src/IGraph/Algorithms/Centrality.chs +++ b/src/IGraph/Algorithms/Centrality.chs @@ -4,19 +4,21 @@ , betweenness , eigenvectorCentrality , pagerank + , hubScore + , authorityScore ) where import Control.Monad import Data.Serialize (Serialize) import Data.List (foldl') import System.IO.Unsafe (unsafePerformIO) -import Data.Maybe import Data.Singletons (SingI) import Foreign import Foreign.C.Types import IGraph +import IGraph.Internal.C2HS {#import IGraph.Internal #} {#import IGraph.Internal.Constants #} @@ -140,4 +142,44 @@ , castPtr `Ptr Vector' , castPtr `Ptr Vector' , id `Ptr ()' + } -> `CInt' void- #} + +-- | Kleinberg's hub scores. +hubScore :: Graph d v e + -> Bool -- ^ scale result such that \(\left|max\ centrality\right|=1\) + -> ([Double],Double) -- ^ (eigenvector,eigenvalue) +hubScore graph scale = unsafePerformIO $ + allocaVector $ \vector -> + alloca $ \value -> + allocaArpackOpt $ \options -> do + igraphHubScore (_graph graph) vector value scale nullPtr options + liftM2 (,) (toList vector) (peekFloatConv value) +{-# INLINE igraphHubScore #-} +{#fun igraph_hub_score as ^ + { `IGraph' + , castPtr `Ptr Vector' + , castPtr `Ptr CDouble' + , `Bool' + , castPtr `Ptr Vector' + , castPtr `Ptr ArpackOpt' + } -> `CInt' void- #} + +-- | Kleinberg's authority scores. +authorityScore :: Graph d v e + -> Bool -- ^ scale result such that \(\left|max\ centrality\right|=1\) + -> ([Double],Double) -- ^ (eigenvector,eigenvalue) +authorityScore graph scale = unsafePerformIO $ + allocaVector $ \vector -> + alloca $ \value -> + allocaArpackOpt $ \options -> do + igraphAuthorityScore (_graph graph) vector value scale nullPtr options + liftM2 (,) (toList vector) (peekFloatConv value) +{-# INLINE igraphAuthorityScore #-} +{#fun igraph_authority_score as ^ + { `IGraph' + , castPtr `Ptr Vector' + , castPtr `Ptr CDouble' + , `Bool' + , castPtr `Ptr Vector' + , castPtr `Ptr ArpackOpt' } -> `CInt' void- #} diff --git a/src/IGraph/Algorithms/Clique.chs b/src/IGraph/Algorithms/Clique.chs --- a/src/IGraph/Algorithms/Clique.chs +++ b/src/IGraph/Algorithms/Clique.chs @@ -6,10 +6,7 @@ , cliqueNumber ) where -import Control.Applicative ((<$>)) import System.IO.Unsafe (unsafePerformIO) - -import qualified Foreign.Ptr as C2HSImp import Foreign import IGraph @@ -18,6 +15,7 @@ #include "haskell_igraph.h" +-- | Find all or some cliques in a graph. cliques :: Graph d v e -> (Int, Int) -- ^ Minimum and maximum size of the cliques to be returned. -- No bound will be used if negative or zero @@ -27,12 +25,16 @@ (map.map) truncate <$> toLists vptr {#fun igraph_cliques as ^ { `IGraph', castPtr `Ptr VectorPtr', `Int', `Int' } -> `CInt' void- #} +-- | Finds the largest clique(s) in a graph. +-- Time complexity: O(3^(|V|/3)) worst case. largestCliques :: Graph d v e -> [[Int]] largestCliques gr = unsafePerformIO $ allocaVectorPtr $ \vptr -> do igraphLargestCliques (_graph gr) vptr (map.map) truncate <$> toLists vptr {#fun igraph_largest_cliques as ^ { `IGraph', castPtr `Ptr VectorPtr' } -> `CInt' void- #} +-- | Find all maximal cliques of a graph. Time complexity: O(d(n-d)3^(d/3)) +-- worst case, d is the degeneracy of the graph. maximalCliques :: Graph d v e -> (Int, Int) -- ^ Minimum and maximum size of the cliques to be returned. -- No bound will be used if negative or zero @@ -42,6 +44,9 @@ (map.map) truncate <$> toLists vpptr {#fun igraph_maximal_cliques as ^ { `IGraph', castPtr `Ptr VectorPtr', `Int', `Int' } -> `CInt' void- #} +-- | Find the clique number of the graph. The clique number of a graph is +-- the size of the largest clique. +-- Time complexity: O(3^(|V|/3)) worst case. cliqueNumber :: Graph d v e -> Int cliqueNumber gr = unsafePerformIO $ igraphCliqueNumber $ _graph gr {#fun igraph_clique_number as ^ diff --git a/src/IGraph/Algorithms/Community.chs b/src/IGraph/Algorithms/Community.chs --- a/src/IGraph/Algorithms/Community.chs +++ b/src/IGraph/Algorithms/Community.chs @@ -2,11 +2,12 @@ {-# LANGUAGE RecordWildCards #-} {-# LANGUAGE DataKinds #-} module IGraph.Algorithms.Community - ( modularity - , findCommunity + ( findCommunity , CommunityMethod(..) - , defaultLeadingEigenvector - , defaultSpinglass + , leadingEigenvector + , spinglass + , leiden + , modularity ) where import Data.Function (on) @@ -14,37 +15,53 @@ import Data.List.Ordered (nubSortBy) import Data.Ord (comparing) import System.IO.Unsafe (unsafePerformIO) +import Data.Serialize (Serialize) import Foreign import Foreign.C.Types import IGraph +import IGraph.Random import IGraph.Internal.C2HS {#import IGraph.Internal #} {#import IGraph.Internal.Constants #} #include "haskell_igraph.h" -modularity :: Graph d v e - -> [[Int]] -- ^ Communities. - -> Maybe [Double] -- ^ Weights - -> Double -modularity gr clusters ws - | length nds /= length (concat clusters) = error "Duplicated nodes" - | nds /= nodes gr = error "Some nodes were not given community assignments" - | otherwise = unsafePerformIO $ withList membership $ \membership' -> - withListMaybe ws (igraphModularity (_graph gr) membership') +-- | Detecting community structure. +findCommunity :: (Serialize v, Serialize e) + => Graph 'U v e + -> Maybe (Node -> v -> Double) -- ^ Function to assign node weights + -> Maybe (e -> Double) -- ^ Function to assign edge weights + -> CommunityMethod -- ^ Community finding algorithms + -> Gen + -> IO [[Int]] +findCommunity gr getNodeW getEdgeW method _ = allocaVector $ \result -> + withListMaybe ew $ \ew' -> do + case method of + LeadingEigenvector n -> allocaArpackOpt $ \arpack -> + igraphCommunityLeadingEigenvector (_graph gr) ew' nullPtr result + n arpack nullPtr False + nullPtr nullPtr nullPtr + nullFunPtr nullPtr + Spinglass{..} -> igraphCommunitySpinglass (_graph gr) ew' nullPtr nullPtr result + nullPtr _nSpins False _startTemp + _stopTemp _coolFact + IgraphSpincommUpdateConfig _gamma + IgraphSpincommImpOrig 1.0 + Leiden{..} -> do + _ <- withListMaybe nw $ \nw' -> igraphCommunityLeiden + (_graph gr) ew' nw' _resolution _beta False result nullPtr + return () + fmap ( map (fst . unzip) . groupBy ((==) `on` snd) + . sortBy (comparing snd) . zip [0..] ) $ toList result where - (membership, nds) = unzip $ nubSortBy (comparing snd) $ concat $ - zipWith f [0 :: Int ..] clusters - where - f i xs = zip (repeat i) xs -{#fun igraph_modularity as ^ - { `IGraph' - , castPtr `Ptr Vector' - , alloca- `Double' peekFloatConv* - , castPtr `Ptr Vector' - } -> `CInt' void- #} + ew = case getEdgeW of + Nothing -> Nothing + Just f -> Just $ map (f . snd) $ labEdges gr + nw = case getNodeW of + Nothing -> Nothing + Just f -> Just $ map (uncurry f) $ labNodes gr data CommunityMethod = LeadingEigenvector @@ -57,38 +74,44 @@ , _coolFact :: Double -- ^ the cooling factor for the simulated annealing , _gamma :: Double -- ^ the gamma parameter of the algorithm. } + | Leiden + { _resolution :: Double + , _beta :: Double + } -defaultLeadingEigenvector :: CommunityMethod -defaultLeadingEigenvector = LeadingEigenvector 10000 +-- | Default parameters for the leading eigenvector algorithm. +leadingEigenvector :: CommunityMethod +leadingEigenvector = LeadingEigenvector 10000 -defaultSpinglass :: CommunityMethod -defaultSpinglass = Spinglass +-- | Default parameters for the spin-glass algorithm. +spinglass :: CommunityMethod +spinglass = Spinglass { _nSpins = 25 , _startTemp = 1.0 , _stopTemp = 0.01 , _coolFact = 0.99 , _gamma = 1.0 } -findCommunity :: Graph 'U v e - -> Maybe [Double] -- ^ node weights - -> CommunityMethod -- ^ Community finding algorithms - -> [[Int]] -findCommunity gr ws method = unsafePerformIO $ allocaVector $ \result -> - withListMaybe ws $ \ws' -> do - case method of - LeadingEigenvector n -> allocaArpackOpt $ \arpack -> - igraphCommunityLeadingEigenvector (_graph gr) ws' nullPtr result - n arpack nullPtr False - nullPtr nullPtr nullPtr - nullFunPtr nullPtr - Spinglass{..} -> igraphCommunitySpinglass (_graph gr) ws' nullPtr nullPtr result - nullPtr _nSpins False _startTemp - _stopTemp _coolFact - IgraphSpincommUpdateConfig _gamma - IgraphSpincommImpOrig 1.0 - - fmap ( map (fst . unzip) . groupBy ((==) `on` snd) - . sortBy (comparing snd) . zip [0..] ) $ toList result +-- | Default parameters for the leiden algorithm. +-- 1 / 2m sum_ij (A_ij - gamma n_i n_j)d(s_i, s_j), where +-- m is the total edge weight, +-- A_ij is the weight of edge (i, j), +-- gamma is the so-called resolution parameter, +-- n_i is the node weight of node i, +-- s_i is the cluster of node i and +-- d(x, y) = 1 if and only if x = y and 0 otherwise. +-- By setting n_i = k_i, the degree of node i, and dividing gamma by 2m, +-- you effectively obtain an expression for modularity. +-- Hence, the standard modularity will be optimized when you supply the degrees +-- as node_weights and by supplying as a resolution parameter 1.0/(2*m), with m the number of edges. +-- +-- RBConfigurationVertexPartition: supplying the degrees as node weights, and +-- a resolution parameter 1.0/(2*m), with m the number of edges. +-- CPM: +leiden :: CommunityMethod +leiden = Leiden + { _resolution = 1 + , _beta = 0.01 } {#fun igraph_community_spinglass as ^ { `IGraph' @@ -124,6 +147,18 @@ , id `Ptr ()' } -> `CInt' void- #} +{#fun igraph_community_leiden as ^ + { `IGraph' + , castPtr `Ptr Vector' + , castPtr `Ptr Vector' + , `Double' + , `Double' + , `Bool' + , castPtr `Ptr Vector' + , alloca- `Int' peekIntConv* + , id `Ptr CDouble' + } -> `CInt' void- #} + type T = FunPtr ( Ptr () -> CLong -> CDouble @@ -132,3 +167,30 @@ -> Ptr () -> Ptr () -> IO CInt) + +-- | Calculate the modularity of a graph with respect to some vertex types. +modularity :: Serialize e + => Graph d v e + -> Maybe (e -> Double) -- ^ Function to assign edge weights + -> [[Int]] -- ^ Communities. + -> Double +modularity gr getEdgeW clusters + | length nds /= length (concat clusters) = error "Duplicated nodes" + | nds /= nodes gr = error "Some nodes were not given community assignments" + | otherwise = unsafePerformIO $ withList membership $ \membership' -> + withListMaybe ws (igraphModularity (_graph gr) membership') + where + (membership, nds) = unzip $ nubSortBy (comparing snd) $ concat $ + zipWith f [0 :: Int ..] clusters + where + f i xs = zip (repeat i) xs + ws = case getEdgeW of + Nothing -> Nothing + Just f -> Just $ map (f . snd) $ labEdges gr +{#fun igraph_modularity as ^ + { `IGraph' + , castPtr `Ptr Vector' + , alloca- `Double' peekFloatConv* + , castPtr `Ptr Vector' + } -> `CInt' void- #} + diff --git a/src/IGraph/Algorithms/Generators.chs b/src/IGraph/Algorithms/Generators.chs --- a/src/IGraph/Algorithms/Generators.chs +++ b/src/IGraph/Algorithms/Generators.chs @@ -5,6 +5,7 @@ ( full , star , ring + , zacharyKarate , ErdosRenyiModel(..) , erdosRenyiGame , degreeSequenceGame @@ -35,7 +36,7 @@ -> Bool -- ^ Whether to include self-edges (loops) -> Graph d () () full n hasLoop = unsafePerformIO $ do - igraphInit + _ <- igraphInit gr <- igraphFull n directed hasLoop initializeNullAttribute gr return $ Graph gr M.empty @@ -52,7 +53,7 @@ star :: Int -- ^ The number of nodes -> Graph 'U () () star n = unsafePerformIO $ do - igraphInit + _ <- igraphInit gr <- igraphStar n IgraphStarUndirected 0 initializeNullAttribute gr return $ Graph gr M.empty @@ -66,7 +67,7 @@ -- | Creates a ring graph, a one dimensional lattice. ring :: Int -> Graph 'U () () ring n = unsafePerformIO $ do - igraphInit + _ <- igraphInit gr <- igraphRing n False False True initializeNullAttribute gr return $ Graph gr M.empty @@ -78,6 +79,20 @@ , `Bool' } -> `CInt' void- #} +-- | Zachary's karate club +zacharyKarate :: Graph 'U () () +zacharyKarate = mkGraph (replicate 34 ()) $ map (\(a, b) -> ((a-1,b-1),())) es + where + es = [ (2,1),(3,1),(3,2),(4,1),(4,2),(4,3),(5,1),(6,1),(7,1),(7,5),(7,6) + , (8,1),(8,2),(8,3),(8,4),(9,1),(9,3),(10,3),(11,1),(11,5),(11,6) + , (12,1),(13,1),(13,4),(14,1),(14,2),(14,3),(14,4),(17,6),(17,7) + , (18,1),(18,2),(20,1),(20,2),(22,1),(22,2),(26,24),(26,25) + , (28,3),(28,24),(28,25),(29,3),(30,24),(30,27),(31,2),(31,9) + , (32,1),(32,25),(32,26),(32,29),(33,3),(33,9),(33,15),(33,16) + , (33,19),(33,21),(33,23),(33,24),(33,30),(33,31),(33,32) + , (34,9),(34,10),(34,14),(34,15),(34,16),(34,19),(34,20),(34,21) + , (34,23),(34,24),(34,27),(34,28),(34,29),(34,30),(34,31),(34,32),(34,33) ] + data ErdosRenyiModel = GNP Int Double -- ^ G(n,p) graph, every possible edge is -- included in the graph with probability p. | GNM Int Int -- ^ G(n,m) graph, m edges are selected @@ -90,7 +105,7 @@ -> Gen -> IO (Graph d () ()) erdosRenyiGame model self _ = do - igraphInit + _ <- igraphInit gr <- case model of GNP n p -> igraphErdosRenyiGame IgraphErdosRenyiGnp n p directed self GNM n m -> igraphErdosRenyiGame IgraphErdosRenyiGnm n (fromIntegral m) @@ -112,7 +127,7 @@ -> Gen -> IO (Graph 'D () ()) degreeSequenceGame out_deg in_deg _ = do - igraphInit + _ <- igraphInit withList out_deg $ \out_deg' -> withList in_deg $ \in_deg' -> do gr <- igraphDegreeSequenceGame out_deg' in_deg' IgraphDegseqSimple diff --git a/src/IGraph/Algorithms/Isomorphism.chs b/src/IGraph/Algorithms/Isomorphism.chs --- a/src/IGraph/Algorithms/Isomorphism.chs +++ b/src/IGraph/Algorithms/Isomorphism.chs @@ -1,8 +1,8 @@ {-# LANGUAGE ForeignFunctionInterface #-} {-# LANGUAGE ScopedTypeVariables #-} module IGraph.Algorithms.Isomorphism - ( getSubisomorphisms - , isomorphic + ( isomorphic + , getSubisomorphisms , isoclassCreate , isoclass3 , isoclass4 @@ -20,6 +20,17 @@ #include "haskell_igraph.h" +-- | Determine whether two graphs are isomorphic. +isomorphic :: Graph d v1 e1 + -> Graph d v2 e2 + -> Bool +isomorphic g1 g2 = unsafePerformIO $ alloca $ \ptr -> do + _ <- igraphIsomorphic (_graph g1) (_graph g2) ptr + x <- peek ptr + return (x /= 0) +{-# INLINE isomorphic #-} +{#fun igraph_isomorphic as ^ { `IGraph', `IGraph', id `Ptr CInt' } -> `CInt' void- #} + getSubisomorphisms :: Graph d v1 e1 -- ^ graph to be searched in -> Graph d v2 e2 -- ^ smaller graph -> [[Int]] @@ -43,16 +54,6 @@ , id `FunPtr (Ptr IGraph -> Ptr IGraph -> CInt -> CInt -> Ptr () -> IO CInt)' , id `Ptr ()' } -> `CInt' void- #} - --- | Determine whether two graphs are isomorphic. -isomorphic :: Graph d v1 e1 - -> Graph d v2 e2 - -> Bool -isomorphic g1 g2 = unsafePerformIO $ alloca $ \ptr -> do - _ <- igraphIsomorphic (_graph g1) (_graph g2) ptr - x <- peek ptr - return (x /= 0) -{#fun igraph_isomorphic as ^ { `IGraph', `IGraph', id `Ptr CInt' } -> `CInt' void- #} -- | Creates a graph from the given isomorphism class. -- This function is implemented only for graphs with three or four vertices. diff --git a/src/IGraph/Algorithms/Layout.chs b/src/IGraph/Algorithms/Layout.chs new file mode 100644 --- /dev/null +++ b/src/IGraph/Algorithms/Layout.chs @@ -0,0 +1,120 @@ +{-# LANGUAGE ForeignFunctionInterface #-} +module IGraph.Algorithms.Layout + ( layout + , LayoutMethod(..) + , kamadaKawai + , lgl + ) where + +import Data.Maybe (isJust, fromMaybe) +import Foreign (nullPtr) +import System.IO.Unsafe (unsafePerformIO) +import IGraph + +import Foreign +import IGraph.Random +{#import IGraph.Internal #} + +#include "haskell_igraph.h" + +layout :: Graph d v e -> LayoutMethod -> Gen -> [(Double, Double)] +layout gr method _ = unsafePerformIO $ case method of + Random -> allocaMatrix $ \mat -> do + igraphLayoutRandom gptr mat + getResult mat + + KamadaKawai seed niter kkconst epsilon -> do + let f mat = igraphLayoutKamadaKawai gptr mat (isJust seed) niter + epsilon (fromMaybe (fromIntegral $ nNodes gr) kkconst) nullPtr + nullPtr nullPtr nullPtr nullPtr + case seed of + Nothing -> allocaMatrix $ \mat -> do + f mat + getResult mat + Just s -> withRowLists ((\(x,y) -> [x,y]) $ unzip s) $ \mat -> do + f mat + getResult mat + + LGL niter delta area coolexp repulserad cellsize -> allocaMatrix $ \mat -> do + igraphLayoutLgl gptr mat niter (delta n) (area n) coolexp + (repulserad n) (cellsize n) (-1) + getResult mat + where + n = nNodes gr + gptr = _graph gr + getResult mat = (\[x, y] -> zip x y) <$> toColumnLists mat + +data LayoutMethod = + Random + | KamadaKawai { kk_seed :: Maybe [(Double, Double)] + , kk_nIter :: Int + , kk_const :: Maybe Double -- ^ The Kamada-Kawai vertex attraction constant + , kk_epsilon :: Double + } -- ^ The Kamada-Kawai algorithm. Time complexity: O(|V|) + -- for each iteration, after an O(|V|^2 log|V|) + -- initialization step. + | LGL { lgl_nIter :: !Int + , lgl_maxdelta :: (Int -> Double) -- ^ The maximum length of the move allowed + -- for a vertex in a single iteration. A reasonable default is the number of vertices. + , lgl_area :: (Int -> Double) -- ^ This parameter gives the area + -- of the square on which the vertices will be placed. A reasonable + -- default value is the number of vertices squared. + , lgl_coolexp :: !Double -- ^ The cooling exponent. A reasonable default value is 1.5. + , lgl_repulserad :: (Int -> Double) -- ^ Determines the radius at which + -- vertex-vertex repulsion cancels out attraction of adjacent vertices. + -- A reasonable default value is area times the number of vertices. + , lgl_cellsize :: (Int -> Double) + } + +-- | Default parameters for the Kamada-Kawai algorithm. +kamadaKawai :: LayoutMethod +kamadaKawai = KamadaKawai + { kk_seed = Nothing + , kk_nIter = 10 + , kk_const = Nothing + , kk_epsilon = 0 } + +-- | Default parameters for the LGL algorithm. +lgl :: LayoutMethod +lgl = LGL + { lgl_nIter = 100 + , lgl_maxdelta = \x -> fromIntegral x + , lgl_area = area + , lgl_coolexp = 1.5 + , lgl_repulserad = \x -> fromIntegral x * area x + , lgl_cellsize = \x -> area x ** 0.25 + } + where + area x = fromIntegral $ x * x + +-- | Places the vertices uniform randomly on a plane. +{#fun igraph_layout_random as ^ + { `IGraph' + , castPtr `Ptr Matrix' + } -> `CInt' void- #} + +{#fun igraph_layout_kamada_kawai as ^ + { `IGraph' -- ^ Graph + , castPtr `Ptr Matrix' -- ^ Pointer to the result matrix + , `Bool' -- ^ Whether to use the seed + , `Int' -- ^ The maximum number of iterations to perform + , `Double' -- ^ epsilon + , `Double' -- ^ kkconst + , castPtr `Ptr Vector' -- ^ edges weights + , castPtr `Ptr Vector' + , castPtr `Ptr Vector' + , castPtr `Ptr Vector' + , castPtr `Ptr Vector' + } -> `CInt' void- #} + +{# fun igraph_layout_lgl as ^ + { `IGraph' + , castPtr `Ptr Matrix' + , `Int' + , `Double' + , `Double' + , `Double' + , `Double' + , `Double' + , `Int' + } -> `CInt' void- #} diff --git a/src/IGraph/Algorithms/Motif.chs b/src/IGraph/Algorithms/Motif.chs --- a/src/IGraph/Algorithms/Motif.chs +++ b/src/IGraph/Algorithms/Motif.chs @@ -1,7 +1,8 @@ {-# LANGUAGE ForeignFunctionInterface #-} {-# LANGUAGE DataKinds #-} module IGraph.Algorithms.Motif - ( triad + ( dyadCensus + , triad , triadCensus ) where @@ -10,10 +11,26 @@ import Foreign import IGraph +import IGraph.Internal.C2HS {#import IGraph.Internal #} #include "haskell_igraph.h" +-- | Dyad census means classifying each pair of vertices of a directed graph +-- into three categories: mutual, there is an edge from a to b and also +-- from b to a; asymmetric, there is an edge either from a to b or +-- from b to a but not the other way; null, no edges between a and b. +dyadCensus :: Graph 'D v e -> (Int, Int, Int) +dyadCensus = unsafePerformIO . igraphDyadCensus . _graph +{-# INLINE dyadCensus #-} + +{#fun igraph_dyad_census as ^ + { `IGraph' + , alloca- `Int' peekIntConv* + , alloca- `Int' peekIntConv* + , alloca- `Int' peekIntConv* + } -> `CInt' void- #} + -- | Every triple of vertices in a directed graph -- 003: A, B, C, the empty graph. -- 012: A->B, C, a graph with a single directed edge. @@ -54,16 +71,18 @@ ] make :: [(Int, Int)] -> Graph 'D () () make xs = mkGraph (replicate 3 ()) $ zip xs $ repeat () +{-# INLINE triad #-} -triadCensus :: (Ord v, Read v) => Graph d v e -> [Int] +-- | Calculating the triad census means classifying every triple of vertices +-- in a directed graph. A triple can be in one of 16 states listed in `triad`. +triadCensus :: (Ord v, Read v) => Graph 'D v e -> [Int] triadCensus gr = unsafePerformIO $ allocaVector $ \result -> do igraphTriadCensus (_graph gr) result map truncate <$> toList result - --- motifsRandesu - +{-# INLINE triadCensus #-} {#fun igraph_triad_census as ^ { `IGraph' , castPtr `Ptr Vector' } -> `CInt' void- #} +-- motifsRandesu {#fun igraph_motifs_randesu as ^ { `IGraph', castPtr `Ptr Vector', `Int' , castPtr `Ptr Vector' } -> `CInt' void- #} diff --git a/src/IGraph/Algorithms/Structure.chs b/src/IGraph/Algorithms/Structure.chs --- a/src/IGraph/Algorithms/Structure.chs +++ b/src/IGraph/Algorithms/Structure.chs @@ -3,20 +3,31 @@ module IGraph.Algorithms.Structure ( -- * Shortest Path Related Functions shortestPath + , averagePathLength + , diameter + , eccentricity + , radius + -- * Graph Components , inducedSubgraph , isConnected , isStronglyConnected , decompose + , articulationPoints + , bridges + -- * Topological Sorting, Directed Acyclic Graphs , isDag , topSort , topSortUnsafe + -- * Other Operations + , density + , reciprocity + -- * Auxiliary types + , Neimode(IgraphOut,IgraphIn,IgraphAll) -- not IgraphTotal ) where import Control.Monad import Data.Serialize (Serialize) -import Data.List (foldl') import System.IO.Unsafe (unsafePerformIO) -import Data.Maybe import Data.Singletons (SingI) import Foreign @@ -29,14 +40,6 @@ #include "haskell_igraph.h" -{#fun igraph_shortest_paths as ^ - { `IGraph' - , castPtr `Ptr Matrix' - , castPtr %`Ptr VertexSelector' - , castPtr %`Ptr VertexSelector' - , `Neimode' - } -> `CInt' void- #} - -- Calculates and returns a single unweighted shortest path from a given vertex -- to another one. If there are more than one shortest paths between the two -- vertices, then an arbitrary one is returned. @@ -53,6 +56,7 @@ Just f -> withList (map (f . snd) $ labEdges gr) $ \ws -> igraphGetShortestPathDijkstra (_graph gr) path nullPtr s t ws IgraphOut map truncate <$> toList path +{-# INLINE shortestPath #-} {#fun igraph_get_shortest_path as ^ { `IGraph' , castPtr `Ptr Vector' @@ -71,13 +75,88 @@ , `Neimode' } -> `CInt' void- #} +-- | Calculates the average shortest path length between all vertex pairs. +averagePathLength :: SingI d + => Graph d v e + -> Bool -- ^ if unconnected, + -- include only connected pairs (True) + -- or return number if vertices (False) + -> Double +averagePathLength graph unconn = + cFloatConv $ igraphAveragePathLength (_graph graph) (isDirected graph) unconn +{-# INLINE igraphAveragePathLength #-} +{#fun pure igraph_average_path_length as ^ + { `IGraph' + , alloca- `CDouble' peek* + , `Bool' + , `Bool' + } -> `CInt' void- #} + +-- | Calculates the diameter of a graph (longest geodesic). +diameter :: SingI d + => Graph d v e + -> Bool -- ^ if unconnected, + -- return largest component diameter (True) + -- or number of vertices (False) + -> (Int, [Node]) +diameter graph unconn = unsafePerformIO $ + alloca $ \pres -> + allocaVector $ \path -> do + igraphDiameter (_graph graph) pres nullPtr nullPtr path (isDirected graph) unconn + liftM2 (,) (peekIntConv pres) (toNodes path) +{-# INLINE igraphDiameter #-} +{#fun igraph_diameter as ^ + { `IGraph' + , castPtr `Ptr CInt' + , castPtr `Ptr CInt' + , castPtr `Ptr CInt' + , castPtr `Ptr Vector' + , `Bool' + , `Bool' + } -> `CInt' void- #} + +-- | Eccentricity of some vertices. +eccentricity :: Graph d v e + -> Neimode -- ^ 'IgraphOut' to follow edges' direction, + -- 'IgraphIn' to reverse it, 'IgraphAll' to ignore + -> [Node] -- ^ vertices for which to calculate eccentricity + -> [Double] +eccentricity graph mode vids = unsafePerformIO $ + allocaVector $ \res -> + withVerticesList vids $ \vs -> do + igraphEccentricity (_graph graph) res vs mode + toList res +{-# INLINE igraphEccentricity #-} +{#fun igraph_eccentricity as ^ + { `IGraph' + , castPtr `Ptr Vector' + , castPtr %`Ptr VertexSelector' + , `Neimode' + } -> `CInt' void- #} + +-- | Radius of a graph. +radius :: Graph d v e + -> Neimode -- ^ 'IgraphOut' to follow edges' direction, + -- 'IgraphIn' to reverse it, 'IgraphAll' to ignore + -> Double +radius graph mode = cFloatConv $ igraphRadius (_graph graph) mode +{-# INLINE igraphRadius #-} +{#fun pure igraph_radius as ^ + { `IGraph' + , alloca- `CDouble' peek* + , `Neimode' + } -> `CInt' void- #} + +-- | Creates a subgraph induced by the specified vertices. This function collects +-- the specified vertices and all edges between them to a new graph. inducedSubgraph :: (Ord v, Serialize v) => Graph d v e - -> [Int] + -> [Node] -> Graph d v e inducedSubgraph gr nds = unsafePerformIO $ withVerticesList nds $ \vs -> igraphInducedSubgraph (_graph gr) vs IgraphSubgraphCreateFromScratch >>= (\g -> return $ Graph g $ mkLabelToId g) +{-# INLINE inducedSubgraph #-} {#fun igraph_induced_subgraph as ^ { `IGraph' , allocaIGraph- `IGraph' addIGraphFinalizer* @@ -88,10 +167,11 @@ -- | Decides whether the graph is weakly connected. isConnected :: Graph d v e -> Bool isConnected gr = igraphIsConnected (_graph gr) IgraphWeak +{-# INLINE isConnected #-} isStronglyConnected :: Graph 'D v e -> Bool isStronglyConnected gr = igraphIsConnected (_graph gr) IgraphStrong - +{-# INLINE isStronglyConnected #-} {#fun pure igraph_is_connected as ^ { `IGraph' , alloca- `Bool' peekBool* @@ -116,7 +196,28 @@ , `Int' } -> `CInt' void- #} +-- | Find the articulation points in a graph. +articulationPoints :: Graph d v e -> [Node] +articulationPoints gr = unsafePerformIO $ allocaVector $ \res -> do + igraphArticulationPoints (_graph gr) res + toNodes res +{-#INLINE igraphArticulationPoints #-} +{#fun igraph_articulation_points as ^ + { `IGraph' + , castPtr `Ptr Vector' + } -> `CInt' void- #} +-- ^ Find all bridges in a graph. +bridges :: Graph d v e -> [Edge] +bridges gr = unsafePerformIO $ allocaVector $ \res -> do + igraphBridges (_graph gr) res + map (getEdgeByEid gr) <$> toNodes res +{-# INLINE igraphBridges #-} +{#fun igraph_bridges as ^ + { `IGraph' + , castPtr `Ptr Vector' + } -> `CInt' void- #} + -- | Checks whether a graph is a directed acyclic graph (DAG) or not. isDag :: Graph d v e -> Bool isDag = igraphIsDag . _graph @@ -124,11 +225,14 @@ { `IGraph' , alloca- `Bool' peekBool* } -> `CInt' void- #} +{-# INLINE isDag #-} --- | Calculate a possible topological sorting of the graph. +-- | Calculate a possible topological sorting of the graph. Raise error if the +-- graph is not acyclic. topSort :: Graph d v e -> [Node] topSort gr | isDag gr = topSortUnsafe gr | otherwise = error "the graph is not acyclic" +{-# INLINE topSort #-} -- | Calculate a possible topological sorting of the graph. If the graph is not -- acyclic (it has at least one cycle), a partial topological sort is returned. @@ -138,8 +242,37 @@ map truncate <$> toList res where n = nNodes gr +{-# INLINE topSortUnsafe #-} {#fun igraph_topological_sorting as ^ { `IGraph' , castPtr `Ptr Vector' , `Neimode' } -> `CInt' void- #} + +-- | Calculate the density of a graph. +density :: Graph d v e + -> Bool -- ^ whether to include loops + -> Double -- ^ the ratio of edges to possible edges +density gr loops = unsafePerformIO $ alloca $ \res -> do + igraphDensity (_graph gr) res loops + peek res +{-# INLINE igraphDensity #-} +{#fun igraph_density as ^ + { `IGraph' + , castPtr `Ptr Double' + , `Bool' + } -> `CInt' void -#} + +-- | Calculates the reciprocity of a directed graph. +reciprocity :: Graph d v e + -> Bool -- ^ whether to ignore loop edges + -> Double -- ^ the proportion of mutual connections +reciprocity gr ignore_loops = unsafePerformIO $ alloca $ \res -> do + igraphReciprocity (_graph gr) res ignore_loops IgraphReciprocityDefault + peek res +{#fun igraph_reciprocity as ^ + { `IGraph' + , castPtr `Ptr Double' + , `Bool' + , `Reciprocity' + } -> `CInt' void -#} diff --git a/src/IGraph/Internal.chs b/src/IGraph/Internal.chs --- a/src/IGraph/Internal.chs +++ b/src/IGraph/Internal.chs @@ -8,6 +8,7 @@ , withList , withListMaybe , toList + , toNodes , igraphVectorNull , igraphVectorFill , igraphVectorE @@ -192,6 +193,10 @@ igraphVectorCopyTo vec ptr map realToFrac <$> peekArray n ptr {-# INLINE toList #-} + +toNodes :: Ptr Vector -> IO [Node] +toNodes = fmap (map truncate) . toList +{-# INLINE toNodes #-} {#fun igraph_vector_copy_to as ^ { castPtr `Ptr Vector', id `Ptr CDouble' } -> `()' #} diff --git a/src/IGraph/Internal/Constants.chs b/src/IGraph/Internal/Constants.chs --- a/src/IGraph/Internal/Constants.chs +++ b/src/IGraph/Internal/Constants.chs @@ -41,3 +41,6 @@ {#enum igraph_degseq_t as Degseq {underscoreToCase} deriving (Show, Read, Eq) #} + +{#enum igraph_reciprocity_t as Reciprocity {underscoreToCase} + deriving (Show, Read, Eq) #} diff --git a/src/IGraph/Mutable.hs b/src/IGraph/Mutable.hs --- a/src/IGraph/Mutable.hs +++ b/src/IGraph/Mutable.hs @@ -23,7 +23,7 @@ import Data.List (foldl', delete) import Data.Primitive.MutVar import Data.Serialize (Serialize, encode) -import Data.Singletons.Prelude (Sing, SingI, fromSing, sing) +import Data.Singletons (Sing, SingI, fromSing, sing) import Foreign hiding (new) import IGraph.Internal diff --git a/src/IGraph/Types.hs b/src/IGraph/Types.hs --- a/src/IGraph/Types.hs +++ b/src/IGraph/Types.hs @@ -13,12 +13,13 @@ {-# LANGUAGE TypeFamilies #-} {-# LANGUAGE TypeOperators #-} {-# LANGUAGE UndecidableInstances #-} +{-# LANGUAGE StandaloneKindSignatures #-} module IGraph.Types where import Data.Serialize (Serialize) -import Data.Singletons.Prelude import Data.Singletons.TH +import Prelude.Singletons import GHC.Generics (Generic) $(singletons [d| diff --git a/stack.yaml b/stack.yaml --- a/stack.yaml +++ b/stack.yaml @@ -1,4 +1,4 @@ packages: - '.' -resolver: lts-15.0 +resolver: lts-24.2 diff --git a/tests/Test/Algorithms.hs b/tests/Test/Algorithms.hs --- a/tests/Test/Algorithms.hs +++ b/tests/Test/Algorithms.hs @@ -1,4 +1,5 @@ {-# LANGUAGE DataKinds #-} +{-# LANGUAGE TypeApplications #-} module Test.Algorithms ( tests ) where @@ -6,6 +7,7 @@ import Control.Arrow import Control.Monad.ST import Data.List +import Control.Monad import qualified Data.Matrix.Unboxed as M import Test.Tasty import Test.Tasty.HUnit @@ -20,9 +22,19 @@ [ graphIsomorphism , motifTest , cliqueTest + , averagePathTest + , diameterTest + , eccentricityTest + , radiusTest , subGraphs , decomposeTest + , articulationTest + , bridgeTest + , communityTest , pagerankTest + , kleinbergTest + , densityTest + , reciprocityTest ] graphIsomorphism :: TestTree @@ -55,6 +67,37 @@ [2,3,4], [2,4,5] ] c4 = [[1, 2, 3, 4], [1, 2, 4, 5]] +averagePathTest :: TestTree +averagePathTest = testGroup "Average path lengths" + [ testCase "clique" $ averagePathLength (full @'U 10 False) True @?= 1 + , testCase "star" $ averagePathLength (star 10) True @?~ 1.8 + , testCase "ring" $ averagePathLength (ring 11) True @?= 3 + ] + +diameterTest :: TestTree +diameterTest = testGroup "Diameters" + [ testCase "clique" $ fst (diameter (full @'U 10 False) True) @?= 1 + , testCase "star" $ fst (diameter (star 10) False) @?= 2 + , testCase "ring" $ fst (diameter (ring 10) False) @?= 5 + ] + +eccentricityTest :: TestTree +eccentricityTest = testGroup "Eccentricity" + [ testCase "clique" $ + eccentricity (full @'U 10 False) IgraphAll [0..9] @?= replicate 10 1 + , testCase "star" $ + eccentricity (star 10) IgraphAll [0..9] @?= (1 : replicate 9 2) + , testCase "ring" $ + eccentricity (ring 10) IgraphAll [0..9] @?= replicate 10 5 + ] + +radiusTest :: TestTree +radiusTest = testGroup "Radius" + [ testCase "clique" $ radius (full @'U 10 False) IgraphAll @?= 1 + , testCase "star" $ radius (star 10) IgraphAll @?= 1 + , testCase "ring" $ radius (ring 10) IgraphAll @?= 5 + ] + subGraphs :: TestTree subGraphs = testGroup "generate induced subgraphs" [ testCase "" $ test case1 ] @@ -83,15 +126,71 @@ ] where es = [ (0,1), (1,2), (2,0) - , (3,4), (4,5), (5,6) - , (8,9), (9,10) ] + , (3,4), (4,5), (5,6) + , (8,9), (9,10) ] gr = mkGraph (replicate 11 ()) $ zip es $ repeat () :: Graph 'U () () +articulationTest :: TestTree +articulationTest = testCase "Articulation points" $ + articulationPoints (star 3) @?= [0] + +bridgeTest :: TestTree +bridgeTest = testCase "Bridges" $ edgeLab g <$> bridges g @?= ["bridge"] + where g = fromLabeledEdges @'U + [ (("a","b"),"ab") , (("b","c"),"bc") , (("c","a"),"ca") + , (("i","j"),"ij") , (("j","k"),"jk") , (("k","i"),"ki") + , (("a","i"),"bridge") + ] + +communityTest :: TestTree +communityTest = testGroup "Community" + [ consistency, consistency2 ] + where + consistency = testCase "Consistency" $ do + rs <- replicateM 50 $ withSeed 134 $ findCommunity zacharyKarate Nothing Nothing spinglass + all (== head rs) rs @=? True + consistency2 = testCase "Consistency -- leiden" $ do + rs <- replicateM 50 $ withSeed 234 $ findCommunity zacharyKarate Nothing Nothing leiden + True @=? all (== head rs) rs + gr = mkGraph (replicate 10 ()) $ map (\(i,j) -> ((i,j),())) + [ (0, 1), (0, 2), (0, 3), (0, 4), (1, 2), (1, 3), (1, 4), (2, 3), (2, 4) + , (3, 4), (5, 6), (5, 7), (5, 8), (5, 9), (6, 7), (6, 8), (6, 9), (7, 8) + , (7, 9), (8, 9), (0, 5) ] :: Graph 'U () () + pagerankTest :: TestTree pagerankTest = testGroup "PageRank" - [ testCase "case 1" $ ranks @=? ranks' ] + [ consistency + , testCase "case 1" $ ranks @=? ranks' ] where + consistency = testCase "Consistency" $ + pagerank gr 0.85 Nothing Nothing @=? + pagerank gr 0.85 Nothing Nothing gr = star 11 ranks = [0.47,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05] ranks' = map ((/100) . fromIntegral . round. (*100)) $ pagerank gr 0.85 Nothing Nothing + +kleinbergTest :: TestTree +kleinbergTest = testGroup "Kleinberg" + [ testCase "Hub score" $ + fst (hubScore (full @'U 16 False) True) @?= replicate 16 1 + , testCase "Authority score" $ + fst (authorityScore (ring 4) False) @?= replicate 4 0.5 + ] + +densityTest :: TestTree +densityTest = testGroup "Density" + [ testCase "clique" $ density (full @'U 16 False) False @?= 1 + , testCase "ring" $ density (ring 9) False @?= 1/4 + ] + +reciprocityTest :: TestTree +reciprocityTest = testGroup "Reciprocity" + [ testCase "clique" $ reciprocity (full @'D 10 False) False @?= 1 + , testCase "ring" $ reciprocity g False @?= 0 + ] + where g = fromLabeledEdges @'D [(("a","b"),()),(("b","c"),()),(("c","a"),())] + +-- approximate equality helper +(@?~) :: (Ord n,Fractional n) => n -> n -> Assertion +a @?~ b = assertBool "" $ abs (b-a) < 1/65536