RNAlien 1.2.5 → 1.2.6

raw patch · 2 files changed

+7/−7 lines, 2 filesdep ~BlastHTTPdep ~EntrezHTTPPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: BlastHTTP, EntrezHTTP

API changes (from Hackage documentation)

Files

• RNAlien.cabal +4/−4
• src/Bio/RNAlienLibrary.hs +3/−3

@@ -2,7 +2,7 @@ -- see http://haskell.org/cabal/users-guide/  name:                RNAlien-version:             1.2.5+version:             1.2.6 synopsis:            Unsupervized construction of RNA family models description:         RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.                      .@@ -53,8 +53,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/RNAlien/tree/1.2.5-  tag:      1.2.5+  location: https://github.com/eggzilla/RNAlien/tree/1.2.6+  tag:      1.2.6                       executable RNAlien   Hs-Source-Dirs:      ./src/Bio/@@ -89,7 +89,7 @@ Library   Hs-Source-Dirs:      ./src/   ghc-options:         -Wall -O2 -fno-warn-unused-do-bind-  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.1, process, directory, blastxml>=0.3.2, biofasta, parsec, random, BlastHTTP, biocore, bytestring, Taxonomy >= 1.0.2, either-unwrap, containers, ClustalParser>=1.1.0, EntrezHTTP>=1.0.2, vector, edit-distance, cassava, matrix, hierarchical-clustering, filepath, HTTP, http-conduit, hxt, network, aeson, text, transformers, pureMD5+  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.1, process, directory, blastxml>=0.3.2, biofasta, parsec, random, BlastHTTP>=1.2.1, biocore, bytestring, Taxonomy >= 1.0.2, either-unwrap, containers, ClustalParser>=1.1.0, EntrezHTTP>=1.0.3, vector, edit-distance, cassava, matrix, hierarchical-clustering, filepath, HTTP, http-conduit, hxt, network, aeson, text, transformers, pureMD5   Exposed-Modules:     Bio.RNAlienData                        Bio.RNAlienLibrary                        Bio.RNAcentralHTTP

@@ -1652,14 +1652,14 @@ -- | Check if alien can connect to NCBI checkNCBIConnection :: IO (Either String String) checkNCBIConnection = do-   response <- simpleHTTP (getRequest "http://www.ncbi.nlm.nih.gov")+   response <- simpleHTTP (getRequest "https://www.ncbi.nlm.nih.gov")    if isRight response      then do        let rightResponse = fromRight response        if rspCode rightResponse == (2,0,0)          then return (Right ("Network connection with NCBI server is ok: "  ++ show (rspCode rightResponse)))-         else return (Left ("Could not connect to NCBI server \"http://www.ncbi.nlm.nih.gov\". Response Code: " ++ show (rspCode rightResponse)))-     else return (Left ("Could not connect to NCBI server: \"http://www.ncbi.nlm.nih.gov\": " ++ show (fromLeft response)))+         else return (Left ("Could not connect to NCBI server \"https://www.ncbi.nlm.nih.gov\". Response Code: " ++ show (rspCode rightResponse)))+     else return (Left ("Could not connect to NCBI server: \"https://www.ncbi.nlm.nih.gov\": " ++ show (fromLeft response)))  -- | Blast evalue is set stricter in inital alignment mode setBlastExpectThreshold :: ModelConstruction -> Double