BiobaseInfernal 0.6.0.0 → 0.6.0.1

raw patch · 3 files changed

+15/−27 lines, 3 files

Files

• Biobase/Infernal/Clan.hs +4/−8
• Biobase/Infernal/RfamFasta.hs +6/−12
• BiobaseInfernal.cabal +5/−7

@@ -16,13 +16,9 @@ -- | Simple Rfam clan data.  data Clan = Clan-  -- | result of the "AC    CL00001" line, keeping "1" in this case.-  { cAccession  :: !ClanAccession-  -- | the "ID    tRNA" line, keeping "tRNA".-  , cIdentifier :: !ClanIdentification-  -- | all the "MB    RF00005;", "MB    RF00023;" lines, keeping "[5,23]".-  , cMembers    :: ![ModelAccession]-  -- | all lines of each clan, without any processing (except being in lines).-  , cStrings    :: ![ByteString]+  { cAccession  :: !ClanAccession       -- ^ result of the "AC    CL00001" line, keeping "1" in this case.+  , cIdentifier :: !ClanIdentification  -- ^ the "ID    tRNA" line, keeping "tRNA".+  , cMembers    :: ![ModelAccession]    -- ^ all the "MB    RF00005;", "MB    RF00023;" lines, keeping "[5,23]".+  , cStrings    :: ![ByteString]        -- ^ all lines of each clan, without any processing (except being in lines).   } deriving (Read,Show,Eq) 

@@ -20,18 +20,12 @@ -- | Rfam FASTA entry.  data RfamFasta = RfamFasta-  -- | Rfam accession number RFxxxxx (the xxxxx part).-  { modelAccession    :: !ModelAccession-  -- | Rfam identifier (like 5S_rRNA).-  , modelIdentifier   :: !ModelIdentification-  -- | EMBL sequence accession identifier and position.-  , sequenceAccession :: !EmblAccession-  -- | Rfam species accession.-  , speciesAccession  :: !SpeciesAccession-  -- | Species name.-  , speciesName       :: !SpeciesName-  -- | FASTA data-  , fastaData         :: !StrictSeqData+  { modelAccession    :: !ModelAccession      -- ^ Rfam accession number RFxxxxx (the xxxxx part).+  , modelIdentifier   :: !ModelIdentification -- ^ Rfam identifier (like 5S_rRNA).+  , sequenceAccession :: !EmblAccession       -- ^ EMBL sequence accession identifier and position.+  , speciesAccession  :: !SpeciesAccession    -- ^ Rfam species accession.+  , speciesName       :: !SpeciesName         -- ^ Species name.+  , fastaData         :: !StrictSeqData       -- ^ FASTA data   } deriving (Show)  -- | Since RfamFasta entries are just fasta entries...

@@ -1,5 +1,5 @@ name:           BiobaseInfernal-version:        0.6.0.0+version:        0.6.0.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -26,6 +26,10 @@                 .                 .                 .+                Changes in 0.6.0.1+                .+                * haddock should finish now+                .                 Changes in 0.6.0.0                 .                 * multiple changes to data representation (mostly newtypes) and@@ -34,12 +38,6 @@                 * load the Rfam.fasta.gz file (and prepare lookup structures)                 .                 * partial biocore integration-                .-                Changes in 0.5.4.1-                .-                * fix-up for VH export-                .-                * half-baked CM type (not useful yet)  extra-source-files: