bioalign 0.0.3 → 0.0.4

raw patch · 2 files changed

+10/−3 lines, 2 files

Files

• bioalign.cabal +1/−1
• src/Bio/Alignment/AlignData.hs +9/−2

@@ -1,5 +1,5 @@ Name:                bioalign-Version:             0.0.3+Version:             0.0.4 Synopsis:            Data structures and helper functions for calculating alignments Description:         Data structures and helper functions for calculating alignments Homepage:	     https://patch-tag.com/r/dfornika/biophd/home

@@ -36,9 +36,16 @@  -- ---------------------------------------- -data Sequence = Seq SeqData (Maybe QualData) -- ^ header and actual sequence+-- Sequence is a header String, plus SeqData and optional QualData+-- Sequence is an instance of the Bio.Core.Sequence.BioSeq class.++data Sequence = Seq SeqLabel SeqData (Maybe QualData)                 deriving Eq +instance BioSeq Sequence where+  seqlabel  (Seq lab seq mqual) = lab+  seqdata   (Seq lab seq mqual) = seq+  seqlength (Seq lab seq mqual) = Offset {unOff = BC.length $ unSD seq}  type Gaps = [Offset] type Alignment = [(Offset, Strand, Sequence, Gaps)]@@ -106,7 +113,7 @@ --   This represents the columns of the alignment matrix, but will only require linear space --   for score calculation. columns :: Selector a -> a -> Sequence -> Sequence -> [[a]]-columns f z (Seq s1 _) (Seq s2 _) = columns' f z s1 s2+columns f z (Seq _ s1 _) (Seq _ s2 _) = columns' f z s1 s2  columns' :: Selector a -> a -> SeqData -> SeqData -> [[a]] columns' f zero s1 s2 = let