seqloc 0.5.0.2 → 0.5.1.0

raw patch · 4 files changed

+30/−6 lines, 4 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• seqloc.cabal +1/−1
• src/Bio/SeqLoc/Location.hs +8/−0
• src/Bio/SeqLoc/SpliceLocation.hs +1/−0
• test/TestMain.hs +20/−5

@@ -1,5 +1,5 @@ Name:                seqloc-Version:             0.5.0.2+Version:             0.5.1.0 Cabal-Version:       >= 1.6 Synopsis:            Handle sequence locations for bioinformatics Description:         Handle sequence locations for bioinformatics

@@ -52,6 +52,10 @@   -- 'startPos'.   endPos :: l -> Pos.Pos +  -- | List of sequence positions in the location, in order from the+  -- 5' end to the 3' end of the location strand.+  allPos :: l -> [Pos.Pos]+   -- | Extract 'Just' the nucleotide 'SeqLike' for the sequence   -- location, or 'Nothing' if f any part of the location lies outside   -- the bounds of the sequence.@@ -157,6 +161,10 @@     = case str of         Plus      -> Pos.Pos (seq5 + len - 1) str         Minus -> Pos.Pos seq5             str+  allPos (ContigLoc seq5 len str) +    = case str of+        Plus ->  [ Pos.Pos (seq5+o)         str | o <- [0..(len - 1)] ]+        Minus -> [ Pos.Pos (seq5+len-(1+o)) str | o <- [0..(len - 1)] ]   clocInto = clocClocInto   clocOutof = clocClocOutof   extend = clocExtend

@@ -88,6 +88,7 @@   posOutof pos = posOutofContigs pos . contigs   startPos = startPos . firstContig   endPos = endPos . lastContig+  allPos = concatMap allPos . contigs   clocInto = slocClocInto   clocOutof = slocClocOutof   extend = slocExtend

@@ -1,4 +1,4 @@-{-# LANGUAGE ExistentialQuantification #-}+{-# LANGUAGE ExistentialQuantification, BangPatterns #-} module Main     where @@ -45,6 +45,7 @@         , T "Contig loc outof/into inverse" property_ContigLocOutofInto         , T "Contig into based on bounds"   test_Contig_IntoBounds         , T "Contig outof based on bounds"  test_Contig_OutofBounds+        , T "Contig allPos/outof equiv"     property_Contig_allPos_outof         , T "Contig seqData"                property_Contig_seqData         , T "Contig seqDataPadded"          property_Contig_seqDataPadded         , T "Contig seqData2"               property_Contig_seqData2@@ -53,13 +54,14 @@         , T "Contig fromBoundsStrand"       property_Contig_fromBoundsStrand         , T "Contig overlaps"               property_Contig_overlaps           , T "Contig repr"                   test_Contig_repr-        +                   , T "Loc revCompl"                  test_Loc_Minus         , T "Loc pos into/outof inverse"    property_LocIntoOutof         , T "Loc pos outof/into inverse"    property_LocOutofInto         , T "Loc outof based on bounds"     test_Loc_OutofBounds         , T "Loc loc outof/into inverse"    property_LocCLocOutofInto         , T "Loc outof association"         property_LocOutofAssoc+        , T "Loc allPos/outof equiv"        property_Loc_allPos_outof                 , T "Loc locOutof"                  property_SpLocOutof         , T "Loc locOutof valid"            property_SpLocOutofGood         , T "Loc within"                    property_Loc_Within@@ -85,9 +87,6 @@ instance Arbitrary SeqLabel where     arbitrary = genName -instance Show SeqLabel where-  show = show . unSeqLabel- test_revCompl :: (Eq s, Stranded s) => s -> Bool test_revCompl s = (revCompl . revCompl) s == s @@ -188,6 +187,14 @@     = let !offset = Pos.offset pos       in (isJust $ Loc.posOutof pos contig) == (offset >= 0 && offset < Loc.length contig) +property_Contig_allPos_outof :: Loc.ContigLoc -> Property+property_Contig_allPos_outof contig+  = forAll (choose (0, fromIntegral $ Loc.length contig - 1)) $ \ioff ->+  let p = drop ioff $ Loc.allPos contig+  in and [ not $ null p+         , Loc.posOutof (Pos.Pos (Pos.Offset $ fromIntegral ioff) Plus) contig == Just (head p)+         ]+ property_Contig_seqData :: Loc.ContigLoc -> Property property_Contig_seqData contig     = forAll (genNonNegOffset >>= genNtByteString . fromIntegral) $ \sequ ->@@ -312,6 +319,14 @@                        mapM (flip Loc.clocOutof outerloc) $                        Loc.toContigs subloc   in (isJust mOutofContigs) ==> mOutofContigs == mContigsOutof++property_Loc_allPos_outof :: SpLoc.SpliceLoc -> Property+property_Loc_allPos_outof sploc+  = forAll (choose (0, fromIntegral $ Loc.length sploc - 1)) $ \ioff ->+  let p = drop ioff $ Loc.allPos sploc+  in and [ not $ null p+         , Loc.posOutof (Pos.Pos (Pos.Offset $ fromIntegral ioff) Plus) sploc == Just (head p)+         ]  property_Loc_seqData :: SpLoc.SpliceLoc -> Property property_Loc_seqData loc