cobot 0.1.1.7 → 0.1.1.8

raw patch · 4 files changed

+25/−9 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +4/−0
• cobot.cabal +9/−3
• src/Bio/Chain/Alignment/Algorithms.hs +6/−0
• test/JuliaSpec.hs +6/−6

@@ -2,6 +2,10 @@  ## Unreleased changes +## [0.1.1.8] - 2023-03-23+### Changed+- Speedup alignment of `Chain Int Char`.+ ## [0.1.1.7] - 2021-10-06 ### Added - `Complementary` instance for `Char`.

@@ -1,13 +1,13 @@ cabal-version: 2.2 --- This file has been generated from package.yaml by hpack version 0.34.4.+-- This file has been generated from package.yaml by hpack version 0.35.0. -- -- see: https://github.com/sol/hpack ----- hash: 09eef6fbd0d4093057c44a56242d5c569842b42a1e49c3625efc6d01f1471d9f+-- hash: 8dc601d166ae8a9d13853f48df9e28fb2c547e46d0d582a6eb091deab3d7a7ba  name:           cobot-version:        0.1.1.7+version:        0.1.1.8 synopsis:       Computational biology toolkit to collaborate with researchers in constructive protein engineering description:    Please see the README on GitHub at <https://github.com/biocad/cobot#readme> category:       Bio@@ -19,6 +19,8 @@ license:        BSD-3-Clause license-file:   LICENSE build-type:     Simple+tested-with:+    GHC ==8.10.7 || ==9.2.5 || ==9.4.4 extra-source-files:     README.md     ChangeLog.md@@ -98,6 +100,8 @@       HandcraftedSpec       JuliaSpec       Paths_cobot+  autogen-modules:+      Paths_cobot   hs-source-dirs:       test   default-extensions:@@ -141,6 +145,8 @@   type: exitcode-stdio-1.0   main-is: Main.hs   other-modules:+      Paths_cobot+  autogen-modules:       Paths_cobot   hs-source-dirs:       bench

@@ -182,6 +182,8 @@     {-# INLINE traceStart #-}     traceStart = const defStart +    {-# SPECIALISE scoreMatrix :: IsGap g => GlobalAlignment g Char Char -> Chain Int Char -> Chain Int Char -> Matrix (Chain Int Char) (Chain Int Char) #-}+    {-# INLINEABLE scoreMatrix #-}     scoreMatrix :: forall m m' . (Alignable m, Alignable m')                 => GlobalAlignment g (IxValue m) (IxValue m')                 -> m@@ -256,6 +258,8 @@     {-# INLINE traceStart #-}     traceStart = const localStart +    {-# SPECIALISE scoreMatrix :: IsGap g => LocalAlignment g Char Char -> Chain Int Char -> Chain Int Char -> Matrix (Chain Int Char) (Chain Int Char) #-}+    {-# INLINEABLE scoreMatrix #-}     scoreMatrix :: forall m m' . (Alignable m, Alignable m')                 => LocalAlignment g (IxValue m) (IxValue m')                 -> m@@ -327,6 +331,8 @@     {-# INLINE traceStart #-}     traceStart = const semiStart +    {-# SPECIALISE scoreMatrix :: IsGap g => SemiglobalAlignment g Char Char -> Chain Int Char -> Chain Int Char -> Matrix (Chain Int Char) (Chain Int Char) #-}+    {-# INLINEABLE scoreMatrix #-}     scoreMatrix :: forall m m' . (Alignable m, Alignable m')                 => SemiglobalAlignment g (IxValue m) (IxValue m')                 -> m

@@ -25,8 +25,8 @@     it "Is symmetric (big): " $   score resBig1   `shouldBe` score resBig2     it "Is symmetric (med): " $   score resMed1   `shouldBe` score resMed2     it "Is symmetric (small): " $ score resSmall1 `shouldBe` score resSmall2-    -- | scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=0, gap_extend=-9);-    -- | pairalign(GlobalAlignment(), a, b, scoremodel)+    -- scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=0, gap_extend=-9);+    -- pairalign(GlobalAlignment(), a, b, scoremodel)     let aAns = "CTCTGCAAGCATAGAGATATTTCACCGGCAATATTTTTCGTTGAAGTGTATTTGTCCCTATTATCACACC\                 \AGTCATTCCGATGTCGTTAGGGCCGCCTGTTTTACTGGAGTTCCCGTTCGATGTACCCTCCTCCATAGA\                 \GATTTAGGGGTATAGACCGCGACGGACGGGGCTTGCGAAAGCTGCCCGATAATGGACTTTGACAATAGA\@@ -111,8 +111,8 @@     it "Is symmetric (big): " $   score resBig1   `shouldBe` score resBig2     it "Is symmetric (med): " $   score resMed1   `shouldBe` score resMed2     it "Is symmetric (small): " $ score resSmall1 `shouldBe` score resSmall2-    -- | scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=0, gap_extend=-3);-    -- | pairalign(OverlapAlignment(), a, b, scoremodel)+    -- scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=0, gap_extend=-3);+    -- pairalign(OverlapAlignment(), a, b, scoremodel)     let aAns = "CTCTGCAAGCATAGAGATATTTCACCGGCAATATTTTTCGTTGAAGTGTATTTGTCCCTATTATCACACC\                 \AGTCATTCCGATGTCGTTAGGGCCGCCTGTTTTACTG--G-AG--TTC--C-CGTTCGATGTACCCTCC\                 \TCCATAGAGA-TTTAGGGGTA-T-AGACCGCGACGGACGGGGCTTGCGAAAGCTGCCCGATAATGGACT\@@ -188,8 +188,8 @@     it "Is symmetric (big): " $   score resBig1   `shouldBe` score resBig2     it "Is symmetric (med): " $   score resMed1   `shouldBe` score resMed2     it "Is symmetric (small): " $ score resSmall1 `shouldBe` score resSmall2-    -- | scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=0, gap_extend=-7);-    -- | pairalign(LocalAlignment(), a, b, scoremodel)+    -- scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=0, gap_extend=-7);+    -- pairalign(LocalAlignment(), a, b, scoremodel)     let aAns = "TGAA-CAGCCATGCCA-TC-CGCAGGATGCGCC-AGGGAAAAGCCACCCCCAAGAACGACTCCA\                 \GGGGCCCAAGTATGATGATAGC-GTTAGGCTTGCTCGAAGGCAAACAACTCCGAGG-ATGC-T\                 \TAGCAGGCCACAACGTGCTCGATAGCACGAGCGTAAGATGCGAACGCAGTAGTACCTAATGCGGGCGAGACATT"