From 6666fd8b18b395d444e7f4c76016231f5a4d3669 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 27 Feb 2017 19:05:26 +0000 Subject: [PATCH] JAL-2416 seqspace.scm and PIDDistanceModel replaced by PIDModel --- resources/scoreModel/seqspace.scm | 31 -------------------- src/jalview/analysis/scoremodels/ScoreModels.java | 4 +-- .../jalview/analysis/scoremodels/PIDModelTest.java | 5 ++++ 3 files changed, 6 insertions(+), 34 deletions(-) delete mode 100644 resources/scoreModel/seqspace.scm diff --git a/resources/scoreModel/seqspace.scm b/resources/scoreModel/seqspace.scm deleted file mode 100644 index a8bdc06..0000000 --- a/resources/scoreModel/seqspace.scm +++ /dev/null @@ -1,31 +0,0 @@ -ScoreMatrix Identity (SeqSpace) -ARNDCQEGHILKMFPSTWYVBZX -# -# The identity substitution matrix, that gives the SeqSpace PCA calculation as in Jalview 2.10.1 -# -# -# A R N D C Q E G H I L K M F P S T W Y V B Z X -# -A 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -R 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -N 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -D 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -C 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -Q 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -E 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -G 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -H 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -I 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 -L 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 -K 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 -M 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 -F 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 -P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 -S 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 -T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 -W 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 -Y 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 -V 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 -B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 -Z 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java index 41b99e2..193d5f4 100644 --- a/src/jalview/analysis/scoremodels/ScoreModels.java +++ b/src/jalview/analysis/scoremodels/ScoreModels.java @@ -49,12 +49,10 @@ public class ScoreModels models = new LinkedHashMap(); BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm"); PAM250 = loadScoreMatrix("scoreModel/pam250.scm"); - // loadScoreMatrix("scoreModel/seqspace.scm"); - // drop seqspace.scm for IdentityScoreModel once JAL-2379 merged in? registerScoreModel(new PIDModel()); DNA = loadScoreMatrix("scoreModel/dna.scm"); registerScoreModel(new FeatureDistanceModel()); - registerScoreModel(new PIDDistanceModel()); + // registerScoreModel(new PIDDistanceModel()); // superseded by PIDModel } /** diff --git a/test/jalview/analysis/scoremodels/PIDModelTest.java b/test/jalview/analysis/scoremodels/PIDModelTest.java index d968e0e..212f825 100644 --- a/test/jalview/analysis/scoremodels/PIDModelTest.java +++ b/test/jalview/analysis/scoremodels/PIDModelTest.java @@ -167,5 +167,10 @@ public class PIDModelTest */ params = new SimilarityParams(false, false, true, false); assertEquals(PIDModel.computePID(s1, s2, params), 20d); + + /* + * no tests for matchGaps=true, includeGaps=false + * as it don't make sense + */ } } -- 1.7.10.2