JAL-2416 seqspace.scm and PIDDistanceModel replaced by PIDModel

diff --git a/resources/scoreModel/seqspace.scm b/resources/scoreModel/seqspace.scm
deleted file mode 100644 (file)
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 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -49,12 +49,10 @@ public class ScoreModels
     models = new LinkedHashMap<String, ScoreModelI>();
     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 (file)
--- 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
+     */
   }
 }