JAL-4386 - Implementation of substitution matrix and test cases.

[jalview.git] / src / jalview / analysis / scoremodels / ScoreModels.java

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index dd1bc9d..1c47968 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -40,6 +40,8 @@ public class ScoreModels
   private final ScoreMatrix PAM250;
 
   private final ScoreMatrix DNA;
+  
+  private final ScoreMatrix SECONDARYSTRUCTURE;
 
   private static ScoreModels instance;
 
@@ -83,7 +85,9 @@ public class ScoreModels
     DNA = loadScoreMatrix("scoreModel/dna.scm");
     registerScoreModel(new PIDModel());
     registerScoreModel(new FeatureDistanceModel());
-    registerScoreModel(new SecondaryStructureDistanceModel());
+    SECONDARYSTRUCTURE = loadScoreMatrix("scoreModel/secondarystructure.scm");
+    registerScoreModel(new SecondaryStructureDistanceModel());   
+
   }
 
   /**
@@ -180,4 +184,9 @@ public class ScoreModels
   {
     return PAM250;
   }
+  
+  public ScoreMatrix getSecondaryStructureMatrix()
+  {
+    return SECONDARYSTRUCTURE;
+  }
 }