Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown

[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 d9648ba..f591c8e 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;
 
@@ -68,7 +70,8 @@ public class ScoreModels
    * <li>PAM250</li>
    * <li>PID</li>
    * <li>DNA</li>
-   * <li>Sequence Feature Similarity</li>
+   * <li>Sequence Feature Similarity</li>   * 
+   * <li>Secondary Structure Similarity</li>
    * </ul>
    */
   private ScoreModels()
@@ -82,6 +85,9 @@ public class ScoreModels
     DNA = loadScoreMatrix("scoreModel/dna.scm");
     registerScoreModel(new PIDModel());
     registerScoreModel(new FeatureDistanceModel());
+    SECONDARYSTRUCTURE = loadScoreMatrix("scoreModel/secondarystructure.scm");
+    registerScoreModel(new SecondaryStructureDistanceModel());   
+
   }
 
   /**
@@ -140,6 +146,9 @@ public class ScoreModels
 
   public void registerScoreModel(ScoreModelI sm)
   {
+    if(sm.getName().equals("SECONDARYSTRUCTURE")) {
+      return;
+    }
     ScoreModelI sm2 = models.get(sm.getName());
     if (sm2 != null)
     {
@@ -178,4 +187,9 @@ public class ScoreModels
   {
     return PAM250;
   }
+  
+  public ScoreMatrix getSecondaryStructureMatrix()
+  {
+    return SECONDARYSTRUCTURE;
+  }
 }