JAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown...

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 5c47703..2a25fa8 100644 (file)
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -103,6 +103,8 @@ public class SimilarityParams implements SimilarityParamsI
   private boolean includeGaps;
 
   private boolean denominateByShortestLength;
+  
+  private String secondaryStructureSource;
 
   /**
    * Constructor
@@ -200,4 +202,16 @@ public class SimilarityParams implements SimilarityParamsI
     }
     return true;
   }
+
+  @Override
+  public String getSecondaryStructureSource()
+  {
+    return secondaryStructureSource;
+  }
+
+  @Override
+  public void setSecondaryStructureSource(String secondaryStructureSource)
+  {
+    this.secondaryStructureSource = secondaryStructureSource;
+  }
 }

diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java
index 8d83a17..43f2866 100644 (file)
--- a/src/jalview/api/analysis/SimilarityParamsI.java
+++ b/src/jalview/api/analysis/SimilarityParamsI.java
@@ -60,4 +60,8 @@ public interface SimilarityParamsI
    * @return
    */
   boolean denominateByShortestLength();
+  
+  String getSecondaryStructureSource();
+
+  void setSecondaryStructureSource(String secondaryStructureSource);
 }