From: Renia Correya <rcorreya001@dundee.ac.uk>
Date: Wed, 24 Apr 2024 14:26:35 +0000 (+0100)
Subject: JAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown... 
X-Git-Tag: Release_2_11_4_0~37^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=98a277d5e5bd7a034b2acbc4d28544210ada392e;p=jalview.git

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

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 5c47703..2a25fa8 100644
--- 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
--- 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);
 }