JAL-1125 option to switch between Jalview and SeqSpace PCA calculation modes

[jalview.git] / src / jalview / viewmodel / PCAModel.java

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 6002c8a..64f2497 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -19,7 +19,7 @@ public class PCAModel
     nucleotide=nucleotide2;
   }
 
-  PCA pca;
+  private volatile PCA pca;
   
   int top;
   
@@ -34,10 +34,18 @@ public class PCAModel
 
   private Vector<SequencePoint> points;
 
+  private boolean jvCalcMode=true;
+
+  public boolean isJvCalcMode()
+  {
+    return jvCalcMode;
+  }
+
   public void run()
   {
     
     pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
+    pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
     // Now find the component coordinates
@@ -188,4 +196,9 @@ public class PCAModel
     return pts;
   }
 
+  public void setJvCalcMode(boolean state)
+  {
+    jvCalcMode=state;
+  }
+
 }