JAL-1632 add score model params to PCAModel and PCA constructors

[jalview.git] / src / jalview / appletgui / PCAPanel.java

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index c5ec0c1..21668d3 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -99,7 +100,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
         return;
       }
     }
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
+            SimilarityParams.SeqSpace);
 
     rc = new RotatableCanvas(av);
     embedMenuIfNeeded(rc);
@@ -116,6 +118,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     // TODO progress indicator
@@ -164,6 +167,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     rc.paint(rc.getGraphics());
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == inputData)
@@ -183,6 +187,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == xCombobox)