JAL-1013 - rename nucleotide and ensure current calculation score model reflected...

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 2171e08..e3959ea 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -52,6 +52,11 @@ public class PCAPanel extends GPCAPanel implements Runnable
   SequenceI[] seqs;
 
   /**
+   * use the identity matrix for calculating similarity between sequences. 
+   */
+  private boolean nucleotide=false;
+
+  /**
    * Creates a new PCAPanel object.
    * 
    * @param av
@@ -67,6 +72,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     boolean sameLength = true;
 
     seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+    nucleotide=av.getAlignment().isNucleotide();
     if (av.getSelectionGroup() == null)
     {
       seqs = av.alignment.getSequencesArray();
@@ -129,7 +135,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
   {
     try
     {
-      pca = new PCA(seqstrings.getSequenceStrings(' '));
+      calcSettings.setEnabled(false);
+      pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
       pca.run();
 
       // Now find the component coordinates
@@ -170,15 +177,30 @@ public class PCAPanel extends GPCAPanel implements Runnable
       rc.repaint();
 
       addKeyListener(rc);
+      nuclSetting.setSelected(nucleotide);
+      protSetting.setSelected(!nucleotide);
 
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("calculating PCA", er);
 
     }
-
+    calcSettings.setEnabled(true);
+  }
+  @Override
+  protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+  {
+    nucleotide=true;
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+  @Override
+  protected void protSetting_actionPerfomed(ActionEvent arg0)
+  {
+    nucleotide=false;
+    Thread worker = new Thread(this);
+    worker.start();
   }
-
   /**
    * DOCUMENT ME!
    */