Merge branch 'JAL-1013_pca_rna_dna' into develop

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index fe0c4f9..9dc73b7 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -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.getAlignment().getSequencesArray();
@@ -100,8 +106,6 @@ public class PCAPanel extends GPCAPanel implements Runnable
       return;
     }
 
-    Desktop.addInternalFrame(this, "Principal component analysis", 400, 400);
-
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     rc = new RotatableCanvas(ap);
@@ -129,7 +133,8 @@ 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
@@ -167,18 +172,37 @@ public class PCAPanel extends GPCAPanel implements Runnable
       }
 
       rc.setPoints(points, pca.getM().rows);
-      rc.repaint();
-
-      addKeyListener(rc);
+      // rc.invalidate();
+      nuclSetting.setSelected(nucleotide);
+      protSetting.setSelected(!nucleotide);
 
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("calculating PCA", er);
-
+      return;
+    }
+    calcSettings.setEnabled(true);
+    repaint();
+    if (getParent()==null)
+    {
+      addKeyListener(rc);
+      Desktop.addInternalFrame(this, "Principal component analysis", 400, 400);
     }
-
   }
-
+  @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!
    */