X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=f470ffc445b9eacd95e80f774bdda7d5a05684eb;hb=8c2ee75d86492f03e4c01404855f9ad2dd305719;hp=1dd05e0e9afe1f82d92d2554a3cfa8e77c1e98e3;hpb=74e53831a61cb5c3d342fa302cd2cd8d16eacf7b;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 1dd05e0..f470ffc 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -35,11 +35,8 @@ public class PCAPanel
   int top;
   RotatableCanvas rc;
   AlignViewport av;
+  SequenceI [] seqs;
 
-  public void run()
-  {
-    // do stuff
-  }
 
   public PCAPanel(AlignViewport av, SequenceI[] s)
   {
@@ -47,65 +44,72 @@ public class PCAPanel
     this.av = av;
     if (av.getSelectionGroup().getSize() > 3)
     {
-      s = new Sequence[av.getSelectionGroup().getSize()];
+      seqs = new Sequence[av.getSelectionGroup().getSize()];
       for (int i = 0; i < s.length; i++)
       {
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
+        seqs[i] = av.getSelectionGroup().getSequenceAt(i);
       }
     }
 
-    if (s == null)
+    if (seqs == null)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
+      seqs = new Sequence[av.getAlignment().getHeight()];
       for (int i = 0; i < av.getAlignment().getHeight(); i++)
       {
-        s[i] = av.getAlignment().getSequenceAt(i);
-      }
-    }
-
-//////////////////////This part was done in PCATHread originally. Is it too slow???
-    pca = new PCA(s);
-    pca.run();
-
-    // Now find the component coordinates
-    int ii = 0;
-    while (ii < s.length && s[ii] != null)
-    {
-      ii++;
-    }
-
-    double[][] comps = new double[ii][ii];
-
-    for (int i = 0; i < ii; i++)
-    {
-      if (pca.getEigenvalue(i) > 1e-4)
-      {
-        comps[i] = pca.component(i);
+        seqs[i] = av.getAlignment().getSequenceAt(i);
       }
     }
-
-    //////////////////
-
-    xCombobox.select(0);
-    yCombobox.select(1);
-    zCombobox.select(2);
-
-    top = pca.getM().rows - 1;
-
-    Vector points = new Vector();
-    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
-    for (int i = 0; i < pca.getM().rows; i++)
-    {
-      SequencePoint sp = new SequencePoint(s[i], scores[i]);
-      points.addElement(sp);
-    }
-
-    rc = new RotatableCanvas(av, points, pca.getM().rows);
-
-    //rc.printPoints();
-
+    rc = new RotatableCanvas(av);
     add(rc, BorderLayout.CENTER);
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+              pca = new PCA(seqs);
+              pca.run();
+
+              // Now find the component coordinates
+              int ii = 0;
+
+              while ((ii < seqs.length) && (seqs[ii] != null))
+              {
+                  ii++;
+              }
+
+              double[][] comps = new double[ii][ii];
+
+              for (int i = 0; i < ii; i++)
+              {
+                  if (pca.getEigenvalue(i) > 1e-4)
+                  {
+                      comps[i] = pca.component(i);
+                  }
+              }
+
+              //////////////////
+              xCombobox.select(0);
+              yCombobox.select(1);
+              zCombobox.select(2);
+
+              top = pca.getM().rows - 1;
+
+              Vector points = new Vector();
+              float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+              for (int i = 0; i < pca.getM().rows; i++)
+              {
+                  SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+                  points.addElement(sp);
+              }
+
+              rc.setPoints(points, pca.getM().rows);
+              rc.repaint();
+              seqs = null;
   }
 
   void doDimensionChange()