Init PCA in thread

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

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