Add header

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 7bda65a..7e893eb 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -28,6 +28,7 @@ import java.awt.*;
 import java.awt.event.*;\r
 \r
 import java.util.*;\r
+import javax.swing.JOptionPane;\r
 \r
 \r
 /**\r
@@ -42,6 +43,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     int top;\r
     RotatableCanvas rc;\r
     AlignViewport av;\r
+    SequenceI [] seqs;\r
 \r
     /**\r
      * Creates a new PCAPanel object.\r
@@ -56,44 +58,58 @@ public class PCAPanel extends GPCAPanel implements Runnable
         if ((av.getSelectionGroup() != null) &&\r
                 (av.getSelectionGroup().getSize() > 3))\r
         {\r
-            s = new Sequence[av.getSelectionGroup().getSize()];\r
+            seqs = new Sequence[av.getSelectionGroup().getSize()];\r
 \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
         {\r
-            s = new Sequence[av.getAlignment().getHeight()];\r
+            seqs = new Sequence[av.getAlignment().getHeight()];\r
 \r
             for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
             {\r
-                s[i] = av.getAlignment().getSequenceAt(i);\r
+                seqs[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
+\r
+        rc = new RotatableCanvas(av);\r
+        add(rc, BorderLayout.CENTER);\r
+        Thread worker = new Thread(this);\r
+        worker.start();\r
+    }\r
+\r
+\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     */\r
+    public void run()\r
+    {\r
+      try{\r
+        pca = new PCA(seqs);\r
         pca.run();\r
 \r
         // Now find the component coordinates\r
         int ii = 0;\r
 \r
-        while ((ii < s.length) && (s[ii] != null))\r
+        while ( (ii < seqs.length) && (seqs[ii] != null))\r
         {\r
-            ii++;\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
+          if (pca.getEigenvalue(i) > 1e-4)\r
+          {\r
+            comps[i] = pca.component(i);\r
+          }\r
         }\r
 \r
         //////////////////\r
@@ -108,22 +124,26 @@ public class PCAPanel extends GPCAPanel implements Runnable
 \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
+          SequencePoint sp = new SequencePoint(seqs[i], scores[i]);\r
+          points.addElement(sp);\r
         }\r
 \r
-        rc = new RotatableCanvas(av, points, pca.getM().rows);\r
-\r
-        //rc.printPoints();\r
-        add(rc, BorderLayout.CENTER);\r
-    }\r
+        rc.setPoints(points, pca.getM().rows);\r
+        rc.repaint();\r
+        seqs = null;\r
+      }\r
+     catch(OutOfMemoryError er)\r
+      { JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                              "Out of memory calculating PCA!!"\r
+                                              +\r
+                                              "\nSee help files for increasing Java Virtual Machine memory."\r
+                                              , "Out of memory",\r
+                                              JOptionPane.WARNING_MESSAGE);\r
+        System.out.println("PCAPanel: "+er);\r
+        System.gc();\r
+\r
+      }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void run()\r
-    {\r
-        // do stuff\r
     }\r
 \r
     /**\r