Init PCA in thread

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 7bda65a..474a158 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -42,6 +42,7 @@ 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
@@ -56,74 +57,78 @@ 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
-        pca.run();\r
 \r
-        // Now find the component coordinates\r
-        int ii = 0;\r
-\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
-            }\r
-        }\r
-\r
-        //////////////////\r
-        xCombobox.setSelectedIndex(0);\r
-        yCombobox.setSelectedIndex(1);\r
-        zCombobox.setSelectedIndex(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
+        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
-        // do stuff\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.setSelectedIndex(0);\r
+                yCombobox.setSelectedIndex(1);\r
+                zCombobox.setSelectedIndex(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
     /**\r