MyGraphics added to enhance applet GUI

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 1dd05e0..026ca09 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -35,77 +35,86 @@ 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
+  public PCAPanel(AlignViewport av)\r
   {\r
-\r
     this.av = av;\r
-    if (av.getSelectionGroup().getSize() > 3)\r
+    if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() > 3)\r
     {\r
-      s = new Sequence[av.getSelectionGroup().getSize()];\r
-      for (int i = 0; i < s.length; i++)\r
+      seqs = new Sequence[av.getSelectionGroup().getSize()];\r
+      for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
       {\r
-        s[i] = av.getSelectionGroup().getSequenceAt(i);\r
+        seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
       }\r
     }\r
-\r
-    if (s == null)\r
+    else\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
+        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
-    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
-\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
+    rc = new RotatableCanvas(av);\r
+    add(rc, BorderLayout.CENTER);\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
+    jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",\r
+                                       400, 400);\r
 \r
-    rc = new RotatableCanvas(av, points, pca.getM().rows);\r
 \r
-    //rc.printPoints();\r
+    Thread worker = new Thread(this);\r
+    worker.start();\r
+  }\r
 \r
-    add(rc, BorderLayout.CENTER);\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
+              this.repaint();\r
   }\r
 \r
   void doDimensionChange()\r
@@ -146,4 +155,20 @@ public class PCAPanel
     doDimensionChange();\r
   }\r
 \r
+  public void values_actionPerformed(ActionEvent actionEvent)\r
+  {\r
+\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);\r
+    Frame frame = new Frame();\r
+    frame.add(cap);\r
+    jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);\r
+\r
+      cap.setText(pca.getDetails());\r
+  }\r
+\r
+  public void labels_itemStateChanged(ItemEvent itemEvent)\r
+  {\r
+    rc.showLabels( labels.getState() );\r
+  }\r
+\r
 }\r