optimize repaints

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 845e880..b121828 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -27,7 +27,6 @@ import java.awt.event.*;
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 \r
-\r
 public class PCAPanel\r
     extends Frame implements Runnable, ActionListener, ItemListener\r
 {\r
@@ -35,10 +34,9 @@ public class PCAPanel
   int top;\r
   RotatableCanvas rc;\r
   AlignViewport av;\r
-  SequenceI [] seqs;\r
+  SequenceI[] seqs;\r
   AlignmentView seqstrings;\r
 \r
-\r
   public PCAPanel(AlignViewport av)\r
   {\r
     try\r
@@ -58,8 +56,8 @@ public class PCAPanel
     }\r
 \r
     this.av = av;\r
-    seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
-    if(av.getSelectionGroup()==null)\r
+    seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);\r
+    if (av.getSelectionGroup() == null)\r
     {\r
       seqs = av.alignment.getSequencesArray();\r
     }\r
@@ -67,7 +65,7 @@ public class PCAPanel
     {\r
       seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
     }\r
-    SeqCigar sq[]=seqstrings.getSequences();\r
+    SeqCigar sq[] = seqstrings.getSequences();\r
     int length = sq[0].getWidth();\r
 \r
     for (int i = 0; i < seqs.length; i++)\r
@@ -79,13 +77,11 @@ public class PCAPanel
       }\r
     }\r
 \r
-\r
     rc = new RotatableCanvas(av);\r
     add(rc, BorderLayout.CENTER);\r
 \r
     jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",\r
-                                       400, 400);\r
-\r
+                                     400, 400);\r
 \r
     Thread worker = new Thread(this);\r
     worker.start();\r
@@ -96,47 +92,47 @@ public class PCAPanel
    */\r
   public void run()\r
   {\r
-              pca = new PCA(seqstrings.getSequenceStrings(' '));\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
+    pca = new PCA(seqstrings.getSequenceStrings(' '));\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
@@ -164,23 +160,32 @@ public class PCAPanel
 \r
   public void actionPerformed(ActionEvent evt)\r
   {\r
-    if(evt.getSource()==inputData)\r
+    if (evt.getSource() == inputData)\r
+    {\r
       showOriginalData();\r
+    }\r
     else\r
+    {\r
       values_actionPerformed();\r
+    }\r
   }\r
 \r
   public void itemStateChanged(ItemEvent evt)\r
   {\r
-    if(evt.getSource()==xCombobox)\r
+    if (evt.getSource() == xCombobox)\r
+    {\r
       xCombobox_actionPerformed();\r
-    else if(evt.getSource()==yCombobox)\r
+    }\r
+    else if (evt.getSource() == yCombobox)\r
+    {\r
       yCombobox_actionPerformed();\r
-    else if(evt.getSource()==zCombobox)\r
+    }\r
+    else if (evt.getSource() == zCombobox)\r
+    {\r
       zCombobox_actionPerformed();\r
+    }\r
   }\r
 \r
-\r
   protected void xCombobox_actionPerformed()\r
   {\r
     doDimensionChange();\r
@@ -204,7 +209,7 @@ public class PCAPanel
     frame.add(cap);\r
     jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);\r
 \r
-      cap.setText(pca.getDetails());\r
+    cap.setText(pca.getDetails());\r
   }\r
 \r
   void showOriginalData()\r
@@ -216,23 +221,23 @@ public class PCAPanel
     Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.\r
         getGapCharacter());\r
 \r
+    if (alAndColsel != null && alAndColsel[0] != null)\r
+    {\r
+      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+      AlignFrame af = new AlignFrame(al,\r
+                                     av.applet,\r
+                                     "Original Data for PCA",\r
+                                     false);\r
 \r
-    if (alAndColsel != null && alAndColsel[0]!=null)\r
-     {\r
-       Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
-       AlignFrame af = new AlignFrame(al,\r
-             av.applet,\r
-             "Original Data for PCA",\r
-             false);\r
-\r
-      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );\r
-     }\r
+      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);\r
+    }\r
   }\r
 \r
   public void labels_itemStateChanged(ItemEvent itemEvent)\r
   {\r
-    rc.showLabels( labels.getState() );\r
+    rc.showLabels(labels.getState());\r
   }\r
+\r
   Panel jPanel2 = new Panel();\r
   Label jLabel1 = new Label();\r
   Label jLabel2 = new Label();\r