merge from 2_4_Release branch

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index ee54478..922941b 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,14 +26,19 @@ import java.awt.event.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-public class PCAPanel
-    extends EmbmenuFrame implements Runnable, ActionListener, ItemListener
+public class PCAPanel extends EmbmenuFrame implements Runnable,
+        ActionListener, ItemListener
 {
   PCA pca;
+
   int top;
+
   RotatableCanvas rc;
+
   AlignViewport av;
+
   SequenceI[] seqs;
+
   AlignmentView seqstrings;
 
   public PCAPanel(AlignViewport av)
@@ -42,8 +46,7 @@ public class PCAPanel
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -72,7 +75,8 @@ public class PCAPanel
     {
       if (sq[i].getWidth() != length)
       {
-        System.out.println("Sequences must be equal length for PCA analysis");
+        System.out
+                .println("Sequences must be equal length for PCA analysis");
         return;
       }
     }
@@ -82,7 +86,7 @@ public class PCAPanel
     add(rc, BorderLayout.CENTER);
 
     jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
-                                     400, 400);
+            400, 400);
 
     Thread worker = new Thread(this);
     worker.start();
@@ -99,7 +103,7 @@ public class PCAPanel
     // Now find the component coordinates
     int ii = 0;
 
-    while ( (ii < seqs.length) && (seqs[ii] != null))
+    while ((ii < seqs.length) && (seqs[ii] != null))
     {
       ii++;
     }
@@ -114,7 +118,7 @@ public class PCAPanel
       }
     }
 
-    //////////////////
+    // ////////////////
     xCombobox.select(0);
     yCombobox.select(1);
     zCombobox.select(2);
@@ -150,7 +154,7 @@ public class PCAPanel
     float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
     for (int i = 0; i < pca.getM().rows; i++)
     {
-      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+      ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
     }
 
     rc.img = null;
@@ -215,28 +219,31 @@ public class PCAPanel
 
   void showOriginalData()
   {
-    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
-    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // decide if av alignment is sufficiently different to original data to
+    // warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions
+    // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
     char gc = '-';
-    try {
+    try
+    {
       // we try to get the associated view's gap character
       // but this may fail if the view was closed...
-      gc = av.
-      getGapCharacter();
-    } catch (Exception ex) {};
+      gc = av.getGapCharacter();
+    } catch (Exception ex)
+    {
+    }
+    ;
     Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
-      Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
-      AlignFrame af = new AlignFrame(al,
-                                     av.applet,
-                                     "Original Data for PCA",
-                                     false);
+      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+      AlignFrame af = new AlignFrame(al, av.applet,
+              "Original Data for PCA", false);
 
-      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+      af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
     }
   }
 
@@ -246,23 +253,36 @@ public class PCAPanel
   }
 
   Panel jPanel2 = new Panel();
+
   Label jLabel1 = new Label();
+
   Label jLabel2 = new Label();
+
   Label jLabel3 = new Label();
+
   protected Choice xCombobox = new Choice();
+
   protected Choice yCombobox = new Choice();
+
   protected Choice zCombobox = new Choice();
+
   FlowLayout flowLayout1 = new FlowLayout();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   MenuBar menuBar1 = new MenuBar();
+
   Menu menu1 = new Menu();
+
   Menu menu2 = new Menu();
+
   protected CheckboxMenuItem labels = new CheckboxMenuItem();
+
   MenuItem values = new MenuItem();
+
   MenuItem inputData = new MenuItem();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(borderLayout1);
     jPanel2.setLayout(flowLayout1);