X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=1dd05e0e9afe1f82d92d2554a3cfa8e77c1e98e3;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=f652aae504245316c29cc2aa225fc00b6b5baa13;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index f652aae..1dd05e0 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,33 +1,35 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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 jalview.datamodel.*;
-import jalview.analysis.PCA;
-import jalview.jbappletgui.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
 
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel
+    extends GPCAPanel implements Runnable
 {
   PCA pca;
   int top;
@@ -39,30 +41,34 @@ public class PCAPanel extends GPCAPanel implements Runnable
     // do stuff
   }
 
-  public PCAPanel(AlignViewport av, SequenceI[] s) {
+  public PCAPanel(AlignViewport av, SequenceI[] s)
+  {
 
     this.av = av;
-    if(av.getSelectionGroup().getSize()>3)
+    if (av.getSelectionGroup().getSize() > 3)
     {
       s = new Sequence[av.getSelectionGroup().getSize()];
-      for(int i=0; i<s.length; i++)
+      for (int i = 0; i < s.length; i++)
+      {
         s[i] = av.getSelectionGroup().getSequenceAt(i);
+      }
     }
 
-
-    if(s==null)
+    if (s == null)
     {
       s = new Sequence[av.getAlignment().getHeight()];
       for (int i = 0; i < av.getAlignment().getHeight(); i++)
+      {
         s[i] = av.getAlignment().getSequenceAt(i);
-     }
+      }
+    }
 
 //////////////////////This part was done in PCATHread originally. Is it too slow???
     pca = new PCA(s);
     pca.run();
 
     // Now find the component coordinates
-    int ii=0;
+    int ii = 0;
     while (ii < s.length && s[ii] != null)
     {
       ii++;
@@ -70,11 +76,11 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
     double[][] comps = new double[ii][ii];
 
-    for (int i=0; i < ii; i++ )
+    for (int i = 0; i < ii; i++)
     {
       if (pca.getEigenvalue(i) > 1e-4)
       {
-        comps[i]  = pca.component(i);
+        comps[i] = pca.component(i);
       }
     }
 
@@ -84,37 +90,39 @@ public class PCAPanel extends GPCAPanel implements Runnable
     yCombobox.select(1);
     zCombobox.select(2);
 
-    top = pca.getM().rows-1;
+    top = pca.getM().rows - 1;
 
     Vector points = new Vector();
-    float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
+    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-    for (int i =0; i < pca.getM().rows; i++ )
+    for (int i = 0; i < pca.getM().rows; i++)
     {
-      SequencePoint sp = new SequencePoint(s[i],scores[i]);
+      SequencePoint sp = new SequencePoint(s[i], scores[i]);
       points.addElement(sp);
     }
 
-    rc = new RotatableCanvas(av,points,pca.getM().rows);
+    rc = new RotatableCanvas(av, points, pca.getM().rows);
 
     //rc.printPoints();
 
     add(rc, BorderLayout.CENTER);
   }
 
-
   void doDimensionChange()
   {
-    if(top==0)
+    if (top == 0)
+    {
       return;
+    }
 
     int dim1 = top - xCombobox.getSelectedIndex();
     int dim2 = top - yCombobox.getSelectedIndex();
     int dim3 = top - zCombobox.getSelectedIndex();
 
-    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];
+    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];
     }
 
     rc.img = null;