X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=6f199c577ad01ab239c5c6e37b9fa691b69522db;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=084311fa6b8942e46247dd52abeb2d55249ad660;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 084311f..6f199c5 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -100,9 +100,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
       return;
     }
 
-    Desktop
-            .addInternalFrame(this, "Principal component analysis", 400,
-                    400);
+    Desktop.addInternalFrame(this, "Principal component analysis", 400, 400);
 
     PaintRefresher.Register(this, av.getSequenceSetId());
 
@@ -244,12 +242,13 @@ public class PCAPanel extends GPCAPanel implements Runnable
   public void outputValues_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    try {
+    try
+    {
       cap.setText(pca.getDetails());
       Desktop.addInternalFrame(cap, "PCA details", 500, 500);
     } catch (OutOfMemoryError oom)
     {
-      new OOMWarning("opening PCA details",oom);
+      new OOMWarning("opening PCA details", oom);
       cap.dispose();
     }
   }
@@ -414,8 +413,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
     else
     {
       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
-              "Make EPS file from PCA", width, height, null, this
-                      .getTitle());
+              "Make EPS file from PCA", width, height, null,
+              this.getTitle());
     }
 
     if (im.getGraphics() != null)
@@ -492,18 +491,24 @@ public class PCAPanel extends GPCAPanel implements Runnable
     associateViewsMenu.add(itemf);
 
   }
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
+   * )
    */
   protected void outputPoints_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    try {
+    try
+    {
       cap.setText(getPointsasCsv(false));
-      Desktop.addInternalFrame(cap, "Points for "+getTitle(), 500, 500);
+      Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
     } catch (OutOfMemoryError oom)
     {
-      new OOMWarning("exporting PCA points",oom);
+      new OOMWarning("exporting PCA points", oom);
       cap.dispose();
     }
   }
@@ -512,36 +517,42 @@ public class PCAPanel extends GPCAPanel implements Runnable
   {
     StringBuffer csv = new StringBuffer();
     csv.append("\"Sequence\"");
-    if (transformed) {
+    if (transformed)
+    {
       csv.append(",");
       csv.append(xCombobox.getSelectedIndex());
       csv.append(",");
       csv.append(yCombobox.getSelectedIndex());
       csv.append(",");
       csv.append(zCombobox.getSelectedIndex());
-    } else {
-      for (int d=1,dmax=pca.component(1).length;d<=dmax;d++)
+    }
+    else
+    {
+      for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++)
       {
-        csv.append(","+d);
+        csv.append("," + d);
       }
     }
     csv.append("\n");
-    for (int s=0;s<seqs.length;s++)
+    for (int s = 0; s < seqs.length; s++)
     {
-      csv.append("\""+seqs[s].getName()+"\"");
+      csv.append("\"" + seqs[s].getName() + "\"");
       double fl[];
-      if (!transformed) {
+      if (!transformed)
+      {
         // output pca in correct order
         fl = pca.component(s);
-        for (int d=fl.length-1; d>=0;d--)
+        for (int d = fl.length - 1; d >= 0; d--)
         {
           csv.append(",");
           csv.append(fl[d]);
         }
-    } else {
-      // output current x,y,z coords for points
+      }
+      else
+      {
+        // output current x,y,z coords for points
         fl = rc.getPointPosition(s);
-        for (int d=0; d<fl.length;d++)
+        for (int d = 0; d < fl.length; d++)
         {
           csv.append(",");
           csv.append(fl[d]);
@@ -552,18 +563,24 @@ public class PCAPanel extends GPCAPanel implements Runnable
     return csv.toString();
   }
 
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event.ActionEvent)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
+   * .ActionEvent)
    */
   protected void outputProjPoints_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    try {
+    try
+    {
       cap.setText(getPointsasCsv(true));
-      Desktop.addInternalFrame(cap, "Transformed points for "+getTitle(), 500, 500);
+      Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
+              500, 500);
     } catch (OutOfMemoryError oom)
     {
-      new OOMWarning("exporting transformed PCA points",oom);
+      new OOMWarning("exporting transformed PCA points", oom);
       cap.dispose();
     }
   }