X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=57a14a0cc38e01ca3047bb47bc318c475c981458;hb=dc1ad37588e94cbc9ebbfaab2e9e49407f464310;hp=cff91041bab8ef15f1159c1bc58b13a8c0861609;hpb=bd318fe40b8d07db486f47d788dcdc2df8cb9e9c;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index cff9104..57a14a0 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,17 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Graphics;
@@ -37,17 +48,6 @@ import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JRadioButtonMenuItem;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.PCAModel;
-
 /**
  * DOCUMENT ME!
  * 
@@ -58,7 +58,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         IProgressIndicator
 {
 
-  private ProgressBar progressBar;
+  private IProgressIndicator progressBar;
 
   RotatableCanvas rc;
 
@@ -113,11 +113,10 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
     if (!sameLength)
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("label.pca_sequences_not_aligned"),
-                      MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.pca_sequences_not_aligned"),
+              MessageManager.getString("label.sequences_not_aligned"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -170,7 +169,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   public void bgcolour_actionPerformed(ActionEvent e)
   {
-    Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_backgroud_colour"),
             rc.bgColour);
 
     if (col != null)
@@ -397,8 +397,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params", new String[]
-                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params",
+                new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -488,15 +488,14 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (type == jalview.util.ImageMaker.TYPE.PNG)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
-              "Make PNG image from PCA", width, height, null, null);
+              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
+              width, height, null, null);
     }
     else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
-              "Make EPS file from PCA", width, height, null,
-              this.getTitle());
+              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
+              width, height, null, this.getTitle());
     }
     else
     {
@@ -597,8 +596,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.points_for_params", new String[]
-              { this.getTitle() }), 500, 500);
+              "label.points_for_params", new String[] { this.getTitle() }),
+              500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting PCA points", oom);
@@ -622,14 +621,15 @@ public class PCAPanel extends GPCAPanel implements Runnable,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.transformed_points_for_params", new String[]
-              { this.getTitle() }), 500, 500);
+              "label.transformed_points_for_params",
+              new String[] { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting transformed PCA points", oom);
       cap.dispose();
     }
   }
+
   /*
    * (non-Javadoc)
    *