X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=b0b8c9c502e0888982111e4bb0af87e25d1006eb;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=78f950b3a5bdf166b6368c41d8fce0cb3ca2d132;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 78f950b..b0b8c9c 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,30 +1,50 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.CheckboxMenuItem;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
 public class PCAPanel extends EmbmenuFrame implements Runnable,
         ActionListener, ItemListener
 {
@@ -85,7 +105,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     embedMenuIfNeeded(rc);
     add(rc, BorderLayout.CENTER);
 
-    jalview.bin.JalviewLite.addFrame(this, MessageManager.getString("label.principal_component_analysis"),
+    jalview.bin.JalviewLite.addFrame(this,
+            MessageManager.getString("label.principal_component_analysis"),
             475, 400);
 
     Thread worker = new Thread(this);
@@ -219,7 +240,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pca_details"), 500, 500);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("label.pca_details"), 500, 500);
 
     cap.setText(pcaModel.getDetails());
   }
@@ -327,7 +349,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     values.setLabel(MessageManager.getString("label.output_values"));
     values.addActionListener(this);
     inputData.setLabel(MessageManager.getString("label.input_data"));
-    nuclSetting.setLabel(MessageManager.getString("label.nucleotide_matrix"));
+    nuclSetting.setLabel(MessageManager
+            .getString("label.nucleotide_matrix"));
     nuclSetting.addItemListener(this);
     protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
     protSetting.addItemListener(this);