JAL-1161 conditional parameters for controlling clipping

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

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 8c87d7c..9ddb132 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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.
- * 
+ *  
  * 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 
@@ -17,12 +17,9 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.viewmodel.PCAModel;
 
@@ -55,11 +52,12 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
 
     this.av = av;
-    AlignmentView seqstrings = av
-            .getAlignmentView(av.getSelectionGroup() != null);
+    boolean selected = av.getSelectionGroup() != null
+            && av.getSelectionGroup().getSize() > 0;
+    AlignmentView seqstrings = av.getAlignmentView(selected);
     boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
-    if (av.getSelectionGroup() == null)
+    if (!selected)
     {
       seqs = av.getAlignment().getSequencesArray();
     }
@@ -132,7 +130,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     {
       return;
     }
-    
+
     int dim1 = top - xCombobox.getSelectedIndex();
     int dim2 = top - yCombobox.getSelectedIndex();
     int dim3 = top - zCombobox.getSelectedIndex();
@@ -176,6 +174,10 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     {
       zCombobox_actionPerformed();
     }
+    else if (evt.getSource() == labels)
+    {
+      labels_itemStateChanged(evt);
+    }
     else if (evt.getSource() == nuclSetting)
     {
       if (!pcaModel.isNucleotide())