From a81cd4fa55b7cade14dc0ee9a0875c63e96d3f44 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 14 Dec 2011 11:12:20 +0000
Subject: [PATCH] JAL-1013 - rename nucleotide and ensure current calculation
 score model reflected in GUI

---
 src/jalview/gui/PCAPanel.java    |   12 +++++++-----
 src/jalview/jbgui/GPCAPanel.java |    4 ++--
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index eec9b6d..e3959ea 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -54,7 +54,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
   /**
    * use the identity matrix for calculating similarity between sequences. 
    */
-  private boolean useidentity=false;
+  private boolean nucleotide=false;
 
   /**
    * Creates a new PCAPanel object.
@@ -72,7 +72,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     boolean sameLength = true;
 
     seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
-    useidentity=av.getAlignment().isNucleotide();
+    nucleotide=av.getAlignment().isNucleotide();
     if (av.getSelectionGroup() == null)
     {
       seqs = av.alignment.getSequencesArray();
@@ -136,7 +136,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     try
     {
       calcSettings.setEnabled(false);
-      pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
+      pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
       pca.run();
 
       // Now find the component coordinates
@@ -177,6 +177,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
       rc.repaint();
 
       addKeyListener(rc);
+      nuclSetting.setSelected(nucleotide);
+      protSetting.setSelected(!nucleotide);
 
     } catch (OutOfMemoryError er)
     {
@@ -188,14 +190,14 @@ public class PCAPanel extends GPCAPanel implements Runnable
   @Override
   protected void nuclSetting_actionPerfomed(ActionEvent arg0)
   {
-    useidentity=true;
+    nucleotide=true;
     Thread worker = new Thread(this);
     worker.start();
   }
   @Override
   protected void protSetting_actionPerfomed(ActionEvent arg0)
   {
-    useidentity=false;
+    nucleotide=false;
     Thread worker = new Thread(this);
     worker.start();
   }
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 10f22bd..8ff42f8 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -72,8 +72,8 @@ public class GPCAPanel extends JInternalFrame
   protected JMenu associateViewsMenu = new JMenu();
 
   protected JMenu calcSettings=new JMenu();
-  JMenuItem nuclSetting=new JMenuItem();
-  JMenuItem protSetting=new JMenuItem();
+  protected JCheckBoxMenuItem nuclSetting=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem protSetting=new JCheckBoxMenuItem();
   public GPCAPanel()
   {
     try
-- 
1.7.10.2