From d3ad666c751eead380676d1c6bf08f7e66f70628 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 13 Dec 2011 12:35:17 +0000
Subject: [PATCH] JAL-1013 - toy menu to switch between nucleotide and blosum
 62 modes of calculation - extend to full matrix parameter
 config menu

---
 src/jalview/gui/PCAPanel.java    |   18 +++++++++++++++--
 src/jalview/jbgui/GPCAPanel.java |   40 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 56 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 4948c22..eec9b6d 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -135,6 +135,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
   {
     try
     {
+      calcSettings.setEnabled(false);
       pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
       pca.run();
 
@@ -182,9 +183,22 @@ public class PCAPanel extends GPCAPanel implements Runnable
       new OOMWarning("calculating PCA", er);
 
     }
-
+    calcSettings.setEnabled(true);
+  }
+  @Override
+  protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+  {
+    useidentity=true;
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+  @Override
+  protected void protSetting_actionPerfomed(ActionEvent arg0)
+  {
+    useidentity=false;
+    Thread worker = new Thread(this);
+    worker.start();
   }
-
   /**
    * DOCUMENT ME!
    */
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 843a4ec..10f22bd 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -71,6 +71,9 @@ public class GPCAPanel extends JInternalFrame
 
   protected JMenu associateViewsMenu = new JMenu();
 
+  protected JMenu calcSettings=new JMenu();
+  JMenuItem nuclSetting=new JMenuItem();
+  JMenuItem protSetting=new JMenuItem();
   public GPCAPanel()
   {
     try
@@ -218,6 +221,30 @@ public class GPCAPanel extends JInternalFrame
       }
     });
     associateViewsMenu.setText("Associate Nodes With");
+    calcSettings.setText("Change Parameters");
+    nuclSetting.setText("Nucleotide matrix");
+    protSetting.setText("Protein matrix");
+    nuclSetting.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        nuclSetting_actionPerfomed(arg0);
+      }
+    });
+    protSetting.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        protSetting_actionPerfomed(arg0);
+      }
+    });calcSettings.add(nuclSetting);
+    calcSettings.add(protSetting);
+    
+    
     this.getContentPane().add(jPanel2, BorderLayout.SOUTH);
     jPanel2.add(jLabel1, null);
     jPanel2.add(xCombobox, null);
@@ -227,6 +254,7 @@ public class GPCAPanel extends JInternalFrame
     jPanel2.add(zCombobox, null);
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(viewMenu);
+    jMenuBar1.add(calcSettings);
     fileMenu.add(saveMenu);
     fileMenu.add(outputValues);
     fileMenu.add(print);
@@ -240,6 +268,18 @@ public class GPCAPanel extends JInternalFrame
     viewMenu.add(associateViewsMenu);
   }
 
+  protected void protSetting_actionPerfomed(ActionEvent arg0)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void outputPoints_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-- 
1.7.10.2