JAL-1013 - toy menu to switch between nucleotide and blosum 62 modes of calculation...

[jalview.git] / src / jalview / jbgui / GPCAPanel.java

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 6ad36e8..10f22bd 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,25 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
@@ -57,6 +57,10 @@ public class GPCAPanel extends JInternalFrame
 
   JMenuItem outputValues = new JMenuItem();
 
+  JMenuItem outputPoints = new JMenuItem();
+
+  JMenuItem outputProjPoints = new JMenuItem();
+
   protected JMenu viewMenu = new JMenu();
 
   protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
@@ -67,6 +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
@@ -149,6 +156,22 @@ public class GPCAPanel extends JInternalFrame
         outputValues_actionPerformed(e);
       }
     });
+    outputPoints.setText("Output points...");
+    outputPoints.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outputPoints_actionPerformed(e);
+      }
+    });
+    outputProjPoints.setText("Output transformed points...");
+    outputProjPoints.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outputProjPoints_actionPerformed(e);
+      }
+    });
     print.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -198,6 +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);
@@ -207,10 +254,13 @@ 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);
     fileMenu.add(originalSeqData);
+    fileMenu.add(outputPoints);
+    fileMenu.add(outputProjPoints);
     saveMenu.add(eps);
     saveMenu.add(png);
     viewMenu.add(showLabels);
@@ -218,6 +268,30 @@ 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
+
+  }
+
+  protected void outputProjPoints_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   protected void xCombobox_actionPerformed(ActionEvent e)
   {
   }