X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPCAPanel.java;h=d63fd5427ada766662bfa8f225b80b08398a81e0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=f2b8fe3b556fd5bc777d0739de56ad228567d1eb;hpb=f8039f1970f67a753809f451756cb1baa0e05d8d;p=jalview.git

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index f2b8fe3..d63fd54 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 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.jbgui;
@@ -54,6 +56,8 @@ public class GPCAPanel extends JInternalFrame
 
   JMenu saveMenu = new JMenu();
 
+  protected JMenu scoreMatrixMenu = new JMenu();
+
   JMenuItem eps = new JMenuItem();
 
   JMenuItem png = new JMenuItem();
@@ -190,7 +194,8 @@ public class GPCAPanel extends JInternalFrame
         outputPoints_actionPerformed(e);
       }
     });
-    outputProjPoints.setText(MessageManager.getString("label.output_transformed_points") + "...");
+    outputProjPoints.setText(MessageManager
+            .getString("label.output_transformed_points") + "...");
     outputProjPoints.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -221,6 +226,23 @@ public class GPCAPanel extends JInternalFrame
       {
       }
     });
+    scoreMatrixMenu.setText(MessageManager
+            .getString("label.select_score_model"));
+    scoreMatrixMenu.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        scoreMatrix_menuSelected();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
     showLabels.setText(MessageManager.getString("label.show_labels"));
     showLabels.addActionListener(new ActionListener()
     {
@@ -230,7 +252,8 @@ public class GPCAPanel extends JInternalFrame
       }
     });
     print.setText(MessageManager.getString("action.print"));
-    bgcolour.setText(MessageManager.getString("label.background_colour") + "...");
+    bgcolour.setText(MessageManager.getString("label.background_colour")
+            + "...");
     bgcolour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -246,9 +269,11 @@ public class GPCAPanel extends JInternalFrame
         originalSeqData_actionPerformed(e);
       }
     });
-    associateViewsMenu.setText(MessageManager.getString("label.associate_nodes_with"));
+    associateViewsMenu.setText(MessageManager
+            .getString("label.associate_nodes_with"));
     calcSettings.setText(MessageManager.getString("action.change_params"));
-    nuclSetting.setText(MessageManager.getString("label.nucleotide_matrix"));
+    nuclSetting
+            .setText(MessageManager.getString("label.nucleotide_matrix"));
     protSetting.setText(MessageManager.getString("label.protein_matrix"));
     nuclSetting.addActionListener(new ActionListener()
     {
@@ -268,7 +293,8 @@ public class GPCAPanel extends JInternalFrame
         protSetting_actionPerfomed(arg0);
       }
     });
-    jvVersionSetting.setText(MessageManager.getString("label.jalview_pca_calculation"));
+    jvVersionSetting.setText(MessageManager
+            .getString("label.jalview_pca_calculation"));
     jvVersionSetting.addActionListener(new ActionListener()
     {
       @Override
@@ -280,6 +306,7 @@ public class GPCAPanel extends JInternalFrame
     calcSettings.add(jvVersionSetting);
     calcSettings.add(nuclSetting);
     calcSettings.add(protSetting);
+    calcSettings.add(scoreMatrixMenu);
     statusPanel.setLayout(statusPanelLayout);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 12));
     // statusPanel.setBackground(Color.lightGray);
@@ -312,6 +339,12 @@ public class GPCAPanel extends JInternalFrame
     viewMenu.add(associateViewsMenu);
   }
 
+  protected void scoreMatrix_menuSelected()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   protected void resetButton_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub