JAL-1503 update version in GPL header

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index 4266c32..d1216b9
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,32 +1,34 @@
 /*
- * 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 2.8.1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
 import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
 /**
@@ -108,7 +110,35 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     Thread worker = new Thread(this);
     worker.start();
   }
-
+  @Override
+  protected void scoreMatrix_menuSelected()
+  {
+    scoreMatrixMenu.removeAll();
+    for (final String sm:ResidueProperties.scoreMatrices.keySet())
+    {
+      JCheckBoxMenuItem jm=new JCheckBoxMenuItem();
+      jm.setText(MessageManager.getStringOrReturn("label.score_model", sm));
+      jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+      if (pcaModel.isNucleotide()==ResidueProperties.scoreMatrices.get(sm).isDNA())
+      {
+        final PCAPanel us = this;
+        jm.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            if (!pcaModel.getScore_matrix().equals((String) sm))
+            {
+              pcaModel.setScore_matrix((String) sm);
+              Thread worker = new Thread(us);
+              worker.start();
+            }
+          }
+        });
+        scoreMatrixMenu.add(jm);
+      }
+    }
+  }
   public void bgcolour_actionPerformed(ActionEvent e)
   {
     Color col = JColorChooser.showDialog(this, "Select Background Colour",
@@ -164,7 +194,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (getParent() == null)
     {
       addKeyListener(rc);
-      Desktop.addInternalFrame(this, "Principal component analysis", 475,
+      Desktop.addInternalFrame(this, MessageManager.getString("label.principal_component_analysis"), 475,
               450);
     }
   }
@@ -175,6 +205,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
+      pcaModel.setScore_matrix("DNA");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -188,6 +219,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
+      pcaModel.setScore_matrix("BLOSUM62");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -260,7 +292,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     try
     {
       cap.setText(pcaModel.getDetails());
-      Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+      Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("opening PCA details", oom);
@@ -334,7 +366,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
         // msaorder);
 
-        Desktop.addInternalFrame(af, "Original Data for " + this.title,
+        Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
                 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -445,6 +477,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
+  
   public void viewMenu_menuSelected()
   {
     buildAssociatedViewMenu();
@@ -523,7 +556,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.setText(pcaModel.getPointsasCsv(false,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
-      Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.points_for_params", new String[]{this.getTitle()}), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting PCA points", oom);
@@ -546,7 +579,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.setText(pcaModel.getPointsasCsv(true,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
-      Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.transformed_points_for_params", new String[]{this.getTitle()}),
               500, 500);
     } catch (OutOfMemoryError oom)
     {
@@ -625,7 +658,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
     if (handler.canCancel())
     {
-      JButton cancel = new JButton("Cancel");
+      JButton cancel = new JButton(MessageManager.getString("action.cancel"));
       final IProgressIndicator us = this;
       cancel.addActionListener(new ActionListener()
       {