X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=3483cc4500c0b359ae3d73f492146d21677d6c08;hb=76139ef711627a3176736af47272ff55be62e720;hp=5c8d08b7ae048452be9afd3110d1757e95b434f8;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 5c8d08b..3483cc4 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,32 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * 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.gui;
 
 import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
+
 import javax.swing.*;
 
 import jalview.datamodel.*;
 import jalview.jbgui.*;
+import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
@@ -94,10 +97,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       JOptionPane
               .showMessageDialog(
                       Desktop.desktop,
-                      "The sequences must be aligned before calculating PCA.\n"
-                              + "Try using the Pad function in the edit menu,\n"
-                              + "or one of the multiple sequence alignment web services.",
-                      "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+                      MessageManager.getString("label.pca_sequences_not_aligned"),
+                      MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -110,9 +111,47 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     worker.start();
   }
 
+  @Override
+  protected void scoreMatrix_menuSelected()
+  {
+    scoreMatrixMenu.removeAll();
+    for (final String sm : ResidueProperties.scoreMatrices.keySet())
+    {
+      if (ResidueProperties.getScoreMatrix(sm) != null)
+      {
+        // create an entry for this score matrix for use in PCA
+        JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+        jm.setText(MessageManager
+                .getStringOrReturn("label.score_model", sm));
+        jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+        if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+                .get(sm).isProtein())
+                || 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",
+    Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
             rc.bgColour);
 
     if (col != null)
@@ -129,11 +168,11 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   {
     long progId = System.currentTimeMillis();
     IProgressIndicator progress = this;
-    String message = "Recalculating PCA";
+    String message = MessageManager.getString("label.pca_recalculating");
     if (getParent() == null)
     {
       progress = ap.alignFrame;
-      message = "Calculating PCA";
+      message = MessageManager.getString("label.pca_calculating");
     }
     progress.setProgressBar(message, progId);
     try
@@ -165,8 +204,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (getParent() == null)
     {
       addKeyListener(rc);
-      Desktop.addInternalFrame(this, MessageManager.getString("label.principal_component_analysis"), 475,
-              450);
+      Desktop.addInternalFrame(this, MessageManager
+              .getString("label.principal_component_analysis"), 475, 450);
     }
   }
 
@@ -176,6 +215,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
+      pcaModel.setScore_matrix("DNA");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -189,6 +229,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
+      pcaModel.setScore_matrix("BLOSUM62");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -261,7 +302,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     try
     {
       cap.setText(pcaModel.getDetails());
-      Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500);
+      Desktop.addInternalFrame(cap,
+              MessageManager.getString("label.pca_details"), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("opening PCA details", oom);
@@ -335,8 +377,10 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
         // msaorder);
 
-        Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
-                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+        Desktop.addInternalFrame(af, MessageManager.formatMessage(
+                "label.original_data_for_params", new String[]
+                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
       }
     }
     /*
@@ -524,7 +568,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.setText(pcaModel.getPointsasCsv(false,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
-      Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.points_for_params", new String[]{this.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);
@@ -547,8 +593,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.setText(pcaModel.getPointsasCsv(true,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
-      Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.transformed_points_for_params", new String[]{this.getTitle()}),
-              500, 500);
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+              "label.transformed_points_for_params", new String[]
+              { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting transformed PCA points", oom);
@@ -619,14 +666,14 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   {
     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
     {
-      throw new Error(
-              "call setProgressBar before registering the progress bar's handler.");
+      throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
     }
     progressBarHandlers.put(new Long(id), handler);
     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
     if (handler.canCancel())
     {
-      JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+      JButton cancel = new JButton(
+              MessageManager.getString("action.cancel"));
       final IProgressIndicator us = this;
       cancel.addActionListener(new ActionListener()
       {
@@ -635,10 +682,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
-          us.setProgressBar(
-                  "Cancelled "
-                          + ((JLabel) progressPanel.getComponent(0))
-                                  .getText(), id);
+          us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);