X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=f07993ca7130c3f41250c5f4eb15e3b2af1144a1;hb=9f822a04881b453114c051b47e133ac43af23c65;hp=38fd74d3c0a5aa45da52e369870f7713ba645e2c;hpb=c460f6a6a2040f07ea8296af95107a8b3a3b6de2;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 38fd74d..f07993c 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * 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;
@@ -28,7 +30,6 @@ import javax.swing.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
@@ -111,35 +112,45 @@ 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())
+    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())
+      if (ResidueProperties.getScoreMatrix(sm) != null)
       {
-        final PCAPanel us = this;
-        jm.addActionListener(new ActionListener()
+        // 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())
         {
-          @Override
-          public void actionPerformed(ActionEvent e)
+          final PCAPanel us = this;
+          jm.addActionListener(new ActionListener()
           {
-            if (!pcaModel.getScore_matrix().equals((String) sm))
+            @Override
+            public void actionPerformed(ActionEvent e)
             {
-              pcaModel.setScore_matrix((String) sm);
-              Thread worker = new Thread(us);
-              worker.start();
+              if (!pcaModel.getScore_matrix().equals((String) sm))
+              {
+                pcaModel.setScore_matrix((String) sm);
+                Thread worker = new Thread(us);
+                worker.start();
+              }
             }
-          }
-        });
-        scoreMatrixMenu.add(jm);
+          });
+          scoreMatrixMenu.add(jm);
+        }
       }
     }
   }
+
   public void bgcolour_actionPerformed(ActionEvent e)
   {
     Color col = JColorChooser.showDialog(this, "Select Background Colour",
@@ -195,8 +206,8 @@ 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);
     }
   }
 
@@ -206,6 +217,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
+      pcaModel.setScore_matrix("DNA");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -219,6 +231,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
+      pcaModel.setScore_matrix("BLOSUM62");
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -291,7 +304,8 @@ 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);
@@ -365,8 +379,10 @@ 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);
       }
     }
     /*
@@ -476,7 +492,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
-  
   public void viewMenu_menuSelected()
   {
     buildAssociatedViewMenu();
@@ -555,7 +570,9 @@ 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);
@@ -578,8 +595,9 @@ 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);
@@ -657,7 +675,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     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()
       {