JAL-1473 show available score matrices for use in PCA calculation

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 5c8d08b..fc32e54 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -19,14 +19,16 @@
 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.schemes.ScoreMatrix;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
@@ -109,7 +111,32 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     Thread worker = new Thread(this);
     worker.start();
   }
-
+  @Override
+  protected void scoreMatrix_menuSelected()
+  {
+    scoreMatrixMenu.removeAll();
+    for (final Object sm:ResidueProperties.scoreMatrices.keySet())
+    {
+      JMenuItem jm=new JMenuItem();
+      jm.setText((String)sm);
+      jm.setSelected(pcaModel.getScore_matrix().equals((String)sm));
+      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",
@@ -446,6 +473,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
+  
   public void viewMenu_menuSelected()
   {
     buildAssociatedViewMenu();