X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=7177e43bfed2c9a5ab4540478f977478dab615e3;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=5ce8e3612dae0b8f50ebdaae7104aa7f76a6cff1;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5ce8e36..7177e43 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,26 +20,47 @@
  */
 package jalview.gui;
 
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-import java.util.List;
-
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import org.jibble.epsgraphics.*;
-import jalview.analysis.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.NewickFile;
+import jalview.jbgui.GTreePanel;
+import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+
+import org.jibble.epsgraphics.EpsGraphics2D;
 
 /**
  * DOCUMENT ME!
@@ -118,7 +139,7 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av.getAlignment();
   }
 
-  public AlignViewport getViewPort()
+  public AlignmentViewport getViewPort()
   {
     return treeCanvas.av;
   }
@@ -222,7 +243,8 @@ public class TreePanel extends GTreePanel
       associateLeavesMenu.add(item);
     }
 
-    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+            "label.all_views");
     buttonGroup.add(itemf);
     itemf.setSelected(treeCanvas.applyToAllViews);
     itemf.addActionListener(new ActionListener()
@@ -293,8 +315,26 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        if (sm instanceof ViewBasedAnalysisI)
+        {
+          try
+          {
+            sm = sm.getClass().newInstance();
+            ((ViewBasedAnalysisI) sm)
+                    .configureFromAlignmentView(treeCanvas.ap);
+          } catch (Exception q)
+          {
+            Cache.log.error("Couldn't create a scoremodel instance for "
+                    + sm.getName());
+          }
+          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+        }
+        else
+        {
+          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+                  end);
+        }
         showDistances(true);
       }
 
@@ -305,7 +345,7 @@ public class TreePanel extends GTreePanel
       av.setCurrentTree(tree);
       if (av.getSortByTree())
       {
-        sortByTree_actionPerformed(null);
+        sortByTree_actionPerformed();
       }
     }
   }
@@ -399,7 +439,7 @@ public class TreePanel extends GTreePanel
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save tree as newick file");
+    chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
@@ -492,8 +532,10 @@ public class TreePanel extends GTreePanel
         // 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 Object[]
+                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
       }
     }
   }
@@ -515,7 +557,8 @@ public class TreePanel extends GTreePanel
    * 
    * @param e
    */
-  public void sortByTree_actionPerformed(ActionEvent e)
+  @Override
+  public void sortByTree_actionPerformed()
   {
 
     if (treeCanvas.applyToAllViews)
@@ -577,7 +620,7 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
-    AlignViewport av = ap.av;
+    AlignmentViewport av = ap.av;
     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(av.getAlignment(), tree);
     CommandI undo;
@@ -693,7 +736,7 @@ public class TreePanel extends GTreePanel
               { "eps" }, new String[]
               { "Encapsulated Postscript" }, "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from tree");
+      chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -740,7 +783,7 @@ public class TreePanel extends GTreePanel
               { "Portable network graphics" }, "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create PNG image from tree");
+      chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);