X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=905a54ad815c372e84c1847a37aaa207b2be79cb;hb=933794f42ed55d57850424e3459a54cd2d92c933;hp=f50c1e8285c7ff9122772b5b06a219f1ade8a0c4;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index f50c1e8..905a54a 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/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.
  * 
@@ -20,14 +20,33 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.analysis.AverageDistanceTree;
+import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.NewickFile;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.ScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
 public class TreePanel extends EmbmenuFrame implements ActionListener,
         ItemListener
 {
@@ -43,17 +62,18 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   TreeCanvas treeCanvas;
 
-  NJTree tree;
+  TreeModel tree;
 
   AlignmentPanel ap;
 
   AlignViewport av;
 
-  public NJTree getTree()
+  public TreeModel getTree()
   {
     return tree;
   }
 
+  @Override
   public void finalize() throws Throwable
   {
     ap = null;
@@ -144,7 +164,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
-    if (tree.seqData != null)
+    if (tree.getOriginalData() != null)
     {
       char gc = '-';
       try
@@ -155,8 +175,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       } catch (Exception ex)
       {
       }
-      ;
-      Object[] alAndColsel = tree.seqData
+
+      Object[] alAndColsel = tree.getOriginalData()
               .getAlignmentAndColumnSelection(gc);
 
       if (alAndColsel != null && alAndColsel[0] != null)
@@ -185,43 +205,21 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       this.newtree = newtree;
     }
 
+    @Override
     public void run()
     {
       if (newtree != null)
       {
-        if (odata == null)
-        {
-          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
-        }
-        else
-        {
-          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
-                  newtree);
-        }
-
+        tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+                newtree);
       }
       else
       {
-        int start, end;
-        SequenceI[] seqs;
-        boolean selview = (av.getSelectionGroup() != null)
-                && (av.getSelectionGroup().getSize() > 1);
-        AlignmentView seqStrings = av.getAlignmentView(selview);
-        if (!selview)
-        {
-          start = 0;
-          end = av.getAlignment().getWidth();
-          seqs = av.getAlignment().getSequencesArray();
-        }
-        else
-        {
-          start = av.getSelectionGroup().getStartRes();
-          end = av.getSelectionGroup().getEndRes() + 1;
-          seqs = av.getSelectionGroup().getSequencesInOrder(
-                  av.getAlignment());
-        }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = configureScoreModel(pwtype);
+        TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+                av, sm, SimilarityParams.Jalview)
+                : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
+        tree = new TreeModel(njtree);
       }
 
       tree.reCount(tree.getTopNode());
@@ -252,6 +250,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == newickOutput)
@@ -268,6 +267,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == fitToWindow)
@@ -358,11 +358,13 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     jMenu2.setLabel(MessageManager.getString("action.view"));
     fontSize.setLabel(MessageManager.getString("action.font"));
     fontSize.addActionListener(this);
-    bootstrapMenu.setLabel(MessageManager.getString("label.show_bootstrap_values"));
+    bootstrapMenu.setLabel(MessageManager
+            .getString("label.show_bootstrap_values"));
     bootstrapMenu.addItemListener(this);
     distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
     distanceMenu.addItemListener(this);
-    placeholdersMenu.setLabel(MessageManager.getString("label.mark_unassociated_leaves"));
+    placeholdersMenu.setLabel(MessageManager
+            .getString("label.mark_unassociated_leaves"));
     placeholdersMenu.addItemListener(this);
     fitToWindow.setState(true);
     fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
@@ -385,4 +387,29 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     inputData.addActionListener(this);
   }
 
+  /**
+   * Gets the score model for the given name. If the score model is one that
+   * requires to get state data from the current view, allow it to do so
+   * 
+   * @param sm
+   * @return
+   */
+  protected ScoreModelI configureScoreModel(String modelName)
+  {
+    ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
+    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());
+      }
+    }
+    return sm;
+  }
+
 }