X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=905a54ad815c372e84c1847a37aaa207b2be79cb;hb=933794f42ed55d57850424e3459a54cd2d92c933;hp=9ac67731216f74c53b7e8fcd42884ab98b1d5478;hpb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 9ac6773..905a54a 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -20,12 +20,16 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AverageDistanceTree;
 import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
 import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.DistanceModelI;
+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.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
@@ -58,13 +62,13 @@ 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;
   }
@@ -160,7 +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
@@ -171,8 +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)
@@ -206,58 +210,16 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     {
       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());
-        }
-        DistanceModelI sm = ScoreModels.getInstance().forName(pwtype);
-        if (sm instanceof ViewBasedAnalysisI)
-        {
-          try
-          {
-            sm = sm.getClass().newInstance();
-            ((ViewBasedAnalysisI) sm)
-                    .configureFromAlignmentView(treeCanvas.ap);
-          } catch (Exception q)
-          {
-            System.err.println("Couldn't create a scoremodel instance for "
-                    + sm.getName());
-            q.printStackTrace();
-          }
-          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
-        }
-        else
-        {
-          tree = new NJTree(seqs, seqStrings, type, pwtype, null, 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());
@@ -425,4 +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;
+  }
+
 }