JAL-1632 refactored NJTree constructor to include SimilarityParams

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 0a33ea8..857e77c 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.NJTree;
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.bin.Cache;
@@ -160,7 +161,7 @@ public class TreePanel extends GTreePanel
                     .println("new alignment sequences vector value is null");
           }
 
-          tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
+          tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
           // rectangles and leafnodes
           repaint();
@@ -300,9 +301,8 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
-        sm = configureScoreModel(sm);
-        tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+        ScoreModelI sm = configureScoreModel(pwtype);
+        tree = new NJTree(av, type, sm, SimilarityParams.Jalview);
         showDistances(true);
       }
 
@@ -367,8 +367,8 @@ public class TreePanel extends GTreePanel
     NewickFile fout = new NewickFile(tree.getTopNode());
     try
     {
-      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-              tree.isHasRootDistance()));
+      cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
+              tree.hasRootDistance()));
       Desktop.addInternalFrame(cap, newTitle, 500, 100);
     } catch (OutOfMemoryError oom)
     {
@@ -406,8 +406,8 @@ public class TreePanel extends GTreePanel
       {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(
                 tree.getTopNode());
-        String output = fout.print(tree.isHasBootstrap(),
-                tree.isHasDistances(), tree.isHasRootDistance());
+        String output = fout.print(tree.hasBootstrap(),
+                tree.hasDistances(), tree.hasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
                 new java.io.FileWriter(choice));
         out.println(output);
@@ -883,14 +883,15 @@ public class TreePanel extends GTreePanel
   }
 
   /**
-   * If the score model is one that requires to get state data from the current
-   * view, allow it to do so
+   * 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(ScoreModelI sm)
+  protected ScoreModelI configureScoreModel(String modelName)
   {
+    ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
     if (sm instanceof ViewBasedAnalysisI)
     {
       try