X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=bd6c5ee5e011780b4dbda61ce9b3e91d35189a42;hb=53b99b41ed7f26f2724f3ed87d524eb83c5208f4;hp=f2d65e54f1e54bdcffa6d9730f303f7eaf157e22;hpb=90ae01c1c1504e0ae42817f78116f1d35b317c47;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f2d65e5..bd6c5ee 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -460,26 +460,26 @@ public class CalculationChooser extends JPanel
   protected void calculate_actionPerformed()
   {
     boolean doPCA = pca.isSelected();
-    String modelName = modelNames.getSelectedItem().toString();
+    String substitutionMatrix = modelNames.getSelectedItem().toString();
     SimilarityParamsI params = getSimilarityParameters(doPCA);
 
     if (doPCA)
     {
-      openPcaPanel(modelName, params);
+      openPcaPanel(substitutionMatrix, params);
     }
     else
     {
-      calculateTree();
-      openTreePanel(modelName, params);
+
+      String treeAlgo = determineTreeAlgo();
+      // TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
+      // substitutionMatrix, params);
+
+      openTreePanel(treeAlgo, substitutionMatrix, params);
     }
 
     // closeFrame();
   }
 
-  protected void calculateTree()
-  {
-
-  }
   protected String determineTreeAlgo() // to be modified & expanded
   {
     String treeAlgorithm = neighbourJoining.isSelected()
@@ -509,7 +509,8 @@ public class CalculationChooser extends JPanel
    * Open a new Tree panel on the desktop
    * 
    */
-  protected void openTreePanel(String modelName, SimilarityParamsI params)
+  protected void openTreePanel(String treeType, String substitutionMatrix,
+          SimilarityParamsI params)
   {
     /*
      * gui validation shouldn't allow insufficient sequences here, but leave
@@ -517,9 +518,9 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-    String treeType = determineTreeAlgo();
 
-    af.newTreePanel(treeType, modelName, params);
+
+    af.newTreePanel(treeType, substitutionMatrix, params);
   }
 
   /**