Start of programmatically creating Aptx trees

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index de4fd37..bae1808 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -479,9 +479,10 @@ public class CalculationChooser extends JPanel
       TreeBuilder calculatedTree = treeCalculator
               .makeTree(af.getViewport());
       TreeModel tree = new TreeModel(calculatedTree);
-      openTreePanel(tree, treeAlgo, params);
+      openTreePanel(tree, treeAlgo, substitutionMatrix);
 
-      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder(
+              tree);
 
 
     }
@@ -522,7 +523,7 @@ public class CalculationChooser extends JPanel
    * @param treeAlgo
    */
   protected void openTreePanel(TreeModel tree, String treeAlgo,
-          SimilarityParamsI params)
+          String substitutionMatrix)
   {
     /*
      * gui validation shouldn't allow insufficient sequences here, but leave
@@ -530,7 +531,7 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-    af.newTreePanel(tree, treeAlgo, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**