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 bd6c5ee..bae1808 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -21,11 +21,14 @@
 package jalview.gui;
 
 import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeCalculator;
+import jalview.analysis.TreeModel;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.SequenceGroup;
+import jalview.ext.archaeopteryx.ArchaeopteryxTreeBuilder;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -471,10 +474,17 @@ public class CalculationChooser extends JPanel
     {
 
       String treeAlgo = determineTreeAlgo();
-      // TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
-      // substitutionMatrix, params);
+      TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
+              substitutionMatrix, params);
+      TreeBuilder calculatedTree = treeCalculator
+              .makeTree(af.getViewport());
+      TreeModel tree = new TreeModel(calculatedTree);
+      openTreePanel(tree, treeAlgo, substitutionMatrix);
+
+      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder(
+              tree);
+
 
-      openTreePanel(treeAlgo, substitutionMatrix, params);
     }
 
     // closeFrame();
@@ -508,9 +518,12 @@ public class CalculationChooser extends JPanel
   /**
    * Open a new Tree panel on the desktop
    * 
+   * @param tree
+   * @param params
+   * @param treeAlgo
    */
-  protected void openTreePanel(String treeType, String substitutionMatrix,
-          SimilarityParamsI params)
+  protected void openTreePanel(TreeModel tree, String treeAlgo,
+          String substitutionMatrix)
   {
     /*
      * gui validation shouldn't allow insufficient sequences here, but leave
@@ -518,9 +531,7 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-
-
-    af.newTreePanel(treeType, substitutionMatrix, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**