JAL-1953 2.11.2 with Archeopteryx!

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index c43d59b..ae92168 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -47,6 +47,7 @@ import java.awt.event.FocusListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -512,6 +513,8 @@ public class CalculationChooser extends JPanel
 
   /**
    * Open and calculate the selected tree or PCA on 'OK'
+   * 
+   * @throws IOException
    */
   protected void calculate_actionPerformed()
   {
@@ -525,7 +528,14 @@ public class CalculationChooser extends JPanel
     }
     else
     {
-      createTree(substitutionMatrix, params);
+      try
+      {
+        createTree(substitutionMatrix, params);
+      } catch (IOException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
 
 
 
@@ -538,17 +548,23 @@ public class CalculationChooser extends JPanel
   }
 
   protected void createTree(String substitutionMatrix,
-          SimilarityParamsI params)
+          SimilarityParamsI params) throws IOException
   {
     String treeAlgo = determineTreeAlgo();
     TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
             substitutionMatrix, params);
     TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
 
-    AptxInit.createInstance(calculatedTree);
+    // AptxInit.createInstanceFromCalculation(calculatedTree);
 
     TreeModel tree = new TreeModel(calculatedTree);
-    openTreePanel(tree, treeAlgo, substitutionMatrix);
+    jalview.io.NewickFile newick = new jalview.io.NewickFile(
+            tree.getTopNode());
+    String output = newick.print(tree.hasBootstrap(), tree.hasDistances(),
+            tree.hasRootDistance());
+    AptxInit.createInstanceFromNhx(af.getTitle(), output, 
+            af.getViewport());
+    // openTreePanel(tree, treeAlgo, substitutionMatrix);
   }