X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=30a9b3d1a95c30907ce1e35892dd6abe7fb88c76;hb=91bea2a1185e438bfd52fc1848cf615068016192;hp=de4fd37e129568ad0ad52dfabd2c58a1487f1af7;hpb=db12baeea5789f5d7c6152f85e432255b460c08b;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index de4fd37..30a9b3d 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -28,7 +28,7 @@ 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.ext.archaeopteryx.AptxInit;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -108,6 +108,11 @@ public class CalculationChooser extends JPanel
 
   List<String> tips = new ArrayList<>();
 
+  /*
+   * the most recently opened PCA results panel
+   */
+  private PCAPanel pcaPanel;
+
   /**
    * Constructor
    * 
@@ -472,16 +477,11 @@ public class CalculationChooser extends JPanel
     }
     else
     {
+      createTree(substitutionMatrix, params);
+
+
 
-      String treeAlgo = determineTreeAlgo();
-      TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
-              substitutionMatrix, params);
-      TreeBuilder calculatedTree = treeCalculator
-              .makeTree(af.getViewport());
-      TreeModel tree = new TreeModel(calculatedTree);
-      openTreePanel(tree, treeAlgo, params);
 
-      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
 
 
     }
@@ -489,6 +489,21 @@ public class CalculationChooser extends JPanel
     // closeFrame();
   }
 
+  protected void createTree(String substitutionMatrix,
+          SimilarityParamsI params)
+  {
+    String treeAlgo = determineTreeAlgo();
+    TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
+            substitutionMatrix, params);
+    TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
+
+    AptxInit.createInstance(calculatedTree);
+
+    TreeModel tree = new TreeModel(calculatedTree);
+    openTreePanel(tree, treeAlgo, substitutionMatrix);
+  }
+
+
   protected String determineTreeAlgo() // to be modified & expanded
   {
     String treeAlgorithm = neighbourJoining.isSelected()
@@ -522,7 +537,7 @@ 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 +545,7 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-    af.newTreePanel(tree, treeAlgo, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**
@@ -561,7 +576,7 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -603,7 +618,6 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
-
     return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
             matchOnShortestLength);
   }
@@ -620,4 +634,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }