X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=ebb12b9c280fd26d2416713595b489a1a5677040;hb=22cc40b671171d958839a9455cba4e6cbe1bae1f;hp=58a28c0843ec9bb57da5452be95864e06ea36676;hpb=0e50368033402ab4eb49fb7473fbb232d7b6091b;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 58a28c0..ebb12b9 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -22,11 +22,13 @@ 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.ArchaeopteryxInit;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -106,6 +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 +479,27 @@ 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());
+
+      ArchaeopteryxInit.createInstance(calculatedTree);
+
+      TreeModel tree = new TreeModel(calculatedTree);
+      openTreePanel(tree, treeAlgo, substitutionMatrix);
+
+
+
 
-      openTreePanel(treeAlgo, substitutionMatrix, params);
     }
 
     // closeFrame();
   }
 
+
+
+
   protected String determineTreeAlgo() // to be modified & expanded
   {
     String treeAlgorithm = neighbourJoining.isSelected()
@@ -510,9 +528,12 @@ 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
@@ -520,9 +541,7 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-
-
-    af.newTreePanel(treeType, substitutionMatrix, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**
@@ -553,7 +572,7 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -595,7 +614,6 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
-
     return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
             matchOnShortestLength);
   }
@@ -612,4 +630,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }