X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=ebb12b9c280fd26d2416713595b489a1a5677040;hb=22cc40b671171d958839a9455cba4e6cbe1bae1f;hp=bae1808c862c3e9ad34566a1832f8ded213629d1;hpb=833fafa77f2f63bea98ce1d6e1e4ee3e46e7bd53;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index bae1808..ebb12b9 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.ArchaeopteryxInit;
 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
    * 
@@ -478,11 +483,13 @@ public class CalculationChooser extends JPanel
               substitutionMatrix, params);
       TreeBuilder calculatedTree = treeCalculator
               .makeTree(af.getViewport());
+
+      ArchaeopteryxInit.createInstance(calculatedTree);
+
       TreeModel tree = new TreeModel(calculatedTree);
       openTreePanel(tree, treeAlgo, substitutionMatrix);
 
-      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder(
-              tree);
+
 
 
     }
@@ -490,6 +497,9 @@ public class CalculationChooser extends JPanel
     // closeFrame();
   }
 
+
+
+
   protected String determineTreeAlgo() // to be modified & expanded
   {
     String treeAlgorithm = neighbourJoining.isSelected()
@@ -562,7 +572,7 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -604,7 +614,6 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
-
     return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
             matchOnShortestLength);
   }
@@ -621,4 +630,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }