X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=fe96eaae318df0caae4ac53b1942afe6ea9b3999;hb=062ebc02980364930ceb26dd6c06448af971fe20;hp=a9f396634a63e9746e8ce405380ada7ec38b087e;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index a9f3966..fe96eaa 100644
--- 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.ArchaeopteryxInit;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -103,7 +106,12 @@ public class CalculationChooser extends JPanel
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 
-  List<String> tips = new ArrayList<String>();
+  List<String> tips = new ArrayList<>();
+
+  /*
+   * the most recently opened PCA results panel
+   */
+  private PCAPanel pcaPanel;
 
   /**
    * Constructor
@@ -370,7 +378,7 @@ public class CalculationChooser extends JPanel
    */
   protected JComboBox<String> buildModelOptionsList()
   {
-    final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+    final JComboBox<String> scoreModelsCombo = new JComboBox<>();
     scoreModelsCombo.setRenderer(renderer);
 
     /*
@@ -413,7 +421,7 @@ public class CalculationChooser extends JPanel
   {
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
-    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
 
     /*
      * now we can actually add entries to the combobox,
@@ -460,34 +468,48 @@ public class CalculationChooser extends JPanel
   protected void calculate_actionPerformed()
   {
     boolean doPCA = pca.isSelected();
-    String modelName = modelNames.getSelectedItem().toString();
+    String substitutionMatrix = modelNames.getSelectedItem().toString();
     SimilarityParamsI params = getSimilarityParameters(doPCA);
 
     if (doPCA)
     {
-      openPcaPanel(modelName, params);
+      openPcaPanel(substitutionMatrix, params);
     }
     else
     {
-      openTreePanel(modelName, 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, substitutionMatrix);
+      ArchaeopteryxInit.createInstance(calculatedTree);
+
+
+
     }
 
     // closeFrame();
   }
 
-  /**
-   * Open a new Tree panel on the desktop
-   * 
-   * @param modelName
-   * @param params
-   */
-  protected void openTreePanel(String modelName, SimilarityParamsI params)
+
+
+
+  protected String determineTreeAlgo() // to be modified & expanded
+  {
+    String treeAlgorithm = neighbourJoining.isSelected()
+            ? TreeBuilder.NEIGHBOUR_JOINING
+            : TreeBuilder.AVERAGE_DISTANCE;
+
+    return treeAlgorithm;
+
+  }
+
+  protected void checkEnoughSequences(AlignViewport viewport)
   {
-    /*
-     * gui validation shouldn't allow insufficient sequences here, but leave
-     * this check in in case this method gets exposed programmatically in future
-     */
-    AlignViewport viewport = af.getViewport();
     SequenceGroup sg = viewport.getSelectionGroup();
     if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
     {
@@ -499,11 +521,25 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
+  }
 
-    String treeType = neighbourJoining.isSelected()
-            ? TreeBuilder.NEIGHBOUR_JOINING
-            : TreeBuilder.AVERAGE_DISTANCE;
-    af.newTreePanel(treeType, modelName, params);
+  /**
+   * Open a new Tree panel on the desktop
+   * 
+   * @param tree
+   * @param params
+   * @param treeAlgo
+   */
+  protected void openTreePanel(TreeModel tree, String treeAlgo,
+          String substitutionMatrix)
+  {
+    /*
+     * gui validation shouldn't allow insufficient sequences here, but leave
+     * this check in in case this method gets exposed programmatically in future
+     */
+    checkEnoughSequences(af.getViewport());
+
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**
@@ -534,7 +570,7 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -576,6 +612,7 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
+
     return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
             matchOnShortestLength);
   }
@@ -592,4 +629,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }