JAL-2795 simplified instance creation from calculation

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 58a28c0..bae4986 100644 (file)
--- 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.AptxInit;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -44,6 +46,7 @@ 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;
 
@@ -106,6 +109,11 @@ public class CalculationChooser extends JPanel
 
   List<String> tips = new ArrayList<>();
 
+  /*
+   * the most recently opened PCA results panel
+   */
+  private PCAPanel pcaPanel;
+
   /**
    * Constructor
    * 
@@ -457,6 +465,8 @@ public class CalculationChooser extends JPanel
 
   /**
    * Open and calculate the selected tree or PCA on 'OK'
+   * 
+   * @throws IOException
    */
   protected void calculate_actionPerformed()
   {
@@ -470,18 +480,46 @@ public class CalculationChooser extends JPanel
     }
     else
     {
+      try
+      {
+        createTree(substitutionMatrix, params);
+      } catch (IOException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
+
+
+
+
 
-      String treeAlgo = determineTreeAlgo();
-      TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
-              substitutionMatrix,
-              params);
 
-      openTreePanel(treeAlgo, substitutionMatrix, params);
     }
 
     // closeFrame();
   }
 
+  protected void createTree(String substitutionMatrix,
+          SimilarityParamsI params) throws IOException
+  {
+    String treeAlgo = determineTreeAlgo();
+    TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
+            substitutionMatrix, params);
+    TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
+
+    // AptxInit.createInstanceFromCalculation(calculatedTree);
+
+    TreeModel tree = new TreeModel(calculatedTree);
+    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);
+  }
+
+
   protected String determineTreeAlgo() // to be modified & expanded
   {
     String treeAlgorithm = neighbourJoining.isSelected()
@@ -510,9 +548,12 @@ 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 +561,7 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-
-
-    af.newTreePanel(treeType, substitutionMatrix, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**
@@ -553,7 +592,7 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -595,7 +634,6 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
-
     return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
             matchOnShortestLength);
   }
@@ -612,4 +650,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }