Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index a41a998..c43d59b 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -21,12 +21,15 @@
 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.bin.Cache;
 import jalview.datamodel.SequenceGroup;
+import jalview.ext.archaeopteryx.AptxInit;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -156,12 +159,15 @@ public class CalculationChooser extends JPanel
     pca = new JRadioButton(
             MessageManager.getString("label.principal_component_analysis"));
     pca.setOpaque(false);
+
     neighbourJoining = new JRadioButton(
             MessageManager.getString("label.tree_calc_nj"));
     neighbourJoining.setSelected(true);
+    neighbourJoining.setOpaque(false);
+
     averageDistance = new JRadioButton(
             MessageManager.getString("label.tree_calc_av"));
-    neighbourJoining.setOpaque(false);
+    averageDistance.setOpaque(false);
 
     JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     calcChoicePanel.setOpaque(false);
@@ -271,9 +277,9 @@ public class CalculationChooser extends JPanel
 
     setMinimumSize(new Dimension(325, height - 10));
     String title = MessageManager.getString("label.choose_calculation");
-    if (af.getViewport().viewName != null)
+    if (af.getViewport().getViewName() != null)
     {
-      title = title + " (" + af.getViewport().viewName + ")";
+      title = title + " (" + af.getViewport().getViewName() + ")";
     }
 
     Desktop.addInternalFrame(frame, title, width, height, false);
@@ -291,6 +297,7 @@ public class CalculationChooser extends JPanel
       };
     });
 
+    validateCalcTypes();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
@@ -420,7 +427,6 @@ public class CalculationChooser extends JPanel
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
     DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
-
     /*
      * select the score models applicable to the alignment type
      */
@@ -510,34 +516,54 @@ 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);
+      createTree(substitutionMatrix, params);
+
+
+
+
+
+
     }
 
     // closeFrame();
   }
 
-  /**
-   * Open a new Tree panel on the desktop
-   * 
-   * @param modelName
-   * @param params
-   */
-  protected void openTreePanel(String modelName, SimilarityParamsI params)
+  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()
+            ? 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)
     {
@@ -549,11 +575,25 @@ 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);
   }
 
   /**