X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=d0315a60d1330916cf806d8e9e01791f52ebed04;hb=6a144c3b2b7f5f04d908c065a017088453bb7fc7;hp=8a95594f133d5d431acd9c0b7485783a25704a7f;hpb=968e71fa2914ce20dd8caca18dd7d4651b636af5;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 8a95594..d0315a6 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.ArchaeopteryxTreeBuilder;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -103,7 +106,7 @@ public class CalculationChooser extends JPanel
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 
-  List<String> tips = new ArrayList<String>();
+  List<String> tips = new ArrayList<>();
 
   /**
    * Constructor
@@ -164,14 +167,14 @@ public class CalculationChooser extends JPanel
     JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     treePanel.setOpaque(false);
 
-    treePanel.setBorder(BorderFactory.createTitledBorder(MessageManager
-            .getString("label.tree")));
+    treePanel.setBorder(BorderFactory
+            .createTitledBorder(MessageManager.getString("label.tree")));
 
     // then copy the inset dimensions for the border-less PCA panel
     JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));
     Insets b = treePanel.getBorder().getBorderInsets(treePanel);
-    pcaBorderless.setBorder(BorderFactory.createEmptyBorder(2, b.left, 2,
-            b.right));
+    pcaBorderless.setBorder(
+            BorderFactory.createEmptyBorder(2, b.left, 2, b.right));
     pcaBorderless.setOpaque(false);
 
     pcaBorderless.add(pca, FlowLayout.LEFT);
@@ -186,7 +189,7 @@ public class CalculationChooser extends JPanel
     calcTypes.add(pca);
     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);
-    
+
     ActionListener calcChanged = new ActionListener()
     {
       @Override
@@ -335,8 +338,8 @@ public class CalculationChooser extends JPanel
    */
   private boolean checkEnabled(JRadioButton calc, int size, int minsize)
   {
-    String ttip = MessageManager.formatMessage(
-            "label.you_need_at_least_n_sequences", minsize);
+    String ttip = MessageManager
+            .formatMessage("label.you_need_at_least_n_sequences", minsize);
 
     calc.setEnabled(size >= minsize);
     if (!calc.isEnabled())
@@ -370,7 +373,7 @@ 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);
 
     /*
@@ -383,7 +386,8 @@ public class CalculationChooser extends JPanel
       @Override
       public void mouseEntered(MouseEvent e)
       {
-        scoreModelsCombo.setToolTipText(tips.get(scoreModelsCombo.getSelectedIndex()));
+        scoreModelsCombo.setToolTipText(
+                tips.get(scoreModelsCombo.getSelectedIndex()));
       }
 
       @Override
@@ -412,7 +416,7 @@ 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,
@@ -459,52 +463,74 @@ 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);
+
+      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+
+
     }
 
     // closeFrame();
   }
 
+  protected String determineTreeAlgo() // to be modified & expanded
+  {
+    String treeAlgorithm = neighbourJoining.isSelected()
+            ? TreeBuilder.NEIGHBOUR_JOINING
+            : TreeBuilder.AVERAGE_DISTANCE;
+
+    return treeAlgorithm;
+
+  }
+
+  protected void checkEnoughSequences(AlignViewport viewport)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
+    {
+      JvOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.formatMessage(
+                      "label.you_need_at_least_n_sequences",
+                      MIN_TREE_SELECTION),
+              MessageManager.getString("label.not_enough_sequences"),
+              JvOptionPane.WARNING_MESSAGE);
+      return;
+    }
+  }
+
   /**
    * Open a new Tree panel on the desktop
    * 
-   * @param modelName
+   * @param tree
    * @param params
+   * @param treeAlgo
    */
-  protected void openTreePanel(String modelName, SimilarityParamsI params)
+  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
      */
-    AlignViewport viewport = af.getViewport();
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
-    {
-      JvOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-              .formatMessage("label.you_need_at_least_n_sequences",
-                      MIN_TREE_SELECTION),
-                      MessageManager
-                              .getString("label.not_enough_sequences"),
-                      JvOptionPane.WARNING_MESSAGE);
-      return;
-    }
+    checkEnoughSequences(af.getViewport());
 
-    String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
-            : TreeBuilder.AVERAGE_DISTANCE;
-    af.newTreePanel(treeType, modelName, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**
@@ -522,14 +548,16 @@ public class CalculationChooser extends JPanel
      * this check in in case this method gets exposed programmatically in future
      */
     if (((viewport.getSelectionGroup() != null)
-            && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) && (viewport
-            .getSelectionGroup().getSize() > 0))
+            && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION)
+            && (viewport.getSelectionGroup().getSize() > 0))
             || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION))
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.you_need_at_least_n_sequences",
-                      MIN_PCA_SELECTION), MessageManager
-              .getString("label.sequence_selection_insufficient"),
+      JvOptionPane.showInternalMessageDialog(this,
+              MessageManager.formatMessage(
+                      "label.you_need_at_least_n_sequences",
+                      MIN_PCA_SELECTION),
+              MessageManager
+                      .getString("label.sequence_selection_insufficient"),
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
@@ -575,7 +603,9 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
-    return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
+
+    return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
+            matchOnShortestLength);
   }
 
   /**