JAL-1632 similarity options on TreeChooser panel affect tree by PID

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

diff --git a/src/jalview/gui/TreeChooser.java b/src/jalview/gui/TreeChooser.java
index 8e2bff0..3542532 100644 (file)
--- a/src/jalview/gui/TreeChooser.java
+++ b/src/jalview/gui/TreeChooser.java
@@ -22,18 +22,24 @@ package jalview.gui;
 
 import jalview.analysis.NJTree;
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.FlowLayout;
 import java.awt.Font;
+import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
+import java.beans.PropertyVetoException;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
@@ -57,6 +63,14 @@ public class TreeChooser extends JPanel
 
   private ButtonGroup treeTypes;
 
+  private JCheckBox includeGaps;
+
+  private JCheckBox matchGaps;
+
+  private JCheckBox includeGappedColumns;
+
+  private JCheckBox shorterSequence;
+
   /**
    * Constructor
    * 
@@ -68,12 +82,22 @@ public class TreeChooser extends JPanel
     init();
   }
 
+  /**
+   * Lays out the panel and adds it to the desktop
+   */
   void init()
   {
     frame = new JInternalFrame();
     frame.setContentPane(this);
     this.setBackground(Color.white);
 
+    /*
+     * Layout consists of 4 panels:
+     * - first with choice of tree method NJ or AV
+     * - second with choice of score model
+     * - third with score model parameter options
+     * - fourth with OK and Cancel
+     */
     neighbourJoining = new JRadioButton(
             MessageManager.getString("label.tree_calc_nj"));
     neighbourJoining.setOpaque(false);
@@ -83,7 +107,14 @@ public class TreeChooser extends JPanel
     treeTypes.add(neighbourJoining);
     treeTypes.add(averageDistance);
     neighbourJoining.setSelected(true);
-
+    JPanel treeChoicePanel = new JPanel();
+    treeChoicePanel.setOpaque(false);
+    treeChoicePanel.add(neighbourJoining);
+    treeChoicePanel.add(averageDistance);
+
+    /*
+     * score model drop-down
+     */
     matrixNames = new JComboBox<String>();
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
@@ -94,7 +125,28 @@ public class TreeChooser extends JPanel
         matrixNames.addItem(sm.getName());
       }
     }
-
+    JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+    scoreModelPanel.setOpaque(false);
+    scoreModelPanel.add(matrixNames, FlowLayout.LEFT);
+
+    /*
+     * score model parameters
+     */
+    JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
+    paramsPanel.setOpaque(false);
+    includeGaps = new JCheckBox("Include gaps");
+    matchGaps = new JCheckBox("Match gaps");
+    includeGappedColumns = new JCheckBox("Include gapped columns");
+    shorterSequence = new JCheckBox("Match on shorter sequence");
+    paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
+    paramsPanel.add(includeGaps);
+    paramsPanel.add(matchGaps);
+    paramsPanel.add(includeGappedColumns);
+    paramsPanel.add(shorterSequence);
+
+    /*
+     * OK / Cancel buttons
+     */
     JButton ok = new JButton(MessageManager.getString("action.ok"));
     ok.setFont(VERDANA_11PT);
     ok.addActionListener(new java.awt.event.ActionListener()
@@ -105,7 +157,6 @@ public class TreeChooser extends JPanel
         ok_actionPerformed(e);
       }
     });
-
     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
     cancel.setFont(VERDANA_11PT);
     cancel.addActionListener(new java.awt.event.ActionListener()
@@ -116,25 +167,18 @@ public class TreeChooser extends JPanel
         cancel_actionPerformed(e);
       }
     });
+    JPanel actionPanel = new JPanel();
+    actionPanel.setOpaque(false);
+    actionPanel.add(ok);
+    actionPanel.add(cancel);
 
-    JPanel p1 = new JPanel();
-    p1.setOpaque(false);
-    p1.add(neighbourJoining);
-    p1.add(averageDistance);
-    this.add(p1);
-    JPanel p2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
-    p2.setOpaque(false);
-    p2.add(matrixNames, FlowLayout.LEFT);
-    this.add(p2);
-    JPanel p3 = new JPanel();
-    p3.setOpaque(false);
-    p3.add(ok);
-    p3.add(cancel);
-    this.add(p3);
+    this.add(treeChoicePanel);
+    this.add(scoreModelPanel);
+    this.add(paramsPanel);
+    this.add(actionPanel);
 
     Desktop.addInternalFrame(frame,
-            MessageManager.getString("label.choose_tree"),
-              400, 200, false);
+            MessageManager.getString("label.choose_tree"), 400, 400, false);
 
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
@@ -146,19 +190,29 @@ public class TreeChooser extends JPanel
    */
   protected void ok_actionPerformed(ActionEvent e)
   {
+    String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
+            : NJTree.AVERAGE_DISTANCE;
+    ScoreModelI sm = ScoreModels.getInstance().forName(
+            matrixNames.getSelectedItem().toString());
+    SimilarityParamsI params = getSimilarityParameters();
+    af.newTreePanel(treeType, sm, params);
+
     try
     {
       frame.setClosed(true);
-      String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
-              : NJTree.AVERAGE_DISTANCE;
-      ScoreModelI sm = ScoreModels.getInstance().forName(
-              matrixNames.getSelectedItem().toString());
-      af.newTreePanel(treeType, sm);
-    } catch (Exception ex)
+    } catch (PropertyVetoException ex)
     {
     }
   }
 
+  private SimilarityParamsI getSimilarityParameters()
+  {
+    SimilarityParamsI params = new SimilarityParams(
+            includeGappedColumns.isSelected(), matchGaps.isSelected(),
+            includeGaps.isSelected(), shorterSequence.isSelected());
+    return params;
+  }
+
   /**
    * Closes dialog on cancel
    *