JAL-1632 first cut of Tree chooser dialog and ScoreModels singleton

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 266cbcb..d6dfd9d 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -82,7 +82,6 @@ import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -360,7 +359,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
-    buildTreeMenu();
+    calculateTree.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        new TreeChooser(AlignFrame.this);
+      }
+    });
     buildColourMenu();
 
     if (Desktop.desktop != null)
@@ -3301,7 +3308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param selected
    */
   @Override
-  protected void applyToAllGroups_actionPerformed(boolean selected)
+  public void applyToAllGroups_actionPerformed(boolean selected)
   {
     viewport.setColourAppliesToAllGroups(selected);
   }
@@ -3359,7 +3366,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void modifyPID_actionPerformed()
   {
     SliderPanel.setPIDSliderSource(alignPanel,
-            viewport.getViewportColourScheme(), "Background");
+            viewport.getResidueShading(), alignPanel.getViewName());
     SliderPanel.showPIDSlider();
   }
 
@@ -3370,7 +3377,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void modifyConservation_actionPerformed()
   {
     SliderPanel.setConservationSlider(alignPanel,
-            viewport.getViewportColourScheme(), "Background");
+            viewport.getResidueShading(), alignPanel.getViewName());
     SliderPanel.showConservationSlider();
   }
 
@@ -3378,11 +3385,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
-  protected void conservationMenuItem_actionPerformed(boolean selected)
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
-    viewport.getViewportColourScheme().setConservationApplied(selected);
+    viewport.getResidueShading().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
     if (selected)
@@ -3403,6 +3410,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     modifyPID.setEnabled(selected);
     viewport.setAbovePIDThreshold(selected);
+    if (!selected)
+    {
+      viewport.getResidueShading().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
     if (selected)
@@ -3575,54 +3587,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * DOCUMENT ME!
    * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("AV", "PID", "Average distance tree using PID");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param type
    *          DOCUMENT ME!
    * @param pwType
@@ -3829,48 +3793,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * call. Listeners are added to remove the menu item when the treePanel is
    * closed, and adjust the tree leaf to sequence mapping when the alignment is
    * modified.
-   * 
-   * @param treePanel
-   *          Displayed tree window.
-   * @param title
-   *          SortBy menu item title.
    */
   @Override
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
-    calculateTree.removeAll();
-    // build the calculate menu
-
-    for (final String type : new String[] { "NJ", "AV" })
-    {
-      String treecalcnm = MessageManager.getString("label.tree_calc_"
-              + type.toLowerCase());
-      for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
-      {
-        JMenuItem tm = new JMenuItem();
-        ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        if (sm.isDNA() == viewport.getAlignment().isNucleotide()
-                || sm.isProtein() == !viewport.getAlignment()
-                        .isNucleotide())
-        {
-          String smn = MessageManager.getStringOrReturn(
-                  "label.score_model_", sm.getName());
-          final String title = MessageManager.formatMessage(
-                  "label.treecalc_title", treecalcnm, smn);
-          tm.setText(title);//
-          tm.addActionListener(new java.awt.event.ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              newTreePanel(type, pwtype, title);
-            }
-          });
-          calculateTree.add(tm);
-        }
-
-      }
-    }
     sortByTreeMenu.removeAll();
 
     List<Component> comps = PaintRefresher.components.get(viewport
@@ -4828,6 +4754,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     /*
+     * 'focus' any colour slider that is open to the selected viewport
+     */
+    if (viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+              viewport.getResidueShading(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+              viewport.getResidueShading(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
+
+    /*
      * If there is a frame linked to this one in a SplitPane, switch it to the
      * same view tab index. No infinite recursion of calls should happen, since
      * tabSelectionChanged() should not get invoked on setting the selected
@@ -5672,6 +5620,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
   }
+
+  public void newTreePanel(String treeType, ScoreModelI sm)
+  {
+    String treecalcnm = MessageManager.getString("label.tree_calc_"
+            + treeType.toLowerCase());
+    String smn = MessageManager.getStringOrReturn("label.score_model_",
+            sm.getName());
+    final String ttl = MessageManager.formatMessage("label.treecalc_title",
+            treecalcnm, smn);
+    newTreePanel(treeType, sm.getName(), ttl);
+  }
 }
 
 class PrintThread extends Thread