JAL-1632 removed ‘tree’ option and changed dialog layout

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index de1d003..8eb09ab 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -34,7 +34,6 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
-import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
@@ -372,7 +371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        new CalculationChooser(AlignFrame.this);
+        openTreePcaDialog();
       }
     });
     buildColourMenu();
@@ -2760,6 +2759,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     newap.av.replaceMappings(viewport.getAlignment());
 
+    /*
+     * start up cDNA consensus (if applicable) now mappings are in place
+     */
+    if (newap.av.initComplementConsensus())
+    {
+      newap.refresh(true); // adjust layout of annotations
+    }
+
     newap.av.viewName = getNewViewName(viewTitle);
 
     addAlignmentPanel(newap, true);
@@ -3337,7 +3344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3358,10 +3365,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
-    if (cs != null)
-    {
-      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, cs);
 
     viewport.setGlobalColourScheme(cs);
 
@@ -3541,35 +3545,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-    if (((viewport.getSelectionGroup() != null)
-            && (viewport.getSelectionGroup().getSize() < 4) && (viewport
-            .getSelectionGroup().getSize() > 0))
-            || (viewport.getAlignment().getHeight() < 4))
-    {
-      JvOptionPane
-              .showInternalMessageDialog(
-                      this,
-                      MessageManager
-                              .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
-                      MessageManager
-                              .getString("label.sequence_selection_insufficient"),
-                      JvOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-
-    new PCAPanel(alignPanel);
-  }
-
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
@@ -3598,16 +3573,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param type
    *          tree type (NJ or AV)
-   * @param sm
-   *          distance or similarity score model used to compute the tree
+   * @param modelName
+   *          name of score model used to compute the tree
    * @param options
    *          parameters for the distance or similarity calculation
    */
-  void newTreePanel(String type, ScoreModelI sm, SimilarityParamsI options)
+  void newTreePanel(String type, String modelName, SimilarityParamsI options)
   {
     String frameTitle = "";
     TreePanel tp;
 
+    boolean onSelection = false;
     if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() > 0)
     {
@@ -3643,36 +3619,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           return;
         }
       }
-
-      tp = new TreePanel(alignPanel, type, sm, options);
-      frameTitle = tp.getPanelTitle() + " on region";
+      onSelection = true;
     }
     else
     {
-      // are the visible sequences aligned?
-      if (!viewport.getAlignment().isAligned(false))
-      {
-        JvOptionPane
-                .showMessageDialog(
-                        Desktop.desktop,
-                        MessageManager
-                                .getString("label.sequences_must_be_aligned_before_creating_tree"),
-                        MessageManager
-                                .getString("label.sequences_not_aligned"),
-                        JvOptionPane.WARNING_MESSAGE);
-
-        return;
-      }
-
       if (viewport.getAlignment().getHeight() < 2)
       {
         return;
       }
-
-      tp = new TreePanel(alignPanel, type, sm, options);
-      frameTitle = tp.getPanelTitle();
     }
 
+    tp = new TreePanel(alignPanel, type, modelName, options);
+    frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
+
     frameTitle += " from ";
 
     if (viewport.viewName != null)
@@ -5634,10 +5593,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
-    String schemeName = colourScheme == null ? null : colourScheme
-            .getSchemeName();
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
+  }
 
-    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+  /**
+   * Open a dialog (if not already open) that allows the user to select and
+   * calculate PCA or Tree analysis
+   */
+  protected void openTreePcaDialog()
+  {
+    if (alignPanel.getCalculationDialog() == null)
+    {
+      new CalculationChooser(AlignFrame.this);
+    }
   }
 }