JAL-1424 recode calls to MessageManager to allow code inspection

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 48bd998..bfaedd0 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2434,7 +2434,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
     viewport.sendSelection();
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -2457,7 +2460,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setSelectionGroup(null);
     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2484,6 +2490,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
 
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
@@ -2831,7 +2840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.explodeViews(this);
+    Desktop.explodeViews(this);
   }
 
   /**
@@ -3210,30 +3219,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Set or clear 'Show Sequence Features'
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
-  {
-    viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
-            .isSelected());
-    if (viewport.isShowSequenceFeaturesHeight())
-    {
-      // ensure we're actually displaying features
-      viewport.setShowSequenceFeatures(true);
-      showSeqFeatures.setSelected(true);
-    }
-    alignPanel.paintAlignment(true);
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-  }
-
-  /**
    * Action on toggle of the 'Show annotations' menu item. This shows or hides
    * the annotations panel as a whole.
    * 
@@ -4691,8 +4676,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param source
    *          the database to show cross-references for
    */
-  protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
-          final String source)
+  protected void showProductsFor(final SequenceI[] sel,
+          final boolean _odna, final String source)
   {
     Runnable foo = new Runnable()
     {
@@ -4711,7 +4696,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           AlignmentI dataset = alignment.getDataset() == null ? alignment
                   : alignment.getDataset();
           boolean dna = alignment.isNucleotide();
-          if (_odna!=dna)
+          if (_odna != dna)
           {
             System.err
                     .println("Conflict: showProducts for alignment originally "
@@ -4720,8 +4705,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                             + " now searching for "
                             + (dna ? "DNA" : "Protein") + " Context.");
           }
-          AlignmentI xrefs = new CrossRef(sel, dataset)
-                  .findXrefSequences(source, dna);
+          AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
+                  source, dna);
           if (xrefs == null)
           {
             return;
@@ -4756,6 +4741,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       xrefsAlignment.getSequencesArray());
               if (copyAlignment.getHeight() == 0)
               {
+                JOptionPane.showMessageDialog(AlignFrame.this,
+                        MessageManager.getString("label.cant_map_cds"),
+                        MessageManager.getString("label.operation_failed"),
+                        JOptionPane.OK_OPTION);
                 System.err.println("Failed to make CDS alignment");
               }