JAL-1855 fail gracefully if XML has no <sequence> element

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 48bd998..b0debf8 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);
   }
 
   /**
@@ -4691,8 +4700,8 @@ 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 +4720,7 @@ 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 +4729,8 @@ 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;