X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c5fb11f32b3ae2776df5064c96479eed26fb94bc;hb=b10330c2e330e409d2fd3812f1001f9542dc1b36;hp=5dba8503830049a731e3ebef266d5263f2d99dbe;hpb=8474e47dc878f83b9b3f45ef6b04eb64ad733e2a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5dba850..c5fb11f 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -473,7 +473,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void focusGained(FocusEvent e)
       {
-        Desktop.setCurrentAlignFrame(AlignFrame.this);
+        Jalview.setCurrentAlignFrame(AlignFrame.this);
       }
     });
 
@@ -4651,7 +4651,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final boolean dna = viewport.getAlignment().isNucleotide();
       List<String> ptypes = (seqs == null || seqs.length == 0) ? null
               : new CrossRef(seqs, dataset)
-                      .findXrefSourcesForSequences();
+                      .findXrefSourcesForSequences(dna);
 
       for (final String source : ptypes)
       {
@@ -4691,7 +4691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param source
    *          the database to show cross-references for
    */
-  protected void showProductsFor(final SequenceI[] sel, final boolean dna,
+  protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
     Runnable foo = new Runnable()
@@ -4710,8 +4710,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   .getAlignment();
           AlignmentI dataset = alignment.getDataset() == null ? alignment
                   : alignment.getDataset();
-          AlignmentI xrefs = new CrossRef(sel, alignment)
-                  .findXrefSequences(source);
+          boolean dna = alignment.isNucleotide();
+          if (_odna!=dna)
+          {
+            System.err
+                    .println("Conflict: showProducts for alignment originally "
+                            + "thought to be "
+                            + (_odna ? "DNA" : "Protein")
+                            + " now searching for "
+                            + (dna ? "DNA" : "Protein") + " Context.");
+          }
+          AlignmentI xrefs = new CrossRef(sel, dataset)
+                  .findXrefSequences(source, dna);
           if (xrefs == null)
           {
             return;
@@ -4891,7 +4901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           sprods[s].updatePDBIds();
         }
         Alignment al = new Alignment(sprods);
-        al.setDataset((Alignment) dataset);
+        al.setDataset(dataset);
         return al;
       }
 
@@ -6078,7 +6088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void runGroovy_actionPerformed()
   {
-    Desktop.setCurrentAlignFrame(this);
+    Jalview.setCurrentAlignFrame(this);
     groovy.ui.Console console = Desktop.getGroovyConsole();
     if (console != null)
     {