X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ea3fdf2c01b9c21afb7056c00e7e989e438e41e2;hb=b21429180fdda3586d67b5d0f43c89d35b504be7;hp=d9d5f279b4ddd73d4ba0e4bbdf54f93eaaa3830c;hpb=1ee9dde6abe6c467f28409fac5b3f06dd67d51bf;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d9d5f27..ea3fdf2 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1313,7 +1313,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {
-      omitHidden = viewport.getViewAsString(false);
+      omitHidden = viewport.getViewAsString(false,
+              settings.isExportHiddenSequences());
     }
 
     int[] alignmentStartEnd = new int[2];
@@ -4646,24 +4647,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       showProducts.removeAll();
       final boolean dna = viewport.getAlignment().isNucleotide();
-      String[] ptypes = (selection == null || selection.length == 0) ? null
-              : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+      List<String> ptypes = (selection == null || selection.length == 0) ? null
+              : CrossRef.findXrefSourcesForSequences(dna, selection, dataset);
 
-      for (int t = 0; ptypes != null && t < ptypes.length; t++)
+      for (final String source : ptypes)
       {
         showp = true;
         final AlignFrame af = this;
-        final String source = ptypes[t];
-        JMenuItem xtype = new JMenuItem(ptypes[t]);
+        JMenuItem xtype = new JMenuItem(source);
         xtype.addActionListener(new ActionListener()
         {
-
           @Override
           public void actionPerformed(ActionEvent e)
           {
             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
           }
-
         });
         showProducts.add(xtype);
       }
@@ -4671,7 +4669,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("canShowProducts threw an exception - please report to help@jalview.org",
                       e);
       return false;
@@ -4679,6 +4677,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return showp;
   }
 
+  /**
+   * Finds and displays cross-references for the selected sequences (protein
+   * products for nucleotide sequences, dna coding sequences for peptides).
+   * 
+   * @param sel
+   *          the sequences to show cross-references for
+   * @param dna
+   *          true if from a nucleotide alignment (so showing proteins)
+   * @param source
+   *          the database to show cross-references for
+   */
   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
           final String source)
   {
@@ -4749,7 +4758,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 System.err.println("Failed to make CDS alignment");
               }
               al.getCodonFrames().clear();
-              al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
+              al.addCodonFrames(copyAlignment.getCodonFrames());
+              al.addCodonFrames(cf);
 
               /*
                * pending getting Embl transcripts to 'align', 
@@ -4767,7 +4777,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               copyAlignment = AlignmentUtils.makeCopyAlignment(
                       sequenceSelection, xrefs.getSequencesArray());
-              copyAlignment.getCodonFrames().addAll(cf);
+              copyAlignment.addCodonFrames(cf);
+              al.addCodonFrames(copyAlignment.getCodonFrames());
+              al.addCodonFrames(cf);
             }
             copyAlignment.setGapCharacter(AlignFrame.this.viewport
                     .getGapCharacter());
@@ -4926,7 +4938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getString("label.error_when_translating_sequences_submit_bug_report");
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
-              + MessageManager.getString("translation_failed");
+              + MessageManager.getString("label.translation_failed");
       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JOptionPane.ERROR_MESSAGE);
       return;