JAL-2110 random stuff

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 895f2f6..477d113 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
+import jalview.analysis.CrossRefs;
 import jalview.analysis.Dna;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
@@ -1313,8 +1314,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {
-      viewport.setExportHiddenSeqs(settings.isExportHiddenSequences());
-      omitHidden = viewport.getViewAsString(false);
+      omitHidden = viewport.getViewAsString(false,
+              settings.isExportHiddenSequences());
     }
 
     int[] alignmentStartEnd = new int[2];
@@ -4647,24 +4648,21 @@ 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);
       }
@@ -4672,7 +4670,7 @@ 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;
@@ -4680,6 +4678,17 @@ 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)
   {
@@ -4697,7 +4706,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           AlignmentI alignment = AlignFrame.this.getViewport()
                   .getAlignment();
-          AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
+          AlignmentI xrefs = CrossRefs.findXrefSequences(sel, dna, source,
                   alignment);
           if (xrefs != null)
           {
@@ -4750,7 +4759,8 @@ 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', 
@@ -4768,7 +4778,9 @@ 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());
@@ -4927,7 +4939,7 @@ 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;