JAL-2089 cleared out old ‘What’s new’

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d9d5f27..bfbc969 100644 (file)
--- 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);
       }
     });
 
@@ -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];
@@ -1324,10 +1325,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       alignmentToExport = viewport.getAlignment();
-      alignmentStartEnd = viewport.getAlignment()
-              .getVisibleStartAndEndIndex(
-                      viewport.getColumnSelection().getHiddenColumns());
     }
+    alignmentStartEnd = alignmentToExport
+            .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+                    .getHiddenColumns());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -4679,6 +4680,17 @@ 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 +4761,8 @@ 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 +4780,9 @@ 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 +4941,7 @@ 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;
@@ -6083,7 +6098,7 @@ 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)
     {