X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=133aab4f59999aec93bac69304a56ad8a1454d8e;hb=0920ff53a47805479a84980bc09886c939c77399;hp=818c15028648966d190884d6b44d9a25a7bcda23;hpb=1f959f4a5bc07769cde4c2577022ad64e55b4a1a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 818c150..133aab4 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);
       }
     });
 
@@ -1313,8 +1313,8 @@ 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];
@@ -1325,10 +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;
@@ -4941,7 +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;
@@ -5960,8 +5960,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignPanel.getAlignment()
+            .getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return;
+    }
+    for (AlignmentAnnotation aa : anns)
     {
       /*
        * don't display non-positional annotations on an alignment
@@ -6098,7 +6103,7 @@ 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)
     {