JAL-1944 bugfix for wrong alignment numbering when exporting an alignment and export...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d548695..7ab8311 100644 (file)
--- 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];
@@ -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;
@@ -4940,7 +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;