Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1970388..8462b8d 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1245,11 +1245,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignmentToExport = viewport.getAlignment();
         alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
                 .getColumnSelection().getHiddenColumns());
+        viewport.setIncludeHiddenRegion(false);
       }
       else
       {
         // export all region including visible
         alignmentToExport = hiddenSeqs.getFullAlignment();
+        viewport.setIncludeHiddenRegion(true);
       }
     }
 
@@ -6121,13 +6123,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     AlignmentI al = viewport.getAlignment();
     HiddenSequences hiddenSeqs = al.getHiddenSequences();
+    boolean hasHiddenRows = false;
     for (SequenceI seq : al.getSequencesArray())
       {
         if (seq.isHidden())
         {
         hiddenSeqs.hideSequence(seq);
+        hasHiddenRows = true;
         }
       }
+    viewport.setHasHiddenRows(hasHiddenRows);
+    firePropertyChange("alignment", null, al.getSequences());
   }
 }