JAL-1944 fix for visible seqs sometimes been replaced with hidden ones while exportin...

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c16fdce..6581bef 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1601,7 +1601,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows())
+      if (hasHiddenRows() && isExportHiddenSeqs)
       {
         iSize = alignment.getHiddenSequences().getFullAlignment()
                 .getHeight();
@@ -2719,4 +2719,18 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
     }
   }
+
+  private boolean isExportHiddenSeqs = true;
+
+  @Override
+  public void setExportHiddenSeqs(boolean isExportHiddenSeqs)
+  {
+    this.isExportHiddenSeqs = isExportHiddenSeqs;
+  }
+
+  @Override
+  public boolean isExportHiddenSeqs()
+  {
+    return isExportHiddenSeqs;
+  }
 }