X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=91ee3c100326bd61b9aa5f307031fe89677c318d;hb=80fa1ace4f6ce0cea9680fd8a6d683270c8b2944;hp=6581bef5ccf9866d3a6ddf7f252a2c9cec59ff25;hpb=3f06233fb50a383439b4e0f28405b8681c2e2d72;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 6581bef..91ee3c1 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1420,11 +1420,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
           boolean visible)
   {
-    for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    if (anns != null)
     {
-      if (ann.sequenceRef == sequenceI)
+      for (AlignmentAnnotation ann : anns)
       {
-        ann.visible = visible;
+        if (ann.sequenceRef == sequenceI)
+        {
+          ann.visible = visible;
+        }
       }
     }
   }
@@ -1588,6 +1592,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
+    return getViewAsString(selectedRegionOnly, true);
+  }
+
+  @Override
+  public String[] getViewAsString(boolean selectedRegionOnly,
+          boolean exportHiddenSeqs)
+  {
     String[] selection = null;
     SequenceI[] seqs = null;
     int i, iSize;
@@ -1601,13 +1612,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows() && isExportHiddenSeqs)
+      if (hasHiddenRows() && exportHiddenSeqs)
       {
-        iSize = alignment.getHiddenSequences().getFullAlignment()
-                .getHeight();
-        seqs = alignment.getHiddenSequences().getFullAlignment()
-                .getSequencesArray();
-        end = alignment.getHiddenSequences().getFullAlignment().getWidth();
+        AlignmentI fullAlignment = alignment.getHiddenSequences()
+                .getFullAlignment();
+        iSize = fullAlignment.getHeight();
+        seqs = fullAlignment.getSequencesArray();
+        end = fullAlignment.getWidth();
       }
       else
       {
@@ -2720,17 +2731,5 @@ 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;
-  }
 }