refactored hidden regions methods and made an AlignmentView preserve

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 15309b7..727bc76 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -23,7 +23,8 @@ public class AlignmentView
   {
     if (!seqcigararray.isSeqCigarArray())
       throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
-    contigs = seqcigararray.applyDeletions();
+    //contigs = seqcigararray.applyDeletions();
+    contigs = seqcigararray.getDeletedRegions();
     sequences = seqcigararray.getSeqCigarArray();
   }
 
@@ -49,7 +50,7 @@ public class AlignmentView
   public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
     ColumnSelection colsel = new ColumnSelection();
 
-    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel), colsel};
+    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
   }
   /**
    * getSequenceStrings