X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=1366ada6cc7acd4188e867b289fb0e6aa827d015;hb=2df0e73f2d10339cd837b0aa3f216ff140cd53e7;hp=8e949a55fb53acb776e6dbf0108af1141acf124e;hpb=173f77ac7161e8866ddfe6b5689d61a83f459cfc;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 8e949a5..1366ada 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -34,7 +34,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
@@ -68,6 +67,7 @@ import java.util.BitSet;
 import java.util.Deque;
 import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -1339,7 +1339,10 @@ public abstract class AlignmentViewport
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
   {
-    changeSupport.removePropertyChangeListener(listener);
+    if (changeSupport != null)
+    {
+      changeSupport.removePropertyChangeListener(listener);
+    }
   }
 
   /**
@@ -1678,13 +1681,6 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    return new CigarArray(alignment, alignment.getHiddenColumns(),
-            (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1745,8 +1741,12 @@ public abstract class AlignmentViewport
     if (alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = alignment.getHiddenColumns()
-              .getVisibleSequenceStrings(start, end, seqs);
+      for (i = 0; i < iSize; i++)
+      {
+        Iterator<int[]> blocks = alignment.getHiddenColumns()
+                .getVisContigsIterator(start, end + 1, false);
+        selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+      }
     }
     else
     {
@@ -1773,10 +1773,10 @@ public abstract class AlignmentViewport
       {
         if (start == 0)
         {
-          start = hidden.adjustForHiddenColumns(start);
+          start = hidden.visibleToAbsoluteColumn(start);
         }
 
-        end = hidden.getHiddenBoundaryRight(start);
+        end = hidden.getNextHiddenBoundary(false, start);
         if (start == end)
         {
           end = max;
@@ -1791,8 +1791,8 @@ public abstract class AlignmentViewport
 
       if (hidden != null && hidden.hasHiddenColumns())
       {
-        start = hidden.adjustForHiddenColumns(end);
-        start = hidden.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.visibleToAbsoluteColumn(end);
+        start = hidden.getNextHiddenBoundary(true, start) + 1;
       }
     } while (end < max);
 
@@ -1814,13 +1814,13 @@ public abstract class AlignmentViewport
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(
+          clone.makeVisibleAnnotation(
                   selectionGroup.getStartRes(), selectionGroup.getEndRes(),
-                  clone);
+                  alignment.getHiddenColumns());
         }
         else
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+          clone.makeVisibleAnnotation(alignment.getHiddenColumns());
         }
         ala.add(clone);
       }
@@ -2786,7 +2786,7 @@ public abstract class AlignmentViewport
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = ranges
-            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+            .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))