X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;fp=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=17e9ea6fc65e17faad9b7f76656fa0f1a30cdf68;hb=04a4d60a50394d846d0479c442facebe360b5b9c;hp=1723f1d45d148bd082b5d9c17ff0661df2e2216d;hpb=653e250e0a2a5dd455ae4c52794c4ce0de340418;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 1723f1d..17e9ea6 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import java.util.List;
+import java.util.Iterator;
 
 public class CigarArray extends CigarBase
 {
@@ -90,9 +90,7 @@ public class CigarArray extends CigarBase
           SequenceGroup selectionGroup)
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
-    constructFromAlignment(alignment,
-            hidden != null ? hidden.getHiddenColumnsCopy() : null,
-            selectionGroup);
+    constructFromAlignment(alignment, hidden, selectionGroup);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,
@@ -154,33 +152,25 @@ public class CigarArray extends CigarBase
    * @param selectionGroup
    */
   private void constructFromAlignment(AlignmentI alignment,
-          List<int[]> list, SequenceGroup selectionGroup)
+          HiddenColumns hidden, SequenceGroup selectionGroup)
   {
     int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
-    int start = _startend[1], end = _startend[2];
+    int start = _startend[1];
+    int end = _startend[2];
     // now construct the CigarArray operations
-    if (list != null)
+    if (hidden != null)
     {
       int[] region;
-      int hideStart, hideEnd;
+      int hideStart;
+      int hideEnd;
       int last = start;
-      for (int j = 0; last < end & j < list.size(); j++)
+
+      Iterator<int[]> regions = hidden.getBoundedIterator(start, end);
+      while (regions.hasNext())
       {
-        region = list.get(j);
+        region = regions.next();
         hideStart = region[0];
         hideEnd = region[1];
-        // edit hidden regions to selection range
-
-        // just move on if hideEnd is before last
-        if (hideEnd < last)
-        {
-          continue;
-        }
-        // exit if next region is after end
-        if (hideStart > end)
-        {
-          break;
-        }
 
         // truncate region at start if last falls in region
         if ((hideStart < last) && (hideEnd >= last))
@@ -204,6 +194,7 @@ public class CigarArray extends CigarBase
         addOperation(CigarArray.D, 1 + hideEnd - hideStart);
         last = hideEnd + 1;
       }
+
       // Final match if necessary.
       if (last <= end)
       {