From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 26 Sep 2017 13:49:16 +0000 (+0100)
Subject: JAL-2674 Changed CigarArray constructor to use HiddenColumns iterator
X-Git-Tag: Release_2_10_4~55^2~1^2~104
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7c70de6dbc24545b9da5aac77896220d15394fb9;p=jalview.git

JAL-2674 Changed CigarArray constructor to use HiddenColumns iterator
---

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index b6224c2..d90b3cd 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,
@@ -154,22 +152,29 @@ 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, true);
+      while (regions.hasNext())
       {
-        region = list.get(j);
+        region = regions.next();
         hideStart = region[0];
         hideEnd = region[1];
+
         // edit hidden regions to selection range
+        // TODO possible bug here in original code: if hideEnd==last we continue
+        // but shouldn't this be a single D at start?
         if (hideStart < last)
         {
           if (hideEnd > last)
@@ -206,6 +211,7 @@ public class CigarArray extends CigarBase
         addOperation(CigarArray.D, 1 + hideEnd - hideStart);
         last = hideEnd + 1;
       }
+
       // Final match if necessary.
       if (last < end)
       {