X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=17e9ea6fc65e17faad9b7f76656fa0f1a30cdf68;hb=0ae965fc73680bdc69b06986c060ff17342c4787;hp=a48a178179221382a27a44a595a374e222af900c;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index a48a178..17e9ea6 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -20,9 +20,7 @@
  */
 package jalview.datamodel;
 
-import htsjdk.samtools.Cigar;
-
-import java.util.List;
+import java.util.Iterator;
 
 public class CigarArray extends CigarBase
 {
@@ -70,7 +68,8 @@ public class CigarArray extends CigarBase
       for (int c = 0; c < cigars.length; c++)
       {
         refCigars[c] = cigars[c];
-        if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
+        if (!((cigars[c] instanceof SeqCigar)
+                || cigars[c] instanceof CigarCigar))
         {
           seqcigararray = false;
         }
@@ -91,9 +90,7 @@ public class CigarArray extends CigarBase
           SequenceGroup selectionGroup)
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
-    constructFromAlignment(alignment,
-            hidden != null ? hidden.getListOfCols()
-                    : null, selectionGroup);
+    constructFromAlignment(alignment, hidden, selectionGroup);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,
@@ -155,48 +152,38 @@ 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
-        if (hideStart < last)
-        {
-          if (hideEnd > last)
-          {
-            hideStart = last;
-          }
-          else
-          {
-            continue;
-          }
-        }
 
-        if (hideStart > end)
+        // truncate region at start if last falls in region
+        if ((hideStart < last) && (hideEnd >= last))
         {
-          break;
+          hideStart = last;
         }
 
-        if (hideEnd > end)
+        // truncate region at end if end falls in region
+        if (hideEnd > end) // already checked that hideStart<=end
         {
           hideEnd = end;
         }
 
-        if (hideStart > hideEnd)
-        {
-          break;
-        }
         /**
          * form operations...
          */
@@ -207,8 +194,9 @@ public class CigarArray extends CigarBase
         addOperation(CigarArray.D, 1 + hideEnd - hideStart);
         last = hideEnd + 1;
       }
+
       // Final match if necessary.
-      if (last < end)
+      if (last <= end)
       {
         addOperation(CigarArray.M, end - last + 1);
       }
@@ -220,7 +208,7 @@ public class CigarArray extends CigarBase
   }
 
   /**
-   * @see Cigar.getSequenceAndDeletions
+   * @see CigarBase.getSequenceAndDeletions
    * @param GapChar
    *          char
    * @return Object[][]