JAL-2738 update spike branch with latest

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index f6e5862..1723f1d 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -68,7 +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;
         }
@@ -85,13 +86,13 @@ public class CigarArray extends CigarBase
    * @param columnSelection
    * @param selectionGroup
    */
-  public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,
+  public CigarArray(AlignmentI alignment, HiddenColumns hidden,
           SequenceGroup selectionGroup)
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
     constructFromAlignment(alignment,
-            columnSelection != null ? columnSelection.getHiddenColumns()
-                    : null, selectionGroup);
+            hidden != null ? hidden.getHiddenColumnsCopy() : null,
+            selectionGroup);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,
@@ -169,32 +170,30 @@ public class CigarArray extends CigarBase
         hideStart = region[0];
         hideEnd = region[1];
         // edit hidden regions to selection range
-        if (hideStart < last)
+
+        // just move on if hideEnd is before last
+        if (hideEnd < last)
         {
-          if (hideEnd > last)
-          {
-            hideStart = last;
-          }
-          else
-          {
-            continue;
-          }
+          continue;
         }
-
+        // exit if next region is after end
         if (hideStart > end)
         {
           break;
         }
 
-        if (hideEnd > end)
+        // truncate region at start if last falls in region
+        if ((hideStart < last) && (hideEnd >= last))
         {
-          hideEnd = end;
+          hideStart = last;
         }
 
-        if (hideStart > hideEnd)
+        // truncate region at end if end falls in region
+        if (hideEnd > end) // already checked that hideStart<=end
         {
-          break;
+          hideEnd = end;
         }
+
         /**
          * form operations...
          */
@@ -206,7 +205,7 @@ public class CigarArray extends CigarBase
         last = hideEnd + 1;
       }
       // Final match if necessary.
-      if (last < end)
+      if (last <= end)
       {
         addOperation(CigarArray.M, end - last + 1);
       }
@@ -218,7 +217,7 @@ public class CigarArray extends CigarBase
   }
 
   /**
-   * @see Cigar.getSequenceAndDeletions
+   * @see CigarBase.getSequenceAndDeletions
    * @param GapChar
    *          char
    * @return Object[][]