Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 1a3d35d..e578f0b 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import java.util.Vector;
+import java.util.List;
 
 public class CigarArray extends CigarBase
 {
@@ -148,25 +148,25 @@ public class CigarArray extends CigarBase
    * internal constructor function - called by CigarArray(AlignmentI, ...);
    * 
    * @param alignment
-   * @param columnSelection
+   * @param list
    *          - vector of visible regions as returned from
    *          columnSelection.getHiddenColumns()
    * @param selectionGroup
    */
   private void constructFromAlignment(AlignmentI alignment,
-          Vector columnSelection, SequenceGroup selectionGroup)
+          List<int[]> list, SequenceGroup selectionGroup)
   {
     int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
     int start = _startend[1], end = _startend[2];
     // now construct the CigarArray operations
-    if (columnSelection != null)
+    if (list != null)
     {
       int[] region;
       int hideStart, hideEnd;
       int last = start;
-      for (int j = 0; last < end & j < columnSelection.size(); j++)
+      for (int j = 0; last < end & j < list.size(); j++)
       {
-        region = (int[]) columnSelection.elementAt(j);
+        region = list.get(j);
         hideStart = region[0];
         hideEnd = region[1];
         // edit hidden regions to selection range