JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index db5a520..61f3c33 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,24 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.Vector;
+import java.util.List;
 
 public class CigarArray extends CigarBase
 {
@@ -95,8 +97,7 @@ public class CigarArray extends CigarBase
   private static int[] _calcStartEndBounds(AlignmentI alignment,
           SequenceGroup selectionGroup)
   {
-    int[] startend = new int[]
-    { 0, 0, 0 };
+    int[] startend = new int[] { 0, 0, 0 };
     if (selectionGroup != null)
     {
       startend[0] = selectionGroup.getSize();
@@ -146,25 +147,25 @@ 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
@@ -341,8 +342,11 @@ public class CigarArray extends CigarBase
           delpos = new java.util.Vector();
         }
         int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
-        delpos.addElement(new int[]
-        { vcursor + offset, range[i] }); // index of right hand column after
+        delpos.addElement(new int[] { vcursor + offset, range[i] }); // index of
+                                                                     // right
+                                                                     // hand
+                                                                     // column
+                                                                     // after
         // hidden region boundary
         offset += range[i] - 1; // shift in visible column coordinates
         System.arraycopy(operation, i + 1, operation, i, length - i);