X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=f6e586227c3c76ef20328b9cdc5a962340620e6b;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=db5a5201dae03b01a3823ea9cb6e1b18b03b087d;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index db5a520..f6e5862 100644
--- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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 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);