X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=3f66aa5c92fafb0df537f055ba2c1d706e20bba5;hb=ee5064ad5cba56f7b2423e8023e5c60204ba0878;hp=5c1d572256ae9fcdfe58b7033466992ca84848dd;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 5c1d572..3f66aa5 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,45 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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
Title: ShiftList
- * - *Description:
- * - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 + * ShiftList Simple way of mapping a linear series to a new linear range with + * new points introduced. Use at your own risk! Now growing to be used for + * interval ranges (position, offset) storing deletions/insertions */ public class ShiftList { - public Vector shifts; + public Vector shifts; + public ShiftList() { shifts = new Vector(); @@ -47,37 +35,51 @@ public class ShiftList /** * addShift - * @param pos start position for shift (in original reference frame) - * @param shift length of shift + * + * @param pos + * start position for shift (in original reference frame) + * @param shift + * length of shift */ public void addShift(int pos, int shift) { int sidx = 0; - int[] rshift=null; - while (sidx