X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FShiftList.java;h=d4d06eeb8d91574f69064e504b9a26339bc1e2a5;hb=5e9c9db95281199bdb29f5716a231283d9e0384c;hp=0c78ca13d74f0db7bfd9fbdc88f3bdaa5527d042;hpb=b2d54d33d6313efd9da96bd7586dfaa7a0d7a182;p=jalview.git
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 0c78ca1..d4d06ee 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,36 +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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 .
*/
package jalview.util;
-import jalview.datamodel.SequenceI;
-
import java.util.*;
/**
- * 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
+ * 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();
@@ -38,37 +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 (sidx0) {
- shiftList=new ShiftList();
- for (int i=0,p=0; i 0)
+ {
+ shiftList = new ShiftList();
+ for (int i = 0, p = 0; i < gapMap.length; p++, i++)
+ {
+ if (p != gapMap[i])
+ {
+ shiftList.addShift(p, gapMap[i] - p);
+ p = gapMap[i];
}
}
}