2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.util;
\r
25 * Simple way of mapping a linear series to a new linear range with new points introduced.
\r
26 * Use at your own risk!
\r
27 * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
\r
29 public class ShiftList
\r
31 public Vector shifts;
\r
34 shifts = new Vector();
\r
39 * @param pos start position for shift (in original reference frame)
\r
40 * @param shift length of shift
\r
42 public void addShift(int pos, int shift)
\r
46 while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
\r
48 if (sidx==shifts.size())
\r
49 shifts.insertElementAt(new int[] { pos, shift}, sidx);
\r
58 * @return int shifted position
\r
60 public int shift(int pos)
\r
62 if (shifts.size()==0)
\r
67 while (sidx<shifts.size()
\r
69 (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
\r
70 shifted += rshift[1];
\r
80 shifts.removeAllElements();
\r
84 * @return ShiftList with inverse shift operations
\r
86 public ShiftList getInverse() {
\r
87 ShiftList inverse=new ShiftList();
\r
89 for (int i=0,j=shifts.size(); i<j; i++) {
\r
90 int[] sh=(int[]) shifts.elementAt(i);
\r
92 inverse.shifts.addElement(new int[] {sh[0], -sh[1]});
\r
99 * parse a 1d map of position 1<i<n to L<pos[i]<N
\r
100 * such as that returned from SequenceI.gapMap()
\r
102 * @return shifts from map index to mapped position
\r
104 public static ShiftList parseMap(int[] gapMap) {
\r
105 ShiftList shiftList = null;
\r
106 if (gapMap!=null && gapMap.length>0) {
\r
107 shiftList=new ShiftList();
\r
108 for (int i=0,p=0; i<gapMap.length; p++,i++) {
\r
109 if (p!=gapMap[i]) {
\r
110 shiftList.addShift(p, gapMap[i]-p);
\r