2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range
26 * Use at your own risk!
27 * TODO: efficient implementation of private posMap method
28 * TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery)
29 * TODO: optimize to use int[][] arrays rather than vectors.
33 public Vector fromShifts;
34 public Vector toShifts;
35 int fromRatio; // number of steps in fromShifts to one toRatio unit
36 int toRatio; // number of steps in toShifts to one fromRatio
37 public MapList(int from[], int to[], int fromRatio, int toRatio)
39 fromShifts = new Vector();
40 for (int i = 0; i < from.length; i += 2)
42 fromShifts.add(new int[]
43 {from[i], from[i + 1]});
45 toShifts = new Vector();
46 for (int i = 0; i < to.length; i += 2)
48 toShifts.add(new int[]
51 this.fromRatio = fromRatio;
52 this.toRatio = toRatio;
56 * get all mapped positions from 'from' to 'to'
57 * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
59 public int[][] makeFromMap()
61 return posMap(fromShifts, fromRatio, toShifts, toRatio);
65 * get all mapped positions from 'to' to 'from'
66 * @return int[to position]=position mapped in from
68 public int[][] makeToMap()
70 return posMap(toShifts, toRatio, fromShifts, fromRatio);
74 * construct an int map for intervals in intVals
76 * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
78 private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
81 Iterator iv = intVals.iterator();
86 int[] intv = (int[]) iv.next();
87 int from = intv[0], to = intv[1];
95 intv = (int[]) iv.next();
114 int mp[][] = new int[to - from + 2][];
115 for (int i = 0; i < mp.length; i++)
117 int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
138 int[][] map = new int[][]
142 from, to, tF, tT}, new int[to - from + 2]};
147 for (int i = 0; i < mp.length; i++)
151 map[1][i] = mp[i][0] - tF;
155 map[1][i] = -1; // indicates an out of range mapping
163 * @param pos start position for shift (in original reference frame)
164 * @param shift length of shift
166 public void addShift(int pos, int shift)
170 while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
172 if (sidx==shifts.size())
173 shifts.insertElementAt(new int[] { pos, shift}, sidx);
179 * shift from pos to To(pos)
182 * @return int shifted position in To, frameshift in From
184 public int[] shiftFrom(int pos)
186 return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
190 * inverse of shiftFrom - maps pos in To to a position in From
192 * @return shifted position in From, frameshift in To
194 public int[] shiftTo(int pos)
196 return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
207 private int[] shift(int pos, Vector fromShifts, int fromRatio,
208 Vector toShifts, int toRatio)
210 int[] fromCount = countPos(fromShifts.iterator(), pos);
211 if (fromCount == null)
215 int fromRemainder = (fromCount[0] - 1) % fromRatio;
216 int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
217 int[] toPos = countToPos(toShifts.iterator(), toCount);
220 return null; // throw new Error("Bad Mapping!");
222 //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
225 toPos[0], fromRemainder};
229 * count how many positions pos is along the series of intervals.
232 * @return number of positions or null if pos is not within intervals
234 private int[] countPos(Iterator intVals, int pos)
236 int count = 0, intv[];
237 while (intVals.hasNext())
239 intv = (int[]) intVals.next();
240 if (intv[0] <= intv[1])
242 if (pos >= intv[0] && pos <= intv[1])
246 count + pos - intv[0] + 1, +1};
250 count += intv[1] - intv[0] + 1;
255 if (pos >= intv[1] && pos <= intv[0])
259 count + intv[0] - pos + 1, -1};
263 count += intv[0] - intv[1] + 1;
271 * count out pos positions into a series of intervals and return the position
274 * @return position pos in interval set
276 private int[] countToPos(Iterator intVals, int pos)
278 int count = 0, diff = 0, intv[] =
281 while (intVals.hasNext())
283 intv = (int[]) intVals.next();
284 diff = intv[1] - intv[0];
287 if (pos <= count + 1 + diff)
291 pos - count - 1 + intv[0], +1};
300 if (pos <= count + 1 - diff)
304 intv[0] - (pos - count - 1), -1};
312 return null; //(diff<0) ? (intv[1]-1) : (intv[0]+1);
315 public static void testMap(MapList ml, int fromS, int fromE)
317 for (int from = 1; from <= 25; from++)
319 int[] too = ml.shiftFrom(from);
320 System.out.print("ShiftFrom(" + from + ")==");
323 System.out.print("NaN\n");
327 System.out.print(too[0] + " % " + too[1]);
328 System.out.print("\t+--+\t");
329 int[] toofrom = ml.shiftTo(too[0]);
332 if (toofrom[0] != from)
334 System.err.println("Mapping not reflexive:" + from + " " + too[0] +
337 System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
342 System.out.println("ShiftTo(" + too[0] + ")==" +
343 "NaN! - not Bijective Mapping!");
347 int mmap[][] = ml.makeFromMap();
348 System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
349 mmap[0][2] + " " + mmap[0][3] + " ");
350 for (int i = 1; i <= mmap[1].length; i++)
352 if (mmap[1][i - 1] == -1)
354 System.out.print(i + "=XXX");
359 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
363 System.out.print("\n");
367 System.out.print(",");
370 System.out.print("\n");
373 public static void main(String argv[])
375 MapList ml = new MapList(new int[]
376 {1, 5, 10, 15, 25, 20},
379 MapList ml1 = new MapList(new int[]
384 // test internal consistency
385 int to[] = new int[51];
386 MapList.testMap(ml, 1, 25);
388 for (int from=1; from<=51; from++) {
389 int[] too=ml.shiftTo(from);
390 int[] toofrom=ml.shiftFrom(too[0]);
391 System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
393 System.out.print("Success?\n"); // if we get here - something must be working!