2 * This file is part of the Vamsas Client version 0.2.
\r
3 * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
\r
4 * Andrew Waterhouse and Dominik Lindner.
\r
6 * Earlier versions have also been incorporated into Jalview version 2.4
\r
7 * since 2008, and TOPALi version 2 since 2007.
\r
9 * The Vamsas Client is free software: you can redistribute it and/or modify
\r
10 * it under the terms of the GNU Lesser General Public License as published by
\r
11 * the Free Software Foundation, either version 3 of the License, or
\r
12 * (at your option) any later version.
\r
14 * The Vamsas Client is distributed in the hope that it will be useful,
\r
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
17 * GNU Lesser General Public License for more details.
\r
19 * You should have received a copy of the GNU Lesser General Public License
\r
20 * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
\r
22 package uk.ac.vamsas.objects.utils;
\r
27 * MapList Simple way of bijectively mapping a non-contiguous linear range to
\r
28 * another non-contiguous linear range Use at your own risk! TODO: efficient
\r
29 * implementation of private posMap method TODO: test/ensure that sense of from
\r
30 * and to ratio start position is conserved (codon start position recovery)
\r
31 * TODO: optimize to use int[][] arrays rather than vectors.
\r
33 public class MapList {
\r
37 * @see java.lang.Object#equals(java.lang.Object)
\r
39 public boolean equals(MapList obj) {
\r
42 if (obj != null && obj.fromRatio == fromRatio && obj.toRatio == toRatio
\r
43 && obj.fromShifts != null && obj.toShifts != null) {
\r
44 int i, iSize = fromShifts.size(), j, jSize = obj.fromShifts.size();
\r
47 for (i = 0, iSize = fromShifts.size(), j = 0, jSize = obj.fromShifts
\r
48 .size(); i < iSize;) {
\r
49 int[] mi = (int[]) fromShifts.elementAt(i++);
\r
50 int[] mj = (int[]) obj.fromShifts.elementAt(j++);
\r
51 if (mi[0] != mj[0] || mi[1] != mj[1])
\r
54 iSize = toShifts.size();
\r
55 jSize = obj.toShifts.size();
\r
58 for (i = 0, j = 0; i < iSize;) {
\r
59 int[] mi = (int[]) toShifts.elementAt(i++);
\r
60 int[] mj = (int[]) obj.toShifts.elementAt(j++);
\r
61 if (mi[0] != mj[0] || mi[1] != mj[1])
\r
69 public Vector fromShifts;
\r
71 public Vector toShifts;
\r
73 int fromRatio; // number of steps in fromShifts to one toRatio unit
\r
75 int toRatio; // number of steps in toShifts to one fromRatio
\r
79 * @return series of intervals mapped in from
\r
81 public int[] getFromRanges() {
\r
82 return getRanges(fromShifts);
\r
85 public int[] getToRanges() {
\r
86 return getRanges(toShifts);
\r
89 private int[] getRanges(Vector shifts) {
\r
90 int[] rnges = new int[2 * shifts.size()];
\r
91 Enumeration e = shifts.elements();
\r
93 while (e.hasMoreElements()) {
\r
94 int r[] = (int[]) e.nextElement();
\r
102 * lowest and highest value in the from Map
\r
104 int[] fromRange = null;
\r
107 * lowest and highest value in the to Map
\r
109 int[] toRange = null;
\r
113 * @return length of mapped phrase in from
\r
115 public int getFromRatio() {
\r
121 * @return length of mapped phrase in to
\r
123 public int getToRatio() {
\r
127 public int getFromLowest() {
\r
128 return fromRange[0];
\r
131 public int getFromHighest() {
\r
132 return fromRange[1];
\r
135 public int getToLowest() {
\r
139 public int getToHighest() {
\r
143 private void ensureRange(int[] limits, int pos) {
\r
144 if (limits[0] > pos)
\r
146 if (limits[1] < pos)
\r
150 public MapList(int from[], int to[], int fromRatio, int toRatio) {
\r
151 fromRange = new int[] { from[0], from[1] };
\r
152 toRange = new int[] { to[0], to[1] };
\r
154 fromShifts = new Vector();
\r
155 for (int i = 0; i < from.length; i += 2) {
\r
156 ensureRange(fromRange, from[i]);
\r
157 ensureRange(fromRange, from[i + 1]);
\r
159 fromShifts.addElement(new int[] { from[i], from[i + 1] });
\r
161 toShifts = new Vector();
\r
162 for (int i = 0; i < to.length; i += 2) {
\r
163 ensureRange(toRange, to[i]);
\r
164 ensureRange(toRange, to[i + 1]);
\r
165 toShifts.addElement(new int[] { to[i], to[i + 1] });
\r
167 this.fromRatio = fromRatio;
\r
168 this.toRatio = toRatio;
\r
171 public MapList(MapList map) {
\r
172 this.fromRange = new int[] { map.fromRange[0], map.fromRange[1] };
\r
173 this.toRange = new int[] { map.toRange[0], map.toRange[1] };
\r
174 this.fromRatio = map.fromRatio;
\r
175 this.toRatio = map.toRatio;
\r
176 if (map.fromShifts != null) {
\r
177 this.fromShifts = new Vector();
\r
178 Enumeration e = map.fromShifts.elements();
\r
179 while (e.hasMoreElements()) {
\r
180 int[] el = (int[]) e.nextElement();
\r
181 fromShifts.addElement(new int[] { el[0], el[1] });
\r
184 if (map.toShifts != null) {
\r
185 this.toShifts = new Vector();
\r
186 Enumeration e = map.toShifts.elements();
\r
187 while (e.hasMoreElements()) {
\r
188 int[] el = (int[]) e.nextElement();
\r
189 toShifts.addElement(new int[] { el[0], el[1] });
\r
195 * get all mapped positions from 'from' to 'to'
\r
197 * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
\r
198 * [fromFinish-fromStart+2] { toStart..toFinish mappings}}
\r
200 public int[][] makeFromMap() {
\r
201 return posMap(fromShifts, fromRatio, toShifts, toRatio);
\r
205 * get all mapped positions from 'to' to 'from'
\r
207 * @return int[to position]=position mapped in from
\r
209 public int[][] makeToMap() {
\r
210 return posMap(toShifts, toRatio, fromShifts, fromRatio);
\r
214 * construct an int map for intervals in intVals
\r
217 * @return int[] { from, to pos in range }, int[range.to-range.from+1]
\r
218 * returning mapped position
\r
220 private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
\r
222 int iv = 0, ivSize = intVals.size();
\r
223 if (iv >= ivSize) {
\r
226 int[] intv = (int[]) intVals.elementAt(iv++);
\r
227 int from = intv[0], to = intv[1];
\r
232 while (iv < ivSize) {
\r
233 intv = (int[]) intVals.elementAt(iv++);
\r
234 if (intv[0] < from) {
\r
237 if (intv[1] < from) {
\r
240 if (intv[0] > to) {
\r
243 if (intv[1] > to) {
\r
247 int tF = 0, tT = 0;
\r
248 int mp[][] = new int[to - from + 2][];
\r
249 for (int i = 0; i < mp.length; i++) {
\r
250 int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
\r
265 int[][] map = new int[][] { new int[] { from, to, tF, tT },
\r
266 new int[to - from + 2] };
\r
271 for (int i = 0; i < mp.length; i++) {
\r
272 if (mp[i] != null) {
\r
273 map[1][i] = mp[i][0] - tF;
\r
275 map[1][i] = -1; // indicates an out of range mapping
\r
285 * start position for shift (in original reference frame)
\r
289 * public void addShift(int pos, int shift) { int sidx = 0; int[]
\r
290 * rshift=null; while (sidx<shifts.size() && (rshift=(int[])
\r
291 * shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())
\r
292 * shifts.insertElementAt(new int[] { pos, shift}, sidx); else
\r
293 * rshift[1]+=shift; }
\r
296 * shift from pos to To(pos)
\r
300 * @return int shifted position in To, frameshift in From, direction of mapped
\r
303 public int[] shiftFrom(int pos) {
\r
304 return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
\r
308 * inverse of shiftFrom - maps pos in To to a position in From
\r
312 * @return shifted position in From, frameshift in To, direction of mapped
\r
315 public int[] shiftTo(int pos) {
\r
316 return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
\r
321 * @param fromShifts
\r
327 private int[] shift(int pos, Vector fromShifts, int fromRatio,
\r
328 Vector toShifts, int toRatio) {
\r
329 int[] fromCount = countPos(fromShifts, pos);
\r
330 if (fromCount == null) {
\r
333 int fromRemainder = (fromCount[0] - 1) % fromRatio;
\r
334 int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
\r
335 int[] toPos = countToPos(toShifts, toCount);
\r
336 if (toPos == null) {
\r
337 return null; // throw new Error("Bad Mapping!");
\r
339 // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
\r
340 return new int[] { toPos[0], fromRemainder, toPos[1] };
\r
344 * count how many positions pos is along the series of intervals.
\r
348 * @return number of positions or null if pos is not within intervals
\r
350 private int[] countPos(Vector intVals, int pos) {
\r
351 int count = 0, intv[], iv = 0, ivSize = intVals.size();
\r
352 while (iv < ivSize) {
\r
353 intv = (int[]) intVals.elementAt(iv++);
\r
354 if (intv[0] <= intv[1]) {
\r
355 if (pos >= intv[0] && pos <= intv[1]) {
\r
356 return new int[] { count + pos - intv[0] + 1, +1 };
\r
358 count += intv[1] - intv[0] + 1;
\r
361 if (pos >= intv[1] && pos <= intv[0]) {
\r
362 return new int[] { count + intv[0] - pos + 1, -1 };
\r
364 count += intv[0] - intv[1] + 1;
\r
372 * count out pos positions into a series of intervals and return the position
\r
376 * @return position pos in interval set
\r
378 private int[] countToPos(Vector intVals, int pos) {
\r
379 int count = 0, diff = 0, iv = 0, ivSize = intVals.size(), intv[] = { 0, 0 };
\r
380 while (iv < ivSize) {
\r
381 intv = (int[]) intVals.elementAt(iv++);
\r
382 diff = intv[1] - intv[0];
\r
384 if (pos <= count + 1 + diff) {
\r
385 return new int[] { pos - count - 1 + intv[0], +1 };
\r
390 if (pos <= count + 1 - diff) {
\r
391 return new int[] { intv[0] - (pos - count - 1), -1 };
\r
397 return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
\r
401 * find series of intervals mapping from start-end in the From map.
\r
404 * position in to map
\r
406 * position in to map
\r
407 * @return series of ranges in from map
\r
409 public int[] locateInFrom(int start, int end) {
\r
410 // inefficient implementation
\r
411 int fromStart[] = shiftTo(start);
\r
412 int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol
\r
414 if (fromStart == null || fromEnd == null)
\r
416 int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
\r
421 * find series of intervals mapping from start-end in the to map.
\r
424 * position in from map
\r
426 * position in from map
\r
427 * @return series of ranges in to map
\r
429 public int[] locateInTo(int start, int end) {
\r
430 // inefficient implementation
\r
431 int toStart[] = shiftFrom(start);
\r
432 int toEnd[] = shiftFrom(end);
\r
433 if (toStart == null || toEnd == null)
\r
435 int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
\r
440 * like shift - except returns the intervals in the given vector of shifts
\r
441 * which were spanned in traversing fromStart to fromEnd
\r
443 * @param fromShifts2
\r
446 * @param fromRatio2
\r
447 * @return series of from,to intervals from from first position of starting
\r
448 * region to final position of ending region inclusive
\r
450 private int[] getIntervals(Vector fromShifts2, int[] fromStart,
\r
451 int[] fromEnd, int fromRatio2) {
\r
452 int startpos, endpos;
\r
453 startpos = fromStart[0]; // first position in fromStart
\r
454 endpos = fromEnd[0]; // last position in fromEnd
\r
455 int endindx = (fromRatio2 - 1); // additional positions to get to last
\r
456 // position from endpos
\r
457 int intv = 0, intvSize = fromShifts2.size();
\r
458 int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
\r
459 // search intervals to locate ones containing startpos and count endindx
\r
460 // positions on from endpos
\r
461 while (intv < intvSize && (fs == -1 || fe == -1))
\r
463 iv = (int[]) fromShifts2.elementAt(intv++);
\r
466 endpos = iv[0]; // start counting from beginning of interval
\r
467 endindx--; // inclusive of endpos
\r
469 if (iv[0] <= iv[1])
\r
471 if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
\r
475 if (endpos >= iv[0] && endpos <= iv[1])
\r
483 if (endpos + endindx <= iv[1])
\r
486 endpos = endpos + endindx; // end of end token is within this
\r
491 endindx -= iv[1] - endpos; // skip all this interval too
\r
498 if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
\r
502 if (endpos <= iv[0] && endpos >= iv[1])
\r
510 if (endpos - endindx >= iv[1])
\r
513 endpos = endpos - endindx; // end of end token is within this
\r
518 endindx -= endpos - iv[1]; // skip all this interval too
\r
525 if (fs == fe && fe == -1)
\r
527 Vector ranges = new Vector();
\r
532 // truncate initial interval
\r
533 iv = (int[]) fromShifts2.elementAt(intv++);
\r
535 { iv[0], iv[1] };// clone
\r
540 ranges.addElement(iv); // add initial range
\r
541 iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
\r
543 { iv[0], iv[1] };// clone
\r
548 ranges.addElement(iv); // add only - or final range
\r
552 // walk from end of interval.
\r
553 i = fromShifts2.size() - 1;
\r
558 iv = (int[]) fromShifts2.elementAt(i);
\r
560 { iv[1], iv[0] };// reverse and clone
\r
561 // truncate initial interval
\r
567 { // fix apparent logic bug when fe==-1
\r
568 ranges.addElement(iv); // add (truncated) reversed interval
\r
569 iv = (int[]) fromShifts2.elementAt(i);
\r
571 { iv[1], iv[0] }; // reverse and clone
\r
575 // interval is already reversed
\r
578 ranges.addElement(iv); // add only - or final range
\r
580 // create array of start end intervals.
\r
581 int[] range = null;
\r
582 if (ranges != null && ranges.size() > 0)
\r
584 range = new int[ranges.size() * 2];
\r
586 intvSize = ranges.size();
\r
588 while (intv < intvSize)
\r
590 iv = (int[]) ranges.elementAt(intv);
\r
591 range[i++] = iv[0];
\r
592 range[i++] = iv[1];
\r
593 ranges.setElementAt(null, intv++); // remove
\r
600 * get the 'initial' position of mpos in To
\r
604 * @return position of first word in to reference frame
\r
606 public int getToPosition(int mpos) {
\r
607 int[] mp = shiftTo(mpos);
\r
615 * get range of positions in To frame for the mpos word in From
\r
619 * @return null or int[] first position in To for mpos, last position in to
\r
622 public int[] getToWord(int mpos) {
\r
623 int[] mp = shiftTo(mpos);
\r
625 return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
\r
631 * get From position in the associated reference frame for position pos in the
\r
632 * associated sequence.
\r
637 public int getMappedPosition(int pos) {
\r
638 int[] mp = shiftFrom(pos);
\r
645 public int[] getMappedWord(int pos) {
\r
646 int[] mp = shiftFrom(pos);
\r
648 return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
\r
654 * test routine. not incremental.
\r
660 public static void testMap(MapList ml, int fromS, int fromE)
\r
662 for (int from = 1; from <= 25; from++)
\r
664 int[] too = ml.shiftFrom(from);
\r
665 System.out.print("ShiftFrom(" + from + ")==");
\r
668 System.out.print("NaN\n");
\r
672 System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
\r
673 System.out.print("\t+--+\t");
\r
674 int[] toofrom = ml.shiftTo(too[0]);
\r
675 if (toofrom != null)
\r
677 if (toofrom[0] != from)
\r
679 System.err.println("Mapping not reflexive:" + from + " "
\r
680 + too[0] + "->" + toofrom[0]);
\r
682 System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
\r
683 + " % " + toofrom[1] + " (" + toofrom[2] + ")");
\r
687 System.out.println("ShiftTo(" + too[0] + ")=="
\r
688 + "NaN! - not Bijective Mapping!");
\r
692 int mmap[][] = ml.makeFromMap();
\r
693 System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
\r
694 + mmap[0][2] + " " + mmap[0][3] + " ");
\r
695 for (int i = 1; i <= mmap[1].length; i++)
\r
697 if (mmap[1][i - 1] == -1)
\r
699 System.out.print(i + "=XXX");
\r
704 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
\r
708 System.out.print("\n");
\r
712 System.out.print(",");
\r
715 // test range function
\r
716 System.out.print("\nTest locateInFrom\n");
\r
718 int f = mmap[0][2], t = mmap[0][3];
\r
721 System.out.println("Range " + f + " to " + t);
\r
722 int rng[] = ml.locateInFrom(f, t);
\r
725 for (int i = 0; i < rng.length; i++)
\r
727 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
\r
732 System.out.println("No range!");
\r
734 System.out.print("\nReversed\n");
\r
735 rng = ml.locateInFrom(t, f);
\r
738 for (int i = 0; i < rng.length; i++)
\r
740 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
\r
745 System.out.println("No range!");
\r
747 System.out.print("\n");
\r
752 System.out.print("\n");
\r
753 mmap = ml.makeToMap();
\r
754 System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
\r
755 + mmap[0][2] + " " + mmap[0][3] + " ");
\r
756 for (int i = 1; i <= mmap[1].length; i++)
\r
758 if (mmap[1][i - 1] == -1)
\r
760 System.out.print(i + "=XXX");
\r
765 System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
\r
769 System.out.print("\n");
\r
773 System.out.print(",");
\r
776 System.out.print("\n");
\r
777 // test range function
\r
778 System.out.print("\nTest locateInTo\n");
\r
780 int f = mmap[0][2], t = mmap[0][3];
\r
783 System.out.println("Range " + f + " to " + t);
\r
784 int rng[] = ml.locateInTo(f, t);
\r
787 for (int i = 0; i < rng.length; i++)
\r
789 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
\r
794 System.out.println("No range!");
\r
796 System.out.print("\nReversed\n");
\r
797 rng = ml.locateInTo(t, f);
\r
800 for (int i = 0; i < rng.length; i++)
\r
802 System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
\r
807 System.out.println("No range!");
\r
811 System.out.print("\n");
\r
817 public static void main(String argv[])
\r
819 MapList ml = new MapList(new int[]
\r
820 { 1, 5, 10, 15, 25, 20 }, new int[]
\r
822 MapList ml1 = new MapList(new int[]
\r
823 { 1, 3, 17, 4 }, new int[]
\r
825 MapList ml2 = new MapList(new int[]
\r
826 { 1, 60 }, new int[]
\r
828 // test internal consistency
\r
829 int to[] = new int[51];
\r
830 MapList.testMap(ml, 1, 60);
\r
831 MapList mldna = new MapList(new int[]
\r
832 { 2, 2, 6, 8, 12, 16 }, new int[]
\r
834 int[] frm = mldna.locateInFrom(1, 1);
\r
835 testLocateFrom(mldna, 1, 1, new int[]
\r
837 MapList.testMap(mldna, 1, 3);
\r
839 * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
\r
840 * toofrom=ml.shiftFrom(too[0]);
\r
841 * System.out.println("ShiftFrom("+from+")=="+too
\r
842 * [0]+" % "+too[1]+"\t+-+\tShiftTo("
\r
843 * +too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
\r
845 System.out.print("Success?\n"); // if we get here - something must be
\r
849 private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
\r
851 int[] frm = mldna.locateInFrom(i, j);
\r
852 if (frm == ks || java.util.Arrays.equals(frm, ks))
\r
854 System.out.println("Success test locate from " + i + " to " + j);
\r
858 System.err.println("Failed test locate from " + i + " to " + j);
\r
859 for (int c = 0; c < frm.length; c++)
\r
861 System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
\r
863 System.err.println("Expected");
\r
864 for (int c = 0; c < ks.length; c++)
\r
866 System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));
\r
873 * @return a MapList whose From range is this maplist's To Range, and vice
\r
876 public MapList getInverse()
\r
878 return new MapList(getToRanges(), getFromRanges(), getToRatio(),
\r
883 * test for containment rather than equivalence to another mapping
\r
884 * @param map to be tested for containment
\r
885 * @return true if local or mapped range map contains or is contained by this mapping
\r
887 public boolean containsEither(boolean local, MapList map)
\r
891 return ((getFromLowest()>=map.getFromLowest() && getFromHighest()<=map.getFromHighest())
\r
892 || (getFromLowest()<=map.getFromLowest() && getFromHighest()>=map.getFromHighest()));
\r
894 return ((getToLowest()>=map.getToLowest() && getToHighest()<=map.getToHighest())
\r
895 || (getToLowest()<=map.getToLowest() && getToHighest()>=map.getToHighest()));
\r