2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.util.ArrayList;
24 import java.util.Arrays;
25 import java.util.List;
28 * A simple way of bijectively mapping a non-contiguous linear range to another
29 * non-contiguous linear range.
31 * Use at your own risk!
33 * TODO: efficient implementation of private posMap method
35 * TODO: test/ensure that sense of from and to ratio start position is conserved
36 * (codon start position recovery)
42 * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
44 private List<int[]> fromShifts = new ArrayList<int[]>();
47 * Same format as fromShifts, for the 'mapped to' sequence
49 private List<int[]> toShifts = new ArrayList<int[]>();
52 * number of steps in fromShifts to one toRatio unit
54 private int fromRatio;
57 * number of steps in toShifts to one fromRatio
62 * lowest and highest value in the from Map
64 private int fromLowest;
66 private int fromHighest;
69 * lowest and highest value in the to Map
73 private int toHighest;
76 * Two MapList objects are equal if they are the same object, or they both
77 * have populated shift ranges and all values are the same.
80 public boolean equals(Object o)
82 if (o == null || !(o instanceof MapList))
87 MapList obj = (MapList) o;
92 if (obj.fromRatio != fromRatio || obj.toRatio != toRatio
93 || obj.fromShifts == null || obj.toShifts == null)
98 .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
100 .deepEquals(toShifts.toArray(), obj.toShifts.toArray());
104 * Returns the flattened 'from' ranges as [start1, end1, start2, end2, ...]
108 public int[] getFromRanges()
110 return getRanges(fromShifts);
114 * Returns the flattened 'to' ranges as [start1, end1, start2, end2, ...]
118 public int[] getToRanges()
120 return getRanges(toShifts);
124 * Flattens a list of [start, end] into a single [start1, end1, start2,
130 protected static int[] getRanges(List<int[]> shifts)
132 int[] rnges = new int[2 * shifts.size()];
134 for (int[] r : shifts)
144 * @return length of mapped phrase in from
146 public int getFromRatio()
153 * @return length of mapped phrase in to
155 public int getToRatio()
160 public int getFromLowest()
165 public int getFromHighest()
170 public int getToLowest()
175 public int getToHighest()
184 * contiguous regions as [start1, end1, start2, end2, ...]
186 * same format as 'from'
188 * phrase length in 'from' (e.g. 3 for dna)
190 * phrase length in 'to' (e.g. 1 for protein)
192 public MapList(int from[], int to[], int fromRatio, int toRatio)
194 fromLowest = from[0];
195 fromHighest = from[1];
196 for (int i = 0; i < from.length; i += 2)
198 fromLowest = Math.min(fromLowest, from[i]);
199 fromHighest = Math.max(fromHighest, from[i + 1]);
201 fromShifts.add(new int[]
202 { from[i], from[i + 1] });
207 for (int i = 0; i < to.length; i += 2)
209 toLowest = Math.min(toLowest, to[i]);
210 toHighest = Math.max(toHighest, to[i + 1]);
211 toShifts.add(new int[]
212 { to[i], to[i + 1] });
214 this.fromRatio = fromRatio;
215 this.toRatio = toRatio;
219 * Copy constructor. Creates an identical mapping.
223 public MapList(MapList map)
225 // TODO not used - remove?
226 this.fromLowest = map.fromLowest;
227 this.fromHighest = map.fromHighest;
228 this.toLowest = map.toLowest;
229 this.toHighest = map.toHighest;
231 this.fromRatio = map.fromRatio;
232 this.toRatio = map.toRatio;
233 if (map.fromShifts != null)
235 for (int[] r : map.fromShifts)
237 fromShifts.add(new int[]
241 if (map.toShifts != null)
243 for (int[] r : map.toShifts)
245 toShifts.add(new int[]
252 * get all mapped positions from 'from' to 'to'
254 * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
255 * [fromFinish-fromStart+2] { toStart..toFinish mappings}}
257 protected int[][] makeFromMap()
259 // TODO not used - remove??
260 return posMap(fromShifts, fromRatio, toShifts, toRatio);
264 * get all mapped positions from 'to' to 'from'
266 * @return int[to position]=position mapped in from
268 protected int[][] makeToMap()
270 // TODO not used - remove??
271 return posMap(toShifts, toRatio, fromShifts, fromRatio);
275 * construct an int map for intervals in intVals
278 * @return int[] { from, to pos in range }, int[range.to-range.from+1]
279 * returning mapped position
281 private int[][] posMap(List<int[]> shiftTo, int ratio,
282 List<int[]> shiftFrom,
285 // TODO not used - remove??
286 int iv = 0, ivSize = shiftTo.size();
291 int[] intv = shiftTo.get(iv++);
292 int from = intv[0], to = intv[1];
300 intv = shiftTo.get(iv++);
319 int mp[][] = new int[to - from + 2][];
320 for (int i = 0; i < mp.length; i++)
322 int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
343 int[][] map = new int[][]
345 { from, to, tF, tT }, new int[to - from + 2] };
350 for (int i = 0; i < mp.length; i++)
354 map[1][i] = mp[i][0] - tF;
358 map[1][i] = -1; // indicates an out of range mapping
368 * start position for shift (in original reference frame)
372 * public void addShift(int pos, int shift) { int sidx = 0; int[]
373 * rshift=null; while (sidx<shifts.size() && (rshift=(int[])
374 * shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())
375 * shifts.insertElementAt(new int[] { pos, shift}, sidx); else
376 * rshift[1]+=shift; }
380 * shift from pos to To(pos)
384 * @return int shifted position in To, frameshift in From, direction of mapped
387 public int[] shiftFrom(int pos)
389 return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
393 * inverse of shiftFrom - maps pos in To to a position in From
397 * @return shifted position in From, frameshift in To, direction of mapped
400 public int[] shiftTo(int pos)
402 return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
413 protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,
414 List<int[]> shiftFrom, int toRatio)
416 // TODO: javadoc; tests
417 int[] fromCount = countPos(shiftTo, pos);
418 if (fromCount == null)
422 int fromRemainder = (fromCount[0] - 1) % fromRatio;
423 int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
424 int[] toPos = countToPos(shiftFrom, toCount);
427 return null; // throw new Error("Bad Mapping!");
429 // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
431 { toPos[0], fromRemainder, toPos[1] };
435 * count how many positions pos is along the series of intervals.
439 * @return number of positions or null if pos is not within intervals
441 protected static int[] countPos(List<int[]> shiftTo, int pos)
443 int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
446 intv = shiftTo.get(iv++);
447 if (intv[0] <= intv[1])
449 if (pos >= intv[0] && pos <= intv[1])
452 { count + pos - intv[0] + 1, +1 };
456 count += intv[1] - intv[0] + 1;
461 if (pos >= intv[1] && pos <= intv[0])
464 { count + intv[0] - pos + 1, -1 };
468 count += intv[0] - intv[1] + 1;
476 * count out pos positions into a series of intervals and return the position
480 * @return position pos in interval set
482 protected static int[] countToPos(List<int[]> shiftFrom, int pos)
484 int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
489 intv = shiftFrom.get(iv++);
490 diff = intv[1] - intv[0];
493 if (pos <= count + 1 + diff)
496 { pos - count - 1 + intv[0], +1 };
505 if (pos <= count + 1 - diff)
508 { intv[0] - (pos - count - 1), -1 };
516 return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
520 * find series of intervals mapping from start-end in the From map.
523 * position mapped 'to'
525 * position mapped 'to'
526 * @return series of [start, end] ranges in sequence mapped 'from'
528 public int[] locateInFrom(int start, int end)
530 // inefficient implementation
531 int fromStart[] = shiftTo(start);
532 // needs to be inclusive of end of symbol position
533 int fromEnd[] = shiftTo(end);
535 return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
539 * find series of intervals mapping from start-end in the to map.
542 * position mapped 'from'
544 * position mapped 'from'
545 * @return series of [start, end] ranges in sequence mapped 'to'
547 public int[] locateInTo(int start, int end)
549 int toStart[] = shiftFrom(start);
550 int toEnd[] = shiftFrom(end);
551 return getIntervals(toShifts, toStart, toEnd, toRatio);
555 * like shift - except returns the intervals in the given vector of shifts
556 * which were spanned in traversing fromStart to fromEnd
562 * @return series of from,to intervals from from first position of starting
563 * region to final position of ending region inclusive
565 protected static int[] getIntervals(List<int[]> shiftFrom,
567 int[] fromEnd, int fromRatio2)
569 if (fromStart == null || fromEnd == null)
573 int startpos, endpos;
574 startpos = fromStart[0]; // first position in fromStart
575 endpos = fromEnd[0]; // last position in fromEnd
576 int endindx = (fromRatio2 - 1); // additional positions to get to last
577 // position from endpos
578 int intv = 0, intvSize = shiftFrom.size();
579 int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
580 // search intervals to locate ones containing startpos and count endindx
581 // positions on from endpos
582 while (intv < intvSize && (fs == -1 || fe == -1))
584 iv = shiftFrom.get(intv++);
587 endpos = iv[0]; // start counting from beginning of interval
588 endindx--; // inclusive of endpos
592 if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
596 if (endpos >= iv[0] && endpos <= iv[1])
604 if (endpos + endindx <= iv[1])
607 endpos = endpos + endindx; // end of end token is within this
612 endindx -= iv[1] - endpos; // skip all this interval too
619 if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
623 if (endpos <= iv[0] && endpos >= iv[1])
631 if (endpos - endindx >= iv[1])
634 endpos = endpos - endindx; // end of end token is within this
639 endindx -= endpos - iv[1]; // skip all this interval too
646 if (fs == fe && fe == -1)
650 List<int[]> ranges = new ArrayList<int[]>();
655 // truncate initial interval
656 iv = shiftFrom.get(intv++);
658 { iv[0], iv[1] };// clone
665 ranges.add(iv); // add initial range
666 iv = shiftFrom.get(intv++); // get next interval
668 { iv[0], iv[1] };// clone
675 ranges.add(iv); // add only - or final range
679 // walk from end of interval.
680 i = shiftFrom.size() - 1;
685 iv = shiftFrom.get(i);
687 { iv[1], iv[0] };// reverse and clone
688 // truncate initial interval
694 { // fix apparent logic bug when fe==-1
695 ranges.add(iv); // add (truncated) reversed interval
696 iv = shiftFrom.get(i);
698 { iv[1], iv[0] }; // reverse and clone
702 // interval is already reversed
705 ranges.add(iv); // add only - or final range
707 // create array of start end intervals.
709 if (ranges != null && ranges.size() > 0)
711 range = new int[ranges.size() * 2];
713 intvSize = ranges.size();
715 while (intv < intvSize)
717 iv = ranges.get(intv);
720 ranges.set(intv++, null); // remove
727 * get the 'initial' position of mpos in To
731 * @return position of first word in to reference frame
733 public int getToPosition(int mpos)
735 // TODO not used - remove??
736 int[] mp = shiftTo(mpos);
745 * get range of positions in To frame for the mpos word in From
749 * @return null or int[] first position in To for mpos, last position in to
752 public int[] getToWord(int mpos)
754 int[] mp = shiftTo(mpos);
758 { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
764 * get From position in the associated reference frame for position pos in the
765 * associated sequence.
770 public int getMappedPosition(int pos)
772 // TODO not used - remove??
773 int[] mp = shiftFrom(pos);
781 public int[] getMappedWord(int pos)
783 // TODO not used - remove??
784 int[] mp = shiftFrom(pos);
788 { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
795 * @return a MapList whose From range is this maplist's To Range, and vice
798 public MapList getInverse()
800 return new MapList(getToRanges(), getFromRanges(), getToRatio(),
805 * test for containment rather than equivalence to another mapping
808 * to be tested for containment
809 * @return true if local or mapped range map contains or is contained by this
812 public boolean containsEither(boolean local, MapList map)
814 // TODO not used - remove?
817 return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
818 .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map
823 return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
824 .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map