2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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 // TODO should also override hashCode to ensure equal objects have equal
84 if (o == null || !(o instanceof MapList))
89 MapList obj = (MapList) o;
94 if (obj.fromRatio != fromRatio || obj.toRatio != toRatio
95 || obj.fromShifts == null || obj.toShifts == null)
100 .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
102 .deepEquals(toShifts.toArray(), obj.toShifts.toArray());
106 * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
110 public List<int[]> getFromRanges()
116 * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
120 public List<int[]> getToRanges()
126 * Flattens a list of [start, end] into a single [start1, end1, start2,
132 protected static int[] getRanges(List<int[]> shifts)
134 int[] rnges = new int[2 * shifts.size()];
136 for (int[] r : shifts)
146 * @return length of mapped phrase in from
148 public int getFromRatio()
155 * @return length of mapped phrase in to
157 public int getToRatio()
162 public int getFromLowest()
167 public int getFromHighest()
172 public int getToLowest()
177 public int getToHighest()
186 * contiguous regions as [start1, end1, start2, end2, ...]
188 * same format as 'from'
190 * phrase length in 'from' (e.g. 3 for dna)
192 * phrase length in 'to' (e.g. 1 for protein)
194 public MapList(int from[], int to[], int fromRatio, int toRatio)
196 this.fromRatio = fromRatio;
197 this.toRatio = toRatio;
198 fromLowest = from[0];
199 fromHighest = from[1];
200 for (int i = 0; i < from.length; i += 2)
202 fromLowest = Math.min(fromLowest, from[i]);
203 fromHighest = Math.max(fromHighest, from[i + 1]);
205 fromShifts.add(new int[]
206 { from[i], from[i + 1] });
211 for (int i = 0; i < to.length; i += 2)
213 toLowest = Math.min(toLowest, to[i]);
214 toHighest = Math.max(toHighest, to[i + 1]);
215 toShifts.add(new int[]
216 { to[i], to[i + 1] });
221 * Copy constructor. Creates an identical mapping.
225 public MapList(MapList map)
227 // TODO not used - remove?
228 this.fromLowest = map.fromLowest;
229 this.fromHighest = map.fromHighest;
230 this.toLowest = map.toLowest;
231 this.toHighest = map.toHighest;
233 this.fromRatio = map.fromRatio;
234 this.toRatio = map.toRatio;
235 if (map.fromShifts != null)
237 for (int[] r : map.fromShifts)
239 fromShifts.add(new int[]
243 if (map.toShifts != null)
245 for (int[] r : map.toShifts)
247 toShifts.add(new int[]
254 * Constructor given ranges as lists of [start, end] positions
261 public MapList(List<int[]> fromRange, List<int[]> toRange,
262 int fromRatio, int toRatio)
264 this.fromShifts = fromRange;
265 this.toShifts = toRange;
266 this.fromRatio = fromRatio;
267 this.toRatio = toRatio;
269 fromLowest = Integer.MAX_VALUE;
271 for (int[] range : fromRange) {
272 fromLowest = Math.min(fromLowest, range[0]);
273 fromHighest = Math.max(fromHighest, range[1]);
276 toLowest = Integer.MAX_VALUE;
278 for (int[] range : toRange)
280 toLowest = Math.min(toLowest, range[0]);
281 toHighest = Math.max(toHighest, range[1]);
286 * get all mapped positions from 'from' to 'to'
288 * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
289 * [fromFinish-fromStart+2] { toStart..toFinish mappings}}
291 protected int[][] makeFromMap()
293 // TODO not used - remove??
294 return posMap(fromShifts, fromRatio, toShifts, toRatio);
298 * get all mapped positions from 'to' to 'from'
300 * @return int[to position]=position mapped in from
302 protected int[][] makeToMap()
304 // TODO not used - remove??
305 return posMap(toShifts, toRatio, fromShifts, fromRatio);
309 * construct an int map for intervals in intVals
312 * @return int[] { from, to pos in range }, int[range.to-range.from+1]
313 * returning mapped position
315 private int[][] posMap(List<int[]> shiftTo, int ratio,
316 List<int[]> shiftFrom,
319 // TODO not used - remove??
320 int iv = 0, ivSize = shiftTo.size();
325 int[] intv = shiftTo.get(iv++);
326 int from = intv[0], to = intv[1];
334 intv = shiftTo.get(iv++);
353 int mp[][] = new int[to - from + 2][];
354 for (int i = 0; i < mp.length; i++)
356 int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
377 int[][] map = new int[][]
379 { from, to, tF, tT }, new int[to - from + 2] };
384 for (int i = 0; i < mp.length; i++)
388 map[1][i] = mp[i][0] - tF;
392 map[1][i] = -1; // indicates an out of range mapping
402 * start position for shift (in original reference frame)
406 * public void addShift(int pos, int shift) { int sidx = 0; int[]
407 * rshift=null; while (sidx<shifts.size() && (rshift=(int[])
408 * shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())
409 * shifts.insertElementAt(new int[] { pos, shift}, sidx); else
410 * rshift[1]+=shift; }
414 * shift from pos to To(pos)
418 * @return int shifted position in To, frameshift in From, direction of mapped
421 public int[] shiftFrom(int pos)
423 return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
427 * inverse of shiftFrom - maps pos in To to a position in From
431 * @return shifted position in From, frameshift in To, direction of mapped
434 public int[] shiftTo(int pos)
436 return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
447 protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,
448 List<int[]> shiftFrom, int toRatio)
450 // TODO: javadoc; tests
451 int[] fromCount = countPos(shiftTo, pos);
452 if (fromCount == null)
456 int fromRemainder = (fromCount[0] - 1) % fromRatio;
457 int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
458 int[] toPos = countToPos(shiftFrom, toCount);
461 return null; // throw new Error("Bad Mapping!");
463 // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
465 { toPos[0], fromRemainder, toPos[1] };
469 * count how many positions pos is along the series of intervals.
473 * @return number of positions or null if pos is not within intervals
475 protected static int[] countPos(List<int[]> shiftTo, int pos)
477 int count = 0, intv[], iv = 0, ivSize = shiftTo.size();
480 intv = shiftTo.get(iv++);
481 if (intv[0] <= intv[1])
483 if (pos >= intv[0] && pos <= intv[1])
486 { count + pos - intv[0] + 1, +1 };
490 count += intv[1] - intv[0] + 1;
495 if (pos >= intv[1] && pos <= intv[0])
498 { count + intv[0] - pos + 1, -1 };
502 count += intv[0] - intv[1] + 1;
510 * count out pos positions into a series of intervals and return the position
514 * @return position pos in interval set
516 protected static int[] countToPos(List<int[]> shiftFrom, int pos)
518 int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
523 intv = shiftFrom.get(iv++);
524 diff = intv[1] - intv[0];
527 if (pos <= count + 1 + diff)
530 { pos - count - 1 + intv[0], +1 };
539 if (pos <= count + 1 - diff)
542 { intv[0] - (pos - count - 1), -1 };
550 return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
554 * find series of intervals mapping from start-end in the From map.
557 * position mapped 'to'
559 * position mapped 'to'
560 * @return series of [start, end] ranges in sequence mapped 'from'
562 public int[] locateInFrom(int start, int end)
564 // inefficient implementation
565 int fromStart[] = shiftTo(start);
566 // needs to be inclusive of end of symbol position
567 int fromEnd[] = shiftTo(end);
569 return getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
573 * find series of intervals mapping from start-end in the to map.
576 * position mapped 'from'
578 * position mapped 'from'
579 * @return series of [start, end] ranges in sequence mapped 'to'
581 public int[] locateInTo(int start, int end)
583 int toStart[] = shiftFrom(start);
584 int toEnd[] = shiftFrom(end);
585 return getIntervals(toShifts, toStart, toEnd, toRatio);
589 * like shift - except returns the intervals in the given vector of shifts
590 * which were spanned in traversing fromStart to fromEnd
596 * @return series of from,to intervals from from first position of starting
597 * region to final position of ending region inclusive
599 protected static int[] getIntervals(List<int[]> shiftFrom,
601 int[] fromEnd, int fromRatio2)
603 if (fromStart == null || fromEnd == null)
607 int startpos, endpos;
608 startpos = fromStart[0]; // first position in fromStart
609 endpos = fromEnd[0]; // last position in fromEnd
610 int endindx = (fromRatio2 - 1); // additional positions to get to last
611 // position from endpos
612 int intv = 0, intvSize = shiftFrom.size();
613 int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
614 // search intervals to locate ones containing startpos and count endindx
615 // positions on from endpos
616 while (intv < intvSize && (fs == -1 || fe == -1))
618 iv = shiftFrom.get(intv++);
621 endpos = iv[0]; // start counting from beginning of interval
622 endindx--; // inclusive of endpos
626 if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
630 if (endpos >= iv[0] && endpos <= iv[1])
638 if (endpos + endindx <= iv[1])
641 endpos = endpos + endindx; // end of end token is within this
646 endindx -= iv[1] - endpos; // skip all this interval too
653 if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
657 if (endpos <= iv[0] && endpos >= iv[1])
665 if (endpos - endindx >= iv[1])
668 endpos = endpos - endindx; // end of end token is within this
673 endindx -= endpos - iv[1]; // skip all this interval too
680 if (fs == fe && fe == -1)
684 List<int[]> ranges = new ArrayList<int[]>();
689 // truncate initial interval
690 iv = shiftFrom.get(intv++);
692 { iv[0], iv[1] };// clone
699 ranges.add(iv); // add initial range
700 iv = shiftFrom.get(intv++); // get next interval
702 { iv[0], iv[1] };// clone
709 ranges.add(iv); // add only - or final range
713 // walk from end of interval.
714 i = shiftFrom.size() - 1;
719 iv = shiftFrom.get(i);
721 { iv[1], iv[0] };// reverse and clone
722 // truncate initial interval
728 { // fix apparent logic bug when fe==-1
729 ranges.add(iv); // add (truncated) reversed interval
730 iv = shiftFrom.get(i);
732 { iv[1], iv[0] }; // reverse and clone
736 // interval is already reversed
739 ranges.add(iv); // add only - or final range
741 // create array of start end intervals.
743 if (ranges != null && ranges.size() > 0)
745 range = new int[ranges.size() * 2];
747 intvSize = ranges.size();
749 while (intv < intvSize)
751 iv = ranges.get(intv);
754 ranges.set(intv++, null); // remove
761 * get the 'initial' position of mpos in To
765 * @return position of first word in to reference frame
767 public int getToPosition(int mpos)
769 // TODO not used - remove??
770 int[] mp = shiftTo(mpos);
779 * get range of positions in To frame for the mpos word in From
783 * @return null or int[] first position in To for mpos, last position in to
786 public int[] getToWord(int mpos)
788 int[] mp = shiftTo(mpos);
792 { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) };
798 * get From position in the associated reference frame for position pos in the
799 * associated sequence.
804 public int getMappedPosition(int pos)
806 // TODO not used - remove??
807 int[] mp = shiftFrom(pos);
815 public int[] getMappedWord(int pos)
817 // TODO not used - remove??
818 int[] mp = shiftFrom(pos);
822 { mp[0], mp[0] + mp[2] * (getToRatio() - 1) };
829 * @return a MapList whose From range is this maplist's To Range, and vice
832 public MapList getInverse()
834 return new MapList(getToRanges(), getFromRanges(), getToRatio(),
839 * test for containment rather than equivalence to another mapping
842 * to be tested for containment
843 * @return true if local or mapped range map contains or is contained by this
846 public boolean containsEither(boolean local, MapList map)
848 // TODO not used - remove?
851 return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
852 .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map
857 return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
858 .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map