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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.util

File MapList.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

188
410
44
1
1,459
829
167
0.41
9.32
44
3.8

Classes

Class Line # Actions
MapList 39 410 167
0.647975164.8%
 

Contributing tests

This file is covered by 223 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.util;
22   
23    import java.util.ArrayList;
24    import java.util.Arrays;
25    import java.util.BitSet;
26    import java.util.List;
27   
28    import jalview.bin.Console;
29   
30    /**
31    * A simple way of bijectively mapping a non-contiguous linear range to another
32    * non-contiguous linear range.
33    *
34    * Use at your own risk!
35    *
36    * TODO: test/ensure that sense of from and to ratio start position is conserved
37    * (codon start position recovery)
38    */
 
39    public class MapList
40    {
41   
42    /*
43    * Subregions (base 1) described as { [start1, end1], [start2, end2], ...}
44    */
45    private List<int[]> fromShifts;
46   
47    /*
48    * Same format as fromShifts, for the 'mapped to' sequence
49    */
50    private List<int[]> toShifts;
51   
52    /*
53    * number of steps in fromShifts to one toRatio unit
54    */
55    private int fromRatio;
56   
57    /*
58    * number of steps in toShifts to one fromRatio
59    */
60    private int toRatio;
61   
62    /*
63    * lowest and highest value in the from Map
64    */
65    private int fromLowest;
66   
67    private int fromHighest;
68   
69    /*
70    * lowest and highest value in the to Map
71    */
72    private int toLowest;
73   
74    private int toHighest;
75   
76    /**
77    * Constructor
78    */
 
79  1238 toggle public MapList()
80    {
81  1238 fromShifts = new ArrayList<>();
82  1238 toShifts = new ArrayList<>();
83    }
84   
85    /**
86    * Two MapList objects are equal if they are the same object, or they both
87    * have populated shift ranges and all values are the same.
88    */
 
89  108 toggle @Override
90    public boolean equals(Object o)
91    {
92  108 if (o == null || !(o instanceof MapList))
93    {
94  2 return false;
95    }
96   
97  106 MapList obj = (MapList) o;
98  106 if (obj == this)
99    {
100  18 return true;
101    }
102  88 if (obj.fromRatio != fromRatio || obj.toRatio != toRatio
103    || obj.fromShifts == null || obj.toShifts == null)
104    {
105  25 return false;
106    }
107  63 return Arrays.deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
108    && Arrays.deepEquals(toShifts.toArray(),
109    obj.toShifts.toArray());
110    }
111   
112    /**
113    * Returns a hashcode made from the fromRatio, toRatio, and from/to ranges
114    */
 
115  39 toggle @Override
116    public int hashCode()
117    {
118  39 int hashCode = 31 * fromRatio;
119  39 hashCode = 31 * hashCode + toRatio;
120  39 for (int[] shift : fromShifts)
121    {
122  59 hashCode = 31 * hashCode + shift[0];
123  59 hashCode = 31 * hashCode + shift[1];
124    }
125  39 for (int[] shift : toShifts)
126    {
127  39 hashCode = 31 * hashCode + shift[0];
128  39 hashCode = 31 * hashCode + shift[1];
129    }
130   
131  39 return hashCode;
132    }
133   
134    /**
135    * Returns the 'from' ranges as {[start1, end1], [start2, end2], ...}
136    *
137    * @return
138    */
 
139  635 toggle public List<int[]> getFromRanges()
140    {
141  635 return fromShifts;
142    }
143   
144    /**
145    * Returns the 'to' ranges as {[start1, end1], [start2, end2], ...}
146    *
147    * @return
148    */
 
149  604 toggle public List<int[]> getToRanges()
150    {
151  604 return toShifts;
152    }
153   
154    /**
155    * Flattens a list of [start, end] into a single [start1, end1, start2,
156    * end2,...] array.
157    *
158    * @param shifts
159    * @return
160    */
 
161  1 toggle protected static int[] getRanges(List<int[]> shifts)
162    {
163  1 int[] rnges = new int[2 * shifts.size()];
164  1 int i = 0;
165  1 for (int[] r : shifts)
166    {
167  2 rnges[i++] = r[0];
168  2 rnges[i++] = r[1];
169    }
170  1 return rnges;
171    }
172   
173    /**
174    *
175    * @return length of mapped phrase in from
176    */
 
177  22114 toggle public int getFromRatio()
178    {
179  22114 return fromRatio;
180    }
181   
182    /**
183    *
184    * @return length of mapped phrase in to
185    */
 
186  432 toggle public int getToRatio()
187    {
188  432 return toRatio;
189    }
190   
 
191  89 toggle public int getFromLowest()
192    {
193  89 return fromLowest;
194    }
195   
 
196  90 toggle public int getFromHighest()
197    {
198  90 return fromHighest;
199    }
200   
 
201  28 toggle public int getToLowest()
202    {
203  28 return toLowest;
204    }
205   
 
206  3619 toggle public int getToHighest()
207    {
208  3619 return toHighest;
209    }
210   
211    /**
212    * Constructor given from and to ranges as [start1, end1, start2, end2,...].
213    * There is no validation check that the ranges do not overlap each other.
214    *
215    * @param from
216    * contiguous regions as [start1, end1, start2, end2, ...]
217    * @param to
218    * same format as 'from'
219    * @param fromRatio
220    * phrase length in 'from' (e.g. 3 for dna)
221    * @param toRatio
222    * phrase length in 'to' (e.g. 1 for protein)
223    */
 
224  1021 toggle public MapList(int from[], int to[], int fromRatio, int toRatio)
225    {
226  1021 this();
227  1021 this.fromRatio = fromRatio;
228  1021 this.toRatio = toRatio;
229  1021 fromLowest = Integer.MAX_VALUE;
230  1021 fromHighest = Integer.MIN_VALUE;
231   
232  2279 for (int i = 0; i < from.length; i += 2)
233    {
234    /*
235    * note lowest and highest values - bearing in mind the
236    * direction may be reversed
237    */
238  1259 fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1]));
239  1259 fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1]));
240  1259 fromShifts.add(new int[] { from[i], from[i + 1] });
241    }
242   
243  1020 toLowest = Integer.MAX_VALUE;
244  1020 toHighest = Integer.MIN_VALUE;
245  2354 for (int i = 0; i < to.length; i += 2)
246    {
247  1335 toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1]));
248  1335 toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1]));
249  1335 toShifts.add(new int[] { to[i], to[i + 1] });
250    }
251    }
252   
253    /**
254    * Copy constructor. Creates an identical mapping.
255    *
256    * @param map
257    */
 
258  23 toggle public MapList(MapList map)
259    {
260  23 this();
261    // TODO not used - remove?
262  23 this.fromLowest = map.fromLowest;
263  23 this.fromHighest = map.fromHighest;
264  23 this.toLowest = map.toLowest;
265  23 this.toHighest = map.toHighest;
266   
267  23 this.fromRatio = map.fromRatio;
268  23 this.toRatio = map.toRatio;
269  23 if (map.fromShifts != null)
270    {
271  23 for (int[] r : map.fromShifts)
272    {
273  35 fromShifts.add(new int[] { r[0], r[1] });
274    }
275    }
276  23 if (map.toShifts != null)
277    {
278  23 for (int[] r : map.toShifts)
279    {
280  28 toShifts.add(new int[] { r[0], r[1] });
281    }
282    }
283    }
284   
285    /**
286    * Constructor given ranges as lists of [start, end] positions. There is no
287    * validation check that the ranges do not overlap each other.
288    *
289    * @param fromRange
290    * @param toRange
291    * @param fromRatio
292    * @param toRatio
293    */
 
294  194 toggle public MapList(List<int[]> fromRange, List<int[]> toRange, int fromRatio,
295    int toRatio)
296    {
297  194 this();
298  194 fromRange = coalesceRanges(fromRange);
299  194 toRange = coalesceRanges(toRange);
300  194 this.fromShifts = fromRange;
301  194 this.toShifts = toRange;
302  194 this.fromRatio = fromRatio;
303  194 this.toRatio = toRatio;
304   
305  194 fromLowest = Integer.MAX_VALUE;
306  194 fromHighest = Integer.MIN_VALUE;
307  194 for (int[] range : fromRange)
308    {
309  239 if (range.length != 2)
310    {
311    // throw new IllegalArgumentException(range);
312  0 Console.error("Invalid format for fromRange "
313    + Arrays.toString(range) + " may cause errors");
314    }
315  239 fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
316  239 fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
317    }
318   
319  194 toLowest = Integer.MAX_VALUE;
320  194 toHighest = Integer.MIN_VALUE;
321  194 for (int[] range : toRange)
322    {
323  346 if (range.length != 2)
324    {
325    // throw new IllegalArgumentException(range);
326  0 Console.error("Invalid format for toRange " + Arrays.toString(range)
327    + " may cause errors");
328    }
329  346 toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
330  346 toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
331    }
332    }
333   
334    /**
335    * Consolidates a list of ranges so that any contiguous ranges are merged.
336    * This assumes the ranges are already in start order (does not sort them).
337    * <p>
338    * The main use case for this method is when mapping cDNA sequence to its
339    * protein product, based on CDS feature ranges which derive from spliced
340    * exons, but are contiguous on the cDNA sequence. For example
341    *
342    * <pre>
343    * CDS 1-20 // from exon1
344    * CDS 21-35 // from exon2
345    * CDS 36-71 // from exon3
346    * 'coalesce' to range 1-71
347    * </pre>
348    *
349    * @param ranges
350    * @return the same list (if unchanged), else a new merged list, leaving the
351    * input list unchanged
352    */
 
353  397 toggle public static List<int[]> coalesceRanges(final List<int[]> ranges)
354    {
355  397 if (ranges == null || ranges.size() < 2)
356    {
357  327 return ranges;
358    }
359   
360  70 boolean changed = false;
361  70 List<int[]> merged = new ArrayList<>();
362  70 int[] lastRange = ranges.get(0);
363  70 int lastDirection = lastRange[1] >= lastRange[0] ? 1 : -1;
364  70 lastRange = new int[] { lastRange[0], lastRange[1] };
365  70 merged.add(lastRange);
366  70 boolean first = true;
367   
368  70 for (final int[] range : ranges)
369    {
370  287 if (first)
371    {
372  70 first = false;
373  70 continue;
374    }
375   
376  217 int direction = range[1] >= range[0] ? 1 : -1;
377   
378    /*
379    * if next range is in the same direction as last and contiguous,
380    * just update the end position of the last range
381    */
382  217 boolean sameDirection = range[1] == range[0]
383    || direction == lastDirection;
384  217 boolean extending = range[0] == lastRange[1] + lastDirection;
385  217 if (sameDirection && extending)
386    {
387  10 lastRange[1] = range[1];
388  10 changed = true;
389    }
390    else
391    {
392  207 lastRange = new int[] { range[0], range[1] };
393  207 merged.add(lastRange);
394    // careful: merging [5, 5] after [7, 6] should keep negative direction
395  207 lastDirection = (range[1] == range[0]) ? lastDirection : direction;
396    }
397    }
398   
399  70 return changed ? merged : ranges;
400    }
401   
402    /**
403    * get all mapped positions from 'from' to 'to'
404    *
405    * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int
406    * [fromFinish-fromStart+2] { toStart..toFinish mappings}}
407    */
 
408  0 toggle protected int[][] makeFromMap()
409    {
410    // TODO only used for test - remove??
411  0 return posMap(fromShifts, fromRatio, toShifts, toRatio);
412    }
413   
414    /**
415    * get all mapped positions from 'to' to 'from'
416    *
417    * @return int[to position]=position mapped in from
418    */
 
419  0 toggle protected int[][] makeToMap()
420    {
421    // TODO only used for test - remove??
422  0 return posMap(toShifts, toRatio, fromShifts, fromRatio);
423    }
424   
425    /**
426    * construct an int map for intervals in intVals
427    *
428    * @param shiftTo
429    * @return int[] { from, to pos in range }, int[range.to-range.from+1]
430    * returning mapped position
431    */
 
432  0 toggle private int[][] posMap(List<int[]> shiftTo, int sourceRatio,
433    List<int[]> shiftFrom, int targetRatio)
434    {
435    // TODO only used for test - remove??
436  0 int iv = 0, ivSize = shiftTo.size();
437  0 if (iv >= ivSize)
438    {
439  0 return null;
440    }
441  0 int[] intv = shiftTo.get(iv++);
442  0 int from = intv[0], to = intv[1];
443  0 if (from > to)
444    {
445  0 from = intv[1];
446  0 to = intv[0];
447    }
448  0 while (iv < ivSize)
449    {
450  0 intv = shiftTo.get(iv++);
451  0 if (intv[0] < from)
452    {
453  0 from = intv[0];
454    }
455  0 if (intv[1] < from)
456    {
457  0 from = intv[1];
458    }
459  0 if (intv[0] > to)
460    {
461  0 to = intv[0];
462    }
463  0 if (intv[1] > to)
464    {
465  0 to = intv[1];
466    }
467    }
468  0 int tF = 0, tT = 0;
469  0 int mp[][] = new int[to - from + 2][];
470  0 for (int i = 0; i < mp.length; i++)
471    {
472  0 int[] m = shift(i + from, shiftTo, sourceRatio, shiftFrom,
473    targetRatio);
474  0 if (m != null)
475    {
476  0 if (i == 0)
477    {
478  0 tF = tT = m[0];
479    }
480    else
481    {
482  0 if (m[0] < tF)
483    {
484  0 tF = m[0];
485    }
486  0 if (m[0] > tT)
487    {
488  0 tT = m[0];
489    }
490    }
491    }
492  0 mp[i] = m;
493    }
494  0 int[][] map = new int[][] { new int[] { from, to, tF, tT },
495    new int[to - from + 2] };
496   
497  0 map[0][2] = tF;
498  0 map[0][3] = tT;
499   
500  0 for (int i = 0; i < mp.length; i++)
501    {
502  0 if (mp[i] != null)
503    {
504  0 map[1][i] = mp[i][0] - tF;
505    }
506    else
507    {
508  0 map[1][i] = -1; // indicates an out of range mapping
509    }
510    }
511  0 return map;
512    }
513   
514    /**
515    * addShift
516    *
517    * @param pos
518    * start position for shift (in original reference frame)
519    * @param shift
520    * length of shift
521    *
522    * public void addShift(int pos, int shift) { int sidx = 0; int[]
523    * rshift=null; while (sidx<shifts.size() && (rshift=(int[])
524    * shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())
525    * shifts.insertElementAt(new int[] { pos, shift}, sidx); else
526    * rshift[1]+=shift; }
527    */
528   
529    /**
530    * shift from pos to To(pos)
531    *
532    * @param pos
533    * int
534    * @return int shifted position in To, frameshift in From, direction of mapped
535    * symbol in To
536    */
 
537  9 toggle public int[] shiftFrom(int pos)
538    {
539  9 return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
540    }
541   
542    /**
543    * inverse of shiftFrom - maps pos in To to a position in From
544    *
545    * @param pos
546    * (in To)
547    * @return shifted position in From, frameshift in To, direction of mapped
548    * symbol in From
549    */
 
550  16338 toggle public int[] shiftTo(int pos)
551    {
552  16338 return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
553    }
554   
555    /**
556    *
557    * @param shiftTo
558    * @param fromRatio
559    * @param shiftFrom
560    * @param toRatio
561    * @return
562    */
 
563  16347 toggle protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,
564    List<int[]> shiftFrom, int toRatio)
565    {
566    // TODO: javadoc; tests
567  16347 int[] fromCount = countPositions(shiftTo, pos);
568  16347 if (fromCount == null)
569    {
570  20 return null;
571    }
572  16327 int fromRemainder = (fromCount[0] - 1) % fromRatio;
573  16327 int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
574  16327 int[] toPos = traverseToPosition(shiftFrom, toCount);
575  16327 if (toPos == null)
576    {
577  0 return null;
578    }
579  16327 return new int[] { toPos[0], fromRemainder, toPos[1] };
580    }
581   
582    /**
583    * Counts how many positions pos is along the series of intervals. Returns an
584    * array of two values:
585    * <ul>
586    * <li>the number of positions traversed (inclusive) to reach {@code pos}</li>
587    * <li>+1 if the last interval traversed is forward, -1 if in a negative
588    * direction</li>
589    * </ul>
590    * Returns null if {@code pos} does not lie in any of the given intervals.
591    *
592    * @param intervals
593    * a list of start-end intervals
594    * @param pos
595    * a position that may lie in one (or more) of the intervals
596    * @return
597    */
 
598  16367 toggle protected static int[] countPositions(List<int[]> intervals, int pos)
599    {
600  16367 int count = 0;
601  16367 int iv = 0;
602  16367 int ivSize = intervals.size();
603   
604  16493 while (iv < ivSize)
605    {
606  16468 int[] intv = intervals.get(iv++);
607  16468 if (intv[0] <= intv[1])
608    {
609    /*
610    * forwards interval
611    */
612  16457 if (pos >= intv[0] && pos <= intv[1])
613    {
614  16336 return new int[] { count + pos - intv[0] + 1, +1 };
615    }
616    else
617    {
618  121 count += intv[1] - intv[0] + 1;
619    }
620    }
621    else
622    {
623    /*
624    * reverse interval
625    */
626  11 if (pos >= intv[1] && pos <= intv[0])
627    {
628  5 return new int[] { count + intv[0] - pos + 1, -1 };
629    }
630    else
631    {
632  6 count += intv[0] - intv[1] + 1;
633    }
634    }
635    }
636  25 return null;
637    }
638   
639    /**
640    * Reads through the given intervals until {@code count} positions have been
641    * traversed, and returns an array consisting of two values:
642    * <ul>
643    * <li>the value at the {@code count'th} position</li>
644    * <li>+1 if the last interval read is forwards, -1 if reverse direction</li>
645    * </ul>
646    * Returns null if the ranges include less than {@code count} positions, or if
647    * {@code count < 1}.
648    *
649    * @param intervals
650    * a list of [start, end] ranges
651    * @param count
652    * the number of positions to traverse
653    * @return
654    */
 
655  16329 toggle protected static int[] traverseToPosition(List<int[]> intervals,
656    final int count)
657    {
658  16329 int traversed = 0;
659  16329 int ivSize = intervals.size();
660  16329 int iv = 0;
661   
662  16329 if (count < 1)
663    {
664  2 return null;
665    }
666   
667  16410 while (iv < ivSize)
668    {
669  16410 int[] intv = intervals.get(iv++);
670  16410 int diff = intv[1] - intv[0];
671  16410 if (diff >= 0)
672    {
673  16410 if (count <= traversed + 1 + diff)
674    {
675  16327 return new int[] { intv[0] + (count - traversed - 1), +1 };
676    }
677    else
678    {
679  83 traversed += 1 + diff;
680    }
681    }
682    else
683    {
684  0 if (count <= traversed + 1 - diff)
685    {
686  0 return new int[] { intv[0] - (count - traversed - 1), -1 };
687    }
688    else
689    {
690  0 traversed += 1 - diff;
691    }
692    }
693    }
694  0 return null;
695    }
696   
697    /**
698    * like shift - except returns the intervals in the given vector of shifts
699    * which were spanned in traversing fromStart to fromEnd
700    *
701    * @param shiftFrom
702    * @param fromStart
703    * @param fromEnd
704    * @param fromRatio2
705    * @return series of from,to intervals from from first position of starting
706    * region to final position of ending region inclusive
707    */
 
708  0 toggle protected static int[] getIntervals(List<int[]> shiftFrom,
709    int[] fromStart, int[] fromEnd, int fromRatio2)
710    {
711  0 if (fromStart == null || fromEnd == null)
712    {
713  0 return null;
714    }
715  0 int startpos, endpos;
716  0 startpos = fromStart[0]; // first position in fromStart
717  0 endpos = fromEnd[0]; // last position in fromEnd
718  0 int endindx = (fromRatio2 - 1); // additional positions to get to last
719    // position from endpos
720  0 int intv = 0, intvSize = shiftFrom.size();
721  0 int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
722    // search intervals to locate ones containing startpos and count endindx
723    // positions on from endpos
724  0 while (intv < intvSize && (fs == -1 || fe == -1))
725    {
726  0 iv = shiftFrom.get(intv++);
727  0 if (fe_s > -1)
728    {
729  0 endpos = iv[0]; // start counting from beginning of interval
730  0 endindx--; // inclusive of endpos
731    }
732  0 if (iv[0] <= iv[1])
733    {
734  0 if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])
735    {
736  0 fs = i;
737    }
738  0 if (endpos >= iv[0] && endpos <= iv[1])
739    {
740  0 if (fe_s == -1)
741    {
742  0 fe_s = i;
743    }
744  0 if (fe_s != -1)
745    {
746  0 if (endpos + endindx <= iv[1])
747    {
748  0 fe = i;
749  0 endpos = endpos + endindx; // end of end token is within this
750    // interval
751    }
752    else
753    {
754  0 endindx -= iv[1] - endpos; // skip all this interval too
755    }
756    }
757    }
758    }
759    else
760    {
761  0 if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
762    {
763  0 fs = i;
764    }
765  0 if (endpos <= iv[0] && endpos >= iv[1])
766    {
767  0 if (fe_s == -1)
768    {
769  0 fe_s = i;
770    }
771  0 if (fe_s != -1)
772    {
773  0 if (endpos - endindx >= iv[1])
774    {
775  0 fe = i;
776  0 endpos = endpos - endindx; // end of end token is within this
777    // interval
778    }
779    else
780    {
781  0 endindx -= endpos - iv[1]; // skip all this interval too
782    }
783    }
784    }
785    }
786  0 i++;
787    }
788  0 if (fs == fe && fe == -1)
789    {
790  0 return null;
791    }
792  0 List<int[]> ranges = new ArrayList<>();
793  0 if (fs <= fe)
794    {
795  0 intv = fs;
796  0 i = fs;
797    // truncate initial interval
798  0 iv = shiftFrom.get(intv++);
799  0 iv = new int[] { iv[0], iv[1] };// clone
800  0 if (i == fs)
801    {
802  0 iv[0] = startpos;
803    }
804  0 while (i != fe)
805    {
806  0 ranges.add(iv); // add initial range
807  0 iv = shiftFrom.get(intv++); // get next interval
808  0 iv = new int[] { iv[0], iv[1] };// clone
809  0 i++;
810    }
811  0 if (i == fe)
812    {
813  0 iv[1] = endpos;
814    }
815  0 ranges.add(iv); // add only - or final range
816    }
817    else
818    {
819    // walk from end of interval.
820  0 i = shiftFrom.size() - 1;
821  0 while (i > fs)
822    {
823  0 i--;
824    }
825  0 iv = shiftFrom.get(i);
826  0 iv = new int[] { iv[1], iv[0] };// reverse and clone
827    // truncate initial interval
828  0 if (i == fs)
829    {
830  0 iv[0] = startpos;
831    }
832  0 while (--i != fe)
833    { // fix apparent logic bug when fe==-1
834  0 ranges.add(iv); // add (truncated) reversed interval
835  0 iv = shiftFrom.get(i);
836  0 iv = new int[] { iv[1], iv[0] }; // reverse and clone
837    }
838  0 if (i == fe)
839    {
840    // interval is already reversed
841  0 iv[1] = endpos;
842    }
843  0 ranges.add(iv); // add only - or final range
844    }
845    // create array of start end intervals.
846  0 int[] range = null;
847  0 if (ranges != null && ranges.size() > 0)
848    {
849  0 range = new int[ranges.size() * 2];
850  0 intv = 0;
851  0 intvSize = ranges.size();
852  0 i = 0;
853  0 while (intv < intvSize)
854    {
855  0 iv = ranges.get(intv);
856  0 range[i++] = iv[0];
857  0 range[i++] = iv[1];
858  0 ranges.set(intv++, null); // remove
859    }
860    }
861  0 return range;
862    }
863   
864    /**
865    * get the 'initial' position of mpos in To
866    *
867    * @param mpos
868    * position in from
869    * @return position of first word in to reference frame
870    */
 
871  3 toggle public int getToPosition(int mpos)
872    {
873  3 int[] mp = shiftTo(mpos);
874  3 if (mp != null)
875    {
876  3 return mp[0];
877    }
878  0 return mpos;
879    }
880   
881    /**
882    *
883    * @return a MapList whose From range is this maplist's To Range, and vice
884    * versa
885    */
 
886  68 toggle public MapList getInverse()
887    {
888  68 return new MapList(getToRanges(), getFromRanges(), getToRatio(),
889    getFromRatio());
890    }
891   
892    /**
893    * String representation - for debugging, not guaranteed not to change
894    */
 
895  12 toggle @Override
896    public String toString()
897    {
898  12 StringBuilder sb = new StringBuilder(64);
899  12 sb.append("[");
900  12 for (int[] shift : fromShifts)
901    {
902  26 sb.append(" ").append(Arrays.toString(shift));
903    }
904  12 sb.append(" ] ");
905  12 sb.append(fromRatio).append(":").append(toRatio);
906  12 sb.append(" to [");
907  12 for (int[] shift : toShifts)
908    {
909  17 sb.append(" ").append(Arrays.toString(shift));
910    }
911  12 sb.append(" ]");
912  12 return sb.toString();
913    }
914   
915    /**
916    * Extend this map list by adding the given map's ranges. There is no
917    * validation check that the ranges do not overlap existing ranges (or each
918    * other), but contiguous ranges are merged.
919    *
920    * @param map
921    */
 
922  12 toggle public void addMapList(MapList map)
923    {
924  12 if (this.equals(map))
925    {
926  3 return;
927    }
928  9 this.fromLowest = Math.min(fromLowest, map.fromLowest);
929  9 this.toLowest = Math.min(toLowest, map.toLowest);
930  9 this.fromHighest = Math.max(fromHighest, map.fromHighest);
931  9 this.toHighest = Math.max(toHighest, map.toHighest);
932   
933  9 for (int[] range : map.getFromRanges())
934    {
935  10 addRange(range, fromShifts);
936    }
937  9 for (int[] range : map.getToRanges())
938    {
939  11 addRange(range, toShifts);
940    }
941    }
942   
943    /**
944    * Adds the given range to a list of ranges. If the new range just extends
945    * existing ranges, the current endpoint is updated instead.
946    *
947    * @param range
948    * @param addTo
949    */
 
950  29 toggle static void addRange(int[] range, List<int[]> addTo)
951    {
952    /*
953    * list is empty - add to it!
954    */
955  29 if (addTo.size() == 0)
956    {
957  1 addTo.add(range);
958  1 return;
959    }
960   
961  28 int[] last = addTo.get(addTo.size() - 1);
962  28 boolean lastForward = last[1] >= last[0];
963  28 boolean newForward = range[1] >= range[0];
964   
965    /*
966    * contiguous range in the same direction - just update endpoint
967    */
968  28 if (lastForward == newForward && last[1] == range[0])
969    {
970  4 last[1] = range[1];
971  4 return;
972    }
973   
974    /*
975    * next range starts at +1 in forward sense - update endpoint
976    */
977  24 if (lastForward && newForward && range[0] == last[1] + 1)
978    {
979  3 last[1] = range[1];
980  3 return;
981    }
982   
983    /*
984    * next range starts at -1 in reverse sense - update endpoint
985    */
986  21 if (!lastForward && !newForward && range[0] == last[1] - 1)
987    {
988  4 last[1] = range[1];
989  4 return;
990    }
991   
992    /*
993    * just add the new range
994    */
995  17 addTo.add(range);
996    }
997   
998    /**
999    * Returns true if mapping is from forward strand, false if from reverse
1000    * strand. Result is just based on the first 'from' range that is not a single
1001    * position. Default is true unless proven to be false. Behaviour is not well
1002    * defined if the mapping has a mixture of forward and reverse ranges.
1003    *
1004    * @return
1005    */
 
1006  3 toggle public boolean isFromForwardStrand()
1007    {
1008  3 return isForwardStrand(getFromRanges());
1009    }
1010   
1011    /**
1012    * Returns true if mapping is to forward strand, false if to reverse strand.
1013    * Result is just based on the first 'to' range that is not a single position.
1014    * Default is true unless proven to be false. Behaviour is not well defined if
1015    * the mapping has a mixture of forward and reverse ranges.
1016    *
1017    * @return
1018    */
 
1019  27 toggle public boolean isToForwardStrand()
1020    {
1021  27 return isForwardStrand(getToRanges());
1022    }
1023   
1024    /**
1025    * A helper method that returns true unless at least one range has start >
1026    * end. Behaviour is undefined for a mixture of forward and reverse ranges.
1027    *
1028    * @param ranges
1029    * @return
1030    */
 
1031  30 toggle private boolean isForwardStrand(List<int[]> ranges)
1032    {
1033  30 boolean forwardStrand = true;
1034  30 for (int[] range : ranges)
1035    {
1036  38 if (range[1] > range[0])
1037    {
1038  20 break; // forward strand confirmed
1039    }
1040  18 else if (range[1] < range[0])
1041    {
1042  8 forwardStrand = false;
1043  8 break; // reverse strand confirmed
1044    }
1045    }
1046  30 return forwardStrand;
1047    }
1048   
1049    /**
1050    *
1051    * @return true if from, or to is a three to 1 mapping
1052    */
 
1053  94 toggle public boolean isTripletMap()
1054    {
1055  94 return (toRatio == 3 && fromRatio == 1)
1056    || (fromRatio == 3 && toRatio == 1);
1057    }
1058   
1059    /**
1060    * Returns a map which is the composite of this one and the input map. That
1061    * is, the output map has the fromRanges of this map, and its toRanges are the
1062    * toRanges of this map as transformed by the input map.
1063    * <p>
1064    * Returns null if the mappings cannot be traversed (not all toRanges of this
1065    * map correspond to fromRanges of the input), or if this.toRatio does not
1066    * match map.fromRatio.
1067    *
1068    * <pre>
1069    * Example 1:
1070    * this: from [1-100] to [501-600]
1071    * input: from [10-40] to [60-90]
1072    * output: from [10-40] to [560-590]
1073    * Example 2 ('reverse strand exons'):
1074    * this: from [1-100] to [2000-1951], [1000-951] // transcript to loci
1075    * input: from [1-50] to [41-90] // CDS to transcript
1076    * output: from [10-40] to [1960-1951], [1000-971] // CDS to gene loci
1077    * </pre>
1078    *
1079    * @param map
1080    * @return
1081    */
 
1082  19 toggle public MapList traverse(MapList map)
1083    {
1084  19 if (map == null)
1085    {
1086  0 return null;
1087    }
1088   
1089    /*
1090    * compound the ratios by this rule:
1091    * A:B with M:N gives A*M:B*N
1092    * reduced by greatest common divisor
1093    * so 1:3 with 3:3 is 3:9 or 1:3
1094    * 1:3 with 3:1 is 3:3 or 1:1
1095    * 1:3 with 1:3 is 1:9
1096    * 2:5 with 3:7 is 6:35
1097    */
1098  19 int outFromRatio = getFromRatio() * map.getFromRatio();
1099  19 int outToRatio = getToRatio() * map.getToRatio();
1100  19 int gcd = MathUtils.gcd(outFromRatio, outToRatio);
1101  19 outFromRatio /= gcd;
1102  19 outToRatio /= gcd;
1103   
1104  19 List<int[]> toRanges = new ArrayList<>();
1105  19 for (int[] range : getToRanges())
1106    {
1107  20 int fromLength = Math.abs(range[1] - range[0]) + 1;
1108  20 int[] transferred = map.locateInTo(range[0], range[1]);
1109  20 if (transferred == null || transferred.length % 2 != 0)
1110    {
1111  0 return null;
1112    }
1113   
1114    /*
1115    * convert [start1, end1, start2, end2, ...]
1116    * to [[start1, end1], [start2, end2], ...]
1117    */
1118  20 int toLength = 0;
1119  169 for (int i = 0; i < transferred.length;)
1120    {
1121  149 toRanges.add(new int[] { transferred[i], transferred[i + 1] });
1122  149 toLength += Math.abs(transferred[i + 1] - transferred[i]) + 1;
1123  149 i += 2;
1124    }
1125   
1126    /*
1127    * check we mapped the full range - if not, abort
1128    */
1129  20 if (fromLength * map.getToRatio() != toLength * map.getFromRatio())
1130    {
1131  1 return null;
1132    }
1133    }
1134   
1135  18 return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
1136    }
1137   
1138    /**
1139    * Answers true if the mapping is from one contiguous range to another, else
1140    * false
1141    *
1142    * @return
1143    */
 
1144  0 toggle public boolean isContiguous()
1145    {
1146  0 return fromShifts.size() == 1 && toShifts.size() == 1;
1147    }
1148   
1149    /**
1150    * <<<<<<< HEAD Returns the [start1, end1, start2, end2, ...] positions in the
1151    * 'from' range that map to positions between {@code start} and {@code end} in
1152    * the 'to' range. Note that for a reverse strand mapping this will return
1153    * ranges with end < start. Returns null if no mapped positions are found in
1154    * start-end.
1155    *
1156    * @param start
1157    * @param end
1158    * @return
1159    */
 
1160  163943 toggle public int[] locateInFrom(int start, int end)
1161    {
1162  163943 return mapPositions(start, end, toShifts, fromShifts, toRatio,
1163    fromRatio);
1164    }
1165   
1166    /**
1167    * Returns the [start1, end1, start2, end2, ...] positions in the 'to' range
1168    * that map to positions between {@code start} and {@code end} in the 'from'
1169    * range. Note that for a reverse strand mapping this will return ranges with
1170    * end < start. Returns null if no mapped positions are found in start-end.
1171    *
1172    * @param start
1173    * @param end
1174    * @return
1175    */
 
1176  25880 toggle public int[] locateInTo(int start, int end)
1177    {
1178  25880 return mapPositions(start, end, fromShifts, toShifts, fromRatio,
1179    toRatio);
1180    }
1181   
1182    /**
1183    * Helper method that returns the [start1, end1, start2, end2, ...] positions
1184    * in {@code targetRange} that map to positions between {@code start} and
1185    * {@code end} in {@code sourceRange}. Note that for a reverse strand mapping
1186    * this will return ranges with end < start. Returns null if no mapped
1187    * positions are found in start-end.
1188    *
1189    * @param start
1190    * @param end
1191    * @param sourceRange
1192    * @param targetRange
1193    * @param sourceWordLength
1194    * @param targetWordLength
1195    * @return
1196    */
 
1197  189821 toggle final static int[] mapPositions(int start, int end,
1198    List<int[]> sourceRange, List<int[]> targetRange,
1199    int sourceWordLength, int targetWordLength)
1200    {
1201  189823 if (end < start)
1202    {
1203  2 int tmp = end;
1204  2 end = start;
1205  2 start = tmp;
1206    }
1207   
1208    /*
1209    * traverse sourceRange and mark offsets in targetRange
1210    * of any positions that lie in [start, end]
1211    */
1212  189823 BitSet offsets = getMappedOffsetsForPositions(start, end, sourceRange,
1213    sourceWordLength, targetWordLength);
1214   
1215    /*
1216    * traverse targetRange and collect positions at the marked offsets
1217    */
1218  189819 List<int[]> mapped = getPositionsForOffsets(targetRange, offsets);
1219   
1220    // TODO: or just return the List and adjust calling code to match
1221  189816 return mapped.isEmpty() ? null : MappingUtils.rangeListToArray(mapped);
1222    }
1223   
1224    /**
1225    * Scans the list of {@code ranges} for any values (positions) that lie
1226    * between start and end (inclusive), and records the <em>offsets</em> from
1227    * the start of the list as a BitSet. The offset positions are converted to
1228    * corresponding words in blocks of {@code wordLength2}.
1229    *
1230    * <pre>
1231    * For example:
1232    * 1:1 (e.g. gene to CDS):
1233    * ranges { [10-20], [31-40] }, wordLengthFrom = wordLength 2 = 1
1234    * for start = 1, end = 9, returns a BitSet with no bits set
1235    * for start = 1, end = 11, returns a BitSet with bits 0-1 set
1236    * for start = 15, end = 35, returns a BitSet with bits 5-15 set
1237    * 1:3 (peptide to codon):
1238    * ranges { [1-200] }, wordLengthFrom = 1, wordLength 2 = 3
1239    * for start = 9, end = 9, returns a BitSet with bits 24-26 set
1240    * 3:1 (codon to peptide):
1241    * ranges { [101-150], [171-180] }, wordLengthFrom = 3, wordLength 2 = 1
1242    * for start = 101, end = 102 (partial first codon), returns a BitSet with bit 0 set
1243    * for start = 150, end = 171 (partial 17th codon), returns a BitSet with bit 16 set
1244    * 3:1 (circular DNA to peptide):
1245    * ranges { [101-150], [21-30] }, wordLengthFrom = 3, wordLength 2 = 1
1246    * for start = 24, end = 40 (spans codons 18-20), returns a BitSet with bits 17-19 set
1247    * </pre>
1248    *
1249    * @param start
1250    * @param end
1251    * @param sourceRange
1252    * @param sourceWordLength
1253    * @param targetWordLength
1254    * @return
1255    */
 
1256  189836 toggle protected final static BitSet getMappedOffsetsForPositions(int start,
1257    int end, List<int[]> sourceRange, int sourceWordLength,
1258    int targetWordLength)
1259    {
1260  189836 BitSet overlaps = new BitSet();
1261  189836 int offset = 0;
1262  189836 final int s1 = sourceRange.size();
1263  379947 for (int i = 0; i < s1; i++)
1264    {
1265  190117 int[] range = sourceRange.get(i);
1266  190118 final int offset1 = offset;
1267  190118 int overlapStartOffset = -1;
1268  190118 int overlapEndOffset = -1;
1269   
1270  190116 if (range[1] >= range[0])
1271    {
1272    /*
1273    * forward direction range
1274    */
1275  190002 if (start <= range[1] && end >= range[0])
1276    {
1277    /*
1278    * overlap
1279    */
1280  176337 int overlapStart = Math.max(start, range[0]);
1281  176338 overlapStartOffset = offset1 + overlapStart - range[0];
1282  176336 int overlapEnd = Math.min(end, range[1]);
1283  176336 overlapEndOffset = offset1 + overlapEnd - range[0];
1284    }
1285    }
1286    else
1287    {
1288    /*
1289    * reverse direction range
1290    */
1291  114 if (start <= range[0] && end >= range[1])
1292    {
1293    /*
1294    * overlap
1295    */
1296  29 int overlapStart = Math.max(start, range[1]);
1297  29 int overlapEnd = Math.min(end, range[0]);
1298  29 overlapStartOffset = offset1 + range[0] - overlapEnd;
1299  29 overlapEndOffset = offset1 + range[0] - overlapStart;
1300    }
1301    }
1302   
1303  190113 if (overlapStartOffset > -1)
1304    {
1305    /*
1306    * found an overlap
1307    */
1308  176364 if (sourceWordLength != targetWordLength)
1309    {
1310    /*
1311    * convert any overlap found to whole words in the target range
1312    * (e.g. treat any partial codon overlap as if the whole codon)
1313    */
1314  21658 overlapStartOffset -= overlapStartOffset % sourceWordLength;
1315  21658 overlapStartOffset = overlapStartOffset / sourceWordLength
1316    * targetWordLength;
1317   
1318    /*
1319    * similar calculation for range end, adding
1320    * (wordLength2 - 1) for end of mapped word
1321    */
1322  21658 overlapEndOffset -= overlapEndOffset % sourceWordLength;
1323  21658 overlapEndOffset = overlapEndOffset / sourceWordLength
1324    * targetWordLength;
1325  21658 overlapEndOffset += targetWordLength - 1;
1326    }
1327  176362 overlaps.set(overlapStartOffset, overlapEndOffset + 1);
1328    }
1329  190113 offset += 1 + Math.abs(range[1] - range[0]);
1330    }
1331  189831 return overlaps;
1332    }
1333   
1334    /**
1335    * Returns a (possibly empty) list of the [start-end] values (positions) at
1336    * offsets in the {@code targetRange} list that are marked by 'on' bits in the
1337    * {@code offsets} bitset.
1338    *
1339    * @param targetRange
1340    * @param offsets
1341    * @return
1342    */
 
1343  189822 toggle protected final static List<int[]> getPositionsForOffsets(
1344    List<int[]> targetRange, BitSet offsets)
1345    {
1346  189822 List<int[]> mapped = new ArrayList<>();
1347  189829 if (offsets.isEmpty())
1348    {
1349  13501 return mapped;
1350    }
1351   
1352    /*
1353    * count of positions preceding ranges[i]
1354    */
1355  176327 int traversed = 0;
1356   
1357    /*
1358    * for each [from-to] range in ranges:
1359    * - find subranges (if any) at marked offsets
1360    * - add the start-end values at the marked positions
1361    */
1362  176328 final int toAdd = offsets.cardinality();
1363  176320 int added = 0;
1364  176320 final int s2 = targetRange.size();
1365  352904 for (int i = 0; added < toAdd && i < s2; i++)
1366    {
1367  176579 int[] range = targetRange.get(i);
1368  176579 added += addOffsetPositions(mapped, traversed, range, offsets);
1369  176580 traversed += Math.abs(range[1] - range[0]) + 1;
1370    }
1371  176323 return mapped;
1372    }
1373   
1374    /**
1375    * Helper method that adds any start-end subranges of {@code range} that are
1376    * at offsets in {@code range} marked by set bits in overlaps.
1377    * {@code mapOffset} is added to {@code range} offset positions. Returns the
1378    * count of positions added.
1379    *
1380    * @param mapped
1381    * @param mapOffset
1382    * @param range
1383    * @param overlaps
1384    * @return
1385    */
 
1386  176586 toggle final static int addOffsetPositions(List<int[]> mapped,
1387    final int mapOffset, final int[] range, final BitSet overlaps)
1388    {
1389  176586 final int rangeLength = 1 + Math.abs(range[1] - range[0]);
1390  176584 final int step = range[1] < range[0] ? -1 : 1;
1391  176584 int offsetStart = 0; // offset into range
1392  176583 int added = 0;
1393   
1394  353073 while (offsetStart < rangeLength)
1395    {
1396    /*
1397    * find the start of the next marked overlap offset;
1398    * if there is none, or it is beyond range, then finished
1399    */
1400  345436 int overlapStart = overlaps.nextSetBit(mapOffset + offsetStart);
1401  345473 if (overlapStart == -1 || overlapStart - mapOffset >= rangeLength)
1402    {
1403    /*
1404    * no more overlaps, or no more within range[]
1405    */
1406  168949 return added;
1407    }
1408  176521 overlapStart -= mapOffset;
1409   
1410    /*
1411    * end of the overlap range is just before the next clear bit;
1412    * restrict it to end of range if necessary;
1413    * note we may add a reverse strand range here (end < start)
1414    */
1415  176521 int overlapEnd = overlaps.nextClearBit(mapOffset + overlapStart + 1);
1416  176525 overlapEnd = (overlapEnd == -1) ? rangeLength - 1
1417    : Math.min(rangeLength - 1, overlapEnd - mapOffset - 1);
1418  176525 int startPosition = range[0] + step * overlapStart;
1419  176524 int endPosition = range[0] + step * overlapEnd;
1420  176524 mapped.add(new int[] { startPosition, endPosition });
1421  176528 offsetStart = overlapEnd + 1;
1422  176531 added += Math.abs(endPosition - startPosition) + 1;
1423    }
1424   
1425  7643 return added;
1426    }
1427   
1428    /*
1429    * Returns the [start, end...] positions in the range mapped from, that are
1430    * mapped to by part or all of the given begin-end of the range mapped to.
1431    * Returns null if begin-end does not overlap any position mapped to.
1432    *
1433    * @param begin
1434    * @param end
1435    * @return
1436    */
 
1437  7 toggle public int[] getOverlapsInFrom(final int begin, final int end)
1438    {
1439  7 int[] overlaps = MappingUtils.findOverlap(toShifts, begin, end);
1440   
1441  7 return overlaps == null ? null : locateInFrom(overlaps[0], overlaps[1]);
1442    }
1443   
1444    /**
1445    * Returns the [start, end...] positions in the range mapped to, that are
1446    * mapped to by part or all of the given begin-end of the range mapped from.
1447    * Returns null if begin-end does not overlap any position mapped from.
1448    *
1449    * @param begin
1450    * @param end
1451    * @return
1452    */
 
1453  15 toggle public int[] getOverlapsInTo(final int begin, final int end)
1454    {
1455  15 int[] overlaps = MappingUtils.findOverlap(fromShifts, begin, end);
1456   
1457  15 return overlaps == null ? null : locateInTo(overlaps[0], overlaps[1]);
1458    }
1459    }
  • Report generated by OpenClover v 4.4.1 on Mon Sep 2 2024 18:05:00 BST using coverage data from Mon Sep 2 2024 18:04:45 BST.
  • OpenClover is free and open-source software.