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.HashMap;
26 import java.util.Iterator;
27 import java.util.List;
30 import jalview.analysis.AlignmentSorter;
31 import jalview.api.AlignViewportI;
32 import jalview.bin.Cache;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.EditCommand.Edit;
37 import jalview.commands.OrderCommand;
38 import jalview.datamodel.AlignedCodonFrame;
39 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
40 import jalview.datamodel.AlignmentI;
41 import jalview.datamodel.AlignmentOrder;
42 import jalview.datamodel.ColumnSelection;
43 import jalview.datamodel.HiddenColumns;
44 import jalview.datamodel.Mapping;
45 import jalview.datamodel.SearchResultMatchI;
46 import jalview.datamodel.SearchResults;
47 import jalview.datamodel.SearchResultsI;
48 import jalview.datamodel.Sequence;
49 import jalview.datamodel.SequenceGroup;
50 import jalview.datamodel.SequenceI;
53 * Helper methods for manipulations involving sequence mappings.
58 public final class MappingUtils
62 * Helper method to map a CUT or PASTE command.
65 * the original command
67 * if true, the command is to be undone
69 * the mapped sequences to apply the mapped command to
71 * the mapped EditCommand to add to
74 protected static void mapCutOrPaste(Edit edit, boolean undo,
75 List<SequenceI> targetSeqs, EditCommand result,
76 List<AlignedCodonFrame> mappings)
78 Action action = edit.getAction();
81 action = action.getUndoAction();
84 Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
88 * Returns a new EditCommand representing the given command as mapped to the
89 * given sequences. If there is no mapping, returns null.
98 public static EditCommand mapEditCommand(EditCommand command,
99 boolean undo, final AlignmentI mapTo, char gapChar,
100 List<AlignedCodonFrame> mappings)
103 * For now, only support mapping from protein edits to cDna
105 if (!mapTo.isNucleotide())
111 * Cache a copy of the target sequences so we can mimic successive edits on
112 * them. This lets us compute mappings for all edits in the set.
114 Map<SequenceI, SequenceI> targetCopies = new HashMap<>();
115 for (SequenceI seq : mapTo.getSequences())
117 SequenceI ds = seq.getDatasetSequence();
120 final SequenceI copy = new Sequence(seq);
121 copy.setDatasetSequence(ds);
122 targetCopies.put(ds, copy);
127 * Compute 'source' sequences as they were before applying edits:
129 Map<SequenceI, SequenceI> originalSequences = command.priorState(undo);
131 EditCommand result = new EditCommand();
132 Iterator<Edit> edits = command.getEditIterator(!undo);
133 while (edits.hasNext())
135 Edit edit = edits.next();
136 if (edit.getAction() == Action.CUT
137 || edit.getAction() == Action.PASTE)
139 mapCutOrPaste(edit, undo, mapTo.getSequences(), result, mappings);
141 else if (edit.getAction() == Action.INSERT_GAP
142 || edit.getAction() == Action.DELETE_GAP)
144 mapInsertOrDelete(edit, undo, originalSequences,
145 mapTo.getSequences(), targetCopies, gapChar, result,
149 return result.getSize() > 0 ? result : null;
153 * Helper method to map an edit command to insert or delete gaps.
156 * the original command
158 * if true, the action is to undo the command
159 * @param originalSequences
160 * the sequences the command acted on
162 * @param targetCopies
165 * the new EditCommand to add mapped commands to
168 protected static void mapInsertOrDelete(Edit edit, boolean undo,
169 Map<SequenceI, SequenceI> originalSequences,
170 final List<SequenceI> targetSeqs,
171 Map<SequenceI, SequenceI> targetCopies, char gapChar,
172 EditCommand result, List<AlignedCodonFrame> mappings)
174 Action action = edit.getAction();
177 * Invert sense of action if an Undo.
181 action = action.getUndoAction();
183 final int count = edit.getNumber();
184 final int editPos = edit.getPosition();
185 for (SequenceI seq : edit.getSequences())
188 * Get residue position at (or to right of) edit location. Note we use our
189 * 'copy' of the sequence before editing for this.
191 SequenceI ds = seq.getDatasetSequence();
196 final SequenceI actedOn = originalSequences.get(ds);
197 final int seqpos = actedOn.findPosition(editPos);
200 * Determine all mappings from this position to mapped sequences.
202 SearchResultsI sr = buildSearchResults(seq, seqpos, mappings);
206 for (SequenceI targetSeq : targetSeqs)
208 ds = targetSeq.getDatasetSequence();
213 SequenceI copyTarget = targetCopies.get(ds);
214 final int[] match = sr.getResults(copyTarget, 0,
215 copyTarget.getLength());
218 final int ratio = 3; // TODO: compute this - how?
219 final int mappedCount = count * ratio;
222 * Shift Delete start position left, as it acts on positions to its
225 int mappedEditPos = action == Action.DELETE_GAP
226 ? match[0] - mappedCount
228 Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
229 mappedEditPos, mappedCount, gapChar);
233 * and 'apply' the edit to our copy of its target sequence
235 if (action == Action.INSERT_GAP)
237 copyTarget.setSequence(new String(
238 StringUtils.insertCharAt(copyTarget.getSequence(),
239 mappedEditPos, mappedCount, gapChar)));
241 else if (action == Action.DELETE_GAP)
243 copyTarget.setSequence(new String(
244 StringUtils.deleteChars(copyTarget.getSequence(),
245 mappedEditPos, mappedEditPos + mappedCount)));
251 * and 'apply' the edit to our copy of its source sequence
253 if (action == Action.INSERT_GAP)
255 actedOn.setSequence(new String(StringUtils.insertCharAt(
256 actedOn.getSequence(), editPos, count, gapChar)));
258 else if (action == Action.DELETE_GAP)
260 actedOn.setSequence(new String(StringUtils.deleteChars(
261 actedOn.getSequence(), editPos, editPos + count)));
267 * Returns a SearchResults object describing the mapped region corresponding
268 * to the specified sequence position.
275 public static SearchResultsI buildSearchResults(SequenceI seq, int index,
276 List<AlignedCodonFrame> seqmappings)
278 SearchResultsI results = new SearchResults();
279 addSearchResults(results, seq, index, seqmappings);
284 * Adds entries to a SearchResults object describing the mapped region
285 * corresponding to the specified sequence position.
292 public static void addSearchResults(SearchResultsI results, SequenceI seq,
293 int index, List<AlignedCodonFrame> seqmappings)
295 if (index >= seq.getStart() && index <= seq.getEnd())
297 for (AlignedCodonFrame acf : seqmappings)
299 acf.markMappedRegion(seq, index, results);
305 * Returns a (possibly empty) SequenceGroup containing any sequences in the
306 * mapped viewport corresponding to the given group in the source viewport.
313 public static SequenceGroup mapSequenceGroup(final SequenceGroup sg,
314 final AlignViewportI mapFrom, final AlignViewportI mapTo)
317 * Note the SequenceGroup holds aligned sequences, the mappings hold dataset
320 boolean targetIsNucleotide = mapTo.isNucleotide();
321 AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
322 List<AlignedCodonFrame> codonFrames = protein.getAlignment()
325 * Copy group name, colours etc, but not sequences or sequence colour scheme
327 SequenceGroup mappedGroup = new SequenceGroup(sg);
328 mappedGroup.setColourScheme(mapTo.getGlobalColourScheme());
331 int minStartCol = -1;
333 final int selectionStartRes = sg.getStartRes();
334 final int selectionEndRes = sg.getEndRes();
335 for (SequenceI selected : sg.getSequences())
338 * Find the widest range of non-gapped positions in the selection range
340 int firstUngappedPos = selectionStartRes;
341 while (firstUngappedPos <= selectionEndRes
342 && Comparison.isGap(selected.getCharAt(firstUngappedPos)))
348 * If this sequence is only gaps in the selected range, skip it
350 if (firstUngappedPos > selectionEndRes)
355 int lastUngappedPos = selectionEndRes;
356 while (lastUngappedPos >= selectionStartRes
357 && Comparison.isGap(selected.getCharAt(lastUngappedPos)))
363 * Find the selected start/end residue positions in sequence
365 int startResiduePos = selected.findPosition(firstUngappedPos);
366 int endResiduePos = selected.findPosition(lastUngappedPos);
367 for (SequenceI seq : mapTo.getAlignment().getSequences())
369 int mappedStartResidue = 0;
370 int mappedEndResidue = 0;
371 for (AlignedCodonFrame acf : codonFrames)
373 for (SequenceToSequenceMapping map: acf.getMappings())
375 if (map.covers(selected) && map.covers(seq))
378 * Found a sequence mapping. Locate the start/end mapped residues.
380 List<AlignedCodonFrame> mapping = Arrays
381 .asList(new AlignedCodonFrame[]
384 SearchResultsI sr = buildSearchResults(selected,
385 startResiduePos, mapping);
386 for (SearchResultMatchI m : sr.getResults())
388 mappedStartResidue = m.getStart();
389 mappedEndResidue = m.getEnd();
391 // locate end - allowing for adjustment of start range
392 sr = buildSearchResults(selected, endResiduePos, mapping);
393 for (SearchResultMatchI m : sr.getResults())
395 mappedStartResidue = Math.min(mappedStartResidue,
397 mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
401 * Find the mapped aligned columns, save the range. Note findIndex
402 * returns a base 1 position, SequenceGroup uses base 0
404 int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
405 minStartCol = minStartCol == -1 ? mappedStartCol
406 : Math.min(minStartCol, mappedStartCol);
407 int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
408 maxEndCol = maxEndCol == -1 ? mappedEndCol
409 : Math.max(maxEndCol, mappedEndCol);
410 mappedGroup.addSequence(seq, false);
416 mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
417 mappedGroup.setEndRes(maxEndCol < 0 ? 0 : maxEndCol);
422 * Returns an OrderCommand equivalent to the given one, but acting on mapped
423 * sequences as described by the mappings, or null if no mapping can be made.
426 * the original order command
428 * if true, the action is to undo the sort
430 * the alignment we are mapping to
432 * the mappings available
435 public static CommandI mapOrderCommand(OrderCommand command, boolean undo,
436 AlignmentI mapTo, List<AlignedCodonFrame> mappings)
438 SequenceI[] sortOrder = command.getSequenceOrder(undo);
439 List<SequenceI> mappedOrder = new ArrayList<>();
443 * Assumption: we are only interested in a cDNA/protein mapping; refactor in
444 * future if we want to support sorting (c)dna as (c)dna or protein as
447 boolean mappingToNucleotide = mapTo.isNucleotide();
448 for (SequenceI seq : sortOrder)
450 for (AlignedCodonFrame acf : mappings)
452 SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
453 : acf.getAaForDnaSeq(seq);
454 if (mappedSeq != null)
456 for (SequenceI seq2 : mapTo.getSequences())
458 if (seq2.getDatasetSequence() == mappedSeq)
460 mappedOrder.add(seq2);
470 * Return null if no mappings made.
478 * Add any unmapped sequences on the end of the sort in their original
481 if (j < mapTo.getHeight())
483 for (SequenceI seq : mapTo.getSequences())
485 if (!mappedOrder.contains(seq))
487 mappedOrder.add(seq);
493 * Have to sort the sequences before constructing the OrderCommand - which
494 * then resorts them?!?
496 final SequenceI[] mappedOrderArray = mappedOrder
497 .toArray(new SequenceI[mappedOrder.size()]);
498 SequenceI[] oldOrder = mapTo.getSequencesArray();
499 AlignmentSorter.sortBy(mapTo, new AlignmentOrder(mappedOrderArray));
500 final OrderCommand result = new OrderCommand(command.getDescription(),
506 * Returns a ColumnSelection in the 'mapTo' view which corresponds to the
507 * given selection in the 'mapFrom' view. We assume one is nucleotide, the
508 * other is protein (and holds the mappings from codons to protein residues).
515 public static void mapColumnSelection(ColumnSelection colsel,
516 HiddenColumns hiddencols, AlignViewportI mapFrom,
517 AlignViewportI mapTo, ColumnSelection newColSel,
518 HiddenColumns newHidden)
520 boolean targetIsNucleotide = mapTo.isNucleotide();
521 AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
522 List<AlignedCodonFrame> codonFrames = protein.getAlignment()
527 return; // mappedColumns;
530 char fromGapChar = mapFrom.getAlignment().getGapCharacter();
533 * For each mapped column, find the range of columns that residues in that
536 List<SequenceI> fromSequences = mapFrom.getAlignment().getSequences();
537 List<SequenceI> toSequences = mapTo.getAlignment().getSequences();
539 for (Integer sel : colsel.getSelected())
541 mapColumn(sel.intValue(), codonFrames, newColSel, fromSequences,
542 toSequences, fromGapChar);
545 Iterator<int[]> regions = hiddencols.iterator();
546 while (regions.hasNext())
548 mapHiddenColumns(regions.next(), codonFrames, newHidden,
549 fromSequences, toSequences, fromGapChar);
551 return; // mappedColumns;
555 * Helper method that maps a [start, end] hidden column range to its mapped
560 * @param mappedColumns
561 * @param fromSequences
565 protected static void mapHiddenColumns(int[] hidden,
566 List<AlignedCodonFrame> mappings, HiddenColumns mappedColumns,
567 List<SequenceI> fromSequences, List<SequenceI> toSequences,
570 for (int col = hidden[0]; col <= hidden[1]; col++)
572 int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
573 toSequences, fromGapChar);
576 * Add the range of hidden columns to the mapped selection (converting
579 if (mappedTo != null)
581 mappedColumns.hideColumns(mappedTo[0] - 1, mappedTo[1] - 1);
587 * Helper method to map one column selection
590 * the column number (base 0)
592 * the sequence mappings
593 * @param mappedColumns
594 * the mapped column selections to add to
595 * @param fromSequences
599 protected static void mapColumn(int col, List<AlignedCodonFrame> mappings,
600 ColumnSelection mappedColumns, List<SequenceI> fromSequences,
601 List<SequenceI> toSequences, char fromGapChar)
603 int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
604 toSequences, fromGapChar);
607 * Add the range of mapped columns to the mapped selection (converting
608 * base 1 to base 0). Note that this may include intron-only regions which
609 * lie between the start and end ranges of the selection.
611 if (mappedTo != null)
613 for (int i = mappedTo[0]; i <= mappedTo[1]; i++)
615 mappedColumns.addElement(i - 1);
621 * Helper method to find the range of columns mapped to from one column.
622 * Returns the maximal range of columns mapped to from all sequences in the
623 * source column, or null if no mappings were found.
627 * @param fromSequences
632 protected static int[] findMappedColumns(int col,
633 List<AlignedCodonFrame> mappings, List<SequenceI> fromSequences,
634 List<SequenceI> toSequences, char fromGapChar)
636 int[] mappedTo = new int[] { Integer.MAX_VALUE, Integer.MIN_VALUE };
637 boolean found = false;
640 * For each sequence in the 'from' alignment
642 for (SequenceI fromSeq : fromSequences)
645 * Ignore gaps (unmapped anyway)
647 if (fromSeq.getCharAt(col) == fromGapChar)
653 * Get the residue position and find the mapped position.
655 int residuePos = fromSeq.findPosition(col);
656 SearchResultsI sr = buildSearchResults(fromSeq, residuePos, mappings);
657 for (SearchResultMatchI m : sr.getResults())
659 int mappedStartResidue = m.getStart();
660 int mappedEndResidue = m.getEnd();
661 SequenceI mappedSeq = m.getSequence();
664 * Locate the aligned sequence whose dataset is mappedSeq. TODO a
665 * datamodel that can do this efficiently.
667 for (SequenceI toSeq : toSequences)
669 if (toSeq.getDatasetSequence() == mappedSeq)
671 int mappedStartCol = toSeq.findIndex(mappedStartResidue);
672 int mappedEndCol = toSeq.findIndex(mappedEndResidue);
673 mappedTo[0] = Math.min(mappedTo[0], mappedStartCol);
674 mappedTo[1] = Math.max(mappedTo[1], mappedEndCol);
677 // note: remove break if we ever want to map one to many sequences
682 return found ? mappedTo : null;
686 * Returns the mapped codon or codons for a given aligned sequence column
690 * an aligned peptide sequence
692 * an aligned column position (base 0)
694 * a set of codon mappings
695 * @return the bases of the mapped codon(s) in the cDNA dataset sequence(s),
696 * or an empty list if none found
698 public static List<char[]> findCodonsFor(SequenceI seq, int col,
699 List<AlignedCodonFrame> mappings)
701 List<char[]> result = new ArrayList<>();
702 int dsPos = seq.findPosition(col);
703 for (AlignedCodonFrame mapping : mappings)
705 if (mapping.involvesSequence(seq))
707 List<char[]> codons = mapping
708 .getMappedCodons(seq.getDatasetSequence(), dsPos);
711 result.addAll(codons);
719 * Converts a series of [start, end] range pairs into an array of individual
720 * positions. This also caters for 'reverse strand' (start > end) cases.
725 public static int[] flattenRanges(int[] ranges)
728 * Count how many positions altogether
731 for (int i = 0; i < ranges.length - 1; i += 2)
733 count += Math.abs(ranges[i + 1] - ranges[i]) + 1;
736 int[] result = new int[count];
738 for (int i = 0; i < ranges.length - 1; i += 2)
740 int from = ranges[i];
741 final int to = ranges[i + 1];
742 int step = from <= to ? 1 : -1;
747 } while (from != to + step);
753 * Returns a list of any mappings that are from or to the given (aligned or
760 public static List<AlignedCodonFrame> findMappingsForSequence(
761 SequenceI sequence, List<AlignedCodonFrame> mappings)
763 return findMappingsForSequenceAndOthers(sequence, mappings, null);
767 * Returns a list of any mappings that are from or to the given (aligned or
768 * dataset) sequence, optionally limited to mappings involving one of a given
776 public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
777 SequenceI sequence, List<AlignedCodonFrame> mappings,
778 List<SequenceI> filterList)
780 List<AlignedCodonFrame> result = new ArrayList<>();
781 if (sequence == null || mappings == null)
785 for (AlignedCodonFrame mapping : mappings)
787 if (mapping.involvesSequence(sequence))
789 if (filterList != null)
791 for (SequenceI otherseq : filterList)
793 SequenceI otherDataset = otherseq.getDatasetSequence();
794 if (otherseq == sequence
795 || otherseq == sequence.getDatasetSequence()
796 || (otherDataset != null && (otherDataset == sequence
797 || otherDataset == sequence
798 .getDatasetSequence())))
800 // skip sequences in subset which directly relate to sequence
803 if (mapping.involvesSequence(otherseq))
805 // selected a mapping contained in subselect alignment
821 * Returns the total length of the supplied ranges, which may be as single
822 * [start, end] or multiple [start, end, start, end ...]
827 public static int getLength(List<int[]> ranges)
834 for (int[] range : ranges)
836 if (range.length % 2 != 0)
839 "Error unbalance start/end ranges: " + ranges.toString());
842 for (int i = 0; i < range.length - 1; i += 2)
844 length += Math.abs(range[i + 1] - range[i]) + 1;
851 * Answers true if any range includes the given value
857 public static boolean contains(List<int[]> ranges, int value)
863 for (int[] range : ranges)
865 if (range[1] >= range[0] && value >= range[0] && value <= range[1])
868 * value within ascending range
872 if (range[1] < range[0] && value <= range[0] && value >= range[1])
875 * value within descending range
884 * Removes a specified number of positions from the start of a ranges list.
885 * For example, could be used to adjust cds ranges to allow for an incomplete
886 * start codon. Subranges are removed completely, or their start positions
887 * adjusted, until the required number of positions has been removed from the
888 * range. Reverse strand ranges are supported. The input array is not
893 * an array of [start, end, start, end...] positions
894 * @return a new array with the first removeCount positions removed
896 public static int[] removeStartPositions(int removeCount,
899 if (removeCount <= 0)
904 int[] copy = Arrays.copyOf(ranges, ranges.length);
907 for (int x = 0; x < copy.length && sxpos == -1; x += 2)
909 cdspos += Math.abs(copy[x + 1] - copy[x]) + 1;
910 if (removeCount < cdspos)
913 * we have removed enough, time to finish
918 * increment start of first exon, or decrement if reverse strand
920 if (copy[x] <= copy[x + 1])
922 copy[x] = copy[x + 1] - cdspos + removeCount + 1;
926 copy[x] = copy[x + 1] + cdspos - removeCount - 1;
935 * we dropped at least one entire sub-range - compact the array
937 int[] nxon = new int[copy.length - sxpos];
938 System.arraycopy(copy, sxpos, nxon, 0, copy.length - sxpos);
945 * Answers true if range's start-end positions include those of queryRange,
946 * where either range might be in reverse direction, else false
951 * a candidate subrange of range (start2-end2)
954 public static boolean rangeContains(int[] range, int[] queryRange)
956 if (range == null || queryRange == null || range.length != 2
957 || queryRange.length != 2)
965 int min = Math.min(range[0], range[1]);
966 int max = Math.max(range[0], range[1]);
968 return (min <= queryRange[0] && max >= queryRange[0]
969 && min <= queryRange[1] && max >= queryRange[1]);
973 * Removes the specified number of positions from the given ranges. Provided
974 * to allow a stop codon to be stripped from a CDS sequence so that it matches
975 * the peptide translation length.
979 * a list of (single) [start, end] ranges
982 public static void removeEndPositions(int positions, List<int[]> ranges)
984 int toRemove = positions;
985 Iterator<int[]> it = new ReverseListIterator<>(ranges);
988 int[] endRange = it.next();
989 if (endRange.length != 2)
992 * not coded for [start1, end1, start2, end2, ...]
995 "MappingUtils.removeEndPositions doesn't handle multiple ranges");
999 int length = endRange[1] - endRange[0] + 1;
1003 * not coded for a reverse strand range (end < start)
1006 "MappingUtils.removeEndPositions doesn't handle reverse strand");
1009 if (length > toRemove)
1011 endRange[1] -= toRemove;
1023 * Converts a list of {@code start-end} ranges to a single array of
1024 * {@code start1, end1, start2, ... } ranges
1029 public static int[] rangeListToArray(List<int[]> ranges)
1031 int rangeCount = ranges.size();
1032 int[] result = new int[rangeCount * 2];
1034 for (int i = 0; i < rangeCount; i++)
1036 int[] range = ranges.get(i);
1037 result[j++] = range[0];
1038 result[j++] = range[1];
1044 * Returns the maximal start-end positions in the given (ordered) list of
1045 * ranges which is overlapped by the given begin-end range, or null if there
1050 * if ranges is {[4, 8], [10, 12], [16, 19]}
1052 * findOverlap(ranges, 1, 20) == [4, 19]
1053 * findOverlap(ranges, 6, 11) == [6, 11]
1054 * findOverlap(ranges, 9, 15) == [10, 12]
1055 * findOverlap(ranges, 13, 15) == null
1063 protected static int[] findOverlap(List<int[]> ranges, final int begin,
1066 boolean foundStart = false;
1071 * traverse the ranges to find the first position (if any) >= begin,
1072 * and the last position (if any) <= end
1074 for (int[] range : ranges)
1078 if (range[0] >= begin)
1081 * first range that starts with, or follows, begin
1084 from = Math.max(range[0], begin);
1086 else if (range[1] >= begin)
1089 * first range that contains begin
1096 if (range[0] <= end)
1098 to = Math.min(end, range[1]);
1102 return foundStart && to >= from ? new int[] { from, to } : null;