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[]
383 SearchResultsI sr = buildSearchResults(selected,
384 startResiduePos, mapping);
385 for (SearchResultMatchI m : sr.getResults())
387 mappedStartResidue = m.getStart();
388 mappedEndResidue = m.getEnd();
390 sr = buildSearchResults(selected, endResiduePos, mapping);
391 for (SearchResultMatchI m : sr.getResults())
393 mappedStartResidue = Math.min(mappedStartResidue,
395 mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
399 * Find the mapped aligned columns, save the range. Note findIndex
400 * returns a base 1 position, SequenceGroup uses base 0
402 int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
403 minStartCol = minStartCol == -1 ? mappedStartCol
404 : Math.min(minStartCol, mappedStartCol);
405 int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
406 maxEndCol = maxEndCol == -1 ? mappedEndCol
407 : Math.max(maxEndCol, mappedEndCol);
408 mappedGroup.addSequence(seq, false);
414 mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
415 mappedGroup.setEndRes(maxEndCol < 0 ? 0 : maxEndCol);
420 * Returns an OrderCommand equivalent to the given one, but acting on mapped
421 * sequences as described by the mappings, or null if no mapping can be made.
424 * the original order command
426 * if true, the action is to undo the sort
428 * the alignment we are mapping to
430 * the mappings available
433 public static CommandI mapOrderCommand(OrderCommand command, boolean undo,
434 AlignmentI mapTo, List<AlignedCodonFrame> mappings)
436 SequenceI[] sortOrder = command.getSequenceOrder(undo);
437 List<SequenceI> mappedOrder = new ArrayList<>();
441 * Assumption: we are only interested in a cDNA/protein mapping; refactor in
442 * future if we want to support sorting (c)dna as (c)dna or protein as
445 boolean mappingToNucleotide = mapTo.isNucleotide();
446 for (SequenceI seq : sortOrder)
448 for (AlignedCodonFrame acf : mappings)
450 SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
451 : acf.getAaForDnaSeq(seq);
452 if (mappedSeq != null)
454 for (SequenceI seq2 : mapTo.getSequences())
456 if (seq2.getDatasetSequence() == mappedSeq)
458 mappedOrder.add(seq2);
468 * Return null if no mappings made.
476 * Add any unmapped sequences on the end of the sort in their original
479 if (j < mapTo.getHeight())
481 for (SequenceI seq : mapTo.getSequences())
483 if (!mappedOrder.contains(seq))
485 mappedOrder.add(seq);
491 * Have to sort the sequences before constructing the OrderCommand - which
492 * then resorts them?!?
494 final SequenceI[] mappedOrderArray = mappedOrder
495 .toArray(new SequenceI[mappedOrder.size()]);
496 SequenceI[] oldOrder = mapTo.getSequencesArray();
497 AlignmentSorter.sortBy(mapTo, new AlignmentOrder(mappedOrderArray));
498 final OrderCommand result = new OrderCommand(command.getDescription(),
504 * Returns a ColumnSelection in the 'mapTo' view which corresponds to the
505 * given selection in the 'mapFrom' view. We assume one is nucleotide, the
506 * other is protein (and holds the mappings from codons to protein residues).
513 public static void mapColumnSelection(ColumnSelection colsel,
514 HiddenColumns hiddencols, AlignViewportI mapFrom,
515 AlignViewportI mapTo, ColumnSelection newColSel,
516 HiddenColumns newHidden)
518 boolean targetIsNucleotide = mapTo.isNucleotide();
519 AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
520 List<AlignedCodonFrame> codonFrames = protein.getAlignment()
525 return; // mappedColumns;
528 char fromGapChar = mapFrom.getAlignment().getGapCharacter();
531 * For each mapped column, find the range of columns that residues in that
534 List<SequenceI> fromSequences = mapFrom.getAlignment().getSequences();
535 List<SequenceI> toSequences = mapTo.getAlignment().getSequences();
537 for (Integer sel : colsel.getSelected())
539 mapColumn(sel.intValue(), codonFrames, newColSel, fromSequences,
540 toSequences, fromGapChar);
543 Iterator<int[]> regions = hiddencols.iterator();
544 while (regions.hasNext())
546 mapHiddenColumns(regions.next(), codonFrames, newHidden,
547 fromSequences, toSequences, fromGapChar);
549 return; // mappedColumns;
553 * Helper method that maps a [start, end] hidden column range to its mapped
558 * @param mappedColumns
559 * @param fromSequences
563 protected static void mapHiddenColumns(int[] hidden,
564 List<AlignedCodonFrame> mappings, HiddenColumns mappedColumns,
565 List<SequenceI> fromSequences, List<SequenceI> toSequences,
568 for (int col = hidden[0]; col <= hidden[1]; col++)
570 int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
571 toSequences, fromGapChar);
574 * Add the range of hidden columns to the mapped selection (converting
577 if (mappedTo != null)
579 mappedColumns.hideColumns(mappedTo[0] - 1, mappedTo[1] - 1);
585 * Helper method to map one column selection
588 * the column number (base 0)
590 * the sequence mappings
591 * @param mappedColumns
592 * the mapped column selections to add to
593 * @param fromSequences
597 protected static void mapColumn(int col, List<AlignedCodonFrame> mappings,
598 ColumnSelection mappedColumns, List<SequenceI> fromSequences,
599 List<SequenceI> toSequences, char fromGapChar)
601 int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
602 toSequences, fromGapChar);
605 * Add the range of mapped columns to the mapped selection (converting
606 * base 1 to base 0). Note that this may include intron-only regions which
607 * lie between the start and end ranges of the selection.
609 if (mappedTo != null)
611 for (int i = mappedTo[0]; i <= mappedTo[1]; i++)
613 mappedColumns.addElement(i - 1);
619 * Helper method to find the range of columns mapped to from one column.
620 * Returns the maximal range of columns mapped to from all sequences in the
621 * source column, or null if no mappings were found.
625 * @param fromSequences
630 protected static int[] findMappedColumns(int col,
631 List<AlignedCodonFrame> mappings, List<SequenceI> fromSequences,
632 List<SequenceI> toSequences, char fromGapChar)
634 int[] mappedTo = new int[] { Integer.MAX_VALUE, Integer.MIN_VALUE };
635 boolean found = false;
638 * For each sequence in the 'from' alignment
640 for (SequenceI fromSeq : fromSequences)
643 * Ignore gaps (unmapped anyway)
645 if (fromSeq.getCharAt(col) == fromGapChar)
651 * Get the residue position and find the mapped position.
653 int residuePos = fromSeq.findPosition(col);
654 SearchResultsI sr = buildSearchResults(fromSeq, residuePos, mappings);
655 for (SearchResultMatchI m : sr.getResults())
657 int mappedStartResidue = m.getStart();
658 int mappedEndResidue = m.getEnd();
659 SequenceI mappedSeq = m.getSequence();
662 * Locate the aligned sequence whose dataset is mappedSeq. TODO a
663 * datamodel that can do this efficiently.
665 for (SequenceI toSeq : toSequences)
667 if (toSeq.getDatasetSequence() == mappedSeq)
669 int mappedStartCol = toSeq.findIndex(mappedStartResidue);
670 int mappedEndCol = toSeq.findIndex(mappedEndResidue);
671 mappedTo[0] = Math.min(mappedTo[0], mappedStartCol);
672 mappedTo[1] = Math.max(mappedTo[1], mappedEndCol);
675 // note: remove break if we ever want to map one to many sequences
680 return found ? mappedTo : null;
684 * Returns the mapped codon or codons for a given aligned sequence column
688 * an aligned peptide sequence
690 * an aligned column position (base 0)
692 * a set of codon mappings
693 * @return the bases of the mapped codon(s) in the cDNA dataset sequence(s),
694 * or an empty list if none found
696 public static List<char[]> findCodonsFor(SequenceI seq, int col,
697 List<AlignedCodonFrame> mappings)
699 List<char[]> result = new ArrayList<>();
700 int dsPos = seq.findPosition(col);
701 for (AlignedCodonFrame mapping : mappings)
703 if (mapping.involvesSequence(seq))
705 List<char[]> codons = mapping
706 .getMappedCodons(seq.getDatasetSequence(), dsPos);
709 result.addAll(codons);
717 * Converts a series of [start, end] range pairs into an array of individual
718 * positions. This also caters for 'reverse strand' (start > end) cases.
723 public static int[] flattenRanges(int[] ranges)
726 * Count how many positions altogether
729 for (int i = 0; i < ranges.length - 1; i += 2)
731 count += Math.abs(ranges[i + 1] - ranges[i]) + 1;
734 int[] result = new int[count];
736 for (int i = 0; i < ranges.length - 1; i += 2)
738 int from = ranges[i];
739 final int to = ranges[i + 1];
740 int step = from <= to ? 1 : -1;
745 } while (from != to + step);
751 * Returns a list of any mappings that are from or to the given (aligned or
758 public static List<AlignedCodonFrame> findMappingsForSequence(
759 SequenceI sequence, List<AlignedCodonFrame> mappings)
761 return findMappingsForSequenceAndOthers(sequence, mappings, null);
765 * Returns a list of any mappings that are from or to the given (aligned or
766 * dataset) sequence, optionally limited to mappings involving one of a given
774 public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
775 SequenceI sequence, List<AlignedCodonFrame> mappings,
776 List<SequenceI> filterList)
778 List<AlignedCodonFrame> result = new ArrayList<>();
779 if (sequence == null || mappings == null)
783 for (AlignedCodonFrame mapping : mappings)
785 if (mapping.involvesSequence(sequence))
787 if (filterList != null)
789 for (SequenceI otherseq : filterList)
791 SequenceI otherDataset = otherseq.getDatasetSequence();
792 if (otherseq == sequence
793 || otherseq == sequence.getDatasetSequence()
794 || (otherDataset != null && (otherDataset == sequence
795 || otherDataset == sequence
796 .getDatasetSequence())))
798 // skip sequences in subset which directly relate to sequence
801 if (mapping.involvesSequence(otherseq))
803 // selected a mapping contained in subselect alignment
819 * Returns the total length of the supplied ranges, which may be as single
820 * [start, end] or multiple [start, end, start, end ...]
825 public static int getLength(List<int[]> ranges)
832 for (int[] range : ranges)
834 if (range.length % 2 != 0)
837 "Error unbalance start/end ranges: " + ranges.toString());
840 for (int i = 0; i < range.length - 1; i += 2)
842 length += Math.abs(range[i + 1] - range[i]) + 1;
849 * Answers true if any range includes the given value
855 public static boolean contains(List<int[]> ranges, int value)
861 for (int[] range : ranges)
863 if (range[1] >= range[0] && value >= range[0] && value <= range[1])
866 * value within ascending range
870 if (range[1] < range[0] && value <= range[0] && value >= range[1])
873 * value within descending range
882 * Removes a specified number of positions from the start of a ranges list.
883 * For example, could be used to adjust cds ranges to allow for an incomplete
884 * start codon. Subranges are removed completely, or their start positions
885 * adjusted, until the required number of positions has been removed from the
886 * range. Reverse strand ranges are supported. The input array is not
891 * an array of [start, end, start, end...] positions
892 * @return a new array with the first removeCount positions removed
894 public static int[] removeStartPositions(int removeCount,
897 if (removeCount <= 0)
902 int[] copy = Arrays.copyOf(ranges, ranges.length);
905 for (int x = 0; x < copy.length && sxpos == -1; x += 2)
907 cdspos += Math.abs(copy[x + 1] - copy[x]) + 1;
908 if (removeCount < cdspos)
911 * we have removed enough, time to finish
916 * increment start of first exon, or decrement if reverse strand
918 if (copy[x] <= copy[x + 1])
920 copy[x] = copy[x + 1] - cdspos + removeCount + 1;
924 copy[x] = copy[x + 1] + cdspos - removeCount - 1;
933 * we dropped at least one entire sub-range - compact the array
935 int[] nxon = new int[copy.length - sxpos];
936 System.arraycopy(copy, sxpos, nxon, 0, copy.length - sxpos);
943 * Answers true if range's start-end positions include those of queryRange,
944 * where either range might be in reverse direction, else false
949 * a candidate subrange of range (start2-end2)
952 public static boolean rangeContains(int[] range, int[] queryRange)
954 if (range == null || queryRange == null || range.length != 2
955 || queryRange.length != 2)
963 int min = Math.min(range[0], range[1]);
964 int max = Math.max(range[0], range[1]);
966 return (min <= queryRange[0] && max >= queryRange[0]
967 && min <= queryRange[1] && max >= queryRange[1]);
971 * Removes the specified number of positions from the given ranges. Provided
972 * to allow a stop codon to be stripped from a CDS sequence so that it matches
973 * the peptide translation length.
977 * a list of (single) [start, end] ranges
980 public static void removeEndPositions(int positions, List<int[]> ranges)
982 int toRemove = positions;
983 Iterator<int[]> it = new ReverseListIterator<>(ranges);
986 int[] endRange = it.next();
987 if (endRange.length != 2)
990 * not coded for [start1, end1, start2, end2, ...]
993 "MappingUtils.removeEndPositions doesn't handle multiple ranges");
997 int length = endRange[1] - endRange[0] + 1;
1001 * not coded for a reverse strand range (end < start)
1004 "MappingUtils.removeEndPositions doesn't handle reverse strand");
1007 if (length > toRemove)
1009 endRange[1] -= toRemove;
1021 * Converts a list of {@code start-end} ranges to a single array of
1022 * {@code start1, end1, start2, ... } ranges
1027 public static int[] rangeListToArray(List<int[]> ranges)
1029 int rangeCount = ranges.size();
1030 int[] result = new int[rangeCount * 2];
1032 for (int i = 0; i < rangeCount; i++)
1034 int[] range = ranges.get(i);
1035 result[j++] = range[0];
1036 result[j++] = range[1];
1042 * Returns the maximal start-end positions in the given (ordered) list of
1043 * ranges which is overlapped by the given begin-end range, or null if there
1048 * if ranges is {[4, 8], [10, 12], [16, 19]}
1050 * findOverlap(ranges, 1, 20) == [4, 19]
1051 * findOverlap(ranges, 6, 11) == [6, 11]
1052 * findOverlap(ranges, 9, 15) == [10, 12]
1053 * findOverlap(ranges, 13, 15) == null
1061 protected static int[] findOverlap(List<int[]> ranges, final int begin,
1064 boolean foundStart = false;
1069 * traverse the ranges to find the first position (if any) >= begin,
1070 * and the last position (if any) <= end
1072 for (int[] range : ranges)
1076 if (range[0] >= begin)
1079 * first range that starts with, or follows, begin
1082 from = Math.max(range[0], begin);
1084 else if (range[1] >= begin)
1087 * first range that contains begin
1094 if (range[0] <= end)
1096 to = Math.min(end, range[1]);
1100 return foundStart && to >= from ? new int[] { from, to } : null;