X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=f5dd88366976c3a028865e8458f44f513b887eda;hb=14193747f3831242bc7dfac12394eb20eb0ba480;hp=1fe452d410d74c305a82c4da04aea41d0b84df71;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java index 1fe452d..f5dd883 100644 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@ -31,8 +31,10 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResults.Match; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -106,7 +108,7 @@ public final class MappingUtils * Cache a copy of the target sequences so we can mimic successive edits on * them. This lets us compute mappings for all edits in the set. */ - Map targetCopies = new HashMap(); + Map targetCopies = new HashMap<>(); for (SequenceI seq : mapTo.getSequences()) { SequenceI ds = seq.getDatasetSequence(); @@ -194,7 +196,7 @@ public final class MappingUtils /* * Determine all mappings from this position to mapped sequences. */ - SearchResults sr = buildSearchResults(seq, seqpos, mappings); + SearchResultsI sr = buildSearchResults(seq, seqpos, mappings); if (!sr.isEmpty()) { @@ -217,8 +219,9 @@ public final class MappingUtils * Shift Delete start position left, as it acts on positions to its * right. */ - int mappedEditPos = action == Action.DELETE_GAP ? match[0] - - mappedCount : match[0]; + int mappedEditPos = action == Action.DELETE_GAP + ? match[0] - mappedCount + : match[0]; Edit e = result.new Edit(action, new SequenceI[] { targetSeq }, mappedEditPos, mappedCount, gapChar); result.addEdit(e); @@ -228,15 +231,15 @@ public final class MappingUtils */ if (action == Action.INSERT_GAP) { - copyTarget.setSequence(new String(StringUtils.insertCharAt( - copyTarget.getSequence(), mappedEditPos, mappedCount, - gapChar))); + copyTarget.setSequence(new String( + StringUtils.insertCharAt(copyTarget.getSequence(), + mappedEditPos, mappedCount, gapChar))); } else if (action == Action.DELETE_GAP) { - copyTarget.setSequence(new String(StringUtils.deleteChars( - copyTarget.getSequence(), mappedEditPos, - mappedEditPos + mappedCount))); + copyTarget.setSequence(new String( + StringUtils.deleteChars(copyTarget.getSequence(), + mappedEditPos, mappedEditPos + mappedCount))); } } } @@ -266,10 +269,10 @@ public final class MappingUtils * @param seqmappings * @return */ - public static SearchResults buildSearchResults(SequenceI seq, int index, + public static SearchResultsI buildSearchResults(SequenceI seq, int index, List seqmappings) { - SearchResults results = new SearchResults(); + SearchResultsI results = new SearchResults(); addSearchResults(results, seq, index, seqmappings); return results; } @@ -283,7 +286,7 @@ public final class MappingUtils * @param index * @param seqmappings */ - public static void addSearchResults(SearchResults results, SequenceI seq, + public static void addSearchResults(SearchResultsI results, SequenceI seq, int index, List seqmappings) { if (index >= seq.getStart() && index <= seq.getEnd()) @@ -319,7 +322,7 @@ public final class MappingUtils * Copy group name, colours etc, but not sequences or sequence colour scheme */ SequenceGroup mappedGroup = new SequenceGroup(sg); - mappedGroup.cs = mapTo.getGlobalColourScheme(); + mappedGroup.setColourScheme(mapTo.getGlobalColourScheme()); mappedGroup.clear(); int minStartCol = -1; @@ -361,8 +364,9 @@ public final class MappingUtils for (AlignedCodonFrame acf : codonFrames) { - SequenceI mappedSequence = targetIsNucleotide ? acf - .getDnaForAaSeq(selected) : acf.getAaForDnaSeq(selected); + SequenceI mappedSequence = targetIsNucleotide + ? acf.getDnaForAaSeq(selected) + : acf.getAaForDnaSeq(selected); if (mappedSequence != null) { for (SequenceI seq : mapTo.getAlignment().getSequences()) @@ -375,16 +379,17 @@ public final class MappingUtils * Found a sequence mapping. Locate the start/end mapped residues. */ List mapping = Arrays - .asList(new AlignedCodonFrame[] { acf }); - SearchResults sr = buildSearchResults(selected, + .asList(new AlignedCodonFrame[] + { acf }); + SearchResultsI sr = buildSearchResults(selected, startResiduePos, mapping); - for (Match m : sr.getResults()) + for (SearchResultMatchI m : sr.getResults()) { mappedStartResidue = m.getStart(); mappedEndResidue = m.getEnd(); } sr = buildSearchResults(selected, endResiduePos, mapping); - for (Match m : sr.getResults()) + for (SearchResultMatchI m : sr.getResults()) { mappedStartResidue = Math.min(mappedStartResidue, m.getStart()); @@ -396,11 +401,11 @@ public final class MappingUtils * returns a base 1 position, SequenceGroup uses base 0 */ int mappedStartCol = seq.findIndex(mappedStartResidue) - 1; - minStartCol = minStartCol == -1 ? mappedStartCol : Math.min( - minStartCol, mappedStartCol); + minStartCol = minStartCol == -1 ? mappedStartCol + : Math.min(minStartCol, mappedStartCol); int mappedEndCol = seq.findIndex(mappedEndResidue) - 1; - maxEndCol = maxEndCol == -1 ? mappedEndCol : Math.max( - maxEndCol, mappedEndCol); + maxEndCol = maxEndCol == -1 ? mappedEndCol + : Math.max(maxEndCol, mappedEndCol); mappedGroup.addSequence(seq, false); break; } @@ -427,11 +432,11 @@ public final class MappingUtils * the mappings available * @return */ - public static CommandI mapOrderCommand(OrderCommand command, - boolean undo, AlignmentI mapTo, List mappings) + public static CommandI mapOrderCommand(OrderCommand command, boolean undo, + AlignmentI mapTo, List mappings) { SequenceI[] sortOrder = command.getSequenceOrder(undo); - List mappedOrder = new ArrayList(); + List mappedOrder = new ArrayList<>(); int j = 0; /* @@ -507,18 +512,19 @@ public final class MappingUtils * @param mapTo * @return */ - public static ColumnSelection mapColumnSelection(ColumnSelection colsel, - AlignViewportI mapFrom, AlignViewportI mapTo) + public static void mapColumnSelection(ColumnSelection colsel, + HiddenColumns hiddencols, AlignViewportI mapFrom, + AlignViewportI mapTo, ColumnSelection newColSel, + HiddenColumns newHidden) { boolean targetIsNucleotide = mapTo.isNucleotide(); AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo; List codonFrames = protein.getAlignment() .getCodonFrames(); - ColumnSelection mappedColumns = new ColumnSelection(); if (colsel == null) { - return mappedColumns; + return; // mappedColumns; } char fromGapChar = mapFrom.getAlignment().getGapCharacter(); @@ -532,16 +538,16 @@ public final class MappingUtils for (Integer sel : colsel.getSelected()) { - mapColumn(sel.intValue(), codonFrames, mappedColumns, fromSequences, + mapColumn(sel.intValue(), codonFrames, newColSel, fromSequences, toSequences, fromGapChar); } - for (int[] hidden : colsel.getHiddenColumns()) + for (int[] hidden : hiddencols.getHiddenColumnsCopy()) { - mapHiddenColumns(hidden, codonFrames, mappedColumns, fromSequences, + mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences, toSequences, fromGapChar); } - return mappedColumns; + return; // mappedColumns; } /** @@ -556,7 +562,7 @@ public final class MappingUtils * @param fromGapChar */ protected static void mapHiddenColumns(int[] hidden, - List mappings, ColumnSelection mappedColumns, + List mappings, HiddenColumns mappedColumns, List fromSequences, List toSequences, char fromGapChar) { @@ -589,10 +595,9 @@ public final class MappingUtils * @param toSequences * @param fromGapChar */ - protected static void mapColumn(int col, - List mappings, ColumnSelection mappedColumns, - List fromSequences, List toSequences, - char fromGapChar) + protected static void mapColumn(int col, List mappings, + ColumnSelection mappedColumns, List fromSequences, + List toSequences, char fromGapChar) { int[] mappedTo = findMappedColumns(col, mappings, fromSequences, toSequences, fromGapChar); @@ -647,8 +652,8 @@ public final class MappingUtils * Get the residue position and find the mapped position. */ int residuePos = fromSeq.findPosition(col); - SearchResults sr = buildSearchResults(fromSeq, residuePos, mappings); - for (Match m : sr.getResults()) + SearchResultsI sr = buildSearchResults(fromSeq, residuePos, mappings); + for (SearchResultMatchI m : sr.getResults()) { int mappedStartResidue = m.getStart(); int mappedEndResidue = m.getEnd(); @@ -692,14 +697,14 @@ public final class MappingUtils public static List findCodonsFor(SequenceI seq, int col, List mappings) { - List result = new ArrayList(); + List result = new ArrayList<>(); int dsPos = seq.findPosition(col); for (AlignedCodonFrame mapping : mappings) { if (mapping.involvesSequence(seq)) { - List codons = mapping.getMappedCodons( - seq.getDatasetSequence(), dsPos); + List codons = mapping + .getMappedCodons(seq.getDatasetSequence(), dsPos); if (codons != null) { result.addAll(codons); @@ -771,7 +776,7 @@ public final class MappingUtils SequenceI sequence, List mappings, List filterList) { - List result = new ArrayList(); + List result = new ArrayList<>(); if (sequence == null || mappings == null) { return result; @@ -787,8 +792,9 @@ public final class MappingUtils SequenceI otherDataset = otherseq.getDatasetSequence(); if (otherseq == sequence || otherseq == sequence.getDatasetSequence() - || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence - .getDatasetSequence()))) + || (otherDataset != null && (otherDataset == sequence + || otherDataset == sequence + .getDatasetSequence()))) { // skip sequences in subset which directly relate to sequence continue; @@ -828,8 +834,8 @@ public final class MappingUtils { if (range.length % 2 != 0) { - System.err.println("Error unbalance start/end ranges: " - + ranges.toString()); + System.err.println( + "Error unbalance start/end ranges: " + ranges.toString()); return 0; } for (int i = 0; i < range.length - 1; i += 2) @@ -933,4 +939,83 @@ public final class MappingUtils } return copy; } + + /** + * Answers true if range's start-end positions include those of queryRange, + * where either range might be in reverse direction, else false + * + * @param range + * a start-end range + * @param queryRange + * a candidate subrange of range (start2-end2) + * @return + */ + public static boolean rangeContains(int[] range, int[] queryRange) + { + if (range == null || queryRange == null || range.length != 2 + || queryRange.length != 2) + { + /* + * invalid arguments + */ + return false; + } + + int min = Math.min(range[0], range[1]); + int max = Math.max(range[0], range[1]); + + return (min <= queryRange[0] && max >= queryRange[0] + && min <= queryRange[1] && max >= queryRange[1]); + } + + /** + * Removes the specified number of positions from the given ranges. Provided + * to allow a stop codon to be stripped from a CDS sequence so that it matches + * the peptide translation length. + * + * @param positions + * @param ranges + * a list of (single) [start, end] ranges + * @return + */ + public static void removeEndPositions(int positions, + List ranges) + { + int toRemove = positions; + Iterator it = new ReverseListIterator<>(ranges); + while (toRemove > 0) + { + int[] endRange = it.next(); + if (endRange.length != 2) + { + /* + * not coded for [start1, end1, start2, end2, ...] + */ + System.err + .println("MappingUtils.removeEndPositions doesn't handle multiple ranges"); + return; + } + + int length = endRange[1] - endRange[0] + 1; + if (length <= 0) + { + /* + * not coded for a reverse strand range (end < start) + */ + System.err + .println("MappingUtils.removeEndPositions doesn't handle reverse strand"); + return; + } + if (length > toRemove) + { + endRange[1] -= toRemove; + toRemove = 0; + } + else + { + toRemove -= length; + it.remove(); + } + } + } }