X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=fe95f4b3f367727bc7031cf3c864554e3074f80c;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=f75286a377a807916eb73a5cb76c8a1537e39e35;hpb=5e8ec77d921ff2d604811e5e4ba7e9211b0f48de;p=jalview.git diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java index f75286a..fe95f4b 100644 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@ -219,8 +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); @@ -230,15 +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))); } } } @@ -363,8 +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()) @@ -377,7 +379,8 @@ public final class MappingUtils * Found a sequence mapping. Locate the start/end mapped residues. */ List mapping = Arrays - .asList(new AlignedCodonFrame[] { acf }); + .asList(new AlignedCodonFrame[] + { acf }); SearchResultsI sr = buildSearchResults(selected, startResiduePos, mapping); for (SearchResultMatchI m : sr.getResults()) @@ -398,11 +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; } @@ -429,8 +432,8 @@ 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<>(); @@ -518,7 +521,6 @@ public final class MappingUtils AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo; List codonFrames = protein.getAlignment() .getCodonFrames(); - // ColumnSelection mappedColumns = new ColumnSelection(); if (colsel == null) { @@ -540,9 +542,11 @@ public final class MappingUtils toSequences, fromGapChar); } - for (int[] hidden : hiddencols) + Iterator regions = hiddencols.iterator(); + while (regions.hasNext()) { - mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences, + mapHiddenColumns(regions.next(), codonFrames, newHidden, + fromSequences, toSequences, fromGapChar); } return; // mappedColumns; @@ -593,10 +597,9 @@ 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); @@ -702,8 +705,8 @@ public final class MappingUtils { if (mapping.involvesSequence(seq)) { - List codons = mapping.getMappedCodons( - seq.getDatasetSequence(), dsPos); + List codons = mapping + .getMappedCodons(seq.getDatasetSequence(), dsPos); if (codons != null) { result.addAll(codons); @@ -791,8 +794,9 @@ 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; @@ -832,8 +836,8 @@ 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) @@ -937,4 +941,158 @@ 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(); + } + } + } + /** + * Adds the given range to a list of ranges. If the new range just extends + * existing ranges, the current endpoint is updated instead. + * + * @param range + * @param addTo + */ + public static void addRange(int[] range, List addTo) + { + /* + * list is empty - add to it! + */ + if (addTo.size() == 0) + { + addTo.add(range); + return; + } + + int[] last = addTo.get(addTo.size() - 1); + boolean lastForward = last[1] >= last[0]; + boolean newForward = range[1] >= range[0]; + + /* + * contiguous range in the same direction - just update endpoint + */ + if (lastForward == newForward && last[1] == range[0]) + { + last[1] = range[1]; + return; + } + + /* + * next range starts at +1 in forward sense - update endpoint + */ + if (lastForward && newForward && range[0] == last[1] + 1) + { + last[1] = range[1]; + return; + } + + /* + * next range starts at -1 in reverse sense - update endpoint + */ + if (!lastForward && !newForward && range[0] == last[1] - 1) + { + last[1] = range[1]; + return; + } + + /* + * just add the new range + */ + addTo.add(range); + } + + /** + * Converts a list of {@code start-end} ranges to a single array of + * {@code start1, end1, start2, ... } ranges + * + * @param ranges + * @return + */ + public static int[] rangeListToArray(List ranges) + { + int rangeCount = ranges.size(); + int[] result = new int[rangeCount * 2]; + int j = 0; + for (int i = 0; i < rangeCount; i++) + { + int[] range = ranges.get(i); + result[j++] = range[0]; + result[j++] = range[1]; + } + return result; + } }