X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=d60d4eb58dc7043a551ba72d75f226e43167c6ad;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=6294ca132ae9ba1b8135bb08b206043e07a81ac1;hpb=c17981672620e0b780a2338bd0c74e55cf9ddec2;p=jalview.git diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java index 6294ca1..d60d4eb 100644 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@ -20,16 +20,10 @@ */ package jalview.util; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; import jalview.analysis.AlignmentSorter; import jalview.api.AlignViewportI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -41,6 +35,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Mapping; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -48,6 +43,12 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; /** * Helper methods for manipulations involving sequence mappings. * @@ -80,7 +81,7 @@ public final class MappingUtils action = action.getUndoAction(); } // TODO write this - Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented"); + Console.error("MappingUtils.mapCutOrPaste not yet implemented"); } /** @@ -364,47 +365,55 @@ public final class MappingUtils int startResiduePos = selected.findPosition(firstUngappedPos); int endResiduePos = selected.findPosition(lastUngappedPos); - for (AlignedCodonFrame acf : codonFrames) + for (SequenceI seq : mapTo.getAlignment().getSequences()) { - for (SequenceI seq : mapTo.getAlignment().getSequences()) + int mappedStartResidue = 0; + int mappedEndResidue = 0; + for (AlignedCodonFrame acf : codonFrames) { - SequenceI peptide = targetIsNucleotide ? selected : seq; - SequenceI cds = targetIsNucleotide ? seq : selected; - SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds, - peptide); - if (s2s == null) - { - continue; - } - int mappedStartResidue = 0; - int mappedEndResidue = 0; - List mapping = Arrays.asList(acf); - SearchResultsI sr = buildSearchResults(selected, startResiduePos, - mapping); - for (SearchResultMatchI m : sr.getResults()) + // rather than use acf.getCoveringMapping() we iterate through all + // mappings to make sure all CDS are selected for a protein + for (SequenceToSequenceMapping map : acf.getMappings()) { - mappedStartResidue = m.getStart(); - mappedEndResidue = m.getEnd(); - } - sr = buildSearchResults(selected, endResiduePos, mapping); - for (SearchResultMatchI m : sr.getResults()) - { - mappedStartResidue = Math.min(mappedStartResidue, m.getStart()); - mappedEndResidue = Math.max(mappedEndResidue, m.getEnd()); - } + if (map.covers(selected) && map.covers(seq)) + { + /* + * Found a sequence mapping. Locate the start/end mapped residues. + */ + List mapping = Arrays + .asList(new AlignedCodonFrame[] + { acf }); + // locate start + SearchResultsI sr = buildSearchResults(selected, + startResiduePos, mapping); + for (SearchResultMatchI m : sr.getResults()) + { + mappedStartResidue = m.getStart(); + mappedEndResidue = m.getEnd(); + } + // locate end - allowing for adjustment of start range + sr = buildSearchResults(selected, endResiduePos, mapping); + for (SearchResultMatchI m : sr.getResults()) + { + mappedStartResidue = Math.min(mappedStartResidue, + m.getStart()); + mappedEndResidue = Math.max(mappedEndResidue, m.getEnd()); + } - /* - * Find the mapped aligned columns, save the range. Note findIndex - * returns a base 1 position, SequenceGroup uses base 0 - */ - int mappedStartCol = seq.findIndex(mappedStartResidue) - 1; - minStartCol = minStartCol == -1 ? mappedStartCol - : Math.min(minStartCol, mappedStartCol); - int mappedEndCol = seq.findIndex(mappedEndResidue) - 1; - maxEndCol = maxEndCol == -1 ? mappedEndCol - : Math.max(maxEndCol, mappedEndCol); - mappedGroup.addSequence(seq, false); - break; + /* + * Find the mapped aligned columns, save the range. Note findIndex + * returns a base 1 position, SequenceGroup uses base 0 + */ + int mappedStartCol = seq.findIndex(mappedStartResidue) - 1; + minStartCol = minStartCol == -1 ? mappedStartCol + : Math.min(minStartCol, mappedStartCol); + int mappedEndCol = seq.findIndex(mappedEndResidue) - 1; + maxEndCol = maxEndCol == -1 ? mappedEndCol + : Math.max(maxEndCol, mappedEndCol); + mappedGroup.addSequence(seq, false); + break; + } + } } } } @@ -444,23 +453,23 @@ public final class MappingUtils { for (AlignedCodonFrame acf : mappings) { - for (SequenceI seq2 : mapTo.getSequences()) + for (SequenceI seq2 : mapTo.getSequences()) + { + /* + * the corresponding peptide / CDS is the one for which there is + * a complete ('covering') mapping to 'seq' + */ + SequenceI peptide = mappingToNucleotide ? seq2 : seq; + SequenceI cds = mappingToNucleotide ? seq : seq2; + SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds, + peptide); + if (s2s != null) { - /* - * the corresponding peptide / CDS is the one for which there is - * a complete ('covering') mapping to 'seq' - */ - SequenceI peptide = mappingToNucleotide ? seq2 : seq; - SequenceI cds = mappingToNucleotide ? seq : seq2; - SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds, - peptide); - if (s2s != null) - { - mappedOrder.add(seq2); - j++; - break; - } + mappedOrder.add(seq2); + j++; + break; } + } } } @@ -522,7 +531,7 @@ public final class MappingUtils if (colsel == null) { - return; + return; // mappedColumns; } char fromGapChar = mapFrom.getAlignment().getGapCharacter(); @@ -544,9 +553,10 @@ public final class MappingUtils while (regions.hasNext()) { mapHiddenColumns(regions.next(), codonFrames, newHidden, - fromSequences, toSequences, fromGapChar); + fromSequences, + toSequences, fromGapChar); } - return; + return; // mappedColumns; } /** @@ -835,7 +845,7 @@ public final class MappingUtils { if (range.length % 2 != 0) { - Cache.log.error( + Console.error( "Error unbalance start/end ranges: " + ranges.toString()); return 0; } @@ -991,7 +1001,7 @@ public final class MappingUtils /* * not coded for [start1, end1, start2, end2, ...] */ - Cache.log.error( + Console.error( "MappingUtils.removeEndPositions doesn't handle multiple ranges"); return; } @@ -1002,7 +1012,7 @@ public final class MappingUtils /* * not coded for a reverse strand range (end < start) */ - Cache.log.error( + Console.error( "MappingUtils.removeEndPositions doesn't handle reverse strand"); return; } @@ -1018,27 +1028,83 @@ public final class MappingUtils } } } + /** + * 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 [start, end] ranges to a single array of [start, end, - * start, end ...] + * Converts a list of {@code start-end} ranges to a single array of + * {@code start1, end1, start2, ... } ranges * * @param ranges * @return */ - public static int[] listToArray(List ranges) + public static int[] rangeListToArray(List ranges) { - int[] result = new int[ranges.size() * 2]; - int i = 0; - for (int[] range : ranges) + int rangeCount = ranges.size(); + int[] result = new int[rangeCount * 2]; + int j = 0; + for (int i = 0; i < rangeCount; i++) { - result[i++] = range[0]; - result[i++] = range[1]; + int[] range = ranges.get(i); + result[j++] = range[0]; + result[j++] = range[1]; } return result; } - /** + /* * Returns the maximal start-end positions in the given (ordered) list of * ranges which is overlapped by the given begin-end range, or null if there * is no overlap.