X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=22714b850d36ce5d21f37069fd484d7c4e7a9d0b;hb=be47cdd2406f63ccb1fcf424194e82302dfc9360;hp=adfd39744b15680e469497c3c6002a9dde688904;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java index adfd397..22714b8 100644 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.util; import jalview.analysis.AlignmentSorter; @@ -18,12 +38,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import java.util.ArrayList; -import java.util.Collections; +import java.util.Arrays; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; -import java.util.Set; /** * Helper methods for manipulations involving sequence mappings. @@ -49,7 +68,7 @@ public final class MappingUtils */ protected static void mapCutOrPaste(Edit edit, boolean undo, List targetSeqs, EditCommand result, - Set mappings) + List mappings) { Action action = edit.getAction(); if (undo) @@ -73,7 +92,7 @@ public final class MappingUtils */ public static EditCommand mapEditCommand(EditCommand command, boolean undo, final AlignmentI mapTo, char gapChar, - Set mappings) + List mappings) { /* * For now, only support mapping from protein edits to cDna @@ -145,7 +164,7 @@ public final class MappingUtils Map originalSequences, final List targetSeqs, Map targetCopies, char gapChar, - EditCommand result, Set mappings) + EditCommand result, List mappings) { Action action = edit.getAction(); @@ -248,7 +267,7 @@ public final class MappingUtils * @return */ public static SearchResults buildSearchResults(SequenceI seq, int index, - Set seqmappings) + List seqmappings) { SearchResults results = new SearchResults(); addSearchResults(results, seq, index, seqmappings); @@ -265,7 +284,7 @@ public final class MappingUtils * @param seqmappings */ public static void addSearchResults(SearchResults results, SequenceI seq, - int index, Set seqmappings) + int index, List seqmappings) { if (index >= seq.getStart() && index <= seq.getEnd()) { @@ -294,7 +313,7 @@ public final class MappingUtils */ boolean targetIsNucleotide = mapTo.isNucleotide(); AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo; - Set codonFrames = protein.getAlignment() + List codonFrames = protein.getAlignment() .getCodonFrames(); /* * Copy group name, colours etc, but not sequences or sequence colour scheme @@ -355,15 +374,15 @@ 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, - startResiduePos, Collections.singleton(acf)); + startResiduePos, mapping); for (Match m : sr.getResults()) { mappedStartResidue = m.getStart(); mappedEndResidue = m.getEnd(); } - sr = buildSearchResults(selected, endResiduePos, - Collections.singleton(acf)); + sr = buildSearchResults(selected, endResiduePos, mapping); for (Match m : sr.getResults()) { mappedStartResidue = Math.min(mappedStartResidue, @@ -408,7 +427,7 @@ public final class MappingUtils * @return */ public static CommandI mapOrderCommand(OrderCommand command, - boolean undo, AlignmentI mapTo, Set mappings) + boolean undo, AlignmentI mapTo, List mappings) { SequenceI[] sortOrder = command.getSequenceOrder(undo); List mappedOrder = new ArrayList(); @@ -492,7 +511,7 @@ public final class MappingUtils { boolean targetIsNucleotide = mapTo.isNucleotide(); AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo; - Set codonFrames = protein.getAlignment() + List codonFrames = protein.getAlignment() .getCodonFrames(); ColumnSelection mappedColumns = new ColumnSelection(); @@ -574,8 +593,8 @@ public final class MappingUtils } /** - * Returns the mapped codon for a given aligned sequence column position (base - * 0). + * Returns the mapped codon or codons for a given aligned sequence column + * position (base 0). * * @param seq * an aligned peptide sequence @@ -583,26 +602,32 @@ public final class MappingUtils * an aligned column position (base 0) * @param mappings * a set of codon mappings - * @return the bases of the mapped codon in the cDNA dataset sequence, or null - * if not found + * @return the bases of the mapped codon(s) in the cDNA dataset sequence(s), + * or an empty list if none found */ - public static char[] findCodonFor(SequenceI seq, int col, - Set mappings) + public static List findCodonsFor(SequenceI seq, int col, + List mappings) { + List result = new ArrayList(); int dsPos = seq.findPosition(col); for (AlignedCodonFrame mapping : mappings) { if (mapping.involvesSequence(seq)) { - return mapping.getMappedCodon(seq.getDatasetSequence(), dsPos); + List codons = mapping.getMappedCodons( + seq.getDatasetSequence(), dsPos); + if (codons != null) + { + result.addAll(codons); + } } } - return null; + return result; } /** - * Converts a series of [start, end] ranges into an array of individual - * positions. + * Converts a series of [start, end] range pairs into an array of individual + * positions. This also caters for 'reverse strand' (start > end) cases. * * @param ranges * @return @@ -615,17 +640,21 @@ public final class MappingUtils int count = 0; for (int i = 0; i < ranges.length - 1; i += 2) { - count += ranges[i + 1] - ranges[i] + 1; + count += Math.abs(ranges[i + 1] - ranges[i]) + 1; } int[] result = new int[count]; int k = 0; for (int i = 0; i < ranges.length - 1; i += 2) { - for (int j = ranges[i]; j <= ranges[i + 1]; j++) + int from = ranges[i]; + final int to = ranges[i + 1]; + int step = from <= to ? 1 : -1; + do { - result[k++] = j; - } + result[k++] = from; + from += step; + } while (from != to + step); } return result; } @@ -639,7 +668,7 @@ public final class MappingUtils * @return */ public static List findMappingsForSequence( - SequenceI sequence, Set mappings) + SequenceI sequence, List mappings) { List result = new ArrayList(); if (sequence == null || mappings == null)