X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=3cca4533fc653e27b11acb497366fb9c7b702fba;hb=HEAD;hp=6103df505c90dfff69a16725189e309e8fb47add;hpb=43e966997685777da741087d56c2067a46757806;p=jalview.git diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 6103df5..3cca453 100644 --- a/src/jalview/datamodel/AlignedCodonFrame.java +++ b/src/jalview/datamodel/AlignedCodonFrame.java @@ -20,13 +20,13 @@ */ package jalview.datamodel; -import jalview.util.MapList; -import jalview.util.MappingUtils; - import java.util.AbstractList; import java.util.ArrayList; import java.util.List; +import jalview.util.MapList; +import jalview.util.MappingUtils; + /** * Stores mapping between the columns of a protein alignment and a DNA alignment * and a list of individual codon to amino acid mappings between sequences. @@ -118,15 +118,50 @@ public class AlignedCodonFrame */ public boolean covers(SequenceI seq) { - List mappedRanges = null; + return covers(seq, false, false); + } + + /** + * + * @param seq + * @param localCover + * - when true - compare extent of seq's dataset sequence rather + * than the local extent + * @param either + * - when true coverage is required for either seq or the mapped + * sequence + * @return true if mapping covers full length of given sequence (or the + * other if either==true) + */ + public boolean covers(SequenceI seq, boolean localCover, boolean either) + { + List mappedRanges = null, otherRanges = null; MapList mapList = mapping.getMap(); + int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend; + ; if (fromSeq == seq || fromSeq == seq.getDatasetSequence()) { + if (localCover && fromSeq != seq) + { + mstart = fromSeq.getStart(); + mend = fromSeq.getEnd(); + } mappedRanges = mapList.getFromRanges(); + otherRanges = mapList.getToRanges(); + ostart = mapping.to.getStart(); + oend = mapping.to.getEnd(); } else if (mapping.to == seq || mapping.to == seq.getDatasetSequence()) { + if (localCover && mapping.to != seq) + { + mstart = mapping.to.getStart(); + mend = mapping.to.getEnd(); + } mappedRanges = mapList.getToRanges(); + otherRanges = mapList.getFromRanges(); + ostart = fromSeq.getStart(); + oend = fromSeq.getEnd(); } else { @@ -134,27 +169,88 @@ public class AlignedCodonFrame } /* - * check that each mapped range lieS with the sequence range + * check that each mapped range lies within the sequence range * (necessary for circular CDS - example EMBL:J03321:AAA91567) * and mapped length covers (at least) sequence length */ + int length = countRange(mappedRanges, mstart, mend); + + if (length != -1) + { + // add 3 to mapped length to allow for a mapped stop codon + if (length + 3 >= (mend - mstart + 1)) + { + return true; + } + } + if (either) + { + // also check coverage of the other range + length = countRange(otherRanges, ostart, oend); + if (length != -1) + { + if (length + 1 >= (oend - ostart + 1)) + { + return true; + } + } + } + return false; + } + + private int countRange(List mappedRanges, int mstart, int mend) + { int length = 0; for (int[] range : mappedRanges) { int from = Math.min(range[0], range[1]); int to = Math.max(range[0], range[1]); - if (from < seq.getStart() || to > seq.getEnd()) + if (from < mstart || to > mend) { - return false; + return -1; } length += (to - from + 1); } - // add 1 to mapped length to allow for a mapped stop codon - if (length + 1 < (seq.getEnd() - seq.getStart() + 1)) + return length; + } + + /** + * Adds any regions mapped to or from position {@code pos} in sequence + * {@code seq} to the given search results Note: recommend first using the + * .covers(,true,true) to ensure mapping covers both sequences + * + * @param seq + * @param pos + * @param sr + */ + public void markMappedRegion(SequenceI seq, int pos, SearchResultsI sr) + { + int[] codon = null; + SequenceI mappedSeq = null; + SequenceI ds = seq.getDatasetSequence(); + if (ds == null) + { + ds = seq; + } + + if (this.fromSeq == seq || this.fromSeq == ds) + { + codon = this.mapping.map.locateInTo(pos, pos); + mappedSeq = this.mapping.to; + } + else if (this.mapping.to == seq || this.mapping.to == ds) { - return false; + codon = this.mapping.map.locateInFrom(pos, pos); + mappedSeq = this.fromSeq; + } + + if (codon != null) + { + for (int i = 0; i < codon.length; i += 2) + { + sr.addResult(mappedSeq, codon[i], codon[i + 1]); + } } - return true; } } @@ -345,7 +441,8 @@ public class AlignedCodonFrame /** * Add search results for regions in other sequences that translate or are - * translated from a particular position in seq + * translated from a particular position in seq (which may be an aligned or + * dataset sequence) * * @param seq * @param index @@ -356,69 +453,18 @@ public class AlignedCodonFrame public void markMappedRegion(SequenceI seq, int index, SearchResultsI results) { - int[] codon; SequenceI ds = seq.getDatasetSequence(); - for (SequenceToSequenceMapping ssm : mappings) + if (ds == null) { - if (ssm.fromSeq == seq || ssm.fromSeq == ds) - { - codon = ssm.mapping.map.locateInTo(index, index); - if (codon != null) - { - for (int i = 0; i < codon.length; i += 2) - { - results.addResult(ssm.mapping.to, codon[i], codon[i + 1]); - } - } - } - else if (ssm.mapping.to == seq || ssm.mapping.to == ds) - { - { - codon = ssm.mapping.map.locateInFrom(index, index); - if (codon != null) - { - for (int i = 0; i < codon.length; i += 2) - { - results.addResult(ssm.fromSeq, codon[i], codon[i + 1]); - } - } - } - } + ds = seq; } - } - - /** - * Returns the DNA codon positions (base 1) for the given position (base 1) in - * a mapped protein sequence, or null if no mapping is found. - * - * Intended for use in aligning cDNA to match aligned protein. Only the first - * mapping found is returned, so not suitable for use if multiple protein - * sequences are mapped to the same cDNA (but aligning cDNA as protein is - * ill-defined for this case anyway). - * - * @param seq - * the DNA dataset sequence - * @param aaPos - * residue position (base 1) in a protein sequence - * @return - */ - public int[] getDnaPosition(SequenceI seq, int aaPos) - { - /* - * Adapted from markMappedRegion(). - */ - MapList ml = null; - int i = 0; for (SequenceToSequenceMapping ssm : mappings) { - if (ssm.fromSeq == seq) + if (ssm.covers(seq, true, true)) { - ml = getdnaToProt()[i]; - break; + ssm.markMappedRegion(ds, index, results); } - i++; } - return ml == null ? null : ml.locateInFrom(aaPos, aaPos); } /** @@ -661,7 +707,8 @@ public class AlignedCodonFrame ds.setSequenceFeatures(dna.getSequenceFeatures()); // dnaSeqs[i] = ds; ssm.fromSeq = ds; - System.out.println("Realised mapped sequence " + ds.getName()); + jalview.bin.Console + .outPrintln("Realised mapped sequence " + ds.getName()); } } } @@ -856,4 +903,34 @@ public class AlignedCodonFrame } return null; } + + /** + * Returns the first mapping found which is between the given dataset sequence + * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent + * of both sequences involved + * + * @param seq + * @return + */ + public SequenceToSequenceMapping getCoveringCodonMapping(SequenceI seq) + { + for (SequenceToSequenceMapping mapping : mappings) + { + if (mapping.getMapping().getMap().isTripletMap() + && mapping.covers(seq)) + { + if (mapping.fromSeq == seq + && mapping.covers(mapping.getMapping().getTo())) + { + return mapping; + } + else if (mapping.getMapping().getTo() == seq + && mapping.covers(mapping.fromSeq)) + { + return mapping; + } + } + } + return null; + } }