X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=6ccc0fc0c663b6458d88377696421e0381026fde;hb=855af27bbb88788ac9c1ee9872a43fbb333ae380;hp=c3d17dc70d5ad9bbecee0aefa0ad36144769f128;hpb=689f9cf4bdb57417fcb93db5b7cf5d9cf8154e3f;p=jalview.git diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index c3d17dc..6ccc0fc 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. @@ -118,19 +118,20 @@ public class AlignedCodonFrame */ public boolean covers(SequenceI seq) { - return covers(seq,false); + return covers(seq,false,false); } /** * * @param seq - * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent - * @return true if mapping covers full length of given sequence + * @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) + public boolean covers(SequenceI seq, boolean localCover,boolean either) { - List mappedRanges = null; + List mappedRanges = null,otherRanges=null; MapList mapList = mapping.getMap(); - int mstart=seq.getStart(),mend=seq.getEnd() + int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend; ; if (fromSeq == seq || fromSeq == seq.getDatasetSequence()) { @@ -140,6 +141,9 @@ public class AlignedCodonFrame 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()) { @@ -149,6 +153,9 @@ public class AlignedCodonFrame mend=mapping.to.getEnd(); } mappedRanges = mapList.getToRanges(); + otherRanges=mapList.getFromRanges(); + ostart=fromSeq.getStart(); + oend=fromSeq.getEnd(); } else { @@ -156,27 +163,86 @@ 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 = 0; + 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 < 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 < (mend - mstart + 1)) + return length; + } + + /** + * Adds any regions mapped to or from position {@code pos} in sequence + * {@code seq} to the given search results + * + * @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) { - return false; + 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) + { + 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; } } @@ -367,7 +433,8 @@ 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 @@ -378,34 +445,14 @@ public class AlignedCodonFrame public void markMappedRegion(SequenceI seq, int index, SearchResultsI results) { - int[] codon; SequenceI ds = seq.getDatasetSequence(); + if (ds == null) + { + ds = seq; + } for (SequenceToSequenceMapping ssm : mappings) { - 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]); - } - } - } - } + ssm.markMappedRegion(ds, index, results); } } @@ -476,11 +523,13 @@ public class AlignedCodonFrame { int mStart=ssm.getMapping().getMap().getFromLowest(),mEnd=ssm.getMapping().map.getFromHighest(); if ((ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence()) - && seq.getStart()>=mStart && seq.getEnd()<=mEnd) + // here AlignmentUtilsTest. testAlignProteinAsDna_incompleteStartCodon fails because mStart/mEnd is contained by seq + // without this filter, we don't get the correct mapping, however + )// && seq.getStart()>=mStart && seq.getEnd()<=mEnd) { for (SequenceI sourceAligned : al.getSequences()) { - if (ssm.covers(sourceAligned,true)) + if (ssm.covers(sourceAligned,true,false)) { if (map != null) { @@ -504,7 +553,7 @@ public class AlignedCodonFrame { for (SequenceI sourceAligned : al.getSequences()) { - if (ssm.covers(sourceAligned,true)) + if (ssm.covers(sourceAligned,true,true)) { if (map != null) { @@ -903,4 +952,34 @@ 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; + } }