X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=f5154ec1da1d151cebd4e240ff86d20914c90c1e;hb=62fb9a3042bdc6daaad8218d47b12cb912907354;hp=1b3c33490c9e50b715a4dbbdef45c05437149092;hpb=ed71ad3c91cd2609f3e91a8027b2c0877b018dea;p=jalview.git diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 1b3c334..f5154ec 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. @@ -118,44 +118,50 @@ public class AlignedCodonFrame */ public boolean covers(SequenceI seq) { - return covers(seq,false,false); + 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) + * @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) + public boolean covers(SequenceI seq, boolean localCover, boolean either) { - List mappedRanges = null,otherRanges=null; + List mappedRanges = null, otherRanges = null; MapList mapList = mapping.getMap(); - int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend; - ; + int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend; + ; if (fromSeq == seq || fromSeq == seq.getDatasetSequence()) { - if (localCover && fromSeq !=seq) + if (localCover && fromSeq != seq) { - mstart=fromSeq.getStart(); - mend=fromSeq.getEnd(); + mstart = fromSeq.getStart(); + mend = fromSeq.getEnd(); } mappedRanges = mapList.getFromRanges(); - otherRanges=mapList.getToRanges(); - ostart=mapping.to.getStart(); - oend=mapping.to.getEnd(); + 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) + if (localCover && mapping.to != seq) { - mstart=mapping.to.getStart(); - mend=mapping.to.getEnd(); + mstart = mapping.to.getStart(); + mend = mapping.to.getEnd(); } mappedRanges = mapList.getToRanges(); - otherRanges=mapList.getFromRanges(); - ostart=fromSeq.getStart(); - oend=fromSeq.getEnd(); + otherRanges = mapList.getFromRanges(); + ostart = fromSeq.getStart(); + oend = fromSeq.getEnd(); } else { @@ -163,16 +169,16 @@ 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); + int length = countRange(mappedRanges, mstart, mend); if (length != -1) { - // add 1 to mapped length to allow for a mapped stop codon - if (length + 1 >= (mend - mstart + 1)) + // add 3 to mapped length to allow for a mapped stop codon + if (length + 3 >= (mend - mstart + 1)) { return true; } @@ -191,9 +197,10 @@ public class AlignedCodonFrame } return false; } - private int countRange(List mappedRanges,int mstart,int mend) + + private int countRange(List mappedRanges, int mstart, int mend) { - int length=0; + int length = 0; for (int[] range : mappedRanges) { int from = Math.min(range[0], range[1]); @@ -206,6 +213,44 @@ public class AlignedCodonFrame } 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) + { + 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]); + } + } } } @@ -396,7 +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 @@ -407,69 +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); } /** @@ -484,37 +479,18 @@ public class AlignedCodonFrame */ public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al) { - return findAlignedSequence(seq, al, null); - } - /** - * Convenience method to return the first aligned sequence in the given - * alignment whose dataset has a mapping with the given (aligned or dataset) - * sequence, and optionally the mapping that relates them - * - * @param seq - * @param al - * @param map - list to add the mapping to - * @return sequence from al that maps to seq - */ - public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al,List map) - { /* * Search mapped protein ('to') sequences first. */ for (SequenceToSequenceMapping ssm : mappings) { - 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) + if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence()) { for (SequenceI sourceAligned : al.getSequences()) { - if (ssm.covers(sourceAligned,true,false)) + if (ssm.mapping.to == sourceAligned.getDatasetSequence() + || ssm.mapping.to == sourceAligned) { - if (map != null) - { - map.add(ssm); - } return sourceAligned; } } @@ -526,19 +502,13 @@ public class AlignedCodonFrame */ for (SequenceToSequenceMapping ssm : mappings) { - int mStart=ssm.getMapping().getMap().getToLowest(),mEnd=ssm.getMapping().map.getToHighest(); - if ((ssm.mapping.to == seq + if (ssm.mapping.to == seq || ssm.mapping.to == seq.getDatasetSequence()) - && seq.getStart()>=mStart && seq.getEnd()<=mEnd) { for (SequenceI sourceAligned : al.getSequences()) { - if (ssm.covers(sourceAligned,true,true)) + if (ssm.fromSeq == sourceAligned.getDatasetSequence()) { - if (map != null) - { - map.add(ssm); - } return sourceAligned; } } @@ -932,4 +902,34 @@ 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; + } }