X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=40401fb69564874b0c72d374d1c9f8a77551394c;hb=9b85e1552fa57f02cf6cd312cfbd7efdfd079ea3;hp=7dcaa17d9e6b1509f6a29e8fedc79536d63437d2;hpb=dfa980fc8e8dd186278e5aa1fcf356964afdf61a;p=jalview.git diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java index 7dcaa17..40401fb 100644 --- a/src/jalview/analysis/CrossRef.java +++ b/src/jalview/analysis/CrossRef.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; @@ -68,11 +69,6 @@ public class CrossRef List rseqs; /** - * mappings constructed - */ - AlignedCodonFrame cf; - - /** * Constructor * * @param seqs @@ -103,7 +99,7 @@ public class CrossRef */ public List findXrefSourcesForSequences(boolean dna) { - List sources = new ArrayList(); + List sources = new ArrayList<>(); for (SequenceI seq : fromSeqs) { if (seq != null) @@ -111,6 +107,16 @@ public class CrossRef findXrefSourcesForSequence(seq, dna, sources); } } + sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in + // redundant datasets + if (dna) + { + sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and + // EnsemblGenomes xref option shown + // from cdna panel + sources.remove(DBRefSource.ENSEMBLGENOMES); + } + // redundant datasets return sources; } @@ -125,6 +131,9 @@ public class CrossRef * * @param seq * the sequence whose dbrefs we are searching against + * @param fromDna + * when true, context is DNA - so sources identifying protein + * products will be returned. * @param sources * a list of sources to add matches to */ @@ -142,21 +151,21 @@ public class CrossRef * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs */ DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs()); - List rseqs = new ArrayList(); + List foundSeqs = new ArrayList<>(); /* * find sequences in the alignment which xref one of these DBRefs * i.e. is xref-ed to a common sequence identifier */ - searchDatasetXrefs(fromDna, seq, lrfs, rseqs, null); + searchDatasetXrefs(fromDna, seq, lrfs, foundSeqs, null); /* * add those sequences' (dna-to-peptide or peptide-to-dna) dbref sources */ - for (SequenceI rs : rseqs) + for (SequenceI rs : foundSeqs) { - DBRefEntry[] xrs = DBRefUtils - .selectDbRefs(!fromDna, rs.getDBRefs()); + DBRefEntry[] xrs = DBRefUtils.selectDbRefs(!fromDna, + rs.getDBRefs()); addXrefsToSources(xrs, sources); } } @@ -209,10 +218,9 @@ public class CrossRef public Alignment findXrefSequences(String source, boolean fromDna) { - rseqs = new ArrayList(); - cf = new AlignedCodonFrame(); - matcher = new SequenceIdMatcher( - dataset.getSequences()); + rseqs = new ArrayList<>(); + AlignedCodonFrame cf = new AlignedCodonFrame(); + matcher = new SequenceIdMatcher(dataset.getSequences()); for (SequenceI seq : fromSeqs) { @@ -222,8 +230,11 @@ public class CrossRef dss = dss.getDatasetSequence(); } boolean found = false; - DBRefEntry[] xrfs = DBRefUtils - .selectDbRefs(!fromDna, dss.getDBRefs()); + DBRefEntry[] xrfs = DBRefUtils.selectDbRefs(!fromDna, + dss.getDBRefs()); + // ENST & ENSP comes in to both Protein and nucleotide, so we need to + // filter them + // out later. if ((xrfs == null || xrfs.length == 0) && dataset != null) { /* @@ -251,11 +262,15 @@ public class CrossRef List sourceRefs = DBRefUtils.searchRefsForSource(xrfs, source); Iterator refIterator = sourceRefs.iterator(); + // At this point, if we are retrieving Ensembl, we still don't filter out + // ENST when looking for protein crossrefs. while (refIterator.hasNext()) { DBRefEntry xref = refIterator.next(); found = false; - if (xref.hasMap()) + // we're only interested in coding cross-references, not + // locus->transcript + if (xref.hasMap() && xref.getMap().getMap().isTripletMap()) { SequenceI mappedTo = xref.getMap().getTo(); if (mappedTo != null) @@ -273,6 +288,15 @@ public class CrossRef * but findInDataset() matches ENSP when looking for Uniprot... */ SequenceI matchInDataset = findInDataset(xref); + if (matchInDataset != null && xref.getMap().getTo() != null + && matchInDataset != xref.getMap().getTo()) + { + System.err.println( + "Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref." + + "Found:" + matchInDataset + "\nExpected:" + + xref.getMap().getTo() + "\nFor xref:" + + xref); + } /*matcher.findIdMatch(mappedTo);*/ if (matchInDataset != null) { @@ -280,24 +304,48 @@ public class CrossRef { rseqs.add(matchInDataset); } + // even if rseqs contained matchInDataset - check mappings between + // these seqs are added + // need to try harder to only add unique mappings + if (xref.getMap().getMap().isTripletMap() + && dataset.getMapping(seq, matchInDataset) == null + && cf.getMappingBetween(seq, matchInDataset) == null) + { + // materialise a mapping for highlighting between these + // sequences + if (fromDna) + { + cf.addMap(dss, matchInDataset, xref.getMap().getMap(), + xref.getMap().getMappedFromId()); + } + else + { + cf.addMap(matchInDataset, dss, + xref.getMap().getMap().getInverse(), + xref.getMap().getMappedFromId()); + } + } + refIterator.remove(); continue; } + // TODO: need to determine if this should be a deriveSequence SequenceI rsq = new Sequence(mappedTo); rseqs.add(rsq); - if (xref.getMap().getMap().getFromRatio() != xref.getMap() - .getMap().getToRatio()) + if (xref.getMap().getMap().isTripletMap()) { // get sense of map correct for adding to product alignment. if (fromDna) { // map is from dna seq to a protein product - cf.addMap(dss, rsq, xref.getMap().getMap()); + cf.addMap(dss, rsq, xref.getMap().getMap(), + xref.getMap().getMappedFromId()); } else { // map should be from protein seq to its coding dna - cf.addMap(rsq, dss, xref.getMap().getMap().getInverse()); + cf.addMap(rsq, dss, xref.getMap().getMap().getInverse(), + xref.getMap().getMappedFromId()); } } } @@ -305,9 +353,11 @@ public class CrossRef if (!found) { - SequenceI matchedSeq = matcher.findIdMatch(xref.getSource() + "|" - + xref.getAccessionId()); - if (matchedSeq != null) + SequenceI matchedSeq = matcher.findIdMatch( + xref.getSource() + "|" + xref.getAccessionId()); + // if there was a match, check it's at least the right type of + // molecule! + if (matchedSeq != null && matchedSeq.isProtein() == fromDna) { if (constructMapping(seq, matchedSeq, xref, cf, fromDna)) { @@ -333,7 +383,7 @@ public class CrossRef */ if (!sourceRefs.isEmpty()) { - retrieveCrossRef(sourceRefs, seq, xrfs, fromDna); + retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf); } } @@ -350,143 +400,269 @@ public class CrossRef } private void retrieveCrossRef(List sourceRefs, SequenceI seq, - DBRefEntry[] xrfs, boolean fromDna) + DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf) { ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher(); SequenceI[] retrieved = null; - SequenceI dss = null; + SequenceI dss = seq.getDatasetSequence() == null ? seq + : seq.getDatasetSequence(); + // first filter in case we are retrieving crossrefs that have already been + // retrieved. this happens for cases where a database record doesn't yield + // protein products for CDS + removeAlreadyRetrievedSeqs(sourceRefs, fromDna); + if (sourceRefs.size() == 0) + { + // no more work to do! We already had all requested sequence records in + // the dataset. + return; + } try { retrieved = sftch.getSequences(sourceRefs, !fromDna); } catch (Exception e) { - System.err - .println("Problem whilst retrieving cross references for Sequence : " + System.err.println( + "Problem whilst retrieving cross references for Sequence : " + seq.getName()); e.printStackTrace(); } if (retrieved != null) { - updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna); + boolean addedXref = false; + List newDsSeqs = new ArrayList<>(), + doNotAdd = new ArrayList<>(); + for (SequenceI retrievedSequence : retrieved) { // dataset gets contaminated ccwith non-ds sequences. why ??! // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL-> - SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence - : retrievedSequence.getDatasetSequence(); - DBRefEntry[] dbr = retrievedSequence.getDBRefs(); - if (dbr != null) + SequenceI retrievedDss = retrievedSequence + .getDatasetSequence() == null ? retrievedSequence + : retrievedSequence.getDatasetSequence(); + addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss, + retrievedDss); + } + if (!addedXref) + { + // try again, after looking for matching IDs + // shouldn't need to do this unless the dbref mechanism has broken. + updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna); + for (SequenceI retrievedSequence : retrieved) + { + // dataset gets contaminated ccwith non-ds sequences. why ??! + // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL-> + SequenceI retrievedDss = retrievedSequence + .getDatasetSequence() == null ? retrievedSequence + : retrievedSequence.getDatasetSequence(); + addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss, + retrievedDss); + } + } + for (SequenceI newToSeq : newDsSeqs) + { + if (!doNotAdd.contains(newToSeq) + && dataset.findIndex(newToSeq) == -1) + { + dataset.addSequence(newToSeq); + matcher.add(newToSeq); + } + } + } + } + + /** + * Search dataset for sequences with a primary reference contained in + * sourceRefs. + * + * @param sourceRefs + * - list of references to filter. + * @param fromDna + * - type of sequence to search for matching primary reference. + */ + private void removeAlreadyRetrievedSeqs(List sourceRefs, + boolean fromDna) + { + DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]); + for (SequenceI sq : dataset.getSequences()) + { + boolean dupeFound = false; + // !fromDna means we are looking only for nucleotide sequences, not + // protein + if (sq.isProtein() == fromDna) + { + for (DBRefEntry dbr : sq.getPrimaryDBRefs()) { - for (DBRefEntry dbref : dbr) + for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr)) { - // find any entry where we should put in the sequence being - // cross-referenced into the map - Mapping map = dbref.getMap(); - if (map != null) + sourceRefs.remove(found); + dupeFound = true; + } + } + } + if (dupeFound) + { + // rebuild the search array from the filtered sourceRefs list + dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]); + } + } + } + + /** + * process sequence retrieved via a dbref on source sequence to resolve and + * transfer data + * + * @param cf + * @param sourceSequence + * @param retrievedSequence + * @return true if retrieveSequence was imported + */ + private boolean importCrossRefSeq(AlignedCodonFrame cf, + List newDsSeqs, List doNotAdd, + SequenceI sourceSequence, SequenceI retrievedSequence) + { + /** + * set when retrievedSequence has been verified as a crossreference for + * sourceSequence + */ + boolean imported = false; + DBRefEntry[] dbr = retrievedSequence.getDBRefs(); + if (dbr != null) + { + for (DBRefEntry dbref : dbr) + { + SequenceI matched = findInDataset(dbref); + if (matched == sourceSequence) + { + // verified retrieved and source sequence cross-reference each other + imported = true; + } + // find any entry where we should put in the sequence being + // cross-referenced into the map + Mapping map = dbref.getMap(); + if (map != null) + { + if (map.getTo() != null && map.getMap() != null) + { + if (map.getTo() == sourceSequence) + { + // already called to import once, and most likely this sequence + // already imported ! + continue; + } + if (matched == null) { - if (map.getTo() != null && map.getMap() != null) + /* + * sequence is new to dataset, so save a reference so it can be added. + */ + newDsSeqs.add(map.getTo()); + continue; + } + + /* + * there was a matching sequence in dataset, so now, check to see if we can update the map.getTo() sequence to the existing one. + */ + + try + { + // compare ms with dss and replace with dss in mapping + // if map is congruent + SequenceI ms = map.getTo(); + // TODO findInDataset requires exact sequence match but + // 'congruent' test is only for the mapped part + // maybe not a problem in practice since only ENA provide a + // mapping and it is to the full protein translation of CDS + // matcher.findIdMatch(map.getTo()); + // TODO addendum: if matched is shorter than getTo, this will fail + // - when it should really succeed. + int sf = map.getMap().getToLowest(); + int st = map.getMap().getToHighest(); + SequenceI mappedrg = ms.getSubSequence(sf, st); + if (mappedrg.getLength() > 0 && ms.getSequenceAsString() + .equals(matched.getSequenceAsString())) { - // TODO findInDataset requires exact sequence match but - // 'congruent' test is only for the mapped part - // maybe not a problem in practice since only ENA provide a - // mapping and it is to the full protein translation of CDS - SequenceI matched = findInDataset(dbref); - // matcher.findIdMatch(map.getTo()); - if (matched != null) + /* + * sequences were a match, + */ + String msg = "Mapping updated from " + ms.getName() + + " to retrieved crossreference " + + matched.getName(); + System.out.println(msg); + + DBRefEntry[] toRefs = map.getTo().getDBRefs(); + if (toRefs != null) { /* - * already got an xref to this sequence; update this - * map to point to the same sequence, and add - * any new dbrefs to it + * transfer database refs */ - DBRefEntry[] toRefs = map.getTo().getDBRefs(); - if (toRefs != null) + for (DBRefEntry ref : toRefs) { - for (DBRefEntry ref : toRefs) + if (dbref.getSrcAccString() + .equals(ref.getSrcAccString())) { - matched.addDBRef(ref); // add or update mapping + continue; // avoid overwriting the ref on source sequence } + matched.addDBRef(ref); // add or update mapping } - map.setTo(matched); } - else - { - matcher.add(map.getTo()); - } - try - { - // compare ms with dss and replace with dss in mapping - // if map is congruent - SequenceI ms = map.getTo(); - int sf = map.getMap().getToLowest(); - int st = map.getMap().getToHighest(); - SequenceI mappedrg = ms.getSubSequence(sf, st); - // SequenceI loc = dss.getSubSequence(sf, st); - if (mappedrg.getLength() > 0 - && ms.getSequenceAsString().equals( - dss.getSequenceAsString())) - // && mappedrg.getSequenceAsString().equals( - // loc.getSequenceAsString())) - { - String msg = "Mapping updated from " + ms.getName() - + " to retrieved crossreference " - + dss.getName(); - System.out.println(msg); - map.setTo(dss); + doNotAdd.add(map.getTo()); + map.setTo(matched); - /* - * give the reverse reference the inverse mapping - * (if it doesn't have one already) - */ - setReverseMapping(dss, dbref, cf); + /* + * give the reverse reference the inverse mapping + * (if it doesn't have one already) + */ + setReverseMapping(matched, dbref, cf); - /* - * copy sequence features as well, avoiding - * duplication (e.g. same variation from two - * transcripts) - */ - SequenceFeature[] sfs = ms.getSequenceFeatures(); - if (sfs != null) + /* + * copy sequence features as well, avoiding + * duplication (e.g. same variation from two + * transcripts) + */ + List sfs = ms.getFeatures() + .getAllFeatures(); + for (SequenceFeature feat : sfs) + { + /* + * make a flyweight feature object which ignores Parent + * attribute in equality test; this avoids creating many + * otherwise duplicate exon features on genomic sequence + */ + SequenceFeature newFeature = new SequenceFeature(feat) + { + @Override + public boolean equals(Object o) { - for (SequenceFeature feat : sfs) - { - /* - * make a flyweight feature object which ignores Parent - * attribute in equality test; this avoids creating many - * otherwise duplicate exon features on genomic sequence - */ - SequenceFeature newFeature = new SequenceFeature( - feat) - { - @Override - public boolean equals(Object o) - { - return super.equals(o, true); - } - }; - dss.addSequenceFeature(newFeature); - } + return super.equals(o, true); } - } - cf.addMap(retrievedDss, map.getTo(), map.getMap()); - } catch (Exception e) - { - System.err - .println("Exception when consolidating Mapped sequence set..."); - e.printStackTrace(System.err); + }; + matched.addSequenceFeature(newFeature); } } + cf.addMap(retrievedSequence, map.getTo(), map.getMap()); + } catch (Exception e) + { + System.err.println( + "Exception when consolidating Mapped sequence set..."); + e.printStackTrace(System.err); } } } - retrievedSequence.updatePDBIds(); - rseqs.add(retrievedDss); - dataset.addSequence(retrievedDss); - matcher.add(retrievedDss); } } + if (imported) + { + retrievedSequence.updatePDBIds(); + rseqs.add(retrievedSequence); + if (dataset.findIndex(retrievedSequence) == -1) + { + dataset.addSequence(retrievedSequence); + matcher.add(retrievedSequence); + } + } + return imported; } + /** * Sets the inverse sequence mapping in the corresponding dbref of the mapped * to sequence (if any). This is used after fetching a cross-referenced @@ -529,9 +705,12 @@ public class CrossRef } /** - * Returns the first identical sequence in the dataset if any, else null + * Returns null or the first sequence in the dataset which is identical to + * xref.mapTo, and has a) a primary dbref matching xref, or if none found, the + * first one with an ID source|xrefacc * * @param xref + * with map and mapped-to sequence * @return */ SequenceI findInDataset(DBRefEntry xref) @@ -543,24 +722,43 @@ public class CrossRef SequenceI mapsTo = xref.getMap().getTo(); String name = xref.getAccessionId(); String name2 = xref.getSource() + "|" + name; - SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo : mapsTo - .getDatasetSequence(); + SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo + : mapsTo.getDatasetSequence(); + // first check ds if ds is directly referenced + if (dataset.findIndex(dss) > -1) + { + return dss; + } + DBRefEntry template = new DBRefEntry(xref.getSource(), null, + xref.getAccessionId()); + /** + * remember the first ID match - in case we don't find a match to template + */ + SequenceI firstIdMatch = null; for (SequenceI seq : dataset.getSequences()) { + // first check primary refs. + List match = DBRefUtils.searchRefs( + seq.getPrimaryDBRefs().toArray(new DBRefEntry[0]), template); + if (match != null && match.size() == 1 && sameSequence(seq, dss)) + { + return seq; + } /* * clumsy alternative to using SequenceIdMatcher which currently * returns sequences with a dbref to the matched accession id * which we don't want */ - if (name.equals(seq.getName()) || seq.getName().startsWith(name2)) + if (firstIdMatch == null && (name.equals(seq.getName()) + || seq.getName().startsWith(name2))) { if (sameSequence(seq, dss)) { - return seq; + firstIdMatch = seq; } } } - return null; + return firstIdMatch; } /** @@ -584,15 +782,15 @@ public class CrossRef { return false; } - char[] c1 = seq1.getSequence(); - char[] c2 = seq2.getSequence(); - if (c1.length != c2.length) + + if (seq1.getLength() != seq2.getLength()) { return false; } - for (int i = 0; i < c1.length; i++) + int length = seq1.getLength(); + for (int i = 0; i < length; i++) { - int diff = c1[i] - c2[i]; + int diff = seq1.getCharAt(i) - seq2.getCharAt(i); /* * same char or differ in case only ('a'-'A' == 32) */ @@ -617,14 +815,14 @@ public class CrossRef void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs, SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna) { - SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved); + SequenceIdMatcher idMatcher = new SequenceIdMatcher(retrieved); for (DBRefEntry xref : xrefs) { if (!xref.hasMap()) { String targetSeqName = xref.getSource() + "|" + xref.getAccessionId(); - SequenceI[] matches = matcher.findAllIdMatches(targetSeqName); + SequenceI[] matches = idMatcher.findAllIdMatches(targetSeqName); if (matches == null) { return; @@ -661,24 +859,28 @@ public class CrossRef DBRefEntry xref, AlignedCodonFrame mappings, boolean fromDna) { MapList mapping = null; - + SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom + : mapFrom.getDatasetSequence(); + SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo + : mapTo.getDatasetSequence(); /* - * look for a reverse mapping, if found make its inverse + * look for a reverse mapping, if found make its inverse. + * Note - we do this on dataset sequences only. */ - if (mapTo.getDBRefs() != null) + if (dsmapTo.getDBRefs() != null) { - for (DBRefEntry dbref : mapTo.getDBRefs()) + for (DBRefEntry dbref : dsmapTo.getDBRefs()) { String name = dbref.getSource() + "|" + dbref.getAccessionId(); - if (dbref.hasMap() && mapFrom.getName().startsWith(name)) + if (dbref.hasMap() && dsmapFrom.getName().startsWith(name)) { /* * looks like we've found a map from 'mapTo' to 'mapFrom' * - invert it to make the mapping the other way */ MapList reverse = dbref.getMap().getMap().getInverse(); - xref.setMap(new Mapping(mapTo, reverse)); - mappings.addMap(mapFrom, mapTo, reverse); + xref.setMap(new Mapping(dsmapTo, reverse)); + mappings.addMap(mapFrom, dsmapTo, reverse); return true; } } @@ -701,9 +903,25 @@ public class CrossRef return false; } xref.setMap(new Mapping(mapTo, mapping)); + + /* + * and add a reverse DbRef with the inverse mapping + */ + if (mapFrom.getDatasetSequence() != null && false) + // && mapFrom.getDatasetSequence().getSourceDBRef() != null) + { + // possible need to search primary references... except, why doesn't xref + // == getSourceDBRef ?? + // DBRefEntry dbref = new DBRefEntry(mapFrom.getDatasetSequence() + // .getSourceDBRef()); + // dbref.setMap(new Mapping(mapFrom.getDatasetSequence(), mapping + // .getInverse())); + // mapTo.addDBRef(dbref); + } + if (fromDna) { - AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping); + // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping); mappings.addMap(mapFrom, mapTo, mapping); } else @@ -724,11 +942,12 @@ public class CrossRef * context was searching from Protein sequences * @param sequenceI * @param lrfs - * @param rseqs + * @param foundSeqs * @return true if matches were found. */ private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI, - DBRefEntry[] lrfs, List rseqs, AlignedCodonFrame cf) + DBRefEntry[] lrfs, List foundSeqs, + AlignedCodonFrame cf) { boolean found = false; if (lrfs == null) @@ -741,7 +960,8 @@ public class CrossRef // add in wildcards xref.setVersion(null); xref.setMap(null); - found |= searchDataset(fromDna, sequenceI, xref, rseqs, cf, false); + found |= searchDataset(fromDna, sequenceI, xref, foundSeqs, cf, + false); } return found; } @@ -753,20 +973,29 @@ public class CrossRef * @param fromDna * true if context was searching for refs *from* dna sequence, false * if context was searching for refs *from* protein sequence - * @param sequenceI + * @param fromSeq * a sequence to ignore (start point of search) * @param xrf * a cross-reference to try to match - * @param rseqs + * @param foundSeqs * result list to add to - * @param cf + * @param mappings * a set of sequence mappings to add to * @param direct - * - search all references or only subset + * - indicates the type of relationship between returned sequences, + * xrf, and sequenceI that is required. + *
    + *
  • direct implies xrf is a primary reference for sequenceI AND + * the sequences to be located (eg a uniprot ID for a protein + * sequence, and a uniprot ref on a transcript sequence).
    • + *
  • indirect means xrf is a cross reference with respect to + * sequenceI or all the returned sequences (eg a genomic reference + * associated with a locus and one or more transcripts)
    • + *
* @return true if relationship found and sequence added. */ - boolean searchDataset(boolean fromDna, SequenceI sequenceI, - DBRefEntry xrf, List rseqs, AlignedCodonFrame cf, + boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf, + List foundSeqs, AlignedCodonFrame mappings, boolean direct) { boolean found = false; @@ -788,10 +1017,13 @@ public class CrossRef { if (nxt.getDatasetSequence() != null) { - System.err - .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!"); + System.err.println( + "Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! (" + + nxt.getDisplayId(true) + " has ds reference " + + nxt.getDatasetSequence().getDisplayId(true) + + ")"); } - if (nxt == sequenceI || nxt == sequenceI.getDatasetSequence()) + if (nxt == fromSeq || nxt == fromSeq.getDatasetSequence()) { continue; } @@ -811,56 +1043,54 @@ public class CrossRef // look for direct or indirect references in common DBRefEntry[] poss = nxt.getDBRefs(); List cands = null; - /* - * TODO does this make any sense? - * if 'direct', search the dbrefs for xrf - * else, filter the dbrefs by type and then search for xrf - * - the result is the same isn't it? - */ - if (direct) - { - cands = DBRefUtils.searchRefs(poss, xrf); - } - else - { - poss = DBRefUtils.selectDbRefs(!fromDna, poss); - cands = DBRefUtils.searchRefs(poss, xrf); - } + + // todo: indirect specifies we select either direct references to nxt + // that match xrf which is indirect to sequenceI, or indirect + // references to nxt that match xrf which is direct to sequenceI + cands = DBRefUtils.searchRefs(poss, xrf); + // else + // { + // poss = DBRefUtils.selectDbRefs(nxt.isProtein()!fromDna, poss); + // cands = DBRefUtils.searchRefs(poss, xrf); + // } if (!cands.isEmpty()) { - if (!rseqs.contains(nxt)) + if (foundSeqs.contains(nxt)) { - found = true; - rseqs.add(nxt); - if (cf != null) + continue; + } + found = true; + foundSeqs.add(nxt); + if (mappings != null && !direct) + { + /* + * if the matched sequence has mapped dbrefs to + * protein product / cdna, add equivalent mappings to + * our source sequence + */ + for (DBRefEntry candidate : cands) { - // don't search if we aren't given a codon map object - for (DBRefEntry candidate : cands) + Mapping mapping = candidate.getMap(); + if (mapping != null) { - Mapping mapping = candidate.getMap(); - if (mapping != null) + MapList map = mapping.getMap(); + if (mapping.getTo() != null + && map.getFromRatio() != map.getToRatio()) { - MapList map = mapping.getMap(); - if (mapping.getTo() != null - && map.getFromRatio() != map.getToRatio()) + /* + * add a mapping, as from dna to peptide sequence + */ + if (map.getFromRatio() == 3) + { + mappings.addMap(nxt, fromSeq, map); + } + else { - // get sense of map correct for adding to product - // alignment. - if (fromDna) - { - // map is from dna seq to a protein product - cf.addMap(sequenceI, nxt, map); - } - else - { - // map should be from protein seq to its coding dna - cf.addMap(nxt, sequenceI, map.getInverse()); - } + mappings.addMap(nxt, fromSeq, map.getInverse()); } } } } - // TODO: add mapping between sequences if necessary } } }