/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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;
import jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.ws.SequenceFetcherFactory;
private SequenceI[] fromSeqs;
/**
+ * matcher built from dataset
+ */
+ SequenceIdMatcher matcher;
+
+ /**
+ * sequences found by cross-ref searches to fromSeqs
+ */
+ List<SequenceI> rseqs;
+
+ /**
* Constructor
*
* @param seqs
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;
}
*
* @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
*/
* find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
*/
DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
- List<SequenceI> rseqs = new ArrayList<SequenceI>();
+ List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
/*
* 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());
public Alignment findXrefSequences(String source, boolean fromDna)
{
- List<SequenceI> rseqs = new ArrayList<SequenceI>();
+ rseqs = new ArrayList<SequenceI>();
AlignedCodonFrame cf = new AlignedCodonFrame();
- SequenceIdMatcher matcher = new SequenceIdMatcher(
- dataset.getSequences());
+ matcher = new SequenceIdMatcher(dataset.getSequences());
for (SequenceI seq : fromSeqs)
{
boolean found = false;
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)
{
/*
List<DBRefEntry> sourceRefs = DBRefUtils.searchRefsForSource(xrfs,
source);
Iterator<DBRefEntry> 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)
* 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)
{
{
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());
}
}
}
{
SequenceI matchedSeq = matcher.findIdMatch(xref.getSource() + "|"
+ xref.getAccessionId());
- if (matchedSeq != null)
+ // 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))
{
*/
if (!sourceRefs.isEmpty())
{
- ASequenceFetcher sftch = SequenceFetcherFactory
- .getSequenceFetcher();
- SequenceI[] retrieved = null;
- try
+ retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf);
+ }
+ }
+
+ Alignment ral = null;
+ if (rseqs.size() > 0)
+ {
+ ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
+ if (!cf.isEmpty())
+ {
+ dataset.addCodonFrame(cf);
+ }
+ }
+ return ral;
+ }
+
+ private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
+ DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf)
+ {
+ ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
+ SequenceI[] retrieved = 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 : "
+ + seq.getName());
+ e.printStackTrace();
+ }
+
+ if (retrieved != null)
+ {
+ boolean addedXref = false;
+ List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(), doNotAdd = new ArrayList<SequenceI>();
+
+ 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);
+ }
+ 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)
{
- retrieved = sftch.getSequences(sourceRefs, !fromDna);
- } catch (Exception e)
+ // 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)
{
- System.err
- .println("Problem whilst retrieving cross references for Sequence : "
- + seq.getName());
- e.printStackTrace();
+ dataset.addSequence(newToSeq);
+ matcher.add(newToSeq);
}
+ }
+ }
+ }
- if (retrieved != null)
+ /**
+ * 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<DBRefEntry> 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 found : DBRefUtils.searchRefs(dbrSourceSet, dbr))
+ {
+ 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<SequenceI> newDsSeqs, List<SequenceI> 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)
{
- updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
- for (SequenceI retrievedSequence : retrieved)
+ if (map.getTo() != null && map.getMap() != null)
{
- SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
- : retrievedSequence.getDatasetSequence();
- DBRefEntry[] dbr = retrievedSequence.getDBRefs();
- if (dbr != null)
+ if (map.getTo() == sourceSequence)
{
- for (DBRefEntry dbref : dbr)
+ // already called to import once, and most likely this sequence
+ // already imported !
+ continue;
+ }
+ if (matched == 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()))
{
- // find any entry where we should put in the sequence being
- // cross-referenced into the map
- Mapping map = dbref.getMap();
- if (map != 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)
{
- if (map.getTo() != null && map.getMap() != null)
+ /*
+ * transfer database refs
+ */
+ for (DBRefEntry ref : toRefs)
{
- // 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)
+ if (dbref.getSrcAccString().equals(
+ ref.getSrcAccString()))
{
- /*
- * already got an xref to this sequence; update this
- * map to point to the same sequence, and add
- * any new dbrefs to it
- */
- DBRefEntry[] toRefs = map.getTo().getDBRefs();
- if (toRefs != null)
- {
- for (DBRefEntry ref : toRefs)
- {
- matched.addDBRef(ref); // add or update mapping
- }
- }
- map.setTo(matched);
+ continue; // avoid overwriting the ref on source sequence
}
- else
- {
- matcher.add(map.getTo());
- }
- try
+ matched.addDBRef(ref); // add or update mapping
+ }
+ }
+ doNotAdd.add(map.getTo());
+ map.setTo(matched);
+
+ /*
+ * 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)
+ {
+ 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)
{
- // 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()))
+ @Override
+ public boolean equals(Object o)
{
- String msg = "Mapping updated from " + ms.getName()
- + " to retrieved crossreference "
- + dss.getName();
- System.out.println(msg);
- map.setTo(dss);
-
- /*
- * give the reverse reference the inverse mapping
- * (if it doesn't have one already)
- */
- setReverseMapping(dss, dbref, cf);
-
- /*
- * copy sequence features as well, avoiding
- * duplication (e.g. same variation from two
- * transcripts)
- */
- SequenceFeature[] sfs = ms.getSequenceFeatures();
- if (sfs != null)
- {
- 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);
}
}
}
}
-
- Alignment ral = null;
- if (rseqs.size() > 0)
+ if (imported)
{
- ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
- if (!cf.isEmpty())
+ retrievedSequence.updatePDBIds();
+ rseqs.add(retrievedSequence);
+ if (dataset.findIndex(retrievedSequence) == -1)
{
- dataset.addCodonFrame(cf);
+ dataset.addSequence(retrievedSequence);
+ matcher.add(retrievedSequence);
}
}
- return ral;
+ return imported;
}
/**
}
/**
- * 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)
String name2 = xref.getSource() + "|" + name;
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<DBRefEntry> 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;
}
/**
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;
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;
}
}
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);
* 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<SequenceI> rseqs, AlignedCodonFrame cf)
+ DBRefEntry[] lrfs, List<SequenceI> foundSeqs, AlignedCodonFrame cf)
{
boolean found = false;
if (lrfs == null)
// 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;
}
* @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.
+ * <ul>
+ * <li>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).</li>
+ * <li>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)</li>
+ * </ul>
* @return true if relationship found and sequence added.
*/
- boolean searchDataset(boolean fromDna, SequenceI sequenceI,
- DBRefEntry xrf, List<SequenceI> rseqs, AlignedCodonFrame cf,
+ boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
+ List<SequenceI> foundSeqs, AlignedCodonFrame mappings,
boolean direct)
{
boolean found = false;
if (nxt.getDatasetSequence() != null)
{
System.err
- .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
+ .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;
}
* complementary type if !direct
*/
{
- boolean isDna = Comparison
- .isNucleotide(new SequenceI[] { nxt });
+ boolean isDna = !nxt.isProtein();
if (direct ? (isDna != fromDna) : (isDna == fromDna))
{
// skip this sequence because it is wrong molecule type
// look for direct or indirect references in common
DBRefEntry[] poss = nxt.getDBRefs();
List<DBRefEntry> 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)
{
- // 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);
+ }
+ else
+ {
+ mappings.addMap(nxt, fromSeq, map.getInverse());
}
}
}
}
- // TODO: add mapping between sequences if necessary
}
}
}
git://source.jalview.org / jalview.git / blobdiff