{
for (DBRefEntry ref : xrefs)
{
- String source = ref.getSource();
+ /*
+ * avoid duplication e.g. ENSEMBL and Ensembl
+ */
+ String source = DBRefUtils.getCanonicalName(ref.getSource());
if (!sources.contains(source))
{
sources.add(source);
}
/**
+ * Attempts to find cross-references from the sequences provided in the
+ * constructor to the given source database. Cross-references may be found
+ * <ul>
+ * <li>in dbrefs on the sequence which hold a mapping to a sequence
+ * <ul>
+ * <li>provided with a fetched sequence (e.g. ENA translation), or</li>
+ * <li>populated previously after getting cross-references</li>
+ * </ul>
+ * <li>as other sequences in the alignment which share a dbref identifier with
+ * the sequence</li>
+ * <li>by fetching from the remote database</li>
+ * </ul>
+ * The cross-referenced sequences, and mappings to them, are added to the
+ * alignment dataset.
*
- * @param seqs
- * sequences whose xrefs are being retrieved
- * @param dna
- * true if sequences are nucleotide
* @param source
- * @param al
- * alignment to search for cross-referenced sequences (and possibly
- * add to)
- * @return products (as dataset sequences)
+ * @return cross-referenced sequences (as dataset sequences)
*/
public Alignment findXrefSequences(String source)
{
+
List<SequenceI> rseqs = new ArrayList<SequenceI>();
AlignedCodonFrame cf = new AlignedCodonFrame();
SequenceIdMatcher matcher = new SequenceIdMatcher(
* for example: UNIPROT {P0CE19, P0CE20} -> EMBL {J03321, X06707}
*/
found = true;
- SequenceI matchInDataset = findInDataset(mappedTo);// matcher.findIdMatch(mappedTo);
+ /*
+ * problem: matcher.findIdMatch() is lenient - returns a sequence
+ * with a dbref to the search arg e.g. ENST for ENSP - wrong
+ * but findInDataset() matches ENSP when looking for Uniprot...
+ */
+ SequenceI matchInDataset = findInDataset(xref);
+ /*matcher.findIdMatch(mappedTo);*/
if (matchInDataset != null)
{
if (!rseqs.contains(matchInDataset))
{
rseqs.add(matchInDataset);
}
+ refIterator.remove();
continue;
}
SequenceI rsq = new Sequence(mappedTo);
if (map.getTo() != null && map.getMap() != null)
{
// TODO findInDataset requires exact sequence match but
- // 'congruent' test only for the mapped part
- SequenceI matched = findInDataset(map.getTo());// matcher.findIdMatch(map.getTo());
+ // '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)
{
/*
+ " to retrieved crossreference "
+ dss.getName();
System.out.println(msg);
- // method to update all refs of existing To on
- // retrieved sequence with dss and merge any props
- // on To onto dss.
- // TODO don't we have to change the mapped to ranges
- // if not to the whole sequence?
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 2
+ * duplication (e.g. same variation from two
* transcripts)
*/
SequenceFeature[] sfs = ms.getSequenceFeatures();
{
/*
* make a flyweight feature object which ignores Parent
- * attribute in equality test, to avoid creating many
+ * attribute in equality test; this avoids creating many
* otherwise duplicate exon features on genomic sequence
*/
SequenceFeature newFeature = new SequenceFeature(
}
}
retrievedSequence.updatePDBIds();
- rseqs.add(retrievedSequence);
+ rseqs.add(retrievedDss);
dataset.addSequence(retrievedDss);
- matcher.add(retrievedSequence);
+ matcher.add(retrievedDss);
}
}
}
if (rseqs.size() > 0)
{
ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
- if (cf != null && !cf.isEmpty())
+ if (!cf.isEmpty())
{
- ral.addCodonFrame(cf);
+ dataset.addCodonFrame(cf);
}
}
return ral;
}
/**
+ * Sets the inverse sequence mapping in the corresponding dbref of the mapped
+ * to sequence (if any). This is used after fetching a cross-referenced
+ * sequence, if the fetched sequence has a mapping to the original sequence,
+ * to set the mapping in the original sequence's dbref.
+ *
+ * @param mapFrom
+ * the sequence mapped from
+ * @param dbref
+ * @param mappings
+ */
+ void setReverseMapping(SequenceI mapFrom, DBRefEntry dbref,
+ AlignedCodonFrame mappings)
+ {
+ SequenceI mapTo = dbref.getMap().getTo();
+ if (mapTo == null)
+ {
+ return;
+ }
+ DBRefEntry[] dbrefs = mapTo.getDBRefs();
+ if (dbrefs == null)
+ {
+ return;
+ }
+ for (DBRefEntry toRef : dbrefs)
+ {
+ if (toRef.hasMap() && mapFrom == toRef.getMap().getTo())
+ {
+ /*
+ * found the reverse dbref; update its mapping if null
+ */
+ if (toRef.getMap().getMap() == null)
+ {
+ MapList inverse = dbref.getMap().getMap().getInverse();
+ toRef.getMap().setMap(inverse);
+ mappings.addMap(mapTo, mapFrom, inverse);
+ }
+ }
+ }
+ }
+
+ /**
* Returns the first identical sequence in the dataset if any, else null
*
- * @param mappedTo
+ * @param xref
* @return
*/
- SequenceI findInDataset(SequenceI mappedTo)
+ SequenceI findInDataset(DBRefEntry xref)
{
- if (mappedTo == null)
+ if (xref == null || !xref.hasMap() || xref.getMap().getTo() == null)
{
return null;
}
- SequenceI dss = mappedTo.getDatasetSequence() == null ? mappedTo
- : mappedTo.getDatasetSequence();
+ SequenceI mapsTo = xref.getMap().getTo();
+ String name = xref.getAccessionId();
+ String name2 = xref.getSource() + "|" + name;
+ SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo : mapsTo
+ .getDatasetSequence();
for (SequenceI seq : dataset.getSequences())
{
- if (sameSequence(seq, dss))
+ /*
+ * 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))
{
- return seq;
+ if (sameSequence(seq, dss))
+ {
+ return seq;
+ }
}
}
return null;
}
/**
- * Tries to make a mapping from dna to protein. If successful, adds the
- * mapping to the dbref and the mappings collection and answers true,
- * otherwise answers false.
+ * Tries to make a mapping between sequences. If successful, adds the mapping
+ * to the dbref and the mappings collection and answers true, otherwise
+ * answers false. The following methods of making are mapping are tried in
+ * turn:
+ * <ul>
+ * <li>if 'mapTo' holds a mapping to 'mapFrom', take the inverse; this is, for
+ * example, the case after fetching EMBL cross-references for a Uniprot
+ * sequence</li>
+ * <li>else check if the dna translates exactly to the protein (give or take
+ * start and stop codons></li>
+ * <li>else try to map based on CDS features on the dna sequence</li>
+ * </ul>
*
* @param mapFrom
* @param mapTo
DBRefEntry xref, AlignedCodonFrame mappings)
{
MapList mapping = null;
+
+ /*
+ * look for a reverse mapping, if found make its inverse
+ */
+ if (mapTo.getDBRefs() != null)
+ {
+ for (DBRefEntry dbref : mapTo.getDBRefs())
+ {
+ String name = dbref.getSource() + "|" + dbref.getAccessionId();
+ if (dbref.hasMap() && mapFrom.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);
+ return true;
+ }
+ }
+ }
+
if (fromDna)
{
mapping = AlignmentUtils.mapCdnaToProtein(mapTo, mapFrom);
git://source.jalview.org / jalview.git / blobdiff