private AlignmentI dataset;
/*
- * true if we are searching for cross-references from nucleotide,
- * i.e. for protein sequences, false if the reverse
- */
- private boolean fromDna;
-
- /*
* the sequences for which we are seeking cross-references
*/
private SequenceI[] fromSeqs;
public CrossRef(SequenceI[] seqs, AlignmentI ds)
{
fromSeqs = seqs;
- fromDna = ds.isNucleotide();
dataset = ds.getDataset() == null ? ds : ds.getDataset();
}
* reference from another sequence in the dataset which has a cross-reference
* to a direct DBRefEntry on the given sequence</li>
* </ul>
+ *
+ * @param dna
+ * - when true, cross-references *from* dna returned. When false,
+ * cross-references *from* protein are returned
* @return
*/
- public List<String> findXrefSourcesForSequences()
+ public List<String> findXrefSourcesForSequences(boolean dna)
{
List<String> sources = new ArrayList<String>();
for (SequenceI seq : fromSeqs)
{
if (seq != null)
{
- findXrefSourcesForSequence(seq, sources);
+ findXrefSourcesForSequence(seq, dna, sources);
}
}
return sources;
* @param sources
* a list of sources to add matches to
*/
- void findXrefSourcesForSequence(SequenceI seq, List<String> sources)
+ void findXrefSourcesForSequence(SequenceI seq, boolean fromDna,
+ List<String> sources)
{
/*
* first find seq's xrefs (dna-to-peptide or peptide-to-dna)
* find sequences in the alignment which xref one of these DBRefs
* i.e. is xref-ed to a common sequence identifier
*/
- searchDatasetXrefs(seq, lrfs, rseqs, null);
+ searchDatasetXrefs(fromDna, seq, lrfs, rseqs, null);
/*
* add those sequences' (dna-to-peptide or peptide-to-dna) dbref sources
{
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)
+ public Alignment findXrefSequences(String source, boolean fromDna)
{
+
List<SequenceI> rseqs = new ArrayList<SequenceI>();
AlignedCodonFrame cf = new AlignedCodonFrame();
SequenceIdMatcher matcher = new SequenceIdMatcher(
* which have a dbref to an accession id for this sequence,
* and add them to the results
*/
- found = searchDatasetXrefs(dss, lrfs, rseqs, cf);
+ found = searchDatasetXrefs(fromDna, dss, lrfs, rseqs, cf);
}
if (xrfs == null && !found)
{
* 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);
+ xref.getAccessionId());
if (matchedSeq != null)
{
- if (constructMapping(seq, matchedSeq, xref, cf))
+ if (constructMapping(seq, matchedSeq, xref, cf, fromDna))
{
found = true;
}
{
// do a bit more work - search for sequences with references matching
// xrefs on this sequence.
- found = searchDataset(dss, xref, rseqs, cf, false);
+ found = searchDataset(fromDna, dss, xref, rseqs, cf, false);
}
if (found)
{
if (retrieved != null)
{
- updateDbrefMappings(seq, xrfs, retrieved, cf);
+ updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
for (SequenceI retrievedSequence : retrieved)
{
SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
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;
* @param retrieved
* @param acf
*/
- void updateDbrefMappings(SequenceI mapFrom,
- DBRefEntry[] xrefs, SequenceI[] retrieved, AlignedCodonFrame acf)
+ void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs,
+ SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna)
{
SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved);
for (DBRefEntry xref : xrefs)
}
for (SequenceI seq : matches)
{
- constructMapping(mapFrom, seq, xref, acf);
+ constructMapping(mapFrom, seq, xref, acf, fromDna);
}
}
}
}
/**
- * 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
* @return
*/
boolean constructMapping(SequenceI mapFrom, SequenceI mapTo,
- DBRefEntry xref, AlignedCodonFrame mappings)
+ DBRefEntry xref, AlignedCodonFrame mappings, boolean fromDna)
{
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);
* dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
* based on source and accession string only - Map and Version are nulled.
*
+ * @param fromDna
+ * - true if context was searching from Dna sequences, false if
+ * context was searching from Protein sequences
* @param sequenceI
* @param lrfs
* @param rseqs
* @return true if matches were found.
*/
- private boolean searchDatasetXrefs(SequenceI sequenceI,
+ private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI,
DBRefEntry[] lrfs, List<SequenceI> rseqs, AlignedCodonFrame cf)
{
boolean found = false;
// add in wildcards
xref.setVersion(null);
xref.setMap(null);
- found |= searchDataset(sequenceI, xref, rseqs, cf, false);
+ found |= searchDataset(fromDna, sequenceI, xref, rseqs, cf, false);
}
return found;
}
* Searches dataset for DBRefEntrys matching the given one (xrf) and adds the
* associated sequence to rseqs
*
+ * @param fromDna
+ * true if context was searching for refs *from* dna sequence, false
+ * if context was searching for refs *from* protein sequence
* @param sequenceI
* a sequence to ignore (start point of search)
* @param xrf
* - search all references or only subset
* @return true if relationship found and sequence added.
*/
- boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
- List<SequenceI> rseqs, AlignedCodonFrame cf, boolean direct)
+ boolean searchDataset(boolean fromDna, SequenceI sequenceI,
+ DBRefEntry xrf, List<SequenceI> rseqs, AlignedCodonFrame cf,
+ boolean direct)
{
boolean found = false;
if (dataset == null)
git://source.jalview.org / jalview.git / blobdiff