/*
* first find seq's xrefs (dna-to-peptide or peptide-to-dna)
*/
- List<DBRefEntry> rfs = DBRefUtils.selectDbRefs(!fromDna, seq.getDBRefs());
+ List<DBRefEntry> rfs = DBRefUtils.selectDbRefs(!fromDna,
+ seq.getDBRefs());
addXrefsToSources(rfs, sources);
if (dataset != null)
{
/*
* find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
*/
- List<DBRefEntry> lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
+ List<DBRefEntry> lrfs = DBRefUtils.selectDbRefs(fromDna,
+ seq.getDBRefs());
List<SequenceI> foundSeqs = new ArrayList<>();
/*
if (matchInDataset != null && xref.getMap().getTo() != null
&& matchInDataset != xref.getMap().getTo())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"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:"
{
// do a bit more work - search for sequences with references matching
// xrefs on this sequence.
- found = searchDataset(fromDna, dss, xref, rseqs, cf, false, DBRefUtils.SEARCH_MODE_FULL);
+ found = searchDataset(fromDna, dss, xref, rseqs, cf, false,
+ DBRefUtils.SEARCH_MODE_FULL);
}
if (found)
{
retrieved = sftch.getSequences(sourceRefs, !fromDna);
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Problem whilst retrieving cross references for Sequence : "
+ seq.getName());
e.printStackTrace();
addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
retrievedDss);
}
+ // JBPNote: What assumptions are made for dbref structures on
+ // retrieved sequences ?
+ // addedXref will be true means importCrossRefSeq found
+ // sequences with dbrefs with mappings to sequences congruent with dss
+
if (!addedXref)
{
// try again, after looking for matching IDs
// protein
if (sq.isProtein() == fromDna)
{
- List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
+ List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
for (int idb = 0, ndb = sqdbrefs.size(); idb < ndb; idb++)
{
- DBRefEntry dbr = sqdbrefs.get(idb);
- List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet, dbr, DBRefUtils.SEARCH_MODE_FULL);
+ DBRefEntry dbr = sqdbrefs.get(idb);
+ List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet,
+ dbr, DBRefUtils.SEARCH_MODE_FULL);
for (int isr = 0, nsr = searchrefs.size(); isr < nsr; isr++)
{
sourceRefs.remove(searchrefs.get(isr));
/**
* process sequence retrieved via a dbref on source sequence to resolve and
- * transfer data
+ * transfer data JBPNote: as of 2022-02-03 - this assumes retrievedSequence
+ * has dbRefs with Mapping references to a sequence congruent with
+ * sourceSequence
*
* @param cf
* @param sourceSequence
List<DBRefEntry> dbr = retrievedSequence.getDBRefs();
if (dbr != null)
{
- for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
+ for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
{
- DBRefEntry dbref = dbr.get(ib);
+ DBRefEntry dbref = dbr.get(ib);
+ // matched will return null if the dbref has no map
SequenceI matched = findInDataset(dbref);
if (matched == sourceSequence)
{
Mapping map = dbref.getMap();
if (map != null)
{
- SequenceI ms = map.getTo();
+ SequenceI ms = map.getTo();
if (ms != null && map.getMap() != null)
{
if (ms == sourceSequence)
String msg = "Mapping updated from " + ms.getName()
+ " to retrieved crossreference "
+ matched.getName();
- System.out.println(msg);
+ jalview.bin.Console.outPrintln(msg);
List<DBRefEntry> toRefs = map.getTo().getDBRefs();
if (toRefs != null)
cf.addMap(retrievedSequence, map.getTo(), map.getMap());
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception when consolidating Mapped sequence set...");
e.printStackTrace(System.err);
}
/**
* 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
+ * first one with an ID source|xrefacc JBPNote: Could refactor this to
+ * AlignmentI/DatasetI
*
* @param xref
* with map and mapped-to sequence
for (SequenceI seq : dataset.getSequences())
{
// first check primary refs.
- List<DBRefEntry> match = DBRefUtils.searchRefs(
- seq.getPrimaryDBRefs(), template, DBRefUtils.SEARCH_MODE_FULL);
+ List<DBRefEntry> match = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(),
+ template, DBRefUtils.SEARCH_MODE_FULL);
if (match != null && match.size() == 1 && sameSequence(seq, dss))
{
return seq;
/**
* Updates any empty mappings in the cross-references with one to a compatible
* retrieved sequence if found, and adds any new mappings to the
- * AlignedCodonFrame
+ * AlignedCodonFrame JBPNote: TODO: this relies on sequence IDs like
+ * UNIPROT|ACCESSION - which do not always happen.
*
* @param mapFrom
* @param xrefs
}
for (int i = 0, n = lrfs.size(); i < n; i++)
{
-// DBRefEntry xref = new DBRefEntry(lrfs.get(i));
-// // add in wildcards
-// xref.setVersion(null);
-// xref.setMap(null);
+ // DBRefEntry xref = new DBRefEntry(lrfs.get(i));
+ // // add in wildcards
+ // xref.setVersion(null);
+ // xref.setMap(null);
found |= searchDataset(fromDna, sequenceI, lrfs.get(i), foundSeqs, cf,
false, DBRefUtils.SEARCH_MODE_NO_MAP_NO_VERSION);
}
* sequenceI or all the returned sequences (eg a genomic reference
* associated with a locus and one or more transcripts)</li>
* </ul>
- * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+ * @param mode
+ * SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
* @return true if relationship found and sequence added.
*/
boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
}
if (dataset.getSequences() == null)
{
- System.err.println("Empty dataset sequence set - NO VECTOR");
+ jalview.bin.Console.errPrintln("Empty dataset sequence set - NO VECTOR");
return false;
}
List<SequenceI> ds = dataset.getSequences();
{
if (nxt.getDatasetSequence() != null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
+ nxt.getDisplayId(true) + " has ds reference "
+ nxt.getDatasetSequence().getDisplayId(true)
git://source.jalview.org / jalview.git / blobdiff