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.DBRefUtils;
-import jalview.ws.SequenceFetcher;
+import jalview.util.MapList;
+import jalview.ws.SequenceFetcherFactory;
import jalview.ws.seqfetcher.ASequenceFetcher;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
/**
- * Functions for cross-referencing sequence databases. user must first specify
- * if cross-referencing from protein or dna (set dna==true)
+ * Functions for cross-referencing sequence databases.
*
* @author JimP
*
*/
public class CrossRef
{
+ /*
+ * the dataset of the alignment for which we are searching for
+ * cross-references; in some cases we may resolve xrefs by
+ * searching in the dataset
+ */
+ private AlignmentI dataset;
+
+ /*
+ * the sequences for which we are seeking cross-references
+ */
+ private SequenceI[] fromSeqs;
+
/**
- * Select just the DNA or protein references for a protein or dna sequence
- *
- * @param fromDna
- * if true, select references from DNA (i.e. Protein databases), else
- * DNA database references
- * @param refs
- * a set of references to select from
- * @return
+ * matcher built from dataset
*/
- public static DBRefEntry[] findXDbRefs(boolean fromDna, DBRefEntry[] refs)
- {
- return DBRefUtils.selectRefs(refs, fromDna ? DBRefSource.PROTEINDBS
- : DBRefSource.DNACODINGDBS);
- // could attempt to find other cross
- // refs here - ie PDB xrefs
- // (not dna, not protein seq)
- }
+ SequenceIdMatcher matcher;
/**
- * @param dna
- * true if seqs are DNA seqs
+ * sequences found by cross-ref searches to fromSeqs
+ */
+ List<SequenceI> rseqs;
+
+ /**
+ * Constructor
+ *
* @param seqs
- * @return a list of sequence database cross reference source types
+ * the sequences for which we are seeking cross-references
+ * @param ds
+ * the containing alignment dataset (may be searched to resolve
+ * cross-references)
*/
- public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)
+ public CrossRef(SequenceI[] seqs, AlignmentI ds)
{
- return findSequenceXrefTypes(dna, seqs, null);
+ fromSeqs = seqs;
+ dataset = ds.getDataset() == null ? ds : ds.getDataset();
}
/**
- * Indirect references are references from other sequences from the dataset to
- * any of the direct DBRefEntrys on the given sequences.
+ * Returns a list of distinct database sources for which sequences have either
+ * <ul>
+ * <li>a (dna-to-protein or protein-to-dna) cross-reference</li>
+ * <li>an indirect cross-reference - a (dna-to-protein or protein-to-dna)
+ * reference from another sequence in the dataset which has a cross-reference
+ * to a direct DBRefEntry on the given sequence</li>
+ * </ul>
*
* @param dna
- * true if seqs are DNA seqs
- * @param seqs
- * @return a list of sequence database cross reference source types
+ * - when true, cross-references *from* dna returned. When false,
+ * cross-references *from* protein are returned
+ * @return
*/
- public static String[] findSequenceXrefTypes(boolean dna,
- SequenceI[] seqs, AlignmentI dataset)
+ public List<String> findXrefSourcesForSequences(boolean dna)
{
- String[] dbrefs = null;
- List<String> refs = new ArrayList<String>();
- for (int s = 0; s < seqs.length; s++)
+ List<String> sources = new ArrayList<String>();
+ for (SequenceI seq : fromSeqs)
{
- if (seqs[s] != null)
+ if (seq != null)
{
- SequenceI dss = seqs[s];
- while (dss.getDatasetSequence() != null)
- {
- dss = dss.getDatasetSequence();
- }
- DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
- for (int r = 0; rfs != null && r < rfs.length; r++)
- {
- if (!refs.contains(rfs[r].getSource()))
- {
- refs.add(rfs[r].getSource());
- }
- }
- if (dataset != null)
- {
- // search for references to this sequence's direct references.
- DBRefEntry[] lrfs = CrossRef
- .findXDbRefs(!dna, seqs[s].getDBRef());
- List<SequenceI> rseqs = new ArrayList<SequenceI>();
- CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
- null); // don't need to specify codon frame for mapping here
- for (SequenceI rs : rseqs)
- {
- DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef()); // not used??
- for (int r = 0; rfs != null && r < rfs.length; r++)
- {
- if (!refs.contains(rfs[r].getSource()))
- {
- refs.add(rfs[r].getSource());
- }
- }
- }
- }
+ findXrefSourcesForSequence(seq, dna, sources);
}
}
- if (refs.size() > 0)
+ sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in
+ // redundant datasets
+ if (dna)
{
- dbrefs = new String[refs.size()];
- refs.toArray(dbrefs);
+ sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and
+ // EnsemblGenomes xref option shown
+ // from cdna panel
+ sources.remove(DBRefSource.ENSEMBLGENOMES);
}
- return dbrefs;
+ // redundant datasets
+ return sources;
}
- /*
- * if (dna) { if (rfs[r].hasMap()) { // most likely this is a protein cross
- * reference if (!refs.contains(rfs[r].getSource())) {
- * refs.addElement(rfs[r].getSource()); } } }
+ /**
+ * Returns a list of distinct database sources for which a sequence has either
+ * <ul>
+ * <li>a (dna-to-protein or protein-to-dna) cross-reference</li>
+ * <li>an indirect cross-reference - a (dna-to-protein or protein-to-dna)
+ * reference from another sequence in the dataset which has a cross-reference
+ * to a direct DBRefEntry on the given sequence</li>
+ * </ul>
+ *
+ * @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
*/
- public static boolean hasCdnaMap(SequenceI[] seqs)
+ void findXrefSourcesForSequence(SequenceI seq, boolean fromDna,
+ List<String> sources)
{
- String[] reftypes = findSequenceXrefTypes(false, seqs);
- for (int s = 0; s < reftypes.length; s++)
+ /*
+ * first find seq's xrefs (dna-to-peptide or peptide-to-dna)
+ */
+ DBRefEntry[] rfs = DBRefUtils.selectDbRefs(!fromDna, seq.getDBRefs());
+ addXrefsToSources(rfs, sources);
+ if (dataset != null)
{
- if (reftypes.equals(DBRefSource.EMBLCDS))
+ /*
+ * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
+ */
+ DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
+ 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, foundSeqs, null);
+
+ /*
+ * add those sequences' (dna-to-peptide or peptide-to-dna) dbref sources
+ */
+ for (SequenceI rs : foundSeqs)
{
- return true;
- // no map
+ DBRefEntry[] xrs = DBRefUtils
+ .selectDbRefs(!fromDna, rs.getDBRefs());
+ addXrefsToSources(xrs, sources);
}
}
- return false;
}
- public static SequenceI[] getCdnaMap(SequenceI[] seqs)
+ /**
+ * Helper method that adds the source identifiers of some cross-references to
+ * a (non-redundant) list of database sources
+ *
+ * @param xrefs
+ * @param sources
+ */
+ void addXrefsToSources(DBRefEntry[] xrefs, List<String> sources)
{
- Vector cseqs = new Vector();
- for (int s = 0; s < seqs.length; s++)
+ if (xrefs != null)
{
- DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
- for (int c = 0; c < cdna.length; c++)
+ for (DBRefEntry ref : xrefs)
{
- if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
+ /*
+ * avoid duplication e.g. ENSEMBL and Ensembl
+ */
+ String source = DBRefUtils.getCanonicalName(ref.getSource());
+ if (!sources.contains(source))
{
- System.err
- .println("TODO: unimplemented sequence retrieval for coding region sequence.");
- // TODO: retrieve CDS dataset sequences
- // need global dataset sequence retriever/resolver to reuse refs
- // and construct Mapping entry.
- // insert gaps in CDS according to peptide gaps.
- // add gapped sequence to cseqs
+ sources.add(source);
}
}
}
- if (cseqs.size() > 0)
- {
- SequenceI[] rsqs = new SequenceI[cseqs.size()];
- cseqs.copyInto(rsqs);
- return rsqs;
- }
- return null;
-
- }
-
- /**
- *
- * @param dna
- * @param seqs
- * @return
- */
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
- String source)
- {
- return findXrefSequences(seqs, dna, source, null);
}
/**
+ * 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
- * @param dna
* @param source
- * @param dataset
- * alignment to search for product sequences.
- * @return products (as dataset sequences)
+ * @return cross-referenced sequences (as dataset sequences)
*/
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
- String source, AlignmentI dataset)
+ public Alignment findXrefSequences(String source, boolean fromDna)
{
- List<SequenceI> rseqs = new ArrayList<SequenceI>();
- Alignment ral = null;
- AlignedCodonFrame cf = new AlignedCodonFrame(); // nominal width
- for (int s = 0; s < seqs.length; s++)
+
+ rseqs = new ArrayList<SequenceI>();
+ AlignedCodonFrame cf = new AlignedCodonFrame();
+ matcher = new SequenceIdMatcher(dataset.getSequences());
+
+ for (SequenceI seq : fromSeqs)
{
- SequenceI dss = seqs[s];
+ SequenceI dss = seq;
while (dss.getDatasetSequence() != null)
{
dss = dss.getDatasetSequence();
}
boolean found = false;
- DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
+ 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)
{
- System.out.println("Attempting to find ds Xrefs refs.");
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
- // less ambiguous would be a 'find primary dbRefEntry' method.
- // filter for desired source xref here
- found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
- rseqs, cf);
+ /*
+ * found no suitable dbrefs on sequence - look for sequences in the
+ * alignment which share a dbref with this one
+ */
+ DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna,
+ seq.getDBRefs());
+
+ /*
+ * find sequences (except this one!), of complementary type,
+ * which have a dbref to an accession id for this sequence,
+ * and add them to the results
+ */
+ found = searchDatasetXrefs(fromDna, dss, lrfs, rseqs, cf);
}
- for (int r = 0; xrfs != null && r < xrfs.length; r++)
+ if (xrfs == null && !found)
{
- if (source != null && !source.equals(xrfs[r].getSource()))
- {
- continue;
- }
- if (xrfs[r].hasMap())
+ /*
+ * no dbref to source on this sequence or matched
+ * complementary sequence in the dataset
+ */
+ continue;
+ }
+ 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;
+ // we're only interested in coding cross-references, not
+ // locus->transcript
+ if (xref.hasMap() && xref.getMap().getMap().isTripletMap())
{
- if (xrfs[r].getMap().getTo() != null)
+ SequenceI mappedTo = xref.getMap().getTo();
+ if (mappedTo != null)
{
- SequenceI rsq = new Sequence(xrfs[r].getMap().getTo());
+ /*
+ * dbref contains the sequence it maps to; add it to the
+ * results unless we have done so already (could happen if
+ * fetching xrefs for sequences which have xrefs in common)
+ * for example: UNIPROT {P0CE19, P0CE20} -> EMBL {J03321, X06707}
+ */
+ found = true;
+ /*
+ * 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);
+ 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)
+ {
+ if (!rseqs.contains(matchInDataset))
+ {
+ 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 (xrfs[r].getMap().getMap().getFromRatio() != xrfs[r]
- .getMap().getMap().getToRatio())
+ if (xref.getMap().getMap().isTripletMap())
{
// get sense of map correct for adding to product alignment.
- if (dna)
+ if (fromDna)
{
// map is from dna seq to a protein product
- cf.addMap(dss, rsq, xrfs[r].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, xrfs[r].getMap().getMap().getInverse());
+ cf.addMap(rsq, dss, xref.getMap().getMap().getInverse(),
+ xref.getMap().getMappedFromId());
}
}
- found = true;
}
}
+
if (!found)
{
- // do a bit more work - search for sequences with references matching
- // xrefs on this sequence.
- if (dataset != 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)
{
- found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
- if (found)
+ if (constructMapping(seq, matchedSeq, xref, cf, fromDna))
{
- xrfs[r] = null; // we've recovered seqs for this one.
+ found = true;
}
}
}
+
+ if (!found)
+ {
+ // do a bit more work - search for sequences with references matching
+ // xrefs on this sequence.
+ found = searchDataset(fromDna, dss, xref, rseqs, cf, false);
+ }
+ if (found)
+ {
+ refIterator.remove();
+ }
+ }
+
+ /*
+ * fetch from source database any dbrefs we haven't resolved up to here
+ */
+ if (!sourceRefs.isEmpty())
+ {
+ 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);
}
- if (!found)
+ }
+ 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)
{
- if (xrfs != null && xrfs.length > 0)
+ // 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)
{
- // Try and get the sequence reference...
- /*
- * Ideal world - we ask for a sequence fetcher implementation here if
- * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (
- */
- ASequenceFetcher sftch = new SequenceFetcher();
- SequenceI[] retrieved = null;
- int l = xrfs.length;
- for (int r = 0; r < xrfs.length; r++)
+ // 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<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))
{
- // filter out any irrelevant or irretrievable references
- if (xrfs[r] == null
- || ((source != null && !source.equals(xrfs[r]
- .getSource())) || !sftch.isFetchable(xrfs[r]
- .getSource())))
- {
- l--;
- xrfs[r] = null;
- }
+ sourceRefs.remove(found);
+ dupeFound = true;
}
- if (l > 0)
+ }
+ }
+ 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)
+ {
+ if (map.getTo() != null && map.getMap() != null)
{
- System.out
- .println("Attempting to retrieve cross referenced sequences.");
- DBRefEntry[] t = new DBRefEntry[l];
- l = 0;
- for (int r = 0; r < xrfs.length; r++)
+ if (map.getTo() == sourceSequence)
{
- if (xrfs[r] != null)
- {
- t[l++] = xrfs[r];
- }
+ // already called to import once, and most likely this sequence
+ // already imported !
+ continue;
}
- xrfs = t;
- try
- {
- retrieved = sftch.getSequences(xrfs); // problem here is we don't
- // know which of xrfs
- // resulted in which
- // retrieved element
- } catch (Exception e)
+ if (matched == null)
{
- System.err
- .println("Problem whilst retrieving cross references for Sequence : "
- + seqs[s].getName());
- e.printStackTrace();
+ /*
+ * sequence is new to dataset, so save a reference so it can be added.
+ */
+ newDsSeqs.add(map.getTo());
+ continue;
}
- if (retrieved != null)
+
+ /*
+ * 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
{
- for (int rs = 0; rs < retrieved.length; rs++)
+ // 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: examine each sequence for 'redundancy'
- jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
- .getDBRef();
- if (dbr != null && dbr.length > 0)
+ /*
+ * 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)
+ {
+ /*
+ * transfer database refs
+ */
+ for (DBRefEntry ref : toRefs)
+ {
+ if (dbref.getSrcAccString().equals(
+ ref.getSrcAccString()))
+ {
+ continue; // avoid overwriting the ref on source sequence
+ }
+ 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 (int di = 0; di < dbr.length; di++)
+ for (SequenceFeature feat : sfs)
{
- // find any entry where we should put in the sequence being
- // cross-referenced into the map
- jalview.datamodel.Mapping map = dbr[di].getMap();
- if (map != null)
+ /*
+ * 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)
{
- if (map.getTo() != null && map.getMap() != null)
+ @Override
+ public boolean equals(Object o)
{
- // should search the local dataset to find any existing
- // candidates for To !
- 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
- && mappedrg.getSequenceAsString().equals(
- loc.getSequenceAsString()))
- {
- System.err
- .println("Mapping updated for retrieved crossreference");
- // method to update all refs of existing To on
- // retrieved sequence with dss and merge any props
- // on To onto dss.
- map.setTo(dss);
- }
- } catch (Exception e)
- {
- System.err
- .println("Exception when consolidating Mapped sequence set...");
- e.printStackTrace(System.err);
- }
+ return super.equals(o, true);
}
- }
+ };
+ matched.addSequenceFeature(newFeature);
}
}
- retrieved[rs].updatePDBIds();
- rseqs.add(retrieved[rs]);
+
}
+ cf.addMap(retrievedSequence, map.getTo(), map.getMap());
+ } catch (Exception e)
+ {
+ System.err
+ .println("Exception when consolidating Mapped sequence set...");
+ e.printStackTrace(System.err);
}
}
}
}
}
- if (rseqs.size() > 0)
+ if (imported)
{
- SequenceI[] rsqs = new SequenceI[rseqs.size()];
- rseqs.toArray(rsqs);
- ral = new Alignment(rsqs);
- if (cf != null && cf.getProtMappings() != null)
+ retrievedSequence.updatePDBIds();
+ rseqs.add(retrievedSequence);
+ if (dataset.findIndex(retrievedSequence) == -1)
{
- ral.addCodonFrame(cf);
+ dataset.addSequence(retrievedSequence);
+ matcher.add(retrievedSequence);
}
}
- return ral;
+ 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
+ * 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 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)
+ {
+ if (xref == null || !xref.hasMap() || xref.getMap().getTo() == null)
+ {
+ return null;
+ }
+ SequenceI mapsTo = xref.getMap().getTo();
+ String name = xref.getAccessionId();
+ 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 (firstIdMatch == null
+ && (name.equals(seq.getName()) || seq.getName().startsWith(
+ name2)))
+ {
+ if (sameSequence(seq, dss))
+ {
+ firstIdMatch = seq;
+ }
+ }
+ }
+ return firstIdMatch;
+ }
+
+ /**
+ * Answers true if seq1 and seq2 contain exactly the same characters (ignoring
+ * case), else false. This method compares the lengths, then each character in
+ * turn, in order to 'fail fast'. For case-sensitive comparison, it would be
+ * possible to use Arrays.equals(seq1.getSequence(), seq2.getSequence()).
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ // TODO move to Sequence / SequenceI
+ static boolean sameSequence(SequenceI seq1, SequenceI seq2)
+ {
+ if (seq1 == seq2)
+ {
+ return true;
+ }
+ if (seq1 == null || seq2 == null)
+ {
+ return false;
+ }
+ char[] c1 = seq1.getSequence();
+ char[] c2 = seq2.getSequence();
+ if (c1.length != c2.length)
+ {
+ return false;
+ }
+ for (int i = 0; i < c1.length; i++)
+ {
+ int diff = c1[i] - c2[i];
+ /*
+ * same char or differ in case only ('a'-'A' == 32)
+ */
+ if (diff != 0 && diff != 32 && diff != -32)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * 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
+ *
+ * @param mapFrom
+ * @param xrefs
+ * @param retrieved
+ * @param acf
+ */
+ void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs,
+ SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna)
+ {
+ SequenceIdMatcher idMatcher = new SequenceIdMatcher(retrieved);
+ for (DBRefEntry xref : xrefs)
+ {
+ if (!xref.hasMap())
+ {
+ String targetSeqName = xref.getSource() + "|"
+ + xref.getAccessionId();
+ SequenceI[] matches = idMatcher.findAllIdMatches(targetSeqName);
+ if (matches == null)
+ {
+ return;
+ }
+ for (SequenceI seq : matches)
+ {
+ constructMapping(mapFrom, seq, xref, acf, fromDna);
+ }
+ }
+ }
+ }
+
+ /**
+ * 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
+ * @param xref
+ * @param mappings
+ * @return
+ */
+ boolean constructMapping(SequenceI mapFrom, SequenceI mapTo,
+ 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.
+ * Note - we do this on dataset sequences only.
+ */
+ if (dsmapTo.getDBRefs() != null)
+ {
+ for (DBRefEntry dbref : dsmapTo.getDBRefs())
+ {
+ String name = dbref.getSource() + "|" + dbref.getAccessionId();
+ 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(dsmapTo, reverse));
+ mappings.addMap(mapFrom, dsmapTo, reverse);
+ return true;
+ }
+ }
+ }
+
+ if (fromDna)
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(mapTo, mapFrom);
+ }
+ else
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(mapFrom, mapTo);
+ if (mapping != null)
+ {
+ mapping = mapping.getInverse();
+ }
+ }
+ if (mapping == null)
+ {
+ 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);
+ mappings.addMap(mapFrom, mapTo, mapping);
+ }
+ else
+ {
+ mappings.addMap(mapTo, mapFrom, mapping.getInverse());
+ }
+
+ return true;
}
/**
* 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 dataset
- * @param rseqs
+ * @param foundSeqs
* @return true if matches were found.
*/
- private static boolean searchDatasetXrefs(SequenceI sequenceI,
- boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
- List<SequenceI> rseqs, AlignedCodonFrame cf)
+ private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI,
+ DBRefEntry[] lrfs, List<SequenceI> foundSeqs, AlignedCodonFrame cf)
{
boolean found = false;
if (lrfs == null)
// add in wildcards
xref.setVersion(null);
xref.setMap(null);
- found = searchDataset(sequenceI, xref, dataset, rseqs, cf, false, dna);
+ found |= searchDataset(fromDna, sequenceI, xref, foundSeqs, cf, false);
}
return found;
}
/**
- * search a given sequence dataset for references matching cross-references to
- * the given sequence
- *
- * @param sequenceI
- * @param xrf
- * @param dataset
- * @param rseqs
- * set of unique sequences
- * @param cf
- * @return true if one or more unique sequences were found and added
- */
- public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
- AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf)
- {
- return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);
- }
-
- /**
- * TODO: generalise to different protein classifications Search dataset for
- * DBRefEntrys matching the given one (xrf) and add the associated sequence to
- * rseq.
+ * Searches dataset for DBRefEntrys matching the given one (xrf) and adds the
+ * associated sequence to rseqs
*
- * @param sequenceI
+ * @param fromDna
+ * true if context was searching for refs *from* dna sequence, false
+ * if context was searching for refs *from* protein sequence
+ * @param fromSeq
+ * a sequence to ignore (start point of search)
* @param xrf
- * @param dataset
- * @param rseqs
+ * a cross-reference to try to match
+ * @param foundSeqs
+ * result list to add to
+ * @param mappings
+ * a set of sequence mappings to add to
* @param direct
- * - search all references or only subset
- * @param dna
- * search dna or protein xrefs (if direct=false)
+ * - 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.
*/
- public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
- AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf,
- boolean direct, boolean dna)
+ boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
+ List<SequenceI> foundSeqs, AlignedCodonFrame mappings,
+ boolean direct)
{
boolean found = false;
- SequenceI[] typer = new SequenceI[1];
if (dataset == null)
{
return 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 == fromSeq || nxt == fromSeq.getDatasetSequence())
+ {
+ continue;
}
- if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
+ /*
+ * only look at same molecule type if 'direct', or
+ * complementary type if !direct
+ */
{
- // check if this is the correct sequence type
+ boolean isDna = !nxt.isProtein();
+ if (direct ? (isDna != fromDna) : (isDna == fromDna))
{
- typer[0] = nxt;
- boolean isDna = jalview.util.Comparison.isNucleotide(typer);
- if ((direct && isDna == dna) || (!direct && isDna != dna))
- {
- // skip this sequence because it is same molecule type
- continue;
- }
+ // skip this sequence because it is wrong molecule type
+ continue;
}
+ }
- // look for direct or indirect references in common
- DBRefEntry[] poss = nxt.getDBRef(), cands = null;
- if (direct)
- {
- cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
- }
- else
+ // look for direct or indirect references in common
+ DBRefEntry[] poss = nxt.getDBRefs();
+ List<DBRefEntry> cands = null;
+
+ // 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 (foundSeqs.contains(nxt))
{
- poss = CrossRef.findXDbRefs(dna, poss); //
- cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+ continue;
}
- if (cands != null)
+ found = true;
+ foundSeqs.add(nxt);
+ if (mappings != null && !direct)
{
- if (!rseqs.contains(nxt))
+ /*
+ * if the matched sequence has mapped dbrefs to
+ * protein product / cdna, add equivalent mappings to
+ * our source sequence
+ */
+ for (DBRefEntry candidate : cands)
{
- rseqs.add(nxt);
- boolean foundmap = cf != null;
- // don't search if we aren't given a codon map object
- for (int r = 0; foundmap && r < cands.length; r++)
+ Mapping mapping = candidate.getMap();
+ if (mapping != null)
{
- if (cands[r].hasMap())
+ MapList map = mapping.getMap();
+ if (mapping.getTo() != null
+ && map.getFromRatio() != map.getToRatio())
{
- if (cands[r].getMap().getTo() != null
- && cands[r].getMap().getMap().getFromRatio() != cands[r]
- .getMap().getMap().getToRatio())
+ /*
+ * add a mapping, as from dna to peptide sequence
+ */
+ if (map.getFromRatio() == 3)
{
- foundmap = true;
- // get sense of map correct for adding to product
- // alignment.
- if (dna)
- {
- // map is from dna seq to a protein product
- cf.addMap(sequenceI, nxt, cands[r].getMap()
- .getMap());
- }
- else
- {
- // map should be from protein seq to its coding dna
- cf.addMap(nxt, sequenceI, cands[r].getMap()
- .getMap().getInverse());
- }
+ mappings.addMap(nxt, fromSeq, map);
+ }
+ else
+ {
+ mappings.addMap(nxt, fromSeq, map.getInverse());
}
}
}
- // TODO: add mapping between sequences if necessary
- found = true;
}
}
-
}
}
}
}
return found;
}
-
- /**
- * precalculate different products that can be found for seqs in dataset and
- * return them.
- *
- * @param dna
- * @param seqs
- * @param dataset
- * @param fake
- * - don't actually build lists - just get types
- * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]
- * seqs, AlignmentI dataset, boolean fake) { String types[] =
- * jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,
- * dataset); if (types != null) { System.out.println("Xref Types for:
- * "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {
- * System.out.println("Type: " + types[t]); SequenceI[] prod =
- * jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
- * System.out.println("Found " + ((prod == null) ? "no" : "" +
- * prod.length) + " products"); if (prod!=null) { for (int p=0;
- * p<prod.length; p++) { System.out.println("Prod "+p+":
- * "+prod[p].getDisplayId(true)); } } } } else {
- * System.out.println("Trying getProducts for
- * "+al.getSequenceAt(0).getDisplayId(true));
- * System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
- * // have a bash at finding the products amongst all the retrieved
- * sequences. SequenceI[] prod =
- * jalview.analysis.CrossRef.findXrefSequences(al
- * .getSequencesArray(), dna, null, ds); System.out.println("Found " +
- * ((prod == null) ? "no" : "" + prod.length) + " products"); if
- * (prod!=null) { // select non-equivalent sequences from dataset list
- * for (int p=0; p<prod.length; p++) { System.out.println("Prod "+p+":
- * "+prod[p].getDisplayId(true)); } } } }
- */
}
git://source.jalview.org / jalview.git / blobdiff