X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=9109fb22f7eef8756c465a02fc1ac56bd229eaaf;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=137c9b065357bcdec1b416e989f5206c25d0f713;hpb=8504d9c48d03acee51397e5fefa3df660ad0a6cc;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 137c9b0..9109fb2 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -1,178 +1,935 @@ package jalview.ext.ensembl; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.Dna; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; +import jalview.datamodel.Mapping; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.exceptions.JalviewException; -import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType; import jalview.io.FastaFile; import jalview.io.FileParse; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.io.gff.SequenceOntologyI; +import jalview.util.Comparison; import jalview.util.DBRefUtils; -import jalview.ws.seqfetcher.DbSourceProxy; -import jalview.ws.seqfetcher.DbSourceProxyImpl; +import jalview.util.MapList; +import java.io.IOException; +import java.net.MalformedURLException; +import java.net.URL; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; +import java.util.Comparator; import java.util.List; -import com.stevesoft.pat.Regex; - -public abstract class EnsemblSeqProxy extends DbSourceProxyImpl implements - DbSourceProxy +/** + * Base class for Ensembl sequence fetchers + * + * @see http://rest.ensembl.org/documentation/info/sequence_id + * @author gmcarstairs + */ +public abstract class EnsemblSeqProxy extends EnsemblRestClient { - SeqFetcher sf; + private static final String ALLELES = "alleles"; + + protected static final String PARENT = "Parent"; + + protected static final String ID = "ID"; + + protected static final String NAME = "Name"; + + protected static final String DESCRIPTION = "description"; + + /* + * enum for 'type' parameter to the /sequence REST service + */ + public enum EnsemblSeqType + { + /** + * type=genomic to fetch full dna including introns + */ + GENOMIC("genomic"), + + /** + * type=cdna to fetch coding dna including UTRs + */ + CDNA("cdna"), + + /** + * type=cds to fetch coding dna excluding UTRs + */ + CDS("cds"), + + /** + * type=protein to fetch peptide product sequence + */ + PROTEIN("protein"); + + /* + * the value of the 'type' parameter to fetch this version of + * an Ensembl sequence + */ + private String type; + + EnsemblSeqType(String t) + { + type = t; + } + + public String getType() + { + return type; + } + + } - public EnsemblSeqProxy() throws Exception + /** + * A comparator to sort ranges into ascending start position order + */ + private class RangeSorter implements Comparator + { + boolean forwards; + + RangeSorter(boolean forward) + { + forwards = forward; + } + + @Override + public int compare(int[] o1, int[] o2) + { + return (forwards ? 1 : -1) * Integer.compare(o1[0], o2[0]); + } + + } + + /** + * Default constructor (to use rest.ensembl.org) + */ + public EnsemblSeqProxy() + { + super(); + } + + /** + * Constructor given the target domain to fetch data from + */ + public EnsemblSeqProxy(String d) { - sf = new SeqFetcher(); - addDbSourceProperty(DBRefSource.MULTIACC); - addDbSourceProperty(DBRefSource.SEQDB); - // decide whether these need to be filtered according to return type - addDbSourceProperty(DBRefSource.PROTSEQDB); - addDbSourceProperty(DBRefSource.DNACODINGSEQDB); - addDbSourceProperty(DBRefSource.DNASEQDB); + super(d); } + /** + * Makes the sequence queries to Ensembl's REST service and returns an + * alignment consisting of the returned sequences. + */ @Override - public String getDbSource() + public AlignmentI getSequenceRecords(String query) throws Exception { - return "ENSEMBL"; + // TODO use a String... query vararg instead? + + // danger: accession separator used as a regex here, a string elsewhere + // in this case it is ok (it is just a space), but (e.g.) '\' would not be + List allIds = Arrays.asList(query + .split(getAccessionSeparator())); + AlignmentI alignment = null; + inProgress = true; + + /* + * execute queries, if necessary in batches of the + * maximum allowed number of ids + */ + int maxQueryCount = getMaximumQueryCount(); + for (int v = 0, vSize = allIds.size(); v < vSize; v += maxQueryCount) + { + int p = Math.min(vSize, v + maxQueryCount); + List ids = allIds.subList(v, p); + try + { + alignment = fetchSequences(ids, alignment); + } catch (Throwable r) + { + inProgress = false; + String msg = "Aborting ID retrieval after " + v + + " chunks. Unexpected problem (" + r.getLocalizedMessage() + + ")"; + System.err.println(msg); + r.printStackTrace(); + break; + } + } + + if (alignment == null) + { + return null; + } + + /* + * fetch and transfer genomic sequence features, + * fetch protein product and add as cross-reference + */ + for (String accId : allIds) + { + addFeaturesAndProduct(accId, alignment); + } + + for (SequenceI seq : alignment.getSequences()) + { + getCrossReferences(seq); + } + + return alignment; } + /** + * Fetches Ensembl features using the /overlap REST endpoint, and adds them to + * the sequence in the alignment. Also fetches the protein product, maps it + * from the CDS features of the sequence, and saves it as a cross-reference of + * the dna sequence. + * + * @param accId + * @param alignment + */ + protected void addFeaturesAndProduct(String accId, AlignmentI alignment) + { + if (alignment == null) + { + return; + } + + try + { + /* + * get 'dummy' genomic sequence with exon, cds and variation features + */ + SequenceI genomicSequence = null; + EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); + EnsemblFeatureType[] features = getFeaturesToFetch(); + AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId, + features); + if (geneFeatures.getHeight() > 0) + { + genomicSequence = geneFeatures.getSequenceAt(0); + } + if (genomicSequence != null) + { + /* + * transfer features to the query sequence + */ + SequenceI querySeq = alignment.findName(accId); + if (transferFeatures(accId, genomicSequence, querySeq)) + { + + /* + * fetch and map protein product, and add it as a cross-reference + * of the retrieved sequence + */ + addProteinProduct(querySeq); + } + } + } catch (IOException e) + { + System.err.println("Error transferring Ensembl features: " + + e.getMessage()); + } + } + /** + * Returns those sequence feature types to fetch from Ensembl. We may want + * features either because they are of interest to the user, or as means to + * identify the locations of the sequence on the genomic sequence (CDS + * features identify CDS, exon features identify cDNA etc). + * + * @return + */ + protected abstract EnsemblFeatureType[] getFeaturesToFetch(); + + /** + * Fetches and maps the protein product, and adds it as a cross-reference of + * the retrieved sequence + */ + protected void addProteinProduct(SequenceI querySeq) + { + String accId = querySeq.getName(); + try + { + AlignmentI protein = new EnsemblProtein(getDomain()) + .getSequenceRecords(accId); + if (protein == null || protein.getHeight() == 0) + { + System.out.println("No protein product found for " + accId); + return; + } + SequenceI proteinSeq = protein.getSequenceAt(0); + + /* + * need dataset sequences (to be the subject of mappings) + */ + proteinSeq.createDatasetSequence(); + querySeq.createDatasetSequence(); + + MapList mapList = AlignmentUtils + .mapCdsToProtein(querySeq, proteinSeq); + if (mapList != null) + { + // clunky: ensure Uniprot xref if we have one is on mapped sequence + SequenceI ds = proteinSeq.getDatasetSequence(); + // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence() + Mapping map = new Mapping(ds, mapList); + DBRefEntry dbr = new DBRefEntry(getDbSource(), + getEnsemblDataVersion(), proteinSeq.getName(), map); + querySeq.getDatasetSequence().addDBRef(dbr); + DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(), + new String[] { DBRefSource.UNIPROT }); + DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(), + new String[] { DBRefSource.UNIPROT }); + if (uprots != null) + { + for (DBRefEntry up : uprots) + { + // locate local uniprot ref and map + List upx = DBRefUtils.searchRefs(upxrefs, + up.getAccessionId()); + DBRefEntry upxref; + if (upx.size() != 0) + { + upxref = upx.get(0); + + if (upx.size() > 1) + { + Cache.log + .warn("Implementation issue - multiple uniprot acc on product sequence."); + } + } + else + { + upxref = new DBRefEntry(DBRefSource.UNIPROT, + getEnsemblDataVersion(), up.getAccessionId()); + } + + Mapping newMap = new Mapping(ds, mapList); + upxref.setVersion(getEnsemblDataVersion()); + upxref.setMap(newMap); + if (upx.size() == 0) + { + // add the new uniprot ref + querySeq.getDatasetSequence().addDBRef(upxref); + } + + } + } + + /* + * copy exon features to protein, compute peptide variants from dna + * variants and add as features on the protein sequence ta-da + */ + AlignmentUtils + .computeProteinFeatures(querySeq, proteinSeq, mapList); + } + } catch (Exception e) + { + System.err + .println(String.format("Error retrieving protein for %s: %s", + accId, e.getMessage())); + } + } + + /** + * Get database xrefs from Ensembl, and attach them to the sequence + * + * @param seq + */ + protected void getCrossReferences(SequenceI seq) + { + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + + EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(), + getEnsemblDataVersion()); + List xrefs = xrefFetcher.getCrossReferences(seq.getName()); + for (DBRefEntry xref : xrefs) + { + seq.addDBRef(xref); + } + + /* + * and add a reference to itself + */ + DBRefEntry self = new DBRefEntry(getDbSource(), + getEnsemblDataVersion(), seq.getName()); + seq.addDBRef(self); + } + + /** + * Fetches sequences for the list of accession ids and adds them to the + * alignment. Returns the extended (or created) alignment. + * + * @param ids + * @param alignment + * @return + * @throws JalviewException + * @throws IOException + */ + protected AlignmentI fetchSequences(List ids, AlignmentI alignment) + throws JalviewException, IOException + { + if (!isEnsemblAvailable()) + { + inProgress = false; + throw new JalviewException("ENSEMBL Rest API not available."); + } + FileParse fp = getSequenceReader(ids); + if (fp == null) + { + return alignment; + } + + FastaFile fr = new FastaFile(fp); + if (fr.hasWarningMessage()) + { + System.out.println(String.format( + "Warning when retrieving %d ids %s\n%s", ids.size(), + ids.toString(), fr.getWarningMessage())); + } + else if (fr.getSeqs().size() != ids.size()) + { + System.out.println(String.format( + "Only retrieved %d sequences for %d query strings", fr + .getSeqs().size(), ids.size())); + } + + if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0) + { + /* + * POST request has returned an empty FASTA file e.g. for invalid id + */ + throw new IOException("No data returned for " + ids); + } + + if (fr.getSeqs().size() > 0) + { + AlignmentI seqal = new Alignment(fr.getSeqsAsArray()); + for (SequenceI sq : seqal.getSequences()) + { + if (sq.getDescription() == null) + { + sq.setDescription(getDbName()); + } + String name = sq.getName(); + if (ids.contains(name) + || ids.contains(name.replace("ENSP", "ENST"))) + { + DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(), + getEnsemblDataVersion(), name); + sq.addDBRef(dbref); + } + } + if (alignment == null) + { + alignment = seqal; + } + else + { + alignment.append(seqal); + } + } + return alignment; + } + + /** + * Returns the URL for the REST call + * + * @return + * @throws MalformedURLException + */ @Override - public String getDbVersion() + protected URL getUrl(List ids) throws MalformedURLException { - return "0"; // sf.getVersion(); + /* + * a single id is included in the URL path + * multiple ids go in the POST body instead + */ + StringBuffer urlstring = new StringBuffer(128); + urlstring.append(getDomain() + "/sequence/id"); + if (ids.size() == 1) + { + urlstring.append("/").append(ids.get(0)); + } + // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats + urlstring.append("?type=").append(getSourceEnsemblType().getType()); + urlstring.append(("&Accept=text/x-fasta")); + + URL url = new URL(urlstring.toString()); + return url; } + /** + * A sequence/id POST request currently allows up to 50 queries + * + * @see http://rest.ensembl.org/documentation/info/sequence_id_post + */ @Override - public String getAccessionSeparator() + public int getMaximumQueryCount() { - return " "; + return 50; } @Override - public Regex getAccessionValidator() + protected boolean useGetRequest() { - return new Regex("((ENSP|ENST|ENSG|CCDS)[0-9.]{3,})"); + return false; } @Override - public String getTestQuery() + protected String getRequestMimeType(boolean multipleIds) { - return "ENSP00000288602"; + return multipleIds ? "application/json" : "text/x-fasta"; } @Override - public boolean isValidReference(String accession) + protected String getResponseMimeType() { - return getAccessionValidator().search(accession); + return "text/x-fasta"; } - private volatile boolean inProgress = false; + /** + * + * @return the configured sequence return type for this source + */ + protected abstract EnsemblSeqType getSourceEnsemblType(); - @Override - public AlignmentI getSequenceRecords(String queries) throws Exception + /** + * Returns a list of [start, end] genomic ranges corresponding to the sequence + * being retrieved. + * + * The correspondence between the frames of reference is made by locating + * those features on the genomic sequence which identify the retrieved + * sequence. Specifically + *
    + *
  • genomic sequence is identified by "transcript" features with + * ID=transcript:transcriptId
    • + *
  • cdna sequence is identified by "exon" features with + * Parent=transcript:transcriptId
    • + *
  • cds sequence is identified by "CDS" features with + * Parent=transcript:transcriptId
    • + *
+ * + * The returned ranges are sorted to run forwards (for positive strand) or + * backwards (for negative strand). Aborts and returns null if both positive + * and negative strand are found (this should not normally happen). + * + * @param sourceSequence + * @param accId + * @param start + * the start position of the sequence we are mapping to + * @return + */ + protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence, + String accId, int start) { - inProgress = true; - List tids, ids = new ArrayList(); - tids = Arrays.asList(queries.split(" +")); - AlignmentI rtn = null; - for (int v = 0, vSize = tids.size(); v < vSize; v += 50) + SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); + if (sfs == null) { - int p = v + 50; - if (p > vSize) - { - p = vSize; - } - ; - ids = tids.subList(v, p); - try + return null; + } + + /* + * generously initial size for number of cds regions + * (worst case titin Q8WZ42 has c. 313 exons) + */ + List regions = new ArrayList(100); + int mappedLength = 0; + int direction = 1; // forward + boolean directionSet = false; + + for (SequenceFeature sf : sfs) + { + /* + * accept the target feature type or a specialisation of it + * (e.g. coding_exon for exon) + */ + if (identifiesSequence(sf, accId)) { - if (!sf.isEnsemblAvailable()) + int strand = sf.getStrand(); + strand = strand == 0 ? 1 : strand; // treat unknown as forward + + if (directionSet && strand != direction) { - inProgress = false; - throw new JalviewException("ENSEMBL Rest API not available."); + // abort - mix of forward and backward + System.err.println("Error: forward and backward strand for " + + accId); + return null; } - FileParse fp = new FileParse(sf.getSequenceReader( - getSourceEnsemblType(), ids)); - FastaFile fr = new FastaFile(fp); - if (fr.hasWarningMessage()) + direction = strand; + directionSet = true; + + /* + * add to CDS ranges, semi-sorted forwards/backwards + */ + if (strand < 0) { - System.out - .println("Warning when retrieving " + ids.size() + " ids" - + ids.toString() + "\n" + fr.getWarningMessage()); + regions.add(0, new int[] { sf.getEnd(), sf.getBegin() }); } - else if (fr.getSeqs().size() != ids.size()) + else { - System.out.println("Only retrieved " + fr.getSeqs().size() - + " sequences for " + ids.size() + " query strings."); + regions.add(new int[] { sf.getBegin(), sf.getEnd() }); } - if (fr.getSeqs().size() > 0) + mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1); + + if (!isSpliceable()) { - AlignmentI seqal = new jalview.datamodel.Alignment( - fr.getSeqsAsArray()); - for (SequenceI sq:seqal.getSequences()) - { - if (ids.contains((sq.getName()))) - { - DBRefUtils.parseToDbRef(sq, "ENSEMBL", "0", sq.getName()); - } - } - if (rtn == null) - { - rtn = seqal; - } - else - { - rtn.append(seqal); - } + /* + * 'gene' sequence is contiguous so we can stop as soon as its + * identifying feature has been found + */ + break; } - } catch (Throwable r) + } + } + + if (regions.isEmpty()) + { + System.out.println("Failed to identify target sequence for " + accId + + " from genomic features"); + return null; + } + + /* + * a final sort is needed since Ensembl returns CDS sorted within source + * (havana / ensembl_havana) + */ + Collections.sort(regions, new RangeSorter(direction == 1)); + + List to = Arrays.asList(new int[] { start, + start + mappedLength - 1 }); + + return new MapList(regions, to, 1, 1); + } + + /** + * Answers true if the sequence being retrieved may occupy discontiguous + * regions on the genomic sequence. + */ + protected boolean isSpliceable() + { + return true; + } + + /** + * Returns true if the sequence feature marks positions of the genomic + * sequence feature which are within the sequence being retrieved. For + * example, an 'exon' feature whose parent is the target transcript marks the + * cdna positions of the transcript. + * + * @param sf + * @param accId + * @return + */ + protected abstract boolean identifiesSequence(SequenceFeature sf, + String accId); + + /** + * Transfers the sequence feature to the target sequence, locating its start + * and end range based on the mapping. Features which do not overlap the + * target sequence are ignored. + * + * @param sf + * @param targetSequence + * @param mapping + * mapping from the sequence feature's coordinates to the target + * sequence + * @param forwardStrand + */ + protected void transferFeature(SequenceFeature sf, + SequenceI targetSequence, MapList mapping, boolean forwardStrand) + { + int start = sf.getBegin(); + int end = sf.getEnd(); + int[] mappedRange = mapping.locateInTo(start, end); + + if (mappedRange != null) + { + SequenceFeature copy = new SequenceFeature(sf); + copy.setBegin(Math.min(mappedRange[0], mappedRange[1])); + copy.setEnd(Math.max(mappedRange[0], mappedRange[1])); + if (".".equals(copy.getFeatureGroup())) { - inProgress = false; - if (rtn != null) + copy.setFeatureGroup(getDbSource()); + } + targetSequence.addSequenceFeature(copy); + + /* + * for sequence_variant on reverse strand, have to convert the allele + * values to their complements + */ + if (!forwardStrand + && SequenceOntologyFactory.getInstance().isA(sf.getType(), + SequenceOntologyI.SEQUENCE_VARIANT)) + { + reverseComplementAlleles(copy); + } + } + } + + /** + * Change the 'alleles' value of a feature by converting to complementary + * bases, and also update the feature description to match + * + * @param sf + */ + static void reverseComplementAlleles(SequenceFeature sf) + { + final String alleles = (String) sf.getValue(ALLELES); + if (alleles == null) + { + return; + } + StringBuilder complement = new StringBuilder(alleles.length()); + for (String allele : alleles.split(",")) + { + reverseComplementAllele(complement, allele); + } + String comp = complement.toString(); + sf.setValue(ALLELES, comp); + sf.setDescription(comp); + + /* + * replace value of "alleles=" in sf.ATTRIBUTES as well + * so 'output as GFF' shows reverse complement alleles + */ + String atts = sf.getAttributes(); + if (atts != null) + { + atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp); + sf.setAttributes(atts); + } + } + + /** + * Makes the 'reverse complement' of the given allele and appends it to the + * buffer, after a comma separator if not the first + * + * @param complement + * @param allele + */ + static void reverseComplementAllele(StringBuilder complement, + String allele) + { + if (complement.length() > 0) + { + complement.append(","); + } + + /* + * some 'alleles' are actually descriptive terms + * e.g. HGMD_MUTATION, PhenCode_variation + * - we don't want to 'reverse complement' these + */ + if (!Comparison.isNucleotideSequence(allele, true)) + { + complement.append(allele); + } + else + { + for (int i = allele.length() - 1; i >= 0; i--) + { + complement.append(Dna.getComplement(allele.charAt(i))); + } + } + } + + /** + * Transfers features from sourceSequence to targetSequence + * + * @param accessionId + * @param sourceSequence + * @param targetSequence + * @return true if any features were transferred, else false + */ + protected boolean transferFeatures(String accessionId, + SequenceI sourceSequence, SequenceI targetSequence) + { + if (sourceSequence == null || targetSequence == null) + { + return false; + } + + // long start = System.currentTimeMillis(); + SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); + MapList mapping = getGenomicRangesFromFeatures(sourceSequence, + accessionId, targetSequence.getStart()); + if (mapping == null) + { + return false; + } + + boolean result = transferFeatures(sfs, targetSequence, mapping, + accessionId); + // System.out.println("transferFeatures (" + (sfs.length) + " --> " + // + targetSequence.getSequenceFeatures().length + ") to " + // + targetSequence.getName() + // + " took " + (System.currentTimeMillis() - start) + "ms"); + return result; + } + + /** + * Transfer features to the target sequence. The start/end positions are + * converted using the mapping. Features which do not overlap are ignored. + * Features whose parent is not the specified identifier are also ignored. + * + * @param features + * @param targetSequence + * @param mapping + * @param parentId + * @return + */ + protected boolean transferFeatures(SequenceFeature[] features, + SequenceI targetSequence, MapList mapping, String parentId) + { + final boolean forwardStrand = mapping.isFromForwardStrand(); + + /* + * sort features by start position (which corresponds to end + * position descending if reverse strand) so as to add them in + * 'forwards' order to the target sequence + */ + sortFeatures(features, forwardStrand); + + boolean transferred = false; + for (SequenceFeature sf : features) + { + if (retainFeature(sf, parentId)) + { + transferFeature(sf, targetSequence, mapping, forwardStrand); + transferred = true; + } + } + return transferred; + } + + /** + * Sort features by start position ascending (if on forward strand), or end + * position descending (if on reverse strand) + * + * @param features + * @param forwardStrand + */ + protected static void sortFeatures(SequenceFeature[] features, + final boolean forwardStrand) + { + Arrays.sort(features, new Comparator() + { + @Override + public int compare(SequenceFeature o1, SequenceFeature o2) + { + if (forwardStrand) { - System.err.println("Aborting ID retrieval after " + v - + " chunks."); - r.printStackTrace(); + return Integer.compare(o1.getBegin(), o2.getBegin()); } else { - - throw new JalviewException("Aborting ID retrieval after " + v - + " chunks. Unexpected problem (" - + r.getLocalizedMessage() + ")", r); + return Integer.compare(o2.getEnd(), o1.getEnd()); } - } - } - inProgress = false; - return rtn; + }); + } + + /** + * Answers true if the feature type is one we want to keep for the sequence. + * Some features are only retrieved in order to identify the sequence range, + * and may then be discarded as redundant information (e.g. "CDS" feature for + * a CDS sequence). + */ + @SuppressWarnings("unused") + protected boolean retainFeature(SequenceFeature sf, String accessionId) + { + return true; // override as required } /** + * Answers true if the feature has a Parent which refers to the given + * accession id, or if the feature has no parent. Answers false if the + * feature's Parent is for a different accession id. * - * @return the configured sequence return type for this source + * @param sf + * @param identifier + * @return */ - protected abstract EnsemblSeqType getSourceEnsemblType(); + protected boolean featureMayBelong(SequenceFeature sf, String identifier) + { + String parent = (String) sf.getValue(PARENT); + // using contains to allow for prefix "gene:", "transcript:" etc + if (parent != null && !parent.contains(identifier)) + { + // this genomic feature belongs to a different transcript + return false; + } + return true; + } @Override - public boolean queryInProgress() + public String getDescription() { - return inProgress; + return "Ensembl " + getSourceEnsemblType().getType() + + " sequence with variant features"; } - @Override - public StringBuffer getRawRecords() + /** + * Returns a (possibly empty) list of features on the sequence which have the + * specified sequence ontology type (or a sub-type of it), and the given + * identifier as parent + * + * @param sequence + * @param type + * @param parentId + * @return + */ + protected List findFeatures(SequenceI sequence, + String type, String parentId) { - return null; + List result = new ArrayList(); + + SequenceFeature[] sfs = sequence.getSequenceFeatures(); + if (sfs != null) + { + SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + for (SequenceFeature sf : sfs) + { + if (so.isA(sf.getType(), type)) + { + String parent = (String) sf.getValue(PARENT); + if (parent.equals(parentId)) + { + result.add(sf); + } + } + } + } + return result; } - @Override - public int getTier() + /** + * Answers true if the feature type is either 'NMD_transcript_variant' or + * 'transcript' or one of its sub-types in the Sequence Ontology. This is + * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl + * although strictly speaking it is not (it is a sub-type of + * sequence_variant). + * + * @param featureType + * @return + */ + public static boolean isTranscript(String featureType) { - return 0; + return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType) + || SequenceOntologyFactory.getInstance().isA(featureType, + SequenceOntologyI.TRANSCRIPT); } }