X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=e4fa53da00a1e97ea485b5bc6046379c4b3b2cb9;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=233707b5de906247c5c8305bedcaab492c87e5f2;hpb=0ed5b947087f831b8673f4c4e423bd4ef2238a89;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 233707b..e4fa53d 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -20,34 +20,37 @@ */ package jalview.ext.ensembl; +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.List; +import java.util.Map; + +import org.json.simple.parser.ParseException; + import jalview.analysis.AlignmentUtils; import jalview.analysis.Dna; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.Alignment; 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.datamodel.features.SequenceFeatures; import jalview.exceptions.JalviewException; -import jalview.io.FastaFile; -import jalview.io.FileParse; +import jalview.io.gff.Gff3Helper; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.util.Comparison; import jalview.util.DBRefUtils; +import jalview.util.IntRangeComparator; import jalview.util.MapList; -import jalview.util.RangeComparator; - -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; /** * Base class for Ensembl sequence fetchers @@ -57,14 +60,6 @@ import java.util.List; */ public abstract class EnsemblSeqProxy extends EnsemblRestClient { - 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"; /* @@ -137,8 +132,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient // 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())); + List allIds = Arrays + .asList(query.split(getAccessionSeparator())); AlignmentI alignment = null; inProgress = true; @@ -175,14 +170,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * fetch and transfer genomic sequence features, * fetch protein product and add as cross-reference */ - for (String accId : allIds) + for (int i = 0, n = allIds.size(); i < n; i++) { - addFeaturesAndProduct(accId, alignment); + addFeaturesAndProduct(allIds.get(i), alignment); } - for (SequenceI seq : alignment.getSequences()) + List seqs = alignment.getSequences(); + for (int i = 0, n = seqs.size(); i < n; i++) { - getCrossReferences(seq); + getCrossReferences(seqs.get(i)); } return alignment; @@ -207,23 +203,30 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient try { /* - * get 'dummy' genomic sequence with exon, cds and variation features + * get 'dummy' genomic sequence with gene, transcript, + * exon, cds and variation features */ SequenceI genomicSequence = null; EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); - EnsemblFeatureType[] features = getFeaturesToFetch(); + EnsemblFeatureType[] features = getFeaturesToFetch(); + + // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK); + AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId, features); if (geneFeatures != null && geneFeatures.getHeight() > 0) { genomicSequence = geneFeatures.getSequenceAt(0); } + + // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK); + if (genomicSequence != null) { /* * transfer features to the query sequence */ - SequenceI querySeq = alignment.findName(accId); + SequenceI querySeq = alignment.findName(accId, true); if (transferFeatures(accId, genomicSequence, querySeq)) { @@ -231,14 +234,16 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * fetch and map protein product, and add it as a cross-reference * of the retrieved sequence */ + // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK); addProteinProduct(querySeq); } } } catch (IOException e) { - System.err.println("Error transferring Ensembl features: " - + e.getMessage()); + System.err.println( + "Error transferring Ensembl features: " + e.getMessage()); } + // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK); } /** @@ -260,6 +265,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String accId = querySeq.getName(); try { + System.out.println("Adding protein product for " + accId); AlignmentI protein = new EnsemblProtein(getDomain()) .getSequenceRecords(accId); if (protein == null || protein.getHeight() == 0) @@ -275,8 +281,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient proteinSeq.createDatasetSequence(); querySeq.createDatasetSequence(); - MapList mapList = AlignmentUtils - .mapCdsToProtein(querySeq, proteinSeq); + MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq, + proteinSeq); if (mapList != null) { // clunky: ensure Uniprot xref if we have one is on mapped sequence @@ -286,10 +292,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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 }); + List uprots = DBRefUtils.selectRefs(ds.getDBRefs(), + new String[] + { DBRefSource.UNIPROT }); + List upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(), + new String[] + { DBRefSource.UNIPROT }); if (uprots != null) { for (DBRefEntry up : uprots) @@ -304,8 +312,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (upx.size() > 1) { - Cache.log - .warn("Implementation issue - multiple uniprot acc on product sequence."); + Console.warn( + "Implementation issue - multiple uniprot acc on product sequence."); } } else @@ -330,8 +338,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * 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); + // JAL-3187 render on the fly instead + // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList); } } catch (Exception e) { @@ -348,25 +356,46 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ protected void getCrossReferences(SequenceI seq) { + + // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK); + + while (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } + // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK); + EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(), getEnsemblDataVersion()); List xrefs = xrefFetcher.getCrossReferences(seq.getName()); - for (DBRefEntry xref : xrefs) + + for (int i = 0, n = xrefs.size(); i < n; i++) { - seq.addDBRef(xref); +// Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK); + // BH 2019.01.25 this next method was taking 174 ms PER addition for a 266-reference example. + // DBRefUtils.ensurePrimaries(seq) + // was at the end of seq.addDBRef, so executed after ever addition! + // This method was moved to seq.getPrimaryDBRefs() + seq.addDBRef(xrefs.get(i)); } +// System.out.println("primaries are " + seq.getPrimaryDBRefs().toString()); /* * and add a reference to itself */ - DBRefEntry self = new DBRefEntry(getDbSource(), - getEnsemblDataVersion(), seq.getName()); + +// Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK); + + DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(), + seq.getName()); + +// Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK); + seq.addDBRef(self); + + // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK); } /** @@ -379,58 +408,50 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * @throws JalviewException * @throws IOException */ - protected AlignmentI fetchSequences(List ids, AlignmentI alignment) - throws JalviewException, 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; - } + // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK); - 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()) + List seqs = parseSequenceJson(ids); + if (seqs == null) + return alignment; + + if (seqs.isEmpty()) { - System.out.println(String.format( - "Only retrieved %d sequences for %d query strings", fr - .getSeqs().size(), ids.size())); + throw new IOException("No data returned for " + ids); } - if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0) + if (seqs.size() != ids.size()) { - /* - * POST request has returned an empty FASTA file e.g. for invalid id - */ - throw new IOException("No data returned for " + ids); + System.out.println(String.format( + "Only retrieved %d sequences for %d query strings", + seqs.size(), ids.size())); } - if (fr.getSeqs().size() > 0) + if (!seqs.isEmpty()) { - AlignmentI seqal = new Alignment(fr.getSeqsAsArray()); - for (SequenceI sq : seqal.getSequences()) + AlignmentI seqal = new Alignment( + seqs.toArray(new SequenceI[seqs.size()])); + for (SequenceI seq : seqs) { - if (sq.getDescription() == null) + if (seq.getDescription() == null) { - sq.setDescription(getDbName()); + seq.setDescription(getDbName()); } - String name = sq.getName(); + String name = seq.getName(); if (ids.contains(name) || ids.contains(name.replace("ENSP", "ENST"))) { - DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(), + // TODO JAL-3077 use true accession version in dbref + DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(), getEnsemblDataVersion(), name); - sq.addDBRef(dbref); + seq.addDBRef(dbref); } } if (alignment == null) @@ -446,6 +467,53 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** + * Parses a JSON response for a single sequence ID query + * + * @param br + * @return a single jalview.datamodel.Sequence + * @see http://rest.ensembl.org/documentation/info/sequence_id + */ + @SuppressWarnings("unchecked") + protected List parseSequenceJson(List ids) + { + List result = new ArrayList<>(); + try + { + /* + * for now, assumes only one sequence returned; refactor if needed + * in future to handle a JSONArray with more than one + */ + // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK); + Map val = (Map) getJSON(null, ids, -1, MODE_MAP, null); + if (val == null) + return null; + Object s = val.get("desc"); + String desc = s == null ? null : s.toString(); + s = val.get("id"); + String id = s == null ? null : s.toString(); + s = val.get("seq"); + String seq = s == null ? null : s.toString(); + Sequence sequence = new Sequence(id, seq); + if (desc != null) + { + sequence.setDescription(desc); + } + // todo JAL-3077 make a DBRefEntry with true accession version + // s = val.get("version"); + // String version = s == null ? "0" : s.toString(); + // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id); + // sequence.addDBRef(dbref); + result.add(sequence); + } catch (ParseException | IOException e) + { + System.err.println("Error processing JSON response: " + e.toString()); + // ignore + } + // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK); + return result; + } + + /** * Returns the URL for the REST call * * @return @@ -466,13 +534,31 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats urlstring.append("?type=").append(getSourceEnsemblType().getType()); - urlstring.append(("&Accept=text/x-fasta")); + urlstring.append(("&Accept=application/json")); + urlstring.append(("&content-type=application/json")); + + String objectType = getObjectType(); + if (objectType != null) + { + urlstring.append("&").append(OBJECT_TYPE).append("=") + .append(objectType); + } URL url = new URL(urlstring.toString()); return url; } /** + * Override this method to specify object_type request parameter + * + * @return + */ + protected String getObjectType() + { + return null; + } + + /** * A sequence/id POST request currently allows up to 50 queries * * @see http://rest.ensembl.org/documentation/info/sequence_id_post @@ -489,18 +575,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return multipleIds ? "application/json" : "text/x-fasta"; - } - - @Override - protected String getResponseMimeType() - { - return "text/x-fasta"; - } - /** * * @return the configured sequence return type for this source @@ -536,8 +610,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence, String accId, int start) { - SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); - if (sfs == null) + List sfs = getIdentifyingFeatures(sourceSequence, + accId); + if (sfs.isEmpty()) { return null; } @@ -546,54 +621,38 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * generously initial size for number of cds regions * (worst case titin Q8WZ42 has c. 313 exons) */ - List regions = new ArrayList(100); + List regions = new ArrayList<>(100); int mappedLength = 0; int direction = 1; // forward boolean directionSet = false; for (SequenceFeature sf : sfs) { + int strand = sf.getStrand(); + strand = strand == 0 ? 1 : strand; // treat unknown as forward + + if (directionSet && strand != direction) + { + // abort - mix of forward and backward + System.err + .println("Error: forward and backward strand for " + accId); + return null; + } + direction = strand; + directionSet = true; + /* - * accept the target feature type or a specialisation of it - * (e.g. coding_exon for exon) + * add to CDS ranges, semi-sorted forwards/backwards */ - if (identifiesSequence(sf, accId)) + if (strand < 0) { - int strand = sf.getStrand(); - strand = strand == 0 ? 1 : strand; // treat unknown as forward - - if (directionSet && strand != direction) - { - // abort - mix of forward and backward - System.err.println("Error: forward and backward strand for " - + accId); - return null; - } - direction = strand; - directionSet = true; - - /* - * add to CDS ranges, semi-sorted forwards/backwards - */ - if (strand < 0) - { - regions.add(0, new int[] { sf.getEnd(), sf.getBegin() }); - } - else - { - regions.add(new int[] { sf.getBegin(), sf.getEnd() }); - } - mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1); - - if (!isSpliceable()) - { - /* - * 'gene' sequence is contiguous so we can stop as soon as its - * identifying feature has been found - */ - break; - } + regions.add(0, new int[] { sf.getEnd(), sf.getBegin() }); + } + else + { + regions.add(new int[] { sf.getBegin(), sf.getEnd() }); } + mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1); } if (regions.isEmpty()) @@ -607,36 +666,32 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * a final sort is needed since Ensembl returns CDS sorted within source * (havana / ensembl_havana) */ - Collections.sort(regions, new RangeComparator(direction == 1)); + Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING + : IntRangeComparator.DESCENDING); - List to = Arrays.asList(new int[] { start, - start + mappedLength - 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 + * Answers a list of sequence features that mark 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. + * cdna positions of the transcript. For a gene sequence, this is trivially + * just the 'gene' feature with matching gene id. * - * @param sf + * @param seq * @param accId * @return */ - protected abstract boolean identifiesSequence(SequenceFeature sf, - String accId); - + protected abstract List getIdentifyingFeatures( + SequenceI seq, String accId); + + int bhtest = 0; + /** * Transfers the sequence feature to the target sequence, locating its start * and end range based on the mapping. Features which do not overlap the @@ -658,22 +713,27 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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())) +// Platform.timeCheck(null, Platform.TIME_SET); + String group = sf.getFeatureGroup(); + if (".".equals(group)) { - copy.setFeatureGroup(getDbSource()); + group = getDbSource(); } + int newBegin = Math.min(mappedRange[0], mappedRange[1]); + int newEnd = Math.max(mappedRange[0], mappedRange[1]); +// Platform.timeCheck(null, Platform.TIME_MARK); + bhtest++; + // 280 ms/1000 here: + SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, group, sf.getScore()); + // 0.175 ms here: 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)) + if (!forwardStrand && SequenceOntologyFactory.getInstance() + .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT)) { reverseComplementAlleles(copy); } @@ -688,7 +748,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ static void reverseComplementAlleles(SequenceFeature sf) { - final String alleles = (String) sf.getValue(ALLELES); + final String alleles = (String) sf.getValue(Gff3Helper.ALLELES); if (alleles == null) { return; @@ -699,19 +759,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient reverseComplementAllele(complement, allele); } String comp = complement.toString(); - sf.setValue(ALLELES, comp); + sf.setValue(Gff3Helper.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); - } } /** @@ -763,21 +812,24 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } - // long start = System.currentTimeMillis(); - SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); +// long start = System.currentTimeMillis(); + List sfs = sourceSequence.getFeatures() + .getPositionalFeatures(); MapList mapping = getGenomicRangesFromFeatures(sourceSequence, accessionId, targetSequence.getStart()); if (mapping == null) - { + { return false; } + // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK); + boolean result = transferFeatures(sfs, targetSequence, mapping, accessionId); - // System.out.println("transferFeatures (" + (sfs.length) + " --> " - // + targetSequence.getSequenceFeatures().length + ") to " - // + targetSequence.getName() - // + " took " + (System.currentTimeMillis() - start) + "ms"); +// System.out.println("transferFeatures (" + (sfs.size()) + " --> " +// + targetSequence.getFeatures().getFeatureCount(true) + ") to " +// + targetSequence.getName() + " took " +// + (System.currentTimeMillis() - start) + "ms"); return result; } @@ -786,13 +838,13 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * 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 sfs * @param targetSequence * @param mapping * @param parentId * @return */ - protected boolean transferFeatures(SequenceFeature[] features, + protected boolean transferFeatures(List sfs, SequenceI targetSequence, MapList mapping, String parentId) { final boolean forwardStrand = mapping.isFromForwardStrand(); @@ -802,45 +854,27 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * position descending if reverse strand) so as to add them in * 'forwards' order to the target sequence */ - sortFeatures(features, forwardStrand); + SequenceFeatures.sortFeatures(sfs, forwardStrand); boolean transferred = false; - for (SequenceFeature sf : features) + + for (int i = 0, n = sfs.size(); i < n; i++) { + +// if ((i%1000) == 0) { +//// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET); +// Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK); +// } + + SequenceFeature sf = sfs.get(i); 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) - { - return Integer.compare(o1.getBegin(), o2.getBegin()); - } - else - { - return Integer.compare(o2.getEnd(), o1.getEnd()); - } - } - }); + return transferred; } /** @@ -867,8 +901,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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)) + if (parent != null + && !parent.equalsIgnoreCase(identifier)) { // this genomic feature belongs to a different transcript return false; @@ -876,6 +910,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return true; } + /** + * Answers a short description of the sequence fetcher + */ @Override public String getDescription() { @@ -885,44 +922,43 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /** * 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 + * specified sequence ontology term (or a sub-type of it), and the given * identifier as parent * * @param sequence - * @param type + * @param term * @param parentId * @return */ protected List findFeatures(SequenceI sequence, - String type, String parentId) + String term, String parentId) { - List result = new ArrayList(); + List result = new ArrayList<>(); - SequenceFeature[] sfs = sequence.getSequenceFeatures(); - if (sfs != null) + List sfs = sequence.getFeatures() + .getFeaturesByOntology(term); + for (SequenceFeature sf : sfs) { - SequenceOntologyI so = SequenceOntologyFactory.getInstance(); - for (SequenceFeature sf : sfs) + String parent = (String) sf.getValue(PARENT); + if (parent != null && parent.equalsIgnoreCase(parentId)) { - if (so.isA(sf.getType(), type)) - { - String parent = (String) sf.getValue(PARENT); - if (parent.equals(parentId)) - { - result.add(sf); - } - } + result.add(sf); } } + return result; } /** * 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 + * 'transcript' (or one of its sub-types in the Sequence Ontology). This is + * because NMD_transcript_variant behaves like 'transcript' in Ensembl * although strictly speaking it is not (it is a sub-type of * sequence_variant). + *

+ * (This test was needed when fetching transcript features as GFF. As we are + * now fetching as JSON, all features have type 'transcript' so the check for + * NMD_transcript_variant is redundant. Left in for any future case arising.) * * @param featureType * @return