--- /dev/null
+package jalview.ext.ensembl;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Dna;
+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.io.FastaFile;
+import jalview.io.FileParse;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.DBRefUtils;
+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;
+
+/**
+ * Base class for Ensembl sequence fetchers
+ *
+ * @see http://rest.ensembl.org/documentation/info/sequence_id
+ * @author gmcarstairs
+ */
+public abstract class EnsemblSeqProxy extends EnsemblRestClient
+{
+ private static final String ALLELES = "alleles";
+
+ private static final List<String> CROSS_REFERENCES = Arrays
+ .asList(new String[] { "CCDS", "Uniprot/SWISSPROT",
+ "Uniprot/SPTREMBL" });
+
+ protected static final String CONSEQUENCE_TYPE = "consequence_type";
+
+ 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 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;
+ }
+
+ }
+
+ /**
+ * A comparator to sort ranges into ascending start position order
+ */
+ private class RangeSorter implements Comparator<int[]>
+ {
+ 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)
+ {
+ super(d);
+ }
+
+ /**
+ * Makes the sequence queries to Ensembl's REST service and returns an
+ * alignment consisting of the returned sequences.
+ */
+ @Override
+ public AlignmentI getSequenceRecords(String query) throws Exception
+ {
+ // 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<String> 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<String> 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);
+ 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();
+ ds.setSourceDBRef(proteinSeq.getSourceDBRef());
+
+ Mapping map = new Mapping(ds, mapList);
+ DBRefEntry dbr = new DBRefEntry(getDbSource(), getDbVersion(),
+ proteinSeq.getName(), map);
+ querySeq.getDatasetSequence().addDBRef(dbr);
+
+ /*
+ * 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());
+ List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName(),
+ getCrossReferenceDatabases());
+ for (DBRefEntry xref : xrefs)
+ {
+ seq.addDBRef(xref);
+ /*
+ * Save any Uniprot xref to be the reference for SIFTS mapping
+ */
+ if (DBRefSource.UNIPROT.equals(xref.getSource()))
+ {
+ seq.setSourceDBRef(xref);
+ }
+ }
+ }
+
+ /**
+ * Returns a list of database names to be used when fetching cross-references.
+ * Specifically, the names are used to filter data returned by the Ensembl
+ * xrefs REST service on the value in field 'dbname'.
+ *
+ * @return
+ */
+ protected List<String> getCrossReferenceDatabases()
+ {
+ return CROSS_REFERENCES;
+ }
+
+ /**
+ * 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<String> ids, AlignmentI alignment)
+ throws JalviewException, IOException
+ {
+ if (!isEnsemblAvailable())
+ {
+ inProgress = false;
+ throw new JalviewException("ENSEMBL Rest API not available.");
+ }
+ FileParse fp = getSequenceReader(ids);
+ 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")))
+ {
+ DBRefUtils.parseToDbRef(sq, DBRefSource.ENSEMBL, "0", name);
+ }
+ }
+ if (alignment == null)
+ {
+ alignment = seqal;
+ }
+ else
+ {
+ alignment.append(seqal);
+ }
+ }
+ return alignment;
+ }
+
+ /**
+ * Returns the URL for the REST call
+ *
+ * @return
+ * @throws MalformedURLException
+ */
+ @Override
+ protected URL getUrl(List<String> ids) throws MalformedURLException
+ {
+ /*
+ * 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 int getMaximumQueryCount()
+ {
+ return 50;
+ }
+
+ @Override
+ protected boolean useGetRequest()
+ {
+ 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
+ */
+ protected abstract EnsemblSeqType getSourceEnsemblType();
+
+ /**
+ * 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
+ * <ul>
+ * <li>genomic sequence is identified by "transcript" features with
+ * ID=transcript:transcriptId</li>
+ * <li>cdna sequence is identified by "exon" features with
+ * Parent=transcript:transcriptId</li>
+ * <li>cds sequence is identified by "CDS" features with
+ * Parent=transcript:transcriptId</li>
+ * </ul>
+ *
+ * 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)
+ {
+ SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
+ if (sfs == null)
+ {
+ return null;
+ }
+
+ /*
+ * generously initial size for number of cds regions
+ * (worst case titin Q8WZ42 has c. 313 exons)
+ */
+ List<int[]> regions = new ArrayList<int[]>(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))
+ {
+ 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;
+ }
+ }
+ }
+
+ 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<int[]> 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]));
+ 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(",");
+ }
+ if ("HGMD_MUTATION".equalsIgnoreCase(allele))
+ {
+ complement.append(allele);
+ }
+ else
+ {
+ char[] alleles = allele.toCharArray();
+ for (int i = alleles.length - 1; i >= 0; i--)
+ {
+ complement.append(Dna.getComplement(alleles[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<SequenceFeature>()
+ {
+ @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());
+ }
+ }
+ });
+ }
+
+ /**
+ * 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.
+ *
+ * @param sf
+ * @param identifier
+ * @return
+ */
+ 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 String getDescription()
+ {
+ return "Ensembl " + getSourceEnsemblType().getType()
+ + " sequence with variant features";
+ }
+
+ /**
+ * 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<SequenceFeature> findFeatures(SequenceI sequence,
+ String type, String parentId)
+ {
+ List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+
+ 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;
+ }
+
+ /**
+ * 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 SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
+ || SequenceOntologyFactory.getInstance().isA(featureType,
+ SequenceOntologyI.TRANSCRIPT);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff