+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * A client to fetch genomic sequence from Ensembl
+ *
+ * TODO: not currently used - delete?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblGenome extends EnsemblSeqProxy
{
+ /*
+ * fetch transcript features on genomic sequence (to identify the transcript
+ * regions) and cds, exon and variation features (to retain)
+ */
+ private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
+ EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
+ EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblGenome()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblGenome(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
- return "ENSEMBL (Genome)";
+ return "ENSEMBL (Genomic)";
}
@Override
return EnsemblSeqType.GENOMIC;
}
+ @Override
+ protected EnsemblFeatureType[] getFeaturesToFetch()
+ {
+ return FEATURES_TO_FETCH;
+ }
+
+ /**
+ * Answers true unless the feature type is 'transcript' (or a sub-type of
+ * transcript in the Sequence Ontology), or has a parent other than the given
+ * accession id. Transcript features are only retrieved in order to identify
+ * the transcript sequence range, and are redundant information on the
+ * transcript sequence itself.
+ */
+ @Override
+ protected boolean retainFeature(SequenceFeature sf, String accessionId)
+ {
+ if (isTranscript(sf.getType()))
+ {
+ return false;
+ }
+ return featureMayBelong(sf, accessionId);
+ }
+
+ /**
+ * Answers a list of sequence features (if any) whose type is 'transcript' (or
+ * a subtype of transcript in the Sequence Ontology), and whose ID is the
+ * accession we are retrieving.
+ * <p>
+ * Note we also include features of type "NMD_transcript_variant", although
+ * not strictly 'transcript' in the SO, as they used in Ensembl as if they
+ * were.
+ */
+ @Override
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
+ {
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures().getFeaturesByOntology(
+ SequenceOntologyI.TRANSCRIPT,
+ SequenceOntologyI.NMD_TRANSCRIPT_VARIANT);
+ for (SequenceFeature sf : sfs)
+ {
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equals(id))
+ {
+ result.add(sf);
+ }
+ }
+ return result;
+ }
+
}