+/*
+ * 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.datamodel.SequenceFeature;
+/**
+ * A client to fetch genomic sequence from Ensembl
+ *
+ * TODO: not currently used - delete?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblGenome extends EnsemblSeqProxy
{
/*
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
/**
* Answers true unless the feature type is 'transcript' (or a sub-type of
- * transcript in the Sequence Ontology). Transcript features are only
- * retrieved in order to identify the transcript sequence range, and are
- * redundant information on the transcript sequence itself.
+ * 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)