+/*
+ * 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.DBRefSource;
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+
+ protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+
/*
* possible values for the 'feature' parameter of the /overlap REST service
* @see http://rest.ensembl.org/documentation/info/overlap_id
constrained, regulatory
}
+ private String domain = ENSEMBL_REST;
+
@Override
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
- return DBRefSource.ENSEMBL; // "ENSEMBL"
- }
-
- @Override
- public String getDbVersion()
- {
- return "0";
+ if (ENSEMBL_GENOMES_REST.equals(getDomain()))
+ {
+ return DBRefSource.ENSEMBLGENOMES;
+ }
+ return DBRefSource.ENSEMBL;
}
@Override
{
return true;
}
+
+ /**
+ * Returns the domain name to query e.g. http://rest.ensembl.org or
+ * http://rest.ensemblgenomes.org
+ *
+ * @return
+ */
+ protected String getDomain()
+ {
+ return domain;
+ }
+
+ protected void setDomain(String d)
+ {
+ domain = d;
+ }
}