+/*
+ * 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.AlignmentI;
import jalview.datamodel.SequenceFeature;
-import java.util.Arrays;
-import java.util.List;
-
import com.stevesoft.pat.Regex;
+/**
+ * A client to fetch protein translated sequence for an Ensembl identifier
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblProtein extends EnsemblSeqProxy
{
/*
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
- private static final List<String> CROSSREFS = Arrays.asList(new String[] {
- "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
-
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblProtein()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblProtein(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
}
@Override
- protected List<String> getCrossReferenceDatabases()
- {
- return CROSSREFS;
- }
-
- @Override
public Regex getAccessionValidator()
{
return ACCESSION_REGEX;