+/*
+ * 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 jalview.datamodel.SequenceI;
-import java.util.Arrays;
+import java.util.ArrayList;
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
{
- // TODO modify to accept other species e.g. ENSMUSPnnn
+ /*
+ * accepts ENSP with 11 digits
+ * or ENSMUSP or similar for other species
+ * or CCDSnnnnn.nn with at least 3 digits
+ */
private static final Regex ACCESSION_REGEX = new Regex(
- "(ENSP|CCDS)[0-9.]{3,}$");
-
- private static final List<String> CROSSREFS = Arrays.asList(new String[] {
- "PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
+ "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ /**
+ * 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 boolean identifiesSequence(SequenceFeature sf, String accId)
- {
- // not applicable - protein sequence is not a 'subset' of genomic sequence
- return false;
- }
-
- @Override
- protected List<String> getCrossReferenceDatabases()
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- return CROSSREFS;
+ return new ArrayList<>();
}
@Override