+/*
+ * 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;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import java.util.Arrays;
-import java.util.List;
-
import com.stevesoft.pat.Regex;
/**
*/
public class EnsemblCdna extends EnsemblSeqProxy
{
- private static final List<String> CROSS_REFERENCES = Arrays
- .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
-
/*
* accepts ENST or ENSTG with 11 digits
* or ENSMUST or similar for other species
*/
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-
+
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
return false;
}
- @Override
- protected List<String> getCrossReferenceDatabases()
- {
- return CROSS_REFERENCES;
- // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
- // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
- }
-
}