X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=6d031b7e8219222d93a3e41e17cbf208147aab8a;hb=833fafa77f2f63bea98ce1d6e1e4ee3e46e7bd53;hp=028492e7da1b5b1405ebf303ae60f98c917d8183;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 028492e..6d031b7 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,10 +1,31 @@
+/*
+ * 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 .
+ * 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.List;
+import java.util.HashMap;
+import java.util.Map;
import com.stevesoft.pat.Regex;
@@ -25,7 +46,14 @@ public class EnsemblCdna extends EnsemblSeqProxy
*/
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-
+
+ private static Map params = new HashMap();
+
+ static
+ {
+ params.put("object_type", "transcript");
+ }
+
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
@@ -110,12 +138,14 @@ public class EnsemblCdna extends EnsemblSeqProxy
return false;
}
+ /**
+ * Parameter object_type=cdna added to ensure cdna and not peptide is returned
+ * (JAL-2529)
+ */
@Override
- protected List getCrossReferenceDatabases()
+ protected Map getAdditionalParameters()
{
- return super.getCrossReferenceDatabases();
- // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
- // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
+ return params;
}
}