X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblCdna.java;h=952f01e9fb57cbfddd4f0b2ac46fbdc090fa6dfe;hb=321caefc5a40cd735c93e0bfa450e0e04abc485d;hp=856be744d8ea8637b28ea6d7654cfe81be33b31e;hpb=6c52cc0b81ae3abdc3c5f6f88a23364a0246351a;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 856be74..952f01e 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,12 +1,29 @@
+/*
+ * 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.Arrays;
-import java.util.List;
-
import com.stevesoft.pat.Regex;
/**
@@ -19,9 +36,6 @@ import com.stevesoft.pat.Regex;
*/
public class EnsemblCdna extends EnsemblSeqProxy
{
- private static final List CROSS_REFERENCES = Arrays
- .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
-
/*
* accepts ENST or ENSTG with 11 digits
* or ENSMUST or similar for other species
@@ -29,7 +43,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
*/
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-
+
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
@@ -114,12 +128,14 @@ public class EnsemblCdna extends EnsemblSeqProxy
return false;
}
+ /**
+ * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+ * returned (JAL-2529)
+ */
@Override
- protected List getCrossReferenceDatabases()
+ protected String getObjectType()
{
- return CROSS_REFERENCES;
- // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
- // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
+ return OBJECT_TYPE_TRANSCRIPT;
}
}