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JAL-1793 update spike build to latest incl stop and synonymous variants on peptides
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblCdna.java
diff --git
a/src/jalview/ext/ensembl/EnsemblCdna.java
b/src/jalview/ext/ensembl/EnsemblCdna.java
index
6d031b7
..
952f01e
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/
src/jalview/ext/ensembl/EnsemblCdna.java
@@
-24,9
+24,6
@@
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import java.util.HashMap;
-import java.util.Map;
-
import com.stevesoft.pat.Regex;
/**
import com.stevesoft.pat.Regex;
/**
@@
-47,13
+44,6
@@
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 final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
- private static Map<String, String> params = new HashMap<String, String>();
-
- static
- {
- params.put("object_type", "transcript");
- }
-
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
@@
-139,13
+129,13
@@
public class EnsemblCdna extends EnsemblSeqProxy
}
/**
}
/**
- * Parameter object_type=cdna added to ensure cdna and not peptide is returned
- * (JAL-2529)
+ * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+ * returned (JAL-2529)
*/
@Override
*/
@Override
- protected Map<String, String> getAdditionalParameters()
+ protected String getObjectType()
{
{
- return params;
+ return OBJECT_TYPE_TRANSCRIPT;
}
}
}
}