import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import java.util.HashMap;
+import java.util.Map;
+
import com.stevesoft.pat.Regex;
/**
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)
return false;
}
+ /**
+ * Parameter object_type=cdna added to ensure cdna and not peptide is returned
+ * (JAL-2529)
+ */
+ @Override
+ protected Map<String, String> getAdditionalParameters()
+ {
+ return params;
+ }
+
}