import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import java.util.ArrayList;
import java.util.List;
+/**
+ * A client for direct fetching of CDS sequences from Ensembl (i.e. that part of
+ * the genomic sequence that is translated to protein)
+ *
+ * TODO: not currently used as CDS sequences are computed from CDS features on
+ * transcripts - delete this class?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblCds extends EnsemblSeqProxy
{
/*
EnsemblFeatureType.variation };
/**
- * Constructor
+ * Default constructor (to use rest.ensembl.org)
*/
public EnsemblCds()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblCds(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
* they are redundant information).
*/
@Override
- protected int getCdsRanges(SequenceI dnaSeq, List<int[]> ranges)
+ protected List<int[]> getCdsRanges(SequenceI dnaSeq)
{
int len = dnaSeq.getLength();
+ List<int[]> ranges = new ArrayList<int[]>();
ranges.add(new int[] { 1, len });
- return len;
+ return ranges;
}
}