package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
+import java.util.Arrays;
+import java.util.List;
import com.stevesoft.pat.Regex;
+/**
+ * A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
+ * sequence that is transcribed to RNA, but not necessarily translated to
+ * protein)
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblCdna extends EnsemblSeqProxy
{
+ private static final List<String> CROSS_REFERENCES = Arrays
+ .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
+
+ /*
+ * accepts ENST or ENSTG with 11 digits
+ * or ENSMUST or similar for other species
+ * or CCDSnnnnn.nn with at least 3 digits
+ */
+ 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 cdnaregions)
+ * fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
*/
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblCdna()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblCdna(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
@Override
public Regex getAccessionValidator()
{
- return new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
+ return ACCESSION_REGEX;
}
@Override
}
/**
- * Answers true unless the feature type is 'transcript' or 'exon' (or a
- * sub-type in the Sequence Ontology). These features are only retrieved in
- * order to identify the exon sequence loci, and are redundant information on
- * the exon sequence itself.
+ * Answers true unless the feature type is 'transcript' (or a sub-type in the
+ * Sequence Ontology).
*/
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- SequenceOntology so = SequenceOntology.getInstance();
- String type = sf.getType();
-
- if (isTranscript(type) || so.isA(type, SequenceOntology.EXON))
+ if (isTranscript(sf.getType()))
{
return false;
}
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.EXON))
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.EXON))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))
return false;
}
+ @Override
+ protected List<String> getCrossReferenceDatabases()
+ {
+ return CROSS_REFERENCES;
+ // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
+ // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
+ }
+
}