package jalview.ext.ensembl;

import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntology;

public class EnsemblGenome extends EnsemblSeqProxy
{
  /*
   * fetch transcript features on genomic sequence (to identify the transcript 
   * regions) and cds, exon and variation features (to retain)
   */
  private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
      EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
      EnsemblFeatureType.cds, EnsemblFeatureType.variation };

  public EnsemblGenome()
  {
    super();
  }

  @Override
  public String getDbName()
  {
    return "ENSEMBL (Genome)";
  }

  @Override
  protected EnsemblSeqType getSourceEnsemblType()
  {
    return EnsemblSeqType.GENOMIC;
  }

  @Override
  protected EnsemblFeatureType[] getFeaturesToFetch()
  {
    return FEATURES_TO_FETCH;
  }

  /**
   * Answers true unless the feature type is 'transcript' (or a sub-type of
   * transcript in the Sequence Ontology). Transcript features are only
   * retrieved in order to identify the transcript sequence range, and are
   * redundant information on the transcript sequence itself.
   */
  @Override
  protected boolean retainFeature(String type)
  {
    return !SequenceOntology.getInstance().isA(type,
            SequenceOntology.TRANSCRIPT);
  }

  /**
   * Answers true if the sequence feature type is 'transcript' (or a subtype of
   * transcript in the Sequence Ontology), and the ID of the feature is the
   * transcript we are retrieving
   */
  @Override
  protected boolean identifiesSequence(SequenceFeature sf, String accId)
  {
    if (SequenceOntology.getInstance().isA(sf.getType(),
            SequenceOntology.TRANSCRIPT))
    {
      String parentFeature = (String) sf.getValue("ID");
      if (("transcript:" + accId).equals(parentFeature))
      {
        return true;
      }
    }
    return false;
  }

}