package jalview.ext.ensembl;

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

import com.stevesoft.pat.Regex;

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

  public EnsemblCdna()
  {
    super();
  }

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

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

  @Override
  public Regex getAccessionValidator()
  {
    return new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
  }

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

  /**
   * 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.
   */
  @Override
  protected boolean retainFeature(SequenceFeature sf, String accessionId)
  {
    SequenceOntology so = SequenceOntology.getInstance();
    String type = sf.getType();

    if (isTranscript(type) || so.isA(type, SequenceOntology.EXON))
    {
      return false;
    }
    return featureMayBelong(sf, accessionId);
  }

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

}