package jalview.ext.ensembl;

import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;

import java.util.List;

import com.stevesoft.pat.Regex;

public class EnsemblCdna extends EnsemblSeqProxy
{
  // TODO modify to accept other species e.g. ENSMUSPnnn
  private static final Regex ACCESSION_REGEX = new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
  
  /*
   * 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 };

  public EnsemblCdna()
  {
    super();
  }

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

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

  @Override
  public Regex getAccessionValidator()
  {
    return ACCESSION_REGEX;
  }

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

  /**
   * Answers true unless the feature type is 'transcript' (or a sub-type in the
   * Sequence Ontology).
   */
  @Override
  protected boolean retainFeature(SequenceFeature sf, String accessionId)
  {
    if (isTranscript(sf.getType()))
    {
      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 (SequenceOntologyFactory.getInstance().isA(sf.getType(),
            SequenceOntologyI.EXON))
    {
      String parentFeature = (String) sf.getValue(PARENT);
      if (("transcript:" + accId).equals(parentFeature))
      {
        return true;
      }
    }
    return false;
  }

  @Override
  protected List<String> getCrossReferenceDatabases()
  {
    return super.getCrossReferenceDatabases();
    // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
    // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
  }

}