Beispiel #1
0
 private void parseEffectName(String effectName) {
   try {
     effect = EffectType.valueOf(effectName);
   } catch (IllegalArgumentException e) {
     parseError(String.format("%s is not a recognized effect type", effectName));
   }
 }
Beispiel #2
0
    public Map<String, Object> getAnnotations() {
      Map<String, Object> annotations =
          new LinkedHashMap<String, Object>(Utils.optimumHashSize(InfoFieldKey.values().length));

      addAnnotation(annotations, InfoFieldKey.EFFECT_KEY.getKeyName(), effect.toString());
      addAnnotation(annotations, InfoFieldKey.IMPACT_KEY.getKeyName(), impact.toString());
      addAnnotation(
          annotations, InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName(), functionalClass.toString());
      addAnnotation(annotations, InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), codonChange);
      addAnnotation(annotations, InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), aminoAcidChange);
      addAnnotation(annotations, InfoFieldKey.GENE_NAME_KEY.getKeyName(), geneName);
      addAnnotation(annotations, InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), geneBiotype);
      addAnnotation(annotations, InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), transcriptID);
      addAnnotation(annotations, InfoFieldKey.EXON_ID_KEY.getKeyName(), exonID);

      return annotations;
    }