private void parseEffectName(String effectName) {
try {
effect = EffectType.valueOf(effectName);
} catch (IllegalArgumentException e) {
parseError(String.format("%s is not a recognized effect type", effectName));
}
}
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;
}
