public boolean isHigherImpactThan(SnpEffEffect other) {
// If one effect is within a coding gene and the other is not, the effect that is
// within the coding gene has higher impact:
if (isCoding() && !other.isCoding()) {
return true;
} else if (!isCoding() && other.isCoding()) {
return false;
}
// Otherwise, both effects are either in or not in a coding gene, so we compare the impacts
// of the effects themselves. Effects with the same impact are tie-broken using the
// functional class of the effect:
if (impact.isHigherImpactThan(other.impact)) {
return true;
} else if (impact.isSameImpactAs(other.impact)) {
return functionalClass.isHigherPriorityThan(other.functionalClass);
}
return false;
}
