Annotation class returns undocumented nulls

[julesjacobsen]

Annotation.getPutativeImpact() and Annotation.getMostPathogenicVarType() can both return a null, yet there are no @Nullable annotations on these methods to enable code inspection tools to make the end-user aware of this hidden gem of excitement.

These stem from the effects field being an empty list:

public VariantEffect getMostPathogenicVarType() {
    return this.effects.isEmpty() ? null : (VariantEffect)this.effects.iterator().next();
}

public PutativeImpact getPutativeImpact() {
    if (this.effects.isEmpty()) {
        return null;
    } else {
        VariantEffect worst = (VariantEffect)this.effects.iterator().next();
        UnmodifiableIterator var2 = this.effects.iterator();
...
}

could these be changed to return the lowest effect/impact:

public VariantEffect getMostPathogenicVarType() {
    return this.effects.isEmpty() ? VariantEffect.SEQUENCE_VARIANT : (VariantEffect) this.effects.iterator().next();
}

public PutativeImpact getPutativeImpact() {
    if (this.effects.isEmpty()) {
        return PutativeImpact.MODIFIER;
    } else {
        VariantEffect worst = (VariantEffect) this.effects.iterator().next();
        UnmodifiableIterator var2 = this.effects.iterator();
...
}

Alternatively the EMPTY_VARIANT_EFFECTS field could be changed to SEQUENCE_VARIANT_EFFECT which is assigned in the constructor:

    private static final ImmutableSet<VariantEffect> EMPTY_VARIANT_EFFECTS = Sets.immutableEnumSet(EnumSet.noneOf(VariantEffect.class));

    this.effects = varTypes == null ? EMPTY_VARIANT_EFFECTS : Sets.immutableEnumSet(varTypes);

becomes:

    private static final ImmutableSet<VariantEffect> SEQUENCE_VARIANT_EFFECT = Sets.immutableEnumSet(VariantEffect.SEQUENCE_VARIANT));

    this.effects = (varTypes == null ||  varTypes.isEmpty()) ? SEQUENCE_VARIANT_EFFECT : Sets.immutableEnumSet(varTypes);

and then getMostPathogenicVarType() and getPutativeImpact() can be simplified:

public VariantEffect getMostPathogenicVarType() {
    return (VariantEffect) this.effects.iterator().next();
}

public PutativeImpact getPutativeImpact() {
    VariantEffect worst = (VariantEffect) this.effects.iterator().next();
    UnmodifiableIterator var2 = this.effects.iterator();
...
}