/**
* Returns the value that corresponds to a given implementation calculator class.
*
* @param clazz the target class.
* @throws IllegalArgumentException if {@code clazz} is {@code null} or if it is abstract.
* @return never {@code null}.
*/
public static AFCalculatorImplementation fromCalculatorClass(
final Class<? extends AFCalculator> clazz) {
Utils.nonNull(clazz, "input class cannot be null");
Utils.validateArg(
!Modifier.isAbstract(clazz.getModifiers()),
"class " + clazz.getCanonicalName() + " should not be abstract");
// Using iteration instead of a static map to avoid static state.
for (final AFCalculatorImplementation impl : AFCalculatorImplementation.values()) {
if (clazz.equals(impl.newInstance().getClass())) {
return impl;
}
}
throw new IllegalArgumentException(
"Attempt to retrieve AFCalculatorImplementation instance from a non-registered calculator class "
+ clazz.getName());
}
/**
* Returns the best (fastest) model give the required ploidy and alternative allele count.
*
* @param requiredPloidy required ploidy
* @param requiredAlternativeAlleleCount required alternative allele count.
* @param preferred a preferred mode if any. A {@code null} indicate that we should be try to use
* the default instead.
* @return never {@code null}
*/
public static AFCalculatorImplementation bestValue(
final int requiredPloidy,
final int requiredAlternativeAlleleCount,
final AFCalculatorImplementation preferred) {
final AFCalculatorImplementation preferredValue = preferred == null ? DEFAULT : preferred;
if (preferredValue.usableForParams(requiredPloidy, requiredAlternativeAlleleCount)) {
return preferredValue;
}
if (EXACT_INDEPENDENT.usableForParams(requiredPloidy, requiredAlternativeAlleleCount)) {
return EXACT_INDEPENDENT;
}
if (EXACT_REFERENCE.usableForParams(
requiredPloidy,
requiredAlternativeAlleleCount)) { // TODO: this seems to be dead code. EXACT_REFERENCE will
// always lose to EXACT_INDEPENDENT.
return EXACT_REFERENCE;
}
return EXACT_GENERAL_PLOIDY;
}