/**
* Helper method that can be used to dynamically figure out enumeration type of given {@link
* EnumSet}, without having access to its declaration. Code is needed to work around design flaw
* in JDK.
*
* @since 1.5
*/
public static Class<? extends Enum<?>> findEnumType(EnumSet<?> s) {
// First things first: if not empty, easy to determine
if (!s.isEmpty()) {
return findEnumType(s.iterator().next());
}
// Otherwise need to locate using an internal field
return EnumTypeLocator.instance.enumTypeFor(s);
}
/**
* the actual constructor. Private access only
*
* @param source source
* @param contig the contig
* @param start the start base (one based)
* @param stop the stop reference base (one based)
* @param alleles alleles
* @param genotypes genotypes map
* @param log10PError qual
* @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes attributes
* @param referenceBaseForIndel padded reference base
* @param validationToPerform set of validation steps to take
*/
protected VariantContext(
String source,
String ID,
String contig,
long start,
long stop,
Collection<Allele> alleles,
GenotypesContext genotypes,
double log10PError,
Set<String> filters,
Map<String, Object> attributes,
Byte referenceBaseForIndel,
EnumSet<Validation> validationToPerform) {
if (contig == null) {
throw new IllegalArgumentException("Contig cannot be null");
}
this.contig = contig;
this.start = start;
this.stop = stop;
// intern for efficiency. equals calls will generate NPE if ID is inappropriately passed in as
// null
if (ID == null || ID.equals(""))
throw new IllegalArgumentException("ID field cannot be the null or the empty string");
this.ID = ID.equals(VCFConstants.EMPTY_ID_FIELD) ? VCFConstants.EMPTY_ID_FIELD : ID;
this.commonInfo = new CommonInfo(source, log10PError, filters, attributes);
REFERENCE_BASE_FOR_INDEL = referenceBaseForIndel;
// todo -- remove me when this check is no longer necessary
if (this.commonInfo.hasAttribute(ID_KEY))
throw new IllegalArgumentException(
"Trying to create a VariantContext with a ID key. Please use provided constructor argument ID");
if (alleles == null) {
throw new IllegalArgumentException("Alleles cannot be null");
}
// we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
this.alleles = makeAlleles(alleles);
if (genotypes == null || genotypes == NO_GENOTYPES) {
this.genotypes = NO_GENOTYPES;
} else {
this.genotypes = genotypes.immutable();
}
// cache the REF and ALT alleles
int nAlleles = alleles.size();
for (Allele a : alleles) {
if (a.isReference()) {
REF = a;
} else if (nAlleles == 2) { // only cache ALT when biallelic
ALT = a;
}
}
if (!validationToPerform.isEmpty()) {
validate(validationToPerform);
}
}
/**
* Checks a function for RESTFful annotations.
*
* @return {@code true} if module contains relevant annotations
* @throws QueryException query exception
*/
boolean analyze() throws QueryException {
// parse all annotations
final EnumSet<HTTPMethod> mth = EnumSet.noneOf(HTTPMethod.class);
final boolean[] declared = new boolean[function.args.length];
boolean found = false;
final int as = function.ann.size();
for (int a = 0; a < as; a++) {
final QNm name = function.ann.names[a];
final Value value = function.ann.values[a];
final byte[] local = name.local();
final byte[] uri = name.uri();
final boolean rexq = eq(uri, QueryText.RESTXQURI);
if (rexq) {
if (eq(PATH, local)) {
// annotation "path"
if (path != null) error(ANN_TWICE, "%", name.string());
path = new RestXqPath(toString(value, name));
for (final String s : path) {
if (s.trim().startsWith("{")) checkVariable(s, AtomType.AAT, declared);
}
} else if (eq(CONSUMES, local)) {
// annotation "consumes"
strings(value, name, consumes);
} else if (eq(PRODUCES, local)) {
// annotation "produces"
strings(value, name, produces);
} else if (eq(QUERY_PARAM, local)) {
// annotation "query-param"
queryParams.add(param(value, name, declared));
} else if (eq(FORM_PARAM, local)) {
// annotation "form-param"
formParams.add(param(value, name, declared));
} else if (eq(HEADER_PARAM, local)) {
// annotation "header-param"
headerParams.add(param(value, name, declared));
} else if (eq(COOKIE_PARAM, local)) {
// annotation "cookie-param"
cookieParams.add(param(value, name, declared));
} else {
// method annotations
final HTTPMethod m = HTTPMethod.get(string(local));
if (m == null) error(ANN_UNKNOWN, "%", name.string());
if (!value.isEmpty()) {
// remember post/put variable
if (requestBody != null) error(ANN_TWICE, "%", name.string());
if (m != POST && m != PUT) error(METHOD_VALUE, m);
requestBody = checkVariable(toString(value, name), declared);
}
if (mth.contains(m)) error(ANN_TWICE, "%", name.string());
mth.add(m);
}
} else if (eq(uri, QueryText.OUTPUTURI)) {
// serialization parameters
final String key = string(local);
final String val = toString(value, name);
if (output.get(key) == null) error(UNKNOWN_SER, key);
output.set(key, val);
}
found |= rexq;
}
if (!mth.isEmpty()) methods = mth;
if (found) {
if (path == null) error(ANN_MISSING, PATH);
for (int i = 0; i < declared.length; i++)
if (!declared[i]) error(VAR_UNDEFINED, function.args[i].name.string());
}
return found;
}
