/**
* according to the order of @param vcfSampleNames, put phenotypes to @param
* phenotypeInOrder
* @param imputePhenotype: if true, we will impute phenotpye to the average
* for
* those have genotype but no phenotype;
* if false, we will drop those samples
*/
void rearrange(const std::map<std::string, double>& phenotype,
const std::vector<std::string>& vcfSampleNames,
std::vector<std::string>* vcfSampleToDrop,
std::vector<std::string>* phenotypeNameInOrder,
std::vector<double>* phenotypeValueInOrder,
bool imputePhenotype) {
vcfSampleToDrop->clear();
phenotypeNameInOrder->clear();
phenotypeValueInOrder->clear();
if (!isUnique(vcfSampleNames)) {
logger->error("VCF file have duplicated sample id. Quitting!");
abort();
}
if (!imputePhenotype) {
for (size_t i = 0; i < vcfSampleNames.size(); i++) {
if (phenotype.count(vcfSampleNames[i]) == 0) {
vcfSampleToDrop->push_back(vcfSampleNames[i]);
} else {
phenotypeNameInOrder->push_back(
phenotype.find(vcfSampleNames[i])->first);
phenotypeValueInOrder->push_back(
phenotype.find(vcfSampleNames[i])->second);
}
}
} else {
double sum = 0.0;
int nMissingPheno = 0;
for (size_t i = 0; i < vcfSampleNames.size(); i++) {
if (phenotype.count(vcfSampleNames[i]) == 0) {
++nMissingPheno;
} else {
sum += phenotype.find(vcfSampleNames[i])->second;
}
}
double avg = sum / (vcfSampleNames.size() - nMissingPheno);
for (size_t i = 0; i < vcfSampleNames.size(); i++) {
if (phenotype.count(vcfSampleNames[i]) == 0) {
logger->info("Impute phenotype of sample [ %s ] to [ %g ]",
vcfSampleNames[i].c_str(), avg);
phenotypeNameInOrder->push_back(vcfSampleNames[i]);
phenotypeValueInOrder->push_back(avg);
} else {
phenotypeNameInOrder->push_back(
phenotype.find(vcfSampleNames[i])->first);
phenotypeValueInOrder->push_back(
phenotype.find(vcfSampleNames[i])->second);
}
}
if (nMissingPheno)
logger->warn(
"Impute [ %d ] missing phenotypes for samples with genotypes but "
"lacks phenotypes",
nMissingPheno);
}
}
int _loadCovariate(const std::string& fn,
const std::vector<std::string>& includedSample,
const std::string& covNameToUse,
DataLoader::HandleMissingCov handleMissingCov,
SimpleMatrix* covariate, std::vector<std::string>* colNames,
std::set<std::string>* sampleToDrop) {
std::vector<std::string> fd;
if (covNameToUse.size()) {
stringTokenize(covNameToUse, ',', &fd);
}
if (!isUnique(fd)) {
logger->error("Remove duplicated covariates in the model before continue");
return -1;
}
if (!isUnique(includedSample)) {
logger->error("Unable to include duplicated samples");
return -1;
}
return _loadCovariate(fn, includedSample, fd, handleMissingCov, covariate,
colNames, sampleToDrop);
}
void SecurityOrigin::grantLoadLocalResources()
{
// Granting privileges to some, but not all, documents in a SecurityOrigin
// is a security hazard because the documents without the privilege can
// obtain the privilege by injecting script into the documents that have
// been granted the privilege.
//
// To be backwards compatible with older versions of WebKit, we also use
// this function to grant the ability to load local resources to documents
// loaded with SubstituteData.
ASSERT(isUnique() || SecurityPolicy::allowSubstituteDataAccessToLocal());
m_canLoadLocalResources = true;
}
bool SecurityOrigin::isThirdParty(const SecurityOrigin* child) const
{
if (child->m_universalAccess)
return false;
if (this == child)
return false;
if (isUnique() || child->isUnique())
return true;
return !isSameSchemeHostPort(child);
}
bool AddDomObject::isUnique(QObject * object, QObject * ownerObject, const QString & name ) const
{
if (!object)
return true;
if (object->objectName() == name && ownerObject!=object)
return false;
for (int i = 0;i < object->children().size();i++)
if (!isUnique(object->children()[i], ownerObject, name))
return false;
return true;
}
bool SecurityOrigin::isPotentiallyTrustworthy() const
{
ASSERT(m_protocol != "data");
if (isUnique())
return m_isUniqueOriginPotentiallyTrustworthy;
if (SchemeRegistry::shouldTreatURLSchemeAsSecure(m_protocol) || isLocal() || isLocalhost())
return true;
if (SecurityPolicy::isOriginWhiteListedTrustworthy(*this))
return true;
return false;
}
void SortedSetContainer<T>::add(const T& elem)
{
string m;
m = "SortedSetContainer object must consist of unique elements.\n";
if(isUnique(elem))
{
this->list.push_back(elem);
++this->size;
sort(this->list.begin(), this->list.end());
}
else
throw m;
}
int main(int argc, char *argv[]){
// Firstly check the arguments
if(argc != 2){
printf("Invalid arguments.n\n");
printf("Usage: %s test_stringn\n",argv[0]);
return 1;
}
// Use the argument as test string
bool testret = isUnique(argv[1]);
if(testret == true)
printf("%s: is unique.n\n",argv[1]);
else
printf("%s: is not unique.n\n",argv[1]);
return 0;
}
TEST(SetManagerTest, isUnique)
{
doim::LocationSetSPtr locations;
ASSERT_TRUE(locations->isUnique());
locations = doim::LocationSet::make();
auto location = doim::Location::obtain(nullptr, "/isUnique");
locations->insert(location);
ASSERT_FALSE(locations->isUnique());
locations = doim::LocationSet::unique(locations);
ASSERT_TRUE(location->isUnique());
}
SortedSetContainer<T>::SortedSetContainer(const vector<T>& orig)
{
this->size = 0;
// setVector function updates the size inside
for (int i = 0; i < orig.size(); i++)
{
if(isUnique(orig.at(i)))
{
this->list.push_back(orig.at(i));
++this->size;
}
}
sort(this->list.begin(), this->list.end());
listIterator = 0;
}
std::string ResourceURIFactory::makeUniqueURI(const std::string &uri)
{
std::lock_guard<std::mutex> lock(m_lock);
if (isUnique(uri))
{
updateUri(uri);
return uri;
}
std::ostringstream os;
os << uri;
if (!uri.empty() && '/' != uri[uri.length() - 1])
os << '/';
os << m_id++;
updateUri(os.str());
return os.str();
}
bool SecurityOrigin::canRequest(const KUrl& url) const
{
if (isUnique())
return false;
WTF::RefPtr<SecurityOrigin> targetOrigin = SecurityOrigin::create(url);
if (targetOrigin->isUnique())
return false;
// We call isSameSchemeHostPort here instead of canAccess because we want
// to ignore document.domain effects.
if (isSameSchemeHostPort(targetOrigin.get()))
return true;
return false;
}
bool SecurityOrigin::canAccess(const SecurityOrigin* other) const
{
if (m_universalAccess)
return true;
if (this == other)
return true;
if (isUnique() || other->isUnique())
return false;
// Here are two cases where we should permit access:
//
// 1) Neither document has set document.domain. In this case, we insist
// that the scheme, host, and port of the URLs match.
//
// 2) Both documents have set document.domain. In this case, we insist
// that the documents have set document.domain to the same value and
// that the scheme of the URLs match.
//
// This matches the behavior of Firefox 2 and Internet Explorer 6.
//
// Internet Explorer 7 and Opera 9 are more strict in that they require
// the port numbers to match when both pages have document.domain set.
//
// FIXME: Evaluate whether we can tighten this policy to require matched
// port numbers.
//
// Opera 9 allows access when only one page has set document.domain, but
// this is a security vulnerability.
bool canAccess = false;
if (m_protocol == other->m_protocol) {
if (!m_domainWasSetInDOM && !other->m_domainWasSetInDOM) {
if (m_host == other->m_host && m_port == other->m_port)
canAccess = true;
} else if (m_domainWasSetInDOM && other->m_domainWasSetInDOM) {
if (m_domain == other->m_domain)
canAccess = true;
}
}
if (canAccess && isLocal())
canAccess = passesFileCheck(other);
return canAccess;
}
bool SecurityOrigin::canAccessStorage(const SecurityOrigin* topOrigin) const
{
if (isUnique())
return false;
// FIXME: This check should be replaced with an ASSERT once we can guarantee that topOrigin is not null.
if (!topOrigin)
return true;
if (m_storageBlockingPolicy == BlockAllStorage || topOrigin->m_storageBlockingPolicy == BlockAllStorage)
return false;
if ((m_storageBlockingPolicy == BlockThirdPartyStorage || topOrigin->m_storageBlockingPolicy == BlockThirdPartyStorage) && topOrigin->isThirdParty(this))
return false;
return true;
}
bool Func::isNameBindingImmutable(const Unit* fromUnit) const {
if (RuntimeOption::EvalJitEnableRenameFunction ||
m_attrs & AttrDynamicInvoke) {
return false;
}
if (isBuiltin()) {
return true;
}
if (isUnique() && RuntimeOption::RepoAuthoritative) {
return true;
}
// Defined at top level, in the same unit as the caller. This precludes
// conditionally defined functions and cross-module calls -- both phenomena
// can change name->Func mappings during the lifetime of a TC.
return top() && (fromUnit == m_unit);
}
/*!
Mark unrequired part of the name with '[' and ']'
characters.
*/
inline void
markUnrequiredPartOfTheName(
//! Name to mark unrequired part.
QString & name,
//! All available names.
const QStringList & rawNames )
{
int index = 1;
while( !isUnique( name.left( index ), rawNames )
&& index < name.length() )
++index;
if( index != name.length() )
{
name.insert( index, QLatin1Char( '[' ) );
name.append( QLatin1Char( ']' ) );
}
} // markUnrequiredPartOfTheName
/*!
Returns a deep-copied clone of the QMofStructuralFeature.
*/
QModelingElement *QMofStructuralFeature::clone() const
{
QMofStructuralFeature *c = new QMofStructuralFeature;
c->asQModelingObject()->setObjectName(this->asQModelingObject()->objectName());
c->asQModelingObject()->setProperty("role", this->asQModelingObject()->property("role"));
foreach (QMofComment *element, ownedComments())
c->addOwnedComment(dynamic_cast<QMofComment *>(element->clone()));
c->setName(name());
c->setVisibility(visibility());
c->setLeaf(isLeaf());
c->setStatic(isStatic());
c->setOrdered(isOrdered());
c->setUnique(isUnique());
if (lowerValue())
c->setLowerValue(dynamic_cast<QMofValueSpecification *>(lowerValue()->clone()));
if (upperValue())
c->setUpperValue(dynamic_cast<QMofValueSpecification *>(upperValue()->clone()));
c->setReadOnly(isReadOnly());
return c;
}
const char *
shMonster::an ()
{
char *buf = GetBuf ();
if (!Hero.canSee (this) and !Hero.canHearThoughts (this)) {
strncpy (buf, hasMind () ? "someone" : "something", SHBUFLEN);
} else if (isUnique ()) {
return the ();
} else if (Hero.is (kXenosHunter) and isXenos ()) {
snprintf (buf, SHBUFLEN, "a xenos scum");
} else if (Hero.is (kXenosHunter) and isHeretic ()) {
snprintf (buf, SHBUFLEN, "a heretic");
} else {
snprintf (buf, SHBUFLEN,
isvowel (myIlk ()->mName[0]) ? "an %s" : "a %s",
myIlk ()->mName);
}
return buf;
}
void UmlRelation::gen_uml_decl()
{
if (isClassMember())
fw.write("static, ");
write(visibility());
writeq(roleName());
fw.write(" : ");
roleType()->write();
QByteArray s;
s = defaultValue();
if (!s.isEmpty()) {
if (s[0] != '=')
fw.write(" = ");
writeq(s);
}
s = multiplicity();
if (!s.isEmpty()) {
fw.write(", multiplicity : ");
writeq(s);
}
if (isDerived())
fw.write((isDerivedUnion()) ? ", derived union" : ", derived");
if (isReadOnly())
fw.write(", read only");
if (isOrdered())
fw.write(", ordered");
if (isUnique())
fw.write(", unique");
}
bool SecurityOrigin::isSameSchemeHostPort(const SecurityOrigin* other) const
{
if (this == other)
return true;
if (isUnique() || other->isUnique())
return false;
if (m_host != other->m_host)
return false;
if (m_protocol != other->m_protocol)
return false;
if (m_port != other->m_port)
return false;
if (isLocal() && !passesFileCheck(other))
return false;
return true;
}
bool SecurityOrigin::canRequest(const KURL& url) const
{
if (m_universalAccess)
return true;
if (isUnique())
return false;
RefPtr<SecurityOrigin> targetOrigin = SecurityOrigin::create(url);
if (targetOrigin->isUnique())
return false;
// We call isSameSchemeHostPort here instead of canAccess because we want
// to ignore document.domain effects.
if (isSameSchemeHostPort(targetOrigin.get()))
return true;
if (SecurityPolicy::isAccessWhiteListed(this, targetOrigin.get()))
return true;
return false;
}
void UmlPinParameter::html(Q3CString pfix, unsigned int rank, unsigned int level) {
if (isUnique()) {
if (isException())
fw.write("<p>Unique, exception</p>");
else
fw.write("<p>Read only</p>");
}
else if (isException())
fw.write("<p>Exception</p>");
fw.write("<p>Direction : ");
write(direction());
fw.write("</p>");
if (effect() != noEffect) {
fw.write("<p>Effect : ");
write(effect());
fw.write("</p>");
}
html_internal(pfix, rank, level);
}
QString SecurityOrigin::toString() const
{
if (isEmpty())
return "null";
if (isUnique())
return "null";
if (m_protocol == "file")
return QString("file://");
QString result;
result += m_protocol;
result += "://";
result += m_host;
if (m_port) {
result += ":";
result += QString::number(m_port);
}
return result;
}
int main()
{
char str[1000];
int len, flag;
while (gets(str)) {
len = strlen(str);
flag = isUnique(str, len);
if (flag)
printf("unique!\n");
else
printf("repeat!\n");
flag = isUniqueBitmap(str, len);
if (flag)
printf("unique!\n");
else
printf("repeat!\n");
}
return 0;
}
String SecurityOrigin::toString() const
{
if (isUnique())
return "null";
if (m_protocol == "file") {
if (m_enforceFilePathSeparation)
return "null";
return "file://";
}
StringBuilder result;
result.reserveCapacity(m_protocol.length() + m_host.length() + 10);
result.append(m_protocol);
result.append("://");
result.append(m_host);
if (m_port) {
result.append(":");
result.append(String::number(m_port));
}
return result.toString();
}
void verifySolution()
{
CPPUNIT_ASSERT(isUnique(std::string("sdfhgf")) == false);
CPPUNIT_ASSERT(isUnique(std::string("abcdef")) == true);
CPPUNIT_ASSERT(isUnique(std::string("aaaaaaaa")) == false);
CPPUNIT_ASSERT(isUnique(std::string("$5^^jdfsg:")) == false);
CPPUNIT_ASSERT(isUnique(std::string(" ")) == false);
CPPUNIT_ASSERT(isUnique(std::string("asd jbv ert")) == false);
auto start = std::chrono::steady_clock::now();
CPPUNIT_ASSERT(isUnique(std::string("1234567890 sdfgpo")) == true);
auto end = std::chrono::steady_clock::now();
auto diff = end - start;
std::cout << std::endl;
std::cout << "Microseconds: " << std::chrono::duration <double,std::micro> (diff).count() << " us" << std::endl;
}
PassRefPtr<UniqueElementData> ElementData::makeUniqueCopy() const
{
if (isUnique())
return adoptRef(new UniqueElementData(toUniqueElementData(*this)));
return adoptRef(new UniqueElementData(toShareableElementData(*this)));
}
bool DDLIndexPopulator::makeIndexStructs( )
{
erydbSelectExecutionPlan csep;
makeCsep(csep);
ResourceManager rm;
if (! fEC)
{
fEC = DistributedEngineComm::instance(rm);
fEC->Open();
}
SJLP jbl = joblist::JobListFactory::makeJobList(&csep, rm);
boost::shared_ptr<erydbSystemCatalog> csc = erydbSystemCatalog::makeerydbSystemCatalog( fSessionID );
csc->identity(erydbSystemCatalog::EC);
jbl->putEngineComm(fEC);
/*
ResultManager * result = jbl->GetResultManager();
result->setRunning(1);
jbl->Execute(); */
jbl->doQuery();
erydbSystemCatalog::TableName tableName;
tableName.schema = fTable.fSchema;
tableName.table = fTable.fName;
erydbSystemCatalog::OID tableOid = (csc->tableRID ( tableName )).objnum;
erydbSystemCatalog::NJLSysDataList sysDataList;
for (;;)
{
TableBand band;
band = jbl->projectTable(tableOid);
if (band.getRowCount() == 0)
{
// No more bands, table is done
break;
}
band.convertToSysDataList(sysDataList, csc);
break;
}
//size_t cnt = fColNames.size();
size_t i = 0;
vector<ColumnResult*>::const_iterator it;
vector<int>::const_iterator oid_iter;
for (it = sysDataList.begin(); it != sysDataList.end(); it++)
{
if (isUnique())
fUniqueColResultList.push_back(*it);
for ( oid_iter = fOidList.begin(); oid_iter != fOidList.end(); oid_iter++ )
{
if ( (*it)->ColumnOID() == *oid_iter )
{
erydbSystemCatalog::ColType coltype = makeIdxStruct(*it, fColNames.size(), csc);
addColumnData(*it, coltype, i);
}
}
i++;
}
return (fIdxValueList.size() && NO_ERROR == fResult.result );
}
void UmlRelation::write_relation_as_attribute(FileOut & out) {
UmlRelation * first = side(TRUE);
Q3CString s;
UmlClass * base;
if ((first->parent()->stereotype() == "stereotype") &&
(first->roleType()->stereotype() == "metaclass")) {
if (this != first)
return;
base = first->roleType();
s = "base_" + base->name();
}
else {
base = 0;
switch (_lang) {
case Uml:
s = roleName();
break;
case Cpp:
if (cppDecl().isEmpty())
return;
s = true_name(roleName(), cppDecl());
break;
default: // Java
if (javaDecl().isEmpty())
return;
s = true_name(roleName(), javaDecl());
}
}
out.indent();
out << "<ownedAttribute xmi:type=\"uml:Property\" name=\"" << s << '"';
out.id(this);
if (base != 0)
out.ref(first, "association", "EXT_");
else {
write_visibility(out);
write_scope(out);
if (isReadOnly())
out << " isReadOnly=\"true\"";
if (isDerived()) {
out << " isDerived=\"true\"";
if (isDerivedUnion())
out << " isDerivedUnion=\"true\"";
}
if (isOrdered())
out << " isOrdered=\"true\"";
if (isUnique())
out << " isUnique=\"true\"";
if (first->_assoc_class != 0)
out.ref(first->_assoc_class, "association");
else
out.ref(first, "association", "ASSOC_");
out << " aggregation=\"";
if (this == first) {
parent()->memo_relation(this);
if (_gen_eclipse) {
switch (relationKind()) {
case anAggregation:
case aDirectionalAggregation:
out << "shared";
break;
case anAggregationByValue:
case aDirectionalAggregationByValue:
out << "composite";
break;
default:
out << "none";
}
}
else
out << "none";
}
else if (_gen_eclipse)
out << "none";
else {
switch (relationKind()) {
case anAggregation:
case aDirectionalAggregation:
out << "shared";
break;
case anAggregationByValue:
case aDirectionalAggregationByValue:
out << "composite";
break;
default:
out << "none";
}
}
out << '"';
}
out << ">\n";
out.indent(+1);
out.indent();
out << "<type xmi:type=\"uml:Class\"";
if (base != 0) {
if (! base->propertyValue("metaclassPath", s))
s = (_uml_20) ? "http://schema.omg.org/spec/UML/2.0/uml.xml"
: "http://schema.omg.org/spec/UML/2.1/uml.xml";
out << " href=\"" << s << '#' << base->name() << '"';
}
else
out.idref(roleType());
out << "/>\n";
write_multiplicity(out, multiplicity(), this);
write_default_value(out, defaultValue(), this);
write_constraint(out);
write_annotation(out);
write_description_properties(out);
out.indent(-1);
out.indent();
out << "</ownedAttribute>\n";
unload();
}
/**
* Rearrange phenotype rows in the order given by @param names
* @param droppedNamed will store sample names who are in @param names but are
* not listed in phenotype.
*
* NOTE: @param names usually is the VCF sample names
* NOTE: Current phenotype data may have NAN values
*/
int DataLoader::arrangePhenotype(const std::vector<std::string>& names,
std::vector<std::string>* droppedNames) {
if (!isUnique(names)) {
logger->error("VCF file have duplicated sample ids. Quitting!");
abort();
}
// not impute phentoype
if (!FLAG_imputePheno) {
std::vector<std::string> noGenotypeSamples =
setSubtract(phenotype.getRowName(), names);
*droppedNames = setSubtract(names, phenotype.getRowName());
const int n = noGenotypeSamples.size();
if (n) {
logger->info("Discard [ %d ] samples as they do not have genotypes", n);
}
phenotype.dropRow(noGenotypeSamples);
phenotype.reorderRow(names);
// TODO: print some info here
return 0;
}
// imputation
std::vector<std::string> noPhenotypeSamples =
setSubtract(names, phenotype.getRowName());
const int n = noPhenotypeSamples.size();
if (n) {
logger->info(
"Impute [ %d ] phenotypes of [ %d ] samples to the mean values",
phenotype.ncol(), n);
phenotype.addRow(noPhenotypeSamples, NAN);
phenotype.imputeMissingToMeanByCol();
}
phenotype.reorderRow(names);
return 0;
#if 0
// phenotype names (vcf sample names) arranged in the same order as in VCF
std::vector<std::string> phenotypeNameInOrder;
std::vector<double>
phenotypeValueInOrder; // phenotype arranged in the same order as in VCF
// TODO: better support for multiple phenotypes
std::map<std::string, double> phenoDict;
for (int i = 0; i < phenotype.nrow(); ++i) {
phenoDict[phenotype.getRowName()[i]] = phenotype[i][0];
}
rearrange(phenoDict, names, droppedNames, &phenotypeNameInOrder,
&phenotypeValueInOrder, FLAG_imputePheno);
// rearrange(phenoDict, vcfSampleNames, &vcfSampleToDrop,
// &phenotypeNameInOrder,
// &phenotypeInOrder, FLAG_imputePheno);
phenotype.resize(phenotypeNameInOrder.size(), 1);
phenotype.setRowName(phenotypeNameInOrder);
phenotype.setCol(0, phenotypeValueInOrder);
if (phenotypeValueInOrder.size() != phenoDict.size()) {
logger->warn(
"Drop [ %d ] samples from phenotype file due to missing genotypes from "
"VCF files",
(int)(phenoDict.size() - phenotypeValueInOrder.size()));
// We may output these samples by comparing keys of phenotype and
// phenotypeNameInOrder
}
#endif
return 0;
}
