/*!
* \brief Read a float vector from a XML subtree.
* \param inIter XML iterator from which the float vector is read.
* \param ioContext Evolutionary context.
* \throw Beagle::IOException If a reading error occured (generally bad file format)!
*/
void GA::IntegerVector::readWithContext(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != "Genotype")) {
throw Beagle_IOExceptionNodeM(*inIter, "tag <Genotype> expected!");
}
std::string lGenotypeType = inIter->getAttribute("type");
if((lGenotypeType.empty() == false) && (lGenotypeType != getType())) {
std::ostringstream lOSS;
lOSS << "type given '" << lGenotypeType << "' mismatch type of the genotype '";
lOSS << getType() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
PACC::XML::ConstIterator lChild = inIter->getFirstChild();
if((!lChild) || (lChild->getType()!=PACC::XML::eString))
throw Beagle_IOExceptionNodeM(*lChild, "expected content for the float vector!");
clear();
std::istringstream lISS(lChild->getValue());
while(lISS.good()) {
int lValue=INT_MAX;
lISS >> lValue;
push_back(lValue);
if(lISS.good()==false) break;
int lDelim=lISS.get();
if((lISS.good()==false) || (lDelim==-1)) break;
}
Beagle_StackTraceEndM("void GA::IntegerVector::readWithContext(PACC::XML::ConstIterator,Context&)");
}
/*!
* \brief Read an ES vector from a XML subtree.
* \param inIter XML iterator from which the ES vector is read.
* \param ioContext Evolutionary context.
* \throw IOException If a reading error occured (generally bad file format)!
*/
void GA::ESVector::readWithContext(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != "Genotype")) {
throw Beagle_IOExceptionNodeM(*inIter, "tag <Genotype> expected!");
}
std::string lGenotypeType = inIter->getAttribute("type");
if((lGenotypeType.empty() == false) && (lGenotypeType != getType())) {
std::ostringstream lOSS;
lOSS << "type given '" << lGenotypeType << "' mismatch type of the genotype '";
lOSS << getType() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
PACC::XML::ConstIterator lChild = inIter->getFirstChild();
if((!lChild) || (lChild->getType()!=PACC::XML::eString)) {
throw Beagle_IOExceptionNodeM(*lChild, "expected content for the ES vector!");
}
clear();
std::istringstream lISS(lChild->getValue());
do {
char lC1='\0', lC2='\0', lC3='\0';
double lValue=DBL_MAX, lStrategy=DBL_MAX;
lISS >> lC1 >> lValue >> lC2 >> lStrategy >> lC3;
if((lC1!='(') || (lC2!=',') || (lC3!=')'))
throw Beagle_IOExceptionNodeM(*lChild, "bad format of ES vector!");
if((lValue==DBL_MAX) || (lStrategy==DBL_MAX))
throw Beagle_IOExceptionNodeM(*lChild, "bad format of ES vector!");
push_back(ESPair(lValue, lStrategy));
} while(lISS.get()==int('/'));
Beagle_StackTraceEndM("void GA::ESVector::readWithContext(PACC::XML::ConstIterator,Context&)");
}
/*!
* \brief Read object from XML using system.
* \param inIter XML iterator of input document.
* \param ioSystem A reference to the system.
* \throw SCHNAPS::Core::IOException if a wrong tag is encountered.
*/
void PrimitiveTree::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem) {
schnaps_StackTraceBeginM();
if (inIter) {
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
if (inIter->getValue() != getName()) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected, but ";
lOSS << "got tag <" << inIter->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
// Get size attribute and reserve size accordingly
std::string lSizeText = inIter->getAttribute("size");
if (lSizeText.empty() == false) {
reserve(str2uint(lSizeText));
}
PACC::XML::ConstIterator lChild = inIter->getFirstChild();
if ((!lChild) || (lChild->getType() != PACC::XML::eData)) {
throw schnaps_IOExceptionNodeM(*lChild, "expected a XML tag for the primitive tree!");
}
clear();
readSubTree(lChild, ioSystem);
}
schnaps_StackTraceEndM("void SCHNAPS::Core::PrimitiveTree::readWithSystem(PACC::XML::ConstIterator, SCHNAPS::Core::System&)");
}
void PopulationManager::readWithSystem(PACC::XML::ConstIterator inIter, SCHNAPS::Core::System& ioSystem) {
schnaps_StackTraceBeginM();
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
if (inIter->getValue() != getName()) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected, but ";
lOSS << "got tag <" << inIter->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
#ifdef SCHNAPS_FULL_DEBUG
printf("Reading population manager\n");
#endif
inIter = inIter->getFirstChild();
// read generator
mGenerator->read(inIter++);
// read population source
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
if (inIter->getValue() != "Population") {
std::ostringstream lOSS;
lOSS << "tag <Population> expected, but ";
lOSS << "got tag <" << inIter->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
for (PACC::XML::ConstIterator lChild = inIter->getFirstChild(); lChild; lChild++) {
if (lChild->getType() == PACC::XML::eData) {
if (lChild->getValue() != "SubPopulation") {
std::ostringstream lOSS;
lOSS << "tag <SubPopulation> expected, but ";
lOSS << "got tag <" << lChild->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*lChild, lOSS.str());
}
if (lChild->getAttribute("time").empty()) {
throw schnaps_IOExceptionNodeM(*lChild, "time attribute expected!");
}
if (lChild->getAttribute("profile").empty()) {
throw schnaps_IOExceptionNodeM(*lChild, "profile attribute expected!");
}
if (lChild->getAttribute("size").empty()) {
throw schnaps_IOExceptionNodeM(*lChild, "size attribute expected!");
}
this->insert(std::pair<unsigned long, Source>(SCHNAPS::str2uint(lChild->getAttribute("time")),
Source(lChild->getAttribute("profile"), SCHNAPS::str2uint(lChild->getAttribute("size")))));
}
}
schnaps_StackTraceEndM("void SCHNAPS::Simulation::PopulationManager::readWithSystem(PACC::XML::ConstIterator, SCHNAPS::Core::System&)");
}
/*!
* \brief Read the state of the quasi-random generator from a XML subtree.
* \param inIter XML iterator to read the mersenne twister randomizer from.
* \param ioSystem
*/
void QuasiRandom::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="QuasiRandom"))
throw Beagle_IOExceptionNodeM(*inIter, "tag <QuasiRandom> expected!");
PACC::XML::ConstIterator lChild = inIter->getFirstChild();
if(lChild) {
if(lChild->getType()!=PACC::XML::eString)
throw Beagle_IOExceptionNodeM(*lChild, "expected quasi-random state!");
setState(lChild->getValue());
} else reset(0);
Beagle_StackTraceEndM("void QuasiRandom::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)");
}
/*!
* \brief Read a Factory, obtain selection of default types for the different families.
* \param inIter Iterator to the XML node to read the Factory from.
* \param ioSystem System to use to read the type selector.
* \throw Beagle::IOException If the format is invalid.
*/
void Factory::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="Factory")) {
throw Beagle_IOExceptionNodeM(*inIter, "tag <Factory> expected!");
}
for(PACC::XML::ConstIterator lChild=inIter->getFirstChild(); lChild; ++lChild) {
if((lChild->getType()==PACC::XML::eData) && (lChild->getValue()=="Concept")) {
std::string lConceptName = lChild->getAttribute("name");
if(lConceptName.empty()) {
throw Beagle_IOExceptionNodeM(*lChild, "no name attribute given for current Concept tag!");
}
std::string lTypeName = lChild->getAttribute("type");
if(lTypeName.empty()) {
throw Beagle_IOExceptionNodeM(*lChild, "no type attribute given for current Concept tag!");
}
Factory::AllocatorMap::const_iterator lIterAllocMap = mAllocatorMap.find(lTypeName);
if(lIterAllocMap == mAllocatorMap.end()) {
std::ostringstream lOSS;
lOSS << "Type named '" << lTypeName;
lOSS << "' does not exists in the internal allocator map of the Factory; ";
lOSS << "could not associated to concept '" << lConceptName << "'.";
throw Beagle_IOExceptionNodeM(*lChild, lOSS.str());
}
setConcept(lConceptName, lTypeName);
Beagle_LogTraceM(
ioSystem.getLogger(),
std::string("Type associated to concept '")+lConceptName+
std::string("' is now '")+lTypeName+std::string("'")
);
}
}
Beagle_StackTraceEndM();
}
/*!
* \brief Read object from XML using system.
* \param inIter XML iterator of input document.
* \param ioSystem A reference to the system.
* \throw SCHNAPS::Core::IOException if a wrong tag is encountered.
* \throw SCHNAPS::Core::IOException if inProbabilities attribute is missing.
* \throw SCHNAPS::Core::RunTimeException if the primitive is undefined for the specific probabilities source.
*/
void BranchMulti::readWithSystem(PACC::XML::ConstIterator inIter, Core::System& ioSystem) {
schnaps_StackTraceBeginM();
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
if (inIter->getValue() != getName()) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected, but ";
lOSS << "got tag <" << inIter->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
// retrieve probabilities of executing each branch
if (inIter->getAttribute("inProbabilities").empty()) {
throw schnaps_IOExceptionNodeM(*inIter, "probabilities of executing each branch expected!");
}
mProbabilities_Ref.assign(inIter->getAttribute("inProbabilities"));
switch (mProbabilities_Ref[0]) {
case '@':
// individual variable value
case '#':
// environment variable value
case '%':
// local variable value
throw schnaps_RunTimeExceptionM("The primitive is undefined for the specific probabilities source!");
break;
case '$':
// parameter value
mProbabilities = Core::castHandleT<Core::Vector>(ioSystem.getParameters().getParameterHandle(mProbabilities_Ref.substr(1)));
break;
default: {
// direct value
std::stringstream lISS(mProbabilities_Ref);
PACC::Tokenizer lTokenizer(lISS);
lTokenizer.setDelimiters("|", "");
std::string lProbability;
double lSum = 0;
mProbabilities = new Core::Vector();
while (lTokenizer.getNextToken(lProbability)) {
mProbabilities->push_back(new Core::Double(SCHNAPS::str2dbl(lProbability)));
lSum += SCHNAPS::str2dbl(lProbability);
}
#ifndef SCHNAPS_NDEBUG
if (lSum != 1) {
std::cout << "Warning: multi branches probabilities must sum to 1 (current sum: " << lSum << "!";
std::cout << "\tIn: void SCHNAPS::Plugins::Control::BranchMulti::readWithSystem(PACC::XML::ConstIterator, SCHNAPS::Core::System&)\n";
}
#endif
break; }
}
setNumberArguments(mProbabilities->size());
schnaps_StackTraceEndM("void SCHNAPS::Plugins::Control::BranchMulti::readWithSystem(PACC::XML::ConstIterator, SCHNAPS::Core::System&)");
}
/*!
* \brief Read a primitive subtree from a XML subtree.
* \param inIter XML iterator to read primitive tree from.
* \param ioSystem A reference to the system.
* \return The size of the subtree read.
* \throw SCHNAPS::Core::IOException if a wrong tag is encountered.
*/
unsigned int PrimitiveTree::readSubTree(PACC::XML::ConstIterator inIter, System& ioSystem) {
schnaps_StackTraceBeginM();
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
Primitive::Alloc::Handle lPrimitiveAlloc = castHandleT<Primitive::Alloc>(ioSystem.getFactory().getAllocator(inIter->getValue()));
if(lPrimitiveAlloc == NULL) {
std::ostringstream lOSS;
lOSS << "no primitive named '" << inIter->getValue();
lOSS << "' found in the factory";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
Primitive::Handle lPrimitive = castHandleT<Primitive>(lPrimitiveAlloc->allocate());
unsigned int lNodeIdx = size();
push_back(Node(lPrimitive, 0));
(*this)[lNodeIdx].mPrimitive->readWithSystem(inIter, ioSystem);
unsigned int lSubTreeSize = 1;
unsigned int lNbChild = 0;
for (PACC::XML::ConstIterator lChild = inIter->getFirstChild(); lChild; lChild++) {
if (lChild->getType() == PACC::XML::eData) {
lSubTreeSize += readSubTree(lChild, ioSystem);
lNbChild++;
}
}
if ((*this)[lNodeIdx].mPrimitive->getNumberArguments() == Primitive::eAny) {
(*this)[lNodeIdx].mPrimitive->setNumberArguments(lNbChild);
} else {
if (lNbChild != (*this)[lNodeIdx].mPrimitive->getNumberArguments()) {
std::ostringstream lOSS;
lOSS << "number of arguments stated by the primitives (";
lOSS << (*this)[lNodeIdx].mPrimitive->getNumberArguments();
lOSS << ") mismatch the number of arguments read for the tree node (";
lOSS << lNbChild << ")!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
}
(*this)[lNodeIdx].mSubTreeSize = lSubTreeSize;
return lSubTreeSize;
schnaps_StackTraceEndM("void SCHNAPS::Core::PrimitiveTree::readSubTree(PACC::XML::ConstIterator, SCHNAPS::Core::System&)");
}
/*!
* \brief Read an instruction super set from a Beagle XML stream.
* \param inIter XML node used to read the super set from.
* \throw Beagle::IOException If size atribute not present.
*/
void LinGP::InstructionSuperSet::read(PACC::XML::ConstIterator inIter)
{
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != "InstructionSuperSet"))
throw Beagle_IOExceptionNodeM((*inIter), "tag <InstructionSuperSet> expected!");
unsigned int lPSIndex = 0;
for(PACC::XML::ConstIterator lChild=inIter->getFirstChild(); lChild; ++lChild) {
if((lChild->getType()==PACC::XML::eData) && (lChild->getValue()=="InstructionSet")) {
mInstructionSets[lPSIndex++]->read(lChild);
}
}
}
/*!
* \brief Read a linear GP mutation operator from XML tree.
* \param inNode XML node to use to read mutation operator.
* \param ioSystem Evolutionary system.
*/
void LinGP::MutationOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string lMutationPbReadName = inIter->getAttribute("mutationpb");
if(lMutationPbReadName.empty() == false) mMutationPbName = lMutationPbReadName;
std::string lInstructMutatePbReadName = inIter->getAttribute("mutinstructpb");
if(lInstructMutatePbReadName.empty() == false) mInstructMutatePbName = lInstructMutatePbReadName;
}
/*!
* \brief Read a sigma adaptation operator from a XML subtree.
* \param inIter XML iterator to use to read adaptation operator.
* \param ioSystem Evolutionary system.
*/
void ES::AdaptOneFifthRuleOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
string lMutateGaussSigmaReadName = inIter->getAttribute("mutgausssigma");
if(lMutateGaussSigmaReadName.empty() == false) mMutateGaussSigmaName = lMutateGaussSigmaReadName;
Beagle_StackTraceEndM();
}
/*!
* \brief Read a initialization operator from a XML subtree.
* \param inIter XML iterator to use to read initialization operator.
* \param ioSystem Evolutionary system.
*/
void InitializationOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string mReproProbaReadName = inIter->getAttribute("repropb");
if(mReproProbaReadName.empty() == false) mReproProbaName = mReproProbaReadName;
Beagle_StackTraceEndM();
}
/*!
* \brief Read object from XML using system.
* \param inIter XML iterator of input document.
* \param ioSystem A reference to the system.
* \throw SCHNAPS::Core::IOException if a wrong tag is encountered.
*/
void Primitive::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem) {
schnaps_StackTraceBeginM();
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
if (inIter->getValue() != getName()) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected, but ";
lOSS << "got tag <" << inIter->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
schnaps_StackTraceEndM("void SCHNAPS::Core::Primitive::readWithSystem(PACC::XML::ConstIterator, SCHNAPS::Core::System&)");
}
/*!
* \brief Read an individual bag with a context.
* \param inIter XML iterator to read the bag from.
* \param ioContext Evolutionary context.
*/
void IndividualBag::readWithContext(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="IndividualBag"))
throw Beagle_IOExceptionNodeM(*inIter, "tag <IndividualBag> expected!");
for(PACC::XML::ConstIterator lChild=inIter->getFirstChild(); lChild; ++lChild) {
if(lChild->getType() == PACC::XML::eData) {
readIndividuals(lChild, ioContext);
break;
}
}
Beagle_StackTraceEndM();
}
/*!
* \brief Read a OversizeOp operator for XML tree.
* \param inIter XML iterator to use to read OversizeOp operator.
* \param ioSystem Evolutionary system.
*/
void OversizeOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
string lOversizeRatioReadName = inIter->getAttribute("ratio_name");
if(lOversizeRatioReadName.empty() == false) mOversizeRatioName = lOversizeRatioReadName;
ReplacementStrategyOp::readWithSystem(inIter, ioSystem);
Beagle_StackTraceEndM("void OversizeOp::readWithSystem(PACC::XML::ConstIterator, System&)");
}
/*!
* \brief Read a bit flip mutation operator from XML subtree.
* \param inIter XML iterator to use to read mutation operator.
* \param ioSystem Evolutionary system.
*/
void BitStr::MutationFlipBitOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string lMutationPbReadName = inIter->getAttribute("mutationpb");
if(lMutationPbReadName.empty() == false) mMutationPbName = lMutationPbReadName;
std::string lBitMutatePbReadName = inIter->getAttribute("mutbitpb");
if(lBitMutatePbReadName.empty() == false) mBitMutatePbName = lBitMutatePbReadName;
Beagle_StackTraceEndM();
}
/*!
* \brief Read a mutation operator from XML subtree.
* \param inIter XML iterator to use to read crossover operator.
* \param ioSystem Evolutionary system.
*/
void GP::MutationSwapSubtreeOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string mMutationPbReadName = inIter->getAttribute("mutationpb");
if(mMutationPbReadName.empty() == false) mMutationPbName = mMutationPbReadName;
std::string mDistribPbReadName = inIter->getAttribute("distrpb");
if(mDistribPbReadName.empty() == false) mDistribPbName = mDistribPbReadName;
Beagle_StackTraceEndM();
}
/*!
* \brief Read a recombination operator from XML tree.
* \param inIter XML iterator to use to read recombination operator.
* \param ioSystem Evolutionary system.
*/
void RecombinationOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string lRecombProbaReadName = inIter->getAttribute("recombpb");
if(lRecombProbaReadName.empty()==false) mRecombProbaName = lRecombProbaReadName;
std::string lNumberRecombReadName = inIter->getAttribute("nbrindrecomb");
if(lNumberRecombReadName.empty()==false) mNumberRecombName = lNumberRecombReadName;
Beagle_StackTraceEndM();
}
void Beagle::WrapperT<T>::read(PACC::XML::ConstIterator inIter)
{
Beagle_StackTraceBeginM();
if(!inIter) mWrappedValue = T();
else {
if(inIter->getType() != PACC::XML::eString)
throw Beagle_IOExceptionNodeM(*inIter, "value of wrapper not found");
if(inIter->getValue().empty()) mWrappedValue = T();
else {
std::istringstream lISS(inIter->getValue());
lISS >> mWrappedValue;
}
}
Beagle_StackTraceEndM();
}
/*!
* \brief Read a max fitness termination operator from a XML subtree.
* \param inIter XML iterator from which the operator is read.
* \param ioSystem Evolutionary system.
* \throw IOException If a reading error occurs.
*/
void TermMaxFitnessOp::readWithSystem(PACC::XML::ConstIterator inIter, System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string lFitnessStr = inIter->getAttribute("fitness");
if(lFitnessStr.empty() == false) {
mMaxFitnessDefault = str2dbl(lFitnessStr);
if(mMaxFitness != NULL) mMaxFitness->getWrappedValue() = mMaxFitnessDefault;
}
Beagle_StackTraceEndM();
}
void Beagle::GP::MutationEphemeralOpT<T>::readWithSystem(PACC::XML::ConstIterator inIter,
Beagle::System& ioSystem)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!=getName())) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected!" << std::flush;
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string lMutationPbReadName = inIter->getAttribute("mutationpb");
if(lMutationPbReadName.empty() == false) mMutationPbName = lMutationPbReadName;
std::string lEphemeralNameParamName = inIter->getAttribute("primitname");
if(lEphemeralNameParamName.empty() == false) mEphemeralNameParamName = lEphemeralNameParamName;
Beagle_StackTraceEndM("void GP::MutationEphemeralOpT<T>::readWithSystem(PACC::XML::ConstIterator, System&)");
}
/*!
* \brief Read genotype from a Beagle XML node.
* \param inIter XML iterator to read the genotype from.
* \param ioContext Evolutionary context.
*/
void Genotype::readWithContext(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != "Genotype")) {
throw Beagle_IOExceptionNodeM(*inIter, "tag <Genotype> expected!");
}
std::string lGenotypeType = inIter->getAttribute("type");
if((lGenotypeType.empty() == false) && (lGenotypeType != getType())) {
std::ostringstream lOSS;
lOSS << "type given '" << lGenotypeType << "' mismatch type of the genotype '";
lOSS << getType() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
Beagle_StackTraceEndM("void Genotype::readWithContext(PACC::XML::ConstIterator,Context&)");
}
/*!
* \brief Read an instruction set from a XML node.
* \param inIter XML node to read the instruction set from.
* \throw IOException If size atribute not present or if the size mismatch.
*/
void LinGP::InstructionSet::read(PACC::XML::ConstIterator inIter)
{
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != "InstructionSet"))
throw Beagle_IOExceptionNodeM(*inIter, "tag <InstructionSet> expected!");
for(PACC::XML::ConstIterator lChild=inIter->getFirstChild(); lChild; ++lChild) {
if(lChild->getType() == PACC::XML::eData) {
Instruction::Handle lInstruction = getInstructionByName(lChild->getValue());
if(lInstruction == NULL) {
std::ostringstream lOSS;
lOSS << "Instruction '" << lChild->getValue();
lOSS << "' is not in the instruction set!";
throw Beagle_IOExceptionNodeM(*lChild, lOSS.str());
}
lInstruction->read(lChild);
}
}
}
/*!
* \brief Read the member instance.
* \param inIter Iterator to XML node to read component from.
* \param ioContext Evolutionary context.
*/
void Member::readWithContext(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType() != PACC::XML::eData) || (inIter->getValue() != getName())) {
std::ostringstream lOSS;
lOSS << "expected to get tag '" << getName() << "' instead of tag '";
lOSS << inIter->getValue() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
std::string lType = inIter->getAttribute("type");
if((lType.empty() == false) && (lType != getType())) {
std::ostringstream lOSS;
lOSS << "type given '" << lType << "' mismatch type of the member '";
lOSS << getType() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
Beagle_StackTraceEndM("void Member::readWithContext(PACC::XML::ConstIterator,Context&)");
}
/*!
* \brief Read vector from a XML subtree.
* \param inIter XML iterator to read the vector from.
*/
void Vector::read(PACC::XML::ConstIterator inIter)
{
Beagle_StackTraceBeginM();
if(inIter->getType()!=PACC::XML::eString)
throw Beagle_IOExceptionNodeM(*inIter,"expected string to read vector!");
clear();
std::istringstream lISS(inIter->getValue());
while(lISS.good()) {
double lValue;
lISS >> lValue;
resize(size()+1);
(*this)[size()-1] = lValue;
if(lISS.good()==false) break;
int lDelim=lISS.get();
if((lISS.good()==false) || (lDelim==-1)) break;
}
Beagle_StackTraceEndM("void Vector::read(PACC::XML::ConstIterator inIter)");
}
/*!
* \brief Read a vivarium population from an XML iterator.
* \param inIter XML iterator to read the vivarium population from.
* \param ioContext Evolutionary context.
* \throw Beagle::IOException If the format is not respected.
*/
void Vivarium::readPopulation(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="Population")) {
throw Beagle_IOExceptionNodeM(*inIter, "tag <Population> expected!");
}
const Factory& lFactory = ioContext.getSystem().getFactory();
unsigned int lPrevDemeIndex = ioContext.getDemeIndex();
Deme::Handle lPrevDemeHandle = ioContext.getDemeHandle();
clear();
for(PACC::XML::ConstIterator lIter=inIter->getFirstChild(); lIter; ++lIter) {
if((lIter->getType()!=PACC::XML::eData) || (lIter->getValue()!="Deme")) continue;
const std::string& lDemeType = lIter->getAttribute("type");
Deme::Alloc::Handle lDemeAlloc = NULL;
if(lDemeType.empty()) {
Deme::Alloc::Handle lDemeAlloc =
castHandleT<Deme::Alloc>(lFactory.getConceptAllocator("Deme"));
if(lDemeAlloc == NULL) {
std::ostringstream lOSS;
lOSS << "Deme object can't be read, ";
lOSS << "it appears that its type is not given and that there is not ";
lOSS << "valid concept allocator associated to it!";
throw Beagle_IOExceptionNodeM(*lIter, lOSS.str());
}
} else {
lDemeAlloc = castHandleT<Deme::Alloc>(lFactory.getAllocator(lDemeType));
if(lDemeAlloc == NULL) {
std::ostringstream lOSS;
lOSS << "Type '" << lDemeType << "' associated to deme object ";
lOSS << "is not valid!";
throw Beagle_IOExceptionNodeM(*lIter, lOSS.str());
}
}
Deme::Handle lDeme = castHandleT<Deme>(lDemeAlloc->allocate());
ioContext.setDemeHandle(lDeme);
ioContext.setDemeIndex(size());
push_back(lDeme);
lDeme->readWithContext(lIter, ioContext);
}
ioContext.setDemeHandle(lPrevDemeHandle);
ioContext.setDemeIndex(lPrevDemeIndex);
Beagle_StackTraceEndM();
}
void SCHNAPS::Core::ArrayT<T>::read(PACC::XML::ConstIterator inIter) {
schnaps_StackTraceBeginM();
if (inIter->getType() != PACC::XML::eString) {
throw schnaps_IOExceptionNodeM(*inIter,"expected string to read array!");
}
std::vector<T>::clear();
std::istringstream lISS(inIter->getValue());
while (lISS.good()) {
T lValue;
lISS >> lValue;
std::vector<T>::push_back(lValue);
if (lISS.good() == false) {
break;
}
int lDelim = lISS.get();
if ((lISS.good() == false) || (lDelim == -1)) {
break;
}
}
schnaps_StackTraceEndM("void SCHNAPS::Core::ArrayT<T>::read(PACC::XML::ConstIterator)");
}
/*!
* \brief Read object from XML using system.
* \param inIter XML iterator of input document.
* \param ioSystem A reference to the system.
* \throw SCHNAPS::Core::IOException if a wrong tag is encountered.
* \throw SCHNAPS::Core::IOException if inProbability attribute is missing.
*/
void Branch::readWithSystem(PACC::XML::ConstIterator inIter, Core::System& ioSystem) {
schnaps_StackTraceBeginM();
if (inIter->getType() != PACC::XML::eData) {
throw schnaps_IOExceptionNodeM(*inIter, "tag expected!");
}
if (inIter->getValue() != getName()) {
std::ostringstream lOSS;
lOSS << "tag <" << getName() << "> expected, but ";
lOSS << "got tag <" << inIter->getValue() << "> instead!";
throw schnaps_IOExceptionNodeM(*inIter, lOSS.str());
}
// retrieve probability of executing the first branch
if (inIter->getAttribute("inProbability").empty()) {
throw schnaps_IOExceptionNodeM(*inIter, "probability of executing first branch expected!");
}
mProbability_Ref = inIter->getAttribute("inProbability");
switch (mProbability_Ref[0]) {
case '@':
// individual variable value
case '#':
// environment variable value
case '%':
// local variable value
mProbability = NULL;
break;
case '$':
// parameter value
mProbability = Core::castHandleT<Core::Double>(ioSystem.getParameters().getParameterHandle(mProbability_Ref.substr(1)));
break;
default:
// direct value
mProbability = new Core::Double();
mProbability->readStr(mProbability_Ref);
break;
}
schnaps_StackTraceEndM("void SCHNAPS::Plugins::Control::Branch::readWithSystem(PACC::XML::ConstIterator, SCHNAPS::Core::System&)");
}
/*!
* \brief Read an individual from an XML node.
* \param inIter XML iterator to read the individual from.
* \param ioContext Evolutionary context to use to read the individual.
* \throw Beagle::IOException If the format is not respected.
*/
void Individual::readWithContext(PACC::XML::ConstIterator inIter, Context& ioContext)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="Individual")) {
throw Beagle_IOExceptionNodeM(*inIter, "tag <Individual> expected!");
}
// Be sure that the types are corresponding
const std::string& lIndivType = inIter->getAttribute("type");
if((lIndivType.empty() == false) && (lIndivType != getType())) {
std::ostringstream lOSS;
lOSS << "type given '" << lIndivType << "' mismatch type of the individual '";
lOSS << getType() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
// Read members
readMembers(inIter->getFirstChild(), ioContext);
// Read fitness
readFitness(inIter->getFirstChild(), ioContext);
// Read genotypes
readGenotypes(inIter->getFirstChild(), ioContext);
Beagle_StackTraceEndM();
}
/*!
* \brief Read a multiobjective fitness from a XML subtree.
* \param inIter XML iterator to use to read the fitness value.
*/
void FitnessMultiObj::read(PACC::XML::ConstIterator inIter)
{
Beagle_StackTraceBeginM();
if((inIter->getType()!=PACC::XML::eData) || (inIter->getValue()!="Fitness"))
throw Beagle_IOExceptionNodeM(*inIter, "tag <Fitness> expected!");
const std::string& lValid = inIter->getAttribute("valid");
if(lValid.empty() || (lValid == "yes")) {
// Check type of fitness read
const std::string& lType = inIter->getAttribute("type");
if((lType.empty() == false) && (lType != getType())) {
std::ostringstream lOSS;
lOSS << "type given '" << lType << "' mismatch type of the fitness '";
lOSS << getType() << "'!";
throw Beagle_IOExceptionNodeM(*inIter, lOSS.str());
}
// Read objective values
clear();
for(PACC::XML::ConstIterator lChild=inIter->getFirstChild(); lChild; ++lChild) {
if((lChild->getType() != PACC::XML::eData) || (lChild->getValue() != "Obj")) continue;
PACC::XML::ConstIterator lChild2 = lChild->getFirstChild();
if(!lChild2) throw Beagle_IOExceptionNodeM(*lChild, "needed a double value in the <Obj> tag!");
if(lChild2->getType() != PACC::XML::eString)
throw Beagle_IOExceptionNodeM(*lChild2, "needed a double value in the <Obj> tag!");
push_back(str2dbl(lChild2->getValue()));
}
setValid();
} else if(lValid == "no") {
clear();
setInvalid();
}
else {
throw Beagle_IOExceptionNodeM(*inIter, "bad fitness validity value!");
}
Beagle_StackTraceEndM();
}