/*!
* \brief Write a history entry into a XML streamer.
* \param ioStreamer XML streamer to use.
* \param inIndent Whether XML output should be indented.
*/
void HistoryEntry::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("Entry", inIndent);
ioStreamer.insertAttribute("var", uint2str(mIndividualVar));
ioStreamer.insertAttribute("generation", uint2str(mGeneration));
for(unsigned int i=0; i<mParents.size(); ++i) {
ioStreamer.openTag("Parent", inIndent);
ioStreamer.insertAttribute("id", uint2str(mParents[i].getID()));
ioStreamer.insertAttribute("var", uint2str(mParents[i].getVar()));
ioStreamer.closeTag();
}
for(unsigned int i=0; i<mOpNames.size(); ++i) {
ioStreamer.openTag("Operations", inIndent);
ioStreamer.insertAttribute("action", mActions[i]);
ioStreamer.insertAttribute("opname", mOpNames[i]);
ioStreamer.closeTag();
}
ioStreamer.closeTag();
Beagle_StackTraceEndM();
}
/*!
* \brief Write an MCC fitness object into a Beagle XML streamer.
* \param ioStreamer XML streamer to use to write the fitness values.
* \param inIndent Whether XML output should be indented.
*/
void GP::FitnessMCC::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("MCC", false);
ioStreamer.insertStringContent(dbl2str(mValue));
ioStreamer.closeTag();
ioStreamer.openTag("TruePositives", false);
ioStreamer.insertStringContent(dbl2str(mTruePositives));
ioStreamer.closeTag();
ioStreamer.openTag("FalsePositives", false);
ioStreamer.insertStringContent(dbl2str(mFalsePositives));
ioStreamer.closeTag();
ioStreamer.openTag("TrueNegatives", false);
ioStreamer.insertStringContent(dbl2str(mTrueNegatives));
ioStreamer.closeTag();
ioStreamer.openTag("FalseNegatives", false);
ioStreamer.insertStringContent(uint2str(mFalseNegatives));
ioStreamer.closeTag();
ioStreamer.openTag("TruePositivesRel", false);
ioStreamer.insertStringContent(dbl2str(mTruePositivesRel));
ioStreamer.closeTag();
ioStreamer.openTag("FalsePositivesRel", false);
ioStreamer.insertStringContent(dbl2str(mFalsePositivesRel));
ioStreamer.closeTag();
ioStreamer.openTag("TrueNegativesRel", false);
ioStreamer.insertStringContent(dbl2str(mTrueNegativesRel));
ioStreamer.closeTag();
ioStreamer.openTag("FalseNegativesRel", false);
ioStreamer.insertStringContent(dbl2str(mFalseNegativesRel));
ioStreamer.closeTag();
Beagle_StackTraceEndM("void GP::FitnessMCC::writeContent(PACC::XML::Streamer&, bool) const");
}
void FitnessNMSE::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("FitnessNMSE", inIndent);
ioStreamer.insertAttribute("NMSE", dbl2str(mNMSE));
for(unsigned i=0; i<size(); ++i) {
ioStreamer.openTag("y" + int2str(i), inIndent);
ioStreamer.insertAttribute("NMSE", dbl2str((*this)[i].nmse));
ioStreamer.insertAttribute("MSE", dbl2str((*this)[i].mse));
ioStreamer.closeTag();
}
ioStreamer.closeTag();
Beagle_StackTraceEndM("void FitnessSimple::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
}
/*!
* \brief Write bag of individuals into XML streamer.
* \param ioStreamer XML streamer.
* \param inIndent Whether XML output should be indented.
*/
void IndividualBag::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("IndividualBag", inIndent);
for(unsigned int i=0; i<size(); ++i) {
if((*this)[i] == NULL) {
ioStreamer.openTag("NullHandle");
ioStreamer.closeTag();
} else {
(*this)[i]->write(ioStreamer, inIndent);
}
}
ioStreamer.closeTag();
Beagle_StackTraceEndM();
}
/*!
* \brief Write switch type operator into an XML stream.
* \param ioStreamer XML stream in which the operator is written.
* \param inIndent Whether XML output should be indented.
*/
void HPC::SwitchTypeOp::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag(getName(), inIndent);
for(OperatorSetMap::const_iterator lIterMap = mOperatorSetMap.begin(); lIterMap != mOperatorSetMap.end(); ++lIterMap){
ioStreamer.openTag(lIterMap->first, inIndent);
for(Operator::Bag::const_iterator lIterBag = lIterMap->second.begin(); lIterBag != lIterMap->second.end(); ++lIterBag){
Operator::Handle lOp = castHandleT<Operator>(*lIterBag);
lOp->write(ioStreamer, inIndent);
}
ioStreamer.closeTag();
}
ioStreamer.closeTag();
Beagle_StackTraceEndM();
}
void PopulationManager::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const {
schnaps_StackTraceBeginM();
// write generator
mGenerator->write(ioStreamer, inIndent);
// write population source
ioStreamer.openTag("Population");
for (PopulationManager::const_iterator lIt = this->begin(); lIt != this->end(); lIt++) {
ioStreamer.openTag("SubPopulation");
ioStreamer.insertAttribute("time", SCHNAPS::uint2str(lIt->first));
ioStreamer.insertAttribute("profile", lIt->second.mProfile);
ioStreamer.insertAttribute("size", SCHNAPS::uint2str(lIt->second.mSize));
ioStreamer.closeTag();
}
ioStreamer.closeTag();
schnaps_StackTraceEndM("void SCHNAPS::Simulation::PopulationManager::writeContent(PACC::XML::Streamer&, bool) const");
}
/*!
* \brief Write a primitive super set into a Beagle XML stream.
* \param ioStreamer XMl streamer to write the super set into.
* \param inIndent Whether XML output should be indented.
*/
void GP::PrimitiveSuperSet::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("GP-PrimitiveSuperSet", inIndent);
for(unsigned int i=0; i<mPrimitSets.size(); i++) mPrimitSets[i]->write(ioStreamer, inIndent);
ioStreamer.closeTag();
Beagle_StackTraceEndM("void GP::PrimitiveSuperSet::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
}
/*!
* \brief Write an instruction super set into a Beagle XML stream.
* \param ioStreamer XMl streamer to write the super set into.
* \param inIndent Whether XML output should be indented.
*/
void LinGP::InstructionSuperSet::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
ioStreamer.openTag("InstructionSuperSet", inIndent);
for(unsigned int i=0; i<mInstructionSets.size(); i++) {
mInstructionSets[i]->write(ioStreamer);
}
ioStreamer.closeTag();
}
/*!
* \brief Write a genotype into a XML streamer.
* \param ioStreamer XML streamer to use.
* \param inIndent Whether XML output should be indented.
*/
void Genotype::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("Genotype", inIndent);
ioStreamer.insertAttribute("type", getType());
writeContent(ioStreamer, inIndent);
ioStreamer.closeTag();
Beagle_StackTraceEndM("void Genotype::write(PACC::XML::Streamer&,bool) const");
}
/*!
* \brief Write an max hits termination operator into a XML stream.
* \param ioStreamer XML streamer in which the operator is written.
* \param inIndent Whether XML output should be indented.
*/
void GP::TermMaxHitsOp::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag(getName(), inIndent);
if(mMaxHits != NULL) ioStreamer.insertAttribute("hits", uint2str(mMaxHits->getWrappedValue()));
else ioStreamer.insertAttribute("hits", uint2str(mMaxHitsDefault));
ioStreamer.closeTag();
Beagle_StackTraceEndM("void GP::TermMaxHitsOp::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
}
/*!
* \brief Write a max fitness termination operator into a XML stream.
* \param ioStreamer XML stream in which the operator is written.
* \param inIndent Whether XML output should be indented.
*/
void TermMaxFitnessOp::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag(getName(), inIndent);
if(mMaxFitness != NULL)
ioStreamer.insertAttribute("fitness", dbl2str(mMaxFitness->getWrappedValue()));
else ioStreamer.insertAttribute("fitness", dbl2str(mMaxFitnessDefault));
ioStreamer.closeTag();
Beagle_StackTraceEndM();
}
/*!
* \brief Write concept map of the factory into a XML streamer.
* \param ioStreamer XML streamer to write factory concept map into.
* \param inIndent Whether XML output should be indented.
*/
void Factory::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("Factory", inIndent);
std::map< std::string, std::string > lSortedMap;
for(Factory::ConceptMap::const_iterator lIter=mConceptMap.begin();
lIter!=mConceptMap.end(); ++lIter) {
lSortedMap[lIter->first] = lIter->second;
}
for(std::map< std::string, std::string >::const_iterator lIterSM=lSortedMap.begin();
lIterSM!=lSortedMap.end(); ++lIterSM) {
ioStreamer.openTag("Concept", false);
ioStreamer.insertAttribute("name", lIterSM->first);
ioStreamer.insertAttribute("type", lIterSM->second);
ioStreamer.closeTag();
}
ioStreamer.closeTag();
Beagle_StackTraceEndM();
}
/*!
* \brief Write a Koza's fitness into a Beagle XML streamer.
* \param ioStreamer XML streamer to use to write the fitness values.
* \param inIndent Whether XML output should be indented.
*/
void GP::FitnessKoza::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("Normalized", false);
ioStreamer.insertStringContent(dbl2str(mValue));
ioStreamer.closeTag();
ioStreamer.openTag("Adjusted", false);
ioStreamer.insertStringContent(dbl2str(mAdjustedFitness));
ioStreamer.closeTag();
ioStreamer.openTag("Standardized", false);
ioStreamer.insertStringContent(dbl2str(mStandardizedFitness));
ioStreamer.closeTag();
ioStreamer.openTag("Raw", false);
ioStreamer.insertStringContent(dbl2str(mRawFitness));
ioStreamer.closeTag();
ioStreamer.openTag("Hits", false);
ioStreamer.insertStringContent(uint2str(mHits));
ioStreamer.closeTag();
Beagle_StackTraceEndM("void GP::FitnessKoza::writeContent(PACC::XML::Streamer&, bool) const");
}
/*!
* \brief Write OversizeOp operator into XML streamer.
* \param ioStreamer XML streamer to write OversizeOp operator into.
* \param inIndent Whether XML output should be indented.
*/
void OversizeOp::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag(getName(), inIndent);
ioStreamer.insertAttribute("ratio_name", mOversizeRatioName);
for(BreederNode::Handle lNode=getRootNode(); lNode!=NULL; lNode=lNode->getNextSibling()) {
lNode->write(ioStreamer, inIndent);
}
ioStreamer.closeTag();
Beagle_StackTraceEndM("void OversizeOp::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
}
/*!
* \brief Write a multiobjective fitness into an XML streamer.
* \param ioStreamer XML streamer to use to write the fitness value.
* \param inIndent Whether XML output should be indented.
*/
void FitnessMultiObj::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.insertAttribute("size", uint2str(size()));
for(unsigned int i=0; i<size(); ++i) {
ioStreamer.openTag("Obj", false);
ioStreamer.insertStringContent(dbl2str((*this)[i]));
ioStreamer.closeTag();
}
Beagle_StackTraceEndM();
}
/*!
* \brief Write fitness of an individual into a XML streamer.
* \param ioStreamer XML streamer to write the fitness into.
* \param inIndent Whether XML output should be indented.
*/
void Individual::writeFitness(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
if(mFitness == NULL) {
ioStreamer.openTag("Fitness", false);
ioStreamer.insertAttribute("valid", "no");
ioStreamer.closeTag();
} else {
mFitness->write(ioStreamer, inIndent);
}
Beagle_StackTraceEndM();
}
/*!
* \brief Write the actual vivarium population in a XML streamer.
* \param ioStreamer XML streamer to write the vivarium population into.
* \param inIndent Whether XML output should be indented.
*/
void Vivarium::writePopulation(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
ioStreamer.openTag("Population", inIndent);
ioStreamer.insertAttribute("size", uint2str(size()));
for(unsigned int i=0; i<size(); ++i) {
Beagle_NonNullPointerAssertM((*this)[i]);
(*this)[i]->write(ioStreamer, inIndent);
}
ioStreamer.closeTag();
Beagle_StackTraceEndM();
}
/*!
* \brief Write members of the vivarium in a XML streamer.
* \param ioStreamer XML streamer to write the members into.
* \param inIndent Whether XML output should be indented.
*/
void Vivarium::writeMembers(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
for(MemberMap::const_iterator lIterMap=mMemberMap.begin();
lIterMap!=mMemberMap.end(); ++lIterMap) {
ioStreamer.openTag(lIterMap->first, inIndent);
Member::Handle lMember = castHandleT<Member>(lIterMap->second);
ioStreamer.insertAttribute("type", lMember->getType());
lMember->writeContent(ioStreamer, inIndent);
ioStreamer.closeTag();
}
Beagle_StackTraceEndM();
}
/*!
* \brief Write a primitive sub-tree into a XML streamer.
* \param ioStreamer A reference to the XML streamer to write the tree into.
* \param inN Index of the actual subtree root node in the vector.
* \param inIndent Whether XML output should be indented.
* \throw SCHNAPS::Core::AssertException if the subtree size doesn't match.
*/
unsigned int PrimitiveTree::writeSubTree(PACC::XML::Streamer& ioStreamer, unsigned int inN, bool inIndent) const {
schnaps_StackTraceBeginM();
schnaps_AssertM(inN < size());
unsigned int lNumberArguments = (*this)[inN].mPrimitive->getNumberArguments();
ioStreamer.openTag((*this)[inN].mPrimitive->getName(), inIndent);
(*this)[inN].mPrimitive->writeContent(ioStreamer, inIndent);
unsigned int lSubTreeSize = 1;
for (unsigned int i = 0; i < lNumberArguments; ++i) {
lSubTreeSize += writeSubTree(ioStreamer, (lSubTreeSize+inN), inIndent);
}
schnaps_AssertM(lSubTreeSize == (*this)[inN].mSubTreeSize);
ioStreamer.closeTag();
return lSubTreeSize;
schnaps_StackTraceEndM("void SCHNAPS::Core::PrimitiveTree::writeSubTree(PACC::XML::Streamer&, bool) const");
}
void TreeSTag::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const {
Beagle_StackTraceBeginM();
ioStreamer.openTag("Genotype", inIndent);
ioStreamer.insertAttribute("type", "gptreetag");
ioStreamer.insertAttribute("structureid", uint2str(mStructureID));
ioStreamer.insertAttribute("size", uint2str(size()));
ioStreamer.insertAttribute("depth", uint2str(getTreeDepth()));
ioStreamer.insertAttribute("primitSetId", uint2str(getPrimitiveSetIndex()));
ioStreamer.insertAttribute("nbArgs", uint2str(getNumberArguments()));
if(size() > 0) {
unsigned int lSizeSubTree = writeSubTree(ioStreamer, 0, inIndent);
Beagle_AssertM(lSizeSubTree == size());
}
ioStreamer.closeTag();
// if(mBondGraph!=NULL) {
// mBondGraph->write(ioStreamer,inIndent);
// }
Beagle_StackTraceEndM("void GP::Tree::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
}
/*!
* \brief Write a stats into a XML streamer.
* \param ioStreamer XML streamer used to write the stats into.
* \param inIndent Whether XML output should be indented.
*/
void Stats::writeContent(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
Beagle_StackTraceBeginM();
if(mValid) {
if(mID.empty() == false) ioStreamer.insertAttribute("id", mID);
ioStreamer.insertAttribute("generation", uint2str(mGeneration));
ioStreamer.insertAttribute("popsize", uint2str(mPopSize));
std::set<std::string> lSortedItemKey;
for(ItemMap::const_iterator lIterMap=mItemMap.begin(); lIterMap!=mItemMap.end(); ++lIterMap) {
lSortedItemKey.insert(lIterMap->first);
}
for(std::set<std::string>::const_iterator lIterSet=lSortedItemKey.begin();
lIterSet!=lSortedItemKey.end(); ++lIterSet) {
ioStreamer.openTag("Item", false);
ioStreamer.insertAttribute("key", *lIterSet);
ItemMap::const_iterator lIterMap = mItemMap.find(*lIterSet);
ioStreamer.insertStringContent(dbl2str(lIterMap->second,12));
ioStreamer.closeTag();
}
for(unsigned int i=0; i<size(); ++i) {
ioStreamer.openTag("Measure", inIndent);
ioStreamer.insertAttribute("id", (*this)[i].mID);
ioStreamer.openTag("Avg", false);
ioStreamer.insertStringContent(dbl2str((*this)[i].mAvg,12));
ioStreamer.closeTag();
ioStreamer.openTag("Std", false);
ioStreamer.insertStringContent(dbl2str((*this)[i].mStd,12));
ioStreamer.closeTag();
ioStreamer.openTag("Max", false);
ioStreamer.insertStringContent(dbl2str((*this)[i].mMax,12));
ioStreamer.closeTag();
ioStreamer.openTag("Min", false);
ioStreamer.insertStringContent(dbl2str((*this)[i].mMin,12));
ioStreamer.closeTag();
ioStreamer.closeTag();
}
} else ioStreamer.insertAttribute("valid", "no");
Beagle_StackTraceEndM("void Stats::writeContent(PACC::XML::Streamer&,bool) const");
}
void BGFitness::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const {
// Beagle_StackTraceBeginM();
ioStreamer.openTag("Fitness", inIndent);
ioStreamer.insertAttribute("type", "LogFitness");
if(isValid()) {
ioStreamer.openTag("Obj", inIndent);
ioStreamer.insertStringContent(dbl2str(mFitness).c_str());
ioStreamer.closeTag();
ioStreamer.openTag("OriObj", inIndent);
ioStreamer.insertStringContent(dbl2str(mOriginalFitness).c_str());
ioStreamer.closeTag();
//State Matrix
ioStreamer.openTag("StateMatrices",inIndent);
// MatrixInterface lInterface;
for(unsigned int i = 0; i < mStateMatrices.size(); ++i) {
mStateMatrices[i].write(ioStreamer);
// lInterface.write(mStateMatrices[i],ioStreamer);
}
ioStreamer.closeTag();
if(mDataSet.size() == 0) {
for(unsigned int i = 0; i < mVariableData.size(); ++i) {
ioStreamer.openTag("Data", false);
ioStreamer.insertAttribute("Name", mVariableName[i]);
ioStreamer.insertAttribute("usize", uint2str(mUncompressedSize[i]));
ioStreamer.insertStringContent(mVariableData[i]);
ioStreamer.closeTag();
}
} else {
for(std::map<unsigned int, double>::const_iterator lIter = mDataSet.begin(); lIter != mDataSet.end(); ++lIter) {
ioStreamer.openTag("DataSet", inIndent);
ioStreamer.insertAttribute("ID", uint2str(lIter->first));
ioStreamer.openTag("Obj", false);
ioStreamer.insertStringContent( dbl2str(lIter->second).c_str() );
ioStreamer.closeTag();
for(unsigned int i = 0; i < mVariableData.size(); ++i) {
if(lIter->first == mVariableDataSet[i]) {
ioStreamer.openTag("Data", false);
ioStreamer.insertAttribute("Name", mVariableName[i]);
ioStreamer.insertAttribute("usize", uint2str(mUncompressedSize[i]));
ioStreamer.insertStringContent(mVariableData[i]);
ioStreamer.closeTag();
}
}
ioStreamer.closeTag();
}
}
if(!mInfo.empty()) {
ioStreamer.openTag("Info", inIndent);
for(std::map<std::string,std::string>::const_iterator lIter = mInfo.begin(); lIter != mInfo.end(); ++lIter) {
ioStreamer.openTag(lIter->first, false);
ioStreamer.insertStringContent( lIter->second );
ioStreamer.closeTag();
}
ioStreamer.closeTag();
}
if(mBondGraph!=NULL) {
mBondGraph->write(ioStreamer,false);
}
if(mSimplifiedBondGraph!=NULL) {
ioStreamer.openTag("SimplifiedBondGraph", inIndent);
mSimplifiedBondGraph->write(ioStreamer,false);
ioStreamer.closeTag();
}
}
else ioStreamer.insertAttribute("valid", "no");
ioStreamer.closeTag();
// Beagle_StackTraceEndM("void LogFitness::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const");
}
/*!
* \brief Write an instruction set into a XML streamer.
* \param ioStreamer XML streamer to use to read the instruction set into.
* \param inIndent Whether XML output should be indented.
*/
void LinGP::InstructionSet::write(PACC::XML::Streamer& ioStreamer, bool inIndent) const
{
ioStreamer.openTag("InstructionSet", inIndent);
for(unsigned int i=0; i<size(); i++) (*this)[i]->write(ioStreamer, inIndent);
ioStreamer.closeTag();
}