bool CEFMMethod::initialize()
{
CEFMTask * pTask = dynamic_cast< CEFMTask * >(getObjectParent());
if (pTask == NULL)
{
CCopasiMessage(CCopasiMessage::ERROR, MCEFMAnalysis + 1);
return false;
}
CEFMProblem * pProblem = dynamic_cast< CEFMProblem *>(pTask->getProblem());
if (pProblem == NULL)
{
CCopasiMessage(CCopasiMessage::ERROR, MCEFMAnalysis + 2);
return false;
}
mpFluxModes = & pProblem->getFluxModes();
mpReorderedReactions = & pProblem->getReorderedReactions();
mpReorderedReactions->clear();
mpFluxModes->clear();
return true;
}
bool CBitPatternTreeMethod::initialize()
{
if (!CEFMMethod::initialize())
{
return false;
}
pdelete(mpStepMatrix);
mReactionForward.clear();
mContinueCombination = true;
CEFMTask * pTask = dynamic_cast< CEFMTask *>(getObjectParent());
if (pTask == NULL) return false;
mpModel = pTask->getProblem()->getModel();
if (mpModel == NULL) return false;
// We first build the kernel matrix
CMatrix< C_INT64 > KernelMatrix;
buildKernelMatrix(KernelMatrix);
#ifdef COPASI_DEBUG
DebugFile << "Original Kernel Matrix:" << std::endl;
DebugFile << KernelMatrix << std::endl;
#endif // COPASI_DEBUG
mMinimumSetSize = KernelMatrix.numCols() - 2;
#ifdef COPASI_DEBUG
DebugFile << "MinSetSize = " << mMinimumSetSize << std::endl;
#endif // COPASI_DEBUG
// Now we create the initial step matrix
mpStepMatrix = new CStepMatrix(KernelMatrix);
mProgressCounter = 0;
mProgressCounterMax = mpStepMatrix->getNumUnconvertedRows();
if (mpCallBack)
mhProgressCounter =
mpCallBack->addItem("Current Step",
CCopasiParameter::UINT,
& mProgressCounter,
& mProgressCounterMax);
return true;
}
void CEFMProblem::printResult(std::ostream * ostream) const
{
CEFMTask * pTask = dynamic_cast< CEFMTask * >(getObjectParent());
if (pTask)
{
const std::vector< CFluxMode > & FluxModes = pTask->getFluxModes();
// List
*ostream << "\tNumber of Modes:\t" << FluxModes.size() << std::endl;
// Column header
*ostream << "#\t\tReactions\tEquations" << std::endl;
std::vector< CFluxMode >::const_iterator itMode = FluxModes.begin();
std::vector< CFluxMode >::const_iterator endMode = FluxModes.end();
unsigned C_INT32 j;
for (j = 0; itMode != endMode; ++itMode, j++)
{
*ostream << j + 1;
if (itMode->isReversible() == true)
*ostream << "\tReversible";
else
*ostream << "\tIrreversible";
std::string Description = pTask->getFluxModeDescription(*itMode);
CFluxMode::const_iterator itReaction = itMode->begin();
CFluxMode::const_iterator endReaction = itMode->end();
std::string::size_type start = 0;
std::string::size_type end = 0;
for (; itReaction != endReaction; ++itReaction)
{
if (itReaction != itMode->begin())
*ostream << "\t";
end = Description.find("\n", start);
*ostream << "\t" << Description.substr(start, end - start);
start = end + 1;
*ostream << "\t" << pTask->getReactionEquation(itReaction) << std::endl;
}
}
*ostream << std::endl;
// Net Reactions
// Column header
*ostream << "#\tNet Reaction\tInternal Species" << std::endl;
itMode = FluxModes.begin();
for (j = 0; itMode != endMode; ++itMode, j++)
{
*ostream << j + 1;
*ostream << "\t" << pTask->getNetReaction(*itMode);
*ostream << "\t" << pTask->getInternalSpecies(*itMode) << std::endl;
}
*ostream << std::endl;
// EFM vs Reaction
std::vector< const CReaction * >::const_iterator itReaction = mReorderedReactions.begin();
std::vector< const CReaction * >::const_iterator endReaction = mReorderedReactions.end();
// Column header
*ostream << "#";
for (; itReaction != endReaction; ++itReaction)
{
*ostream << "\t" << (*itReaction)->getObjectName();
}
*ostream << std::endl;
itMode = FluxModes.begin();
size_t k;
for (j = 0; itMode != endMode; ++itMode, j++)
{
itReaction = mReorderedReactions.begin();
*ostream << j + 1;
for (k = 0; itReaction != endReaction; ++itReaction, k++)
{
*ostream << "\t" << itMode->getMultiplier(k);
}
*ostream << std::endl;
}
*ostream << std::endl;
if (mpModel == NULL) return;
// EFM vs Species
std::vector< CMetab * >::const_iterator itSpecies = mpModel->getMetabolites().begin();
std::vector< CMetab * >::const_iterator endSpecies = mpModel->getMetabolites().end();
// Column header
*ostream << "#";
for (; itSpecies != endSpecies; ++itSpecies)
{
*ostream << "\t" << CMetabNameInterface::getDisplayName(mpModel, **itSpecies);
}
*ostream << std::endl;
itMode = FluxModes.begin();
for (j = 0; itMode != endMode; ++itMode, j++)
{
itSpecies = mpModel->getMetabolites().begin();
*ostream << j + 1;
for (; itSpecies != endSpecies; ++itSpecies)
{
std::pair< C_FLOAT64, C_FLOAT64 > Changes =
pTask->getSpeciesChanges(*itMode, **itSpecies);
*ostream << "\t";
if (Changes.first > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() ||
Changes.second > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
{
*ostream << "-" << Changes.first << " | +" << Changes.second;
}
}
*ostream << std::endl;
}
*ostream << std::endl;
}
}
bool CEFMAlgorithm::initialize()
{
if (!CEFMMethod::initialize())
{
return false;
}
CEFMTask * pTask = dynamic_cast< CEFMTask *>(getObjectParent());
if (pTask == NULL) return false;
mpModel = pTask->getProblem()->getModel();
if (mpModel == NULL) return false;
mpFluxModes->clear();
/* ModelStoi is the transpose of the models stoichiometry matrix */
const CTransposeView< CMatrix< C_FLOAT64 > > ModelStoi(mpModel->getStoi());
size_t row, numRows = ModelStoi.numRows();
size_t col, numCols = ModelStoi.numCols();
/* Size the stoichiometry matrix passed to the algorithm */
mStoi.resize(numRows);
std::vector< std::vector< C_FLOAT64 > >::iterator it = mStoi.begin();
std::vector< std::vector< C_FLOAT64 > >::iterator end = mStoi.end();
for (; it != end; ++it)
it->resize(numCols);
/* Get the reactions from the model */
/* Note: We have as many reactions as we have rows in ModelStoi */
const CCopasiVectorNS < CReaction > & Reaction = mpModel->getReactions();
/* Vector to keep track of the rearrangements necessary to put the */
/* reversible reactions to the top of stoichiometry matrix */
mpReorderedReactions->resize(numRows);
/* Reversible reaction counter */
mReversible = 0;
size_t Insert;
size_t InsertReversible = 0;
size_t InsertIrreversible = numRows - 1;
/* Build the transpose of the stoichiometry matrix, */
/* sort reversible reactions to the top, count them */
/* and keep track of the rearrangement */
for (row = 0; row < numRows; row++)
{
if (Reaction[row]->isReversible())
{
Insert = InsertReversible++;
mReversible++;
}
else
Insert = InsertIrreversible--;
(*mpReorderedReactions)[Insert] = Reaction[row];
for (col = 0; col < numCols; col++)
mStoi[Insert][col] = ModelStoi(row, col);
}
mStep = 0;
mStepProcess = 0;
mMaxStep = (unsigned C_INT32) numCols;
if (mpCallBack)
mhSteps =
mpCallBack->addItem("Current Step",
mStepProcess,
& mMaxStep);
return true;
}
