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;
}
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;
}