void CEFMAlgorithm::calculateFluxModes()
{
bool Continue = true;
if (mStoi.size())
{
/* initialize the current tableau matrix */
pdelete(mpCurrentTableau);
mpCurrentTableau = new CTableauMatrix(mStoi, mReversible);
/* Do the iteration */
mIndexSet.resize(mMaxStep);
for (mStep = 0; mStep < mMaxStep; mStep++)
mIndexSet[mStep] = mStep;
while (findMinimalCombinationIndex() && Continue)
{
calculateNextTableau();
mStepProcess++;
if (mpCallBack)
Continue &= mpCallBack->progressItem(mhSteps);
static_cast<CCopasiTask *>(getObjectParent())->output(COutputInterface::DURING);
}
/* Build the elementary flux modes to be returned */
if (Continue)
buildFluxModes();
/* Delete the current / final tableau matrix */
pdelete(mpCurrentTableau);
}
if (mpCallBack)
Continue &= mpCallBack->finishItem(mhSteps);
}
bool CBitPatternTreeMethod::calculate()
{
bool Continue = true;
if (!initialize())
{
if (mpCallBack)
mpCallBack->finishItem(mhProgressCounter);
return false;
}
while (mpStepMatrix->getNumUnconvertedRows() > 0 &&
Continue)
{
#ifdef COPASI_DEBUG
DebugFile << "Step Matrix:" << std::endl;
DebugFile << *mpStepMatrix << std::endl;
#endif // COPASI_DEBUG
mStep = mpStepMatrix->getFirstUnconvertedRow();
std::vector< CStepMatrixColumn * > PositiveColumns;
std::vector< CStepMatrixColumn * > NegativeColumns;
std::vector< CStepMatrixColumn * > NullColumns;
if (mpStepMatrix->splitColumns(PositiveColumns,
NegativeColumns,
NullColumns))
{
// Process each step.
// We need to update the bit pattern tree.
pdelete(mpNullTree);
mpNullTree = new CBitPatternTree(NullColumns);
// Bit pattern tree containing the positive columns
CBitPatternTree PositiveTree(PositiveColumns);
// Convert the negative columns into a bit pattern tree
CBitPatternTree NegativeTree(NegativeColumns);
// Iterate over all combinations and add/remove columns to the step matrix
mProgressCounter2 = 0;
mProgressCounter2Max = PositiveTree.size() * NegativeTree.size();
if (mpCallBack)
mhProgressCounter2 =
mpCallBack->addItem("Combinations",
CCopasiParameter::UINT,
& mProgressCounter2,
& mProgressCounter2Max);
combine(PositiveTree.getRoot(), NegativeTree.getRoot());
if (mpCallBack)
mpCallBack->finishItem(mhProgressCounter2);
Continue &= mContinueCombination;
if (Continue)
{
// We can now destroy all negative columns, which removes them from
// the step matrix.
mpStepMatrix->removeInvalidColumns(NegativeColumns);
// Remove columns of the step matrix which are no longer extreme rays.
findRemoveInvalidColumns(NullColumns);
// We compact the step matrix which has empty columns due to the removal of columns above.
mpStepMatrix->compact();
// Now we can convert the processed row.
mpStepMatrix->convertRow();
}
}
mProgressCounter = mProgressCounterMax - mpStepMatrix->getNumUnconvertedRows();
if (mpCallBack)
Continue &= mpCallBack->progressItem(mhProgressCounter);
}
if (Continue)
{
buildFluxModes();
}
if (mpCallBack)
Continue &= mpCallBack->finishItem(mhProgressCounter);
return true;
}