void
address_book_aliases::OK ()
{
// map [email => addr_id] of aliases to m_email in the database
std::map<QString,int> alias_map;
mail_address address;
bool found;
address.fetchByEmail (m_email, &found);
if (!found) {
close();
return;
}
// remove the aliases marked for removal
std::set<QString>::const_iterator iter1;
for (iter1 = m_remove_list.begin(); iter1 != m_remove_list.end(); iter1++) {
address.remove_alias (*(iter1));
}
mail_address_list aliases_list;
address.fetch_aliases (&aliases_list);
// fill in alias_map
std::list<mail_address>::const_iterator iter;
for (iter = aliases_list.begin(); iter != aliases_list.end(); iter++) {
alias_map[iter->get()] = iter->id();
}
// find the entries of the aliases widget that are not in the alias
// map and add these aliases to the database
Q3ListViewItemIterator it (m_aliases_list_w);
for ( ; it.current(); ++it ) {
std::map<QString,int>::const_iterator iter =
alias_map.find (it.current()->text(0));
if (iter == alias_map.end())
address.add_alias (it.current()->text(0));
}
close();
}
void
address_book_aliases::add_aliases ()
{
const Q3ListView* l = m_result_list_w;
Q3ListViewItem* i =l->firstChild();
while (i) {
if (i->isSelected()) {
QString email = i->text(0);
// add only if the item isn't already part of the alias list
bool found=false;
Q3ListViewItemIterator it (m_aliases_list_w);
for ( ; it.current() && !found; ++it )
found = (it.current()->text(0) == email);
if (!found)
Q3ListViewItem* inew = new Q3ListViewItem (m_aliases_list_w, email);
}
i = i->nextSibling();
}
}
/*
* build the population tree
*/
void CCopasiSimpleSelectionTree::populateTree(const CModel * pModel,
const ObjectClasses & classes)
{
if (!pModel) return;
const CCopasiObject * pObject;
Q3ListViewItem * pItem;
// find all kinds of time
pObject = pModel->getObject(CCopasiObjectName("Reference=Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "Model Time");
treeItems[pItem] = pObject;
}
pObject = pModel->getObject(CCopasiObjectName("Reference=Initial Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "Model Initial Time");
treeItems[pItem] = pObject;
}
pObject = pModel->getObjectDataModel()->getObject(CCopasiObjectName("Timer=CPU Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "CPU time");
treeItems[pItem] = pObject;
}
pObject = pModel->getObjectDataModel()->getObject(CCopasiObjectName("Timer=Wall Clock Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "real time");
treeItems[pItem] = pObject;
}
removeEmptySubTree(&mpTimeSubtree);
// find all species (aka metabolites) and create items in the metabolite subtree
const CCopasiVector<CMetab>& metabolites = pModel->getMetabolites();
unsigned int counter;
unsigned int maxCount = metabolites.size();
for (counter = maxCount; counter != 0; --counter)
{
const CMetab* metab = metabolites[counter - 1];
std::string name = metab->getObjectName();
bool unique = isMetaboliteNameUnique(name, metabolites);
if (!unique)
{
const CCompartment* comp = metab->getCompartment();
if (comp)
{
name = name + "(" + comp->getObjectName() + ")";
}
}
pObject = metab->getObject(CCopasiObjectName("Reference=InitialParticleNumber"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteInitialNumberSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = metab->getObject(CCopasiObjectName("Reference=ParticleNumber"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteTransientNumberSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (metab->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = metab->getObject(CCopasiObjectName("Reference=ParticleNumberRate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteRateNumberSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
name = "[" + name + "]"; // Concentration
pObject = metab->getObject(CCopasiObjectName("Reference=InitialConcentration"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteInitialConcentrationSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = metab->getObject(CCopasiObjectName("Reference=Concentration"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteTransientConcentrationSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (metab->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = metab->getObject(CCopasiObjectName("Reference=Rate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteRateConcentrationSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
}
removeEmptySubTree(&mpMetaboliteInitialNumberSubtree);
removeEmptySubTree(&mpMetaboliteTransientNumberSubtree);
removeEmptySubTree(&mpMetaboliteRateNumberSubtree);
removeEmptySubTree(&mpMetaboliteInitialConcentrationSubtree);
removeEmptySubTree(&mpMetaboliteTransientConcentrationSubtree);
removeEmptySubTree(&mpMetaboliteRateConcentrationSubtree);
removeEmptySubTree(&mpMetaboliteSubtree);
// find all reactions and create items in the reaction subtree
const CCopasiVectorNS<CReaction>& reactions = pModel->getReactions();
maxCount = reactions.size();
for (counter = maxCount; counter != 0; --counter)
{
const CReaction* react = reactions[counter - 1];
std::string name = "flux(" + react->getObjectName() + ")";
pObject = react->getObject(CCopasiObjectName("Reference=Flux"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpReactionFluxConcentrationSubtree, FROM_UTF8(name));
treeItems[pItem] = pObject;
}
pObject = react->getObject(CCopasiObjectName("Reference=ParticleFlux"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpReactionFluxNumberSubtree, FROM_UTF8("particle " + name));
treeItems[pItem] = pObject;
}
// create items for the reaction parameters
pItem = new Q3ListViewItem(mpReactionParameterSubtree,
FROM_UTF8(react->getObjectName()));
const CCopasiParameterGroup & Parameters = react->getParameters();
unsigned int j;
unsigned int numParameters = Parameters.size();
for (j = numParameters; j != 0; --j)
{
const CCopasiParameter * pParameter = Parameters.getParameter(j - 1);
// We skip local parameters which ar covered by global parameters
if (!react->isLocalParameter(pParameter->getObjectName()))
continue;
pObject = pParameter->getObject(CCopasiObjectName("Reference=Value"));
if (filter(classes, pObject))
{
Q3ListViewItem * pParameterItem =
new Q3ListViewItem(pItem, FROM_UTF8(pParameter->getObjectName()));
treeItems[pParameterItem] = pObject;
}
}
removeEmptySubTree(&pItem);
}
removeEmptySubTree(&mpReactionFluxNumberSubtree);
removeEmptySubTree(&mpReactionFluxConcentrationSubtree);
removeEmptySubTree(&mpReactionParameterSubtree);
removeEmptySubTree(&mpReactionSubtree);
// find all global parameters (aka model values) variables
const CCopasiVector<CModelValue>& objects = pModel->getModelValues();
maxCount = objects.size();
for (counter = maxCount; counter != 0; --counter)
{
const CModelEntity* object = objects[counter - 1];
std::string name = object->getObjectName();
pObject = object->getObject(CCopasiObjectName("Reference=InitialValue"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpModelQuantityInitialValueSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = object->getObject(CCopasiObjectName("Reference=Value"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpModelQuantityTransientValueSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (object->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = object->getObject(CCopasiObjectName("Reference=Rate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpModelQuantityRateSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
}
removeEmptySubTree(&mpModelQuantityRateSubtree);
removeEmptySubTree(&mpModelQuantityInitialValueSubtree);
removeEmptySubTree(&mpModelQuantityTransientValueSubtree);
removeEmptySubTree(&mpModelQuantitySubtree);
// find all compartments
const CCopasiVector<CCompartment>& objects2 = pModel->getCompartments();
maxCount = objects2.size();
for (counter = maxCount; counter != 0; --counter)
{
const CModelEntity* object = objects2[counter - 1];
std::string name = object->getObjectName();
pObject = object->getObject(CCopasiObjectName("Reference=InitialVolume"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpCompartmentInitialVolumeSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = object->getObject(CCopasiObjectName("Reference=Volume"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpCompartmentTransientVolumeSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (object->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = object->getObject(CCopasiObjectName("Reference=Rate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpCompartmentRateSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
}
removeEmptySubTree(&mpCompartmentRateSubtree);
removeEmptySubTree(&mpCompartmentInitialVolumeSubtree);
removeEmptySubTree(&mpCompartmentTransientVolumeSubtree);
removeEmptySubTree(&mpCompartmentSubtree);
pObject = pModel->getObject(CCopasiObjectName("Reference=Avogadro Constant"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(this, "Avogadro Constant");
treeItems[pItem] = pObject;
}
pObject = pModel->getObject(CCopasiObjectName("Reference=Quantity Conversion Factor"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(this, "Quantity Conversion Factor");
treeItems[pItem] = pObject;
}
// find all model matrices
const CMatrix<C_FLOAT64> &StoiMatrix = pModel->getStoi();
if (StoiMatrix.array())
{
pObject = pModel->getObject(CCopasiObjectName("Array=Stoichiometry(ann)"));
if (filter(classes, pObject))
{
// pItem = new QListViewItem(matrixSubtree, "Stoichiometry(ann)");
pItem = new Q3ListViewItem(mpModelMatrixSubtree, FROM_UTF8(pObject->getObjectName()));
treeItems[pItem] = pObject;
}
}
const CMatrix<C_FLOAT64> &RedStoiMatrix = pModel->getRedStoi();
if (RedStoiMatrix.array())
{
pObject = pModel->getObject(CCopasiObjectName("Array=Reduced stoichiometry(ann)"));
if (filter(classes, pObject))
{
// pItem = new QListViewItem(matrixSubtree, "Reduced stoichiometry(ann)");
pItem = new Q3ListViewItem(mpModelMatrixSubtree, FROM_UTF8(pObject->getObjectName()));
treeItems[pItem] = pObject;
}
}
const CMatrix<C_FLOAT64> &LinkMatrix = pModel->getL0();
if (LinkMatrix.array())
{
pObject = pModel->getObject(CCopasiObjectName("Array=Link matrix(ann)"));
if (filter(classes, pObject))
{
// pItem = new QListViewItem(matrixSubtree, "Link matrix(ann)");
pItem = new Q3ListViewItem(mpModelMatrixSubtree, FROM_UTF8(pObject->getObjectName()));
treeItems[pItem] = pObject;
}
}
removeEmptySubTree(&mpModelMatrixSubtree);
// find all result matrices
// Metabolic Control Analysis
CCopasiTask *task;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
// MCA
task = dynamic_cast<CCopasiTask*>((*pDataModel->getTaskList())["Metabolic Control Analysis"]);
try
{
if (task && task->updateMatrices())
{
//for mca the result is in the method
CMCAMethod* pMethod = dynamic_cast<CMCAMethod *>(task->getMethod());
const CCopasiContainer::objectMap * pObjects = & pMethod->getObjects();
CCopasiContainer::objectMap::const_iterator its = pObjects->begin();
CArrayAnnotation *ann;
for (; its != pObjects->end(); ++its)
{
ann = dynamic_cast<CArrayAnnotation*>(its->second);
if (!ann) continue;
if (!ann->isEmpty() && filter(classes, ann))
{
pItem = new Q3ListViewItem(this->mpResultMCASubtree, FROM_UTF8(ann->getObjectName()));
treeItems[pItem] = ann;
}
}
}
}
catch (...)
{}
// Steady State
task = dynamic_cast<CCopasiTask *>((*pDataModel->getTaskList())["Steady-State"]);
try
{
if (task && task->updateMatrices())
{
//for steady state the results are in the task
const CCopasiContainer::objectMap * pObjects = & task->getObjects();
CCopasiContainer::objectMap::const_iterator its = pObjects->begin();
CArrayAnnotation *ann;
for (; its != pObjects->end(); ++its)
{
ann = dynamic_cast<CArrayAnnotation*>(its->second);
if (!ann) continue;
if (!ann->isEmpty() && filter(classes, ann))
{
pItem = new Q3ListViewItem(this->mpResultSteadyStateSubtree, FROM_UTF8(ann->getObjectName()));
treeItems[pItem] = ann;
}
}
}
}
catch (...)
{}
// Sensitivities
task = dynamic_cast<CCopasiTask *>((*pDataModel->getTaskList())["Sensitivities"]);
try
{
if (task && task->updateMatrices())
{
//for sensitivities the result is in the problem
CSensProblem *sens = dynamic_cast<CSensProblem *>(task->getProblem());
const CCopasiContainer::objectMap * pObjects = & sens->getObjects();
CCopasiContainer::objectMap::const_iterator its = pObjects->begin();
CArrayAnnotation *ann;
for (; its != pObjects->end(); ++its)
{
ann = dynamic_cast<CArrayAnnotation*>(its->second);
if (!ann) continue;
if (!ann->isEmpty() && filter(classes, ann))
{
pItem = new Q3ListViewItem(this->mpResultSensitivitySubtree, FROM_UTF8(ann->getObjectName()));
treeItems[pItem] = (CCopasiObject *) ann;
}
}
}
}
catch (...)
{}
removeEmptySubTree(&mpResultMCASubtree);
removeEmptySubTree(&mpResultSensitivitySubtree);
removeEmptySubTree(&mpResultSteadyStateSubtree);
removeEmptySubTree(&mpResultMatrixSubtree);
if (selectionMode() == Q3ListView::NoSelection)
{
// see if some objects are there, if yes set to single selection
Q3ListViewItemIterator it = Q3ListViewItemIterator(this);
while (it.current())
{
if (treeItems.find(it.current()) != treeItems.end())
{
setSelectionMode(Q3ListView::Single);
setCurrentItem(it.current());
it.current()->setSelected(true);
Q3ListViewItem* parent = it.current()->parent();
while (parent)
{
parent->setOpen(true);
parent = parent->parent();
}
break;
}
++it;
}
}
}
