void SliderDialog::editSlider()
{
SliderSettingsDialog* pSettingsDialog = new SliderSettingsDialog(this);
// set the list of sliders that is already known
CCopasiObject* object = (CCopasiObject*)getTaskForFolderId(mCurrentFolderId);
if (!object) return;
CCopasiDataModel * pDataModel = object->getObjectDataModel();
assert(pDataModel != NULL);
pSettingsDialog->setModel(pDataModel->getModel());
std::vector<CSlider*>* pVector = getCSlidersForCurrentFolderId();
pSettingsDialog->setDefinedSliders(*pVector);
//pSettingsDialog->disableObjectChoosing(true);
pSettingsDialog->setSlider(mpCurrSlider->getCSlider());
if (pSettingsDialog->exec() == QDialog::Accepted)
{
addSlider(pSettingsDialog->getSlider());
mpCurrSlider->updateSliderData();
/*
if ((!mpCurrSlider->isEnabled()) && mpCurrSlider->getCSlider()->compile())
{
mpCurrSlider->setEnabled(true);
}
*/
}
delete pSettingsDialog;
delete pVector;
}
/**
* This method is used for the export of several layout elements.
* Layout elements can reference model elements, but when a referenced model element
* is deleted, the layout is not infomred about this yet, so we end up with dnagling
* references.
* In order to not write these dangling references to file, we check if the reference
* belongs to a valid object in the same datamodel. If not, we issue a warning.
* This warning is only issued once during a save process.
*
* If the key belongs to an object in the same datamodel, true is returned, else false is returned.
*/
bool CLGraphicalObject::hasValidModelReference() const
{
bool result = false;
// check if the object for this key actually exists
// TODO This is only a workaround because it is theoretically
// TODO possible that the key no longer belongs to the same object it
// TODO originally did.
CCopasiObject* pObj = CCopasiRootContainer::getKeyFactory()->get(this->mModelObjectKey);
if (pObj != NULL)
{
// check if the object actually belongs to the same
// model as the text glyph
const CCopasiDataModel* pDM1 = NULL;
const CCopasiDataModel* pDM2 = NULL;
const CCopasiContainer* pParent = pObj->getObjectParent();
while (pParent != NULL)
{
pDM1 = dynamic_cast<const CCopasiDataModel*>(pParent);
if (pDM1 != NULL)
{
break;
}
pParent = pParent->getObjectParent();
}
pParent = this->getObjectParent();
while (pParent != NULL)
{
pDM2 = dynamic_cast<const CCopasiDataModel*>(pParent);
if (pDM2 != NULL)
{
break;
}
pParent = pParent->getObjectParent();
}
//assert(pDM2 != NULL);
if (pDM1 != NULL && pDM2 == NULL)
{
// if we have been able to resolve the model reference, but
// don't have a datamodel parent, that is good enough
return true;
}
if (pDM1 != NULL && pDM1 == pDM2)
{
result = true;
}
}
return result;
}
std::string CLGraphicalObject::getModelObjectName() const
{
CCopasiObject * tmp = getModelObject();
if (tmp)
return tmp->getObjectName();
else
return "";
}
std::string
SEDMLUtils::getXPathForObject(const CCopasiObject& object)
{
const std::string& type = object.getObjectName();
const CCopasiDataModel* dm = object.getObjectDataModel();
std::string yAxis = object.getObjectDisplayName();
std::string targetXPathString = getXPathAndName(yAxis, type,
dm->getModel(), *dm);
return targetXPathString;
}
bool CModelAdd::copyInitialExpression(const CModelEntity * sourceEntity, CModelEntity * newEntity)
{
bool info = false;
const CExpression* pExpression = sourceEntity->getInitialExpressionPtr();
if (pExpression == NULL) return info;
CExpression* tmp;
tmp = new CExpression(*pExpression, mmModel);
const std::vector<CEvaluationNode*>& objectNodes = tmp->getNodeList();
size_t j, jmax = objectNodes.size();
for (j = 0; j < jmax; ++j)
{
if (CEvaluationNode::type(objectNodes[j]->getType()) == CEvaluationNode::OBJECT)
{
CEvaluationNodeObject* pObjectNode = dynamic_cast<CEvaluationNodeObject*>(objectNodes[j]);
if (pObjectNode == NULL) return info;
CCopasiObjectName cn = pObjectNode->getObjectCN();
const CCopasiObject* mObject =
static_cast< const CCopasiObject * >(mmModel->getObjectDataModel()->getObject(cn));
if (mObject == NULL) return info;
std::string host = "";
if (mObject->isReference())
{
host = ",Reference=" + mObject->getObjectName();
mObject = mObject->getObjectParent();
}
if (mObject == NULL) return info;
std::string key = keyMap[(dynamic_cast<const CModelEntity * >(mObject))->getKey()];
CCopasiObject* pObject = (CCopasiRootContainer::getKeyFactory()->get(key));
cn = pObject->getCN() + host;
pObjectNode->setData("<" + cn + ">");
}
}
tmp->updateTree();
newEntity->setInitialExpression(tmp->getInfix().c_str());
return info;
}
bool CModelMerging::mergeInExpression(std::string toKey, std::string key, CExpression *pExpression)
{
bool info = false;
if (pExpression == NULL) return info;
const std::vector<CEvaluationNode*>& objectNodes = pExpression->getNodeList();
size_t j, jmax = objectNodes.size();
for (j = 0; j < jmax; ++j)
{
if (CEvaluationNode::type(objectNodes[j]->getType()) == CEvaluationNode::OBJECT)
{
CEvaluationNodeObject* pObjectNode = dynamic_cast<CEvaluationNodeObject*>(objectNodes[j]);
if (pObjectNode == NULL) return info;
CCopasiObjectName cn = pObjectNode->getObjectCN();
const CCopasiObject* mObject =
static_cast< const CCopasiObject * >(mpModel->getObjectDataModel()->getObject(cn));
if (mObject == NULL) return info;
std::string host = "";
if (mObject->isReference())
{
host = ",Reference=" + mObject->getObjectName();
mObject = mObject->getObjectParent();
}
if (mObject == NULL) return info;
CCopasiObject* pObject;
std::string ikey = (dynamic_cast<const CModelEntity * >(mObject))->getKey();
if (ikey == key)
{
pObject = (CCopasiRootContainer::getKeyFactory()->get(toKey));
cn = pObject->getCN() + host;
pObjectNode->setData("<" + cn + ">");
}
}
}
pExpression->updateTree();
return true;
}
void CMoiety::initObjects()
{
mpINumberReference = new CTotalNumberReference("InitialValue", this, mINumber);
mpNumberReference = new CTotalNumberReference("Value", this, mNumber);
mpDNumberReference = new CDependentNumberReference("DependentValue", this, mNumber);
mpDNumberReference->addDirectDependency(this);
CCopasiObject * pObject = addObjectReference("Amount", mIAmount, CCopasiObject::ValueDbl);
pObject->addDirectDependency(mpNumberReference);
return;
}
std::string CLGraphicalObject::getModelObjectDisplayName(bool /* regular */, bool /* richtext */) const
{
CCopasiObject * tmp = getModelObject();
if (tmp)
{
return tmp->getObjectName();
}
else
{
return "";
}
}
/**
* Returns a pointer to the CCopasiDataModel the element belongs to.
* If there is no instance of CCopasiDataModel in the ancestor tree, NULL
* is returned.
*/
CCopasiDataModel* CCopasiObject::getObjectDataModel()
{
CCopasiObject * pObject = this;
while (pObject != NULL)
{
if (pObject->isDataModel())
return static_cast<CCopasiDataModel *>(pObject);
pObject = pObject->getObjectParent();
}
return NULL;
}
void CMIRIAMInfo::load(const std::string& key)
{
pdelete(mpRDFGraph);
mKey = key;
CCopasiObject * pCopasiObject = dynamic_cast< CCopasiObject * >(CCopasiRootContainer::getKeyFactory()->get(mKey));
if (pCopasiObject != NULL)
{
const std::string * pMiriamAnnotation = NULL;
CAnnotation * pAnnotation = CAnnotation::castObject(pCopasiObject);
if (pAnnotation != NULL)
{
pMiriamAnnotation = &pAnnotation->getMiriamAnnotation();
}
if (pMiriamAnnotation && *pMiriamAnnotation != "")
mpRDFGraph = CRDFParser::graphFromXml(*pMiriamAnnotation);
}
if (mpRDFGraph == NULL)
mpRDFGraph = new CRDFGraph;
// We make sure that we always have an about node.
if (pCopasiObject != NULL)
mTriplet.pObject = mpRDFGraph->createAboutNode(pCopasiObject->getKey());
else
mTriplet.pObject = mpRDFGraph->createAboutNode("");
// Load the created date if set;
CRDFPredicate::Path Path = mTriplet.pObject->getPath();
std::set< CRDFTriplet > Triples =
mTriplet.pObject->getDescendantsWithPredicate(CRDFPredicate::dcterms_created);
if (Triples.size() > 0)
mCreated = *Triples.begin();
else
mCreated = CRDFTriplet(); // This is an invalid triplet, i.e., !mCreated is true.
loadCreators();
loadReferences();
loadModifications();
loadBiologicalDescriptions();
return;
}
void ObjectBrowserWidget::loadField(ObjectBrowserItem* parent, CCopasiVector <CCopasiObject>* copaParent)
{
unsigned int i;
ObjectBrowserItem* lastFieldItem = NULL;
CCopasiObject* currentFieldObject = NULL;
ObjectBrowserItem* lastObjectItem = NULL;
CCopasiObject* currentObject = NULL;
if ((copaParent->size() < 1) || (!(*copaParent)[0]->isContainer())) return; //empty list
const CCopasiContainer::objectMap * pFieldList =
&(static_cast< CCopasiContainer * >((*copaParent)[0])->getObjects());
CCopasiContainer::objectMap::const_iterator fieldIt = pFieldList->begin();
CCopasiContainer::objectMap::const_iterator fieldEnd = pFieldList->end();
while (fieldIt != fieldEnd)
{
currentFieldObject = fieldIt->second;
ObjectBrowserItem* currentFieldItem = new ObjectBrowserItem(parent, lastFieldItem, NULL, objectItemList);
currentFieldItem->attachKey();
currentFieldItem->setObjectType(FIELDATTR);
currentFieldItem->setText(0, FROM_UTF8(currentFieldObject->getObjectName()));
lastFieldItem = currentFieldItem;
lastObjectItem = NULL;
for (i = 0; i < copaParent->size(); i++)
{
CCopasiObject* pSubField;
currentObject = (*static_cast< CCopasiVector < CCopasiObject > * >(copaParent))[i];
if (currentObject->isContainer())
pSubField =
getFieldCopasiObject(static_cast< CCopasiContainer * >(currentObject),
FROM_UTF8(currentFieldObject->getObjectName()));
else
{
pSubField = NULL; // this shall be an exception error
}
ObjectBrowserItem* currentItem = new ObjectBrowserItem(currentFieldItem, lastObjectItem, pSubField, objectItemList);
currentItem->setText(0, FROM_UTF8(currentObject->getObjectName()));
// if ((pSubField)&&(pSubField->isVector()))
// currentItem->setText(0, currentItem->text(0) + "[]");
currentItem->setObjectType(FIELDATTR);
currentItem->attachKey();
if (pSubField)
if (pSubField->isContainer()) //container field recursively to find all possible items
{
loadChild(currentItem, static_cast< CCopasiContainer * >(pSubField), false); // wont show the attribute and field list
}
lastObjectItem = currentItem;
}
fieldIt++;
}
}
bool CExperimentObjectMap::compile(const std::vector< CCopasiContainer * > listOfContainer)
{
size_t i, imax = size();
size_t Column;
// We need to find out the size of the object map
if (imax == 0)
mLastColumn = C_INVALID_INDEX;
else
{
mLastColumn = strtoul(getName(0).c_str(), NULL, 0);
for (i = 1; i < imax; i++)
{
Column = strtoul(getName(i).c_str(), NULL, 0);
if (mLastColumn < Column)
mLastColumn = Column;
}
}
mObjects.resize(mLastColumn + 1);
mObjects = NULL;
CCopasiObject * pObject = NULL;
std::string CN;
for (i = 0; i < imax; i++)
{
if ((CN = getObjectCN(i)) == "") continue;
if ((pObject =
getObjectDataModel()->ObjectFromName(listOfContainer, CN)) != NULL &&
pObject->isValueDbl())
{
Column = strtoul(getName(i).c_str(), NULL, 0);
mObjects[Column] = pObject;
}
else
return false;
}
return true;
}
/**
* Since labels are not part of the model, we can't use the new method for
* getting the text but have to fall back to the old
* behavior.
* Hopefully I can get rid of this implementation sonner than later.
*/
std::string CLabel::getText() const
{
if (mIsTextSet)
{
return mText;
}
else
{
CCopasiObject* pObject = CCopasiRootContainer::getKeyFactory()->get(this->mModelObjectKey);
if (pObject)
{
return pObject->getObjectName();
}
else
{
return "unset";
}
}
}
void printNameForKey(std::ostringstream& stream, CKeyFactory* kf, const std::string& key, const std::string prefix = "")
{
CCopasiObject* obj = kf->get(key);
if (obj != NULL)
{
stream << "\"" << prefix << obj->getObjectName() << "\", ";
}
else if (startsWith(key, "sm_"))
{
printNameForKey(stream, kf, key.substr(3), "");
}
else if (startsWith(key, "ode_"))
{
printNameForKey(stream, kf, key.substr(4), "ODE ");
}
else
{
stream << "\"" << prefix << key << "\", ";
}
}
std::vector<CCopasiObject*> CSensItem::getVariablesPointerList(CCopasiDataModel* pDataModel)
{
std::vector<CCopasiObject*> ret;
if (isSingleObject())
{
CCopasiObject * tmpObject = const_cast<CCopasiObject *>(pDataModel->getObject(getSingleObjectCN()));
if (!tmpObject) {return ret;} //return empty list
if (!tmpObject->isValueDbl()) {return ret;} //return empty list
ret.push_back(tmpObject);
}
else
{
ret = CObjectLists::getListOfObjects(getListType(), pDataModel->getModel());
}
return ret;
}
void DefaultPlotDialog::slotCreate()
{
if (!mpTask) return;
CCopasiDataModel* pDataModel = ListViews::dataModel(parent());
assert(pDataModel != NULL);
CCopasiObject* result = COutputAssistant::createDefaultOutput(mIndex, mpTask, pDataModel);
if (result != NULL)
{
QString current = lineEditTitle->text();
int count = 0;
while (!result->setObjectName(TO_UTF8(current)))
current = QString("%1 %2").arg(lineEditTitle->text()).arg(++count);
this->accept();
}
else
this->reject();
}
void ObjectBrowserWidget::loadChild(ObjectBrowserItem* parent,
const CCopasiContainer* copaParent,
bool nField)
{
unsigned int i;
ObjectBrowserItem* last = NULL;
CCopasiObject* current = NULL;
ObjectList* childStack = new ObjectList();
const CCopasiContainer::objectMap * pObjectList = & copaParent->getObjects();
CCopasiContainer::objectMap::const_iterator it = pObjectList->begin();
CCopasiContainer::objectMap::const_iterator end = pObjectList->end();
if ((copaParent->isVector()) && (nField))
{
if ((static_cast< const CCopasiVector < CCopasiObject > * >(copaParent)->size() >= 1) &&
((*static_cast< const CCopasiVector < CCopasiObject > * >(copaParent))[0]->isContainer()))
{//add attribute list
ObjectBrowserItem* fieldChild = new ObjectBrowserItem(parent, NULL, NULL, objectItemList);
fieldChild->setObjectType(FIELDATTR);
fieldChild->setText(0, "Select by attribute");
fieldChild->setSelectable(false);
loadField(fieldChild, const_cast<CCopasiVector < CCopasiObject > *>(static_cast< const CCopasiVector < CCopasiObject > * >(copaParent)));
fieldChild->attachKey();
last = fieldChild;
}
}
if (copaParent->isVector())
{
for (i = 0; i < static_cast< const CCopasiVector < CCopasiObject > * >(copaParent)->size(); i++)
{
current = (*static_cast< const CCopasiVector < CCopasiObject > * >(copaParent))[i];
ObjectBrowserItem* currentItem = new ObjectBrowserItem(parent, last, current, objectItemList);
last = currentItem;
currentItem->setText(0, FROM_UTF8(current->getObjectName()));
if (current->isContainer())
{
currentItem->setObjectType(CONTAINERATTR);
currentItem->attachKey();
if (current->isVector())
currentItem->setText(0, currentItem->text(0) + "[]");
loadChild(currentItem, static_cast< CCopasiContainer * >(current), nField);
}
else
{
currentItem->setObjectType(OBJECTATTR);
childStack->insert(currentItem); //attach the key later
}
}
}
else
{
while (it != end)
{
current = it->second;
// Skip all strings
if (dynamic_cast<CCopasiStaticString *>(current))
{
it++;
continue;
}
ObjectBrowserItem* currentItem = new ObjectBrowserItem(parent, last, current, objectItemList);
last = currentItem;
currentItem->setText(0, FROM_UTF8(current->getObjectName()));
if (current->isContainer())
{
currentItem->setObjectType(CONTAINERATTR);
currentItem->attachKey();
if (current->isVector())
currentItem->setText(0, currentItem->text(0) + "[]");
loadChild(currentItem, static_cast< CCopasiContainer * >(current), nField);
}
else
{
currentItem->setObjectType(OBJECTATTR);
childStack->insert(currentItem); //attach the key later
}
it++;
}
}
ObjectBrowserItem* pCurrent;
while (childStack->len() > 0)
{
pCurrent = childStack->pop();
pCurrent->attachKey();
}
pdelete(childStack);
}
// virtual
bool COPASIHandler::processEnd(const XML_Char * pszName)
{
bool finished = false;
switch (mCurrentElement.first)
{
case COPASI:
{
// We need to handle the unmapped parameters of type key.
std::vector< std::string >::iterator it = mpData->UnmappedKeyParameters.begin();
std::vector< std::string >::iterator end = mpData->UnmappedKeyParameters.end();
for (; it != end; ++it)
{
CCopasiParameter * pParameter =
dynamic_cast< CCopasiParameter * >(CCopasiRootContainer::getKeyFactory()->get(*it));
if (pParameter != NULL &&
pParameter->getType() == CCopasiParameter::KEY)
{
CCopasiObject * pObject =
mpData->mKeyMap.get(pParameter->getValue< std::string >());
if (pObject != NULL)
pParameter->setValue(pObject->getKey());
else
pParameter->setValue(std::string(""));
}
}
// We need to remove the no longer needed expression "Objective Function" from the function list.
if (mpData->pFunctionList != NULL &&
mpData->pFunctionList->getIndex("Objective Function") != C_INVALID_INDEX)
{
mpData->pFunctionList->remove("Objective Function");
}
}
finished = true;
break;
case ParameterGroup:
finished = true;
break;
case ListOfFunctions:
case Model:
case ListOfTasks:
case ListOfReports:
case ListOfPlots:
case ListOfLayouts:
case SBMLReference:
case ListOfUnitDefinitions:
break;
case GUI:
if (mpData->pGUI == NULL)
{
CCopasiMessage::getLastMessage();
}
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return finished;
}
// virtual
bool CModelParameter::updateModel()
{
bool success = true;
if (mpObject != NULL)
{
switch (mType)
{
case Model:
{
CModel * pModel = static_cast< CModel * >(mpObject);
if (!pModel->isAutonomous())
{
pModel->setInitialValue(mValue);
}
else
{
pModel->setInitialValue(0.0);
}
}
break;
case Compartment:
case Species:
case ModelValue:
{
CModelEntity * pEntity = static_cast< CModelEntity * >(mpObject);
if (pEntity->getStatus() != CModelEntity::ASSIGNMENT)
{
pEntity->setInitialValue(mValue);
if (mIsInitialExpressionValid)
{
pEntity->setInitialExpression(getInitialExpression());
}
}
}
break;
case ReactionParameter:
{
CCopasiParameter * pParameter = static_cast< CCopasiParameter * >(mpObject);
CReaction * pReaction = static_cast< CReaction * >(mpObject->getObjectAncestor("Reaction"));
if (mIsInitialExpressionValid &&
getInitialExpression() != "")
{
CModel * pModel = mpParent->getModel();
assert(pModel != NULL);
std::vector< CCopasiContainer * > ListOfContainer;
ListOfContainer.push_back(pModel);
CCopasiObjectName CN = static_cast< CEvaluationNodeObject * >(mpInitialExpression->getRoot())->getObjectCN();
CCopasiObject * pObject = pModel->getObjectDataModel()->ObjectFromName(ListOfContainer, CN);
assert(pObject != NULL);
// We assign the object value
pParameter->setValue(* (C_FLOAT64 *) pObject->getValuePointer());
// We map the parameter to the global quantity
pReaction->setParameterMapping(pParameter->getObjectName(), pObject->getObjectParent()->getKey());
}
else
{
pParameter->setValue(mValue);
// We need to remove the existing mapping to a global quantity1.
pReaction->setParameterMapping(pParameter->getObjectName(), pParameter->getKey());
}
}
break;
default:
success = false;
break;
}
}
return success;
}
// virtual
CXMLHandler * ParameterHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
const char * cValue = NULL;
const char * cType = NULL;
std::string name;
std::string sValue("");
bool UnmappedKey = false;
void * pValue = NULL;
CCopasiParameter::Type type;
C_FLOAT64 d;
C_INT32 i;
size_t ui;
bool b;
switch (mCurrentElement.first)
{
case Parameter:
// Parameter has attributes name, type and value
name = mpParser->getAttributeValue("name", papszAttrs);
cType = mpParser->getAttributeValue("type", papszAttrs);
type = toEnum(cType, CCopasiParameter::XMLType, CCopasiParameter::INVALID);
cValue = mpParser->getAttributeValue("value", papszAttrs);
if (cValue != NULL)
{
sValue = cValue;
}
switch (type)
{
case CCopasiParameter::DOUBLE:
d = CCopasiXMLInterface::DBL(sValue.c_str());
pValue = &d;
break;
case CCopasiParameter::UDOUBLE:
d = CCopasiXMLInterface::DBL(sValue.c_str());
pValue = &d;
break;
case CCopasiParameter::INT:
i = strToInt(sValue.c_str());
pValue = &i;
break;
case CCopasiParameter::UINT:
ui = strToUnsignedInt(sValue.c_str());
pValue = &ui;
break;
case CCopasiParameter::BOOL:
if (sValue == "0" || sValue == "false")
{
b = false;
}
else
{
b = true;
}
pValue = &b;
break;
case CCopasiParameter::STRING:
case CCopasiParameter::FILE:
case CCopasiParameter::CN:
pValue = &sValue;
break;
case CCopasiParameter::KEY:
{
if (sValue != "" &&
CKeyFactory::isValidKey(sValue))
{
CCopasiObject * pObject = mpData->mKeyMap.get(sValue);
if (pObject)
{
sValue = pObject->getKey();
}
else
{
UnmappedKey = true;
}
}
pValue = &sValue;
}
break;
default:
CCopasiMessage(CCopasiMessage::ERROR, MCXML + 16, name.c_str(), cType, mpParser->getCurrentLineNumber());
pValue = NULL;
break;
}
mpData->pCurrentParameter = new CCopasiParameter(name, type, pValue);
if (UnmappedKey)
{
mpData->UnmappedKeyParameters.push_back(mpData->pCurrentParameter->getKey());
}
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
bool CODEExporterC::exportTitleData(const CModel* copasiModel, std::ostream & os)
{
size_t metab_size = copasiModel->getMetabolitesX().size();
size_t indep_size = copasiModel->getNumIndependentReactionMetabs();
size_t ode_size = copasiModel->getNumODEMetabs();
size_t comps_size = copasiModel->getCompartments().size();
size_t modvals_size = copasiModel->getModelValues().size();
size_t reacs_size = copasiModel->getReactions().size();
size_t i, j, num_params, count;
const CCopasiVector< CReaction > & reacs = copasiModel->getReactions();
const CReaction* reac;
count = 0;
for (i = 0; i < reacs_size; ++i)
{
reac = &reacs[i];
num_params = reac->getParameters().size();
for (j = 0; j < num_params; ++j)
{
if (reac->isLocalParameter(j))
++count;
}
}
size_t numX = 0;
size_t numY = 0;
size_t numXC = 0;
size_t numYC = 0;
size_t numPC = 0;
size_t numP = 0;
size_t numDX = 0;
size_t numCT = 0;
std::ostringstream p_names; p_names << "const char* p_names[] = {";
std::ostringstream x_names; x_names << "const char* x_names[] = {";
std::ostringstream y_names; y_names << "const char* y_names[] = {";
std::ostringstream xc_names; xc_names << "const char* xc_names[] = {";
std::ostringstream pc_names; pc_names << "const char* pc_names[] = {";
std::ostringstream yc_names; yc_names << "const char* yc_names[] = {";
std::ostringstream dx_names; dx_names << "const char* dx_names[] = {";
std::ostringstream ct_names; ct_names << "const char* ct_names[] = {";
CKeyFactory* kf = CCopasiRootContainer::getKeyFactory();
std::map< std::string, std::string >::const_iterator it = NameMap.begin();
std::map< std::string, std::string > reverse_map;
while (it != NameMap.end())
{
const std::string& abbrev = it->second;
const std::string& key = it->first;
if (startsWith(abbrev, "p["))
{
reverse_map[abbrev] = key;
++numP;
}
else if (startsWith(abbrev, "x["))
{
reverse_map[abbrev] = key;
++numX;
}
else if (startsWith(abbrev, "y["))
{
reverse_map[abbrev] = key;
++numY;
}
else if (startsWith(abbrev, "dx["))
{
reverse_map[abbrev] = key;
++numDX;
}
else if (startsWith(abbrev, "ct["))
{
reverse_map[abbrev] = key;
++numCT;
}
else if (startsWith(abbrev, "x_c["))
{
CCopasiObject* obj = kf->get(key);
if (obj != NULL)
{
reverse_map[abbrev] = obj->getObjectName();
}
else
{
reverse_map[abbrev] = key;
}
++numXC;
}
else if (startsWith(abbrev, "p_c["))
{
CCopasiObject* obj = kf->get(key);
if (obj != NULL)
{
reverse_map[abbrev] = obj->getObjectName();
}
else
{
reverse_map[abbrev] = key;
}
++numPC;
}
else if (startsWith(abbrev, "y_c["))
{
CCopasiObject* obj = kf->get(key);
if (obj != NULL)
{
reverse_map[abbrev] = obj->getObjectName();
}
else
{
reverse_map[abbrev] = key;
}
++numYC;
}
++it;
}
for (size_t i = 0; i < numP; ++i)
{
std::stringstream str; str << "p[" << i << "]";
printNameForKey(p_names, kf, reverse_map[str.str()]);
}
for (size_t i = 0; i < numX; ++i)
{
std::stringstream str; str << "x[" << i << "]";
printNameForKey(x_names, kf, reverse_map[str.str()]);
}
for (size_t i = 0; i < numY; ++i)
{
std::stringstream str; str << "y[" << i << "]";
printNameForKey(y_names, kf, reverse_map[str.str()]);
}
for (size_t i = 0; i < numDX; ++i)
{
std::stringstream str; str << "dx[" << i << "]";
printNameForKey(dx_names, kf, reverse_map[str.str()]);
}
for (size_t i = 0; i < numCT; ++i)
{
std::stringstream str; str << "ct[" << i << "]";
printNameForKey(ct_names, kf, reverse_map[str.str()]);
}
for (size_t i = 0; i < numXC; ++i)
{
std::stringstream str; str << "x_c[" << i << "]";
xc_names << "\"" << reverse_map[str.str()] << "\", ";
}
for (size_t i = 0; i < numPC; ++i)
{
std::stringstream str; str << "p_c[" << i << "]";
pc_names << "\"" << reverse_map[str.str()] << "\", ";
}
for (size_t i = 0; i < numYC; ++i)
{
std::stringstream str; str << "y_c[" << i << "]";
yc_names << "\"" << reverse_map[str.str()] << "\", ";
}
os << "#ifdef SIZE_DEFINITIONS" << std::endl;
os << "#define N_METABS " << metab_size << std::endl;
os << "#define N_ODE_METABS " << ode_size << std::endl;
os << "#define N_INDEP_METABS " << indep_size << std::endl;
os << "#define N_COMPARTMENTS " << comps_size << std::endl;
os << "#define N_GLOBAL_PARAMS " << modvals_size << std::endl;
os << "#define N_KIN_PARAMS " << count << std::endl;
os << "#define N_REACTIONS " << reacs_size << std::endl << std::endl;
os << "#define N_ARRAY_SIZE_P " << numP << "\t// number of parameters" << std::endl;
os << "#define N_ARRAY_SIZE_X " << numX << "\t// number of initials" << std::endl;
os << "#define N_ARRAY_SIZE_Y " << numY << "\t// number of assigned elements" << std::endl;
os << "#define N_ARRAY_SIZE_XC " << numXC << "\t// number of x concentration" << std::endl;
os << "#define N_ARRAY_SIZE_PC " << numPC << "\t// number of p concentration" << std::endl;
os << "#define N_ARRAY_SIZE_YC " << numYC << "\t// number of y concentration" << std::endl;
os << "#define N_ARRAY_SIZE_DX " << numDX << "\t// number of ODEs " << std::endl;
os << "#define N_ARRAY_SIZE_CT " << numCT << "\t// number of conserved totals" << std::endl << std::endl;
os << "#endif // SIZE_DEFINITIONS" << std::endl;
os << std::endl;
os << "#ifdef TIME" << std::endl;
os << "#define T <set here a user name for the time variable> " << std::endl;
os << "#endif // TIME" << std::endl;
os << std::endl;
os << "#ifdef NAME_ARRAYS" << std::endl;
os << p_names.str() << " \"\" };" << std::endl;
os << x_names.str() << " \"\" };" << std::endl;
os << y_names.str() << " \"\" };" << std::endl;
os << xc_names.str() << " \"\" };" << std::endl;
os << pc_names.str() << " \"\" };" << std::endl;
os << yc_names.str() << " \"\" };" << std::endl;
os << dx_names.str() << " \"\" };" << std::endl;
os << ct_names.str() << " \"\" };" << std::endl;
os << "#endif // NAME_ARRAYS" << std::endl;
return true;
}
std::string CODEExporterC::KineticFunction2ODEmember(const CReaction *reac)
{
std::ostringstream equation;
if (reac->getFunction()->getType() != CEvaluationTree::MassAction)
{
const CFunctionParameters & params = reac->getFunctionParameters();
size_t k, params_size = params.size();
const std::vector<std::vector<std::string> > & keyMap = reac->getParameterMappings();
std::string name;
equation << NameMap[reac->getFunction()->getKey()] << "(";
for (k = 0; k < params_size; ++k)
{
CFunctionParameter::Role role = params[k]->getUsage();
CCopasiObject * obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[k][0]);
if ((role == CFunctionParameter::SUBSTRATE)
|| (role == CFunctionParameter::PRODUCT)
|| (role == CFunctionParameter::MODIFIER))
{
if (obj)
name = NameMap[obj->getKey()];
else
name = "unknown";
}
if (role == CFunctionParameter::PARAMETER)
{
if (!(reac->isLocalParameter(k)))
{
CModelValue* modval;
modval = dynamic_cast< CModelValue * >(obj);
name = NameMap[modval->getKey()];
}
else
{
CCopasiParameter* param;
param = dynamic_cast< CCopasiParameter * >(obj);
name = NameMap[param->getKey()];
}
}
if (role == CFunctionParameter::VOLUME)
{
CCompartment* comp;
comp = dynamic_cast< CCompartment * >(obj);
name = NameMap[comp->getKey()];
}
if (role == CFunctionParameter::TIME)
{
name = "T";
}
if (name.empty())
{
std::string message = "Could not export C code, since one of the arguments could not be resolved. Please consider filing a bug with the COPASI tracker: http://www.copasi.org/tracker";
CCopasiMessage(CCopasiMessage::EXCEPTION, message.c_str());
}
equation << name;
if (k != params_size - 1)
equation << ", ";
}
equation << ")";
}
else
{
const CCopasiVector<CChemEqElement> & substrs = reac->getChemEq().getSubstrates();
const CCopasiVector<CChemEqElement> & prods = reac->getChemEq().getProducts();
const std::vector<std::vector<std::string> > & keyMap = reac->getParameterMappings();
CCopasiObject * obj;
size_t substrs_size = substrs.size(), prods_size = prods.size();
size_t k, m, mult;
const CChemEqElement* substr;
const CChemEqElement* prod;
const CMassAction & cMassAction = *static_cast<const CMassAction*>(reac->getFunction());
equation << "(";
obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[0][0]);
if (!(reac->isLocalParameter(0)))
{
CModelValue* modval;
modval = dynamic_cast< CModelValue * >(obj);
equation << NameMap[modval->getKey()];
}
else
{
CCopasiParameter* param;
param = dynamic_cast< CCopasiParameter * >(obj);
equation << NameMap[param->getKey()];
}
for (k = 0; k < substrs_size; ++k)
{
substr = &substrs[k];
mult = (size_t) substr->getMultiplicity();
assert(substr->getMetabolite());
equation << " * " << NameMap[substr->getMetabolite()->getKey()];
if (mult > 1)
for (m = 1; m < mult; ++m)
equation << " * " << NameMap[substr->getMetabolite()->getKey()];
}
if (cMassAction.isReversible() == TriTrue)
{
equation << " - ";
obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[2][0]);
if (!(reac->isLocalParameter(2)))
{
CModelValue* modval;
modval = dynamic_cast< CModelValue * >(obj);
equation << NameMap[modval->getKey()];
}
else
{
CCopasiParameter* param;
param = dynamic_cast< CCopasiParameter * >(obj);
equation << NameMap[param->getKey()];
}
for (k = 0; k < prods_size; ++k)
{
prod = &prods[k];
mult = (size_t) prod->getMultiplicity();
assert(prod->getMetabolite());
equation << " * " << NameMap[prod->getMetabolite()->getKey()];
if (mult > 1)
for (m = 1; m < mult; ++m)
equation << " * " << NameMap[prod->getMetabolite()->getKey()];
}
}
equation << ") ";
}
return equation.str();
}
void CMMLOutput::createParameterMapping(const CReaction* pReac,
std::vector<std::vector<std::string> > & params,
bool numbers)
{
assert(pReac);
assert(pReac->getFunction());
const CFunctionParameters & functionParams = pReac->getFunctionParameters();
size_t j, jmax;
size_t i, imax = functionParams.size();
params.resize(imax);
for (i = 0; i < imax; ++i)
{
params[i].resize(1);
std::string name;
//std::ostringstream number;
switch (functionParams[i]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
if (functionParams[i]->getType() == CFunctionParameter::FLOAT64)
{
CCopasiObject * pObject = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0]);
if (pObject != NULL)
{
name = pObject->getObjectDisplayName();
}
else
{
name = "unknown";
}
//params[i][0] = "<mi>"+ CMathMl::fixName(name)+"</mi>";
params[i][0] = "<mi>[" + CMathMl::fixName(name) + "]</mi>";
}
else if (functionParams[i]->getType() == CFunctionParameter::VFLOAT64)
{
jmax = pReac->getParameterMappings()[i].size();
params[i].resize(jmax);
for (j = 0; j < jmax; ++j)
{
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][j])->getObjectDisplayName();
//params[i][j] = "<mi>"+ CMathMl::fixName(name)+"</mi>";
params[i][j] = "<mi>[" + CMathMl::fixName(name) + "]</mi>";
}
}
else assert(false);
break;
case CFunctionParameter::PARAMETER:
if (pReac->isLocalParameter(i))
{
if (numbers)
{
std::ostringstream number;
number << pReac->getParameterValue(functionParams[i]->getObjectName());
params[i][0] = "<mn>" + number.str() + "</mn>";
}
else
{
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0])->getObjectName();
//params[i][0] = "<mi>" + CMathMl::fixName(name) + "</mi>";
params[i][0] = "<msub><mi>" + CMathMl::fixName(name) + "</mi><mi>("
+ CMathMl::fixName(pReac->getObjectName()) + ")</mi></msub>";
}
}
else
{
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0])->getObjectName();
params[i][0] = "<mi>" + CMathMl::fixName(name) + "</mi>";
//params[i][0] = "<mi>ggg</mi>";
}
break;
case CFunctionParameter::VOLUME:
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0])->getObjectName();
params[i][0] = "<msub><mi>V</mi><mi>" + CMathMl::fixName(name)
+ "</mi></msub>";
break;
case CFunctionParameter::TIME:
params[i][0] = "<mi>time</mi>";
break;
default:
break;
}
}
}
void SliderDialog::createNewSlider()
{
// allow the user to create more than one slider
std::vector<const CCopasiObject*> objects = CCopasiSelectionDialog::getObjectVector(this,
CQSimpleSelectionTree::InitialTime |
CQSimpleSelectionTree::Parameters);
std::vector<CSlider*>* pVector = getCSlidersForCurrentFolderId();
std::vector<const CCopasiObject*>::const_iterator it = objects.begin(), endit = objects.end();
bool yesToAll = false;
bool noToAll = false;
// create the sliders for all the selected objects
// first we need the task object because we need it later to associate the
// later with the correct task
CCopasiObject* object = (CCopasiObject*)getTaskForFolderId(mCurrentFolderId);
if (!object) return;
CCopasiObject* pTmpObject = NULL;
while (it != endit)
{
// create a new slider
assert((*it) != NULL);
pTmpObject = const_cast<CCopasiObject*>(determineCorrectObjectForSlider(*it));
CSlider* pCSlider = new CSlider("slider", (*CCopasiRootContainer::getDatamodelList())[0]);
if (pCSlider)
{
pCSlider->setSliderObject(pTmpObject);
pCSlider->setAssociatedEntityKey(object->getKey());
// check if a slider for that object already exists and if so, prompt
// the user what to do
CSlider* pEquivalentSlider = equivalentSliderExists(pCSlider);
if (pEquivalentSlider != NULL)
{
CopasiSlider* pCopasiSlider = NULL;
// if the user has specified yesToAll, we reset the ranges of all
// duplicate sliders
if (yesToAll)
{
pEquivalentSlider->resetRange();
// update the slider widget
pCopasiSlider = findCopasiSliderForCSlider(pEquivalentSlider);
assert(pCopasiSlider != NULL);
if (pCopasiSlider != NULL)
{
pCopasiSlider->updateSliderData();
}
}
// if the user has not specified noToAll, we need to prompt
else if (!noToAll)
{
QMessageBox::StandardButton result = CQMessageBox::information(NULL, "Slider Exists",
"A slider for this object already exists.\n\nDo you want to reset the range of the slider?",
QMessageBox::Yes | QMessageBox::No | QMessageBox::YesToAll | QMessageBox::NoToAll, QMessageBox::No);
// check the answer and maybe set some flags
switch (result)
{
case QMessageBox::YesToAll:
// set the flag
yesToAll = true;
case QMessageBox::Yes:
// reset the range
pEquivalentSlider->resetRange();
// update the slider widget
pCopasiSlider = findCopasiSliderForCSlider(pEquivalentSlider);
assert(pCopasiSlider != NULL);
if (pCopasiSlider != NULL)
{
pCopasiSlider->updateSliderData();
}
break;
case QMessageBox::NoToAll:
// set the flag
noToAll = true;
break;
case QMessageBox::No:
// do nothing else
break;
default:
// do nothing
break;
}
}
delete pCSlider;
}
else
{
std::vector<CCopasiContainer*> listOfContainers;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
listOfContainers.push_back((*CCopasiRootContainer::getDatamodelList())[0]->getModel());
pCSlider->compile(listOfContainers);
pCSlider->resetRange();
addSlider(pCSlider);
mChanged = true;
}
}
++it;
}
delete pVector;
}
void CQEventWidget1::addEvent(UndoEventData *pSData)
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
//reinsert the Event
CEvent *pEvent = pModel->createEvent(pSData->getName());
//set the expressions
pEvent->setTriggerExpression(pSData->getTriggerExpression());
pEvent->setDelayExpression(pSData->getDelayExpression());
pEvent->setPriorityExpression(pSData->getPriorityExpression());
QList <UndoEventAssignmentData *> *assignmentData = pSData->getEventAssignmentData();
QList <UndoEventAssignmentData *>::const_iterator i;
for (i = assignmentData->begin(); i != assignmentData->end(); ++i)
{
UndoEventAssignmentData * assignData = *i;
CCopasiObject * pObject = NULL;
bool speciesExist = false;
size_t ci;
for (ci = 0; ci < pModel->getCompartments().size(); ci++)
{
CCompartment * pCompartment = pModel->getCompartments()[ci];
if (pCompartment->getMetabolites().getIndex(assignData->getName()) != C_INVALID_INDEX)
speciesExist = true;
}
if (speciesExist)
{
size_t index = pModel->findMetabByName(assignData->getName());
pObject = pModel->getMetabolites()[index];
}
else if (pModel->getModelValues().getIndex(assignData->getName()) != C_INVALID_INDEX)
{
pObject = pModel->getModelValues()[assignData->getName()];
}
else if (pModel->getReactions().getIndex(assignData->getName()) != C_INVALID_INDEX)
{
pObject = pModel->getReactions()[assignData->getName()];
}
const CModelEntity * pEntity = dynamic_cast< const CModelEntity * >(pObject);
CEventAssignment *eventAssign = new CEventAssignment(pObject->getKey(), pEvent->getObjectParent());
eventAssign->setExpression(assignData->getExpression());
eventAssign->getExpressionPtr()->compile();
pEvent->getAssignments().add(eventAssign);
}
std::string key = pEvent->getKey();
protectedNotify(ListViews::EVENT, ListViews::ADD, key);
mpListView->switchToOtherWidget(C_INVALID_INDEX, key);
}
/**
* Creates the data generators for SEDML.
*/
void CSEDMLExporter::createDataGenerators(CCopasiDataModel & dataModel,
std::string & taskId,
CCopasiTask* task)
{
const CModel* pModel = dataModel.getModel();
std::vector<std::string> stringsContainer; //split string container
if (pModel == NULL)
CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No model for this SED-ML document. An SBML model must exist for every SED-ML document.");
SedPlot2D* pPSedPlot;
SedCurve* pCurve; // = pPSedPlot->createCurve();
//create generator for special varibale time
const CCopasiObject* pTime = static_cast<const CCopasiObject *>(dataModel.getModel()->getObject(CCopasiObjectName("Reference=Time")));
SedDataGenerator *pTimeDGenp = this->mpSEDMLDocument->createDataGenerator();
pTimeDGenp->setId("time");
pTimeDGenp->setName(pTime->getObjectName());
SedVariable *pTimeVar = pTimeDGenp->createVariable();
pTimeVar->setId("var_time");
pTimeVar->setTaskReference(taskId);
pTimeVar->setSymbol(SEDML_TIME_URN);
pTimeDGenp->setMath(SBML_parseFormula(pTimeVar->getId().c_str()));
size_t i, imax = dataModel.getPlotDefinitionList()->size();
SedDataGenerator *pPDGen;
if (imax == 0 && (task == NULL || task->getReport().getTarget().empty()))
CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No plot/report definition for this SED-ML document.");
// export report
if (task != NULL && !task->getReport().getTarget().empty())
{
CReportDefinition* def = task->getReport().getReportDefinition();
if (def != NULL)
{
SedReport* pReport = mpSEDMLDocument->createReport();
std::string name = def->getObjectName();
SEDMLUtils::removeCharactersFromString(name, "[]");
//
pReport->setId(SEDMLUtils::getNextId("report", mpSEDMLDocument->getNumOutputs()));
pReport->setName(name);
std::vector<CRegisteredObjectName> header = *def->getHeaderAddr();
std::vector<CRegisteredObjectName> body =
def->isTable() ? *def->getTableAddr() :
*def->getBodyAddr();
int dsCount = 0;
for (size_t i = 0; i < body.size(); ++i)
{
CRegisteredObjectName& current = body[i];
if (current == def->getSeparator().getCN()) continue;
CCopasiObject *object = dataModel.getDataObject(current);
if (object == NULL) continue;
const std::string& typeX = object->getObjectName();
std::string xAxis = object->getObjectDisplayName();
std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
pModel, dataModel);
if (object->getCN() == pTime->getCN())
pPDGen = pTimeDGenp;
else
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
xAxis,
targetXPathStringX,
taskId,
i,
0
);
SedDataSet* pDS = pReport->createDataSet();
pDS->setId(SEDMLUtils::getNextId("ds", ++dsCount));
if (def->isTable())
{
CCopasiObject *headerObj = NULL;
if (header.size() > i)
headerObj = dataModel.getDataObject(header[i]);
else
headerObj = dataModel.getDataObject(body[i]);
if (headerObj != NULL)
pDS->setLabel(headerObj->getObjectDisplayName());
else
pDS->setLabel(xAxis);
}
else
pDS->setLabel(xAxis);
pDS->setDataReference(pPDGen->getId());
}
}
}
// export plots
for (i = 0; i < imax; i++)
{
pPSedPlot = this->mpSEDMLDocument->createPlot2D();
const CPlotSpecification* pPlot = (*dataModel.getPlotDefinitionList())[i];
std::string plotName = pPlot->getObjectName();
SEDMLUtils::removeCharactersFromString(plotName, "[]");
pPSedPlot->setId(SEDMLUtils::getNextId("plot", mpSEDMLDocument->getNumOutputs()));
pPSedPlot->setName(plotName);
size_t j, jmax = pPlot->getItems().size();
for (j = 0; j < jmax; j++)
{
const CPlotItem* pPlotItem = pPlot->getItems()[j];
CCopasiObject *objectX, *objectY;
if (pPlotItem->getChannels().size() >= 1)
{
objectX = dataModel.getDataObject(pPlotItem->getChannels()[0]);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s', as it has no data channel.", pPlotItem->getObjectName().c_str());
continue;
}
if (objectX == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as it cannot be resolved.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[0].c_str());
continue;
}
bool xIsTime = objectX->getCN() == pTime->getCN();
if (pPlotItem->getChannels().size() >= 2)
{
objectY = dataModel.getDataObject(pPlotItem->getChannels()[1]);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s', as it has only 1 data channel.", pPlotItem->getObjectName().c_str());
continue;
}
if (objectY == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as it cannot be resolved.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[1].c_str());
continue;
}
const std::string& type = objectY->getObjectName();
std::string yAxis = objectY->getObjectDisplayName();
std::string sbmlId = yAxis;
std::string targetXPathString = SEDMLUtils::getXPathAndName(sbmlId, type,
pModel, dataModel);
if (targetXPathString.empty())
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as no xpath expression for it could be generated.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[1].c_str());
continue;
}
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
sbmlId,
targetXPathString,
taskId,
i,
j
);
pPDGen->setName(yAxis);
pCurve = pPSedPlot->createCurve();
std::ostringstream idCurveStrStream;
idCurveStrStream << "p";
idCurveStrStream << i + 1;
idCurveStrStream << "_curve_";
idCurveStrStream << j + 1;
pCurve->setId(idCurveStrStream.str());
pCurve->setLogX(pPlot->isLogX());
pCurve->setLogY(pPlot->isLogY());
pCurve->setName(yAxis);
pCurve->setYDataReference(pPDGen->getId());
if (xIsTime)
{
pCurve->setXDataReference(pTimeDGenp->getId());
}
else
{
const std::string& typeX = objectX->getObjectName();
std::string xAxis = objectX->getObjectDisplayName();
std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
pModel, dataModel);
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
xAxis,
targetXPathStringX,
taskId,
i,
j
);
pCurve->setXDataReference(pPDGen->getId());
}
}
}
}
