#include <DataModelGUI.h>

Inheritance diagram for DataModelGUI:

Collaboration diagram for DataModelGUI:

Public Slots
void	exportMathModelFinished ()

void	exportSBMLFinished ()

void	exportSBMLToStringFinished ()

void	importSBMLFinished ()

void	importSBMLFromStringFinished ()

void	loadModelFinished ()

void	miriamDownloadFinished (QNetworkReply *)

void	miriamDownloadProgress (qint64 received, qint64 total)

void	saveModelFinished ()

Signals
void	finished (bool success)

void	notifyView (ListViews::ObjectType objectType, ListViews::Action action, std::string key="")

void	updateCompleteView ()

Public Member Functions
void	buildChangedObjects ()

void	commit ()

bool	createModel ()

	DataModelGUI (QObject *parent)

void	deregisterListView (ListViews *pListView)

void	exportMathModel (const std::string &fileName, const std::string &filter, bool overwriteFile=false)

void	exportMathModelRun ()

void	exportSBML (const std::string &fileName, bool overwriteFile, int sbmlLevel, int sbmlVersion, bool exportIncomplete, bool exportCOPASIMIRIAM=true)

void	exportSBMLRun ()

void	exportSBMLToString (std::string &sbmlDocumentText)

void	exportSBMLToStringRun ()

COutputDefinitionVector &	getPlotDefinitionList ()

void	importCellDesigner ()

void	importSBML (const std::string &fileName)

void	importSBMLFromString (const std::string &sbmlDocumentText)

void	importSBMLFromStringRun ()

void	importSBMLRun ()

void	loadFunctionDB (const std::string &fileName)

void	loadModel (const std::string &fileName)

void	loadModelRun ()

bool	notify (ListViews::ObjectType objectType, ListViews::Action action, const std::string &key="")

void	refreshInitialValues ()

void	registerListView (ListViews *pListView)

void	saveFunctionDB (const std::string &fileName)

void	saveModel (const std::string &fileName, bool overwriteFile=false)

void	saveModelRun ()

void	setFramework (int framework)

bool	updateMIRIAM (CMIRIAMResources &miriamResources)

void	updateMIRIAMResourceContents ()

virtual	~DataModelGUI ()

Private Member Functions
void	linkDataModelToGUI ()

void	threadFinished ()

Private Attributes
std::set< const CCopasiObject * >	mChangedObjects

unsigned int	mDownloadedBytes

unsigned int	mDownloadedTotalBytes

std::string	mExportFormat

std::string	mFileName

int	mFramework

std::set< ListViews * >	mListViews

COutputHandlerPlot	mOutputHandlerPlot

bool	mOverWrite

QApplication *	mpApp

CMIRIAMResources *	mpMiriamResources

CProgressBar *	mpProgressBar

std::string *	mpSBMLExportString

CQThread *	mpThread

bool	mSBMLExportCOPASIMIRIAM

bool	mSBMLExportIncomplete

std::string	mSBMLImportString

int	mSBMLLevel

int	mSBMLVersion

bool	mSuccess

size_t	mUpdateItem

std::vector< Refresh * >	mUpdateVector

Detailed Description

Definition at line 34 of file DataModelGUI.h.

Constructor & Destructor Documentation

DataModelGUI::DataModelGUI ( QObject * parent )

Definition at line 79 of file DataModelGUI.cpp.

References CCopasiRootContainer::getDatamodelList(), and mOutputHandlerPlot.

                                           :
   QObject(parent),
   mpApp(NULL),
   mOutputHandlerPlot(),
   mListViews(),
   mFramework(0),
   mUpdateVector(),
   mChangedObjects(),
   mpThread(NULL),
   mpProgressBar(NULL),
   mSuccess(false),
   mSBMLImportString(),
   mpSBMLExportString(NULL),
   mFileName(),
   mOverWrite(false),
   mSBMLLevel(2),
   mSBMLVersion(4),
   mSBMLExportIncomplete(true),
   mSBMLExportCOPASIMIRIAM(true),
   mExportFormat()
 
 #ifdef COPASI_SEDML
   , mSEDMLImportString()
   , mpSEDMLExportString(NULL)
   , mSEDMLLevel(1)
   , mSEDMLVersion(1)
   , mSEDMLExportIncomplete(true)
   , mSEDMLExportCOPASIMIRIAM(true)
 #endif
 
 {
   assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
   (*CCopasiRootContainer::getDatamodelList())[0]->addInterface(&mOutputHandlerPlot);
 
   //mpMathModel = NULL;
   //mMathModelUpdateScheduled = false;
 }

DataModelGUI::~DataModelGUI ( )

virtual

Definition at line 117 of file DataModelGUI.cpp.

118 {

119 }

Member Function Documentation

void DataModelGUI::buildChangedObjects ( )

Definition at line 634 of file DataModelGUI.cpp.

References CArrayAnnotation::appendElementReferences(), CModelEntity::ASSIGNMENT, CCopasiVector< T >::begin(), CModel::buildInitialRefreshSequence(), CCopasiMessage::clearDeque(), CModel::compileIfNecessary(), CQMessageBox::critical(), CCopasiVector< T >::end(), CStateTemplate::endFixed(), FROM_UTF8, CCopasiRootContainer::getDatamodelList(), CStateTemplate::getEntities(), CMetab::getInitialConcentration(), CMetab::getInitialConcentrationReference(), CModelEntity::getInitialValueReference(), CCopasiMessage::getLastMessage(), CCopasiContainer::getObject(), CCopasiParameterGroup::getParameter(), CModel::getReactions(), CModel::getStateTemplate(), CMetab::isInitialConcentrationChangeAllowed(), mChangedObjects, mFramework, mUpdateVector, and CCopasiParameterGroup::size().

Referenced by refreshInitialValues().

 {
   assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
   CModel * pModel = (*CCopasiRootContainer::getDatamodelList())[0]->getModel();
   pModel->compileIfNecessary(NULL);
 
   mChangedObjects.clear();
 
   CModelEntity ** ppEntity = pModel->getStateTemplate().getEntities();
   CModelEntity ** ppEntityEnd = pModel->getStateTemplate().endFixed();
 
   CMetab * pMetab;
   std::set< const CCopasiObject * > Objects;
 
   // The objects which are changed are all initial values of of all model entities including
   // fixed and unused once. Additionally, all kinetic parameters are possibly changed.
   // This is basically all the parameters in the parameter overview whose value is editable.
 
   // :TODO: Theoretically, it is possible that also task parameters influence the initial
   // state of a model but that is currently not handled.
 
   for (; ppEntity != ppEntityEnd; ++ppEntity)
     {
       // If we have an initial expression we have no initial values
       if ((*ppEntity)->getInitialExpression() != "" ||
           (*ppEntity)->getStatus() == CModelEntity::ASSIGNMENT)
         continue;
 
       // Metabolites have two initial values
       if (mFramework == 0 &&
           (pMetab = dynamic_cast< CMetab * >(*ppEntity)) != NULL)
         {
           // The concentration is assumed to be fix accept when this would lead to circular dependencies,
           // for the parent's compartment's initial volume.
           if (pMetab->isInitialConcentrationChangeAllowed() &&
               !isnan(pMetab->getInitialConcentration()))
             mChangedObjects.insert(pMetab->getInitialConcentrationReference());
           else
             mChangedObjects.insert(pMetab->getInitialValueReference());
         }
       else
         mChangedObjects.insert((*ppEntity)->getInitialValueReference());
     }
 
   // The reaction parameters
   CCopasiVector< CReaction >::const_iterator itReaction = pModel->getReactions().begin();
   CCopasiVector< CReaction >::const_iterator endReaction = pModel->getReactions().end();
   size_t i, imax;
 
   for (; itReaction != endReaction; ++itReaction)
     {
       const CCopasiParameterGroup & Group = (*itReaction)->getParameters();
 
       for (i = 0, imax = Group.size(); i < imax; i++)
         mChangedObjects.insert(static_cast< const CCopasiObject * >(Group.getParameter(i)->getObject(CCopasiObjectName("Reference=Value"))));
     }
 
   // Fix for Issue 1170: We need to add elements of the stoichiometry, reduced stoichiometry,
   // and link matrices.
   const CArrayAnnotation * pMatrix = NULL;
   pMatrix = dynamic_cast<const CArrayAnnotation *>(pModel->getObject(std::string("Array=Stoichiometry(ann)")));
 
   if (pMatrix != NULL)
     pMatrix->appendElementReferences(mChangedObjects);
 
   pMatrix = dynamic_cast<const CArrayAnnotation *>(pModel->getObject(std::string("Array=Reduced stoichiometry(ann)")));
 
   if (pMatrix != NULL)
     pMatrix->appendElementReferences(mChangedObjects);
 
   pMatrix = dynamic_cast<const CArrayAnnotation *>(pModel->getObject(std::string("Array=Link matrix(ann)")));
 
   if (pMatrix != NULL)
     pMatrix->appendElementReferences(mChangedObjects);
 
   try
     {
       mUpdateVector = pModel->buildInitialRefreshSequence(mChangedObjects);
     }
 
   catch (...)
     {
       QString Message = "Error while updating the initial values!\n\n";
       Message += FROM_UTF8(CCopasiMessage::getLastMessage().getText());
 
       CQMessageBox::critical(NULL, QString("COPASI Error"), Message,
                              QMessageBox::Ok, QMessageBox::Ok);
       CCopasiMessage::clearDeque();
 
       mUpdateVector.clear();
       return;
     }
 }

void DataModelGUI::commit ( )

Definition at line 768 of file DataModelGUI.cpp.

References mListViews.

 {
   std::set< ListViews * >::iterator it = mListViews.begin();
   std::set< ListViews * >::iterator end = mListViews.end();
 
   for (; it != end; ++it)
     {
       (*it)->commit();
     }
 }

bool DataModelGUI::createModel ( )

Definition at line 200 of file DataModelGUI.cpp.

References CCopasiRootContainer::getDatamodelList(), getPlotDefinitionList(), linkDataModelToGUI(), mOutputHandlerPlot, and COutputHandlerPlot::setOutputDefinitionVector().

Referenced by CopasiUI3Window::newDoc(), CopasiUI3Window::slotFileOpenFinished(), CopasiUI3Window::slotImportSBMLFinished(), and CopasiUI3Window::slotImportSBMLFromStringFinished().

 {
   assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
 
   if (!(*CCopasiRootContainer::getDatamodelList())[0]->newModel(NULL, false)) return false;
 
   mOutputHandlerPlot.setOutputDefinitionVector((*CCopasiRootContainer::getDatamodelList())[0]->getPlotDefinitionList());
 
   linkDataModelToGUI();
   return true;
 }

void DataModelGUI::deregisterListView ( ListViews * pListView )

Definition at line 628 of file DataModelGUI.cpp.

References mListViews, and ListViews::setDataModel().

Referenced by CopasiUI3Window::~CopasiUI3Window().

 {
   pListView->setDataModel(NULL);
   mListViews.erase(pListView);
 }

void DataModelGUI::exportMathModel	(	const std::string &	fileName,
		const std::string &	filter,
		bool	overwriteFile = `false`
	)

Definition at line 487 of file DataModelGUI.cpp.

References CProgressBar::create(), exportMathModelFinished(), exportMathModelRun(), finished(), mExportFormat, mFileName, mOverWrite, mpProgressBar, mpThread, and mSuccess.

Referenced by exportMathModelRun(), and CopasiUI3Window::slotExportMathModel().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mFileName = fileName;
   mOverWrite = overwriteFile;
   mExportFormat = filter;
 
   mpThread = new CQThread(this, &DataModelGUI::exportMathModelRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(exportMathModelFinished()));
   mpThread->start();
 }

void DataModelGUI::exportMathModelFinished ( )

slot

Definition at line 515 of file DataModelGUI.cpp.

References finished(), mpThread, and threadFinished().

Referenced by exportMathModel().

 {
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(exportMathModelFinished()));
 
   threadFinished();
 }

void DataModelGUI::exportMathModelRun ( )

Definition at line 501 of file DataModelGUI.cpp.

References exportMathModel(), CCopasiRootContainer::getDatamodelList(), mExportFormat, mFileName, mOverWrite, mpProgressBar, and mSuccess.

Referenced by exportMathModel().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       mSuccess = (*CCopasiRootContainer::getDatamodelList())[0]->exportMathModel(mFileName, mpProgressBar, mExportFormat, mOverWrite);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::exportSBML	(	const std::string &	fileName,
		bool	overwriteFile,
		int	sbmlLevel,
		int	sbmlVersion,
		bool	exportIncomplete,
		bool	exportCOPASIMIRIAM = `true`
	)

Definition at line 446 of file DataModelGUI.cpp.

References CProgressBar::create(), exportSBMLFinished(), exportSBMLRun(), finished(), mFileName, mOverWrite, mpProgressBar, mpThread, mSBMLExportCOPASIMIRIAM, mSBMLExportIncomplete, mSBMLLevel, mSBMLVersion, and mSuccess.

Referenced by exportSBMLRun(), and CopasiUI3Window::slotExportSBML().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mFileName = fileName;
   mOverWrite = overwriteFile;
   mSBMLLevel = sbmlLevel;
   mSBMLVersion = sbmlVersion;
   mSBMLExportIncomplete = exportIncomplete;
   mSBMLExportCOPASIMIRIAM = exportCOPASIMIRIAM;
 
   mpThread = new CQThread(this, &DataModelGUI::exportSBMLRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(exportSBMLFinished()));
   mpThread->start();
 }

void DataModelGUI::exportSBMLFinished ( )

slot

Definition at line 477 of file DataModelGUI.cpp.

References CRecentFiles::addFile(), finished(), CCopasiRootContainer::getConfiguration(), CConfigurationFile::getRecentSBMLFiles(), mFileName, mpThread, mSuccess, and threadFinished().

Referenced by exportSBML().

 {
   if (mSuccess)
     CCopasiRootContainer::getConfiguration()->getRecentSBMLFiles().addFile(mFileName);
 
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(exportSBMLFinished()));
 
   threadFinished();
 }

void DataModelGUI::exportSBMLRun ( )

Definition at line 463 of file DataModelGUI.cpp.

References exportSBML(), CCopasiRootContainer::getDatamodelList(), mFileName, mOverWrite, mpProgressBar, mSBMLExportCOPASIMIRIAM, mSBMLExportIncomplete, mSBMLLevel, mSBMLVersion, and mSuccess.

Referenced by exportSBML().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       mSuccess = (*CCopasiRootContainer::getDatamodelList())[0]->exportSBML(mFileName, mOverWrite, mSBMLLevel, mSBMLVersion, mSBMLExportIncomplete, mSBMLExportCOPASIMIRIAM, mpProgressBar);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::exportSBMLToString ( std::string & sbmlDocumentText )

Definition at line 395 of file DataModelGUI.cpp.

References CProgressBar::create(), exportSBMLToStringFinished(), exportSBMLToStringRun(), finished(), mpProgressBar, mpSBMLExportString, mpThread, and mSuccess.

Referenced by CopasiUI3Window::exportSBMLToString(), and exportSBMLToStringRun().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mpSBMLExportString = & sbmlDocumentText;
 
   mpThread = new CQThread(this, &DataModelGUI::exportSBMLToStringRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(exportSBMLToStringFinished()));
   mpThread->start();
 }

void DataModelGUI::exportSBMLToStringFinished ( )

slot

Definition at line 421 of file DataModelGUI.cpp.

References finished(), mpThread, and threadFinished().

Referenced by exportSBMLToString().

 {
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(exportSBMLToStringFinished()));
 
   threadFinished();
 }

void DataModelGUI::exportSBMLToStringRun ( )

Definition at line 407 of file DataModelGUI.cpp.

References exportSBMLToString(), CCopasiRootContainer::getDatamodelList(), mpProgressBar, mpSBMLExportString, and mSuccess.

Referenced by exportSBMLToString().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       *mpSBMLExportString = (*CCopasiRootContainer::getDatamodelList())[0]->exportSBMLToString(mpProgressBar, 2, 4);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::finished ( bool success )

signal

Referenced by exportMathModel(), exportMathModelFinished(), exportSBML(), exportSBMLFinished(), exportSBMLToString(), exportSBMLToStringFinished(), importSBML(), importSBMLFinished(), importSBMLFromString(), importSBMLFromStringFinished(), loadModel(), loadModelFinished(), miriamDownloadFinished(), saveModel(), saveModelFinished(), threadFinished(), and updateMIRIAM().

COutputDefinitionVector& DataModelGUI::getPlotDefinitionList ( )

Referenced by createModel(), importSBMLFinished(), importSBMLFromStringFinished(), and loadModelFinished().

void DataModelGUI::importCellDesigner ( )

This method tries to import CellDesigner annotations.

Definition at line 782 of file DataModelGUI.cpp.

References CListOfLayouts::addLayout(), SBMLDocumentLoader::createLayout(), CCellDesignerImporter::determineVersion(), CCellDesignerImporter::findCellDesignerAnnotation(), CCellDesignerImporter::findCellDesignerNamespace(), CCopasiDataModel::getCopasi2SBMLMap(), CCopasiDataModel::getCurrentSBMLDocument(), CCopasiRootContainer::getDatamodelList(), SBMLUtils::getIdFromSBase(), CCellDesignerImporter::getLayout(), CCopasiDataModel::getListOfLayouts(), CQMessageBox::question(), CCopasiMessage::RAW, and CCopasiMessage::WARNING.

Referenced by importSBMLFinished(), and importSBMLFromStringFinished().

 {
   // add code to check for CellDesigner annotations
   // ask the user if the annotations should be imported
   CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
   assert(pDataModel != NULL);
 
   if (pDataModel != NULL)
     {
       SBMLDocument* pSBMLDocument = pDataModel->getCurrentSBMLDocument();
 
       if (pSBMLDocument != NULL &&
           pSBMLDocument->getModel() != NULL &&
           pSBMLDocument->getModel()->getAnnotation() != NULL)
         {
           // check for the CellDesigner namespace
           std::pair<bool, std::string> foundNamespace = CCellDesignerImporter::findCellDesignerNamespace(pSBMLDocument);
 
           if (foundNamespace.first == true)
             {
               const XMLNode* pAnno = CCellDesignerImporter::findCellDesignerAnnotation(pSBMLDocument, pSBMLDocument->getModel()->getAnnotation());
 
               // first we check if there are supported cell designer annotations
               if (pAnno != NULL)
                 {
                   // check if the file contains the correct version
                   double version = CCellDesignerImporter::determineVersion(pAnno);
 
                   if (version < 4.0)
                     {
                       CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
                     }
                   else
                     {
                       bool importCD = false;
 #if LIBSBML_VERSION >= 50400
                       // if we don't have a layout import it!
                       LayoutModelPlugin* mplugin = (LayoutModelPlugin*)pSBMLDocument->getModel()->getPlugin("layout");
 
                       if (mplugin == NULL || (mplugin != NULL && mplugin->getNumLayouts() == 0))
                         importCD = true;
 
 #endif
 
                       // ask the user if the CellDesigner annotation should be imported
                       if (importCD || CQMessageBox::question(NULL, "CellDesigner import", "A CellDesigner diagram was found in this file.\nDo you want to import the diagram?" , QMessageBox::Yes | QMessageBox::No , QMessageBox::No) == QMessageBox::Yes)
                         {
                           // do the import
                           CCellDesignerImporter cd_importer(pSBMLDocument);
 
                           if (cd_importer.getLayout() == NULL)
                             {
                               CCopasiMessage(CCopasiMessage::WARNING, "Sorry, CellDesigner annotations could not be imported.");
                             }
                           else
                             {
                               // now we have to import the created layout
                               // create the model map
                               std::string s1, s2;
                               std::map<std::string, std::string> modelmap;
                               std::map<CCopasiObject*, SBase*>::const_iterator it;
                               std::map<CCopasiObject*, SBase*>::const_iterator itEnd = pDataModel->getCopasi2SBMLMap().end();
 
                               for (it = pDataModel->getCopasi2SBMLMap().begin(); it != itEnd; ++it)
                                 {
                                   s1 = SBMLUtils::getIdFromSBase(it->second);
 
                                   if (it->first)
                                     {
                                       s2 = it->first->getKey();
                                     }
                                   else
                                     {
                                       s2 = "";
                                     }
 
                                   if ((s1 != "") && (s2 != ""))
                                     {
                                       modelmap[s1] = s2;
                                     }
                                 }
 
                               // the layout map and the id to key map can be empty
                               std::map<std::string, std::string> layoutmap;
                               std::map<std::string, std::string> idToKeyMap;
                               CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap, idToKeyMap);
 
                               // add the layout to the DataModel
                               if (pLayout != NULL && pDataModel->getListOfLayouts() != NULL)
                                 {
                                   // the addLayout methods expects a map as the second argument which currently is
                                   // ignored, so we just pass an empty one
                                   // TODO maybe the methods actually expects one of the maps above (layoutmap or idToKeyMap), but
                                   // TODO this is not documented in CListOfLayouts
                                   std::map<std::string, std::string> tmp;
                                   pDataModel->getListOfLayouts()->addLayout(pLayout, tmp);
                                 }
                               else
                                 {
                                   CCopasiMessage(CCopasiMessage::WARNING, "Sorry, Layout from CellDesigner annotations could not be created.");
                                 }
                             }
                         }
                     }
                 }
               else
                 {
                   CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
                 }
             }
         }
     }
 }

void DataModelGUI::importSBML ( const std::string & fileName )

Definition at line 354 of file DataModelGUI.cpp.

References CProgressBar::create(), finished(), importSBMLFinished(), importSBMLRun(), mFileName, mpProgressBar, mpThread, and mSuccess.

Referenced by importSBMLRun(), and CopasiUI3Window::slotImportSBML().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mFileName = fileName;
   mpThread = new CQThread(this, &DataModelGUI::importSBMLRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(importSBMLFinished()));
   mpThread->start();
 }

void DataModelGUI::importSBMLFinished ( )

slot

Definition at line 379 of file DataModelGUI.cpp.

References CRecentFiles::addFile(), finished(), CCopasiRootContainer::getConfiguration(), CCopasiRootContainer::getDatamodelList(), getPlotDefinitionList(), CConfigurationFile::getRecentSBMLFiles(), importCellDesigner(), linkDataModelToGUI(), mFileName, mOutputHandlerPlot, mpThread, mSuccess, COutputHandlerPlot::setOutputDefinitionVector(), and threadFinished().

Referenced by importSBML().

 {
   if (mSuccess)
     {
       this->importCellDesigner();
       CCopasiRootContainer::getConfiguration()->getRecentSBMLFiles().addFile(mFileName);
 
       mOutputHandlerPlot.setOutputDefinitionVector((*CCopasiRootContainer::getDatamodelList())[0]->getPlotDefinitionList());
       linkDataModelToGUI();
     }
 
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(importSBMLFinished()));
 
   threadFinished();
 }

void DataModelGUI::importSBMLFromString ( const std::string & sbmlDocumentText )

Definition at line 290 of file DataModelGUI.cpp.

References CProgressBar::create(), finished(), importSBMLFromStringFinished(), importSBMLFromStringRun(), mpProgressBar, mpThread, mSBMLImportString, and mSuccess.

Referenced by CopasiUI3Window::importSBMLFromString(), and importSBMLFromStringRun().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mSBMLImportString = sbmlDocumentText;
 
   mpThread = new CQThread(this, &DataModelGUI::importSBMLFromStringRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(importSBMLFromStringFinished()));
   mpThread->start();
 }

void DataModelGUI::importSBMLFromStringFinished ( )

slot

Definition at line 316 of file DataModelGUI.cpp.

References finished(), CCopasiRootContainer::getDatamodelList(), getPlotDefinitionList(), importCellDesigner(), linkDataModelToGUI(), mOutputHandlerPlot, mpThread, mSBMLImportString, mSuccess, COutputHandlerPlot::setOutputDefinitionVector(), and threadFinished().

Referenced by importSBMLFromString().

 {
   mSBMLImportString = "";
 
   if (mSuccess)
     {
       // can't run this in a separate thread because it uses GUI routines
       // TODO maybe put the main part of this routine in a separate thread after
       // TODO asking the user
       this->importCellDesigner();
       mOutputHandlerPlot.setOutputDefinitionVector((*CCopasiRootContainer::getDatamodelList())[0]->getPlotDefinitionList());
       linkDataModelToGUI();
     }
 
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(importSBMLFromStringFinished()));
 
   threadFinished();
 }

void DataModelGUI::importSBMLFromStringRun ( )

Definition at line 302 of file DataModelGUI.cpp.

References CCopasiRootContainer::getDatamodelList(), importSBMLFromString(), mpProgressBar, mSBMLImportString, and mSuccess.

Referenced by importSBMLFromString().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       mSuccess = (*CCopasiRootContainer::getDatamodelList())[0]->importSBMLFromString(mSBMLImportString, mpProgressBar, false);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::importSBMLRun ( )

Definition at line 365 of file DataModelGUI.cpp.

References CCopasiRootContainer::getDatamodelList(), importSBML(), mFileName, mpProgressBar, and mSuccess.

Referenced by importSBML().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       mSuccess = (*CCopasiRootContainer::getDatamodelList())[0]->importSBML(mFileName, mpProgressBar, false);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::linkDataModelToGUI ( )

private

Definition at line 123 of file DataModelGUI.cpp.

References CCopasiDataModel::deleteOldData(), CCopasiRootContainer::getDatamodelList(), and mListViews.

Referenced by createModel(), importSBMLFinished(), importSBMLFromStringFinished(), and loadModelFinished().

 {
   assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
   CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
   assert(pDataModel != NULL);
 
   std::set< ListViews * >::iterator it = mListViews.begin();
   std::set< ListViews * >::iterator end = mListViews.end();
 
   for (; it != end; ++it)
     {
       (*it)->setDataModel(this);
     }
 
   pDataModel->deleteOldData();
 }

void DataModelGUI::loadFunctionDB ( const std::string & fileName )

Definition at line 344 of file DataModelGUI.cpp.

References ListViews::DELETE, ListViews::FUNCTION, CCopasiRootContainer::getFunctionList(), CFunctionDB::load(), and notify().

Referenced by CopasiUI3Window::slotFunctionDBLoad().

 {
   CFunctionDB* pFunctionDB = CCopasiRootContainer::getFunctionList();
 
   if (pFunctionDB == NULL) return;
 
   if (pFunctionDB->load(fileName))
     emit notify(ListViews::FUNCTION, ListViews::DELETE, "");
 }

void DataModelGUI::loadModel ( const std::string & fileName )

Definition at line 212 of file DataModelGUI.cpp.

References CProgressBar::create(), finished(), loadModelFinished(), loadModelRun(), mFileName, mpProgressBar, mpThread, and mSuccess.

Referenced by loadModelRun(), and CopasiUI3Window::slotFileOpen().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mFileName = fileName;
 
   mpThread = new CQThread(this, &DataModelGUI::loadModelRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(loadModelFinished()));
   mpThread->start();
 }

void DataModelGUI::loadModelFinished ( )

slot

Definition at line 238 of file DataModelGUI.cpp.

References CRecentFiles::addFile(), finished(), CCopasiRootContainer::getConfiguration(), CCopasiRootContainer::getDatamodelList(), getPlotDefinitionList(), CConfigurationFile::getRecentFiles(), linkDataModelToGUI(), mFileName, mOutputHandlerPlot, mpThread, mSuccess, COutputHandlerPlot::setOutputDefinitionVector(), and threadFinished().

Referenced by loadModel().

 {
   if (mSuccess)
     {
       CCopasiRootContainer::getConfiguration()->getRecentFiles().addFile(mFileName);
 
       mOutputHandlerPlot.setOutputDefinitionVector((*CCopasiRootContainer::getDatamodelList())[0]->getPlotDefinitionList());
       linkDataModelToGUI();
     }
 
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(loadModelFinished()));
 
   threadFinished();
 }

void DataModelGUI::loadModelRun ( )

Definition at line 224 of file DataModelGUI.cpp.

References CCopasiRootContainer::getDatamodelList(), loadModel(), mFileName, mpProgressBar, and mSuccess.

Referenced by loadModel().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       mSuccess = (*CCopasiRootContainer::getDatamodelList())[0]->loadModel(mFileName, mpProgressBar, false);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::miriamDownloadFinished ( QNetworkReply * reply )

slot

Definition at line 522 of file DataModelGUI.cpp.

References finished(), COptions::getValue(), mDownloadedBytes, mpMiriamResources, mpProgressBar, mUpdateItem, pdelete, CProgressBar::progressItem(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

Referenced by updateMIRIAM().

 {
   bool success = true;
   mDownloadedBytes = 100;
   mpProgressBar->progressItem(mUpdateItem);
 
   CMIRIAMResources & miriamResources = *mpMiriamResources;
 
   if (reply != NULL && reply->error() == QNetworkReply::NoError)
     {
       std::string filename;
       COptions::getValue("ConfigDir", filename);
       filename += "/miriam.xml";
 
       QFile *miriamFile = new QFile(filename.c_str());
 
       if (miriamFile->open(QFile::WriteOnly))
         {
           miriamFile->write(reply->readAll());
           miriamFile->flush();
           miriamFile->close();
           success = miriamResources.updateMIRIAMResourcesFromFile(mpProgressBar, filename);
         }
 
       delete miriamFile;
     }
   else
     {
       success = false;
     }
 
   reply->deleteLater();
 
   pdelete(mpProgressBar);
 
   // notify UI to pick up
   emit finished(success);
 }

void DataModelGUI::miriamDownloadProgress	(	qint64	received,
		qint64	total
	)

slot

Definition at line 561 of file DataModelGUI.cpp.

References mDownloadedBytes, mpProgressBar, mUpdateItem, and CProgressBar::progressItem().

Referenced by updateMIRIAM().

 {
   if (total != -1)
     {
       mDownloadedBytes = 100 * double(received) / double(total);
     }
   else
     {
       ++mDownloadedBytes;
     }
 
   if (!mpProgressBar->progressItem(mUpdateItem))
     {
       QNetworkReply *reply = dynamic_cast<QNetworkReply*>(sender());
 
       if (reply != NULL) reply->abort();
     }
 }

bool DataModelGUI::notify	(	ListViews::ObjectType	objectType,
		ListViews::Action	action,
		const std::string &	key = `""`
	)

Definition at line 607 of file DataModelGUI.cpp.

References mpProgressBar, notifyView(), refreshInitialValues(), and ListViews::RENAME.

 {
   // The GUI is inactive whenever a progress bar exist. We wait with updates
   // until then.
   if (mpProgressBar != NULL) return false;
 
   // update all initial value
   if (action != ListViews::RENAME)
     refreshInitialValues();
 
   emit notifyView(objectType, action, key);
 
   return true;
 }

void DataModelGUI::notifyView	(	ListViews::ObjectType	objectType,
		ListViews::Action	action,
		std::string	key = `""`
	)

signal

Referenced by notify().

void DataModelGUI::refreshInitialValues ( )

Definition at line 728 of file DataModelGUI.cpp.

References buildChangedObjects(), CCopasiRootContainer::getDatamodelList(), mUpdateVector, and CModel::refreshActiveParameterSet().

Referenced by notify(), CopasiSlider::setValue(), SliderDialog::updateAllSliders(), and CopasiSlider::updateValue().

 {
   buildChangedObjects();
 
   std::vector< Refresh * >::iterator it = mUpdateVector.begin();
   std::vector< Refresh * >::iterator end = mUpdateVector.end();
 
   for (; it != end; ++it)
     (**it)();
 
   assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
   CModel * pModel = (*CCopasiRootContainer::getDatamodelList())[0]->getModel();
 
   pModel->refreshActiveParameterSet();
 }

void DataModelGUI::registerListView ( ListViews * pListView )

Definition at line 622 of file DataModelGUI.cpp.

References mListViews, and ListViews::setDataModel().

Referenced by CopasiUI3Window::CopasiUI3Window().

 {
   pListView->setDataModel(this);
   mListViews.insert(pListView);
 }

void DataModelGUI::saveFunctionDB ( const std::string & fileName )

Definition at line 335 of file DataModelGUI.cpp.

References CCopasiRootContainer::getFunctionList(), and CFunctionDB::save().

Referenced by CopasiUI3Window::slotFunctionDBSave().

 {
   CFunctionDB* pFunctionDB = CCopasiRootContainer::getFunctionList();
 
   if (pFunctionDB == NULL) return;
 
   pFunctionDB->save(fileName);
 }

void DataModelGUI::saveModel	(	const std::string &	fileName,
		bool	overwriteFile = `false`
	)

Definition at line 253 of file DataModelGUI.cpp.

References CProgressBar::create(), finished(), mFileName, mOverWrite, mpProgressBar, mpThread, mSuccess, saveModelFinished(), and saveModelRun().

Referenced by saveModelRun(), CopasiUI3Window::slotFileSave(), and CopasiUI3Window::slotFileSaveAs().

 {
   mpProgressBar = CProgressBar::create();
 
   mSuccess = true;
   mFileName = fileName;
   mOverWrite = overwriteFile;
 
   mpThread = new CQThread(this, &DataModelGUI::saveModelRun);
   connect(mpThread, SIGNAL(finished()), this, SLOT(saveModelFinished()));
   mpThread->start();
 }

void DataModelGUI::saveModelFinished ( )

slot

Definition at line 280 of file DataModelGUI.cpp.

References CRecentFiles::addFile(), finished(), CCopasiRootContainer::getConfiguration(), CConfigurationFile::getRecentFiles(), mFileName, mpThread, mSuccess, and threadFinished().

Referenced by saveModel().

 {
   if (mSuccess)
     CCopasiRootContainer::getConfiguration()->getRecentFiles().addFile(mFileName);
 
   disconnect(mpThread, SIGNAL(finished()), this, SLOT(saveModelFinished()));
 
   threadFinished();
 }

void DataModelGUI::saveModelRun ( )

Definition at line 266 of file DataModelGUI.cpp.

References CCopasiRootContainer::getDatamodelList(), mFileName, mOverWrite, mpProgressBar, mSuccess, and saveModel().

Referenced by saveModel().

 {
   try
     {
       assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
       mSuccess = (*CCopasiRootContainer::getDatamodelList())[0]->saveModel(mFileName, mpProgressBar, mOverWrite);
     }
 
   catch (...)
     {
       mSuccess = false;
     }
 }

void DataModelGUI::setFramework ( int framework )

Definition at line 744 of file DataModelGUI.cpp.

References mFramework, and mListViews.

Referenced by CopasiUI3Window::slotFrameworkChanged().

 {
   mFramework = framework;
 
   std::set< ListViews * >::iterator it = mListViews.begin();
   std::set< ListViews * >::iterator end = mListViews.end();
 
   for (; it != end; ++it)
     {
       (*it)->setFramework(mFramework);
     }
 }

void DataModelGUI::threadFinished ( )

private

Definition at line 428 of file DataModelGUI.cpp.

References CProgressBar::finish(), finished(), mpProgressBar, mpThread, and mSuccess.

Referenced by exportMathModelFinished(), exportSBMLFinished(), exportSBMLToStringFinished(), importSBMLFinished(), importSBMLFromStringFinished(), loadModelFinished(), and saveModelFinished().

 {
   if (mpThread != NULL)
     {
       mpThread->deleteLater();
       mpThread = NULL;
     }
 
   if (mpProgressBar != NULL)
     {
       mpProgressBar->finish();
       mpProgressBar->deleteLater();
       mpProgressBar = NULL;
     }
 
   emit finished(mSuccess);
 }

void DataModelGUI::updateCompleteView ( )

signal

bool DataModelGUI::updateMIRIAM ( CMIRIAMResources & miriamResources )

Definition at line 580 of file DataModelGUI.cpp.

References CProgressBar::create(), finished(), mDownloadedBytes, mDownloadedTotalBytes, miriamDownloadFinished(), miriamDownloadProgress(), mpMiriamResources, mpProgressBar, mUpdateItem, and CProgressBar::setName().

Referenced by CopasiUI3Window::slotUpdateMIRIAM().

 {
   bool success = true;
 
   mpMiriamResources = &miriamResources;
 
   mpProgressBar = CProgressBar::create();
   mpProgressBar->setName("MIRIAM Resources Update...");
   mDownloadedBytes = 0; mDownloadedTotalBytes = 100;
   mUpdateItem = ((CProcessReport*)mpProgressBar)->addItem("Download MIRIAM info", mDownloadedBytes, &mDownloadedTotalBytes);
 
   QNetworkAccessManager *manager = new QNetworkAccessManager(this);
 
   connect(manager, SIGNAL(finished(QNetworkReply*)),
           this, SLOT(miriamDownloadFinished(QNetworkReply*)));
 
   QNetworkReply* reply = manager->get(QNetworkRequest(QUrl("http://www.ebi.ac.uk/miriam/main/export/xml/")));
   connect(reply, SIGNAL(downloadProgress(qint64, qint64)),
           this, SLOT(miriamDownloadProgress(qint64, qint64)));
 
   return success;
 }

void DataModelGUI::updateMIRIAMResourceContents ( )

Definition at line 757 of file DataModelGUI.cpp.

References mListViews.

Referenced by CopasiUI3Window::slotUpdateMIRIAMFinished().

 {
   std::set< ListViews * >::iterator it = mListViews.begin();
   std::set< ListViews * >::iterator end = mListViews.end();
 
   for (; it != end; ++it)
     {
       (*it)->updateMIRIAMResourceContents();
     }
 }