#include <arguments.h>

Collaboration diagram for Arguments:

Public Member Functions
	Arguments (int argc, char *argv[])

const std::string &	getFilename () const

const std::string &	getFileType () const

char **	getInitArgs () const

const std::string &	getOutputDir () const

int	getOutputToGenerate () const

const std::string &	getReportFile () const

const std::string &	getTaskName () const

int	getTaskToSwitchTo () const

bool	handleCommandLine () const

bool	haveFile () const

bool	haveOutputDir () const

bool	haveReportFile () const

bool	haveTaskName () const

bool	isDisablePlots () const

bool	isDisableRandomizeStartValues () const

bool	isDisableStatistic () const

bool	isGenerateOutput () const

bool	isHideWindow () const

bool	isQuitAfterTaskExecution () const

bool	isRunScheduled () const

bool	isSaveLayout () const

bool	isSolutionStatistic () const

bool	isSwitchToTask () const

bool	isValid () const

std::string	prepareModel () const

Static Public Member Functions
static CCopasiTask *	getFirstScheduledTask ()

Private Member Functions
CCopasiTask *	getTask () const

CCopasiTask *	getTaskForName (const std::string &name) const

void	parseArgs (int arc, char *argv[])

Private Attributes
int	mArgc

char **	mArgv

bool	mClearTargets

bool	mDisablePlots

bool	mDisableRandomizeStartValues

bool	mDisableStatistic

std::string	mFilename

std::string	mFileType

int	mGenerateOutput

bool	mHideWindow

std::string	mOutputDir

bool	mQuitAfterTaskExecution

std::string	mReportFile

bool	mRunScheduled

bool	mSaveLayout

bool	mSetSolutionStatistic

int	mSwitchToTask

std::string	mTask

Detailed Description

Definition at line 13 of file arguments.h.

Constructor & Destructor Documentation

Arguments::Arguments	(	int	argc,
		char *	argv[]
	)

Definition at line 31 of file arguments.cpp.

References parseArgs().

   : mFilename("")
   , mOutputDir("")
   , mTask("")
   , mReportFile("")
   , mFileType("pdf")
   , mRunScheduled(false)
   , mSetSolutionStatistic(false)
   , mDisableStatistic(false)
   , mDisablePlots(false)
   , mDisableRandomizeStartValues(false)
   , mHideWindow(false)
   , mQuitAfterTaskExecution(false)
   , mClearTargets(false)
   , mSwitchToTask(-1)
   , mGenerateOutput(-1)
   , mArgc(argc)
   , mArgv(argv)
 {
   parseArgs(argc, argv);
 }

Member Function Documentation

const std::string & Arguments::getFilename ( ) const

Definition at line 255 of file arguments.cpp.

References mFilename.

Referenced by prepareModel(), and Worker::Worker().

 {
   return mFilename;
 }

const std::string & Arguments::getFileType ( ) const

Definition at line 260 of file arguments.cpp.

References mFileType.

Referenced by Worker::slotNotify().

 {
   return mFileType;
 }

CCopasiTask * Arguments::getFirstScheduledTask ( )

static

Definition at line 53 of file arguments.cpp.

References CCopasiRootContainer::getDatamodelList(), CCopasiTask::isScheduled(), and CCopasiVector< T >::size().

Referenced by Worker::finishedLoading(), and getTask().

 {
   CCopasiVectorN<CCopasiTask> &taskList = *(*CCopasiRootContainer::getDatamodelList())[0]->getTaskList();
 
   for (size_t i = 0; i < taskList.size(); ++i)
     {
       CCopasiTask *current = taskList[i];
 
       if (current->isScheduled())
         return current;
     }
 
   return NULL;
 }

char ** Arguments::getInitArgs ( ) const

Definition at line 247 of file arguments.cpp.

References mArgv, and mFilename.

 {
   char ** result = (char**)malloc(sizeof(char*) * 2);
   result[0] = strdup(mArgv[0]);
   result[1] = strdup((mFilename + ".view.cps").c_str());
   return result;
 }

const std::string & Arguments::getOutputDir ( ) const

Definition at line 106 of file arguments.cpp.

References mOutputDir.

Referenced by Worker::slotNotify().

 {
   return mOutputDir;
 }

int Arguments::getOutputToGenerate ( ) const

Definition at line 96 of file arguments.cpp.

References mGenerateOutput.

 {
   return mGenerateOutput;
 }

const std::string & Arguments::getReportFile ( ) const

Definition at line 151 of file arguments.cpp.

References mReportFile.

 {
   return mReportFile;
 }

CCopasiTask * Arguments::getTask ( ) const

private

Definition at line 83 of file arguments.cpp.

References getFirstScheduledTask(), getTaskForName(), haveTaskName(), and mTask.

Referenced by prepareModel().

 {
   if (haveTaskName())
     return getTaskForName(mTask);
 
   return getFirstScheduledTask();
 }

CCopasiTask * Arguments::getTaskForName ( const std::string & name ) const

private

Definition at line 68 of file arguments.cpp.

References CCopasiRootContainer::getDatamodelList(), CCopasiObject::getObjectName(), and CCopasiVector< T >::size().

Referenced by getTask().

 {
   CCopasiVectorN<CCopasiTask> &taskList = *(*CCopasiRootContainer::getDatamodelList())[0]->getTaskList();
 
   for (size_t i = 0; i < taskList.size(); ++i)
     {
       CCopasiTask *current = taskList[i];
 
       if (current->getObjectName() == name)
         return current;
     }
 
   return NULL;
 }

const std::string & Arguments::getTaskName ( ) const

Definition at line 280 of file arguments.cpp.

References mTask.

 {
   return mTask;
 }

int Arguments::getTaskToSwitchTo ( ) const

Definition at line 242 of file arguments.cpp.

References mSwitchToTask.

Referenced by Worker::finishedLoading().

 {
   return mSwitchToTask;
 }

bool Arguments::handleCommandLine ( ) const

Definition at line 116 of file arguments.cpp.

References CCopasiRootContainer::addDatamodel(), CCopasiMessage::getAllMessageText(), CCopasiDataModel::getListOfLayouts(), CCopasiException::getMessage(), CCopasiObject::getObjectName(), haveFile(), haveOutputDir(), CCopasiDataModel::importSBML(), CCopasiRootContainer::init(), CCopasiDataModel::loadModel(), mFilename, mFileType, mOutputDir, mSaveLayout, CQLayoutScene::recreate(), CQLayoutScene::saveToFile(), and CCopasiVector< T >::size().

Referenced by main().

 {
   if (!(mSaveLayout && haveFile() && haveOutputDir()))
     return false;
 
   CCopasiRootContainer::init(0, NULL, false);
   CCopasiDataModel& model = *CCopasiRootContainer::addDatamodel();
 
   try
     {
       if (!model.importSBML(mFilename, NULL))
         model.loadModel(mFilename, NULL);
     }
   catch (CCopasiException &ex)
     {
       std::cerr << ex.getMessage().getAllMessageText() << std::endl;
       return true;
     }
 
   for (size_t i = 0; i < model.getListOfLayouts()->size(); ++i)
     {
       CLayout* layout = (*model.getListOfLayouts())[i];
       CQLayoutScene scene(layout, &model);
       scene.recreate();
       scene.saveToFile(mOutputDir + "/" + QFileInfo(mFilename.c_str()).baseName().toStdString() + "_" + layout->getObjectName() + "." + mFileType, mFileType);
     }
 
   return true;
 }

bool Arguments::haveFile ( ) const

Definition at line 265 of file arguments.cpp.

References mFilename.

Referenced by handleCommandLine(), and isValid().

 {
   return !mFilename.empty();
 }

bool Arguments::haveOutputDir ( ) const

Definition at line 101 of file arguments.cpp.

References mOutputDir.

Referenced by handleCommandLine(), and Worker::slotNotify().

 {
   return !mOutputDir.empty();
 }

bool Arguments::haveReportFile ( ) const

Definition at line 111 of file arguments.cpp.

References mReportFile.

Referenced by prepareModel().

 {
   return !mReportFile.empty();
 }

bool Arguments::haveTaskName ( ) const

Definition at line 275 of file arguments.cpp.

References mTask.

Referenced by getTask().

 {
   return !mTask.empty();
 }

bool Arguments::isDisablePlots ( ) const

Definition at line 300 of file arguments.cpp.

References mDisablePlots.

 {
   return mDisablePlots;
 }

bool Arguments::isDisableRandomizeStartValues ( ) const

Definition at line 295 of file arguments.cpp.

References mDisableRandomizeStartValues.

Referenced by prepareModel().

 {
   return mDisableRandomizeStartValues;
 }

bool Arguments::isDisableStatistic ( ) const

Definition at line 290 of file arguments.cpp.

References mDisableStatistic.

Referenced by prepareModel().

 {
   return mDisableStatistic;
 }

bool Arguments::isGenerateOutput ( ) const

Definition at line 91 of file arguments.cpp.

References mGenerateOutput.

Referenced by prepareModel().

 {
   return mGenerateOutput != -1;
 }

bool Arguments::isHideWindow ( ) const

Definition at line 305 of file arguments.cpp.

References mHideWindow.

Referenced by Worker::finishedLoading().

 {
   return mHideWindow;
 }

bool Arguments::isQuitAfterTaskExecution ( ) const

Definition at line 310 of file arguments.cpp.

References mQuitAfterTaskExecution.

Referenced by Worker::slotNotify().

 {
   return mQuitAfterTaskExecution;
 }

bool Arguments::isRunScheduled ( ) const

Definition at line 270 of file arguments.cpp.

References mRunScheduled.

Referenced by Worker::finishedLoading().

 {
   return mRunScheduled;
 }

bool Arguments::isSaveLayout ( ) const

Definition at line 146 of file arguments.cpp.

References mSaveLayout.

 {
   return mSaveLayout;
 }

bool Arguments::isSolutionStatistic ( ) const

Definition at line 285 of file arguments.cpp.

References mSetSolutionStatistic.

 {
   return mSetSolutionStatistic;
 }

bool Arguments::isSwitchToTask ( ) const

Definition at line 237 of file arguments.cpp.

References mSwitchToTask.

Referenced by Worker::finishedLoading().

 {
   return mSwitchToTask != -1;
 }

bool Arguments::isValid ( ) const

Definition at line 315 of file arguments.cpp.

References haveFile(), and mFilename.

Referenced by main(), and prepareModel().

 {
   if (!haveFile()) return false;
 
   if (!QFile(mFilename.c_str()).exists()) return false;
 
   return true;
 }

void Arguments::parseArgs	(	int	arc,
		char *	argv[]
	)

private

Definition at line 156 of file arguments.cpp.

References mClearTargets, mDisablePlots, mDisableRandomizeStartValues, mDisableStatistic, mFilename, mFileType, mGenerateOutput, mHideWindow, mOutputDir, mQuitAfterTaskExecution, mReportFile, mRunScheduled, mSaveLayout, mSetSolutionStatistic, mSwitchToTask, and mTask.

Referenced by Arguments().

 {
   for (int i = 1; i < argc; ++i)
     {
       QString current(argv[i]);
       QString lower = current.toLower();
 
       if (lower == "-r" || lower == "--run-scheduled")
         {
           mRunScheduled = true;
         }
       else if (lower == "-q" || lower == "--quit-after-task-execution")
         {
           mQuitAfterTaskExecution = true;
         }
       else if (i + 1 < argc && (lower == "--switch-to-task"))
         {
           mSwitchToTask = QString(argv[i + 1]).toInt();
           ++i;
         }
       else if (i + 1 < argc && (lower == "--task"))
         {
           mTask = argv[i + 1];
           ++i;
         }
       else if (lower == "--set-solution-statistic")
         {
           mSetSolutionStatistic = true;
         }
       else if (lower == "--disable-calculate-statistic")
         {
           mDisableStatistic = true;
         }
       else if (lower == "--disable-other-plots")
         {
           mDisablePlots = true;
         }
       else if (lower == "--hide")
         {
           mHideWindow = true;
         }
       else if (lower == "--clear-targets")
         {
           mClearTargets = true;
         }
       else if (lower == "--disable-randomize-startvalues")
         {
           mDisableRandomizeStartValues = true;
         }
       else if (lower == "--save-layout")
         {
           mSaveLayout = true;
         }
       else if (i + 1 < argc && (lower == "-g" || lower == "--generate-output"))
         {
           mGenerateOutput = QString(argv[i + 1]).toInt();
           ++i;
         }
       else if (i + 1 < argc && (lower == "-f" || lower == "--set-report-file"))
         {
           mReportFile = argv[i + 1];
           ++i;
         }
       else if (i + 1 < argc && (lower == "-o" || lower == "--set-output-dir"))
         {
           mOutputDir = argv[i + 1];
           ++i;
         }
       else if (i + 1 < argc && (lower == "-t" || lower == "--set-file-type"))
         {
           mFileType = argv[i + 1];
           ++i;
         }
       else if (QFile(current).exists() && mFilename.empty())
         {
           // only if we don't have a file yet, we assume this to be the copasi file
           mFilename = current.toStdString();
         }
     }
 }

std::string Arguments::prepareModel ( ) const

Definition at line 324 of file arguments.cpp.

References COutputAssistant::createDefaultOutput(), CCopasiRootContainer::getDatamodelList(), getFilename(), COutputAssistant::getListOfDefaultOutputDescriptions(), CCopasiDataModel::getPlotDefinitionList(), CCopasiTask::getProblem(), CCopasiTask::getReport(), getTask(), CCopasiDataModel::getTaskList(), haveReportFile(), isDisableRandomizeStartValues(), isDisableStatistic(), isGenerateOutput(), isValid(), CCopasiDataModel::loadModel(), mClearTargets, mDisablePlots, mGenerateOutput, mReportFile, mSetSolutionStatistic, CCopasiDataModel::saveModel(), COptProblem::setCalculateStatistics(), COptTask::setMethodType(), COptProblem::setRandomizeStartValues(), CReport::setTarget(), CCopasiVector< T >::size(), and CCopasiMethod::Statistics.

Referenced by main().

 {
   if (!isValid()) return "";
 
   CCopasiDataModel* model = (*CCopasiRootContainer::getDatamodelList())[0];
   model->loadModel(getFilename(), NULL);
 
   if (mDisablePlots)
     {
       for (size_t index = 0; index < model->getPlotDefinitionList()->size(); ++index)
         {
           (*model->getPlotDefinitionList())[index]->setActive(false);
         }
     }
 
   if (mClearTargets)
     {
       for (size_t index = 0; index < model->getTaskList()->size(); ++index)
         {
           (*model->getTaskList())[index]->getReport().setTarget("");
         }
     }
 
   CCopasiTask *task = getTask();
 
   if (task != NULL)
     {
       if (isGenerateOutput())
         {
           // calls initialize which is private
           COutputAssistant::getListOfDefaultOutputDescriptions();
 
           // generate the output
           COutputAssistant::createDefaultOutput(mGenerateOutput, task, model);
         }
 
       if (haveReportFile())
         task->getReport().setTarget(mReportFile);
 
       COptTask* optTask = dynamic_cast<COptTask*>(task);
 
       if (optTask != NULL)
         {
           COptProblem *problem = (COptProblem *)optTask->getProblem();
 
           if (mSetSolutionStatistic)
             optTask->setMethodType(CCopasiMethod::Statistics);
 
           if (isDisableRandomizeStartValues())
             problem->setRandomizeStartValues(false);
 
           if (isDisableStatistic())
             problem->setCalculateStatistics(false);
         }
     }
 
   model->saveModel(getFilename() + ".view.cps", NULL, true);
   return getFilename() + ".view.cps";
 }