public static IDimension TryGetDimension(this IDimensionFactory dimensionFactory, string dimensionName)
{
try
{
return(dimensionFactory.Dimension(dimensionName));
}
catch (KeyNotFoundException)
{
return(null);
}
}
public FormulaTask(
IObjectPathFactory objectPathFactory,
IObjectBaseFactory objectBaseFactory,
IAliasCreator aliasCreator,
IDimensionFactory dimensionFactory)
{
_objectPathFactory = objectPathFactory;
_objectBaseFactory = objectBaseFactory;
_aliasCreator = aliasCreator;
_dimensionFactory = dimensionFactory;
}
protected ParameterIdentificationChartFeedbackPresenter(IParameterIdentificationChartFeedbackView view, IChartDisplayPresenter chartDisplayPresenter, IDimensionFactory dimensionFactory, IDisplayUnitRetriever displayUnitRetriever, TChart chart) : base(view)
{
_chartDisplayPresenter = chartDisplayPresenter;
_displayUnitRetriever = displayUnitRetriever;
_view.AddChartView(chartDisplayPresenter.View);
AddSubPresenters(_chartDisplayPresenter);
_dimensionFactory = dimensionFactory;
_chart = chart;
_outputMappingComparer = new OutputMappingByFullOutputPathComparer();
_chartDisplayPresenter.Edit(_chart, new ChartFontAndSizeSettings().ForParameterIdentificationFeedback());
}
public Converter52To531(ISolverSettingsFactory solverSettingsFactory, ISimulationResultsLoader simulationResultsLoader,
ICompoundConverter52 compoundConverter, IObjectPathFactory objectPathFactory, IoC container, IDimensionFactory dimensionFactory)
{
_solverSettingsFactory = solverSettingsFactory;
_simulationResultsLoader = simulationResultsLoader;
_compoundConverter = compoundConverter;
_objectPathFactory = objectPathFactory;
_container = container;
_dimensionFactory = dimensionFactory;
_simulationChartElementCache = new List <XElement>();
}
public DataFactory(
IDimensionFactory dimensionFactory,
IObjectPathFactory objectPathFactory,
IDisplayUnitRetriever displayUnitRetriever,
IDataRepositoryTask dataRepositoryTask)
{
_dimensionFactory = dimensionFactory;
_objectPathFactory = objectPathFactory;
_displayUnitRetriever = displayUnitRetriever;
_dataRepositoryTask = dataRepositoryTask;
}
public PKParameterTask(
IPKParameterRepository pkParameterRepository,
IDimensionTask dimensionTask,
IDimensionFactory dimensionFactory,
IOSPSuiteLogger logger)
{
_pkParameterRepository = pkParameterRepository;
_dimensionTask = dimensionTask;
_dimensionFactory = dimensionFactory;
_logger = logger;
}
protected override void Context()
{
_dialogCreator = A.Fake <IDialogCreator>();
_dataRepositoryTask = A.Fake <IDataRepositoryTask>();
_quantityDisplayPathMapper = A.Fake <IQuantityPathToQuantityDisplayPathMapper>();
_pkAnalysesTask = A.Fake <IPKAnalysesTask>();
_globalPKAnalysisMapper = A.Fake <IGlobalPKAnalysisToDataTableMapper>();
_dimensionFactory = A.Fake <IDimensionFactory>();
sut = new PKAnalysisExportTask(_dialogCreator, _dataRepositoryTask, _quantityDisplayPathMapper, _globalPKAnalysisMapper, _dimensionFactory);
}
protected override void Context()
{
_dimensionFactory = A.Fake <IDimensionFactory>();
_view = A.Fake <IParameterIdentificationErrorHistoryFeedbackView>();
_chartDisplayPresenter = A.Fake <IChartDisplayPresenter>();
sut = new ParameterIdentificationErrorHistoryFeedbackPresenter(_view, _chartDisplayPresenter, _dimensionFactory);
_runState = A.Fake <ParameterIdentificationRunState>();
_errorHistory = new List <float>();
A.CallTo(() => _runState.ErrorHistory).Returns(_errorHistory);
}
public ObjectBaseFactory(
Utility.Container.IContainer container,
IDimensionFactory dimensionFactory,
IIdGenerator idGenerator,
ICreationMetaDataFactory creationMetaDataFactory)
{
_container = container;
_dimensionFactory = dimensionFactory;
_idGenerator = idGenerator;
_creationMetaDataFactory = creationMetaDataFactory;
}
public CompartmentImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory,
IMoBiSpatialStructureFactory spatialStructureFactory, IMoBiDimensionFactory moBiDimensionFactory,
ASTHandler astHandler, IMoBiContext context, IFormulaFactory formulaFactory, IUnitDefinitionImporter unitDefinitionImporter)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_objectBaseFactory = objectBaseFactory;
_spatialStructureFactory = spatialStructureFactory;
_dimensionFactory = moBiDimensionFactory;
_formulaFactory = formulaFactory;
_unitDefinitionImporter = unitDefinitionImporter;
}
public override void GlobalContext()
{
base.GlobalContext();
_dialogCreator = A.Fake <IDialogCreator>();
_importer = A.Fake <IImporter>();
_applicationController = A.Fake <IApplicationController>();
_reloadPresenter = A.Fake <IImporterReloadPresenter>();
_dimensionFactory = A.Fake <IDimensionFactory>();
A.CallTo(() => _applicationController.Start <IImporterReloadPresenter>()).Returns(_reloadPresenter);
A.CallTo(() => _reloadPresenter.Canceled()).Returns(false);
}
public SerializationContextFactory(
IDimensionFactory dimensionFactory,
IObjectBaseFactory objectBaseFactory,
ICloneManagerForModel cloneManagerForModel,
IContainer container
)
{
_dimensionFactory = dimensionFactory;
_objectBaseFactory = objectBaseFactory;
_cloneManagerForModel = cloneManagerForModel;
_container = container;
}
protected override void Context()
{
_context = A.Fake <IInteractionTaskContext>();
_simulationPersitor = A.Fake <ISimulationPersistor>();
_dialogCreator = A.Fake <IDialogCreator>();
_forbiddenNamesRetriever = A.Fake <IForbiddenNamesRetriever>();
_dataRepositoryTask = A.Fake <IDataRepositoryTask>();
_simulationModelExporter = A.Fake <ISimModelExporter>();
_reportCreator = A.Fake <IModelReportCreator>();
_dimensionFactory = A.Fake <IDimensionFactory>();
sut = new EditTasksForSimulation(_context, _simulationPersitor, _dialogCreator, _forbiddenNamesRetriever, _dataRepositoryTask, _reportCreator, _simulationModelExporter, _dimensionFactory);
}
public SimulationTransferLoader(IDimensionFactory dimensionFactory, IObjectBaseFactory objectBaseFactory,
ISimulationPersistor simulationPersister, IProjectRetriever projectRetriever, IDialogCreator dialogCreator, IJournalTask journalTask,
ICloneManagerForModel cloneManagerForModel)
{
_dimensionFactory = dimensionFactory;
_objectBaseFactory = objectBaseFactory;
_simulationPersister = simulationPersister;
_projectRetriever = projectRetriever;
_dialogCreator = dialogCreator;
_journalTask = journalTask;
_cloneManagerForModel = cloneManagerForModel;
}
protected override void Context()
{
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_formulaMapper = A.Fake <IFormulaBuilderToFormulaMapper>();
_parameterMapper = A.Fake <IParameterBuilderCollectionToParameterCollectionMapper>();
_keywordReplacerTask = A.Fake <IKeywordReplacerTask>();
_formulaFactory = A.Fake <IFormulaFactory>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
sut = new MoleculeBuilderToMoleculeAmountMapper(_objectBaseFactory, _formulaMapper, _parameterMapper, _dimensionFactory,
_keywordReplacerTask, _formulaFactory, _parameterFactory);
}
public EditTasksForSimulation(IInteractionTaskContext interactionTaskContext, ISimulationPersistor simulationPersistor, IDialogCreator dialogCreator,
IForbiddenNamesRetriever forbiddenNamesRetriver, IDataRepositoryTask dataRepositoryTask,
IModelReportCreator reportCreator, ISimModelExporter simModelExporter, IDimensionFactory dimensionFactory) : base(interactionTaskContext)
{
_simulationPersistor = simulationPersistor;
_dialogCreator = dialogCreator;
_forbiddenNamesRetriver = forbiddenNamesRetriver;
_dataRepositoryTask = dataRepositoryTask;
_reportCreator = reportCreator;
_simModelExporter = simModelExporter;
_dimensionFactory = dimensionFactory;
}
protected override void Context()
{
_chartDisplayView = A.Fake <IChartDisplayView>();
_curveBinderFactory = A.Fake <ICurveBinderFactory>();
_exceptionManager = A.Fake <IExceptionManager>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_axisBinderFactory = A.Fake <IAxisBinderFactory>();
_dataModeMapper = A.Fake <ICurveToDataModeMapper>();
_contextMenuFactory = A.Fake <IViewItemContextMenuFactory>();
_chartExportTask = A.Fake <ICurveChartExportTask>();
_applicationSettings = A.Fake <IApplicationSettings>();
sut = new ChartDisplayPresenter(_chartDisplayView, _curveBinderFactory, _contextMenuFactory, _axisBinderFactory, _dataModeMapper, _chartExportTask, _applicationSettings);
var dataRepository = DomainHelperForSpecs.SimulationDataRepositoryFor("Sim");
A.CallTo(() => _dimensionFactory.MergedDimensionFor(A <DataColumn> ._)).ReturnsLazily(x => x.GetArgument <DataColumn>(0).Dimension);
_curve = new Curve();
_curve.SetxData(dataRepository.BaseGrid, _dimensionFactory);
_curve.SetyData(dataRepository.AllButBaseGrid().First(), _dimensionFactory);
A.CallTo(_curveBinderFactory).WithReturnType <ICurveBinder>().ReturnsLazily(x =>
{
var curve = x.GetArgument <Curve>(0);
var curveBinder = A.Fake <ICurveBinder>();
A.CallTo(() => curveBinder.SeriesIds).Returns(SeriesIdsFor(curve));
A.CallTo(() => curveBinder.LLOQ).Returns(LLOQFor(curve));
A.CallTo(() => curveBinder.ContainsSeries(curve.Id)).Returns(true);
A.CallTo(() => curveBinder.Id).Returns(curve.Id);
A.CallTo(() => curveBinder.Curve).Returns(curve);
return(curveBinder);
});
_curveChart = new CurveChart();
_curveChart.AddAxis(new Axis(AxisTypes.X)
{
Dimension = _curve.xDimension
});
_curveChart.AddAxis(new Axis(AxisTypes.Y)
{
Dimension = _curve.yDimension
});
_xAxisBinder = createAxisBinderFor(_curveChart.AxisBy(AxisTypes.X));
_yAxisBinder = createAxisBinderFor(_curveChart.AxisBy(AxisTypes.Y));
A.CallTo(() => _axisBinderFactory.Create(_curveChart.AxisBy(AxisTypes.X), _chartDisplayView.ChartControl, _curveChart)).Returns(_xAxisBinder);
A.CallTo(() => _axisBinderFactory.Create(_curveChart.AxisBy(AxisTypes.Y), _chartDisplayView.ChartControl, _curveChart)).Returns(_yAxisBinder);
SetupChart();
sut.Edit(_curveChart);
}
public static IDimension OptimalDimension(this IDimensionFactory dimensionFactory, IDimension defaultDimension)
{
if (defaultDimension == null)
{
return(null);
}
var templateColumn = new DataColumn {
Dimension = defaultDimension
};
return(dimensionFactory.MergedDimensionFor(templateColumn));
}
protected override void Context()
{
_context = A.Fake <IInteractionTaskContext>();
_simulationPersistor = A.Fake <ISimulationPersistor>();
_dialogCreator = A.Fake <IDialogCreator>();
_dataRepositoryTask = A.Fake <IDataRepositoryExportTask>();
_simulationModelExporter = A.Fake <ISimModelExporter>();
_reportCreator = A.Fake <IModelReportCreator>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_parameterIdentificationSimulationPathUpdater = A.Fake <IParameterIdentificationSimulationPathUpdater>();
sut = new EditTasksForSimulation(_context, _simulationPersistor, _dialogCreator, _dataRepositoryTask, _reportCreator, _simulationModelExporter, _dimensionFactory, _parameterIdentificationSimulationPathUpdater);
}
public ReactionImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context, IReactionBuildingBlockFactory reactionBuildingBlockFactory, IFunctionDefinitionImporter functionDefinitionImporter, ISpeciesImporter speciesImporter, IUnitDefinitionImporter unitDefinitionImporter)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_dimensionFactory = moBiDimensionFactory;
ReactionBuilderList = new List <IReactionBuilder>();
_passiveTransportList = new List <ITransportBuilder>();
_reactionBuildingBlock = reactionBuildingBlockFactory.Create().WithName(SBMLConstants.SBML_REACTION_BB);
_passiveTransportBuildingBlock = ObjectBaseFactory.Create <IPassiveTransportBuildingBlock>()
.WithName(SBMLConstants.SBML_PASSIVETRANSPORTS_BB);
_functionDefinitionImporter = functionDefinitionImporter;
_speciesImporter = speciesImporter;
_unitDefinitionImporter = unitDefinitionImporter;
}
protected override void Context()
{
_view = A.Fake <IAxisSettingsView>();
_dimensionFactory = A.Fake <IDimensionFactory>();
sut = new AxisSettingsPresenter(_view, _dimensionFactory);
_axisX = new Axis(AxisTypes.X);
_axisY = new Axis(AxisTypes.Y);
_axes = new List <Axis> {
_axisX, _axisY
};
sut.Edit(_axes);
}
public ChartPresenterContext(IChartEditorAndDisplayPresenter chartEditorAndDisplayPresenter, ICurveNamer curveNamer,
IDataColumnToPathElementsMapper dataColumnToPathElementsMapper, IChartTemplatingTask chartTemplatingTask, IPresentationSettingsTask presentationSettingsTask,
IChartEditorLayoutTask chartEditorLayoutTask, IProjectRetriever projectRetriever, IDimensionFactory dimensionFactory)
{
EditorAndDisplayPresenter = chartEditorAndDisplayPresenter;
DataColumnToPathElementsMapper = dataColumnToPathElementsMapper;
TemplatingTask = chartTemplatingTask;
PresenterSettingsTask = presentationSettingsTask;
EditorLayoutTask = chartEditorLayoutTask;
ProjectRetriever = projectRetriever;
DimensionFactory = dimensionFactory;
CurveNamer = curveNamer;
}
protected override void Context()
{
_dimensionFactory = A.Fake <IDimensionFactory>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_withIdRepository = A.Fake <IWithIdRepository>();
_dataRepositories = new List <DataRepository>();
_cloneManagerForModel = A.Fake <ICloneManagerForModel>();
_container = A.Fake <Utility.Container.IContainer>();
sut = new SerializationContext(_dimensionFactory, _objectBaseFactory, _withIdRepository, _dataRepositories, _cloneManagerForModel, _container);
_formula1 = new ExplicitFormula().WithId("1");
_formula2 = new ExplicitFormula().WithId("1");
}
public PKAnalysisExportTask(
IDialogCreator dialogCreator,
IDataRepositoryExportTask dataRepositoryTask,
IQuantityPathToQuantityDisplayPathMapper quantityDisplayPathMapper,
IGlobalPKAnalysisToDataTableMapper globalPKAnalysisToDataTableMapper,
IDimensionFactory dimensionFactory)
{
_dialogCreator = dialogCreator;
_dataRepositoryTask = dataRepositoryTask;
_globalPKAnalysisToDataTableMapper = globalPKAnalysisToDataTableMapper;
_dimensionFactory = dimensionFactory;
_quantityDisplayPathMapper = quantityDisplayPathMapper;
}
protected override void Context()
{
_view = A.Fake <IEditFormulaPathListView>();
_moBiFormulaTask = A.Fake <IMoBiFormulaTask>();
_context = A.Fake <IMoBiContext>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_userSettings = A.Fake <IUserSettings>();
_contextMenuFactory = A.Fake <IViewItemContextMenuFactory>();
_circularReferenceChecker = A.Fake <ICircularReferenceChecker>();
_formulaUsablePathDTOMapper = A.Fake <IFormulaUsablePathToFormulaUsablePathDTOMapper>();
sut = new EditFormulaPathListPresenter(_view, _moBiFormulaTask, _context, _dimensionFactory, _userSettings, _contextMenuFactory, _circularReferenceChecker, _formulaUsablePathDTOMapper);
}
private static void setUpDimensionMergings(IDimensionFactory factory)
{
var concentrationDimension = factory.Dimension(Constants.Dimension.MASS_CONCENTRATION);
var molarConcentrationDimomension = factory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION);
factory.AddMergingInformation(new MoBiDimensionMergingInformation <IQuantity>(concentrationDimension, molarConcentrationDimomension,
new MolWeightDimensionConverterForFormulaUsable(concentrationDimension, molarConcentrationDimomension)));
factory.AddMergingInformation(new MoBiDimensionMergingInformation <DataColumn>(concentrationDimension, molarConcentrationDimomension,
new ConcentrationToMolarConcentrationConverterForDataColumn(concentrationDimension, molarConcentrationDimomension)));
factory.AddMergingInformation(new MoBiDimensionMergingInformation <DataColumn>(molarConcentrationDimomension, concentrationDimension,
new MolarConcentrationToConcentrationConverterForDataColumn(molarConcentrationDimomension, concentrationDimension)));
}
public SimpleChartPresenter(ISimpleChartView view, IChartDisplayPresenter chartDisplayPresenter, IChartFactory chartFactory,
IEventPublisher eventPublisher, IPresentationUserSettings presentationUserSettings, IDimensionFactory dimensionFactory)
: base(view)
{
_chartDisplayPresenter = chartDisplayPresenter;
_chartFactory = chartFactory;
_eventPublisher = eventPublisher;
_presentationUserSettings = presentationUserSettings;
_dimensionFactory = dimensionFactory;
_view.AddView(_chartDisplayPresenter.View);
_chartDisplayPresenter.DisableCurveAndAxisEdits();
LogLinSelectionEnabled = false;
AddSubPresenters(_chartDisplayPresenter);
}
private IDimension yDimensionFor(IDimensionFactory dimensionFactory)
{
if (yData.ContainsRelatedColumn(AuxiliaryType.GeometricMeanPop))
{
return(dimensionFactory.MergedDimensionFor(yData.GetRelatedColumn(AuxiliaryType.GeometricMeanPop)));
}
if (yData.ContainsRelatedColumn(AuxiliaryType.ArithmeticMeanPop))
{
return(dimensionFactory.MergedDimensionFor(yData.GetRelatedColumn(AuxiliaryType.ArithmeticMeanPop)));
}
return(dimensionFactory.MergedDimensionFor(yData));
}
public MoleculeBuilderToMoleculeAmountMapper(IObjectBaseFactory objectBaseFactory,
IFormulaBuilderToFormulaMapper formulaMapper,
IParameterBuilderToParameterMapper parameterMapper,
IDimensionFactory dimensionFactory, IKeywordReplacerTask keywordReplacerTask, IFormulaFactory formulaFactory,
IParameterFactory parameterFactory)
{
_objectBaseFactory = objectBaseFactory;
_formulaMapper = formulaMapper;
_parameterMapper = parameterMapper;
_keywordReplacerTask = keywordReplacerTask;
_formulaFactory = formulaFactory;
_parameterFactory = parameterFactory;
_amountDimension = dimensionFactory.Dimension(Constants.Dimension.MOLAR_AMOUNT);
}
protected override void Context()
{
_presentationSettingsTask = A.Fake <IPresentationSettingsTask>();
_view = A.Fake <IParameterIdentificationMultipleRunsAnalysisView>();
_chartEditorAndDisplayPresenter = A.Fake <IChartEditorAndDisplayPresenter>();
_curveNamer = A.Fake <ICurveNamer>();
_pathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>();
_chartTemplatingTask = A.Fake <IChartTemplatingTask>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
_chartEditorLayoutTask = A.Fake <IChartEditorLayoutTask>();
_projectRetreiver = A.Fake <IProjectRetriever>();
_chartPresenterContext = A.Fake <ChartPresenterContext>();
A.CallTo(() => _chartPresenterContext.EditorAndDisplayPresenter).Returns(_chartEditorAndDisplayPresenter);
A.CallTo(() => _chartPresenterContext.CurveNamer).Returns(_curveNamer);
A.CallTo(() => _chartPresenterContext.DataColumnToPathElementsMapper).Returns(_pathElementsMapper);
A.CallTo(() => _chartPresenterContext.TemplatingTask).Returns(_chartTemplatingTask);
A.CallTo(() => _chartPresenterContext.PresenterSettingsTask).Returns(_presentationSettingsTask);
A.CallTo(() => _chartPresenterContext.DimensionFactory).Returns(_dimensionFactory);
A.CallTo(() => _chartPresenterContext.EditorLayoutTask).Returns(_chartEditorLayoutTask);
A.CallTo(() => _chartPresenterContext.ProjectRetriever).Returns(_projectRetreiver);
sut = new ParameterIdentificationTimeProfileChartPresenter(_view, _chartPresenterContext, _displayUnitRetriever);
_timeProfileAnalysis = new ParameterIdentificationTimeProfileChart();
_outputMapping1 = A.Fake <OutputMapping>();
_outputMapping2 = A.Fake <OutputMapping>();
_observedData1 = DomainHelperForSpecs.ObservedData();
_observedData2 = DomainHelperForSpecs.ObservedData();
A.CallTo(() => _outputMapping1.WeightedObservedData).Returns(new WeightedObservedData(_observedData1));
A.CallTo(() => _outputMapping2.WeightedObservedData).Returns(new WeightedObservedData(_observedData2));
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddOutputMapping(_outputMapping1);
_parameterIdentification.AddOutputMapping(_outputMapping2);
_parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>();
_parameterIdentification.AddResult(_parameterIdentificationRunResult);
_optimizationRunResult = new OptimizationRunResult();
_parameterIdentificationRunResult.BestResult = _optimizationRunResult;
_parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>();
_parameterIdentification.AddResult(_parameterIdentificationRunResult);
_optimizationRunResult2 = new OptimizationRunResult();
_parameterIdentificationRunResult.BestResult = _optimizationRunResult2;
}