private void checkChartTemplatesIn(ISimulationSettings simulationSettings) { var chartTemplates = simulationSettings.ChartTemplates.ToList(); if (!referencesOldName(chartTemplates)) { return; } var newChartTemplates = new List <CurveChartTemplate>(); foreach (var chartTemplate in simulationSettings.ChartTemplates) { var newChartTemplate = chartTemplate; if (referencesOldName(chartTemplate)) { newChartTemplate = _cloneManager.Clone(chartTemplate); foreach (var curveTemplate in newChartTemplate.Curves) { curveTemplate.xData.Path = stringReplace(curveTemplate.xData.Path); curveTemplate.yData.Path = stringReplace(curveTemplate.yData.Path); } } newChartTemplates.Add(newChartTemplate); } _changes.Add(simulationSettings, _buildingBlock, new ReplaceBuildingBlockTemplatesCommand(simulationSettings, newChartTemplates)); }
public override void GlobalContext() { base.GlobalContext(); _compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>(); _cloneManager = IoC.Resolve <ICloneManager>(); _enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>(); _transporterFactory = IoC.Resolve <IIndividualTransporterFactory>(); _modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>(); _modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>(); _compound = DomainFactoryForSpecs.CreateStandardCompound(); _individual = DomainFactoryForSpecs.CreateStandardIndividual(); _protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol(); _enzyme = _enzymeFactory.AddMoleculeTo(_individual, "CYP").DowncastTo <IndividualEnzyme>(); _allExpressionParameters = _individual.AllExpressionParametersFor(_enzyme); _allExpressionParameters[CoreConstants.Compartment.PLASMA].Value = _relExpPls; _allExpressionParameters[CoreConstants.Compartment.BLOOD_CELLS].Value = _relExpBloodCells; _allExpressionParameters[CoreConstants.Compartment.VASCULAR_ENDOTHELIUM].Value = _relExpVascEndo; _hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value; _metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository .ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>()); _metabolizationProcess.Name = "My Partial Process"; _metabolizationProcess.Parameter(ConverterConstants.Parameters.CLspec).Value = 15; _compound.AddProcess(_metabolizationProcess); _simulationRunOptions = new SimulationRunOptions { RaiseEvents = false }; }
public override void UpdatePropertiesFrom(IUpdatable sourceObject, ICloneManager cloneManager) { base.UpdatePropertiesFrom(sourceObject, cloneManager); var sourceSimulation = sourceObject as Simulation; if (sourceSimulation == null) { return; } Properties = sourceSimulation.Properties.Clone(cloneManager); sourceSimulation.UsedBuildingBlocks.Each(bb => AddUsedBuildingBlock(bb.Clone(cloneManager))); Model = cloneManager.Clone(sourceSimulation.Model); sourceSimulation.UsedObservedData.Each(data => AddUsedObservedData(data.Clone())); Reactions = cloneManager.Clone(sourceSimulation.Reactions); SimulationSettings = cloneManager.Clone(sourceSimulation.SimulationSettings); ReactionDiagramModel = sourceSimulation.ReactionDiagramModel.CreateCopy(); updateBuildingBlockReferences(sourceSimulation); }
protected override void Context() { base.Context(); _cloneManager = A.Fake <ICloneManager>(); _sourceMolecule = new IndividualEnzyme { Ontogeny = new UserDefinedOntogeny() }; _clonedOntogeny = new UserDefinedOntogeny(); A.CallTo(() => _cloneManager.Clone(_sourceMolecule.Ontogeny)).Returns(_clonedOntogeny); }
public UserDisplayUnitsPresenter(IUserDisplayUnitsView view, IDisplayUnitsPresenter displayUnitsPresenter, IUserSettings userSettings, ICloneManager cloneManager) : base(view) { _displayUnitsPresenter = displayUnitsPresenter; _userSettings = userSettings; _cloneManager = cloneManager; AddSubPresenters(_displayUnitsPresenter); _view.AddView(_displayUnitsPresenter.View); _settingsToEdit = cloneManager.Clone(_userSettings.DisplayUnits); }
public ImportPopulationSettings Clone(ICloneManager cloneManager) { var settings = new ImportPopulationSettings { BaseIndividual = cloneManager.Clone(BaseIndividual) }; _allFiles.Each(f => settings.AddFile(f.Clone())); return(settings); }
public RandomPopulationSettings Clone(ICloneManager cloneManager) { var clone = new RandomPopulationSettings { BaseIndividual = cloneManager.Clone(BaseIndividual), NumberOfIndividuals = NumberOfIndividuals }; _genderRatios.Each(gr => clone.AddGenderRatio(gr.Clone())); _parameterRanges.Each(pr => clone.AddParameterRange(pr.Clone())); return(clone); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var intervalGrouping = source as IntervalGroupingDefinition; if (intervalGrouping == null) { return; } intervalGrouping.Items.Each(item => AddItem(cloneManager.Clone(item))); }
public virtual UsedBuildingBlock Clone(ICloneManager cloneManager) { return(new UsedBuildingBlock(TemplateId, BuildingBlockType) { Altered = Altered, Version = Version, StructureVersion = StructureVersion, BuildingBlock = cloneManager.Clone(BuildingBlock), Name = Name }); }
protected override void Context() { _cloneManager = A.Fake <ICloneManager>(); _view = A.Fake <IUserDisplayUnitsView>(); _displayUnitPresenter = A.Fake <IDisplayUnitsPresenter>(); _userSettings = A.Fake <IUserSettings>(); _cloneDisplayUnitsManager = new DisplayUnitsManager(); A.CallTo(() => _cloneManager.Clone(_userSettings.DisplayUnits)).Returns(_cloneDisplayUnitsManager); sut = new UserDisplayUnitsPresenter(_view, _displayUnitPresenter, _userSettings, _cloneManager); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var userDefinedOntogeny = source as UserDefinedOntogeny; if (userDefinedOntogeny == null) { return; } Table = cloneManager.Clone(userDefinedOntogeny.Table); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var valueMapping = source as ValueMappingGroupingDefinition; if (valueMapping == null) { return; } valueMapping.Mapping.KeyValues.Each(kv => Mapping.Add(kv.Key, cloneManager.Clone(kv.Value))); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var covariateField = source as PopulationAnalysisCovariateField; if (covariateField == null) { return; } Covariate = covariateField.Covariate; covariateField.GroupingItems.Each(x => AddGroupingItem(cloneManager.Clone(x))); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var sourceSpatialStructure = source as ISpatialStructure; if (sourceSpatialStructure == null) { return; } sourceSpatialStructure.TopContainers.Each(c => AddTopContainer(cloneManager.Clone(c))); NeighborhoodsContainer = cloneManager.Clone(sourceSpatialStructure.NeighborhoodsContainer); foreach (var neighborhoodBuilder in Neighborhoods) { var sourceNeighborhood = neighborhoodBuilderSourceFor(neighborhoodBuilder, sourceSpatialStructure.Neighborhoods); updateNeighborsReferences(sourceNeighborhood, neighborhoodBuilder); } GlobalMoleculeDependentProperties = cloneManager.Clone(sourceSpatialStructure.GlobalMoleculeDependentProperties); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var statisticalAnalysis = source as PopulationStatisticalAnalysis; if (statisticalAnalysis == null) { return; } statisticalAnalysis.Statistics.Each(s => AddStatistic(cloneManager.Clone(s))); TimeUnit = statisticalAnalysis.TimeUnit; }
private T createClone <T>(T objectToClone, ICloneManager cloneManager) where T : class, IUpdatable { var clone = cloneManager.Clone(objectToClone); var buildingBlock = clone as IPKSimBuildingBlock; if (buildingBlock != null) { _buildingBlockFinalizer.Finalize(buildingBlock); } return(clone); }
private void rebind(ISimulationSettings simulationSettings) { var chartTemplatesToEdit = simulationSettings.ChartTemplates.Select(x => { var curveChartTemplate = _cloneManager.Clone(x); // setting IsDefault is not part of general cloning and is done when cloning the set only curveChartTemplate.IsDefault = x.IsDefault; return(curveChartTemplate); }); _chartTemplateManagerPresenter.EditTemplates(chartTemplatesToEdit.OrderBy(x => x.Name)); }
public void EditTemplates(IEnumerable <CurveChartTemplate> chartTemplates) { var chartTemplatesToEdit = chartTemplates.Select(x => { var curveChartTemplate = _cloneManager.Clone(x); // setting IsDefault is not part of general cloning and is done when cloning the set only curveChartTemplate.IsDefault = x.IsDefault; return(curveChartTemplate); }); _chartTemplateManagerPresenter.EditTemplates(chartTemplatesToEdit); }
public virtual void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { var sourceAnalysis = source as PopulationAnalysisChart; if (sourceAnalysis == null) { return; } Name = sourceAnalysis.Name; Description = sourceAnalysis.Description; ChartSettings = cloneManager.Clone(sourceAnalysis.ChartSettings); ObservedDataCollection = cloneManager.Clone(sourceAnalysis.ObservedDataCollection); Title = sourceAnalysis.Title; FontAndSize.UpdatePropertiesFrom(sourceAnalysis.FontAndSize); IncludeOriginData = sourceAnalysis.IncludeOriginData; OriginText = sourceAnalysis.OriginText; PrimaryXAxisSettings.UpdatePropertiesFrom(sourceAnalysis.PrimaryXAxisSettings, cloneManager); PrimaryYAxisSettings.UpdatePropertiesFrom(sourceAnalysis.PrimaryYAxisSettings, cloneManager); sourceAnalysis.SecondaryYAxisSettings.Each((axisSettings, index) => { AxisSettingsForSecondaryYAxis(index).UpdatePropertiesFrom(axisSettings, cloneManager); }); }
protected override void Context() { base.Context(); _sourceParameterIdentification = new ParameterIdentification(); _identificationParameter = new IdentificationParameter(); _cloneOfIdentificationParameter = new IdentificationParameter(); _sourceParameterIdentification.AddSimulation(_simulation); _sourceParameterIdentification.AddOutputMapping(_outputMapping); _sourceParameterIdentification.AddIdentificationParameter(_identificationParameter); _cloneManager = A.Fake <ICloneManager>(); A.CallTo(() => _cloneManager.Clone(_identificationParameter)).Returns(_cloneOfIdentificationParameter); }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var groupingField = source as PopulationAnalysisGroupingField; if (groupingField == null) { return; } GroupingDefinition = cloneManager.Clone(groupingField.GroupingDefinition); //Reference grouping item will be set on the fly when creating flat data table and does not need to be cloned //ReferenceGroupingItem }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var sourceStartValeBuidlingBlock = source as IStartValuesBuildingBlock <T>; if (sourceStartValeBuidlingBlock == null) { return; } sourceStartValeBuidlingBlock.Each(startValue => Add(cloneManager.Clone(startValue))); MoleculeBuildingBlockId = sourceStartValeBuidlingBlock.MoleculeBuildingBlockId; SpatialStructureId = sourceStartValeBuidlingBlock.SpatialStructureId; }
public virtual IEnumerable <ISchemaItem> ExpandedSchemaItems(ICloneManager cloneManager) { { double offset = TimeBetweenRepetitions.Value; for (int repetition = 0; repetition < NumberOfRepetitions.Value; repetition++) { foreach (var schemaItem in SchemaItems) { var expandedItem = cloneManager.Clone(schemaItem); expandedItem.StartTime.Value += StartTime.Value + repetition * offset; yield return(expandedItem); } } } }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var srcAppMoleculeBuilder = source as IApplicationMoleculeBuilder; if (srcAppMoleculeBuilder == null) { return; } RelativeContainerPath = srcAppMoleculeBuilder.RelativeContainerPath.Clone <IObjectPath>(); Formula = cloneManager.Clone(srcAppMoleculeBuilder.Formula); Dimension = srcAppMoleculeBuilder.Dimension; }
protected override void Context() { base.Context(); _cloneManager = A.Fake <ICloneManager>(); _sourceTemplate = new CurveChartTemplate { Name = "TOTO", ChartSettings = { BackColor = Color.Red } }; _sourceTemplate.AddAxis(new Axis(AxisTypes.X)); var curveTemplate = new CurveTemplate { Name = "XX" }; _cloneCurve = new CurveTemplate(); _sourceTemplate.Curves.Add(curveTemplate); A.CallTo(() => _cloneManager.Clone(curveTemplate)).Returns(_cloneCurve); }
public void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { var sourceChartTemplate = source as CurveChartTemplate; if (sourceChartTemplate == null) { return; } FontAndSize.UpdatePropertiesFrom(sourceChartTemplate.FontAndSize, cloneManager); ChartSettings.UpdatePropertiesFrom(sourceChartTemplate.ChartSettings, cloneManager); Name = sourceChartTemplate.Name; _axes.Clear(); Curves.Clear(); sourceChartTemplate.Axes.Each(axis => AddAxis(axis.Clone())); sourceChartTemplate.Curves.Each(curve => Curves.Add(cloneManager.Clone(curve))); IsDefault = sourceChartTemplate.IsDefault; PreviewSettings = sourceChartTemplate.PreviewSettings; }
public override void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { base.UpdatePropertiesFrom(source, cloneManager); var sourceMoleculeBuilder = source as IMoleculeBuilder; if (sourceMoleculeBuilder == null) { return; } IsFloating = sourceMoleculeBuilder.IsFloating; QuantityType = sourceMoleculeBuilder.QuantityType; IsXenobiotic = sourceMoleculeBuilder.IsXenobiotic; DisplayUnit = sourceMoleculeBuilder.DisplayUnit; Dimension = sourceMoleculeBuilder.Dimension; DefaultStartFormula = cloneManager.Clone(sourceMoleculeBuilder.DefaultStartFormula); _usedCalculationMethods.Clear(); sourceMoleculeBuilder.UsedCalculationMethods.Each(x => AddUsedCalculationMethod(x.Clone())); }
public override void GlobalContext() { base.GlobalContext(); _compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>(); _cloneManager = IoC.Resolve <ICloneManager>(); _enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>(); _transporterFactory = IoC.Resolve <IIndividualTransporterFactory>(); _modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>(); _modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>(); _compound = DomainFactoryForSpecs.CreateStandardCompound(); _individual = DomainFactoryForSpecs.CreateStandardIndividual(); _protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol(); _enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP"); _enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls; _enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells; _enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo; _individual.AddMolecule(_enzyme); _hct = _individual.Organism.Parameter(CoreConstants.Parameter.HCT).Value; _metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>()); _metabolizationProcess.Name = "My Partial Process"; _metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15; _compound.AddProcess(_metabolizationProcess); }
public override void UpdatePropertiesFrom(IUpdatable sourceObject, ICloneManager cloneManager) { base.UpdatePropertiesFrom(sourceObject, cloneManager); var sourceMolecule = sourceObject as IndividualMolecule; if (sourceMolecule == null) { return; } QueryConfiguration = sourceMolecule.QueryConfiguration; MoleculeType = sourceMolecule.MoleculeType; var sourceOntogeny = sourceMolecule.Ontogeny; if (sourceOntogeny.IsUserDefined()) { Ontogeny = cloneManager.Clone(sourceOntogeny); } else { Ontogeny = sourceMolecule.Ontogeny; } }
public virtual void UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager) { var populationAnalysis = source as PopulationAnalysis; populationAnalysis?.AllFields.Each(f => Add(cloneManager.Clone(f))); }