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)));
}