public SetValuePointXValueCommand(TableFormula tableFormula, ValuePoint valuePoint, double newBaseValue, IBuildingBlock buildingBlock)
: base(tableFormula, valuePoint, newBaseValue, buildingBlock)
{
_oldBaseValue = valuePoint.X;
}
public RemoveActiveTransportBuilderCommand(TransporterMoleculeContainer parent, ITransportBuilder itemToRemove, IBuildingBlock buildingBlock)
: base(parent, itemToRemove, buildingBlock)
{
}
public RemoveMatchAllConditionCommand(T taggedObject, IBuildingBlock buildingBlock, Func <T, DescriptorCriteria> descriptorCriteriaRetriever)
: base(string.Empty, taggedObject, buildingBlock, descriptorCriteriaRetriever)
{
ObjectType = AppConstants.Commands.MatchAllCondition;
}
public bool Uses(IBuildingBlock buildingBlock)
{
return((refersTo(buildingBlock, SpatialStructureId)) ||
(refersTo(buildingBlock, MoleculeBuildingBlockId)));
}
public override IMoBiCommand GetRemoveCommand(IEventGroupBuilder eventGroupBuilderToRemove, IEventGroupBuildingBlock parent, IBuildingBlock buildingBlock)
{
return(new RemoveRootEventGroupBuilderCommand(parent, eventGroupBuilderToRemove));
}
private void checkBuildingBlock <TBuildingBlock>(TBuildingBlock buildingBlock) where TBuildingBlock : IBuildingBlock
{
// We keep actual BB to provide Information to user
_buildingBlock = buildingBlock;
checkObjectBase(buildingBlock);
}
private async Task exportToFolder(string exportFolder)
{
var project = new Project();
var individual = await _snapshotObjectCreator.DefaultIndividual();
project.Individuals = new[] { individual };
var compound = await _snapshotObjectCreator.StandardCompound(lipophilicity : 3, fractionUnbound : 0.1, molWeight : 400, name : "Standard Molecule");
compound.Name = "Standard Molecule";
project.Compounds = new[] { compound };
var intrevanousBolusMgPerKg = await _snapshotObjectCreator.SimpleProtocol(dose : 1, doseUnit : "mg/kg", applicationType : ApplicationTypes.IntravenousBolus);
var intrevanousBolusMg = await _snapshotObjectCreator.SimpleProtocol(dose : 1, doseUnit : "mg", applicationType : ApplicationTypes.IntravenousBolus);
project.Protocols = new[] { intrevanousBolusMgPerKg, intrevanousBolusMg };
var snapshotConfiguration = new SimulationConstruction
{
Individual = individual,
Compounds = new[] { compound },
Protocols = new [] { intrevanousBolusMgPerKg },
ModelName = CoreConstants.Model.FourComp,
};
var fourCompIvBolusMgPerKg = await configurationFrom(snapshotConfiguration);
snapshotConfiguration.ModelName = CoreConstants.Model.TwoPores;
var twoPore = await configurationFrom(snapshotConfiguration);
snapshotConfiguration.Protocols = new[] { intrevanousBolusMg };
snapshotConfiguration.ModelName = CoreConstants.Model.FourComp;
var fourCompIvBolusMg = await configurationFrom(snapshotConfiguration);
twoPore.SpatialStructure.Name = "Human 2 Pores";
twoPore.PassiveTransports.Name = "2 Pores Passive Transports";
fourCompIvBolusMgPerKg.SpatialStructure.Name = "Human Standard";
fourCompIvBolusMgPerKg.PassiveTransports.Name = "Standard Passive Transports";
fourCompIvBolusMgPerKg.EventGroups.Name = "IV Bolus";
fourCompIvBolusMgPerKg.Molecules.Name = "Standard Molecule";
fourCompIvBolusMgPerKg.Observers.Name = "Standard Observer";
fourCompIvBolusMg.EventGroups.Name = "IV Bolus (mg)";
var defaultCompound = fourCompIvBolusMgPerKg.Molecules.First();
defaultCompound.Name = string.Empty;
defaultCompound.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameters.MOLECULAR_WEIGHT).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameters.FRACTION_UNBOUND_PLASMA_REFERENCE_VALUE).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH).Value = double.NaN;
_moBiExportTask.UpdateObserverForAllFlag(fourCompIvBolusMgPerKg.Observers);
var buildingBlocks = new IBuildingBlock[]
{
twoPore.SpatialStructure,
twoPore.PassiveTransports,
fourCompIvBolusMgPerKg.SpatialStructure,
fourCompIvBolusMgPerKg.PassiveTransports,
fourCompIvBolusMgPerKg.EventGroups,
fourCompIvBolusMgPerKg.Molecules,
fourCompIvBolusMgPerKg.Observers,
fourCompIvBolusMg.EventGroups
};
buildingBlocks.Each(bb => saveToPKML(bb, exportFolder));
}
protected RemoveChildFromEventGroupCommand(IEventGroupBuilder parent, TChild itemToRemove, IBuildingBlock buildingBlock)
: base(parent, itemToRemove, buildingBlock)
{
}
public RemoveContainerFromEventGroupCommand(IEventGroupBuilder parent, IContainer itemToRemove, IBuildingBlock buildingBlock) : base(parent, itemToRemove, buildingBlock)
{
}
public AddActiveTransportBuilderContainerCommand(IMoleculeBuilder parent, TransporterMoleculeContainer itemToAdd, IBuildingBlock buildingBlock)
: base(parent, itemToAdd, buildingBlock)
{
}
protected ChangeTableFormulaWithReferencePathCommandBase(TFormula tableFormulaWithReference,
IFormulaUsablePath newFormulaUsablePath, IBuildingBlock buildingBlock, Func <TFormula, string> aliasFunc, Action <IFormulaUsablePath> addAction)
: base(buildingBlock)
{
_tableFormulaWithReference = tableFormulaWithReference;
_tableFormulaWithReferenceId = _tableFormulaWithReference.Id;
_newFormulaUsablePath = newFormulaUsablePath;
_aliasFunc = aliasFunc;
_addAction = addAction;
}
protected override void Because()
{
_result = sut.Active <IBuildingBlock>();
}
public AddInteracionContainerCommand(IMoleculeBuilder parent, InteractionContainer itemToAdd, IBuildingBlock buildingBlock) : base(parent, itemToAdd, buildingBlock)
{
}
public RemoveInteracionContainerCommand(IMoleculeBuilder parent, InteractionContainer itemToRemove, IBuildingBlock buildingBlock) : base(parent, itemToRemove, buildingBlock)
{
}
public TestAddObjectBaseCommand(IObjectBase parent, IObjectBase itemToAdd, IBuildingBlock buildingBlock) : base(parent, itemToAdd, buildingBlock)
{
}
public AddContainerToEventGroupCommand(IEventGroupBuilder parent, IContainer itemToAdd, IBuildingBlock buildingBlock) : base(parent, itemToAdd, buildingBlock)
{
}
public void Visit(IBuildingBlock buildingBlock)
{
checkBuildingBlock(buildingBlock);
}
protected AddChildToEventGroupCommand(IEventGroupBuilder parent, TChild itemToAdd, IBuildingBlock buildingBlock) : base(parent, itemToAdd, buildingBlock)
{
}
private void saveToPKML(IBuildingBlock buildingBlock, string folder)
{
var fileName = Path.Combine(folder, buildingBlock.Name + ".pkml");
_pkmlPersistor.SaveToPKML(buildingBlock, fileName);
}
public RemoveTransportBuilderFromApplicationBuilderCommand(IApplicationBuilder parent, ITransportBuilder itemToRemove, IBuildingBlock buildingBlock)
: base(parent, itemToRemove, buildingBlock)
{
}
private void setMoleculeStartValueFormula(IFormula formula, IMoleculeStartValue moleculeStartValue, IBuildingBlock moleculesStartValues)
{
if (!formula.IsConstant())
{
moleculeStartValue.Formula = _cloneManagerForBuildingBlock.Clone(formula, moleculesStartValues.FormulaCache);
}
}
public AddTransportBuilderToApplicationBuilderCommand(IApplicationBuilder parent, ITransportBuilder itemToAdd, IBuildingBlock buildingBlock)
: base(parent, itemToAdd, buildingBlock)
{
}
private bool refersTo(IBuildingBlock buildingBlock, string idToCheck)
{
return(string.Equals(idToCheck, buildingBlock.Id));
}
public AddEventGroupBuilderCommand(IEventGroupBuilder parent, IEventGroupBuilder itemToAdd, IBuildingBlock buildingBlock) : base(parent, itemToAdd, buildingBlock)
{
}
public override IMoBiCommand GetAddCommand(IEventGroupBuilder eventGroupBuilder, IEventGroupBuildingBlock parent, IBuildingBlock buildingBlock)
{
return(GetAddCommand(eventGroupBuilder, buildingBlock as IEventGroupBuildingBlock));
}
public RemoveEventGroupBuilderCommand(IEventGroupBuilder parent, IEventGroupBuilder itemToRemove, IBuildingBlock buildingBlock) : base(parent, itemToRemove, buildingBlock)
{
}
protected RemoveTagConditionCommandBase(string tagToRemove, T taggedObject, IBuildingBlock buildingBlock, Func <T, DescriptorCriteria> descriptorCriteriaRetriever)
: base(tagToRemove, taggedObject, buildingBlock, descriptorCriteriaRetriever)
{
CommandType = AppConstants.Commands.DeleteCommand;
}
/// <summary>
/// Initializes a new instance of the <see cref="ValidationMessage" /> class.
/// </summary>
/// <param name="notificationType">Type of the message.</param>
/// <param name="text">The text describing the validation problem</param>
/// <param name="objectBase">The invalid object .</param>
/// <param name="buildingBlock">Building block where the invalid object is defined. </param>
public ValidationMessage(NotificationType notificationType, string text, IObjectBase objectBase, IBuildingBlock buildingBlock)
{
NotificationType = notificationType;
Text = text;
Object = objectBase;
BuildingBlock = buildingBlock;
_details = new List <string>();
}
public RemoveInContainerConditionCommand(string tag, T taggedObject, IBuildingBlock buildingBlock, Func <T, DescriptorCriteria> descriptorCriteriaRetriever)
: base(tag, taggedObject, buildingBlock, descriptorCriteriaRetriever)
{
ObjectType = AppConstants.Commands.InContainerCondition;
}
private bool containsEntity(IBuildingBlock buildingBlock)
{
buildingBlock.AcceptVisitor(this);
return(_found);
}
