protected override void PerformExecuteWith(IExecutionContext context)
{
//Retrieve building block id in execute only since molecule might have been added in a macro command and bbid was not available in constructor
BuildingBlockId = context.BuildingBlockIdContaining(_molecule);
var allRelExpressionContainer = _molecule.AllExpressionsContainers().ToList();
var max = allRelExpressionContainer.Select(x => x.RelativeExpression).Max();
allRelExpressionContainer.Each(relExp => relExp.RelativeExpressionNorm = max == 0 ? 0 : relExp.RelativeExpression / max);
}
public SetTissueLocationCommand(IndividualProtein protein, TissueLocation tissueLocation, IExecutionContext context)
{
_protein = protein;
BuildingBlockId = context.BuildingBlockIdContaining(protein);
_newTissuleLocation = tissueLocation;
ObjectType = PKSimConstants.ObjectTypes.Protein;
CommandType = PKSimConstants.Command.CommandTypeEdit;
_proteinId = _protein.Id;
context.UpdateBuildinBlockProperties(this, context.BuildingBlockContaining(protein));
}
public SetSchemaItemTargetCompartmentCommand(ISchemaItem schemaItem, string newTargetCompartment, IExecutionContext context)
{
_schemaItem = schemaItem;
_newTargetCompartment = newTargetCompartment;
_schemaItemId = _schemaItem.Id;
ObjectType = PKSimConstants.ObjectTypes.AdministrationProtocol;
CommandType = PKSimConstants.Command.CommandTypeEdit;
BuildingBlockId = context.BuildingBlockIdContaining(schemaItem);
context.UpdateBuildinBlockProperties(this, context.BuildingBlockContaining(schemaItem));
}
public SetSchemaItemFormulationKeyCommand(ISchemaItem schemaItem, string newFormulationKey, IExecutionContext context)
{
_schemaItem = schemaItem;
_newFormulationKey = newFormulationKey;
_schemaItemId = _schemaItem.Id;
ObjectType = PKSimConstants.ObjectTypes.AdministrationProtocol;
CommandType = PKSimConstants.Command.CommandTypeEdit;
BuildingBlockId = context.BuildingBlockIdContaining(schemaItem);
context.UpdateBuildinBlockPropertiesInCommand(this, context.BuildingBlockContaining(schemaItem));
}
public RenameDataSourceCommand(CompoundProcess compoundProcess, string newDataSource, IExecutionContext context)
{
_processId = compoundProcess.Id;
BuildingBlockId = context.BuildingBlockIdContaining(compoundProcess);
_newDataSource = newDataSource;
_compoundProcess = compoundProcess;
ObjectType = context.TypeFor(compoundProcess);
CommandType = PKSimConstants.Command.CommandTypeEdit;
context.UpdateBuildingBlockPropertiesInCommand(this, context.BuildingBlockContaining(compoundProcess));
}
public ChangeApplicationTypeCommand(ISchemaItem schemaItem, ApplicationType newApplicationType, IExecutionContext context)
{
_schemaItem = schemaItem;
_schemaItemId = _schemaItem.Id;
_newApplicationType = newApplicationType;
ObjectType = PKSimConstants.ObjectTypes.AdministrationProtocol;
CommandType = PKSimConstants.Command.CommandTypeEdit;
BuildingBlockId = context.BuildingBlockIdContaining(schemaItem);
context.UpdateBuildinBlockProperties(this, context.BuildingBlockContaining(schemaItem));
}
public SetProteinIntracellularVascularEndoLocationCommand(IndividualProtein protein, IntracellularVascularEndoLocation newVascularEndoLocation, IExecutionContext context)
{
_protein = protein;
_newVascularEndoLocation = newVascularEndoLocation;
BuildingBlockId = context.BuildingBlockIdContaining(protein);
ObjectType = PKSimConstants.ObjectTypes.Protein;
CommandType = PKSimConstants.Command.CommandTypeEdit;
_proteinId = _protein.Id;
context.UpdateBuildinBlockProperties(this, context.BuildingBlockContaining(_protein));
}
public RenameMoleculeInPartialProcessCommand(PKSim.Core.Model.PartialProcess partialProcess, string newMoleculeName, IExecutionContext context)
{
_partialPocessId = partialProcess.Id;
BuildingBlockId = context.BuildingBlockIdContaining(partialProcess);
_newMoleculeName = newMoleculeName;
_partialProcess = partialProcess;
ObjectType = PKSimConstants.ObjectTypes.PartialProcess;
CommandType = PKSimConstants.Command.CommandTypeEdit;
context.UpdateBuildinBlockPropertiesInCommand(this, context.BuildingBlockContaining(partialProcess));
}
public SetProteinMembraneLocationCommand(PKSim.Core.Model.IndividualProtein protein, MembraneLocation membraneLocation, IExecutionContext context)
{
_protein = protein;
BuildingBlockId = context.BuildingBlockIdContaining(protein);
_newMembraneLocation = membraneLocation;
ObjectType = PKSimConstants.ObjectTypes.Protein;
CommandType = PKSimConstants.Command.CommandTypeEdit;
_proteinId = _protein.Id;
context.UpdateBuildinBlockPropertiesInCommand(this, context.BuildingBlockContaining(_protein));
}
public NormalizeSimulationRelativeExpressionCommand(IParameter parameter, IExecutionContext context)
{
_parameter = parameter;
ParameterId = parameter.Id;
CommandType = PKSimConstants.Command.CommandTypeEdit;
ObjectType = PKSimConstants.ObjectTypes.Protein;
BuildingBlockId = context.BuildingBlockIdContaining(parameter);
context.UpdateBuildingBlockPropertiesInCommand(this, context.BuildingBlockContaining(parameter));
//This command is necessary to insure consitency but does not need to be seen
Visible = false;
}
public RenameEntityCommand(IEntity entity, string newName, IExecutionContext context)
{
_entity = entity;
_newName = newName;
_entityId = entity.Id;
BuildingBlockId = context.BuildingBlockIdContaining(entity);
ObjectType = context.TypeFor(entity);
CommandType = PKSimConstants.Command.CommandTypeEdit;
Description = PKSimConstants.Command.RenameEntityCommandDescripiton(ObjectType, entity.Name, _newName);
}
public ChangeCompoundProcessInternalNameCommand(CompoundProcess compoundProcess, string internalName, IExecutionContext context)
{
_compoundProcess = compoundProcess;
_internalName = internalName;
_processId = compoundProcess.Id;
_oldInternalName = _compoundProcess.InternalName;
BuildingBlockId = context.BuildingBlockIdContaining(_compoundProcess);
//This command is necessary to insure consitency but does not need to be seen
context.UpdateBuildinBlockPropertiesInCommand(this, context.BuildingBlockContaining(_compoundProcess));
Visible = false;
}
public ChangeEnzymaticProcessMetaboliteNameCommand(EnzymaticProcess process, string newMetabolite, IExecutionContext context)
{
_process = process;
BuildingBlockId = context.BuildingBlockIdContaining(_process);
_processId = process.Id;
_newMetabolite = newMetabolite;
CommandType = PKSimConstants.Command.CommandTypeEdit;
Description = PKSimConstants.Command.SetMetaboliteForProcess(_newMetabolite, process.Name, process.MetaboliteName);
ObjectType = PKSimConstants.ObjectTypes.MetabolizingEnzyme;
context.UpdateBuildinBlockProperties(this, context.BuildingBlockContaining(_process));
}
public SetSpeciesInSpeciesDependentEntityCommand(ISpeciesDependentEntity entity, Species species, IExecutionContext context)
{
_entity = entity;
_entityId = entity.Id;
BuildingBlockId = context.BuildingBlockIdContaining(entity);
ObjectType = context.TypeFor(entity);
CommandType = PKSimConstants.Command.CommandTypeEdit;
_oldSpecies = entity.Species;
_newSpecies = species;
Description = PKSimConstants.Command.SetSpeciesInSpeciesDependentEntityDescription(context.TypeFor(_entity), entity.Name, _oldSpecies.Name, _newSpecies.Name);
context.UpdateBuildingBlockPropertiesInCommand(this, context.BuildingBlockContaining(entity));
}
public RenameEntityCommand(IEntity entity, string newName, IExecutionContext context)
{
_entity = entity;
_newName = newName;
_entityId = entity.Id;
BuildingBlockId = context.BuildingBlockIdContaining(entity);
//per default, should not change the version of the renamed entity
ShouldChangeVersion = false;
ObjectType = context.TypeFor(entity);
CommandType = PKSimConstants.Command.CommandTypeEdit;
Description = PKSimConstants.Command.RenameEntityCommandDescripiton(ObjectType, entity.Name, _newName);
}
public SetDefaultAlternativeParameterCommand(ParameterAlternativeGroup parameterGroup, ParameterAlternative parameterAlternative, IExecutionContext context)
{
_parameterGroup = parameterGroup;
_parameterGroupId = _parameterGroup.Id;
_parameterAlternative = parameterAlternative;
_oldDefaultAlternative = parameterGroup.DefaultAlternative;
_oldDefaultAlternativeId = _oldDefaultAlternative.Id;
ObjectType = PKSimConstants.ObjectTypes.Compound;
CommandType = PKSimConstants.Command.CommandTypeEdit;
BuildingBlockId = context.BuildingBlockIdContaining(parameterGroup);
Description = PKSimConstants.Command.SetDefaultAlternativeParameterDescription(context.DisplayNameFor(parameterGroup), _oldDefaultAlternative.Name, parameterAlternative.Name);
ShouldChangeVersion = false;
context.UpdateBuildingBlockPropertiesInCommand(this, context.BuildingBlockContaining(parameterGroup));
}
public EditObjectBaseDescriptionCommand(IObjectBase objectBase, string newDescription, IExecutionContext context)
{
_objectBase = objectBase;
_newDescription = newDescription;
_objectBaseId = objectBase.Id;
var entity = objectBase as IEntity;
if (entity != null)
{
_buildingBlockId = context.BuildingBlockIdContaining(entity);
context.UpdateBuildingBlockPropertiesInCommand(this, context.BuildingBlockContaining(entity));
}
ObjectType = context.TypeFor(objectBase);
CommandType = PKSimConstants.Command.CommandTypeEdit;
Description = PKSimConstants.Command.EditEntityDescriptionCommandDescripiton(ObjectType, objectBase.Name);
}
public SetExpressionLocalizationInProteinCommand(
IndividualProtein protein,
Localization localization,
ISimulationSubject simulationSubject,
IExecutionContext context, bool setAsFlag = true)
{
_protein = protein;
_simulationSubject = simulationSubject;
BuildingBlockId = context.BuildingBlockIdContaining(protein);
_newLocalization = setAsFlag ? _protein.Localization ^ localization : localization;
ObjectType = PKSimConstants.ObjectTypes.Protein;
CommandType = PKSimConstants.Command.CommandTypeEdit;
_proteinId = _protein.Id;
context.UpdateBuildingBlockPropertiesInCommand(this, context.BuildingBlockContaining(protein));
//This command is not visible. Only required to ensure that we can undo
Visible = false;
}
protected AddEntityToContainerCommand(TEntity entityToAdd, TContainer parentContainer, IExecutionContext context, Func <TContainer, Action <TEntity> > addFunction)
{
_entityToAdd = entityToAdd;
_parentContainer = parentContainer;
_addFunction = addFunction;
_entityToAddId = _entityToAdd.Id;
_parentContainerId = _parentContainer.Id;
IncrementVersion = true;
BuildingBlockId = context.BuildingBlockIdContaining(parentContainer);
ObjectType = context.TypeFor(entityToAdd);
CommandType = PKSimConstants.Command.CommandTypeAdd;
var buildingBlock = context.BuildingBlockContaining(parentContainer);
context.UpdateBuildinBlockProperties(this, buildingBlock);
string containerName = string.IsNullOrEmpty(parentContainer.Name) ? CoreConstants.ContainerName.NameTemplate : parentContainer.Name;
Description = PKSimConstants.Command.AddEntityToContainer(ObjectType, entityToAdd.Name, context.TypeFor(parentContainer), containerName);
}
protected override void PerformExecuteWith(IExecutionContext context)
{
//Retrieve building block id in execute only since parameter might have been added in a macro command and building block id was not available in constructor
BuildingBlockId = context.BuildingBlockIdContaining(_parameter);
//Model parameter in simulation might not be found as belonging to a building block, In that case, we set
//the building block id equal to the simulation id, which is also a building block
if (string.IsNullOrEmpty(BuildingBlockId))
{
BuildingBlockId = SimulationId;
}
udpateBuildingBlockProperties(context);
setBuildingBlockAlteredFlag(context);
//Command dependent implementation
ExecuteUpdateParameter(context);
//Once values have been updated, update dependent objects
UpdateDependenciesOnParameter(context);
}
protected override void PerformExecuteWith(IExecutionContext context)
{
//Retrieve building block id in execute only since molecule might have been added in a macro command and bbid was not available in constructor
BuildingBlockId = context.BuildingBlockIdContaining(_molecule);
NormalizeExpressions(_simulationSubject, _molecule);
}