private IEnumerable <object> processSelection(ProcessSelectionGroup processSelectionGroup, StructureElement element)
{
if (!processSelectionGroup.AllEnabledProcesses().Any())
{
yield break;
}
yield return(element);
yield return(processSelectionGroup);
}
private void addSystemicProcesses(Model.Compound compound, ProcessSelectionGroup processSelectionGroup, SystemicProcessType systemicProcessType)
{
//add all systemic processes
compound.AllSystemicProcessesOfType(systemicProcessType).Each(systemicProcess =>
{
var processSelection = new SystemicProcessSelection {
ProcessName = systemicProcess.Name, ProcessType = systemicProcess.SystemicProcessType
};
processSelectionGroup.AddSystemicProcessSelection(processSelection);
});
}
private void removeOldStaticInhibitionReferences(ProcessSelectionGroup processSelectionGroup, Compound compound, List <string> oldMappedInhibitionProcessList)
{
var allInhibitionProcesses = compound.AllProcesses <PartialProcess>().Where(x => x.InternalName.Contains("Inhibition"));
foreach (var inhibitionProcess in allInhibitionProcesses)
{
var inhibitionSelection = processSelectionGroup.AllPartialProcesses()
.FirstOrDefault(x => string.Equals(x.ProcessName, inhibitionProcess.Name));
if (inhibitionSelection == null)
{
continue;
}
processSelectionGroup.RemovePartialProcessSelection(inhibitionSelection);
oldMappedInhibitionProcessList.Add(inhibitionProcess.Name);
}
}
private ProcessSelectionGroup selectionGroup <TPartialProcess>(ProcessSelectionGroup processSelectionGroup, Model.CompoundProcess process, params SystemicProcessType[] systemicProcessTypes) where TPartialProcess : PartialProcess
{
if (process.IsAnImplementationOf <TPartialProcess>())
{
return(processSelectionGroup);
}
var systemicProcess = process as SystemicProcess;
if (systemicProcess == null)
{
return(null);
}
if (systemicProcess.SystemicProcessType.IsOneOf(systemicProcessTypes))
{
return(processSelectionGroup);
}
return(null);
}
private void updateCompoundNameInProcess(ProcessSelectionGroup processSelectionGroup, Compound compound)
{
processSelectionGroup.AllPartialProcesses().Each(p => p.CompoundName = compound.Name);
processSelectionGroup.AllSystemicProcesses().Each(p => p.CompoundName = compound.Name);
}
private void addPartialProcesses <TPartialProcess, TIndividualMolecule, TProcessSelection>(Model.Compound compound, Model.Individual individual, ProcessSelectionGroup processSelectionGroup)
where TPartialProcess : Model.PartialProcess
where TIndividualMolecule : IndividualMolecule
where TProcessSelection : ProcessSelection, new()
{
//default mapping with processes: Mapping done only by name
foreach (var process in compound.AllProcesses <TPartialProcess>())
{
var molecule = individual.MoleculeByName <TIndividualMolecule>(process.MoleculeName);
//enzyme not found in individual
if (molecule == null)
{
_batchLogger.AddDebug($"Molecule '{process.MoleculeName}' not found in individual but is defined in compound for process '{process.Name}'");
continue;
}
_batchLogger.AddDebug($"Adding process {process.Name} for molecule {molecule.Name}");
processSelectionGroup.AddPartialProcessSelection(new TProcessSelection {
ProcessName = process.Name, MoleculeName = molecule.Name, CompoundName = compound.Name
});
}
}
protected void SaveProcessSelectionGroup(ProcessSelectionGroup processSelectionGroup)
{
processSelectionGroup.ClearProcesses();
_allPartialProcessesDTO.Each(process => processSelectionGroup.AddPartialProcessSelection(MapPartialProcessFrom(process)));
_allSystemicProcessesDTO.Each(process => processSelectionGroup.AddSystemicProcessSelection(MapSystemicProcessFrom(process)));
}
private void addPartialProcesses <TPartialProcess, TIndividualMolecule, TProcessSelection>(Compound compound, Individual individual, ProcessSelectionGroup processSelectionGroup)
where TPartialProcess : PartialProcess
where TIndividualMolecule : IndividualMolecule
where TProcessSelection : ProcessSelection, new()
{
//default mapping with processes: Mapping done only by name
foreach (var process in compound.AllProcesses <TPartialProcess>())
{
var molecule = individual.MoleculeByName <TIndividualMolecule>(process.MoleculeName);
//enzyme not found in individual
if (molecule == null)
{
continue;
}
processSelectionGroup.AddPartialProcessSelection(new TProcessSelection {
ProcessName = process.Name, MoleculeName = molecule.Name, CompoundName = compound.Name
});
}
}
private ProcessSelection getFirstPartialProcessFor(ProcessSelectionGroup processSelectionGroup)
{
return(processSelectionGroup.AllPartialProcesses().ElementAt(0));
}
