public async Task <GeneEditorViewModel> OptimizeDNASequence(GeneEditorViewModel geneEditorViewModel)
{
string optimizedDNASequence = null;
geneEditorViewModel.InitialSequence = geneEditorViewModel.InitialSequence.Trim().Replace(" ", string.Empty).ToUpper();
if (geneEditorViewModel.SelectedInitialSequenceType == InitialSequenceType.ProteinInitialSequence)
{
optimizedDNASequence = await codonOptimizationService.OptimizeProteinSequence(
geneEditorViewModel.InitialSequence, geneEditorViewModel.SelectedOrganismId);
}
else if (geneEditorViewModel.SelectedInitialSequenceType == InitialSequenceType.DNAInitialSequence)
{
optimizedDNASequence = await codonOptimizationService.OptimizeDNASequence(
geneEditorViewModel.InitialSequence, geneEditorViewModel.SelectedOrganismId);
}
geneEditorViewModel.OptimizedDNASequence = optimizedDNASequence;
Gene gene = CreateGene(geneEditorViewModel.Name, geneEditorViewModel.OptimizedDNASequence,
geneEditorViewModel.SelectedOrganismId, geneEditorViewModel.KPlusConcentration, geneEditorViewModel.DMSO);
geneEditorViewModel.GeneId = gene.Id;
geneEditorViewModel.GeneFragmentLength = DefaultOligoLength;
geneEditorViewModel.GeneFragmentOverlappingLength = DefaultOverlappingLength;
geneEditorViewModel.IsGeneOptimized = true;
Organism organism = unitOfWork.GetById <Organism>(geneEditorViewModel.SelectedOrganismId);
geneEditorViewModel.SelectedOrganismName = organism.Name;
return(geneEditorViewModel);
}
public GeneEditorViewModel GetGeneEditorViewModel(string geneId)
{
Gene gene = unitOfWork.GetById <Gene>(geneId);
GeneEditorViewModel geneEditorViewModel = new GeneEditorViewModel();
geneEditorViewModel.IsGeneOptimized = true;
geneEditorViewModel.Name = gene.Name;
geneEditorViewModel.GeneId = gene.Id;
geneEditorViewModel.OptimizedDNASequence = gene.DNASequence;
Organism organism = unitOfWork.GetById <Organism>(gene.OrganismId);
geneEditorViewModel.AllOrganisms = new List <ListItem>()
{
new ListItem {
Id = organism.Id, Text = organism.Name
}
};
geneEditorViewModel.SelectedOrganismId = organism.Id;
geneEditorViewModel.SelectedOrganismName = organism.Name;
geneEditorViewModel.KPlusConcentration = gene.KPlusConcentration;
geneEditorViewModel.DMSO = gene.DMSO;
var geneFragment = gene.GeneFragments.First();
geneEditorViewModel.GeneFragmentLength = geneFragment.OligoLength;
geneEditorViewModel.GeneFragmentOverlappingLength = geneFragment.OverlappingLength;
return(geneEditorViewModel);
}
public async Task <GeneEditorViewModel> GetGeneEditorViewModel()
{
GeneEditorViewModel geneEditorViewModel = new GeneEditorViewModel();
geneEditorViewModel.SelectedInitialSequenceType = InitialSequenceType.ProteinInitialSequence;
IEnumerable <Organism> organisms = await unitOfWork.GetAll <Organism>().ToListAsync();
geneEditorViewModel.AllOrganisms = organisms.Select(x => new ListItem()
{
Id = x.Id, Text = x.Name
});
if (geneEditorViewModel.AllOrganisms.Any())
{
ListItem defaultOrganism = geneEditorViewModel.AllOrganisms.First();
geneEditorViewModel.SelectedOrganismId = defaultOrganism.Id;
}
geneEditorViewModel.KPlusConcentration = DefaultKPlusConcentration;
geneEditorViewModel.DMSO = DefaultDMSO;
geneEditorViewModel.IsGeneOptimized = false;
return(geneEditorViewModel);
}
public async Task <JsonResult> UpdateGeneFragments(GeneEditorViewModel geneEditorViewModel)
{
await geneEditorService.UpdateGeneFragments(
geneEditorViewModel.GeneId, geneEditorViewModel.OptimizedDNASequence,
geneEditorViewModel.GeneFragmentLength, geneEditorViewModel.GeneFragmentOverlappingLength,
geneEditorViewModel.KPlusConcentration, geneEditorViewModel.DMSO);
return(JsonSuccess(geneEditorViewModel.GeneId));
}
public async Task <JsonResult> OptimizeGene(GeneEditorViewModel geneEditorViewModel)
{
// if (string.IsNullOrWhiteSpace(geneEditorViewModel.ProteinInitialSequence) &&
// (string.IsNullOrWhiteSpace(geneEditorViewModel.DNAInitialSequence) || geneEditorViewModel.DNAInitialSequence.Length % 3 != 0))
// {
// ModelState.AddModelError(string.Empty, "Wrong sequence");
// return View(geneEditorViewModel);
// }
// ModelState.Clear();
try
{
geneEditorViewModel = await geneEditorService.OptimizeDNASequence(geneEditorViewModel);
return(Json(geneEditorViewModel));
}
catch (Exception ex)
{
return(JsonError());
}
}
public JsonResult GetGeneEditorViewModel(string geneId)
{
GeneEditorViewModel geneEditorViewModel = geneEditorService.GetGeneEditorViewModel(geneId);
return(Json(geneEditorViewModel, JsonRequestBehavior.AllowGet));
}
public async Task <ActionResult> Index(string genesProjectName)
{
GeneEditorViewModel geneEditorViewModel = await geneEditorService.GetGeneEditorViewModel();
return(View(geneEditorViewModel));
}
public async Task <ActionResult> Index()
{
GeneEditorViewModel geneEditorViewModel = await geneEditorService.GetGeneEditorViewModel();
return(View(geneEditorViewModel));
}
