/// <summary>
/// Apply a list of variants to intervals within this gene model
/// </summary>
/// <param name="variants"></param>
/// <returns></returns>
public List <Transcript> ApplyVariants(List <Variant> variants)
{
// Must add variants before applying them to this gene model
if (PreviouslyAddedVariants != variants)
{
AddVariantAnnotations(variants);
}
return(ApplyVariants(variants, Genes.SelectMany(g => g.Transcripts).ToList()));
}
public void RebuildModelFollowingGenes()
{
var activeModels = Genes.SelectMany(g => g.Parts.Where(p => p.Active)).Select(gp => gp.Model);
var collectionToAdd = _settings.CombinationCollection(_model);
collectionToAdd.Clear();
foreach (var activeModel in activeModels)
{
collectionToAdd.Add(activeModel);
}
}
public List <Protein> Translate(bool translateCodingDomains, HashSet <string> incompleteTranscriptAccessions = null, Dictionary <string, string> selenocysteineContaining = null)
{
return(Genes.SelectMany(g => g.Translate(translateCodingDomains, incompleteTranscriptAccessions, selenocysteineContaining)).ToList());
}