public List <ProteoformFamily> construct_families()
{
ProteoformFamily.reset_family_counter();
Stack <Proteoform> remaining = new Stack <Proteoform>(this.experimental_proteoforms.ToArray());
List <ProteoformFamily> running_families = new List <ProteoformFamily>();
List <Proteoform> running = new List <Proteoform>();
List <Thread> active = new List <Thread>();
while (remaining.Count > 0 || active.Count > 0)
{
while (remaining.Count > 0 && active.Count < Environment.ProcessorCount)
{
Proteoform root = remaining.Pop();
ProteoformFamily fam = new ProteoformFamily(root);
Thread t = new Thread(new ThreadStart(fam.construct_family));
t.Start();
running_families.Add(fam);
running.Add(root);
active.Add(t);
}
foreach (Thread t in active)
{
t.Join();
}
List <Proteoform> cumulative_proteoforms = new List <Proteoform>();
foreach (ProteoformFamily family in running_families.ToList())
{
if (cumulative_proteoforms.Contains(family.proteoforms.First()))
{
running_families.Remove(family); // check for duplicates due to arbitrary seed selection
}
else
{
cumulative_proteoforms.AddRange(family.proteoforms);
Parallel.ForEach(family.proteoforms, p => { lock (p) p.family = family; });
}
}
this.families.AddRange(running_families);
remaining = new Stack <Proteoform>(remaining.Except(cumulative_proteoforms));
running_families.Clear();
running.Clear();
active.Clear();
}
if (Sweet.lollipop.gene_centric_families)
{
families = combine_gene_families(families).ToList();
}
Sweet.lollipop.theoretical_database.aaIsotopeMassList = new AminoAcidMasses(Sweet.lollipop.carbamidomethylation, Sweet.lollipop.neucode_labeled).AA_Masses;
Parallel.ForEach(families, f => f.identify_experimentals());
return(families);
}
public List <ProteoformFamily> construct_families()
{
Stack <Proteoform> remaining = new Stack <Proteoform>(this.experimental_proteoforms.Where(e => e.accepted).ToArray());
List <ProteoformFamily> running_families = new List <ProteoformFamily>();
List <Proteoform> running = new List <Proteoform>();
List <Thread> active = new List <Thread>();
while (remaining.Count > 0 || active.Count > 0)
{
while (remaining.Count > 0 && active.Count < Environment.ProcessorCount)
{
Proteoform root = remaining.Pop();
ProteoformFamily fam = new ProteoformFamily(root);
Thread t = new Thread(new ThreadStart(fam.construct_family));
t.Start();
running_families.Add(fam);
running.Add(root);
active.Add(t);
}
foreach (Thread t in active)
{
t.Join();
}
List <Proteoform> cumulative_proteoforms = new List <Proteoform>();
foreach (ProteoformFamily family in running_families.ToList())
{
if (cumulative_proteoforms.Contains(family.proteoforms.First()))
{
running_families.Remove(family); // check for duplicates due to arbitrary seed selection
}
else
{
cumulative_proteoforms.AddRange(family.proteoforms);
Parallel.ForEach(family.proteoforms, p => { lock (p) p.family = family; });
}
}
this.families.AddRange(running_families);
remaining = new Stack <Proteoform>(remaining.Except(cumulative_proteoforms));
running_families.Clear();
running.Clear();
active.Clear();
}
if (gene_centric_families)
{
families = combine_gene_families(families).ToList();
}
Parallel.ForEach(families, f => f.identify_experimentals());
return(families);
}
public IEnumerable <ProteoformFamily> combine_gene_families(IEnumerable <ProteoformFamily> families)
{
Stack <ProteoformFamily> remaining = new Stack <ProteoformFamily>(families);
List <ProteoformFamily> running = new List <ProteoformFamily>();
HashSet <Proteoform> cumulative_proteoforms = new HashSet <Proteoform>();
List <Thread> active = new List <Thread>();
while (remaining.Count > 0 || active.Count > 0)
{
while (remaining.Count > 0 && active.Count < Environment.ProcessorCount)
{
ProteoformFamily fam = remaining.Pop();
Thread t = new Thread(() => fam.merge_families(this.families));
t.Start();
running.Add(fam);
active.Add(t);
}
foreach (Thread t in active)
{
t.Join();
}
foreach (ProteoformFamily family in running)
{
if (!family.proteoforms.Any(p => cumulative_proteoforms.Contains(p)))
{
foreach (Proteoform p in family.proteoforms)
{
cumulative_proteoforms.Add(p);
}
Parallel.ForEach(family.proteoforms, p => { lock (p) p.family = family; });
yield return(family);
}
}
remaining = new Stack <ProteoformFamily>(remaining.Except(remaining.Where(f => f.proteoforms.Any(p => cumulative_proteoforms.Contains(p)))));
running.Clear();
active.Clear();
}
}
public List <ProteoformFamily> construct_families()
{
ProteoformFamily.reset_family_counter();
Stack <Proteoform> remaining = new Stack <Proteoform>(this.experimental_proteoforms.Where(e => e.accepted).ToArray());
List <ProteoformFamily> running_families = new List <ProteoformFamily>();
List <Proteoform> running = new List <Proteoform>();
List <Thread> active = new List <Thread>();
while (remaining.Count > 0 || active.Count > 0)
{
while (remaining.Count > 0 && active.Count < Environment.ProcessorCount)
{
Proteoform root = remaining.Pop();
ProteoformFamily fam = new ProteoformFamily(root);
Thread t = new Thread(new ThreadStart(fam.construct_family));
t.Start();
running_families.Add(fam);
running.Add(root);
active.Add(t);
}
foreach (Thread t in active)
{
t.Join();
}
List <Proteoform> cumulative_proteoforms = new List <Proteoform>();
foreach (ProteoformFamily family in running_families.ToList())
{
if (cumulative_proteoforms.Contains(family.proteoforms.First()))
{
running_families.Remove(family); // check for duplicates due to arbitrary seed selection
}
else
{
cumulative_proteoforms.AddRange(family.proteoforms);
Parallel.ForEach(family.proteoforms, p => { lock (p) p.family = family; });
}
}
this.families.AddRange(running_families);
remaining = new Stack <Proteoform>(remaining.Except(cumulative_proteoforms));
running_families.Clear();
running.Clear();
active.Clear();
}
if (Lollipop.gene_centric_families)
{
families = combine_gene_families(families).ToList();
}
Sweet.lollipop.theoretical_database.aaIsotopeMassList = new AminoAcidMasses(Sweet.lollipop.carbamidomethylation, Sweet.lollipop.neucode_labeled).AA_Masses;
Parallel.ForEach(families, f => f.identify_experimentals());
//read in BU results if available, map to proteoforms.
//Sweet.lollipop.BottomUpPSMList.Clear();
//BottomUpReader.bottom_up_PTMs_not_in_dictionary.Clear();
//foreach (InputFile file in Sweet.lollipop.input_files.Where(f => f.purpose == Purpose.BottomUp))
//{
// Sweet.lollipop.BottomUpPSMList.AddRange(BottomUpReader.ReadBUFile(file.complete_path, theoreticals_by_accession.Values.ToList()));
//}
return(families);
}
