public override MyTaskResults RunSpecific(string OutputFolder, List <DbForDigestion> dbFileList)
{
PeptideByFile =
new Dictionary <string, Dictionary <string, Dictionary <Protein, List <InSilicoPep> > > >(dbFileList.Count);
int threads_1 = Environment.ProcessorCount - 1 > dbFileList.Count() ? dbFileList.Count : Environment.ProcessorCount - 1;
int[] threadArray_1 = Enumerable.Range(0, threads_1).ToArray();
Parallel.ForEach(threadArray_1, (j) =>
{
for (; j < dbFileList.Count(); j += threads_1)
{
var database = dbFileList[j];
Status("Loading Protein Database(s)...", "loadDbs");
List <Protein> proteins = LoadProteins(database);
int maxThreads = Environment.ProcessorCount - 1;
int[] threads = Enumerable.Range(0, maxThreads).ToArray();
Parallel.ForEach(threads, (i) =>
{
for (; i < DigestionParameters.ProteasesForDigestion.Count; i += maxThreads)
{
Status("Digesting Proteins...", "digestDbs");
var peptides = DigestDatabase(proteins, DigestionParameters.ProteasesForDigestion[i], DigestionParameters);
var peptidesFormatted = DeterminePeptideStatus(database.FileName, peptides, DigestionParameters);
lock (PeptideByFile)
{
if (PeptideByFile.ContainsKey(database.FileName))
{
PeptideByFile[database.FileName].Add(DigestionParameters.ProteasesForDigestion[i].Name, peptidesFormatted);
}
else
{
Dictionary <string, Dictionary <Protein, List <InSilicoPep> > > peptidesByProtease = new Dictionary <string, Dictionary <Protein, List <InSilicoPep> > >();
peptidesByProtease.Add(DigestionParameters.ProteasesForDigestion[i].Name, peptidesFormatted);
PeptideByFile.Add(database.FileName, peptidesByProtease);
}
}
}
});
}
});
Status("Writing Peptide Output...", "peptides");
WritePeptidesToTsv(PeptideByFile, OutputFolder, DigestionParameters);
MyTaskResults myRunResults = new MyTaskResults(this);
Status("Writing Results Summary...", "summary");
return(myRunResults);
}
public override MyTaskResults RunSpecific(string OutputFolder, List <DbForDigestion> dbFileList)
{
PeptideByFile =
new Dictionary <string, Dictionary <string, Dictionary <Protein, List <InSilicoPep> > > >(dbFileList.Count);
foreach (var database in dbFileList)
{
PeptideByFile.Add(database.FileName, new Dictionary <string, Dictionary <Protein, List <InSilicoPep> > >(DigestionParameters.ProteasesForDigestion.Count));
Dictionary <string, Dictionary <Protein, List <InSilicoPep> > > peptidesByProtease = new Dictionary <string, Dictionary <Protein, List <InSilicoPep> > >();
List <Protein> proteins = LoadProteins(database);
foreach (var protease in DigestionParameters.ProteasesForDigestion)
{
PeptideByFile[database.FileName].Add(protease.Name, DeterminePeptideStatus(database.FileName, DigestDatabase(proteins, protease, DigestionParameters), DigestionParameters));
}
}
PeptideByFile = WritePeptidesToTsv(PeptideByFile, OutputFolder, DigestionParameters);
MyTaskResults myRunResults = new MyTaskResults(this);
return(myRunResults);
}
public override MyTaskResults RunSpecific(string OutputFolder, List <DbForDigestion> dbFileList)
{
Dictionary <string, Dictionary <Protease, Dictionary <Protein, List <InSilicoPeptide> > > > peptideByFile =
new Dictionary <string, Dictionary <Protease, Dictionary <Protein, List <InSilicoPeptide> > > >();
foreach (var database in dbFileList)
{
Dictionary <Protease, Dictionary <Protein, List <InSilicoPeptide> > > peptidesByProtease = new Dictionary <Protease, Dictionary <Protein, List <InSilicoPeptide> > >();
List <Protein> proteins = LoadProteins(database);
foreach (var protease in DigestionParameters.ProteasesForDigestion)
{
var peptides = DigestDatabase(proteins, protease, DigestionParameters);
var inSilicoPeptidesByFile = DeterminePeptideStatus(peptides, DigestionParameters);
peptidesByProtease.Add(protease, inSilicoPeptidesByFile);
}
peptideByFile.Add(database.FileName, peptidesByProtease);
}
MyTaskResults myRunResults = new MyTaskResults(this);
return(myRunResults);
}
public override MyTaskResults RunSpecific(MyTaskResults digestionResults, List <string> peptideFilePaths)
{
throw new NotImplementedException();
}
public abstract MyTaskResults RunSpecific(MyTaskResults digestionResults, List <string> peptideFilePaths);
public override MyTaskResults RunSpecific(MyTaskResults digestionResults, List <string> peptideFilePaths)
{
MyTaskResults results = new MyTaskResults(this);
return(results);
}