public static void Start(IProtease protease, int maxMissed = 3, int minLength = 5, int maxLength = 35)
{
Console.WriteLine("**Start Morpheus Search**");
Stopwatch watch = new Stopwatch();
watch.Start();
List<int> hashCodes = new List<int>();
// Generate peptide candidates
HashSet<Peptide> peptides = new HashSet<Peptide>();
using (FastaReader reader = new FastaReader("Resources/yeast_uniprot_120226.fasta"))
{
foreach (Protein protein in reader.ReadNextProtein())
{
foreach (Peptide peptide in protein.Digest(protease, maxMissed, minLength, maxLength))
{
peptides.Add(peptide);
}
}
}
MSSearchEngine engine = new MorpheusSearchEngine();
engine.PrecursorMassTolerance = Tolerance.FromPPM(100);
engine.ProductMassTolerance = Tolerance.FromPPM(10);
engine.LoadPeptides(peptides);
watch.Stop();
Console.WriteLine("Time elapsed: {0}", watch.Elapsed);
Console.WriteLine("Memory used: {0:N0} MB", Environment.WorkingSet/(1024*1024));
Console.WriteLine("**End Morpheus Search**");
}
public static void Start(IProtease protease, int maxMissed = 3, int minLength = 5, int maxLength = 35)
{
Console.WriteLine("**Start Morpheus Search**");
Stopwatch watch = new Stopwatch();
watch.Start();
List<int> hashCodes = new List<int>();
// Generate peptide candidates
HashSet<Peptide> peptides = new HashSet<Peptide>();
using (FastaReader reader = new FastaReader("Resources/yeast_uniprot_120226.fasta"))
{
foreach (Protein protein in reader.ReadNextProtein())
{
foreach (Peptide peptide in protein.Digest(protease, maxMissed, minLength, maxLength))
{
peptides.Add(peptide);
}
}
}
MSSearchEngine engine = new MorpheusSearchEngine();
engine.PrecursorMassTolerance = Tolerance.FromPPM(100);
engine.ProductMassTolerance = Tolerance.FromPPM(10);
engine.LoadPeptides(peptides);
using (MSDataFile msDataFile = new ThermoRawFile("Resources/ThermoRawFileMS1MS2.raw"))
{
//SortedMaxSizedContainer<PeptideSpectralMatch> psms = engine.Search(msDataFile.Where(scan => scan.MsnOrder > 1));
//foreach (MSDataScan scan in msDataFile.Where(scan => scan.MsnOrder > 1))
//{
// List<PeptideSpectralMatch> psms = engine.Search(scan);
// Console.WriteLine("{0} {1}", scan.SpectrumNumber, psms.Count);
//}
}
watch.Stop();
Console.WriteLine("Time elapsed: {0}", watch.Elapsed);
Console.WriteLine("Memory used: {0:N0} MB", System.Environment.WorkingSet / (1024 * 1024));
Console.WriteLine("**End Morpheus Search**");
}
