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 void ToleranceWithin2()
{
var tol = Tolerance.FromPPM(10, ToleranceType.FullWidth);
Assert.IsFalse(tol.Within(500, 500.005));
}
public void ToleranceWithin1()
{
var tol = Tolerance.FromPPM(10);
Assert.IsTrue(tol.Within(500, 500.005));
}