public void Run()
{
IGlycoPeptideSearchParameter parameter = GlycoPeptideSearchParameter.Parameter;
List <string> enzymes = new List <string>();
enzymes.Add("Trypsin");
enzymes.Add("GluC");
parameter.SetDigestionEnzyme(enzymes);
parameter.SetReportLocation(@"C:\Users\iruiz\Downloads\FDR4.csv");
parameter.SetAlphaFactor(1.0);
parameter.SetBetaFactor(0.1);
parameter.SetMS1Tolereance(10);
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
IGlycoPeptideSearchEngine engine = new FDREThcDGlycoPeptideSearchEngine();
//IGlycoPeptideSearchEngine engine = new CIDGlycoPeptideSearchEngine();
engine.Read(@"C:\Users\iruiz\Downloads\HP.fasta", @"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
engine.RunRange(7859, 7861);
engine.AnalyzeRange(7859, 7861);
//engine.RunRange(1, 7861);
//engine.AnalyzeRange(1, 7861);
//engine.RunRange(1, 19918);
//engine.AnalyzeRange(1, 19918);
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
public void Run()
{
IGlycoPeptideSearchParameter parameter = GlycoPeptideSearchParameter.Parameter;
List <string> enzymes = new List <string>();
enzymes.Add("Trypsin");
enzymes.Add("GluC");
parameter.SetDigestionEnzyme(enzymes);
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
if (parameter.GetReportType() == "Search")
{
IGlycoPeptideSearchEngine engine = new EThcDGlycoPeptideSearchEngine();
engine.Read(@"C:\Users\iruiz\Downloads\HP.fasta", @"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
engine.RunRange(7859, 7861);
engine.Analyze(7861);
}
watch.Stop();
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
public ConfigureWindow()
{
parameter = GlycoPeptideSearchParameter.Parameter;
digestion = new List <string>();
types = new List <string>();
InitializeComponent();
InitWindow();
}
public void SetParameter(IGlycoPeptideSearchParameter parameter)
{
this.parameter = parameter;
}
public GeneralGlycoPeptideSearchEngineInitalizer()
{
parameter = GlycoPeptideSearchParameter.Parameter;
CreateInitNGlycan.Creator.SetGeneratedTypes(parameter.GetGlycanTypes());
}
