public static void Uptimize()
{
string fastaFile = @"C:\_IRIC\Data\NB\peptide.fasta";
DBOptions dbOptions = PositionnalIsomerSolver.CreateOptions(fastaFile, @"C:\_IRIC\Data\NB\Units2\", 8, 0.05, new PeptidAce.Utilities.Interfaces.ConSolCommandLine());
dbOptions.dProduct = 0.0917981081138356;
dbOptions.dPrecursor = 0.345789190542786;
dbOptions.dMatchingProductFraction = 0.427418045898628;
dbOptions.dMatchingProduct = 0;
dbOptions.dIntensityFraction = 0.429418127252449;
dbOptions.dIntensity = 0;
dbOptions.dProtein = 0.692270441303156;
dbOptions.dPeptideScore = 0.636739763262095;
dbOptions.dFragmentScore = 0.0229058195943506;
dbOptions.fullFragment = new FullFragments(true);
string project = @"C:\_IRIC\Data\NB\ProjectTest_AllAce_Spiked_QEPlus_Apr21.csv";
Samples samples = new Samples(project, 0, dbOptions);
Uptimizer.Run(samples, dbOptions);
dbOptions.Save(dbOptions.OutputFolder + "UptimizedOptions.csv");
}
public static void Run(Samples samples, DBOptions options)
{
//PeptidAce.Utilities.Methods.UptimizeOptions upper = new Utilities.Methods.UptimizeOptions(options, samples);
//upper.Run();
Ace ace = new Ace(options, samples);
ace.Preload(false, false);
ace.PrepareQueries();
bool keepUptimizing = true;
int bestCount = 0;
while (keepUptimizing)
{
try
{
foreach (Query query in ace.AllQueries)
{
query.psms.Clear();
query.precursor.psms_AllPossibilities.Clear();
if (query.precursor.psms != null)
{
query.precursor.psms.Clear();
}
}
Result rez = ace.LaunchSearch(ace.AllQueries);
int nbCorrectMatches = 0;
int nbTarget = 0;
foreach (Query query in rez.queries)
{
if (query.psms.Count > 0)
{
if (query.Target)
{
nbTarget++;
if (query.psms[0].Peptide.Sequence.CompareTo(query.sample.nameColumn) == 0)
{
nbCorrectMatches++;
}
}
}
}
options.ConSole.WriteLine("NbCorrectMatches : " + nbCorrectMatches + " (" + nbTarget + " targets)");//332
if (nbCorrectMatches > bestCount)
{
bestCount = nbCorrectMatches;
options.Save(options.OutputFolder + "Options_" + bestCount + ".csv");
}
options.RandomizeParams();
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
}
}
options.Save(options.OutputFolder + "UptimizedOptions.csv");
//*/
}
