private void WriteScoreMap(StreamWriter sw, DatasetList BuildResult, ProteinFdrFilteredItem item)
{
if (item.ProteinCount == 0)
{
return;
}
BuildResult.BuildSpectrumBin();
BuildResult.KeepOptimalResultInSetOnly(item.AcceptedSpectra);
sw.WriteLine(MyConvert.Format("Filtering condition = {0}, PeptideFdr = {1}", item.ProteinCondition, item.PeptideFdr));
BuildResult.ForEach(ds =>
{
sw.WriteLine("Dataset {0}", ds.Options.Name);
OptimalResultConditionUtils.WriteSpectrumBin(sw, ds, f1, f2);
});
sw.WriteLine();
}
public ProteinFdrFilteredItem GetOptimalResultForGroupFilter(DatasetList dsList, double initFdr, double maxProteinFdr, IIdentifiedProteinGroupFilter groupFilter)
{
double curFdr = initFdr;
var result = new ProteinFdrFilteredItem();
result.PeptideBeforeFdr = dsList.GetOptimalSpectrumCount();
while (true)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
string condition = groupFilter == null ? "[]" : "[" + groupFilter.FilterCondition + "]";
string task = MyConvert.Format("Filtering {0} protein ... PeptideFdr={1:0.0000}", condition, curFdr);
Progress.SetMessage(task);
GC.Collect();
GC.WaitForPendingFinalizers();
var filteredSpectra = dsList.FilterByFdr(curFdr).Spectra;
filteredSpectra.TrimExcess();
GC.Collect();
GC.WaitForPendingFinalizers();
Progress.SetMessage(task + ", building protein list from peptides...");
List <IIdentifiedProtein> proteins = proteinBuilder.Build(filteredSpectra);
Progress.SetMessage(task + ", building protein group from protein list...");
List <IIdentifiedProteinGroup> groups = groupBuilder.Build(proteins);
List <IIdentifiedProteinGroup> filteredGroups = groupFilter == null ? groups : groups.FindAll(g => groupFilter.Accept(g));
Progress.SetMessage(task + ", calculating protein fdr...");
double proteinFdr = CalculateProteinGroupFdr(filteredGroups);
if (proteinFdr <= maxProteinFdr)
{
//using (StreamWriter sw = new StreamWriter(@"e:\temp\protein.txt", true))
//{
// sw.WriteLine(task + " kept proteins");
// foreach (var g in filteredGroups)
// {
// foreach (var p in g)
// {
// sw.WriteLine(p.Name);
// }
// }
// sw.WriteLine();
//}
result.ProteinCondition = condition;
result.PeptideFdr = curFdr;
result.ProteinFdr = proteinFdr;
result.ProteinCount = filteredGroups.Count;
Progress.SetMessage(task + ", accepted, processing corresponding PSMs...");
foreach (IIdentifiedProteinGroup group in filteredGroups)
{
result.AcceptedSpectra.UnionWith(group[0].GetSpectra());
}
result.AcceptedSpectra.TrimExcess();
//删除已经被包含在通过筛选的group对应的spectra
filteredSpectra.RemoveAll(m => result.AcceptedSpectra.Contains(m));
//删除对应于已通过筛选的蛋白质的spectra（但未通过初始的肽段筛选）
var proteinList = new HashSet <string>((from g in filteredGroups
from p in g
select p.Name).Distinct());
filteredSpectra.RemoveAll(m =>
{
foreach (var pep in m.Peptides)
{
foreach (var p in pep.Proteins)
{
if (proteinList.Contains(p))
{
return(true);
}
}
}
return(false);
});
filteredSpectra.TrimExcess();
result.RejectedSpectra = filteredSpectra;
List <IIdentifiedProtein> rejectProteins = proteinBuilder.Build(filteredSpectra);
List <IIdentifiedProteinGroup> rejectGroups = groupBuilder.Build(rejectProteins);
//using (StreamWriter sw = new StreamWriter(@"e:\temp\protein.txt", true))
//{
// sw.WriteLine(task + " rejected proteins");
// foreach (var g in rejectGroups)
// {
// foreach (var p in g)
// {
// sw.WriteLine(p.Name);
// }
// }
// sw.WriteLine();
//}
GC.Collect();
GC.WaitForPendingFinalizers();
Progress.SetMessage(task + " finished.");
return(result);
}
else
{
double stepFdr = CalculateStepFdr(curFdr);
curFdr -= stepFdr;
}
}
}
