public void Log(string message)
{
if (filter.Accept(message))
{
logger.Log(message);
}
}
protected Action <ActionContext> WrapFilter(Action <ActionContext> handler, IFilter filter)
{
return((ActionContext ctx) =>
{
filter.Accept(handler, ctx);
});
}
public static void AssignDecoy <T>(List <T> peptides, IFilter <IIdentifiedSpectrum> decoyFilter) where T : IIdentifiedSpectrum
{
foreach (T phit in peptides)
{
phit.FromDecoy = decoyFilter.Accept(phit);
}
}
public override IEnumerable <string> Process(string fileName)
{
IFilter <FastqSequence> filter = options.GetFilter();
using (GzipTextReader gz1 = new GzipTextReader(options.Gzip, options.FastqFiles[0]))
using (GzipTextReader gz2 = new GzipTextReader(options.Gzip, options.FastqFiles[1]))
using (StreamWriter sw1 = new StreamWriter(options.OutputFiles[0]))
using (StreamWriter sw2 = new StreamWriter(options.OutputFiles[1]))
{
FastqReader reader = new FastqReader();
FastqWriter writer = new FastqWriter();
var count = 0;
while (true)
{
var q1 = reader.Parse(gz1.Reader);
var q2 = reader.Parse(gz2.Reader);
if (q1 == null || q2 == null)
{
break;
}
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (filter.Accept(q1) && filter.Accept(q2))
{
writer.Write(sw1, q1);
writer.Write(sw2, q2);
}
}
}
return(options.OutputFiles);
}
private void visitSelect(SelectBuilder item)
{
bool needsParentheses = level > 0;
if (needsParentheses)
{
writer.Write("(");
}
writer.Write("SELECT ");
if (item.Distinct != DistinctQualifier.Default)
{
DistinctQualifierConverter converter = new DistinctQualifierConverter();
writer.Write(converter.ToString(item.Distinct));
writer.Write(" ");
}
if (item.Top != null)
{
IVisitableBuilder top = item.Top;
top.Accept(forSubCommand().forValueContext(ValueReferenceType.Reference));
writer.Write(" ");
}
forValueContext(ValueReferenceType.Declaration).join(", ", item.Projection);
if (item.From.Any())
{
writer.Write(" FROM ");
forSourceContext(SourceReferenceType.Declaration).join(", ", item.From);
}
if (item.WhereFilterGroup.HasFilters)
{
writer.Write(" WHERE ");
IFilter where = item.WhereFilterGroup;
where.Accept(forSubCommand().forValueContext(ValueReferenceType.Reference));
}
if (item.GroupBy.Any())
{
writer.Write(" GROUP BY ");
forValueContext(ValueReferenceType.Reference).join(", ", item.GroupBy);
}
if (item.HavingFilterGroup.HasFilters)
{
writer.Write(" HAVING ");
IFilter having = item.HavingFilterGroup;
having.Accept(forSubCommand().forValueContext(ValueReferenceType.Reference));
}
if (item.OrderBy.Any())
{
writer.Write(" ORDER BY ");
forValueContext(ValueReferenceType.Alias).join(", ", item.OrderBy);
}
if (needsParentheses)
{
writer.Write(")");
}
}
public PeakList <T> Filter(IFilter <T> filter)
{
PeakList <T> result = NewSubPeakList();
foreach (T peak in this)
{
if (filter.Accept(peak))
{
result.Add(peak);
}
}
return(result);
}
protected override void VisitSelect(SelectBuilder item)
{
this.QueryExpression = CreateDefaultQueryExpression();
CurrentRequest.Query = this.QueryExpression;
if (!item.From.Any())
{
throw new InvalidOperationException("The query does not have a valid FROM clause");
}
Mode = VisitMode.From;
if (item.From.Count() == 1)
{
IsSingleSource = true;
}
VisitEach(item.From);
Mode = VisitMode.Projection;
NavigateProjections(item.Projection);
Mode = VisitMode.Filter;
if (item.WhereFilterGroup != null)
{
IFilter where = item.WhereFilterGroup;
where.Accept(this);
}
else
{
//TODO: Should only be one where clause?
foreach (IVisitableBuilder where in item.Where)
{
where.Accept(this);
}
}
if (item.Top != null)
{
Mode = VisitMode.Top;
IVisitableBuilder top = item.Top;
top.Accept(this);
}
if (item.OrderBy != null)
{
Mode = VisitMode.OrderBy;
foreach (IVisitableBuilder order in item.OrderBy)
{
order.Accept(this);
}
}
}
public List <Pair <char, char> > getSiteListByFilter(
IFilter <Pair <char, char> > filter)
{
List <Pair <char, char> > result = new List <Pair <char, char> >();
for (int i = 0; i < sites.Count; i++)
{
if (filter.Accept(sites[i]))
{
result.Add(new Pair <char, char>(sites[i]));
}
}
return(result);
}
private void CreateHideVesselCommands(CommandSet commands)
{
var vessels = FlightGlobals.Vessels;
for (int i = 0; i < vessels.Count; i++)
{
var vessel = vessels[i];
var needCommand = m_configuration.HideVesselIcons | m_configuration.HideVesselOrbits;
if (needCommand && m_vesselFilter.Accept(vessel))
{
var command = new HideOrbitCommand(vessel.orbitRenderer, m_configuration.HideVesselIcons, m_configuration.HideVesselOrbits);
commands.Add(command);
}
}
}
private void CreateHideBodiesCommands(CommandSet commands)
{
var bodies = FlightGlobals.Bodies;
for (int i = 0; i < bodies.Count; i++)
{
var body = bodies[i];
var needCommand = m_configuration.HideCelestialBodyIcons | m_configuration.HideCelestialBodyOrbits;
if (needCommand && m_celestialBodyFilter.Accept(body))
{
var command = new HideOrbitCommand(body.GetOrbitDriver().Renderer, m_configuration.HideCelestialBodyIcons, m_configuration.HideCelestialBodyOrbits);
commands.Add(command);
}
}
}
private void visitDelete(DeleteBuilder item)
{
writer.Write("DELETE ");
if (options.VerboseDeleteStatement)
{
writer.Write("FROM ");
}
forSourceContext(SourceReferenceType.Declaration).visitAliasedSource(item.Table);
if (item.WhereFilterGroup.HasFilters)
{
writer.Write(" WHERE ");
IFilter filterGroup = item.WhereFilterGroup;
filterGroup.Accept(forSubCommand().forValueContext(ValueReferenceType.Reference));
}
}
protected override void VisitSelect(SelectBuilder item)
{
this.QueryExpression = new QueryExpression();
CurrentRequest.Query = this.QueryExpression;
if (!item.From.Any())
{
throw new InvalidOperationException("The query does not have a valid FROM clause");
}
Mode = VisitMode.From;
if (item.From.Count() == 1)
{
IsSingleSource = true;
}
VisitEach(item.From);
Mode = VisitMode.Projection;
NavigateProjections(item.Projection);
Mode = VisitMode.Filter;
if (item.WhereFilterGroup != null)
{
IFilter where = item.WhereFilterGroup;
where.Accept(this);
}
else
{
//TODO: Should only be one where clause?
foreach (IVisitableBuilder where in item.Where)
{
where.Accept(this);
}
}
if (item.Top != null)
{
Mode = VisitMode.Top;
IVisitableBuilder top = item.Top;
top.Accept(this);
}
else
{
// xrm wont let you use paging and top for some reason..
if (QueryExpression.PageInfo == null)
{
QueryExpression.PageInfo = new PagingInfo();
}
QueryExpression.PageInfo.PageNumber = 1;
//todo take this from the connection string..
QueryExpression.PageInfo.Count = 500;
QueryExpression.PageInfo.ReturnTotalRecordCount = true;
}
if (item.OrderBy != null)
{
Mode = VisitMode.OrderBy;
foreach (IVisitableBuilder order in item.OrderBy)
{
order.Accept(this);
}
}
}
protected override List <IIdentifiedSpectrum> DoParse()
{
IAccessNumberParser parser = options.Parent.Database.GetAccessNumberParser();
var peptideFormat = new SequestPeptideTextFormat()
{
Progress = this.Progress
};
Progress.SetRange(0, options.PathNames.Count + 1);
var result = new List <IIdentifiedSpectrum>();
IFilter <IIdentifiedSpectrum> spectrumFilter = options.GetFilter();
SequestOutDirectoryParser outDirParser;
SequestOutsParser outsParser;
SequestOutZipParser outZipParser;
string modStr = "";
if (options.SkipSamePeptideButDifferentModificationSite)
{
modStr = MyConvert.Format(".M{0:0.00}", options.MaxModificationDeltaCn);
outsParser = new SequestOutsParser(true, options.MaxModificationDeltaCn);
outDirParser = new SequestOutDirectoryParser(true, options.MaxModificationDeltaCn);
outZipParser = new SequestOutZipParser(true, options.MaxModificationDeltaCn);
}
else
{
outsParser = new SequestOutsParser(true);
outDirParser = new SequestOutDirectoryParser(true);
outZipParser = new SequestOutZipParser(true);
}
outsParser.Progress = Progress;
outDirParser.Progress = Progress;
outZipParser.Progress = Progress;
long afterFirstMemory = 0;
DateTime afterFirstTime = DateTime.Now;
int stepCount = 0;
foreach (string pathName in options.PathNames)
{
stepCount++;
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
AbstractSequestSpectraDistiller distiller;
string engine;
if (Directory.Exists(pathName))
{
var dir = new DirectoryInfo(pathName);
if (dir.GetFiles("*.outs").Length > 0 || dir.GetFiles("*.outs.zip").Length > 0)
{
distiller = new SequestOutsDistiller(outsParser, peptideFormat);
}
else
{
distiller = new SequestOutDirectoryDistiller(outDirParser, peptideFormat);
}
engine = "SEQUEST";
}
else if (pathName.ToLower().EndsWith(".xml"))
{
distiller = new CometSpectraDistiller(peptideFormat);
engine = "COMET";
}
else if (pathName.ToLower().EndsWith(".msf"))
{
distiller = new MsfSpectraDistiller(peptideFormat);
engine = "PD";
}
else //zipfile
{
ISpectrumParser zipParser;
if (ZipUtils.HasFile(pathName, m => m.ToLower().EndsWith(".out")))
{
zipParser = outZipParser;
}
else
{
zipParser = outsParser;
}
distiller = new SequestOutZipDistiller(zipParser, peptideFormat);
engine = "SEQUEST";
}
distiller.Progress = this.Progress;
List <IIdentifiedSpectrum> curPeptides = distiller.ParseSpectra(pathName, modStr, stepCount, options.PathNames.Count);
int curPeptideCount = curPeptides.Count;
if (null != spectrumFilter)
{
curPeptides.RemoveAll(m => !spectrumFilter.Accept(m));
}
curPeptides.ForEach(m =>
{
m.Tag = options.Name;
m.Engine = engine;
});
result.AddRange(curPeptides);
curPeptides = null;
GC.Collect();
GC.WaitForPendingFinalizers();
if (stepCount == 1)
{
afterFirstMemory = Process.GetCurrentProcess().WorkingSet64 / (1024 * 1024);
afterFirstTime = DateTime.Now;
}
else
{
long currMemory = Process.GetCurrentProcess().WorkingSet64 / (1024 * 1024);
double averageCost = (double)(currMemory - afterFirstMemory) / (stepCount - 1);
double estimatedCost = afterFirstMemory + averageCost * options.PathNames.Count;
DateTime currTime = DateTime.Now;
var averageTime = currTime.Subtract(afterFirstTime).TotalMinutes / (stepCount - 1);
var finishTime = afterFirstTime.AddMinutes(averageTime * (options.PathNames.Count - 1));
Console.WriteLine("{0}/{1}, cost {2}M, avg {3:0.0}M, need {4:0.0}M, will finish at {5:MM-dd HH:mm:ss}", stepCount, options.PathNames.Count, currMemory, averageCost, estimatedCost, finishTime.ToString());
}
}
return(result);
}
public PropertyTree ApplyFilter(IFilter <PropertyTree> f)
{
return(new PropertyTree(
Entity, Properties, Children.Where(child => f.Accept(child)).Select(child => child.ApplyFilter(f)).ToImmutableList()));
}
