public void InitializeByResult(IIdentifiedResult identifiedResult)
{
string oldProteinHeader = ProteinFormat == null?GetDefaultProteinHeader() : ProteinFormat.GetHeader();
InitializeProteinFormat(identifiedResult, oldProteinHeader);
string oldPeptideHeader = PeptideFormat == null?GetDefaultPeptideHeader() : PeptideFormat.GetHeader();
InitializePeptideFormat(identifiedResult, oldPeptideHeader);
}
private IIdentifiedProteinGroup ReadNextProteinGroup(StreamReader filein, Dictionary <string, IIdentifiedSpectrum> peptideMap, ref string lastLine)
{
Progress.SetPosition(filein.BaseStream.Position);
while (!IdentifiedResultUtils.IsProteinLine(lastLine) && (lastLine = filein.ReadLine()) != null)
{
}
if (lastLine == null)
{
return(null);
}
IIdentifiedProteinGroup result = new IdentifiedProteinGroup();
while (IdentifiedResultUtils.IsProteinLine(lastLine))
{
IIdentifiedProtein protein = ProteinFormat.ParseString(lastLine);
result.Add(protein);
protein.GroupIndex = IdentifiedResultUtils.GetGroupIndex(lastLine);
lastLine = filein.ReadLine();
}
List <IIdentifiedSpectrum> peptides = new List <IIdentifiedSpectrum>();
while (!IdentifiedResultUtils.IsProteinLine(lastLine))
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
IIdentifiedSpectrum mphit = PeptideFormat.ParseString(lastLine);
string id = string.Format("{0}-{1}-{2}-{3}", mphit.Query.FileScan.LongFileName, mphit.Rank, mphit.Engine, mphit.Tag);
if (!peptideMap.ContainsKey(id))
{
peptideMap[id] = mphit;
}
else
{
mphit = peptideMap[id];
}
peptides.Add(mphit);
lastLine = filein.ReadLine();
if (lastLine == null || lastLine.Trim().Length == 0)
{
break;
}
}
foreach (IIdentifiedSpectrum hit in peptides)
{
result.AddIdentifiedSpectrum(hit);
}
return(result);
}
public override void WriteToFile(string fileName, IIdentifiedResult identifiedResult)
{
CheckFormat(identifiedResult);
List <IIdentifiedSpectrum> allSpectra = identifiedResult.GetSpectra();
for (int i = 0; i < allSpectra.Count; i++)
{
allSpectra[i].Id = i.ToString();
}
string linkFilename = GetLinkFileName(fileName);
HashSet <IIdentifiedSpectrum> spectra = new HashSet <IIdentifiedSpectrum>();
using (var linkWriter = new StreamWriter(linkFilename))
{
linkWriter.WriteLine("PeptideId\tGroupId");
using (var sw = new StreamWriter(fileName))
{
sw.WriteLine(ProteinFormat.GetHeader());
var groups = GetValidGroups(identifiedResult);
foreach (IIdentifiedProteinGroup mpg in groups)
{
GroupWriter.WriteToStream(sw, mpg);
var validSpectra = GetValidSpectra(mpg.GetSortedPeptides());
foreach (var spectrum in validSpectra)
{
linkWriter.WriteLine(spectrum.Id + "\t" + mpg.Index);
}
spectra.UnionWith(validSpectra);
}
}
}
var finalSpectra = from s in spectra
orderby s.Id
select s;
string peptideFile = GetPeptideFileName(fileName);
if (!PeptideFormat.GetHeader().Contains("Id\t"))
{
PeptideFormat = new PeptideLineFormat("Id\t" + PeptideFormat.GetHeader());
}
using (var sw = new StreamWriter(peptideFile))
{
WritePeptideHeader(sw);
foreach (IIdentifiedSpectrum mph in finalSpectra)
{
WritePeptide(sw, mph);
}
}
if (identifiedResult.Count > 0 && identifiedResult[0][0].Sequence != null)
{
string fastaFilename = fileName + ".fasta";
WriteFastaFile(fastaFilename, identifiedResult);
}
}
