public override IIdentifiedResult ReadFromFile(string fileName)
{
if (!File.Exists(fileName))
{
throw new FileNotFoundException("Protein file not exist : " + fileName);
}
string peptideFilename = GetPeptideFileName(fileName);
if (!File.Exists(peptideFilename))
{
throw new FileNotFoundException("Peptide file not exist : " + peptideFilename);
}
string linkFileName = GetLinkFileName(fileName);
if (!File.Exists(linkFileName))
{
throw new FileNotFoundException("Peptide2group file not exist : " + linkFileName);
}
var pepFileReader = new PeptideTextReader(GetEngineName());
List <IIdentifiedSpectrum> spectra = pepFileReader.ReadFromFile(peptideFilename);
this.PeptideFormat = pepFileReader.PeptideFormat;
var proFileReader = new ProteinTextReader(GetEngineName());
List <IIdentifiedProtein> proteins = proFileReader.ReadFromFile(fileName);
this.ProteinFormat = proFileReader.ProteinFormat;
var peptideMap = spectra.ToDictionary(m => m.Id);
var proteinMap = proteins.GroupBy(m => m.GroupIndex);
IIdentifiedResult result = Allocate();
foreach (var pros in proteinMap)
{
var group = new IdentifiedProteinGroup();
pros.ToList().ForEach(m => group.Add(m));
result.Add(group);
}
new Peptide2GroupTextReader().LinkPeptideToGroup(linkFileName, peptideMap, result.ToDictionary(m => m.Index));
string fastaFile = fileName + ".fasta";
if (File.Exists(fastaFile))
{
IdentifiedResultUtils.FillSequenceFromFasta(fastaFile, result, null);
}
return(result);
}
protected override bool FillSequence(IIdentifiedResult groups)
{
if (File.Exists(fastaFilename))
{
try
{
IdentifiedResultUtils.FillSequenceFromFasta(acParser, fastaFilename, groups, Progress);
}
catch (Exception ex)
{
Progress.SetMessage("ERROR: fill sequence failed, file = {0}, error = {1}, trace = {2}", fastaFilename, ex.Message, ex.StackTrace);
return(false);
}
return(true);
}
return(false);
}
public override IIdentifiedResult ReadFromFile(string fileName)
{
if (!File.Exists(fileName))
{
throw new FileNotFoundException("File not exist : " + fileName);
}
IIdentifiedResult result = Allocate();
Dictionary <string, IIdentifiedSpectrum> peptideMap = new Dictionary <string, IIdentifiedSpectrum>();
using (StreamReader filein = new StreamReader(new FileStream(fileName, FileMode.Open, FileAccess.Read)))
{
Progress.SetRange(0, filein.BaseStream.Length);
IIdentifiedProteinGroup group;
string lastLine = filein.ReadLine();
if (lastLine == null)
{
return(result);
}
if (ProteinFormat != null)
{
ProteinFormat = new LineFormat <IIdentifiedProtein>(ProteinFormat.Factory, lastLine, GetEngineName());
}
else
{
ProteinFormat = new ProteinLineFormat(lastLine, GetEngineName());
}
lastLine = filein.ReadLine();
if (lastLine == null)
{
return(result);
}
if (PeptideFormat != null)
{
PeptideFormat = new LineFormat <IIdentifiedSpectrum>(PeptideFormat.Factory, lastLine, GetEngineName());
}
else
{
PeptideFormat = new PeptideLineFormat(lastLine, GetEngineName());
}
lastLine = null;
while ((group = ReadNextProteinGroup(filein, peptideMap, ref lastLine)) != null)
{
result.Add(group);
}
}
string fastaFile = fileName + ".fasta";
if (File.Exists(fastaFile))
{
IdentifiedResultUtils.FillSequenceFromFasta(fastaFile, result, null);
}
return(result);
}
