public static HashSet <string> GetTags(string fileName, bool isProteinFile)
{
HashSet <string> result = new HashSet <string>();
using (StreamReader sr = new StreamReader(fileName))
{
if (isProteinFile)
{
sr.ReadLine();
}
var line = sr.ReadLine();
var parts = line.Split('\t');
var tagIndex = Array.IndexOf(parts, "Tag");
if (tagIndex >= 0)
{
while ((line = sr.ReadLine()) != null)
{
if (isProteinFile && IdentifiedResultUtils.IsProteinLine(line))
{
continue;
}
parts = line.Split('\t');
if (parts.Length <= tagIndex)
{
break;
}
result.Add(parts[tagIndex]);
}
}
}
return(result);
}
public HashSet <string> ReadFromFile(string fileName)
{
HashSet <string> result = new HashSet <string>();
SequestFilename sf = new SequestFilename();
using (StreamReader sr = new StreamReader(fileName))
{
//ignore header lines
string line;
while ((line = sr.ReadLine()) != null)
{
string[] parts = line.Trim().Split(chars);
try
{
sf.ShortFileName = parts[0];
break;
}
catch (Exception)
{ }
}
if (line != null)
{
result.Add(sf.Experimental);
}
while ((line = sr.ReadLine()) != null)
{
line = line.Trim();
if (line.Length == 0)
{
break;
}
if (IdentifiedResultUtils.IsProteinLine(line))
{
continue;
}
string[] parts = line.Split(chars);
sf.ShortFileName = parts[0];
result.Add(sf.Experimental);
}
}
return(result);
}
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);
}
