private static CensusPeptideItem Parse(string line)
{
var result = new CensusPeptideItem();
if (line.StartsWith("S\t"))
{
result.Singleton = false;
}
else if (line.StartsWith("&S\t"))
{
result.Singleton = true;
}
else
{
return(null);
}
string[] parts = line.Split(new[] { '\t' });
if (parts.Length < 13)
{
return(null);
}
result.Unique = parts[1];
result.Sequence = parts[2];
result.Ratio = MyConvert.ToDouble(parts[3]);
result.RegressionFactor = MyConvert.ToDouble(parts[4]);
result.DeterminantFactor = MyConvert.ToDouble(parts[5]);
result.Score = MyConvert.ToDouble(parts[6]);
result.DeltaScore = MyConvert.ToDouble(parts[7]);
result.SampleIntensity = MyConvert.ToDouble(parts[8]);
result.ReferenceIntensity = MyConvert.ToDouble(parts[9]);
result.AreaRatio = MyConvert.ToDouble(parts[10]);
result.SingletonScore = MyConvert.ToDouble(parts[11]);
if (parts[12].EndsWith("."))
{
result.Filename = SequestFilename.Parse(parts[12]);
}
else
{
result.Filename = SequestFilename.Parse(parts[12] + ".");
}
return(result);
}
public bool IsSameChro(CensusPeptideItem another)
{
if (null == another)
{
return(false);
}
return(Filename.Experimental.Equals(another.Filename.Experimental) &&
Filename.Charge.Equals(another.Filename.Charge) &&
Sequence.Equals(another.Sequence) &&
Ratio.Equals(another.Ratio) &&
SampleIntensity.Equals(another.SampleIntensity) &&
ReferenceIntensity.Equals(another.ReferenceIntensity));
}
private List <CensusProteinItem> ReadProteins(string filename)
{
var result = new List <CensusProteinItem>();
var peptideMap = new Dictionary <string, CensusPeptideItem>();
var lastItem = new CensusProteinItem();
using (var sr = new StreamReader(filename))
{
string lastLine = sr.ReadLine();
while (lastLine != null)
{
lastLine = lastLine.Trim();
if (lastLine.StartsWith("S") || (lastLine.StartsWith("&S") && this.readSingleton))
{
CensusPeptideItem pepItem = this.peptideFormat.ParseString(lastLine);
if (pepItem.Ratio != 0.0)
{
string longFilename = pepItem.Filename.LongFileName;
if (peptideMap.ContainsKey(longFilename))
{
lastItem.Peptides.Add(peptideMap[longFilename]);
}
else
{
peptideMap[longFilename] = pepItem;
lastItem.Peptides.Add(pepItem);
}
}
}
else if (lastLine.StartsWith("P"))
{
lastItem = this.proteinFormat.ParseString(lastLine);
result.Add(lastItem);
}
lastLine = sr.ReadLine();
}
}
result.ForEach(m => m.ValidatePeptides());
result.RemoveAll(m => m.Peptides.Count == 0);
return(result);
}
public List <CensusPeptideItem> ReadPeptides(string filename)
{
var peptideMap = new Dictionary <string, CensusPeptideItem>();
List <string> headers = CensusUtils.ReadHeaders(filename);
InitFormat(headers);
using (var sr = new StreamReader(filename))
{
string lastLine;
while ((lastLine = sr.ReadLine()) != null)
{
lastLine = lastLine.Trim();
if (lastLine.StartsWith("S") || lastLine.StartsWith("&S"))
{
CensusPeptideItem pepItem = this.peptideFormat.ParseString(lastLine);
if (pepItem.Ratio != 0.0)
{
string longFilename = pepItem.Filename.LongFileName;
if (peptideMap.ContainsKey(longFilename))
{
continue;
}
else
{
peptideMap[longFilename] = pepItem;
}
}
}
}
}
return(new List <CensusPeptideItem>(peptideMap.Values));
}
