public static CensusProteinItem Parse(string line)
{
Match m = proteinRegex.Match(line);
if (!m.Success)
{
throw new Exception(
"Cannot recognize protein line format, contact with author please. And, provide this line to author :" + line);
}
var result = new CensusProteinItem();
result.Locus = m.Groups[1].Value;
result.AverageRatio = MyConvert.ToDouble(m.Groups[2].Value);
if (m.Groups[3].Length == 0 || m.Groups[3].Value.Equals("NA"))
{
result.StandardDeviation = 0;
}
else
{
result.StandardDeviation = MyConvert.ToDouble(m.Groups[3].Value);
}
result.WeightedAverage = MyConvert.ToDouble(m.Groups[4].Value);
result.PeptideNumber = int.Parse(m.Groups[5].Value);
result.SpectraCount = int.Parse(m.Groups[6].Value);
result.Description = m.Groups[7].Value;
return(result);
}
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);
}
