public void WriteToFile(string proteinFile, IIdentifiedResult mr)
{
var proteinWriter =
new IdentifiedProteinTextWriter(GetProteinHeader());
using (var sw = new StreamWriter(proteinFile))
{
sw.WriteLine("\tName\tDescription" + proteinWriter.GetHeader());
foreach (IIdentifiedProteinGroup mpg in mr)
{
if (mpg[0].IsEnabled(true))
{
mpg[0].InitUniquePeptideCount(mph => mph.Spectrum.IsEnabled(true));
this.WriteFunction(sw, mpg, proteinWriter);
}
}
}
string peptideFile = GetPeptideFileName(proteinFile);
var peptideWriter = new MascotPeptideTextFormat(GetPeptideHeader());
using (var sw = new StreamWriter(peptideFile))
{
sw.WriteLine(peptideWriter.PeptideFormat.GetHeader());
foreach (IIdentifiedProteinGroup mpg in mr)
{
if (mpg[0].IsEnabled(true))
{
foreach (IIdentifiedSpectrum mph in mpg[0].GetSpectra())
{
if (mph.IsEnabled(false))
{
sw.WriteLine(peptideWriter.PeptideFormat.GetString(mph));
}
}
}
}
}
}
private void WriteProteinMultipleLines(StreamWriter sw, IIdentifiedProteinGroup mpg, IdentifiedProteinTextWriter proteinWriter)
{
for (int proteinIndex = 0; proteinIndex < mpg.Count; proteinIndex++)
{
IIdentifiedProtein mpro = mpg[proteinIndex];
mpro.UniquePeptideCount = mpg[0].UniquePeptideCount;
sw.WriteLine("${0}-{1}\t{2}\t{3}\t{4}",
mpg.Index,
proteinIndex + 1,
mpro.Name,
mpro.Description,
proteinWriter.GetString(mpro));
}
}
private void WriteProteinOneLine(StreamWriter sw, IIdentifiedProteinGroup mpg, IdentifiedProteinTextWriter proteinWriter)
{
//find user-defined protein
IIdentifiedProtein filtered = null;
foreach (Regex reg in this.perferAccessNumberRegexs)
{
foreach (IIdentifiedProtein mp in mpg)
{
if (reg.Match(mp.Name).Success)
{
filtered = mp;
break;
}
}
if (filtered != null)
{
break;
}
}
string name;
string reference;
if (filtered != null)
{
name = filtered.Name;
reference = filtered.Description;
filtered.UniquePeptideCount = mpg[0].UniquePeptideCount;
}
else
{
var names = new StringBuilder();
var refs = new StringBuilder();
for (int proteinIndex = 0; proteinIndex < mpg.Count; proteinIndex++)
{
names.Append(" ! ").Append(mpg[proteinIndex].Name);
refs.Append(" ! ").Append(mpg[proteinIndex].Description);
IIdentifiedProtein mpro = mpg[proteinIndex];
mpro.UniquePeptideCount = mpg[0].UniquePeptideCount;
}
filtered = mpg[0];
name = names.ToString().Substring(3);
reference = refs.ToString().Substring(3);
}
sw.WriteLine("${0}-1\t{1}\t{2}{3}",
mpg.Index,
name,
reference,
proteinWriter.GetString(filtered));
}
