public void LoadData(string dtaFile, string outFile)
{
ExperimentalPeakList = DtaIO.ReadFromDta <MatchedPeak>(dtaFile);
SequestOutHeaderParser parser = new SequestOutHeaderParser();
string[] lines = FileUtils.ReadFile(outFile).ToArray();
int index = ParseMassType(lines, 0, parser);
index = ParseModification(lines, index, parser);
IIdentifiedSpectrum spectrum = new OutParser().ParseFromFile(outFile);
ScoreMap = new Dictionary <string, string>();
if (spectrum != null)
{
Peptide = spectrum.Sequence;
ScoreMap["Xcorr"] = MyConvert.Format("{0:0.0000}", spectrum.Score);
ScoreMap["DeltaCn"] = MyConvert.Format("{0:0.0000}", spectrum.DeltaScore);
InitTheoreticalPeaks();
}
}
private int ParseMassType(string[] lines, int index, SequestOutHeaderParser parser)
{
while (index < lines.Length)
{
bool precursorIsMono, peakIsMono;
if (parser.ParseMassType(lines[index], out precursorIsMono, out peakIsMono))
{
return(index + 1);
}
index++;
}
throw new ArgumentException("Cannot find mass type information");
}
private int ParseModification(string[] lines, int index, SequestOutHeaderParser parser)
{
while (index < lines.Length)
{
if (lines[index].IndexOf("Enzyme:") != -1)
{
DynamicModification = parser.ParseDynamicModification(lines[index]);
StaticModification = parser.ParseStaticModification(lines[index]);
return(index + 1);
}
index++;
}
throw new ArgumentException("Cannot find modification information");
}
public void TestParseModification()
{
var dm = new SequestOutHeaderParser().ParseStaticModification(" (STY* +79.9663) (M# -15.9949) C=160.0307 Enzyme:Trypsin(KR) (2)");
Assert.AreEqual(dm['C'], 160.0307, 0.0001);
}
