protected override ISpectrumParser GetSpectrumParser()
{
var datParser = new XTandemSpectrumXmlParser(options.GetTitleParser(), options.Parent.Database.GetAccessNumberParser());
datParser.Progress = Progress;
return(datParser);
}
protected override string GetTitleSample()
{
if (datFiles.SelectFileNames.Length > 0)
{
return(XTandemSpectrumXmlParser.GetTitleSample(datFiles.SelectFileNames[0]));
}
return(base.GetTitleSample());
}
public void TestParsePeptides()
{
List<IIdentifiedSpectrum> spectra = new XTandemSpectrumXmlParser().ReadFromFile(@"../../../data/xtandem.xml");
Assert.AreEqual(2, spectra.Count);
Assert.AreEqual("K.DLGEEHFK.G", spectra[0].Sequence);
Assert.AreEqual(32.2, spectra[0].Score, 0.1);
Assert.AreEqual(5.1e-003, spectra[0].ExpectValue, 0.001);
Assert.AreEqual(974.458, spectra[0].TheoreticalMH, 0.001);
Assert.AreEqual(975.773, spectra[0].ExperimentalMH, 0.001);
Assert.AreEqual(2, spectra[0].Query.Charge);
Assert.AreEqual("K.DDDEEHFK.G", spectra[1].Sequence);
}
public static void FindXtandemSourceXml(ListView lvDatFiles)
{
lvDatFiles.BeginUpdate();
try
{
foreach (ListViewItem item in lvDatFiles.Items)
{
string xmlFile = item.Text;
if (File.Exists(xmlFile))
{
while (item.SubItems.Count < 2)
{
item.SubItems.Add("");
}
item.SubItems[1].Text = new FileInfo(XTandemSpectrumXmlParser.GetSourceFile(xmlFile)).Name;
}
}
}
finally
{
lvDatFiles.EndUpdate();
}
}