static void WiffToMzML()
{
string wiffPath = @"C:\Work\primaqdev\testdata\C2 Sol SWATH4.wiff";
string runID = "sample=0";
string mzMLOutPath = @"C:\Work\primaqdev\testdata\test.mzML";
using (var wiff = new WiffFileReader(wiffPath))
using (ITransactionScope txn = wiff.BeginTransaction())
using (var mzML = new MzMLWriter(mzMLOutPath))
{
mzML.BeginMzML(wiff.Model);
mzML.BeginRun(wiff.Model.Runs[runID]);
var spectra = wiff.ReadMassSpectra(runID).Take(1);
int spectrumCount = spectra.Count();
int specIdx = 0;
mzML.BeginSpectrumList(spectrumCount);
foreach (var ms in spectra)
{
var bd = wiff.ReadSpectrumPeaks(ms.ID);
mzML.WriteSpectrum(ms, bd, specIdx);
specIdx++;
}
mzML.EndSpectrumList();
mzML.EndRun();
mzML.EndMzML();
mzML.Close();
}
}
public void MzMLWriteTest(string inPath, string outFolderName, int expectedSpectra)
{
var sourceFile = new FileInfo(Path.Combine(TestPath.ExtTestDataDirectory, inPath));
if (!sourceFile.Exists)
{
Console.WriteLine("File not found: " + sourceFile.FullName);
return;
}
if (sourceFile.DirectoryName == null)
{
throw new DirectoryNotFoundException("Cannot determine the parent folder of " + sourceFile.FullName);
}
var outFolder = new DirectoryInfo(Path.Combine(sourceFile.DirectoryName, outFolderName));
if (!outFolder.Exists)
{
outFolder.Create();
}
var outFile = new FileInfo(Path.Combine(outFolder.FullName, sourceFile.Name));
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, inPath));
var mzMLData = reader.Read();
Console.WriteLine("Spectrum count: " + mzMLData.run.spectrumList.count);
Console.WriteLine("Array length: " + mzMLData.run.spectrumList.spectrum.Count);
Assert.AreEqual(expectedSpectra.ToString(), mzMLData.run.spectrumList.count, "Spectrum Count");
Assert.AreEqual(expectedSpectra, mzMLData.run.spectrumList.spectrum.Count, "Array length");
var writer = new MzMLWriter(Path.Combine(TestPath.ExtTestDataDirectory, outFile.FullName))
{
MzMLType = MzMLSchemaType.MzML
};
writer.Write(mzMLData);
}
