private void TestReadMzML(FileSystemInfo mzMLFile, int expectedSpectra)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName, mzMLFile.Name);
var timer = new Stopwatch();
timer.Start();
var reader = new MzMLReader(mzMLFile.FullName);
var constTime = timer.Elapsed;
Console.WriteLine(@"Constructor time: " + constTime);
var numSpectra = reader.NumSpectra;
var metaTime = timer.Elapsed - constTime;
Console.WriteLine(@"Metadata read time: " + metaTime);
var spectra = reader.ReadAllSpectra();
var spectraCount = spectra.Count();
timer.Stop();
reader.Close();
Console.WriteLine(@"Spectra Read time: " + (timer.Elapsed - metaTime));
Console.WriteLine(@"Time: " + timer.Elapsed);
Assert.AreEqual(expectedSpectra, numSpectra, "NumSpectra");
Assert.AreEqual(expectedSpectra, spectraCount, "SpectraCount");
}
/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
break;
}
return(reader);
}
public void MzMLIndexedReadTest(string inputFileRelativePath, int expectedSpectra)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, sourceFile.FullName));
//mzMLType mzMLData = reader.Read();
var mzMLData = new MSData(reader.Read());
Console.WriteLine("Spectrum count: " + mzMLData.Run.SpectrumList.Spectra.Count);
Assert.AreEqual(expectedSpectra, mzMLData.Run.SpectrumList.Spectra.Count, "Spectrum count");
}
public void MzMLIndexedReadTest(string inputFileRelativePath, int expectedSpectra)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var reader = new MzMLReader(sourceFile.FullName);
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");
}
public void MzMLIndexedReadTest(string path, int expectedSpectra)
{
var sourceFile = new FileInfo(Path.Combine(TestPath.ExtTestDataDirectory, path));
if (!sourceFile.Exists)
{
Console.WriteLine("File not found: " + sourceFile.FullName);
return;
}
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, sourceFile.FullName));
//mzMLType mzMLData = reader.Read();
var mzMLData = new MSData(reader.Read());
Console.WriteLine("Spectrum count: " + mzMLData.Run.SpectrumList.Spectra.Count);
Assert.AreEqual(expectedSpectra, mzMLData.Run.SpectrumList.Spectra.Count, "Spectrum count");
}
public void MzMLIndexedReadTest(string path, int expectedSpectra)
{
var sourceFile = new FileInfo(Path.Combine(TestPath.ExtTestDataDirectory, path));
if (!sourceFile.Exists)
{
Console.WriteLine("File not found: " + sourceFile.FullName);
return;
}
var reader = new MzMLReader(sourceFile.FullName);
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");
}
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);
}
/// <summary>
/// Gets the appropriate IMassSpecDataReader for the supplied path.
/// It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
/// <remarks>It is recommended that "NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static IMassSpecDataReader GetMassSpecDataReader(string filePath)
{
filePath = NormalizeDatasetPath(filePath);
var type = GetMassSpecDataType(filePath);
IMassSpecDataReader reader = null;
switch (type)
{
case MassSpecDataType.XCaliburRun:
reader = new XCaliburReader(filePath);
break;
case MassSpecDataType.MzMLFile:
reader = new MzMLReader(filePath);
break;
case MassSpecDataType.PbfFile:
reader = new PbfLcMsRun(filePath);
break;
case MassSpecDataType.DeconvolutedPbfFile:
reader = new DPbfLcMsRun(filePath);
break;
case MassSpecDataType.Unknown:
if (_pwizAvailable)
{
reader = new ProteoWizardReader(filePath);
}
else
{
ConsoleMsgUtils.ShowWarning(string.Format("WARNING: Could not find a reader for file \"{0}\"." +
" Is MSFileReader and/or ProteoWizard installed?", filePath));
}
break;
}
return(reader);
}
[TestCase(@"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MZML\VA139IMSMS_compressed.mzML", 3145)] // Centroid, Agilent QTOF, compressed binary data
public void TestReadMzML(string filePath, int expectedSpectra)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName, filePath);
Stopwatch timer = new Stopwatch();
timer.Start();
var reader = new MzMLReader(filePath);
var constTime = timer.Elapsed;
Console.WriteLine(@"Constructor time: " + constTime);
var numSpectra = reader.NumSpectra;
var metaTime = timer.Elapsed - constTime;
Console.WriteLine(@"Metadata read time: " + metaTime);
var spectra = reader.ReadAllSpectra();
var spectraCount = spectra.Count();
timer.Stop();
Console.WriteLine(@"Spectra Read time: " + (timer.Elapsed - metaTime));
Console.WriteLine(@"Time: " + timer.Elapsed);
Assert.AreEqual(expectedSpectra, numSpectra, "NumSpectra");
Assert.AreEqual(expectedSpectra, spectraCount, "SpectraCount");
Assert.AreEqual(numSpectra, spectraCount, "NumSpectra vs. SpectraCount");
reader.Close();
}
public MainViewModel()
{
/*/
* Window mainWindow;
* Canvas myParentCanvas;
* Canvas myCanvas1;
* Canvas myCanvas2;
* Canvas myCanvas3;
*
* // Create the application's main window
* mainWindow = new Window();
* mainWindow.Title = "Canvas Sample";
*
* // Create the Canvas
* myParentCanvas = new Canvas();
* myParentCanvas.Width = 400;
* myParentCanvas.Height = 400;
*
* // Define child Canvas elements
* myCanvas1 = new Canvas();
* myCanvas1.Background = Brushes.Red;
* myCanvas1.Height = 100;
* myCanvas1.Width = 100;
* Canvas.SetTop(myCanvas1, 0);
* Canvas.SetLeft(myCanvas1, 0);
*
* myCanvas2 = new Canvas();
* myCanvas2.Background = Brushes.Green;
* myCanvas2.Height = 100;
* myCanvas2.Width = 100;
* Canvas.SetTop(myCanvas2, 100);
* Canvas.SetLeft(myCanvas2, 100);
*
* myCanvas3 = new Canvas();
* myCanvas3.Background = Brushes.Blue;
* myCanvas3.Height = 100;
* myCanvas3.Width = 100;
* Canvas.SetTop(myCanvas3, 50);
* Canvas.SetLeft(myCanvas3, 50);
*
* // Add child elements to the Canvas' Children collection
* myParentCanvas.Children.Add(myCanvas1);
* myParentCanvas.Children.Add(myCanvas2);
* myParentCanvas.Children.Add(myCanvas3);
*
* // Add the parent Canvas as the Content of the Window Object
* mainWindow.Content = myParentCanvas;
* mainWindow.Show();
* /*/
const string datasetPathName = @"..\..\..\ExampleData\2016-07-28_QC-digest_HCD_01";
const string identFile = datasetPathName + "_msgfplus.mzid.gz";
const string dataFileFixed = datasetPathName + "_FIXED.mzML.gz";
Console.WriteLine("Loading data from {0}", identFile);
var reader = new MzIdentMLReader();
var psmResults = reader.Read(identFile);
var haveScanTimes = reader.HaveScanTimes;
var dataFileExists = false;
if (File.Exists(dataFileFixed))
{
Console.WriteLine();
Console.WriteLine("Loading data from {0}", dataFileFixed);
var mzML = new MzMLReader(dataFileFixed);
mzML.ReadSpectraData(psmResults);
dataFileExists = true;
haveScanTimes = true;
}
//this.OrigScanId = IdentDataPlotter.ScatterPlot(scanData, "ScanIdInt", "PpmError", "Scan Number: Original", OxyColors.Blue);
//this.OrigCalcMz = IdentDataPlotter.ScatterPlot(scanData, "CalcMz", "PpmError", "M/Z: Original", OxyColors.Green);
//this.FixScanId = IdentDataPlotter.ScatterPlot(scanData, "ScanIdInt", "PpmErrorFixed", "Scan Number: Refined", OxyColors.Blue);
//this.FixCalcMz = IdentDataPlotter.ScatterPlot(scanData, "CalcMz", "PpmErrorFixed", "M/Z: Refined", OxyColors.Green);
//this.OrigPpmErrorHist = IdentDataPlotter.Histogram(scanData, "PpmError", "Original", OxyColors.Blue, 0.5);
//this.FixPpmErrorHist = IdentDataPlotter.Histogram(scanData, "PpmErrorFixed", "Refined", OxyColors.Green, 0.5);
var options = new ErrorCharterOptions();
var plotter = new IdentDataPlotter(options, datasetPathName);
plotter.GeneratePNGPlots(psmResults, dataFileExists, haveScanTimes);
AllVis = plotter.ErrorScatterPlotBitmap;
ErrHist = plotter.ErrorHistogramBitmap;
}
