public static void IndexUimfFile(string uimfFileLocation)
{
bool indexed = false;
using (var uimfReader = new DataReader(uimfFileLocation))
{
if (uimfReader.DoesContainBinCentricData())
{
indexed = true;
Console.WriteLine("Bin centric data found in dataset {0}.", uimfFileLocation);
}
else
{
Console.WriteLine("No bin centric data found for file {0}.", uimfFileLocation);
}
uimfReader.Dispose();
}
if (!indexed)
{
Console.WriteLine("Creating bin centric data for {0}.", uimfFileLocation);
using (DataWriter dataWriter = new DataWriter(uimfFileLocation))
{
dataWriter.CreateBinCentricTables();
dataWriter.Dispose();
}
}
}
public void TestCreateBinCentricTables()
{
DataReaderTests.DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
var fiSource = new FileInfo(FileRefs.BinCentricTest1);
if (!fiSource.Exists)
{
return;
}
var fiTarget = DuplicateUIMF(fiSource, "_BinCentric");
if (fiTarget == null)
{
return;
}
var executingAssembly = System.Reflection.Assembly.GetExecutingAssembly();
using (var uimfWriter = new DataWriter(fiTarget.FullName, executingAssembly))
{
uimfWriter.CreateBinCentricTables();
}
Console.WriteLine("Added bin centric tables to " + fiTarget.FullName);
}
/// <summary>
///
/// </summary>
/// <param name="uimf"></param>
/// <param name="frameNumber"></param>
/// <param name="xicMz"></param>
/// <param name="tolerance"></param>
/// <param name="getMsms"></param>
/// <returns></returns>
private IEnumerable <KeyValuePair <double, double> > GetXicInfo(
DataReader uimf,
int frameNumber,
double xicMz,
double tolerance,
bool getMsms)
{
const DataReader.ToleranceType Tolerance = DataReader.ToleranceType.PPM;
var frametype = getMsms ? DataReader.FrameType.MS2 : DataReader.FrameType.MS1;
if (!uimf.DoesContainBinCentricData())
{
Console.WriteLine(uimf.UimfFilePath + " Does not have bin centric data which is required to get XiC");
Console.WriteLine("starting to create it, this may take some time");
var fileName = uimf.UimfFilePath;
uimf.Dispose(); // why is this being disposed -- this is INSIDE a using statement! SAP 4/4/2016
using (var dataWriter = new DataWriter(fileName))
{
dataWriter.CreateBinCentricTables();
}
uimf = new DataReader(fileName); // WHY IS THIS BEING SET?! This is inside a using statement!
Console.WriteLine("Finished Creating bin centric tables for " + uimf.UimfFilePath);
}
var data = new List <KeyValuePair <double, double> >();
try
{
var xic = uimf.GetXic(xicMz, tolerance, frametype, Tolerance);
var frameData = xic.Where(point => point.ScanLc == frameNumber - 1);
// I think this is more readable with a regular loop than a very long linq query
foreach (var intensityPoint in frameData)
{
var driftTime = uimf.GetDriftTime(intensityPoint.ScanLc + 1, intensityPoint.ScanIms, true);
data.Add(new KeyValuePair <double, double>(driftTime, intensityPoint.Intensity));
}
}
catch (Exception)
{
Console.Error.WriteLine("Unable to get XiC on first attempt for " + uimf.UimfFilePath);
}
return(data);
}
public SaturationDetector(string uimfFileLocation)
{
_uimfReader = new DataReader(uimfFileLocation);
_smoother = new SavitzkyGolaySmoother(9, 2);
_peakDetector = new ChromPeakDetector(0.0001, 0.0001);
_theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
if (!_uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
IterativeTFFParameters msFeatureFinderParameters = new IterativeTFFParameters
{
MinimumRelIntensityForForPeakInclusion = 0.0000000001,
PeakDetectorMinimumPeakBR = 0,
PeakDetectorPeakBR = 5.00000000000002,
PeakBRStep = 0.25,
PeakDetectorSigNoiseRatioThreshold = 0.00000000001,
ToleranceInPPM = 50
};
_msFeatureFinder = new IterativeTFF(msFeatureFinderParameters);
}
/// <summary>
/// Initializes a new instance of the <see cref="LibraryMatchWorkflow"/> class.
/// </summary>
/// <param name="uimfFileLocation">
/// The UIMF file location.
/// </param>
/// <param name="outputDirectory">
/// The output directory.
/// </param>
/// <param name="resultFileName">
/// The result file name.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
public LibraryMatchWorkflow(string uimfFileLocation, string outputDirectory, string resultFileName, LibraryMatchParameters parameters)
{
this.uimfReader = new DataReader(uimfFileLocation);
// Append bin-centric table to the uimf if not present.
if (!this.uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
this.Parameters = parameters;
this.smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
this.NumberOfFrames = this.uimfReader.GetGlobalParams().NumFrames;
this.NumberOfScans = this.uimfReader.GetFrameParams(1).Scans;
this.DatasetName = Path.GetFileNameWithoutExtension(uimfFileLocation);
this.Parameters = parameters;
this.ResultFileName = resultFileName;
if (outputDirectory == string.Empty)
{
outputDirectory = Directory.GetCurrentDirectory();
}
if (!outputDirectory.EndsWith("\\"))
{
outputDirectory += "\\";
}
if (!Directory.Exists(outputDirectory))
{
try
{
Directory.CreateDirectory(outputDirectory);
}
catch (Exception)
{
Console.WriteLine("Failed to create directory.");
throw;
}
}
this.OutputPath = outputDirectory;
Trace.Listeners.Clear();
ConsoleTraceListener consoleTraceListener = new ConsoleTraceListener(false);
consoleTraceListener.TraceOutputOptions = TraceOptions.DateTime;
string result = this.OutputPath + this.ResultFileName;
this.resultFileWriter = File.AppendText(result);
TextWriterTraceListener resultFileTraceListener = new TextWriterTraceListener(this.resultFileWriter)
{
Name = "this.DatasetName" + "_Result",
TraceOutputOptions = TraceOptions.ThreadId | TraceOptions.DateTime
};
Trace.Listeners.Add(consoleTraceListener);
Trace.Listeners.Add(resultFileTraceListener);
Trace.AutoFlush = true;
}
/// <summary>
/// Initializes a new instance of the <see cref="LcImsPeptideSearchWorkfow"/> class.
/// </summary>
/// <param name="uimfFileLocation">
/// The uimf file location.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
public LcImsPeptideSearchWorkfow(string uimfFileLocation, LcImsPeptideSearchParameters parameters)
{
this._buildWatershedStopWatch = new Stopwatch();
this._smoothStopwatch = new Stopwatch();
this._featureFindStopWatch = new Stopwatch();
this._featureFindCount = 0;
this._pointCount = 0;
this._uimfFileLocation = uimfFileLocation;
this._uimfReader = new DataReader(uimfFileLocation);
// Append bin-centric table to the uimf if not present.
if (!this._uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
this._parameters = parameters;
this._smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
this._theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
this._leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
this._peakDetector = new ChromPeakDetector(0.0001, 0.0001);
this._isotopicPeakFitScoreCalculator = new PeakLeastSquaresFitter();
IterativeTFFParameters msFeatureFinderParameters = new IterativeTFFParameters
{
MinimumRelIntensityForForPeakInclusion = 0.0001,
PeakDetectorMinimumPeakBR = 0.0001,
PeakDetectorPeakBR = 5.0002,
PeakBRStep = 0.25,
PeakDetectorSigNoiseRatioThreshold = 0.0001,
ToleranceInPPM = parameters.MassToleranceInPpm
};
this._msFeatureFinder = new IterativeTFF(msFeatureFinderParameters);
this.NumberOfFrames = this._uimfReader.GetGlobalParams().NumFrames;
this.NumberOfScans = this._uimfReader.GetFrameParams(1).Scans;
}
/// <summary>
/// Initializes a new instance of the <see cref="CrossSectionWorkfow"/> class.
/// </summary>
/// <param name="uimfFileLocation">
/// The uimf file location.
/// </param>
/// <param name="outputDirectory">
/// The output directory.
/// </param>
/// <param name="logFileName">
/// The log file name.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
public CrossSectionWorkfow(string uimfFileLocation, string outputDirectory, CrossSectionSearchParameters parameters)
{
this.uimfReader = new DataReader(uimfFileLocation);
// Append bin-centric table to the uimf if not present.
if (!this.uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
this.Parameters = parameters;
this.smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 5);
this.theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
this.peakDetector = new ChromPeakDetector(0.0001, 0.0001);
this.NumberOfFrames = this.uimfReader.GetGlobalParams().NumFrames;
this.NumberOfScans = this.uimfReader.GetFrameParams(1).Scans;
this.SampleCollectionDate = this.uimfReader.GetGlobalParams().GetValue(GlobalParamKeyType.DateStarted);
this.DatasetName = Path.GetFileNameWithoutExtension(uimfFileLocation);
this.OutputPath = outputDirectory;
this.DatasetPath = uimfFileLocation;
this.Parameters = parameters;
if (outputDirectory == string.Empty)
{
outputDirectory = Directory.GetCurrentDirectory();
}
if (!outputDirectory.EndsWith("\\"))
{
outputDirectory += "\\";
}
if (!Directory.Exists(outputDirectory))
{
try
{
Directory.CreateDirectory(outputDirectory);
}
catch (Exception)
{
Console.WriteLine("Failed to create directory.");
throw;
}
}
this.OutputPath = outputDirectory;
}