FileReader

Remarks

Reads spectra and chromatograms from an MS data file, choosing the reader by file extension. Enumerating it yields each spectrum in file order.

Implements

IEnumerable

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Constructors

Syntax	Description
FileReader(MSFilter filter = MSFilter.MS1 | MSFilter.MS2 | MSFilter.MS3)	Creates a reader with no file open.
FileReader(string filename, MSFilter filter = MSFilter.MS1 | MSFilter.MS2 | MSFilter.MS3)	Creates a reader and opens the file.

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Properties

Identifier	Type	Description
ChromatCount	int	Number of chromatograms in the open file, or 0 for formats that carry none.
FileName	string	The name of the file currently being read.
FirstScan	int	The scan number of the first spectrum in the file.
Format	FileFormat	Identifies the format of the most recently opened file.
LastScan	int	The scan number of the last spectrum in the file.
MaxRetentionTime	double	The retention time at the end of the run, in minutes.
ScanCount	int	The number of spectra in the open file.

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Methods

Method	Returns	Description
static CheckFileFormat(string fileName)	FileFormat	Reads a file name string and returns the FileFormat value based on the file extension characters.
GetEnumerator()	IEnumerator	Yields each spectrum in the open file in file order, subject to the current filter, then resets the reader.
OpenSpectrumFile(string fileName)	bool	Opens a file for reading, closing any file already open.
ReadChromatogram(string fileName = “”, int chromatIndex = -1)	Chromatogram	Reads a chromatogram, opening the file first if it is not the current one.
ReadSpectrum(string fileName = “”, int scanNumber = -1, bool centroid = true)	Spectrum	Reads a spectrum, opening the file first if it is not the current one.
ReadSpectrumEx(string fileName = “”, int scanNumber = -1, bool centroid = true)	SpectrumEx	Reads a spectrum with the extended per-peak data where the format provides it, opening the file first if it is not the current one.
Reset()	void	Returns to the start of the open file for sequential reading.
SetFilter(MSFilter filter)	void	Sets the MS levels to read, for this reader and any file it has open.

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Example

using Nova.Io.Read;
using Nova.Data;

// Reads all MS1 scans from a Thermo Fisher Scientific data file
FileReader reader = new FileReader("DDA.raw", MSFilter.MS1);
foreach (Spectrum spec in reader)
{
  // Report each scan number and number of data points
  Console.WriteLine(spec.ScanNumber + " has " + spec.Count + " data points.");
}