FileReader

Remarks

A versatile class for reading multiple formats of mass spectrometry data. Internally, FileReader implements the SpectrumFileReaderFactory to support all Nova compatible spectra files. Additional functionality has been added beyond the individual file reader classes in Nova.

Implements

IEnumerable

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Constructors

Syntax	Description
FileReader(MSFilter filter = MSFilter.MS1	MSFilter.MS2	MSFilter.MS3)	Initializes the FileReader class and defaults to parsing all MS, MS/MS, and MS3 scans.
FileReader(string filename,MSFilter filter = MSFilter.MS1	MSFilter.MS2	MSFilter.MS3)	Initializes the FileReader class and opens the requeested file, defaults to parsing all MS, MS/MS, and MS3 scans.

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Properties

Identifier	Type	Description
FileName	string	The names of the file currently being read, or empty if no file has been opened.
FirstScanNumber	int	Number of the first scan event in the file.
LastScanNumber	int	Number of the last scan event in the file.
MaxRetentionTime	double	Retention time (in minutes) of the last scan event in the file.
ScanCount	int	Total number of scan events in the file.

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Methods

Method	Returns	Description
CheckFileFormat(string fileName)	FileFormat	Reads a file name string and returns the FileFormat value based on the file extension characters. FormatException thrown if file doesn’t have an exception or the extension isn’t recognized.
Close()	void	Closes an open MS data file.
OpenSpectrumFile(string fileName)	bool	Opens an mzML file and parses the index and meta information.
ReadSpectrum(string filename=””, int scanNumber = -1, bool centroid = true)	Spectrum	Opens and/or reads the requested spectrum or the next spectrum if a valid scanNumber is not given. Data are returned in centroid, if possible, unless otherwise requested. Providing an empty string for the file name reads from the previously opened data file, or throws an exception if a file has not been previously opened.
ReadSpectrumEx(string filename=””, int scanNumber = -1, bool centroid = true)	SpectrumEx	Opens and/or reads the requested spectrum or the next spectrum if a valid scanNumber is not given, and returns the data in the extended spectrum format. Data are returned in centroid, if possible, unless otherwise requested. Providing an empty string for the file name reads from the previously opened data file, or throws an exception if a file has not been previously opened.
Reset()	void	Resets the reader to the beginning of the file if sequentially reading the spectra.
SetFilter(MSFilter filter)	void	Sets the spectrum type filter to the values requested.

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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.");
}