io.github.msdk.datamodel

Interface RawDataFile

All Known Implementing Classes:

MzDBRawDataFile, MzMLRawDataFile, MzXMLRawDataFile, NetCDFRawDataFile, SimpleRawDataFile

public interface RawDataFile

Raw data file, typically obtained by loading data from one of the supported file formats. A raw data file is a collection of scans (MsScan).

See Also:

MsScan

Method Summary

Modifier and Type	Method and Description
void	dispose() Remove all data associated with this file from the disk.
List<Chromatogram>	getChromatograms() Returns an immutable list of all chromatograms.
List<String>	getMsFunctions() Returns all MS functions found in this raw data file.
String	getName() Returns the name of this raw data file.
Optional<File>	getOriginalFile() Returns the original file (i.e.
default String	getOriginalFilename() Returns the filename of the original filename.
FileType	getRawDataFileType() Returns the file type of this raw data file.
List<MsScan>	getScans() Returns an immutable list of all scans.

Method Detail

getName

@Nonnull
String getName()

Returns the name of this raw data file. This can be any descriptive name, not necessarily the original file name.

Returns:

Raw data file name

getOriginalFile

@Nonnull
Optional<File> getOriginalFile()

Returns the original file (i.e. filename and path), or Optional.empty() if this file was created by MSDK.

Returns:

Original file.

getOriginalFilename

@Nonnull
default String getOriginalFilename()

Returns the filename of the original filename. Default implementations return "Unknown."

Returns:

Filename of original file.

getRawDataFileType

@Nonnull
FileType getRawDataFileType()

Returns the file type of this raw data file.

Returns:

Raw data file type

getMsFunctions

@Nonnull
List<String> getMsFunctions()

Returns all MS functions found in this raw data file.

Returns:

A list of MS functions.

getScans

@Nonnull
List<MsScan> getScans()

Returns an immutable list of all scans. The list can be safely iterated over, as it cannot be modified by another thread.

Returns:

A list of all scans.

getChromatograms

@Nonnull
List<Chromatogram> getChromatograms()

Returns an immutable list of all chromatograms. The list can be safely iterated over, as it cannot be modified by another thread.

Returns:

A list of all chromatograms.

dispose

void dispose()

Remove all data associated with this file from the disk. After this method is called, any subsequent method calls on this object will throw IllegalStateException.