io.github.msdk.datamodel

Class SimpleRawDataFile

java.lang.Object

io.github.msdk.datamodel.SimpleRawDataFile

All Implemented Interfaces:

RawDataFile

Direct Known Subclasses:

NetCDFRawDataFile

public class SimpleRawDataFile
extends Object
implements RawDataFile

Implementation of the RawDataFile interface.

Constructor Summary

Constructors

Constructor and Description
SimpleRawDataFile(String rawDataFileName, Optional<File> originalRawDataFile, FileType rawDataFileType) Constructor for SimpleRawDataFile.

Method Summary

Modifier and Type	Method and Description
void	addChromatogram(Chromatogram chromatogram)
void	addScan(MsScan scan)
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.
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.
void	removeChromatogram(Chromatogram chromatogram)
void	removeScan(MsScan scan)
void	setName(String name)
void	setOriginalFile(File newOriginalFile)
void	setRawDataFileType(FileType rawDataFileType)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleRawDataFile

public SimpleRawDataFile(@Nonnull
                         String rawDataFileName,
                         @Nonnull
                         Optional<File> originalRawDataFile,
                         @Nonnull
                         FileType rawDataFileType)

Constructor for SimpleRawDataFile.

Parameters:

rawDataFileName - a String object.

originalRawDataFile - a Optional object.

rawDataFileType - a FileType object.

Method Detail

getName

@Nonnull
public String getName()

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

Specified by:

getName in interface RawDataFile

Returns:

a String object.

setName

public void setName(@Nonnull
                    String name)

Parameters:

name - a String object.

getOriginalFile

@Nullable
public Optional<File> getOriginalFile()

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

Specified by:

getOriginalFile in interface RawDataFile

Returns:

Original file.

getOriginalFilename

@Nonnull
public String getOriginalFilename()

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

Specified by:

getOriginalFilename in interface RawDataFile

Returns:

Filename of original file.

setOriginalFile

public void setOriginalFile(@Nullable
                            File newOriginalFile)

Parameters:

newOriginalFile - a File object.

getRawDataFileType

@Nonnull
public FileType getRawDataFileType()

Returns the file type of this raw data file.

Specified by:

getRawDataFileType in interface RawDataFile

Returns:

Raw data file type

setRawDataFileType

public void setRawDataFileType(@Nonnull
                               FileType rawDataFileType)

Parameters:

rawDataFileType - a FileType object.

getMsFunctions

@Nonnull
public List<String> getMsFunctions()

Returns all MS functions found in this raw data file.

Specified by:

getMsFunctions in interface RawDataFile

Returns:

A list of MS functions.

getScans

@Nonnull
public 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.

Specified by:

getScans in interface RawDataFile

Returns:

A list of all scans.

addScan

public void addScan(@Nonnull
                    MsScan scan)

Parameters:

scan - a MsScan object.

removeScan

public void removeScan(@Nonnull
                       MsScan scan)

Parameters:

scan - a MsScan object.

getChromatograms

@Nonnull
public 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.

Specified by:

getChromatograms in interface RawDataFile

Returns:

A list of all chromatograms.

addChromatogram

public void addChromatogram(@Nonnull
                            Chromatogram chromatogram)

Parameters:

chromatogram - a Chromatogram object.

removeChromatogram

public void removeChromatogram(@Nonnull
                               Chromatogram chromatogram)

Parameters:

chromatogram - a Chromatogram object.

dispose

public 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.

Specified by:

dispose in interface RawDataFile