uk.ac.ebi.pride.utilities.data.utils

Class Constants

java.lang.Object

uk.ac.ebi.pride.utilities.data.utils.Constants

public final class Constants
extends Object

Constants contain a set of functions for SpectraData validation and also the constants used by mzTab and mzIdentML to reference the Ids and type file formats.

Author:

Yasset Perez-Riverol, Rui Wang

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Constants.SpecFileFormat An enum of the supported spectra file types
static class	Constants.SpecIdFormat Supported id format used in the spectrum file.

Field Summary

Fields

Modifier and Type	Field and Description
static String	APL_EXT
static String	DTA_EXT
static String	INTEGER integer expression
static String	MGF_EXT
static String	MS2_EXT
static String	MZML_EXT
static String	MZTAB_EXT
static String	MZXML_EXT
static String	NOT_AVAILABLE
static String	PKL_EXT
static String	WIFF_EXT
static String	XML_EXT

Method Summary

Methods

Modifier and Type	Method and Description
static Constants.SpecFileFormat	getDataFormatFromFileExtension(SpectraData spectradata) Return the Spectrum File format beased onf the SpectraData object name
static Class	getFileType(File file) Check the file type
static List<Constants.SpecFileFormat>	getFileTypeSupported(SpectraData spectraData) Return the set of file format supported for an ambiguous SpectraData Object
static Constants.SpecFileFormat	getSpecFileFormat(String fileFormat) Retrieve the Spectrum File format for an specific fileformat.
static Constants.SpecFileFormat	getSpecFileFormatFromLocation(String path) Return the SpectrumFile format for an specific path such as: /myppath/spectrum_file.mgf
static Constants.SpecFileFormat	getSpectraDataFormat(SpectraData spectraData) This function returns the Spectrum File format for an specific SpectraData ob object
static Constants.SpecIdFormat	getSpectraDataIdFormat(String accession) Spectrum Id format for an specific CVterm accession

Methods inherited from class java.lang.Object

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

Field Detail

INTEGER

public static final String INTEGER

integer expression

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Constant Field Values

NOT_AVAILABLE

public static final String NOT_AVAILABLE

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Constant Field Values

MGF_EXT

public static final String MGF_EXT

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Constant Field Values

DTA_EXT

public static final String DTA_EXT

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Constant Field Values

MS2_EXT

public static final String MS2_EXT

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Constant Field Values

PKL_EXT

public static final String PKL_EXT

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Constant Field Values

MZXML_EXT

public static final String MZXML_EXT

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Constant Field Values

APL_EXT

public static final String APL_EXT

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Constant Field Values

XML_EXT

public static final String XML_EXT

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Constant Field Values

MZML_EXT

public static final String MZML_EXT

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Constant Field Values

MZTAB_EXT

public static final String MZTAB_EXT

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Constant Field Values

WIFF_EXT

public static final String WIFF_EXT

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Constant Field Values

Method Detail

getSpecFileFormat

public static Constants.SpecFileFormat getSpecFileFormat(String fileFormat)

Retrieve the Spectrum File format for an specific fileformat.

Parameters:

fileFormat - file format such mgf ms2, mzid or other file formats

Returns:

the SpectrumFile format such as MZXML or PKL

getSpecFileFormatFromLocation

public static Constants.SpecFileFormat getSpecFileFormatFromLocation(String path)

Return the SpectrumFile format for an specific path such as: /myppath/spectrum_file.mgf

Parameters:

path - the specific path

Returns:

the SpectrumFile format such as MZXML or PKL

getSpectraDataFormat

public static Constants.SpecFileFormat getSpectraDataFormat(SpectraData spectraData)

This function returns the Spectrum File format for an specific SpectraData ob object

Parameters:

spectraData - The SpectraData object

Returns:

the Spectrum File format

getSpectraDataIdFormat

public static Constants.SpecIdFormat getSpectraDataIdFormat(String accession)

Spectrum Id format for an specific CVterm accession

Parameters:

accession - CvTerm Accession

Returns:

Specific Spectrum Id Format

getFileTypeSupported

public static List<Constants.SpecFileFormat> getFileTypeSupported(SpectraData spectraData)

Return the set of file format supported for an ambiguous SpectraData Object

Parameters:

spectraData - SpectraData Object

Returns:

Set of file formats supported

getDataFormatFromFileExtension

public static Constants.SpecFileFormat getDataFormatFromFileExtension(SpectraData spectradata)

Return the Spectrum File format beased onf the SpectraData object name

Parameters:

spectradata - SpectraData Object

Returns:

Spectrum File Format

getFileType

public static Class getFileType(File file)

Check the file type

Parameters:

file - input file

Returns:

Class the class type of the data access controller