uk.ac.ebi.pride.utilities.util.file

Enum MassSpecFileFormat

java.lang.Object

java.lang.Enum<MassSpecFileFormat>

uk.ac.ebi.pride.utilities.util.file.MassSpecFileFormat

All Implemented Interfaces:

Serializable, Comparable<MassSpecFileFormat>

public enum MassSpecFileFormat
extends Enum<MassSpecFileFormat>

Different mass spec file format, also include support methods for detecting the format

Version:

$Id$

todo: add quant file formats

Author:

Rui Wang

Enum Constant Summary

Enum Constants

Enum Constant and Description
ABI_MTD
ABI_SCAN
ABI_WIFF
AGILENT_MASSHUNTER_RAW
BRUKER_BAF
BRUKER_FID
BRUKER_YEP
CRUX
DAT
FASTA
GIF
HDR
IBD
IMG
IMZML
JPG
MGF
MS2
MSGF
MZDATA
MZIDENTML
MZML
MZTAB
MZXML
OMSSA_OMX
PEPTIDE_PROPHET
PKL
PKL_SPO
PNG
PRIDE
PROTEIN_PILOT
PROTEIN_PROPHET
RAW
SEQUEST_DTA
SEQUEST_OUT
SPECTRAST
TIF
VEMS_PKX
XTANDEM

Method Summary

Methods

Modifier and Type	Method and Description
static MassSpecFileFormat	checkFormat(File file) Detect mass spec file format
static MassSpecFileFormat	checkFormat(URL url) Detect mass spec file format
String	getFileExtension()
boolean	isFileFormat()
static boolean	isMassSpecDataFolder(File folder) Check whether a folder is a recognized mass spec data folder
static MassSpecFileFormat	valueOf(String name) Returns the enum constant of this type with the specified name.
static MassSpecFileFormat[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

MGF

public static final MassSpecFileFormat MGF

MZML

public static final MassSpecFileFormat MZML

MZIDENTML

public static final MassSpecFileFormat MZIDENTML

PRIDE

public static final MassSpecFileFormat PRIDE

DAT

public static final MassSpecFileFormat DAT

XTANDEM

public static final MassSpecFileFormat XTANDEM

PKL

public static final MassSpecFileFormat PKL

PKL_SPO

public static final MassSpecFileFormat PKL_SPO

SEQUEST_DTA

public static final MassSpecFileFormat SEQUEST_DTA

SEQUEST_OUT

public static final MassSpecFileFormat SEQUEST_OUT

OMSSA_OMX

public static final MassSpecFileFormat OMSSA_OMX

MSGF

public static final MassSpecFileFormat MSGF

SPECTRAST

public static final MassSpecFileFormat SPECTRAST

CRUX

public static final MassSpecFileFormat CRUX

PEPTIDE_PROPHET

public static final MassSpecFileFormat PEPTIDE_PROPHET

PROTEIN_PROPHET

public static final MassSpecFileFormat PROTEIN_PROPHET

PROTEIN_PILOT

public static final MassSpecFileFormat PROTEIN_PILOT

VEMS_PKX

public static final MassSpecFileFormat VEMS_PKX

MS2

public static final MassSpecFileFormat MS2

MZDATA

public static final MassSpecFileFormat MZDATA

MZXML

public static final MassSpecFileFormat MZXML

MZTAB

public static final MassSpecFileFormat MZTAB

BRUKER_BAF

public static final MassSpecFileFormat BRUKER_BAF

BRUKER_FID

public static final MassSpecFileFormat BRUKER_FID

BRUKER_YEP

public static final MassSpecFileFormat BRUKER_YEP

ABI_WIFF

public static final MassSpecFileFormat ABI_WIFF

ABI_SCAN

public static final MassSpecFileFormat ABI_SCAN

ABI_MTD

public static final MassSpecFileFormat ABI_MTD

RAW

public static final MassSpecFileFormat RAW

AGILENT_MASSHUNTER_RAW

public static final MassSpecFileFormat AGILENT_MASSHUNTER_RAW

IBD

public static final MassSpecFileFormat IBD

IMG

public static final MassSpecFileFormat IMG

IMZML

public static final MassSpecFileFormat IMZML

HDR

public static final MassSpecFileFormat HDR

FASTA

public static final MassSpecFileFormat FASTA

TIF

public static final MassSpecFileFormat TIF

GIF

public static final MassSpecFileFormat GIF

PNG

public static final MassSpecFileFormat PNG

JPG

public static final MassSpecFileFormat JPG

Method Detail

values

public static MassSpecFileFormat[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (MassSpecFileFormat c : MassSpecFileFormat.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static MassSpecFileFormat valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

getFileExtension

public String getFileExtension()

isFileFormat

public boolean isFileFormat()

isMassSpecDataFolder

public static boolean isMassSpecDataFolder(File folder)
                                    throws IOException

Check whether a folder is a recognized mass spec data folder

Parameters:

folder - input folder

Returns:

boolean true means mass spec data folder

Throws:

IOException

checkFormat

public static MassSpecFileFormat checkFormat(File file)
                                      throws IOException

Detect mass spec file format

Parameters:

file - input file

Returns:

MassSpecFileFormat mass spec file format

Throws:

IOException

checkFormat

public static MassSpecFileFormat checkFormat(URL url)
                                      throws IOException

Detect mass spec file format

Parameters:

url - input URL

Returns:

MassSpecFileFormat mass spec file format

Throws:

IOException