MsFormat (computational omics utilities 4.5.7 API)

java.lang.Object
- java.lang.Enum<MsFormat>
- - com.compomics.util.experiment.massspectrometry.proteowizard.MsFormat

All Implemented Interfaces:

Serializable, Comparable<MsFormat>
```
public enum MsFormat
extends Enum<MsFormat>
```
The mass spectrometry formats supported by ProteoWizard.

Author:

Marc Vaudel, Harald Barsnes

Enum Constant Summary

Enum Constants
Enum Constant and Description
`baf` Bruker FID format.
`bms2` Binary bms2 format.
`cms1` cms1 format.
`cms2` cms2 format.
`d` Agilent/Bruker d format.
`fid` Bruker FID format.
`mgf` Mascot generic format.
`ms1` ms1 format.
`ms2` ms2 format.
`mz5` Implementation of the PSI mzML ontology that is based on HDF5.
`mzML` mzML generic PSI format.
`mzXML` mzXML format.
`raw` Thermo/Waters raw format.
`wiff` Applied Biosystems wiff format.
`yep` Bruker FID format.

Field Summary

Fields
Modifier and Type	Field and Description
`String`	`commandLineOption` The command line option name.
`String`	`description` A brief description of the format.
`String`	`fileNameEnding` The file name ending of the format.
`int`	`index` The index of the format.
`String`	`name` The name of the format.
`boolean`	`outputFormat` Boolean indicating if this in a format that can be used as output.
`boolean`	`rawFormat` Boolean indicating if this in a format for raw data, false means that it is a peak list format.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static Vector<MsFormat>`	`getDataFormats(Boolean raw, Boolean outputFormat)` Returns a list of formats.
`String`	`toString()`
`static MsFormat`	`valueOf(String name)` Returns the enum constant of this type with the specified name.
`static MsFormat[]`	`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, valueOf

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Enum Constant Detail
  - mgf
```
public static final MsFormat mgf
```
    Mascot generic format.
  - ms1
```
public static final MsFormat ms1
```
    ms1 format.
  - ms2
```
public static final MsFormat ms2
```
    ms2 format.
  - cms1
```
public static final MsFormat cms1
```
    cms1 format.
  - cms2
```
public static final MsFormat cms2
```
    cms2 format.
  - bms2
```
public static final MsFormat bms2
```
    Binary bms2 format.
  - mzML
```
public static final MsFormat mzML
```
    mzML generic PSI format.
  - mzXML
```
public static final MsFormat mzXML
```
    mzXML format.
  - mz5
```
public static final MsFormat mz5
```
    Implementation of the PSI mzML ontology that is based on HDF5.
  - raw
```
public static final MsFormat raw
```
    Thermo/Waters raw format.
  - d
```
public static final MsFormat d
```
    Agilent/Bruker d format.
  - fid
```
public static final MsFormat fid
```
    Bruker FID format.
  - yep
```
public static final MsFormat yep
```
    Bruker FID format.
  - baf
```
public static final MsFormat baf
```
    Bruker FID format.
  - wiff
```
public static final MsFormat wiff
```
    Applied Biosystems wiff format.
- Field Detail
  - index
```
public final int index
```
    The index of the format.
  - commandLineOption
```
public final String commandLineOption
```
    The command line option name.
  - name
```
public final String name
```
    The name of the format.
  - description
```
public final String description
```
    A brief description of the format.
  - rawFormat
```
public final boolean rawFormat
```
    Boolean indicating if this in a format for raw data, false means that it is a peak list format.
  - fileNameEnding
```
public final String fileNameEnding
```
    The file name ending of the format.
  - outputFormat
```
public final boolean outputFormat
```
    Boolean indicating if this in a format that can be used as output.
- Method Detail
  - values
```
public static MsFormat[] 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 (MsFormat c : MsFormat.values())
    System.out.println(c);
```
    Returns:
    
    an array containing the constants of this enum type, in the order they are declared
  - valueOf
```
public static MsFormat 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
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Enum<MsFormat>
  - getDataFormats
```
public static Vector<MsFormat> getDataFormats(Boolean raw,
                                              Boolean outputFormat)
```
    Returns a list of formats.
    
    Parameters:
    
    raw - get raw formats, null returns both
    
    outputFormat - get output formats, null return both
    
    Returns:
    
    the list formats

Enum MsFormat

Enum Constant Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

mgf

ms1

ms2

cms1

cms2

bms2

mzML

mzXML

mz5

raw

d

fid

yep

baf

wiff

Field Detail

index

commandLineOption

name

description

rawFormat

fileNameEnding

outputFormat

Method Detail

values

valueOf

toString

getDataFormats