Advocate (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.Advocate

```
public class Advocate
extends Object
```
The advocate of a hit can be a search engine, a sequencing algorithm, a rescoring algorithm, etc.

Author:

Marc Vaudel, Harald Barsnes

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Advocate.AdvocateType
The different types of advocates.

Nested Classes
Modifier and Type	Class and Description
`static class`	`Advocate.AdvocateType` The different types of advocates.

Field Summary

Fields
Modifier and Type	Field and Description
`static Advocate`	`andromeda` The Andromeda search engine.
`static Advocate`	`byonic` The Byonic search engine integrated in the Byonic protein metrics interface.
`static Advocate`	`comet` The Comet search engine, free version of Sequest.
`static Advocate`	`direcTag` The DirecTag sequencing algorithm.
`static Advocate`	`genericMzId` Advocate type for mzId files where no software is annotated.
`static Advocate`	`mascot` The Mascot search engine.
`static Advocate`	`msAmanda` The MS Amanda search engine.
`static Advocate`	`msFit` The MS-Fit search engine, old school peptide mass fingerprinting.
`static Advocate`	`msgf` The MS-GF+ search engine.
`static Advocate`	`myriMatch` The MyriMatch search engine, old school peptide mass fingerprinting.
`static Advocate`	`novor` The Novor de novo sequencing algorithm.
`static Advocate`	`omssa` The OMSSA search engine.
`static Advocate`	`peaks` The PEAKS sequencing algorithm.
`static Advocate`	`pepnovo` The PepNovo+ de novo sequencing algorithm.
`static Advocate`	`peptideShaker` The PeptideShaker multiple algorithm software.
`static Advocate`	`percolator` The percolator rescoring algorithm.
`static Advocate`	`phenyx` The phenyx search engine.
`static Advocate`	`pNovo` The pNovo+ de novo sequencing algorithm.
`static Advocate`	`proFound` The profound search engine.
`static Advocate`	`proteinLynx` The ProteinLynx search engine, waters instruments.
`static Advocate`	`proteinProspector` The search engine results of protein prospector.
`static Advocate`	`proteinScape` The search engine integrated in protein scape, Bruker instruments.
`static Advocate`	`scaffold` The scaffold multiple search engine data interpretation software.
`static Advocate`	`sequest` The sequest search engine.
`static Advocate`	`sonar` The sonar search engine, integrated in radars.
`static Advocate`	`spectraST` The SpectraST spectral library search engine (TPP).
`static Advocate`	`spectrumMill` The Spectrum Mill search engine, Agilent.
`static Advocate`	`sqid` The SeQuence IDentfication (SQID) search engine.
`static Advocate`	`tide` The Tide search engine.
`static Advocate`	`xtandem` The X!Tandem search engine.
`static Advocate`	`zCore` The ZCore search engine, ETD search engine.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static Advocate`	`addUserAdvocate(String advocateName)` Adds a user advocate and returns it.
`static Advocate`	`getAdvocate(int index)` Returns the advocate corresponding to the given index.
`static Advocate`	`getAdvocate(String advocateName)` Returns the advocate with the given name.
`static HashMap<Integer,Color>`	`getAdvocateColorMap()` Returns the advocate color map.
`static Advocate`	`getAdvocateFromFile(String idFileName)` Returns the advocate based on the identification file name.
`static HashMap<Integer,String>`	`getAdvocateToolTipMap()` Returns the advocate tool tip map.
`Color`	`getColor()` Returns the color of the advocate.
`int`	`getIndex()` Returns the index of the advocate.
`String`	`getName()` Returns the name of the advocate.
`String`	`getPmid()` Returns the PubMed id of the reference of the advocate of interest.
`Advocate.AdvocateType`	`getType()` Returns the type of advocate.
`static HashMap<Integer,Advocate>`	`getUserAdvocates()` Returns the map of user advocates imported.
`static void`	`setUserAdvocates(HashMap<Integer,Advocate> userAdvocates)` Returns the map of user advocates imported.
`String`	`toString()`
`static Advocate[]`	`values()` Returns the implemented advocates in an array.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - mascot
```
public static final Advocate mascot
```
    The Mascot search engine.
  - omssa
```
public static final Advocate omssa
```
    The OMSSA search engine.
  - xtandem
```
public static final Advocate xtandem
```
    The X!Tandem search engine.
  - pepnovo
```
public static final Advocate pepnovo
```
    The PepNovo+ de novo sequencing algorithm.
  - andromeda
```
public static final Advocate andromeda
```
    The Andromeda search engine.
  - msAmanda
```
public static final Advocate msAmanda
```
    The MS Amanda search engine.
  - peptideShaker
```
public static final Advocate peptideShaker
```
    The PeptideShaker multiple algorithm software.
  - msgf
```
public static final Advocate msgf
```
    The MS-GF+ search engine.
  - direcTag
```
public static final Advocate direcTag
```
    The DirecTag sequencing algorithm.
  - byonic
```
public static final Advocate byonic
```
    The Byonic search engine integrated in the Byonic protein metrics interface.
  - comet
```
public static final Advocate comet
```
    The Comet search engine, free version of Sequest.
  - proteinLynx
```
public static final Advocate proteinLynx
```
    The ProteinLynx search engine, waters instruments.
  - msFit
```
public static final Advocate msFit
```
    The MS-Fit search engine, old school peptide mass fingerprinting.
  - myriMatch
```
public static final Advocate myriMatch
```
    The MyriMatch search engine, old school peptide mass fingerprinting.
  - peaks
```
public static final Advocate peaks
```
    The PEAKS sequencing algorithm.
  - phenyx
```
public static final Advocate phenyx
```
    The phenyx search engine.
  - proFound
```
public static final Advocate proFound
```
    The profound search engine.
  - proteinProspector
```
public static final Advocate proteinProspector
```
    The search engine results of protein prospector.
  - proteinScape
```
public static final Advocate proteinScape
```
    The search engine integrated in protein scape, Bruker instruments.
  - sequest
```
public static final Advocate sequest
```
    The sequest search engine.
  - sqid
```
public static final Advocate sqid
```
    The SeQuence IDentfication (SQID) search engine.
  - scaffold
```
public static final Advocate scaffold
```
    The scaffold multiple search engine data interpretation software.
  - sonar
```
public static final Advocate sonar
```
    The sonar search engine, integrated in radars.
  - spectraST
```
public static final Advocate spectraST
```
    The SpectraST spectral library search engine (TPP).
  - spectrumMill
```
public static final Advocate spectrumMill
```
    The Spectrum Mill search engine, Agilent.
  - zCore
```
public static final Advocate zCore
```
    The ZCore search engine, ETD search engine.
  - percolator
```
public static final Advocate percolator
```
    The percolator rescoring algorithm.
  - pNovo
```
public static final Advocate pNovo
```
    The pNovo+ de novo sequencing algorithm.
  - tide
```
public static final Advocate tide
```
    The Tide search engine.
  - novor
```
public static final Advocate novor
```
    The Novor de novo sequencing algorithm.
  - genericMzId
```
public static final Advocate genericMzId
```
    Advocate type for mzId files where no software is annotated.
- Method Detail
  - getIndex
```
public int getIndex()
```
    Returns the index of the advocate.
    
    Returns:
    
    the index of the advocate
  - getName
```
public String getName()
```
    Returns the name of the advocate.
    
    Returns:
    
    the name of the advocate
  - getType
```
public Advocate.AdvocateType getType()
```
    Returns the type of advocate.
    
    Returns:
    
    the type of advocate
  - getColor
```
public Color getColor()
```
    Returns the color of the advocate.
    
    Returns:
    
    the color of the advocate
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - values
```
public static Advocate[] values()
```
    Returns the implemented advocates in an array.
    
    Returns:
    
    the implemented advocates in an array
  - getAdvocate
```
public static Advocate getAdvocate(int index)
```
    Returns the advocate corresponding to the given index. Null if not found.
    
    Parameters:
    
    index - the index of the advocate
    
    Returns:
    
    the advocate of interest
  - getAdvocate
```
public static Advocate getAdvocate(String advocateName)
```
    Returns the advocate with the given name. Null if not recognized.
    
    Parameters:
    
    advocateName - the name of the advocate of interest
    
    Returns:
    
    the advocate with the given name
  - addUserAdvocate
```
public static Advocate addUserAdvocate(String advocateName)
```
    Adds a user advocate and returns it.
    
    Parameters:
    
    advocateName - the name of the advocate
    
    Returns:
    
    the new advocate
  - getUserAdvocates
```
public static HashMap<Integer,Advocate> getUserAdvocates()
```
    Returns the map of user advocates imported.
    
    Returns:
    
    the map of user advocates imported
  - setUserAdvocates
```
public static void setUserAdvocates(HashMap<Integer,Advocate> userAdvocates)
```
    Returns the map of user advocates imported.
    
    Parameters:
    
    userAdvocates - the map of user advocates
  - getPmid
```
public String getPmid()
```
    Returns the PubMed id of the reference of the advocate of interest.
    
    Returns:
    
    the PubMed id of the reference of the advocate of interest
  - getAdvocateColorMap
```
public static HashMap<Integer,Color> getAdvocateColorMap()
```
    Returns the advocate color map. Key is the advocate index and the element the advocate color.
    
    Returns:
    
    the advocate color map
  - getAdvocateToolTipMap
```
public static HashMap<Integer,String> getAdvocateToolTipMap()
```
    Returns the advocate tool tip map. Key is the advocate index and the element the advocate name.
    
    Returns:
    
    the advocate tool tip map
  - getAdvocateFromFile
```
public static Advocate getAdvocateFromFile(String idFileName)
```
    Returns the advocate based on the identification file name. Null if not found. Note: this method implements a limited number of algorithms and does not support generic files. Use the IdfileReader when possible. Implemented formats: omx > OMSSA dat > Mascot xml > X!Tandem csv > MS-Amanda.
    
    Parameters:
    
    idFileName - the name of the identification file
    
    Returns:
    
    the advocate likely to have been used to create the given file

Class Advocate

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

mascot

omssa

xtandem

pepnovo

andromeda

msAmanda

peptideShaker

msgf

direcTag

byonic

comet

proteinLynx

msFit

myriMatch

peaks

phenyx

proFound

proteinProspector

proteinScape

sequest

sqid

scaffold

sonar

spectraST

spectrumMill

zCore

percolator

pNovo

tide

novor

genericMzId

Method Detail

getIndex

getName

getType

getColor

toString

values

getAdvocate

getAdvocate

addUserAdvocate

getUserAdvocates

setUserAdvocates

getPmid

getAdvocateColorMap

getAdvocateToolTipMap

getAdvocateFromFile