Uses of Class
com.compomics.util.experiment.identification.Advocate

Packages that use Advocate

Package	Description
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.gui.parameters.identification	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.

Uses of Advocate in com.compomics.util.experiment.identification

Fields in com.compomics.util.experiment.identification declared as Advocate

Modifier and Type	Field	Description
static final Advocate	Advocate.andromeda	The Andromeda search engine.
static final Advocate	Advocate.byonic	The Byonic search engine integrated in the Byonic protein metrics interface.
static final Advocate	Advocate.comet	The Comet search engine, free version of Sequest.
static final Advocate	Advocate.coss	The CompOmics Spectral Searching (COSS) engine.
static final Advocate	Advocate.direcTag	The DirecTag sequencing algorithm.
static final Advocate	Advocate.genericMzId	Advocate type for mzId files where no software is annotated.
static final Advocate	Advocate.identiPy	The IdentiPy search engine.
static final Advocate	Advocate.mascot	The Mascot search engine.
static final Advocate	Advocate.metaMorpheus	The MetaMorpheus search engine.
static final Advocate	Advocate.morpheus	The Morpheus search engine.
static final Advocate	Advocate.msAmanda	The MS Amanda search engine.
static final Advocate	Advocate.msFit	The MS-Fit search engine, old school peptide mass fingerprinting.
static final Advocate	Advocate.msFragger	The MSFragger search engine.
static final Advocate	Advocate.msgf	The MS-GF+ search engine.
static final Advocate	Advocate.myriMatch	The MyriMatch search engine, old school peptide mass fingerprinting.
static final Advocate	Advocate.novor	The Novor de novo sequencing algorithm.
static final Advocate	Advocate.omssa	The OMSSA search engine.
static final Advocate	Advocate.onyaseEngine	The Onyase engine script.
static final Advocate	Advocate.peaks	The PEAKS sequencing algorithm.
static final Advocate	Advocate.pepnovo	The PepNovo+ de novo sequencing algorithm.
static final Advocate	Advocate.peptideShaker	The PeptideShaker multiple algorithm software.
static final Advocate	Advocate.percolator	The Percolator rescoring algorithm.
static final Advocate	Advocate.phenyx	The Phenyx search engine.
static final Advocate	Advocate.pNovo	The pNovo+ de novo sequencing algorithm.
static final Advocate	Advocate.proFound	The Profound search engine.
static final Advocate	Advocate.proteinLynx	The ProteinLynx search engine, waters instruments.
static final Advocate	Advocate.proteinPilot	The ProteinPilot search engine.
static final Advocate	Advocate.proteinProspector	The search engine results of Protein Prospector.
static final Advocate	Advocate.proteinScape	The search engine integrated in Protein Scape, Bruker instruments.
static final Advocate	Advocate.sage	The Sage search engine.
static final Advocate	Advocate.scaffold	The Scaffold multiple search engine data interpretation software.
static final Advocate	Advocate.sequest	The Sequest search engine.
static final Advocate	Advocate.sonar	The Sonar search engine, integrated in radars.
static final Advocate	Advocate.spectraST	The SpectraST spectral library search engine (TPP).
static final Advocate	Advocate.spectrumMill	The Spectrum Mill search engine, Agilent.
static final Advocate	Advocate.sqid	The SeQuence IDentfication (SQID) search engine.
static final Advocate	Advocate.tide	The Tide search engine.
static final Advocate	Advocate.xtandem	The X! Tandem search engine.
static final Advocate	Advocate.zCore	The ZCore search engine, ETD search engine.

Methods in com.compomics.util.experiment.identification that return Advocate

Modifier and Type	Method	Description
static Advocate	Advocate.addUserAdvocate(String advocateName)	Adds a user advocate and returns it.
static Advocate	Advocate.getAdvocate(int index)	Returns the advocate corresponding to the given index.
static Advocate	Advocate.getAdvocate(String advocateName)	Returns the advocate with the given name.
static Advocate	Advocate.getAdvocateFromFile(String idFileName)	Deprecated. no longer used
static Advocate[]	Advocate.values()	Returns the implemented advocates in an array.

Methods in com.compomics.util.experiment.identification that return types with arguments of type Advocate

Modifier and Type	Method	Description
static HashMap<Integer,Advocate>	Advocate.getUserAdvocates()	Returns the map of user advocates imported.

Method parameters in com.compomics.util.experiment.identification with type arguments of type Advocate

Modifier and Type	Method	Description
static void	Advocate.setUserAdvocates(HashMap<Integer,Advocate> userAdvocates)	Returns the map of user advocates imported.

Uses of Advocate in com.compomics.util.gui.parameters.identification

Methods in com.compomics.util.gui.parameters.identification that return Advocate

Modifier and Type	Method	Description
Advocate	IdentificationAlgorithmParameter.getAlgorithm()	Returns the identification algorithm.

Uses of Advocate in com.compomics.util.parameters.identification.tool_specific

Methods in com.compomics.util.parameters.identification.tool_specific that return Advocate

Modifier and Type	Method	Description
Advocate	AndromedaParameters.getAlgorithm()
Advocate	CometParameters.getAlgorithm()
Advocate	DirecTagParameters.getAlgorithm()
Advocate	MetaMorpheusParameters.getAlgorithm()
Advocate	MsAmandaParameters.getAlgorithm()
Advocate	MsgfParameters.getAlgorithm()
Advocate	MyriMatchParameters.getAlgorithm()
Advocate	NovorParameters.getAlgorithm()
Advocate	OmssaParameters.getAlgorithm()
Advocate	PepnovoParameters.getAlgorithm()
Advocate	PNovoParameters.getAlgorithm()
Advocate	SageParameters.getAlgorithm()
Advocate	TideParameters.getAlgorithm()
Advocate	XtandemParameters.getAlgorithm()