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