Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
|
com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
|
Modifier and Type | Field and 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.direcTag
The DirecTag sequencing algorithm.
|
static Advocate |
Advocate.genericMzId
Advocate type for mzId files where no software is annotated.
|
static Advocate |
Advocate.mascot
The Mascot 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.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.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.
|
Modifier and Type | Method and 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)
Returns the advocate based on the identification file name.
|
static Advocate[] |
Advocate.values()
Returns the implemented advocates in an array.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Advocate> |
Advocate.getUserAdvocates()
Returns the map of user advocates imported.
|
Modifier and Type | Method and Description |
---|---|
static void |
Advocate.setUserAdvocates(HashMap<Integer,Advocate> userAdvocates)
Returns the map of user advocates imported.
|
Modifier and Type | Method and Description |
---|---|
Advocate |
IdentificationAlgorithmParameter.getAlgorithm()
Returns the identification algorithm.
|
Modifier and Type | Method and Description |
---|---|
Advocate |
XtandemParameters.getAlgorithm() |
Advocate |
TideParameters.getAlgorithm() |
Advocate |
PNovoParameters.getAlgorithm() |
Advocate |
PepnovoParameters.getAlgorithm() |
Advocate |
OmssaParameters.getAlgorithm() |
Advocate |
NovorParameters.getAlgorithm() |
Advocate |
MyriMatchParameters.getAlgorithm() |
Advocate |
MsgfParameters.getAlgorithm() |
Advocate |
MsAmandaParameters.getAlgorithm() |
Advocate |
DirecTagParameters.getAlgorithm() |
Advocate |
CometParameters.getAlgorithm() |
Advocate |
AndromedaParameters.getAlgorithm() |
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