Class Advocate
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.Advocate
- All Implemented Interfaces:
Serializable
public class Advocate extends ExperimentObject
The advocate of a hit can be a search engine, a sequencing algorithm, a
rescoring algorithm, etc.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Advocate.AdvocateType
The different types of advocates. -
Field Summary
Fields Modifier and Type Field 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
coss
The CompOmics Spectral Searching (COSS) engine.static Advocate
direcTag
The DirecTag sequencing algorithm.static Advocate
genericMzId
Advocate type for mzId files where no software is annotated.static Advocate
identiPy
The IdentiPy search engine.static Advocate
mascot
The Mascot search engine.static Advocate
metaMorpheus
The MetaMorpheus search engine.static Advocate
morpheus
The Morpheus 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
onyaseEngine
The Onyase engine script.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
proteinPilot
The ProteinPilot search engine.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. -
Constructor Summary
Constructors Constructor Description Advocate()
Empty default constructor -
Method Summary
Modifier and Type Method 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)
Deprecated.no longer usedstatic 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 com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
-
Field Details
-
mascot
The Mascot search engine. -
omssa
The OMSSA search engine. -
xtandem
The X! Tandem search engine. -
pepnovo
The PepNovo+ de novo sequencing algorithm. -
andromeda
The Andromeda search engine. -
msAmanda
The MS Amanda search engine. -
peptideShaker
The PeptideShaker multiple algorithm software. -
msgf
The MS-GF+ search engine. -
direcTag
The DirecTag sequencing algorithm. -
byonic
The Byonic search engine integrated in the Byonic protein metrics interface. -
comet
The Comet search engine, free version of Sequest. -
proteinLynx
The ProteinLynx search engine, waters instruments. -
msFit
The MS-Fit search engine, old school peptide mass fingerprinting. -
myriMatch
The MyriMatch search engine, old school peptide mass fingerprinting. -
peaks
The PEAKS sequencing algorithm. -
phenyx
The Phenyx search engine. -
proFound
The Profound search engine. -
proteinProspector
The search engine results of Protein Prospector. -
proteinScape
The search engine integrated in Protein Scape, Bruker instruments. -
sequest
The Sequest search engine. -
sqid
The SeQuence IDentfication (SQID) search engine. -
scaffold
The Scaffold multiple search engine data interpretation software. -
sonar
The Sonar search engine, integrated in radars. -
spectraST
The SpectraST spectral library search engine (TPP). -
spectrumMill
The Spectrum Mill search engine, Agilent. -
zCore
The ZCore search engine, ETD search engine. -
percolator
The Percolator rescoring algorithm. -
pNovo
The pNovo+ de novo sequencing algorithm. -
tide
The Tide search engine. -
novor
The Novor de novo sequencing algorithm. -
morpheus
The Morpheus search engine. -
proteinPilot
The ProteinPilot search engine. -
onyaseEngine
The Onyase engine script. -
metaMorpheus
The MetaMorpheus search engine. -
identiPy
The IdentiPy search engine. -
coss
The CompOmics Spectral Searching (COSS) engine. -
genericMzId
Advocate type for mzId files where no software is annotated.
-
-
Constructor Details
-
Advocate
public Advocate()Empty default constructor
-
-
Method Details
-
getIndex
public int getIndex()Returns the index of the advocate.- Returns:
- the index of the advocate
-
getName
Returns the name of the advocate.- Returns:
- the name of the advocate
-
getType
Returns the type of advocate.- Returns:
- the type of advocate
-
getColor
Returns the color of the advocate.- Returns:
- the color of the advocate
-
toString
-
values
Returns the implemented advocates in an array.- Returns:
- the implemented advocates in an array
-
getAdvocate
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
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
Adds a user advocate and returns it.- Parameters:
advocateName
- the name of the advocate- Returns:
- the new advocate
-
getUserAdvocates
Returns the map of user advocates imported.- Returns:
- the map of user advocates imported
-
setUserAdvocates
Returns the map of user advocates imported.- Parameters:
userAdvocates
- the map of user advocates
-
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
Returns the advocate color map. Key is the advocate index and the element the advocate color.- Returns:
- the advocate color map
-
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
Deprecated.no longer usedReturns 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
-