Package | Description |
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.identification_parameters |
Modifier and Type | Field and Description |
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static Advocate |
Advocate.andromeda
The Andromeda search engine.
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static Advocate |
Advocate.direcTag
The DirecTag sequencing algorithm.
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static Advocate |
Advocate.mascot
The Mascot search engine.
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static Advocate |
Advocate.msAmanda
The MS Amanda search engine.
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static Advocate |
Advocate.msgf
The MS-GF+ search engine.
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static Advocate |
Advocate.omssa
The OMSSA search engine.
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static Advocate |
Advocate.pepnovo
The pepnovo+ de novo sequencing algorithm.
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static Advocate |
Advocate.peptideShaker
The PeptideShaker multiple algorithm software.
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static Advocate |
Advocate.xtandem
The X!Tandem search engine.
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Modifier and Type | Method and Description |
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static Advocate |
Advocate.addUserAdvocate(String advocateName)
Adds a user advocate and returns it.
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static Advocate |
Advocate.getAdvocate(int index)
Returns the advocate corresponding to the given index.
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static Advocate |
Advocate.getAdvocate(String advocateName)
Returns the advocate with the given name.
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Advocate |
IdentificationAlgorithmParameter.getAlgorithm()
Returns the identification algorithm.
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static Advocate[] |
Advocate.values()
Returns the implemented advocates in an array.
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Modifier and Type | Method and Description |
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static HashMap<Integer,Advocate> |
Advocate.getUserAdvocates()
Returns the map of user advocates imported.
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Modifier and Type | Method and Description |
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static void |
Advocate.setUserAdvocates(HashMap<Integer,Advocate> userAdvocates)
Returns the map of user advocates imported.
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Modifier and Type | Method and Description |
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Advocate |
XtandemParameters.getAlgorithm() |
Advocate |
PepnovoParameters.getAlgorithm() |
Advocate |
OmssaParameters.getAlgorithm() |
Advocate |
MsgfParameters.getAlgorithm() |
Advocate |
MsAmandaParameters.getAlgorithm() |
Advocate |
DirecTagParameters.getAlgorithm() |
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