Package | Description |
---|---|
com.compomics.util.denovo | |
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
com.compomics.util.experiment.personalization |
This package contains experiment customization classes.
|
com.compomics.util.experiment.quantification |
This package contains experiment classes related to quantification.
|
com.compomics.util.experiment.refinementparameters |
This package contains experiment classes related to specific parametrization of experiment objects.
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideAssumptionDetails
This class contains the de novo specific details of a spectrum match
|
Modifier and Type | Field and Description |
---|---|
protected java.util.HashMap<java.lang.String,java.util.HashMap<java.lang.String,UrParameter>> |
Identification.urParameters
Deprecated.
use the database instead
|
Modifier and Type | Method and Description |
---|---|
UrParameter |
Identification.getMatchParameter(java.lang.String matchKey,
UrParameter urParameter)
Deprecated.
use the database match specific methods instead
|
UrParameter |
IdentificationDB.getMatchPArameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Deprecated.
use match specific mapping instead
|
UrParameter |
Identification.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired peptide match parameter.
|
UrParameter |
IdentificationDB.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter.
|
UrParameter |
Identification.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter.
|
UrParameter |
Identification.getProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired protein match parameter.
|
UrParameter |
IdentificationDB.getProteinMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter.
|
UrParameter |
Identification.getProteinMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter.
|
UrParameter |
Identification.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired spectrum match parameter.
|
UrParameter |
IdentificationDB.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter.
|
UrParameter |
Identification.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationDB.addMatchParameter(java.lang.String key,
UrParameter urParameter)
Deprecated.
use match specific mapping instead
|
void |
Identification.addMatchParameter(java.lang.String key,
UrParameter urParameter)
Deprecated.
use the database match specific methods instead
|
void |
IdentificationDB.addPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a peptide match parameter to the database.
|
void |
Identification.addPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a peptide match parameter to the database.
|
void |
IdentificationDB.addProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a protein match parameter to the database.
|
void |
Identification.addProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a protein match parameter to the database.
|
void |
IdentificationDB.addSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database.
|
void |
Identification.addSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database.
|
UrParameter |
Identification.getMatchParameter(java.lang.String matchKey,
UrParameter urParameter)
Deprecated.
use the database match specific methods instead
|
UrParameter |
IdentificationDB.getMatchPArameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Deprecated.
use match specific mapping instead
|
java.lang.String |
IdentificationDB.getParameterTable(UrParameter urParameter)
Deprecated.
use match specific mapping instead
|
UrParameter |
Identification.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired peptide match parameter.
|
UrParameter |
IdentificationDB.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter.
|
UrParameter |
Identification.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter.
|
java.lang.String |
IdentificationDB.getPeptideParameterTable(UrParameter urParameter)
Returns the table name associated with the given peptide parameter.
|
UrParameter |
Identification.getProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired protein match parameter.
|
UrParameter |
IdentificationDB.getProteinMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter.
|
UrParameter |
Identification.getProteinMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter.
|
java.lang.String |
IdentificationDB.getProteinParameterTable(UrParameter urParameter)
Returns the table name associated with the given protein parameter.
|
UrParameter |
Identification.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired spectrum match parameter.
|
UrParameter |
IdentificationDB.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter.
|
UrParameter |
Identification.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter.
|
java.lang.String |
IdentificationDB.getSpectrumParameterTable(java.lang.String spectrumKey,
UrParameter urParameter)
Returns the table name associated with the given spectrum parameter.
|
void |
IdentificationDB.loadPeptideMatchParameters(java.util.ArrayList<java.lang.String> peptideKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads the desired peptide match parameters of the given type in the cache
of the database.
|
void |
Identification.loadPeptideMatchParameters(java.util.ArrayList<java.lang.String> peptideKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads the desired peptide match parameters of the given type in the cache
of the database.
|
void |
IdentificationDB.loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all peptide match parameters of the given type in the cache of the
database.
|
void |
Identification.loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all peptide match parameters of the given type in the cache of the
database.
|
void |
IdentificationDB.loadProteinMatchParameters(java.util.ArrayList<java.lang.String> proteinKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads the desired protein match parameters of the given type in the cache
of the database.
|
void |
Identification.loadProteinMatchParameters(java.util.ArrayList<java.lang.String> proteinKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads the desired protein match parameters of the given type in the cache
of the database.
|
void |
IdentificationDB.loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all protein match parameters of the given type in the cache of the
database.
|
void |
Identification.loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all protein match parameters of the given type in the cache of the
database.
|
void |
IdentificationDB.loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
Identification.loadSpectrumMatchParameters(java.util.ArrayList<java.lang.String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
IdentificationDB.loadSpectrumMatchParameters(java.lang.String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the
database.
|
void |
Identification.loadSpectrumMatchParameters(java.lang.String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the
database
|
void |
Identification.updatePeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Updates a peptide match parameter in the database.
|
void |
IdentificationDB.updatePeptideParameter(java.lang.String key,
UrParameter urParameter)
Updates a peptide match parameter.
|
void |
Identification.updateProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Updates a protein match parameter in the database.
|
void |
IdentificationDB.updateProteinParameter(java.lang.String key,
UrParameter urParameter)
Updates a protein match parameter.
|
void |
Identification.updateSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Updates a spectrum match parameter in the database.
|
void |
IdentificationDB.updateSpectrumParameter(java.lang.String key,
UrParameter urParameter)
Updates a spectrum match parameter.
|
Modifier and Type | Method and Description |
---|---|
UrParameter |
ExperimentObject.getUrParam(UrParameter parameter)
Method which returns the refinement parameter.
|
Modifier and Type | Method and Description |
---|---|
void |
ExperimentObject.addUrParam(UrParameter parameter)
Method to add a user refinement parameter.
|
static java.lang.String |
ExperimentObject.getParameterKey(UrParameter parameter)
Returns the key of a personalization parameter.
|
UrParameter |
ExperimentObject.getUrParam(UrParameter parameter)
Method which returns the refinement parameter.
|
Modifier and Type | Method and Description |
---|---|
UrParameter |
QuantificationDB.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired peptide match parameter.
|
UrParameter |
QuantificationDB.getProteinMatchPArameter(java.lang.String key,
UrParameter urParameter)
Returns the desired protein match parameter.
|
UrParameter |
QuantificationDB.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired spectrum match parameter.
|
Modifier and Type | Method and Description |
---|---|
void |
QuantificationDB.addPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a peptide match parameter to the database.
|
void |
QuantificationDB.addProteinMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a protein match parameter to the database.
|
void |
QuantificationDB.addSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database.
|
UrParameter |
QuantificationDB.getPeptideMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired peptide match parameter.
|
java.lang.String |
QuantificationDB.getPeptideParameterTable(UrParameter urParameter)
Returns the table name associated to the given peptide parameter.
|
UrParameter |
QuantificationDB.getProteinMatchPArameter(java.lang.String key,
UrParameter urParameter)
Returns the desired protein match parameter.
|
java.lang.String |
QuantificationDB.getProteinParameterTable(UrParameter urParameter)
Returns the table name associated to the given protein parameter.
|
UrParameter |
QuantificationDB.getSpectrumMatchParameter(java.lang.String key,
UrParameter urParameter)
Returns the desired spectrum match parameter.
|
java.lang.String |
QuantificationDB.getSpectrumParameterTable(java.lang.String spectrumKey,
UrParameter urParameter)
Returns the table name associated to the given spectrum parameter.
|
void |
QuantificationDB.updatePeptideParameter(java.lang.String key,
UrParameter urParameter)
Updates a peptide match parameter.
|
void |
QuantificationDB.updateProteinParameter(java.lang.String key,
UrParameter urParameter)
Updates a protein match parameter.
|
void |
QuantificationDB.updateSpectrumParameter(java.lang.String key,
UrParameter urParameter)
Updates a spectrum match parameter.
|
Modifier and Type | Class and Description |
---|---|
class |
MascotScore
This class will contain the mascot score.
|
Copyright © 2013. All Rights Reserved.