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Packages that use UrParameter | |
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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. |
Uses of UrParameter in com.compomics.util.denovo |
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Classes in com.compomics.util.denovo that implement UrParameter | |
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class |
PeptideAssumptionDetails
This class contains the de novo specific details of a spectrum match. |
Uses of UrParameter in com.compomics.util.experiment.identification |
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Fields in com.compomics.util.experiment.identification with type parameters of type UrParameter | |
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protected HashMap<String,HashMap<String,UrParameter>> |
Identification.urParameters
Deprecated. use the database instead |
Methods in com.compomics.util.experiment.identification that return UrParameter | |
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UrParameter |
Identification.getMatchParameter(String matchKey,
UrParameter urParameter)
Deprecated. use the database match specific methods instead |
UrParameter |
IdentificationDB.getMatchPArameter(String key,
UrParameter urParameter,
boolean useDB)
Deprecated. use match specific mapping instead |
UrParameter |
Identification.getPeptideMatchParameter(String key,
UrParameter urParameter)
Returns the desired peptide match parameter. |
UrParameter |
IdentificationDB.getPeptideMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter. |
UrParameter |
Identification.getPeptideMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter. |
UrParameter |
Identification.getProteinMatchParameter(String key,
UrParameter urParameter)
Returns the desired protein match parameter. |
UrParameter |
IdentificationDB.getProteinMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter. |
UrParameter |
Identification.getProteinMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter. |
UrParameter |
Identification.getSpectrumMatchParameter(String key,
UrParameter urParameter)
Returns the desired spectrum match parameter. |
UrParameter |
IdentificationDB.getSpectrumMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter. |
UrParameter |
Identification.getSpectrumMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter. |
Methods in com.compomics.util.experiment.identification with parameters of type UrParameter | |
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void |
IdentificationDB.addMatchParameter(String key,
UrParameter urParameter)
Deprecated. use match specific mapping instead |
void |
Identification.addMatchParameter(String key,
UrParameter urParameter)
Deprecated. use the database match specific methods instead |
void |
IdentificationDB.addPeptideMatchParameter(String key,
UrParameter urParameter)
Adds a peptide match parameter to the database. |
void |
Identification.addPeptideMatchParameter(String key,
UrParameter urParameter)
Adds a peptide match parameter to the database. |
void |
IdentificationDB.addProteinMatchParameter(String key,
UrParameter urParameter)
Adds a protein match parameter to the database. |
void |
Identification.addProteinMatchParameter(String key,
UrParameter urParameter)
Adds a protein match parameter to the database. |
void |
IdentificationDB.addSpectrumMatchParameter(String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database. |
void |
Identification.addSpectrumMatchParameter(String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database. |
UrParameter |
Identification.getMatchParameter(String matchKey,
UrParameter urParameter)
Deprecated. use the database match specific methods instead |
UrParameter |
IdentificationDB.getMatchPArameter(String key,
UrParameter urParameter,
boolean useDB)
Deprecated. use match specific mapping instead |
String |
IdentificationDB.getParameterTable(UrParameter urParameter)
Deprecated. use match specific mapping instead |
UrParameter |
Identification.getPeptideMatchParameter(String key,
UrParameter urParameter)
Returns the desired peptide match parameter. |
UrParameter |
IdentificationDB.getPeptideMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter. |
UrParameter |
Identification.getPeptideMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired peptide match parameter. |
String |
IdentificationDB.getPeptideParameterTable(UrParameter urParameter)
Returns the table name associated with the given peptide parameter. |
UrParameter |
Identification.getProteinMatchParameter(String key,
UrParameter urParameter)
Returns the desired protein match parameter. |
UrParameter |
IdentificationDB.getProteinMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter. |
UrParameter |
Identification.getProteinMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired protein match parameter. |
String |
IdentificationDB.getProteinParameterTable(UrParameter urParameter)
Returns the table name associated with the given protein parameter. |
UrParameter |
Identification.getSpectrumMatchParameter(String key,
UrParameter urParameter)
Returns the desired spectrum match parameter. |
UrParameter |
IdentificationDB.getSpectrumMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter. |
UrParameter |
Identification.getSpectrumMatchParameter(String key,
UrParameter urParameter,
boolean useDB)
Returns the desired spectrum match parameter. |
String |
IdentificationDB.getSpectrumParameterTable(String spectrumKey,
UrParameter urParameter)
Returns the table name associated with the given spectrum parameter. |
void |
IdentificationDB.loadPeptideMatchParameters(ArrayList<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(ArrayList<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(ArrayList<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(ArrayList<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(ArrayList<String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database. |
void |
Identification.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all desired spectrum match parameters in the cache of the database. |
void |
IdentificationDB.loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the database. |
void |
Identification.loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler)
Loads all spectrum match parameters of the given type in the cache of the database |
void |
Identification.updatePeptideMatchParameter(String key,
UrParameter urParameter)
Updates a peptide match parameter in the database. |
void |
IdentificationDB.updatePeptideParameter(String key,
UrParameter urParameter)
Updates a peptide match parameter. |
void |
Identification.updateProteinMatchParameter(String key,
UrParameter urParameter)
Updates a protein match parameter in the database. |
void |
IdentificationDB.updateProteinParameter(String key,
UrParameter urParameter)
Updates a protein match parameter. |
void |
Identification.updateSpectrumMatchParameter(String key,
UrParameter urParameter)
Updates a spectrum match parameter in the database. |
void |
IdentificationDB.updateSpectrumParameter(String key,
UrParameter urParameter)
Updates a spectrum match parameter. |
Uses of UrParameter in com.compomics.util.experiment.personalization |
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Methods in com.compomics.util.experiment.personalization that return UrParameter | |
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UrParameter |
ExperimentObject.getUrParam(UrParameter parameter)
Method which returns the refinement parameter. |
Methods in com.compomics.util.experiment.personalization with parameters of type UrParameter | |
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void |
ExperimentObject.addUrParam(UrParameter parameter)
Method to add a user refinement parameter. |
static String |
ExperimentObject.getParameterKey(UrParameter parameter)
Returns the key of a personalization parameter. |
UrParameter |
ExperimentObject.getUrParam(UrParameter parameter)
Method which returns the refinement parameter. |
Uses of UrParameter in com.compomics.util.experiment.quantification |
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Methods in com.compomics.util.experiment.quantification that return UrParameter | |
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UrParameter |
QuantificationDB.getPeptideMatchParameter(String key,
UrParameter urParameter)
Returns the desired peptide match parameter. |
UrParameter |
QuantificationDB.getProteinMatchPArameter(String key,
UrParameter urParameter)
Returns the desired protein match parameter. |
UrParameter |
QuantificationDB.getSpectrumMatchParameter(String key,
UrParameter urParameter)
Returns the desired spectrum match parameter. |
Methods in com.compomics.util.experiment.quantification with parameters of type UrParameter | |
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void |
QuantificationDB.addPeptideMatchParameter(String key,
UrParameter urParameter)
Adds a peptide match parameter to the database. |
void |
QuantificationDB.addProteinMatchParameter(String key,
UrParameter urParameter)
Adds a protein match parameter to the database. |
void |
QuantificationDB.addSpectrumMatchParameter(String key,
UrParameter urParameter)
Adds a spectrum match parameter to the database. |
UrParameter |
QuantificationDB.getPeptideMatchParameter(String key,
UrParameter urParameter)
Returns the desired peptide match parameter. |
String |
QuantificationDB.getPeptideParameterTable(UrParameter urParameter)
Returns the table name associated to the given peptide parameter. |
UrParameter |
QuantificationDB.getProteinMatchPArameter(String key,
UrParameter urParameter)
Returns the desired protein match parameter. |
String |
QuantificationDB.getProteinParameterTable(UrParameter urParameter)
Returns the table name associated to the given protein parameter. |
UrParameter |
QuantificationDB.getSpectrumMatchParameter(String key,
UrParameter urParameter)
Returns the desired spectrum match parameter. |
String |
QuantificationDB.getSpectrumParameterTable(String spectrumKey,
UrParameter urParameter)
Returns the table name associated to the given spectrum parameter. |
void |
QuantificationDB.updatePeptideParameter(String key,
UrParameter urParameter)
Updates a peptide match parameter. |
void |
QuantificationDB.updateProteinParameter(String key,
UrParameter urParameter)
Updates a protein match parameter. |
void |
QuantificationDB.updateSpectrumParameter(String key,
UrParameter urParameter)
Updates a spectrum match parameter. |
Uses of UrParameter in com.compomics.util.experiment.refinementparameters |
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Classes in com.compomics.util.experiment.refinementparameters that implement UrParameter | |
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class |
MascotScore
This class will contain the mascot score. |
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