Uses of Interface
com.compomics.util.experiment.personalization.UrParameter

Packages that use UrParameter
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
 

Classes in com.compomics.util.denovo that implement UrParameter
 class PeptideAssumptionDetails
          This class contains the de novo specific details of a spectrum match
 

Uses of UrParameter in com.compomics.util.experiment.identification
 

Fields in com.compomics.util.experiment.identification with type parameters of type UrParameter
protected  HashMap<String,HashMap<String,UrParameter>> Identification.urParameters
          Deprecated. use the database instead
 

Methods in com.compomics.util.experiment.identification that return UrParameter
 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
 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
 

Methods in com.compomics.util.experiment.personalization that return UrParameter
 UrParameter ExperimentObject.getUrParam(UrParameter parameter)
          Method which returns the refinement parameter.
 

Methods in com.compomics.util.experiment.personalization with parameters of type UrParameter
 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
 

Methods in com.compomics.util.experiment.quantification that return UrParameter
 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
 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
 

Classes in com.compomics.util.experiment.refinementparameters that implement UrParameter
 class MascotScore
          This class will contain the mascot score.
 



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