Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches_iterators |
Identification match iterators.
|
com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
|
com.compomics.util.experiment.personalization |
Experiment customization classes.
|
com.compomics.util.experiment.refinementparameters |
Experiment classes related to specific parametrization of experiment objects.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.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,
boolean displayProgress)
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,
boolean displayProgress)
Loads the desired peptide match parameters of the given type in the cache
of the database.
|
void |
IdentificationDB.loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all peptide match parameters of the given type in the cache of the
database.
|
void |
Identification.loadPeptideMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
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,
boolean displayProgress)
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,
boolean displayProgress)
Loads the desired protein match parameters of the given type in the cache
of the database.
|
void |
IdentificationDB.loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all protein match parameters of the given type in the cache of the
database.
|
void |
Identification.loadProteinMatchParameters(UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
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,
boolean displayProgress)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
Identification.loadSpectrumMatchParameters(ArrayList<String> spectrumKeys,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all desired spectrum match parameters in the cache of the database.
|
void |
IdentificationDB.loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
Loads all spectrum match parameters of the given type in the cache of the
database.
|
void |
Identification.loadSpectrumMatchParameters(String fileName,
UrParameter urParameter,
WaitingHandler waitingHandler,
boolean displayProgress)
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.
|
Modifier and Type | Method and Description |
---|---|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(ArrayList<String> peptideKeys,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator.
|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(ArrayList<String> peptideKeys,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator.
|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator iterating all peptides.
|
PeptideMatchesIterator |
Identification.getPeptideMatchesIterator(ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a peptide matches iterator iterating all peptides.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<String> proteinKeys,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<String> proteinKeys,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<String> proteinKeys,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator iterating all protein matches.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator iterating all protein matches.
|
ProteinMatchesIterator |
Identification.getProteinMatchesIterator(ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a protein matches iterator iterating all protein matches.
|
PsmIterator |
Identification.getPsmIterator(ArrayList<String> spectrumKeys,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
Identification.getPsmIterator(boolean loadAssumptions,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
PsmIterator |
Identification.getPsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator.
|
PsmIterator |
Identification.getPsmIterator(String spectrumFile,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Returns a PSM iterator iterating all PSMs in a file.
|
Constructor and Description |
---|
PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(ArrayList<String> peptideKeys,
Identification identification,
ArrayList<UrParameter> peptideParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
PeptideMatchesIterator(Identification identification,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(ArrayList<String> proteinKeys,
Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(ArrayList<String> proteinKeys,
Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(ArrayList<String> proteinKeys,
Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
ProteinMatchesIterator(Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor for an iterator iterating all protein keys.
|
ProteinMatchesIterator(Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor for an iterator iterating all protein keys.
|
ProteinMatchesIterator(Identification identification,
ArrayList<UrParameter> proteinParameters,
boolean loadPeptides,
ArrayList<UrParameter> peptideParameters,
boolean loadPsms,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor for an iterator iterating all protein keys.
|
PsmIterator(ArrayList<String> spectrumKeys,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
ArrayList<String> spectrumKeys,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
ArrayList<UrParameter> psmParameters,
boolean loadAssumptions,
WaitingHandler waitingHandler)
Constructor.
|
PsmIterator(String spectrumFile,
Identification identification,
boolean loadAssumptions,
ArrayList<UrParameter> psmParameters,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Class and Description |
---|---|
class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
|
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 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 | Class and Description |
---|---|
class |
PepnovoAssumptionDetails
This class contains pepnovo assumption details which are not contained in the
tag assumption class which will be saved as additional parameter.
|
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