Class AssumptionFilter
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.filtering.MatchFilter
com.compomics.util.experiment.identification.filtering.AssumptionFilter
- All Implemented Interfaces:
Filter
,Serializable
public class AssumptionFilter extends MatchFilter
Peptide Assumption filter.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
-
Nested Class Summary
Nested classes/interfaces inherited from class com.compomics.util.experiment.identification.filtering.MatchFilter
MatchFilter.FilterType
-
Field Summary
Fields inherited from class com.compomics.util.experiment.identification.filtering.MatchFilter
comparatorsMap, condition, description, exceptions, filterType, MANUAL_SELECTION, manualValidation, name, reportFailed, reportPassed, valuesMap
-
Constructor Summary
Constructors Constructor Description AssumptionFilter()
Constructor.AssumptionFilter(String name)
Constructor.AssumptionFilter(String name, String description)
Constructor.AssumptionFilter(String name, String description, String condition, String reportPassed, String reportFailed)
Constructor. -
Method Summary
Modifier and Type Method Description FilterItem
getFilterItem(String itemName)
Returns the filter item corresponding to the given name.protected MatchFilter
getNew()
Returns a new empty filter.FilterItem[]
getPossibleFilterItems()
Returns the filter items accepted by this filter.boolean
isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
Tests whether a match is validated by this filter.boolean
isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.boolean
isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.Methods inherited from class com.compomics.util.experiment.identification.filtering.MatchFilter
addException, addManualValidation, clear, clone, getComparatorForItem, getCondition, getDescription, getExceptions, getItemsNames, getManualValidation, getName, getPossibleFilterItemsNames, getReport, getType, getValue, isActive, isSameAs, isValidated, removeException, removeFilterItem, removeManualValidation, setActive, setComparatorForItem, setCondition, setDescription, setExceptions, setFilterItem, setManualValidation, setName, setReportFailed, setReportPassed, setType, setValueForItem
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
-
Constructor Details
-
AssumptionFilter
public AssumptionFilter()Constructor. -
AssumptionFilter
Constructor.- Parameters:
name
- the name of the filter
-
AssumptionFilter
Constructor.- Parameters:
name
- the name of the filterdescription
- the description of the filter
-
AssumptionFilter
public AssumptionFilter(String name, String description, String condition, String reportPassed, String reportFailed)Constructor.- Parameters:
name
- the name of the filterdescription
- the description of the filtercondition
- a description of the condition to be met to pass the filterreportPassed
- a report for when the filter is passedreportFailed
- a report for when the filter is not passed
-
-
Method Details
-
getNew
Description copied from class:MatchFilter
Returns a new empty filter.- Specified by:
getNew
in classMatchFilter
- Returns:
- a new empty filter
-
isValidated
public boolean isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)Description copied from class:MatchFilter
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.- Specified by:
isValidated
in classMatchFilter
- Parameters:
itemName
- the name of the item to filter onfilterItemComparator
- the comparator to usevalue
- the value to use as a thresholdspectrumMatchKey
- the key of the match of interestidentification
- the identification objects where to get identification matches fromgeneMaps
- the gene mapsidentificationFeaturesGenerator
- the identification feature generator where to get identification featuresidentificationParameters
- the identification parameters usedsequenceProvider
- the protein sequence providerproteinDetailsProvider
- the protein details providerspectrumProvider
- the spectrum provider- Returns:
- a boolean indicating whether the match designated by the protein key validates the given item using the given comparator and value threshold.
-
isValidated
public boolean isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)Tests whether a match is validated by this filter.- Parameters:
spectrumMatchKey
- the key of the matchspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumpeptideAssumption
- the peptide assumptionidentification
- the identification where to get the information fromsequenceProvider
- the sequence providerspectrumProvider
- the spectrum provideridentificationFeaturesGenerator
- the identification features generator providing identification featuresidentificationParameters
- the identification parameters- Returns:
- a boolean indicating whether a match is validated by a given filter
-
isValidated
public boolean isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.- Parameters:
itemName
- the name of the item to filter onfilterItemComparator
- the comparator to usevalue
- the value to use as a thresholdspectrumMatchKey
- the key of the match of interestspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumpeptideAssumption
- the assumption to validateidentification
- the identification objects where to get identification matches fromsequenceProvider
- the sequence providerspectrumProvider
- the spectrum provideridentificationFeaturesGenerator
- the identification feature generator where to get identification featuresidentificationParameters
- the identification parameters used- Returns:
- a boolean indicating whether the match designated by the protein key validates the given item using the given comparator and value threshold.
-
getPossibleFilterItems
Description copied from class:MatchFilter
Returns the filter items accepted by this filter.- Specified by:
getPossibleFilterItems
in classMatchFilter
- Returns:
- the filter items accepted by this filter
-
getFilterItem
Description copied from class:MatchFilter
Returns the filter item corresponding to the given name.- Specified by:
getFilterItem
in classMatchFilter
- Parameters:
itemName
- the name of the filter item- Returns:
- the filter item corresponding to the given name
-