public class AssumptionFilter extends MatchFilter
MatchFilter.FilterType
comparatorsMap, condition, description, exceptions, filterType, MANUAL_SELECTION, manualValidation, name, reportFailed, reportPassed, valuesMap
NO_KEY
Constructor and Description |
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AssumptionFilter()
Constructor.
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AssumptionFilter(String name)
Constructor.
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AssumptionFilter(String name,
String description)
Constructor.
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AssumptionFilter(String name,
String description,
String condition,
String reportPassed,
String reportFailed)
Constructor.
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Modifier and Type | Method and Description |
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FilterItem |
getFilterItem(String itemName)
Returns the filter item corresponding to the given name.
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protected MatchFilter |
getNew()
Returns a new empty filter.
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FilterItem[] |
getPossibleFilterItems()
Returns the filter items accepted by this filter.
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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.
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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.
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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.
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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
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public AssumptionFilter()
public AssumptionFilter(String name)
name
- the name of the filterpublic AssumptionFilter(String name, String description)
name
- the name of the filterdescription
- the description of the filterpublic AssumptionFilter(String name, String description, String condition, String reportPassed, String reportFailed)
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 passedprotected MatchFilter getNew()
MatchFilter
getNew
in class MatchFilter
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)
MatchFilter
isValidated
in class MatchFilter
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 providerpublic boolean isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
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 parameterspublic 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)
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 usedpublic FilterItem[] getPossibleFilterItems()
MatchFilter
getPossibleFilterItems
in class MatchFilter
public FilterItem getFilterItem(String itemName)
MatchFilter
getFilterItem
in class MatchFilter
itemName
- the name of the filter itemCopyright © 2021. All rights reserved.