public class PsmFilter extends MatchFilter
MatchFilter.FilterType
comparatorsMap, condition, description, exceptions, filterType, MANUAL_SELECTION, manualValidation, name, reportFailed, reportPassed, valuesMap
Constructor and Description |
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PsmFilter()
Constructor.
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PsmFilter(String name)
Constructor.
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PsmFilter(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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AssumptionFilter |
getAssumptionFilter()
Returns the filter used to filter at the assumption level.
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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(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider)
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
public PsmFilter(String name)
name
- the name of the filterpublic PsmFilter()
public PsmFilter(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 passedpublic AssumptionFilter getAssumptionFilter()
protected MatchFilter getNew()
MatchFilter
getNew
in class MatchFilter
public boolean isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider)
MatchFilter
isValidated
in class MatchFilter
itemName
- the name of the item to filter onfilterItemComparator
- the comparator to usevalue
- the value to use as a thresholdmatchKey
- 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 providerpublic FilterItem[] getPossibleFilterItems()
MatchFilter
getPossibleFilterItems
in class MatchFilter
public FilterItem getFilterItem(String itemName)
MatchFilter
getFilterItem
in class MatchFilter
itemName
- the name of the filter itemCopyright © 2018. All rights reserved.