Package com.compomics.util.experiment.identification.filtering

Class ProteinFilter

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.filtering.MatchFilter

com.compomics.util.experiment.identification.filtering.ProteinFilter

All Implemented Interfaces:

Filter, Serializable

public class ProteinFilter
extends MatchFilter

Protein filter.

Author:

Marc Vaudel, Harald Barsnes

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

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
ProteinFilter()	Constructor.
ProteinFilter(String name)	Constructor.
ProteinFilter(String name, String description)	Constructor.
ProteinFilter(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(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, 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.

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

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ProteinFilter

public ProteinFilter()

Constructor.

ProteinFilter

public ProteinFilter(String name)

Constructor.

Parameters:

name - the name of the filter

ProteinFilter

public ProteinFilter(String name,
 String description)

Constructor.

Parameters:

name - the name of the filter

description - the description of the filter

ProteinFilter

public ProteinFilter(String name,
 String description,
 String condition,
 String reportPassed,
 String reportFailed)

Constructor.

Parameters:

name - the name of the filter

description - the description of the filter

condition - a description of the condition to be met to pass the filter

reportPassed - a report for when the filter is passed

reportFailed - a report for when the filter is not passed

Method Details

getNew

protected MatchFilter getNew()

Description copied from class: MatchFilter

Returns a new empty filter.

Specified by:

getNew in class MatchFilter

Returns:

a new empty filter

isValidated

public boolean isValidated(String itemName,
 FilterItemComparator filterItemComparator,
 Object value,
 long matchKey,
 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 class MatchFilter

Parameters:

itemName - the name of the item to filter on

filterItemComparator - the comparator to use

value - the value to use as a threshold

matchKey - the key of the match of interest

identification - the identification objects where to get identification matches from

geneMaps - the gene maps

identificationFeaturesGenerator - the identification feature generator where to get identification features

identificationParameters - the identification parameters used

sequenceProvider - the protein sequence provider

proteinDetailsProvider - the protein details provider

spectrumProvider - 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.

getPossibleFilterItems

public FilterItem[] getPossibleFilterItems()

Description copied from class: MatchFilter

Returns the filter items accepted by this filter.

Specified by:

getPossibleFilterItems in class MatchFilter

Returns:

the filter items accepted by this filter

getFilterItem

public FilterItem getFilterItem(String itemName)

Description copied from class: MatchFilter

Returns the filter item corresponding to the given name.

Specified by:

getFilterItem in class MatchFilter

Parameters:

itemName - the name of the filter item

Returns:

the filter item corresponding to the given name