Uses of Interface
psidev.psi.mi.jami.model.Range

Packages that use Range

Package	Description
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher.impl.minimal
psidev.psi.mi.jami.enricher.listener.impl
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.enricher.util
psidev.psi.mi.jami.json.elements
psidev.psi.mi.jami.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone
psidev.psi.mi.jami.utils.comparator
psidev.psi.mi.jami.utils.comparator.feature
psidev.psi.mi.jami.utils.comparator.range
psidev.psi.mi.jami.xml.io.writer.elements
psidev.psi.mi.jami.xml.io.writer.elements.impl
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300
psidev.psi.mi.jami.xml.model.reference

Uses of Range in psidev.psi.mi.jami.crosslink.extension

Classes in psidev.psi.mi.jami.crosslink.extension that implement Range

Modifier and Type	Class	Description
class	CsvRange	Crosslink CSV extension of Range It contains a FileSourceLocator

Uses of Range in psidev.psi.mi.jami.enricher.impl.minimal

Methods in psidev.psi.mi.jami.enricher.impl.minimal with parameters of type Range

Modifier and Type	Method	Description
protected void	MinimalFeatureEnricher.onInvalidRange(F feature, Range range, Collection<String> errorMessages)	onInvalidRange.
protected void	MinimalFeatureEvidenceUpdater.onInvalidRange(FeatureEvidence feature, Range range, Collection<String> errorMessages)	onInvalidRange.
protected void	MinimalFeatureUpdater.onInvalidRange(F feature, Range range, Collection<String> errorMessages)	onInvalidRange.
protected void	MinimalFeatureEnricher.onOutOfDateRange(F feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.
protected void	MinimalFeatureEvidenceUpdater.onOutOfDateRange(FeatureEvidence feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.
protected void	MinimalFeatureUpdater.onOutOfDateRange(F feature, Range range, Collection<String> errorMessages, String oldSequence)	onOutOfDateRange.

Uses of Range in psidev.psi.mi.jami.enricher.listener.impl

Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type Range

Modifier and Type	Method	Description
void	FeatureEnricherListenerManager.onAddedRange(T feature, Range added)	onAddedRange
void	FeatureEnricherListenerManager.onRemovedRange(T feature, Range removed)	onRemovedRange
void	FeatureEnricherListenerManager.onUpdatedRangePositions(T feature, Range range, Position position, Position position2)	onUpdatedRangePositions

Uses of Range in psidev.psi.mi.jami.enricher.listener.impl.writer

Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type Range

Modifier and Type	Method	Description
void	FeatureEnricherStatisticsWriter.onAddedRange(T feature, Range added)	onAddedRange
void	FeatureEnricherStatisticsWriter.onRemovedRange(T feature, Range removed)	onRemovedRange
void	FeatureEnricherStatisticsWriter.onUpdatedRangePositions(T feature, Range range, Position position, Position position2)	onUpdatedRangePositions

Uses of Range in psidev.psi.mi.jami.enricher.util

Method parameters in psidev.psi.mi.jami.enricher.util with type arguments of type Range

Modifier and Type	Method	Description
static <T extends Feature> void	EnricherUtils.mergeRanges(T termToEnrich, Collection<Range> toEnrichRanges, Collection<Range> fetchedRanges, boolean remove, FeatureChangeListener<T> featureListener)	mergeRanges.

Uses of Range in psidev.psi.mi.jami.json.elements

Methods in psidev.psi.mi.jami.json.elements with parameters of type Range

Modifier and Type	Method	Description
void	JsonRangeWriter.write(Range object, Feature parent)	write.
void	SimpleJsonRangeWriter.write(Range object)	write.
void	SimpleJsonRangeWriter.write(Range object, Feature parent)	write.

Uses of Range in psidev.psi.mi.jami.listener

Methods in psidev.psi.mi.jami.listener with parameters of type Range

Modifier and Type	Method	Description
void	FeatureChangeListener.onAddedRange(F feature, Range added)	onAddedRange
void	FeatureChangeListener.onRemovedRange(F feature, Range removed)	onRemovedRange
void	FeatureChangeListener.onUpdatedRangePositions(F feature, Range range, Position oldStart, Position oldEnd)	onUpdatedRangePositions

Uses of Range in psidev.psi.mi.jami.listener.impl

Methods in psidev.psi.mi.jami.listener.impl with parameters of type Range

Modifier and Type	Method	Description
void	FeatureChangeLogger.onAddedRange(T feature, Range added)	onAddedRange
void	FeatureChangeLogger.onRemovedRange(T feature, Range removed)	onRemovedRange
void	FeatureChangeLogger.onUpdatedRangePositions(T feature, Range range, Position oldStart, Position oldEnd)	onUpdatedRangePositions

Uses of Range in psidev.psi.mi.jami.model

Methods in psidev.psi.mi.jami.model with type parameters of type Range

Modifier and Type	Method	Description
<R extends Range> Collection<R>	Feature.getRanges()	The ranges which locate the feature in the interactor sequence/structure.

Uses of Range in psidev.psi.mi.jami.model.impl

Classes in psidev.psi.mi.jami.model.impl that implement Range

Modifier and Type	Class	Description
class	DefaultRange	Default implementation for Range Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousRangeAndResultingSequenceComparator

Methods in psidev.psi.mi.jami.model.impl that return types with arguments of type Range

Modifier and Type	Method	Description
Collection<Range>	AbstractFeature.getRanges()	Getter for the field ranges.

Method parameters in psidev.psi.mi.jami.model.impl with type arguments of type Range

Modifier and Type	Method	Description
protected void	AbstractFeature.initialiseRangesWith(Collection<Range> ranges)	initialiseRangesWith

Uses of Range in psidev.psi.mi.jami.tab.extension

Classes in psidev.psi.mi.jami.tab.extension that implement Range

Modifier and Type	Class	Description
class	MitabRange	Mitab extension of Range It contains a FileSourceLocator

Uses of Range in psidev.psi.mi.jami.utils

Methods in psidev.psi.mi.jami.utils that return Range

Modifier and Type	Method	Description
static Range	RangeUtils.createCertainRange(int position)	createCertainRange
static Range	RangeUtils.createCertainRange(int start, int end)	createCertainRange
static Range	RangeUtils.createCTerminalRange()	createCTerminalRange
static Range	RangeUtils.createCTerminusRange(int lastPosition)	createCTerminusRange
static Range	RangeUtils.createFuzzyRange(int position)	createFuzzyRange
static Range	RangeUtils.createFuzzyRange(int start, int end)	createFuzzyRange
static Range	RangeUtils.createFuzzyRange(int fromStart, int fromEnd, int toStart, int toEnd)	createFuzzyRange
static Range	RangeUtils.createGreaterThanRange(int position)	createGreaterThanRange
static Range	RangeUtils.createGreaterThanRange(int start, int end)	createGreaterThanRange
static Range	RangeUtils.createLessThanRange(int position)	createLessThanRange
static Range	RangeUtils.createLessThanRange(int start, int end)	createLessThanRange
static Range	RangeUtils.createLinkedCertainRange(int position)	createLinkedCertainRange
static Range	RangeUtils.createLinkedCertainRange(int start, int end)	createLinkedCertainRange
static Range	RangeUtils.createLinkedFuzzyRange(int position)	createLinkedFuzzyRange
static Range	RangeUtils.createLinkedFuzzyRange(int start, int end)	createLinkedFuzzyRange
static Range	RangeUtils.createLinkedFuzzyRange(int fromStart, int fromEnd, int toStart, int toEnd)	createLinkedFuzzyRange
static Range	RangeUtils.createLinkedRaggedNTerminusRange(int position)	createLinkedRaggedNTerminusRange
static Range	RangeUtils.createLinkedRaggedNTerminusRange(int start, int end)	createLinkedRaggedNTerminusRange
static Range	RangeUtils.createLinkedRange(String statusName, String statusMi, int position)	createLinkedRange
static Range	RangeUtils.createLinkedRange(String statusName, String statusMi, int start, int end)	createLinkedRange
static Range	RangeUtils.createNTerminalRange()	createNTerminalRange
static Range	RangeUtils.createNTerminusRange()	createNTerminusRange
static Range	RangeUtils.createRaggedNTerminusRange(int position)	createRaggedNTerminusRange
static Range	RangeUtils.createRaggedNTerminusRange(int start, int end)	createRaggedNTerminusRange
static Range	RangeUtils.createRange(String statusName, String statusMi, int position)	createRange
static Range	RangeUtils.createRange(String statusName, String statusMi, int start, int end)	createRange
static Range	RangeUtils.createRangeFromString(String rangeString)	Create a Range from a String
static Range	RangeUtils.createRangeFromString(String rangeString, boolean linked)	Create a range with a given linked property from a String
static Range	RangeUtils.createUndeterminedRange()	createUndeterminedRange

Methods in psidev.psi.mi.jami.utils with parameters of type Range

Modifier and Type	Method	Description
static boolean	RangeUtils.areRangePositionsOverlapping(Range range)	Checks if the interval positions of the range are overlapping
static boolean	RangeUtils.areRangeStatusInconsistent(Range range)	areRangeStatusInconsistent
static String	RangeUtils.convertRangeToString(Range range)	Converts a range in a String.
static Feature	FeatureUtils.createDefaultFeature(String name, CvTerm featureType, Range range)	createDefaultFeature
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Collection<CvTerm> detectionMethods, Range range)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, CvTerm detectionMethod, Range range)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Range range)	createFeatureEvidence
static ModelledFeature	FeatureUtils.createModelledFeature(String name, CvTerm featureType, Range range)	createModelledFeature
static String	RangeUtils.extractRangeSequence(Range range, String sequence)	Extract a sub-sequence from the sequence given a Range object
static List<String>	RangeUtils.validateRange(Range range, String sequence)	Method to check if the range is valid or not.

Method parameters in psidev.psi.mi.jami.utils with type arguments of type Range

Modifier and Type	Method	Description
static Feature	FeatureUtils.createDefaultFeature(String name, CvTerm featureType, Collection<Range> ranges)	createDefaultFeature
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, Collection<Range> ranges)	createFeatureEvidence
static FeatureEvidence	FeatureUtils.createFeatureEvidence(String name, CvTerm featureType, CvTerm detectionMethod, Collection<Range> ranges)	createFeatureEvidence
static ModelledFeature	FeatureUtils.createModelledFeature(String name, CvTerm featureType, Collection<Range> ranges)	createModelledFeature

Uses of Range in psidev.psi.mi.jami.utils.clone

Methods in psidev.psi.mi.jami.utils.clone with parameters of type Range

Modifier and Type	Method	Description
static void	RangeCloner.copyAndOverrideRangeProperties(Range source, Range target)	All properties are copied from source to target excepted the participant
static void	RangeCloner.copyAndOverrideRangePropertiesWithParticipant(Range source, Range target)	All properties are copied from source to target

Uses of Range in psidev.psi.mi.jami.utils.comparator

Method parameters in psidev.psi.mi.jami.utils.comparator with type arguments of type Range

Modifier and Type	Method	Description
static boolean	ComparatorUtils.areRangesEqual(Collection<? extends Range> method1, Collection<? extends Range> method2)	areRangesEqual

Uses of Range in psidev.psi.mi.jami.utils.comparator.feature

Methods in psidev.psi.mi.jami.utils.comparator.feature that return types with arguments of type Range

Modifier and Type	Method	Description
CollectionComparator<Range>	FeatureBaseComparator.getRangeCollectionComparator()	Getter for the field rangeCollectionComparator.

Uses of Range in psidev.psi.mi.jami.utils.comparator.range

Methods in psidev.psi.mi.jami.utils.comparator.range with parameters of type Range

Modifier and Type	Method	Description
static boolean	DefaultRangeAndResultingSequenceComparator.areEquals(Range range1, Range range2)	Use DefaultRangeComparator to know if two ranges are equals.
static boolean	DefaultRangeComparator.areEquals(Range range1, Range range2)	Use DefaultRangeComparator to know if two ranges are equals.
static boolean	UnambiguousRangeAndResultingSequenceComparator.areEquals(Range range1, Range range2)	Use DefaultRangeComparator to know if two ranges are equals.
static boolean	UnambiguousRangeComparator.areEquals(Range range1, Range range2)	Use DefaultRangeComparator to know if two ranges are equals.
int	RangeAndResultingSequenceComparator.compare(Range range1, Range range2)	It compares first the start Position, then the end Position using a PositionComparator, If start/end positions are equals, the linked ranges will always come before the ranges that are not linked.
int	RangeComparator.compare(Range range1, Range range2)	It compares first the start Position, then the end Position using a PositionComparator, If start/end positions are equals, the linked ranges will always come before the ranges that are not linked.
int	UnambiguousRangeAndResultingSequenceComparator.compare(Range range1, Range range2)	It compares first the start Position, then the end Position using a UnambiguousPositionComparator, If start/end positions are equals, the linked ranges will always come before the ranges that are not linked.
int	UnambiguousRangeComparator.compare(Range range1, Range range2)
static int	UnambiguousRangeAndResultingSequenceComparator.hashCode(Range range)	hashCode
static int	UnambiguousRangeComparator.hashCode(Range range)	hashCode

Uses of Range in psidev.psi.mi.jami.xml.io.writer.elements

Methods in psidev.psi.mi.jami.xml.io.writer.elements that return types with arguments of type Range

Modifier and Type	Method	Description
static PsiXmlElementWriter<Range>	PsiXmlElementWriterFactory.createRangeWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlObjectCache objectIndex, PsiXmlVersion version, PsiXmlXrefWriter refWriter, PsiXmlVariableNameWriter<CvTerm> statusWriter)	createRangeWriter.

Uses of Range in psidev.psi.mi.jami.xml.io.writer.elements.impl

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl with parameters of type Range

Modifier and Type	Method	Description
protected void	XmlRangeWriter.writeOtherProperties(Range object)	writeOtherProperties.

Uses of Range in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts that return types with arguments of type Range

Modifier and Type	Method	Description
PsiXmlElementWriter<Range>	AbstractXmlFeatureWriter.getRangeWriter()	Getter for the field rangeWriter.

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with parameters of type Range

Modifier and Type	Method	Description
void	AbstractXmlRangeWriter.write(Range object)	write.
protected abstract void	AbstractXmlRangeWriter.writeOtherProperties(Range object)	writeOtherProperties.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with type arguments of type Range

Modifier and Type	Method	Description
void	AbstractXmlFeatureWriter.setRangeWriter(PsiXmlElementWriter<Range> rangeWriter)	Setter for the field rangeWriter.

Uses of Range in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25 with parameters of type Range

Modifier and Type	Method	Description
protected void	XmlRangeWriter.writeOtherProperties(Range object)	writeOtherProperties.

Uses of Range in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 with parameters of type Range

Modifier and Type	Method	Description
protected void	XmlRangeWriter.writeOtherProperties(Range object)	writeOtherProperties.

Uses of Range in psidev.psi.mi.jami.xml.model.extension.xml253

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Range

Modifier and Type	Class	Description
class	XmlRange	Xml implementation of Range The JAXB binding is designed to be read-only and is not designed for writing

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return types with arguments of type Range

Modifier and Type	Method	Description
List<Range>	AbstractXmlFeature.JAXBRangeWrapper.getJAXBRanges()
Collection<Range>	AbstractXmlFeature.getRanges()	getRanges.
Collection<Range>	XmlFeatureEvidenceWrapper.getRanges()	The ranges which locate the feature in the interactor sequence/structure.
Collection<Range>	XmlFeatureWrapper.getRanges()	The ranges which locate the feature in the interactor sequence/structure.

Uses of Range in psidev.psi.mi.jami.xml.model.extension.xml254

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Range

Modifier and Type	Class	Description
class	XmlRange	Xml implementation of Range The JAXB binding is designed to be read-only and is not designed for writing

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return types with arguments of type Range

Modifier and Type	Method	Description
List<Range>	AbstractXmlFeature.JAXBRangeWrapper.getJAXBRanges()
Collection<Range>	AbstractXmlFeature.getRanges()	getRanges.
Collection<Range>	XmlFeatureEvidenceWrapper.getRanges()	The ranges which locate the feature in the interactor sequence/structure.
Collection<Range>	XmlFeatureWrapper.getRanges()	The ranges which locate the feature in the interactor sequence/structure.

Uses of Range in psidev.psi.mi.jami.xml.model.extension.xml300

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Range

Modifier and Type	Class	Description
class	XmlRange	Xml implementation of Range The JAXB binding is designed to be read-only and is not designed for writing

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return types with arguments of type Range

Modifier and Type	Method	Description
List<Range>	AbstractXmlFeature.JAXBRangeWrapper.getJAXBRanges()
Collection<Range>	AbstractXmlFeature.getRanges()	getRanges.
Collection<Range>	XmlFeatureEvidenceWrapper.getRanges()	The ranges which locate the feature in the interactor sequence/structure.
Collection<Range>	XmlFeatureWrapper.getRanges()	The ranges which locate the feature in the interactor sequence/structure.

Uses of Range in psidev.psi.mi.jami.xml.model.reference

Methods in psidev.psi.mi.jami.xml.model.reference that return types with arguments of type Range

Modifier and Type	Method	Description
Collection<Range>	AbstractFeatureRef.getRanges()	getRanges.