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

Packages that use Position

Package	Description
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher.listener.impl
psidev.psi.mi.jami.enricher.listener.impl.writer
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.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.extended
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300

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

Constructors in psidev.psi.mi.jami.crosslink.extension with parameters of type Position

Constructor	Description
CsvRange(Position start, Position end)	Constructor for CsvRange.
CsvRange(Position start, Position end, boolean isLink)	Constructor for CsvRange.
CsvRange(Position start, Position end, boolean isLink, Participant participant)	Constructor for CsvRange.
CsvRange(Position start, Position end, boolean isLink, ResultingSequence resultingSequence)	Constructor for CsvRange.
CsvRange(Position start, Position end, Participant participant)	Constructor for CsvRange.
CsvRange(Position start, Position end, ResultingSequence resultingSequence)	Constructor for CsvRange.

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

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

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

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

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

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

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

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

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

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

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

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

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

Methods in psidev.psi.mi.jami.model that return Position

Modifier and Type	Method	Description
Position	Range.getEnd()	The end position of the feature range in the interactor sequence It cannot be null
Position	Range.getStart()	The start position of the feature range in the interactor sequence It cannot be null

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

Modifier and Type	Method	Description
void	Range.setPositions(Position start, Position end)	Set the positions of the feature range in the interactor sequence

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

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

Modifier and Type	Class	Description
class	DefaultPosition	Default implementation for Position Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousPositionComparator

Methods in psidev.psi.mi.jami.model.impl that return Position

Modifier and Type	Method	Description
Position	DefaultRange.getEnd()	Getter for the field end.
Position	DefaultRange.getStart()	Getter for the field start.

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

Modifier and Type	Method	Description
void	DefaultRange.setPositions(Position start, Position end)	Set the positions of the feature range in the interactor sequence

Constructors in psidev.psi.mi.jami.model.impl with parameters of type Position

Constructor	Description
DefaultRange(Position start, Position end)	Constructor for DefaultRange.
DefaultRange(Position start, Position end, boolean isLink)	Constructor for DefaultRange.
DefaultRange(Position start, Position end, boolean isLink, Participant participant)	Constructor for DefaultRange.
DefaultRange(Position start, Position end, boolean isLink, ResultingSequence resultingSequence)	Constructor for DefaultRange.
DefaultRange(Position start, Position end, Participant participant)	Constructor for DefaultRange.
DefaultRange(Position start, Position end, ResultingSequence resultingSequence)	Constructor for DefaultRange.

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

Constructors in psidev.psi.mi.jami.tab.extension with parameters of type Position

Constructor	Description
MitabRange(Position start, Position end)	Constructor for MitabRange.
MitabRange(Position start, Position end, boolean isLink)	Constructor for MitabRange.
MitabRange(Position start, Position end, boolean isLink, Participant participant)	Constructor for MitabRange.
MitabRange(Position start, Position end, boolean isLink, ResultingSequence resultingSequence)	Constructor for MitabRange.
MitabRange(Position start, Position end, Participant participant)	Constructor for MitabRange.
MitabRange(Position start, Position end, ResultingSequence resultingSequence)	Constructor for MitabRange.

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

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

Modifier and Type	Method	Description
static Position	PositionUtils.createCertainPosition(int position)	createCertainPosition
static Position	PositionUtils.createCTerminalPosition(int lastPosition)	createCTerminalPosition
static Position	PositionUtils.createCTerminalRangePosition()	createCTerminalRangePosition
static Position	PositionUtils.createFuzzyPosition(int position)	createFuzzyPosition
static Position	PositionUtils.createFuzzyPosition(int start, int end)	createFuzzyPosition
static Position	PositionUtils.createGreaterThanPosition(int position)	createGreaterThanPosition
static Position	PositionUtils.createLessThanPosition(int position)	createLessThanPosition
static Position	PositionUtils.createNTerminalPosition()	createNTerminalPosition
static Position	PositionUtils.createNTerminalRangePosition()	createNTerminalRangePosition
static Position	PositionUtils.createPosition(String statusName, String statusMi, int start)	createPosition
static Position	PositionUtils.createPositionFromString(String pos)	createPositionFromString
static Position	PositionUtils.createRaggedNTerminusPosition(int position)	createRaggedNTerminusPosition
static Position	PositionUtils.createUndeterminedPosition()	createUndeterminedPosition

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

Modifier and Type	Method	Description
static String	PositionUtils.convertPositionToString(Position position)	Converts a given position in a String using specific mnemonic for encoding the position status
static boolean	PositionUtils.isCertain(Position position)	Check if a position is certain (MI:0335)
static boolean	PositionUtils.isCTerminal(Position position)	Check if a position is C-terminal position (MI:0334)
static boolean	PositionUtils.isCTerminalRange(Position position)	Check if a position is C-terminal range (MI:1039)
static boolean	PositionUtils.isFuzzyRange(Position position)	Check if a position is fuzzy range (MI:0338)
static boolean	PositionUtils.isGreaterThan(Position position)	Check if a position is greater-than (MI:0336)
static boolean	PositionUtils.isLessThan(Position position)	Check if a position is less-than (MI:0337)
static boolean	PositionUtils.isNTerminal(Position position)	Check if a position is N-terminal position (MI:0340)
static boolean	PositionUtils.isNTerminalRange(Position position)	Check if a position is N-terminal range (MI:1040)
static boolean	PositionUtils.isRaggedNTerminal(Position position)	Check if a position is ragged N-terminal position (MI:0341)
static boolean	PositionUtils.isUndetermined(Position position)	Check if a position is undetermined (MI:0339)
static List<String>	PositionUtils.validateRangePosition(Position position, String sequence)	Check if the positions and the position status are consistent.

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

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

Modifier and Type	Method	Description
static boolean	DefaultPositionComparator.areEquals(Position position1, Position position2)	Use DefaultPositionComparator to know if two positions are equals.
static boolean	UnambiguousPositionComparator.areEquals(Position pos1, Position pos2)	Use UnabmbiguousPositionComparator to know if two positions are equals.
int	PositionComparator.compare(Position position1, Position position2)	It will first compare the status and then will check if the position is undetermined.
int	UnambiguousPositionComparator.compare(Position position1, Position position2)	It will first compare the status and then will check if the position is undetermined.
static int	UnambiguousPositionComparator.hashCode(Position pos)	hashCode

Uses of Position 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 Position

Modifier and Type	Method	Description
static PsiXmlElementWriter<Position>[]	PsiXmlElementWriterFactory.createPositionsWriter(XMLStreamWriter streamWriter, boolean extended, PsiXmlVariableNameWriter<CvTerm> statusWriter)	createPositionsWriter.

Uses of Position 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 Position

Modifier and Type	Method	Description
protected void	XmlBeginPositionWriter.writeStatus(Position object)	writeStatus.
protected void	XmlEndPositionWriter.writeStatus(Position object)	writeStatus.

Uses of Position 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 Position

Modifier and Type	Method	Description
PsiXmlElementWriter<Position>	AbstractXmlRangeWriter.getEndPositionWriter()	Getter for the field endPositionWriter.
PsiXmlElementWriter<Position>	AbstractXmlRangeWriter.getStartPositionWriter()	Getter for the field startPositionWriter.

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

Modifier and Type	Method	Description
void	AbstractXmlPositionWriter.write(Position object)	write.
protected abstract void	AbstractXmlPositionWriter.writeStatus(Position object)	writeStatus.

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

Modifier and Type	Method	Description
void	AbstractXmlRangeWriter.setEndPositionWriter(PsiXmlElementWriter<Position> endPositionWriter)	Setter for the field endPositionWriter.
void	AbstractXmlRangeWriter.setStartPositionWriter(PsiXmlElementWriter<Position> startPositionWriter)	Setter for the field startPositionWriter.

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

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

Modifier and Type	Method	Description
protected void	XmlBeginPositionWriter.writeStatus(Position object)	writeStatus.
protected void	XmlEndPositionWriter.writeStatus(Position object)	writeStatus.

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

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

Modifier and Type	Class	Description
class	AbstractXmlPosition	Abstract class for XmlPosition
class	XmlInterval	Xml implementation of a position which is an interval The JAXB binding is designed to be read-only and is not designed for writing
class	XmlPosition	Xml implementation of a simple Position 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 Position

Modifier and Type	Method	Description
Position	XmlRange.getEnd()	Getter for the field end.
Position	XmlRange.getStart()	Getter for the field start.

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Position

Modifier and Type	Method	Description
void	XmlRange.setPositions(Position start, Position end)	Set the positions of the feature range in the interactor sequence

Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Position

Constructor	Description
XmlRange(Position start, Position end)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink, Participant participant)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink, ResultingSequence resultingSequence)	Constructor for XmlRange.
XmlRange(Position start, Position end, Participant participant)	Constructor for XmlRange.
XmlRange(Position start, Position end, ResultingSequence resultingSequence)	Constructor for XmlRange.

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

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

Modifier and Type	Class	Description
class	AbstractXmlPosition	Abstract class for XmlPosition
class	XmlInterval	Xml implementation of a position which is an interval The JAXB binding is designed to be read-only and is not designed for writing
class	XmlPosition	Xml implementation of a simple Position 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 Position

Modifier and Type	Method	Description
Position	XmlRange.getEnd()	Getter for the field end.
Position	XmlRange.getStart()	Getter for the field start.

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Position

Modifier and Type	Method	Description
void	XmlRange.setPositions(Position start, Position end)	Set the positions of the feature range in the interactor sequence

Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Position

Constructor	Description
XmlRange(Position start, Position end)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink, Participant participant)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink, ResultingSequence resultingSequence)	Constructor for XmlRange.
XmlRange(Position start, Position end, Participant participant)	Constructor for XmlRange.
XmlRange(Position start, Position end, ResultingSequence resultingSequence)	Constructor for XmlRange.

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

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

Modifier and Type	Class	Description
class	AbstractXmlPosition	Abstract class for XmlPosition
class	XmlInterval	Xml implementation of a position which is an interval The JAXB binding is designed to be read-only and is not designed for writing
class	XmlPosition	Xml implementation of a simple Position 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 Position

Modifier and Type	Method	Description
Position	XmlRange.getEnd()	Getter for the field end.
Position	XmlRange.getStart()	Getter for the field start.

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Position

Modifier and Type	Method	Description
void	XmlRange.setPositions(Position start, Position end)	Set the positions of the feature range in the interactor sequence

Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Position

Constructor	Description
XmlRange(Position start, Position end)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink, Participant participant)	Constructor for XmlRange.
XmlRange(Position start, Position end, boolean isLink, ResultingSequence resultingSequence)	Constructor for XmlRange.
XmlRange(Position start, Position end, Participant participant)	Constructor for XmlRange.
XmlRange(Position start, Position end, ResultingSequence resultingSequence)	Constructor for XmlRange.