Uses of Interface
org.biojavax.bio.seq.Position

Packages that use Position

org.biojavax.bio.seq

Rich implementations of Sequences, Locations and Features.

Uses of Position in org.biojavax.bio.seq

Classes in org.biojavax.bio.seq that implement Position

class

SimplePosition A simple implementation of the Position interface.

Fields in org.biojavax.bio.seq declared as Position

static Position

Position.EMPTY_POSITION The empty position lies nowhere.

Methods in org.biojavax.bio.seq that return Position

Position	SimpleRichLocation.getMaxPosition() Retrieves the end position of this location.
Position	RichLocation.getMaxPosition() Retrieves the end position of this location.
Position	MultiSourceCompoundRichLocation.getMaxPosition() Retrieves the end position of this location. ALWAYS RETURNS A POINT POSITION AT POINT EQUIVALENT TO COMBINED LENGTH OF MEMBERS
Position	EmptyRichLocation.getMaxPosition() Retrieves the end position of this location. ALWAYS RETURNS THE EMPTY POSITION
Position	SimpleRichLocation.getMinPosition() Retrieves the start position of this location.
Position	RichLocation.getMinPosition() Retrieves the start position of this location.
Position	MultiSourceCompoundRichLocation.getMinPosition() Retrieves the start position of this location. ALWAYS RETURNS A POINT POSITION AT POINT 1
Position	EmptyRichLocation.getMinPosition() Retrieves the start position of this location. ALWAYS RETURNS THE EMPTY POSITION
protected Position	SimpleRichLocation.posmax(Position a, Position b)
protected Position	SimpleRichLocation.posmin(Position a, Position b)
Position	SimplePosition.translate(int distance) Takes this position and returns a copy translated by 'distance' bases.
Position	Position.translate(int distance) Takes this position and returns a copy translated by 'distance' bases.

Methods in org.biojavax.bio.seq with parameters of type Position

int	PositionResolver.getMax(Position end) Resolves the maximum possible base for this position.
int	PositionResolver.MaximalResolver.getMax(Position e) Resolves the maximum possible base for this position. ALWAYS RETURNS e.getEnd()
int	PositionResolver.MinimalResolver.getMax(Position e) Resolves the maximum possible base for this position. ALWAYS RETURNS e.getStart()
int	PositionResolver.AverageResolver.getMax(Position e) Resolves the maximum possible base for this position. ALWAYS RETURNS e.getStart()+e.getEnd() / 2
int	PositionResolver.getMin(Position start) Resolves the minimum possible base for this position.
int	PositionResolver.MaximalResolver.getMin(Position s) Resolves the minimum possible base for this position. ALWAYS RETURNS s.getStart()
int	PositionResolver.MinimalResolver.getMin(Position s) Resolves the minimum possible base for this position. ALWAYS RETURNS s.getEnd()
int	PositionResolver.AverageResolver.getMin(Position s) Resolves the minimum possible base for this position. ALWAYS RETURNS s.getStart()+s.getEnd() / 2
protected Position	SimpleRichLocation.posmax(Position a, Position b)
protected Position	SimpleRichLocation.posmin(Position a, Position b)
protected void	SimpleRichLocation.setMaxPosition(Position max)
protected void	SimpleRichLocation.setMinPosition(Position min)

Constructors in org.biojavax.bio.seq with parameters of type Position

SimpleRichLocation(Position pos, int rank)
Creates a new instance of SimpleRichSequenceLocation that points to a single position on the positive strand.

SimpleRichLocation(Position pos, int rank, RichLocation.Strand strand)
Creates a new instance of SimpleRichSequenceLocation that points to a single position.

SimpleRichLocation(Position pos, int rank, RichLocation.Strand strand, CrossRef crossRef)
Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence.

SimpleRichLocation(Position min, Position max, int rank)
Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand.

SimpleRichLocation(Position min, Position max, int rank, RichLocation.Strand strand)
Creates a new instance of SimpleRichSequenceLocation that points to a range position.

SimpleRichLocation(Position min, Position max, int rank, RichLocation.Strand strand, CrossRef crossRef)
Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence.