Uses of Interface
org.biojava.nbio.core.sequence.location.template.Point

Packages that use Point

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template

Uses of Point in org.biojava.nbio.core.alignment

Methods in org.biojava.nbio.core.alignment that return Point

Modifier and Type	Method and Description
Point	SimpleAlignedSequence.getEnd()
Point	SimpleAlignedSequence.getStart()

Uses of Point in org.biojava.nbio.core.alignment.template

Methods in org.biojava.nbio.core.alignment.template that return Point

Modifier and Type	Method and Description
Point	AlignedSequence.getEnd() Returns the Point within an alignment of the last element of the original Sequence.
Point	AlignedSequence.getStart() Returns the Point within an alignment of the first element of the original Sequence.

Uses of Point in org.biojava.nbio.core.sequence.location

Classes in org.biojava.nbio.core.sequence.location that implement Point

Modifier and Type	Class and Description
class	FuzzyPoint Implementation for resolving fuzzy locations.
class	SimplePoint Basic implementation of the Point interface.

Methods in org.biojava.nbio.core.sequence.location that return Point

Modifier and Type	Method and Description
Point	SimplePoint.clonePoint()
static Point	LocationHelper.detectEnd(List<Location> subLocations, boolean isCircular) This will attempt to find what the last point is and returns that position.
static Point	LocationHelper.detectStart(List<Location> subLocations) Assumes that the first element is the start & clones it
Point	FuzzyPoint.offset(int distance)
Point	SimplePoint.offset(int distance)
Point	FuzzyPoint.reverse(int length)
Point	SimplePoint.reverse(int length)

Methods in org.biojava.nbio.core.sequence.location with parameters of type Point

Modifier and Type	Method and Description
int	FuzzyPoint.compareTo(Point point)
int	SimplePoint.compareTo(Point o)
boolean	SimplePoint.isHigher(Point point)
boolean	SimplePoint.isLower(Point point)

Constructors in org.biojava.nbio.core.sequence.location with parameters of type Point

Constructor and Description
GroupLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)
GroupLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
GroupLocation(Point start, Point end, Strand strand, List<Location> subLocations)
GroupLocation(Point start, Point end, Strand strand, Location... subLocations)
OrderLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)
OrderLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
OrderLocation(Point start, Point end, Strand strand, List<Location> subLocations)
OrderLocation(Point start, Point end, Strand strand, Location... subLocations)
SequenceLocation(Point start, Point end, S sequence, Strand strand)
SimpleLocation(Point start, Point end)
SimpleLocation(Point start, Point end, Strand strand)
SimpleLocation(Point start, Point end, Strand strand, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, boolean betweenCompounds, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenBases)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenBases, List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
SimpleLocation(Point start, Point end, Strand strand, List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, Location... subLocations)

Uses of Point in org.biojava.nbio.core.sequence.location.template

Classes in org.biojava.nbio.core.sequence.location.template with type parameters of type Point

Modifier and Type	Interface and Description
static interface	Point.Resolver<T extends Point> Used to resolve a position about a point

Methods in org.biojava.nbio.core.sequence.location.template that return Point

Modifier and Type	Method and Description
Point	Point.clonePoint() Returns a copy of this point
Point	AbstractLocation.getEnd()
Point	Location.getEnd() End of the location
Point	AbstractLocation.getStart()
Point	Location.getStart() Start of the location
Point	Point.offset(int distance) Returns a new point offset by the given distance
Point	Point.reverse(int length) Returns the equivalent position on the reverse strand

Methods in org.biojava.nbio.core.sequence.location.template with parameters of type Point

Modifier and Type	Method and Description
boolean	Point.isHigher(Point point) Returns true if the point is higher in value to the current point
boolean	Point.isLower(Point point) Returns true if the current point is at a lower position than the point given.
protected void	AbstractLocation.setEnd(Point end)
protected void	AbstractLocation.setStart(Point start)

Constructors in org.biojava.nbio.core.sequence.location.template with parameters of type Point

Constructor and Description
AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations) Default constructor
AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations) Default constructor