org.biojava.nbio.core.sequence.location

Class SimplePoint

java.lang.Object

org.biojava.nbio.core.sequence.location.SimplePoint

All Implemented Interfaces:

Comparable<Point>, Point

Direct Known Subclasses:

FuzzyPoint

public class SimplePoint
extends Object
implements Point

Basic implementation of the Point interface.

Author:

ayates

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.Point

Point.Resolver<T extends Point>

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimplePoint()
	SimplePoint(int position)
	SimplePoint(int position, boolean unknown, boolean uncertain)

Method Summary

Methods

Modifier and Type	Method and Description
Point	clonePoint() Returns a copy of this point
int	compareTo(Point o)
boolean	equals(Object obj)
Integer	getPosition() Returns the position held by this object
int	hashCode()
boolean	isHigher(Point point) Returns true if the point is higher in value to the current point
boolean	isLower(Point point) Returns true if the current point is at a lower position than the point given.
boolean	isUncertain() Returns a true if the exact point is unknown.
boolean	isUnknown() Returns true if the current position is unknown but is beyond the position encoded for.
Point	offset(int distance) Returns a new point offset by the given distance
Point	reverse(int length) Returns the equivalent position on the reverse strand
protected int	reverse(int position, int length)
protected void	setPosition(int position)
protected void	setUncertain(boolean uncertain)
protected void	setUnknown(boolean unknown)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SimplePoint

protected SimplePoint()

SimplePoint

public SimplePoint(int position)

SimplePoint

public SimplePoint(int position,
           boolean unknown,
           boolean uncertain)

Method Detail

getPosition

public Integer getPosition()

Description copied from interface: Point

Returns the position held by this object

Specified by:

getPosition in interface Point

setPosition

protected void setPosition(int position)

isUnknown

public boolean isUnknown()

Description copied from interface: Point

Returns true if the current position is unknown but is beyond the position encoded for. This is the same as the position

>80

as encoded by UniProt.

Specified by:

isUnknown in interface Point

setUnknown

protected void setUnknown(boolean unknown)

isUncertain

public boolean isUncertain()

Description copied from interface: Point

Returns a true if the exact point is unknown. Equivalent position from UniProt is

?80

.

Specified by:

isUncertain in interface Point

setUncertain

protected void setUncertain(boolean uncertain)

reverse

public Point reverse(int length)

Description copied from interface: Point

Returns the equivalent position on the reverse strand

Specified by:

reverse in interface Point

Parameters:

length - Length of the sequence to translate to

offset

public Point offset(int distance)

Description copied from interface: Point

Returns a new point offset by the given distance

Specified by:

offset in interface Point

reverse

protected int reverse(int position,
          int length)

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

compareTo

public int compareTo(Point o)

Specified by:

compareTo in interface Comparable<Point>

isLower

public boolean isLower(Point point)

Description copied from interface: Point

Returns true if the current point is at a lower position than the point given.

Specified by:

isLower in interface Point

isHigher

public boolean isHigher(Point point)

Description copied from interface: Point

Returns true if the point is higher in value to the current point

Specified by:

isHigher in interface Point

clonePoint

public Point clonePoint()

Description copied from interface: Point

Returns a copy of this point

Specified by:

clonePoint in interface Point