org.biojava.nbio.core.sequence.location

Class FuzzyPoint

java.lang.Object

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

org.biojava.nbio.core.sequence.location.FuzzyPoint

All Implemented Interfaces:

Comparable<Point>, Point

public class FuzzyPoint
extends SimplePoint

Implementation for resolving fuzzy locations. Caches the calculated value.

Author:

ayates

Nested Class Summary

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

Point.Resolver<T extends Point>

Field Summary

Fields

Modifier and Type	Field and Description
static Point.Resolver<FuzzyPoint>	MAX_RESOLVER Always uses the max point to resolve a location
static Point.Resolver<FuzzyPoint>	MEAN_RESOLVER Combines min and max and then gets the mean of it
static Point.Resolver<FuzzyPoint>	MIN_RESOLVER Always uses the min point to resolve a location

Constructor Summary

Constructors

Constructor and Description
FuzzyPoint(int minPoint, int maxPoint)
FuzzyPoint(int minPoint, int maxPoint, Point.Resolver<FuzzyPoint> resolver)
FuzzyPoint(int minPoint, int maxPoint, Point.Resolver<FuzzyPoint> resolver, boolean unknown, boolean uncertain)

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(Point point)
boolean	equals(Object obj)
protected Integer	getMax()
protected Integer	getMin()
Integer	getPosition() Returns the position held by this object
protected Point.Resolver<FuzzyPoint>	getResolver()
int	hashCode()
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

Methods inherited from class org.biojava.nbio.core.sequence.location.SimplePoint

clonePoint, isHigher, isLower, isUncertain, isUnknown, reverse, setPosition, setUncertain, setUnknown, toString

Methods inherited from class java.lang.Object

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

Field Detail

MIN_RESOLVER

public static final Point.Resolver<FuzzyPoint> MIN_RESOLVER

Always uses the min point to resolve a location

MAX_RESOLVER

public static final Point.Resolver<FuzzyPoint> MAX_RESOLVER

Always uses the max point to resolve a location

MEAN_RESOLVER

public static final Point.Resolver<FuzzyPoint> MEAN_RESOLVER

Combines min and max and then gets the mean of it

Constructor Detail

FuzzyPoint

public FuzzyPoint(int minPoint,
          int maxPoint)

FuzzyPoint

public FuzzyPoint(int minPoint,
          int maxPoint,
          Point.Resolver<FuzzyPoint> resolver)

FuzzyPoint

public FuzzyPoint(int minPoint,
          int maxPoint,
          Point.Resolver<FuzzyPoint> resolver,
          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

Overrides:

getPosition in class SimplePoint

getMax

protected Integer getMax()

getMin

protected Integer getMin()

getResolver

protected Point.Resolver<FuzzyPoint> getResolver()

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

Overrides:

reverse in class SimplePoint

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

Overrides:

offset in class SimplePoint

equals

public boolean equals(Object obj)

Overrides:

equals in class SimplePoint

hashCode

public int hashCode()

Overrides:

hashCode in class SimplePoint

compareTo

public int compareTo(Point point)

Specified by:

compareTo in interface Comparable<Point>

Overrides:

compareTo in class SimplePoint