com.pacbio.secondary.vis.data.interval

Class Interval

java.lang.Object

com.pacbio.secondary.vis.data.interval.Interval

All Implemented Interfaces:

IntervalScale<Interval>, java.lang.Comparable<Interval>

public class Interval
extends java.lang.Object
implements IntervalScale<Interval>

Field Summary

Fields

Modifier and Type	Field and Description
int	from
int	strand
int	to

Constructor Summary

Constructors

Constructor and Description
Interval()
Interval(Interval interval)
Interval(long from, long to)
Interval(long from, long to, int strand)

Method Summary

Methods

Modifier and Type	Method and Description
long	borderDist(long x)
int	compareTo(Interval interval)
boolean	contains(Interval I)
boolean	containsValue(long x)
long	distance(long x)
long	epiprodistance(Interval interval)
boolean	equals(Interval obj)
int	from()
int	getCenter()
int	getGFFLength()
int	getLength()
Interval	intersection(Interval interval)
boolean	intersects(Interval I)
boolean	intersects(int start, int end)
int	to()
java.lang.String	toString()
Interval	union(Interval interval)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

from

public int from

to

public int to

strand

public int strand

Constructor Detail

Interval

public Interval()

Interval

public Interval(long from,
        long to)

Interval

public Interval(long from,
        long to,
        int strand)

Interval

public Interval(Interval interval)

Method Detail

getLength

public int getLength()

Returns:

The length of the interval.

getGFFLength

public int getGFFLength()

Returns:

A gff interval is inclusive

containsValue

public boolean containsValue(long x)

Parameters:

x -

Returns:

True if the value x lies in the interval [A,B]

contains

public boolean contains(Interval I)

Parameters:

I -

Returns:

Returns true if this interval contains I.

intersects

public boolean intersects(Interval I)

Parameters:

I -

Returns:

Returns true if the two intervals intersects.

intersects

public boolean intersects(int start,
                 int end)

Parameters:

I -

Returns:

Returns true if the two intervals intersects.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(Interval obj)

compareTo

public int compareTo(Interval interval)

Specified by:

compareTo in interface java.lang.Comparable<Interval>

union

public Interval union(Interval interval)

borderDist

public long borderDist(long x)

Parameters:

x -

Returns:

The distance of a given point to the interval borders min(|x-A|,|x-B|).

distance

public long distance(long x)

Parameters:

x -

Returns:

The distance of a given point to an interval which is 0 if x is in [A,B] or the smaller distance from the ends of the interval: min(|x-A|,|x-B|).

epiprodistance

public long epiprodistance(Interval interval)

intersection

public Interval intersection(Interval interval)

from

public int from()

Specified by:

from in interface IntervalScale<Interval>

to

public int to()

Specified by:

to in interface IntervalScale<Interval>

getCenter

public int getCenter()