org.utgenome.gwt.utgb.client.bio
Class Interval

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Interval

All Implemented Interfaces:

Serializable, Comparable<Interval>, OnGenome

Direct Known Subclasses:

CDS, Exon, Gap, Read, ReadCoverage, ReadList, RepeatChainFinder.FlippedInterval2D, RepeatChainFinder.Interval2D, SAMReadLight, SAMReadPair, SAMReadPairFragment

public class Interval
extends Object
implements OnGenome, Comparable<Interval>, Serializable

An interval in a genome sequence.

Author:

leo

See Also:

Serialized Form

Constructor Summary

Interval()

Interval(Interval other)

Interval(int start, int end)

Method Summary

void	accept(OnGenomeDataVisitor visitor)
void	adjustToOneOrigin()
void	atomicSetStartAndEnd(int start, int end)
int	compareTo(Interval other)
boolean	contains(int pos)
boolean	contains(Interval other)
protected void	correctInterval()
boolean	follows(Interval other)
String	getColor()
int	getEnd() Get the end position of the locus (start <= end)
String	getName()
int	getStart() Get the start position of the locus.
boolean	hasOverlap(Interval other)
Interval	intersect(Interval other) Return the intersected interval with the other
boolean	intersectsWith(Interval other)
boolean	isAntiSense()
boolean	isSense()
int	length() return the length of the data
boolean	precedes(Interval other)
void	setEnd(int end)
void	setStart(int start)
String	toJSONArray()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Interval

public Interval()

Interval

public Interval(int start,
                int end)

Interval

public Interval(Interval other)

Method Detail

getName

public String getName()

Specified by:

getName in interface OnGenome

adjustToOneOrigin

public void adjustToOneOrigin()

isSense

public boolean isSense()

isAntiSense

public boolean isAntiSense()

getColor

public String getColor()

getStart

public int getStart()

Get the start position of the locus. (start <= end)

Specified by:

getStart in interface OnGenome

Returns:

the start position

setStart

public void setStart(int start)

atomicSetStartAndEnd

public void atomicSetStartAndEnd(int start,
                                 int end)

correctInterval

protected void correctInterval()

getEnd

public int getEnd()

Get the end position of the locus (start <= end)

Specified by:

getEnd in interface OnGenome

Returns:

the end position

setEnd

public void setEnd(int end)

length

public int length()

Description copied from interface: OnGenome

return the length of the data

Specified by:

length in interface OnGenome

Returns:

hasOverlap

public boolean hasOverlap(Interval other)

intersectsWith

public boolean intersectsWith(Interval other)

intersect

public Interval intersect(Interval other)

Return the intersected interval with the other

Parameters:

other -

Returns:

contains

public boolean contains(int pos)

contains

public boolean contains(Interval other)

precedes

public boolean precedes(Interval other)

follows

public boolean follows(Interval other)

accept

public void accept(OnGenomeDataVisitor visitor)

Specified by:

accept in interface OnGenome

compareTo

public int compareTo(Interval other)

Specified by:

compareTo in interface Comparable<Interval>

toJSONArray

public String toJSONArray()

toString

public String toString()

Overrides:

toString in class Object