util.bio.annotation
Class Coordinates

java.lang.Object
  util.bio.annotation.Coordinates

All Implemented Interfaces:

java.lang.Comparable

public class Coordinates

extends java.lang.Object

implements java.lang.Comparable

Base class for holding info about a genomic coordinate.

Constructor Summary

Coordinates(java.lang.String chromosome, int start, int stop)

Method Summary

int	compareTo(java.lang.Object other) Sorts by chromsome, start position, length (smallest to largest).
java.lang.String	getChromosome()
int	getStart()
int	getStop()
static Coordinates[]	readBinary(java.io.File file) Reads a binary Coordinate[] file.
void	setChromosome(java.lang.String chromosome)
void	setStart(int start)
void	setStop(int stop)
java.lang.String	toString()
static boolean	writeBinary(Coordinates[] c, java.io.File file) Writes a binary Coordinate[].

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Coordinates

public Coordinates(java.lang.String chromosome,
                   int start,
                   int stop)

Method Detail

compareTo

public int compareTo(java.lang.Object other)

Sorts by chromsome, start position, length (smallest to largest).

Specified by:

compareTo in interface java.lang.Comparable

toString

public java.lang.String toString()

writeBinary

public static boolean writeBinary(Coordinates[] c,
                                  java.io.File file)

Writes a binary Coordinate[].

Returns:

true if sucessful, false if something bad happened.

readBinary

public static Coordinates[] readBinary(java.io.File file)

Reads a binary Coordinate[] file.

Returns:

null if something bad happened.

getChromosome

public java.lang.String getChromosome()

setChromosome

public void setChromosome(java.lang.String chromosome)

getStart

public int getStart()

setStart

public void setStart(int start)

getStop

public int getStop()

setStop

public void setStop(int stop)