util.bio.seq
Class IndexedSequence

java.lang.Object
  util.bio.seq.IndexedSequence

All Implemented Interfaces:

java.lang.Comparable

public class IndexedSequence

extends java.lang.Object

implements java.lang.Comparable

Field Summary

static java.util.regex.Pattern

nameParser

Constructor Summary

IndexedSequence(java.io.File binarySeqFile)

Method Summary

int	compareTo(java.lang.Object obj) Assumes starts are unique.
boolean	contained(int basePosition)
java.lang.String	getChromosome()
java.lang.String	getSequence()
int	getStart()
int	getStop()
void	setSequence(java.lang.String sequence)

Methods inherited from class java.lang.Object

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

Field Detail

nameParser

public static final java.util.regex.Pattern nameParser

Constructor Detail

IndexedSequence

public IndexedSequence(java.io.File binarySeqFile)

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Assumes starts are unique.

Specified by:

compareTo in interface java.lang.Comparable

contained

public boolean contained(int basePosition)

getChromosome

public java.lang.String getChromosome()

getSequence

public java.lang.String getSequence()

getStart

public int getStart()

getStop

public int getStop()

setSequence

public void setSequence(java.lang.String sequence)