org.biojava.nbio.genome.parsers.twobit

Class TwoBitFacade

java.lang.Object

org.biojava.nbio.genome.parsers.twobit.TwoBitFacade

public class TwoBitFacade
extends java.lang.Object

A facade that makes it easier to work with a 2bit file. Created by yana on 3/27/17.

Constructor Summary

Constructors

Constructor and Description
TwoBitFacade(java.io.File file) Reads a genome from a locally stored .2bit file.

Method Summary

Modifier and Type	Method and Description
void	close() Closes .2bit file twoBitParser.
java.lang.String	getSequence(java.lang.String chromosomeName, int start, int end) Extract a sequence from a chromosome, using chromosomal coordinates
void	setChromosome(java.lang.String chr) Sets a chromosome for TwoBitParser.

Methods inherited from class java.lang.Object

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

Constructor Detail

TwoBitFacade

public TwoBitFacade(java.io.File file)
             throws java.lang.Exception

Reads a genome from a locally stored .2bit file.

Parameters:

file - the File to a .2bit file.

Throws:

java.lang.Exception

Method Detail

close

public void close()
           throws java.lang.Exception

Closes .2bit file twoBitParser.

Throws:

java.lang.Exception

setChromosome

public void setChromosome(java.lang.String chr)
                   throws java.lang.Exception

Sets a chromosome for TwoBitParser.

Parameters:

chr - The chromosome name (e.g. chr21)

Throws:

java.lang.Exception

getSequence

public java.lang.String getSequence(java.lang.String chromosomeName,
                                    int start,
                                    int end)
                             throws java.lang.Exception

Extract a sequence from a chromosome, using chromosomal coordinates

Parameters:

chromosomeName -

start -

end -

Returns:

the DNASequence from the requested coordinates.

Throws:

java.lang.Exception