org.biojava.nbio.genome.parsers.twobit

Class TwoBitParser

java.lang.Object

java.io.InputStream

org.biojava.nbio.genome.parsers.twobit.TwoBitParser

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class TwoBitParser
extends java.io.InputStream

downloaded from http://storage.bioinf.fbb.msu.ru/~roman/TwoBitParser.java Class is a parser of UCSC Genome Browser file format .2bit used to store nucleotide sequence information. This class extends InputStream and can be used as it after choosing one of names of containing sequences. This parser can be used to do some work like UCSC tool named twoBitToFa. For it just run this class with input file path as single parameter and set stdout stream into output file. If you have any problems or ideas don't hesitate to contact me through email: rsutormin[at]gmail.com.

Author:

Roman Sutormin

Field Summary

Fields

Modifier and Type	Field and Description
int	DEFAULT_BUFFER_SIZE

Constructor Summary

Constructors

Constructor and Description
TwoBitParser(java.io.File f)

Method Summary

Modifier and Type	Method and Description
int	available()
void	close() Method closes current sequence and it's necessary to invoke it before setting new current sequence.
void	closeParser() Method closes random access file descriptor.
long	getCurrentSequencePosition()
java.io.File	getFile()
java.lang.String[]	getSequenceNames()
java.lang.String	loadFragment(long seq_pos, int len)
static void	main(java.lang.String[] args)
void	printFastaSequence()
void	printFastaSequence(long len)
int	read() Method reads 1 nucleotide from sequence stream.
void	reset() Method resets current position to the begining of sequence stream.
void	setCurrentSequence(java.lang.String seq_name) Method open nucleotide stream for sequence with given name.
void	setCurrentSequencePosition(long pos)
long	skip(long n) Method skips n nucleotides in sequence stream.

Methods inherited from class java.io.InputStream

mark, markSupported, read, read

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_BUFFER_SIZE

public int DEFAULT_BUFFER_SIZE

Constructor Detail

TwoBitParser

public TwoBitParser(java.io.File f)
             throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

getSequenceNames

public java.lang.String[] getSequenceNames()

setCurrentSequence

public void setCurrentSequence(java.lang.String seq_name)
                        throws java.lang.Exception

Method open nucleotide stream for sequence with given name.

Parameters:

seq_name - name of sequence (one of returned by getSequenceNames()).

Throws:

java.lang.Exception

reset

public void reset()
           throws java.io.IOException

Method resets current position to the begining of sequence stream.

Overrides:

reset in class java.io.InputStream

Throws:

java.io.IOException

getCurrentSequencePosition

public long getCurrentSequencePosition()

Returns:

number (starting from 0) of next readable nucleotide in sequence stream.

setCurrentSequencePosition

public void setCurrentSequencePosition(long pos)
                                throws java.io.IOException

Throws:

java.io.IOException

read

public int read()
         throws java.io.IOException

Method reads 1 nucleotide from sequence stream. You should set current sequence before use it.

Specified by:

read in class java.io.InputStream

Throws:

java.io.IOException

skip

public long skip(long n)
          throws java.io.IOException

Method skips n nucleotides in sequence stream. You should set current sequence before use it.

Overrides:

skip in class java.io.InputStream

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Method closes current sequence and it's necessary to invoke it before setting new current sequence.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.InputStream

Throws:

java.io.IOException

available

public int available()
              throws java.io.IOException

Overrides:

available in class java.io.InputStream

Throws:

java.io.IOException

closeParser

public void closeParser()
                 throws java.lang.Exception

Method closes random access file descriptor. You can't use any reading methods after it.

Throws:

java.lang.Exception

getFile

public java.io.File getFile()

loadFragment

public java.lang.String loadFragment(long seq_pos,
                                     int len)
                              throws java.io.IOException

Throws:

java.io.IOException

printFastaSequence

public void printFastaSequence()
                        throws java.io.IOException

Throws:

java.io.IOException

printFastaSequence

public void printFastaSequence(long len)
                        throws java.io.IOException

Throws:

java.io.IOException

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception