Package org.biojava.nbio.genome.parsers.twobit

Class TwoBitParser

java.lang.Object

java.io.InputStream

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

All Implemented Interfaces:

Closeable, AutoCloseable

public class TwoBitParser
extends 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	Description
int	DEFAULT_BUFFER_SIZE

Constructor Summary

Constructors

Constructor	Description
TwoBitParser(File f)

Method Summary

Modifier and Type	Method	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()
File	getFile()
String[]	getSequenceNames()
String	loadFragment(long seq_pos, int len)
static void	main(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(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, nullInputStream, read, read, readAllBytes, readNBytes, readNBytes, skipNBytes, transferTo

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_BUFFER_SIZE

public int DEFAULT_BUFFER_SIZE

Constructor Details

TwoBitParser

public TwoBitParser(File f)
             throws Exception

Throws:

Exception

Method Details

getSequenceNames

public String[] getSequenceNames()

setCurrentSequence

public void setCurrentSequence(String seq_name)
                        throws Exception

Method open nucleotide stream for sequence with given name.

Parameters:

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

Throws:

Exception

reset

public void reset()
           throws IOException

Method resets current position to the begining of sequence stream.

Overrides:

reset in class InputStream

Throws:

IOException

getCurrentSequencePosition

public long getCurrentSequencePosition()

Returns:

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

setCurrentSequencePosition

public void setCurrentSequencePosition(long pos)
                                throws IOException

Throws:

IOException

read

public int read()
         throws IOException

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

Specified by:

read in class InputStream

Throws:

IOException

skip

public long skip(long n)
          throws IOException

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

Overrides:

skip in class InputStream

Throws:

IOException

close

public void close()
           throws IOException

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

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class InputStream

Throws:

IOException

available

public int available()
              throws IOException

Overrides:

available in class InputStream

Throws:

IOException

closeParser

public void closeParser()
                 throws Exception

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

Throws:

Exception

getFile

public File getFile()

loadFragment

public String loadFragment(long seq_pos,
 int len)
                    throws IOException

Throws:

IOException

printFastaSequence

public void printFastaSequence()
                        throws IOException

Throws:

IOException

printFastaSequence

public void printFastaSequence(long len)
                        throws IOException

Throws:

IOException

main

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

Throws:

Exception