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

Fields
Modifier and Type	Field and Description
`int`	`DEFAULT_BUFFER_SIZE`

Constructor Summary

Constructors
Constructor and Description

TwoBitParser(java.io.File f)

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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

Class TwoBitParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.io.InputStream

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_BUFFER_SIZE

Constructor Detail

TwoBitParser

Method Detail

getSequenceNames

setCurrentSequence

reset

getCurrentSequencePosition

setCurrentSequencePosition

read

skip

close

available

closeParser

getFile

loadFragment

printFastaSequence

printFastaSequence

main