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 Details

    • DEFAULT_BUFFER_SIZE

      public int DEFAULT_BUFFER_SIZE

  • Constructor Details

  • 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