org.utgenome.format.fasta
Class CompactACGTWriter

java.lang.Object
  org.utgenome.format.fasta.CompactACGTWriter

public class CompactACGTWriter
extends Object

ACGT sequence compressor

Author:

leo

Constructor Summary

CompactACGTWriter(OutputStream seqOut, OutputStream nSeqOut)

Method Summary

void	append(char ch)
void	append(String sequence)
void	close()
static void	generateCharTo2BitACGTTable() This method is used to generate source code for the charToACGTCodeTable
long	getSequenceLength()
static byte	to2bitCode(char acgt)

Methods inherited from class java.lang.Object

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

Constructor Detail

CompactACGTWriter

public CompactACGTWriter(OutputStream seqOut,
                         OutputStream nSeqOut)

Method Detail

getSequenceLength

public long getSequenceLength()

close

public void close()
           throws IOException

Throws:

IOException

append

public void append(String sequence)
            throws IOException

Throws:

IOException

append

public void append(char ch)
            throws IOException

Throws:

IOException

to2bitCode

public static byte to2bitCode(char acgt)

generateCharTo2BitACGTTable

public static void generateCharTo2BitACGTTable()

This method is used to generate source code for the charToACGTCodeTable