Class BWT

java.lang.Object

BWT

public class BWT
extends java.lang.Object

A BWT object represents a Burrows-Wheeler Transform of a sequence in a Fasta file.

Field Summary

Fields

Modifier and Type	Field and Description
static int	NUM_CHARS The number of nucleotide characters in our alphabet: A, C, G, T, $

Constructor Summary

Constructors

Constructor and Description
BWT(java.lang.String filename) Creates a BWT object from the sequence in a Fasta file.

Method Summary

Methods

Modifier and Type	Method and Description
static int	charToInt(char c) Returns an integer representation of the specified character.
int	getLength() Returns the length of the genome sequence (plus 1 to account for '$').
int	getNumberCharactersLessThan(char c) Returns number of characters lexographically less than c.
int	getNumberOccurrencesPriorToIndex(char c, int i) Returns number of occurrences of character c up to but not including index i.
static void	main(java.lang.String[] args) The main method tests the BWT class by creating a BWT based on the sequence in the specified Fasta file.

Methods inherited from class java.lang.Object

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

Field Detail

NUM_CHARS

public static final int NUM_CHARS

The number of nucleotide characters in our alphabet: A, C, G, T, $

See Also:

Constant Field Values

Constructor Detail

BWT

public BWT(java.lang.String filename)

Creates a BWT object from the sequence in a Fasta file.

Parameters:

filename - the name of the Fasta file

Method Detail

getLength

public int getLength()

Returns the length of the genome sequence (plus 1 to account for '$').

getNumberCharactersLessThan

public int getNumberCharactersLessThan(char c)

Returns number of characters lexographically less than c.

getNumberOccurrencesPriorToIndex

public int getNumberOccurrencesPriorToIndex(char c,
                                   int i)

Returns number of occurrences of character c up to but not including index i.

charToInt

public static int charToInt(char c)

Returns an integer representation of the specified character.

'A' returns 0
'C' returns 1
'G' returns 2
'T' returns 3
'$' returns 4
Otherwise, -1 is returned.

Parameters:

c - character to be converted to an integer

Returns:

an integer representation of the input character

main

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

The main method tests the BWT class by creating a BWT based on the sequence in the specified Fasta file. The original sequence is output along with the BWT sequene and the unpermuted BWT (i.e., the original sequence re-created).

Parameters:

args - a String array of any command line arguments