B C G M N

B

BWT - Class in <Unnamed>

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

BWT(String) - Constructor for class BWT

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

C

charToInt(char) - Static method in class BWT

Returns an integer representation of the specified character.

G

getLength() - Method in class BWT

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

getNumberCharactersLessThan(char) - Method in class BWT

Returns number of characters lexographically less than c.

getNumberOccurrencesPriorToIndex(char, int) - Method in class BWT

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

M

main(String[]) - Static method in class BWT

The main method tests the BWT class by creating a BWT based on the sequence in the specified Fasta file.

N

NUM_CHARS - Static variable in class BWT

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

B C G M N