A B C G M O S T 

A

Alignment - Class in <Unnamed>
An instance of the Alignment class represents an optimal pairwise alignment for two genomic sequences.
Alignment(File, File) - Constructor for class Alignment
Creates an Alignment from the genomic sequences found in the two specified FASTA files.
Alignment(String, String) - Constructor for class Alignment
Creates an Alignment from the two specified genomic sequences.
alignmentTableToString() - Method in class Alignment
Returns a String representation of the alignment table generated during alignment computation.

B

backtrackTableToString() - Method in class Alignment
Returns a String representation of the backtrack table generated during alignment computation.

C

calculatePValue() - Method in class Alignment
Estimates the p-value of this Alignment.
computeAlignment() - Method in class Alignment
Computes the optimal pairwise alignment of two genomic sequences.

G

getAlignment() - Method in class Alignment
Returns the optimal pairwise alignment.
getAlignmentScore() - Method in class Alignment
Returns the optimal pairwise alignment score for this Alignment.
getPValue() - Method in class Alignment
Returns the p-value of this Alignment.

M

main(String[]) - Static method in class Alignment
The main method creates an optimal pairwise alignment for two genomic sequences.

O

outputHistogramOfRandomAlignmentScores(String, Vector<Integer>) - Static method in class Alignment
Outputs a histogram of optimal pairwise alignment scores to a file.

S

sequence1() - Method in class Alignment
Returns the first of two genomic sequences in this Alignment.
sequence2() - Method in class Alignment
Returns the second of two genomic sequences in this Alignment.
setAffineGaps(int, int) - Method in class Alignment
Score gaps in this Alignment using an affine model.
setFastAlignment(int) - Method in class Alignment
Indicate that a fast linear-time pairwise alignment should be performed.
setFixedScoring(int, int) - Method in class Alignment
When aligning two characters, one from each genomic sequence, if the two characters are identical then the alignment score of the two characters should be the match score.
setGlobalAlignment() - Method in class Alignment
Indicate that a global pairwise alignment should be performed.
setLinearGaps(int) - Method in class Alignment
Score gaps in this Alignment using a linear model.
setLocalAlignment() - Method in class Alignment
Indicate that a local pairwise alignment should be performed.
setMatrixScoring(String) - Method in class Alignment
When aligning two characters, one from each genomic sequence, the alignment score of the two characters should be determined from a matrix of scores found in a file with the specified name.

T

toString() - Method in class Alignment
Returns a String representation of this Alignment.
A B C G M O S T