Uses of Class
jaligner.matrix.Matrix

Packages that use Matrix

jaligner	Core classes for the implementation of Smith-Waterman-Gotoh algorithm
jaligner.matrix	Scoring matrices package.

Uses of Matrix in jaligner

Methods in jaligner that return Matrix

Matrix

Alignment.getMatrix()

Methods in jaligner with parameters of type Matrix

static Alignment	SmithWatermanGotoh.align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) Aligns two sequences by Smith-Waterman (local)
static Alignment	NeedlemanWunschGotoh.align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) Aligns two sequences by Needleman-Wunsch (global)
static Alignment	NeedlemanWunsch.align(Sequence s1, Sequence s2, Matrix matrix, float gap) Aligns two sequences by Needleman-Wunsch (global)
void	Alignment.setMatrix(Matrix matrix)

Uses of Matrix in jaligner.matrix

Methods in jaligner.matrix that return Matrix

static Matrix	MatrixLoader.load(java.lang.String matrix) Loads scoring matrix from Jar file or file system.
static Matrix	MatrixLoader.load(NamedInputStream nis) Loads scoring matrix from InputStream
static Matrix	MatrixGenerator.generate(float match, float mismatch) Returns scoring matrix from a fixed match/mismatch scoring scheme.