Uses of Class
org.biojava.bio.alignment.SubstitutionMatrix

Packages that use SubstitutionMatrix

org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.structure.io	Input and Output of Structures

Uses of SubstitutionMatrix in org.biojava.bio.alignment

Fields in org.biojava.bio.alignment declared as SubstitutionMatrix

protected SubstitutionMatrix

NeedlemanWunsch.subMatrix A matrix with the size length(alphabet) times length(alphabet)

Methods in org.biojava.bio.alignment that return SubstitutionMatrix

static SubstitutionMatrix	SubstitutionMatrix.getSubstitutionMatrix(BufferedReader reader) This constructor can be used to guess the alphabet of this substitution matrix.
SubstitutionMatrix	SubstitutionMatrix.normalizeMatrix() With this method you can get a “normalized” SubstitutionMatrix object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten.

Methods in org.biojava.bio.alignment with parameters of type SubstitutionMatrix

void	NeedlemanWunsch.setSubstitutionMatrix(SubstitutionMatrix matrix) Sets the substitution matrix to be used to the specified one.

Constructors in org.biojava.bio.alignment with parameters of type SubstitutionMatrix

NeedlemanWunsch(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix subMat)
Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.

SmithWaterman(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object.

Uses of SubstitutionMatrix in org.biojava.bio.structure.io

Methods in org.biojava.bio.structure.io that return SubstitutionMatrix

static SubstitutionMatrix

SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet)