Uses of Interface
org.biojava.nbio.core.alignment.template.SubstitutionMatrix

Packages that use SubstitutionMatrix

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template

Uses of SubstitutionMatrix in org.biojava.nbio.core.alignment

Fields in org.biojava.nbio.core.alignment declared as SubstitutionMatrix

Modifier and Type	Field	Description
protected static SubstitutionMatrix<AminoAcidCompound>	SimpleProfile.matrix

Uses of SubstitutionMatrix in org.biojava.nbio.core.alignment.matrices

Classes in org.biojava.nbio.core.alignment.matrices that implement SubstitutionMatrix

Modifier and Type	Class	Description
class	ScaledSubstitutionMatrix	The biojava-alignment module represents substitution matrices with short values.
class	SimpleSubstitutionMatrix<C extends Compound>	Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.

Methods in org.biojava.nbio.core.alignment.matrices that return SubstitutionMatrix

Modifier and Type	Method	Description
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix(String name)	Returns a substitution matrix for amino acids given by the name name.
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum100()	Returns Blosum 100 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum30()	Returns Blosum 30 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum35()	Returns Blosum 35 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum40()	Returns Blosum 40 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum45()	Returns Blosum 45 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum50()	Returns Blosum 50 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum55()	Returns Blosum 55 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum60()	Returns Blosum 60 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SimpleSubstitutionMatrix.getBlosum62()
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum62()	Returns Blosum 62 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum65()	Returns Blosum 65 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum70()	Returns Blosum 70 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum75()	Returns Blosum 75 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum80()	Returns Blosum 80 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum85()	Returns Blosum 85 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getBlosum90()	Returns Blosum 90 matrix by Henikoff & Henikoff
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getGonnet250()	Returns PAM 250 matrix by Gonnet, Cohen & Benner
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getIdentity()	Gets identity matrix where matches score 1 and mismatches score -10000
SubstitutionMatrix<AminoAcidCompound>	AAIndexProvider.getMatrix(String matrixName)	Gets a substitution matrix by its name.
SubstitutionMatrix<AminoAcidCompound>	DefaultAAIndexProvider.getMatrix(String matrixName)
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getMatrixFromAAINDEX(String matrixName)	Returns any matrix from the AAINDEX database file
static SubstitutionMatrix<NucleotideCompound>	SubstitutionMatrixHelper.getNuc4_2()	Returns Nuc 4.2 matrix by Lowe Only the first nucleotide sequence to align can contain ambiguous nucleotides
static SubstitutionMatrix<NucleotideCompound>	SubstitutionMatrixHelper.getNuc4_4()	Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides
static SubstitutionMatrix<AminoAcidCompound>	SubstitutionMatrixHelper.getPAM250()	Returns PAM 250 matrix by Dayhoff
SubstitutionMatrix<AminoAcidCompound>	ScaledSubstitutionMatrix.normalizeMatrix(short scale)
SubstitutionMatrix<C>	SimpleSubstitutionMatrix.normalizeMatrix(short scale)

Methods in org.biojava.nbio.core.alignment.matrices that return types with arguments of type SubstitutionMatrix

Modifier and Type	Method	Description
Map<String,SubstitutionMatrix<AminoAcidCompound>>	AAIndexFileParser.getMatrices()

Uses of SubstitutionMatrix in org.biojava.nbio.core.alignment.template

Methods in org.biojava.nbio.core.alignment.template that return SubstitutionMatrix

Modifier and Type	Method	Description
SubstitutionMatrix<C>	SubstitutionMatrix.normalizeMatrix(short scale)	Rescales the matrix so that to getMaxValue() - getMinValue() = scale.