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 and 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 and 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 and 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()
SubstitutionMatrix<AminoAcidCompound>	DefaultAAIndexProvider.getMatrix(String matrixName)
SubstitutionMatrix<AminoAcidCompound>	AAIndexProvider.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 and 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 and Description
SubstitutionMatrix<C>	SubstitutionMatrix.normalizeMatrix(short scale) Rescales the matrix so that to getMaxValue() - getMinValue() = scale.