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

Packages that use SubstitutionMatrix

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template
org.biojava.nbio.phylo
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.cluster

Uses of SubstitutionMatrix in org.biojava.nbio.alignment

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

Modifier and Type	Method	Description
static <S extends Sequence<C>, C extends Compound> List<SequencePair<S,C>>	Alignments.getAllPairsAlignments(List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence alignment for all Sequence pairs in the given List.
static <S extends Sequence<C>, C extends Compound> List<PairwiseSequenceScorer<S,C>>	Alignments.getAllPairsScorers(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
static <S extends Sequence<C>, C extends Compound> double[]	Alignments.getAllPairsScores(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence pair score for all Sequence pairs in the given List.
static <S extends Sequence<C>, C extends Compound> PairwiseSequenceAligner<S,C>	Alignments.getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which constructs a pairwise sequence aligner.
static <S extends Sequence<C>, C extends Compound> SequencePair<S,C>	Alignments.getPairwiseAlignment(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method which computes a sequence alignment for the given Sequence pair.
static <S extends Sequence<C>, C extends Compound> Profile<S,C>	Alignments.getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.

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

Modifier	Constructor	Description
	NeedlemanWunsch(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
	SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
	SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
	SimpleProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
	SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment.
	SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise local sequence alignment.
	SubstitutionMatrixScorer(SequencePair<S,C> pair, SubstitutionMatrix<C> matrix)

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

Constructors in org.biojava.nbio.alignment.routines with parameters of type SubstitutionMatrix

Modifier	Constructor	Description
	AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
	AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int[] anchors)	Prepares for a pairwise global sequence alignment.
	GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
	GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection)	Prepares for a pairwise global sequence alignment.

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

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

Modifier and Type	Method	Description
SubstitutionMatrix<C>	AbstractMatrixAligner.getSubstitutionMatrix()	Returns the substitution matrix.

Methods in org.biojava.nbio.alignment.template with parameters of type SubstitutionMatrix

Modifier and Type	Method	Description
void	AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix<C> subMatrix)	Sets the substitution matrix.

Constructors in org.biojava.nbio.alignment.template with parameters of type SubstitutionMatrix

Modifier	Constructor	Description
protected	AbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for an alignment.
protected	AbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local)	Prepares for an alignment.
protected	AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
protected	AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local)	Prepares for a pairwise sequence alignment.
protected	AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
protected	AbstractProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment.

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 final 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.

Uses of SubstitutionMatrix in org.biojava.nbio.phylo

Methods in org.biojava.nbio.phylo with parameters of type SubstitutionMatrix

Modifier and Type	Method	Description
static <C extends Sequence<D>, D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.dissimilarityScore(MultipleSequenceAlignment<C,D> msa, SubstitutionMatrix<D> M)	The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
static <C extends Sequence<D>, D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.fractionalDissimilarityScore(MultipleSequenceAlignment<C,D> msa, SubstitutionMatrix<D> M)	The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.

Uses of SubstitutionMatrix in org.biojava.nbio.structure.align.ce

Fields in org.biojava.nbio.structure.align.ce declared as SubstitutionMatrix

Modifier and Type	Field	Description
protected SubstitutionMatrix<AminoAcidCompound>	CeParameters.substitutionMatrix

Methods in org.biojava.nbio.structure.align.ce that return SubstitutionMatrix

Modifier and Type	Method	Description
SubstitutionMatrix<AminoAcidCompound>	CeParameters.getSubstitutionMatrix()	Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

Methods in org.biojava.nbio.structure.align.ce with parameters of type SubstitutionMatrix

Modifier and Type	Method	Description
void	CeParameters.setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)	Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

Uses of SubstitutionMatrix in org.biojava.nbio.structure.cluster

Methods in org.biojava.nbio.structure.cluster with parameters of type SubstitutionMatrix

Modifier and Type	Method	Description
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix)	Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).