Uses of Interface
org.biojava.nbio.alignment.template.GapPenalty

Packages that use GapPenalty

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template
org.biojava.nbio.structure.cluster

Uses of GapPenalty in org.biojava.nbio.alignment

Classes in org.biojava.nbio.alignment that implement GapPenalty

Modifier and Type	Class	Description
class	SimpleGapPenalty	Implements a data structure for the gap penalties used during a sequence alignment routine.

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

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 GapPenalty

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.

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

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

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 GapPenalty in org.biojava.nbio.alignment.template

Fields in org.biojava.nbio.alignment.template declared as GapPenalty

Modifier and Type	Field	Description
protected GapPenalty	AbstractMatrixAligner.gapPenalty

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

Modifier and Type	Method	Description
GapPenalty	AbstractMatrixAligner.getGapPenalty()	Returns the gap penalties.

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

Modifier and Type	Method	Description
void	AbstractMatrixAligner.setGapPenalty(GapPenalty gapPenalty)	Sets the gap penalties.

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

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 GapPenalty in org.biojava.nbio.structure.cluster

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

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).