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

Packages that use SequencePair

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.search.io
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of SequencePair in org.biojava.nbio.alignment

Methods in org.biojava.nbio.alignment that return SequencePair

Modifier and Type	Method and Description
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.

Methods in org.biojava.nbio.alignment that return types with arguments of type SequencePair

Modifier and Type	Method and 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.

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

Constructor and Description
FractionalIdentityScorer(SequencePair<S,C> pair) Creates a fractional identity scorer for an aligned pair of sequences.
FractionalSimilarityScorer(SequencePair<S,C> pair) Creates a fractional similarity scorer for an aligned pair of sequences.
SubstitutionMatrixScorer(SequencePair<S,C> pair, SubstitutionMatrix<C> matrix)

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

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

Modifier and Type	Field and Description
protected SequencePair<S,C>	AbstractPairwiseSequenceAligner.pair

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

Modifier and Type	Method and Description
SequencePair<S,C>	CallablePairwiseSequenceAligner.call()
SequencePair<S,C>	AbstractPairwiseSequenceAligner.getPair()
SequencePair<S,C>	PairwiseSequenceAligner.getPair() Returns sequence alignment pair.

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

Classes in org.biojava.nbio.core.alignment that implement SequencePair

Modifier and Type	Class and Description
class	SimpleSequencePair<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of pairwise sequence alignment.

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

Subinterfaces of SequencePair in org.biojava.nbio.core.alignment.template

Modifier and Type	Interface and Description
interface	MutableSequencePair<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for the results of pairwise sequence alignment.

Uses of SequencePair in org.biojava.nbio.core.search.io

Methods in org.biojava.nbio.core.search.io that return SequencePair

Modifier and Type	Method and Description
SequencePair<S,C>	Hsp.getAlignment()

Uses of SequencePair in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io with parameters of type SequencePair

Modifier and Type	Method and Description
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2) Provided only for convenience.