Uses of Interface
org.biojava.nbio.core.alignment.template.SequencePair
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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 -
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Uses of SequencePair in org.biojava.nbio.alignment
Methods in org.biojava.nbio.alignment that return SequencePair Modifier and Type Method 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 givenSequence
pair.Methods in org.biojava.nbio.alignment that return types with arguments of type SequencePair 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)
Constructors in org.biojava.nbio.alignment with parameters of type SequencePair Constructor 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)
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Uses of SequencePair in org.biojava.nbio.alignment.template
Fields in org.biojava.nbio.alignment.template declared as SequencePair Modifier and Type Field Description protected SequencePair<S,C>
AbstractPairwiseSequenceAligner. pair
Methods in org.biojava.nbio.alignment.template that return SequencePair Modifier and Type Method 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 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 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 Description SequencePair<S,C>
Hsp. getAlignment()
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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 Description static AFPChain
FastaAFPChainConverter. fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2)
Provided only for convenience.
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