Uses of Class
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
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Packages that use Alignments.PairwiseSequenceAlignerType Package Description org.biojava.nbio.alignment org.biojava.nbio.structure.cluster -
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Uses of Alignments.PairwiseSequenceAlignerType in org.biojava.nbio.alignment
Methods in org.biojava.nbio.alignment that return Alignments.PairwiseSequenceAlignerType Modifier and Type Method Description static Alignments.PairwiseSequenceAlignerType
Alignments.PairwiseSequenceAlignerType. valueOf(String name)
Returns the enum constant of this type with the specified name.static Alignments.PairwiseSequenceAlignerType[]
Alignments.PairwiseSequenceAlignerType. values()
Returns an array containing the constants of this enum type, in the order they are declared.Methods in org.biojava.nbio.alignment with parameters of type Alignments.PairwiseSequenceAlignerType 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)
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 givenSequence
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Uses of Alignments.PairwiseSequenceAlignerType in org.biojava.nbio.structure.cluster
Methods in org.biojava.nbio.structure.cluster with parameters of type Alignments.PairwiseSequenceAlignerType 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).
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