Uses of Class
org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
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Packages that use Alignments.ProfileProfileAlignerType Package Description org.biojava.nbio.alignment org.biojava.nbio.alignment.template -
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Uses of Alignments.ProfileProfileAlignerType in org.biojava.nbio.alignment
Methods in org.biojava.nbio.alignment that return Alignments.ProfileProfileAlignerType Modifier and Type Method Description Alignments.ProfileProfileAlignerType
StandardRescoreRefiner. getProfileProfileAligner()
static Alignments.ProfileProfileAlignerType
Alignments.ProfileProfileAlignerType. valueOf(String name)
Returns the enum constant of this type with the specified name.static Alignments.ProfileProfileAlignerType[]
Alignments.ProfileProfileAlignerType. 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.ProfileProfileAlignerType Modifier and Type Method Description 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 Alignments.ProfileProfileAlignerType Constructor Description StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)
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Uses of Alignments.ProfileProfileAlignerType in org.biojava.nbio.alignment.template
Methods in org.biojava.nbio.alignment.template that return Alignments.ProfileProfileAlignerType Modifier and Type Method Description Alignments.ProfileProfileAlignerType
PartitionRefiner. getProfileProfileAligner()
Returns class type of profile-profile alignment subroutine.Alignments.ProfileProfileAlignerType
RescoreRefiner. getProfileProfileAligner()
Returns class type of profile-profile alignment subroutine.
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