Package | Description |
---|---|
org.biojava.nbio.alignment | |
org.biojava.nbio.alignment.template |
Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
---|---|
static <S extends Sequence<C>,C extends Compound> |
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.
|
Constructor and Description |
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StandardRescoreRefiner(Alignments.PairInProfileScorerType pips,
Alignments.ProfileProfileAlignerType ppa) |
Modifier and Type | Method and 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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