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Hierarchy For Package org.biojava3.alignment
Package Hierarchies:
All Packages
Class Hierarchy
java.lang.Object
org.biojava3.alignment.template.
AbstractScorer
(implements org.biojava3.alignment.template.
Scorer
)
org.biojava3.alignment.template.
AbstractMatrixAligner
<S,C> (implements org.biojava3.alignment.template.
MatrixAligner
<S,C>)
org.biojava3.alignment.template.
AbstractPairwiseSequenceAligner
<S,C> (implements org.biojava3.alignment.template.
PairwiseSequenceAligner
<S,C>)
org.biojava3.alignment.
NeedlemanWunsch
<S,C>
org.biojava3.alignment.
SmithWaterman
<S,C>
org.biojava3.alignment.template.
AbstractProfileProfileAligner
<S,C> (implements org.biojava3.alignment.template.
ProfileProfileAligner
<S,C>)
org.biojava3.alignment.
SimpleProfileProfileAligner
<S,C>
org.biojava3.alignment.
FractionalIdentityScorer
<S,C> (implements org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava3.alignment.
FractionalIdentityInProfileScorer
<S,C> (implements org.biojava3.alignment.template.
PairInProfileScorer
<S,C>)
org.biojava3.alignment.
FractionalSimilarityScorer
<S,C> (implements org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava3.alignment.
FractionalSimilarityInProfileScorer
<S,C> (implements org.biojava3.alignment.template.
PairInProfileScorer
<S,C>)
org.biojava3.alignment.
StandardRescoreRefiner
<S,C> (implements org.biojava3.alignment.template.
RescoreRefiner
<S,C>)
org.biojava3.alignment.
Alignments
org.biojava3.alignment.
GuideTree
<S,C> (implements java.lang.Iterable<T>)
org.biojava3.alignment.
GuideTree.Node
(implements org.biojava3.alignment.template.
GuideTreeNode
<S,C>)
org.biojava3.alignment.
SimpleAlignedSequence
<S,C> (implements org.biojava3.alignment.template.
AlignedSequence
<S,C>)
org.biojava3.alignment.
SimpleGapPenalty
(implements org.biojava3.alignment.template.
GapPenalty
)
org.biojava3.alignment.
SimpleProfile
<S,C> (implements org.biojava3.alignment.template.
Profile
<S,C>)
org.biojava3.alignment.
SimpleProfilePair
<S,C> (implements org.biojava3.alignment.template.
ProfilePair
<S,C>)
org.biojava3.alignment.
SimpleSequencePair
<S,C> (implements org.biojava3.alignment.template.
SequencePair
<S,C>)
org.biojava3.alignment.
SimpleSubstitutionMatrix
<C> (implements org.biojava3.alignment.template.
SubstitutionMatrix
<C>)
org.biojava3.alignment.
SubstitutionMatrixHelper
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava3.alignment.
Alignments.PairInProfileScorerType
org.biojava3.alignment.
Alignments.PairwiseSequenceAlignerType
org.biojava3.alignment.
Alignments.PairwiseSequenceScorerType
org.biojava3.alignment.
Alignments.ProfileProfileAlignerType
org.biojava3.alignment.
Alignments.RefinerType
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