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Hierarchy For Package org.biojava.nbio.alignment.template
Package Hierarchies:
All Packages
Class Hierarchy
java.lang.Object
org.biojava.nbio.alignment.template.
AbstractScorer
(implements org.biojava.nbio.alignment.template.
Scorer
)
org.biojava.nbio.alignment.template.
AbstractMatrixAligner
<S,C> (implements org.biojava.nbio.alignment.template.
MatrixAligner
<S,C>)
org.biojava.nbio.alignment.template.
AbstractPairwiseSequenceAligner
<S,C> (implements org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C>)
org.biojava.nbio.alignment.template.
AbstractProfileProfileAligner
<S,C> (implements org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C>)
org.biojava.nbio.alignment.template.
CallablePairwiseSequenceAligner
<S,C> (implements java.util.concurrent.Callable<V>)
org.biojava.nbio.alignment.template.
CallablePairwiseSequenceScorer
<S,C> (implements java.util.concurrent.Callable<V>)
org.biojava.nbio.alignment.template.
CallableProfileProfileAligner
<S,C> (implements java.util.concurrent.Callable<V>)
Interface Hierarchy
org.biojava.nbio.core.sequence.template.
Accessioned
org.biojava.nbio.core.sequence.template.
Sequence
<C> (also extends java.lang.Iterable<T>)
org.biojava.nbio.alignment.template.
AlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
GapPenalty
org.biojava.nbio.alignment.template.
HierarchicalClusterer
<S,C>
java.lang.Iterable<T>
org.biojava.nbio.alignment.template.
Profile
<S,C>
org.biojava.nbio.alignment.template.
MutableProfile
<S,C>
org.biojava.nbio.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava.nbio.alignment.template.
ProfilePair
<S,C>)
org.biojava.nbio.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava.nbio.alignment.template.
SequencePair
<S,C>)
org.biojava.nbio.alignment.template.
ProfilePair
<S,C>
org.biojava.nbio.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava.nbio.alignment.template.
MutableProfile
<S,C>)
org.biojava.nbio.alignment.template.
ProfileView
<S,C>
org.biojava.nbio.alignment.template.
SequencePair
<S,C>
org.biojava.nbio.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava.nbio.alignment.template.
MutableProfile
<S,C>)
org.biojava.nbio.core.sequence.template.
Sequence
<C> (also extends org.biojava.nbio.core.sequence.template.
Accessioned
)
org.biojava.nbio.alignment.template.
AlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
Scorer
org.biojava.nbio.alignment.template.
Aligner
<S,C>
org.biojava.nbio.alignment.template.
MatrixAligner
<S,C>
org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava.nbio.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava.nbio.alignment.template.
RescoreRefiner
<S,C>
org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>
org.biojava.nbio.alignment.template.
PairInProfileScorer
<S,C>
org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>
org.biojava.nbio.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>)
org.biojava.nbio.alignment.template.
SubstitutionMatrix
<C>
javax.swing.tree.TreeNode
org.biojava.nbio.alignment.template.
GuideTreeNode
<S,C>
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.alignment.template.
GapPenalty.Type
org.biojava.nbio.alignment.template.
Profile.StringFormat
org.biojava.nbio.alignment.template.
AlignedSequence.Step
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