Package org.biojava.nbio.core.alignment.template

Interface Summary

Interface	Description
AlignedSequence<S extends Sequence<C>,C extends Compound>	Defines a data structure for a Sequence within an alignment.
MutableAlignedSequence<S extends Sequence<C>,C extends Compound>	Defines a mutable (editable) data structure for an AlignedSequence.
MutableProfile<S extends Sequence<C>,C extends Compound>	Defines a mutable (editable) data structure for a Profile.
MutableProfilePair<S extends Sequence<C>,C extends Compound>	Defines a mutable (editable) data structure for a ProfilePair.
MutableSequencePair<S extends Sequence<C>,C extends Compound>	Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
Profile<S extends Sequence<C>,C extends Compound>	Defines a data structure for the results of sequence alignment.
ProfilePair<S extends Sequence<C>,C extends Compound>	Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileView<S extends Sequence<C>,C extends Compound>	Defines a data structure for a view of sequence alignment.
SequencePair<S extends Sequence<C>,C extends Compound>	Defines a data structure for the results of pairwise sequence alignment.
SubstitutionMatrix<C extends Compound>	Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.

Enum Summary

Enum	Description
AlignedSequence.Step	Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
Profile.StringFormat	List of output formats.