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

Packages that use org.biojava.nbio.core.alignment.template

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.search.io

Classes in org.biojava.nbio.core.alignment.template used by org.biojava.nbio.core.alignment

Class	Description
AlignedSequence	Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step	Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
Profile	Defines a data structure for the results of sequence alignment.
Profile.StringFormat	List of output formats.
ProfilePair	Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileView	Defines a data structure for a view of sequence alignment.
SequencePair	Defines a data structure for the results of pairwise sequence alignment.
SubstitutionMatrix	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.

Classes in org.biojava.nbio.core.alignment.template used by org.biojava.nbio.core.alignment.matrices

Class	Description
SubstitutionMatrix	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.

Classes in org.biojava.nbio.core.alignment.template used by org.biojava.nbio.core.alignment.template

Class	Description
AlignedSequence	Defines a data structure for a Sequence within an alignment.
AlignedSequence.Step	Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
MutableProfile	Defines a mutable (editable) data structure for a Profile.
Profile	Defines a data structure for the results of sequence alignment.
Profile.StringFormat	List of output formats.
ProfilePair	Defines a data structure for the results of the alignment of a pair of Profiles.
ProfileView	Defines a data structure for a view of sequence alignment.
SequencePair	Defines a data structure for the results of pairwise sequence alignment.
SubstitutionMatrix	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.

Classes in org.biojava.nbio.core.alignment.template used by org.biojava.nbio.core.search.io

Class	Description
SequencePair	Defines a data structure for the results of pairwise sequence alignment.