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

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

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.search.io
org.biojava.nbio.phylo
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.io	Input and Output of Structures

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

Class	Description
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.
ProfilePair	Defines a data structure for the results of the alignment of a pair of Profiles.
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.alignment.routines

Class	Description
AlignedSequence.Step	Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
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.alignment.template

Class	Description
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.
ProfilePair	Defines a data structure for the results of the alignment of a pair of Profiles.
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

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.

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

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.structure.align.ce

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.structure.cluster

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.structure.io

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