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