Name | Description | Type | Package | Framework |
AlignedSequence | Defines a data structure for a Sequence within an alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
AlignedSequence .Step | Defines an alignment step in order to pass alignment information from an Aligner to a constructor. | Class | org.biojava.nbio.core.alignment.template | BioJava |
MutableAlignedSequence | Defines a mutable (editable) data structure for an AlignedSequence. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
MutableProfile | Defines a mutable (editable) data structure for a Profile. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
MutableProfilePair | Defines a mutable (editable) data structure for a ProfilePair. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
MutableSequencePair | Defines a mutable (editable) data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
Profile | Defines a data structure for the results of sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
Profile .StringFormat | List of output formats. | Class | org.biojava.nbio.core.alignment.template | BioJava |
ProfilePair | Defines a data structure for the results of the alignment of a pair of Profiles. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
ProfileView | Defines a data structure for a view of sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
SequencePair | Defines a data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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. | Interface | org.biojava.nbio.core.alignment.template | BioJava |