Search Java Classes and Packages
#Org.biojava.nbio.core.alignment Classes and Interfaces - 23 results found.
| Name | Description | Type | Package | Framework |
| AAindexFactory | Factory class to get Providers for substitution matrices the are provided by the AAINDEX database. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
| AAIndexFileParser | Class | org.biojava.nbio.core.alignment.matrices | BioJava | |
| AAIndexProvider | Interface | org.biojava.nbio.core.alignment.matrices | BioJava | |
| 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 |
| DefaultAAIndexProvider | The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directoryAuthor:Andreas Prlic | Class | org.biojava.nbio.core.alignment.matrices | 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 |
| ScaledSubstitutionMatrix | The biojava-alignment module represents substitution matrices with short values. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
| SequencePair | Defines a data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| SimpleAlignedSequence | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleProfile | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleProfilePair | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleSequencePair | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleSubstitutionMatrix | Compound in a sequence for another. | Class | org.biojava.nbio.core.alignment.matrices | 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 |
| SubstitutionMatrixHelper | Static utility to access substitution matrices that come bundled with BioJava. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |