|
Class Summary |
| AbstractFixedLengthSequenceModel |
Abstract stub implementation of the FixedLengthSequenceModel interface. |
| Alphabet |
Class representing an alphabet of symbols. |
| AlphabetRegistry |
Central (singleton) registry of alphabets. |
| AtomicCharSymbol |
An atomic char symbol is an atomic symbol associated to a character 'image'. |
| ByteArraySequence |
Implementation of Sequence in which the sequence of symbols
is translated into an array of bytes s.t. |
| CharSymbol |
Abstract class for symbols associated to a character (either atomic or
higher order). |
| DNAAlphabet |
Class representing the basic DNA nucleotide alphabet {a,g,c,t}. |
| ExtendedDNAAlphabet |
Class representing the extended DNA nucleotide alphabet. |
| FactorTrie |
A factor trie is a trie representing all factors of a given length
of a set of sequences. |
| GibbsMotifSiteSampler |
Implementation of the simple Gibbs motif site sampler using
motif trie-based K-order Markov models. |
| HighOrderCharSymbol |
A high order symbol that is associated to a character 'image'. |
| MarkovFixedLengthSequenceModel |
Probabilistic model for sequences of a fixed length W, in which
they are assumed to be generated from a non-homogeneous Markov chain of
order K, that is
Pr(x1...xW) = prod_{i=1}^W Pr(xi|xi-1...xi-K).
|
| Sequence |
Abstract class representing a sequence of symbols from a fixed alphabet. |
| SequenceFactory |
Singleton sequence factory. |
| SymbolArraySequence |
Basic high-level implementation of Sequence using an array of symbols. |
| Trie |
Class representing an extended character trie over a given alphabet. |
| TrieForest |
Class representing a trie forest. |
| UniformFixedLengthSequenceModel |
This class represents a uniform model for words of a fixed length W
over a given alphabet A. |