org.biojava.bio.symbol
Interface CrossProductAlphabet
- public interface CrossProductAlphabet
- extends Alphabet
Cross product of a list of alphabets. This is provided primarily
to assist in the implemention of a `multi-headed' hidden markov
model. For instance, in a pair HMM intended for aligning DNA
sequence, the emmision alphabet will be (DNA, gap) x (DNA, gap).
To actualy make a CrossProductAlphabet, either roll your own, or use
the CrossProductAlphabetFactory object.
- Author:
- Thomas Down
Method Summary |
java.util.List |
getAlphabets()
Return an ordered List of the alphabets which make up this
compound alphabet. |
CrossProductSymbol |
getSymbol(java.util.List rl)
Get a symbol from the CrossProductAlphabet which corresponds
to the specified ordered list of symbols. |
getAlphabets
public java.util.List getAlphabets()
- Return an ordered List of the alphabets which make up this
compound alphabet. The returned list should be immutable.
getSymbol
public CrossProductSymbol getSymbol(java.util.List rl)
throws IllegalSymbolException
- Get a symbol from the CrossProductAlphabet which corresponds
to the specified ordered list of symbols.
- Parameters:
rl
- A list of symbols.- Throws:
- IllegalSymbolException - if the members of rl are
not Symbols over the alphabets returned from
getAlphabets