Interface Alphabet

    • Field Detail

      • SYMBOLS

        static final ChangeType SYMBOLS

        This ChangeType indicates that some symbols have been added or removed from the alphabet. The current and previous fields should indicate what symbols were there originally, and what they have been replaced with.

        If the alphabet wishes to propagate that the symbol has changed state, then previous and current should be null, but the chainedEvent property should rever to the ChangeEvent on the unerlying Symbol.

      • PARSERS

        static final ChangeType PARSERS
        This signals that the available parsers have changed. If a parser is added, it will appear in getChanged(). If it is removed, it will appear in getPrevious().
    • Method Detail

      • getName

        String getName()
        Get the name of the alphabet.
        the name as a string.
      • getAlphabets

        Return an ordered List of the alphabets which make up a compound alphabet. For simple alphabets, this will return a singleton list of itself. The returned list should be immutable.
        a List of alphabets
      • getSymbol

        Symbol getSymbol​(List<Symbol> rl)
                  throws IllegalSymbolException

        Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.

        The symbol at i in the list must be a member of the i'th alphabet in getAlphabets. If all of the symbols in rl are atomic, then the resulting symbol will also be atomic. If any one of them is an ambiguity symbol then the resulting symbol will be the appropriate ambiguity symbol.

        rl - A list of Symbol instances
        IllegalSymbolException - if the members of rl are not Symbols over the alphabets returned from getAlphabets
      • getAmbiguity

        Symbol getAmbiguity​(Set<Symbol> syms)
                     throws IllegalSymbolException

        Get a symbol that represents the set of symbols in syms.

        Syms must be a set of Symbol instances each of which is contained within this alphabet. This method is used to retrieve ambiguity symbols.

        syms - the Set of Symbols that will be found in getMatches of the returned symbol
        a Symbol (possibly fly-weighted) for the Set of symbols in syms
      • getGapSymbol

        Symbol getGapSymbol()

        Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.

        In general, this will be a BasisSymbol that represents a list of AlphabetManager.getGapSymbol() the same length as the getAlphabets list.

        the appropriate gap Symbol instance
      • contains

        boolean contains​(Symbol s)

        Returns whether or not this Alphabet contains the symbol.

        An alphabet contains an ambiguity symbol iff the ambiguity symbol's getMatches() returns an alphabet that is a proper sub-set of this alphabet. That means that every one of the symbols that could match the ambiguity symbol is also a member of this alphabet.

        s - the Symbol to check
        boolean true if the Alphabet contains the symbol and false otherwise
      • validate

        void validate​(Symbol s)
               throws IllegalSymbolException

        Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

        This function is used all over the code to validate symbols as they enter a method. Also, the code is littered with catches for IllegalSymbolException. There is a preferred style of handling this, which should be covererd in the package documentation.

        s - the Symbol to validate
        IllegalSymbolException - if r is not contained in this alphabet
      • getTokenization

        SymbolTokenization getTokenization​(String name)
                                    throws BioException

        Get a SymbolTokenization by name.

        The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.

        Every alphabet should have a SymbolTokenzation under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolTokenization under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behavior of the returned SymbolTokenization is not defined here.

        A SymbolTokenization under the name 'default' should be defined for all sequences, that determines the behavior when printing out a sequence. Standard behavior is to define the 'token' SymbolTokenization as default if it exists, else to define the 'name' SymbolTokenization as the default, but others are possible.

        name - the name of the parser
        a parser for that name
        NoSuchElementException - if the name is unknown
        BioException - if for any reason the tokenization could not be built