Class DoubleAlphabet.SubDoubleAlphabet

    • Method Detail

      • readResolve

        protected Object readResolve()
                              throws ObjectStreamException
        To prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.
        Throws:
        ObjectStreamException
      • getName

        public String getName()
        Description copied from interface: Alphabet
        Get the name of the alphabet.
        Specified by:
        getName in interface Alphabet
        Returns:
        the name as a string.
      • getAlphabets

        public List getAlphabets()
        Description copied from interface: Alphabet
        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.
        Specified by:
        getAlphabets in interface Alphabet
        Returns:
        a List of alphabets
      • getSymbol

        public Symbol getSymbol​(List rl)
                         throws IllegalSymbolException
        Description copied from interface: Alphabet

        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.

        Specified by:
        getSymbol in interface Alphabet
        Parameters:
        rl - A list of Symbol instances
        Throws:
        IllegalSymbolException - if the members of rl are not Symbols over the alphabets returned from getAlphabets
      • getAmbiguity

        public Symbol getAmbiguity​(Set syms)
        Description copied from interface: Alphabet

        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.

        Specified by:
        getAmbiguity in interface Alphabet
        Parameters:
        syms - the Set of Symbols that will be found in getMatches of the returned symbol
        Returns:
        a Symbol (possibly fly-weighted) for the Set of symbols in syms
      • getGapSymbol

        public Symbol getGapSymbol()
        Description copied from interface: Alphabet

        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.

        Specified by:
        getGapSymbol in interface Alphabet
        Returns:
        the appropriate gap Symbol instance
      • contains

        public boolean contains​(Symbol s)
        Description copied from interface: Alphabet

        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.

        Specified by:
        contains in interface Alphabet
        Parameters:
        s - the Symbol to check
        Returns:
        boolean true if the Alphabet contains the symbol and false otherwise
      • validate

        public void validate​(Symbol sym)
                      throws IllegalSymbolException
        Description copied from interface: Alphabet

        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.

        Specified by:
        validate in interface Alphabet
        Parameters:
        sym - the Symbol to validate
        Throws:
        IllegalSymbolException - if r is not contained in this alphabet
      • getTokenization

        public SymbolTokenization getTokenization​(String name)
                                           throws BioException
        Description copied from interface: Alphabet

        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.

        Specified by:
        getTokenization in interface Alphabet
        Parameters:
        name - the name of the parser
        Returns:
        a parser for that name
        Throws:
        BioException - if for any reason the tokenization could not be built