Package org.biojava.bio.symbol

Class IntegerAlphabet

  • All Implemented Interfaces:
    Serializable, Annotatable, Alphabet, Changeable
    public final class IntegerAlphabet
extends Unchangeable
implements Alphabet, Serializable

    An efficient implementation of an Alphabet over the infinite set of integer values.

    This class can be used to represent lists of integer numbers as a SymbolList with the alphabet IntegerAlphabet. These lists can then be annotated with features, or fed into dynamic-programming algorithms, or processed as per any other SymbolList object.

    Object identity should be used to decide if two IntegerSymbol objects are the same. IntegerAlphabet ensures that all IntegerSymbol instances are canonicalized.

    Author:
    Matthew Pocock, Mark Schreiber, Thomas Down
    See Also:
    Serialized Form

    • Method Detail

      • fromArray

        public static SymbolList fromArray​(int[] iArray)
        Retrieve a SymbolList view of an array of integers.

        The returned object is a view onto the underlying array, and does not copy it. Changes made to the original array will alter the symulting SymbolList.

        Parameters:
        iArray - the array of integers to view
        Returns:
        a SymbolList over the IntegerAlphabet that represent the values in iArray

      • getInstance

        public static IntegerAlphabet getInstance()
        Retrieve the single IntegerAlphabet instance.
        Returns:
        the singleton IntegerAlphabet instance

      • 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

      • 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 symList)
                 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:
        symList - 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 symSet)
                    throws IllegalSymbolException
        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:
        symSet - 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
        Throws:
        IllegalSymbolException

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

      • 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.

      • getTokenization

        public SymbolTokenization getTokenization​(String name)
        Creates a new parser (Mark Schreiber 3 May 2001).
        Specified by:
        getTokenization in interface Alphabet
        Parameters:
        name - Currently only "token" is supported. You may also use "default" as a synonym of "token"
        Returns:
        an IntegerParser.