Class IntegerAlphabet

java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.symbol.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:
  • Field Details

  • Method Details

    • getSubAlphabet

      Construct a finite contiguous subset of the IntegerAlphabet. Useful for making CrossProductAlphabets with other FiniteAlphabets.
      Parameters:
      min - the lower bound of the Alphabet
      max - the upper bound of the Alphabet
      Returns:
      A FiniteAlphabet from min to max inclusive.
      Throws:
      IllegalArgumentException - if max invalid input: '<' min
    • 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
    • getSymbol

      Retrieve the Symbol for an int.
      Parameters:
      val - the int to view
      Returns:
      a IntegerSymbol embodying val
    • 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
    • getAnnotation

      Description copied from interface: Annotatable
      Should return the associated annotation object.
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      an Annotation object, never null
    • 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

      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

      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.