## org.biojava.bio.symbol
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:
  Serialized Form

Nested Class Summary
`static class` `IntegerAlphabet.IntegerSymbol` A single int value.
`static class` `IntegerAlphabet.SubIntegerAlphabet` A class to represent a finite contiguous subset of the infinite IntegerAlphabet

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Field Summary
`static IntegerAlphabet` `INSTANCE` The singleton instance of the IntegerAlphabet class.

Fields inherited from interface org.biojava.bio.symbol.Alphabet
`EMPTY_ALPHABET, PARSERS, SYMBOLS`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Method Summary
`boolean` `contains(Symbol s)` Returns whether or not this Alphabet contains the symbol.
`static SymbolList` `fromArray(int[] iArray)` Retrieve a SymbolList view of an array of integers.
`List` `getAlphabets()` Return an ordered List of the alphabets which make up a compound alphabet.
`Symbol` `getAmbiguity(Set symSet)` Get a symbol that represents the set of symbols in syms.
`Annotation` `getAnnotation()` Should return the associated annotation object.
`Symbol` `getGapSymbol()` Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
`static IntegerAlphabet` `getInstance()` Retrieve the single IntegerAlphabet instance.
`String` `getName()` Get the name of the alphabet.
`static IntegerAlphabet.SubIntegerAlphabet` `getSubAlphabet(int min, int max)` Construct a finite contiguous subset of the `IntegerAlphabet`.
`IntegerAlphabet.IntegerSymbol` `getSymbol(int val)` Retrieve the Symbol for an int.
`Symbol` `getSymbol(List symList)` Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
`SymbolTokenization` `getTokenization(String name)` Creates a new parser (Mark Schreiber 3 May 2001).
`void` `validate(Symbol s)` Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

Methods inherited from class org.biojava.utils.Unchangeable
`addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Field Detail

### INSTANCE

    public static IntegerAlphabet INSTANCE

  The singleton instance of the IntegerAlphabet class.

Method Detail

### getSubAlphabet

    public static IntegerAlphabet.SubIntegerAlphabet getSubAlphabet(int min,
                                                                    int max)
                                                             throws IllegalArgumentException

  Construct a finite contiguous subset of the `IntegerAlphabet`. Useful for making CrossProductAlphabets with other `FiniteAlphabet`s.

  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 < 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

    public IntegerAlphabet.IntegerSymbol getSymbol(int val)

  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

    public Annotation 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

    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.