org.biojava.bio.symbol
Class Alphabet.EmptyAlphabet

java.lang.Object
  |
  +--org.biojava.bio.symbol.Alphabet.EmptyAlphabet
Enclosing class:
Alphabet

public static class Alphabet.EmptyAlphabet
extends java.lang.Object
implements FiniteAlphabet, java.io.Serializable

The class that implements Alphabet and is empty.

See Also:
Serialized Form

Inner classes inherited from class org.biojava.bio.symbol.Alphabet
Alphabet.EmptyAlphabet
 
Fields inherited from interface org.biojava.bio.symbol.Alphabet
EMPTY_ALPHABET
 
Constructor Summary
Alphabet.EmptyAlphabet()
           
 
Method Summary
 boolean contains(Symbol s)
          Returns whether or not this Alphabet contains the symbol.
 Annotation getAnnotation()
          Should return the associated annotation object.
 java.lang.String getName()
          Get the name of the alphabet.
 SymbolParser getParser(java.lang.String name)
          Get a parser by name.
 java.util.Iterator iterator()
          Retrieve an Iterator over the Symbols in this FiniteAlphabet.
 int size()
          The number of symbols in the alphabet.
 SymbolList symbols()
          A list of symbols that make up this alphabet.
 void validate(Symbol res)
          Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Alphabet.EmptyAlphabet

public Alphabet.EmptyAlphabet()
Method Detail

getName

public java.lang.String getName()
Description copied from interface: Alphabet
Get the name of the alphabet.
Tags copied from interface: Alphabet
Returns:
the name as a string.

getAnnotation

public Annotation getAnnotation()
Description copied from interface: Annotatable
Should return the associated annotation object.
Tags copied from interface: Annotatable
Returns:
an Annotation object, never null

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 getMemberAlphabet() returns an alphabe that is a propper sub-set of this alphabet. That means that every one of the symbols that could mach the ambiguity symbol is also a member of this alphabet.

Tags copied from interface: Alphabet
Parameters:
r - the Symbol to check
Returns:
boolean true if the Alphabet contains the symbol and false otherwise

validate

public void validate(Symbol res)
              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.

Tags copied from interface: Alphabet
Parameters:
r - the Symbol to validate
Throws:
IllegalSymbolException - if r is not contained in this alphabet

getParser

public SymbolParser getParser(java.lang.String name)
                       throws java.util.NoSuchElementException
Description copied from interface: Alphabet
Get a parser by name.

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

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

Tags copied from interface: Alphabet
Parameters:
name - the name of the parser
Returns:
a parser for that name
Throws:
java.util.NoSuchElementException - if the name is unknown
BioException - if for any reason the parser could not be built

size

public int size()
Description copied from interface: FiniteAlphabet
The number of symbols in the alphabet.
Specified by:
size in interface FiniteAlphabet
Tags copied from interface: FiniteAlphabet
Returns:
the size of the alphabet

iterator

public java.util.Iterator iterator()
Description copied from interface: FiniteAlphabet
Retrieve an Iterator over the Symbols in this FiniteAlphabet.

Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.

Specified by:
iterator in interface FiniteAlphabet
Tags copied from interface: FiniteAlphabet
Returns:
an Iterator over the contained AtomicSymbol objects

symbols

public SymbolList symbols()
Description copied from interface: FiniteAlphabet
A list of symbols that make up this alphabet.

Subsequent calls to this method are not required to return either the same symbol list, or even a symbol list with the symbols in the same order.

Specified by:
symbols in interface FiniteAlphabet
Tags copied from interface: FiniteAlphabet
Returns:
a SymbolList containing one AtomicSymbol for each AtomicSymbol in this alphabet