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## org.biojava.bio.symbol
Class AbstractAlphabet

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.symbol.AbstractAlphabet

All Implemented Interfaces:
  Serializable, Annotatable, Alphabet, FiniteAlphabet, Changeable

Direct Known Subclasses:
  IntegerAlphabet.SubIntegerAlphabet, SimpleAlphabet, SingletonAlphabet

    public abstract class AbstractAlphabet

extends AbstractChangeable
implements FiniteAlphabet, Serializable

An abstract implementation of `Alphabet`.

This provides the frame-work for maintaining the SymbolParser <-> name mappings and also for the ChangeListeners.

This class is for developers to derive from, not for use directly.

Since:
  1.1
Author:
  Matthew Pocock, Greg Cox, Francois Pepin, Mark Schreiber
See Also:
  Serialized Form

Nested Class Summary

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

Field Summary
`static long` | `serialVersionUID`

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

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

Constructor Summary
`protected` | `AbstractAlphabet()`

Method Summary
`void` | `addSymbol(Symbol s)` Adds a symbol to this alphabet.
`protected abstract void` | `addSymbolImpl(AtomicSymbol s)`
`boolean` | `contains(Symbol sym)` Returns whether or not this Alphabet contains the symbol.
`protected abstract boolean` | `containsImpl(AtomicSymbol s)`
`Symbol` | `getAmbiguity(Set syms)` Get a symbol that represents the set of symbols in syms.
`protected Symbol` | `getAmbiguityImpl(Set syms)` Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
`Symbol` | `getGapSymbol()` Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
`Symbol` | `getSymbol(List syms)` Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
`protected abstract AtomicSymbol` | `getSymbolImpl(List symList)`
`SymbolTokenization` | `getTokenization(String name)` Get a SymbolTokenization by name.
`void` | `putTokenization(String name, SymbolTokenization parser)` Assigns a symbol parser to a String object.
`protected Object` | `readResolve()` To prevent duplication of a what should be a single instance of an existing alphabet.
`String` | `toString()`
`void` | `validate(Symbol sym)` Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

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

Methods inherited from interface org.biojava.bio.symbol.FiniteAlphabet
`iterator, removeSymbol, size`

Methods inherited from interface org.biojava.bio.symbol.Alphabet
`getAlphabets, getName`

Methods inherited from interface org.biojava.bio.Annotatable
`getAnnotation`

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

Field Detail

### serialVersionUID

    public static final long serialVersionUID

See Also:
  Constant Field Values

Constructor Detail

### AbstractAlphabet

    protected AbstractAlphabet()

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`

### putTokenization

    public void putTokenization(String name,
                                SymbolTokenization parser)

  Assigns a symbol parser to a String object.

  Afterwards, the parser can be retrieved using the getTokenization(Sting name) method.

### getTokenization

    public SymbolTokenization getTokenization(String name)
                                       throws NoSuchElementException,
                                              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 behaviour 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:
    `NoSuchElementException` - if the name is unknown
    `BioException` - if for any reason the tokenization could not be built

### getAmbiguity

    public final Symbol getAmbiguity(Set syms)
                              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:
    `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
  Throws:
    `IllegalSymbolException`

### getAmbiguityImpl

    protected Symbol getAmbiguityImpl(Set syms)
                               throws IllegalSymbolException

  Backend for getAmbiguity, called when it is actually necessarly to create a new symbol. By default, calls AlphabetManager.createSymbol.

  Throws:
    `IllegalSymbolException`
  Since:
    1.3

### getSymbol

    public final Symbol getSymbol(List syms)
                           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:
    `syms` - A list of Symbol instances
  Throws:
    `IllegalSymbolException` - if the members of rl are not Symbols over the alphabets returned from `getAlphabets`

### getSymbolImpl

    protected abstract AtomicSymbol getSymbolImpl(List symList)
                                           throws IllegalSymbolException

  Throws:
    `IllegalSymbolException`

### addSymbolImpl

    protected abstract void addSymbolImpl(AtomicSymbol s)
                                   throws IllegalSymbolException,
                                          ChangeVetoException

  Throws:
    `IllegalSymbolException`
    `ChangeVetoException`

### addSymbol

    public final void addSymbol(Symbol s)
                         throws IllegalSymbolException,
                                ChangeVetoException

  Description copied from interface: `FiniteAlphabet`
  Adds a symbol to this alphabet.

  If the symbol matches more than one AtomicSymbol, then each symbol matching it will be added.

  Specified by:
    `addSymbol` in interface `FiniteAlphabet`
  Parameters:
    `s` - the Symbol to add
  Throws:
    `IllegalSymbolException` - if the symbol is null, or if for any reason it can't be added
    `ChangeVetoException` - if either the alphabet doesn't allow symbols to be added, or the change was vetoed

### contains

    public final boolean contains(Symbol sym)

  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:
    `sym` - the Symbol to check
  Returns:
    boolean true if the Alphabet contains the symbol and false otherwise

### getGapSymbol

    public final 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

### validate

    public final 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

### containsImpl

    protected abstract boolean containsImpl(AtomicSymbol s)

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

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