org.biojava.bio.symbol
Class AbstractAlphabet

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.symbol.AbstractAlphabet
All Implemented Interfaces:
Alphabet, Annotatable, Changeable, FiniteAlphabet, java.io.Serializable
Direct Known Subclasses:
IntegerAlphabet.SubIntegerAlphabet, SimpleAlphabet, SingletonAlphabet

public abstract class AbstractAlphabet
extends AbstractChangeable
implements FiniteAlphabet, java.io.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
See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
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(java.util.Set syms)
           Get a symbol that represents the set of symbols in syms.
protected  Symbol getAmbiguityImpl(java.util.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(java.util.List syms)
           Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
protected abstract  AtomicSymbol getSymbolImpl(java.util.List symList)
           
 SymbolTokenization getTokenization(java.lang.String name)
           Get a SymbolTokenization by name.
 void putTokenization(java.lang.String name, SymbolTokenization parser)
           Assigns a symbol parser to a String object.
protected  java.lang.Object readResolve()
          To prevent duplication of a what should be a single instance of an existing alphabet.
 java.lang.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, 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
 

Constructor Detail

AbstractAlphabet

protected AbstractAlphabet()
Method Detail

readResolve

protected java.lang.Object readResolve()
                                throws java.io.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:
java.io.ObjectStreamException

putTokenization

public void putTokenization(java.lang.String name,
                            SymbolTokenization parser)

Assigns a symbol parser to a String object.

Afterwards, the parser can be retrieved using the getParser method.


getTokenization

public SymbolTokenization getTokenization(java.lang.String name)
                                   throws java.util.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.

Specified by:
getTokenization in 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 tokenization could not be built

getAmbiguity

public final Symbol getAmbiguity(java.util.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(java.util.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(java.util.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(java.util.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 java.lang.String toString()