org.biojava.bio.symbol
Class DoubleAlphabet.SubDoubleAlphabet

java.lang.Object
  org.biojava.utils.Unchangeable
      org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet

All Implemented Interfaces:

Serializable, Annotatable, Alphabet, Changeable

Enclosing class:

DoubleAlphabet

public static class DoubleAlphabet.SubDoubleAlphabet
extends Unchangeable
implements Alphabet, Serializable

A class to represent a contiguous range of double symbols.

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface 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

Method Summary

boolean	contains(Symbol s) Returns whether or not this Alphabet contains the symbol.
List	getAlphabets() Return an ordered List of the alphabets which make up a compound alphabet.
Symbol	getAmbiguity(Set syms) 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.
String	getName() Get the name of the alphabet.
DoubleAlphabet.DoubleSymbol	getSymbol(double val)
Symbol	getSymbol(List rl) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
SymbolTokenization	getTokenization(String name) Get a SymbolTokenization by name.
protected Object	readResolve() To prevent duplication of a what should be a single instance of an existing alphabet.
void	validate(Symbol sym) 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

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

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.

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 rl)
                 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:

rl - A list of Symbol instances

Throws:

IllegalSymbolException - if the members of rl are not Symbols over the alphabets returned from getAlphabets

getSymbol

public DoubleAlphabet.DoubleSymbol getSymbol(double val)
                                      throws IllegalSymbolException

Throws:

IllegalSymbolException

getAmbiguity

public Symbol getAmbiguity(Set syms)

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

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

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 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

getTokenization

public SymbolTokenization getTokenization(String name)
                                   throws 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:

BioException - if for any reason the tokenization could not be built