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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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 behavior 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

Class DoubleAlphabet.SubDoubleAlphabet

Nested Class Summary

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

Field Summary

Fields inherited from interface org.biojava.bio.symbol.Alphabet

Fields inherited from interface org.biojava.bio.Annotatable

Method Summary

Methods inherited from class org.biojava.utils.Unchangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Method Detail

readResolve

getName

getAnnotation

getAlphabets

getSymbol

getSymbol

getAmbiguity

getGapSymbol

contains

validate

getTokenization