Class DoubleAlphabet.SubDoubleAlphabet
- All Implemented Interfaces:
Serializable
,Annotatable
,Alphabet
,Changeable
- Enclosing class:
DoubleAlphabet
- Author:
- Matthew Pocock
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
Fields inherited from interface org.biojava.bio.symbol.Alphabet
EMPTY_ALPHABET, PARSERS, SYMBOLS
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptionboolean
Returns whether or not this Alphabet contains the symbol.Return an ordered List of the alphabets which make up a compound alphabet.getAmbiguity
(Set syms) Get a symbol that represents the set of symbols in syms.Should return the associated annotation object.Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.getName()
Get the name of the alphabet.getSymbol
(double val) Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.getTokenization
(String name) Get a SymbolTokenization by name.protected Object
To prevent duplication of a what should be a single instance of an existing alphabet.void
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
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Method Details
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readResolve
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
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getName
Description copied from interface:Alphabet
Get the name of the alphabet. -
getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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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 interfaceAlphabet
- Returns:
- a List of alphabets
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getSymbol
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 interfaceAlphabet
- Parameters:
rl
- A list of Symbol instances- Throws:
IllegalSymbolException
- if the members of rl are not Symbols over the alphabets returned fromgetAlphabets
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getSymbol
- Throws:
IllegalSymbolException
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getAmbiguity
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 interfaceAlphabet
- 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
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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 interfaceAlphabet
- Returns:
- the appropriate gap Symbol instance
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contains
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.
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validate
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 interfaceAlphabet
- Parameters:
sym
- the Symbol to validate- Throws:
IllegalSymbolException
- if r is not contained in this alphabet
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getTokenization
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 interfaceAlphabet
- 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
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