Class AbstractAlphabet
- All Implemented Interfaces:
Serializable
,Annotatable
,Alphabet
,FiniteAlphabet
,Changeable
- Direct Known Subclasses:
IntegerAlphabet.SubIntegerAlphabet
,SimpleAlphabet
,SingletonAlphabet
An abstract implementation of Alphabet
.
This provides the frame-work for maintaining the SymbolParser invalid input: '<'-> 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:
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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
FieldsFields 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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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfinal void
Adds a symbol to this alphabet.protected abstract void
final boolean
Returns whether or not this Alphabet contains the symbol.protected abstract boolean
final 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.final Symbol
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.final Symbol
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.protected abstract AtomicSymbol
getSymbolImpl
(List symList) getTokenization
(String name) Get a SymbolTokenization by name.void
putTokenization
(String name, SymbolTokenization parser) Assigns a symbol parser to a String object.protected Object
To prevent duplication of a what should be a single instance of an existing alphabet.toString()
final void
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.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
Methods inherited from interface org.biojava.bio.symbol.FiniteAlphabet
iterator, removeSymbol, size
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Field Details
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serialVersionUID
- See Also:
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Constructor Details
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AbstractAlphabet
protected AbstractAlphabet()
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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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putTokenization
Assigns a symbol parser to a String object.
Afterwards, the parser can be retrieved using the getTokenization(Sting name) method.
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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:
NoSuchElementException
- if the name is unknownBioException
- if for any reason the tokenization could not be built
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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
- Throws:
IllegalSymbolException
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getAmbiguityImpl
Backend for getAmbiguity, called when it is actually necessarly to create a new symbol. By default, calls AlphabetManager.createSymbol.- Throws:
IllegalSymbolException
- Since:
- 1.3
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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:
syms
- A list of Symbol instances- Throws:
IllegalSymbolException
- if the members of rl are not Symbols over the alphabets returned fromgetAlphabets
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getSymbolImpl
- Throws:
IllegalSymbolException
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addSymbolImpl
protected abstract void addSymbolImpl(AtomicSymbol s) throws IllegalSymbolException, ChangeVetoException -
addSymbol
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 interfaceFiniteAlphabet
- Parameters:
s
- the Symbol to add- Throws:
IllegalSymbolException
- if the symbol is null, or if for any reason it can't be addedChangeVetoException
- if either the alphabet doesn't allow symbols to be added, or the change was vetoed
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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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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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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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containsImpl
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toString
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