Class IntegerAlphabet.SubIntegerAlphabet
- All Implemented Interfaces:
Serializable
,Annotatable
,Alphabet
,FiniteAlphabet
,Changeable
- Enclosing class:
IntegerAlphabet
- Since:
- 1.3
- Author:
- Mark Schreiber, 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 class org.biojava.bio.symbol.AbstractAlphabet
serialVersionUID
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 TypeMethodDescriptionprotected void
protected boolean
containsImpl
(AtomicSymbol sym) Return an ordered List of the alphabets which make up a compound alphabet.Should return the associated annotation object.getName()
Get the name of the alphabet.getSymbol
(int val) protected AtomicSymbol
getSymbolImpl
(List symL) getTokenization
(String name) Get a SymbolTokenization by name.iterator()
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.void
removeSymbol
(Symbol sym) Remove a symbol from this alphabet.int
size()
The number of symbols in the alphabet.Methods inherited from class org.biojava.bio.symbol.AbstractAlphabet
addSymbol, contains, getAmbiguity, getAmbiguityImpl, getGapSymbol, getSymbol, putTokenization, readResolve, toString, validate
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.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Method Details
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getName
Description copied from interface:Alphabet
Get the name of the alphabet.- Returns:
- the name as a string.
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containsImpl
- Specified by:
containsImpl
in classAbstractAlphabet
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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
- Overrides:
getTokenization
in classAbstractAlphabet
- Parameters:
name
- Currently only "token" is supported.- Returns:
- an IntegerParser.
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getSymbol
- Throws:
IllegalSymbolException
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size
Description copied from interface:FiniteAlphabet
The number of symbols in the alphabet.- Returns:
- the size of the alphabet
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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.- Returns:
- a List of alphabets
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getSymbolImpl
- Specified by:
getSymbolImpl
in classAbstractAlphabet
- Throws:
IllegalSymbolException
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addSymbolImpl
- Specified by:
addSymbolImpl
in classAbstractAlphabet
- Throws:
ChangeVetoException
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removeSymbol
Description copied from interface:FiniteAlphabet
Remove a symbol from this alphabet.If the symbol matches multiple AtomicSymbols, then each matching symbol it will be removed.
- Parameters:
sym
- the Symbol to removeintGot- Throws:
ChangeVetoException
- if either the alphabet doesn't allow symbols to be added, or the change was vetoed
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iterator
Description copied from interface:FiniteAlphabet
Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.Each AtomicSymbol as for which this.contains(as) is true will be returned exactly once by this iterator in no specified order.
- Returns:
- an Iterator over the contained AtomicSymbol objects
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getAnnotation
Description copied from interface:Annotatable
Should return the associated annotation object.- Returns:
- an Annotation object, never null
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