Package org.biojava.bio.symbol
Class SimpleReversibleTranslationTable
java.lang.Object
org.biojava.bio.symbol.AbstractReversibleTranslationTable
org.biojava.bio.symbol.SimpleReversibleTranslationTable
- All Implemented Interfaces:
Serializable
,ReversibleTranslationTable
,TranslationTable
public class SimpleReversibleTranslationTable
extends AbstractReversibleTranslationTable
implements Serializable
A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.
- Author:
- Matthew Pocock, David Huen (refactoring)
- See Also:
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Field Summary
Fields inherited from interface org.biojava.bio.symbol.TranslationTable
ALT_YEAST_NUC, ASCID_MITO, BACTERIAL, BLEPH_MNUC, CHLORO_MITO, CILIATE_NUC, ECHIN_MITO, EUPL_NUC, FWORM_MITO, INVERT_MITO, MOLD_MITO, SCENE_MITO, TREMA_MITO, UNIVERSAL, VERT_MITO, YEAST_MITO
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Constructor Summary
ConstructorsConstructorDescriptionSimpleReversibleTranslationTable
(FiniteAlphabet source, FiniteAlphabet target) Construct a new translation table. -
Method Summary
Modifier and TypeMethodDescriptionprotected Symbol
doTranslate
(Symbol sym) this method is expected to translate any symbol in the source alphabet.protected Symbol
doUntranslate
(Symbol sym) this method is expected to reverse-translate any symbol in the source alphabet.The alphabet of Symbols that can be translated.The alphabet of Symbols that will be produced.void
setTranslation
(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.Translate a single symbol from source alphabet to the target alphabet.Methods inherited from class org.biojava.bio.symbol.AbstractReversibleTranslationTable
untranslate
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.bio.symbol.TranslationTable
translate
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Constructor Details
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SimpleReversibleTranslationTable
public SimpleReversibleTranslationTable(FiniteAlphabet source, FiniteAlphabet target) throws IllegalAlphabetException Construct a new translation table.- Parameters:
source
- the source FiniteAlphabettarget
- the target FiniteAlphabet- Throws:
IllegalAlphabetException
- if the alphabets are of different sizes
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Method Details
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getSourceAlphabet
Description copied from interface:TranslationTable
The alphabet of Symbols that can be translated.- Specified by:
getSourceAlphabet
in interfaceTranslationTable
- Specified by:
getSourceAlphabet
in classAbstractReversibleTranslationTable
- Returns:
- the source Alphabet
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getTargetAlphabet
Description copied from interface:TranslationTable
The alphabet of Symbols that will be produced.- Specified by:
getTargetAlphabet
in interfaceTranslationTable
- Specified by:
getTargetAlphabet
in classAbstractReversibleTranslationTable
- Returns:
- the target Alphabet
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doTranslate
this method is expected to translate any symbol in the source alphabet. Failure can be indicated by returning a null if, for example, your method only handles AtomicSymbols and you want BasisSymbols to be taken apart. If you are sure the symbol is illegal, you can throw the IllegalSymbolException immediately to bypass further processing.As an optimisation, if your method is capable of immediately translating an ambiguity Symbol, just return it and the alternate route of establishing the translation through doing an ambiguity lookup will be avoided.
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doUntranslate
Description copied from class:AbstractReversibleTranslationTable
this method is expected to reverse-translate any symbol in the source alphabet. Failure can be indicated by returning a null if, for example, your method only handles AtomicSymbols and you want BasisSymbols to be taken apart. If you are sure the symbol is illegal, you can throw the IllegalSymbolException immediately to bypass further processing.As an optimisation, if your method is capable of immediately translating an ambiguity Symbol, just return it and the alternate route of establishing the translation through doing an ambiguity lookup will be avoided.
- Specified by:
doUntranslate
in classAbstractReversibleTranslationTable
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setTranslation
Alter the translation mapping.- Parameters:
from
- source AtomicSymbolto
- target AtomicSymbol to be returned by translate(from)- Throws:
IllegalSymbolException
- if either from is not in the source alphabet or to is not in the target alphabet
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translate
Description copied from interface:TranslationTable
Translate a single symbol from source alphabet to the target alphabet.- Specified by:
translate
in interfaceTranslationTable
- Parameters:
sym
- the Symbol to translate (member of source alphabet)- Returns:
- the translated version of sym (member of target alphabet)
- Throws:
IllegalSymbolException
- if sym is not a member of the source alphabet
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