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java.lang.Objectorg.biojava.bio.symbol.AbstractReversibleTranslationTable
public abstract class AbstractReversibleTranslationTable
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
Field Summary |
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Fields inherited from interface org.biojava.bio.symbol.TranslationTable |
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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 |
Constructor Summary | |
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AbstractReversibleTranslationTable()
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Method Summary | |
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protected abstract Symbol |
doTranslate(Symbol sym)
this method is expected to translate any symbol in the source alphabet. |
protected abstract Symbol |
doUntranslate(Symbol sym)
this method is expected to reverse-translate any symbol in the source alphabet. |
abstract Alphabet |
getSourceAlphabet()
The alphabet of Symbols that can be translated. |
abstract Alphabet |
getTargetAlphabet()
The alphabet of Symbols that will be produced. |
Symbol |
translate(Symbol sym)
Translate a single symbol from source alphabet to the target alphabet. |
Symbol |
untranslate(Symbol sym)
Translate a single symbol from target alphabet to the source alphabet. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.bio.symbol.TranslationTable |
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translate |
Constructor Detail |
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public AbstractReversibleTranslationTable()
Method Detail |
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public abstract Alphabet getSourceAlphabet()
TranslationTable
getSourceAlphabet
in interface TranslationTable
public abstract Alphabet getTargetAlphabet()
TranslationTable
getTargetAlphabet
in interface TranslationTable
protected abstract Symbol doUntranslate(Symbol sym) throws IllegalSymbolException
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.
IllegalSymbolException
public Symbol untranslate(Symbol sym) throws IllegalSymbolException
ReversibleTranslationTable
untranslate
in interface ReversibleTranslationTable
sym
- the Symbol to translate (member of target alphabet)
IllegalSymbolException
- if sym is not a member of the target
alphabetprotected abstract Symbol doTranslate(Symbol sym) throws IllegalSymbolException
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.
IllegalSymbolException
public Symbol translate(Symbol sym) throws IllegalSymbolException
TranslationTable
translate
in interface TranslationTable
sym
- the Symbol to translate (member of source alphabet)
IllegalSymbolException
- if sym is not a member of the source
alphabet
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