Interface TranslationTable
- All Known Subinterfaces:
ManyToOneTranslationTable
,ReversibleTranslationTable
- All Known Implementing Classes:
AbstractManyToOneTranslationTable
,AbstractReversibleTranslationTable
,SimpleGeneticCodeTable
,SimpleManyToOneTranslationTable
,SimpleReversibleTranslationTable
,SimpleTranslationTable
Encapsulates the mapping from a source to a destination alphabet.
A TranslationTable is in effect a map or function with the source domain being getSourceAlphabet() and the target domain being getTargetAlphabet(). The method translate() maps a single symbol from source to target.
It is presumed that there will be some explicit declaration of the mapping for attomic symbols, and that the mapping for all other symbols will be infered from these.
If you wish to translate every symbol in a symbol list then use TranslatedSymbolList to automate the job. If you want to translate windowed regions then first construct a WindowedSymbolList from the original sequence and then build a TranslatedSymbolList from this windowed view.
There are a range of named tables available. Their names are specified by the public static final fields in this interface. Each table can be retrieved by calling the static method RNATools.getGeneticCode(name) which will return the appropriate TanslationTable instance.
- Author:
- Matthew Pocock, Keith James
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
Translation table name for the alternative yeast nuclear genetic code.static final String
Translation table name for the ascidian mitochondrial genetic code.static final String
Translation table name for the bacterial and plant plastid genetic code.static final String
Translation table name for the blepharisma macronuclear genetic code.static final String
Translation table name for the chlorophycean mitochondrial genetic code.static final String
Translation table name for the ciliate nuclear genetic code.static final String
Translation table name for the echinoderm mitochondrial genetic code.static final String
Translation table name for the euplotid nuclear genetic code.static final String
Translation table name for the flatworm mitochondrial genetic code.static final String
Translation table name for the invertebrate mitochondrial genetic code.static final String
Translation table name for the mold mitochondrial genetic code.static final String
Translation table name for the scenedesmus obliquus mitochondrial genetic code.static final String
Translation table name for the trematode mitochondrial genetic code.static final String
Translation table name for the universal genetic code.static final String
Translation table name for the vertebrate mitochondrial genetic code.static final String
Translation table name for the yeast mitochondrial genetic code. -
Method Summary
Modifier and TypeMethodDescriptionThe alphabet of Symbols that can be translated.The alphabet of Symbols that will be produced.Translate a single symbol from source alphabet to the target alphabet.
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Field Details
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UNIVERSAL
Translation table name for the universal genetic code.- See Also:
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VERT_MITO
Translation table name for the vertebrate mitochondrial genetic code.- See Also:
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YEAST_MITO
Translation table name for the yeast mitochondrial genetic code.- See Also:
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MOLD_MITO
Translation table name for the mold mitochondrial genetic code.- See Also:
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INVERT_MITO
Translation table name for the invertebrate mitochondrial genetic code.- See Also:
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CILIATE_NUC
Translation table name for the ciliate nuclear genetic code.- See Also:
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ECHIN_MITO
Translation table name for the echinoderm mitochondrial genetic code.- See Also:
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EUPL_NUC
Translation table name for the euplotid nuclear genetic code.- See Also:
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BACTERIAL
Translation table name for the bacterial and plant plastid genetic code.- See Also:
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ALT_YEAST_NUC
Translation table name for the alternative yeast nuclear genetic code.- See Also:
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ASCID_MITO
Translation table name for the ascidian mitochondrial genetic code.- See Also:
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FWORM_MITO
Translation table name for the flatworm mitochondrial genetic code.- See Also:
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BLEPH_MNUC
Translation table name for the blepharisma macronuclear genetic code.- See Also:
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CHLORO_MITO
Translation table name for the chlorophycean mitochondrial genetic code.- See Also:
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TREMA_MITO
Translation table name for the trematode mitochondrial genetic code.- See Also:
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SCENE_MITO
Translation table name for the scenedesmus obliquus mitochondrial genetic code.- See Also:
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Method Details
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getSourceAlphabet
The alphabet of Symbols that can be translated.- Returns:
- the source Alphabet
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getTargetAlphabet
The alphabet of Symbols that will be produced.- Returns:
- the target Alphabet
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translate
Translate a single symbol from source alphabet to the target alphabet.- 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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