Interface TranslationTable
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- All Known Subinterfaces:
ManyToOneTranslationTable
,ReversibleTranslationTable
- All Known Implementing Classes:
AbstractManyToOneTranslationTable
,AbstractReversibleTranslationTable
,SimpleGeneticCodeTable
,SimpleManyToOneTranslationTable
,SimpleReversibleTranslationTable
,SimpleTranslationTable
public interface TranslationTable
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
Fields Modifier and Type Field Description static String
ALT_YEAST_NUC
Translation table name for the alternative yeast nuclear genetic code.static String
ASCID_MITO
Translation table name for the ascidian mitochondrial genetic code.static String
BACTERIAL
Translation table name for the bacterial and plant plastid genetic code.static String
BLEPH_MNUC
Translation table name for the blepharisma macronuclear genetic code.static String
CHLORO_MITO
Translation table name for the chlorophycean mitochondrial genetic code.static String
CILIATE_NUC
Translation table name for the ciliate nuclear genetic code.static String
ECHIN_MITO
Translation table name for the echinoderm mitochondrial genetic code.static String
EUPL_NUC
Translation table name for the euplotid nuclear genetic code.static String
FWORM_MITO
Translation table name for the flatworm mitochondrial genetic code.static String
INVERT_MITO
Translation table name for the invertebrate mitochondrial genetic code.static String
MOLD_MITO
Translation table name for the mold mitochondrial genetic code.static String
SCENE_MITO
Translation table name for the scenedesmus obliquus mitochondrial genetic code.static String
TREMA_MITO
Translation table name for the trematode mitochondrial genetic code.static String
UNIVERSAL
Translation table name for the universal genetic code.static String
VERT_MITO
Translation table name for the vertebrate mitochondrial genetic code.static String
YEAST_MITO
Translation table name for the yeast mitochondrial genetic code.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Alphabet
getSourceAlphabet()
The alphabet of Symbols that can be translated.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.
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Field Detail
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UNIVERSAL
static final String UNIVERSAL
Translation table name for the universal genetic code.- See Also:
- Constant Field Values
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VERT_MITO
static final String VERT_MITO
Translation table name for the vertebrate mitochondrial genetic code.- See Also:
- Constant Field Values
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YEAST_MITO
static final String YEAST_MITO
Translation table name for the yeast mitochondrial genetic code.- See Also:
- Constant Field Values
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MOLD_MITO
static final String MOLD_MITO
Translation table name for the mold mitochondrial genetic code.- See Also:
- Constant Field Values
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INVERT_MITO
static final String INVERT_MITO
Translation table name for the invertebrate mitochondrial genetic code.- See Also:
- Constant Field Values
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CILIATE_NUC
static final String CILIATE_NUC
Translation table name for the ciliate nuclear genetic code.- See Also:
- Constant Field Values
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ECHIN_MITO
static final String ECHIN_MITO
Translation table name for the echinoderm mitochondrial genetic code.- See Also:
- Constant Field Values
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EUPL_NUC
static final String EUPL_NUC
Translation table name for the euplotid nuclear genetic code.- See Also:
- Constant Field Values
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BACTERIAL
static final String BACTERIAL
Translation table name for the bacterial and plant plastid genetic code.- See Also:
- Constant Field Values
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ALT_YEAST_NUC
static final String ALT_YEAST_NUC
Translation table name for the alternative yeast nuclear genetic code.- See Also:
- Constant Field Values
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ASCID_MITO
static final String ASCID_MITO
Translation table name for the ascidian mitochondrial genetic code.- See Also:
- Constant Field Values
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FWORM_MITO
static final String FWORM_MITO
Translation table name for the flatworm mitochondrial genetic code.- See Also:
- Constant Field Values
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BLEPH_MNUC
static final String BLEPH_MNUC
Translation table name for the blepharisma macronuclear genetic code.- See Also:
- Constant Field Values
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CHLORO_MITO
static final String CHLORO_MITO
Translation table name for the chlorophycean mitochondrial genetic code.- See Also:
- Constant Field Values
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TREMA_MITO
static final String TREMA_MITO
Translation table name for the trematode mitochondrial genetic code.- See Also:
- Constant Field Values
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SCENE_MITO
static final String SCENE_MITO
Translation table name for the scenedesmus obliquus mitochondrial genetic code.- See Also:
- Constant Field Values
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Method Detail
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getSourceAlphabet
Alphabet getSourceAlphabet()
The alphabet of Symbols that can be translated.- Returns:
- the source Alphabet
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getTargetAlphabet
Alphabet getTargetAlphabet()
The alphabet of Symbols that will be produced.- Returns:
- the target Alphabet
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translate
Symbol translate(Symbol sym) throws IllegalSymbolException
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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