org.biojava.bio.symbol

Class SimpleGeneticCodeTable

java.lang.Object

org.biojava.bio.symbol.AbstractManyToOneTranslationTable

org.biojava.bio.symbol.SimpleManyToOneTranslationTable

org.biojava.bio.symbol.SimpleGeneticCodeTable

All Implemented Interfaces:

Serializable, ManyToOneTranslationTable, TranslationTable

public class SimpleGeneticCodeTable
extends SimpleManyToOneTranslationTable

A genetic code translation table representing a translation table in the DDBJ/EMBL/GenBank Feature Table (appendix V).

Since:

1.5

Author:

gwaldon

See Also:

Serialized Form

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

Constructor Summary

Constructors

Constructor and Description
SimpleGeneticCodeTable(FiniteAlphabet source, FiniteAlphabet target) Creates a new instance of SimpleGeneticCodeTable

Method Summary

Modifier and Type	Method and Description
String	getDescription()
int	getTableNumber()
void	setDescription(String description)
void	setTableNumber(int num)
Symbol	translate(Symbol sym) Translate a single symbol from source alphabet to the target alphabet.

Methods inherited from class org.biojava.bio.symbol.SimpleManyToOneTranslationTable

doTranslate, doUntranslate, getSourceAlphabet, getTargetAlphabet, setTranslation

Methods inherited from class org.biojava.bio.symbol.AbstractManyToOneTranslationTable

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

Constructor Detail

SimpleGeneticCodeTable

public SimpleGeneticCodeTable(FiniteAlphabet source,
                              FiniteAlphabet target)

Creates a new instance of SimpleGeneticCodeTable

Method Detail

setTableNumber

public void setTableNumber(int num)

getTableNumber

public int getTableNumber()

Returns:

the value for the feature qualifier table_num found in the DDBJ/EMBL/GenBank Feature Table. The associated feature key is CDS.

setDescription

public void setDescription(String description)

getDescription

public String getDescription()

Returns:

A string descripting this table, normally the one found in the DDBJ/EMBL/GenBank Feature Table.

translate

public Symbol translate(Symbol sym)
                 throws IllegalSymbolException

Description copied from interface: TranslationTable

Translate a single symbol from source alphabet to the target alphabet.

Specified by:

translate in interface TranslationTable

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