org.biojava.bio.symbol
Class SimpleGeneticCodeTable

java.lang.Object
  extended by org.biojava.bio.symbol.AbstractManyToOneTranslationTable
      extended by org.biojava.bio.symbol.SimpleManyToOneTranslationTable
          extended by 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
SimpleGeneticCodeTable(FiniteAlphabet source, FiniteAlphabet target)
          Creates a new instance of SimpleGeneticCodeTable
 
Method Summary
 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