SimpleGeneticCodeTable (biojava-legacy 1.9.5 API)

SimpleGeneticCodeTable (biojava-legacy 1.9.5 API)

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 Description

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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
```
    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