AbstractReversibleTranslationTable (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.bio.symbol.AbstractReversibleTranslationTable

All Implemented Interfaces:

ReversibleTranslationTable, TranslationTable

Direct Known Subclasses:

SimpleReversibleTranslationTable
```
public abstract class AbstractReversibleTranslationTable
extends Object
implements ReversibleTranslationTable
```
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.

Author:

Matthew Pocock, Keith James (docs), Thomas Down, Greg Cox, Mark Schreiber, David Huen (refactoring)

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

AbstractReversibleTranslationTable()

Constructors
Constructor	Description
`AbstractReversibleTranslationTable()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected abstract Symbol`	`doTranslate(Symbol sym)`	this method is expected to translate any symbol in the source alphabet.
`protected abstract Symbol`	`doUntranslate(Symbol sym)`	this method is expected to reverse-translate any symbol in the source alphabet.
`abstract Alphabet`	`getSourceAlphabet()`	The alphabet of Symbols that can be translated.
`abstract 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.
`Symbol`	`untranslate(Symbol sym)`	Translate a single symbol from target alphabet to the source alphabet.

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
  - AbstractReversibleTranslationTable
```
public AbstractReversibleTranslationTable()
```
- Method Detail
  - getSourceAlphabet
```
public abstract Alphabet getSourceAlphabet()
```
    The alphabet of Symbols that can be translated.
    
    Specified by:
    
    getSourceAlphabet in interface TranslationTable
    
    Returns:
    
    the source Alphabet
  - getTargetAlphabet
```
public abstract Alphabet getTargetAlphabet()
```
    The alphabet of Symbols that will be produced.
    
    Specified by:
    
    getTargetAlphabet in interface TranslationTable
    
    Returns:
    
    the target Alphabet
  - doUntranslate
```
protected abstract Symbol doUntranslate(Symbol sym)
                                 throws IllegalSymbolException
```
    this method is expected to reverse-translate any symbol in the source alphabet. Failure can be indicated by returning a null if, for example, your method only handles AtomicSymbols and you want BasisSymbols to be taken apart. If you are sure the symbol is illegal, you can throw the IllegalSymbolException immediately to bypass further processing.
    As an optimisation, if your method is capable of immediately translating an ambiguity Symbol, just return it and the alternate route of establishing the translation through doing an ambiguity lookup will be avoided.
    
    Throws:
    
    IllegalSymbolException
  - untranslate
```
public Symbol untranslate(Symbol sym)
                   throws IllegalSymbolException
```
    Translate a single symbol from target alphabet to the source alphabet.
    
    Specified by:
    
    untranslate in interface ReversibleTranslationTable
    
    Parameters:
    
    sym - the Symbol to translate (member of target alphabet)
    
    Returns:
    
    the translated version of sym (member of source alphabet)
    
    Throws:
    
    IllegalSymbolException - if sym is not a member of the target alphabet
  - doTranslate
```
protected abstract Symbol doTranslate(Symbol sym)
                               throws IllegalSymbolException
```
    this method is expected to translate any symbol in the source alphabet. Failure can be indicated by returning a null if, for example, your method only handles AtomicSymbols and you want BasisSymbols to be taken apart. If you are sure the symbol is illegal, you can throw the IllegalSymbolException immediately to bypass further processing.
    As an optimisation, if your method is capable of immediately translating an ambiguity Symbol, just return it and the alternate route of establishing the translation through doing an ambiguity lookup will be avoided.
    
    Throws:
    
    IllegalSymbolException
  - 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

Field Summary

Fields inherited from interface org.biojava.bio.symbol.TranslationTable

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.bio.symbol.TranslationTable

Constructor Detail

AbstractReversibleTranslationTable

Method Detail

getSourceAlphabet

getTargetAlphabet

doUntranslate

untranslate

doTranslate

translate