org.biojava.bio.symbol
Class AbstractReversibleTranslationTable

java.lang.Object
  extended by org.biojava.bio.symbol.AbstractReversibleTranslationTable
All Implemented Interfaces:
ReversibleTranslationTable, TranslationTable
Direct Known Subclasses:
SimpleReversibleTranslationTable

public abstract class AbstractReversibleTranslationTable
extends java.lang.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
AbstractReversibleTranslationTable()
           
 
Method Summary
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()
Description copied from interface: TranslationTable
The alphabet of Symbols that can be translated.

Specified by:
getSourceAlphabet in interface TranslationTable
Returns:
the source Alphabet

getTargetAlphabet

public abstract Alphabet getTargetAlphabet()
Description copied from interface: TranslationTable
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
Description copied from interface: ReversibleTranslationTable
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
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