Package org.biojava.bio.symbol

Class AbstractReversibleTranslationTable

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()

Method Summary

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()

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