Package org.biojava.bio.symbol

Class SimpleReversibleTranslationTable

java.lang.Object

org.biojava.bio.symbol.AbstractReversibleTranslationTable

org.biojava.bio.symbol.SimpleReversibleTranslationTable

All Implemented Interfaces:

Serializable, ReversibleTranslationTable, TranslationTable

public class SimpleReversibleTranslationTable
extends AbstractReversibleTranslationTable
implements Serializable

A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.

Author:

Matthew Pocock, David Huen (refactoring)

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
SimpleReversibleTranslationTable(FiniteAlphabet source, FiniteAlphabet target)	Construct a new translation table.

Method Summary

Modifier and Type	Method	Description
protected Symbol	doTranslate(Symbol sym)	this method is expected to translate any symbol in the source alphabet.
protected Symbol	doUntranslate(Symbol sym)	this method is expected to reverse-translate any symbol in the source alphabet.
Alphabet	getSourceAlphabet()	The alphabet of Symbols that can be translated.
Alphabet	getTargetAlphabet()	The alphabet of Symbols that will be produced.
void	setTranslation(AtomicSymbol from, AtomicSymbol to)	Alter the translation mapping.
Symbol	translate(Symbol sym)	Translate a single symbol from source alphabet to the target alphabet.

Methods inherited from class org.biojava.bio.symbol.AbstractReversibleTranslationTable

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

SimpleReversibleTranslationTable

public SimpleReversibleTranslationTable(FiniteAlphabet source,
                                        FiniteAlphabet target)
                                 throws IllegalAlphabetException

Construct a new translation table.

Parameters:

source - the source FiniteAlphabet

target - the target FiniteAlphabet

Throws:

IllegalAlphabetException - if the alphabets are of different sizes

Method Detail

getSourceAlphabet

public Alphabet getSourceAlphabet()

Description copied from interface: TranslationTable

The alphabet of Symbols that can be translated.

Specified by:

getSourceAlphabet in interface TranslationTable

Specified by:

getSourceAlphabet in class AbstractReversibleTranslationTable

Returns:

the source Alphabet

getTargetAlphabet

public Alphabet getTargetAlphabet()

Description copied from interface: TranslationTable

The alphabet of Symbols that will be produced.

Specified by:

getTargetAlphabet in interface TranslationTable

Specified by:

getTargetAlphabet in class AbstractReversibleTranslationTable

Returns:

the target Alphabet

doTranslate

protected Symbol doTranslate(Symbol sym)

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.

doUntranslate

protected Symbol doUntranslate(Symbol sym)

Description copied from class: AbstractReversibleTranslationTable

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.

Specified by:

doUntranslate in class AbstractReversibleTranslationTable

setTranslation

public void setTranslation(AtomicSymbol from,
                           AtomicSymbol to)
                    throws IllegalSymbolException

Alter the translation mapping.

Parameters:

from - source AtomicSymbol

to - target AtomicSymbol to be returned by translate(from)

Throws:

IllegalSymbolException - if either from is not in the source alphabet or to is not in the target alphabet

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