org.biojava.bio.symbol
Class AbstractManyToOneTranslationTable

java.lang.Object
  org.biojava.bio.symbol.AbstractManyToOneTranslationTable

All Implemented Interfaces:

ManyToOneTranslationTable, TranslationTable

Direct Known Subclasses:

SimpleManyToOneTranslationTable

public abstract class AbstractManyToOneTranslationTable
extends Object
implements ManyToOneTranslationTable

an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.

The mapping between the alphabets can be either one-to-one or many-to one.

Author:

David Huen

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

AbstractManyToOneTranslationTable()

Method Summary

protected abstract Symbol	doTranslate(Symbol sym) this method is expected to translate any symbol in the source alphabet.
protected abstract Set	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.
Set	untranslate(Symbol sym) returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target 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

AbstractManyToOneTranslationTable

public AbstractManyToOneTranslationTable()

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 Set 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 Set untranslate(Symbol sym)
                throws IllegalSymbolException

returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.

Specified by:

untranslate in interface ManyToOneTranslationTable

Parameters:

sym - the Symbol to reverse-translate (member of target alphabet)

Returns:

a Set containing symbols that translate to the specified Symbol.

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