org.biojava.bio.symbol
Class SimpleReversibleTranslationTable

java.lang.Object
  |
  +--org.biojava.bio.symbol.SimpleTranslationTable
        |
        +--org.biojava.bio.symbol.SimpleReversibleTranslationTable

All Implemented Interfaces:

ReversibleTranslationTable, java.io.Serializable, TranslationTable

public class SimpleReversibleTranslationTable

extends SimpleTranslationTable

implements ReversibleTranslationTable, java.io.Serializable

A no-frills implementation of ReversibleTranslationTable that uses two Maps to map between symbols in a finite source alphabet into a finite target alphabet.

Author:

Matthew Pocock

See Also:

Serialized Form

Field Summary

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

ALT_YEAST_NUC, ASCID_MITO, BLEPH_MNUC, CILIATE_NUC, ECHIN_MITO, EUPL_NUC, FWORM_MITO, INVERT_MITO, MOLD_MITO, UNIVERSAL, VERT_MITO, YEAST_MITO

Constructor Summary

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

Method Summary

void	setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.
Symbol	untranslate(Symbol sym) Translate a single symbol from target alphabet to the source alphabet.

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

getSourceAlphabet, getTargetAlphabet, translate

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

getSourceAlphabet, getTargetAlphabet, 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

setTranslation

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

Description copied from class: SimpleTranslationTable

Alter the translation mapping.

Overrides:

setTranslation in class SimpleTranslationTable

Parameters:

from - source AtomicSymbol

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

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