org.biojava.bio.symbol
Class SimpleTranslationTable

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

public class SimpleTranslationTable
extends java.lang.Object
implements TranslationTable, java.io.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
See Also:
Serialized Form

Constructor Summary
SimpleTranslationTable(FiniteAlphabet source, Alphabet target)
          Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet source, Alphabet target, java.util.Map transMap)
          Create a new translation table that will translate symbols from source to target.
 
Method Summary
 Alphabet getSourceAlphabet()
          The alphabet of Symbols that can be translated.
 Alphabet getTargetAlphabet()
          The alphabet of Symbols that will be produced.
 void setTranslation(Symbol from, Symbol to)
          Alter the translation mapping.
 Symbol translate(Symbol res)
          Translate a single symbol from source alphabet to the target alphabet.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleTranslationTable

public SimpleTranslationTable(FiniteAlphabet source,
                              Alphabet target)
Create a new translation table that will translate symbols from source to target.

The source alphabet must be finite, as a Map object is used to associate a source Symbol with a target Symbol. The target alphabet need not be finite.

Parameters:
source - the FiniteAlphabet to translate from
target - the Alphabet to translate into

SimpleTranslationTable

public SimpleTranslationTable(FiniteAlphabet source,
                              Alphabet target,
                              java.util.Map transMap)
Create a new translation table that will translate symbols from source to target.

The Map transMap should contain keys in the source alphabet with values in the target alphabet. However, this is not currently checked.

The source alphabet must be finite, as a Map object is used to associate a source Symbol with a target Symbol. The target alphabet need not be finite.

Parameters:
source - the FiniteAlphabet to translate from
target - the Alphabet to translate into
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
Tags copied from interface: TranslationTable
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
Tags copied from interface: TranslationTable
Returns:
the target Alphabet

translate

public Symbol translate(Symbol res)
                 throws IllegalSymbolException
Description copied from interface: TranslationTable
Translate a single symbol from source alphabet to the target alphabet.
Specified by:
translate in interface TranslationTable
Tags copied from 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

setTranslation

public void setTranslation(Symbol from,
                           Symbol to)
                    throws IllegalSymbolException
Alter the translation mapping.
Parameters:
from - source Symbol
to - target Symbol to be returned by translate(from)
Throws:
IllefalSymbolException - if either from is not in the source alphabet or to is not in the target alphabet