org.biojava.bio.symbol
Class NameParser

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

public class NameParser
extends java.lang.Object
implements SymbolParser, java.io.Serializable

This uses Symbol names to parse characters into symbols.

Author:
Matthew Pocock
See Also:
Serialized Form

Constructor Summary
NameParser(FiniteAlphabet alpha)
           
NameParser(java.util.Map nameToSymbol)
           
 
Method Summary
 Alphabet getAlphabet()
          The alphabet that all Symbols produced will belong to.
 SymbolList parse(java.lang.String seq)
          Parse an entire string into a SymbolList.
 Symbol parseToken(java.lang.String token)
          Returns the symbol for a single token.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NameParser

public NameParser(FiniteAlphabet alpha)

NameParser

public NameParser(java.util.Map nameToSymbol)
Method Detail

getAlphabet

public Alphabet getAlphabet()
Description copied from interface: SymbolParser
The alphabet that all Symbols produced will belong to.
Specified by:
getAlphabet in interface SymbolParser
Tags copied from interface: SymbolParser
Returns:
the Alphabet

parse

public SymbolList parse(java.lang.String seq)
                 throws IllegalSymbolException
Description copied from interface: SymbolParser
Parse an entire string into a SymbolList.

The SymbolList produced will have the same Alphabet as this SymbolParser.

Specified by:
parse in interface SymbolParser
Tags copied from interface: SymbolParser
Parameters:
seq - the String to parse
Returns:
the SymbolList containing the parsed value of the String
Throws:
IllegalSymbolException - if any part of the String can not be parsed

parseToken

public Symbol parseToken(java.lang.String token)
                  throws IllegalSymbolException
Description copied from interface: SymbolParser
Returns the symbol for a single token.

The Symbol will be a member of the alphabet. If the token is not recognized as mapping to a symbol, an exception will be thrown.

Specified by:
parseToken in interface SymbolParser
Tags copied from interface: SymbolParser
Parameters:
token - the token to retrieve a Symbol for
Returns:
the Symbol for that token
Throws:
IllegalSymbolException - if there is no Symbol for the token