org.biojava.bio.symbol
Class FixedWidthParser

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

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

A parser that uses a fixed width window of characters to look up the associated symbol.

The string will be chunked up into substrings the size of the window, and each substring will be converted into a Symbol object.

Author:
Matthew Pocock
See Also:
Serialized Form

Constructor Summary
FixedWidthParser(Alphabet alpha, int tokenLength)
           
 
Method Summary
 void addTokenMap(java.lang.String token, Symbol symbol)
          Maps a string (one or more characters) onto a symbol
 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

FixedWidthParser

public FixedWidthParser(Alphabet alpha,
                        int tokenLength)
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

addTokenMap

public void addTokenMap(java.lang.String token,
                        Symbol symbol)
                 throws IllegalSymbolException,
                        java.lang.IllegalArgumentException
Maps a string (one or more characters) onto a symbol
Parameters:
token - the string to be mapped
symbol - the symbol to be mapped onto