uk.ac.man.bioinf.io.parsers
Class AbstractProteinSequenceInputParser

java.lang.Object
  |
  +--uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser
All Implemented Interfaces:
SequenceInputParser
Direct Known Subclasses:
FastaSequenceParser

public abstract class AbstractProteinSequenceInputParser
extends Object
implements SequenceInputParser

AbstractProteinSequenceInputParser.java Provides a root class for all protein sequence parsers. Created: Wed Feb 7 15:08:25 2001

Version:
$Id: AbstractProteinSequenceInputParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $
Author:
Phillip Lord

Constructor Summary
AbstractProteinSequenceInputParser()
           
 
Method Summary
protected  UnknownElementException createException(int position, char elem)
           
protected  Element[] toElements(String seq, ParserExceptionHandler eh)
           
protected  Sequence toSequence(Identifier ident, String seq, ParserExceptionHandler eh)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface uk.ac.man.bioinf.io.SequenceInputParser
getDescription, parse
 

Constructor Detail

AbstractProteinSequenceInputParser

public AbstractProteinSequenceInputParser()
Method Detail

toSequence

protected Sequence toSequence(Identifier ident,
                              String seq,
                              ParserExceptionHandler eh)

toElements

protected Element[] toElements(String seq,
                               ParserExceptionHandler eh)

createException

protected UnknownElementException createException(int position,
                                                  char elem)