Package uk.ac.man.bioinf.io

Interface Summary

AlignmentInputParser	This is an interface that provides a definition for any sequence parsers.
AlignmentOutputParser	This is an interface that provides a definition for any sequence output parsing.
ParserExceptionHandler	Handles exceptions generated by any sequence parsers.
SequenceInputParser	SequenceInputParser.java This class defines the basic interface for parsing sequence files.

Class Summary

DefaultParserExceptionHandler	This parser exception handler does very little.
NarrowedInputStream	NarrowedInputStream.java This InputStream wraps another and puts a limits access to that stream.
NullParserExceptionHandler	NullParserExceptionHandler.java An exception handler for all seasons Created: Thu Feb 8 21:24:57 2001

Exception Summary

InvalidSequenceTypeParserException	This exception is cast when there is a mismatch of sequence types when dealing with parsers.
ParserException	A general exception thrown up when parsing a sequence.
SequenceWriterException	An exception cast when an IOException is thrown in writing the sequence out from CINEMA.
UnknownElementException	An exception to flag an unrecognised element in a string.