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.