Phoenix EMBL Parser README

INTRODUCTION
------------

Phoenix is a non-validating parser for the EMBL flat-file format. 

The format of EMBL flat files is described in the EMBL User Manual, available at:
 
	http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
 
and the format of the Feature Table element is further described in the
Feature Table Definition document, available at: 

	http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

To retrieve EMBL flat file records you can use either EBI dbfetch: 

	http://www.ebi.ac.uk/cgi-bin/emblfetch
	
or consult the EMBL information pages at:

	http://www.ebi.ac.uk/embl/Access/index.html

In the context of Phoenix the term non-validating means that the parser
is only concerned with the file being well-formed and does not attempt 
to perform any semantic validation of the content of the file.

For this very reason Phoenix is ideal for all those people who only want to
extract information from the publicly available flat files.


VERSION
-------

This is version 0.8 of Phoenix. 


WHAT IS PROVIDED
----------------

In order to be portable across platforms the Phoenix parser is built as
a static library. 

The sources of the Phoenix parser can be found under 

	src\libphoenix

As a user of Phoenix you will typically only need to #include <Phoenix.hpp>


PHOENIX SAMPLE APPLICATIONS
---------------------------

The following sample applications are provided:

	1) checkff
	2) showevents
	3) Showxml
	4) ff2xml
	5) efmt

checkff is the minimal Phoenix application. It just reads the input file and outputs
errors and warnings if the file is not well-formed.

showevents hooks into the Phoenix parser and displays on screen all the events that 
the parser generates while reading an input file. ShowEvents is particularly useful
to get an idea of what is happening under the hood while Phoenix parses a file.

Showxml and ff2xml show how Phoenix can be used to write a flat-file to XML conversion
utility. 

efmt is a Unix-style pipe that can be used to remove the artifacts produced by 
text editors (even though EMBL flat files are text files, they do have some 
unusual requirements that conflict with the way most text editor save files). 


DISCLAIMER
-----------

If you want to contact me about bugs in Phoenix please send an e-mail to:

	phoenix@renatomancuso.com

Palermo, 7 June 2005

Renato Mancuso