[Bioperl-l] EMBOSS ACD parsing

[Heikki Lehvaslaiho]

I added Bio::Tools::Run::EMBOSSacd.pm and modified other EMBOSS modules
to take that into account. Now if you set EMBOSSApplication verbose > 0
(or in the factory; the value is passed to new application objects), the 
input argument hash is compared to possible program options.

Following Peter Rice's suggestion  EMBOSS ACD (Ajax Command Definition)
files are read in using command 'acdc $program -help -verbose -acdtable'. 
That seems to be only way to get absolutely all available options out of 
EMBOSS. The output is a HTML table, which I decided to convert into XHTML 
and use XML::Twig to parse it. The EMBOSS modules should work even without 
XML::Twig but without error checking.

Verbose setting is used to print out various other debugging messages, too. 
The output is a bit messy and should be cleaned.

	-Heikki



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       _/      _/                      http://www.ebi.ac.uk/mutations/
      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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