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#
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Alignment::Proda - Object for the calculation of sets
of multiple sequence alignments from a set of unaligned sequences or
alignments using the Proda program. 

=head1 SYNOPSIS

  # Build a Proda alignment factory
  $factory = Bio::Tools::Run::Alignment::Proda->new(@params);

  # Pass the factory a list of sequences to be aligned.
  $inputfilename = 't/cysprot.fa';
  # @alns is an array of SimpleAlign objects.
  @alns = $factory->align($inputfilename);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  @alns = $factory->align($seq_array_ref);

  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:

  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.

  $factory = Bio::Tools::Run::Alignment::Proda->new();
  @alns = $factory->align($seq_array_ref);

=head1 DESCRIPTION

You can get it and see information about it at this URL
http://proda.stanford.edu

This program will return one or more local alignments for the
different repeated or rearranged regions in the sequences. If a
sequences contains more than one of those patterns, it will be present
more than once in the alignment. The difference will be in that the id
contain the start and end, like myseqid(123-456) and myseqid(567-890),
instead of simply myseqid as in the original input file. This is true
for all the output ids, even if they are present only once.

=head2 Helping the module find your executable 

You will need to enable Proda to find the proda program. This can be
done in (at least) three ways:

  1. Make sure the proda executable is in your path (i.e. 
     'which proda' returns a valid program
  2. define an environmental variable PRODADIR which points to a 
     directory containing the 'proda' app:
   In bash 
	export PRODADIR=/home/progs/proda   or
   In csh/tcsh
        setenv PRODADIR /home/progs/proda

  3. include a definition of an environmental variable PRODADIR 
      in every script that will
     BEGIN {$ENV{PRODADIR} = '/home/progs/proda'; }
     use Bio::Tools::Run::Alignment::Proda;


=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the web:

 http://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR -  Albert Vilella

Email avilella-at-gmail-dot-com

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut

package Bio::Tools::Run::Alignment::Proda;

use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS
            @PRODA_PARAMS @PRODA_SWITCHES @OTHER_SWITCHES 
            %OK_FIELD
            );
use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;