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  #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.

  #To run amap with training, try something like:

  #First round to generate train.params
  $factory = Bio::Tools::Run::Alignment::Amap->new
      (
       'iterative-refinement'  => '1000',
       'consistency'   => '5',
       'pre-training' => '20',
       'emissions' => '',
       'verbose' => '',
       'train'   => "$dir/$subdir/$outdir/train.params",
      );
  $factory->outfile_name("$dir/$subdir/$outdir/train.params");

  #Second round to use train.params to get a high qual alignment

  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);
  $aln = '';
  $factory = '';

  $factory = Bio::Tools::Run::Alignment::Amap->new
      (
       'iterative-refinement'  => '1000',
       'consistency'   => '5',
       'pre-training' => '20',
       'verbose' => '',
       'paramfile'   => "$dir/$subdir/$outdir/train.params",
      );
  $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
  $aln = $factory->align($seq_array_ref);

=head1 DESCRIPTION

Amap uses a Sequence Annealing algorithm which is an incremental
method for building multiple alignments. You can get it and see
information about it at this URL http://bio.math.berkeley.edu/amap/


=head2 Helping the module find your executable 

FIXME: Amap uses the same parameters as Probcons, plus a few others. I
haven't had time to check all the changes from the Probcons.pm
runnable. Feel free to do it.

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

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

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

=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 foo@bar.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::Amap;

use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS
            @AMAP_PARAMS @AMAP_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;
use Bio::Factory::ApplicationFactoryI;