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Many methods common to all analyses are inherited from
Bio::Tools::Analysis::SimpleAnalysisBase.

=back

=head1 SEE ALSO

L<Bio::SimpleAnalysisI>, 
L<Bio::Tools::Analysis::SimpleAnalysisBase>, 
L<Bio::Seq::Meta::Array>, 
L<Bio::WebAgent>

=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:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk, 

=head1 APPENDIX

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


=cut


use strict;
package Bio::Tools::Analysis::Protein::Domcut;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw(GET);
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;

use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);

my $URL = 'http://www.Bork.EMBL-Heidelberg.DE/Docu/mikita/domplot.cgi?';
my $ANALYSIS_NAME = 'Domcut';
my $ANALYSIS_SPEC =
    {
     'name'        => 'Domcut',
     'type'        => 'protein', #compulsory entry as is used for seq checking
     'version'     => 'n/a',
     'supplier'    => 'Ohara lab, Laboratory of DNA technology, 
                       Kazusa DNA Research Institute, 1532-3 Yana,
                       Kisarazu, Japan',
     'description' => 'to predict domain boundaries in proteins',
     'reference'   => 'Bioinformatics 19, 673-674 (2003)',
    };


my $INPUT_SPEC =
    [
     {
      'mandatory' => 'true',
      'type'      => 'Bio::PrimarySeqI',
      'name'      => 'seq',
     },
    ];

my  $RESULT_SPEC =
    {
     ''                 => 'bulk',              # same as undef
     'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic',
     'parsed'           => "Array of {'score' =>, 'rank'=> ]",
     'meta'             => 'Bio::Seq::Meta::Array object'
    };

=head2 result

 Name    : result
 Purpose : To retrieve results of analysis in one of several formats.
 Usage   : $job->result (...)
 Returns : a result created by running an analysis
 Args    : various - see keysin $RESULT_SPEC. 

The method returns a result of an executed job. If the job was
terminated by an error the result may contain an error message instead
of the real data.

This implementation returns differently processed data depending on
argument:

=over 3

=item undef

Returns the raw ASCII data stream but without HTML tags

=item 'Bio::SeqFeatureI'