=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

package XrefMapper::Methods::LocalExonerateGappedBest1;

use strict;
use File::Basename;

use XrefMapper::Methods::ExonerateBasic;

use vars '@ISA';

@ISA = qw{XrefMapper::Methods::ExonerateBasic};

our $exonerate_path = 'exonerate'; # Make sure exonerate binary is in
                                   # $PATH

sub options {

  return ('--model', 'affine:local', '--subopt', 'no', '--bestn', '1');

}

sub query_identity_threshold {

  #return 90;
  return 50;
}

sub target_identity_threshold {

  #return 90;
  return 50;
}

sub submit_exonerate{
  my ($self, $query, $target, $root_dir, @options) = @_;

  # Exonerate can run individual chunks of a large job.
  # Determine the number of chunks that will be used, and add to total
  my $num_jobs 
      = XrefMapper::Methods::ExonerateBasic::calculate_num_jobs($query);
  $self->jobcount($self->jobcount()+$num_jobs);

  # Determine the output filename
  my $queryfile = basename($query);
  my $targetfile = basename($target);
  my $query_alphabet = $queryfile =~ /peptide/ ? 'peptide' : 'dna';
  my $outfile = join( '_',
                      $self->get_class_name() , 
                      $query_alphabet, 
                      q[%s.map] # Substitute the chunk ID
                      );

  # Build a template representing the exonerate command
  my $options_str = join(" ", @options);
  my $exonerate_command = join
      ( " \\\n ", 
        $exonerate_path, 
        qq[--target $target],
        qq[--query $query], 
        qq[--querychunktotal $num_jobs],
        q [--querychunkid %s], # Substitute the chunk ID
        q [--showvulgar false],
        q [--showalignment FALSE],
        q [--ryo "%s"],
        $options_str );
  my $ryo_format = 'xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n';
  my $shell_command = qq[%s \\\n| grep '^xref' \\\n> %s/%s];

  # Run exonerate for each job chunk
  foreach( my $i=1; $i<=$num_jobs; $i++ ){
    my $command = sprintf( $shell_command, 
                           sprintf($exonerate_command, $i, $ryo_format),
                           $root_dir,
                           sprintf($outfile, $i) );
    my $status = system( $command );
    unless( $status == 0 ){ warn( "Bad exit status ($?) from:\n $command" )}
  }
}

sub submit_depend_job{
  die;
}

1;