<commit_before>=head1 NAME - Bio::EnsEMBL::Compara::PeptideAlignFeature

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 CONTACT

Describe contact details here

=head1 APPENDIX

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

=cut

my $_paf_build_homology_idx = 1; #global index counter

package Bio::EnsEMBL::Compara::PeptideAlignFeature;

use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Compara::Homology;
use Bio::EnsEMBL::Compara::Attribute;

#se overload '<=>' => "sort_by_score_evalue_and_pid";   # named method

@ISA = qw(Bio::EnsEMBL::Root);

sub new {
  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);

  $self->query_member(new Bio::EnsEMBL::Compara::Member);
  $self->hit_member(new Bio::EnsEMBL::Compara::Member);

  if (scalar @args) {
    my ($query_stable_id,$hit_stable_id,
        $query_member_id,$hit_member_id,
        $analysis,
        $qstart,$hstart,$qend,$hend,<commit_msg>changed method for calculating homology stable_id to use time() to get starting number for index counter<commit_after>=head1 NAME - Bio::EnsEMBL::Compara::PeptideAlignFeature

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 CONTACT

Describe contact details here

=head1 APPENDIX

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

=cut

my $_paf_build_homology_idx = time(); #global index counter

package Bio::EnsEMBL::Compara::PeptideAlignFeature;

use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Compara::Homology;
use Bio::EnsEMBL::Compara::Attribute;

#se overload '<=>' => "sort_by_score_evalue_and_pid";   # named method

@ISA = qw(Bio::EnsEMBL::Root);

sub new {
  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);

  $self->query_member(new Bio::EnsEMBL::Compara::Member);
  $self->hit_member(new Bio::EnsEMBL::Compara::Member);

  if (scalar @args) {
    my ($query_stable_id,$hit_stable_id,
        $query_member_id,$hit_member_id,
        $analysis,
        $qstart,$hstart,$qend,$hend,
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