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lib/Bio/Polloc/LocusIO/gff3.pm  view on Meta::CPAN

   }
   if(defined $genomes){
      my $genome;
      # Search the genome by name:
      if(defined $genome_name){
	 for my $g (@$genomes){
	    $genome = $g if $g->name eq $genome_name;
	    last if defined $genome;
	 }
      }
      # Search the genome by sequence name (prone to errors, but it's a guess):
      unless(defined $genome){
	 for my $g (@$genomes){
	    $genome = $g if defined $g->search_sequence($seqid);
	    last if defined $genome;
	 }
      }
      $locus->genome($genome);
   }
   $locus->comments(@comments);
   return $self->_save_locus($locus);

lib/Bio/Polloc/RuleI.pm  view on Meta::CPAN

   1 => with respect to the start of the sequence
   0 => somewhere within the sequence (ignores the second)
  -1 => with respect to the end of the sequence

And the second being the number of residues from the reference point.  The second
value can be positive, negative, or zero.

=item Arguments

Three integers, or one integer equal to zero.  Please note that this function is
extremely tolerant, and tries to guess the context regardless of the input.

=item Returns

A reference to the array described above.

=back

=cut

sub context {