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Bio/SeqEvolution/Factory.pm  view on Meta::CPAN

 Returns : an array of sequences mutated from the reference sequence
           according to evolutionary parameters given
 Args    : -

=cut

sub each_seq{
   my $self = shift;
   my $number = shift;

   $self->throw("[$number] ". ' should be a positive integer')
       unless $number =~ /^[+\d]+$/;

   my @array;
   for (my $count=1; $count<$number; $count++) {
       push @array, $self->next_seq();

   }
   return @array;
}



=head2 each_mutation

  Title   : each_mutation
  Usage   : $obj->each_mutation
  Function: return the mutations leading to the last generated 
            sequence in objects 
  Returns : an array of Bio::Variation::DNAMutation objects
  Args    : optional argument to return an array of  stringified names

=cut

sub each_mutation {
    my $self = shift;
    my $string = shift;

    return @{$self->{'_mutations'}} if $string;

    return map {
        /(\d+)(\w*)>(\w*)/;
#        print;
        my $dnamut = Bio::Variation::DNAMutation->new
            ('-start'         => $1,
             '-end'           => $1,
             '-length'        => 1,
             '-isMutation'    => 1
            );
        $dnamut->allele_ori( Bio::Variation::Allele->new(-seq => $2,
                                                         -alphabet => 'dna') );
        $dnamut->add_Allele( Bio::Variation::Allele->new(-seq => $3,
                                                         -alphabet => 'dna') );
        $dnamut;
    } @{$self->{'_mutations'}}
}


sub get_alignment_identity  {
    my $self = shift;
    return $self->{'_align'}->overall_percentage_identity;
}


sub get_alignmet {
   my $self = shift;
   return $self->{'_align'}->remove_gaps('-', 'all-gaps');
}


=head1 Internal methods

=cut


=head2 _increase_mutation_counter

 Title   : _increase_mutation_counter
 Usage   : $obj->_increase_mutation_counter()
 Function: Internal method to increase the counter of mutations performed
 Returns : value of counter
 Args    : -

=cut

sub _increase_mutation_counter{
   return shift->{'_mutation_counter'}++;
}



=head2 _increase_sequence_counter

 Title   : _increase_sequence_counter
 Usage   : $obj->_increase_sequence_counter()
 Function: Internal method to increase the counter of sequences created
 Returns : value of counter
 Args    : -

=cut

sub _increase_sequence_counter{
   return shift->{'_sequence_counter'}++;
}


1;