File Coverage

blib/lib/BioX/SeqUtils/Promoter/Sequence.pm

Criterion	Covered	Total	%
statement	3	3	100.0
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	4	4	100.0

package BioX::SeqUtils::Promoter::Sequence;
####################################################################
#	               Charles Stephen Embry			   #
#	            MidSouth Bioinformatics Center		   #
#	        University of Arkansas Little Rock	           #
####################################################################
use base qw(BioX::SeqUtils::Promoter::Base);
use Class::Std;
use Class::Std::Utils;

use warnings;
use strict;
use Carp;

use version; our $VERSION = qv('0.1.1');

{
        my %base_list_of   :ATTR( :get   :set   :default<[]>    :init_arg );
        my %color_list_of  :ATTR( :get  :set  :default<[]>    :init_arg );
        my %label_of       :ATTR( :get       :set       :default<''>    :init_arg );




        sub BUILD {
                my ($self, $ident, $arg_ref) = @_;


                return;
        }

        sub START {
                my ($self, $ident, $arg_ref) = @_;
		#assigned default value
		my $sequence = defined $arg_ref->{sequence} ?  $arg_ref->{sequence} : '';
		#splits a list on every character
		my @sequence = split('',$sequence);
		#reference a list
		$self->set_base_list(\@sequence);
                return;
        }

	sub get_sequence {
		my ($self, $arg_ref) = @_;
		my $base_list = $self->get_base_list();
		#returns the list of nucleotides as a single string
                return join('',@$base_list);
        }

	sub get_labels {
		my ($self, $arg_ref) = @_;
		my $label = $self->get_label();
                return join('',@$label);
        }
	sub add_segment {
		my ($self, $arg_ref) = @_;
		#takes a sequence and adds it to base_list
		my $sequence = defined $arg_ref->{sequence} ?  $arg_ref->{sequence} : '';
		my @sequence = split('',$sequence);

		my $base_list = $self->get_base_list();
		my @base_list = @$base_list;

		push @base_list, @sequence;
		$self->set_base_list(\@base_list);
	}

	sub set_color {
                my ($self, $arg_ref) = @_;

		my $bases = defined $arg_ref->{bases} ?  $arg_ref->{bases} : '';
		my $colors = defined $arg_ref->{colors} ?  $arg_ref->{colors} : '';

		my $color_list = $self->get_color_list({colors => $colors});

		my $count = @$bases;
		for (my $i = 0; $i< $count; $i++) {
			my $base = $bases->[$i];
			my $color = $colors->[$i];
			$color_list->[$base] = $color;

			}

		$self->set_color_list($color_list);
		#color list will be used to give each character from a mulitple alignment file a color
                return;
        }

	sub add_tag {
		my ($self, $arg_ref) = @_;
		my $tag = defined $arg_ref->{tag} ?  $arg_ref->{tag} : '';
		my @tag = split('',$tag);

		my $label = $self->get_label();
		my @label = @$label;

		push @label, @tag;
		$self->set_label(\@label);
	}


}

1; # Magic true value required at end of module
__END__