File Coverage

blib/lib/BioX/CLPM/Fragments.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::CLPM::Fragments;
use base qw(BioX::CLPM::Base);
use BioX::CLPM::Fragments::Simple;
use Class::Std;
use Class::Std::Utils;

use warnings;
use strict;
use Carp;

use version; our $VERSION = qv('0.0.1');

{
        my %sequence_id_of  :ATTR( :get   :set   :default<''>    :init_arg );
        my %list_of         :ATTR( :get          :set          :default<[]>    :init_arg );
        my %index_of        :ATTR( :get         :set         :default<'1'>   :init_arg );
        my %type_of         :ATTR( :get          :set          :default<''>    :init_arg );

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

        sub START {
                my ($self, $ident, $arg_ref) = @_;
                return;
        }

        sub list { my ( $self ) = @_; return @{ $self->get_list() }; }
        sub next_index { my ( $self ) = @_; my $index = $self->get_index(); $self->set_index( $index + 1 ); return $index; }

        sub add {
                my ( $self, $arg_ref ) = @_;
		my @fragments   = $self->list();
		my $fragment;
		if ( $self->get_type() eq 'simple' ) {
			my $sequence    = defined $arg_ref->{sequence}   ? $arg_ref->{sequence}   : '';
			my $mass        = defined $arg_ref->{mass}   ? $arg_ref->{mass}   : '';
			my $fragment_id = defined $arg_ref->{fragment_id} ? $arg_ref->{fragment_id} : $self->next_index();
			   $fragment    = BioX::CLPM::Fragments::Simple->new({
			             sequence    => $sequence,
        		             mass        => $mass,
        		             fragment_id => $fragment_id,
        		             sequence_id => $self->get_sequence_id() });
		}
		elsif ( $self->get_type() eq 'linked' ) {
			my $fragment_id_1 = defined $arg_ref->{fragment_id_1} ? $arg_ref->{fragment_id_1} : '';
			my $fragment_id_2 = defined $arg_ref->{fragment_id_2} ? $arg_ref->{fragment_id_2} : '';
			my $mass          = defined $arg_ref->{mass}   ? $arg_ref->{mass}   : '';
			my $mods          = defined $arg_ref->{mods}   ? $arg_ref->{mods}   : '';
			   $fragment      = BioX::CLPM::Fragments::Linked->new({
        		             fragment_id_1 => $fragment_id_1,
        		             fragment_id_2 => $fragment_id_2,
        		             mass          => $mass,
        		             mods          => $mods });
		}
		push( @fragments, $fragment );
		$self->set_list( \@fragments );
                return;
        }

}

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