File Coverage

blib/lib/BioX/CLPM/Base.pm

Criterion	Covered	Total	%
statement	1	3	33.3
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	2	4	50.0

package BioX::CLPM::Base;
use Class::Std;
use Class::Std::Utils;
use DBIx::MySperqlOO;
use File::Spec;
use YAML qw(DumpFile LoadFile);

use warnings;
use strict;
use Carp;

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

our $config_filename = '.clpm/config';

{
        #my %attribute_of  :ATTR( :get   :set   :default<''>    :init_arg );
        my %storage_of    :ATTR( :get     :set     :default<'db'>      :init_arg );
        my %lookups_of    :ATTR( :get     :set     :default<'local'>   :init_arg );
	my %data_dbh_of   : ATTR();

        sub BUILD {
                my ($self, $ident, $arg_ref) = @_;
		my $config              = $self->_load_config();
        	   $data_dbh_of{$ident} = DBIx::MySperqlOO->new( $config->{data} );
                return;
        }

	sub get_config_filename  { return File::Spec->catfile( $ENV{HOME}, $config_filename ); }

	sub sqlexec {
		my ( $self, $sql, $return ) = @_;
		my $data   = $data_dbh_of{ident $self};
		   $sql    = $sql    ? $sql    : '';
		   $return = $return ? $return : '';
		if ( $return eq '\@@' ) {
			my $rows_ref;
			if ( $sql ) { $rows_ref = $data->sqlexec( $sql, $return ); }
			return $rows_ref;
		}
		elsif ( $return eq '@' ) {
			my @data;
			if ( $sql ) { @data = $data->sqlexec( $sql, $return ); }
			return @data;
		}
	}

	# UTIL
	sub load_masses {
		my ( $self ) = @_;
		my $rows_ref = $self->sqlexec( 'select letter, mass from amino_acids', '\@@' );
		my %aa_masses;
		foreach my $row_ref ( @$rows_ref ) {
			my ( $letter, $mass ) = @$row_ref;
			$aa_masses{$letter} = $mass;
		}
		return \%aa_masses;
	}

	sub _load_config {
		my ( $self ) = @_;
		return LoadFile( $self->get_config_filename() );
	}

	sub _sql_escape {
		my ( $self, $string ) = @_;
		if ($string) { $string =~ s/(['"\\])/\\$1/g; }
		return $string;
	}

}

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