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lib/GenOO/RegionCollection/Type/DBIC.pm  view on Meta::CPAN

# POD documentation - main docs before the code

=head1 NAME

GenOO::RegionCollection::Type::DBIC - Class for a collection of GenOO::Region objects stored in a database.

=head1 SYNOPSIS

    # Object that corresponds to a collection of GenOO::Region objects.
    # To initialize 
    my $region_collection = GenOO::RegionCollection::DB->new(
        driver      => undef,
        host        => undef,
        database    => undef,
        table       => undef,
        user        => undef,
        password    => undef,
        port        => undef,
        name        => undef,
        species     => undef,
        description => undef,
        extra       => undef,
    );


=head1 DESCRIPTION

    This class consumes the L<GenOO::RegionCollection> role.
    An instance of this class corresponds to a collection of records consuming the L<GenOO::Region>
    role.The records are stored in a database (ie MySQL, SQLite, etc) and the class offers methods 
    for quering them and accessing specific characteristics (eg. longest record). Internally the class
    rests on DBIx::Class for the database access and for defining the appropriate result objects.
    Note that the columns which correspond to the required attributes of L<GenOO::Region> must exist
    in the table schema (ie. strand, rname, start, stop, copy_number)

=head1 EXAMPLES

    # Get the records contained in a specific region
    my @records = $region_collection->records_contained_in_region(1,'chr3',127726308,127792250);
    
    # Get the longest record
    my $longest_record = $region_collection->longest_record;
    
=cut

# Let the code begin...

package GenOO::RegionCollection::Type::DBIC;
$GenOO::RegionCollection::Type::DBIC::VERSION = '1.5.2';

#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Modern::Perl;
use autodie;
use Moose;
use namespace::autoclean;


#######################################################################
########################   Load GenOO modules   #######################
#######################################################################
use GenOO::Data::DB::DBIC::Species::Schema;


#######################################################################
#######################   Interface attributes   ######################
#######################################################################
has 'dsn' => (
	isa      => 'Str',
	is       => 'ro',
);

has 'user' => (
	isa => 'Maybe[Str]',
	is => 'ro'
);

has 'password' => (
	isa => 'Maybe[Str]',
	is  => 'ro'
);

has 'attributes' => (
	traits    => ['Hash'],
	is        => 'ro',
	isa       => 'HashRef[Str]',
	default   => sub { {} },
);

has 'table' => (
	isa      => 'Str',
	is       => 'ro',
);

has 'records_class' => (
	is        => 'ro',
	default   => 'GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v1',
);

has 'name' => (
	isa => 'Str',
	is => 'rw'
);

has 'species' => (
	isa => 'Str',
	is => 'rw'
);

has 'description' => (
	isa => 'Str',
	is => 'rw'
);