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lib/Bio/SeqAlignment/Components/SeqMapping/Mapper/Generic.pm  view on Meta::CPAN

package Bio::SeqAlignment::Components::SeqMapping::Mapper::Generic;
$Bio::SeqAlignment::Components::SeqMapping::Mapper::Generic::VERSION = '0.03';
use strict;
use warnings;

#ABSTRACT: A generic sequence mapper for sequence mapping
use Carp;
use Module::Runtime 'use_module';
use Module::Find;
use Scalar::Util 'blessed';
use Moose;
use namespace::autoclean;
###############################################################################
## Searching/Mapping related methods
has 'init_sim_search' => (
    is      => 'rw',
    isa     => 'CodeRef',
    default => sub {
        sub { }
    },
    trigger => sub { $_[0]->_nondefault_set( 'init_sim_search', @_ ) },
);

has 'seq_align' => (
    is      => 'rw',
    isa     => 'CodeRef',
    default => sub {
        sub { }
    },
    trigger => sub { $_[0]->_nondefault_set( 'seq_align', @_ ) },
);

has 'extract_sim_metric' => (
    is      => 'rw',
    isa     => 'CodeRef',
    default => sub {
        sub { }
    },
    trigger => sub { $_[0]->_nondefault_set( 'extract_sim_metric', @_ ) },
);

has 'reduce_sim_metric' => (
    is      => 'rw',
    isa     => 'CodeRef',
    default => sub {
        sub { }
    },
    trigger => sub { $_[0]->_nondefault_set( 'reduce_sim_metric', @_ ) },
);

has 'cleanup' => (
    is      => 'rw',
    isa     => 'CodeRef',
    default => sub {
        sub { }
    },
    trigger => sub { $_[0]->_nondefault_set( 'cleanup', @_ ) },
);

###############################################################################
## Reference Database related methods
has 'create_refDB' => (
    is      => 'rw',
    isa     => 'CodeRef',
    default => sub {
        sub { }
    },
    trigger => sub { $_[0]->_nondefault_set( 'create_refDB', @_ ) },
);

has 'use_refDB' => (
    is      => 'rw',