Bio-SeqAlignment-Components-SeqMapping

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META.json  view on Meta::CPAN

      "runtime" : {
         "requires" : {
            "Carp" : "0",
            "MCE" : "0",
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            "Module::Find" : "0",
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            "Moose" : "0",
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            "namespace::autoclean" : "0",
            "strict" : "0",
            "warnings" : "0"
         }
      },
      "test" : {
         "recommends" : {
            "CPAN::Meta" : "2.120900"
         },
         "requires" : {
            "ExtUtils::MakeMaker" : "0",

META.yml  view on Meta::CPAN

    version: '0.03'
requires:
  Carp: '0'
  MCE: '0'
  MCE::Candy: '0'
  Module::Find: '0'
  Module::Runtime: '0'
  Moose: '0'
  Moose::Role: '0'
  Scalar::Util: '0'
  namespace::autoclean: '0'
  strict: '0'
  warnings: '0'
version: '0.03'
x_generated_by_perl: v5.38.0
x_serialization_backend: 'YAML::Tiny version 1.74'
x_spdx_expression: 'Artistic-1.0-Perl OR GPL-1.0-or-later'

Makefile.PL  view on Meta::CPAN

  "NAME" => "Bio::SeqAlignment::Components::SeqMapping",
  "PREREQ_PM" => {
    "Carp" => 0,
    "MCE" => 0,
    "MCE::Candy" => 0,
    "Module::Find" => 0,
    "Module::Runtime" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Scalar::Util" => 0,
    "namespace::autoclean" => 0,
    "strict" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {
    "ExtUtils::MakeMaker" => 0,
    "File::Spec" => 0,
    "Test::More" => 0
  },
  "VERSION" => "0.03",
  "test" => {

lib/Bio/SeqAlignment/Components/SeqMapping/Dataflow/LinearGeneric.pm  view on Meta::CPAN

package Bio::SeqAlignment::Components::SeqMapping::Dataflow::LinearGeneric;
$Bio::SeqAlignment::Components::SeqMapping::Dataflow::LinearGeneric::VERSION = '0.03';
use strict;
use warnings;

use Moose::Role;
use Carp;
use MCE;
use MCE::Candy;
use namespace::autoclean;

requires 'seq_align';    ## the method that does (pseudo)alignment mapping & reductions
requires 'cleanup';

sub sim_seq_search {

    my ( $self, $workload, %args ) = @_;

    croak 'expect an array(ref) as workload' unless ref $workload eq 'ARRAY';

lib/Bio/SeqAlignment/Components/SeqMapping/Dataflow/LinearLinear.pm  view on Meta::CPAN

package Bio::SeqAlignment::Components::SeqMapping::Dataflow::LinearLinear;
$Bio::SeqAlignment::Components::SeqMapping::Dataflow::LinearLinear::VERSION = '0.03';
use strict;
use warnings;

use Moose::Role;
use Carp;
use MCE;
use MCE::Candy;
use namespace::autoclean;

requires 'seq_align';          ## the method that does (pseudo)alignment
requires 'extract_sim_metric'; ## extract the similarity metric from the search
requires 'reduce_sim_metric';  ## reduce the similarity metric to a single value
requires 'cleanup';

sub sim_seq_search {

    my ( $self, $workload, %args ) = @_;

lib/Bio/SeqAlignment/Components/SeqMapping/Dataflow/LinearLinearGeneric.pm  view on Meta::CPAN

package Bio::SeqAlignment::Components::SeqMapping::Dataflow::LinearLinearGeneric;
$Bio::SeqAlignment::Components::SeqMapping::Dataflow::LinearLinearGeneric::VERSION = '0.03';
use strict;
use warnings;

use Moose::Role;
use Carp;
use MCE;
use MCE::Candy;
use namespace::autoclean;

requires 'seq_align';          ## the method that does (pseudo)alignment
requires 'extract_sim_metric'; ## extract the similarity metric from the search
requires 'reduce_sim_metric';  ## reduce the similarity metric to a single value
requires 'cleanup';

sub sim_seq_search {

    my ( $self, $workload, %args ) = @_;

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

$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', @_ ) },
);

t/00-report-prereqs.dd  view on Meta::CPAN

       'runtime' => {
                      'requires' => {
                                      'Carp' => '0',
                                      'MCE' => '0',
                                      'MCE::Candy' => '0',
                                      'Module::Find' => '0',
                                      'Module::Runtime' => '0',
                                      'Moose' => '0',
                                      'Moose::Role' => '0',
                                      'Scalar::Util' => '0',
                                      'namespace::autoclean' => '0',
                                      'strict' => '0',
                                      'warnings' => '0'
                                    }
                    },
       'test' => {
                   'recommends' => {
                                     'CPAN::Meta' => '2.120900'
                                   },
                   'requires' => {
                                   'ExtUtils::MakeMaker' => '0',

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