Bio-Palantir

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META.yml  view on Meta::CPAN

  POSIX: '0'
  Path::Class: '0'
  Smart::Comments: '0'
  Template: '0'
  Test::Most: '0'
  XML::Bare: '0.53'
  XML::Hash::XS: '0'
  aliased: '0'
  autodie: '0'
  feature: '0'
  namespace::autoclean: '0'
  perl: '5.013002'
  strict: '0'
  warnings: '0'
version: '0.211420'
x_generated_by_perl: v5.22.0
x_serialization_backend: 'YAML::Tiny version 1.73'
x_spdx_expression: 'Artistic-1.0-Perl OR GPL-1.0-or-later'

Makefile.PL  view on Meta::CPAN

    "POSIX" => 0,
    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Template" => 0,
    "Test::Most" => 0,
    "XML::Bare" => "0.53",
    "XML::Hash::XS" => 0,
    "aliased" => 0,
    "autodie" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0,
    "strict" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {
    "Test::Most" => 0
  },
  "VERSION" => "0.211420",
  "test" => {
    "TESTS" => "t/*.t"
  }

lib/Bio/Palantir/Explorer/GeneFasta.pm  view on Meta::CPAN

package Bio::Palantir::Explorer::GeneFasta;
# ABSTRACT: Explorer internal class for handling GeneFasta objects
$Bio::Palantir::Explorer::GeneFasta::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use Data::UUID;
use List::AllUtils qw(each_array);

use aliased 'Bio::Palantir::Refiner::DomainPlus';
with 'Bio::Palantir::Roles::Fillable';


# public attributes

lib/Bio/Palantir/Parser.pm  view on Meta::CPAN

package Bio::Palantir::Parser;
# ABSTRACT: front-end class for Bio::Palantir::Parser module, wich handles the parsing of biosynML.xml and regions.js antiSMASH reports
$Bio::Palantir::Parser::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use autodie;

use Carp;
use File::Basename 'fileparse';
use File::Temp;
use JSON::Parse 'json_file_to_perl';
use POSIX 'ceil';
use XML::Bare;
use XML::Hash::XS;

lib/Bio/Palantir/Parser/Cluster.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Cluster;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Cluster::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);
use Data::UUID;

use aliased 'Bio::Palantir::Parser::Gene';
use aliased 'Bio::Palantir::Parser::Location';

lib/Bio/Palantir/Parser/Domain.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Domain;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Domain::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);
use Data::UUID;

use aliased 'Bio::Palantir::Parser::Motif';
use aliased 'Bio::Palantir::Parser::Location';

lib/Bio/Palantir/Parser/Gene.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Gene;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Gene::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);
use Data::UUID;

use aliased 'Bio::Palantir::Parser::Domain';
use aliased 'Bio::Palantir::Parser::Motif';
use aliased 'Bio::Palantir::Parser::Qualifier';
use aliased 'Bio::Palantir::Parser::Location';

lib/Bio/Palantir/Parser/Location.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Location;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Location::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);
use POSIX;



# private attributes
has '_root' => (

lib/Bio/Palantir/Parser/Motif.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Motif;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Motif::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);
use Data::UUID;

use aliased 'Bio::Palantir::Parser::Qualifier';
use aliased 'Bio::Palantir::Parser::Location';

lib/Bio/Palantir/Parser/Qualifier.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Qualifier;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Qualifier::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);



# private attributes
has '_root' => (
    is       => 'ro',

lib/Bio/Palantir/Parser/Root.pm  view on Meta::CPAN

package Bio::Palantir::Parser::Root;
# ABSTRACT: BiosynML DTD-derived internal class
$Bio::Palantir::Parser::Root::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);
use POSIX;

use aliased 'Bio::Palantir::Parser::Cluster';
use aliased 'Bio::Palantir::Parser::Gene';
use aliased 'Bio::Palantir::Parser::Domain';
use aliased 'Bio::Palantir::Parser::Motif';

lib/Bio/Palantir/Refiner.pm  view on Meta::CPAN

package Bio::Palantir::Refiner;
# ABSTRACT: front-end class for Bio::Palantir::Refiner module, wich handles the refinement of NRPS/PKS BGC annotations
$Bio::Palantir::Refiner::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use Data::UUID;

use aliased 'Bio::Palantir::Parser';
use aliased 'Bio::Palantir::Refiner::ClusterPlus';
extends 'Bio::FastParsers::Base';


# ATTRIBUTES

lib/Bio/Palantir/Refiner/ClusterPlus.pm  view on Meta::CPAN

package Bio::Palantir::Refiner::ClusterPlus;
# ABSTRACT: Refiner internal class for handling ClusterPlus objects
$Bio::Palantir::Refiner::ClusterPlus::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use Data::UUID;

use aliased 'Bio::Palantir::Refiner::GenePlus';


# private attributes

has '_cluster' => (
    is      => 'ro',

lib/Bio/Palantir/Refiner/DomainPlus.pm  view on Meta::CPAN

package Bio::Palantir::Refiner::DomainPlus;
# ABSTRACT: Refiner internal class for handling DomainPlus objects
$Bio::Palantir::Refiner::DomainPlus::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use Data::UUID;


# public attributes

has 'uui' => (
    is       => 'ro',
    isa      => 'Str',
    init_arg => undef,

lib/Bio/Palantir/Refiner/GenePlus.pm  view on Meta::CPAN

package Bio::Palantir::Refiner::GenePlus;
# ABSTRACT: Refiner internal class for handling GenePlus objects
$Bio::Palantir::Refiner::GenePlus::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use Data::UUID;
use List::AllUtils qw(each_array);

use aliased 'Bio::Palantir::Refiner::DomainPlus';


# private attributes

has '_gene' => (

lib/Bio/Palantir/Roles/Modulable/Component.pm  view on Meta::CPAN

package Bio::Palantir::Roles::Modulable::Component;
$Bio::Palantir::Roles::Modulable::Component::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use aliased 'Bio::Palantir::Parser::Domain';
use aliased 'Bio::Palantir::Refiner::DomainPlus';


# private attributes

has 'uui' => (
    is       => 'ro',
    isa      => 'Str',

lib/Bio/Palantir/Roles/Modulable/Module.pm  view on Meta::CPAN

package Bio::Palantir::Roles::Modulable::Module;
$Bio::Palantir::Roles::Modulable::Module::VERSION = '0.211420';
use Moose;
use namespace::autoclean;

use aliased 'Bio::Palantir::Parser::Domain';
use aliased 'Bio::Palantir::Refiner::DomainPlus';


# private attributes

has 'uui' => (
    is       => 'ro',
    isa      => 'Str',

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