/usr/share/perl5/Bio/Chado/Schema/Result/Sequence/FeatureRelationship.pm is in libbio-chado-schema-perl 0.20000-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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BEGIN {
$Bio::Chado::Schema::Result::Sequence::FeatureRelationship::AUTHORITY = 'cpan:RBUELS';
}
{
$Bio::Chado::Schema::Result::Sequence::FeatureRelationship::VERSION = '0.20000';
}
# Created by DBIx::Class::Schema::Loader
# DO NOT MODIFY THE FIRST PART OF THIS FILE
use strict;
use warnings;
use base 'DBIx::Class::Core';
=head1 NAME
Bio::Chado::Schema::Result::Sequence::FeatureRelationship
=head1 DESCRIPTION
Features can be arranged in
graphs, e.g. "exon part_of transcript part_of gene"; If type is
thought of as a verb, the each arc or edge makes a statement
[Subject Verb Object]. The object can also be thought of as parent
(containing feature), and subject as child (contained feature or
subfeature). We include the relationship rank/order, because even
though most of the time we can order things implicitly by sequence
coordinates, we can not always do this - e.g. transpliced genes. It is also
useful for quickly getting implicit introns.
=cut
__PACKAGE__->table("feature_relationship");
=head1 ACCESSORS
=head2 feature_relationship_id
data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'feature_relationship_feature_relationship_id_seq'
=head2 subject_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0
The subject of the subj-predicate-obj sentence. This is typically the subfeature.
=head2 object_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0
The object of the subj-predicate-obj sentence. This is typically the container feature.
=head2 type_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0
Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.
=head2 value
data_type: 'text'
is_nullable: 1
Additional notes or comments.
=head2 rank
data_type: 'integer'
default_value: 0
is_nullable: 0
The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.
=cut
__PACKAGE__->add_columns(
"feature_relationship_id",
{
data_type => "integer",
is_auto_increment => 1,
is_nullable => 0,
sequence => "feature_relationship_feature_relationship_id_seq",
},
"subject_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 0 },
"object_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 0 },
"type_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 0 },
"value",
{ data_type => "text", is_nullable => 1 },
"rank",
{ data_type => "integer", default_value => 0, is_nullable => 0 },
);
__PACKAGE__->set_primary_key("feature_relationship_id");
__PACKAGE__->add_unique_constraint(
"feature_relationship_c1",
["subject_id", "object_id", "type_id", "rank"],
);
=head1 RELATIONS
=head2 subject
Type: belongs_to
Related object: L<Bio::Chado::Schema::Result::Sequence::Feature>
=cut
__PACKAGE__->belongs_to(
"subject",
"Bio::Chado::Schema::Result::Sequence::Feature",
{ feature_id => "subject_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
=head2 object
Type: belongs_to
Related object: L<Bio::Chado::Schema::Result::Sequence::Feature>
=cut
__PACKAGE__->belongs_to(
"object",
"Bio::Chado::Schema::Result::Sequence::Feature",
{ feature_id => "object_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
=head2 type
Type: belongs_to
Related object: L<Bio::Chado::Schema::Result::Cv::Cvterm>
=cut
__PACKAGE__->belongs_to(
"type",
"Bio::Chado::Schema::Result::Cv::Cvterm",
{ cvterm_id => "type_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
=head2 feature_relationshipprops
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Sequence::FeatureRelationshipprop>
=cut
__PACKAGE__->has_many(
"feature_relationshipprops",
"Bio::Chado::Schema::Result::Sequence::FeatureRelationshipprop",
{
"foreign.feature_relationship_id" => "self.feature_relationship_id",
},
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 feature_relationship_pubs
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Sequence::FeatureRelationshipPub>
=cut
__PACKAGE__->has_many(
"feature_relationship_pubs",
"Bio::Chado::Schema::Result::Sequence::FeatureRelationshipPub",
{
"foreign.feature_relationship_id" => "self.feature_relationship_id",
},
{ cascade_copy => 0, cascade_delete => 0 },
);
# Created by DBIx::Class::Schema::Loader v0.07010 @ 2011-03-16 23:09:59
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:NyvyWCI4DfPZrKeQuyx1CQ
# You can replace this text with custom content, and it will be preserved on regeneration
1;
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