Bio::Chado::Schema::Result::Phylogeny::Phylonode - Bio::Chado::Schema::Result::Phylogeny::Phylonode documentation
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Code Index:
NAME
Bio::Chado::Schema::Result::Phylogeny::Phylonode
DESCRIPTION
This is the most pervasive
element in the phylogeny module, cataloging the "phylonodes" of
tree graphs. Edges are implied by the parent_phylonode_id
reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.
NAME
Bio::Chado::Schema::Result::Phylogeny::Phylonode
ACCESSORS
phylonode_id
data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'phylonode_phylonode_id_seq'
phylotree_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0
parent_phylonode_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 1
Root phylonode can have null parent_phylonode_id value.
left_idx
data_type: 'integer'
is_nullable: 0
right_idx
data_type: 'integer'
is_nullable: 0
type_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 1
Type: e.g. root, interior, leaf.
feature_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 1
Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.
label
data_type: 'varchar'
is_nullable: 1
size: 255
distance
data_type: 'double precision'
is_nullable: 1
RELATIONS
feature
type
parent_phylonode
phylonodes
phylotree
phylonode_dbxrefs
phylonode_organism
phylonodeprops
phylonode_pubs
phylonode_relationship_objects
phylonode_relationship_subjects
NESTEDSET OPERATIONS
Phylonodes support DBIx::Class::Tree::NestedSet operations for
working with this tree-structured data. See
DBIx::Class::Tree::NestedSet for details.
CAVEAT: As of DBIx::Class::Tree::NestedSet 0.07, an important caveat of
these operations is that they cannot be chained with other resultsets.
This shortcoming is being addressed at the level of DBIx::Class and
DBIx::Class::Tree::NestedSet modules.
AUTHOR
Robert Buels <rbuels@cpan.org>
COPYRIGHT AND LICENSE
This software is copyright (c) 2011 by Robert Buels.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.
package Bio::Chado::Schema::Result::Phylogeny::Phylonode;
BEGIN {
$Bio::Chado::Schema::Result::Phylogeny::Phylonode::AUTHORITY = 'cpan:RBUELS';
}
BEGIN {
$Bio::Chado::Schema::Result::Phylogeny::Phylonode::VERSION = '0.08100';
}
# Created by DBIx::Class::Schema::Loader
# DO NOT MODIFY THE FIRST PART OF THIS FILE
use strict;
use warnings;
use base 'DBIx::Class::Core';
__PACKAGE__->table("phylonode");
__PACKAGE__->add_columns(
"phylonode_id",
{
data_type => "integer",
is_auto_increment => 1,
is_nullable => 0,
sequence => "phylonode_phylonode_id_seq",
},
"phylotree_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 0 },
"parent_phylonode_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 1 },
"left_idx",
{ data_type => "integer", is_nullable => 0 },
"right_idx",
{ data_type => "integer", is_nullable => 0 },
"type_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 1 },
"feature_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 1 },
"label",
{ data_type => "varchar", is_nullable => 1, size => 255 },
"distance",
{ data_type => "double precision", is_nullable => 1 },
);
__PACKAGE__->set_primary_key("phylonode_id");
__PACKAGE__->add_unique_constraint("phylonode_phylotree_id_key1", ["phylotree_id", "right_idx"]);
__PACKAGE__->add_unique_constraint("phylonode_phylotree_id_key", ["phylotree_id", "left_idx"]);
__PACKAGE__->belongs_to(
"feature",
"Bio::Chado::Schema::Result::Sequence::Feature",
{ feature_id => "feature_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
join_type => "LEFT",
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
__PACKAGE__->belongs_to(
"type",
"Bio::Chado::Schema::Result::Cv::Cvterm",
{ cvterm_id => "type_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
join_type => "LEFT",
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
__PACKAGE__->belongs_to(
"parent_phylonode",
"Bio::Chado::Schema::Result::Phylogeny::Phylonode",
{ phylonode_id => "parent_phylonode_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
join_type => "LEFT",
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
__PACKAGE__->has_many(
"phylonodes",
"Bio::Chado::Schema::Result::Phylogeny::Phylonode",
{ "foreign.parent_phylonode_id" => "self.phylonode_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
__PACKAGE__->belongs_to(
"phylotree",
"Bio::Chado::Schema::Result::Phylogeny::Phylotree",
{ phylotree_id => "phylotree_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
__PACKAGE__->has_many(
"phylonode_dbxrefs",
"Bio::Chado::Schema::Result::Phylogeny::PhylonodeDbxref",
{ "foreign.phylonode_id" => "self.phylonode_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
__PACKAGE__->might_have(
"phylonode_organism",
"Bio::Chado::Schema::Result::Phylogeny::PhylonodeOrganism",
{ "foreign.phylonode_id" => "self.phylonode_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
__PACKAGE__->has_many(
"phylonodeprops",
"Bio::Chado::Schema::Result::Phylogeny::Phylonodeprop",
{ "foreign.phylonode_id" => "self.phylonode_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
__PACKAGE__->has_many(
"phylonode_pubs",
"Bio::Chado::Schema::Result::Phylogeny::PhylonodePub",
{ "foreign.phylonode_id" => "self.phylonode_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
__PACKAGE__->has_many(
"phylonode_relationship_objects",
"Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship",
{ "foreign.object_id" => "self.phylonode_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
__PACKAGE__->has_many(
"phylonode_relationship_subjects",
"Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship",
{ "foreign.subject_id" => "self.phylonode_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:lDVljDfIraP9A4Fx0agxbw
__PACKAGE__->load_components(qw( Tree::NestedSet ));
__PACKAGE__->tree_columns({qw{
root_column phylotree_id
left_column left_idx
right_column right_idx
level_column distance
}});
# distance is not usually reliable, so use a null parent ID to
# determine whether something is a root node
sub is_root { ! defined shift->parent_id }
# You can replace this text with custom content, and it will be preserved on regeneration
1;
__END__