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: belongs_to
Related object: Bio::Chado::Schema::Result::Sequence::Feature
type
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Cv::Cvterm
parent_phylonode
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonode
phylonodes
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonode
phylotree
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylotree
phylonode_dbxrefs
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeDbxref
phylonode_organism
Type: might_have
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeOrganism
phylonodeprops
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonodeprop
phylonode_pubs
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodePub
phylonode_relationship_objects
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship
phylonode_relationship_subjects
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship
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.