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.

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.

cpanm Bio::Chado::Schema

perl -MCPAN -e shell
install Bio::Chado::Schema