NAME

Bio::Chado::Schema::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
default_value: nextval('phylonode_phylonode_id_seq'::regclass)
is_auto_increment: 1
is_nullable: 0

phylotree_id

data_type: integer
default_value: undef
is_foreign_key: 1
is_nullable: 0

parent_phylonode_id

data_type: integer
default_value: undef
is_foreign_key: 1
is_nullable: 1

Root phylonode can have null parent_phylonode_id value.

left_idx

data_type: integer
default_value: undef
is_nullable: 0

right_idx

data_type: integer
default_value: undef
is_nullable: 0

type_id

data_type: integer
default_value: undef
is_foreign_key: 1
is_nullable: 1

Type: e.g. root, interior, leaf.

feature_id

data_type: integer
default_value: undef
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: character varying
default_value: undef
is_nullable: 1
size: 255

distance

data_type: double precision
default_value: undef
is_nullable: 1

RELATIONS

feature

Type: belongs_to

Related object: Bio::Chado::Schema::Sequence::Feature

type

Type: belongs_to

Related object: Bio::Chado::Schema::Cv::Cvterm

parent_phylonode

Type: belongs_to

Related object: Bio::Chado::Schema::Phylogeny::Phylonode

phylonodes

Type: has_many

Related object: Bio::Chado::Schema::Phylogeny::Phylonode

phylotree

Type: belongs_to

Related object: Bio::Chado::Schema::Phylogeny::Phylotree

phylonode_dbxrefs

Type: has_many

Related object: Bio::Chado::Schema::Phylogeny::PhylonodeDbxref

phylonode_organism

Type: might_have

Related object: Bio::Chado::Schema::Phylogeny::PhylonodeOrganism

phylonodeprops

Type: has_many

Related object: Bio::Chado::Schema::Phylogeny::Phylonodeprop

phylonode_pubs

Type: has_many

Related object: Bio::Chado::Schema::Phylogeny::PhylonodePub

phylonode_relationship_objects

Type: has_many

Related object: Bio::Chado::Schema::Phylogeny::PhylonodeRelationship

phylonode_relationship_subjects

Type: has_many

Related object: Bio::Chado::Schema::Phylogeny::PhylonodeRelationship

cpanm Bio::Chado::Schema

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