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.

NAME

Bio::Chado::Schema::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

NESTEDSET OPERATIONS

Phylonodes support the DBIx::Class::Tree::NestedSet manpage operations for working with this tree-structured data. See the DBIx::Class::Tree::NestedSet manpage for details.

CAVEAT: As of the DBIx::Class::Tree::NestedSet manpage 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 the DBIx::Class manpage and the DBIx::Class::Tree::NestedSet manpage modules.

AUTHOR

Robert Buels <rbuels@cpan.org>

COPYRIGHT AND LICENSE

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

Bio::Chado::Schema::Phylogeny::Phylonode