Chado Phylotree

Provides API functions specificially for managing phylogenetic and taxonomic tree records in Chado. The API consists of functions for creation, retrieval, update and deltion (CRUD) for phylogenetic tree records as well as importing of trees in the newick file format.

Parent topics

Chado API
The Tripal Chado (tripal_chado) module provides an application programming interface (API) to support customizations and creation of new extensions using the Chado database schem as a data store.

File

tripal_chado/api/modules/tripal_chado.phylotree.api.inc, line 9
Provides API functions specificially for managing phylogenetic and taxonomic tree records in Chado.

Functions

Namesort descending Location Description
chado_assign_phylogeny_tree_indices tripal_chado/api/modules/tripal_chado.phylotree.api.inc Iterates through the tree and sets the left and right indicies.
chado_delete_phylotree tripal_chado/api/modules/tripal_chado.phylotree.api.inc Deletes a phylotree record from Chado.
chado_insert_phylotree tripal_chado/api/modules/tripal_chado.phylotree.api.inc Inserts a phylotree record into Chado.
chado_phylogeny_get_node_types_vocab tripal_chado/api/modules/tripal_chado.phylotree.api.inc Get the vocabulary terms used to describe nodes in the tree.
chado_phylogeny_import_tree tripal_chado/api/modules/tripal_chado.phylotree.api.inc Iterates through the tree array and creates phylonodes in Chado.
chado_phylogeny_import_tree_file tripal_chado/api/modules/tripal_chado.phylotree.api.inc Imports a tree file.
chado_update_phylotree tripal_chado/api/modules/tripal_chado.phylotree.api.inc Updates a phylotree record into Chado.
chado_validate_phylotree tripal_chado/api/modules/tripal_chado.phylotree.api.inc Validates an $options array for insert or update of a phylotree record.