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