mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
1.8 KiB
1.8 KiB
obitax Package: Taxonomic Data Management
The obitax package provides a robust framework for managing hierarchical taxonomic classifications. Its core component is the Taxonomy struct, which encapsulates metadata (name, code), taxon identifiers (ids, ranks), names and name classes (names, nameclasses), node hierarchy (nodes, root), indexing for fast lookup, and validation logic.
Key Functionalities
- Initialization:
NewTaxonomy()creates a new taxonomy with configurable identifier alphabet and initializes internal data structures. - Identifier Handling:
Id()validates and converts string-based taxon IDs to internal representations;TaxidString()retrieves formatted identifiers (e.g.,"code:id [name]"). - Taxon Access:
Taxon()fetches a taxon by ID, returning whether it's an alias;AsTaxonSet()exposes the full taxonomic node collection. - Structure Management:
AddTaxon()inserts a new taxon with parent, rank, and root flags.AddAlias()maps alternative IDs to existing taxa (supporting replacement).
- Metadata Queries: Methods like
RankList(),Name(), andCode()expose taxonomy metadata. - Root Control:
SetRoot()/Root()manage the root node;HasRoot()checks its presence. - Path Insertion:
InsertPathString()builds or extends a taxonomy from an ordered list of taxon strings, enforcing parent-child consistency. - Phylogenetic Export:
AsPhyloTree()converts the taxonomy into a phylogeny-compatible tree (obiphylo.PhyloNode), enabling downstream evolutionary analysis.
All operations gracefully handle nil receivers via an internal .OrDefault() helper, ensuring safe usage in pipelines. Error reporting is explicit and contextualized (e.g., duplicate taxon, missing parent).