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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

`obitax` Package: Taxonomic Node Representation and Management

The obitax package provides a lightweight, pointer-based Go implementation for representing taxonomic nodes in biological classification systems.

Core Data Structure

TaxNode: Represents a single taxon (e.g., species, genus) with the following fields:
- id: Unique taxon identifier (pointer to string).
- parent: Identifier of the parent node in the taxonomy hierarchy.
- rank: Taxonomic rank (e.g., "species", "family").
- scientificname: Canonical scientific name (e.g., Homo sapiens).
- alternatenames: Map of alternative names keyed by name class (e.g., "common_name", "synonym").

String Representation
String(taxonomyCode) returns a formatted label like "NCBI:12345 [Homo sapiens]@species" (or raw ID if enabled via obidefault.UseRawTaxids()).
Accessors
- Id(), ParentId(): Retrieve identifiers.
- ScientificName() / Rank(): Return name or rank (defaulting to "NA" if missing).
- Name(class): Fetch name by class ("scientific name" or alternate).
Mutators
- SetName(name, class): Assign scientific name or add/update alternate names.
Name Matching & Validation
- IsNameEqual(name, ignoreCase): Exact or case-insensitive match against scientific/alternate names.
- IsNameMatching(pattern): Regex-based pattern matching over all available names.

Uses pointers for optional fields (enables nil semantics).
Graceful handling of missing data (NA, empty strings, safe dereferencing with nil checks).
Integrates logging via Logrus (log.Panic on misuse, e.g., setting name of nil node).
Designed for use in larger OBITools pipelines (e.g., with obidefault configuration).