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37 lines
1.8 KiB
Markdown
37 lines
1.8 KiB
Markdown
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# `obitax` Package: Taxonomic Node Representation and Management
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The `obitax` package provides a lightweight, pointer-based Go implementation for representing taxonomic nodes in biological classification systems.
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## Core Data Structure
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- **`TaxNode`**: Represents a single taxon (e.g., species, genus) with the following fields:
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- `id`: Unique taxon identifier (pointer to string).
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- `parent`: Identifier of the parent node in the taxonomy hierarchy.
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- `rank`: Taxonomic rank (e.g., `"species"`, `"family"`).
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- `scientificname`: Canonical scientific name (e.g., *Homo sapiens*).
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- `alternatenames`: Map of alternative names keyed by name class (e.g., `"common_name"`, `"synonym"`).
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## Key Functionalities
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- **String Representation**
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`String(taxonomyCode)` returns a formatted label like `"NCBI:12345 [Homo sapiens]@species"` (or raw ID if enabled via `obidefault.UseRawTaxids()`).
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- **Accessors**
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- `Id()`, `ParentId()`: Retrieve identifiers.
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- `ScientificName()` / `Rank()`: Return name or rank (defaulting to `"NA"` if missing).
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- `Name(class)`: Fetch name by class (`"scientific name"` or alternate).
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- **Mutators**
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- `SetName(name, class)`: Assign scientific name or add/update alternate names.
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- **Name Matching & Validation**
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- `IsNameEqual(name, ignoreCase)`: Exact or case-insensitive match against scientific/alternate names.
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- `IsNameMatching(pattern)`: Regex-based pattern matching over all available names.
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## Design Notes
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- Uses pointers for optional fields (enables `nil` semantics).
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- Graceful handling of missing data (`NA`, empty strings, safe dereferencing with `nil` checks).
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- Integrates logging via Logrus (`log.Panic` on misuse, e.g., setting name of `nil` node).
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- Designed for use in larger OBITools pipelines (e.g., with `obidefault` configuration).
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