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25 lines
1.6 KiB
Markdown
25 lines
1.6 KiB
Markdown
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# TaxonSet: Semantic Description of Functionality
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The `TaxonSet` type manages a collection of taxonomic entities within a hierarchical taxonomy system. It stores mappings from unique identifiers (pointers to strings) to `TaxNode` instances, supporting both canonical taxa and aliases.
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- **Construction**: Created via `(Taxonomy).NewTaxonSet()`, initializing an empty set and linking it to a specific taxonomy.
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- **Basic Queries**:
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- `Get(id)`: Retrieves the corresponding taxon (or nil).
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- `Len()`: Returns count of *unique* taxa, excluding aliases.
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- `Contains(id)`, `IsATaxon(id)`, and `IsAlias(id)` enable precise taxon/alias distinction.
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- **Insertion & Management**:
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- `Insert(node)`: Adds or updates a taxon node.
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- `InsertTaxon(taxon)`: Safe insertion with taxonomy validation; auto-creates set if nil.
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- `Alias(id, taxon)`: Registers an alias (non-canonical ID pointing to a real node), incrementing internal `nalias` counter.
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- **Hierarchy & Iteration**:
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- `Sort()`: Returns a topologically sorted slice of taxa (parents before children), respecting tree structure.
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- `Taxonomy()`: Provides access to the parent taxonomy.
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- **Phylogenetic Export**:
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- `AsPhyloTree(root)`: Converts the set into a rooted phylogenetic tree (`obiphylo.PhyloNode`), embedding taxon names, ranks, and parent relationships as node attributes.
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In essence, `TaxonSet` enables efficient storage, lookup, validation, and structural manipulation of taxonomic data—supporting both biological classification logic (e.g., alias resolution, hierarchy traversal) and downstream interoperability with phylogenetic tools.
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