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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)
30 lines
1.4 KiB
Markdown
30 lines
1.4 KiB
Markdown
# ObiTax Lua Module Documentation
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This Go package (`obilua`) provides **Lua bindings** for the `obitax` taxonomy management module of OBItools4, enabling scripting in Lua with rich taxonomic operations.
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## Core Features
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- **Type Registration**: Registers two main types in the Lua state: `Taxonomy` and `Taxon`.
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- **Factory Functions**:
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- `obitax.Taxonomy.new(name, code [, charset])`: Creates a new taxonomy instance.
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- `obitax.Taxonomy.default()`: Returns the globally configured default taxonomy (raises error if none exists).
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- `obitax.Taxonomy.has_default()`: Boolean check for existence of a default taxonomy.
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- `obitax.Taxonomy.nil`: Represents the nil taxon (used for missing data).
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## Taxonomy Object Methods
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- `name()`: Returns the taxonomy name (e.g., `"NCBI"`).
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- `code()`: Returns the internal code used for taxonomic identifiers (e.g., `"txid"`).
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- `taxon(id)`: Retrieves a taxonomic node by ID; returns:
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- the corresponding *Taxon* object,
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- raises an error if not found or on alias resolution when `FailOnTaxonomy()` is enabled.
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## Taxon Object Support
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- A dedicated `registerTaxonType` (not shown here) exposes a Lua-accessible *Taxon* type with methods like `rank`, `parent`, and string representation.
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## Integration
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- Built on top of standard OBItools4 types (`obitax.Taxonomy`, `obiutils.AsciiSetFromString`).
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- Leverages GopherLua for seamless interoperability between Go and Lua.
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