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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)
20 lines
1.3 KiB
Markdown
20 lines
1.3 KiB
Markdown
# `obitax` Package: Taxonomic Identifier Handling
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The `obitax` package provides a lightweight, type-safe abstraction for handling taxonomic identifiers (`Taxid`) in the OBITools4 ecosystem.
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- **`Taxid` type**: A pointer to a string, representing an opaque taxonomic ID (e.g., NCBI TaxID).
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- **`TaxidFactory`**: A factory for constructing `Taxid`s from strings or integers, enforcing validation and normalization.
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Key features:
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- **Code prefix enforcement**: `FromString` validates that the input string starts with a required taxonomy code (e.g., `"tx"`), returning an error otherwise.
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- **String parsing**: Automatically strips leading whitespace and extracts the suffix after `':'`.
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- **Alphabet filtering**: Uses an ASCII set to extract only valid characters (e.g., digits), ensuring clean, standardized IDs.
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- **String interning**: Internally uses `Innerize` (via `InnerString`) to deduplicate strings—improving memory efficiency and comparison speed.
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- **Type safety**: `Taxid` is a distinct type (not raw string), reducing misuse and enabling future extension.
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Supported conversions:
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- `FromString(string)`: Parses `"tx:12345"` → internalized `"12345"`.
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- `FromInt(int)`: Converts e.g., `12345` → internalized `"12345"`.
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Designed for high-performance pipelines where many taxonomic IDs are processed and reused.
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