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Eric Coissac
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- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
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obitax Package: Taxonomic Identifier Handling
The obitax package provides a lightweight, type-safe abstraction for handling taxonomic identifiers (Taxid) in the OBITools4 ecosystem.
Taxidtype: A pointer to a string, representing an opaque taxonomic ID (e.g., NCBI TaxID).TaxidFactory: A factory for constructingTaxids from strings or integers, enforcing validation and normalization.
Key features:
- Code prefix enforcement:
FromStringvalidates that the input string starts with a required taxonomy code (e.g.,"tx"), returning an error otherwise. - String parsing: Automatically strips leading whitespace and extracts the suffix after
':'. - Alphabet filtering: Uses an ASCII set to extract only valid characters (e.g., digits), ensuring clean, standardized IDs.
- String interning: Internally uses
Innerize(viaInnerString) to deduplicate strings—improving memory efficiency and comparison speed. - Type safety:
Taxidis a distinct type (not raw string), reducing misuse and enabling future extension.
Supported conversions:
FromString(string): Parses"tx:12345"→ internalized"12345".FromInt(int): Converts e.g.,12345→ internalized"12345".
Designed for high-performance pipelines where many taxonomic IDs are processed and reused.