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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)
26 lines
1.5 KiB
Markdown
26 lines
1.5 KiB
Markdown
# `obitax` Package: Taxonomic Data Handling
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The `obitax` package provides structured support for managing collections of taxon nodes in a biological taxonomy.
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- **Core Type**: `TaxonSlice` encapsulates an ordered list of `*TaxNode`s and a reference to their parent `Taxonomy`.
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- **Construction**: Created via `(taxonomy *Taxonomy).NewTaxonSlice(size, capacity)`, initializing a typed slice with optional pre-allocation.
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- **Accessors**:
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- `Get(i int) *TaxNode`: retrieves the raw node at index.
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- `Taxon(i int) *Taxon`: wraps a node with its taxonomy context, enabling richer operations.
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- `Len() int`: returns the current number of nodes.
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- **Mutation Methods**:
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- `Set(index, taxon)`: replaces a node at given index (taxonomy-mismatch panics).
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- `Push(taxon)`: appends a taxon to the end (also enforces taxonomy consistency).
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- `ReduceToSize(n)`: truncates slice to first *n* elements.
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- **Utility Features**:
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- `Reverse(inplace)`: reverses node order — either in-place or as a new slice.
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- `String() string`: formats the entire path as `"id@sci_name@rank"` entries, separated by `|`, in *reverse* (leaf-to-root) order — ideal for lineage strings.
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- **Safety & Semantics**:
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- Nil-safety in all methods (returns `nil` or zero).
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- Enforces taxonomy coherence: mixing taxa from different taxonomies triggers a panic.
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This package enables efficient, type-safe manipulation of hierarchical biological classification paths (e.g., for sequence annotation or metabarcoding output).
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