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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)
31 lines
1.5 KiB
Markdown
31 lines
1.5 KiB
Markdown
# `obiphylo` Package: Semantic Description
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The `obiphylo` package provides a minimal yet expressive data structure and utilities for representing **phylogenetic trees** in Go.
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## Core Type: `PhyloNode`
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- Represents a node (taxon or internal branch point) in a phylogeny.
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- Fields:
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- `Name`: Optional label (e.g., species name, OTU ID).
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- `Children`: A map of child nodes to **branch lengths** (evolutionary distances).
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- `Attributes`: A flexible key-value store for metadata (e.g., bootstrap support, posterior probability).
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## Key Functionalities
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- **Tree Construction**:
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- `NewPhyloNode()`: Instantiates an empty node.
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- `AddChild(child, distance)`: Appends a child with associated branch length (supports NaN for unlabeled branches).
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- **Metadata Access**:
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- `SetAttribute(key, value)` / `GetAttribute(key)`: Enables extensible node annotation.
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- Supports arbitrary types (via `any`), ideal for dynamic metadata.
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## Output: Newick Format
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- Recursive method `Newick(level int)` generates a **human-readable, standard phylogenetic tree string**:
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- Properly indented for readability.
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- Supports branch lengths (`:distance`) on edges (skips if `NaN`).
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- Terminates with semicolon (`;`) at root level.
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- Designed for interoperability (e.g., export to tools like RAxML, FigTree).
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## Design Notes
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- Lightweight and dependency-free.
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- Uses Go’s idiomatic maps for efficient child lookup (O(1) average).
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- Recursive Newick generation ensures correct nesting and formatting.
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