mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
31 lines
1.5 KiB
Markdown
31 lines
1.5 KiB
Markdown
|
# `obiphylo` Package: Semantic Description
|
|||
|
|
|
|||
|
|
The `obiphylo` package provides a minimal yet expressive data structure and utilities for representing **phylogenetic trees** in Go.
|
|||
|
|
|
|||
|
|
## Core Type: `PhyloNode`
|
|||
|
|
- Represents a node (taxon or internal branch point) in a phylogeny.
|
|||
|
|
- Fields:
|
|||
|
|
- `Name`: Optional label (e.g., species name, OTU ID).
|
|||
|
|
- `Children`: A map of child nodes to **branch lengths** (evolutionary distances).
|
|||
|
|
- `Attributes`: A flexible key-value store for metadata (e.g., bootstrap support, posterior probability).
|
|||
|
|
|
|||
|
|
## Key Functionalities
|
|||
|
|
- **Tree Construction**:
|
|||
|
|
- `NewPhyloNode()`: Instantiates an empty node.
|
|||
|
|
- `AddChild(child, distance)`: Appends a child with associated branch length (supports NaN for unlabeled branches).
|
|||
|
|
- **Metadata Access**:
|
|||
|
|
- `SetAttribute(key, value)` / `GetAttribute(key)`: Enables extensible node annotation.
|
|||
|
|
- Supports arbitrary types (via `any`), ideal for dynamic metadata.
|
|||
|
|
|
|||
|
|
## Output: Newick Format
|
|||
|
|
- Recursive method `Newick(level int)` generates a **human-readable, standard phylogenetic tree string**:
|
|||
|
|
- Properly indented for readability.
|
|||
|
|
- Supports branch lengths (`:distance`) on edges (skips if `NaN`).
|
|||
|
|
- Terminates with semicolon (`;`) at root level.
|
|||
|
|
- Designed for interoperability (e.g., export to tools like RAxML, FigTree).
|
|||
|
|
|
|||
|
|
## Design Notes
|
|||
|
|
- Lightweight and dependency-free.
|
|||
|
|
- Uses Go’s idiomatic maps for efficient child lookup (O(1) average).
|
|||
|
|
- Recursive Newick generation ensures correct nesting and formatting.
|