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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)
62 lines
3.1 KiB
Markdown
62 lines
3.1 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, prioritizing simplicity, extensibility, and interoperability with standard phylogenetic formats.
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## Core Type: `PhyloNode`
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Represents a node in a phylogenetic tree—either an operational taxonomic unit (leaf) or an internal branching point.
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### Public Fields
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- `Name string`: Optional identifier for the node (e.g., species name, OTU label). May be empty.
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- `Children map[*PhyloNode]float64`: Maps child nodes to their associated **branch lengths** (evolutionary distances). Supports `NaN` for unspecified or unmeasured branches.
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- `Attributes map[string]any`: A flexible key-value store for arbitrary metadata (e.g., bootstrap values, posterior probabilities, geographic origin). Values may be of any type.
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> ⚠️ *All fields are exported for direct read/write access, but users should prefer the provided methods to ensure consistency (e.g., `AddChild`, `SetAttribute`).*
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## Public Methods
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### Construction & Mutation
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- **`NewPhyloNode(name string) *PhyloNode`**
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Instantiates a new node with optional name. Initializes `Children` and `Attributes` as empty maps.
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- **`AddChild(child *PhyloNode, distance float64)`**
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Appends a child node to the current one with specified branch length. If `distance` is `NaN`, it is stored as-is (and omitted in Newick output).
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→ *Enables incremental tree building from leaves to root.*
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- **`SetAttribute(key string, value any)`**
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Stores or updates a metadata entry on the node. Overwrites existing keys.
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- **`GetAttribute(key string) (any, bool)`**
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Retrieves a metadata value and reports presence via boolean. Returns zero `value` if key absent.
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### Tree Serialization
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- **`Newick(level int) string`**
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Recursively generates a Newick-formatted subtree rooted at the current node.
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- Nodes without children appear as `Name` (or empty string if unnamed).
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- Internal nodes are rendered with comma-separated children in parentheses.
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- Branch lengths (`:distance`) appear *only if finite* (i.e., `!math.IsNaN(distance)`).
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- Indentation (`level * "\t"`) improves human readability.
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- Root-level calls (e.g., `root.Newick(0)`) append a final semicolon (`;`).
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→ *Designed for export to tools like RAxML, FigTree, or Iq-TREE.*
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## Design Principles
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- **Zero external dependencies**: Pure Go implementation.
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- **Idiomatic efficiency**: Child lookup via `map` ensures O(1) average access.
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- **Extensibility over rigidity**: Arbitrary metadata via `any` supports evolving annotation needs without API changes.
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- **Format compliance**: Newick output adheres to widely accepted syntax (with optional branch lengths), enabling seamless integration with phylogenetic software ecosystems.
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## Usage Example
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```go
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root := obiphylo.NewPhyloNode("Root")
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leafA := obiphylo.NewPhyloNode("Species_A")
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leafB := obiphylo.NewPhyloNode("Species_B")
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root.AddChild(leafA, 1.2)
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root.AddChild(leafB, math.NaN()) // distance omitted in output
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leafA.SetAttribute("bootstrap", 95)
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root.Newick(0) // → "\t(Species_A:1.2,Species_B);"
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```
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