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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)
29 lines
1.6 KiB
Markdown
29 lines
1.6 KiB
Markdown
# `obidist` Package: Semantic Feature Overview
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The `obidist` Go package provides two core data structures for managing **distance** and **similarity matrices**, with built-in guarantees suitable for scientific computing (e.g., clustering, phylogenetics). Key features include:
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- **`DistMatrix`**: A symmetric `n×n` matrix representing pairwise distances, where:
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- Diagonal entries are *always* `0.0` (self-distance).
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- Off-diagonals obey symmetry: `dist(i, j) == dist(j, i)`.
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- Automatic enforcement via dedicated `Set()`/`Get()` methods.
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- **`SimilarityMatrix`**: A symmetric matrix where:
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- Diagonal entries are *always* `1.0`.
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- Off-diagonals represent similarity scores (e.g., between `0` and `1`, though not enforced).
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- Symmetry is similarly guaranteed.
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Both matrix types support:
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- **Optional labels**: Associate human-readable identifiers (e.g., sample names) with rows/columns.
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- **Safe bounds checking**: Panics on out-of-range access (tested via `defer/recover`).
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- **Deep copy support**: Ensures isolation between original and copied instances.
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- **Utility methods**:
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- `MinDistance()` / `MaxDistance()`: Return extremal values and their indices.
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- `GetRow(i)`: Retrieve a full row as a slice (symmetric copy).
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- `ToFullMatrix()`: Export the matrix as an immutable 2D slice.
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Edge cases are rigorously handled:
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- Empty (`n=0`) and singleton (`n=1`) matrices return `(0.0, -1, -1)` for min/max.
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- Label mutations do not affect internal state via defensive copying.
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All behaviors are validated through comprehensive unit tests, emphasizing correctness and robustness.
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