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23 lines
1.9 KiB
Markdown
23 lines
1.9 KiB
Markdown
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# BioSequence Attribute Management API
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This Go package (`obiseq`) provides a rich set of methods for managing metadata and structural attributes associated with biological sequences (`BioSequence`). Below is a semantic overview of the core functionalities:
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- **Key Discovery & Existence Checks**:
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- `Keys()` and `AttributeKeys()` return all attribute names (optionally excluding container/statistics fields or the `"definition"` key).
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- `HasAttribute(key)` verifies presence of a given attribute (including standard fields: `"id"`, `"sequence"`, `"qualities"`).
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- **Generic Attribute Access**:
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- `GetAttribute(key)` retrieves any attribute value (as `interface{}`), with thread-safe locking.
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- `SetAttribute(key, value)` assigns values to attributes (including automatic conversion for `"id"`, `"sequence"` and `"qualities"`).
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- **Typed Attribute Retrieval**:
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- Type-specific getters (`GetIntAttribute`, `GetFloatAttribute`, `GetStringAttribute`, etc.) ensure safe conversion and *auto-upgrade* of stored values (e.g., string `"42"` → integer `42`).
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- Supports maps (`GetIntMap`, `GetStringMap`) and slices (`GetIntSlice`).
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- **Convenience & Domain-Specific Helpers**:
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- `Count()` / `SetCount()`: manage observation frequency (default = 1).
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- OBITag indexing: `OBITagRefIndex()` / `SetOBITagRefIndex()`, and geometry variants (`geomref`). Supports flexible input map types with dynamic conversion.
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- Coordinate & landmark support: `GetCoordinate()` / `SetCoordinate()`, and `landmark_id`-based operations (`IsALandmark()`, `GetLandmarkID()`).
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All methods are designed for robustness: they handle type conversions gracefully, use locking to ensure concurrency safety, and provide fallbacks (e.g., default count = 1). The API abstracts internal storage (`annotations` map) while exposing a clean, consistent interface for sequence annotation manipulation.
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