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30 lines
1.6 KiB
Markdown
30 lines
1.6 KiB
Markdown
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# BioSequenceBatch: A Container for Ordered Biological Sequences
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`BioSequenceBatch` is a structured data type encapsulating an ordered collection of biological sequences (`obiseq.BioSequenceSlice`) along with metadata: a `source` identifier and an integer `order`. It serves as a lightweight, immutable-friendly container for batch processing in bioinformatics pipelines.
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## Core Properties
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- **`source`**: String identifying the origin (e.g., file, pipeline stage).
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- **`order`**: Integer defining processing sequence or priority.
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- **`slice`**: Holds the actual sequences via `obiseq.BioSequenceSlice`.
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## Key Functionalities
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- **Construction**:
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`MakeBioSequenceBatch(source, order, sequences)` creates a new batch.
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- **Accessors**:
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`Source()`, `Order()` return metadata; `Slice()` exposes the sequence slice.
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- **Mutation (via copy)**:
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`Reorder(newOrder)` returns a new batch with updated order.
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- **Size & emptiness**:
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`Len()` gives sequence count; `NotEmpty()` checks non-emptiness.
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- **Consumption**:
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`Pop0()` removes and returns the first sequence (FIFO behavior).
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- **Safety**:
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`IsNil()` detects uninitialized batches; a global `NilBioSequenceBatch` sentinel exists.
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## Design Notes
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- Instances are value types (struct), enabling safe copying.
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- Operations follow Go idioms: methods return updated values rather than mutating in place (except internal slice mutation via `Pop0`).
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- Designed for interoperability with the OBITools4 ecosystem (`obiseq` package).
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This abstraction supports modular, traceable sequence processing workflows—ideal for pipeline stages where ordering and provenance matter.
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