obitools4/autodoc/docmd/pkg/obiiter/batch.md

BioSequenceBatch: A Container for Ordered Biological Sequences

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.

Core Properties

• source: String identifying the origin (e.g., file, pipeline stage).
• order: Integer defining processing sequence or priority.
• slice: Holds the actual sequences via obiseq.BioSequenceSlice.

Key Functionalities

• Construction:
  MakeBioSequenceBatch(source, order, sequences) creates a new batch.
• Accessors:
  Source(), Order() return metadata; Slice() exposes the sequence slice.
• Mutation (via copy):
  Reorder(newOrder) returns a new batch with updated order.
• Size & emptiness:
  Len() gives sequence count; NotEmpty() checks non-emptiness.
• Consumption:
  Pop0() removes and returns the first sequence (FIFO behavior).
• Safety:
  IsNil() detects uninitialized batches; a global NilBioSequenceBatch sentinel exists.

Design Notes

• Instances are value types (struct), enabling safe copying.
• Operations follow Go idioms: methods return updated values rather than mutating in place (except internal slice mutation via Pop0).
• Designed for interoperability with the OBITools4 ecosystem (obiseq package).

This abstraction supports modular, traceable sequence processing workflows—ideal for pipeline stages where ordering and provenance matter.