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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)
36 lines
1.7 KiB
Markdown
36 lines
1.7 KiB
Markdown
# `obiseq` Package: Sequence Concatenation via `.Join()`
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The `BioSequence.Join()` method enables semantic concatenation of two biological sequences (e.g., DNA, RNA, or protein strings).
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- **Signature**:
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```go
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func (sequence *BioSequence) Join(seq2 *BioSequence, inplace bool) *BioSequence
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```
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- **Purpose**:
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Combines the current sequence (`sequence`) with a second one (`seq2`), returning a new or modified `BioSequence`.
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- **Parameters**:
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- `seq2`: The sequence to append. Must be a valid `*BioSequence`.
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- `inplace`: Boolean flag: if `true`, modifies the receiver in-place; otherwise, operates on a copy.
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- **Semantics**:
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- If `inplace == false`, the method first creates a deep copy of the original sequence to avoid side effects.
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- It then appends `seq2.Sequence()` (the underlying string/byte representation) to the target sequence using an internal `.Write()` method.
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- The final concatenated result is returned as a `*BioSequence`.
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- **Behavioral Guarantees**:
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- *Pure operation*: When `inplace = false`, the original sequences remain unaltered.
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- *Chaining-friendly*: Returns a pointer, enabling method chaining (e.g., `seq.Join(a, false).Join(b, true)`).
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- **Use Cases**:
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- Building multi-domain proteins or gene fusions.
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- Merging fragments from sequencing reads.
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- Constructing synthetic constructs in silico.
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- **Assumptions**:
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- `BioSequence.Sequence()` returns a valid string/byte slice.
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- `.Write(...)` handles appending correctly (e.g., no validation of biological compatibility — e.g., frame shifts are not checked).
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This method supports flexible, functional-style sequence manipulation while preserving memory safety via optional in-place mutation.
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