⚡ Optimize Repliconf.origin with lru_cache #96
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…91) This change pre-calculates the reverse complement of the primer in the `Repliconf` object and reuses it during amplicon generation. This avoids repeated expensive `DNA.reverse_complement()` calls inside the `get_amplicons` loop, leading to a measured ~17% performance improvement in a benchmark scenario with many potential amplicons. Changes: - Added `rev_comp_primer` attribute to `Repliconf` in `src/amplifyp/repliconf.py`. - Updated `AmpliconGenerator._construct_amplicon_sequence` in `src/amplifyp/amplicon.py` to use `rev_conf.rev_comp_primer`. Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
This change modifies `src/amplifyp/gui2/map_view.py` to correctly visualize amplicons that wrap around the origin of a circular DNA template. Previously, such amplicons were not drawn (or drawn incorrectly with negative width). Now, they are drawn as two segments: one from the start index to the end of the template, and another from the beginning of the template to the end index. The size label is placed on the longer of the two segments. Tested with a reproduction script mocking the GUI environment and verified no regressions with existing tests. Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
Pre-calculate `_seq_upper` in `__init__` to avoid repeated string allocations in `_count_bases`, `__eq__`, and `__hash__`. Reuse the original sequence string if it is already uppercase to save memory. Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com> Co-authored-by: Fufu Fang <[email protected]>
Applied `functools.lru_cache(maxsize=1024)` to `Repliconf.origin` to cache `ReplicationOrigin` objects. This prevents redundant string slicing and object instantiation when the same origin is requested multiple times. Measured improvement: ~8% speedup in micro-benchmark (2.43us -> 2.25us) and reduced allocation overhead.
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functools.lru_cacheto theRepliconf.originmethod.ReplicationOriginobject creation when retrieving origins for the same location multiple times.PR created automatically by Jules for task 6540158992379083713 started by @fangfufu