⚡ Optimize lookup_keys creation in Repliconf #94
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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 <fangfufu2003@gmail.com>
- Replace set creation and update loop with a single set construction from concatenated strings. - Reduces allocation overhead and improves performance of Repliconf.search initialization. - Benchmark showed ~2.6x speedup for this specific operation (0.22s -> 0.085s for 100k iters).
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💡 What: Optimized the creation of
lookup_keysset inRepliconf.search.🎯 Why: The previous implementation used
set(Nucleotides.TEMPLATE)followed byupdatewith a list comprehension, which involved redundant list allocation and Python-level iteration.📊 Measured Improvement:
lookup_keyscreation showed a significant speedup:Repliconf.searchinitialization, which can be beneficial when performing many searches.PR created automatically by Jules for task 42424823925354820 started by @fangfufu