⚡ Optimize AmpliconGenerator.add_repliconf performance #95
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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>
Introduced a private set `_repliconfs_set` to store `Repliconf` objects for fast membership testing. Updated `add_repliconf` and `remove_repliconf` to maintain synchronization between the public list `repliconfs` and the new set. This reduces the complexity of checking for duplicates from O(N) to O(1), significantly improving performance when adding many replication configurations. Benchmarks showed a reduction from ~4.02s to ~0.02s for adding 5000 repliconfs. Added `tests/test_amplicon_generator_optimization.py` to verify internal consistency and regression testing.
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⚡ Optimize AmpliconGenerator.add_repliconf with O(1) checks
What:
self._repliconfs_set(set) toAmpliconGenerator.add_repliconfto use the set for membership check (O(1)) instead of the list (O(N)).repliconfs(list) and_repliconfs_setinadd_repliconfandremove_repliconf.Why:
add_repliconfwas performing a linear scan ofrepliconfsto prevent duplicates, leading to O(N^2) complexity when adding N repliconfs.Measured Improvement:
PR created automatically by Jules for task 17538939382487651922 started by @fangfufu