Merge correlate_preloaded into correlate with auto-detection of PSM spectrum property#262
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RalfG merged 4 commits intorelease/4.2from Apr 15, 2026
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Make `correlate` auto-detect whether PSMs carry preloaded spectra (MS2Spectrum/AnnotatedMS2Spectrum) or need file-based loading, removing the need for a separate `correlate_preloaded` function.
Validate peptidoforms before passing to ms2rescore-rs: check for unsupported amino acids, sequence length (4-100), and missing charge. Invalid PSMs are skipped with an empty ProcessingResult and a single summarized warning log message, matching the old silent-skip behavior.
- Replace np.corrcoef with direct dot-product Pearson formula - Consolidate pearson() in correlation.py, reuse in result.py - Cache proforma_to_mass_shift with lru_cache (avoids recomputation) - Use model_construct for internal ObservedSpectrum creation
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Merge
correlate_preloadedintocorrelatewith auto-detection, skip invalid peptidoforms with summarized warnings, and optimize performance.Changed
correlatenow auto-detects preloaded spectra on PSMs (MS2Spectrum/AnnotatedMS2Spectrum), removing the need for a separatecorrelate_preloadedfunctionProcessingResultand a summarized warningread_psmsacceptslist[PSM]in addition toPSMList,str, andPathnp.corrcoefwith direct Pearson formula (~60% faster per call)proforma_to_mass_shiftwithlru_cachemodel_constructfor internalObservedSpectrumcreation (skips Pydantic validation)pearson()incorrelation.py, reused byms2pip_pearsonandcalculate_correlationsresolve_spectradispatcher andMatchedSpectrumNamedTuple in_spectrum_processing_preprocess_spectrumhelper to deduplicate preprocessing logic_load_and_match_spectra,_preloaded_to_annotations,_read_raw_spectra,_to_observed_spectrum)validate_peptidoformandfilter_valid_psmstopsm_inputRemoved
correlate_preloadedfrom public API