LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
alphadia/__init__.py
alphadia/cli.py
alphadia/exceptions.py
alphadia/search_plan.py
alphadia/search_step.py
alphadia/utils.py
alphadia.egg-info/PKG-INFO
alphadia.egg-info/SOURCES.txt
alphadia.egg-info/dependency_links.txt
alphadia.egg-info/entry_points.txt
alphadia.egg-info/requires.txt
alphadia.egg-info/top_level.txt
alphadia/calibration/__init__.py
alphadia/calibration/estimator.py
alphadia/calibration/models.py
alphadia/calibration/plot.py
alphadia/constants/__init__.py
alphadia/constants/default.yaml
alphadia/constants/default_rust.yaml
alphadia/constants/keys.py
alphadia/constants/multistep.yaml
alphadia/constants/settings.py
alphadia/constants/classifier/fa9945ae23db872d.pth
alphadia/fdr/__init__.py
alphadia/fdr/classifiers.py
alphadia/fdr/fdr.py
alphadia/fdr/plotting.py
alphadia/fdr/utils.py
alphadia/fdr/_fdrx/__init__.py
alphadia/fdr/_fdrx/base.py
alphadia/fdr/_fdrx/plotting.py
alphadia/fdr/_fdrx/stats.py
alphadia/fdr/_fdrx/models/__init__.py
alphadia/fdr/_fdrx/models/logistic_regression.py
alphadia/fdr/_fdrx/models/two_step_classifier.py
alphadia/fragcomp/__init__.py
alphadia/fragcomp/fragcomp.py
alphadia/fragcomp/utils.py
alphadia/libtransform/__init__.py
alphadia/libtransform/base.py
alphadia/libtransform/decoy.py
alphadia/libtransform/fasta_digest.py
alphadia/libtransform/flatten.py
alphadia/libtransform/harmonize.py
alphadia/libtransform/loader.py
alphadia/libtransform/mbr.py
alphadia/libtransform/multiplex.py
alphadia/libtransform/prediction.py
alphadia/outputtransform/__init__.py
alphadia/outputtransform/df_builders.py
alphadia/outputtransform/grouping.py
alphadia/outputtransform/outputaccumulator.py
alphadia/outputtransform/protein_fdr.py
alphadia/outputtransform/search_plan_output.py
alphadia/outputtransform/utils.py
alphadia/outputtransform/quantification/__init__.py
alphadia/outputtransform/quantification/fragment_accumulator.py
alphadia/outputtransform/quantification/quant_builder.py
alphadia/outputtransform/quantification/quant_output_builder.py
alphadia/raw_data/__init__.py
alphadia/raw_data/alpharaw_wrapper.py
alphadia/raw_data/bruker.py
alphadia/raw_data/dia_cycle.py
alphadia/reporting/__init__.py
alphadia/reporting/logging.py
alphadia/reporting/reporting.py
alphadia/search/__init__.py
alphadia/search/jitclasses/__init__.py
alphadia/search/jitclasses/alpharaw_jit.py
alphadia/search/jitclasses/bruker_jit.py
alphadia/search/jitclasses/fragment_container.py
alphadia/search/jitclasses/jit_config.py
alphadia/search/jitclasses/utils.py
alphadia/search/scoring/__init__.py
alphadia/search/scoring/config.py
alphadia/search/scoring/output.py
alphadia/search/scoring/quadrupole.py
alphadia/search/scoring/scoring.py
alphadia/search/scoring/scoring_utils.py
alphadia/search/scoring/utils.py
alphadia/search/scoring/containers/__init__.py
alphadia/search/scoring/containers/candidate.py
alphadia/search/scoring/containers/score_group.py
alphadia/search/scoring/features/__init__.py
alphadia/search/scoring/features/features_utils.py
alphadia/search/scoring/features/fragment_features.py
alphadia/search/scoring/features/location_features.py
alphadia/search/scoring/features/precursor_features.py
alphadia/search/scoring/features/profile_features.py
alphadia/search/scoring/features/reference_features.py
alphadia/search/scoring/plotting/__init__.py
alphadia/search/scoring/plotting/cycle.py
alphadia/search/scoring/plotting/debug.py
alphadia/search/selection/__init__.py
alphadia/search/selection/config_df.py
alphadia/search/selection/fft.py
alphadia/search/selection/kernel.py
alphadia/search/selection/selection.py
alphadia/search/selection/utils.py
alphadia/transferlearning/__init__.py
alphadia/transferlearning/metrics.py
alphadia/transferlearning/train.py
alphadia/validation/__init__.py
alphadia/validation/base.py
alphadia/validation/schemas.py
alphadia/workflow/__init__.py
alphadia/workflow/base.py
alphadia/workflow/config.py
alphadia/workflow/manager.py
alphadia/workflow/managers/__init__.py
alphadia/workflow/managers/base.py
alphadia/workflow/managers/calibration_manager.py
alphadia/workflow/managers/fdr_manager.py
alphadia/workflow/managers/optimization_manager.py
alphadia/workflow/managers/raw_file_manager.py
alphadia/workflow/managers/timing_manager.py
alphadia/workflow/optimizers/__init__.py
alphadia/workflow/optimizers/automatic.py
alphadia/workflow/optimizers/base.py
alphadia/workflow/optimizers/optimization_lock.py
alphadia/workflow/optimizers/targeted.py
alphadia/workflow/peptidecentric/__init__.py
alphadia/workflow/peptidecentric/column_name_handler.py
alphadia/workflow/peptidecentric/extraction_handler.py
alphadia/workflow/peptidecentric/library_init.py
alphadia/workflow/peptidecentric/multiplexing_requantification_handler.py
alphadia/workflow/peptidecentric/optimization_handler.py
alphadia/workflow/peptidecentric/peptidecentric.py
alphadia/workflow/peptidecentric/recalibration_handler.py
alphadia/workflow/peptidecentric/transfer_library_requantification_handler.py
alphadia/workflow/peptidecentric/utils.py
alphadia/workflow/peptidecentric/ng/__init__.py
alphadia/workflow/peptidecentric/ng/ng_mapper.py
docs/conf.py
misc/distributed_search/discover_project_files.py
misc/distributed_search/parse_parameters.py
misc/distributed_search/speclib_config.py
release/pyinstaller/cli_hook.py
release/pyinstaller/hookdir/hook-huggingface_hub.py
release/pyinstaller/hookdir/hook-rocket_fft.py
requirements/_requirements.freeze.txt
requirements/requirements.txt
requirements/requirements_development.txt
requirements/requirements_docs.txt
requirements/requirements_tests.txt