Index

_

__init__() (alphadia.calibration.estimator.CalibrationEstimator method) (alphadia.calibration.estimator.CalibrationModelProvider method) (alphadia.calibration.models.LOESSRegression method) (alphadia.fdr._fdrx.base.TargetDecoyFDR method) (alphadia.fdr.classifiers.BinaryClassifierLegacyNewBatching method) (alphadia.fdr.classifiers.FeedForwardNN method) (alphadia.fragcomp.fragcomp.FragmentCompetition method) (alphadia.libtransform.base.ProcessingPipeline method) (alphadia.libtransform.base.ProcessingStep method) (alphadia.libtransform.decoy.DecoyGenerator method) (alphadia.libtransform.fasta_digest.FastaDigest method) (alphadia.libtransform.flatten.FlattenLibrary method) (alphadia.libtransform.flatten.InitFlatColumns method) (alphadia.libtransform.flatten.LogFlatLibraryStats method) (alphadia.libtransform.harmonize.AnnotateFasta method) (alphadia.libtransform.harmonize.IsotopeGenerator method) (alphadia.libtransform.harmonize.PrecursorInitializer method) (alphadia.libtransform.harmonize.RTNormalization method) (alphadia.libtransform.loader.DynamicLoader method) (alphadia.libtransform.mbr.IndexBuilder method) (alphadia.libtransform.mbr.MbrLibraryBuilder method) (alphadia.libtransform.multiplex.MultiplexLibrary method) (alphadia.libtransform.prediction.PeptDeepPrediction method) (alphadia.outputtransform.outputaccumulator.AccumulationBroadcaster method) (alphadia.outputtransform.outputaccumulator.TransferLearningAccumulator method) (alphadia.outputtransform.search_plan_output.SearchPlanOutput method) (alphadia.search.scoring.config.CandidateScoringConfig method) (alphadia.search.scoring.quadrupole.SimpleQuadrupole method) (alphadia.search.scoring.scoring.CandidateScoring method) (alphadia.search.selection.config_df.CandidateSelectionConfig method) (alphadia.search.selection.kernel.GaussianKernel method) (alphadia.search.selection.selection.CandidateSelection method) (alphadia.search_step.SearchStep method) (alphadia.validation.base.Optional method) (alphadia.validation.base.Property method) (alphadia.validation.base.Required method) (alphadia.validation.base.Schema method) (alphadia.workflow.base.WorkflowBase method) (alphadia.workflow.config.Config method) (alphadia.workflow.managers.base.BaseManager method) (alphadia.workflow.managers.calibration_manager.CalibrationManager method) (alphadia.workflow.managers.fdr_manager.FDRManager method) (alphadia.workflow.managers.optimization_manager.OptimizationManager method) (alphadia.workflow.managers.raw_file_manager.RawFileManager method) (alphadia.workflow.managers.timing_manager.TimingManager method)

A

AccumulationBroadcaster (class in alphadia.outputtransform.outputaccumulator) add_frag_start_stop_idx() (in module alphadia.fragcomp.utils) add_module() (alphadia.fdr.classifiers.FeedForwardNN method) add_q_values() (in module alphadia.fdr._fdrx.stats) alphadia.calibration.estimator module alphadia.calibration.models module alphadia.fdr._fdrx.base module alphadia.fdr._fdrx.plotting module alphadia.fdr._fdrx.stats module alphadia.fdr.classifiers module alphadia.fdr.fdr module alphadia.fdr.plotting module alphadia.fdr.utils module alphadia.fragcomp.fragcomp module alphadia.fragcomp.utils module alphadia.libtransform.base module alphadia.libtransform.decoy module alphadia.libtransform.fasta_digest module alphadia.libtransform.flatten module alphadia.libtransform.harmonize module alphadia.libtransform.loader module alphadia.libtransform.mbr module alphadia.libtransform.multiplex module alphadia.libtransform.prediction module alphadia.outputtransform.df_builders module alphadia.outputtransform.outputaccumulator module alphadia.outputtransform.protein_fdr module alphadia.outputtransform.search_plan_output module alphadia.outputtransform.utils module alphadia.search.scoring.config module alphadia.search.scoring.containers module alphadia.search.scoring.features.features_utils module alphadia.search.scoring.features.fragment_features module alphadia.search.scoring.features.location_features module

alphadia.search.scoring.features.precursor_features module alphadia.search.scoring.features.profile_features module alphadia.search.scoring.features.reference_features module alphadia.search.scoring.output module alphadia.search.scoring.quadrupole module alphadia.search.scoring.scoring module alphadia.search.scoring.scoring_utils module alphadia.search.scoring.utils module alphadia.search.selection.config_df module alphadia.search.selection.fft module alphadia.search.selection.kernel module alphadia.search.selection.selection module alphadia.search.selection.utils module alphadia.search_step module alphadia.utils module alphadia.validation.base module alphadia.validation.schemas module alphadia.workflow.base module alphadia.workflow.config module alphadia.workflow.managers.base module alphadia.workflow.managers.calibration_manager module alphadia.workflow.managers.fdr_manager module alphadia.workflow.managers.optimization_manager module alphadia.workflow.managers.raw_file_manager module alphadia.workflow.managers.timing_manager module alphadia.workflow.optimizers module amean1() (in module alphadia.search.selection.utils) AnnotateFasta (class in alphadia.libtransform.harmonize) apply() (alphadia.fdr.classifiers.FeedForwardNN method) (alphadia.libtransform.mbr.IndexBuilder method) apply_output_column_names() (in module alphadia.outputtransform.utils) apply_protein_inference() (in module alphadia.outputtransform.utils) assemble_fragments() (alphadia.search.scoring.scoring.CandidateScoring method) assemble_isotope_mz() (in module alphadia.search.selection.utils) assemble_score_group_container() (alphadia.search.scoring.scoring.CandidateScoring method) astd1() (in module alphadia.search.selection.utils)

B

BaseAccumulator (class in alphadia.outputtransform.outputaccumulator) BaseManager (class in alphadia.workflow.managers.base) bfloat16() (alphadia.fdr.classifiers.FeedForwardNN method) BinaryClassifierLegacyNewBatching (class in alphadia.fdr.classifiers)

buffers() (alphadia.fdr.classifiers.FeedForwardNN method) build() (alphadia.outputtransform.search_plan_output.SearchPlanOutput method) build_run_internal_df() (in module alphadia.outputtransform.df_builders) build_run_stat_df() (in module alphadia.outputtransform.df_builders) build_speclibflat_from_quant() (in module alphadia.outputtransform.outputaccumulator)

C

calc_deviation() (alphadia.calibration.estimator.CalibrationEstimator method) calculate_observation_importance_single() (in module alphadia.search.scoring.quadrupole) calculate_score_groups() (in module alphadia.search.scoring.utils) calculate_template_single() (in module alphadia.search.scoring.quadrupole) calibration_manager (alphadia.workflow.base.WorkflowBase property) CALIBRATION_MANAGER_PKL_NAME (alphadia.workflow.base.WorkflowBase attribute) CalibrationEstimator (class in alphadia.calibration.estimator) CalibrationEstimators (class in alphadia.workflow.managers.calibration_manager) CalibrationGroups (class in alphadia.workflow.managers.calibration_manager) CalibrationManager (class in alphadia.workflow.managers.calibration_manager) CalibrationModelProvider (class in alphadia.calibration.estimator) call_super_init (alphadia.fdr.classifiers.FeedForwardNN attribute) candidate_container_to_df() (in module alphadia.search.selection.config_df) candidate_count (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) candidate_features_to_candidates() (in module alphadia.search.scoring.utils) candidate_hash() (in module alphadia.fragcomp.utils) candidate_start_idx (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) candidate_stop_idx (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) CandidateContainer (class in alphadia.search.selection.config_df) CandidateScoring (class in alphadia.search.scoring.scoring) CandidateScoringConfig (class in alphadia.search.scoring.config) CandidateScoringConfigJIT (class in alphadia.search.scoring.config) CandidateSelection (class in alphadia.search.selection.selection) CandidateSelectionConfig (class in alphadia.search.selection.config_df) CandidateSelectionConfigJIT (class in alphadia.search.selection.config_df) center_envelope_1d() (in module alphadia.search.scoring.features.fragment_features) center_fraction (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

charge (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) children() (alphadia.fdr.classifiers.FeedForwardNN method) ci() (alphadia.calibration.estimator.CalibrationEstimator method) class_type (alphadia.search.scoring.config.CandidateScoringConfigJIT attribute) (alphadia.search.scoring.output.OutputPsmDF attribute) (alphadia.search.scoring.quadrupole.SimpleQuadrupoleJit attribute) (alphadia.search.selection.config_df.CandidateContainer attribute) (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) Classifier (class in alphadia.fdr.classifiers) classifier_version (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) collect_candidates() (alphadia.search.scoring.scoring.CandidateScoring method) collect_fragments (alphadia.search.scoring.config.CandidateScoringConfig property) collect_fragments() (alphadia.search.scoring.scoring.CandidateScoring method) column_hash() (in module alphadia.workflow.managers.fdr_manager) compile() (alphadia.fdr.classifiers.FeedForwardNN method) config (alphadia.search.scoring.scoring.CandidateScoring property) (alphadia.search_step.SearchStep property) (alphadia.workflow.base.WorkflowBase property) Config (class in alphadia.workflow.config) construct_polynomial_regression() (in module alphadia.calibration.models) convolve_fourier() (in module alphadia.search.selection.fft) copy() (alphadia.workflow.config.Config method) correlation_coefficient() (in module alphadia.search.scoring.scoring_utils) cosine_similarity_a1() (in module alphadia.search.scoring.features.features_utils) cpu() (alphadia.fdr.classifiers.FeedForwardNN method) cuda() (alphadia.fdr.classifiers.FeedForwardNN method) current_version (alphadia.workflow.managers.fdr_manager.FDRManager property)

D

DecoyGenerator (class in alphadia.libtransform.decoy) determine_mobility_sigma() (alphadia.search.selection.kernel.GaussianKernel method) determine_rt_sigma() (alphadia.search.selection.kernel.GaussianKernel method) dia_data (alphadia.search.scoring.scoring.CandidateScoring property) (alphadia.workflow.base.WorkflowBase property)

docstring() (alphadia.validation.base.Schema method) double() (alphadia.fdr.classifiers.FeedForwardNN method) dump_patches (alphadia.fdr.classifiers.FeedForwardNN attribute) DynamicLoader (class in alphadia.libtransform.loader)

E

error_callback() (in module alphadia.outputtransform.outputaccumulator) estimator_groups (alphadia.workflow.managers.calibration_manager.CalibrationManager property) eval() (alphadia.fdr.classifiers.FeedForwardNN method) exclude_shared_ions (alphadia.search.scoring.config.CandidateScoringConfig property) (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

expand_cycle() (in module alphadia.search.scoring.quadrupole) expand_path() (in module alphadia.utils) experimental_xic (alphadia.search.scoring.config.CandidateScoringConfig property) extra_repr() (alphadia.fdr.classifiers.FeedForwardNN method)

F

f_mobility (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) f_rt (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) FastaDigest (class in alphadia.libtransform.fasta_digest) FDR_MANAGER_PKL_NAME (alphadia.workflow.base.WorkflowBase attribute) fdr_to_q_values() (in module alphadia.fdr._fdrx.stats) FDRManager (class in alphadia.workflow.managers.fdr_manager) feature_mean (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) feature_std (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) feature_weight (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) FeedForwardNN (class in alphadia.fdr.classifiers) find_peaks_1d() (in module alphadia.search.selection.utils) find_peaks_2d() (in module alphadia.search.selection.utils) fit() (alphadia.calibration.estimator.CalibrationEstimator method) (alphadia.calibration.models.LOESSRegression method) (alphadia.fdr.classifiers.BinaryClassifierLegacyNewBatching method) (alphadia.fdr.classifiers.Classifier method) (alphadia.search.scoring.quadrupole.SimpleQuadrupole method) (alphadia.workflow.managers.calibration_manager.CalibrationManager method) fit_classifier() (alphadia.fdr._fdrx.base.TargetDecoyFDR method) fit_predict() (alphadia.workflow.managers.fdr_manager.FDRManager method) fit_predict_qval() (alphadia.fdr._fdrx.base.TargetDecoyFDR method) fitted (alphadia.fdr.classifiers.Classifier attribute) FlattenLibrary (class in alphadia.libtransform.flatten) float() (alphadia.fdr.classifiers.FeedForwardNN method) forward() (alphadia.fdr.classifiers.FeedForwardNN method) (alphadia.libtransform.base.ProcessingStep method) (alphadia.libtransform.decoy.DecoyGenerator method) (alphadia.libtransform.fasta_digest.FastaDigest method) (alphadia.libtransform.flatten.FlattenLibrary method) (alphadia.libtransform.flatten.InitFlatColumns method) (alphadia.libtransform.flatten.LogFlatLibraryStats method) (alphadia.libtransform.harmonize.AnnotateFasta method) (alphadia.libtransform.harmonize.IsotopeGenerator method) (alphadia.libtransform.harmonize.PrecursorInitializer method) (alphadia.libtransform.harmonize.RTNormalization method) (alphadia.libtransform.loader.DynamicLoader method) (alphadia.libtransform.mbr.MbrLibraryBuilder method) (alphadia.libtransform.multiplex.MultiplexLibrary method) (alphadia.libtransform.prediction.PeptDeepPrediction method)

frag_start_idx (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) frag_stop_idx (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) FRAGMENT (alphadia.workflow.managers.calibration_manager.CalibrationGroups attribute) fragment_correlation() (in module alphadia.search.scoring.utils) fragment_correlation_different() (in module alphadia.search.scoring.utils) fragment_features() (in module alphadia.search.scoring.features.fragment_features) fragment_mobility_correlation() (in module alphadia.search.scoring.features.fragment_features) fragment_mz_tolerance (alphadia.search.scoring.config.CandidateScoringConfig property) (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) FragmentCompetition (class in alphadia.fragcomp.fragcomp) fragments_flat_df (alphadia.search.scoring.scoring.CandidateScoring property) frame_profile_1d() (in module alphadia.search.scoring.utils) frame_profile_2d() (in module alphadia.search.scoring.utils) from_file() (alphadia.calibration.estimator.CalibrationEstimator class method) from_json() (alphadia.workflow.config.Config method) from_state_dict() (alphadia.fdr.classifiers.BinaryClassifierLegacyNewBatching method) (alphadia.fdr.classifiers.Classifier method) from_yaml() (alphadia.workflow.config.Config method) fwhm_mobility (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) fwhm_rt (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute)

G

gaussian_kernel_2d() (alphadia.search.selection.kernel.GaussianKernel static method) GaussianKernel (class in alphadia.search.selection.kernel) get_buffer() (alphadia.fdr.classifiers.FeedForwardNN method) get_calibrated_cycle() (alphadia.search.scoring.quadrupole.SimpleQuadrupole method) get_channels_from_config() (in module alphadia.outputtransform.utils) get_classifier() (alphadia.workflow.managers.fdr_manager.FDRManager method) get_dense_matrix() (alphadia.search.selection.kernel.GaussianKernel method) get_dia_data_object() (alphadia.workflow.managers.raw_file_manager.RawFileManager method) get_estimator() (alphadia.workflow.managers.calibration_manager.CalibrationManager method) get_extra_state() (alphadia.fdr.classifiers.FeedForwardNN method)

get_group_columns() (in module alphadia.workflow.managers.fdr_manager) get_isotope_columns() (in module alphadia.utils) get_model() (alphadia.calibration.estimator.CalibrationModelProvider method) get_parameter() (alphadia.fdr.classifiers.FeedForwardNN method) get_params() (alphadia.search.scoring.quadrupole.SimpleQuadrupole method) get_pep() (in module alphadia.fdr._fdrx.stats) get_q_values() (in module alphadia.fdr.fdr) get_submodule() (alphadia.fdr.classifiers.FeedForwardNN method) get_torch_device() (in module alphadia.utils) group_channels (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

H

half() (alphadia.fdr.classifiers.FeedForwardNN method)

I

IndexBuilder (class in alphadia.libtransform.mbr) InitFlatColumns (class in alphadia.libtransform.flatten) INTERNAL_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) ipu() (alphadia.fdr.classifiers.FeedForwardNN method)

is_loaded_from_file (alphadia.workflow.managers.base.BaseManager property) isotope_tolerance (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) IsotopeGenerator (class in alphadia.libtransform.harmonize) isotopes (alphadia.search.selection.config_df.PrecursorFlatContainer attribute)

J

join_close_candidates (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

join_close_candidates_cycle_threshold (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) join_close_candidates_scan_threshold (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

K

keep_best() (in module alphadia.fdr._fdrx.stats) (in module alphadia.fdr.fdr)

kernel_size (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

L

LIBRARY_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) load() (alphadia.workflow.base.WorkflowBase method) (alphadia.workflow.managers.base.BaseManager method) load_classifier_store() (alphadia.workflow.managers.fdr_manager.FDRManager method) load_library() (alphadia.search_step.SearchStep method) load_psm_files_from_folders() (in module alphadia.outputtransform.utils) load_state_dict() (alphadia.fdr.classifiers.FeedForwardNN method)

location_features() (in module alphadia.search.scoring.features.location_features) LOESSRegression (class in alphadia.calibration.models) log_protein_fdr_summary() (in module alphadia.outputtransform.utils) log_stat_df() (in module alphadia.outputtransform.df_builders) LogFlatLibraryStats (class in alphadia.libtransform.flatten) logistic() (in module alphadia.search.scoring.quadrupole) logistic_rectangle() (in module alphadia.search.scoring.quadrupole)

M

manage_torch_threads() (in module alphadia.fdr.utils) max_size_mobility (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) max_size_rt (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) MbrLibraryBuilder (class in alphadia.libtransform.mbr) median_axis() (in module alphadia.search.scoring.scoring_utils) merge_candidate_data() (alphadia.search.scoring.scoring.CandidateScoring static method) merge_missing_columns() (in module alphadia.search.scoring.utils) merge_precursor_data() (alphadia.search.scoring.scoring.CandidateScoring static method) merge_quant_levels_to_psm() (in module alphadia.outputtransform.utils) min_size_mobility (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) min_size_rt (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) mobility (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) MOBILITY (alphadia.workflow.managers.calibration_manager.CalibrationEstimators attribute) mobility_error (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) mobility_tolerance (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) module alphadia.calibration.estimator alphadia.calibration.models alphadia.fdr._fdrx.base alphadia.fdr._fdrx.plotting alphadia.fdr._fdrx.stats alphadia.fdr.classifiers alphadia.fdr.fdr alphadia.fdr.plotting alphadia.fdr.utils alphadia.fragcomp.fragcomp alphadia.fragcomp.utils alphadia.libtransform.base alphadia.libtransform.decoy alphadia.libtransform.fasta_digest alphadia.libtransform.flatten alphadia.libtransform.harmonize alphadia.libtransform.loader alphadia.libtransform.mbr alphadia.libtransform.multiplex alphadia.libtransform.prediction alphadia.outputtransform.df_builders alphadia.outputtransform.outputaccumulator alphadia.outputtransform.protein_fdr alphadia.outputtransform.search_plan_output alphadia.outputtransform.utils alphadia.search.scoring.config alphadia.search.scoring.containers alphadia.search.scoring.features.features_utils alphadia.search.scoring.features.fragment_features alphadia.search.scoring.features.location_features alphadia.search.scoring.features.precursor_features alphadia.search.scoring.features.profile_features alphadia.search.scoring.features.reference_features alphadia.search.scoring.output alphadia.search.scoring.quadrupole alphadia.search.scoring.scoring alphadia.search.scoring.scoring_utils alphadia.search.scoring.utils alphadia.search.selection.config_df alphadia.search.selection.fft alphadia.search.selection.kernel alphadia.search.selection.selection alphadia.search.selection.utils alphadia.search_step alphadia.utils alphadia.validation.base alphadia.validation.schemas alphadia.workflow.base alphadia.workflow.config alphadia.workflow.managers.base alphadia.workflow.managers.calibration_manager alphadia.workflow.managers.fdr_manager alphadia.workflow.managers.optimization_manager alphadia.workflow.managers.raw_file_manager alphadia.workflow.managers.timing_manager alphadia.workflow.optimizers

modules() (alphadia.fdr.classifiers.FeedForwardNN method) ms1_error (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) ms2_error (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) ms2_quality_control() (in module alphadia.outputtransform.outputaccumulator) mtia() (alphadia.fdr.classifiers.FeedForwardNN method) multiplex_candidates() (in module alphadia.search.scoring.utils) MultiplexLibrary (class in alphadia.libtransform.multiplex) multivariate_normal() (in module alphadia.search.selection.kernel) mz (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) MZ (alphadia.workflow.managers.calibration_manager.CalibrationEstimators attribute)

N

named_buffers() (alphadia.fdr.classifiers.FeedForwardNN method) named_children() (alphadia.fdr.classifiers.FeedForwardNN method) named_modules() (alphadia.fdr.classifiers.FeedForwardNN method) named_parameters() (alphadia.fdr.classifiers.FeedForwardNN method)

normalize_profiles() (in module alphadia.search.scoring.scoring_utils) normalize_rt_delta_max() (in module alphadia.outputtransform.outputaccumulator) normalize_rt_max() (in module alphadia.outputtransform.outputaccumulator) num_candidates (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) NumbaContextOnly

O

optimization_manager (alphadia.workflow.base.WorkflowBase property) OPTIMIZATION_MANAGER_PKL_NAME (alphadia.workflow.base.WorkflowBase attribute) OptimizationManager (class in alphadia.workflow.managers.optimization_manager)

Optional (class in alphadia.validation.base) or_envelope_1d() (in module alphadia.search.scoring.utils) or_envelope_2d() (in module alphadia.search.scoring.utils) OutputPsmDF (class in alphadia.search.scoring.output)

P

parameters() (alphadia.fdr.classifiers.FeedForwardNN method) path (alphadia.workflow.base.WorkflowBase property) (alphadia.workflow.managers.base.BaseManager property) peak_len_mobility (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) peak_len_rt (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) PeptDeepPrediction (class in alphadia.libtransform.prediction) perform_protein_fdr() (in module alphadia.outputtransform.protein_fdr) PG_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) plot_fdr() (in module alphadia.fdr.plotting) post_process() (alphadia.outputtransform.outputaccumulator.BaseAccumulator method) (alphadia.outputtransform.outputaccumulator.TransferLearningAccumulator method) PRECURSOR (alphadia.workflow.managers.calibration_manager.CalibrationGroups attribute) precursor_features() (in module alphadia.search.scoring.features.precursor_features) precursor_idx (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) precursor_mz_tolerance (alphadia.search.scoring.config.CandidateScoringConfig property) (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) PRECURSOR_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) PrecursorFlatContainer (class in alphadia.search.selection.config_df)

PrecursorInitializer (class in alphadia.libtransform.harmonize) precursors_flat_df (alphadia.search.scoring.scoring.CandidateScoring property) predict() (alphadia.calibration.estimator.CalibrationEstimator method) (alphadia.calibration.models.LOESSRegression method) (alphadia.fdr.classifiers.BinaryClassifierLegacyNewBatching method) (alphadia.fdr.classifiers.Classifier method) (alphadia.search.scoring.quadrupole.SimpleQuadrupole method) (alphadia.workflow.managers.calibration_manager.CalibrationManager method) predict_classifier() (alphadia.fdr._fdrx.base.TargetDecoyFDR method) predict_proba() (alphadia.fdr.classifiers.BinaryClassifierLegacyNewBatching method) (alphadia.fdr.classifiers.Classifier method) predict_qval() (alphadia.fdr._fdrx.base.TargetDecoyFDR method) prepare_psm_dataframe() (in module alphadia.outputtransform.utils) ProcessingPipeline (class in alphadia.libtransform.base) ProcessingStep (class in alphadia.libtransform.base) profile_features() (in module alphadia.search.scoring.features.profile_features) Property (class in alphadia.validation.base) PSM_INPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute)

Q

quadrupole_calibration (alphadia.search.scoring.scoring.CandidateScoring property) quadrupole_transfer_function_single() (in module alphadia.search.scoring.quadrupole)

quant_all (alphadia.search.scoring.config.CandidateScoringConfig property) quant_window (alphadia.search.scoring.config.CandidateScoringConfig property)

R

RAW_FILE_MANAGER_PKL_NAME (alphadia.workflow.base.WorkflowBase attribute) RawFileManager (class in alphadia.workflow.managers.raw_file_manager) read_df() (in module alphadia.outputtransform.utils) reference_channel (alphadia.search.scoring.config.CandidateScoringConfig property) reference_features() (in module alphadia.search.scoring.features.reference_features) register_backward_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_buffer() (alphadia.fdr.classifiers.FeedForwardNN method) register_forward_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_forward_pre_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_full_backward_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_full_backward_pre_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_load_state_dict_post_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_load_state_dict_pre_hook() (alphadia.fdr.classifiers.FeedForwardNN method)

register_model() (alphadia.calibration.estimator.CalibrationModelProvider method) register_module() (alphadia.fdr.classifiers.FeedForwardNN method) register_parameter() (alphadia.fdr.classifiers.FeedForwardNN method) register_state_dict_post_hook() (alphadia.fdr.classifiers.FeedForwardNN method) register_state_dict_pre_hook() (alphadia.fdr.classifiers.FeedForwardNN method) Required (class in alphadia.validation.base) requires_grad_() (alphadia.fdr.classifiers.FeedForwardNN method) rt (alphadia.search.selection.config_df.PrecursorFlatContainer attribute) RT (alphadia.workflow.managers.calibration_manager.CalibrationEstimators attribute) rt_error (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) rt_tolerance (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) RTNormalization (class in alphadia.libtransform.harmonize) run() (alphadia.outputtransform.outputaccumulator.AccumulationBroadcaster method) (alphadia.search_step.SearchStep method)

S

save() (alphadia.calibration.estimator.CalibrationEstimator method) (alphadia.workflow.managers.base.BaseManager method) save_classifier_store() (alphadia.workflow.managers.fdr_manager.FDRManager method) save_corrcoeff() (in module alphadia.search.scoring.utils) scan_profile_1d() (in module alphadia.search.scoring.utils) scan_profile_2d() (in module alphadia.search.scoring.utils) Schema (class in alphadia.validation.base) score_cutoff (alphadia.workflow.managers.optimization_manager.OptimizationManager attribute) score_grouped (alphadia.search.scoring.config.CandidateScoringConfig property) SearchPlanOutput (class in alphadia.outputtransform.search_plan_output) SearchStep (class in alphadia.search_step) set_end_time() (alphadia.workflow.managers.timing_manager.TimingManager method) set_extra_state() (alphadia.fdr.classifiers.FeedForwardNN method) set_fit_request() (alphadia.calibration.models.LOESSRegression method) set_params() (alphadia.search.scoring.quadrupole.SimpleQuadrupole method) set_predict_request() (alphadia.calibration.models.LOESSRegression method) set_score_request() (alphadia.calibration.models.LOESSRegression method)

set_start_time() (alphadia.workflow.managers.timing_manager.TimingManager method) set_submodule() (alphadia.fdr.classifiers.FeedForwardNN method) set_value() (alphadia.workflow.config.Config method) setup_estimator_groups() (alphadia.workflow.managers.calibration_manager.CalibrationManager method) share_memory() (alphadia.fdr.classifiers.FeedForwardNN method) sigma_scale_mobility (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) sigma_scale_rt (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) SimpleQuadrupole (class in alphadia.search.scoring.quadrupole) SimpleQuadrupoleJit (class in alphadia.search.scoring.quadrupole) slice() (in module alphadia.search.scoring.utils) slice_manual() (in module alphadia.search.selection.utils) spectral_library (alphadia.search_step.SearchStep property) (alphadia.workflow.base.WorkflowBase property) STAT_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) state_dict() (alphadia.fdr.classifiers.FeedForwardNN method) subscribe() (alphadia.outputtransform.outputaccumulator.AccumulationBroadcaster method) symetric_limits_2d() (in module alphadia.search.selection.utils)

T

T_destination (alphadia.fdr.classifiers.FeedForwardNN attribute) TargetDecoyFDR (class in alphadia.fdr._fdrx.base) tile() (in module alphadia.search.scoring.utils) timing_manager (alphadia.workflow.base.WorkflowBase property) TIMING_MANAGER_PKL_NAME (alphadia.workflow.base.WorkflowBase attribute) TimingManager (class in alphadia.workflow.managers.timing_manager) to() (alphadia.fdr.classifiers.FeedForwardNN method) to_empty() (alphadia.fdr.classifiers.FeedForwardNN method) to_json() (alphadia.workflow.config.Config method) to_state_dict() (alphadia.fdr.classifiers.BinaryClassifierLegacyNewBatching method) (alphadia.fdr.classifiers.Classifier method) to_yaml() (alphadia.workflow.config.Config method)

top_k_fragments (alphadia.search.scoring.config.CandidateScoringConfig property) (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) top_k_isotopes (alphadia.search.scoring.config.CandidateScoringConfig property) top_k_precursors (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute) train() (alphadia.fdr.classifiers.FeedForwardNN method) train_test_split_() (in module alphadia.fdr.utils) training (alphadia.fdr.classifiers.FeedForwardNN attribute) transfer_library_stat_df() (in module alphadia.outputtransform.df_builders) TRANSFER_MODEL (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) TRANSFER_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) TRANSFER_STATS_OUTPUT (alphadia.outputtransform.search_plan_output.SearchPlanOutput attribute) TransferLearningAccumulator (class in alphadia.outputtransform.outputaccumulator) type() (alphadia.fdr.classifiers.FeedForwardNN method)

U

update() (alphadia.outputtransform.outputaccumulator.BaseAccumulator method) (alphadia.outputtransform.outputaccumulator.TransferLearningAccumulator method) (alphadia.workflow.config.Config method) (alphadia.workflow.managers.optimization_manager.OptimizationManager method)

use_weighted_score (alphadia.search.selection.config_df.CandidateSelectionConfigJIT attribute)

V

validate() (alphadia.libtransform.base.ProcessingStep method) (alphadia.libtransform.decoy.DecoyGenerator method) (alphadia.libtransform.fasta_digest.FastaDigest method) (alphadia.libtransform.flatten.FlattenLibrary method) (alphadia.libtransform.flatten.InitFlatColumns method) (alphadia.libtransform.flatten.LogFlatLibraryStats method) (alphadia.libtransform.harmonize.AnnotateFasta method) (alphadia.libtransform.harmonize.IsotopeGenerator method) (alphadia.libtransform.harmonize.PrecursorInitializer method) (alphadia.libtransform.harmonize.RTNormalization method) (alphadia.libtransform.loader.DynamicLoader method) (alphadia.libtransform.mbr.MbrLibraryBuilder method) (alphadia.libtransform.multiplex.MultiplexLibrary method) (alphadia.libtransform.prediction.PeptDeepPrediction method) (alphadia.search.scoring.config.CandidateScoringConfig method) (alphadia.search.selection.config_df.CandidateSelectionConfig method) (alphadia.validation.base.Schema method)

W

weighted_center_mean() (in module alphadia.search.scoring.features.features_utils) weighted_center_mean_2d() (in module alphadia.search.scoring.features.features_utils) weighted_center_of_mass() (in module alphadia.search.scoring.features.fragment_features) weighted_center_of_mass_1d() (in module alphadia.search.scoring.features.fragment_features)

weighted_mean_a1() (in module alphadia.search.scoring.features.fragment_features) WorkflowBase (class in alphadia.workflow.base) wrap0() (in module alphadia.search.selection.utils) wrap1() (in module alphadia.search.selection.utils) write_df() (in module alphadia.outputtransform.utils)

X

xpu() (alphadia.fdr.classifiers.FeedForwardNN method)

Z

zero_grad() (alphadia.fdr.classifiers.FeedForwardNN method)