Index

_

_extract_features() (fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser.PeakMzmine3Parser static method)

_extract_samples() (fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser.PeakMzmine3Parser static method) _extract_stats() (fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser.PeakMzmine3Parser static method)

A

aa_frags (fermo_core.config.class_default_settings.CharFragments attribute) aa_frags_src (fermo_core.config.class_default_settings.CharFragments attribute) abbr (fermo_core.config.class_default_settings.Loss attribute) Ac (fermo_core.config.class_default_settings.DefaultMasses attribute) accepted (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser attribute) acetate_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) activate_module (fermo_core.input_output.param_handlers.AdductAnnotationParameters attribute) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams attribute) (fermo_core.input_output.param_handlers.AsKcbDeepscoreMatchingParams attribute) (fermo_core.input_output.param_handlers.BlankAssignmentParameters attribute) (fermo_core.input_output.param_handlers.FeatureFilteringParameters attribute) (fermo_core.input_output.param_handlers.FragmentAnnParameters attribute) (fermo_core.input_output.param_handlers.GroupFactAssignmentParameters attribute) (fermo_core.input_output.param_handlers.NeutralLossParameters attribute) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingDeepscoreParameters attribute) active_features (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2query_annotator.MS2QueryAnnotator attribute) (fermo_core.data_processing.class_stats.Stats attribute) add() (fermo_core.data_processing.class_repository.Repository method) add_activity_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_adduct_info() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator static method) add_adduct_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_annotation() (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator static method) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator static method) add_annotation_attribute() (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner static method) (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss static method) add_blank_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_fragment_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_group_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_loss_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_match_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_networks_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_phenotype_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) add_sample_info_csv() (fermo_core.input_output.class_export_manager.CsvExporter method) Adduct (class in fermo_core.data_processing.builder_feature.dataclass_feature) adduct_type (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) AdductAnnotationParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) AdductAnnotator (class in fermo_core.data_analysis.annotation_manager.class_adduct_annotator) adducts (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations attribute) algorithm (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.SimNetworks attribute) (fermo_core.data_processing.class_stats.SpecSimNet attribute) (fermo_core.input_output.param_handlers.BlankAssignmentParameters attribute) (fermo_core.input_output.param_handlers.GroupFactAssignmentParameters attribute) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute)

ammonium() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) AnalysisManager (class in fermo_core.data_analysis.class_analysis_manager) analyze() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) annotate_adducts_neg() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) annotate_adducts_pos() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) annotate_feature_neg() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) annotate_feature_pos() (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator method) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) AnnotationManager (class in fermo_core.data_analysis.annotation_manager.class_annotation_manager) Annotations (class in fermo_core.data_processing.builder_feature.dataclass_feature) (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) area (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) area_max (fermo_core.data_processing.class_stats.Stats attribute) area_min (fermo_core.data_processing.class_stats.Stats attribute) area_per_sample (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) ArgparseManager (class in fermo_core.input_output.class_argparse_manager) AsKcbCosineMatchingParams (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) AsKcbDeepscoreMatchingParams (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) AsResultsParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) assays (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) assemble_summary() (fermo_core.input_output.class_summary_writer.SummaryWriter method) assign_adduct_annotation() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_as_kcb_matching_cosine() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_as_kcb_matching_deepscore() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_as_results() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_blank_assignment() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_feature_filtering() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_feature_info() (fermo_core.data_analysis.annotation_manager.class_ms2query_annotator.MS2QueryAnnotator method) assign_feature_scores() (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner method) assign_fragment_annotation() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_group_factor_assignment() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_group_factors() (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner method) assign_group_metadata() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_groups() (fermo_core.data_analysis.group_assigner.class_group_assigner.GroupAssigner method) assign_ms2query_results() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_msms() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_neutral_loss_annotation() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_parameters_cli() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_params() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_peaktable() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_phenotype() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_phenotype_qualitative() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_phenotype_quant_concentration() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_phenotype_quant_percent() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_relative_intensity() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) assign_results() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss method) assign_sample_scores() (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner method) assign_spec_lib_matching_cosine() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_spec_lib_matching_ms2deepscore() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_spec_sim_networking_cosine() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_spec_sim_networking_ms2deepscore() (fermo_core.input_output.class_parameter_manager.ParameterManager method) assign_spectral_library() (fermo_core.input_output.class_parameter_manager.ParameterManager method)

B

bicarbonate_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) bin_intersection() (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner method) blank (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) blank_f_ids (fermo_core.data_processing.class_stats.GroupMData attribute) blank_s_ids (fermo_core.data_processing.class_stats.GroupMData attribute)

BlankAssigner (class in fermo_core.data_analysis.blank_assigner.class_blank_assigner) BlankAssignmentParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) build_csv_output() (fermo_core.input_output.class_export_manager.CsvExporter method) build_json_dict() (fermo_core.input_output.class_export_manager.JsonExporter method)

C

C13_12 (fermo_core.config.class_default_settings.DefaultMasses attribute) calc_rprsnt() (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner method) calc_rt_left_fwhm() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) calc_rt_left_kink() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) calc_rt_right_fwhm() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) calc_rt_right_kink() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) calculate_correlation() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss method) calculate_scores_mod_cosine() (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator method) calculate_scores_ms2deepscore() (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator method) category (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype attribute) (fermo_core.data_processing.class_stats.PhenoData attribute) CharFrag (class in fermo_core.data_processing.builder_feature.dataclass_feature) CharFragments (class in fermo_core.config.class_default_settings) check_ms2deepscore_req() (fermo_core.utils.utility_method_manager.UtilityMethodManager method) chloride_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) chrom_trace (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator attribute) ChromTraceCalculator (class in fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator) ChromTraceData (class in fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator) Cl35 (fermo_core.config.class_default_settings.DefaultMasses attribute) coeff_cutoff (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute)

collect_area() (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) collect_height() (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) collect_sample_spec_networks() (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner method) collect_sets() (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner method) configure_logger_results() (in module fermo_core.main) construct_mzmine3() (fermo_core.data_processing.builder_feature.class_general_feature_director.GeneralFeatureDirector static method) (fermo_core.data_processing.builder_feature.class_specific_feature_director.SpecificFeatureDirector static method) (fermo_core.data_processing.builder_sample.class_samples_director.SamplesDirector static method) contains_values() (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser method) correct_p_val() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss method) create_mibig_spec_lib() (fermo_core.utils.utility_method_manager.UtilityMethodManager static method) create_network() (fermo_core.data_analysis.sim_networks_manager.class_mod_cosine_networker.ModCosineNetworker static method) (fermo_core.data_analysis.sim_networks_manager.class_ms2deepscore_networker.Ms2deepscoreNetworker static method) create_spectrum_object() (fermo_core.utils.utility_method_manager.UtilityMethodManager static method) create_trace_int() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) create_trace_rt() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) CsvExporter (class in fermo_core.input_output.class_export_manager) ctgrs (fermo_core.data_processing.class_stats.GroupMData attribute) cutoff (fermo_core.data_analysis.annotation_manager.class_ms2query_annotator.MS2QueryAnnotator attribute)

D

datatype (fermo_core.data_processing.class_stats.PhenoData attribute) default_s_ids (fermo_core.data_processing.class_stats.GroupMData attribute) DefaultMasses (class in fermo_core.config.class_default_settings) DefaultPaths (class in fermo_core.config.class_default_settings) define_argparse_args() (fermo_core.input_output.class_argparse_manager.ArgparseManager static method) dereplicate_adducts() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) descr (fermo_core.config.class_default_settings.Fragment attribute) (fermo_core.config.class_default_settings.Loss attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype attribute) destination (fermo_core.input_output.class_summary_writer.SummaryWriter attribute) determine_blank() (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) df (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser attribute) (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser attribute) (fermo_core.input_output.class_export_manager.CsvExporter attribute) diff (fermo_core.data_processing.builder_feature.dataclass_feature.CharFrag attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.NeutralLoss attribute) diff_mz (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute)

diff_ppm (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) dimer_double() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) dimer_sodium_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) directory_path (fermo_core.input_output.param_handlers.AsResultsParameters attribute) (fermo_core.input_output.param_handlers.OutputParameters attribute) dirpath (fermo_core.input_output.param_handlers.SpecLibParameters attribute) dirpath_frags (fermo_core.config.class_default_settings.DefaultPaths attribute) dirpath_losses (fermo_core.config.class_default_settings.DefaultPaths attribute) dirpath_ms2deepscore_pos (fermo_core.config.class_default_settings.DefaultPaths attribute) diversity (fermo_core.data_processing.builder_sample.dataclass_sample.Scores attribute) double_dimer_pair_neg() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) double_plus1() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) double_plus2() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) double_plus3() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) double_plus4() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) double_plus5() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) download_file() (fermo_core.utils.utility_method_manager.UtilityMethodManager static method)

E

entries (fermo_core.data_processing.class_repository.Repository attribute) export_features_json() (fermo_core.input_output.class_export_manager.JsonExporter method) export_metadata_json() (fermo_core.input_output.class_export_manager.JsonExporter method) export_params_json() (fermo_core.input_output.class_export_manager.JsonExporter method) export_samples_json() (fermo_core.input_output.class_export_manager.JsonExporter method) export_stats_json() (fermo_core.input_output.class_export_manager.JsonExporter method)

ExportManager (class in fermo_core.input_output.class_export_manager) extract_as_kcb_results() (fermo_core.utils.utility_method_manager.UtilityMethodManager static method) extract_blanks() (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser method) extract_mibig_scores() (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator method) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator method) extract_userlib_scores() (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator method) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator method)

F

f (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser attribute) f_id (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) f_ids (fermo_core.data_processing.class_stats.Group attribute) f_ids_intersect (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner attribute) f_ids_positive (fermo_core.data_processing.class_stats.PhenoData attribute) factor (fermo_core.data_processing.builder_feature.dataclass_feature.GroupFactor attribute) (fermo_core.input_output.param_handlers.BlankAssignmentParameters attribute) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams attribute) fdr_corr (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute) Fe56 (fermo_core.config.class_default_settings.DefaultMasses attribute) Feature (class in fermo_core.data_processing.builder_feature.dataclass_feature) feature (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder attribute) feature_id (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) feature_ids (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) FeatureBuilder (class in fermo_core.data_processing.builder_feature.class_feature_builder) FeatureFilter (class in fermo_core.data_analysis.feature_filter.class_feature_filter) FeatureFilteringParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) features (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager attribute) (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2query_annotator.MS2QueryAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser attribute) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator attribute) (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner attribute) (fermo_core.data_analysis.class_analysis_manager.AnalysisManager attribute) (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter attribute) (fermo_core.data_analysis.group_assigner.class_group_assigner.GroupAssigner attribute) (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager attribute) (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner attribute) (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager attribute) (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) (fermo_core.data_processing.class_stats.Stats attribute) (fermo_core.data_processing.parser.class_general_parser.GeneralParser attribute) (fermo_core.data_processing.parser.msms_parser.class_mgf_parser.MgfParser attribute) (fermo_core.input_output.class_export_manager.CsvExporter attribute) (fermo_core.input_output.class_export_manager.ExportManager attribute) (fermo_core.input_output.class_export_manager.JsonExporter attribute) fermo_core module fermo_core.config module fermo_core.config.class_default_settings module fermo_core.data_analysis module fermo_core.data_analysis.annotation_manager module fermo_core.data_analysis.annotation_manager.class_adduct_annotator module fermo_core.data_analysis.annotation_manager.class_annotation_manager module fermo_core.data_analysis.annotation_manager.class_fragment_annotator module fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator module fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator module fermo_core.data_analysis.annotation_manager.class_ms2query_annotator module fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser module fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator module fermo_core.data_analysis.blank_assigner module fermo_core.data_analysis.blank_assigner.class_blank_assigner module fermo_core.data_analysis.chrom_trace_calculator module fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator module fermo_core.data_analysis.class_analysis_manager module fermo_core.data_analysis.feature_filter module fermo_core.data_analysis.feature_filter.class_feature_filter module fermo_core.data_analysis.group_assigner module fermo_core.data_analysis.group_assigner.class_group_assigner module fermo_core.data_analysis.group_factor_assigner module fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner module fermo_core.data_analysis.phenotype_manager module fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner module fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass module fermo_core.data_analysis.phenotype_manager.class_phenotype_manager module fermo_core.data_analysis.score_assigner module fermo_core.data_analysis.score_assigner.class_score_assigner module fermo_core.data_analysis.sim_networks_manager module fermo_core.data_analysis.sim_networks_manager.class_mod_cosine_networker module fermo_core.data_analysis.sim_networks_manager.class_ms2deepscore_networker module

fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager module fermo_core.data_processing module fermo_core.data_processing.builder_feature module fermo_core.data_processing.builder_feature.class_feature_builder module fermo_core.data_processing.builder_feature.class_general_feature_director module fermo_core.data_processing.builder_feature.class_specific_feature_director module fermo_core.data_processing.builder_feature.dataclass_feature module fermo_core.data_processing.builder_sample module fermo_core.data_processing.builder_sample.class_sample_builder module fermo_core.data_processing.builder_sample.class_samples_director module fermo_core.data_processing.builder_sample.dataclass_sample module fermo_core.data_processing.class_repository module fermo_core.data_processing.class_stats module fermo_core.data_processing.parser module fermo_core.data_processing.parser.class_general_parser module fermo_core.data_processing.parser.group_metadata_parser module fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser module fermo_core.data_processing.parser.msms_parser module fermo_core.data_processing.parser.msms_parser.class_mgf_parser module fermo_core.data_processing.parser.peaktable_parser module fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser module fermo_core.data_processing.parser.phenotype_parser module fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser module fermo_core.data_processing.parser.spec_library_parser module fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser module fermo_core.input_output module fermo_core.input_output.class_argparse_manager module fermo_core.input_output.class_export_manager module fermo_core.input_output.class_file_manager module fermo_core.input_output.class_parameter_manager module fermo_core.input_output.class_summary_writer module fermo_core.input_output.class_validation_manager module fermo_core.input_output.param_handlers module fermo_core.main module fermo_core.utils module fermo_core.utils.utility_method_manager module FileManager (class in fermo_core.input_output.class_file_manager) filepath (fermo_core.input_output.param_handlers.GroupMetadataParameters attribute) (fermo_core.input_output.param_handlers.MS2QueryResultsParameters attribute) (fermo_core.input_output.param_handlers.MsmsParameters attribute) (fermo_core.input_output.param_handlers.PeaktableParameters attribute) (fermo_core.input_output.param_handlers.PhenotypeParameters attribute) filter() (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter method) filter_features_for_range() (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter method) filter_for_ms2deepscore() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager static method) filter_input_spectra() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager method) filter_match() (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator method) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator method) filter_rel_area_range() (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter method) filter_rel_area_range_max (fermo_core.input_output.param_handlers.FeatureFilteringParameters attribute) filter_rel_area_range_min (fermo_core.input_output.param_handlers.FeatureFilteringParameters attribute) filter_rel_int_range() (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter method) filter_rel_int_range_max (fermo_core.input_output.param_handlers.FeatureFilteringParameters attribute) filter_rel_int_range_min (fermo_core.input_output.param_handlers.FeatureFilteringParameters attribute) find_relevant_f_ids() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss method) format (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype attribute) (fermo_core.input_output.param_handlers.GroupMetadataParameters attribute) (fermo_core.input_output.param_handlers.MsmsParameters attribute) (fermo_core.input_output.param_handlers.PeaktableParameters attribute) (fermo_core.input_output.param_handlers.PhenotypeParameters attribute) (fermo_core.input_output.param_handlers.SpecLibParameters attribute) format_network_for_storage() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager static method) frag_det (fermo_core.data_processing.builder_feature.dataclass_feature.CharFrag attribute) frag_ex (fermo_core.data_processing.builder_feature.dataclass_feature.CharFrag attribute) Fragment (class in fermo_core.config.class_default_settings) fragment_tol (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters attribute) FragmentAnnotator (class in fermo_core.data_analysis.annotation_manager.class_fragment_annotator) FragmentAnnParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) fragments (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations attribute) frags (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator attribute) fwhm (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute)

G

gen_bio_pos (fermo_core.config.class_default_settings.NeutralLosses attribute) gen_bio_pos_src (fermo_core.config.class_default_settings.NeutralLosses attribute) gen_other_neg (fermo_core.config.class_default_settings.NeutralLosses attribute) gen_other_neg_src (fermo_core.config.class_default_settings.NeutralLosses attribute) gen_other_pos (fermo_core.config.class_default_settings.NeutralLosses attribute) gen_other_pos_src (fermo_core.config.class_default_settings.NeutralLosses attribute) GeneralFeatureDirector (class in fermo_core.data_processing.builder_feature.class_general_feature_director) GeneralParser (class in fermo_core.data_processing.parser.class_general_parser) get() (fermo_core.data_processing.class_repository.Repository method) get_result() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder method) get_value() (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner method) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner method) glycoside (fermo_core.config.class_default_settings.NeutralLosses attribute)

glycoside_src (fermo_core.config.class_default_settings.NeutralLosses attribute) Group (class in fermo_core.data_processing.class_stats) group1 (fermo_core.data_processing.builder_feature.dataclass_feature.GroupFactor attribute) group2 (fermo_core.data_processing.builder_feature.dataclass_feature.GroupFactor attribute) group_factors (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) GroupAssigner (class in fermo_core.data_analysis.group_assigner.class_group_assigner) GroupFactAssignmentParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) GroupFactor (class in fermo_core.data_processing.builder_feature.dataclass_feature) GroupFactorAssigner (class in fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner) GroupMData (class in fermo_core.data_processing.class_stats) (fermo_core.data_processing.class_stats.Stats attribute) GroupMetadataParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) groups (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute)

H

H (fermo_core.config.class_default_settings.DefaultMasses attribute) H2O (fermo_core.config.class_default_settings.DefaultMasses attribute)

HCO2 (fermo_core.config.class_default_settings.DefaultMasses attribute) height_per_sample (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute)

I

id (fermo_core.data_processing.builder_feature.dataclass_feature.CharFrag attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.NeutralLoss attribute) inactive_features (fermo_core.data_processing.class_stats.Stats attribute) inchikey (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) int_apex (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) int_begin (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute)

int_end (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) int_left_fwhm (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) int_left_kink (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) int_right_fwhm (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) int_right_kink (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) intensity (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) iron56() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method)

J

JsonExporter (class in fermo_core.input_output.class_export_manager)

K

K (fermo_core.config.class_default_settings.DefaultMasses attribute)

L

library (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) library_mibig_pos (fermo_core.config.class_default_settings.DefaultPaths attribute) library_name (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) load_json_file() (fermo_core.input_output.class_file_manager.FileManager static method) log_complete_module() (fermo_core.input_output.class_export_manager.ExportManager static method) log_filtered_feature_no_msms() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager static method) log_filtered_feature_nr_fragments() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager static method) log_malformed_parameters_skip() (fermo_core.input_output.class_parameter_manager.ParameterManager static method) log_passed_modules() (fermo_core.input_output.class_parameter_manager.ParameterManager static method) log_skipped_modules() (fermo_core.input_output.class_parameter_manager.ParameterManager static method) log_start_module() (fermo_core.input_output.class_export_manager.ExportManager static method) logger (in module fermo_core.data_analysis.annotation_manager.class_adduct_annotator) (in module fermo_core.data_analysis.annotation_manager.class_annotation_manager) (in module fermo_core.data_analysis.annotation_manager.class_fragment_annotator) (in module fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator) (in module fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator) (in module fermo_core.data_analysis.annotation_manager.class_ms2query_annotator) (in module fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser) (in module fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator) (in module fermo_core.data_analysis.blank_assigner.class_blank_assigner) (in module fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator) (in module fermo_core.data_analysis.class_analysis_manager) (in module fermo_core.data_analysis.feature_filter.class_feature_filter) (in module fermo_core.data_analysis.group_assigner.class_group_assigner) (in module fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner) (in module fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner) (in module fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass) (in module fermo_core.data_analysis.phenotype_manager.class_phenotype_manager) (in module fermo_core.data_analysis.score_assigner.class_score_assigner) (in module fermo_core.data_analysis.sim_networks_manager.class_mod_cosine_networker) (in module fermo_core.data_analysis.sim_networks_manager.class_ms2deepscore_networker) (in module fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager) (in module fermo_core.data_processing.builder_feature.class_feature_builder) (in module fermo_core.data_processing.builder_feature.dataclass_feature) (in module fermo_core.data_processing.builder_sample.class_sample_builder) (in module fermo_core.data_processing.builder_sample.dataclass_sample) (in module fermo_core.data_processing.parser.class_general_parser) (in module fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser) (in module fermo_core.data_processing.parser.msms_parser.class_mgf_parser) (in module fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser) (in module fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser) (in module fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser) (in module fermo_core.input_output.class_export_manager) (in module fermo_core.input_output.class_file_manager) (in module fermo_core.input_output.class_parameter_manager) (in module fermo_core.input_output.class_summary_writer) (in module fermo_core.input_output.class_validation_manager) (in module fermo_core.input_output.param_handlers) (in module fermo_core.utils.utility_method_manager)

Loss (class in fermo_core.config.class_default_settings) loss (fermo_core.config.class_default_settings.Loss attribute) loss_det (fermo_core.data_processing.builder_feature.dataclass_feature.NeutralLoss attribute) loss_ex (fermo_core.data_processing.builder_feature.dataclass_feature.NeutralLoss attribute) losses (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations attribute)

M

main() (in module fermo_core.main) main_cli() (in module fermo_core.main) mass (fermo_core.config.class_default_settings.Fragment attribute) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator attribute) mass_dev_ppm (fermo_core.input_output.param_handlers.AdductAnnotationParameters attribute) (fermo_core.input_output.param_handlers.FragmentAnnParameters attribute) (fermo_core.input_output.param_handlers.NeutralLossParameters attribute) mass_deviation() (fermo_core.utils.utility_method_manager.UtilityMethodManager static method) Match (class in fermo_core.data_processing.builder_feature.dataclass_feature) matches (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations attribute) max_area (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) max_intensity (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) max_nr_links (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters attribute) max_precursor_mass_diff (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams attribute) (fermo_core.input_output.param_handlers.AsKcbDeepscoreMatchingParams attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingDeepscoreParameters attribute) mean_novelty (fermo_core.data_processing.builder_sample.dataclass_sample.Scores attribute) message() (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser static method) MetadataFermoParser (class in fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser) MgfParser (class in fermo_core.data_processing.parser.msms_parser.class_mgf_parser) min_nr_matched_peaks (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters attribute) ModCosAnnotator (class in fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator) ModCosineNetworker (class in fermo_core.data_analysis.sim_networks_manager.class_mod_cosine_networker) mode (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) modify() (fermo_core.data_processing.class_repository.Repository method) modify_features() (fermo_core.data_processing.parser.msms_parser.class_mgf_parser.MgfParser method) modify_features_in_sample() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) modify_samples() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method) modify_stats() (fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser.SpecLibMgfParser method) module fermo_core fermo_core.config fermo_core.config.class_default_settings fermo_core.data_analysis fermo_core.data_analysis.annotation_manager fermo_core.data_analysis.annotation_manager.class_adduct_annotator fermo_core.data_analysis.annotation_manager.class_annotation_manager fermo_core.data_analysis.annotation_manager.class_fragment_annotator fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator fermo_core.data_analysis.annotation_manager.class_ms2query_annotator fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator fermo_core.data_analysis.blank_assigner fermo_core.data_analysis.blank_assigner.class_blank_assigner fermo_core.data_analysis.chrom_trace_calculator fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator fermo_core.data_analysis.class_analysis_manager fermo_core.data_analysis.feature_filter fermo_core.data_analysis.feature_filter.class_feature_filter fermo_core.data_analysis.group_assigner fermo_core.data_analysis.group_assigner.class_group_assigner fermo_core.data_analysis.group_factor_assigner fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner fermo_core.data_analysis.phenotype_manager fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass fermo_core.data_analysis.phenotype_manager.class_phenotype_manager fermo_core.data_analysis.score_assigner fermo_core.data_analysis.score_assigner.class_score_assigner fermo_core.data_analysis.sim_networks_manager fermo_core.data_analysis.sim_networks_manager.class_mod_cosine_networker fermo_core.data_analysis.sim_networks_manager.class_ms2deepscore_networker fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager fermo_core.data_processing fermo_core.data_processing.builder_feature fermo_core.data_processing.builder_feature.class_feature_builder fermo_core.data_processing.builder_feature.class_general_feature_director fermo_core.data_processing.builder_feature.class_specific_feature_director fermo_core.data_processing.builder_feature.dataclass_feature fermo_core.data_processing.builder_sample fermo_core.data_processing.builder_sample.class_sample_builder fermo_core.data_processing.builder_sample.class_samples_director fermo_core.data_processing.builder_sample.dataclass_sample fermo_core.data_processing.class_repository fermo_core.data_processing.class_stats fermo_core.data_processing.parser fermo_core.data_processing.parser.class_general_parser fermo_core.data_processing.parser.group_metadata_parser fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser fermo_core.data_processing.parser.msms_parser fermo_core.data_processing.parser.msms_parser.class_mgf_parser fermo_core.data_processing.parser.peaktable_parser fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser fermo_core.data_processing.parser.phenotype_parser fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser fermo_core.data_processing.parser.spec_library_parser fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser fermo_core.input_output fermo_core.input_output.class_argparse_manager fermo_core.input_output.class_export_manager fermo_core.input_output.class_file_manager fermo_core.input_output.class_parameter_manager fermo_core.input_output.class_summary_writer fermo_core.input_output.class_validation_manager fermo_core.input_output.param_handlers fermo_core.main fermo_core.utils fermo_core.utils.utility_method_manager

module (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) module_passed (fermo_core.input_output.param_handlers.AdductAnnotationParameters attribute) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams attribute) (fermo_core.input_output.param_handlers.AsKcbDeepscoreMatchingParams attribute) (fermo_core.input_output.param_handlers.BlankAssignmentParameters attribute) (fermo_core.input_output.param_handlers.FeatureFilteringParameters attribute) (fermo_core.input_output.param_handlers.FragmentAnnParameters attribute) (fermo_core.input_output.param_handlers.GroupFactAssignmentParameters attribute) (fermo_core.input_output.param_handlers.NeutralLossParameters attribute) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingDeepscoreParameters attribute) Ms2deepscoreAnnotator (class in fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator) Ms2deepscoreNetworker (class in fermo_core.data_analysis.sim_networks_manager.class_ms2deepscore_networker) MS2QueryAnnotator (class in fermo_core.data_analysis.annotation_manager.class_ms2query_annotator) MS2QueryResultsParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) msms_min_frag_nr (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters attribute) MsmsParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) mz (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) mz_frag (fermo_core.data_processing.builder_feature.dataclass_feature.NeutralLoss attribute) MzmineAnnParser (class in fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser)

N

Na (fermo_core.config.class_default_settings.DefaultMasses attribute) network (fermo_core.data_processing.class_stats.SpecSimNet attribute) network_id (fermo_core.data_processing.builder_feature.dataclass_feature.SimNetworks attribute) networks (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) (fermo_core.data_processing.class_stats.Stats attribute) NeutralLoss (class in fermo_core.data_processing.builder_feature.dataclass_feature) NeutralLossAnnotator (class in fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator)

NeutralLosses (class in fermo_core.config.class_default_settings) NeutralLossParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) NH4 (fermo_core.config.class_default_settings.DefaultMasses attribute) nonblank_f_ids (fermo_core.data_processing.class_stats.GroupMData attribute) nonblank_s_ids (fermo_core.data_processing.class_stats.GroupMData attribute) nonribo (fermo_core.config.class_default_settings.NeutralLosses attribute) nonribo_src (fermo_core.config.class_default_settings.NeutralLosses attribute) novelty (fermo_core.data_processing.builder_feature.dataclass_feature.Scores attribute) npc_class (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute)

O

OutputParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute)

P

p_val_cutoff (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute) p_value (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype attribute) p_value_corr (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype attribute) ParameterManager (class in fermo_core.input_output.class_parameter_manager) params (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager attribute) (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2query_annotator.MS2QueryAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser attribute) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator attribute) (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner attribute) (fermo_core.data_analysis.class_analysis_manager.AnalysisManager attribute) (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter attribute) (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager attribute) (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner attribute) (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager attribute) (fermo_core.data_processing.parser.msms_parser.class_mgf_parser.MgfParser attribute) (fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser.SpecLibMgfParser attribute) (fermo_core.input_output.class_export_manager.CsvExporter attribute) (fermo_core.input_output.class_export_manager.ExportManager attribute) (fermo_core.input_output.class_export_manager.JsonExporter attribute) (fermo_core.input_output.class_summary_writer.SummaryWriter attribute) parse() (fermo_core.data_processing.parser.msms_parser.class_mgf_parser.MgfParser method) (fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser.PeakMzmine3Parser method) (fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser.SpecLibMgfParser method) parse_group_metadata() (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) parse_ion_ident() (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser method) parse_msms() (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) parse_mzmine3() (fermo_core.data_processing.class_stats.Stats method) parse_parameters() (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) parse_peaktable() (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) parse_phenotype() (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) parse_qualitative() (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser method) parse_quantitative_concentration() (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser method)

parse_quantitative_percentage() (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser method) parse_spectral_db() (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser method) parse_spectral_library() (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) partner_adduct (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) partner_id (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) partner_mz (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) PeakMzmine3Parser (class in fermo_core.data_processing.parser.peaktable_parser.class_mzmine3_parser) PeaktableParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) pearson_concentration() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss static method) pearson_percentage() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss static method) PhenoData (class in fermo_core.data_processing.class_stats) PhenoQualAssgnParams (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) PhenoQuantConcAssgnParams (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) PhenoQuantPercentAssgnParams (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) Phenotype (class in fermo_core.data_processing.builder_feature.dataclass_feature) phenotype (fermo_core.data_processing.builder_feature.dataclass_feature.Scores attribute) PhenotypeManager (class in fermo_core.data_analysis.phenotype_manager.class_phenotype_manager) PhenotypeParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) PhenotypeParser (class in fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser) phenotypes (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations attribute) (fermo_core.data_processing.class_stats.Stats attribute) PhenQualAssigner (class in fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner) PhenQuantAss (class in fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass) plus1_isotope() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) plus2_isotope() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) plus3_isotope() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) plus4_isotope() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) plus5_isotope() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) polarity (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) (fermo_core.input_output.param_handlers.PeaktableParameters attribute) potassium() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) prepare_ctgrs() (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser method) prepare_queries() (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator method) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator method)

Q

queries (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute)

R

read_files() (fermo_core.config.class_default_settings.CharFragments method) (fermo_core.config.class_default_settings.NeutralLosses method) rel_area (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) rel_int_from (fermo_core.input_output.param_handlers.MsmsParameters attribute) rel_intensity (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) relevant_f_ids (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) remove() (fermo_core.data_processing.class_repository.Repository method) remove_filtered_features() (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter method) Repository (class in fermo_core.data_processing.class_repository) return_attributes() (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator method) (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser method) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner method) (fermo_core.data_processing.parser.class_general_parser.GeneralParser method) return_attrs() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) (fermo_core.data_analysis.group_assigner.class_group_assigner.GroupAssigner method) (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager method) (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager method) return_dfs() (fermo_core.input_output.class_export_manager.CsvExporter method) return_features() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator method) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator method) (fermo_core.data_analysis.annotation_manager.class_ms2query_annotator.MS2QueryAnnotator method) (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner method) (fermo_core.data_processing.parser.msms_parser.class_mgf_parser.MgfParser method) return_session() (fermo_core.input_output.class_export_manager.JsonExporter method) return_stats() (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser method) (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser method) (fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser.SpecLibMgfParser method) return_values() (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter method) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner method) (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss method) ribosomal (fermo_core.config.class_default_settings.NeutralLosses attribute) ribosomal_src (fermo_core.config.class_default_settings.NeutralLosses attribute) rt (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) rt_apex (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_begin (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_end (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_left_fwhm (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_left_kink (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_max (fermo_core.data_processing.class_stats.Stats attribute) rt_min (fermo_core.data_processing.class_stats.Stats attribute) rt_range (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) (fermo_core.data_processing.class_stats.Stats attribute)

rt_right_fwhm (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_right_kink (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) rt_start (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) rt_stop (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) run() (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser method) (fermo_core.input_output.class_export_manager.ExportManager method) run_analysis() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator method) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) (fermo_core.data_analysis.group_assigner.class_group_assigner.GroupAssigner method) (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner method) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner method) (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss method) (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager method) (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner method) (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager method) run_annotation_manager() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_argparse() (fermo_core.input_output.class_argparse_manager.ArgparseManager method) run_as_kcb_cosine_annotation() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_as_kcb_deepscore_annotation() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_assigner_qualitative() (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager method) run_assigner_quant_concentration() (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager method) run_assigner_quant_percentage() (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager method) run_blank_assignment() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_chrom_trace_calculator() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_feature_adduct_annotation() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_feature_filter() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_fragment_annotation() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_group_assignment() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_group_factor_assignment() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_modified_cosine_alg() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager method) run_ms2deepscore_alg() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager method) run_ms2query_results_assignment() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_mzmine_assignment() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_neutral_loss_annotation() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_parser() (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser method) run_phenotype_manager() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_sample_group_analysis() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_score_assignment() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_sim_networks_manager() (fermo_core.data_analysis.class_analysis_manager.AnalysisManager method) run_user_lib_mod_cosine_matching() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) run_user_lib_ms2deepscore_matching() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method)

S

s_id (fermo_core.data_processing.builder_feature.dataclass_feature.SampleInfo attribute) (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) (fermo_core.data_processing.class_stats.SamplePhenotype attribute) s_ids (fermo_core.data_processing.class_stats.Group attribute) s_negative (fermo_core.data_processing.class_stats.PhenoData attribute) s_phen_data (fermo_core.data_processing.class_stats.PhenoData attribute) Sample (class in fermo_core.data_processing.builder_sample.dataclass_sample) sample (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder attribute) sample_avg (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute) sample_id (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceData attribute) sample_set (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct attribute) SampleBuilder (class in fermo_core.data_processing.builder_sample.class_sample_builder) SampleInfo (class in fermo_core.data_processing.builder_feature.dataclass_feature) SamplePhenotype (class in fermo_core.data_processing.class_stats) samples (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager attribute) (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator attribute) (fermo_core.data_analysis.class_analysis_manager.AnalysisManager attribute) (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager attribute) (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner attribute) (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) (fermo_core.data_processing.class_stats.Stats attribute) (fermo_core.data_processing.parser.class_general_parser.GeneralParser attribute) (fermo_core.input_output.class_export_manager.CsvExporter attribute) (fermo_core.input_output.class_export_manager.ExportManager attribute) (fermo_core.input_output.class_export_manager.JsonExporter attribute) SamplesDirector (class in fermo_core.data_processing.builder_sample.class_samples_director) score (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype attribute) score_cutoff (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams attribute) (fermo_core.input_output.param_handlers.AsKcbDeepscoreMatchingParams attribute) (fermo_core.input_output.param_handlers.MS2QueryResultsParameters attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters attribute) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters attribute) (fermo_core.input_output.param_handlers.SpectralLibMatchingDeepscoreParameters attribute) ScoreAssigner (class in fermo_core.data_analysis.score_assigner.class_score_assigner) Scores (class in fermo_core.data_processing.builder_feature.dataclass_feature) (class in fermo_core.data_processing.builder_sample.dataclass_sample) scores (fermo_core.data_analysis.annotation_manager.class_mod_cos_annotator.ModCosAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_ms2deepscore_annotator.Ms2deepscoreAnnotator attribute) Scores (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) (fermo_core.data_processing.builder_sample.dataclass_sample.Sample attribute) session (fermo_core.input_output.class_export_manager.JsonExporter attribute) set_area() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_area_per_sample() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_f_id() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_feature_ids() (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder method) set_features_mzmine3() (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder method) set_fwhm() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_height_per_sample() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_intensity() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_max_area_mzmine3() (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder method) set_max_intensity_mzmine3() (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder method) set_mz() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_rel_area() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_rel_intensity() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_rt() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_rt_range() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_rt_start() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_rt_stop() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) set_s_id() (fermo_core.data_processing.builder_sample.class_sample_builder.SampleBuilder method) set_samples() (fermo_core.data_processing.builder_feature.class_feature_builder.FeatureBuilder method) similarity_cutoff (fermo_core.input_output.param_handlers.AsResultsParameters attribute)

SimNetworks (class in fermo_core.data_processing.builder_feature.dataclass_feature) SimNetworksManager (class in fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager) smiles (fermo_core.data_processing.builder_feature.dataclass_feature.Match attribute) sodium_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) sort_entries() (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations method) spec_sim_networking() (fermo_core.data_analysis.sim_networks_manager.class_mod_cosine_networker.ModCosineNetworker static method) (fermo_core.data_analysis.sim_networks_manager.class_ms2deepscore_networker.Ms2deepscoreNetworker static method) SpecificFeatureDirector (class in fermo_core.data_processing.builder_feature.class_specific_feature_director) specificity (fermo_core.data_processing.builder_sample.dataclass_sample.Scores attribute) SpecLibMgfParser (class in fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser) SpecLibParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) SpecSimNet (class in fermo_core.data_processing.class_stats) SpecSimNetworkCosineParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) SpecSimNetworkDeepscoreParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) spectral_library (fermo_core.data_processing.class_stats.Stats attribute) SpectralLibMatchingCosineParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) SpectralLibMatchingDeepscoreParameters (class in fermo_core.input_output.param_handlers) (fermo_core.input_output.class_parameter_manager.ParameterManager attribute) Spectrum (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) starttime (fermo_core.input_output.class_export_manager.JsonExporter attribute) Stats (class in fermo_core.data_processing.class_stats) stats (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager attribute) (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator attribute) (fermo_core.data_analysis.annotation_manager.class_mzmine_ann_parser.MzmineAnnParser attribute) (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator attribute) (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner attribute) (fermo_core.data_analysis.class_analysis_manager.AnalysisManager attribute) (fermo_core.data_analysis.feature_filter.class_feature_filter.FeatureFilter attribute) (fermo_core.data_analysis.group_assigner.class_group_assigner.GroupAssigner attribute) (fermo_core.data_analysis.group_factor_assigner.class_group_factor_assigner.GroupFactorAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_qual_assigner.PhenQualAssigner attribute) (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss attribute) (fermo_core.data_analysis.phenotype_manager.class_phenotype_manager.PhenotypeManager attribute) (fermo_core.data_analysis.score_assigner.class_score_assigner.ScoreAssigner attribute) (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager attribute) (fermo_core.data_processing.parser.class_general_parser.GeneralParser attribute) (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser attribute) (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser attribute) (fermo_core.data_processing.parser.spec_library_parser.class_spec_lib_mgf_parser.SpecLibMgfParser attribute) (fermo_core.input_output.class_export_manager.CsvExporter attribute) (fermo_core.input_output.class_export_manager.ExportManager attribute) (fermo_core.input_output.class_export_manager.JsonExporter attribute) store_network_data() (fermo_core.data_analysis.sim_networks_manager.class_sim_networks_manager.SimNetworksManager method) subnetworks (fermo_core.data_processing.class_stats.SpecSimNet attribute) summarize_adductannotationparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_askcbcosinematchingparams() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_askcbdeepscorematchingparams() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_asresultsparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_blankassignmentparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_featurefilteringparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_fragmentannparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_groupfactassignmentparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_groupmetadataparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_ms2queryresultsparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_msmsparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_neutrallossparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_peaktableparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_phenoqualassgnparams() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_phenoquantconcassgnparams() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_phenoquantpercentassgnparams() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_phenotypeparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_speclibparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_specsimnetworkcosineparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_specsimnetworkdeepscoreparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_spectrallibmatchingcosineparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summarize_spectrallibmatchingdeepscoreparameters() (fermo_core.input_output.class_summary_writer.SummaryWriter method) summary (fermo_core.data_processing.class_stats.SpecSimNet attribute) (fermo_core.input_output.class_summary_writer.SummaryWriter attribute) SummaryWriter (class in fermo_core.input_output.class_summary_writer)

T

TFA (fermo_core.config.class_default_settings.DefaultMasses attribute) tfa_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) to_json() (fermo_core.data_processing.builder_feature.dataclass_feature.Adduct method) (fermo_core.data_processing.builder_feature.dataclass_feature.Annotations method) (fermo_core.data_processing.builder_feature.dataclass_feature.CharFrag method) (fermo_core.data_processing.builder_feature.dataclass_feature.Feature method) (fermo_core.data_processing.builder_feature.dataclass_feature.GroupFactor method) (fermo_core.data_processing.builder_feature.dataclass_feature.Match method) (fermo_core.data_processing.builder_feature.dataclass_feature.NeutralLoss method) (fermo_core.data_processing.builder_feature.dataclass_feature.Phenotype method) (fermo_core.data_processing.builder_feature.dataclass_feature.SampleInfo method) (fermo_core.data_processing.builder_feature.dataclass_feature.Scores method) (fermo_core.data_processing.builder_feature.dataclass_feature.SimNetworks method) (fermo_core.data_processing.builder_sample.dataclass_sample.Sample method) (fermo_core.data_processing.builder_sample.dataclass_sample.Scores method) (fermo_core.data_processing.class_stats.Group method) (fermo_core.data_processing.class_stats.GroupMData method) (fermo_core.data_processing.class_stats.PhenoData method) (fermo_core.data_processing.class_stats.SamplePhenotype method) (fermo_core.data_processing.class_stats.SpecSimNet method) (fermo_core.data_processing.class_stats.Stats method) (fermo_core.input_output.class_parameter_manager.ParameterManager method) (fermo_core.input_output.param_handlers.AdductAnnotationParameters method) (fermo_core.input_output.param_handlers.AsKcbCosineMatchingParams method) (fermo_core.input_output.param_handlers.AsKcbDeepscoreMatchingParams method) (fermo_core.input_output.param_handlers.AsResultsParameters method) (fermo_core.input_output.param_handlers.BlankAssignmentParameters method) (fermo_core.input_output.param_handlers.FeatureFilteringParameters method) (fermo_core.input_output.param_handlers.FragmentAnnParameters method) (fermo_core.input_output.param_handlers.GroupFactAssignmentParameters method) (fermo_core.input_output.param_handlers.GroupMetadataParameters method) (fermo_core.input_output.param_handlers.MS2QueryResultsParameters method) (fermo_core.input_output.param_handlers.MsmsParameters method) (fermo_core.input_output.param_handlers.NeutralLossParameters method) (fermo_core.input_output.param_handlers.OutputParameters method) (fermo_core.input_output.param_handlers.PeaktableParameters method) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams method) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams method) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams method) (fermo_core.input_output.param_handlers.PhenotypeParameters method) (fermo_core.input_output.param_handlers.SpecLibParameters method) (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters method) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters method) (fermo_core.input_output.param_handlers.SpectralLibMatchingCosineParameters method) (fermo_core.input_output.param_handlers.SpectralLibMatchingDeepscoreParameters method)

trace_int (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) trace_rt (fermo_core.data_processing.builder_feature.dataclass_feature.Feature attribute) triple_h_adduct() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method)

U

unassign_default_set() (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser method)

url_ms2deepscore_pos (fermo_core.config.class_default_settings.DefaultPaths attribute) UtilityMethodManager (class in fermo_core.utils.utility_method_manager)

V

val() (fermo_core.input_output.param_handlers.AdductAnnotationParameters method) (fermo_core.input_output.param_handlers.AsResultsParameters method) (fermo_core.input_output.param_handlers.BlankAssignmentParameters method) (fermo_core.input_output.param_handlers.FragmentAnnParameters method) (fermo_core.input_output.param_handlers.GroupFactAssignmentParameters method) (fermo_core.input_output.param_handlers.GroupMetadataParameters method) (fermo_core.input_output.param_handlers.MS2QueryResultsParameters method) (fermo_core.input_output.param_handlers.MsmsParameters method) (fermo_core.input_output.param_handlers.NeutralLossParameters method) (fermo_core.input_output.param_handlers.OutputParameters method) (fermo_core.input_output.param_handlers.PeaktableParameters method) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams method) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams method) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams method) (fermo_core.input_output.param_handlers.PhenotypeParameters method) (fermo_core.input_output.param_handlers.SpecLibParameters method) (fermo_core.input_output.param_handlers.SpecSimNetworkCosineParameters method) (fermo_core.input_output.param_handlers.SpecSimNetworkDeepscoreParameters method) valid_constant() (fermo_core.data_analysis.phenotype_manager.class_phen_quant_ass.PhenQuantAss static method) validate_allowed() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_assignment() (fermo_core.data_analysis.blank_assigner.class_blank_assigner.BlankAssigner method) validate_attrs() (fermo_core.input_output.param_handlers.FeatureFilteringParameters method) validate_csv_file() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_csv_has_rows() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_file_exists() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_file_extension() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_file_vs_jsonschema() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_float_zero_one() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_fwhm_rt() (fermo_core.data_analysis.chrom_trace_calculator.class_chrom_trace_calculator.ChromTraceCalculator method)

validate_gen_bio_pos_losses() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) validate_gen_other_neg_losses() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) validate_gen_other_pos_losses() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) validate_glycoside_losses() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) validate_group_metadata_fermo() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_mass_deviation_ppm() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_mgf_file() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_ms2query_results() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_no_duplicate_entries_csv_column() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_nonribosomal_losses() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) validate_output_created() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_peaktable_mzmine() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_pheno_qualitative() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_pheno_quant_concentration() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_pheno_quant_percentage() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_pos_aa_fragments() (fermo_core.data_analysis.annotation_manager.class_fragment_annotator.FragmentAnnotator method) validate_range_zero_one() (fermo_core.input_output.class_validation_manager.ValidationManager static method) validate_ribosomal_losses() (fermo_core.data_analysis.annotation_manager.class_neutral_loss_annotator.NeutralLossAnnotator method) validate_sample_names() (fermo_core.data_processing.parser.group_metadata_parser.class_fermo_metadata_parser.MetadataFermoParser method) (fermo_core.data_processing.parser.phenotype_parser.class_phenotype_parser.PhenotypeParser method) ValidationManager (class in fermo_core.input_output.class_validation_manager) value (fermo_core.data_processing.builder_feature.dataclass_feature.SampleInfo attribute) (fermo_core.data_processing.class_stats.SamplePhenotype attribute) (fermo_core.input_output.param_handlers.BlankAssignmentParameters attribute) (fermo_core.input_output.param_handlers.GroupFactAssignmentParameters attribute) (fermo_core.input_output.param_handlers.PhenoQualAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantConcAssgnParams attribute) (fermo_core.input_output.param_handlers.PhenoQuantPercentAssgnParams attribute) verify_user_lib_params() (fermo_core.data_analysis.annotation_manager.class_annotation_manager.AnnotationManager method) version (fermo_core.input_output.class_export_manager.JsonExporter attribute)

W

water_add() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) water_loss() (fermo_core.data_analysis.annotation_manager.class_adduct_annotator.AdductAnnotator method) write_csv_output() (fermo_core.input_output.class_export_manager.ExportManager method)

write_cytoscape_output() (fermo_core.input_output.class_export_manager.ExportManager method) write_fermo_json() (fermo_core.input_output.class_export_manager.ExportManager method) write_summary() (fermo_core.input_output.class_summary_writer.SummaryWriter method) write_summary_output() (fermo_core.input_output.class_export_manager.ExportManager method)