Index

A

alter() (sm.engine.db.DB method) arg_dict() (in module sm.webapp.handlers.feedback)

AuthenticateClient (class in sm.webapp.handlers.auth)

B

BatchConfig (class in sm.engine.metabolights)

C

calc_metrics() (sm.engine.msm_basic.msm_basic_search.MSMBasicSearch method) (sm.engine.search_algorithm.SearchAlgorithm method) Centroids (class in sm.engine.isocalc_wrapper) check_formula_uniqueness() (sm.engine.formulas_segm.FormulasSegm static method) clean() (sm.engine.work_dir.LocalWorkDir method) (sm.engine.work_dir.S3WorkDir method) (sm.engine.work_dir.WorkDirManager method) clean_target_decoy_table() (sm.engine.fdr.FDR method) cleanup() (sm.engine.metabolights.MetabolightsBatch method) close() (sm.engine.db.DB method) (sm.engine.queue.Queue method) cmd() (in module sm.engine.util) cmd_check() (in module sm.engine.util)

compute_sf_images() (in module sm.engine.msm_basic.formula_imager) (in module sm.engine.msm_basic.formula_imager_segm) compute_sf_peak_images() (in module sm.engine.msm_basic.formula_imager) convert() (sm.engine.imzml_txt_converter.ImzmlTxtConverter method) cookie_name (sm.webapp.handlers.results_table.ResultsTableHandler attribute) coord_path (sm.engine.work_dir.LocalWorkDir attribute) (sm.engine.work_dir.S3WorkDir attribute) (sm.engine.work_dir.WorkDirManager attribute) copy() (sm.engine.db.DB method) (sm.engine.work_dir.LocalWorkDir method) (sm.engine.work_dir.S3WorkDir method) copy_input_data() (sm.engine.work_dir.WorkDirManager method) copy_read_data() (sm.engine.dataset.Dataset method) create_index() (sm.engine.es_export.ESExporter method)

D

Dataset (class in sm.engine.dataset) dataset_config() (in module sm.webapp.handlers.misc) DB (class in sm.engine.db) db (sm.webapp.handlers.misc.SFPeakMZsHandler attribute) (sm.webapp.handlers.misc.SpectrumLineChartHandler attribute) (sm.webapp.handlers.results_table.ResultsTableHandler attribute) db_decor() (in module sm.engine.db)

decoy_adduct_selection() (sm.engine.fdr.FDR method) delete_ds() (sm.engine.es_export.ESExporter method) delete_index() (sm.engine.es_export.ESExporter method) ds_config_path (sm.engine.work_dir.LocalWorkDir attribute) (sm.engine.work_dir.S3WorkDir attribute) (sm.engine.work_dir.WorkDirManager attribute) ds_metadata_path (sm.engine.work_dir.LocalWorkDir attribute) (sm.engine.work_dir.WorkDirManager attribute)

E

empty (sm.engine.isocalc_wrapper.Centroids attribute) encode_coord_line() (in module sm.engine.imzml_txt_converter) encode_data_line() (in module sm.engine.imzml_txt_converter) es (sm.webapp.handlers.results_table.ResultsTableHandler attribute)

ESExporter (class in sm.engine.es_export) estimate_fdr() (sm.engine.fdr.FDR method) (sm.engine.msm_basic.msm_basic_search.MSMBasicSearch method) (sm.engine.search_algorithm.SearchAlgorithm method) exists() (sm.engine.work_dir.LocalWorkDir method) (sm.engine.work_dir.S3WorkDir method) (sm.engine.work_dir.WorkDirManager method)

F

fabfile (module) FDR (class in sm.engine.fdr) FeedbackComment (class in sm.webapp.handlers.feedback) FeedbackRating (class in sm.webapp.handlers.feedback) filter_sf_images() (sm.engine.search_algorithm.SearchAlgorithm method)

filter_sf_metrics() (sm.engine.msm_basic.msm_basic_search.MSMBasicSearch method) (sm.engine.search_algorithm.SearchAlgorithm method) find_mz_segments() (in module sm.engine.msm_basic.formula_imager_segm) find_sf_adduct_cand() (sm.engine.theor_peaks_gen.TheorPeaksGenerator method) formatted_iso_peaks() (sm.engine.isocalc_wrapper.IsocalcWrapper method) FormulasSegm (class in sm.engine.formulas_segm)

G

gen_iso_peak_images() (in module sm.engine.msm_basic.formula_imager_segm) gen_iso_sf_images() (in module sm.engine.msm_basic.formula_imager_segm) generate_theor_peaks() (sm.engine.theor_peaks_gen.TheorPeaksGenerator method) get() (sm.webapp.handlers.feedback.FeedbackComment method) (sm.webapp.handlers.feedback.FeedbackRating method) (sm.webapp.handlers.misc.IndexHandler method) (sm.webapp.handlers.misc.MinMaxIntHandler method) (sm.webapp.handlers.misc.SFPeakMZsHandler method) (sm.webapp.handlers.misc.SpectrumLineChartHandler method) (sm.webapp.handlers.results_table.ResultsTableHandler method) get_compute_img_metrics() (in module sm.engine.msm_basic.formula_img_validator) get_conf() (sm.engine.util.SMConfig class method) get_current_user() (sm.webapp.handlers.misc.MinMaxIntHandler method) get_dims() (sm.engine.dataset.Dataset method)

get_norm_img_pixel_inds() (sm.engine.dataset.Dataset method) get_sample_area_mask() (sm.engine.dataset.Dataset method) get_sf_adduct_peaksn() (sm.engine.formulas_segm.FormulasSegm method) get_sf_adduct_sorted_df() (sm.engine.formulas_segm.FormulasSegm method) get_sf_peak_df() (sm.engine.formulas_segm.FormulasSegm method) get_sf_peak_ints() (sm.engine.formulas_segm.FormulasSegm method) get_spectra() (sm.engine.dataset.Dataset method) get_track_progress() (in module sm.engine.imzml_txt_converter)

H

handlers (module)

I

ImgMeasures (class in sm.engine.msm_basic.formula_img_validator) imzml_path (sm.engine.work_dir.LocalWorkDir attribute) ImzmlTxtConverter (class in sm.engine.imzml_txt_converter) index_ds() (sm.engine.es_export.ESExporter method) IndexHandler (class in sm.webapp.handlers.misc) init_logger() (in module sm.engine.util)

initialize() (sm.webapp.handlers.results_table.ResultsTableHandler method) insert() (sm.engine.db.DB method) insert_return() (sm.engine.db.DB method) IsocalcWrapper (class in sm.engine.isocalc_wrapper) isotope_peaks() (sm.engine.isocalc_wrapper.IsocalcWrapper method)

L

list_of_floats_to_str() (in module sm.engine.isocalc_wrapper) local_path() (in module sm.engine.util)

LocalWorkDir (class in sm.engine.work_dir)

M

make_datatable_dict() (sm.webapp.handlers.results_table.ResultsTableHandler method) MetabolightsBatch (class in sm.engine.metabolights) MIN_MAX_INT_SEL (sm.webapp.handlers.misc.MinMaxIntHandler attribute)

MinMaxIntHandler (class in sm.webapp.handlers.misc) MSMBasicSearch (class in sm.engine.msm_basic.msm_basic_search)

P

parse_save_spectrum() (sm.engine.imzml_txt_converter.ImzmlTxtConverter method) post() (sm.webapp.handlers.auth.AuthenticateClient method) (sm.webapp.handlers.feedback.FeedbackComment method) (sm.webapp.handlers.feedback.FeedbackRating method) (sm.webapp.handlers.results_table.ResultsTableHandler method) preprocess_spectrum() (in module sm.engine.imzml_txt_converter)

proj_root() (in module sm.engine.util) publish() (sm.engine.queue.Queue method)

Q

Queue (class in sm.engine.queue)

R

read_json() (in module sm.engine.util) ResultsTableHandler (class in sm.webapp.handlers.results_table)

run() (sm.engine.metabolights.MetabolightsBatch method) (sm.engine.search_job.SearchJob method) (sm.engine.theor_peaks_gen.TheorPeaksGenerator method)

S

s3_path() (in module sm.engine.util) S3WorkDir (class in sm.engine.work_dir) sample_centr_ints_norm() (sm.webapp.handlers.misc.SpectrumLineChartHandler static method) SAMPLE_INTENS_SQL (sm.webapp.handlers.misc.SpectrumLineChartHandler attribute) sample_spectra() (in module sm.engine.msm_basic.formula_imager) search() (sm.engine.msm_basic.msm_basic_search.MSMBasicSearch method) (sm.engine.search_algorithm.SearchAlgorithm method) (sm.webapp.handlers.results_table.ResultsTableHandler method) SearchAlgorithm (class in sm.engine.search_algorithm) SearchJob (class in sm.engine.search_job) SearchResults (class in sm.engine.search_results) select() (sm.engine.db.DB method) select_one() (sm.engine.db.DB method) set_path() (sm.engine.util.SMConfig class method) setupQueue() (in module sm.engine.metabolights) sf_image_metrics() (in module sm.engine.msm_basic.formula_img_validator) sf_image_metrics_est_fdr() (in module sm.engine.msm_basic.formula_img_validator) sf_peak_gen() (sm.engine.formulas_segm.FormulasSegm static method) SFPeakMZsHandler (class in sm.webapp.handlers.misc) sign_in() (sm.webapp.handlers.auth.AuthenticateClient method) sign_out() (sm.webapp.handlers.auth.AuthenticateClient method) slice_array() (sm.engine.isocalc_wrapper.IsocalcWrapper static method) sm (module) sm.engine (module) sm.engine.dataset (module) sm.engine.db (module) sm.engine.es_export (module) sm.engine.fdr (module) sm.engine.formulas_segm (module) sm.engine.imzml_txt_converter (module) sm.engine.isocalc_wrapper (module) sm.engine.metabolights (module)

sm.engine.msm_basic (module) sm.engine.msm_basic.formula_imager (module) sm.engine.msm_basic.formula_imager_segm (module) sm.engine.msm_basic.formula_img_validator (module) sm.engine.msm_basic.msm_basic_search (module) sm.engine.queue (module) sm.engine.search_algorithm (module) sm.engine.search_job (module) sm.engine.search_results (module) sm.engine.theor_peaks_gen (module) sm.engine.util (module) sm.engine.work_dir (module) sm.webapp (module) sm.webapp.handlers (module) sm.webapp.handlers.auth (module) sm.webapp.handlers.feedback (module) sm.webapp.handlers.misc (module) sm.webapp.handlers.results_table (module) sm_engine_config() (in module sm.engine.metabolights) SMConfig (class in sm.engine.util) spectrum_chart() (sm.engine.isocalc_wrapper.Centroids method) SpectrumLineChartHandler (class in sm.webapp.handlers.misc) split_local_path() (in module sm.engine.work_dir) split_s3_path() (in module sm.engine.work_dir) start_consuming() (sm.engine.queue.Queue method) store() (sm.engine.search_results.SearchResults method) store_job_meta() (sm.engine.search_job.SearchJob method) store_sf_img_metrics() (sm.engine.search_results.SearchResults method) store_sf_iso_images() (sm.engine.search_results.SearchResults method) study() (sm.engine.metabolights.MetabolightsBatch method)

T

TheorPeaksGenerator (class in sm.engine.theor_peaks_gen) to_space_separated_string() (in module sm.engine.imzml_txt_converter) to_tuple() (sm.engine.msm_basic.formula_img_validator.ImgMeasures method)

trim_centroids() (in module sm.engine.isocalc_wrapper) txt_path (sm.engine.work_dir.LocalWorkDir attribute) (sm.engine.work_dir.S3WorkDir attribute) (sm.engine.work_dir.WorkDirManager attribute) txt_to_spectrum_non_cum() (sm.engine.dataset.Dataset static method)

U

upload_to_remote() (sm.engine.work_dir.WorkDirManager method)

upsert_feedback() (in module sm.webapp.handlers.feedback)

V

validate_id_token() (sm.webapp.handlers.auth.AuthenticateClient static method)

W

WorkDirManager (class in sm.engine.work_dir)