# Generated by roxygen2: do not edit by hand

S3method(colnames,databaseClass)
S3method(dim,databaseClass)
S3method(filter,databaseClass)
S3method(ncol,databaseClass)
S3method(nrow,databaseClass)
S3method(print,metid_conflicts)
export(analyze_metabolite_origins)
export(annotate_metabolites)
export(annotate_metabolites_mass_dataset)
export(annotate_peaks_mz_rt_ms2)
export(annotate_single_peak_mass_dataset)
export(calculate_confidence_level)
export(calculate_dotproduct)
export(calculate_ms2_matching_score)
export(calculate_mz_match_score)
export(calculate_rt_match_score)
export(calculate_total_score)
export(check_adduct_table)
export(check_database)
export(check_mass_dataset)
export(check_ms1_ms2_info)
export(check_object4metablite_origin)
export(check_parameters4annotate_metabolites)
export(check_parameters4calculate_total_score)
export(construct_database)
export(construct_massbank_database)
export(construct_mona_database)
export(correct_database_rt)
export(extract_database_name)
export(extract_ms1_database)
export(extract_ms1_info)
export(extract_ms2_database)
export(extract_ms2_info)
export(filter)
export(filter_adducts)
export(filter_identification)
export(getIdentificationTable2)
export(getMS2spectrum)
export(get_iden_info)
export(get_identification_table)
export(get_identification_table_all)
export(get_ms2_spectrum)
export(get_ms2_spectrum_from_object)
export(get_parameters)
export(get_parameters_metid)
export(identify_metabolite_all)
export(identify_metabolites)
export(identify_metabolites_params)
export(identify_ms2_only)
export(identify_peak)
export(identify_single_peak)
export(load_adduct_table)
export(match_ms2_fragments)
export(match_ms2_temp)
export(metIdentification)
export(metIdentify)
export(metIdentify_mass_dataset)
export(metabolite_origin_network)
export(metabolite_origin_upsetplot)
export(metid)
export(metid_conflicts)
export(metid_logo)
export(metid_packages)
export(ms2_plot_mass_dataset)
export(ms2plot)
export(mzIdentify)
export(mzIdentifyParam)
export(mzIdentify_mass_dataset)
export(plot_ms2_matching)
export(readMGF)
export(readMSP)
export(readMSP_MoNA)
export(readMZXML)
export(read_mgf_experiment)
export(read_mgf_gnps)
export(read_mgf_mona)
export(read_msp)
export(read_msp_database)
export(read_msp_gnps)
export(read_msp_mona)
export(remove_impossible_annotations)
export(remove_noise)
export(source_metabolite_network)
export(source_network)
export(specific_source_network)
export(summary_annotation_table)
export(trans_to_new_style)
export(which_has_identification)
export(write_mgf_gnps)
export(write_mgf_massbank)
export(write_mgf_mona)
export(write_msp)
export(write_msp_gnps)
export(write_msp_massbank)
export(write_msp_mona)
exportClasses(databaseClass)
exportClasses(metIdentifyClass)
import(ggplot2)
import(grDevices)
import(utils)
importClassesFrom(massdataset,mass_dataset)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(MSnbase,readMSData)
importFrom(cli,cat_line)
importFrom(cli,rule)
importFrom(cli,symbol)
importFrom(crayon,bgRed)
importFrom(crayon,green)
importFrom(crayon,red)
importFrom(crayon,yellow)
importFrom(dplyr,all_of)
importFrom(dplyr,anti_join)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,lag)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,ungroup)
importFrom(furrr,future_map)
importFrom(furrr,future_map2)
importFrom(future,multisession)
importFrom(future,plan)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(ggraph,create_layout)
importFrom(ggraph,geom_edge_diagonal)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,geom_node_text)
importFrom(ggraph,ggraph)
importFrom(ggraph,scale_edge_color_manual)
importFrom(ggraph,theme_graph)
importFrom(igraph,V)
importFrom(igraph,bipartite_mapping)
importFrom(magrittr,"%>%")
importFrom(massdataset,extract_variable_info)
importFrom(masstools,get_os)
importFrom(masstools,get_spectra_match_score)
importFrom(masstools,ms2_match)
importFrom(masstools,mz_rt_match)
importFrom(masstools,read_mgf)
importFrom(masstools,read_mzxml)
importFrom(pbapply,pblapply)
importFrom(pbapply,pboptions)
importFrom(plyr,.)
importFrom(plyr,dlply)
importFrom(progress,progress_bar)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(readr,cols)
importFrom(readr,read_csv)
importFrom(rlang,"!!!")
importFrom(rlang,quos)
importFrom(rstudioapi,getThemeInfo)
importFrom(rstudioapi,hasFun)
importFrom(rstudioapi,isAvailable)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,predict)
importFrom(stringr,str_c)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_trim)
importFrom(tibble,as_tibble)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidygraph,activate)
importFrom(tidygraph,mutate)
importFrom(tidygraph,tbl_graph)
importFrom(tidyr,pivot_longer)
