Method List
Search:
-
#aa_deletion GappedAligner
-
#accessions Bio::SPTR
-
#add ManageDBTool
-
#add_information EuPathDBGeneInformation
-
add_retention_times OMSSAUtil
-
#add_table EuPathDBGeneInformation
-
#align GappedAligner
-
#all_database_names ManageDBTool
-
#altnames Bio::SPTR
-
#as_rows ProtXML
-
#asaprationpvalueparser Constants
-
#asapratiopeptideparser Constants
-
#asapratioproteinparser Constants
-
#bin Constants
-
#blast_root Constants
-
#calculate_dp GappedAligner
-
#cd Bio::SPTR
-
#check_options Tool
-
#convert ProteinAnnotator
-
#copyBook Spreadsheet::Workbook
-
create FastaDB
-
#current_database SearchTool
-
#current_database_for_name Constants
-
#data_lib_dir Constants
-
#database_downloads Constants
-
#dbexist? Constants
-
#disease Bio::SPTR
-
#domain Bio::SPTR
-
#each EuPathDBGeneInformationTable
-
#end PeptideFragment
-
#ensembl Bio::SPTR
-
#ensembl_link Bio::SPTR
-
ensure_mzml_indexed ConvertUtil
-
#env ProteinAnnotator
-
#env CommandRunner
-
#executepipeline Constants
-
#extract_db ProphetTool
-
#extract_engine ProphetTool
-
#extract_gene_info EuPathDBGeneInformationFileExtractor
-
#feature_dump Bio::SPTR
-
#featurefinderisotopewavelet Constants
-
#featurefinderisotopewavelet OpenMSDefaults
-
#fetch FastaDB
-
#filename EuPathDBGeneInformationFileExtractor
-
#find_pep_xml ProtXML
-
#find_runs PepXML
-
for_galaxy? GalaxyUtil
-
#fragments PeptideToGeneAlignment
-
#function Bio::SPTR
-
#gaps PeptideToGeneAlignment
-
#gene_seq PeptideToGeneAlignment
-
#get_by_id FastaDB
-
#get_entry_for_name SwissprotDatabase
-
#get_entry_for_name PlasmoDB
-
#get_info EuPathDBGeneInformation
-
#get_predefined_definition ManageDBTool
-
#get_rows BioToolsExcelConverter
-
#get_table EuPathDBGeneInformation
-
#gpmtandem Constants
-
#groups ProtXML
-
#hasAccession ProteinAnnotator
-
#idconvert Constants
-
#import_fasta_database Constants
-
index_mgf_times MascotUtil
-
index_mzml ConvertUtil
-
#info EuPathDBGeneInformation
-
#info_level Constants
-
#init_groups ProtXML
-
#initialize ProteinAnnotator
-
#initialize OpenMSDefaults
-
#initialize UniprotMapper
-
#initialize SwissprotDatabase
-
#initialize PeptideToGeneAlignment
-
#initialize XTandemDefaults
-
#initialize PlasmoDB
-
#initialize BioToolsExcelConverter
-
#initialize ManageDBTool
-
#initialize GalaxyStager
-
#initialize ProtXML
-
#initialize FastaDB
-
#initialize PepXML
-
#initialize Tool
-
#initialize EuPathDBGeneInformationFileExtractor
-
#initialize CommandRunner
-
#initialize GappedAligner
-
#initialize Constants
-
#initialize ProphetTool
-
#initialize EuPathDBGeneInformationTable
-
#initialize SearchTool
-
#initialize_loggers Constants
-
#input_base_path Tool
-
input_basename MascotUtil
-
#insert_column Spreadsheet::Worksheet
-
#inspect PeptideToGeneAlignment
-
#install SetupTool
-
#intact Bio::SPTR
-
#intact_link Bio::SPTR
-
#interprophetparser Constants
-
#ipi Bio::SPTR
-
#isBioToolsFile ProteinAnnotator
-
isBiotools BioToolsExcelConverter
-
#isExcelFile ProteinAnnotator
-
#isProtXMLFile ProteinAnnotator
-
#jobid_from_filename Tool
-
#jobid_from_filename SearchTool
-
#jobid_prefix Tool
-
#jobid_prefix= Tool
-
#librapeptideparser Constants
-
#libraproteinratioparser Constants
-
#location Bio::SPTR
-
#log Constants
-
#log_file Constants
-
make_decoys Decoymaker
-
make_decoys Randomize
-
#make_index FastaDB
-
#makeblastdb Constants
-
#map UniprotMapper
-
#mascot2xml Constants
-
#method_missing Constants
-
#method_missing Tool
-
#msconvert Constants
-
#msgfplus_root Constants
-
#msgfplusjar Constants
-
#next_frame GappedAligner
-
#next_gene EuPathDBGeneInformationTable
-
#nextbio Bio::SPTR
-
#nextbio_link Bio::SPTR
-
#num_transmem Bio::SPTR
-
#omssa2pepxml Constants
-
#omssa_root Constants
-
#omssacl Constants
-
#openms_root Constants
-
#option_parser Tool
-
#options Tool
-
#outputBookFromBiotoolsExcel ProteinAnnotator
-
#outputBookFromExcelInput ProteinAnnotator
-
#outputBookFromProtXML ProteinAnnotator
-
#outputBookFromProtXMLAndPepXML ProteinAnnotator
-
#outputBookFromWarpLCInput ProteinAnnotator
-
#output_base_path Tool
-
#path XTandemDefaults
-
#path_for_builtin_database Constants
-
#pep_seq PeptideToGeneAlignment
-
#peptide_sequences_from_protein ProtXML
-
#peptides_from_protein ProtXML
-
#predefined_databases_help ManageDBTool
-
#predefined_names ManageDBTool
-
#pride Bio::SPTR
-
#pride_link Bio::SPTR
-
#protein_database_root Constants
-
#protein_to_row ProtXML
-
#proteinprophet Constants
-
#proteins_from_group ProtXML
-
#protk_dir Constants
-
#pwiz_root Constants
-
#rakefile_path ManageDBTool
-
#recname Bio::SPTR
-
#ref_dump Bio::SPTR
-
remove_charge_from_title_string MascotUtil
-
#renameValuesInColumn ProteinAnnotator
-
replace_references GalaxyStager
-
#replace_references GalaxyStager
-
#restore_references GalaxyStager
-
#row_is_empty ProteinAnnotator
-
#rubygems Top Level Namespace
-
#run Tool
-
#run_batch CommandRunner
-
#run_local CommandRunner
-
#run_local Constants
-
#safely_get_drentry_for_key Bio::SPTR
-
#save_matrix GappedAligner
-
#score_match GappedAligner
-
#score_na_deletion GappedAligner
-
#searchblastdb Constants
-
#seq PeptideFragment
-
#seq_dump Bio::SPTR
-
#signalp Bio::SPTR
-
#similarity Bio::SPTR
-
#species_dump Bio::SPTR
-
stage_protxml GalaxyUtil
-
#staged_path GalaxyStager
-
#start PeptideFragment
-
#subunit Bio::SPTR
-
#tandem2xml Constants
-
#tandem_root Constants
-
#tax_dump Bio::SPTR
-
#taxonomy_path XTandemDefaults
-
#tissues Bio::SPTR
-
#tpp_root Constants
-
#trace PeptideToGeneAlignment
-
#traceback GappedAligner
-
#translate_na_at GappedAligner
-
#trf_path OpenMSDefaults
-
unindexed_mzml? ConvertUtil
-
#uniprot_link Bio::SPTR
-
#update_user_config Constants
-
#xinteract Constants
-
#xpresspeptideparser Constants
-
#xpressproteinratioparser Constants
-
#xtandem Constants