Method List
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#<=> Bio::GFF::GFF3::Record
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#accessions Bio::SPTR
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#add ManageDBTool
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#add_boolean_option Tool
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#add_putative_nterm_to_gff ProtXMLToGFFTool
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add_retention_times OMSSAUtil
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#add_value_option Tool
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#all_database_names ManageDBTool
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#altnames Bio::SPTR
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#bin Constants
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#blast_root Constants
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#blastdbcmd Constants
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#cd Bio::SPTR
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#cds_info_from_fasta ProtXMLToGFFTool
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#charge Peptide
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#check_options Tool
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#coding_sequences ProtXMLToGFFTool::CDSInfo
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#coords_in_protein Peptide
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create FastaDB
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create GFFDB
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#current_database_for_name Constants
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#data_lib_dir Constants
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#database_downloads Constants
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#database_info Tool
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#dbexist? Constants
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#default_data_path TandemSearchTool
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default_output_path Tool
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#defaults_path TandemSearchTool
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#disease Bio::SPTR
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#domain Bio::SPTR
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#end ProtXMLToGFFTool::CDSInfo
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#ensembl Bio::SPTR
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#ensembl_link Bio::SPTR
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ensure_mzml_indexed ConvertUtil
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#env CommandRunner
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#extract_db PepXML
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#extract_engine PepXML
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#extract_enzyme PepXML
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#fasta_id ProtXMLToGFFTool::CDSInfo
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#feature_dump Bio::SPTR
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#featurefinderisotopewavelet OpenMSDefaults
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#fetch FastaDB
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#file_name PepXML
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#find_runs PepXML
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for_galaxy? GalaxyUtil
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#fragment_coords_from_protein_coords ProtXMLToGFFTool
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#frame ProtXMLToGFFTool::CDSInfo
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from_protxml Protein
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from_protxml Peptide
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from_sequence Peptide
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#function Bio::SPTR
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#gene_id ProtXMLToGFFTool::CDSInfo
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#generate_fragment_gffs_for_coords ProtXMLToGFFTool
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#generate_gff_for_peptide_mapped_to_protein ProtXMLToGFFTool
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#generate_protein_gff ProtXMLToGFFTool
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#get_by_id FastaDB
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#get_by_id GFFDB
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#get_cds_by_parent_id GFFDB
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#get_cterm_coords_for_peptide ProtXMLToGFFTool
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#get_dna_sequence ProtXMLToGFFTool
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#get_entry_for_name SwissprotDatabase
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#get_entry_for_name PlasmoDB
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#get_fasta_record ProtXMLToGFFTool
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#get_nterm_peptide_for_peptide ProtXMLToGFFTool
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#get_peptide_coordinates ProtXMLToGFFTool
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#get_peptide_coordinates_from_transcript_info ProtXMLToGFFTool
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#get_peptide_coordinates_sixframe ProtXMLToGFFTool
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#get_predefined_definition ManageDBTool
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#get_start_codon_coords_for_peptide ProtXMLToGFFTool
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#gff_record_for_peptide_fragment Peptide
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#go_entries Bio::SPTR
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#go_terms Bio::SPTR
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#group_number Protein
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#group_probability Protein
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#id_to_records_map GFFDB
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#import_fasta_database Constants
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index_mgf_times MascotUtil
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index_mzml ConvertUtil
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#info_level Constants
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#initialize PlasmoDB
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#initialize Protein
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#initialize SwissprotDatabase
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#initialize Peptide
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#initialize FastaDB
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#initialize PepXML
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#initialize GFFDB
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#initialize UniprotMapper
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#initialize Tool
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#initialize TandemSearchTool
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#initialize FastaDatabase
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#initialize SearchTool
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#initialize GalaxyStager
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#initialize ProphetTool
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#initialize Constants
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#initialize OpenMSDefaults
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#initialize ProtXMLToGFFTool
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#initialize ManageDBTool
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#initialize CommandRunner
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#initialize MzMLParser
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#initialize_loggers Constants
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input_basename MascotUtil
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#install SetupTool
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#intact Bio::SPTR
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#intact_link Bio::SPTR
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#ipi Bio::SPTR
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#is_new_genome_location ProtXMLToGFFTool
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#is_sixframe ProtXMLToGFFTool::CDSInfo
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#is_valid_type PepXML
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#jobid_prefix Tool
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#jobid_prefix= Tool
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#length Bio::GFF::GFF3::Record
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#location Bio::SPTR
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#log Constants
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#log_file Constants
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make_decoys Randomize
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make_decoys Decoymaker
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#make_index FastaDB
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#make_index GFFDB
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#makeblastdb Constants
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#map UniprotMapper
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#mascot2xml Constants
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#method_missing Constants
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#method_missing Tool
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#msgfplus_root Constants
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#msgfplusjar Constants
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#n_indistinguishable_proteins Protein
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#name ProtXMLToGFFTool::CDSInfo
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#name FastaDatabase
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#ncbi_taxon_id Bio::SPTR
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#next_spectrum MzMLParser
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#nextbio Bio::SPTR
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#nextbio_link Bio::SPTR
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#nsp_adjusted_probability Peptide
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#num_transmem Bio::SPTR
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#omssa_root Constants
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#openms_root Constants
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#option_parser Tool
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#options Tool
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#overlap ProtXMLToGFFTool::CDSInfo
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#params_doc TandemSearchTool
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#path FastaDatabase
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#path_for_builtin_database Constants
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#peptide_gff_is_duplicate ProtXMLToGFFTool
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#peptide_is_in_sixframe ProtXMLToGFFTool
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#peptide_nodes ProtXMLToGFFTool
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#peptides Protein
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#percent_coverage Protein
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#predefined_databases_help ManageDBTool
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#predefined_names ManageDBTool
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#pride Bio::SPTR
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#pride_link Bio::SPTR
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#probability Protein
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#protein_database_root Constants
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#protein_name Protein
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#protein_name Peptide
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#protein_names ProtXMLToGFFTool
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#protk_dir Constants
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#pwiz_root Constants
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#rakefile_path ManageDBTool
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#recname Bio::SPTR
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#ref_dump Bio::SPTR
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remove_charge_from_title_string MascotUtil
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replace_references GalaxyStager
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#replace_references GalaxyStager
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#representative_peptides Protein
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#restore_references GalaxyStager
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#rubygems Top Level Namespace
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#run Tool
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#run_batch CommandRunner
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#run_local Constants
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#run_local CommandRunner
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#safely_get_drentry_for_key Bio::SPTR
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#scaffold ProtXMLToGFFTool::CDSInfo
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#seq_dump Bio::SPTR
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#sequence Protein
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#sequence Peptide
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#signalp Bio::SPTR
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#similarity Bio::SPTR
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#species_dump Bio::SPTR
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#spectrum_as_hash MzMLParser
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stage_fasta GalaxyUtil
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stage_pepxml GalaxyUtil
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#staged_base_path GalaxyStager
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#staged_path GalaxyStager
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#start ProtXMLToGFFTool::CDSInfo
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#strand ProtXMLToGFFTool::CDSInfo
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#subunit Bio::SPTR
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#supported_options Tool
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#supported_xtandem_keys TandemSearchTool
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#tandem_root Constants
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#taxonomy_doc TandemSearchTool
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#taxonomy_path TandemSearchTool
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#tissues Bio::SPTR
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#to_gff3_records Peptide
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#tpp_root Constants
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#trf_path OpenMSDefaults
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#type_from_base_name PepXML
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unindexed_mzml? ConvertUtil
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#uniprot_link Bio::SPTR
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#update_user_config Constants
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xinteract_code_for_enzyme ProphetTool
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#xtandem_modification_motif? String