Table of Contents - genevalidatorapp-2.1.8 Documentation
Classes and Modules
- GeneValidatorApp
- GeneValidatorApp::BIN_DIR_NOT_FOUND
- GeneValidatorApp::BLAST_DATABASE_ERROR
- GeneValidatorApp::BLAST_NOT_COMPATIBLE
- GeneValidatorApp::BLAST_NOT_EXECUTABLE
- GeneValidatorApp::BLAST_NOT_INSTALLED
- GeneValidatorApp::CONFIG_FILE_ERROR
- GeneValidatorApp::Config
- GeneValidatorApp::DATABASE_DIR_NOT_FOUND
- GeneValidatorApp::DATABASE_DIR_NOT_SET
- GeneValidatorApp::Database
- GeneValidatorApp::ENOENT
- GeneValidatorApp::EXTENSION_FILE_NOT_FOUND
- GeneValidatorApp::Logger
- GeneValidatorApp::Logger::Formatter
- GeneValidatorApp::MAFFT_NOT_INSTALLED
- GeneValidatorApp::NO_BLAST_DATABASE_FOUND
- GeneValidatorApp::NO_PROTEIN_BLAST_DATABASE_FOUND
- GeneValidatorApp::NUM_THREADS_INCORRECT
- GeneValidatorApp::Routes
- GeneValidatorApp::RunGeneValidator
- GeneValidatorApp::RunGeneValidator::ArgumentError
- GeneValidatorApp::RunGeneValidator::RuntimeError
- GeneValidatorApp::Server
Methods
- ::<< — GeneValidatorApp::Database
- ::[] — GeneValidatorApp::Database
- ::all — GeneValidatorApp::Database
- ::assert_blast_databases_present_in_database_dir — GeneValidatorApp
- ::assert_blast_installed_and_compatible — GeneValidatorApp
- ::assert_input_file_present — GeneValidatorApp::RunGeneValidator
- ::assert_json_output_file_produced — GeneValidatorApp::RunGeneValidator
- ::assert_mafft_installed — GeneValidatorApp
- ::call — GeneValidatorApp
- ::check_database_params_present — GeneValidatorApp::RunGeneValidator
- ::check_host — GeneValidatorApp
- ::check_max_characters — GeneValidatorApp
- ::check_num_threads — GeneValidatorApp
- ::check_seq_length — GeneValidatorApp::RunGeneValidator
- ::check_seq_param_present — GeneValidatorApp::RunGeneValidator
- ::check_validations_param_present — GeneValidatorApp::RunGeneValidator
- ::collection — GeneValidatorApp::Database
- ::command? — GeneValidatorApp
- ::create_gv_log_file — GeneValidatorApp::RunGeneValidator
- ::create_run_dir — GeneValidatorApp::RunGeneValidator
- ::create_unique_id — GeneValidatorApp::RunGeneValidator
- ::default_db — GeneValidatorApp::Database
- ::each — GeneValidatorApp::Database
- ::ensure_fasta_valid — GeneValidatorApp::RunGeneValidator
- ::ensure_unique_id — GeneValidatorApp::RunGeneValidator
- ::ensure_unix_line_ending — GeneValidatorApp::RunGeneValidator
- ::environment — GeneValidatorApp
- ::export_bin_dir — GeneValidatorApp
- ::first — GeneValidatorApp::Database
- ::group_by — GeneValidatorApp::Database
- ::gv_params — GeneValidatorApp::RunGeneValidator
- ::ids — GeneValidatorApp::Database
- ::include? — GeneValidatorApp::Database
- ::individual_json_path — GeneValidatorApp::RunGeneValidator
- ::init — GeneValidatorApp
- ::init — GeneValidatorApp::RunGeneValidator
- ::init_binaries — GeneValidatorApp
- ::init_bins — GeneValidatorApp
- ::init_database — GeneValidatorApp
- ::init_dirs — GeneValidatorApp
- ::init_public_dir — GeneValidatorApp
- ::is_compatible — GeneValidatorApp
- ::load_extension — GeneValidatorApp
- ::logger — GeneValidatorApp
- ::multipart_database_name? — GeneValidatorApp::Database
- ::new — GeneValidatorApp::Config
- ::new — GeneValidatorApp::Database
- ::new — GeneValidatorApp::CONFIG_FILE_ERROR
- ::new — GeneValidatorApp::ENOENT
- ::new — GeneValidatorApp::BIN_DIR_NOT_FOUND
- ::new — GeneValidatorApp::EXTENSION_FILE_NOT_FOUND
- ::new — GeneValidatorApp::DATABASE_DIR_NOT_FOUND
- ::new — GeneValidatorApp::BLAST_NOT_COMPATIBLE
- ::new — GeneValidatorApp::NO_BLAST_DATABASE_FOUND
- ::new — GeneValidatorApp::NO_PROTEIN_BLAST_DATABASE_FOUND
- ::new — GeneValidatorApp::BLAST_DATABASE_ERROR
- ::new — GeneValidatorApp::Logger
- ::new — GeneValidatorApp::Logger::Formatter
- ::new — GeneValidatorApp::Server
- ::non_default_dbs — GeneValidatorApp::Database
- ::obtain_db_path — GeneValidatorApp::RunGeneValidator
- ::obtain_original_structure — GeneValidatorApp::Database
- ::on_start — GeneValidatorApp
- ::on_stop — GeneValidatorApp
- ::open_in_browser — GeneValidatorApp
- ::output_json_file_path — GeneValidatorApp::RunGeneValidator
- ::parse_output_json — GeneValidatorApp::RunGeneValidator
- ::parse_version — GeneValidatorApp
- ::produce_json_url_link — GeneValidatorApp::RunGeneValidator
- ::produce_result_url_link — GeneValidatorApp::RunGeneValidator
- ::root — GeneValidatorApp
- ::run — GeneValidatorApp::Server
- ::run — GeneValidatorApp
- ::run — GeneValidatorApp::RunGeneValidator
- ::run_genevalidator — GeneValidatorApp::RunGeneValidator
- ::run_gv — GeneValidatorApp::RunGeneValidator
- ::scan_databases_dir — GeneValidatorApp::Database
- ::server_url — GeneValidatorApp
- ::set_database_from_env — GeneValidatorApp
- ::ssl? — GeneValidatorApp
- ::using_ssh? — GeneValidatorApp
- ::validate_params — GeneValidatorApp::RunGeneValidator
- ::verbose? — GeneValidatorApp
- ::write_seq_to_file — GeneValidatorApp::RunGeneValidator
- ::xdg? — GeneValidatorApp
- #[] — GeneValidatorApp::Config
- #[]= — GeneValidatorApp::Config
- #base_url — GeneValidatorApp::Routes
- #call — GeneValidatorApp::Logger::Formatter
- #default_config_file — GeneValidatorApp::Config
- #defaults — GeneValidatorApp::Config
- #file? — GeneValidatorApp::Config
- #host — GeneValidatorApp::Routes
- #host_with_port — GeneValidatorApp::Routes
- #include? — GeneValidatorApp::Config
- #logdev — GeneValidatorApp::Server
- #options — GeneValidatorApp::Server
- #parse_config_file — GeneValidatorApp::Config
- #setup_signal_handlers — GeneValidatorApp::Server
- #start — GeneValidatorApp::Server
- #stop — GeneValidatorApp::Server
- #symbolise — GeneValidatorApp::Config
- #to_s — GeneValidatorApp::Database
- #to_s — GeneValidatorApp::CONFIG_FILE_ERROR
- #to_s — GeneValidatorApp::NUM_THREADS_INCORRECT
- #to_s — GeneValidatorApp::ENOENT
- #to_s — GeneValidatorApp::MAFFT_NOT_INSTALLED
- #to_s — GeneValidatorApp::BLAST_NOT_INSTALLED
- #to_s — GeneValidatorApp::BLAST_NOT_EXECUTABLE
- #to_s — GeneValidatorApp::BLAST_NOT_COMPATIBLE
- #to_s — GeneValidatorApp::DATABASE_DIR_NOT_SET
- #to_s — GeneValidatorApp::NO_BLAST_DATABASE_FOUND
- #to_s — GeneValidatorApp::NO_PROTEIN_BLAST_DATABASE_FOUND
- #to_s — GeneValidatorApp::BLAST_DATABASE_ERROR
- #uri — GeneValidatorApp::Routes
- #write_config_file — GeneValidatorApp::Config