Table of Contents - sequenceserver-3.1.2 Documentation
Classes and Modules
- Hash
- Pool
- SequenceServer
- SequenceServer::BLAST
- SequenceServer::BLAST::Error
- SequenceServer::BLAST::Formatter
- SequenceServer::BLAST::Job
- SequenceServer::BLAST::Report
- SequenceServer::BLAST::Tasks
- SequenceServer::BLAST_DATABASE_ERROR
- SequenceServer::BLAST_NOT_COMPATIBLE
- SequenceServer::BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE
- SequenceServer::CONFIG_FILE_ERROR
- SequenceServer::CommandFailed
- SequenceServer::Config
- SequenceServer::DATABASE_DIR_NOT_SET
- SequenceServer::Database
- SequenceServer::DatabaseUnreachableError
- SequenceServer::Doctor
- SequenceServer::ENOENT
- SequenceServer::INCOMPATIBLE_BLAST_DATABASES
- SequenceServer::InputError
- SequenceServer::InvalidParameterError
- SequenceServer::InvalidSequenceIdError
- SequenceServer::Job
- SequenceServer::JobRemover
- SequenceServer::Links
- SequenceServer::Logger
- SequenceServer::Logger::Formatter
- SequenceServer::MAKEBLASTDB
- SequenceServer::NO_BLAST_DATABASE_FOUND
- SequenceServer::NUM_THREADS_INCORRECT
- SequenceServer::NotFound
- SequenceServer::Report
- SequenceServer::Routes
- SequenceServer::Sequence
- SequenceServer::Sequence::Retriever
- SequenceServer::Sequence::Retriever::IO
- SequenceServer::Server
- SequenceServer::SystemError
- ZipFileGenerator
Methods
- ::[] — SequenceServer::Database
- ::all — SequenceServer::Database
- ::all — SequenceServer::Job
- ::all_sequence_ids — SequenceServer::Doctor
- ::assert_blast_installed_and_compatible — SequenceServer
- ::bullet_list — SequenceServer::Doctor
- ::call — SequenceServer
- ::check_database_compatibility — SequenceServer
- ::check_num_threads — SequenceServer
- ::clear — SequenceServer::Database
- ::collection — SequenceServer::Database
- ::collection= — SequenceServer::Database
- ::command? — SequenceServer
- ::composition — SequenceServer::Sequence
- ::create — SequenceServer::Job
- ::delete — SequenceServer::Job
- ::development? — SequenceServer
- ::each — SequenceServer::Database
- ::enqueue — SequenceServer::Job
- ::environment — SequenceServer
- ::extract_tasks — SequenceServer::BLAST::Tasks
- ::extract_tasks_from_paragraph — SequenceServer::BLAST::Tasks
- ::fetch — SequenceServer::Job
- ::first — SequenceServer::Database
- ::group_by — SequenceServer::Database
- ::guess_type — SequenceServer::Sequence
- ::hostname — SequenceServer
- ::ids — SequenceServer::Database
- ::include? — SequenceServer::Database
- ::init — SequenceServer
- ::init_binaries — SequenceServer
- ::init_database — SequenceServer
- ::inspect_parse_seqids — SequenceServer::Doctor
- ::inspect_seqids — SequenceServer::Doctor
- ::ip_address — SequenceServer
- ::irb — SequenceServer
- ::is_compatible — SequenceServer
- ::load_extension — SequenceServer
- ::logger — SequenceServer
- ::makeblastdb — SequenceServer
- ::new — SequenceServer::DatabaseUnreachableError
- ::new — SequenceServer::InvalidSequenceIdError
- ::new — SequenceServer::InvalidParameterError
- ::new — SequenceServer::InputError
- ::new — SequenceServer::SystemError
- ::new — SequenceServer::BLAST::Error
- ::new — SequenceServer::BLAST::Formatter
- ::new — SequenceServer::BLAST::Job
- ::new — SequenceServer::BLAST::Report
- ::new — SequenceServer::Config
- ::new — SequenceServer::Doctor
- ::new — SequenceServer::CONFIG_FILE_ERROR
- ::new — SequenceServer::ENOENT
- ::new — SequenceServer::BLAST_NOT_COMPATIBLE
- ::new — SequenceServer::NO_BLAST_DATABASE_FOUND
- ::new — SequenceServer::INCOMPATIBLE_BLAST_DATABASES
- ::new — SequenceServer::BLAST_DATABASE_ERROR
- ::new — SequenceServer::CommandFailed
- ::new — SequenceServer::Job
- ::new — SequenceServer::JobRemover
- ::new — SequenceServer::Logger
- ::new — SequenceServer::Logger::Formatter
- ::new — SequenceServer::MAKEBLASTDB
- ::new — Pool
- ::new — SequenceServer::Report
- ::new — SequenceServer::Sequence::Retriever
- ::new — SequenceServer::Server
- ::new — ZipFileGenerator
- ::on_start — SequenceServer
- ::on_stop — SequenceServer
- ::open_in_browser — SequenceServer
- ::parse_version — SequenceServer
- ::pool — SequenceServer::Job
- ::retrieve — SequenceServer::Database
- ::run — SequenceServer::Server
- ::run — SequenceServer
- ::serializable_classes — SequenceServer::Job
- ::server_url — SequenceServer
- ::show_message — SequenceServer::Doctor
- ::sys — SequenceServer
- ::to_h — SequenceServer::BLAST::Tasks
- ::to_json — SequenceServer::Database
- ::tree — SequenceServer::Database
- ::using_ssh? — SequenceServer
- ::verbose? — SequenceServer
- ::xdg? — SequenceServer
- #[] — SequenceServer::Config
- #[]= — SequenceServer::Config
- #_make_blast_database — SequenceServer::MAKEBLASTDB
- #any_formatted? — SequenceServer::MAKEBLASTDB
- #any_to_format? — SequenceServer::MAKEBLASTDB
- #any_to_format_or_reformat? — SequenceServer::MAKEBLASTDB
- #any_to_reformat? — SequenceServer::MAKEBLASTDB
- #blastdbcmd — SequenceServer::MAKEBLASTDB
- #call — SequenceServer::Logger::Formatter
- #check_id_format — SequenceServer::Doctor
- #check_numeric_ids — SequenceServer::Doctor
- #check_parse_seqids — SequenceServer::Doctor
- #command — SequenceServer::Job
- #confirm_database_title — SequenceServer::MAKEBLASTDB
- #convert_deprecated_options — SequenceServer::Config
- #create_entry_batch_file — SequenceServer::Sequence::Retriever
- #database_names — SequenceServer::Sequence::Retriever
- #database_titles — SequenceServer::Sequence::Retriever
- #dbtype — SequenceServer::BLAST::Report
- #dbtype_from_program — SequenceServer::BLAST::Report
- #deep_copy — Hash
- #deep_merge — Hash
- #defaults — SequenceServer::Config
- #diagnose — SequenceServer::Doctor
- #dir — SequenceServer::Job
- #display_large_result_warning? — SequenceServer::Routes
- #done! — SequenceServer::Job
- #done? — SequenceServer::BLAST::Report
- #done? — SequenceServer::Job
- #error_msgs — SequenceServer::Sequence::Retriever
- #extract_fasta — SequenceServer::MAKEBLASTDB
- #extract_params — SequenceServer::BLAST::Report
- #extract_stats — SequenceServer::BLAST::Report
- #extract_taxid_map — SequenceServer::MAKEBLASTDB
- #fastas_to_format — SequenceServer::MAKEBLASTDB
- #fastas_to_reformat — SequenceServer::MAKEBLASTDB
- #fetch — SequenceServer::Job
- #fetch_job — SequenceServer::Routes
- #file — SequenceServer::Sequence::Retriever::IO
- #file? — SequenceServer::Config
- #filename — SequenceServer::BLAST::Formatter
- #filename — SequenceServer::Sequence::Retriever::IO
- #filepath — SequenceServer::BLAST::Formatter
- #first_text — SequenceServer::BLAST::Report
- #format — SequenceServer::MAKEBLASTDB
- #formatted_fastas — SequenceServer::MAKEBLASTDB
- #get_categories — SequenceServer::MAKEBLASTDB
- #guess_sequence_type_in_fasta — SequenceServer::MAKEBLASTDB
- #hsps — SequenceServer::BLAST::Report
- #http_status — SequenceServer::DatabaseUnreachableError
- #http_status — SequenceServer::InvalidSequenceIdError
- #http_status — SequenceServer::InvalidParameterError
- #http_status — SequenceServer::NotFound
- #http_status — SequenceServer::InputError
- #http_status — SequenceServer::SystemError
- #include? — SequenceServer::Config
- #large_result_warning_payload — SequenceServer::Routes
- #logdev — SequenceServer::Server
- #logid — SequenceServer::JobRemover
- #make_blast_database — SequenceServer::MAKEBLASTDB
- #make_blast_database? — SequenceServer::MAKEBLASTDB
- #make_db_title — SequenceServer::MAKEBLASTDB
- #message — SequenceServer::DatabaseUnreachableError
- #message — SequenceServer::InvalidSequenceIdError
- #message — SequenceServer::InvalidParameterError
- #message — SequenceServer::NotFound
- #message — SequenceServer::InputError
- #message — SequenceServer::SystemError
- #mime — SequenceServer::Sequence::Retriever::IO
- #more_info — SequenceServer::NotFound
- #multipart_database_name? — SequenceServer::MAKEBLASTDB
- #ncbi — SequenceServer::Links
- #no_fastas? — SequenceServer::MAKEBLASTDB
- #node_to_array — SequenceServer::BLAST::Report
- #node_to_hash — SequenceServer::BLAST::Report
- #node_to_value — SequenceServer::BLAST::Report
- #normalize — SequenceServer::Config
- #options — SequenceServer::Server
- #params — SequenceServer::BLAST::Report
- #parse_advanced — SequenceServer::BLAST::Report
- #parse_config_file — SequenceServer::Config
- #parse_tsv — SequenceServer::BLAST::Report
- #parse_xml — SequenceServer::BLAST::Report
- #pfam — SequenceServer::Links
- #probably_fasta? — SequenceServer::MAKEBLASTDB
- #probably_fastas — SequenceServer::MAKEBLASTDB
- #program — SequenceServer::BLAST::Report
- #program_version — SequenceServer::BLAST::Report
- #put_into_archive — ZipFileGenerator
- #queries — SequenceServer::BLAST::Report
- #query_hits — SequenceServer::BLAST::Report
- #querydb — SequenceServer::BLAST::Report
- #queue — Pool
- #raise! — SequenceServer::BLAST::Error
- #raise! — SequenceServer::Job
- #read_file — SequenceServer::BLAST::Formatter
- #recursively_deflate_directory — ZipFileGenerator
- #reformat — SequenceServer::MAKEBLASTDB
- #remove_invalid_databases — SequenceServer::Doctor
- #rfam — SequenceServer::Links
- #root_path_prefix — SequenceServer::Routes
- #run — SequenceServer::BLAST::Formatter
- #run — SequenceServer::Job
- #run — SequenceServer::MAKEBLASTDB
- #run — SequenceServer::Sequence::Retriever
- #sample_sequences — SequenceServer::MAKEBLASTDB
- #save — SequenceServer::Job
- #setup_signal_handlers — SequenceServer::Server
- #shutdown — Pool
- #size — SequenceServer::BLAST::Formatter
- #spawn_cleanup — SequenceServer::JobRemover
- #start — SequenceServer::Server
- #stats — SequenceServer::BLAST::Report
- #stderr — SequenceServer::Job
- #stdout — SequenceServer::Job
- #stop — SequenceServer::Server
- #store — SequenceServer::Job
- #taxid — SequenceServer::MAKEBLASTDB
- #taxid_map — SequenceServer::MAKEBLASTDB
- #title — SequenceServer::DatabaseUnreachableError
- #title — SequenceServer::InvalidSequenceIdError
- #title — SequenceServer::InvalidParameterError
- #title — SequenceServer::NotFound
- #title — SequenceServer::InputError
- #title — SequenceServer::SystemError
- #to_json — SequenceServer::BLAST::Report
- #to_json — SequenceServer::Sequence::Retriever
- #to_s — SequenceServer::CONFIG_FILE_ERROR
- #to_s — SequenceServer::ENOENT
- #to_s — SequenceServer::NUM_THREADS_INCORRECT
- #to_s — SequenceServer::BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE
- #to_s — SequenceServer::BLAST_NOT_COMPATIBLE
- #to_s — SequenceServer::DATABASE_DIR_NOT_SET
- #to_s — SequenceServer::NO_BLAST_DATABASE_FOUND
- #to_s — SequenceServer::INCOMPATIBLE_BLAST_DATABASES
- #to_s — SequenceServer::BLAST_DATABASE_ERROR
- #tsv_formatter — SequenceServer::BLAST::Report
- #tsv_ir — SequenceServer::BLAST::Report
- #uniprot — SequenceServer::Links
- #update_searchdata_from_job — SequenceServer::Routes
- #validate — SequenceServer::Sequence::Retriever
- #write — ZipFileGenerator
- #write — SequenceServer::Sequence::Retriever::IO
- #write_config_file — SequenceServer::Config
- #write_entries — ZipFileGenerator
- #write_error_msgs — SequenceServer::Sequence::Retriever::IO
- #write_sequences — SequenceServer::Sequence::Retriever::IO
- #xml_file_size — SequenceServer::BLAST::Report
- #xml_formatter — SequenceServer::BLAST::Report
- #xml_ir — SequenceServer::BLAST::Report
- #yfile — SequenceServer::Job