Table of Contents - sequenceserver-1.0.14 Documentation
Classes and Modules
- SequenceServer
- SequenceServer::BIN_DIR_NOT_FOUND
- SequenceServer::BLAST
- SequenceServer::BLAST::ArgumentError
- SequenceServer::BLAST::Formatter
- SequenceServer::BLAST::HSP
- SequenceServer::BLAST::HSP::BLASTN
- SequenceServer::BLAST::HSP::BLASTP
- SequenceServer::BLAST::HSP::BLASTX
- SequenceServer::BLAST::HSP::TBLASTN
- SequenceServer::BLAST::HSP::TBLASTX
- SequenceServer::BLAST::Report
- SequenceServer::BLAST::RuntimeError
- SequenceServer::BLAST_DATABASE_ERROR
- SequenceServer::BLAST_NOT_COMPATIBLE
- SequenceServer::BLAST_NOT_EXECUTABLE
- SequenceServer::BLAST_NOT_INSTALLED
- SequenceServer::CONFIG_FILE_ERROR
- SequenceServer::Config
- SequenceServer::DATABASE_DIR_NOT_FOUND
- SequenceServer::DATABASE_DIR_NOT_SET
- SequenceServer::Database
- SequenceServer::ENOENT
- SequenceServer::EXTENSION_FILE_NOT_FOUND
- SequenceServer::Links
- SequenceServer::Logger
- SequenceServer::Logger::Formatter
- SequenceServer::NO_BLAST_DATABASE_FOUND
- SequenceServer::NUM_THREADS_INCORRECT
- SequenceServer::Routes
- SequenceServer::Search
- SequenceServer::Sequence
- SequenceServer::Sequence::Retriever
- SequenceServer::Sequence::Retriever::IO
- SequenceServer::Server
Methods
- ::<< — SequenceServer::Database
- ::<< — SequenceServer::Search
- ::[] — SequenceServer::Database
- ::_make_blast_database — SequenceServer::Database
- ::all — SequenceServer::Database
- ::allowed_chars — SequenceServer::BLAST
- ::assert_blast_installed_and_compatible — SequenceServer
- ::call — SequenceServer
- ::check_host — SequenceServer
- ::check_num_threads — SequenceServer
- ::clear — SequenceServer::Database
- ::collection — SequenceServer::Database
- ::command? — SequenceServer
- ::composition — SequenceServer::Sequence
- ::data — SequenceServer::Search
- ::defaults — SequenceServer::BLAST
- ::disallowed_options — SequenceServer::BLAST
- ::each — SequenceServer::Database
- ::environment — SequenceServer
- ::export_bin_dir — SequenceServer
- ::fetch_tax_id — SequenceServer::Database
- ::first — SequenceServer::Database
- ::get_database_title — SequenceServer::Database
- ::group_by — SequenceServer::Database
- ::guess_sequence_type_in_fasta — SequenceServer::Database
- ::guess_type — SequenceServer::Sequence
- ::ids — SequenceServer::Database
- ::include? — SequenceServer::Database
- ::init — SequenceServer
- ::init_binaries — SequenceServer
- ::init_database — SequenceServer
- ::irb — SequenceServer
- ::load_extension — SequenceServer
- ::logger — SequenceServer
- ::make_blast_database — SequenceServer::Database
- ::make_blast_database? — SequenceServer::Database
- ::make_blast_databases — SequenceServer::Database
- ::make_db_title — SequenceServer::Database
- ::multipart_database_name? — SequenceServer::Database
- ::new — SequenceServer::BLAST::RuntimeError
- ::new — SequenceServer::BLAST::Formatter
- ::new — SequenceServer::BLAST::Report
- ::new — SequenceServer::Config
- ::new — SequenceServer::CONFIG_FILE_ERROR
- ::new — SequenceServer::ENOENT
- ::new — SequenceServer::BIN_DIR_NOT_FOUND
- ::new — SequenceServer::DATABASE_DIR_NOT_FOUND
- ::new — SequenceServer::EXTENSION_FILE_NOT_FOUND
- ::new — SequenceServer::BLAST_NOT_COMPATIBLE
- ::new — SequenceServer::NO_BLAST_DATABASE_FOUND
- ::new — SequenceServer::BLAST_DATABASE_ERROR
- ::new — SequenceServer::Logger
- ::new — SequenceServer::Logger::Formatter
- ::new — SequenceServer::Sequence::Retriever
- ::new — SequenceServer::Server
- ::on_start — SequenceServer
- ::on_stop — SequenceServer
- ::open_in_browser — SequenceServer
- ::parse_version — SequenceServer
- ::pre_process — SequenceServer::BLAST
- ::probably_fasta? — SequenceServer::Database
- ::root — SequenceServer
- ::run — SequenceServer::Server
- ::run — SequenceServer
- ::run — SequenceServer::BLAST
- ::sample_sequences — SequenceServer::Database
- ::scan_databases_dir — SequenceServer::Database
- ::server_url — SequenceServer
- ::throw_scan_error — SequenceServer::Database
- ::unformatted_fastas — SequenceServer::Database
- ::using_ssh? — SequenceServer
- ::validate_blast_databases — SequenceServer::BLAST
- ::validate_blast_method — SequenceServer::BLAST
- ::validate_blast_options — SequenceServer::BLAST
- ::validate_blast_params — SequenceServer::BLAST
- ::validate_blast_sequences — SequenceServer::BLAST
- ::verbose? — SequenceServer
- ::xdg? — SequenceServer
- #[] — SequenceServer::Config
- #[]= — SequenceServer::Config
- #a — SequenceServer::Routes
- #absolute? — SequenceServer::Routes
- #call — SequenceServer::Logger::Formatter
- #database_names — SequenceServer::Sequence::Retriever
- #database_titles — SequenceServer::Sequence::Retriever
- #default_config_file — SequenceServer::Config
- #defaults — SequenceServer::Config
- #error_msgs — SequenceServer::Sequence::Retriever
- #fasta_download — SequenceServer::Links
- #file — SequenceServer::BLAST::Formatter
- #file — SequenceServer::Sequence::Retriever::IO
- #file? — SequenceServer::Config
- #filename — SequenceServer::BLAST::Formatter
- #filename — SequenceServer::Sequence::Retriever::IO
- #float? — SequenceServer::Routes
- #get_archive_file — SequenceServer::BLAST::Formatter
- #in_scientific_or_twodecimal — SequenceServer::Routes
- #include? — SequenceServer::Config
- #logdev — SequenceServer::Server
- #mime — SequenceServer::Sequence::Retriever::IO
- #ncbi — SequenceServer::Links
- #normalize — SequenceServer::Config
- #nqseq — SequenceServer::BLAST::HSP::BLASTN
- #nsseq — SequenceServer::BLAST::HSP::BLASTN
- #options — SequenceServer::Server
- #parse_config_file — SequenceServer::Config
- #prettify — SequenceServer::Routes
- #prettify_float — SequenceServer::Routes
- #prettify_tuple — SequenceServer::Routes
- #qframe_unit — SequenceServer::BLAST::HSP::BLASTX
- #qframe_unit — SequenceServer::BLAST::HSP::TBLASTX
- #run — SequenceServer::BLAST::Formatter
- #run — SequenceServer::Sequence::Retriever
- #sequence_viewer — SequenceServer::Links
- #setup_signal_handlers — SequenceServer::Server
- #sframe_unit — SequenceServer::BLAST::HSP::TBLASTX
- #sframe_unit — SequenceServer::BLAST::HSP::TBLASTN
- #start — SequenceServer::Server
- #stats — SequenceServer::BLAST::HSP::BLASTX
- #stats — SequenceServer::BLAST::HSP::BLASTP
- #stats — SequenceServer::BLAST::HSP::BLASTN
- #stats — SequenceServer::BLAST::HSP::TBLASTX
- #stats — SequenceServer::BLAST::HSP::TBLASTN
- #stop — SequenceServer::Server
- #to_json — SequenceServer::Sequence::Retriever
- #to_s — SequenceServer::BLAST::RuntimeError
- #to_s — SequenceServer::CONFIG_FILE_ERROR
- #to_s — SequenceServer::ENOENT
- #to_s — SequenceServer::NUM_THREADS_INCORRECT
- #to_s — SequenceServer::BLAST_NOT_INSTALLED
- #to_s — SequenceServer::BLAST_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::BLAST_DATABASE_ERROR
- #tuple? — SequenceServer::Routes
- #uniprot — SequenceServer::Links
- #validate — SequenceServer::BLAST::Formatter
- #validate — SequenceServer::Sequence::Retriever
- #write — SequenceServer::Sequence::Retriever::IO
- #write_config_file — SequenceServer::Config
- #write_error_msgs — SequenceServer::Sequence::Retriever::IO
- #write_sequences — SequenceServer::Sequence::Retriever::IO