Method List
Search:
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#== SequenceServer::Database
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[] SequenceServer::Database
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#[] SequenceServer::Config
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#[]= SequenceServer::Config
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#accession SequenceServer::BLAST::Hit
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#accession SequenceServer::Sequence
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#advanced SequenceServer::BLAST::Job
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#advanced_params SequenceServer::BLAST::Job
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#alias? SequenceServer::Database
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all SequenceServer::Database
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all SequenceServer::Job
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#all_seqids SequenceServer::Doctor
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all_sequence_ids SequenceServer::Doctor
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#any_formatted? SequenceServer::MAKEBLASTDB
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#any_to_format? SequenceServer::MAKEBLASTDB
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#any_to_format_or_reformat? SequenceServer::MAKEBLASTDB
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#app SequenceServer::Server
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#as_archived_file SequenceServer::BLAST::Job
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#bit_score SequenceServer::BLAST::HSP
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bullet_list SequenceServer::Doctor
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call SequenceServer
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#call SequenceServer::Logger::Formatter
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#categories SequenceServer::Database
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#check_id_format SequenceServer::Doctor
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#check_numeric_ids SequenceServer::Doctor
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#check_parse_seqids SequenceServer::Doctor
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clear SequenceServer::Database
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#cmd SequenceServer::BLAST_DATABASE_ERROR
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collection SequenceServer::Database
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collection= SequenceServer::Database
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#command SequenceServer::Job
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#command SequenceServer::BLAST::Job
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#completed_at SequenceServer::Job
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composition SequenceServer::Sequence
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config SequenceServer
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#config_file SequenceServer::Config
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#coordinates SequenceServer::BLAST::Hit
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create SequenceServer::Job
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#data SequenceServer::Config
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#database_dir SequenceServer::INCOMPATIBLE_BLAST_DATABASES
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#database_dir SequenceServer::NO_BLAST_DATABASE_FOUND
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#database_dir SequenceServer::MAKEBLASTDB
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#database_ids SequenceServer::Sequence::Retriever
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#databases SequenceServer::BLAST::Job
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#databases_ncharacters_total SequenceServer::BLAST::Job
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#dbtype SequenceServer::BLAST::Hit
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#dbtype SequenceServer::BLAST::Report
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#deep_copy Hash
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#deep_merge Hash
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#def SequenceServer::BLAST::Query
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delete SequenceServer::Job
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#des SequenceServer::ENOENT
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development? SequenceServer
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#diagnose SequenceServer::Doctor
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#dir SequenceServer::Job
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#done? SequenceServer::Job
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#done? SequenceServer::BLAST::Report
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each SequenceServer::Database
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enqueue SequenceServer::Job
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#ent SequenceServer::CONFIG_FILE_ERROR
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#ent SequenceServer::ENOENT
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environment SequenceServer
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#err SequenceServer::CONFIG_FILE_ERROR
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#evalue SequenceServer::BLAST::HSP
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#exitstatus SequenceServer::Job
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#exitstatus SequenceServer::BLAST::Error
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#exitstatus SequenceServer::CommandFailed
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#fasta SequenceServer::Sequence
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fetch SequenceServer::Job
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#file SequenceServer::Sequence::Retriever::IO
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#filename SequenceServer::Sequence::Retriever::IO
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#filename SequenceServer::BLAST::Formatter
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#filepath SequenceServer::BLAST::Formatter
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first SequenceServer::Database
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#format SequenceServer::MAKEBLASTDB
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#format SequenceServer::BLAST::Formatter
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#format SequenceServer::Database
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#formatted_fastas SequenceServer::MAKEBLASTDB
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#gaps SequenceServer::BLAST::HSP
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generate SequenceServer::Report
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#gi SequenceServer::Sequence
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group_by SequenceServer::Database
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guess_type SequenceServer::Sequence
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#hit SequenceServer::BLAST::HSP
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#hits SequenceServer::BLAST::Query
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#hsps SequenceServer::BLAST::Hit
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#http_status SequenceServer::InputError
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#http_status SequenceServer::SystemError
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#http_status SequenceServer::NotFound
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#id SequenceServer::BLAST::Hit
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#id SequenceServer::Sequence
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#id SequenceServer::Job
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#id SequenceServer::Database
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#id SequenceServer::BLAST::Query
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#identity SequenceServer::BLAST::HSP
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ids SequenceServer::Database
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#imported_xml_file SequenceServer::BLAST::Job
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#in_file SequenceServer::Sequence::Retriever
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#include? SequenceServer::Config
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#include? SequenceServer::Database
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include? SequenceServer::Database
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#info SequenceServer::Sequence
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init SequenceServer
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#initialize SequenceServer::BLAST::Error
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#initialize SequenceServer::Sequence
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#initialize SequenceServer::BLAST::Report
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#initialize SequenceServer::BLAST_NOT_COMPATIBLE
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#initialize SequenceServer::InputError
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#initialize SequenceServer::Database
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#initialize SequenceServer::BLAST::Query
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#initialize SequenceServer::CONFIG_FILE_ERROR
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#initialize SequenceServer::INCOMPATIBLE_BLAST_DATABASES
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#initialize SequenceServer::MAKEBLASTDB
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#initialize SequenceServer::BLAST::HSP
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#initialize SequenceServer::Report
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#initialize SequenceServer::Logger
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#initialize SequenceServer::Logger::Formatter
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#initialize SequenceServer::NO_BLAST_DATABASE_FOUND
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#initialize SequenceServer::Doctor
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#initialize SequenceServer::Server
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#initialize SequenceServer::Config
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#initialize SequenceServer::ENOENT
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#initialize SequenceServer::BLAST::Job
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#initialize SequenceServer::JobRemover
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#initialize Pool
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#initialize SequenceServer::BLAST_DATABASE_ERROR
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#initialize SequenceServer::Job
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#initialize SequenceServer::SystemError
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#initialize SequenceServer::Sequence::Retriever
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#initialize SequenceServer::BLAST::Hit
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#initialize SequenceServer::BLAST::Formatter
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#initialize SequenceServer::DatabaseUnreachableError
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#initialize ZipFileGenerator
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#initialize SequenceServer::CommandFailed
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inspect_parse_seqids SequenceServer::Doctor
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inspect_seqids SequenceServer::Doctor
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#invalids SequenceServer::Doctor
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irb SequenceServer
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#job SequenceServer::Report
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#length SequenceServer::BLAST::HSP
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#length SequenceServer::Sequence
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#length SequenceServer::BLAST::Query
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#length SequenceServer::BLAST::Hit
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#links SequenceServer::BLAST::Hit
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logger SequenceServer
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makeblastdb SequenceServer
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#message SequenceServer::DatabaseUnreachableError
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#message SequenceServer::SystemError
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#message SequenceServer::InputError
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#message SequenceServer::NotFound
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#method SequenceServer::BLAST::Job
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#midline SequenceServer::BLAST::HSP
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#mime SequenceServer::BLAST::Formatter
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#mime SequenceServer::Sequence::Retriever::IO
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#more_info SequenceServer::DatabaseUnreachableError
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#more_info SequenceServer::SystemError
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#more_info SequenceServer::NotFound
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#more_info SequenceServer::InputError
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#name SequenceServer::Database
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#ncbi SequenceServer::Links
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#ncharacters SequenceServer::Database
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#no_fastas? SequenceServer::MAKEBLASTDB
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#non_parse_seqids? SequenceServer::Database
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#nsequences SequenceServer::Database
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#num_threads SequenceServer::BLAST::Job
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#number SequenceServer::BLAST::Query
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#number SequenceServer::BLAST::Hit
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#number SequenceServer::BLAST::HSP
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#number_of_query_sequences SequenceServer::BLAST::Job
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on_start SequenceServer
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on_stop SequenceServer
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#options SequenceServer::Server
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#options SequenceServer::BLAST::Job
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#out SequenceServer::BLAST_DATABASE_ERROR
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#params SequenceServer::BLAST::Report
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#pfam SequenceServer::Links
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#positives SequenceServer::BLAST::HSP
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#program SequenceServer::BLAST::Report
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#program_version SequenceServer::BLAST::Report
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#qcovhsp SequenceServer::BLAST::HSP
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#qcovs SequenceServer::BLAST::Hit
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#qend SequenceServer::BLAST::HSP
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#qfile SequenceServer::BLAST::Job
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#qframe SequenceServer::BLAST::HSP
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#qseq SequenceServer::BLAST::HSP
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#qstart SequenceServer::BLAST::HSP
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#queries SequenceServer::BLAST::Report
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#query SequenceServer::BLAST::Hit
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#query_length SequenceServer::BLAST::Job
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#querydb SequenceServer::BLAST::Report
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#queue Pool
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#raise! SequenceServer::BLAST::Job
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#raise! SequenceServer::BLAST::Error
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#raise! SequenceServer::Job
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#read_file SequenceServer::BLAST::Formatter
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#reformat SequenceServer::MAKEBLASTDB
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#remove_invalid_databases SequenceServer::Doctor
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#report SequenceServer::BLAST::Query
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retrieve SequenceServer::Database
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#retrieve SequenceServer::Database
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#rfam SequenceServer::Links
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#run SequenceServer::MAKEBLASTDB
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run SequenceServer::Server
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#run SequenceServer::Job
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run SequenceServer
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#sciname SequenceServer::BLAST::Hit
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#score SequenceServer::BLAST::HSP
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#send SequenceServer::BLAST::HSP
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#seqid SequenceServer::Sequence
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#sequence_ids SequenceServer::Sequence::Retriever
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#sequences SequenceServer::Sequence::Retriever
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serializable_classes SequenceServer::Job
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#sframe SequenceServer::BLAST::HSP
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show_message SequenceServer::Doctor
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#shutdown Pool
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#size SequenceServer::BLAST::Formatter
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#specifiers SequenceServer::BLAST::Formatter
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#sseq SequenceServer::BLAST::HSP
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#sstart SequenceServer::BLAST::HSP
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#start SequenceServer::Server
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#stats SequenceServer::BLAST::Report
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#stderr SequenceServer::Job
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#stderr SequenceServer::CommandFailed
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#stderr SequenceServer::BLAST::Error
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#stdout SequenceServer::CommandFailed
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#stdout SequenceServer::Job
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#stdout SequenceServer::BLAST::Error
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#stop SequenceServer::Server
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#submitted_at SequenceServer::Job
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sys SequenceServer
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#title SequenceServer::BLAST::Hit
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#title SequenceServer::BLAST::Query
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#title SequenceServer::Sequence
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#title SequenceServer::Database
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#title SequenceServer::SystemError
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#title SequenceServer::InputError
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#title SequenceServer::DatabaseUnreachableError
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#title SequenceServer::NotFound
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#to_json SequenceServer::BLAST::HSP
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#to_json SequenceServer::BLAST::Hit
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#to_json SequenceServer::Sequence::Retriever
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to_json SequenceServer::Database
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#to_json SequenceServer::Database
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#to_json SequenceServer::BLAST::Report
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#to_json SequenceServer::BLAST::Query
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#to_s SequenceServer::Sequence
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#to_s SequenceServer::Database
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#to_s SequenceServer::INCOMPATIBLE_BLAST_DATABASES
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#to_s SequenceServer::DATABASE_DIR_NOT_SET
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#to_s SequenceServer::BLAST_NOT_COMPATIBLE
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#to_s SequenceServer::BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE
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#to_s SequenceServer::NUM_THREADS_INCORRECT
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#to_s SequenceServer::NO_BLAST_DATABASE_FOUND
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#to_s SequenceServer::BLAST_DATABASE_ERROR
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#to_s SequenceServer::CONFIG_FILE_ERROR
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#to_s SequenceServer::ENOENT
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#total_score SequenceServer::BLAST::Hit
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tree SequenceServer::Database
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#type SequenceServer::Database
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#uniprot SequenceServer::Links
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#update_searchdata_from_job SequenceServer::Routes
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#updated_on SequenceServer::Database
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#v4? SequenceServer::Database
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#v5? SequenceServer::Database
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#value SequenceServer::Sequence
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#version SequenceServer::BLAST_NOT_COMPATIBLE
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#whichdb SequenceServer::BLAST::Hit
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#write ZipFileGenerator
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#write_config_file SequenceServer::Config
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#xml_file_size SequenceServer::BLAST::Report