Method List
-
#== Color
-
GET_params2hash Misc
-
IUPAC_to_base Misc
-
#R TSV
-
#R_interactive TSV
-
#[] IndiferentHash
-
#[] FixWidthTable
-
#[] TSV
-
#[] Path
-
#[] AnnotatedArray
-
#[] Resource
-
#[] NamedArray
-
#[]= TSV
-
#[]= NamedArray
-
#a Color
-
#abort Task::Job
-
#abort Step
-
#aborted? Step
-
#aborted? Task::Job
-
#add FixWidthTable
-
add FileCache
-
#add KnowledgeBase
-
#add Filtered::Filter
-
add_cache Open
-
add_consummable_annotation AnnotatedModule
-
add_defaults Misc
-
#add_field TSV
-
#add_filter Filtered
-
#add_index KnowledgeBase
-
#add_point FixWidthTable
-
#add_range FixWidthTable
-
add_reciprocal Association
-
#add_to_data_flat TSV::Parser
-
#add_to_data_flat_merge TSV::Parser
-
#add_to_data_merge TSV::Parser
-
#add_to_data_merge_zipped TSV::Parser
-
#add_to_data_no_merge_double TSV::Parser
-
#add_to_data_no_merge_list TSV::Parser
-
#add_to_data_zipped TSV::Parser
-
#add_unsaved Filtered::Filter
-
#all KnowledgeBase
-
all SOPT
-
#all_databases KnowledgeBase
-
#all_fields TSV::Parser
-
#all_fields Path
-
#all_fields TSV
-
#all_inputs Task::Job
-
#annotate Path
-
#annotate Annotated
-
#annotate TSV
-
#annotate KnowledgeBase
-
#annotation Annotation
-
#annotation_md5 Annotated
-
#annotation_types Annotated
-
#annotation_values Annotated
-
#annotations Annotation
-
#annotations Annotated
-
#arguments Task::Job
-
array2hash Misc
-
#asynchronous WorkflowSOAP
-
#asynchronous_exports Workflow
-
#attach TSV
-
#attach_index TSV
-
#attach_same_key TSV
-
#b Color
-
#basename Path
-
benchmark Misc
-
binary_include? Misc
-
#bindings Step
-
#blend Color
-
blend Color
-
#blend! Color
-
#block Task::Job
-
#byte Path
-
cachedir FileCache
-
cachedir Persist
-
cachedir Open
-
cachedir= FileCache
-
cachedir= Open
-
calculate_headers Association
-
caller_lib_dir Path
-
can_open? Open
-
#cast TSV::Parser
-
#cast? TSV::Parser
-
#cast_values_double TSV::Parser
-
#cast_values_list TSV::Parser
-
#cast_values_single TSV::Parser
-
chain_methods_extended ChainMethods
-
#change_key TSV
-
change_key TSV
-
#child Step
-
#children KnowledgeBase
-
#chop_line TSV::Parser
-
#chunked_values_at FixWidthTable
-
#chunked_values_at Hash
-
#claim Resource
-
#clean Filtered::Filter
-
#clean Task::Job
-
#clean Step
-
#clean_and_setup_hash Annotation
-
#clean_annotations Annotated
-
clean_cache Open
-
#clean_name Step
-
#close CMD::SmartIO
-
#close FixWidthTable
-
#closest FixWidthTable
-
cmd CMD
-
#cmd CMD::SmartIO
-
collapse_ranges Misc
-
#collect NamedArray
-
#collect TSV
-
#collect AnnotatedArray
-
colors_for Misc
-
#column TSV
-
command SOPT
-
common_path Misc
-
#config SimpleDSL
-
consolidate Misc
-
#container Annotated
-
#container_index Annotated
-
continuous Colorize
-
correct_vcf_mutation Misc
-
counts Misc
-
#darken Color
-
#darken! Color
-
#data Filtered::Filter
-
#databases KnowledgeBase
-
databases Association
-
#ddd Top Level Namespace
-
debug Log
-
del FileCache
-
#delete IndiferentHash
-
#dep Workflow
-
#dependencies Step
-
#desc Workflow
-
description SOPT
-
#description Workflow
-
#description Task
-
#description KnowledgeBase
-
#detach TSV
-
#detach NamedArray
-
#detach_annotations Annotated
-
digest Misc
-
digest_url Open
-
#dir KnowledgeBase
-
#dirname Path
-
distinct Colorize
-
divide Misc
-
do_once Misc
-
#doc Task
-
#doc Workflow
-
doc SOPT
-
#doc_file Path
-
#done? Step
-
#done? Task::Job
-
#double_array AnnotatedArray
-
dump TSV::FloatArraySerializer
-
dump TSV::StringDoubleArraySerializer
-
dump TSV::StringSerializer
-
dump TSV::TSVMarshalSerializer
-
dump TSV::IntegerArraySerializer
-
#dump FixWidthTable
-
dump TSV::TSVSerializer
-
dump TSV::StringArraySerializer
-
dump TSV::IntegerSerializer
-
dump TSV::FloatSerializer
-
#each NamedArray
-
#each AnnotatedArray
-
#each TSV
-
#empty? TSV
-
ensembl_server Misc
-
#entities KnowledgeBase
-
#entity_options TSV
-
#entity_options KnowledgeBase
-
#entity_options NamedArray
-
#entity_options_for KnowledgeBase
-
entity_property_cache Entity
-
#entity_templates NamedArray
-
#entity_types KnowledgeBase
-
entry TSV
-
env_add Misc
-
#err CMD::SmartIO
-
error Log
-
#error? Task::Job
-
#error? Step
-
excel TSV
-
#excel TSV
-
excel2tsv TSV
-
#exec Task
-
#exec Step
-
#exec_exports Workflow
-
#exec_in Task
-
#exists? Path
-
exists? Open
-
exists_in_repo Open
-
#export_asynchronous Workflow
-
#export_exec Workflow
-
#export_synchronous Workflow
-
extended Annotation
-
extended TSV
-
extended Resource::WithKey
-
extended ChainMethods
-
extended Workflow
-
extended Filtered
-
extended Resource
-
extended Entity
-
fast_align Misc
-
#fast_setup Annotation
-
#fff Top Level Namespace
-
field_position Misc
-
#field_positions TSV::Parser
-
#fieldnum Filtered::Filter
-
#fields NamedArray
-
#fields TSV
-
#fields Path
-
#fields TSV::Parser
-
#fields= TSV
-
#file FixWidthTable
-
#file Step
-
file_open Open
-
file_write Open
-
#filename FixWidthTable
-
#filename Path
-
filename? Misc
-
#files Step
-
#files Task::Job
-
#files_dir Step
-
#filter TSV
-
#filtered_collect Filtered
-
#filtered_delete Filtered
-
#filtered_each Filtered
-
#filtered_filename Filtered
-
#filtered_keys Filtered
-
#filtered_set Filtered
-
#filtered_values Filtered
-
#filters Filtered::FilterArray
-
#find Path
-
#find_all Path
-
find_path TSV
-
find_repo_dir Open
-
find_traversal TSV
-
fingerprint Misc
-
#first AnnotatedArray
-
#first_line TSV::Parser
-
#fix TSV::Parser
-
#fix_fields TSV::Parser
-
fixascii Misc
-
fixutf8 Misc
-
flatten Annotated
-
#force_close CMD::SmartIO
-
#fork Step
-
#fork Task::Job
-
fork_each_on_semaphore RbbtSemaphore
-
#format FixWidthTable
-
#format KnowledgeBase
-
formats Entity
-
found FileCache
-
from_name Colorize
-
#g Color
-
get FileCache
-
get FixWidthTable
-
get SOPT
-
#get_database KnowledgeBase
-
get_filename TSV
-
get_index Association
-
#get_index KnowledgeBase
-
#get_point FixWidthTable
-
#get_range FixWidthTable
-
get_repo_from_dir Open
-
get_stream TSV
-
get_stream_from_repo Open
-
#get_values_double TSV::Parser
-
#get_values_flat TSV::Parser
-
#get_values_flat_inverse TSV::Parser
-
#get_values_list TSV::Parser
-
#get_values_single TSV::Parser
-
#get_values_single_from_flat TSV::Parser
-
#glob Path
-
google_venn Misc
-
#grayscale Color
-
#grayscale! Color
-
#grayscale? Color
-
grep Open
-
gunzip Open
-
gzip? Open
-
#has_rake Resource
-
hash2GET_params Misc
-
hash2md5 Misc
-
hash2string Misc
-
#header_hash TSV::Parser
-
#helper Workflow
-
#helpers Workflow
-
high Log
-
hostname Misc
-
html_tag Misc
-
humanize Misc
-
#id Annotated
-
#id Task::Job
-
id2name Task::Job
-
#id_for Workflow
-
#identifier_files Path
-
#identify KnowledgeBase
-
identify_field TSV
-
#identify_field TSV
-
#identify_source KnowledgeBase
-
#identify_target KnowledgeBase
-
#ids Filtered::Filter
-
#ids Filtered::FilterArray
-
#in CMD::SmartIO
-
in_cache Open
-
in_dir Misc
-
#in_dir? Path
-
incidence AssociationItem
-
#include? IndiferentHash
-
#included Annotation
-
index Association
-
index TSV
-
#index TSV
-
#index Path
-
#index KnowledgeBase
-
#index_fields KnowledgeBase
-
#indices KnowledgeBase
-
#info RBBTError
-
#info Annotated
-
info Log
-
#info Task::Job
-
#info Step
-
#info_file Task::Job
-
#info_file Step
-
#initialize FixWidthTable
-
#initialize TSV::Traverser
-
#initialize Filtered::Filter
-
#initialize TSV::Parser
-
#initialize KnowledgeBase
-
#initialize Task::Job
-
#initialize Step
-
#initialize WorkflowSOAP
-
#initialize Color
-
#input AnnotatedModule
-
#input Task::Job
-
input_defaults SOPT
-
#input_defaults Task
-
input_descriptions SOPT
-
#input_descriptions Task
-
input_doc SOPT
-
input_format SOPT
-
#input_options Task
-
input_shortcuts SOPT
-
#input_types Task
-
input_types SOPT
-
inputs SOPT
-
#inputs Step
-
#inputs Task
-
insist Misc
-
#inspect Color
-
is_filename? Misc
-
is_persisted? Persist
-
#job WorkflowSOAP
-
#job Workflow
-
#jobs Workflow
-
#join Step
-
#join Path
-
#join Task::Job
-
#key Filtered::Filter
-
#key NamedArray
-
#key_field TSV::Parser
-
#key_position TSV::Parser
-
#keys Path
-
#keys TSV
-
knowledge_base_dir KnowledgeBase
-
#last AnnotatedArray
-
#last_pos FixWidthTable
-
#last_task Workflow
-
#length TSV
-
#libdir Workflow
-
#lighten Color
-
#lighten! Color
-
#list Filtered::Filter
-
#list Path
-
#list_id AnnotatedArray
-
load TSV::StringSerializer
-
load TSV::TSVMarshalSerializer
-
load TSV::StringArraySerializer
-
load TSV::FloatSerializer
-
#load Step
-
load Task::Job
-
load TSV::TSVSerializer
-
#load Task::Job
-
load TSV::IntegerArraySerializer
-
load TSV::IntegerSerializer
-
load TSV::FloatArraySerializer
-
load TSV::StringDoubleArraySerializer
-
#load_config SimpleDSL
-
#load_dependencies Task::Job
-
load_entity Annotated
-
load_file Persist
-
#load_file Step
-
#load_id Workflow
-
load_info Annotated
-
#load_step Workflow
-
load_tsv Annotated
-
load_tsv Association
-
load_tsv_values Annotated
-
load_workflow_file Workflow
-
#local_persist LocalPersist
-
#local_persist_dir LocalPersist
-
#local_persist_setup Workflow
-
#local_persist_tsv LocalPersist
-
#local_workdir_setup Workflow
-
#located? Path
-
lock Open
-
lock Misc
-
lock_dir TSV
-
lock_in_repo Misc
-
#log Workflow
-
log Log
-
#log CMD::SmartIO
-
#log Step
-
log2 Misc
-
log_relay_step Step
-
logfile Log
-
low Log
-
#make_list Annotated
-
#make_local Workflow
-
#masked_annotations Annotation
-
#masked_annotations Annotated
-
#match Filtered::Filter
-
#match Association::Index
-
#matches Association::Index
-
max Misc
-
mean Misc
-
medium Log
-
memprof Misc
-
#merge NamedArray
-
merge_paste TSV
-
merge_row_fields TSV
-
merge_sorted_arrays Misc
-
#message Step
-
#messages Task::Job
-
#messages Step
-
#method_missing Path
-
#method_missing Filtered::FilterArray
-
#method_missing Resource::WithKey
-
#method_missing Resource
-
#monitor TSV
-
#name Step
-
name SOPT
-
#name Task
-
#name Task::Job
-
#namespace TSV::Parser
-
#namespace KnowledgeBase
-
#namespace= TSV
-
#neighbours KnowledgeBase
-
#new_field_names TSV::Traverser
-
#new_fields TSV::Traverser
-
#new_key_field TSV::Traverser
-
#new_key_field_name TSV::Traverser
-
newer? Persist
-
#old_method_missing Resource::WithKey
-
#old_to_s RBBTError
-
#opaque? Color
-
#open Path
-
open Association
-
open Open
-
open TSV
-
#open Task::Job
-
#open_options KnowledgeBase
-
open_tokyocabinet Persist
-
open_tsv Association
-
#options Task::Job
-
#options TSV
-
ordered_divide Misc
-
#out CMD::SmartIO
-
#overlap FixWidthTable
-
#page TSV
-
#param_options Task
-
#parents KnowledgeBase
-
parse Color
-
parse SOPT
-
#parse SimpleDSL
-
parse TSV
-
#parse_description Task
-
parse_field_specification Association
-
#parse_header TSV::Parser
-
parse_header TSV
-
#parse_key_field Association::Index
-
#path Task::Job
-
path FileCache
-
#path Step
-
path_relative_to Misc
-
pdftotext PDF2Text
-
persist Persist
-
#persist_exec Task
-
#persist_exec_in Task
-
persist_tsv Persist
-
#persistence Filtered::Filter
-
persistence_path Persist
-
#pid Task::Job
-
#pid Step
-
#pid CMD::SmartIO
-
pid_exists? Misc
-
#pipe_to Path
-
#pkgdir Path
-
#pop_filter Filtered
-
#pos FixWidthTable
-
#pos_end FixWidthTable
-
#pos_index Path
-
#pos_index TSV
-
pos_index TSV
-
positional2hash Misc
-
#positions NamedArray
-
#post CMD::SmartIO
-
#ppp Top Level Namespace
-
#prepare_entity TSV
-
#prepare_entity NamedArray
-
prepare_entity Misc
-
#prepare_result Step
-
#previous_jobs Task::Job
-
#previous_jobs_rec Task::Job
-
#process TSV::Parser
-
#process TSV
-
#process_key TSV
-
#process_null TSV::Traverser
-
process_options Misc
-
#process_reorder_double TSV::Traverser
-
#process_reorder_double_uniq TSV::Traverser
-
#process_reorder_flat TSV::Traverser
-
#process_reorder_list TSV::Traverser
-
#process_subset_all_but_double TSV::Traverser
-
#process_subset_all_but_list TSV::Traverser
-
#process_subset_double TSV::Traverser
-
#process_subset_list TSV::Traverser
-
process_to_hash Misc
-
#produce Path
-
#produce Resource
-
profile Misc
-
profile_graph Misc
-
profile_html Misc
-
proportions Misc
-
pull_keys Misc
-
purge Annotated
-
#r Color
-
#rake_for Resource
-
random_name TmpFile
-
#range FixWidthTable
-
#range_index Path
-
#range_index TSV
-
range_index TSV
-
#read Path
-
#read FixWidthTable
-
read Open
-
#read CMD::SmartIO
-
#read Task::Job
-
#real_dependencies Workflow
-
#rec_dependencies Workflow
-
#rec_dependencies Step
-
#rec_input_defaults Workflow
-
#rec_input_descriptions Workflow
-
#rec_input_options Workflow
-
#rec_input_types Workflow
-
#rec_inputs Workflow
-
record SOPT
-
#record_size FixWidthTable
-
#recursive_clean Step
-
#recursive_clean Task::Job
-
#recursive_done? Task::Job
-
#register KnowledgeBase
-
#registry KnowledgeBase
-
registry KnowledgeBase
-
#reject AnnotatedArray
-
#relay_log Step
-
remote? Open
-
#remove AnnotatedArray
-
remove_from_cache Open
-
remove_from_repo Open
-
remove_long_items Misc
-
#reorder TSV
-
#report NamedArray
-
repository_dirs Open
-
require_local_workflow Workflow
-
require_remote_workflow Workflow
-
require_workflow Workflow
-
#required_files Task::Job
-
#rescue_first_line TSV::Parser
-
#reset Annotated
-
#reset Filtered::Filter
-
reset SOPT
-
reset_do_once Misc
-
#reset_filters TSV
-
resolve_array Annotated
-
resolve_field Association
-
resolve_locals Workflow
-
#resource Path
-
#result_description Task
-
#result_type Task
-
#returns Workflow
-
#reverse Association::Index
-
#rgb Top Level Namespace
-
rm Open
-
rm_rf Open
-
#root Resource
-
ruby2R R
-
run Rake
-
run R
-
#run Step
-
#run Task::Job
-
#run_dependencies Task::Job
-
#run_rake Resource
-
#running? Step
-
sample Misc
-
sanitize_filename Misc
-
#save Filtered::Filter
-
save_content_in_repo Open
-
#save_dependencies Task::Job
-
#save_file Step
-
save_file Persist
-
#save_options Task::Job
-
#saved Filtered::Filter
-
sd Misc
-
#select TSV::Parser
-
#select AnnotatedArray
-
#select TSV
-
#select_by AnnotatedArray
-
#select_entities Association::Index
-
#self_md5 Annotated
-
send_email Misc
-
sensiblewrite Misc
-
#sep TSV::Parser
-
#sep2 TSV::Parser
-
#serializer TSV::Parser
-
#set Color
-
#set_extension Path
-
#set_info Step
-
#set_info Task::Job
-
#set_software_env Resource
-
setup Association::Index
-
setup Path
-
#setup Annotation
-
#setup TSV::Parser
-
setup IndiferentHash
-
setup TSV
-
#setup KnowledgeBase
-
setup NamedArray
-
setup Task
-
#setup_array TSV
-
#setup_hash Annotation
-
#setup_positional Annotation
-
severity Log
-
short_for SOPT
-
shortcuts SOPT
-
#size TSV
-
#size FixWidthTable
-
#slice TSV
-
snake_case Misc
-
#sort AnnotatedArray
-
#sort TSV
-
#sort_by TSV
-
sorted_array_hits Misc
-
#source KnowledgeBase
-
#source_field Association::Index
-
#source_for_doc_file Path
-
#source_type KnowledgeBase
-
specs Association
-
#start Task::Job
-
#started? Step
-
#status Step
-
#status= Step
-
#step Step
-
#step Task::Job
-
#step_path Workflow
-
#straight TSV::Parser
-
string2const Misc
-
string2hash Misc
-
string2hash_old Misc
-
#subset Association::Index
-
#subset AnnotatedArray
-
#subset KnowledgeBase
-
#subset_entities Association::Index
-
sum Misc
-
#summary TSV
-
summary SOPT
-
swap_id TSV
-
#swap_id TSV
-
#synchronous WorkflowSOAP
-
#synchronous_exports Workflow
-
synopsys SOPT
-
#take_all TSV::Parser
-
#take_input_values Task
-
#target KnowledgeBase
-
#target_field Association::Index
-
#target_type KnowledgeBase
-
#task Task::Job
-
#task Workflow
-
#task Step
-
#task_dependencies Workflow
-
#task_description Workflow
-
#task_for Workflow
-
#task_info Workflow
-
#task_name Step
-
#tasks Workflow
-
#through TSV
-
tie CMD::SmartIO
-
tmp_file TmpFile
-
tmpdir TmpFile
-
tmpdir= TmpFile
-
#to_double TSV
-
#to_flat TSV
-
#to_hash TSV
-
#to_rgb Color
-
#to_rgba Color
-
#to_s Path
-
#to_s TSV
-
#to_s Color
-
#to_s RBBTError
-
#to_s LaterString
-
to_utf8 Misc
-
#to_yaml Path
-
total_length Misc
-
#trans? Color
-
#translate KnowledgeBase
-
translate_tsv Association
-
#transpose TSV
-
try3times Misc
-
tsv Colorize
-
#tsv Path
-
tsv Annotated
-
#tsv_sort TSV
-
#tsv_values Annotated
-
#type TSV::Parser
-
#type TSV::Traverser
-
#undirected KnowledgeBase
-
#undirected Association::Index
-
#unformat FixWidthTable
-
#uniq TSV::Traverser
-
#unmasked_annotations Annotation
-
#unmasked_annotations Annotated
-
#unnamed TSV
-
#unsaved Filtered::Filter
-
unzip Open
-
#update Filtered::Filter
-
#value FixWidthTable
-
#value Filtered::Filter
-
#value_peek TSV
-
#value_size FixWidthTable
-
#values TSV
-
#values_at NamedArray
-
#values_at FixWidthTable
-
#values_at TSV
-
#values_at IndiferentHash
-
#values_to_s TSV
-
#version KnowledgeBase
-
wait Open
-
#wait_and_status CMD::SmartIO
-
warn Log
-
wget Open
-
with_dir TmpFile
-
with_file TmpFile
-
#with_key Resource
-
#with_monitor TSV
-
with_semaphore RbbtSemaphore
-
#with_unnamed TSV
-
#workdir Workflow
-
#workflow WorkflowSOAP
-
#workflow_description Workflow
-
workflows Workflow
-
#write KnowledgeBase
-
#write Path
-
write Open
-
#yaml Path
-
zip2hash Misc
-
zip? Open
-
#zip_fields NamedArray
-
zip_fields TSV
-
zip_fields Misc
-
#zipped TSV::Parser