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Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree Member List
This is the complete list of members for Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree, including all inherited members.
_slurp()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
analysis()Bio::EnsEMBL::Hive::Process
analyze_genepairlink()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
ancient_residual_test()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
catch()Bio::EnsEMBL::Utils::Exception
check_homology_consistency()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
check_if_exit_cleanly()Bio::EnsEMBL::Hive::Process
compara_dba()Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable
data_dbc()Bio::EnsEMBL::Hive::Process
dataflow_output_id()Bio::EnsEMBL::Hive::Process
db()Bio::EnsEMBL::Hive::Process
dbc()Bio::EnsEMBL::Hive::Process
debug()Bio::EnsEMBL::Hive::Process
delete_old_homologies()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
delete_old_homologies_old()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
delete_old_orthotree_tags()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
deprecate()Bio::EnsEMBL::Utils::Exception
DESTROY()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
direct_ortholog_test()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
display_link_analysis()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
duplication_confidence_score()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
fetch_input()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
genepairlink_check_dups()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
genepairlink_fetch_homology()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
generate_attribute_arguments()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
get_ancestor_species_hash()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
get_ancestor_taxon_level()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
get_matrix_hash()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
get_species_tree_string()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
go_figure_compara_dba()Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable
go_figure_dbc()Bio::EnsEMBL::Hive::Process
info()Bio::EnsEMBL::Utils::Exception
input_id()Bio::EnsEMBL::Hive::Process
input_job()Bio::EnsEMBL::Hive::Process
inspecies_paralog_test()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
load_species_tree_from_string()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
new()Bio::EnsEMBL::Hive::Process
one2many_ortholog_test()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
output()Bio::EnsEMBL::Hive::Process
outspecies_test()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
param()Bio::EnsEMBL::Hive::Process
param_defaults()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
param_substitute()Bio::EnsEMBL::Hive::Process
parameters()Bio::EnsEMBL::Hive::Process
queen()Bio::EnsEMBL::Hive::Process
run()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
run_analysis()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
runnable()Bio::EnsEMBL::Hive::Process
stack_trace()Bio::EnsEMBL::Utils::Exception
stack_trace_dump()Bio::EnsEMBL::Utils::Exception
store_gene_link_as_homology()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
store_homologies()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree
strict_hash_format()Bio::EnsEMBL::Hive::Process
throw()Bio::EnsEMBL::Utils::Exception
try()Bio::EnsEMBL::Utils::Exception
verbose()Bio::EnsEMBL::Utils::Exception
warning()Bio::EnsEMBL::Hive::Process
worker()Bio::EnsEMBL::Hive::Process
worker_temp_directory()Bio::EnsEMBL::Hive::Process
write_output()Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree