add_options() const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
Aligner_algorithm typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
Alignment_engine typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
Alignment_type typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
Base typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
check_options(std::string &message) const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
clone(const Self_ *s) const | Module_base | inline |
delete_options(void) | T_Module_option_description< Dummy > | inlinestatic |
FT typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
get_aligner_algorithm(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_aligner_algorithm(void) const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_alignment(void) const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_alignment_engine(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_alignment_engine(void) const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_alignment_viewer_name(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinestatic |
get_first_structure(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_module_instance_name(void) const | Module_base | inline |
get_name(void) const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
get_options(void) | T_Module_option_description< Dummy > | inlinestatic |
get_output_prefix(void) const | T_Module_option_description< Dummy > | inlinevirtual |
get_percentage_length_type(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinestatic |
get_report_mode(void) const | Module_base | inline |
get_second_structure(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
get_substition_matrix_type(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinestatic |
has_options(void) | T_Module_option_description< Dummy > | inlinestatic |
initialize_engine(void) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inline |
initialize_options(const std::string &caption) | T_Module_option_description< Dummy > | inlinestatic |
is_condition_module(void) const | Module_base | inlineprotectedvirtual |
is_logical_module(void) const | Module_base | inlineprotectedvirtual |
is_modules_collection(void) const | Module_base | inlineprotectedvirtual |
is_runnable(void) const | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
Module_base(void) | Module_base | inline |
Molecular_distance typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
operator()(void) | Module_base | inlineprotectedvirtual |
report(const std::string &prefix) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
run(unsigned verbose, std::ostream &out) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
Self typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
Sequence_length_type typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
set_module_instance_name(const std::string &module_instance_name) | Module_base | inline |
set_report_mode(std::ios_base::openmode report_mode) | Module_base | inline |
set_report_mode(std::ios_base::openmode &report_mode) | Module_base | inline |
statistics(std::ostream &out) | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | inlinevirtual |
Structure typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
Structure_unit typedef | T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > | |
~Module_base(void) | Module_base | inlinevirtual |