T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures > Member List

This is the complete list of members for T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, including all inherited members.

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_filesystem_directory_exists(const std::string &output_prefix)	Module_base	inline
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