options_description get_section_options(const string section_name, const string group_caption, const options_description &original_options_descriptions)
{
const std::vector< shared_ptr<option_description> >&original_options = original_options_descriptions.options();
options_description new_options(group_caption.c_str());
std::vector< shared_ptr<option_description> >::const_iterator options_it;
for(options_it = original_options.begin(); options_it != original_options.end(); ++options_it)
{
const option_description &t_option = *(*options_it);
string new_name(section_name + ".");
new_name += t_option.long_name();
// IMPORTANT: in order for this line not to crash the original_options_descriptions needs to be a static declaration
// otherwise t_option.semantic().get() will point to an invalid memory direction and
// the application will raise a segmentation fault
new_options.add_options()
(new_name.c_str(), t_option.semantic().get(), t_option.description().c_str());
}
return new_options;
}
basic_parsed_options<charT>
parse_config_file(std::basic_istream<charT>& is,
const options_description& desc,
bool allow_unregistered)
{
set<string> allowed_options;
const vector<shared_ptr<option_description> >& options = desc.options();
for (unsigned i = 0; i < options.size(); ++i)
{
const option_description& d = *options[i];
if (d.long_name().empty())
pdalboost::throw_exception(
error("long name required for config file"));
allowed_options.insert(d.long_name());
}
// Parser return char strings
parsed_options result(&desc);
copy(detail::basic_config_file_iterator<charT>(
is, allowed_options, allow_unregistered),
detail::basic_config_file_iterator<charT>(),
back_inserter(result.options));
// Convert char strings into desired type.
return basic_parsed_options<charT>(result);
}
/// \brief Add the block's non-hidden options to the provided options_description
///
/// This is a concrete definition of a virtual method that's pure in options_block
void old_ssap_options_block::do_add_visible_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
const string dir_varname { "<dir>" };
const string file_varname { "<file>" };
const string score_varname{ "<score>" };
const string set_varname { "<set>" };
const string protein_file_combns_str = join( get_all_protein_file_combn_strings(), ", " );
arg_desc.add_options()
( PO_DEBUG.c_str(), bool_switch ( &debug ) ->default_value(DEF_BOOL ), "Output debugging information" )
((PO_OUT_FILE+",o").c_str(), value<path> ( &output_filename )->value_name(file_varname ), ( "[DEPRECATED] Output scores to " + file_varname + " rather than to stdout" ).c_str() )
( PO_CLIQUE_FILE.c_str(), value<path> ( &clique_file )->value_name(file_varname ), ( "Read clique from " + file_varname ).c_str() )
( PO_DOMIN_FILE.c_str(), value<path> ( &domin_file )->value_name(file_varname ), ( "Read domin from " + file_varname ).c_str() )
( PO_MAX_SCORE_TO_REFAST.c_str(), value<double> ( &max_score_to_fast_ssap_rerun )->value_name(score_varname)->default_value(DEF_REFAST ), ( "Run a second fast SSAP with looser cutoffs if the first fast SSAP's score falls below " + score_varname ).c_str() )
( PO_MAX_SCORE_TO_RESLOW.c_str(), value<double> ( &max_score_to_slow_ssap_rerun )->value_name(score_varname)->default_value(DEF_RESLOW ), ( "Perform a slow SSAP if the (best) fast SSAP score falls below " + score_varname ).c_str() )
( PO_SLOW_SSAP_ONLY.c_str(), bool_switch ( &slow_ssap_only ) ->default_value(DEF_BOOL ), "Don't try any fast SSAPs; only use slow SSAP" )
( PO_LOC_SSAP_SCORE.c_str(), bool_switch ( &use_local_ssap_score ) ->default_value(DEF_BOOL ), "[DEPRECATED] Normalise the SSAP score over the length of the smallest domain rather than the largest" )
( PO_ALL_SCORES.c_str(), bool_switch ( &write_all_scores ) ->default_value(DEF_BOOL ), "[DEPRECATED] Output all SSAP scores from fast and slow runs, not just the highest" )
( PO_PROTEIN_SOURCE_FILES.c_str(), value<protein_file_combn>( &protein_source_files )->value_name( set_varname )->default_value(DEF_PROT_SRCS ), ( "Read the protein data from the set of files "+set_varname+", of available sets:\n" + protein_file_combns_str ).c_str() )
( PO_SUPN_DIR.c_str(), value<path> ( &superposition_dir )->value_name( dir_varname ), ( "[DEPRECATED] Output a superposition to directory " + dir_varname ).c_str() )
( PO_ALIGN_DIR.c_str(), value<path> ( &alignment_dir )->value_name( dir_varname )->default_value( path(".") ), ( "Write alignment to directory " + dir_varname ).c_str() )
( PO_MIN_OUT_SCORE.c_str(), value<double> ( &min_score_for_writing_files )->value_name(score_varname)->default_value(DEF_FILE_SC ), ( "Only output alignment/superposition files if the SSAP score exceeds " + score_varname ).c_str() )
( PO_MIN_SUP_SCORE.c_str(), value<double> ( &min_score_for_superposition )->value_name(score_varname)->default_value(DEF_SUP ), ( "[DEPRECATED] Calculate superposition based on the residue-pairs with scores greater than " + score_varname ).c_str() )
( PO_RASMOL_SCRIPT.c_str(), bool_switch ( &write_rasmol_script ) ->default_value(DEF_BOOL ), "[DEPRECATED] Write a rasmol superposition script to load and colour the superposed structures" )
( PO_XML_SUP.c_str(), bool_switch ( &write_xml_sup ) ->default_value(DEF_BOOL ), "[DEPRECATED] Write a small xml superposition file, from which a larger superposition file can be reconstructed" );
}
void http_client_plugin::set_program_options(options_description&, options_description& cfg) {
cfg.add_options()
("https-client-root-cert", boost::program_options::value<vector<string>>()->composing()->multitoken(),
"PEM encoded trusted root certificate (or path to file containing one) used to validate any TLS connections made. (may specify multiple times)\n")
("https-client-validate-peers", boost::program_options::value<bool>()->default_value(true),
"true: validate that the peer certificates are valid and trusted, false: ignore cert errors")
;
}
/// \brief Add this block's options to the provided options_description
void superposition_output_options_block::do_add_visible_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
arg_desc.add_options()
(PO_SUP_FILE.c_str(), value<path>(&sup_to_pdb_file), "Write the superposed structures to a single PDB file arg, separated using faked chain codes" )
(PO_SUP_FILES_DIR.c_str(), value<path>(&sup_to_pdb_files_dir), "Write the superposed structures to separate PDB files in directory arg" )
(PO_SUP_TO_STDOUT.c_str(), bool_switch(&sup_to_stdout)->default_value(false), "Print the superposed structures to stdout, separated using faked chain codes" )
(PO_SUP_TO_PYMOL.c_str(), bool_switch(&sup_to_pymol )->default_value(false), "Start up PyMOL for viewing the superposition" )
(PO_PYMOL_PROGRAM.c_str(), value<path>(&pymol_program)->default_value(DEFAULT_PYMOL_PROGRAM), "Use arg as the PyMOL executable for viewing; may optionally include the full path" )
(PO_SUP_TO_PYMOL_FILE.c_str(), value<path>(&sup_to_pymol_file), "Write the superposition to a PyMOL script arg\n(Recommended filename extension: .pml)" )
(PO_SUP_TO_JSON_FILE.c_str(), value<path>(&json_file), "Write the superposition to JSON superposition file\n(Recommended filename extension: .sup_json)" );
}
basic_parsed_options<charT>
parse_config_file(std::basic_istream<charT>& is,
const options_description& desc)
{
set<string> allowed_options;
set<string> pm = desc.primary_keys();
for (set<string>::iterator i = pm.begin(); i != pm.end(); ++i) {
const option_description& d = desc.find(*i);
if (d.long_name().empty())
throw error("long name required for config file");
allowed_options.insert(d.long_name());
}
// Parser return char strings
parsed_options result(&desc);
copy(detail::basic_config_file_iterator<charT>(is, allowed_options),
detail::basic_config_file_iterator<charT>(),
back_inserter(result.options));
// Convert char strings into desired type.
return basic_parsed_options<charT>(result);
}
/// \brief Add this block's options to the provided options_description
void alignment_input_options_block::do_add_visible_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
const string file_varname { "<file>" };
const auto residue_name_align_notifier = [&] (const bool &x) { the_alignment_input_spec.set_residue_name_align ( x ); };
const auto fasta_alignment_file_notifier = [&] (const path &x) { the_alignment_input_spec.set_fasta_alignment_file( x ); };
const auto ssap_alignment_file_notifier = [&] (const path &x) { the_alignment_input_spec.set_ssap_alignment_file ( x ); };
const auto cora_alignment_file_notifier = [&] (const path &x) { the_alignment_input_spec.set_cora_alignment_file ( x ); };
const auto ssap_scores_file_notifier = [&] (const path &x) { the_alignment_input_spec.set_ssap_scores_file ( x ); };
arg_desc.add_options()
(
PO_RES_NAME_ALIGN.c_str(),
bool_switch()
->notifier ( residue_name_align_notifier )
->default_value( alignment_input_spec::DEFAULT_RESIDUE_NAME_ALIGN ),
"Align residues by simply matching their names (numbers+insert)\n(for multiple models of the same structure)"
)
(
PO_FASTA_ALIGN_INFILE.c_str(),
value<path>()
->value_name( file_varname )
->notifier ( fasta_alignment_file_notifier ),
( "Read FASTA alignment from file " + file_varname ).c_str()
)
(
PO_SSAP_ALIGN_INFILE.c_str(),
value<path>()
->value_name( file_varname )
->notifier ( ssap_alignment_file_notifier ),
( "Read SSAP alignment from file " + file_varname ).c_str()
)
(
PO_CORA_ALIGN_INFILE.c_str(),
value<path>()
->value_name( file_varname )
->notifier ( cora_alignment_file_notifier ),
( "Read CORA alignment from file " + file_varname ).c_str()
)
(
PO_SSAP_SCORE_INFILE.c_str(),
value<path>()
->value_name( file_varname )
->notifier ( ssap_scores_file_notifier ),
( "Read SSAP scores from file " + file_varname + "\nAssumes all .list alignment files in same directory" ).c_str()
);
static_assert( ! alignment_input_spec::DEFAULT_RESIDUE_NAME_ALIGN,
"If alignment_input_spec::DEFAULT_RESIDUE_NAME_ALIGN isn't false, it might mess up the bool switch in here" );
}
/// \brief Add this block's options to the provided options_description
void display_options_block::do_add_visible_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
const string colrs_varname{ "<colrs>" };
const auto display_colours_string_notifier = [&] (const string &x) { the_display_spec.set_display_colours_string ( x ); };
const auto gradient_colour_alignment_notifier = [&] (const bool &x) { the_display_spec.set_gradient_colour_alignment( x ); };
const auto show_scores_if_present_notifier = [&] (const bool &x) { the_display_spec.set_show_scores_if_present ( x ); };
const auto scores_to_equivs_notifier = [&] (const bool &x) { the_display_spec.set_scores_to_equivs ( x ); };
const auto normalise_scores_notifier = [&] (const bool &x) { the_display_spec.set_normalise_scores ( x ); };
arg_desc.add_options()
(
PO_VIEWER_COLOURS.c_str(),
value<string>()
->value_name( colrs_varname )
->notifier ( display_colours_string_notifier ),
( "Use " + colrs_varname + " to colour successive entries in the viewer\n"
"(format: colon-separated list of comma-separated triples of RGB values between 0 and 1)\n"
"(will wrap-around when it runs out of colours)" ).c_str()
)
(
PO_GRADIENT_COLOUR_ALIGNMENT.c_str(),
bool_switch()
->notifier ( gradient_colour_alignment_notifier )
->default_value( false ),
"Colour the length of the alignment with a rainbow gradient (blue -> red)"
)
(
PO_SHOW_SCORES_IF_PRESENT.c_str(),
bool_switch()
->notifier ( show_scores_if_present_notifier )
->default_value( false ),
( "Show the alignment scores\n(use with " + PO_GRADIENT_COLOUR_ALIGNMENT + ")" ).c_str()
)
(
PO_SCORES_TO_EQUIVS.c_str(),
bool_switch()
->notifier ( scores_to_equivs_notifier )
->default_value( false ),
( "Show the alignment scores to equivalent positions, which increases relative scores where few entries are aligned\n"
"(use with --" + PO_GRADIENT_COLOUR_ALIGNMENT + " and --" + PO_SHOW_SCORES_IF_PRESENT + ")" ).c_str()
)
(
PO_NORMALISE_SCORES.c_str(),
bool_switch()
->notifier ( normalise_scores_notifier )
->default_value( false ),
( "When showing scores, normalise them to the highest score in the alignment\n"
"(use with --" + PO_GRADIENT_COLOUR_ALIGNMENT + " and --" + PO_SHOW_SCORES_IF_PRESENT + ")" ).c_str()
);
}
basic_parsed_options<charT>
parse_xml(const options_description& desc) {
using boost::shared_ptr;
set<string> allowed_options;
const vector<shared_ptr<option_description> >& options = desc.options();
for (unsigned i = 0; i < options.size(); ++i) {
const option_description& d = *options[i];
if (d.long_name().empty())
boost::throw_exception(
error("long name required for config file"));
allowed_options.insert(d.long_name());
}
// Parser return char strings
parsed_options result(&desc);
result.options.push_back(basic_option<charT>("my_double", vector<string>(1, "10.1214")));
//result.options.push_back(basic_option<charT>("my_string", vector<string>(1, "hello world")));
return basic_parsed_options<charT>(result);
}
explicit AddOption(options_description& desc) : AddOptionBase(desc.add_options()) {}
inline AddOptionBase add(options_description& desc) {
return desc.add_options();
}
void history_plugin::set_program_options(options_description& cli, options_description& cfg) {
cfg.add_options()
("filter_on_accounts,f", bpo::value<vector<string>>()->composing(),
"Track only transactions whose scopes involve the listed accounts. Default is to track all transactions.")
;
}
/// \brief Add this block's hidden options to the provided options_description
void check_pdb_options_block::do_add_hidden_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
arg_desc.add_options()
( PO_PDB_FILE.c_str(), value<path>( &pdb_file ), "PDB file to check" );
}
/// \brief Add this block's options to the provided options_description
///
/// This is a concrete definition of a virtual method that's pure in options_block
void check_pdb_options_block::do_add_visible_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
arg_desc.add_options()
( PO_PERMIT.c_str(), bool_switch( &permit_no_atoms )->default_value( false ), "Permit success for a file that has no ATOM records" );
}
void prepareParseMotorId(options_description& desc) {
using namespace boost::program_options;
desc.add_options()
("motor_id,i", value<int>()->default_value(1)->implicit_value(false)->required(), "the CAN id of the motor to test");
}
/// \brief Add any hidden options to the provided options_description
void old_ssap_options_block::do_add_hidden_options_to_description(options_description &arg_desc ///< The options_description to which the options are added
) {
arg_desc.add_options()
( PO_NAME.c_str(), value<str_vec>( &names ), "Structure names" );
}
