colvarparse.cpp
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Created: Sun, Jul 28, 13:11

colvarparse.cpp
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	#include <sstream>
	#include <iostream>

	#include "colvarmodule.h"
	#include "colvarvalue.h"
	#include "colvarparse.h"


	// space & tab
	std::string const colvarparse::white_space = " \t";

	std::string colvarparse::dummy_string = "";
	size_t colvarparse::dummy_pos = 0;


	// definition of single-value keyword parsers

	template<typename TYPE> bool colvarparse::_get_keyval_scalar_(std::string const &conf,
	char const *key,
	TYPE &value,
	TYPE const &def_value,
	Parse_Mode const parse_mode)
	{
	std::string data;
	bool b_found = false, b_found_any = false;
	size_t save_pos = 0, found_count = 0;

	do {
	std::string data_this = "";
	b_found = key_lookup(conf, key, data_this, save_pos);
	if (b_found) {
	if (!b_found_any)
	b_found_any = true;
	found_count++;
	data = data_this;
	}
	} while (b_found);

	if (found_count > 1)
	cvm::log("Warning: found more than one instance of \""+
	std::string(key)+"\".\n");

	if (data.size()) {
	std::istringstream is(data);
	TYPE x(def_value);
	if (is >> x) {
	value = x;
	} else {
	cvm::error("Error: in parsing \""+
	std::string(key)+"\".\n", INPUT_ERROR);
	}
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = "+
	cvm::to_str(value)+"\n");
	}
	} else {

	if (b_found_any) {
	cvm::error("Error: improper or missing value "
	"for \""+std::string(key)+"\".\n", INPUT_ERROR);
	}
	value = def_value;
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = "+
	cvm::to_str(def_value)+" [default]\n");
	}
	}

	return b_found_any;
	}


	bool colvarparse::_get_keyval_scalar_string_(std::string const &conf,
	char const *key,
	std::string &value,
	std::string const &def_value,
	Parse_Mode const parse_mode)
	{
	std::string data;
	bool b_found = false, b_found_any = false;
	size_t save_pos = 0, found_count = 0;

	do {
	std::string data_this = "";
	b_found = key_lookup(conf, key, data_this, save_pos);
	if (b_found) {
	if (!b_found_any)
	b_found_any = true;
	found_count++;
	data = data_this;
	}
	} while (b_found);

	if (found_count > 1)
	cvm::log("Warning: found more than one instance of \""+
	std::string(key)+"\".\n");

	if (data.size()) {
	std::istringstream is(data);
	size_t data_count = 0;
	std::string x(def_value);
	while (is >> x) {
	value = x;
	data_count++;
	}
	if (data_count == 0)
	cvm::error("Error: in parsing \""+
	std::string(key)+"\".\n", INPUT_ERROR);
	if (data_count > 1) {
	cvm::error("Error: multiple values "
	"are not allowed for keyword \""+
	std::string(key)+"\".\n", INPUT_ERROR);
	}
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = \""+
	cvm::to_str(value)+"\"\n");
	}
	} else {

	if (b_found_any) {
	cvm::error("Error: improper or missing value "
	"for \""+std::string(key)+"\".\n", INPUT_ERROR);
	}
	value = def_value;
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = \""+
	cvm::to_str(def_value)+"\" [default]\n");
	}
	}

	return b_found_any;
	}


	// multiple-value keyword parsers

	template<typename TYPE> bool colvarparse::_get_keyval_vector_(std::string const &conf,
	char const *key,
	std::vector<TYPE> &values,
	std::vector<TYPE> const &def_values,
	Parse_Mode const parse_mode)
	{
	std::string data;
	bool b_found = false, b_found_any = false;
	size_t save_pos = 0, found_count = 0;

	do {
	std::string data_this = "";
	b_found = key_lookup(conf, key, data_this, save_pos);
	if (b_found) {
	if (!b_found_any)
	b_found_any = true;
	found_count++;
	data = data_this;
	}
	} while (b_found);

	if (found_count > 1)
	cvm::log("Warning: found more than one instance of \""+
	std::string(key)+"\".\n");

	if (data.size()) {
	std::istringstream is(data);

	if (values.size() == 0) {

	std::vector<TYPE> x;
	if (def_values.size())
	x = def_values;
	else
	x.assign(1, TYPE());

	for (size_t i = 0;
	( is >> x[ ((i<x.size()) ? i : x.size()-1) ] );
	i++) {
	values.push_back(x[ ((i<x.size()) ? i : x.size()-1) ]);
	}

	} else {

	size_t i = 0;
	for ( ; i < values.size(); i++) {
	TYPE x(values[i]);
	if (is >> x) {
	values[i] = x;
	} else {
	cvm::error("Error: in parsing \""+
	std::string(key)+"\".\n", INPUT_ERROR);
	}
	}
	}

	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = "+
	cvm::to_str(values)+"\n");
	}

	} else {

	if (b_found_any) {
	cvm::error("Error: improper or missing values for \""+
	std::string(key)+"\".\n", INPUT_ERROR);
	}

	for (size_t i = 0; i < values.size(); i++)
	values[i] = def_values[ (i > def_values.size()) ? 0 : i ];

	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = "+
	cvm::to_str(def_values)+" [default]\n");
	}
	}

	return b_found_any;
	}


	// single-value keyword parsers


	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	int &value,
	int const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<int>(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	size_t &value,
	size_t const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<size_t>(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	long &value,
	long const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<long>(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::string &value,
	std::string const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_string_(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	cvm::real &value,
	cvm::real const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<cvm::real>(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	cvm::rvector &value,
	cvm::rvector const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<cvm::rvector>(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	cvm::quaternion &value,
	cvm::quaternion const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<cvm::quaternion>(conf, key, value, def_value, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	colvarvalue &value,
	colvarvalue const &def_value,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_scalar_<colvarvalue>(conf, key, value, def_value, parse_mode);
	}


	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	bool &value,
	bool const &def_value,
	Parse_Mode const parse_mode)
	{
	std::string data;
	bool b_found = false, b_found_any = false;
	size_t save_pos = 0, found_count = 0;

	do {
	std::string data_this = "";
	b_found = key_lookup(conf, key, data_this, save_pos);
	if (b_found) {
	if (!b_found_any)
	b_found_any = true;
	found_count++;
	data = data_this;
	}
	} while (b_found);

	if (found_count > 1)
	cvm::log("Warning: found more than one instance of \""+
	std::string(key)+"\".\n");

	if (data.size()) {
	if ( (data == std::string("on")) \|\|
	(data == std::string("yes")) \|\|
	(data == std::string("true")) ) {
	value = true;
	} else if ( (data == std::string("off")) \|\|
	(data == std::string("no")) \|\|
	(data == std::string("false")) ) {
	value = false;
	} else
	cvm::error("Error: boolean values only are allowed "
	"for \""+std::string(key)+"\".\n", INPUT_ERROR);
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = "+
	(value ? "on" : "off")+"\n");
	}
	} else {

	if (b_found_any) {
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = on\n");
	}
	value = true;
	} else {
	value = def_value;
	if (parse_mode != parse_silent) {
	cvm::log("# "+std::string(key)+" = "+
	(def_value ? "on" : "off")+" [default]\n");
	}
	}
	}

	return b_found_any;
	}


	// multiple-value keyword parsers

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<int> &values,
	std::vector<int> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<int>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<size_t> &values,
	std::vector<size_t> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<size_t>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<long> &values,
	std::vector<long> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<long>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<std::string> &values,
	std::vector<std::string> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<std::string>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<cvm::real> &values,
	std::vector<cvm::real> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<cvm::real>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<cvm::rvector> &values,
	std::vector<cvm::rvector> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<cvm::rvector>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<cvm::quaternion> &values,
	std::vector<cvm::quaternion> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<cvm::quaternion>(conf, key, values, def_values, parse_mode);
	}

	bool colvarparse::get_keyval(std::string const &conf,
	char const *key,
	std::vector<colvarvalue> &values,
	std::vector<colvarvalue> const &def_values,
	Parse_Mode const parse_mode)
	{
	return _get_keyval_vector_<colvarvalue>(conf, key, values, def_values, parse_mode);
	}


	void colvarparse::add_keyword(char const *key)
	{
	for (std::list<std::string>::iterator ki = allowed_keywords.begin();
	ki != allowed_keywords.end(); ki++) {
	if (to_lower_cppstr(std::string(key)) == *ki)
	return;
	}
	// not found in the list
	// if (cvm::debug())
	// cvm::log("Registering a new keyword, \""+std::string (key)+"\".\n");
	allowed_keywords.push_back(to_lower_cppstr(std::string(key)));
	}


	void colvarparse::strip_values(std::string &conf)
	{
	size_t offset = 0;
	data_begin_pos.sort();
	data_end_pos.sort();

	std::list<size_t>::iterator data_begin = data_begin_pos.begin();
	std::list<size_t>::iterator data_end = data_end_pos.begin();

	for ( ; (data_begin != data_begin_pos.end()) &&
	(data_end != data_end_pos.end()) ;
	data_begin++, data_end++) {

	// std::cerr << "data_begin, data_end "
	// << data_begin << ", " << data_end
	// << "\n";

	size_t const nchars = data_end-data_begin;

	// std::cerr << "conf[data_begin:data_end] = \""
	// << std::string (conf, *data_begin - offset, nchars)
	// << "\"\n";

	conf.erase(*data_begin - offset, nchars);
	offset += nchars;

	// std::cerr << ("Stripped config = \"\n"+conf+"\"\n");

	}
	}


	void colvarparse::clear_keyword_registry()
	{
	allowed_keywords.clear();
	data_begin_pos.clear();
	data_end_pos.clear();
	}


	int colvarparse::check_keywords(std::string &conf, char const *key)
	{
	if (cvm::debug())
	cvm::log("Configuration string for \""+std::string(key)+
	"\": \"\n"+conf+"\".\n");

	strip_values(conf);
	// after stripping, the config string has either empty lines, or
	// lines beginning with a keyword

	std::string line;
	std::istringstream is(conf);
	while (std::getline(is, line)) {
	if (line.size() == 0)
	continue;
	if (line.find_first_not_of(white_space) ==
	std::string::npos)
	continue;

	std::string uk;
	std::istringstream line_is(line);
	line_is >> uk;
	// if (cvm::debug())
	// cvm::log ("Checking the validity of \""+uk+"\" from line:\n" + line);
	uk = to_lower_cppstr(uk);

	bool found_keyword = false;
	for (std::list<std::string>::iterator ki = allowed_keywords.begin();
	ki != allowed_keywords.end(); ki++) {
	if (uk == *ki) {
	found_keyword = true;
	break;
	}
	}
	if (!found_keyword) {
	cvm::error("Error: keyword \""+uk+"\" is not supported, "
	"or not recognized in this context.\n", INPUT_ERROR);
	return INPUT_ERROR;
	}
	}

	clear_keyword_registry();

	return COLVARS_OK;
	}


	std::istream & colvarparse::getline_nocomments(std::istream &is,
	std::string &line,
	char const delim)
	{
	std::getline(is, line, delim);
	size_t const comment = line.find('#');
	if (comment != std::string::npos) {
	line.erase(comment);
	}
	return is;
	}


	bool colvarparse::key_lookup(std::string const &conf,
	char const *key_in,
	std::string &data,
	size_t &save_pos)
	{
	if (cvm::debug()) {
	cvm::log("Looking for the keyword \""+std::string(key_in)+"\" and its value.\n");
	}

	// add this keyword to the register (in its camelCase version)
	add_keyword(key_in);

	// use the lowercase version from now on
	std::string const key(to_lower_cppstr(key_in));

	// "conf_lower" is only used to lookup the keyword, but its value
	// will be read from "conf", in order not to mess up file names
	std::string const conf_lower(to_lower_cppstr(conf));

	// by default, there is no value, unless we found one
	data = "";

	// when the function is invoked without save_pos, ensure that we
	// start from zero
	colvarparse::dummy_pos = 0;

	// start from the first occurrence of key
	size_t pos = conf_lower.find(key, save_pos);

	// iterate over all instances of the substring until it finds it as isolated keyword
	while (true) {

	if (pos == std::string::npos) {
	// no valid instance of the keyword has been found
	if (cvm::debug()) {
	cvm::log("Keyword \""+std::string(key_in)+"\" not found.\n");
	}
	return false;
	}

	bool b_isolated_left = true, b_isolated_right = true;

	if (pos > 0) {
	if ( std::string("\n"+white_space+
	"}").find(conf[pos-1]) ==
	std::string::npos ) {
	// none of the valid delimiting characters is on the left of key
	b_isolated_left = false;
	}
	}

	if (pos < conf.size()-key.size()-1) {
	if ( std::string("\n"+white_space+
	"{").find(conf[pos+key.size()]) ==
	std::string::npos ) {
	// none of the valid delimiting characters is on the right of key
	b_isolated_right = false;
	}
	}

	// check that there are matching braces between here and the end of conf
	bool const b_not_within_block = brace_check(conf, pos);

	bool const b_isolated = (b_isolated_left && b_isolated_right &&
	b_not_within_block);

	if (b_isolated) {
	// found it
	break;
	} else {
	// try the next occurrence of key
	pos = conf_lower.find(key, pos+key.size());
	}
	}

	// save the pointer for a future call (when iterating over multiple
	// valid instances of the same keyword)
	save_pos = pos + key.size();

	// get the remainder of the line
	size_t pl = conf.rfind("\n", pos);
	size_t line_begin = (pl == std::string::npos) ? 0 : pos;
	size_t nl = conf.find("\n", pos);
	size_t line_end = (nl == std::string::npos) ? conf.size() : nl;
	std::string line(conf, line_begin, (line_end-line_begin));

	size_t data_begin = (to_lower_cppstr(line)).find(key) + key.size();
	data_begin = line.find_first_not_of(white_space, data_begin+1);

	if (data_begin != std::string::npos) {

	size_t data_end = line.find_last_not_of(white_space) + 1;
	data_end = (data_end == std::string::npos) ? line.size() : data_end;

	size_t brace = line.find('{', data_begin); // look for an opening brace
	size_t brace_last = brace;

	if (brace != std::string::npos) {

	// find the matching closing brace

	if (cvm::debug()) {
	cvm::log("Multi-line value, config is now \""+line+"\".\n");
	}

	int brace_count = 1;

	while (brace_count > 0) {

	brace = line.find_first_of("{}", brace_last+1);
	// find all braces within this line
	while (brace < std::string::npos) {
	brace_last = brace;
	if (line[brace] == '{') brace_count++;
	if (line[brace] == '}') brace_count--;
	if (brace_count == 0) {
	data_end = brace+1;
	break;
	}
	brace = line.find_first_of("{}", brace+1);
	}

	if (brace_count == 0) {
	data_end = brace+1;
	break;
	}

	if (brace == std::string::npos) {

	// add a new line
	if (line_end >= conf.size()) {
	cvm::error("Parse error: reached the end while "
	"looking for closing brace; until now "
	"the following was parsed: \"\n"+
	line+"\".\n", INPUT_ERROR);
	return false;
	}

	line_begin = line_end;
	nl = conf.find('\n', line_begin+1);
	if (nl == std::string::npos)
	line_end = conf.size();
	else
	line_end = nl;
	line.append(conf, line_begin, (line_end-line_begin));

	if (cvm::debug()) {
	cvm::log("Added a new line, config is now \""+line+"\".\n");
	}
	}

	if (brace_count < 0) {
	cvm::error("Error: found closing brace without opening brace.\n", INPUT_ERROR);
	}
	}

	// strip the leading and trailing braces
	data_begin = line.find_first_of('{') + 1;
	data_begin = line.find_first_not_of(white_space,
	data_begin);

	data_end = line.find_last_of('}', line.size()) - 1;
	data_end = line.find_last_not_of(white_space,
	data_end) + 1;
	}

	data.append(line, data_begin, (data_end-data_begin));

	if (cvm::debug()) {
	cvm::log("Keyword value = \""+data+"\".\n");
	}

	if (data.size() && save_delimiters) {
	data_begin_pos.push_back(conf.find(data, pos+key.size()));
	data_end_pos.push_back(data_begin_pos.back()+data.size());
	}
	}

	save_pos = line_end;

	return true;
	}


	std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
	{
	size_t start_pos = is.tellg();
	std::string read_key, next;

	if ( !(is >> read_key) \|\| !(read_key == rb.key) \|\|
	!(is >> next) ) {
	// the requested keyword has not been found, or it is not possible
	// to read data after it
	is.clear();
	is.seekg(start_pos, std::ios::beg);
	is.setstate(std::ios::failbit);
	return is;
	}

	if (next != "{") {
	(*rb.data) = next;
	return is;
	}

	size_t brace_count = 1;
	std::string line;
	while (colvarparse::getline_nocomments(is, line)) {
	size_t br = 0, br_old = 0;
	while ( (br = line.find_first_of("{}", br)) != std::string::npos) {
	if (line[br] == '{') brace_count++;
	if (line[br] == '}') brace_count--;
	br_old = br;
	br++;
	}
	if (brace_count) (*rb.data).append(line + "\n");
	else {
	(*rb.data).append(line, 0, br_old);
	break;
	}
	}
	if (brace_count) {
	// end-of-file reached
	// restore initial position
	is.clear();
	is.seekg(start_pos, std::ios::beg);
	is.setstate(std::ios::failbit);
	}
	return is;
	}


	bool colvarparse::brace_check(std::string const &conf,
	size_t const start_pos)
	{
	size_t brace_count = 0;
	size_t brace = start_pos;
	while ( (brace = conf.find_first_of("{}", brace)) != std::string::npos) {
	if (conf[brace] == '{') brace_count++;
	if (conf[brace] == '}') brace_count--;
	brace++;
	}

	if (brace_count != 0)
	return false;
	else
	return true;
	}

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