pyEQL 1.4.0rc9__cp310-cp310-macosx_10_9_x86_64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/src/phreeqcpp/common/Parser.cxx

@@ -0,0 +1,1331 @@
+// Parser.cpp: implementation of the CParser class.
+//
+//////////////////////////////////////////////////////////////////////
+#ifdef _DEBUG
+#pragma warning(disable : 4786)	// disable truncation warning (Only used by debugger)
+#endif
+
+#include <algorithm>			// std::transform
+#include <map>					// std::map
+#include <cassert>				// assert
+#include <stdlib.h>
+#include <iostream>				// std::cout std::cerr
+#include "Utils.h"
+#include <stdio.h>
+#include "Parser.h"
+#include "PHRQ_io.h"
+
+#if defined(PHREEQCI_GUI)
+#ifdef _DEBUG
+#define new DEBUG_NEW
+#undef THIS_FILE
+static char THIS_FILE[] = __FILE__;
+#endif
+#endif
+
+//////////////////////////////////////////////////////////////////////
+// Construction/Destruction
+//////////////////////////////////////////////////////////////////////
+CParser::CParser(PHRQ_io *io):
+PHRQ_base(io),
+m_input_stream(std::cin), 
+m_input_error(0),
+m_next_keyword(Keywords::KEY_NONE)
+{
+	if (!io)
+	{
+		error_msg("This parser constructor requires non-null phrq_io", PHRQ_io::OT_STOP);
+		echo_file = EO_ALL;
+		echo_stream = EO_NONE;
+		accumulate = false;
+		phrq_io_only = true;
+		m_line_type = PHRQ_io::LT_EMPTY;
+	}
+	else
+	{
+		m_line_save = io->Get_m_line();
+		m_line = io->Get_m_line();
+		m_line_type = io->Get_m_line_type();
+		m_line_iss.str(m_line);
+		m_line_iss.seekg(0, std::ios_base::beg);
+		m_line_iss.clear();
+		echo_file = EO_ALL;
+		echo_stream = EO_NONE;
+		accumulate = false;
+		phrq_io_only = true;
+	}
+}
+
+CParser::CParser(std::istream & input, PHRQ_io *io):
+PHRQ_base(io),
+m_input_stream(input), 
+m_input_error(0),
+m_next_keyword(Keywords::KEY_NONE)
+{
+	m_line_save.reserve(80);
+	m_line.reserve(80);
+	echo_file = EO_ALL;
+	echo_stream = EO_NONE;
+	accumulate = false;
+	phrq_io_only = false;
+	m_line_type = PHRQ_io::LT_EMPTY;
+}
+
+CParser::~CParser()
+{
+}
+
+PHRQ_io::LINE_TYPE CParser::check_line(const std::string & str,
+									   bool allow_empty, bool allow_eof,
+									   bool allow_keyword, bool print)
+{
+	PHRQ_io::LINE_TYPE
+		i;
+
+	// Get line
+	do
+	{
+		i = get_line();
+		// reset iss
+		m_line_iss.str(m_line);
+		m_line_iss.seekg(0, std::ios_base::beg);
+		m_line_iss.clear();
+
+		// output for stream
+		switch (this->echo_stream)
+		{
+		case EO_NONE:
+			break;
+		case EO_ALL:
+			if (i != PHRQ_io::LT_EOF)
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				//get_output() << msg;
+				io->output_msg(msg.str().c_str());
+			}
+			break;
+		case EO_KEYWORDS:
+			if (i == PHRQ_io::LT_KEYWORD)
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				//get_output() << msg;
+				io->output_msg(msg.str().c_str());
+			}
+			break;
+		case EO_NOKEYWORDS:
+			if (i != PHRQ_io::LT_KEYWORD && i != PHRQ_io::LT_EOF)
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				//get_output() << msg;
+				io->output_msg(msg.str().c_str());
+			}
+			break;
+		}
+		// output for file
+		switch (this->echo_file)
+		{
+		case EO_NONE:
+			break;
+		case EO_ALL:
+			if (i != PHRQ_io::LT_EOF)
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				this->echo_msg(msg.str());
+			}
+			break;
+		case EO_KEYWORDS:
+			if (i == PHRQ_io::LT_KEYWORD)
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				this->echo_msg(msg.str());
+			}
+			break;
+
+		case EO_NOKEYWORDS:
+			if (i != PHRQ_io::LT_KEYWORD && i != PHRQ_io::LT_EOF)
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				this->echo_msg(msg.str().c_str());
+			}
+			break;
+		}
+	}
+	while (i == PHRQ_io::LT_EMPTY && allow_empty == false);
+
+	// Check eof
+	if (i == PHRQ_io::LT_EOF && allow_eof == false)
+	{
+		std::ostringstream msg;
+		msg << "Unexpected eof while reading " << str <<
+			"\nExecution terminated.\n";
+		error_msg(msg.str().c_str(), PHRQ_io::OT_STOP);
+	}
+
+	// Check keyword
+	if (i == PHRQ_io::LT_KEYWORD && allow_keyword == false)
+	{
+		std::ostringstream msg;
+		msg << "Expected data for " << str <<
+			", but got a keyword ending data block.";
+		error_msg(msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+		incr_input_error();
+	}
+	m_line_type = i;
+	return i;
+}
+PHRQ_io::LINE_TYPE CParser::get_line_phrq_io()
+{
+	m_line_type = io->get_line();
+	m_line_save = io->Get_m_line_save();
+	m_line = io->Get_m_line();
+	m_next_keyword = io->Get_m_next_keyword();
+	if (accumulate)
+	{
+		this->accumulated.append(m_line_save);
+		this->accumulated.append("\n");
+	}
+	return m_line_type;
+}
+
+PHRQ_io::LINE_TYPE CParser::get_line()
+{
+	if (this->phrq_io_only)
+	{
+		return get_line_phrq_io();
+	}
+	PHRQ_io::LINE_TYPE return_value = PHRQ_io::LT_EMPTY;
+	while (return_value == PHRQ_io::LT_EMPTY)
+	{
+		//
+		// Eliminate all characters after # sign as a comment
+		//
+
+		//
+		// Get line, check for eof
+		//
+		if (get_logical_line() == PHRQ_io::LT_EOF)
+		{
+			if (!m_input_stream.eof())
+			{
+				error_msg("Reading input file.", PHRQ_io::OT_CONTINUE);
+				error_msg("istream::get() returned an error.", PHRQ_io::OT_STOP);
+			}
+			else
+			{
+				//{{MOD
+				m_line.erase(m_line.begin(), m_line.end());	// m_line.clear();
+				//}}MOD
+				m_next_keyword = Keywords::KEY_END;
+				return PHRQ_io::LT_EOF;
+			}
+		}
+
+		//
+		// Get long lines
+		//
+		bool
+			empty = true;
+		m_line = m_line_save.substr(0, m_line_save.find_first_of('#'));
+		for (unsigned int i = 0; i < m_line.size(); ++i)
+		{
+			if (!::isspace(m_line[i]))
+			{
+				empty = false;
+				break;
+			}
+		}
+
+		if (this->accumulate)
+		{
+			this->accumulated.append(m_line_save);
+			this->accumulated.append("\n");
+		}
+		//
+		// New line character encountered 
+		//
+		return_value = (empty ? PHRQ_io::LT_EMPTY : PHRQ_io::LT_OK);
+	}
+
+	//
+	// Determine return_value
+	// 
+	if (return_value == PHRQ_io::LT_OK)
+	{
+		if (check_key(m_line.begin(), m_line.end()))
+		{
+			return_value = PHRQ_io::LT_KEYWORD;
+		}
+		else
+		{
+			std::string::iterator beg = m_line.begin();
+			std::string::iterator end = m_line.end();
+			std::string token;
+			copy_token(token, beg, end);
+
+			if (token.size() > 1 && token[0] == '-' &&::isalpha(token[1]))
+			{
+				return_value = PHRQ_io::LT_OPTION;
+			}
+		}
+	}
+	return return_value;
+}
+
+/**
+        Reads input stream until end of line, ";", or eof
+        stores characters in line_save
+
+        returns:
+                EOF on empty line on end of file or
+                OK otherwise
+*/
+PHRQ_io::LINE_TYPE CParser::get_logical_line()
+{
+	int
+		j;
+	unsigned int
+		pos;
+	char
+		c;
+
+	m_line_save.erase(m_line_save.begin(), m_line_save.end());	// m_line_save.clear();
+
+	while ((j = m_input_stream.get()) != std::char_traits < char >::eof())
+	{
+		c = (char) j;
+		if (c == '#')
+		{
+			// ignore all chars after # until newline
+			do
+			{
+				c = (char) j;
+				if (c == '\n')
+				{
+					break;
+				}
+				m_line_save += c;
+			}
+			while ((j =
+					m_input_stream.get()) != std::char_traits <
+				   char >::eof());
+		}
+		if (c == ';')
+			break;
+		if (c == '\n')
+		{
+			break;
+		}
+		if (c == '\\')
+		{
+			pos = (int) m_line_save.size();
+			m_line_save += c;
+			while ((j =
+					m_input_stream.get()) != std::char_traits < char >::eof())
+			{
+				c = (char) j;
+				if (c == '\\')
+				{
+					pos = (int) m_line_save.size();
+					m_line_save += c;
+					continue;
+				}
+				if (c == '\n')
+				{
+					// remove '\\'
+					for (; pos < m_line_save.size(); pos++)
+					{
+						m_line_save[pos] = m_line_save[(size_t) pos + 1];
+					}
+					m_line_save.erase(m_line_save.size() - 1, 1);
+					break;
+				}
+				m_line_save += c;
+				if (!::isspace(j))
+					break;
+			}
+		}
+		else
+		{
+			m_line_save += c;
+		}
+	}
+	if (j == std::char_traits < char >::eof() && m_line_save.size() == 0)
+	{
+		return (PHRQ_io::LT_EOF);
+	}
+	return (PHRQ_io::LT_OK);
+}
+
+bool
+CParser::check_key(std::string::iterator begin, std::string::iterator end)
+{
+	std::string lowercase;
+	copy_token(lowercase, begin, end);
+	std::transform(lowercase.begin(), lowercase.end(), lowercase.begin(),
+				   tolower);
+	m_next_keyword = Keywords::Keyword_search(lowercase);
+	if (m_next_keyword == Keywords::KEY_NONE)
+	{
+		return false;
+	}
+	return true;
+}
+CParser::STATUS_TYPE CParser::check_units(std::string & tot_units,
+										  bool alkalinity,
+										  bool check_compatibility,
+										  const std::string & default_units,
+										  bool print)
+{
+/*
+ *   Check if legitimate units
+ *   Input:
+ *           tot_units           character string to check,
+ *           alkalinity          true if alkalinity, false if any other total,
+ *           check_compatibility true check alk and default units, false otherwise
+ *           default_units       character string of default units (check /L, /kg, etc)
+ *           print               true print warning messages
+ *   Output:
+ *           tot_units           standard form for unit
+ */
+	using
+		Utilities::str_tolower;
+	using
+		Utilities::replace;
+	using
+		Utilities::squeeze_white;
+
+	static const char *
+		units[] = {
+		"Mol/l",				/* 0 */
+		"mMol/l",				/* 1 */
+		"uMol/l",				/* 2 */
+		"g/l",					/* 3 */
+		"mg/l",					/* 4 */
+		"ug/l",					/* 5 */
+		"Mol/kgs",				/* 6 */
+		"mMol/kgs",				/* 7 */
+		"uMol/kgs",				/* 8 */
+		"g/kgs",				/* 9 = ppt */
+		"mg/kgs",				/* 10 = ppm */
+		"ug/kgs",				/* 11 = ppb */
+		"Mol/kgw",				/* 12 = mol/kg H2O */
+		"mMol/kgw",				/* 13 = mmol/kg H2O */
+		"uMol/kgw",				/* 14 = umol/kg H2O */
+		"g/kgw",				/* 15 = mol/kg H2O */
+		"mg/kgw",				/* 16 = mmol/kg H2O */
+		"ug/kgw",				/* 17 = umol/kg H2O */
+		"eq/l",					/* 18 */
+		"meq/l",				/* 19 */
+		"ueq/l",				/* 20 */
+		"eq/kgs",				/* 21 */
+		"meq/kgs",				/* 22 */
+		"ueq/kgs",				/* 23 */
+		"eq/kgw",				/* 24 */
+		"meq/kgw",				/* 25 */
+		"ueq/kgw",				/* 26 */
+	};
+
+	squeeze_white(tot_units);
+	str_tolower(tot_units);
+	replace("milli", "m", tot_units);
+	replace("micro", "u", tot_units);
+	replace("grams", "g", tot_units);
+	replace("gram", "g", tot_units);
+	replace("moles", "Mol", tot_units);
+	replace("mole", "Mol", tot_units);
+	replace("mol", "Mol", tot_units);
+	replace("liter", "l", tot_units);
+	replace("kgh", "kgw", tot_units);
+	replace("ppt", "g/kgs", tot_units);
+	replace("ppm", "mg/kgs", tot_units);
+	replace("ppb", "ug/kgs", tot_units);
+	replace("equivalents", "eq", tot_units);
+	replace("equivalent", "eq", tot_units);
+	replace("equiv", "eq", tot_units);
+
+	std::string::size_type end;
+	if ((end = tot_units.find("/l")) != std::string::npos)
+	{
+		tot_units.resize(end + 2);
+	}
+	if ((end = tot_units.find("/kgs")) != std::string::npos)
+	{
+		tot_units.resize(end + 4);
+	}
+	if ((end = tot_units.find("/kgw")) != std::string::npos)
+	{
+		tot_units.resize(end + 4);
+	}
+
+	//
+	//  Check if unit in list
+	//
+	bool
+		found = false;
+	for (unsigned int i = 0; i < sizeof(units) / sizeof(char *); ++i)
+	{
+		if (tot_units.compare(units[i]) == 0)
+		{
+			found = true;
+			break;
+		}
+	}
+	if (!found)
+	{
+		if (print)
+		{
+			std::ostringstream err;
+			err << "Unknown unit, " << tot_units;
+			this->error_msg(err.str().c_str(), PHRQ_io::OT_CONTINUE);
+		}
+		return PARSER_ERROR;
+	}
+
+	//
+	//   Check if units are compatible with default_units
+	//
+	if (check_compatibility == false)
+		return PARSER_OK;
+
+	//
+	//   Special cases for alkalinity
+	//
+	if (alkalinity == true && tot_units.find("Mol") != std::string::npos)
+	{
+		if (print)
+		{
+			this->warning_msg
+				("Alkalinity given in moles, assumed to be equivalents.");
+		}
+		replace("Mol", "eq", tot_units);
+	}
+	if (alkalinity == false && tot_units.find("eq") != std::string::npos)
+	{
+		if (print)
+		{
+			this->error_msg("Only alkalinity can be entered in equivalents.",
+					  PHRQ_io::OT_CONTINUE);
+		}
+		return PARSER_ERROR;
+	}
+
+	//
+	//  See if default_units are compatible with tot_units
+	//
+	if (default_units.find("/l") != std::string::npos
+		&& tot_units.find("/l") != std::string::npos)
+		return PARSER_OK;
+	if (default_units.find("/kgs") != std::string::npos
+		&& tot_units.find("/kgs") != std::string::npos)
+		return PARSER_OK;
+	if (default_units.find("/kgw") != std::string::npos
+		&& tot_units.find("/kgw") != std::string::npos)
+		return PARSER_OK;
+
+	std::string str = default_units;
+	replace("kgs", "kg solution", str);
+	replace("kgs", "kg solution", tot_units);
+	replace("kgw", "kg water", str);
+	replace("kgw", "kg water", tot_units);
+	replace("/l", "/L", str);
+	replace("Mol", "mol", str);
+	replace("/l", "/L", tot_units);
+	replace("Mol", "mol", tot_units);
+
+	if (print)
+	{
+		std::ostringstream err;
+		err << "Units for master species, " << tot_units <<
+			", are not compatible with default units, " << str << ".";
+		this->error_msg(err.str().c_str(), PHRQ_io::OT_CONTINUE);
+	}
+	return PARSER_ERROR;
+}
+CParser::TOKEN_TYPE CParser::token_type(const std::string & token)
+{
+	if (!token.empty())
+	{
+		if (::isupper(token[0]))
+		{
+			return CParser::TT_UPPER;
+		}
+		else if (::islower(token[0]))
+		{
+			return CParser::TT_LOWER;
+		}
+		else if (::isdigit(token[0]) || token[0] == '.' || token[0] == '-')
+		{
+			return CParser::TT_DIGIT;
+		}
+		else
+		{
+			assert(!::isspace(token[0]));
+			return CParser::TT_UNKNOWN;
+		}
+	}
+	else
+	{
+		return CParser::TT_EMPTY;
+	}
+}
+
+CParser::TOKEN_TYPE CParser::peek_token()
+{
+	std::istringstream::pos_type pos = m_line_iss.tellg();
+	std::string token;
+	m_line_iss >> token;
+	m_line_iss.seekg(pos);
+	return token_type(token);
+}
+
+CParser::TOKEN_TYPE CParser::copy_token(std::string & token,
+										std::string::iterator & begin,
+										std::string::iterator & end)
+{
+	if (begin != end)
+	{
+		std::string::iterator b = begin;
+		for (; b < end &&::isspace(*b); ++b);
+
+		begin = b;
+		for (; begin < end && !::isspace(*begin); ++begin);
+
+		token.assign(b, begin);
+	}
+	else
+	{
+		token.resize(0);
+	}
+
+	return token_type(token);
+}
+
+CParser::TOKEN_TYPE CParser::copy_token(std::string & token,
+										std::istream & is)
+{
+	is >> token;
+	return token_type(token);
+}
+
+CParser::TOKEN_TYPE CParser::copy_token(std::string & token,
+										std::istream::pos_type & pos)
+{
+	m_line_iss.seekg(pos);
+	if (!(m_line_iss >> token))
+	{
+		token.erase(token.begin(), token.end());	// token.clear();
+	}
+	pos = m_line_iss.tellg();
+	return token_type(token);
+}
+
+CParser::FIND_TYPE CParser::find_option(const std::string & item, int *n,
+										const std::vector < std::string >
+										&list, bool exact)
+{
+	std::string token(item);
+	std::transform(token.begin(), token.end(), token.begin(), tolower);
+	for (unsigned int i = 0; i < list.size(); i++)
+	{
+		if (exact == true)
+		{
+			if (list[i].compare(token) == 0)
+			{
+				*n = i;
+				return FT_OK;
+			}
+		}
+		else
+		{
+			if (list[i].find(token) == 0)
+			{
+				*n = i;
+				return FT_OK;
+			}
+		}
+	}
+
+	*n = -1;
+	return FT_ERROR;
+}
+
+int
+CParser::get_option(const std::vector < std::string > &opt_list,
+					std::string::iterator & next_char)
+{
+	//
+	// Read a line and check for options
+	//
+	int j;
+	int /*  opt_l,  */ opt;
+	std::string::iterator opt_ptr;
+	std::string option;
+
+#if !defined(R_SO)
+	fprintf(stderr, "Did not think this get_option was called\n");
+#endif
+	//
+	// Read line
+	//
+	PHRQ_io::LINE_TYPE lt = check_line("get_option", false, true, true, true);
+	if (lt == PHRQ_io::LT_EOF)
+	{
+		j = OPT_EOF;
+	}
+	else if (lt == PHRQ_io::LT_KEYWORD)
+	{
+		j = OPT_KEYWORD;
+	}
+	else if (lt == PHRQ_io::LT_OPTION)
+	{
+		opt_ptr = m_line.begin();
+		std::string::iterator end = m_line.end();
+		copy_token(option, opt_ptr, end);
+		if (find_option(option, &opt, opt_list, false) == CParser::FT_OK)
+		{
+			j = opt;
+			m_line_save.replace(m_line_save.find(option), option.size(),
+								opt_list[opt]);
+			m_line.replace(m_line.find(option), option.size(), opt_list[opt]);
+			opt_ptr = m_line.begin();
+			std::string::iterator end = m_line.end();
+			copy_token(option, opt_ptr, end);
+			next_char = opt_ptr;
+			if (true)			// pr.echo_input == TRUE
+			{
+				if (true)		// database_file == NULL
+				{
+					//get_output() << "\t" << m_line_save << "\n";
+					std::ostringstream msg;
+					msg << "\t" << m_line_save << "\n";
+					io->output_msg(msg.str().c_str());
+				}
+			}
+		}
+		else
+		{
+			if (true)			// (database_file == NULL)
+			{
+				//get_output() << "\t" << m_line_save << "\n";
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				io->output_msg(msg.str().c_str());
+			}
+
+			std::ostringstream err;
+			err << "Unknown option." << "\n";
+			err << m_line_save << "\n";
+			error_msg(err.str().c_str());
+
+			j = OPT_ERROR;
+			next_char = m_line.begin();
+		}
+	}
+	else
+	{
+		opt_ptr = m_line.begin();
+		std::string::iterator end = m_line.end();
+		copy_token(option, opt_ptr, end);
+		if (find_option(option, &opt, opt_list, true) == FT_OK)
+		{
+			j = opt;
+			next_char = opt_ptr;
+		}
+		else
+		{
+			j = OPT_DEFAULT;
+			next_char = m_line.begin();
+		}
+		if (true)				// pr.echo_input == TRUE
+		{
+			if (true)			// database_file == NULL
+			{
+#if !defined(R_SO)
+				std::cout << "\t" << m_line_save << "\n";
+#endif
+			}
+		}
+	}
+	return (j);
+}
+
+int
+CParser::get_option(const std::vector < std::string > &opt_list,
+					std::istream::pos_type & next_pos)
+{
+	//
+	// Read a line and check for options
+	//
+	int j;
+	int opt;
+	std::istream::pos_type pos_ptr;
+	std::string option;
+
+	//
+	// Read line
+	//
+	PHRQ_io::LINE_TYPE lt = check_line("get_option", false, true, true, true);
+	if (lt == PHRQ_io::LT_EOF)
+	{
+		j = OPT_EOF;
+	}
+	else if (lt == PHRQ_io::LT_KEYWORD)
+	{
+		j = OPT_KEYWORD;
+	}
+	else if (lt == PHRQ_io::LT_OPTION)
+	{
+		std::string::iterator opt_ptr = m_line.begin();
+		std::string::iterator end = m_line.end();
+		copy_token(option, opt_ptr, end);
+		if (find_option(option.substr(1), &opt, opt_list, false) == FT_OK)
+		{
+			// replace -option with option
+			j = opt;
+			m_line_save.replace(m_line_save.find(option), option.size(),
+								opt_list[opt]);
+			m_line.replace(m_line.find(option), option.size(), opt_list[opt]);
+
+			// reset iss
+			m_line_iss.str(m_line);
+			m_line_iss.seekg(0, std::ios_base::beg);
+			m_line_iss.clear();
+
+			pos_ptr = 0;
+			copy_token(option, pos_ptr);
+			next_pos = pos_ptr;
+		}
+		else
+		{
+			j = OPT_ERROR;
+			next_pos = pos_ptr;
+		}
+	}
+	else
+	{
+		pos_ptr = m_line_iss.tellg();
+		m_line_iss >> option;
+		if (find_option(option, &opt, opt_list, true) == FT_OK)
+		{
+			j = opt;
+			next_pos = m_line_iss.tellg();
+		}
+		else
+		{
+			j = OPT_DEFAULT;
+			m_line_iss.seekg(pos_ptr);
+			m_line_iss.clear();
+			next_pos = pos_ptr;
+		}
+	}
+	return (j);
+}
+CParser::STATUS_TYPE CParser::get_elt(std::string::iterator & begin,
+									  const std::string::iterator end,
+									  std::string & element)
+{
+	element.erase(element.begin(), element.end());	// element.clear();
+
+	if (begin == end)
+	{
+		error_msg("Empty string in get_elt.  Expected an element name.",
+				  PHRQ_io::OT_CONTINUE);
+		return PARSER_ERROR;
+	}
+
+	//
+	// Load name into char array element
+	//
+	char
+		c = *begin;
+	++begin;
+	element.insert(element.end(), c);	// element.push_back(c);
+	if (c == '[')
+	{
+		while ((c = *begin) != ']')
+		{
+			element.insert(element.end(), c);	// element.push_back(c);
+			++begin;
+			if ((c = *begin) == ']')
+			{
+				element.insert(element.end(), c);	// element.push_back(c);
+				++begin;
+				break;
+			}
+			else if (begin == end)
+			{
+				error_msg("No ending bracket (]) for element name",
+						  PHRQ_io::OT_CONTINUE);
+				incr_input_error();
+				return PARSER_ERROR;
+			}
+		}
+		while (::islower(c = *begin) || c == '_')
+		{
+			element.insert(element.end(), c);	// element.push_back(c);
+			++begin;
+			if (begin == end)
+				break;
+		}
+	}
+	else
+	{
+		while (::islower(c = *begin) || c == '_')
+		{
+			element.insert(element.end(), c);	// element.push_back(c);
+			++begin;
+			if (begin == end)
+				break;
+		}
+	}
+	return PARSER_OK;
+}
+
+CParser::STATUS_TYPE CParser::parse_couple(std::string & token)
+{
+	// Parse couple puts redox couples in standard form
+	// "+" is removed and couples are rewritten in sort
+	// order.
+
+	if (Utilities::strcmp_nocase_arg1(token.c_str(), "pe") == 0)
+	{
+		Utilities::str_tolower(token);
+		return PARSER_OK;
+	}
+
+	while (Utilities::replace("(+", "(", token));
+
+	std::string::iterator ptr = token.begin();
+	std::string elt1;
+	get_elt(ptr, token.end(), elt1);
+
+	if (*ptr != '(')
+	{
+		std::ostringstream err_msg;
+		err_msg << "Element name must be followed by " <<
+			"parentheses in redox couple, " << token << ".";
+		error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+		incr_input_error();
+		return PARSER_ERROR;
+	}
+
+	int
+		paren_count = 1;
+	std::string paren1 = "(";
+	while (ptr != token.end())
+	{
+		++ptr;
+		if (*ptr == '/' || ptr == token.end())
+		{
+			std::ostringstream err_msg;
+			err_msg << "End of line or  " "/"
+				" encountered before end of parentheses, " << token << ".";
+			error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+			return PARSER_ERROR;
+		}
+		paren1.insert(paren1.end(), *ptr);	// element.push_back(c);
+		if (*ptr == '(')
+			++paren_count;
+		if (*ptr == ')')
+			--paren_count;
+		if (paren_count == 0)
+			break;
+	}
+
+	++ptr;
+	if (ptr == token.end() || *ptr != '/')
+	{
+		std::ostringstream err_msg;
+		err_msg << " " "/" " must follow parentheses " <<
+			"ending first half of redox couple, " << token << ".";
+		error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+		return PARSER_ERROR;
+	}
+	++ptr;
+	std::string elt2;
+	get_elt(ptr, token.end(), elt2);
+	if (elt1.compare(elt2) != 0)
+	{
+		std::ostringstream err_msg;
+		err_msg << "Redox couple must be two redox states " <<
+			"of the same element, " << token << ".";
+		error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+		return PARSER_ERROR;
+	}
+	if (*ptr != '(')
+	{
+		std::ostringstream err_msg;
+		err_msg << "Element name must be followed by "
+			"parentheses in redox couple, " << token << ".";
+		error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+		incr_input_error();
+		return PARSER_ERROR;
+	}
+	std::string paren2 = "(";
+	paren_count = 1;
+
+	while (ptr != token.end())
+	{
+		++ptr;
+		if (*ptr == '/' || ptr == token.end())
+		{
+			std::ostringstream err_msg;
+			err_msg << "End of line or  " "/"
+				" encountered before end of parentheses, " << token << ".";
+			error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+			return PARSER_ERROR;
+		}
+		paren2.insert(paren2.end(), *ptr);	// element.push_back(c);
+		if (*ptr == '(')
+			++paren_count;
+		if (*ptr == ')')
+			--paren_count;
+		if (paren_count == 0)
+			break;
+	}
+	if (paren1.compare(paren2) < 0)
+	{
+		token = elt1 + paren1 + std::string("/") + elt2 + paren2;
+	}
+	else if (paren1.compare(paren2) > 0)
+	{
+		token = elt2 + paren2 + std::string("/") + elt1 + paren1;
+	}
+	else
+	{
+		std::ostringstream err_msg;
+		err_msg << "Both parts of redox couple are the same, " <<
+			token << ".";
+		error_msg(err_msg.str().c_str(), PHRQ_io::OT_CONTINUE);
+		return PARSER_ERROR;
+	}
+	return PARSER_OK;
+}
+
+template <class T>
+CParser::STATUS_TYPE CParser::addPair(std::map < std::string, T >&totals,
+									  std::istream::pos_type & pos)
+{
+	std::string token;
+	T d;
+	CParser::TOKEN_TYPE j;
+
+	m_line_iss.seekg(pos);
+
+	j = copy_token(token, pos);
+
+	if (j == CParser::TT_EMPTY)
+		return PARSER_OK;
+
+	if (!(m_line_iss >> d))
+	{
+		return PARSER_ERROR;
+	}
+	totals[token] = d;
+	return PARSER_OK;
+}
+
+int
+CParser::getOptionFromLastLine(const std::vector < std::string > &opt_list,
+							   std::string::iterator & next_char, bool flag_error)
+{
+	//
+	// Read a line and check for options
+	//
+	int j;
+	int /*  opt_l,  */ opt;
+	std::string::iterator opt_ptr;
+	std::string option;
+
+	//
+	// Read line
+	//
+	PHRQ_io::LINE_TYPE lt = m_line_type;
+	if (lt == PHRQ_io::LT_EOF)
+	{
+		j = OPT_EOF;
+	}
+	else if (lt == PHRQ_io::LT_KEYWORD)
+	{
+		j = OPT_KEYWORD;
+	}
+	else if (lt == PHRQ_io::LT_OPTION)
+	{
+		opt_ptr = m_line.begin();
+		std::string::iterator end = m_line.end();
+		copy_token(option, opt_ptr, end);
+		if (find_option(option, &opt, opt_list, false) == CParser::FT_OK)
+		{
+			j = opt;
+			m_line_save.replace(m_line_save.find(option), option.size(),
+								opt_list[opt]);
+			m_line.replace(m_line.find(option), option.size(), opt_list[opt]);
+			opt_ptr = m_line.begin();
+			std::string::iterator end = m_line.end();
+			copy_token(option, opt_ptr, end);
+			next_char = opt_ptr;
+			if (true)			// pr.echo_input == TRUE
+			{
+				if (true)		// database_file == NULL
+				{
+					std::ostringstream msg;
+					msg << "\t" << m_line_save << "\n";
+					io->output_msg(msg.str().c_str());
+				}
+			}
+		}
+		else
+		{
+			if (flag_error)
+			{
+				if (true)			// (database_file == NULL)
+				{
+					std::ostringstream msg;
+					msg << "\t" << m_line_save << "\n";
+					io->output_msg(msg.str().c_str());
+				}
+				std::ostringstream err;
+				err << "Unknown option." << "\n";
+				err << m_line_save << "\n";
+				error_msg(err.str().c_str());
+			}
+			j = OPT_ERROR;
+			next_char = m_line.begin();
+		}
+	}
+	else
+	{
+		opt_ptr = m_line.begin();
+		std::string::iterator end = m_line.end();
+		copy_token(option, opt_ptr, end);
+		if (find_option(option, &opt, opt_list, true) == FT_OK)
+		{
+			j = opt;
+			next_char = opt_ptr;
+		}
+		else
+		{
+			j = OPT_DEFAULT;
+			next_char = m_line.begin();
+		}
+		if (true)				// pr.echo_input == TRUE
+		{
+			if (true)			// database_file == NULL
+			{
+#if !defined(R_SO)
+				std::cout << "\t" << m_line_save << "\n";
+#endif
+			}
+		}
+	}
+	return (j);
+}
+
+int
+CParser::getOptionFromLastLine(const std::vector < std::string > &opt_list,
+							   std::istream::pos_type & next_pos, bool flag_error)
+{
+	//
+	// Read a line and check for options
+	//
+	int j;
+	int opt;
+	std::istream::pos_type pos_ptr;
+	std::string option;
+
+	//
+	// Read line
+	//
+	PHRQ_io::LINE_TYPE lt = m_line_type;
+	if (lt == PHRQ_io::LT_EOF)
+	{
+		j = OPT_EOF;
+	}
+	else if (lt == PHRQ_io::LT_KEYWORD)
+	{
+		j = OPT_KEYWORD;
+	}
+	else if (lt == PHRQ_io::LT_OPTION)
+	{
+		std::string::iterator opt_ptr = m_line.begin();
+		std::string::iterator end = m_line.end();
+		copy_token(option, opt_ptr, end);
+		if (find_option(option.substr(1), &opt, opt_list, false) == FT_OK)
+		{
+			// replace -option with option
+			j = opt;
+			m_line_save.replace(m_line_save.find(option), option.size(),
+								opt_list[opt]);
+			m_line.replace(m_line.find(option), option.size(), opt_list[opt]);
+
+			// reset iss
+			m_line_iss.str(m_line);
+			m_line_iss.seekg(0, std::ios_base::beg);
+			m_line_iss.clear();
+
+			pos_ptr = 0;
+			copy_token(option, pos_ptr);
+			next_pos = pos_ptr;
+			//if (this->echo_file)			// pr.echo_input == TRUE
+			if (false)
+			{
+				if (true)		// database_file == NULL
+				{
+					std::ostringstream msg;
+					msg << "\t" << m_line_save << "\n";
+					io->output_msg(msg.str().c_str());
+				}
+			}
+		}
+		else
+		{
+			if (flag_error) // don`t throw error
+			{
+				if (true)			// (database_file == NULL)
+				{
+					std::ostringstream msg;
+					msg << "\t" << m_line_save << "\n";
+					io->output_msg(msg.str().c_str());
+				}
+				error_msg("Unknown option.", PHRQ_io::OT_CONTINUE);
+				error_msg(m_line_save.c_str(), PHRQ_io::OT_CONTINUE);
+				incr_input_error();
+			}
+			j = OPT_ERROR;
+			next_pos = pos_ptr;
+		}
+	}
+	else
+	{
+		pos_ptr = 0;
+		copy_token(option, pos_ptr);
+		if (find_option(option, &opt, opt_list, true) == FT_OK)
+		{
+			j = opt;
+			next_pos = pos_ptr;
+		}
+		else
+		{
+			j = OPT_DEFAULT;
+			next_pos = 0;
+		}
+		if (true)				// pr.echo_input == TRUE
+		{
+			if (true)			// database_file == NULL
+			{
+				std::ostringstream msg;
+				msg << "\t" << m_line_save << "\n";
+				io->output_msg(msg.str().c_str());
+			}
+		}
+	}
+	return (j);
+}
+int CParser::
+incr_input_error()
+{
+	return ++m_input_error;
+}
+
+CParser::TOKEN_TYPE CParser::copy_title(std::string & token,
+										std::string::iterator & begin,
+										std::string::iterator & end)
+{
+	if (begin != end)
+	{
+		std::string::iterator b = begin;
+		std::string::iterator e = end;
+		for (; b < end && (::isspace(*b) || (*b == ',')); ++b);
+		begin = b;
+		if (*begin == '"')
+		{
+			begin = ++b;
+			for (; begin != end && !(*begin == '"'); ++begin);
+			e = begin;
+			if (begin != end && *begin == '"')
+			{
+				e = begin++;
+			}
+		}
+		else if (*begin == '\'')
+		{
+			begin = ++b;
+			for (; begin != end && !(*begin == '\''); ++begin);
+			e = begin;
+			if (begin != end && *begin == '\'')
+			{
+				e = begin++;
+			}
+		}
+		else
+		{
+			for (; begin < end && !(*begin == ',') && !(::isspace(*begin)); ++begin);
+			e = begin;
+		}
+		token.assign(b, e);
+	}
+	else
+	{
+		token.resize(0);
+	}
+	token = trim(token);
+	return token_type(token);
+}
+bool CParser::get_true_false(std::istream::pos_type & pos, bool def)
+{
+	std::string token;
+	this->copy_token(token, pos);
+	std::string::iterator b = token.begin();
+	for (; b != token.end() && (::isspace(*b)); ++b);
+	if (b != token.end())
+	{
+		if (*b == 'f' || *b == 'F')
+		{
+			return false;
+		}
+		else if (*b == 't' || *b == 'T')
+		{
+			return true;
+		}
+	}
+	return def;
+}
+CParser::TOKEN_TYPE CParser::get_rest_of_line(std::string &token)
+{
+	token.clear();
+	int j;
+	while ((j = m_line_iss.get()) != std::char_traits < char >::eof())
+	{
+		char c = (char) j;
+		token += c;
+	}
+	token = trim(token);
+	return token_type(token);
+}
+CParser::TOKEN_TYPE CParser::parse_delimited(std::string & source, std::string & result,
+										const std::string& t = " \t")
+{
+
+	size_t pos = source.find_first_of(t);
+	std::string temp;
+	if (pos != std::string::npos)
+	{
+		result = source.substr(0, pos);
+		temp = source.substr(pos+1);
+		source = temp;
+	}
+	else
+	{
+		result = source;
+		source.clear();
+	}
+	std::string str = result;
+
+	return token_type(trim_left(str));
+}