utility.cpp File Reference

#include <algorithm>
#include <cmath>
#include <limits>
#include <string>
#include <sstream>
#include <iostream>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "copasi.h"
#include "utility.h"
#include "CCopasiMessage.h"

Include dependency graph for utility.cpp:

Go to the source code of this file.

Macros
#define	toBeEscaped   "\\\""

Functions
void	FixSName (const std::string &original, std::string &fixed)
bool	isNumber (const std::string &str)
std::string	ISODateTime (tm *pTime)
std::string	LocalTimeStamp ()
std::string	nameToSbmlId (const std::string &name)
std::string	pointerToString (const void *pVoid)
std::string	quote (const std::string &name, const std::string &additionalEscapes)
std::string	StringPrint (const char *format,...)
bool	stringReplace (std::string &str, const std::string &target, const std::string &replacement)
void *	stringToPointer (const std::string str)
double	strToDouble (const char *str, char const **pTail)
C_INT32	strToInt (const char *str, char const **pTail)
unsigned C_INT32	strToUnsignedInt (const char *str, char const **pTail)
std::string	unQuote (const std::string &name)
std::string	UTCTimeStamp ()

Macro Definition Documentation

#define toBeEscaped   "\\\""

Referenced by quote().

Function Documentation

void FixSName	(	const std::string &	original,
		std::string &	fixed
	)

Definition at line 188 of file utility.cpp.

{
  size_t i, len;

  // check reserved names
  if (original == "abs") {fixed = "_abs"; return;}

  if (original == "acos") {fixed = "_acos"; return;}

  if (original == "and") {fixed = "_and"; return;}

  if (original == "asin") {fixed = "_asin"; return;}

  if (original == "atan") {fixed = "_atan"; return;}

  if (original == "ceil") {fixed = "_ceil"; return;}

  if (original == "cos") {fixed = "_cos"; return;}

  if (original == "exp") {fixed = "_exp"; return;}

  if (original == "floor") {fixed = "_floor"; return;}

  if (original == "hilli") {fixed = "_hilli"; return;}

  if (original == "hillmmr") {fixed = "_hillmmr"; return;}

  if (original == "hillmr") {fixed = "_hillmr"; return;}

  if (original == "hillr") {fixed = "_hillr"; return;}

  if (original == "isouur") {fixed = "_isouur"; return;}

  if (original == "log") {fixed = "_log"; return;}

  if (original == "log10") {fixed = "_log10"; return;}

  if (original == "massi") {fixed = "_massi"; return;}

  if (original == "massr") {fixed = "_massr"; return;}

  if (original == "not") {fixed = "_not"; return;}

  if (original == "or") {fixed = "_or"; return;}

  if (original == "ordbbr") {fixed = "_ordbbr"; return;}

  if (original == "ordbur") {fixed = "_ordbur"; return;}

  if (original == "ordubr") {fixed = "_ordubr"; return;}

  if (original == "pow") {fixed = "_pow"; return;}

  if (original == "ppbr") {fixed = "_ppbr"; return;}

  if (original == "sin") {fixed = "_sin"; return;}

  if (original == "sqr") {fixed = "_sqr"; return;}

  if (original == "sqrt") {fixed = "_sqrt"; return;}

  if (original == "substance") {fixed = "_substance"; return;}

  if (original == "time") {fixed = "_time"; return;}

  if (original == "tan") {fixed = "_tan"; return;}

  if (original == "umai") {fixed = "_umai"; return;}

  if (original == "umar") {fixed = "_umar"; return;}

  if (original == "uai") {fixed = "_uai"; return;}

  if (original == "ualii") {fixed = "_ualii"; return;}

  if (original == "uar") {fixed = "_uar"; return;}

  if (original == "ucii") {fixed = "_ucii"; return;}

  if (original == "ucir") {fixed = "_ucir"; return;}

  if (original == "ucti") {fixed = "_ucti"; return;}

  if (original == "uctr") {fixed = "_uctr"; return;}

  if (original == "uhmi") {fixed = "_uhmi"; return;}

  if (original == "uhmr") {fixed = "_uhmr"; return;}

  if (original == "umi") {fixed = "_umi"; return;}

  if (original == "unii") {fixed = "_unii"; return;}

  if (original == "unir") {fixed = "_unir"; return;}

  if (original == "uuhr") {fixed = "_uuhr"; return;}

  if (original == "umr") {fixed = "_umr"; return;}

  if (original == "usii") {fixed = "_usii"; return;}

  if (original == "usir") {fixed = "_usir"; return;}

  if (original == "uuci") {fixed = "_uuci"; return;}

  if (original == "uucr") {fixed = "_uucr"; return;}

  if (original == "uui") {fixed = "_uui"; return;}

  if (original == "uur") {fixed = "_uur"; return;}

  if (original == "volume") {fixed = "_volume"; return;}

  if (original == "xor") {fixed = "_xor"; return;}

  len = original.length();

  // check rule for initial characters
  // if first not a letter...
  if (((original[0] < 'A') || (original[0] > 'z')) && (original[0] != '_'))
    {
      if ((original[0] >= '0') && (original[0] <= '9'))
        fixed = "_" + original;
      else
        {fixed = original; fixed [0] = '_';}
    }
  else
    fixed = original;

  len = fixed.length();

  for (i = 1; i < len; i++)
    if ((fixed [i] != '_') && ((fixed [i] < 'A') || (fixed [i] > 'z')) &&
        ((fixed [i] < '0') || (fixed [i] > '9')))
      fixed [i] = '_';
}

bool isNumber

(

const std::string &

str

)

Check whether the given string represents a number

Parameters

const

std::string & str

Returns

bool isNumber

Definition at line 75 of file utility.cpp.

References strToDouble().

Referenced by COptItem::compileLowerBound(), COptItem::compileUpperBound(), ConverterASTNode::ConverterASTNode(), CMetabNameInterface::getDisplayName(), CQFittingItemWidget::loadSelection(), CQFittingItemWidget::saveSelection(), COptItem::setLowerBound(), CQFittingItemWidget::setTableText(), COptItem::setUpperBound(), CQFittingItemWidget::slotCheckLowerInf(), CQFittingItemWidget::slotCheckUpperInf(), CQFittingItemWidget::slotLowerLostFocus(), CQFittingItemWidget::slotStartLostFocus(), CQFittingItemWidget::slotUpperLostFocus(), and CChemEqInterface::writeElement().

{
  if (str.find_first_of("+-.0123456789")) return false;

  const char * Tail;
  strToDouble(str.c_str(), & Tail);

  if (*Tail) return false;

  return true;
}

std::string ISODateTime

(

tm *

pTime

)

Returns the time pointed to by pTime in ISO format

Definition at line 31 of file utility.cpp.

Referenced by LocalTimeStamp(), and UTCTimeStamp().

{
  char str[20];

  if (pTime)
    {
      sprintf(str, "%d-%.02d-%.02d %.02d:%.02d:%.02d",
              pTime->tm_year + 1900,
              pTime->tm_mon + 1,
              pTime->tm_mday,
              pTime->tm_hour,
              pTime->tm_min,
              pTime->tm_sec);
    }
  else
    {
      sprintf(str, "0000-00-00 00:00:00");
    }

  return (std::string) str;
}

std::string LocalTimeStamp

(

)

Returns the current local time in ISO format

Definition at line 53 of file utility.cpp.

References ISODateTime().

Referenced by CCopasiMessage::handler().

{
  time_t Time;
  time(&Time);

  tm *sTime = NULL;
  sTime = localtime(&Time);

  return ISODateTime(sTime);
}

std::string nameToSbmlId

(

const std::string &

name

)

Convert a utf8 encoded name to a XmlId

Parameters

const

std::string & name

Returns

std::string SbmlId

Definition at line 437 of file utility.cpp.

Referenced by CSBMLExporter::createUniqueId().

{
  // We convert all non allowed characters to '_'
  // letter ::= ’a’..’z’,’A’..’Z’
  // digit  ::= ’0’..’9’
  // idChar ::= letter | digit | ’_’
  // SId    ::= (letter | ’_’ ) idChar*

  std::ostringstream IdStream;

  std::string::const_iterator it = name.begin();
  std::string::const_iterator end = name.end();

  if ('0' <= *it && *it <= '9')
    {
      IdStream << '_';
    }

  for (; it != end; ++it)
    {
      // second, third or forth character of a multi-byte encoding
      if (0x80 == (*it & 0xc0))
        {
          continue;
        }

      if (('0' <= *it && *it <= '9') ||
          ('a' <= *it && *it <= 'z') ||
          ('A' <= *it && *it <= 'Z'))
        {
          IdStream << *it;
        }
      else
        {
          IdStream << '_';
        }
    }

  std::string Id = IdStream.str();

  if (Id[Id.length() - 1] != '_')
    {
      return Id;
    }

  return Id.substr(0, Id.length() - 1);
}

std::string pointerToString

(

const void *

pVoid

)

Convert a void pointer to a string

Parameters

const

void * pVoid

Returns

std::string str

Definition at line 423 of file utility.cpp.

References fatalError.

Referenced by CEvaluationNodeObject::CEvaluationNodeObject(), and CEvaluationNodeObject::setObjectValuePtr().

{
  char String[19];

  int Printed = sprintf(String, "%p", pVoid);

  if (Printed < 0 || 18 < Printed)
    {
      fatalError();
    }

  return String;
}

std::string quote	(	const std::string &	name,
		const std::string &	additionalEscapes = ""
	)

Surround a name with quotes if the name contains a space or double quote else the name is returned unmodified. In the quoted name " and \ are escaped. The parameter additionalEscapes forces quotes around names containing any of the character in the parameter.

Parameters

const	std::string & name
const	std::string & additionalEscapes (default: "")

Returns

std::string quote

Definition at line 144 of file utility.cpp.

References toBeEscaped.

Referenced by CChemEqInterface::addModifier(), CEvaluationNodeCall::CEvaluationNodeCall(), CEvaluationNodeCall::getBerkeleyMadonnaString(), CEvaluationNodeCall::getCCodeString(), CEvaluationNodeCall::getData(), CMetabNameInterface::getDisplayName(), CEvaluationNodeCall::getDisplayString(), CEvaluationNodeCall::getInfix(), CEvaluationNodeCall::getMMLString(), CEvaluationNodeCall::getXPPString(), CEvaluationNodeCall::setData(), and CMetabNameInterface::splitDisplayName().

{
  if (name.find_first_of(" \"" + additionalEscapes) == std::string::npos)
    return name;

#define toBeEscaped "\\\""
  std::string Escaped(name);
  std::string::size_type pos = Escaped.find_first_of(toBeEscaped);

  while (pos != std::string::npos)
    {
      Escaped.insert(pos, "\\");
      pos += 2;
      pos = Escaped.find_first_of(toBeEscaped, pos);
    }

  return "\"" + Escaped + "\"";
#undef toBeEscaped
}

std::string StringPrint	(	const char *	format,
			...
	)

sprintf like function for strings

Parameters

const char *	format sprintf like format string
...

Returns

"string"

Definition at line 87 of file utility.cpp.

References C_INT32, and INITIALTEXTSIZE.

Referenced by CExperimentSet::addExperiment(), CExperiment::elevateChildren(), CExperimentObjectMap::getDefaultScale(), CExperimentObjectMap::getName(), CExperimentObjectMap::getObjectCN(), CExperimentObjectMap::getRole(), CExperimentObjectMap::getScale(), CCopasiTimeVariable::LL2String(), CQExperimentData::load(), CReaction::loadOld(), CReaction::loadOneRole(), CExperimentObjectMap::setNumCols(), CExperimentObjectMap::setObjectCN(), CExperimentObjectMap::setRole(), CExperimentObjectMap::setScale(), CVersion::setString(), CQExperimentData::slotFileAdd(), and CCopasiXMLParser::ParameterDescriptionElement::start().

{
  C_INT32 TextSize = INITIALTEXTSIZE;
  C_INT32 Printed = 0;

  char *Text = NULL;

  Text = new char[TextSize + 1];

  va_list Arguments; // = NULL;
  va_start(Arguments, format);
  Printed = vsnprintf(Text, TextSize + 1, format, Arguments);
  va_end(Arguments);

  while (Printed < 0 || TextSize < Printed)
    {
      delete [] Text;

      (Printed < 0) ? TextSize *= 2 : TextSize = Printed;
      Text = new char[TextSize + 1];

      va_list Arguments; // = NULL;
      va_start(Arguments, format);
      Printed = vsnprintf(Text, TextSize + 1, format, Arguments);
      va_end(Arguments);
    }

  std::string Result = Text;

  delete [] Text;
  return Result;
}

bool stringReplace	(	std::string &	str,
		const std::string &	target,
		const std::string &	replacement
	)

Replaces the all occurrences of target string in str with the replacement and returns true if the target string was replaced

Parameters

std::string	& str
const	std::string & target
const	std::string & replacement

Returns

bool replaced

Definition at line 165 of file utility.cpp.

Referenced by CModel::convert2NonReversible().

{
  bool replaced = false;

  std::string::size_type pos = str.find(target, 0);

  while (pos != std::string::npos)
    {
      replaced = true;

      str.replace(pos, target.length(), replacement, 0, std::string::npos);
      pos = str.find(target, 0);
    }

  return replaced;
}

void* stringToPointer

(

const std::string

str

)

Convert a character sequence to a void pointer

Parameters

const

std::string str

Returns

void * pVoid

Definition at line 414 of file utility.cpp.

Referenced by CEvaluationNodeObject::compile(), CMathExpression::compile(), and CMathExpression::copy().

{
  void * pPointer;

  sscanf(str.c_str(), "%p", &pPointer);

  return pPointer;
}

double strToDouble	(	const char *	str,
		char const **	pTail = NULL
	)

Convert a character sequence to a double

Parameters

const	char * str
char	const ** pTail (default: NULL)

Returns

double

Definition at line 325 of file utility.cpp.

Referenced by CEvaluationNodeNumber::CEvaluationNodeNumber(), COptItem::compileLowerBound(), COptItem::compileUpperBound(), CReadConfig::getVariable(), isNumber(), CMiaseParser::newSimulation(), operator>>(), COptItem::setLowerBound(), COptItem::setUpperBound(), CCopasiXMLParser::RectangleElement::start(), CCopasiXMLParser::EllipseElement::start(), CCopasiXMLParser::TextElement::start(), CCopasiXMLParser::RenderCurveElement::start(), CCopasiXMLParser::PolygonElement::start(), CCopasiXMLParser::GroupElement::start(), test000087::test_simulate_reaction_flux_reference_1(), CEvaluationNodeNumber::toAST(), and CChemEqParserBase::yyparse().

{
  double Value = std::numeric_limits<C_FLOAT64>::quiet_NaN();

  if (pTail != NULL)
    {
      *pTail = str;
    }

  if (str == NULL || *str == 0x0)
    {
      return Value;
    }

  std::istringstream in;

  in.imbue(std::locale::classic());
  in.str(str);

  in >> Value;

  if (pTail != NULL && !isnan(Value))
    {
      *pTail = str + std::min< size_t >(in.tellg(), strlen(str));
    }

  return Value;
}

C_INT32 strToInt	(	const char *	str,
		char const **	pTail = NULL
	)

Convert a character sequence to a double

Parameters

const	char * str
char	const ** pTail (default: NULL)

Returns

C_INT32

Definition at line 354 of file utility.cpp.

References C_INT32.

Referenced by CCopasiXMLParser::ParameterElement::start(), and CCopasiXMLParser::COPASIElement::start().

{
  C_INT32 Value = std::numeric_limits< C_INT32 >::quiet_NaN();

  if (pTail != NULL)
    {
      *pTail = str;
    }

  if (str == NULL || *str == 0x0)
    {
      return Value;
    }

  std::istringstream in;

  in.imbue(std::locale::classic());
  in.str(str);

  in >> Value;

  if (pTail != NULL && !isnan(Value))
    {
      *pTail = str + std::min< size_t >(in.tellg(), strlen(str));
    }

  return Value;
}

unsigned C_INT32 strToUnsignedInt	(	const char *	str,
		char const **	pTail = NULL
	)

Convert a character sequence to a double

Parameters

const	char * str
char	const ** pTail (default: NULL)

Returns

unsigned C_INT32

Definition at line 384 of file utility.cpp.

References C_INT32.

Referenced by CCopasiParameterGroup::getObject(), CCopasiXMLParser::CompartmentElement::start(), CCopasiXMLParser::ParameterElement::start(), CCopasiXMLParser::ReportElement::start(), CCopasiXMLParser::ParameterDescriptionElement::start(), and CCopasiXMLParser::SliderElement::start().

{
  unsigned C_INT32 Value = std::numeric_limits< unsigned C_INT32 >::quiet_NaN();

  if (pTail != NULL)
    {
      *pTail = str;
    }

  if (str == NULL || *str == 0x0)
    {
      return Value;
    }

  std::istringstream in;

  in.imbue(std::locale::classic());
  in.str(str);

  in >> Value;

  if (pTail != NULL && !isnan(Value))
    {
      *pTail = str + std::min< size_t >(in.tellg(), strlen(str));
    }

  return Value;
}

std::string unQuote

(

const std::string &

name

)

Unesacape a quoted name. If the name is surrounded by quotes these are removed and included escape sequences '.' are reduced to '.' else the name is returned unmodified.

Parameters

const

std::string & name

Returns

std::string unQuote

Definition at line 120 of file utility.cpp.

Referenced by CEvaluationNodeCall::CEvaluationNodeCall(), CModel::findMetabByName(), CEvaluationNodeCall::getData(), CCopasiVectorN< CReportDefinition >::getIndex(), CEvaluationNodeCall::setData(), and CChemEqParser::yylex().

{
  std::string Name = name;
  std::string::size_type len = Name.length();

  if (len > 1 && Name[0] == '"' && Name[len - 1] == '"')
    {
      // Remove surrounding double quotes.
      Name = Name.substr(1, len - 2);

      // Remove escape sequences.
      std::string::size_type pos = Name.find("\\");

      while (pos != std::string::npos)
        {
          Name.erase(pos, 1);
          pos++;
          pos = Name.find("\\", pos);
        }
    }

  return Name;
}

std::string UTCTimeStamp

(

)

Returns the current time in ISO format

Definition at line 64 of file utility.cpp.

References ISODateTime().

Referenced by createParameterSetsForExperiment(), CCopasiXML::save(), and CConfigurationFile::CXML::save().

{
  time_t Time;
  time(&Time);

  tm *sTime = NULL;
  sTime = gmtime(&Time);

  return ISODateTime(sTime);
}