void PatchParser::parseMatrix(parser::DefTokeniser& tok, IPatch& patch) const
{
tok.assertNextToken("(");
// For each row
for (std::size_t c = 0; c < patch.getWidth(); c++)
{
tok.assertNextToken("(");
// For each column
for (std::size_t r=0; r < patch.getHeight(); r++)
{
tok.assertNextToken("(");
// Parse vertex coordinates
patch.ctrlAt(r, c).vertex[0] = strToDouble(tok.nextToken());
patch.ctrlAt(r, c).vertex[1] = strToDouble(tok.nextToken());
patch.ctrlAt(r, c).vertex[2] = strToDouble(tok.nextToken());
// Parse texture coordinates
patch.ctrlAt(r, c).texcoord[0] = strToDouble(tok.nextToken());
patch.ctrlAt(r, c).texcoord[1] = strToDouble(tok.nextToken());
tok.assertNextToken(")");
}
tok.assertNextToken(")");
}
tok.assertNextToken(")");
}
boost::shared_ptr<HazardRateStructure> qlHazardRateFactory::hazardRateTS(TiXmlNode* node)
{
boost::shared_ptr<HazardRateStructure> hazardCurve;
Date referenceDate = Settings::instance().evaluationDate();
std::vector<boost::shared_ptr<DefaultProbabilityHelper> > instruments;
qlCalendarFactory calFactory = qlCalendarFactory();
qlTimeUnitFactory timeUnitFactory = qlTimeUnitFactory();
qlYieldTermStructureFactory tsFactory = qlYieldTermStructureFactory();
Calendar calendar = calFactory.calendar(node->FirstChildElement("calendar")->GetText());
Real recoveryRate = strToDouble(node->FirstChildElement("recoveryRate")->GetText());
TiXmlElement* rateNode = node->FirstChildElement("rateData");
std::vector<Period> periods;
std::vector<Real> spreadRates;
if(rateNode)
{
for(rateNode; rateNode; rateNode = rateNode->NextSiblingElement("rateData"))
{
periods.push_back(timeUnitFactory.timeUnit(rateNode));
spreadRates.push_back(strToDouble(rateNode->FirstChildElement("data")->GetText()));
}
}
for (Size i=0; i<periods.size(); i++) {
instruments.push_back(boost::shared_ptr<DefaultProbabilityHelper>(
new SpreadCdsHelper(
Handle<Quote>(boost::shared_ptr<Quote>(
new SimpleQuote(spreadRates[i]))),
periods[i],
0,
calendar,
Quarterly,
Following,
DateGeneration::TwentiethIMM,
Actual365Fixed(),
recoveryRate,
tsCurve_)));
}
// Bootstrap hazard rates
std::string curveType = "HazardRate";
std::string interpolationType = "BackwardFlat";
boost::shared_ptr<PiecewiseDefaultCurve<HazardRate, BackwardFlat> >
hazardRateStructure(
new PiecewiseDefaultCurve<HazardRate, BackwardFlat>(
referenceDate,
instruments,
Actual365Fixed()));
return hazardCurve;
}
/**
* Convert parameter to double (64 bit)
* @param context
* @param parameter
* @param value result
* @return TRUE if succesful
*/
scpi_bool_t SCPI_ParamToDouble(scpi_t * context, scpi_parameter_t * parameter, double * value) {
scpi_bool_t result;
uint64_t valint;
if (!value) {
SCPI_ErrorPush(context, SCPI_ERROR_SYSTEM_ERROR);
return FALSE;
}
switch (parameter->type) {
case SCPI_TOKEN_HEXNUM:
case SCPI_TOKEN_OCTNUM:
case SCPI_TOKEN_BINNUM:
result = SCPI_ParamToUInt64(context, parameter, &valint);
*value = valint;
break;
case SCPI_TOKEN_DECIMAL_NUMERIC_PROGRAM_DATA:
case SCPI_TOKEN_DECIMAL_NUMERIC_PROGRAM_DATA_WITH_SUFFIX:
result = strToDouble(parameter->ptr, value) > 0 ? TRUE : FALSE;
break;
default:
result = FALSE;
}
return result;
}
// Get Widget data as an double (entry, textview)
bool
GtkAReViWidget::getWidgetDouble(const StlString &propName,double &propValueOut)
{
StlString strValue;
if (!getWidgetString(propName,strValue))
return false;
return strToDouble(propValueOut,strValue);
}
ASTNode* CEvaluationNodeNumber::toAST(const CDataModel* /* pDataModel */) const
{
SubType subType = (SubType)this->subType();
ASTNode* node = new ASTNode();
double num1;
double num2;
const char * end;
const char * str = mData.c_str();
switch (subType)
{
case SubType::DOUBLE:
node->setType(AST_REAL);
node->setValue(*mpValue);
break;
case SubType::INTEGER:
node->setType(AST_INTEGER);
node->setValue((long)*mpValue);
break;
case SubType::ENOTATION:
node->setType(AST_REAL_E);
num2 = floor(log10(*mpValue));
num1 = pow(10.0, log10(*mpValue) - num2);
node->setValue(num1, (long)num2);
break;
case SubType::RATIONALE:
node->setType(AST_RATIONAL);
str++; // Skip the '('
num1 = strToDouble(str, &end);
end++; // Skip the '/'
num2 = strToDouble(end, NULL);
node->setValue((long)num1, (long)num2);
break;
case SubType::INVALID:
break;
}
return node;
}
double Parser::evaluateToNumber(Expr* e)
{
switch (e->tag()) {
case TAG_literalUndefined: return MathUtils::kNaN;
case TAG_literalNull: return 0.0;
case TAG_literalBoolean: return ((LiteralBoolean*)e)->value ? 1.0 : 0.0;
case TAG_literalDouble: return ((LiteralDouble*)e)->value;
case TAG_literalInt: return (double)(((LiteralInt*)e)->value);
case TAG_literalUInt: return (double)(((LiteralUInt*)e)->value);
case TAG_literalString: return strToDouble(((LiteralString*)e)->value);
default:
failNonConstant(e);
return 0;
}
}
CEvaluationNodeNumber::CEvaluationNodeNumber(const SubType & subType,
const Data & data):
CEvaluationNode(MainType::NUMBER, subType, data)
{
mPrecedence = PRECEDENCE_NUMBER;
mValueType = ValueType::Number;
const char * end;
const char * str = mData.c_str();
switch (subType)
{
case SubType::DOUBLE:
case SubType::INTEGER:
case SubType::ENOTATION:
{
//mValue = strToDouble(str, NULL);
std::istringstream in;
in.imbue(std::locale::classic());
in.str(str);
in >> mValue;
}
break;
case SubType::RATIONALE:
str++; // Skip the '('
mValue = strToDouble(str, &end);
end++; // Skip the '/'
mValue /= strToDouble(end, NULL);
break;
case SubType::INVALID:
fatalError();
break;
}
}
CDatum::operator double () const
// double cast operator
{
switch (m_dwData & AEON_TYPE_MASK)
{
case AEON_TYPE_STRING:
return (m_dwData == 0 ? 0.0 : strToDouble(raw_GetString()));
case AEON_TYPE_NUMBER:
switch (m_dwData & AEON_NUMBER_TYPE_MASK)
{
case AEON_NUMBER_CONSTANT:
{
switch (m_dwData)
{
case constTrue:
return 1.0;
default:
ASSERT(false);
return 0.0;
}
}
case AEON_NUMBER_28BIT:
return (double)((int)(m_dwData & AEON_NUMBER_MASK) >> 4);
case AEON_NUMBER_32BIT:
return (double)(int)g_IntAlloc.Get(GetNumberIndex());
case AEON_NUMBER_DOUBLE:
return g_DoubleAlloc.Get(GetNumberIndex());
default:
ASSERT(false);
return 0.0;
}
case AEON_TYPE_COMPLEX:
return 0.0;
default:
ASSERT(false);
return 0.0;
}
}
bool CDatum::CreateFromStringValue (const CString &sValue, CDatum *retdDatum)
// CreateFromStringValue
//
// Creates either a string or a number depending on the value.
{
CDatum dDatum;
switch (GetStringValueType(sValue))
{
case typeNil:
break;
case typeInteger32:
dDatum = CDatum(strToInt(sValue, 0));
break;
case typeIntegerIP:
{
CIPInteger Value;
Value.InitFromString(sValue);
CDatum::CreateIPIntegerFromHandoff(Value, &dDatum);
break;
}
case typeDouble:
dDatum = CDatum(strToDouble(sValue));
break;
case typeString:
dDatum = CDatum(sValue);
break;
default:
return false;
}
if (retdDatum)
*retdDatum = dDatum;
return true;
}
/**
* Parse double parameter
* @param context
* @param value
* @param mandatory
* @return
*/
scpi_bool_t SCPI_ParamDouble(scpi_t * context, double * value, scpi_bool_t mandatory) {
const char * param;
size_t param_len;
size_t num_len;
if (!value) {
return FALSE;
}
if (!SCPI_ParamString(context, ¶m, ¶m_len, mandatory)) {
return FALSE;
}
num_len = strToDouble(param, value);
if (num_len != param_len) {
SCPI_ErrorPush(context, SCPI_ERROR_SUFFIX_NOT_ALLOWED);
return FALSE;
}
return TRUE;
}
/**
* Parse parameter as number, number with unit or special value (min, max, default, ...)
* @param context
* @param value return value
* @param mandatory if the parameter is mandatory
* @return
*/
scpi_bool_t SCPIParser::SCPI_ParamNumber(scpi_number_t * value, scpi_bool_t mandatory) {
scpi_bool_t result;
const char * param;
size_t len;
size_t numlen;
/* read parameter and shift to the next one */
result = SCPI_ParamString(¶m, &len, mandatory);
/* value not initializes */
if (!value) {
return FALSE;
}
value->type = SCPI_NUM_DEF;
/* if parameter was not found, return TRUE or FALSE according
* to fact that parameter was mandatory or not */
if (!result) {
return mandatory ? FALSE : TRUE;
}
/* convert string to special number type */
if (translateSpecialNumber(context.special_numbers, param, len, value)) {
/* found special type */
return TRUE;
}
/* convert text from double - no special type */
numlen = strToDouble(param, &value->value);
/* transform units of value */
if (numlen <= len) {
return transformNumber(param + numlen, len - numlen, value);
}
return FALSE;
}
/**
* Parses the postfix expression for the given code line in the parameter.
* While doing this, prints the intermediate states of the number stack
* using printNumberStackContent function.
* @param codeLine The code line which will be calculated.
* @param destination The name of destination variable.
*/
void parsePostfixExpression(struct code_line *codeLine, char destination) {
int i = 0;
while (i < codeLine->lineContentPostfix.postfixLength) {
if (isspace(codeLine->lineContentPostfix.postfixExpression[i])) {
i++;
} else {
if (isNumberOrVariable(
codeLine->lineContentPostfix.postfixExpression[i])) {
if (isalpha(
(codeLine->lineContentPostfix.postfixExpression[i]))) { // if the character is a variable
pushNumber(
variableValues[tolower(
codeLine->lineContentPostfix.postfixExpression[i++])
- 'a']);
} else { // if the character is a number
char numberString[NUMBER_LENGTH];
size_t j = 0;
while (!isspace(
codeLine->lineContentPostfix.postfixExpression[i])) {
numberString[j++] =
codeLine->lineContentPostfix.postfixExpression[i++];
}
numberString[j] = '\0';
double numberValue = strToDouble(numberString, j);
pushNumber(numberValue);
}
} else { // if the character is an operation sign character
double number1, number2;
number2 = popNumber();
number1 = popNumber();
switch (codeLine->lineContentPostfix.postfixExpression[i++]) {
case '+':
pushNumber(number1 + number2);
break;
case '-':
pushNumber(number1 - number2);
break;
case '*':
pushNumber(number1 * number2);
break;
case '/':
if (number2 == 0) {
fprintf(stderr, "ERROR: You can not divide by zero.");
exit(EXIT_FAILURE);
}
pushNumber(number1 / number2);
break;
default:
fprintf(stderr,
"ERROR: Unexpected character in the postfix expression.");
exit(EXIT_FAILURE);
break;
}
}
printf("Stack: ");
printNumberStackContent();
printf("\n");
}
}
double finalValue = popNumber();
variableValues[tolower(destination) - 'a'] = finalValue;
codeLine->finalValue = finalValue;
}
std::string stringCalc(std::string expression)
{
std::string subExpression, subExpression2, result, result2;
int startPos, endPos;
double val1, val2;
if (expression.compare(varNotFound) == 0)
return "";
do // Searches for (), calculates the expression inside, then
{ // replaces the () with the result. Will start from the
startPos = -1; // innermost (). Repeats until there are no more ().
endPos = -1;
for(register int i = 0 ; unsigned(i) < expression.length() ; i++)
{
if (expression[i] == '(')
{
startPos = i;
for (register int j = i; unsigned(j) < expression.length() ; j++)
{
if (expression[j] == ')')
{
endPos = j;
break;
}
}
}
}
if (startPos != -1) // () found
{
subExpression = expression.substr(startPos+1, endPos-startPos-1);
result = stringCalc(subExpression); // Calls same function with expression inside ()
expression.erase(startPos, endPos-startPos+1);
expression.insert(startPos, result);
}
}
while(startPos != -1);
// At this point the expression will have no ( or ) and only numbers, +, -, *, /
do // Searches for + and - then calculates the rest of the expression
{ // Will calculate last the + or - that is most to the right
startPos = -1;
for(register int i = 0 ; unsigned(i) < expression.length() ; i++)
{
if ((expression[i] == '+')||(expression[i] == '-'))
{
startPos = i;
}
}
// Expression[startPos] is the last + or - found in the entire string
if (startPos != -1)
{
if(expression[startPos]=='-') // Special case for negative numbers
{
if(startPos > 0)
{
if(!isdigit(expression[startPos-1]))
{
endPos = startPos;
for(register int i = 0 ; unsigned(i) < startPos ; i++)
{
if ((expression[i] == '+')||(expression[i] == '-'))
{
startPos = i;
}
}
if (startPos == endPos)
{
break;
}
}
}
else
{
break;
}
}
// Separates the 2 expressions before and after the + or -
subExpression = expression.substr(0, startPos);
subExpression2 = expression.substr(startPos+1, expression.length()-startPos);
result = stringCalc(subExpression); // Calls the same function for
result2 = stringCalc(subExpression2); // each of the new expressions
val1 = strToDouble(result);
val2 = strToDouble(result2);
if (expression[startPos] == '+')
{
expression = doubleToStr(val1 + val2);
}
else
{
expression = doubleToStr(val1 - val2);
}
}
}
while(startPos != -1);
do // Searches for * and / then calculates the rest of the expression
{ // Same logic as the +- block
startPos = -1;
for(register int i = 0 ; unsigned(i) < expression.length() ; i++)
{
if ((expression[i] == '*')||(expression[i] == '/'))
{
startPos = i;
}
}
if (startPos != -1)
{
subExpression = expression.substr(0, startPos);
subExpression2 = expression.substr(startPos+1, expression.length()-startPos);
result = stringCalc(subExpression);
result2 = stringCalc(subExpression2);
val1 = strToDouble(result);
val2 = strToDouble(result2);
if(expression[startPos] == '*')
{
expression = doubleToStr(val1 * val2);
}
else
{
expression = doubleToStr(val1 / val2);
}
}
}
while(startPos != -1);
return expression;
}
//hacky code for week 10 checkoffs
SensorData CrashDetectionThread::parseData(char *buffer){
SensorData data;
char *token = (char *)malloc(10*sizeof(char));
token = strtok(buffer, ",");
for (int i=0; token != NULL; i++) {
if (i == 0) {
data.accelerometerX = strToDouble(token);
}
else if (i == 1) {
data.accelerometerY = strToDouble(token);
}
else if (i == 2) {
data.accelerometerZ = strToDouble(token);
}
else if (i == 3) {
data.gyroX = strToDouble(token);
}
else if (i == 4) {
data.gyroY = strToDouble(token);
}
else if (i == 5) {
data.gyroZ = strToDouble(token);
}
else if (i == 6) {
data.fix = atoi(token);
}
else if (i == 7) {
data.satellites = atoi(token);
}
else if (i == 8) {
data.hour = (time_t)atoi(token);
}
else if (i == 9) {
data.minute = (time_t)atoi(token);
}
else if (i == 10) {
data.second = (time_t)atoi(token);
}
else if (i == 11) {
data.month = (time_t)atoi(token);
}
else if (i == 12) {
data.day = (time_t)atoi(token);
}
else if (i == 13) {
data.year = (time_t)atoi(token);
}
else if (i == 14) {
data.lattitude = strToDouble(token);
}
else if (i == 15) {
data.longitude = strToDouble(token);
}
else if (i == 16) {
data.speed = atoi(token);
}
else if (i == 17) {
//strcpy(data.command, token);
}
else if (i == 18) {
//data.value = atoi(token);
}
token = strtok(NULL, ",");
}
return data;
}
// virtual
CXMLHandler * RenderCurveHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
const char * Transform;
const char * Stroke;
const char * StrokeWidth;
const char * StrokeDashArray;
const char * StartHead;
const char * EndHead;
switch (mCurrentElement.first)
{
case RenderCurve:
mpData->pRenderCurve = new CLRenderCurve();
Transform = mpParser->getAttributeValue("transform", papszAttrs, false);
Stroke = mpParser->getAttributeValue("stroke", papszAttrs, false);
StrokeWidth = mpParser->getAttributeValue("stroke-width", papszAttrs, false);
StrokeDashArray = mpParser->getAttributeValue("stroke-dasharray", papszAttrs, false);
StartHead = mpParser->getAttributeValue("startHead", papszAttrs, false);
EndHead = mpParser->getAttributeValue("endHead", papszAttrs, false);
if (Transform != NULL)
{
mpData->pRenderCurve->parseTransformation(Transform);
}
if (Stroke != NULL)
{
mpData->pRenderCurve->setStroke(Stroke);
}
if (StrokeWidth != NULL)
{
double width = strToDouble(StrokeWidth, NULL);
mpData->pRenderCurve->setStrokeWidth(width);
}
if (StrokeDashArray != NULL)
{
mpData->pRenderCurve->parseDashArray(StrokeDashArray);
}
if (StartHead != NULL)
{
mpData->pRenderCurve->setStartHead(StartHead);
}
if (EndHead != NULL)
{
mpData->pRenderCurve->setEndHead(EndHead);
}
break;
case ListOfElements:
mpData->pListOfCurveElements = mpData->pRenderCurve->getListOfCurveElements();
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
int main(void)
{
int i = 0;
float vx;
float vy;
DoubleInt dTemp;
int count = 0;
char temp[100];
char tempStr[24];
ssize_t ret = 0;
Coords* c = NULL;
ret = allocate(PAGE_SIZE, 0, (void**)(&c));
if (ret != 0)
{
return (-1);
}
do
{
printfstr(STDOUT, "Initial Velocity X: ");
ret = readLine(STDIN, temp, 100);
if (ret < 0)
{
return (-1);
}
dTemp.d = strToDouble(temp);
} while (dTemp.u == NAN.u);
vx = (float)dTemp.d;
do
{
printfstr(STDOUT, "Initial Velocity Y: ");
ret = readLine(STDIN, temp, 100);
if (ret < 0)
{
return (-1);
}
dTemp.d = strToDouble(temp);
} while (dTemp.u == NAN.u);
vy = (float)dTemp.d;
printfstr(STDOUT, "Initial Count: ");
ret = readLine(STDIN, temp, 100);
if (ret < 0)
{
return (-1);
}
count = strToUint32(temp);
do
{
fillPage(vx, vy, c, &count, 10);
ret = readLine(STDIN, temp, 100);
if (ret < 0)
{
return (-1);
}
if (temp[0] == 'p')
{
for (i = 0; i < 510; i++)
{
tempStr[0] = 'x';
tempStr[1] = '=';
tempStr[2] = '\0';
snprintfloat(tempStr+2, 24, c[i].x);
printfstr(STDOUT, tempStr);
printfstr(STDOUT, ", ");
tempStr[0] = 'y';
tempStr[1] = '=';
tempStr[2] = '\0';
snprintfloat(tempStr+2, 24, c[i].y);
printfstr(STDOUT, tempStr);
printfstr(STDOUT, "\n");
}
}
} while ( (temp[0] == 'c') || (temp[0] == 'p') );
}
int main(int argc, char *argv[])
{
// Parse the commandline options
// first argument is the SBML filename
// second argument is the endtime
// third argument is the step number
// fourth argument is the filename where the results are to be written
// fifth argument is the tmp directory (this is not needed)
// the rest of the arguments are species names for the result
try
{
// Create the root container.
CCopasiRootContainer::init(0, NULL, false);
}
catch (copasi::autoexcept &e)
{}
catch (copasi::option_error &e)
{}
if (argc < 5)
{
std::cout << "Usage: semantic-test-suite SBMLFILENAME ENDTIME STEPNUMBER OUTFILENAME TMPDIR SPECIESID1 SPECIESID2 ..." << std::endl;
exit(1);
}
char* pSBMLFilename = argv[1];
const char* pEndTime = argv[2];
const char* pStepNumber = argv[3];
char* pOutputFilename = argv[4];
//char* pTmpDirectory=argv[5];
char** pSBMLSpeciesIds = new char * [argc - 6];
unsigned int i, iMax = argc;
CTrajectoryTask* pTrajectoryTask = NULL;
std::string CWD = COptions::getPWD();
double endTime = strToDouble(pEndTime, &pEndTime);
double stepNumber = strToDouble(pStepNumber, &pStepNumber);
if (endTime == 0.0)
{
std::cerr << "Invalid endtime " << pEndTime << std::endl;
exit(1);
}
if (stepNumber == 0.0)
{
std::cerr << "Invalid step number " << pStepNumber << std::endl;
exit(1);
}
for (i = 6; i < iMax; ++i)
{
pSBMLSpeciesIds[i - 6] = argv[i];
//std::cout << "Copying pointer to " << argv[i] << "." << std::endl;
}
try
{
// Create the global data model.
CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
// Import the SBML File
pDataModel->importSBML(pSBMLFilename);
//pDataModel->getModel()->forceCompile();
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for SBML testsuite run");
pReport->setTaskType(CCopasiTask::timeCourse);
pReport->setIsTable(true);
std::vector<CRegisteredObjectName>* pTable = pReport->getTableAddr();
pTable->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
iMax = iMax - 6;
const CCopasiVector<CMetab>& metabolites = pDataModel->getModel()->getMetabolites();
for (i = 0; i < iMax; ++i)
{
unsigned int j, jMax = metabolites.size();
for (j = 0; j < jMax; ++j)
{
if (metabolites[j]->getSBMLId() == pSBMLSpeciesIds[i])
{
pTable->push_back(metabolites[j]->getObject(CCopasiObjectName("Reference=Concentration"))->getCN());
//std::cout << "adding metabolite " << metabolites[j]->getObjectName() << " to report." << std::endl;
break;
}
}
if (j == jMax)
{
std::cerr << "Could not find a metabolite for the SBML id " << pSBMLSpeciesIds[i] << std::endl;
exit(1);
}
}
// create a trajectory task
pTrajectoryTask = new CTrajectoryTask();
pTrajectoryTask->getProblem()->setModel(pDataModel->getModel());
pTrajectoryTask->setScheduled(true);
pTrajectoryTask->getReport().setReportDefinition(pReport);
pTrajectoryTask->getReport().setTarget(CWD + "/" + pOutputFilename);
pTrajectoryTask->getReport().setAppend(false);
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
pProblem->setStepNumber((const unsigned C_INT32)stepNumber);
pProblem->setDuration((const C_FLOAT64)endTime);
pProblem->setTimeSeriesRequested(true);
//pProblem->setInitialState(pDataModel->getModel()->getInitialState());
CTrajectoryMethod* pMethod = dynamic_cast<CTrajectoryMethod*>(pTrajectoryTask->getMethod());
pMethod->getParameter("Absolute Tolerance")->setValue(1.0e-20);
CCopasiVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();
TaskList.remove("Time-Course");
TaskList.add(pTrajectoryTask, true);
// save the file for control purposes
std::string saveFilename = pSBMLFilename;
saveFilename = saveFilename.substr(0, saveFilename.length() - 4) + ".cps";
pDataModel->saveModel(saveFilename, NULL, true);
// Run the trajectory task
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pDataModel, NULL);
pTrajectoryTask->process(true);
pTrajectoryTask->restore();
// create another report that will write to the directory where the input file came from
// this can be used for debugging
// create a trajectory task
pTrajectoryTask->getReport().setTarget(pOutputFilename);
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pDataModel, NULL);
pTrajectoryTask->process(true);
pTrajectoryTask->restore();
}
catch (CCopasiException Exception)
{
std::cerr << Exception.getMessage().getText() << std::endl;
}
CCopasiRootContainer::destroy();
return 0;
}
void test000087::test_simulate_reaction_flux_reference_1()
{
try
{
bool result = pCOPASIDATAMODEL->importSBMLFromString(test000087::MODEL_STRING5);
CPPUNIT_ASSERT(result = true);
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
CModel* pModel = pCOPASIDATAMODEL->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 2);
CPPUNIT_ASSERT(pModel->getReactions().size() == 1);
const CReaction* pReaction = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction != NULL);
CModelValue* pConstParameter = NULL;
CModelValue* pNonConstParameter = NULL;
unsigned int i, iMax = pModel->getModelValues().size();
for (i = 0; i < iMax; ++i)
{
if (pModel->getModelValues()[i]->getStatus() == CModelEntity::FIXED)
{
pConstParameter = pModel->getModelValues()[i];
}
if (pModel->getModelValues()[i]->getStatus() == CModelEntity::ASSIGNMENT)
{
pNonConstParameter = pModel->getModelValues()[i];
}
}
CPPUNIT_ASSERT(pConstParameter != NULL);
CPPUNIT_ASSERT(pNonConstParameter != NULL);
// check if the kinetic law is mass action with const global parameter as the kinetic constant
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == false);
const CFunction* pKineticLaw = pReaction->getFunction();
CPPUNIT_ASSERT(pKineticLaw != NULL);
CPPUNIT_ASSERT(pKineticLaw->getType() == CEvaluationTree::MassAction);
const std::vector< std::vector<std::string> > & parameterMappings = pReaction->getParameterMappings();
CPPUNIT_ASSERT(parameterMappings.size() == 2);
CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
CPPUNIT_ASSERT(parameterMappings[0][0] == pConstParameter->getKey());
CPPUNIT_ASSERT(parameterMappings[1].size() == 1);
std::string substrateKey = parameterMappings[1][0];
const CCopasiObject* pTempObject = CCopasiRootContainer::getKeyFactory()->get(substrateKey);
CPPUNIT_ASSERT(pTempObject != NULL);
const CMetab* pSubstrate = dynamic_cast<const CMetab*>(pTempObject);
CPPUNIT_ASSERT(pSubstrate != NULL);
// check that the assignment consists of only one object node that is a reference to the reaction flux
const CExpression* pExpression = pNonConstParameter->getExpressionPtr();
CPPUNIT_ASSERT(pExpression != NULL);
const CEvaluationNode* pRoot = pExpression->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(CEvaluationNode::type(pRoot->getType()) == CEvaluationNode::OBJECT);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pRoot);
CPPUNIT_ASSERT(pObjectNode != NULL);
const CRegisteredObjectName cn = pObjectNode->getObjectCN();
std::vector<CCopasiContainer*> listOfContainers;
listOfContainers.push_back(pCOPASIDATAMODEL->getModel());
const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, cn);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == "Flux");
CPPUNIT_ASSERT(pObject->getObjectParent() == pReaction);
// Simulate the model (5 steps, stepsize 1 and check that at each step, the value of the variable parameter
// is the same as the flux through the reaction.
std::ostringstream result;
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pCOPASIDATAMODEL->getReportDefinitionList();
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for simulation");
pReport->setTaskType(CCopasiTask::timeCourse);
pReport->setIsTable(false);
pReport->setSeparator(CCopasiReportSeparator(", "));
std::vector<CRegisteredObjectName>* pHeader = pReport->getHeaderAddr();
std::vector<CRegisteredObjectName>* pBody = pReport->getBodyAddr();
pHeader->push_back(CCopasiStaticString("time").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
pHeader->push_back(CCopasiStaticString("substrate").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
pHeader->push_back(CCopasiStaticString("reaction flux").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
pHeader->push_back(CCopasiStaticString("variable model value").getCN());
pBody->push_back(CCopasiObjectName(pCOPASIDATAMODEL->getModel()->getCN() + ",Reference=Time"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pBody->push_back(CCopasiObjectName(pSubstrate->getCN() + ",Reference=Concentration"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pBody->push_back(CCopasiObjectName(pReaction->getCN() + ",Reference=Flux"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pBody->push_back(CCopasiObjectName(pNonConstParameter->getCN() + ",Reference=Value"));
//
// create a trajectory task
CTrajectoryTask* pTrajectoryTask = new CTrajectoryTask();
// use LSODAR from now on since we will have events pretty soon
pTrajectoryTask->setMethodType(CCopasiMethod::LSODAR);
pTrajectoryTask->getProblem()->setModel(pCOPASIDATAMODEL->getModel());
pTrajectoryTask->setScheduled(true);
pTrajectoryTask->getReport().setReportDefinition(pReport);
// the target needs to be set in order to get output on the stream
// object passed to the task in the call to initialize below
pTrajectoryTask->getReport().setTarget("test.tmp");
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
pProblem->setStepNumber((const unsigned C_INT32)30);
pCOPASIDATAMODEL->getModel()->setInitialTime((const C_FLOAT64)0.0);
pProblem->setDuration((const C_FLOAT64)30);
pProblem->setTimeSeriesRequested(true);
CTrajectoryMethod* pMethod = dynamic_cast<CTrajectoryMethod*>(pTrajectoryTask->getMethod());
pMethod->getParameter("Absolute Tolerance")->setValue(1.0e-12);
CCopasiVectorN< CCopasiTask > & TaskList = * pCOPASIDATAMODEL->getTaskList();
TaskList.remove("Time-Course");
TaskList.add(pTrajectoryTask, true);
try
{
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pCOPASIDATAMODEL, &result);
pTrajectoryTask->process(true);
pTrajectoryTask->restore();
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
// analyse the result
CPPUNIT_ASSERT(!result.str().empty());
std::string result_string = result.str();
std::string delimiter = "\n";
std::string delimiter2 = ",";
std::size_t lastPos = result_string.find_first_not_of(delimiter);
std::size_t pos;
std::string line, number_string;
unsigned int index = 0;
unsigned int index2;
std::size_t lastPos2;
std::size_t pos2;
double last = std::numeric_limits<double>::max(), current = std::numeric_limits<double>::max();
while (lastPos != std::string::npos)
{
pos = result_string.find_first_of(delimiter, lastPos);
line = result_string.substr(lastPos, pos - lastPos);
lastPos = result_string.find_first_not_of(delimiter, pos);
lastPos2 = line.find_first_not_of(delimiter2);
// skip the header line
if (index != 0)
{
index2 = 0;
while (lastPos2 != std::string::npos)
{
pos2 = line.find_first_of(delimiter2, lastPos2);
number_string = line.substr(lastPos2, pos2 - lastPos2);
lastPos2 = line.find_first_not_of(delimiter2, pos2);
// skip the time column
if (index2 != 0)
{
//check that all values in the row (besides the time)
// are always the same
if (index2 == 1)
{
last = strToDouble(number_string.c_str(), NULL);
if (index == 1)
{
// just make sure that we don't compare all zeros
// The initial value of the substrate hould be higher than 1
CPPUNIT_ASSERT(fabs(pSubstrate->getInitialValue()) > 1);
// the first rwo should correspond the the initial value of the substrate
// We check this to make sure that the whole timeseries does not consist of zeros
CPPUNIT_ASSERT(fabs((last - pSubstrate->getInitialConcentration()) / pSubstrate->getInitialConcentration()) < 1e-20);
}
}
else
{
current = strToDouble(number_string.c_str(), NULL);
CPPUNIT_ASSERT(fabs((current - last) / last) < 1e-20);
last = current;
}
}
++index2;
}
}
++index;
}
// make sure there actually were datapoints
CPPUNIT_ASSERT(index > 1);
// the simulation is set to run until all substrate is depleted, so in the end
// last should be below the absolute tolerance for the simulation
CPPUNIT_ASSERT(last < *pMethod->getParameter("Absolute Tolerance")->getValue().pDOUBLE);
}
/*
// Example Primitive
{
brushDef3
{
( 0 0 1 -604 ) ( ( 0.015625 0 255.9375 ) ( 0 0.015625 0 ) ) "textures/darkmod/stone/brick/blocks_brown" 0 0 0
( 0 1 0 -1528 ) ( ( 0.015625 0 0 ) ( 0 0.015625 1 ) ) "textures/darkmod/stone/brick/blocks_brown" 0 0 0
( 1 0 0 -1312 ) ( ( 0.015625 0 255.9375 ) ( 0 0.015625 1 ) ) "textures/darkmod/stone/brick/blocks_brown" 0 0 0
( 0 0 -1 -0 ) ( ( 0.015625 0 255.9375 ) ( 0 0.015625 0 ) ) "textures/darkmod/stone/brick/blocks_brown" 0 0 0
( -1 0 0 -1264 ) ( ( 0.015625 0 0.0625 ) ( 0 0.015625 1 ) ) "textures/darkmod/stone/brick/blocks_brown" 0 0 0
( -0 -1 -0 1524 ) ( ( 0.015625 0 0 ) ( 0 0.015625 1 ) ) "textures/darkmod/stone/brick/blocks_brown" 0 0 0
}
}
*/
scene::INodePtr BrushDef3Parser::parse(parser::DefTokeniser& tok) const
{
// Create a new brush
scene::INodePtr node = GlobalBrushCreator().createBrush();
// Cast the node, this must succeed
IBrushNodePtr brushNode = boost::dynamic_pointer_cast<IBrushNode>(node);
assert(brushNode != NULL);
IBrush& brush = brushNode->getIBrush();
tok.assertNextToken("{");
// Parse face tokens until a closing brace is encountered
while (1)
{
std::string token = tok.nextToken();
// Token should be either a "(" (start of face) or "}" (end of brush)
if (token == "}")
{
break; // end of brush
}
else if (token == "(") // FACE
{
// Construct a plane and parse its values
Plane3 plane;
plane.normal().x() = strToDouble(tok.nextToken());
plane.normal().y() = strToDouble(tok.nextToken());
plane.normal().z() = strToDouble(tok.nextToken());
plane.dist() = -strToDouble(tok.nextToken()); // negate d
tok.assertNextToken(")");
// Parse TexDef
Matrix4 texdef;
tok.assertNextToken("(");
tok.assertNextToken("(");
texdef.xx() = strToDouble(tok.nextToken());
texdef.yx() = strToDouble(tok.nextToken());
texdef.tx() = strToDouble(tok.nextToken());
tok.assertNextToken(")");
tok.assertNextToken("(");
texdef.xy() = strToDouble(tok.nextToken());
texdef.yy() = strToDouble(tok.nextToken());
texdef.ty() = strToDouble(tok.nextToken());
tok.assertNextToken(")");
tok.assertNextToken(")");
// Parse Shader
std::string shader = tok.nextToken();
// Parse Contents Flags (and ignore them)
tok.skipTokens(3);
// Finally, add the new face to the brush
IFace& face = brush.addFace(plane, texdef, shader);
}
else {
std::string text = (boost::format(_("BrushDef3Parser: invalid token '%s'")) % token).str();
throw parser::ParseException(text);
}
}
// Final outer "}"
tok.assertNextToken("}");
return node;
}
void GameScene::update()
{
ColeScene::update();
p->update();
std::string result = p->clientNetworkUpdate();
while (result != "")
{
if(result == "ERROR") std::cout << "TODO!!!" << std::endl;
if (result != "")
{
result = result.substr(0, result.length()-1); // Remove the ;
std::string command = result.substr(0, result.find("§"));
std::vector<std::string> arguments;
std::string argumentsString = result.substr(result.find("§")+2);
while (argumentsString.length()>0)
{
arguments.push_back(argumentsString.substr(0, argumentsString.find("§")));
argumentsString = argumentsString.substr(argumentsString.find("§")+2); //it appears that § takes up 2 characters, so +2
}
if (command=="join" && arguments[0] != p->name)
{
std::cout << "New player joining" << std::endl;
std::shared_ptr<OtherPlayer> newPlayer = std::make_shared<OtherPlayer>(arguments[0], strToInt(arguments[3]));
newPlayer->x = strToInt(arguments[1]);
newPlayer->y = strToInt(arguments[2]);
otherPlayers.push_back(newPlayer);
w->addChild(newPlayer);
}
if (command == "move" && getOtherPlayerByName(arguments[0]) != NULL)
{
std::shared_ptr<OtherPlayer> thePlayer = getOtherPlayerByName(arguments[0]);
thePlayer->x = strToInt(arguments[1]);
thePlayer->y = strToInt(arguments[2]);
}
if (command == "leave" && getOtherPlayerByName(arguments[0]) != NULL)
{
std::shared_ptr<OtherPlayer> thePlayer = getOtherPlayerByName(arguments[0]);
otherPlayers.remove(thePlayer);
w->removeChild(thePlayer);
}
if (command == "world")
{
int worldSize = strToInt(arguments[0]);
int tilex = 0;
int tiley = 0;
for (int i=1; i<arguments.size(); i++) {
w->setTile(tilex, tiley, strToInt(arguments[i]));
tiley++;
if (tiley == worldSize)
{
tiley = 0;
tilex++;
}
}
}
if (command == "newbullet" && arguments[0] != p->name)
{
std::shared_ptr<BulletClient> b = std::make_shared<BulletClient>();
//s.broadcast("newbullet§"+p->name+"§"+doubleToStr(b->x)+"§"+doubleToStr(b->y)+"§"+doubleToStr(b->angle)+"§"+doubleToStr(b->speed)+"§"+doubleToStr(b->ttl)+"§"+doubleToStr(b->bulletType)+";");
b->owner = arguments[0];
b->setPos(strToDouble(arguments[1]), strToDouble(arguments[2]));
b->angle = strToDouble(arguments[3]);
b->speed = strToDouble(arguments[4]);
b->ttl = strToDouble(arguments[5]);
b->bulletType = strToInt(arguments[6]);
b->tag = 1;
w->addChild(b);
}
}
result = p->clientNetworkUpdate();
}
int futurex = 0, futurey = 0;
const Uint8 *state = SDL_GetKeyboardState( NULL );
if (state[SDL_SCANCODE_W]) futurey--;
if (state[SDL_SCANCODE_S]) futurey++;
if (state[SDL_SCANCODE_A]) futurex--;
if (state[SDL_SCANCODE_D]) futurex++;
if (futurex != 0 || futurey != 0)
p->move(futurex, futurey);
int mousex, mousey;
Uint32 mouseState = SDL_GetMouseState(&mousex, &mousey);
if (mouseState&SDL_BUTTON(1))
{
int altMouseX = mousex+p->x-(RenderManager::getInstance()->getScreenX()/2);
int altMouseY = mousey+p->y-(RenderManager::getInstance()->getScreenY()/2);
if (p->shootTowards(altMouseX, altMouseY))
{
std::shared_ptr<BulletClient> b = std::make_shared<BulletClient>();
b->setPos(p->x, p->y);
b->speed = 5;
b->ttl = 100;
b->angle = angleBetween(p->x, p->y, altMouseX, altMouseY);
b->owner = p->name;
b->tag = 1;
w->addChild(b);
}
}
}
int getToken(tToken *Token, FILE* source) {
//prvne zkontroluji frontu tokenu
if (TQueue != NULL) {//nema cenu si neco na frontu zkouset kdyz je NULL
TQDequeue(Token);
if (Token != NULL) {//token byl ve fronte
return 1;
}
}
//alokace pameti pro cteny token
tToken tok = (tToken)malloc(sizeof(struct stToken));
*Token = tok;
/* @var c int actual character*/
int c = -1;
/* @var prevRest int poslední načtený znak (Zbytek posledního průchodu) */
static int pom = -1;
/* @var string s Uklada aktualne cteny string pokud je treba, pri kazdem
* konci teto funkce musi byt volano strFree.
*/
string s;
//strInit vraci 1 při chybe
if (strInit(&s)) {
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
//string kam se ukladaji sekvence pro escape sekvence
string escape;
//nastavime vychozi stav
int state = START;
while (1) {
if (pom > 0) {//pozustatek z minuleho cteni
c = pom;
pom = -1;//-1 je jedina hodnota kterou by nemela pomocna promenna nabyt pokud v ni opravdu je pozustatek
//pokud je v ni opravdu EOF tak pomoci getc() ho stejne dostanu znovu
}
else {
c = getc(source);
character++;
if (c == '\n') {//pokud ctu dalsi radek tak vynuluji citadlo znaku a inkrementuji citadlo radku
line++;
character = 0;
}
}
switch (state)
{
case START:
//pocatecni bile znaky nic nezmeni
if (isspace(c)) {
state = START;
}
//zacatek identifikatoru
else if (isalpha(c) || c == '_') {
state = IDENTIFICATOR;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//ulozi prvni nulu v cisle
else if (c == '0') {
state = FLOAT_OR_INT;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//platna cislice na zacatku retezce znamena celou cast cisla
else if (c >= '1' && c <= '9') {
state = INT_PART;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//strednik ulozi token strednik
else if (c == ';') {
tok->typ = SEMICOLON;
strFree(&s);
return 1;
}
//zacatek escape sekvenci rozsireni BASE
else if (c == '\\') {
state = ESCAPE;
}
//string zacina uvozovkami
else if (c == '\"') {
state = STRING;
}
//lomeno muze byt operatro nebo zacatek komentare
else if (c == '/') {
state = DIVISION_COMMENT;
}
//unarni minus, odcitani nebo dekremenrace
else if (c == '-') {
//jsem schopny rozlisit jen dekrementaci a minus
//unarni minus ani rozdil mezi postfix/prefix neurcim
state = DECREMENT_OPERATOR;
}
//scitani nebo inkrementace
else if (c == '+') {
state = INCREMENT_OPERATOR;
}
//nasobeni znamena jedine nasobeni
else if (c == '*') {
tok->typ = MULTIPLY;
strFree(&s);
return 1;
}
//toto mohou byt opertary se dvema znaky i jednim
else if (c == '!' || c == '<' || c == '>' || c == '=') {
state = TWO_CHAR_OPER;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//zaovrky ihned ulozime jako token
else if (c == ')') {
tok->typ = PARENTHESIS_CLOSING;
strFree(&s);
return 1;
}
else if (c == '(') {
tok->typ = PARENTHESIS_OPENING;
strFree(&s);
return 1;
}
else if (c == '}') {
tok->typ = BRACES_CLOSING;
strFree(&s);
return 1;
}
else if (c == '{') {
tok->typ = BRACES_OPENING;
strFree(&s);
return 1;
}
//logicky or
else if (c == '|') {
state = LOGICAL_OR;
}
//logicky and
else if (c == '&') {
state = LOGICAL_AND;
}
//carka (comma) operator ulozime do tokenu
else if (c == ',') {
tok->typ = COMMA;
strFree(&s);
return 1;
}
//konec souboru cas vyhlasit chyby pokud nastaly jinak ulozit do tokenu EOF
else if (c==EOF) {
tok->typ = END_OF_FILE;
strFree(&s);
if (errorFlag) {
freeTokenMem(&tok);
return 42;
}
return 1;
}
else {//pokud na zacatku tokenu prislo cokoli jineho tak scanner nevi co se deje
errorFlag = 1;
Warning("%sLine - %d:%d\t- Unknown symbol.\n", ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
break;
case INT_PART:
//cteni cele casti cisla
//cislice ukladam
if (c >= '0' && c <= '9') {
state = INT_PART;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//zacatek exponentu
else if (c == 'e' || c == 'E') {
state = EXPONENT_CHECK;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//zacatek desetine casti
else if (c == '.') {
//vlozen testovaci stav pro podminku ze za des. teckou musi byt cislice
state = FLOAT_CHECK;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//uloz cele cislo
else {
int val;
if (!strToInt(&s, &val)) {
freeTokenMem(&tok);
strFree(&s);
FatalError(99, "%s-%d: Chyba pri nacteni celeho cisla.", ERR_MESSAGES[ERR_ALLOC], line);
return 42;
}
pom = c;
tok->typ = TYPE_INTEGER;
tok->value.intVal = val;
strFree(&s);
return 1;
}
break;
case FLOAT_OR_INT:
//prvni nula byla ulozena pocatecnim stavu ted je necham byt
if (c == '0') {
state = FLOAT_OR_INT;
}
else if (c >= '1' && c<='9') {//pokud nasleduje cislice ctu cele cislo
state = INT_PART;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else if (c == '.') {
//zacatek desetine casti
state = FLOAT_CHECK;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else if (c == 'e' || c == 'E') {
//zacatek exponentu
state = EXPONENT_CHECK;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
//konec celeho cisla
int val;
if (!strToInt(&s, &val)) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Nepodarilo se nacist ciselny literal.\n",ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
tok->typ = TYPE_INTEGER;
tok->value.intVal = val;
strFree(&s);
pom = c;
return 1;
}
break;
case FLOAT_CHECK:
//tento stav slouzi ke kontrole neprazdnosti desetine casti
if (c >= '0' && c <= '9') {
state = FLOAT_PART;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//pokud za teckou neni cislice je to chyba
else {
pom = c;
errorFlag = 1;
Warning("%sLine - %d:%d\t- Nepodarilo se nacist ciselny literal. Desetina cast nesmi byt prazdna.\n", ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
break;
case FLOAT_PART:
if (c >= '0' && c <= '9') {
//ulozi cislo a pokracuje ve cteni
state = FLOAT_PART;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else if (c == 'e' || c == 'E') {
//zacatek exponentu
state = EXPONENT_CHECK;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
//konec desetineho cisla, ulozme jej
double val;
if (!strToDouble(&s, &val)) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Nepodarilo se nacist ciselny literal.\n",ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
tok->typ = TYPE_DOUBLE;
tok->value.doubleVal = val;
strFree(&s);
pom = c;
return 1;
}
break;
case EXPONENT_CHECK:
if (c >= '0' && c <= '9') {
//prislo cislo, ulozi jej a pokracuje j*z ve cteni exponentu
state = EXPONENT;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else if (c == '+' || c == '-') {
//znamenko na zacatku exponentu
state = EXPONENT_PLUS_MINUS_CHECK;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//nemuzeme napsat exponent a neudat ho
else{
errorFlag = 1;
Warning("%sLine - %d:%d\t- Exponent musi obsahovat validni cislici.\n",ERR_MESSAGES[ERR_LEX], line, character);
pom = c;
strFree(&s);
freeTokenMem(&tok);
return 42;
}
break;
case EXPONENT_PLUS_MINUS_CHECK:
if (c >= '0' && c <= '9') {
//spravne bylo za znamenkem exponentu cislo
//pokracuji ve cteni expoenntu
state = EXPONENT;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
//nemuzem napsat znamenko exponentu a neudat jeho hodnotu
errorFlag = 1;
Warning("%sLine - %d:%d\t- Exponent musi obsahovat validni cislici.\n",ERR_MESSAGES[ERR_LEX], line, character);
pom = c;
strFree(&s);
freeTokenMem(&tok);
return 42;
}
break;
case EXPONENT:
if (c >= '0' && c <= '9') {
//cte cisla dokud prichazi
state = EXPONENT;
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
//prislo cokoli jineho nez cislo
double val = 42;
if (!strToDouble(&s, &val)) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Nepodarilo se nacist ciselny literal.\n",ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
tok->typ = TYPE_DOUBLE;
tok->value.doubleVal = val;
pom = c;//dalsi znak patri dalsimu tokenu
strFree(&s);
return 1;
}
break;
case ESCAPE:
//escape sekvence celociselne konstanty
switch (c) {
//binarni escape sekvence
case 'b':
case 'B':
state = BINARY_NUMBER;
break;
//oktalova escape sekvence
case '0':
state = OCTAL_NUMBER;
break;
//hexadecimalni escape sekvence
case 'x':
case 'X':
state = HEX_DEC_NUMBER;
break;
//cokoli jineho je chybou
default:
errorFlag = 1;
Warning("%sLine - %d:%d\t- Ocekavan symbol pro ciselnou soustavu.\n",ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
break;
}
break;
case BINARY_NUMBER:
//escape sekvence obsahujici binarni cislo
if (c == '0' || c == '1') {
//zahazuji nevyznamne nuly
if (!(c == '0' && strGetLength(&s) == 0)) {
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
}
else {
pom = c;
int val = 0;
if (!strBinToInt(&s, &val)) {
strFree(&s);
freeTokenMem(&tok);
return 42;
}
tok->typ = TYPE_INTEGER;
tok->value.intVal = val;
strFree(&s);
return 1;
}
break;
case OCTAL_NUMBER:
//escape sekvence obsahujici oktalove cislo
if (c >= '0' && c <= '7') {
//zahazuji nevyznamne nuly
if (!(c == '0' && strGetLength(&s) == 0)) {
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
}
else {
pom = c;
int val = 0;
if (!strOctToInt(&s, &val)) {
strFree(&s);
freeTokenMem(&tok);
return 42;
}
tok->typ = TYPE_INTEGER;
tok->value.intVal = val;
strFree(&s);
return 1;
}
break;
case HEX_DEC_NUMBER:
//escape sekvence obsahujici hexadecimalni cislo
if ((c >= '0' && c <= '9') || (c >= 'a' && c <= 'f') || (c >= 'A' && c <= 'F')) {
//zahazuji nevyznamne nuly
if (!(c == '0' && strGetLength(&s)==0)) {
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
}
else {
pom = c;
int val = 0;
if (!strHexToInt(&s, &val)) {
strFree(&s);
freeTokenMem(&tok);
return 42;
}
tok->typ = TYPE_INTEGER;
tok->value.intVal = val;
strFree(&s);
return 1;
}
break;
case LOGICAL_AND:
//logicky and
//v IFJ2015 neexistuje binarni and proto jediny prijatelny znak
//v tuto chvili je &
if (c == '&') {
tok->typ = LOG_AND_OPER;
strFree(&s);
return 1;
}
else {
pom = c;
errorFlag = 1;
Warning("%sLine - %d:%d\t- Binarni and neni podporovan v IFJ2015.\n",ERR_MESSAGES[ERR_LEX], line, character-1);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
break;
case LOGICAL_OR:
//logicky or
//v IFJ2015 neexistuje binarni or proto jediny prijatelny znak
//v tuto chvili je |
if (c == '|') {
tok->typ = LOG_OR_OPER;
strFree(&s);
return 1;
}
else {
/*Abych se zotavil po teto chybe a docetl soubor*/
errorFlag = 1;
Warning("%sLine - %d:%d\t- Binarni or neni podporovan v IFJ2015.\n",ERR_MESSAGES[ERR_LEX], line, character - 1);
pom = c;
strFree(&s);
freeTokenMem(&tok);
return 42;
}
break;
case STRING:
if (c == EOF) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Necekany konec souboru.\n",ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
else if (c == '\\') {
state = STRING_ESCAPE;
}
else if (c == '"') {//konec retezce uloz ho
tok->typ = TYPE_STRING;
if (strInit(&tok->value.stringVal)) {
//return stringval
}
if (strCopyString(&tok->value.stringVal, &s)) {
//return error;
}
strFree(&s);
return 1;
}
else if (c < 1 || c>255) {//nejaky znak mimo ASCII chyba
}
else {//uloz si znak
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
break;
case STRING_ESCAPE:
//escape sekvence ve stringu
switch (c) {
//binarni escape sekvence
case 'b':
case 'B':
if (strInit(&escape)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING_BINARY_NUMBER;
break;
//oktalova escape sekvence
case '0':
if (strInit(&escape)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING_OCTAL_NUMBER;
break;
case 'x':
case 'X':
//hexadecimalni escape sekvence
if (strInit(&escape)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING_HEX_DEC_NUMBER;
break;
case '\\':
//escape sekvence backslash
if (strAddChar(&s, '\\')) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING;
break;
case 'n':
//escape sekvence noveho radku
if (strAddChar(&s, '\n')) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING;
break;
case 't':
//escape sekvence tabulatoru
if (strAddChar(&s, '\t')) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING;
break;
case '\"':
//escape sekvence uvozovek
if (strAddChar(&s, '\"')) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
state = STRING;
break;
default:
//cokoliv jineho je chybnym zapsani escape sekvence
errorFlag = 1;
Warning("%sLine - %d:%d\t- Ocekavana escape sekvence\n", ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
break;
}
break;
case STRING_BINARY_NUMBER:
if ((c == '0' || c == '1')) {//ctu validni vstup
if (strGetLength(&escape) < 8) {//jeste nemam 8 cislic tak ctu dal
if (strAddChar(&escape, c)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {//mam 8 cislic
pom = c;
int val;
if (strBinToInt(&escape, &val) && val >= 1 && val <= 255) {
if (strAddChar(&s, (char)val)) {//precteny znak pridam do stringu
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {//nepodarilo se prevest escape na string
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
strFree(&escape);
state = STRING;
}
}
else {
if (strGetLength(&escape) < 8) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
if (strGetLength(&escape) == 8) {
int val;
if (strBinToInt(&escape, &val) && val >= 1 && val <= 255) {
if (strAddChar(&s, (char)val)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
}
pom = c;
strFree(&escape);
state = STRING;
}
break;
case STRING_OCTAL_NUMBER:
if ((c >= '0' && c <= '7')) {//ctu validni vstup
if (strGetLength(&escape) < 3) {
if (strAddChar(&escape, c)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
pom = c;
int val;
if (strOctToInt(&escape, &val) && val >= 1 && val <= 255) {
if (strAddChar(&s, (char)val)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
strFree(&escape);
state = STRING;
}
}
else {
if (strGetLength(&escape) < 3) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
if (strGetLength(&escape) == 3) {
int val;
if (strOctToInt(&escape, &val) && val >= 1 && val <= 255) {
if (strAddChar(&s, (char)val)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
}
pom = c;
strFree(&escape);
state = STRING;
}
break;
case STRING_HEX_DEC_NUMBER:
if ((c >= '0' && c <= '9')||(c >= 'a' && c <= 'f')|| (c >= 'A' && c <= 'F')) {//ctu validni vstup
if (strGetLength(&escape) < 2) {
if (strAddChar(&escape, c)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
int val;
pom = c;
if (strHexToInt(&escape, &val) && val >= 1 && val <= 255) {
if (strAddChar(&s, (char)val)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
strFree(&escape);
state = STRING;
}
}
else {
if (strGetLength(&escape) < 2) {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
if (strGetLength(&escape) == 2) {
int val;
if (strHexToInt(&escape, &val) && val >= 1 && val <= 255) {
if (strAddChar(&s, (char)val)) {
freeTokenMem(&tok);
strFree(&escape);
strFree(&s);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
else {
errorFlag = 1;
Warning("%sLine - %d:%d\t- Retezec \"%s\" neni platnou escape sekvenci.\n", ERR_MESSAGES[ERR_LEX], line, character, escape.str);
}
}
pom = c;
strFree(&escape);
state = STRING;
}
break;
case IDENTIFICATOR:
//ctu cislice, pismena nebo podtrzitka
if (isalnum(c) || c == '_') {
if (strAddChar(&s, c)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
//konec identifikatoru
else {
pom = c;
int isIdent = isKeyWord(&s);
tok->typ = isIdent;
if (isIdent == TYPE_IDENTIFICATOR) {
if (strInit(&(tok->value.stringVal))) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
if (strCopyString(&(tok->value.stringVal), &s)) {
strFree(&s);
freeTokenMem(&tok);
FatalError(99, ERR_MESSAGES[ERR_ALLOC]);
}
}
if (isIdent == KEYW_FALSE) {
tok->typ = TYPE_BOOL;
tok->value.boolVal = false;
}
if (isIdent == KEYW_TRUE) {
tok->typ = TYPE_BOOL;
tok->value.boolVal = true;
}
strFree(&s);
return 1;
}
break;
case DIVISION_COMMENT:
if (c == '*') {
state = BLOCK_COMMENT;
}
else if (c == '/') {
state = LINE_COMMENT;
}
else {//jednoznakovy operator deleni
tok->typ = DIVISION;
pom = c;
strFree(&s);
return 1;
}
break;
case LINE_COMMENT:
if (c == '\n') {//konec radkoveho komentare hledame dalsi lexem
state = START;
}
else if (c == EOF) {//nemusi byt lf pred koncem souboru
pom = c;
state = START;
}
else {//komentar pokracuje
//reflection nepodporujeme takže komentáře zahodíme
}
break;
case BLOCK_COMMENT:
if (c == EOF) {
Warning("%sLine - %d:%d\t- Necekany konec souboru.\n", ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
/*else if (c=='/') {
state = NESTED_BLOCK_COMMENT_CHECK;
}*/
else if (c=='*') {
state = END_BLOCK_COMMENT;
}
break;
case END_BLOCK_COMMENT:
if (c == '*') {
//zůstaneme tady komentář může končit x hvězdičkama
}
else if (c == EOF) {
Warning("%sLine - %d:%d\t- Necekany konec souboru.\n", ERR_MESSAGES[ERR_LEX], line, character);
strFree(&s);
freeTokenMem(&tok);
return 42;
}
else if (c == '/') {//konec blokového komentáře jdeme hledat další lexém
state = START;
}
else {
state = BLOCK_COMMENT;
}
break;
//dvouznakove operatry
case TWO_CHAR_OPER:
//jako druhy znak muze jen rovna se
//dle prvniho znaku rozhodneme co ulozime
if (c == '=') {
switch (s.str[0]) {
case '!':
tok->typ = NOT_EQUAL_OPER;
break;
case '<':
tok->typ = LESS_EQUAL;
break;
case '>':
tok->typ = GREATER_EQUAL;
break;
case '=':
tok->typ = EQUAL;
break;
default:
break;
}
}
//pokud prislo cokoli jineho tak dle prvniho znaku rozhodneme co ulozime
else {
pom = c;
switch (s.str[0]) {
case '!':
tok->typ = LOG_NOT_OPER;
break;
case '<':
tok->typ = LESS;
break;
case '>':
tok->typ = GREATER;
break;
case '=':
tok->typ = SET_OPER;
break;
default:
break;
}
}
strFree(&s);
return 1;
break;
case DECREMENT_OPERATOR:
//druhe minus v rade znamena dekrementaci
if (c == '-') {
tok->typ = DECREMENTATION;
strFree(&s);
return 1;
}
//cokoli jineho znamena pouze minus
else {
pom = c;
tok->typ = MINUS;
strFree(&s);
return 1;
}
break;
case INCREMENT_OPERATOR:
//druhe plus v rade je inkrementace
if (c == '+') {
tok->typ = INCREMENTATION;
strFree(&s);
return 1;
}
//pouze scitani
else {
pom = c;
tok->typ = PLUS;
strFree(&s);
return 1;
}
break;
default:
break;
}
}
}
bool NumberParser::tryParseFloat(const std::string& s, double& value, char decSep, char thSep)
{
return strToDouble(s.c_str(), value, decSep, thSep);
}
int main(int argc, char *argv[])
{
// Parse the commandline options
// first argument is the SBML filename
// second argument is the endtime
// third argument is the step number
// fourth argument is the filename where the results are to be written
// fifth argument is the tmp directory (this is not needed)
// the rest of the arguments are species names for the result
try
{
// Create the root container.
CCopasiRootContainer::init(0, NULL, false);
}
catch (copasi::autoexcept &e)
{}
catch (copasi::option_error &e)
{}
if (argc < 5)
{
std::cout << "Usage: stochastic-testsuite METHOD SBMLFILENAME ENDTIME STEPNUMBER REPEATS OUTFILENAME SPECIESID1 SPECIESID2 ..." << std::endl;
exit(1);
}
const char* pMethodType = argv[1];
const char* pSBMLFilename = argv[2];
const char* pEndTime = argv[3];
const char* pStepNumber = argv[4];
const char* pRepeats = argv[5];
const char* pOutputFilename = argv[6];
unsigned int NUMARGS = 7;
/*
std::cout << "Input : " << pSBMLFilename << std::endl;
std::cout << "Endtime : " << pEndTime << std::endl;
std::cout << "Stepnumber: " << pStepNumber << std::endl;
std::cout << "Repeats : " << pRepeats << std::endl;
std::cout << "Output file: " << pOutputFilename << std::endl;
*/
char** pSBMLSpeciesIds = new char * [argc - NUMARGS];
unsigned int i, iMax = argc;
CTrajectoryTask* pTrajectoryTask = NULL;
CScanTask* pScanTask = NULL;
std::string CWD = COptions::getPWD();
double endTime = strToDouble(pEndTime, &pEndTime);
double stepNumber = strToDouble(pStepNumber, &pStepNumber);
char** pTmpP = (char**)(&pRepeats);
long int repeats = strtol(pRepeats, pTmpP , 10);
CCopasiMethod::SubType MethodType;
if (!strcmp(pMethodType, "stochastic"))
{
MethodType = CCopasiMethod::stochastic;
}
else if (!strcmp(pMethodType, "directMethod"))
{
MethodType = CCopasiMethod::directMethod;
}
else if (!strcmp(pMethodType, "tauLeap"))
{
MethodType = CCopasiMethod::tauLeap;
}
else if (!strcmp(pMethodType, "adaptiveSA"))
{
MethodType = CCopasiMethod::adaptiveSA;
}
else if (!strcmp(pMethodType, "LSODA"))
{
MethodType = CCopasiMethod::deterministic;
}
else
{
std::cerr << "Invalid method type. Valid options are:" << std::endl;
std::cerr << " stochastic" << std::endl;
std::cerr << " directMethod" << std::endl;
std::cerr << " tauLeap" << std::endl;
}
if (endTime == 0.0)
{
std::cerr << "Invalid endtime " << pEndTime << std::endl;
exit(1);
}
if (stepNumber == 0.0)
{
std::cerr << "Invalid step number " << pStepNumber << std::endl;
exit(1);
}
for (i = NUMARGS; i < iMax; ++i)
{
pSBMLSpeciesIds[i - NUMARGS] = argv[i];
//std::cout << "Copying pointer to " << argv[i] << "." << std::endl;
}
try
{
// Create the global data model.
CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
// Import the SBML File
pDataModel->importSBML(pSBMLFilename);
//pDataModel->getModel()->forceCompile();
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for stochastic testsuite run");
pReport->setTaskType(CCopasiTask::timeCourse);
pReport->setIsTable(false);
CCopasiReportSeparator Separator(std::string(","));
pReport->setSeparator(Separator);
std::vector<CRegisteredObjectName> * pHeader = pReport->getHeaderAddr();
std::vector<CRegisteredObjectName> * pBody = pReport->getBodyAddr();
// Add time column
pHeader->push_back(CCopasiStaticString("time").getCN());
pBody->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
iMax = iMax - NUMARGS;
const CCopasiVector<CMetab>& metabolites = pDataModel->getModel()->getMetabolites();
for (i = 0; i < iMax; ++i)
{
pHeader->push_back(Separator.getCN());
pBody->push_back(Separator.getCN());
unsigned int j, jMax = metabolites.size();
std::string SBMLId = unQuote(pSBMLSpeciesIds[i]);
for (j = 0; j < jMax; ++j)
{
if (metabolites[j]->getSBMLId() == SBMLId)
{
break;
}
}
if (j == jMax)
{
std::cerr << "Could not find a metabolite for the SBML id \"" << pSBMLSpeciesIds[i] << "\"" << std::endl;
exit(1);
}
pHeader->push_back(CCopasiStaticString(SBMLId).getCN());
pBody->push_back(metabolites[j]->getObject(CCopasiObjectName("Reference=ParticleNumber"))->getCN());
}
// create a trajectory task
pTrajectoryTask = new CTrajectoryTask();
pTrajectoryTask->setMethodType(MethodType);
pTrajectoryTask->getProblem()->setModel(pDataModel->getModel());
pTrajectoryTask->setScheduled(false);
//pTrajectoryTask->getReport().setReportDefinition(pReport);
//pTrajectoryTask->getReport().setTarget(CWD + "/" + pOutputFilename);
//pTrajectoryTask->getReport().setAppend(false);
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
pProblem->setStepNumber((const unsigned C_INT32)stepNumber);
pProblem->setDuration((const C_FLOAT64)endTime);
pProblem->setTimeSeriesRequested(true);
pProblem->setTimeSeriesRequested(false);
//pProblem->setInitialState(pDataModel->getModel()->getInitialState());
CCopasiVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();
TaskList.remove("Time-Course");
TaskList.add(pTrajectoryTask, true);
// create a scan task
pScanTask = new CScanTask(pDataModel);
CScanProblem* pScanProblem = dynamic_cast<CScanProblem*>(pScanTask->getProblem());
pScanProblem->setModel(pDataModel->getModel());
pScanTask->setScheduled(true);
pScanTask->getReport().setReportDefinition(pReport);
pScanTask->getReport().setTarget(CWD + "/" + pOutputFilename);
pScanTask->getReport().setAppend(false);
pScanProblem->setSubtask(CCopasiTask::timeCourse);
pScanProblem->createScanItem(CScanProblem::SCAN_REPEAT, repeats);
pScanProblem->setOutputInSubtask(true);
pScanProblem->setContinueFromCurrentState(false);
TaskList.remove("Scan");
TaskList.add(pScanTask, true);
// save the file for control purposes
std::string saveFilename = pSBMLFilename;
saveFilename = saveFilename.substr(0, saveFilename.length() - 4) + ".cps";
pDataModel->saveModel(saveFilename, NULL, true);
// Run the trajectory task
pScanTask->initialize(CCopasiTask::OUTPUT_SE, pDataModel, NULL);
pScanTask->process(true);
pScanTask->restore();
// create another report that will write to the directory where the input file came from
// this can be used for debugging
// create a trajectory task
// pScanTask->getReport().setTarget(pOutputFilename);
// pScanTask->initialize(CCopasiTask::OUTPUT_SE, pDataModel, NULL);
// pScanTask->process(true);
// pScanTask->restore();
}
catch (CCopasiException Exception)
{
std::cerr << Exception.getMessage().getText() << std::endl;
}
CCopasiRootContainer::destroy();
return 0;
}
