void CMetab::initObjects()
{
// We need to have mpIValueRefernce point to a CParticleReference object.
pdelete(mpIValueReference);
mpIValueReference = new CParticleReference("InitialParticleNumber", this, mIValue);
// We need to have mpValueRefernce point to a CParticleReference object.
pdelete(mpValueReference);
mpValueReference = new CParticleReference("ParticleNumber", this, mValue);
mpRateReference->setObjectName("ParticleNumberRate");
mpIConcReference = new CConcentrationReference("InitialConcentration", this, mIConc);
mpConcReference = new CConcentrationReference("Concentration", this, mConc);
mpConcRateReference =
static_cast<CCopasiObjectReference<C_FLOAT64> *>(addObjectReference("Rate", mConcRate, CCopasiObject::ValueDbl));
mpIntensiveNoiseReference =
static_cast<CCopasiObjectReference<C_FLOAT64> *>(addObjectReference("IntensiveNoise", mIntensiveNoise, CCopasiObject::ValueDbl));
mpTTReference =
static_cast<CCopasiObjectReference<C_FLOAT64> *>(addObjectReference("TransitionTime", mTT, CCopasiObject::ValueDbl));
}
void CCrossSectionTask::initObjects()
{
addObjectReference("Period", mPeriod, CCopasiObject::ValueDbl);
addObjectReference("Average Period", mAveragePeriod, CCopasiObject::ValueDbl);
addObjectReference("Last Period", mLastPeriod, CCopasiObject::ValueDbl);
addObjectReference("Periodicity", mPeriodicity, CCopasiObject::ValueInt);
addObjectReference("Last Frequency", mLastFreq, CCopasiObject::ValueDbl);
addObjectReference("Frequency", mFreq, CCopasiObject::ValueDbl);
addObjectReference("Average Frequency", mAverageFreq, CCopasiObject::ValueDbl);
}
void CILDMMethod::initializeParameter()
{
addObjectReference("Number of slow variables", mSlow, CCopasiObject::ValueInt);
addMatrixReference("Contribution of Species to Slow Space", mVslow, CCopasiObject::ValueDbl);
initializeIntegrationsParameter();
assertParameter("Deuflhard Tolerance", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0e-6);
createAnnotationsM();
emptyVectors();
}
void CMoiety::initObjects()
{
mpINumberReference = new CTotalNumberReference("InitialValue", this, mINumber);
mpNumberReference = new CTotalNumberReference("Value", this, mNumber);
mpDNumberReference = new CDependentNumberReference("DependentValue", this, mNumber);
mpDNumberReference->addDirectDependency(this);
CCopasiObject * pObject = addObjectReference("Amount", mIAmount, CCopasiObject::ValueDbl);
pObject->addDirectDependency(mpNumberReference);
return;
}
void CCopasiTask::initObjects()
{
addObjectReference("Output counter", mOutputCounter, CCopasiObject::ValueInt);
new CCopasiTimer(CCopasiTimer::WALL, this);
new CCopasiTimer(CCopasiTimer::PROCESS, this);
CCopasiDataModel *pDataModel = getObjectDataModel();
if (pDataModel != NULL)
{
if (pDataModel->getModel() != NULL)
{
setMathContainer(&pDataModel->getModel()->getMathContainer());
}
}
}
/** Begin Code emulation ********************************************************************/
void startFunction(FILE * logf, struct SCRIPT * script,
struct TYPING * types, int funcindex, struct LINE * line){
char * tokens = (char *) calloc(TOKENMAXNB*TOKENSIZE,sizeof(char));
int parameters[10];
char arguments[10][TOKENSIZE];
int i, j, retobj, nbtokens, nbarg, nextparam, pos = 0;
//Jump to function
printf("[+] Jump inside function %s\n",
script->functionslist[funcindex].name);
//Merge parameters with local aliases from the signature
nbarg = script->functionslist[funcindex].nbarg;
nbtokens = decomposeLine(line->line,(char*)tokens,TOKENMAXNB,TOKENSIZE);
for(i=0;i<nbtokens;i++){
if(!strcasecmp(ACCESS(tokens,i),script->functionslist[funcindex].name)) break;
}
nextparam = i+1;
for(j=1;j<=nbarg;j++){
processExpression(logf,script,types,FUNCLEVEL|funcindex,
line,nextparam,0,arguments[j-1],&nextparam);
parameters[j-1] = updateTypesBeforeLocCall(types, arguments[j-1],
script->functionslist[funcindex].arguments[j-1]);
}
//Following the execution path
while(pos<script->functionslist[funcindex].nblines){
//Analyze code
pos = processLines(logf,script,types,FUNCLEVEL|funcindex,pos);
}//while
//Return from function
printf("[+] Return from function %s\n",script->functionslist[funcindex].name);
//Unmerge parameters with local aliases from the signature
for(j=1;j<=nbarg;j++){
removeObjectReference(types, parameters[j-1],
script->functionslist[funcindex].arguments[j-1]);
}
retobj = isKnownObject(types,script->functionslist[funcindex].name);
if(retobj>-1){
removeObjectReference(types,retobj,script->functionslist[funcindex].name);
//If the return value is affected
if(i>1 && ((char*)ACCESS(tokens,i-1))[0]== '='){
addObjectReference(types,retobj,ACCESS(tokens,i-2));
}//if affectation
}
free(tokens);
}
void CLyapTask::initObjects()
{
unsigned C_INT32 i;
mExponents.resize(LYAP_NUM_REF);
for (i = 0; i < LYAP_NUM_REF; ++i) mExponents[i] = 0.0;
mvExpRef.resize(LYAP_NUM_REF);
mLocalExponents.resize(LYAP_NUM_REF);
for (i = 0; i < LYAP_NUM_REF; ++i) mLocalExponents[i] = 0.0;
mvLocExpRef.resize(LYAP_NUM_REF);
addVectorReference("Exponents", mExponents, CCopasiObject::ValueDbl);
addVectorReference("Local exponents", mLocalExponents, CCopasiObject::ValueDbl);
for (i = 0; i < LYAP_NUM_REF; ++i)
{
std::ostringstream sss;
sss << "Exponent " << i + 1;
mvExpRef[i] = dynamic_cast<CCopasiObjectReference<C_FLOAT64> *>
(addObjectReference(sss.str(), mExponents.array()[i], CCopasiObject::ValueDbl));
assert(mvExpRef[i]);
std::ostringstream sss2;
sss2 << "Local exponent " << i + 1;
mvLocExpRef[i] = dynamic_cast<CCopasiObjectReference<C_FLOAT64> *>
(addObjectReference(sss2.str(), mLocalExponents.array()[i], CCopasiObject::ValueDbl));
assert(mvLocExpRef[i]);
}
addObjectReference("Sum of exponents", mSumOfExponents, CCopasiObject::ValueDbl);
addObjectReference("Sum of local exponents", mSumOfLocalExponents, CCopasiObject::ValueDbl);
//addObjectReference("Local divergence", mDivergence, CCopasiObject::ValueDbl);
addObjectReference("Interval divergence", mIntervalDivergence, CCopasiObject::ValueDbl);
addObjectReference("Average divergence", mAverageDivergence, CCopasiObject::ValueDbl);
}
void COptPopulationMethod::initObjects()
{
if (getSubType() != CTaskEnum::Method::ParticleSwarm && getSubType() != CTaskEnum::Method::ScatterSearch)
addObjectReference("Current Generation", mCurrentGeneration, CDataObject::ValueInt);
}
void CEFMAlgorithm::initObjects()
{
addObjectReference("Current Step", mStep, CCopasiObject::ValueInt);
}
void COptMethodNelderMead::initObjects()
{
addObjectReference("Current Iteration", mIteration, CCopasiObject::ValueInt);
}
void CFunctionDB::initObjects()
{
addObjectReference("File", mFilename);
}
int monitorFileControl(FILE * logf, struct SCRIPT * script, struct TYPING * types,
unsigned long location, struct LINE * line){
char tokens[TOKENMAXNB][TOKENSIZE]; char exp[TOKENSIZE]; int next = 1;
static char driveobj[TOKENSIZE];
static int drives = 0; static int driveset;
int i, obj1, nbtokens, unknown = -1;
struct LINE combined; static int combinnb = 45;
char combinid[TOKENSIZE]; char * combinline;
struct MANAG_ENTRY * localmanagers = accessManagers(script,location);
nbtokens = decomposeLine(line->line,(char*)tokens,TOKENMAXNB,TOKENSIZE);
for(i=0;i<nbtokens;i++){
unknown = isUnknownManager(&script->managers,tokens[i]);
//File system manager
if((isFileManager(&script->managers,tokens[i])>-1)
|| (isFileManager(localmanagers,tokens[i])>-1)
|| (unknown>-1)){
//Open command
if(!strcasecmp(tokens[i+1],OPENF1)//file
|| !strcasecmp(tokens[i+1],OPENF2)
|| !strcasecmp(tokens[i+1],OPENF3)){
line->type = SYSCALL;
processExpression(logf,script,types,location,
line,i+2,OBJ_FILE,exp,&next);
obj1 = updateTypesAfterSysCall(types,exp,
NULL,OBJ_FILE,OBJ_EXIST);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
//Checks combined call
combinline = strstr(line->line,tokens[next]);
if((nbtokens-2>=next)&&combinline){
char * found;
combinline--;
found = strchr(combinline,'.');
if(!found){
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in")))
addObjectReference(types,obj1,tokens[i-2]);
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
}
sprintf_s(combinid,TOKENSIZE,"INT%08X",combinnb); combinnb++;
addObjectReference(types,obj1,combinid);
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in"))){
sprintf_s(combined.line,LINE_LENGTH,"%s = %s.%s",
tokens[i-2],combinid,found);
}else{
sprintf_s(combined.line,LINE_LENGTH,"%s.%s",combinid,found);
}
if(!monitorFileIO(logf,script,types,location,&combined)){
removeObjectReference(types,obj1,combinid);
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in")))
addObjectReference(types,obj1,tokens[i-2]);
}
}else{
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in")))
addObjectReference(types,obj1,tokens[i-2]);
}
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
//File existence command
}else if(!strcasecmp(tokens[i+1],OPENFT)){
line->type = SYSCALL;
processExpression(logf,script,types,location,
line,i+2,OBJ_FILE,exp,NULL);
obj1 = updateTypesAfterSysCall(types,exp,
NULL,OBJ_FILE,OBJ_CREATED);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
//Drive commands
}else if(!strcasecmp(tokens[i+1],OPEND1)){
line->type = SYSCALL;
obj1 = updateTypesAfterSysCall(types,COM_DRIVE,
tokens[i-2],OBJ_DRIVE,OBJ_EXIST);
sprintf_s(types->objects[obj1].ObjectName, NAME_MAX_LENGTH,
"Drive(ref:%s)",tokens[i-2]);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
}else if(!strcasecmp(tokens[i+1],OPEND2)){
if((i+2<nbtokens&&!strcasecmp(tokens[i+2],"Item"))
||(i-2>=0&&!strcasecmp(tokens[i-1],"In"))){
line->type = SYSCALL;
obj1 = updateTypesAfterSysCall(types,COM_DRIVE,
tokens[i-2],OBJ_DRIVE,OBJ_EXIST);
sprintf_s(types->objects[obj1].ObjectName, NAME_MAX_LENGTH,
"Drive(ref:%s)",tokens[i-2]);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
}else if(i-2>=0&&tokens[i-1][0]=='='){
drives = 1;
strcpy_s(driveobj,TOKENSIZE,tokens[i-2]);
line->type = SYSCALL;
}else{
line->type = SYSCALL;
}
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
}//if open
//Creation command
if(!strcasecmp(tokens[i+1],CREATEF2)
|| !strcasecmp(tokens[i+1],CREATEF3)){
line->type = SYSCALL;
processExpression(logf,script,types,location,
line,i+2,OBJ_FILE,exp,&next);
obj1 = updateTypesAfterSysCall(types,exp,
NULL,OBJ_FILE,OBJ_CREATED);
printLogEntry(logf, types, OP_CREA, obj1, 0);
//Checks combined call
combinline = strstr(line->line,tokens[next]);
if((nbtokens-2>=next)&&combinline){
char * found = strchr(combinline,'.');
if(!found){
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in")))
addObjectReference(types,obj1,tokens[i-2]);
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
}
sprintf_s(combinid,TOKENSIZE,"INT%08X",combinnb); combinnb++;
addObjectReference(types,obj1,combinid);
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in"))){
sprintf_s(combined.line,LINE_LENGTH,"%s = %s.%s",tokens[i-2],combinid,found);
}else{
sprintf_s(combined.line,LINE_LENGTH,"%s.%s",combinid,found);
}
if(!monitorFileIO(logf,script,types,location,&combined)){
removeObjectReference(types,obj1,combinid);
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in")))
addObjectReference(types,obj1,tokens[i-2]);
}
}else{
if(i>=2&&(tokens[i-1][0]=='='||!strcasecmp(tokens[i-1],"in")))
addObjectReference(types,obj1,tokens[i-2]);
}
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
}//if creation
//Delete command
if(!strcasecmp(tokens[i+1],DELETEF1)
|| !strcasecmp(tokens[i+1],DELETEF2)){
line->type = SYSCALL;
processExpression(logf,script,types,location,
line,i+2,OBJ_FILE,exp,NULL);
obj1 = updateTypesAfterSysCall(types,exp,
tokens[i-2],OBJ_FILE,OBJ_EXIST);
printLogEntry(logf, types, OP_DEL, obj1, 0);
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TFSO,tokens[i]);
return 1;
}//if delete
}//if file system manager
//Drive set object
if(drives && !strcasecmp(driveobj,tokens[i])){
if((i+1<nbtokens && (!strcasecmp(tokens[i+1],"Item")||
!strcasecmp(tokens[i+1],"Files")))|| !strcasecmp(tokens[i-1],"in")){
line->type = SYSCALL;
obj1 = updateTypesAfterSysCall(types,COM_DRIVE,
tokens[i-2],OBJ_DRIVE,OBJ_EXIST);
sprintf_s(types->objects[obj1].ObjectName, NAME_MAX_LENGTH,
"Drive(ref:%s)",tokens[i-2]);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
return 1;
}
}//if drive set
//Document object
if((nbtokens-i>2) && !strcasecmp(tokens[i],"Document")){
if(!strcasecmp(tokens[i+1],"Body")&&!strcasecmp(tokens[i+2],OPENDOC)){
line->type = SYSCALL;
obj1 = updateTypesAfterSysCall(types,HTM_DOC,
NULL,OBJ_FILE,OBJ_EXIST);
if(i>=2) addObjectReference(types,obj1,tokens[i-2]);
setObjectStatus(types,obj1,OBJ_EXIST);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
return 1;
}
}
//Shell manager
if((isShellManager(&script->managers,tokens[i])>-1)
|| (isShellManager(localmanagers,tokens[i])>-1)){
//Open command
if(!strcasecmp(tokens[i+1],OPENRUN)){
line->type = SYSCALL;
processExpression(logf,script,types,location,
line,i+2,OBJ_FILE,exp,&next);
obj1 = updateTypesAfterSysCall(types,exp,
NULL,OBJ_FILE,OBJ_EXIST);
printLogEntry(logf, types, OP_OPEN, obj1, 0);
if(unknown>1) //learn manager class
addManagerObject(&script->managers,TSHELL,tokens[i]);
return 1;
}
}
}//for
return 0;
}
void processLine(FILE * logf, struct SCRIPT * script, struct TYPING * types,
unsigned long location, struct LINE * line){
char * tokens = (char *) calloc(TOKENMAXNB*TOKENSIZE,sizeof(char));
int nbtokens, i, j, index, storobj=-1, valobj=-1; int calldetected;
//Detect system calls
calldetected = monitorSytemCalls(logf,script,types,location,line);
//Parse line
nbtokens = decomposeLine(line->line,tokens,TOKENMAXNB,TOKENSIZE);
for(i=0;i<nbtokens;i++){
//Monitor string and processing and treat dependency
if(!strcasecmp(ACCESS(tokens,i),"Mid")
||!strcasecmp(ACCESS(tokens,i),"Left")
||!strcasecmp(ACCESS(tokens,i),"Ucase")
||!strcasecmp(ACCESS(tokens,i),"Lcase")
||!strcasecmp(ACCESS(tokens,i),"LTrim")
||!strcasecmp(ACCESS(tokens,i),"RTrim")
||!strcasecmp(ACCESS(tokens,i),"Replace")){
int newstor = 0;
int obj = isKnownObject(types,ACCESS(tokens,i+1));
if(obj>-1 && i>=2 && ((char *)ACCESS(tokens,i-1))[0]=='='){
int storobj = isKnownObject(types,ACCESS(tokens,i-2));
if(storobj==-1){
newstor = 1,
storobj = addNewObject(types,NULL,getObjectNature(types,obj));
addObjectReference(types,storobj,ACCESS(tokens,i-2));
setObjectType(types,storobj,getObjectType(types,obj));
}else{
setObjectNature(types,storobj,getObjectNature(types,obj));
setObjectType(types,storobj,getObjectType(types,obj));
}
if(newstor){strcpy_s(types->objects[storobj].ObjectName,
NAME_MAX_LENGTH,types->objects[obj].ObjectName);}
printLogEntry(logf, types, OP_AFF, storobj, obj);
}
}
//Detect string proceclocal procedure and function calls
index = isLocalProcedure(script,ACCESS(tokens,i));
if(index>-1){
//Avoid recursive calls
//if((location&0xF0000000)==PROCLEVEL
// && index==(location&0x0FFFFFFF)){
if(script->procedureslist[index].beingexecuted){
printf("[+] Block recursive call to procedure %s\n",
script->procedureslist[index].name);
}else{
script->procedureslist[index].beingexecuted = 1;
//No return value, so can not be an affectation
startProcedure(logf,script,types,index,line);
script->procedureslist[index].beingexecuted = 0;
}
free(tokens); return;
}else{
index = isLocalFunction(script,ACCESS(tokens,i));
if(index>-1){
if(strcmp(ACCESS(tokens,i+1),"=")){//Avoid return values
//Avoid recursive calls
if(script->functionslist[index].beingexecuted){
printf("[+] Block recursive call to function %s\n",
script->functionslist[index].name);
}else{
script->functionslist[index].beingexecuted = 1;
startFunction(logf,script,types,index,line);
script->functionslist[index].beingexecuted = 0;
}
free(tokens); return;
}else{
line->type = AFFECTATION;
updateReturnStorage(types,
script->functionslist[index].name, ACCESS(tokens,i+2));
free(tokens); return;
}//if call or return
}
}
} if(calldetected) return;
//Detect affectation of known object
for(i=0;i<nbtokens;i++){
if(((char *)ACCESS(tokens,i))[0]=='='||!strcasecmp(ACCESS(tokens,i),"in")){
int maxobj = -1; int maxtype; int nullnat = 0; int newstor = 0;
int nbconselem; //Number of consecutive elements must
int isarray = 0;//be < 2 except using & and array to concatenate
//Either creation or retrieving of store object
storobj = isKnownObject(types,ACCESS(tokens,i-1));
if(storobj==-1){
newstor = 1;
storobj = addNewObject(types,NULL,0);
addObjectReference(types,storobj,ACCESS(tokens,i-1));
}//if unknown
maxtype = getObjectType(types,storobj);
nbconselem = 0;
//Look for significant passing value
for(j=i+1;j<nbtokens;j++){
if(!strcasecmp(ACCESS(tokens,j),"Array")){
isarray = 1; j++;
}//if
if(((char *)ACCESS(tokens,j))[0]=='&'){
nbconselem = 0;
}else{
//Checks if access to a static attribute
char stataccess[TOKENSIZE+5];
strcpy_s(stataccess,5+TOKENSIZE,ACCESS(tokens,j));
strcat_s(stataccess,5+TOKENSIZE,".");
if(strcasestr(line->line,stataccess)){
nbconselem = 0;
}else{
nbconselem++;
}
}//if
if(!isarray && nbconselem>1) break;
valobj = isKnownObject(types,ACCESS(tokens,j));
if(valobj>-1){//known objects
//Update store type when significant
if(getObjectType(types,valobj)>maxtype){
maxtype = getObjectType(types,valobj);
maxobj = valobj;
}
}else if(ClassifyObject(ACCESS(tokens,j),&nullnat)>maxtype){//typed object
maxobj = addNewObject(types,ACCESS(tokens,j),nullnat);
maxtype = getObjectType(types,maxobj);
}//if
}//for
if(maxobj>-1){
line->type = AFFECTATION;
setObjectType(types,storobj,getObjectType(types,maxobj));
setObjectNature(types,storobj,getObjectNature(types,maxobj));
if(newstor){strcpy_s(types->objects[storobj].ObjectName,
NAME_MAX_LENGTH,types->objects[maxobj].ObjectName);}
printLogEntry(logf, types, OP_AFF, storobj, maxobj);
}
}//if '=' found
}//for
free(tokens);
}
void COptMethodSteepestDescent::initObjects()
{
addObjectReference("Current Iteration", mCurrentIteration, CCopasiObject::ValueInt);
}
void CBitPatternTreeMethod::initObjects()
{
addObjectReference("Current Step", mProgressCounter, CCopasiObject::ValueInt);
}
void COptMethodPraxis::initObjects()
{
addObjectReference("Current Iteration", mIteration, CDataObject::ValueInt);
}
void CCopasiTask::initObjects()
{
addObjectReference("Output counter", mOutputCounter, CCopasiObject::ValueInt);
new CCopasiTimer(CCopasiTimer::WALL, this);
new CCopasiTimer(CCopasiTimer::PROCESS, this);
}
void COptMethodEP::initObjects()
{
addObjectReference("Current Generation", mGeneration, CCopasiObject::ValueInt);
}
void CChemEqElement::initObjects()
{
addObjectReference("Multiplicity", mMultiplicity, CCopasiObject::ValueDbl);
addObjectReference("Metab Key", mMetaboliteKey);
}