bool CMassAction::setInfix(const std::string & infix)
{
if (infix == "k1*PRODUCT<substrate_i>-k2*PRODUCT<product_j>")
setReversible(TriTrue);
else if (infix == "k1*PRODUCT<substrate_i>")
setReversible(TriFalse);
else
return false;
CFunction::setInfix(infix);
getVariables().cleanup();
getVariables().add("k1",
CFunctionParameter::FLOAT64,
CFunctionParameter::PARAMETER);
getVariables().add("substrate",
CFunctionParameter::VFLOAT64,
CFunctionParameter::SUBSTRATE);
if (isReversible() == TriTrue)
{
getVariables().add("k2",
CFunctionParameter::FLOAT64,
CFunctionParameter::PARAMETER);
getVariables().add("product",
CFunctionParameter::VFLOAT64,
CFunctionParameter::PRODUCT);
}
return true;
}
bool Session::getVariables(const QStringList &oids, QValueVector<QVariant> &retvars, uint32_t &status)
{
QMutexLocker ml(&m_mutex);
int maxIterations = oids.count() / 5;
for(int i = 0; i < maxIterations; i++)
if ( ! getVariables(oids, retvars, status, i*5) )
return false;
return getVariables(oids, retvars, status, maxIterations*5);
}
void CFunction::createListOfParametersForMathML(std::vector<std::vector<std::string> > & env)
{
unsigned C_INT32 i, imax = getVariables().size();
env.clear();
env.resize(imax);
for (i = 0; i < imax; ++i)
{
env[i].push_back("<mi>" + getVariables()[i]->getObjectName() + "</mi>");
}
}
static void OnCloseClicked(WndButton* pWnd){
if(pWnd) {
WndForm * pForm = pWnd->GetParentWndForm();
bool bIdenti = false;
getVariables();
for (unsigned int i=0 ; i < NO_WP_FILES-1; i++)
{
if((szWaypointFile[i] != NULL) && (_tcslen (szWaypointFile[i])> 0))
for (unsigned int j=(i+1) ; j < NO_WP_FILES; j++)
{
TCHAR tmp[MAX_PATH];
if((szWaypointFile[j] != NULL) && (_tcslen (szWaypointFile[j])> 0))
{
if(_tcscmp(szWaypointFile[i],szWaypointFile[j])==0)
{
_sntprintf(tmp, MAX_PATH, _T("%s %u %s %u %s!"), MsgToken(2340), // _@M2340_ "Waypoint Files"
i+1,
MsgToken(2345) , //_@M2345_ "and"
j+1,
MsgToken(2346) //_@M2346_ "are identical"
);
MessageBoxX( tmp, MsgToken(356), mbOk) ; // _@M356_ "Information"
bIdenti = true;
}
}
}
}
if( bIdenti) return ;
if(pForm) {
pForm->SetModalResult(mrOK);
}
}
}
void glsl_program :: LinkProgram()
{
if (!m_num)
{
error("can't link zero shaders");
return;
}
if(GLEW_VERSION_2_0)
LinkGL2();
else
LinkARB();
//post("getting variables");
getVariables();
#ifdef __APPLE__
// call API to check if linked program is running on hardware or in software emulation
GemCGLint vertexGPUProcessing, fragmentGPUProcessing;
CGLGetParameter (CGLGetCurrentContext(), kCGLCPGPUVertexProcessing, &vertexGPUProcessing);
CGLGetParameter (CGLGetCurrentContext(), kCGLCPGPUFragmentProcessing, &fragmentGPUProcessing);
post("vertex shader running in %sware", vertexGPUProcessing?"hard":"soft");
post("fragment shader running in %sware", fragmentGPUProcessing?"hard":"soft");
#endif //__APPLE__
// send program ID to outlet
/* JMZ: shouldn't this be only done, when we have a linked program? */
t_atom a;
gem::utils::glsl::atom_setshader(a, (GLEW_VERSION_2_0)?m_program:m_programARB);
outlet_list(m_outProgramID, 0, 1, &a);
}
double RateFree::targetFunk(double x[]) {
getVariables(x);
if (optimizing_params != 2)
// only clear partial_lh if optimizing rates
phylo_tree->clearAllPartialLH();
return -phylo_tree->computeLikelihood();
}
void CFunction::writeMathML(std::ostream & out,
const std::vector<std::vector<std::string> > & env,
bool expand, bool fullExpand,
unsigned C_INT32 l) const
{
if (expand && mpRoot)
{
bool flag = false; //TODO include check if parantheses are necessary
if (flag) out << SPC(l) << "<mfenced>" << std::endl;
mpRoot->writeMathML(out, env, fullExpand, l + 1);
if (flag) out << SPC(l) << "</mfenced>" << std::endl;
}
else //no expand
{
out << SPC(l) << "<mrow>" << std::endl;
out << SPC(l + 1) << CMathMl::fixName(getObjectName()) << std::endl;
out << SPC(l + 1) << "<mfenced>" << std::endl;
unsigned C_INT32 i, imax = getVariables().size();
for (i = 0; i < imax; ++i)
{
out << SPC(l + 2) << env[i][0] << std::endl;
}
out << SPC(l + 1) << "</mfenced>" << std::endl;
out << SPC(l) << "</mrow>" << std::endl;
}
}
bool PadeConstraints::put(xmlNodePtr cur) {
bool success=getVariables(cur);
map<string,pair<string,RealType> >::iterator vit(inVars.find("B"));
if(vit == inVars.end()) return false; //disaster, need to abort
ID=(*vit).second.first; B=(*vit).second.second;
return true;
}
Monome* Monome::primitive(Variable* v) const
{
if(v != *getVariables().begin()) return clone();
//assert(m_exposant != -1); pas besoin tant que exposant m_uint
//TODO return new Monome(v, m_multiplicateur/(m_exposant+1), m_exposant+1);
return 0;
}
bool CmdVariable::onServer(DebuggerProxy &proxy) {
if (m_type == KindOfVariableAsync) {
//we only do variable inspection on continuation wait handles
auto frame = getWaitHandleAtAsyncStackPosition(m_frame);
if (frame != nullptr) {
auto fp = frame->actRec();
if (fp != nullptr) {
m_variables = getVariables(fp);
}
}
}
else if (m_frame < 0) {
m_variables = g_context->m_globalVarEnv->getDefinedVariables();
m_global = true;
} else {
m_variables = g_context->getLocalDefinedVariables(m_frame);
m_global = g_context->getVarEnv(m_frame) == g_context->m_globalVarEnv;
}
if (m_global) {
m_variables.remove(s_GLOBALS);
}
if (m_version == 1) {
// Remove the values before sending to client.
ArrayInit ret(m_variables->size(), ArrayInit::Map{});
Variant v;
for (ArrayIter iter(m_variables); iter; ++iter) {
ret.add(iter.first().toString(), v);
}
m_variables = ret.toArray();
m_version = 2;
} else if (m_version == 2) {
// Remove entries that do not match a non empty m_varName.
if (!m_varName.empty()) {
ArrayInit ret(1, ArrayInit::Map{});
ret.add(m_varName, m_variables[m_varName]);
m_variables = ret.toArray();
}
// Remove entries whose name or contents do not match a non empty m_filter
if (!m_filter.empty()) {
ArrayInit ret(m_variables.size(), ArrayInit::Map{});
for (ArrayIter iter(m_variables); iter; ++iter) {
String name = iter.first().toString();
if (name.find(m_filter, 0, false) < 0) {
String fullvalue = DebuggerClient::FormatVariable(iter.second(), -1);
if (fullvalue.find(m_filter, 0, false) < 0) {
continue;
}
}
ret.add(name, iter.second());
}
m_variables = ret.toArray();
}
}
return proxy.sendToClient(this);
}
double RateGammaInvar::optimizeParameters(double gradient_epsilon) {
int ndim = getNDim();
// return if nothing to be optimized
if (ndim == 0)
return phylo_tree->computeLikelihood();
if (verbose_mode >= VB_MED)
cout << "Optimizing " << name << " model parameters by " << optimize_alg << " algorithm..." << endl;
if (optimize_alg.find("EM_RR") != string::npos) {
return randomRestartOptimization(gradient_epsilon);
} else if (optimize_alg.find("Brent") != string::npos || phylo_tree->aln->frac_const_sites == 0.0 || isFixPInvar() || isFixGammaShape()) {
double lh = phylo_tree->computeLikelihood();
cur_optimize = 0;
double gamma_lh = RateGamma::optimizeParameters(gradient_epsilon);
ASSERT(gamma_lh >= lh-0.1);
cur_optimize = 1;
double invar_lh = -DBL_MAX;
invar_lh = RateInvar::optimizeParameters(gradient_epsilon);
ASSERT(invar_lh >= gamma_lh-0.1);
cur_optimize = 0;
return invar_lh;
} else if (optimize_alg.find("EM") != string::npos) {
return optimizeWithEM(gradient_epsilon);
} else if (optimize_alg.find("BFGS") != string::npos) {
//if (freq_type == FREQ_ESTIMATE) scaleStateFreq(false);
double *variables = new double[ndim+1];
double *upper_bound = new double[ndim+1];
double *lower_bound = new double[ndim+1];
bool *bound_check = new bool[ndim+1];
double score;
// by BFGS algorithm
setVariables(variables);
setBounds(lower_bound, upper_bound, bound_check);
score = -minimizeMultiDimen(variables, ndim, lower_bound, upper_bound, bound_check, max(gradient_epsilon, TOL_GAMMA_SHAPE));
getVariables(variables);
phylo_tree->clearAllPartialLH();
score = phylo_tree->computeLikelihood();
delete [] bound_check;
delete [] lower_bound;
delete [] upper_bound;
delete [] variables;
return score;
} else {
string errMsg = "Unknown optimization algorithm: " + optimize_alg;
outError(errMsg.c_str());
return 0.0;
}
}
bool ScaledPadeConstraints::put(xmlNodePtr cur) {
bool success=getVariables(cur);
map<string,pair<string,RealType> >::iterator bit(inVars.find("B"));
map<string,pair<string,RealType> >::iterator cit(inVars.find("C"));
if(bit == inVars.end() || cit == inVars.end()) return false;
BID=(*bit).second.first; B=(*bit).second.second;
CID=(*cit).second.first; C=(*cit).second.second;
return true;
}
void script::parseStringScript(std::string in)
{
//FIX: Do we really need 4 functions when they all run at the same time anyway?
getVariables(in);
getFunctions(in);
getRules(in);
findSeed(in);
rawStorage = seed;
}
void CFunction::writeMathML(std::ostream & out, unsigned C_INT32 l) const
{
//out << "<math>" << std::endl;
out << SPC(l) << "<mrow>" << std::endl;
out << SPC(l + 1) << CMathMl::fixName(getObjectName()) << std::endl;
out << SPC(l + 1) << "<mfenced>" << std::endl;
unsigned C_INT32 i, imax = getVariables().size();
for (i = 0; i < imax; ++i)
{
out << SPC(l + 2) << "<mi>" << getVariables()[i]->getObjectName() << "</mi>" << std::endl;
}
out << SPC(l + 1) << "</mfenced>" << std::endl;
out << SPC(l) << "</mrow>" << std::endl;
//out << "</math>" << std::endl;
}
void BaseRunTimeConfig::dump()
{
getVariables();
string::size_type longestName = 0;
for( RunTimeVariableMap::iterator itr = m_variables.begin(); itr != m_variables.end(); ++itr )
if( itr->first.length() > longestName )
longestName = itr->first.length();
for( RunTimeVariableMap::iterator itr = m_variables.begin(); itr != m_variables.end(); ++itr )
{
cout.width( (streamsize) longestName + 2 );
stringstream s;
s << right << itr->first << ": ";
cout << s.str() << boolalpha << "\"" << itr->second << "\"" << endl;
}
}
void script::getVariables(std::string in, unsigned startPos)
{
//Find first instance of "var" in the string
startPos = in.find("var", startPos);
if(startPos != std::string::npos)
{
//If not at end of string, we have found a variable, find the end of the it by finding the next ";"
unsigned nameEnd = in.find_first_of(";", startPos); //FIX: Do we need to find ; since it is only one character?
//Store the variables identity in name
char name = in.at(nameEnd-1);
//Put the variable in the vector for variables in the script class
variables.push_back(name);
//Function runs itself from the point after the found variable
getVariables(in, nameEnd);
}
//If we are here we have found all the variables in the script and should exit
}
double NGSRateCat::optimizeParameters(double epsilon) {
int ndim = getNDim();
// return if nothing to be optimized
if (ndim == 0) return 0.0;
cout << "Optimizing " << name << " model parameters..." << endl;
double *variables = new double[ndim+1];
double *upper_bound = new double[ndim+1];
double *lower_bound = new double[ndim+1];
bool *bound_check = new bool[ndim+1];
int i;
double score;
// by BFGS algorithm
setVariables(variables);
for (i = 1; i <= ndim; i++) {
//cout << variables[i] << endl;
lower_bound[i] = 1e-4;
upper_bound[i] = 100.0;
bound_check[i] = false;
}
for (i = ndim-ncategory+2; i <= ndim; i++)
upper_bound[i] = 1.0;
//packData(variables, lower_bound, upper_bound, bound_check);
score = -minimizeMultiDimen(variables, ndim, lower_bound, upper_bound, bound_check, max(epsilon, 1e-6));
getVariables(variables);
delete [] bound_check;
delete [] lower_bound;
delete [] upper_bound;
delete [] variables;
return score;
}
std::pair<unsigned,unsigned> HttpInterface::sendGetVariables(const std::string nodeName, const strings& args)
{
unsigned nodePos, varPos;
for (strings::const_iterator it(args.begin()); it != args.end(); ++it)
{
// get node id, variable position and length
if (verbose)
cerr << "getVariables " << nodeName << " " << *it;
const bool exists(getNodeAndVarPos(nodeName, *it, nodePos, varPos));
if (!exists)
continue;
VariablesMap vm = allVariables[nodeName];
const unsigned length(vm[UTF8ToWString(*it)].second);
if (verbose)
cerr << " (" << nodePos << "," << varPos << "):" << length << "\n";
// send the message
GetVariables getVariables(nodePos, varPos, length);
getVariables.serialize(asebaStream);
}
asebaStream->flush();
return std::pair<unsigned,unsigned>(nodePos,varPos); // just last one
}
double RateInvar::targetFunk(double x[]) {
getVariables(x);
// fix bug: computeTip... will update ptn_invar vector
phylo_tree->computePtnInvar();
return -phylo_tree->computeLikelihood();
}
void BaseRunTimeConfig::initializeFromBuffer( const string& cfgStr )
{ TRACER_OP_START("BaseRunTimeConfig::initializeFromBuffer"); TRACER(cfgStr, READ, HEAP, "Configuration string");
if (&cfgStr != &this->cfgStr)
this->cfgStr = cfgStr;
m_warnings.str("");
RunTimeVariableMap newVars;
int lineNum = 0;
try
{
getVariables();
istringstream cfgStream(cfgStr);
string line;
while (getline(cfgStream, line))
{
++lineNum;
bal::trim(line); // trim whitespace
// skip blank or comment lines
if (line.empty() || line.find_first_of("#[") == 0)
continue;
// otherwise, the line must be in the form "Key=Value" and Key must be in the variables map
if (!bal::contains(line, "="))
{
m_warnings << "Line " << lineNum << ": line does not define a parameter in the \"Parameter = Value\" format.\n";
continue;
}
size_t predIdx = line.find_first_of('=') + 1;
TRACER_OP_START("get value for key"); TRACER_BI;
string key = line.substr(0, predIdx-1); TRACER(key, WRITE, STACK, "Parameter name");
bal::trim(key);
if (m_variables.count(key) == 0)
{
m_warnings << "Line " << lineNum << ": \"" << key << "\" is not a supported parameter.\n";
continue;
}
RunTimeVariableMap::iterator itr = newVars.find(key);
if (itr != newVars.end())
{
m_warnings << "Line " << lineNum << ": \"" << key << "\" has already been defined.\n";
continue;
}
size_t valBegin = line.find_first_not_of("\t ", predIdx);
size_t valEnd = valBegin;
bool inQuote = false;
for (valEnd = valBegin; valEnd < line.size(); ++valEnd)
{
if (line[valEnd] == '"' && line[valEnd-1] != '\\')
inQuote = !inQuote;
else if ((line[valEnd] == '#') && !inQuote)
break; // stop at unquoted comment token
}
if (valEnd == valBegin || valBegin == string::npos)
{
m_warnings << "Line " << lineNum << ": no value set for \"" << key << "\"; did you mean to use an empty string (\"\")?\n";
continue;
}
string& value = newVars[key];
value = TrimWhitespace(line.substr(valBegin, valEnd-valBegin));
if (value.empty())
{
m_warnings << "Line " << lineNum << ": no value set for \"" << key << "\"; did you mean to use an empty string (\"\")?\n";
continue;
}
value = UnquoteString(value);
bal::replace_all(value, "\\\"", "\"");
bal::replace_all(value, "true", "1");
bal::replace_all(value, "false", "0"); TRACER(value, WRITE, HEAP, std::string("Value for ")+std::string(key)); TRACER_BO; TRACER_OP_END("get value for key");
}
}
catch (exception& e)
{
m_warnings << "Line " << lineNum << ": " << e.what() << "\n";
}
// apply the new variable values
setVariables(newVars); TRACER_OP_END("BaseRunTimeConfig::initializeFromBuffer");
}
// This is only used when reading Gepasi Files
void CKinFunction::createParameters()
{
CCopasiVectorN < CFunctionParameter > Substrates;
CCopasiVectorN < CFunctionParameter > Products;
CCopasiVectorN < CFunctionParameter > Modifiers;
CCopasiVectorN < CFunctionParameter > Parameters;
CCopasiVectorN < CFunctionParameter > Volumes;
size_t i, imax = mNodes.size();
CFunctionParameter *pParameter;
for (i = 0; i < imax; i++)
{
if (mNodes[i]->getType() == N_IDENTIFIER)
{
// We need to check that we have no reserved name.
const char *Reserved[] =
{"pi", "exponentiale", "true", "false", "infinity", "nan",
"PI", "EXPONENTIALE", "TRUE", "FALSE", "INFINITY", "NAN"
};
std::string Name = mNodes[i]->getName();
size_t j, jmax = 12;
for (j = 0; j < jmax; j++)
if (Name == Reserved[j]) break;
if (j != jmax)
{
// It is save to prepend the identifyer with '_' since this is not allowed in
// Gepasi but within COPASI.
std::string OldName = Name;
Name = "_" + Name;
// We have to replace the corresponding CEvaluationNodes to reflect the change.
std::vector< CEvaluationNode * >::iterator it = mpNodeList->begin();
std::vector< CEvaluationNode * >::iterator end = mpNodeList->end();
for (; it != end; ++it)
if (((*it)->getType() & 0xFF000000) == CEvaluationNode::CONSTANT &&
(*it)->getData() == OldName)
(*it)->setData(Name);
// The Infix has changed we need to update it.
setInfix(mpRoot->buildInfix());
}
pParameter = new CFunctionParameter(Name);
pParameter->setType(CFunctionParameter::FLOAT64);
switch (mNodes[i]->getSubtype())
{
case N_SUBSTRATE:
pParameter->setUsage(CFunctionParameter::SUBSTRATE);
if (Substrates.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Substrates.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_PRODUCT:
pParameter->setUsage(CFunctionParameter::PRODUCT);
if (Products.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Products.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_MODIFIER:
pParameter->setUsage(CFunctionParameter::MODIFIER);
if (Modifiers.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Modifiers.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_KCONSTANT:
case N_NOP:
pParameter->setUsage(CFunctionParameter::PARAMETER);
if (Parameters.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Parameters.add(pParameter, false);
else
pdelete(pParameter);
break;
case N_VOLUME:
pParameter->setUsage(CFunctionParameter::VOLUME);
if (Volumes.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
Volumes.add(pParameter, false);
else
pdelete(pParameter);
break;
default:
pdelete(pParameter);
fatalError();
}
}
}
getVariables().cleanup();
imax = Substrates.size();
for (i = 0; i < imax; i++)
getVariables().add(Substrates[i], true);
Substrates.cleanup();
imax = Products.size();
for (i = 0; i < imax; i++)
getVariables().add(Products[i], true);
Products.cleanup();
imax = Modifiers.size();
for (i = 0; i < imax; i++)
getVariables().add(Modifiers[i], true);
Modifiers.cleanup();
imax = Parameters.size();
for (i = 0; i < imax; i++)
getVariables().add(Parameters[i], true);
Parameters.cleanup();
imax = Volumes.size();
for (i = 0; i < imax; i++)
getVariables().add(Volumes[i], true);
Volumes.cleanup();
}
/**
optimize parameters. Default is to optimize gamma shape
@return the best likelihood
*/
double RateFree::optimizeParameters(double gradient_epsilon) {
int ndim = getNDim();
// return if nothing to be optimized
if (ndim == 0)
return phylo_tree->computeLikelihood();
if (verbose_mode >= VB_MED)
cout << "Optimizing " << name << " model parameters by " << optimize_alg << " algorithm..." << endl;
// TODO: turn off EM algorithm for +ASC model
if ((optimize_alg.find("EM") != string::npos && phylo_tree->getModelFactory()->unobserved_ptns.empty()))
if (fix_params == 0)
return optimizeWithEM();
//if (freq_type == FREQ_ESTIMATE) scaleStateFreq(false);
double *variables = new double[ndim+1];
double *upper_bound = new double[ndim+1];
double *lower_bound = new double[ndim+1];
bool *bound_check = new bool[ndim+1];
double score;
// score = optimizeWeights();
int left = 1, right = 2;
if (fix_params == 1) // fix proportions
right = 1;
if (optimize_alg.find("1-BFGS") != string::npos) {
left = 0;
right = 0;
}
// changed to Wi -> Ri by Thomas on Sept 11, 15
for (optimizing_params = right; optimizing_params >= left; optimizing_params--) {
ndim = getNDim();
// by BFGS algorithm
setVariables(variables);
setBounds(lower_bound, upper_bound, bound_check);
// if (optimizing_params == 2 && optimize_alg.find("-EM") != string::npos)
// score = optimizeWeights();
// else
if (optimize_alg.find("BFGS-B") != string::npos)
score = -L_BFGS_B(ndim, variables+1, lower_bound+1, upper_bound+1, max(gradient_epsilon, TOL_FREE_RATE));
else
score = -minimizeMultiDimen(variables, ndim, lower_bound, upper_bound, bound_check, max(gradient_epsilon, TOL_FREE_RATE));
getVariables(variables);
// sort the rates in increasing order
if (sorted_rates)
quicksort(rates, 0, ncategory-1, prop);
phylo_tree->clearAllPartialLH();
score = phylo_tree->computeLikelihood();
}
optimizing_params = 0;
delete [] bound_check;
delete [] lower_bound;
delete [] upper_bound;
delete [] variables;
return score;
}
double RateGamma::targetFunk(double x[]) {
getVariables(x);
phylo_tree->clearAllPartialLH();
return -phylo_tree->computeLikelihood();
}
/**
the target function which needs to be optimized
@param x the input vector x
@return the function value at x
*/
double NGSRateCat::targetFunk(double x[]) {
getVariables(x);
if (proportion[ncategory-1] <= 1e-6) return 1e9;
return -phylo_tree->computeLikelihood();
}
bool PolyConstraints::put(xmlNodePtr cur) {
//get generic parameters and grid information
bool success=getVariables(cur);
return success;
}
