double RungeKuttaSolver::SolveEquation()
{
double h = GetStepSize();
double t_previous = GetInitialTime();
double t1 = GetFinalTime();
double y_previous = getInitialValue();
double y_current = getInitialValue();
double k1, k2, k3, k4;
while (t_previous + h < t1)
{
k1 = h * RightHandSide(y_previous, t_previous);
k2 = h * RightHandSide(y_previous + 0.5 * k1, t_previous + 0.5 * h);
k3 = h * RightHandSide(y_previous + 0.5 * k2, t_previous + 0.5 * h);
k4 = h * RightHandSide(y_previous + k3, t_previous + h);
y_current = y_previous + (1.0 / 6.0) * (k1 + 2 * k2 + 2 * k3 + k4);
t_previous += h;
y_previous = y_current;
}
return y_current;
}
void AminoModelJump::resetState(TreeAln &traln)
{
auto primVar = getPrimaryParameterView();
assert(primVar.size() == 1 );
auto partitions = primVar[0]->getPartitions();
for(auto p: partitions )
traln.setProteinModel(p,savedMod);
// necessary, if we have fixed branch lengths
for(auto ¶m : getBranchLengthsParameterView() )
{
if( not param->getPrior()->needsIntegration() )
{
auto prior = param->getPrior() ;
for(auto &b : traln.extractBranches(param))
{
auto content = prior->getInitialValue();
b.setLength(InternalBranchLength::fromAbsolute(content.values[0], param->getMeanSubstitutionRate()));
if(not BoundsChecker::checkBranch(b))
BoundsChecker::correctBranch(b);
traln.setBranch(b,param);
}
}
else
{
// TODO inefficient =/ but cannot use the _oldFcs. That
// would cause trouble in proposal sets
param->updateMeanSubstRate(traln);
}
}
}
static void initializePoints(double * * points, int rowFrom, int howMany, int numPointsPerDimension)
{
int i, j;
for (i = rowFrom; i < rowFrom + howMany; ++i)
{
for (j = 0; j < numPointsPerDimension; ++j)
{
points[i-rowFrom][j] = getInitialValue(i, j, numPointsPerDimension);
}
}
}
// virtual
LLXMLNodePtr LLSlider::getXML(bool save_children) const
{
LLXMLNodePtr node = LLUICtrl::getXML();
node->createChild("initial_val", TRUE)->setFloatValue(getInitialValue());
node->createChild("min_val", TRUE)->setFloatValue(getMinValue());
node->createChild("max_val", TRUE)->setFloatValue(getMaxValue());
node->createChild("increment", TRUE)->setFloatValue(getIncrement());
node->createChild("volume", TRUE)->setBoolValue(mVolumeSlider);
return node;
}
// virtual
LLXMLNodePtr LLMultiSlider::getXML(bool save_children) const
{
LLXMLNodePtr node = LLUICtrl::getXML();
node->setName(LL_MULTI_SLIDER_TAG);
node->createChild("initial_val", TRUE)->setFloatValue(getInitialValue());
node->createChild("min_val", TRUE)->setFloatValue(getMinValue());
node->createChild("max_val", TRUE)->setFloatValue(getMaxValue());
node->createChild("increment", TRUE)->setFloatValue(getIncrement());
return node;
}
// virtual
LLXMLNodePtr LLSlider::getXML(bool save_children) const
{
LLXMLNodePtr node = LLUICtrl::getXML();
if (mVolumeSlider)
{
node->setName(LL_VOLUME_SLIDER_CTRL_TAG);
}
else
{
node->setName(LL_SLIDER_TAG);
}
node->createChild("initial_val", TRUE)->setFloatValue(getInitialValue());
node->createChild("min_val", TRUE)->setFloatValue(getMinValue());
node->createChild("max_val", TRUE)->setFloatValue(getMaxValue());
node->createChild("increment", TRUE)->setFloatValue(getIncrement());
node->createChild("volume", TRUE)->setBoolValue(mVolumeSlider);
return node;
}
/**
* Set attributes of the node that represents this class
* in the XMI document.
*/
void CodeParameter::setAttributesOnNode ( QDomDocument & doc, QDomElement & blockElement)
{
// set local attributes
blockElement.setAttribute("parent_id",getID());
// setting ID's takes special treatment
// as UMLRoles arent properly stored in the XMI right now.
// (change would break the XMI format..save for big version change )
UMLRole * role = dynamic_cast<UMLRole*>(m_parentObject);
if(role)
blockElement.setAttribute("role_id", role->role());
else
blockElement.setAttribute("role_id","-1");
blockElement.setAttribute("initialValue",getInitialValue());
// a comment which we will store in its own separate child node block
QDomElement commElement = doc.createElement( "header" );
getComment()->saveToXMI(doc, commElement); // comment
blockElement.appendChild( commElement);
}
QString
vleSmDT::getData()
{
QString tpl = "/**\n" \
" * @file {{classname}}.cpp\n" \
" * @author ...\n" \
" * ...\n" \
" */\n\n" \
"/*\n" \
" * @@tagdynamic@@\n" \
" * @@tagdepends: vle.discrete-time @@endtagdepends\n" \
"*/\n\n" \
"#include <vle/DiscreteTimeDbg.hpp>\n" \
"#include <vle/devs/DynamicsDbg.hpp>\n\n" \
"{{includes}}" \
"namespace vd = vle::devs;\n\n" \
"namespace vv = vle::value;\n\n" \
"namespace vle {\n" \
"namespace discrete_time {\n" \
"namespace {{namespace}} {\n\n" \
"class {{classname}} : public DiscreteTimeDyn\n" \
"{\n" \
"public:\n" \
"{{classname}}(\n" \
" const vd::DynamicsInit& init,\n" \
" const vd::InitEventList& evts)\n" \
" : DiscreteTimeDyn(init, evts)\n" \
"{\n" \
"{{for i in var}}" \
" {{var^i}}.init(this, \"{{var^i}}\", evts);\n" \
"{{end for}}" \
"{{for i in init_value_var}}" \
" {{init_value_var^i}}.init_value({{init_value_val^i}});\n" \
"{{end for}}" \
"{{construct}}" \
"\n" \
"}\n" \
"\n" \
"virtual ~{{classname}}()\n" \
"{}\n" \
"\n" \
"void compute(const vle::devs::Time& t)\n" \
"{\n" \
"{{compute}}" \
"}\n" \
"\n" \
"{{for i in var}}" \
" Var {{var^i}};\n" \
"{{end for}}" \
"{{userSection}}" \
"};\n\n" \
"} // namespace {{namespace}}\n" \
"} // namespace discrete_time\n" \
"} // namespace vle\n\n" \
"DECLARE_DYNAMICS(" \
"vle::discrete_time::{{namespace}}::{{classname}})\n\n";
vle::utils::Template vleTpl(tpl.toStdString());
vleTpl.stringSymbol().append("classname", getClassName().toStdString());
vleTpl.stringSymbol().append("namespace", getNamespace().toStdString());
vleTpl.listSymbol().append("var");
vleTpl.listSymbol().append("init_value_var");
vleTpl.listSymbol().append("init_value_val");
QDomNodeList variablesXml = variablesFromDoc();
for (int i = 0; i < variablesXml.length(); i++) {
QDomNode variable = variablesXml.item(i);
QString varName = variable.attributes().namedItem("name").nodeValue();
vle::value::Value* val = getInitialValue(varName);
if (val) {
vleTpl.listSymbol().append("init_value_var", varName.toStdString());
vleTpl.listSymbol().append("init_value_val", val->writeToString());
delete val;
}
vleTpl.listSymbol().append("var", varName.toStdString());
}
vleTpl.stringSymbol().append("includes", "");
vleTpl.stringSymbol().append("compute", getComputeBody().toStdString());
vleTpl.stringSymbol().append("construct","");
vleTpl.stringSymbol().append("userSection","");
std::ostringstream out;
vleTpl.process(out);
return QString(out.str().c_str());
}
