bool interpolator::update( const double currentTime, float& p )
{
bool bContinue;
if( currentTime >= _dDestTime )
{
p = _fDestValue;
if( m_listParams.size () )
{
interpolatorParam& item = m_listParams.front();
set(_fDestValue, item.fDestValue, item.type, item.dDuration );
m_listParams.pop_front();
bContinue = true;
}
else
{
bContinue = false;
}
}
else
{
float t = (float)(currentTime - _dStartTime);
float d = (float)(_dDestTime - _dStartTime);
float b = _fStartValue;
float c = _fDestValue - _fStartValue;
p = getFormula(_type, t, b, d, c);
bContinue = true;
}
return bContinue;
}
void Residue::setModification(const String & modification)
{
//modification_ = modification;
ModificationsDB * mod_db = ModificationsDB::getInstance();
ResidueModification mod = mod_db->getModification(one_letter_code_, modification, ResidueModification::ANYWHERE);
modification_ = mod.getId();
// update all the members
if (mod.getAverageMass() != 0)
{
average_weight_ = mod.getAverageMass();
}
if (mod.getMonoMass() != 0)
{
mono_weight_ = mod.getMonoMass();
}
bool updated_formula(false);
if (!mod.getDiffFormula().isEmpty())
{
updated_formula = true;
setFormula(getFormula() + mod.getDiffFormula());
}
if (mod.getFormula() != "" && !updated_formula)
{
updated_formula = true;
String formula = mod.getFormula();
formula.removeWhitespaces();
formula_ = EmpiricalFormula(formula);
}
if (updated_formula)
{
average_weight_ = formula_.getAverageWeight();
mono_weight_ = formula_.getMonoWeight();
}
else
{
if (mod.getAverageMass() != 0)
{
average_weight_ = mod.getAverageMass();
}
if (mod.getMonoMass() != 0)
{
mono_weight_ = mod.getMonoMass();
}
}
// neutral losses
loss_formulas_.clear();
loss_names_.clear();
if (mod.hasNeutralLoss())
{
loss_formulas_.push_back(mod.getNeutralLossDiffFormula());
loss_names_.push_back(mod.getNeutralLossDiffFormula().toString());
}
is_modified_ = true;
}
string itsProblem::getInformations()
{
// separator used to format output
string sep = ":\t";
// put all in the stream
stringstream msg;
msg << "Key" << sep << getKey() << endl;
msg << "Name" << sep << getName() << endl;
msg << "Description" << sep << getDescription() << endl;
msg << "Formula" << sep << getFormula() << endl;
msg << "Dimension" << sep << getDimension() << (isDimensionFixed()?" (fixed)":" (not fixed)") << endl;
if ( getOptima().size() <= 0 ) {
msg << "Optimum Unknown" << endl;
} else {
// print vectors of the optimums
for(unsigned int i=0;i<getOptima().size();i++) {
if(getOptima().size()>1) {
msg << "Optimum " << i << sep;
} else {
msg << "Optimum " << sep;
}
msg << "<"
<< print(getOptima()[i].getValues()," ");
msg << "> @ <"
<< print(getOptima()[i].getSolution()," ");
msg << ">";
msg << endl;
}
}
// print vectors of bounds
msg << "Bounds" << sep << "[";
for(unsigned int i=0;i<getBounds().size();i++) {
msg << "["
<< print(getBounds()[i]," ");
msg << "]";
}
msg << "]" << endl;
msg << "Reference" << sep << getCitation() << endl;
// return only the string
return msg.str();
}
string itsProblem::getInformations_XML()
{
// put all in the stream
stringstream msg;
msg << "<problem>" << endl;
msg << "<key>" << getKey() << "</key>" << endl;
msg << "<name>" << getName() << "</name>" << endl;
msg << "<description>" << getDescription() << "</description>" << endl;
msg << "<formula>" << getFormula() << "</formula>" << endl;
msg << "<dimension>" << getDimension() << "</dimension>" << endl;
msg << "<accuracy>" << getAccuracy() << "</accuracy>" << endl;
msg << "<optimums>" << endl;
if ( getOptima().size() <= 0 ) {
msg << "Unknown";
} else {
// print vectors of the optimums
for(unsigned int i=0;i<getOptima().size();i++) {
if(getOptima().size()>1) {
msg << "<point id=\"" << i << "\">" << "<values>";
} else {
msg << "<point>" << "<values>";
}
msg << print(getOptima()[i].getValues()," ");
msg << "</values>" << "<solution>";
msg << print(getOptima()[i].getSolution()," ");
msg << "</solution>" << "</point>" << endl;
}
}
msg << "</optimums>" << endl;
// print vectors of bounds
msg << "<bounds>" << endl;
msg << "<minimums>";
msg << "<point>" << "<solution>";
msg << print( getBoundsMinima(), " ");
msg << "</solution>" << "</point>";
msg << "</minimums>" << endl;
msg << "<maximums>";
msg << "<point>" << "<solution>";
msg << print( getBoundsMaxima(), " ");
msg << "</solution>" << "</point>";
msg << "</maximums>" << endl;
msg << "</bounds>" << endl;
// references
msg << "<reference>" << getCitation() << "</reference>" << endl;
msg << "</problem>" << endl;
// return only the string
return msg.str();
}
