Filter::Filter(void)
{
m_resonance = ONE_OVER_SQRT2;
m_r2 = 1/m_resonance;
m_h = 0.5f;
m_c_low=m_c_band=m_c_high=0.0f;
#ifdef VSTI
m_samplerate = SAMPLERATE;
#endif
m_base_freq=0.0f;
m_mod=0.0f;
m_staticmod=0.0f;
m_bandwidth=2.0f;
setMode(0.0f);
setCutoff(0.5f);
setMod(0.0f,0.0f);
setBandwidth(2.0f);
setDrive(0.0f);
m_staticmod = 0.0f;
setOutputLevel(1.0f);
m_cutoff = 0.0f;
calculateCoefficients();
m_calc_coefficients = false;
m_calc_interval = STATE_CALC_INTERVAL;
reset();
}
void BranchAcceptor::load(istream &is)
{
double cutoff;
Strand strand;
SignalType signalType;
BOOM::String p;
int consensusOffset;
is >> signalType;
is >> p;
cutoff=p.asDouble();
is >> strand;
is >> consensusOffset;
setSignalType(signalType);
setStrand(strand);
setCutoff(cutoff);
BOOM::String dummy;
is>>dummy; // will always be "WWAM"
branchPoint=new WWAM(getGC(),is);
is>>dummy; // will always be "WAM"
acceptor=new WAM(getGC(),is);
int contextWindowLength=branchPoint->getContextWindowLength()+
acceptor->getContextWindowLength();
setSizes(2,consensusOffset,contextWindowLength);
}
Light::Light(LIGHT_TYPE type)
{
lights.push_back(this);
if(availableLights.size() > 0)
{
lightNum = availableLights[0];
availableLights.erase(availableLights.begin());
Visible(true);
setLightType(type);
setPosition(0, 0, 0);
setCutoff(45);
setExponent(12);
setSpotDirection(0, -1, 0);
setAmbient(0, 0, 0, 1);
setDiffuse(1, 1, 1, 1);
setSpecular(1, 1, 1, 1);
updateLight();
}
else
{
lightNum = 0;
Visible(false);
}
}
FENE(real _K, real _r0, real _rMax,
real _cutoff)
: K(_K), r0(_r0), rMax(_rMax) {
autoShift = false;
setCutoff(_cutoff);
setAutoShift();
}
VSpherePair(real _epsilon, real _cutoff)
: epsilon(_epsilon) {
autoShift = false;
setCutoff(_cutoff);
preset();
setAutoShift();
}
LennardJonesCapped(real _epsilon, real _sigma,
real _cutoff, real _caprad, real _shift)
: epsilon(_epsilon), sigma(_sigma), caprad(_caprad) {
setShift(_shift);
setCutoff(_cutoff);
preset();
}
FENECapped(real _K, real _r0, real _rMax,
real _cutoff, real _caprad)
: K(_K), r0(_r0), rMax(_rMax), caprad(_caprad) {
autoShift = false;
setCutoff(_cutoff);
setAutoShift();
}
ReactionFieldGeneralized()
: prefactor(1), kappa(0.0),
epsilon1(1.0), epsilon2(80.0),
rc(1.0){
setShift(0.0);
setCutoff(infinity);
initialize();
}
Light::Light(int number, Vector pos, Vector dir, float cutoff, float exponent) {
setNumber(number);
this->pos = pos;
this->dir = dir;
setCutoff(cutoff);
setExponent(exponent);
initAttenuation();
}
LennardJonesCapped(real _epsilon, real _sigma,
real _cutoff, real _caprad)
: epsilon(_epsilon), sigma(_sigma), caprad(_caprad) {
autoShift = false;
setCutoff(_cutoff);
preset();
setAutoShift();
}
ReactionFieldGeneralizedTI()
: prefactor(0.0), kappa(0.0),
epsilon1(1.0), epsilon2(80.0),
rc(1.0), lambdaTI(0.0), annihilate(1) {
setShift(0.0);
autoShift = false;
setCutoff(infinity);
initialize();
}
void PBSynthFilter::reset() {
int i;
for (i = 0; i < 4; i++)
xbuffer[i] = ybuffer[i] = 0;
setCutoff(1.0f, -1.0f);
}
Light::Light(int number, Vector pos, Vector dir, float* attenuation, float cutoff, float exponent) {
setNumber(number);
this->pos = pos;
this->dir = dir;
setAttenuation(0, attenuation[0]);
setAttenuation(1, attenuation[1]);
setAttenuation(2, attenuation[2]);
setCutoff(cutoff);
setExponent(exponent);
}
ReactionFieldGeneralized(
real _prefactor,
real _kappa,
real _eps1,
real _eps2,
real _cutoff,
real _shift)
: prefactor(_prefactor),kappa(_kappa),
epsilon1(_eps1), epsilon2(_eps2),
rc(_cutoff) {
setShift(_shift);//setShift(_shift);
setCutoff(_cutoff);
initialize();
}
ReactionFieldGeneralized(
real _prefactor,
real _kappa,
real _eps1,
real _eps2,
real _cutoff)
: prefactor(_prefactor), kappa(_kappa),
epsilon1(_eps1), epsilon2(_eps2),
rc(_cutoff) {
autoShift = false;
setCutoff(_cutoff);
/*Note: AutoShift cannot be used here since the shift
* has to depend on the product of charges */
//setAutoShift();
initialize();
}
// Drag/move curve.
void samplv1widget_filt::dragCurve ( const QPoint& pos )
{
const int h = height();
const int w = width();
const int dx = (pos.x() - m_posDrag.x());
const int dy = (pos.y() - m_posDrag.y());
if (dx || dy) {
const int h2 = (h >> 1);
const int x = int(cutoff() * float(w));
const int y = int(reso() * float(h2));
setCutoff(float(x + dx) / float(w));
setReso(float(y - dy) / float(h2));
m_posDrag = pos;
}
}
ReactionFieldGeneralizedTI(
real _prefactor,
real _kappa,
real _eps1,
real _eps2,
real _cutoff,
real _lambdaTI,
bool _annihilate)
: prefactor(_prefactor),kappa(_kappa),
epsilon1(_eps1), epsilon2(_eps2),
rc(_cutoff), lambdaTI(_lambdaTI),
annihilate(_annihilate) {
setShift(0.0);
autoShift = false;
/*Note: AutoShift cannot be used here since the shift
* has to depend on the product of charges */
setCutoff(_cutoff);
initialize();
}
bool
DcModel::setBestSolution(DC_Message how,
double & objectiveValue,
const double * solution,
bool fixVariables)
{
double cutoff = getCutoff();
// Double check the solution to catch pretenders.
if (objectiveValue >= cutoff) { // Bad news
if (objectiveValue > 1.0e30)
handler_->message(DC_NOTFEAS1, messages_) << CoinMessageEol;
else
handler_->message(DC_NOTFEAS2, messages_)
<< objectiveValue << cutoff << CoinMessageEol;
return false;
}
else { // Better solution
bestObjective_ = objectiveValue;
int numberColumns = solver_->getNumCols();
if (bestSolution_ == 0) {
bestSolution_ = new double[numberColumns];
}
memcpy(bestSolution_, solution, numberColumns*sizeof(double));
cutoff = bestObjective_ - dblParam_[DcCutoffIncrement];
setCutoff(cutoff);
if (how == DC_ROUNDING)
numberHeuristicSolutions_++;
numberSolutions_++;
// std::cout << "cutoff = " << getCutoff()
// << "; objVal = " << bestObjective_
// << "; cutoffInc = " << dblParam_[DcCutoffIncrement]
// << std::endl;
handler_->message(how, messages_)
<< bestObjective_ << numberIterations_
<< numberNodes_
<< CoinMessageEol;
return true;
}
}
void Light::setLightType(LIGHT_TYPE type)
{
lightType = type;
if(lightType == LIGHT_SPOT)
{
position[3] = 1.0f;
}
else if (lightType == LIGHT_POINT)
{
position[3] = 1.0f;
setCutoff(180.0f);
}
else if(lightType == LIGHT_DIRECTIONAL)
{
position[3] = 0.0f;
}
updateLight();
}
LennardJonesCapped()
: epsilon(0.0), sigma(0.0) {
setShift(0.0);
setCutoff(infinity);
preset();
}
FENECapped()
: K(0.0), r0(0.0), rMax(0.0), caprad(0.0) {
setShift(0.0);
setCutoff(infinity);
}
FENE()
: K(0.0), r0(0.0), rMax(0.0) {
setShift(0.0);
setCutoff(infinity);
}
void PBSynthFilter::setParameters(void *p) {
memcpy(¶meters, p, sizeof(parameters));
setCutoff(parameters.cutoff, parameters.resonance);
}
VSpherePair()
: epsilon(0.0) {
setShift(0.0);
setCutoff(infinity);
preset();
}
FENE(real _K, real _r0, real _rMax,
real _cutoff, real _shift)
: K(_K), r0(_r0), rMax(_rMax) {
setShift(_shift);
setCutoff(_cutoff);
}
void Light::modifyCutoff(float cutoff) {
setCutoff(this->cutoff + cutoff);
}
void AnalysisDialog::createResultsAnalysis() {
QVBoxLayout* resultsAnalysisLayout = new QVBoxLayout();
QGridLayout* resultsTopLayout = new QGridLayout();
QGridLayout* resultsBottomLayout = new QGridLayout();
thresholdEdit = new QLineEdit(this);
thresholdEdit ->setText(QString::number( 0 ));
thresholdEdit->setValidator( new QDoubleValidator(thresholdEdit) );
connect(thresholdEdit, SIGNAL(textChanged(QString)), this, SLOT(updateResultsAnalysis()));
QPushButton* defaultThresholdButton = new QPushButton("Default");
connect(defaultThresholdButton, SIGNAL(clicked()), this, SLOT(reset_epi_threshold()));
allNEdit = new QLineEdit(this);
allMinEdit = new QLineEdit(this);
allMaxEdit = new QLineEdit(this);
allMeanEdit = new QLineEdit(this);
allSDEdit = new QLineEdit(this);
outNEdit = new QLineEdit(this);
outMinEdit = new QLineEdit(this);
outMaxEdit = new QLineEdit(this);
outMeanEdit = new QLineEdit(this);
outSDEdit = new QLineEdit(this);
epiNEdit = new QLineEdit(this);
epiMinEdit = new QLineEdit(this);
epiMaxEdit = new QLineEdit(this);
epiMeanEdit = new QLineEdit(this);
epiSDEdit = new QLineEdit(this);
QLabel* thresholdLabel = new QLabel("Outbreak/epidemic threshold:", this);
resultsTopLayout->addWidget(thresholdLabel, 1, 0, 1, 2);
resultsTopLayout->addWidget(thresholdEdit, 1, 2);
resultsTopLayout->addWidget(defaultThresholdButton, 1, 3);
QLabel* allLabel = new QLabel("All simulations", this);
QLabel* outLabel = new QLabel("Outbreaks only", this);
QLabel* epiLabel = new QLabel("Epidemics only", this);
resultsTopLayout->addWidget(allLabel, 2, 1);
resultsTopLayout->addWidget(outLabel, 2, 2);
resultsTopLayout->addWidget(epiLabel, 2, 3);
_addResultsAnalysisRow(resultsTopLayout, "N", allNEdit, outNEdit, epiNEdit);
_addResultsAnalysisRow(resultsTopLayout, "Min" , allMinEdit, outMinEdit, epiMinEdit);
_addResultsAnalysisRow(resultsTopLayout, "Max" , allMaxEdit, outMaxEdit, epiMaxEdit);
_addResultsAnalysisRow(resultsTopLayout, "Mean" , allMeanEdit, outMeanEdit, epiMeanEdit);
_addResultsAnalysisRow(resultsTopLayout, "SD" , allSDEdit, outSDEdit, epiSDEdit);
QGroupBox* resultsAnalysisTop = new QGroupBox();
resultsAnalysisTop->setLayout(resultsTopLayout);
QLabel* nbins = new QLabel("Number of bins", this);
QLabel* minRange = new QLabel("Range minimum", this);
QLabel* maxRange = new QLabel("Range maximum", this);
resultsBottomLayout->addWidget(nbins, 1, 0);
resultsBottomLayout->addWidget(minRange, 1, 1);
resultsBottomLayout->addWidget(maxRange, 1, 2);
QLineEdit* nbinsLineEdit = new QLineEdit(this);
QLineEdit* minRangeLineEdit = new QLineEdit(this);
QLineEdit* maxRangeLineEdit = new QLineEdit(this);
resultsBottomLayout->addWidget(nbinsLineEdit, 2, 0);
resultsBottomLayout->addWidget(minRangeLineEdit, 2, 1);
resultsBottomLayout->addWidget(maxRangeLineEdit, 2, 2);
QGroupBox* resultsAnalysisBottom = new QGroupBox();
resultsAnalysisBottom->setLayout(resultsBottomLayout);
resultsHistPlot = new PlotView(this, "Epidemic size distribution", "Epidemic size", "Frequency");
resultsHistPlot->setPlotType(PlotView::RESULTS_HISTPLOT);
connect(thresholdEdit, SIGNAL(textChanged(QString)), resultsHistPlot, SLOT(setCutoff(QString)));
connect(thresholdEdit, SIGNAL(textEdited(QString)), this, SLOT(setThresholdEdited()));
connect(nbinsLineEdit, SIGNAL(textChanged(QString)), resultsHistPlot, SLOT(setNBins(QString)));
connect(minRangeLineEdit, SIGNAL(textChanged(QString)), resultsHistPlot, SLOT(setRangeMin(QString)));
connect(maxRangeLineEdit, SIGNAL(textChanged(QString)), resultsHistPlot, SLOT(setRangeMax(QString)));
// add a close window button
QPushButton* closeButton = new QPushButton("Close analysis", this);
connect(closeButton, SIGNAL(clicked()), this, SLOT(close()));
QHBoxLayout* buttonBoxLayout = new QHBoxLayout();
QWidget* buttonBox = new QWidget();
buttonBoxLayout->addStretch(1);
buttonBoxLayout->addWidget(closeButton);
buttonBox->setLayout(buttonBoxLayout);
resultsAnalysisLayout->addWidget(resultsAnalysisTop);
resultsAnalysisLayout->addWidget(resultsHistPlot);
resultsAnalysisLayout->addWidget(resultsAnalysisBottom);
resultsAnalysisLayout->addWidget(buttonBox);
this->setLayout(resultsAnalysisLayout);
}
VSpherePair(real _epsilon, real _cutoff, real _shift)
: epsilon(_epsilon) {
setShift(_shift);
setCutoff(_cutoff);
preset();
}
Quartic(real _K, real _r0, real _cutoff) : K(_K), r0(_r0) {
autoShift = false;
setCutoff(_cutoff);
setAutoShift();
}
FENECapped(real _K, real _r0, real _rMax,
real _cutoff, real _caprad, real _shift)
: K(_K), r0(_r0), rMax(_rMax), caprad(_caprad) {
setShift(_shift);
setCutoff(_cutoff);
}