void TimeWarp::createCombinedMatrix(DoubleMatrix myChromaMatrix, DoubleVector energyVector, DoubleMatrix* chromaEnergyMatrix){
chromaEnergyMatrix->clear();
int sizeRatio = energyVector.size() / myChromaMatrix.size();//
printf("COMBINE: size of my chroma is %i\n", (int) myChromaMatrix.size());// energyVector.size() / myChromaMatrix.size();
printf("COMBINED: size ratio of energy to chroma is %i \n", sizeRatio);
int chromaSize = myChromaMatrix.size();
// printf("index is %i\n", index);
for (int i = 0;i < energyVector.size();i++){
DoubleVector d;
int index = min(chromaSize-1, (int) floor(i/sizeRatio));
for (int y = 0;y < 12;y++){
d.push_back(myChromaMatrix[index][y]);//
}
d.push_back(energyVector[i]);
(*chromaEnergyMatrix).push_back(d);
}
printf("COMBINED: size of chroma energy is %i\n", (int)(*chromaEnergyMatrix).size());
// int x = (int)(*chromaEnergyMatrix).size()/3;
// printf("energy[%i] %f \n", x, energyVector[x]);
/*
for (int y = 0;y < 13;y++){
printf("chroma[%i][%i] %f \n", x, y, myChromaMatrix[x/sizeRatio][y]);
printf("c[%i][%i] %f \n", x, y, (*chromaEnergyMatrix)[x][y]);
}
printf("\n");
*/
}
std::vector<double> ContinuousVariable_Impl::incrementalValues() const {
DoubleVector result;
if (m_minimum && m_maximum && (m_increment || m_nSteps)) {
// empty range
if (*m_minimum > *m_maximum) { return result; }
// degenerate range (single point)
if (equal(*m_minimum,*m_maximum)) {
result.push_back((*m_minimum + *m_maximum)/2.0);
return result;
}
// otherwise get incremental values
if (m_increment) {
for (double value = *m_minimum; lessThanOrEqual(value,*m_maximum); value += *m_increment) {
result.push_back(value);
}
}
else {
// m_nSteps
double inc = (*m_maximum - *m_minimum)/static_cast<double>(*m_nSteps);
for (double value = *m_minimum; lessThanOrEqual(value,*m_maximum); value += inc) {
result.push_back(value);
}
}
}
return result;
}
DoubleVector QuantitationRatio::getIntensityRatios () const
{
DoubleVector dv;
for ( int i = 0 ; i < numRatios ; i++ ) {
if ( quanPep )
dv.push_back ( getQuanRatio ( lightHeavyIntRatio [i][0], lightHeavyIntRatioType [i][0] ) );
else
dv.push_back ( 0.0 );
}
return dv;
}
TEST(String,NumFractionalDigits) {
DoubleVector values;
values.push_back(128196.198);
values.push_back(19671.281);
values.push_back(218528.28);
values.push_back(192.186);
std::pair<unsigned,unsigned> result = numFractionalDigits(values,3u);
EXPECT_EQ(0u,result.first); EXPECT_EQ(0u,result.second);
result = numFractionalDigits(values,4u);
EXPECT_EQ(0u,result.first); EXPECT_EQ(1u,result.second);
result = numFractionalDigits(values,7u);
EXPECT_EQ(1u,result.first); EXPECT_EQ(4u,result.second);
values.clear();
values.push_back(0.189678);
values.push_back(0.001869168);
values.push_back(0.7198);
result = numFractionalDigits(values,2u);
EXPECT_EQ(2u,result.first); EXPECT_EQ(4u,result.second);
result = numFractionalDigits(values,8u);
EXPECT_EQ(8u,result.first); EXPECT_EQ(10u,result.second);
values.clear();
values.push_back(0.07592);
values.push_back(198.82);
values.push_back(210.28);
values.push_back(0.628);
result = numFractionalDigits(values,2u);
EXPECT_EQ(0u,result.first); EXPECT_EQ(3u,result.second);
result = numFractionalDigits(values,3u);
EXPECT_EQ(0u,result.first); EXPECT_EQ(4u,result.second);
result = numFractionalDigits(values,5u);
EXPECT_EQ(2u,result.first); EXPECT_EQ(6u,result.second);
values.clear();
values.push_back(0.0);
result = numFractionalDigits(values,2u);
EXPECT_EQ(1u,result.first); EXPECT_EQ(1u,result.second);
result = numFractionalDigits(values,5u);
EXPECT_EQ(4u,result.first); EXPECT_EQ(4u,result.second);
}
DoubleVector MSMSFragmentation::getLossMasses ()
{
DoubleVector dv;
dv.push_back ( 0.0 );
for ( int i = 0 ; i < ionTypes.size () ; i++ ) {
string it = ionTypes [i];
if ( isPrefix ( it, "M+" ) || isPrefix ( it, "M-" ) ) {
string loss = it.substr ( 1 );
if ( loss.length () > 1 && isdigit ( loss [1] ) ) {
dv.push_back ( atof ( loss.c_str () ) );
}
}
}
return dv;
}
bool TimeWarp::extendRestrictedAlignmentAlong(const int& endIndexX, DoubleMatrix* alignmentMatrix, DoubleMatrix* simMatrix){
DoubleVector d;
//firstMatrix.size()
int widthSize = (*alignmentMatrix).size();
if (widthSize < endIndexX){//firstMatrix.size()
// printf("restruicted along %i\n", widthSize);
//then we can extend along
double value = getDistanceFromMatrix(widthSize, 0, simMatrix);
value += getMinimumFromMatrix(widthSize, 0, value, alignmentMatrix);
d.push_back(value);
(*alignmentMatrix).push_back(d);
for (int j = 1;j < (*alignmentMatrix)[widthSize - 1].size();j++){
// printf("restruicted along %i %i\n", widthSize, j);
value = getDistanceFromMatrix(widthSize, j, simMatrix);
value += getMinimumFromMatrix(widthSize, j, value, alignmentMatrix);
(*alignmentMatrix)[widthSize].push_back(value);
}
}
if ((*alignmentMatrix).size() == endIndexX)
return true;
else
return false;
}
void TimeWarp::calculatePartAlignmentMatrix(const int& endIndexX, const int& endIndexY, DoubleMatrix* alignmentMatrix, DoubleMatrix* simMatrix){
// printf("starting PART Alignment calculation : sim matrix size %i %i endX %i Y %i\n", (int)(*simMatrix).size(), (int)(*simMatrix)[0].size(), endIndexX, endIndexY);
//initialise alignment
alignmentMatrix->clear();
DoubleVector d;
d.push_back(getDistanceFromMatrix(0, 0, simMatrix));
// printf("first distance %f\n", d[0]);
(*alignmentMatrix).push_back(d);
bool chromaCalculated = false;
bool secondCalculated = false;
while (!chromaCalculated || !secondCalculated) {
if (!chromaCalculated)
chromaCalculated = extendRestrictedAlignmentAlong(endIndexX, alignmentMatrix, simMatrix);
if (!secondCalculated)
secondCalculated = extendRestrictedAlignmentUp(endIndexY, alignmentMatrix, simMatrix);
}
// printf("PART Alignment matrix calculated, size %i by %i\n", (int) (*alignmentMatrix).size() , (int) (*alignmentMatrix)[0].size());
// printf("PART Alignment ends at x %i y %i\n", (int) (*alignmentMatrix)[0][(*alignmentMatrix)[0].size()-1], (int)(*alignmentMatrix)[0][(*alignmentMatrix)[1].size()-1]);
}
void TimeWarp::calculatePartSimilarityMatrix(DoubleMatrix* firstChromaMatrix, DoubleMatrix* secondChromaMatrix, DoubleMatrix* simMatrix, int startX, int startY, int endX){
// printf("Calculate similarity : pointers : size %i x %i ", (int) firstChromaMatrix.size(), (int) secondChromaMatrix.size());
simMatrix->clear();
double distance, firstSum, secondSum;
endX = min (endX, (int)(*firstChromaMatrix).size()-1);//in case out of size
for (int x = startX;x <= endX;x++){
DoubleVector d;
for (int y = startY;y < (*secondChromaMatrix).size();y++){
if (useDotProduct)
distance = getChromaSimilarity(x, y, firstChromaMatrix, secondChromaMatrix);
else
distance = getEuclideanDistance(x, y, firstChromaMatrix, secondChromaMatrix);
d.push_back( distance);
} //end for y
(*simMatrix).push_back(d);
}//end for x
printf("..part sim size: %i, height: %i \n", (int) (*simMatrix).size(), (int) (*simMatrix)[0].size());
}//end self sim
void TimeWarp::calculateSimilarityMatrixWithPointers(DoubleMatrix* firstChromaMatrix, DoubleMatrix* secondChromaMatrix, DoubleMatrix* simMatrix){
printf("Calculate similarity : pointers : size %i x %i ", (int) (*firstChromaMatrix).size(), (int) (*secondChromaMatrix).size());
simMatrix->clear();
double distance, firstSum, secondSum;
for (int x = 0;x < (*firstChromaMatrix).size();x++){
DoubleVector d;
for (int y = 0;y < (*secondChromaMatrix).size();y++){
if (useDotProduct)
distance = getChromaSimilarity(x, y, firstChromaMatrix, secondChromaMatrix);
else
distance = getEuclideanDistance(x, y, firstChromaMatrix, secondChromaMatrix);
d.push_back( distance);
} //end for y
(*simMatrix).push_back(d);
}//end for x
printf("..sim size: %i, height: %i \n", (int) (*simMatrix).size(), (int) (*simMatrix)[0].size());
}//end self sim
int main(int argc, char **argv)
{
std::string cornerString=" 0.1 0.1 0.1 20 20 10";
typedef boost::tokenizer<boost::char_separator<char> > Tokenizer;
typedef std::vector<double> DoubleVector;
typedef boost::tokenizer<boost::char_separator<char> >::iterator TokIterator;
boost::char_separator<char> sep(", ");
Tokenizer tok(cornerString, sep);
DoubleVector corners;
corners.clear();
for (TokIterator it=tok.begin(); it!=tok.end(); ++it ) {
double q;
printf("");
sscanf(it->c_str(), "%lf", &q);
//DPrintf(DebugReaction," %lf ['%s']; ", q, it->c_str());
corners.push_back( q );
}
printf("the corners are:\n ");
printf("%e", corners[0]);
for(int i=1; i<corners.size(); ++i ) {
printf(", %e", corners[i]);
}
printf("\n");
}
void testApp::addToFFT(float sample) {
//window
fftSampleBuffer.push_back(sample);
if (fftSampleBuffer.size() == fftSize) {
setFFTinput();
//do FFT using Accelerate
audiofft->forward_FFT_d(fftInput, fftOutput);//Result);//&fftRealResult[0], &fftImagResult[0]);
DoubleVector v;
for (int i = 0; i < bufferSize; i++) {
v.push_back(sqrt(fftOutput[i][0]*fftOutput[i][0] + fftOutput[i][1]*fftOutput[i][1]));
}
magnitudeSpectrum.push_back(v);
/*
//see what it's doing for low frequencies
for (int j = 0; j < 4; j++){
printf("%i %.3f, ", j, v[j]);
}
printf("\n");
*/
//now remove many samples
for (int removeIndex = 0; removeIndex < fftHopsize; removeIndex++) {
fftSampleBuffer.erase(fftSampleBuffer.begin());//just need first to go each time
}
}
}
DoubleVector* ImageFeature::toJF(int channel) {
DoubleVector* dv = new DoubleVector(0);
for (uint i = 0; i < xsize_ * ysize_; i++) {
dv->push_back(data_[channel][i]);
}
return dv;
}
std::vector<double> OSArgument::domainAsDouble() const {
if (!hasDomain()) {
LOG_AND_THROW("No domain set for OSArgument '" << name() << "'.");
}
DoubleVector result;
BOOST_FOREACH(const QVariant& value,m_domain) {
result.push_back(value.toDouble());
}
FastbSequence *FastbReader::nextSequence()
{
String defline, ID;
// Read defline
if(!nextDefline.isEmpty()) {
defline=nextDefline;
nextDefline="";
}
else {
bool found=false;
while(!file.eof()) {
String line=file.getline();
if(!line.isEmpty()) {defline=line; found=true; break;}
}
if(!found) return NULL;
}
FastbSeqType seqType;
Regex *regex;
if(discreteRegex.match(defline)) {
ID=discreteRegex[1];
seqType=FASTB_DISCRETE;}
else if(continuousRegex.match(defline)) {
ID=continuousRegex[1];
seqType=FASTB_CONTINUOUS;}
else throw String("Bad defline in FASTB file: ")+defline;
// Read sequence data
String discreteSeq;
DoubleVector continuousSeq;
while(!file.eof()) {
String line=file.getline();
line.trimWhitespace();
if(file.eof() && line.isEmpty()) break;
if(discreteRegex.match(line) || continuousRegex.match(line))
{nextDefline=line; break;}
else switch(seqType)
{
case FASTB_DISCRETE:
discreteSeq+=line;
break;
case FASTB_CONTINUOUS:
{
const double d=line.asDouble();
//continuousSeq.push_back(isFinite(d) ? d : 0);
continuousSeq.push_back(d);//###
if(!isFinite(d)) //### represents "missing data"
cerr<<"warning: non-finite value encountered: "<<d<<endl;//###
}
break;
}
}
if(seqType==FASTB_DISCRETE)
return new FastbDiscreteSeq(discreteSeq,defline,ID);
else
return new FastbContinuousSeq(continuousSeq,defline,ID);
}
DoubleVector
Line2D::intersectsAtLengths(const Position2DVector &v) {
Position2DVector p = v.intersectsAtPoints(myP1, myP2);
DoubleVector ret;
for (size_t i=0; i<p.size(); i++) {
ret.push_back(myP1.distanceTo(p[int(i)]));
}
return ret;
}
DoubleVector QuantitationMulti::getIntensityRatios () const
{
DoubleVector dv;
for ( int i = 0 ; i < numQuanPks ; i++ ) {
if ( i != iTRAQRefPk && iTRAQPks [i] ) {
dv.push_back ( getQuanRatio ( lightHeavyIntRatio [0][i], lightHeavyIntRatioType [0][i] ) );
}
}
return dv;
}
void TimeWarp::calculateJointSimilarityMatrix(DoubleVector* energyVectorOne, DoubleVector* energyVectorTwo, DoubleMatrix* chromaSimilarityMatrix, DoubleMatrix* simMatrix){
//requires a chromagram similarity first this already done
//calculateSimilarityMatrixWithPointers(chromaMatrixOne, chromaMatrixTwo, &chromaSimilarityMatrix);
conversionFactor = (int) round((*energyVectorOne).size() / (*chromaSimilarityMatrix).size() );
printf("tw.ROUNDED CONVERSION FACTOR IS %i\n", conversionFactor);
printf("tw.CHROMA SIM SIZE %i\n", (int) (*chromaSimilarityMatrix).size());
simMatrix->clear();
double energyProportion = 0.3;
double chromaProportion = 1 - energyProportion;
double distance, firstSum, secondSum;
//lets try not actually doing calculation
for (int x = 0;x < (*energyVectorOne).size();x++){
DoubleVector d;
for (int y = 0;y < (*energyVectorTwo).size();y++){
//create chroma similarity first
// distance = (*energyVectorOne)[x] * (*energyVectorTwo)[y];//energy similarity
//now need the chroma part
int chromaIndexX = min(x / conversionFactor, (int)(*chromaSimilarityMatrix).size()-1);
int chromaIndexY = min(y / conversionFactor, (int)(*chromaSimilarityMatrix)[chromaIndexX].size()-1);
double chromaComponent = (*chromaSimilarityMatrix)[chromaIndexX][chromaIndexY];
// getChromaSimilarity(chromaIndexX, chromaIndexY, firstChromaMatrix, secondChromaMatrix);
distance *= energyProportion;
distance += chromaProportion * chromaComponent;
//distance = getJointChromaAndEnergyDistance(energyVectorOne, firstChromaMatrix, energyVectorTwo, secondChromaMatrix, x, y, conversionFactor, energyProportion, chromaProportion);
d.push_back( distance);
} //end for y
(*simMatrix).push_back(d);
}//end for x
printf("..sim size: %i, height: %i \n", (int) (*simMatrix).size(), (int) (*simMatrix)[0].size());
}
void LowessSmoothing::smoothData(const DoubleVector& input_x, const DoubleVector& input_y, DoubleVector& smoothed_output)
{
if (input_x.size() != input_y.size())
{
throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Sizes of x and y values not equal! Aborting... ", String(input_x.size()));
}
// unable to smooth over 2 or less data points (we need at least 3)
if (input_x.size() <= 2)
{
smoothed_output = input_y;
return;
}
Size input_size = input_y.size();
// const Size q = floor( input_size * alpha );
const Size q = (window_size_ < input_size) ? static_cast<Size>(window_size_) : input_size - 1;
DoubleVector distances(input_size, 0.0);
DoubleVector sortedDistances(input_size, 0.0);
for (Size outer_idx = 0; outer_idx < input_size; ++outer_idx)
{
// Compute distances.
// Size inner_idx = 0;
for (Size inner_idx = 0; inner_idx < input_size; ++inner_idx)
{
distances[inner_idx] = std::fabs(input_x[outer_idx] - input_x[inner_idx]);
sortedDistances[inner_idx] = distances[inner_idx];
}
// Sort distances in order from smallest to largest.
std::sort(sortedDistances.begin(), sortedDistances.end());
// Compute weigths.
std::vector<double> weigths(input_size, 0);
for (Size inner_idx = 0; inner_idx < input_size; ++inner_idx)
{
weigths.at(inner_idx) = tricube_(distances[inner_idx], sortedDistances[q]);
}
//calculate regression
Math::QuadraticRegression qr;
std::vector<double>::const_iterator w_begin = weigths.begin();
qr.computeRegressionWeighted(input_x.begin(), input_x.end(), input_y.begin(), w_begin);
//smooth y-values
double rt = input_x[outer_idx];
smoothed_output.push_back(qr.eval(rt));
}
return;
}
void Fresnel::spiral (DoubleVector &spiralX, DoubleVector &spiralY) const
{
spiralX.clear ();
spiralY.clear ();
spiralX.push_back (0.0);
spiralY.push_back (0.0);
Complex sp;
int fn = currentFresnelNumber;
double R = holeRadius;
double b = observerDistance;
double b2 = b * b;
double innerR = 0.0;
double outerR = 0.0;
double innerD = b;
double outerD = 0.0;
double dd = 0.0;
for (int n = 0; n < fn + 1; ++n) {
outerR = zoneOuterRadius (n);
outerD = sqrt (outerR*outerR + b2);
dd = (outerD - innerD) / accuracySpiral;
bool stop = false;
for (int i = 0; i < accuracySpiral && !stop; ++i) {
innerR = sqrt (innerD*innerD - b2);
innerD += dd;
outerR = sqrt (innerD*innerD - b2);
if (outerR >= R) {
outerR = R;
stop = true;
}
sp += amplitude (innerR, outerR);
spiralX.push_back (sp.im);
spiralY.push_back (sp.re);
}
}
}
ResultVector cluster(vector<LocalFeatures*> &locfeat, bool clusterWithPositions, string splitMode, uint maxSplit, uint stopWithNClusters, string disturbMode, string poolMode, uint dontSplitBelow, uint iterationsBetweenSplits, uint minObservationsPerCluster, double epsilon, string distanceMaker, string saveModelTo, bool saveBeforeSplits, string loadModelFrom)
{
BaseClusterer *clusterer = new EM();
if(loadModelFrom!="")
{
clusterer->loadModel(loadModelFrom);
}
setupClusterer(dynamic_cast<EM*>(clusterer), splitMode, maxSplit, stopWithNClusters, disturbMode, poolMode, dontSplitBelow,
iterationsBetweenSplits, minObservationsPerCluster, epsilon, distanceMaker, saveBeforeSplits);
ResultVector clusterinformation;
if (clusterWithPositions)
{
DBG(10) << "clustering with position information included" << endl;
}
DoubleVectorVector localFeaturesData;
for (uint j = 0; j < locfeat.size(); j++)
{
LocalFeatures* localFeatures = locfeat[j];
int xSize = localFeatures->imageSizeX();
int ySize = localFeatures->imageSizeY();
for (uint i = 0; i < localFeatures->numberOfFeatures(); i++)
{
DoubleVector* lfvector = &((*localFeatures)[i]);
if (clusterWithPositions)
{
pair<double, double> pos = localFeatures->relativePosition(i);
lfvector->push_back((double) localFeatures->position(i).x / (double) xSize);
lfvector->push_back((double) localFeatures->position(i).y / (double) ySize);
}
localFeaturesData.push_back( lfvector );
}
}
if(saveModelTo!="")
{
dynamic_cast<EM*>(clusterer)->run(localFeaturesData, clusterinformation, saveModelTo);
clusterer->saveModel(saveModelTo);
}
else
{
clusterer->run(localFeaturesData, clusterinformation);
}
delete clusterer;
return clusterinformation;
}
DoubleVectorVector QuanMSMSXMLData::getFormulaPurityCoefficients ( const string& name ) const
{
DoubleVectorVector dvv;
StringVector f = getQuanMSMSInfo ( name ).formulae;
DoubleVector m = getQuanMSMSInfo ( name ).masses;
for ( int i = 0 ; i < f.size () ; i++ ) {
DoubleVector dv;
if ( f [i] != "" ) {
IsotopePeakStats ips ( f [i], 1 );
int index = ips.getProbabilityIndexForMass ( m [i] );
if ( index >= 2 ) dv.push_back ( ips.getProbability ( index - 2 ) );
else dv.push_back ( 0.0 );
if ( index >= 1 ) dv.push_back ( ips.getProbability ( index - 1 ) );
else dv.push_back ( 0.0 );
dv.push_back ( ips.getProbability ( index + 1 ) );
dv.push_back ( ips.getProbability ( index + 2 ) );
}
else { // No formulae so assume no correction
for ( int j = 0 ; j < 4 ; j++ ) {
dv.push_back ( 0.0 );
}
}
dvv.push_back ( dv );
}
return dvv;
}
void testSingleRateModel(Params ¶ms, NGSAlignment &aln, NGSTree &tree, string model,
double *freq, DoubleVector &rate_info, StrVector &rate_name,
bool write_info, const char *report_file)
{
char model_name[20];
NGSAlignment sum_aln(aln.num_states, 1, freq);
ModelsBlock *models_block = new ModelsBlock;
NGSTree sum_tree(params, &sum_aln);
sum_aln.tree = &sum_tree;
if (model == "")
sprintf(model_name, "GTR+F1");
else
sprintf(model_name, "%s+F1", model.c_str());
try {
params.model_name = model_name;
sum_tree.setModelFactory(new ModelFactory(params, &sum_tree, models_block));
sum_tree.setModel(sum_tree.getModelFactory()->model);
sum_tree.setRate(sum_tree.getModelFactory()->site_rate);
double bestTreeScore = sum_tree.getModelFactory()->optimizeParameters(false, write_info);
cout << "LogL: " << bestTreeScore;
cout << " / Rate: " << sum_tree.getRate()->getRate(0) << endl;
} catch (...) {
cout << "Skipped due to sparse matrix" << endl;
//rate_info.push_back(MIN_SITE_RATE);
rate_info.insert(rate_info.end(), rate_name.size(), MIN_SITE_RATE);
return;
}
//return sum_tree.getRate()->getRate(0);
rate_info.push_back(sum_tree.getRate()->getRate(0));
double *rate_mat = new double[aln.num_states*aln.num_states];
memset(rate_mat, 0, aln.num_states*aln.num_states*sizeof(double));
sum_tree.getModel()->getRateMatrix(rate_mat);
rate_info.insert(rate_info.end(), rate_mat, rate_mat+sum_tree.getModel()->getNumRateEntries());
if (tree.getModel()->isReversible()) {
sum_tree.getModel()->getStateFrequency(rate_mat);
rate_info.insert(rate_info.end(), rate_mat, rate_mat+aln.num_states);
}
delete [] rate_mat;
delete models_block;
if (report_file) {
DoubleMatrix tmp(1);
tmp[0] = rate_info;
reportNGSAnalysis(report_file, params, sum_aln, sum_tree, tmp, rate_name);
}
}
void MainWindow::gradient()
{
DoubleVector x;
x.push_back(-1.0);
x.push_back(+1.2);
SampleGradient gm;
connect(&gm, SIGNAL(showCoordinares(const DoubleVector &)), this, SLOT(showCoordinares(const DoubleVector &)));
gm.setEpsilon1(0.00001);
gm.setEpsilon2(0.00001);
gm.setEpsilon3(0.00001);
gm.setR1MinimizeEpsilon(0.01, 0.00001);
gm.calculate(x);
}
void TimeWarp::calculateCausalChromaSimilarityMatrix(DoubleMatrix& firstChromaMatrix, DoubleMatrix& secondChromaMatrix, DoubleMatrix& simMatrix){
//calculates the chroma only similarity matrix
//but we have already done some, so is extending it...
int size = 0;
if (simMatrix.size() > 0){
size = simMatrix[0].size();
}
if (secondChromaMatrix.size() > size ){
for (int x = 0;x < firstChromaMatrix.size();x++){
if (x < simMatrix.size()){
//i.e. entries already exist
for (int y = (int)simMatrix[x].size();y < secondChromaMatrix.size();y++){
double distance;
if (useDotProduct)
distance = getChromaSimilarity(x, y, &firstChromaMatrix, &secondChromaMatrix);
else
distance = getEuclideanDistance(x, y, &firstChromaMatrix, &secondChromaMatrix);
printf("putting one back X %i Y %i dist %f \n", x, y, distance);
simMatrix[x].push_back(distance);
}
}
else {
DoubleVector d;
for (int y = 0;y < secondChromaMatrix.size();y++){
double distance;
if (useDotProduct)
distance = getChromaSimilarity(x, y, &firstChromaMatrix, &secondChromaMatrix);
else
distance = getEuclideanDistance(x, y, &firstChromaMatrix, &secondChromaMatrix);
printf("new row X %i Y %i dist %f\n", x, y, distance);
d.push_back( distance);
}
simMatrix.push_back(d);
}
}
}
if (size > 0)
printf("Causial CHROMA ONLY SIM SIZE %i x %i; ", (int)simMatrix.size(), (int) simMatrix[0].size());
printf("First matrix SIZE %i , SECOND size %i\n", (int)firstChromaMatrix.size(), (int) secondChromaMatrix.size());
}
bool ThermochromicGlazing_Impl::setThickness(double value) {
GlazingVector glazings = mf_glazings();
DoubleVector rollbackValues;
for (unsigned i = 0,n = glazings.size(); i < n; ++ i) {
rollbackValues.push_back(glazings[i].thickness());
bool ok = glazings[i].setThickness(value);
if (!ok) {
// rollback previous values
for (int j = i-1; j >= 0; --j) {
glazings[j].setThickness(rollbackValues[j]);
}
return false;
}
}
return true;
}
DoubleVector RRSchedule::reconfigureWeek(DoubleVector _week, Vector _permute)
// Creates a new week based on the current week and a permutation
{
DoubleVector newWeek;
for (Vector::const_iterator tSlotNum = _permute.begin(); tSlotNum != _permute.end(); ++tSlotNum)
{
// For week0, there are not enough timeslots
if ((week0 and *tSlotNum < max_times - skip_first) or (not week0))
{
newWeek.push_back(_week[*tSlotNum]);
}
}
return newWeek;
}
CosSimilarity::CosSimilarity ( const string& formulaString, int charge, const DoubleVector& intensity, const DoubleVector& area ) :
cosSimilarityIntensity ( -100.0 ),
cosSimilarityArea ( -100.0 )
{
IsotopePeakStats id ( formulaString, charge );
int np = id.getNumPeaks ();
int ind1 = id.getProbabilityIndexForIdealMonoisotopicMZ ();
int distSize = genMax ( intensity.size (), area.size () );
DoubleVector dv;
for ( int i = ind1 ; i < np ; i++ ) {
dv.push_back ( id.getProbability ( i ) );
if ( dv.size () == distSize ) break;
}
if ( dv.size () > 1 ) {
if ( intensity.size () > 1 ) cosSimilarityIntensity = cosSimilarity ( intensity, dv );
if ( area.size () > 1 ) cosSimilarityArea = cosSimilarity ( area, dv );
}
}
void RddtClust::getDimData(DoubleVector& dimData, int idx){
using namespace Rcpp;
XmdvToolMainWnd* m_mwd = this->m_rddtOp->m_pm->getMainWnd();
RInside r = m_mwd->getRinstance();
//qDebug()<<"idx qt "<<idx;
r["currentDim"] = idx;
std::string cmd = "currentDim <- as.integer(currentDim)+1;\n"
//"print(currentDim);\n"
"dimData <- M[,currentDim];\n"
"dimData";
SEXP evals = r.parseEval(cmd);
NumericVector rDimData(evals);
dimData.clear();
for(int i = 0; i< rDimData.length(); i++){
dimData.push_back(rDimData[i]);
}
}
void TimeWarp::calculateAlignmentMatrix(DoubleMatrix firstMatrix, DoubleMatrix secondMatrix, DoubleMatrix* alignmentMatrix){//, DoubleMatrix simMatrix
printf("starting Alignment calculation\n");
//initialise alignment
alignmentMatrix->clear();
DoubleVector d;
d.push_back(getDistance(0,0));
(*alignmentMatrix).push_back(d);
bool chromaCalculated = false;
bool secondCalculated = false;
while (!chromaCalculated || !secondCalculated) {
if (!chromaCalculated)
chromaCalculated = extendAlignmentAlong((int) firstMatrix.size(), alignmentMatrix);
if (!secondCalculated)
secondCalculated = extendAlignmentUp((int) secondMatrix.size(), alignmentMatrix);
}
printf("Alignment matrix calculated, size %i\n", (int) (*alignmentMatrix).size());
}
void Application::reestimate(EmissionSequence &seq,MultiGauss &dist)
{
int dim=seq.getSchema().getNumContinuous();
GSL::Vector means(dim);
GSL::Matrix covM(dim,dim);
int L=seq.length();
for(int d=0 ; d<dim ; ++d) {
DoubleVector V;
for(int pos=0 ; pos<L ; ++pos) {
const Emission &s=seq[pos];
const GSL::Vector &v=s.getContinuous();
V.push_back(v[d]);
}
SummaryStats stats(V);
means[d]=stats.getMean();
covM(d,d)=stats.getVar();
}
for(int d1=0 ; d1<dim ; ++d1) {
double sd1=sqrt(covM(d1,d1));
for(int d2=0 ; d2<dim ; ++d2) {
if(d2==d1) continue;
double sd2=sqrt(covM(d2,d2));
DoubleVector V1, V2;
for(int pos=0 ; pos<L ; ++pos) {
const Emission &s=seq[pos];
const GSL::Vector &v=s.getContinuous();
V1.push_back(v[d1]);
V2.push_back(v[d2]);
}
Correlation cor(V1,V2);
covM(d1,d2)=cor.getR()*sd1*sd2;
}
}
cout<<"REESTIMATING FROM: "<<means<<"\n"<<covM<<endl;
dist=MultiGauss(means,covM);
}