void AbstractMixedSubstitutionModel::setVRates(const Vdouble& vd)
{
if (vd.size()!=modelsContainer_.size())
throw Exception("AbstractMixedSubstitutionModel::setVRates bad size of Vdouble argument.");
for (unsigned int i=0;i<vd.size();i++)
vRates_[i]=vd[i];
normalizeVRates();
}
generalGammaDistributionFixedCategories::generalGammaDistributionFixedCategories(const Vdouble& fixedRates, const Vdouble& boundaries, MDOUBLE alpha, MDOUBLE beta) :
generalGammaDistribution()
{
if ((fixedRates.size() + 1) != boundaries.size())
errorMsg::reportError("error in generalGammaDistributionFixedCategories constructor");
_alpha = alpha;
_beta = beta;
_rates = fixedRates;
_bonderi = boundaries;
computeRatesProbs();
}
void generalGammaDistributionFixedCategories::setFixedCategories(const Vdouble& fixedBoundaries){
if (fixedBoundaries.size()<2)
errorMsg::reportError("Error in generalGammaDistributionFixedCategories::setFixedCategories : at least two boundaries are required");
if (fixedBoundaries[0] > 0.0)
errorMsg::reportError("Error in generalGammaDistributionFixedCategories::setFixedCategories : first boundary should be zero");
_bonderi = fixedBoundaries;
if (_bonderi[_bonderi.size()] > VERYBIG/10000.0)
_bonderi[_bonderi.size()] = VERYBIG/10000.0; // to avoid overflow
setFixedCategories();
}
Vdouble TreeTemplateTools::getBranchLengths(const Node& node) throw (NodePException)
{
Vdouble brLen(1);
brLen[0] = node.getDistanceToFather();
for (size_t i = 0; i < node.getNumberOfSons(); i++)
{
Vdouble sonBrLen = getBranchLengths(*node.getSon(i));
for (size_t j = 0; j < sonBrLen.size(); j++)
{
brLen.push_back(sonBrLen[j]);
}
}
return brLen;
}
///////////////////////////////////////////////////////////////////////////////////////////////////////////
//findBestParamManyStarts: Finds the best gammaMixture from many starting points.
//The function starts form few starting points.
//For each point it tries to optimize the likellihood doing only a small number of iterations.
//It then picks the best points (highest likelihood) and continue the maximization for these points only.
//The best gammaMixture is stored in _sp and the best likelihood is returned.
//input Parameters:
//startPointsNum = the number of starting points.
//bestStartsNum = the number of best points to continue with the full optimization.
//startIter = the number of iterations to perform with all starting points.
//maxIterations = the maximum number of iterations to continue with the best points
//epsilon = for determining convergence in the maximization process.
MDOUBLE optGammaMixtureEM::findBestParamManyStarts(const int startPointsNum, const int bestStartsNum, const int startIter, const int maxIterations, const MDOUBLE epsilon, const MDOUBLE epsilomQopt, ofstream* pOutF)
{
vector<mixtureDistribution> distVec;
Vdouble likelihoodVec(startPointsNum);
mixtureDistribution * pMixture = static_cast<mixtureDistribution*>(_pSp->distr());
//create starting distributions
int i;
for (i = 0; i < startPointsNum; ++i)
{
//the first distribution will be the current one
if (i == 0)
distVec.push_back(*pMixture);
else
distVec.push_back(mixtureDistribution(pMixture->getComponentsNum(), pMixture->categoriesForOneComponent(), LAGUERRE, 15, 15));
}
//make a small number of iterations for all random starts
for (i = 0; i < distVec.size(); ++i)
{
likelihoodVec[i] = optimizeParam(&distVec[i], startIter, epsilon, epsilomQopt, pOutF);
}
//sort results and make full optimization only on the best starts
Vdouble sortedL = likelihoodVec;
sort(sortedL.begin(),sortedL.end());
MDOUBLE threshold = sortedL[sortedL.size()- bestStartsNum];
MDOUBLE bestL = sortedL[0];
int bestDistNum = 0;
for (i = 0; i < distVec.size(); ++i)
{
if (likelihoodVec[i] >= threshold)
{
MDOUBLE newL = optimizeParam(&distVec[i], maxIterations, epsilon, epsilomQopt, pOutF);
if (newL > bestL)
{
bestL = newL;
bestDistNum = i;
}
}
}
_pSp->setDistribution(&distVec[bestDistNum]);
distVec.clear();
return bestL;
}
//Input: alf = the alpha parameter of the Laguerre polynomials
// pointsNum = the polynom order
//Output: the abscissas and weights are stored in the vecotrs x and w, respectively.
//Discreption: given alf, the alpha parameter of the Laguerre polynomials, the function returns the abscissas and weights
// of the n-point Guass-Laguerre quadrature formula.
// The smallest abscissa is stored in x[0], the largest in x[pointsNum - 1].
void GLaguer::gaulag(Vdouble &x, Vdouble &w, const MDOUBLE alf, const int pointsNum)
{
x.resize(pointsNum, 0.0);
w.resize(pointsNum, 0.0);
const int MAXIT=10000;
const MDOUBLE EPS=1.0e-6;
int i,its,j;
MDOUBLE ai,p1,p2,p3,pp,z=0.0,z1;
int n= x.size();
for (i=0;i<n;i++) {
//loops over the desired roots
if (i == 0) { //initial guess for the smallest root
z=(1.0+alf)*(3.0+0.92*alf)/(1.0+2.4*n+1.8*alf);
} else if (i == 1) {//initial guess for the second smallest root
z += (15.0+6.25*alf)/(1.0+0.9*alf+2.5*n);
} else { //initial guess for the other roots
ai=i-1;
z += ((1.0+2.55*ai)/(1.9*ai)+1.26*ai*alf/
(1.0+3.5*ai))*(z-x[i-2])/(1.0+0.3*alf);
}
for (its=0;its<MAXIT;its++) { //refinement by Newton's method
p1=1.0;
p2=0.0;
for (j=0;j<n;j++) { //Loop up the recurrence relation to get the Laguerre polynomial evaluated at z.
p3=p2;
p2=p1;
p1=((2*j+1+alf-z)*p2-(j+alf)*p3)/(j+1);
}
//p1 is now the desired Laguerre polynomial. We next compute pp, its derivative,
//by a standard relation involving also p2, the polynomial of one lower order.
pp=(n*p1-(n+alf)*p2)/z;
z1=z;
z=z1-p1/pp; //Newton's formula
if (fabs(z-z1) <= EPS)
break;
}
if (its >= MAXIT)
errorMsg::reportError("too many iterations in gaulag");
x[i]=z;
w[i] = -exp(gammln(alf+n)-gammln(MDOUBLE(n)))/(pp*n*p2);
}
}
Vdouble TreeTools::getBranchLengths(const Tree& tree, int nodeId) throw (NodeNotFoundException, NodeException)
{
if (!tree.hasNode(nodeId))
throw NodeNotFoundException("TreeTools::getBranchLengths", nodeId);
Vdouble brLen(1);
if (tree.hasDistanceToFather(nodeId))
brLen[0] = tree.getDistanceToFather(nodeId);
else
throw NodeException("TreeTools::getbranchLengths(). No branch length.", nodeId);
vector<int> sons = tree.getSonsId(nodeId);
for (size_t i = 0; i < sons.size(); i++)
{
Vdouble sonBrLen = getBranchLengths(tree, sons[i]);
for (size_t j = 0; j < sonBrLen.size(); j++)
{
brLen.push_back(sonBrLen[j]);
}
}
return brLen;
}
// a file with color-coding from Ka/Ks values to color-bins
void kaks2Color(const Vdouble & kaksVec, const Vdouble &lowerBoundV,
const sequence & refSeq, string fileName,codon *co) {
vector<int> colors;
int numOfSitesinAln = kaksVec.size();
Vdouble negativesKaksVec,negativesSite;
negativesKaksVec.clear();
negativesSite.clear();
int i,gapsInRefSeq=0;
for (i=0;i<numOfSitesinAln;i++){
if (codonUtility::aaOf(refSeq[i],*co) == -1) gapsInRefSeq++;
}
// first dealing with positive selection
colors.resize(numOfSitesinAln-gapsInRefSeq);
int gap=0;
for (i=0;i<numOfSitesinAln;i++){
if (codonUtility::aaOf(refSeq[i],*co) == -1){
gap++;
continue;
}
if (lowerBoundV[i]>1) // color 1 (positive selection) : if confidence interval lower bound > 1
colors[i-gap]=1;
else if (kaksVec[i]>1) // color 2(positive selection) : "non-significant"
colors[i-gap]=2;
else {
negativesKaksVec.push_back(kaksVec[i]); //add the value of kaks < 1
negativesSite.push_back(i-gap); //add the number of site of the kaks
}
}
// now dealing with purifying selection
Vdouble orderVec = negativesKaksVec;
if (orderVec.size()>0) // this is since once the whole protein was positive selection... (anomaly)
sort(orderVec.begin(), orderVec.end()); //sort the kaks values to be divided to 5 groups
MDOUBLE percentileNum = 5.0;
int percentileNumInt = 5;
Vdouble maxScoreForPercentile(percentileNumInt);
if (orderVec.size()>0) {
maxScoreForPercentile[0] = orderVec[0];
for (int c = 1; c < percentileNumInt; ++c){
int place = (int)((c / percentileNum) * negativesKaksVec.size());
MDOUBLE maxScore = orderVec[place];
maxScoreForPercentile[c] = maxScore;
}
}
//loop over all the Ka/Ks < 1
for (int j=0; j < negativesKaksVec.size(); ++j){
MDOUBLE r = negativesKaksVec[j]; //the kaks of the site.
int s = (int)negativesSite[j]; //the site.
if (r > maxScoreForPercentile[4])
colors[s] = 3;
else if (r > maxScoreForPercentile[3])
colors[s] = 4;
else if (r> maxScoreForPercentile[2])
colors[s] = 5;
else if (r > maxScoreForPercentile[1])
colors[s] = 6;
else if (r >= maxScoreForPercentile[0])
colors[s] = 7;
}
//print to file
ofstream out(fileName.c_str());
gap=0;
amino aminoAcid;
LOG(5,<<"Printing selection color bins to file"<<endl);
for (i=0;i<refSeq.seqLen();i++){
int aa = codonUtility::aaOf(refSeq[i], *co);
if (aa==-1){
gap++;
continue;
}
string aaStr = aminoAcid.fromInt(aa);
out<<i+1-gap <<"\t"<<aaStr<<"\t"<<colors[i-gap];
out<<endl;
}
out.close();
}