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// $Id: simulateTree.cpp 8508 2010-08-12 15:21:04Z rubi $
#include "definitions.h"
#include "treeUtil.h"
#include "simulateTree.h"
#include "talRandom.h"
#include "gammaDistribution.h"
#include "codon.h"
simulateTree::simulateTree(const tree& _inEt,
const stochasticProcess& sp,
const alphabet* alph) :
_et(_inEt), _sp(sp),_alph(alph),_avgSubtitutionsPerSite(0.0) {};
simulateTree::~simulateTree() {}
void simulateTree::generate_seq(int seqLength) {
sequence justAseq(_alph);
_simulatedSequences.resize(_et.getNodesNum(),justAseq);
for (int i=0; i < _simulatedSequences.size(); ++i) {
_simulatedSequences[i].resize(seqLength);
}
generateRootSeq(seqLength);
vector<MDOUBLE> rateVec(seqLength);
for (int h = 0; h < seqLength; h++) {
int theRanCat = getRandCategory(h);
rateVec[h] = _sp.rates(theRanCat);
}
_avgSubtitutionsPerSite = 0.0;
for (int p=0 ; p < _et.getRoot()->getNumberOfSons() ; ++p) {
recursiveGenerateSpecificSeq(rateVec, seqLength, _et.getRoot()->getSon(p));
}
_avgSubtitutionsPerSite /= 1.0*seqLength;
}
void simulateTree::generate_rates_continuous_gamma(const int seqLength,const MDOUBLE alpha, Vdouble rates)
{
rates.clear();
rates.resize(seqLength);
for (int h = 0; h < seqLength; h++) {
rates[h] = talRandom::SampleGamma(alpha);
}
}
void simulateTree::generate_seq_continuous_gamma(int seqLength) {
sequence justAseq(_alph);
_simulatedSequences.resize(_et.getNodesNum(),justAseq);
for (int i=0; i < _simulatedSequences.size(); ++i) {
_simulatedSequences[i].resize(seqLength);
}
generateRootSeq(seqLength);
vector<MDOUBLE> rateVec(seqLength);
MDOUBLE alpha= (static_cast<gammaDistribution*>(_sp.distr()))->getAlpha();
for (int h = 0; h < seqLength; h++) {
rateVec[h] = talRandom::SampleGamma(alpha);
}
_avgSubtitutionsPerSite = 0.0;
for (int p=0 ; p < _et.getRoot()->getNumberOfSons() ; ++p) {
recursiveGenerateSpecificSeq(rateVec, seqLength, _et.getRoot()->getSon(p));
}
_avgSubtitutionsPerSite /= 1.0*seqLength;
}
void simulateTree::generate_seqWithRateVectorNoStopCodon(const Vdouble& simRates, int seqLength)
{
if (_alph->size() != 4)
errorMsg::reportError("generate_seqWithRateVectorNoStopCodon is applicable only for nucleotide process");
if (seqLength %3 != 0)
errorMsg::reportError("generate_seqWithRateVectorNoStopCodon: seqLenth should be a multiplicative of 3");
if (simRates.size() != seqLength)
errorMsg::reportError("generate_seqWithRateVectorNoStopCodon: the size of simRates should be identical to seqLenth");
// sequence justAseq(_alph);
// vector<sequence> simulatedSequences(_et.getNodesNum(),justAseq);
vector<sequence> simulatedSequences;
//generate three nucleotide positions at a time. Repeat each position if the generated sequences contain stop codon
Vdouble rateVec(3);
bool bStopCodonFound = false;
codon codonAlph;
for (int p = 0; p < seqLength; p+=3)
{
rateVec[0] = simRates[p];
rateVec[1] = simRates[p+1];
rateVec[2] = simRates[p+2];
//generate 3 nucleotide positions with no stop codon
for (int loop = 0; loop < 1000; ++loop)
{
bStopCodonFound = false;
generate_seqWithRateVector(rateVec, 3);
for (int s = 0; s < _simulatedSequences.size(); ++s)
{
string codonStr = _simulatedSequences[s].toString();
if (codonAlph.isStopCodon(codonStr))
{
bStopCodonFound = true;
break;
}
}
if (!bStopCodonFound)
break;
}
if (bStopCodonFound)
errorMsg::reportError("Could not generate a position without stop codon");
//append positions to the positions generated so far
if (p == 0)
simulatedSequences = _simulatedSequences; //this will copy also the names of the sequences
else
{
for (int i = 0; i < simulatedSequences.size(); ++i)
simulatedSequences[i] += _simulatedSequences[i];
}
}
_simulatedSequences = simulatedSequences;
}
void simulateTree::generate_seqWithRateVector(const Vdouble& rateVec, const int seqLength) {
sequence justAseq(_alph);
_simulatedSequences.resize(_et.getNodesNum(),justAseq);
for (int i=0; i < _simulatedSequences.size(); ++i) {
_simulatedSequences[i].resize(seqLength);
}
generateRootSeq(seqLength);
_avgSubtitutionsPerSite = 0.0;
for (int p=0 ; p < _et.getRoot()->getNumberOfSons() ; ++p) {
recursiveGenerateSpecificSeq(rateVec,seqLength,_et.getRoot()->getSon(p));
}
_avgSubtitutionsPerSite /= 1.0*seqLength;
}
void simulateTree::generateRootSeq(int seqLength) {
for (int i = 0; i < seqLength; i++) {
_simulatedSequences[_et.getRoot()->id()][i] = giveRandomChar();
}
_simulatedSequences[_et.getRoot()->id()].setAlphabet(_alph);
_simulatedSequences[_et.getRoot()->id()].setName(_et.getRoot()->name());
_simulatedSequences[_et.getRoot()->id()].setID(_et.getRoot()->id());
}
void simulateTree::recursiveGenerateSpecificSeq(
const vector<MDOUBLE> &rateVec,
const int seqLength,
tree::nodeP myNode) {
for (int y = 0; y < seqLength; y++) {
MDOUBLE lenFromFather=myNode->dis2father()*rateVec[y];
int aaInFather = _simulatedSequences[myNode->father()->id()][y];
int newChar = giveRandomChar(aaInFather,lenFromFather,y);
if(newChar != aaInFather) _avgSubtitutionsPerSite += 1;
_simulatedSequences[myNode->id()][y] = newChar;
}
_simulatedSequences[myNode->id()].setAlphabet(_alph);
_simulatedSequences[myNode->id()].setName(myNode->name());
_simulatedSequences[myNode->id()].setID(myNode->id());
for (int x =0 ; x < myNode->getNumberOfSons(); ++x) {
recursiveGenerateSpecificSeq(rateVec, seqLength, myNode->getSon(x));
}
}
int simulateTree::giveRandomChar() const {
for (int loop =0 ;loop<100000 ;loop++) {
MDOUBLE theRandNum = talRandom::giveRandomNumberBetweenZeroAndEntry(1.0);
MDOUBLE sum = 0.0;
for (int j=0;j<_sp.alphabetSize();++j) {
sum+=_sp.freq(j);
if (theRandNum<sum) return j;
}
}
errorMsg::reportError("Could not give random character. The reason is probably that the P_i do not sum to one.");
return 1;
}
int simulateTree::giveRandomChar(const int letterInFatherNode,
const MDOUBLE length,
const int pos) const {
assert(letterInFatherNode>=0);
assert(letterInFatherNode<_sp.alphabetSize());
for (int loop =0 ;loop<100000 ;loop++) {
MDOUBLE theRandNum = talRandom::giveRandomNumberBetweenZeroAndEntry(1.0);
MDOUBLE sum = 0.0;
for (int j=0;j<_sp.alphabetSize();++j) {
sum+=_sp.Pij_t(letterInFatherNode,j, length);
if (theRandNum<sum) return j;
}
}
errorMsg::reportError("Could not give random character. The reason is probably that the Pij_t do not sum to one.");
return 1;
}
int simulateTree::getRandCategory(const int pos) const {
MDOUBLE theRandNum = talRandom::giveRandomNumberBetweenZeroAndEntry(1);
MDOUBLE sum = 0.0;
for (int j=0;j<_sp.categories() ;++j) {
sum+=_sp.ratesProb(j);
if (theRandNum<sum) return j;
}
errorMsg::reportError(" error in function simulateTree::getRandCategory() ");// also quit the program
return -1;
}
sequenceContainer simulateTree::toSeqData() {
sequenceContainer myseqData;
for (int i=0; i < _simulatedSequences.size(); ++i) {
myseqData.add(_simulatedSequences[i]);
}
return myseqData;
}
sequenceContainer simulateTree::toSeqDataWithoutInternalNodes() {
sequenceContainer myseqData;
for (int i=0; i < _simulatedSequences.size(); ++i) {
tree::nodeP theCurNode = _et.findNodeByName(_simulatedSequences[i].name());
if (theCurNode == NULL)
errorMsg::reportError("could not find the specified name: " + _simulatedSequences[i].name());
if (theCurNode->isInternal()) continue;
myseqData.add(_simulatedSequences[i]);
}
return myseqData;
}
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