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F3Result.cpp
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F3Result.cpp
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/*
* F3Result
* Date: Mar-15-2013
* Author : Gabriel Renaud gabriel.reno [at sign here ] gmail.com
*
*/
#include "F3Result.h"
F3Result::F3Result(){
all.reinitializedCounters();
noCpg.reinitializedCounters();
onlyCpg.reinitializedCounters();
transitions.reinitializedCounters();
transversions.reinitializedCounters();
noDamage.reinitializedCounters();
// noDamage.reinitializedCounters();
}
F3Result::F3Result(const F3Result & other){
all = other.all;
noCpg = other.noCpg;
onlyCpg = other.onlyCpg;
transitions = other.transitions;
transversions = other.transversions;
noDamage = other.noDamage;
}
F3Result::~F3Result(){
}
string F3Result::printWithBootstrap(list<vector< vector< vector<F3Result> > > > & boostraps,unsigned int i,unsigned int j,unsigned int k,unsigned int numberOfBootstraps){
stringstream toreturn;
vector<double> allBoot;
vector<double> nocpgBoot;
vector<double> onlycpgBoot;
vector<double> transitionsBoot;
vector<double> transversionsBoot;
vector<double> noDamageBoot;
//all
for (list< vector< vector< vector<F3Result> > > >::iterator it=boostraps.begin();
it != boostraps.end(); it++){
allBoot.push_back( (*it)[i][j][k].all.computeF3() );
nocpgBoot.push_back( (*it)[i][j][k].noCpg.computeF3() );
onlycpgBoot.push_back( (*it)[i][j][k].onlyCpg.computeF3() );
transitionsBoot.push_back( (*it)[i][j][k].transitions.computeF3() );
transversionsBoot.push_back( (*it)[i][j][k].transversions.computeF3() );
noDamageBoot.push_back( (*it)[i][j][k].noDamage.computeF3() );
}
//cout<<vectorToString(allBoot)<<endl;
pair<double,double> allDEV = computeMeanSTDDEV(allBoot);
pair<double,double> noCpgDEV = computeMeanSTDDEV(nocpgBoot);
pair<double,double> onlyCpgDEV = computeMeanSTDDEV(onlycpgBoot);
pair<double,double> transitionsDEV = computeMeanSTDDEV(transitionsBoot);
pair<double,double> transversionsDEV = computeMeanSTDDEV(transversionsBoot);
pair<double,double> noDamageDEV = computeMeanSTDDEV(transversionsBoot);
//cout<<allBootDEV.first<<"\t"<<allBootDEV.second<<endl;
toreturn<<":\t" <<all.headerForCount() <<"\n";
toreturn<<"all_sites:\t" <<all <<"\t"<<allDEV.first <<"\t"<<allDEV.second <<"\t"<<all.computeF3() / allDEV.second <<"\n";
toreturn<<"nocpg_sites:\t" <<noCpg <<"\t"<<noCpgDEV.first <<"\t"<<noCpgDEV.second <<"\t"<<noCpg.computeF3() / noCpgDEV.second <<"\n";
toreturn<<"onlycpg_sites:\t" <<onlyCpg <<"\t"<<onlyCpgDEV.first <<"\t"<<onlyCpgDEV.second <<"\t"<<onlyCpg.computeF3() / onlyCpgDEV.second <<"\n";
toreturn<<"transitions:\t" <<transitions <<"\t"<<transitionsDEV.first <<"\t"<<transitionsDEV.second <<"\t"<<transitions.computeF3() / transitionsDEV.second <<"\n";
toreturn<<"transversions:\t" <<transversions <<"\t"<<transversionsDEV.first <<"\t"<<transversionsDEV.second <<"\t"<<transversions.computeF3() / transversionsDEV.second <<"\n";
toreturn<<"noDamage:\t" <<noDamage <<"\t"<<noDamageDEV.first <<"\t"<<noDamageDEV.second <<"\t"<<noDamage.computeF3() / noDamageDEV.second <<"\n";
return toreturn.str();
}
void F3Result::addIfNotInfinity( vector<double> * target , double val ){
if(val != std::numeric_limits<double>::infinity()){
target->push_back(val);
}
}
string F3Result::printWithJacknife(const vector<const F3Result * > * jacknife){
stringstream toreturn;
vector<double> allBoot;
vector<double> nocpgBoot;
vector<double> onlycpgBoot;
vector<double> transitionsBoot;
vector<double> transversionsBoot;
vector<double> noDamageBoot;
// vector<double> counterReferenceB;
// vector<double> counterBothB;
//all
//for (vector< AvgCoaResult * > ::iterator it=jacknife->begin(); it != jacknife->end(); it++){
for (unsigned int k=0;k<jacknife->size(); k++){
//cout<<"jack "<<jacknife->at(k)->all.avgCoaRefSam()<<endl;
addIfNotInfinity( &allBoot, jacknife->at(k)->all.computeF3() );
addIfNotInfinity( &nocpgBoot, jacknife->at(k)->noCpg.computeF3() );
addIfNotInfinity( &onlycpgBoot, jacknife->at(k)->onlyCpg.computeF3() );
addIfNotInfinity( &transitionsBoot, jacknife->at(k)->transitions.computeF3() );
addIfNotInfinity( &transversionsBoot, jacknife->at(k)->transversions.computeF3() );
addIfNotInfinity( &noDamageBoot, jacknife->at(k)->noDamage.computeF3() );
}
pair<double,double> allJK = computeJackknifeConfIntervals(all.computeF3(), allBoot );
pair<double,double> noCpgJK = computeJackknifeConfIntervals(noCpg.computeF3(), nocpgBoot );
pair<double,double> onlyCpgJK = computeJackknifeConfIntervals(onlyCpg.computeF3(), onlycpgBoot );
pair<double,double> transitionsJK = computeJackknifeConfIntervals(transitions.computeF3(), transitionsBoot );
pair<double,double> transversionsJK = computeJackknifeConfIntervals(transversions.computeF3(),transversionsBoot);
pair<double,double> noDamageJK = computeJackknifeConfIntervals(noDamage.computeF3(), transversionsBoot);
// cout<<"jk size"<<jacknife->size()<<"\t"<<allDEVRefSam.first <<"\t"<<allDEVRefSam.second <<"\t"<<( (all.avgCoaRefSam()-allDEVRefSam.first) / allDEVRefSam.second)<<"\t"<<ppp.first<<"\t"<<ppp.second<<"\tlb"<<pppRef.first<<"\tub"<<pppRef.second<<"\t"<<pppBoth.first<<"\t"<<pppBoth.second<<"\t"<<(pppRef.first/pppBoth.second)<<"\t"<<(pppRef.second/pppBoth.first)<<"\t"<<all.counterReference<<"\t"<<(all.counterReference+all.counterCommon)<<endl;
//exit(1);
toreturn
<<all<<"\t"
<<allJK.first <<"\t"<<allJK.second <<"\t"
<<onlyCpg<<"\t"
<<onlyCpgJK.first <<"\t"<<onlyCpgJK.second <<"\t"
<<noCpg<<"\t"
<<noCpgJK.first <<"\t"<<noCpgJK.second <<"\t"
<<transitions<<"\t"
<<transitionsJK.first <<"\t"<<transitionsJK.second <<"\t"
<<transversions<<"\t"
<<transversionsJK.first <<"\t"<<transversionsJK.second <<"\t"
<<noDamage<<"\t"
<<noDamageJK.first <<"\t"<<noDamageJK.second ;
return toreturn.str();
}
F3Result & F3Result::operator+=(const F3Result & other){
this->all += other.all;
this->noCpg += other.noCpg;
this->onlyCpg += other.onlyCpg;
this->transversions += other.transversions;
this->transitions += other.transitions;
this->noDamage += other.noDamage;
return *this;
}
F3Result & F3Result::operator-=(const F3Result & other){
this->all -= other.all;
this->noCpg -= other.noCpg;
this->onlyCpg -= other.onlyCpg;
this->transversions -= other.transversions;
this->transitions -= other.transitions;
this->noDamage -= other.noDamage;
return *this;
}