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#ifndef OUTPUTFILE_H
#define OUTPUTFILE_H
#include <QtXml>
#include <QtGui>
#include "paramqt.h"
//
using namespace std;
//
class OutputFile
{
public:
OutputFile(QStringList qstrs,bool makeVectors=true);
inline int getL() {return blocks.split(",").last().toInt();}
inline int getB() {return blocks.split(",").size()-1;}
inline QString getBlocks() {return blocks;}
bool getIt(ParamQt * p);
void startOver();
void reset();
inline int getCurIt() {return currentIteration;}
void addOtherData(string name,double val);
inline vector<double>*getThetas(){vector<double> *v=new vector<double>(thetas);return v;}
inline vector<double>*getRhos(){vector<double> *v=new vector<double>(rhos);return v;}
inline vector<double>*getDeltas(){vector<double> *v=new vector<double>(deltas);return v;}
inline vector<double>*getLikelihoods(){vector<double> *v=new vector<double>(likelihoods);return v;}
inline vector<double>*getPriors(){vector<double> *v=new vector<double>(priors);return v;}
inline vector<double>*getNumRecEdges(){vector<double> *v=new vector<double>(numrecedges);return v;}
inline vector<double>*getGenoRec(){vector<double> *v=new vector<double>(genorec);return v;}
vector<double>*getRelGenoRec(ParamQt*param);
vector<double>*getGenoRec(int id,bool getto);
vector<double>*getRelGenoRec(ParamQt*param,int id);
inline vector<double>*getGenoBeg(){vector<double> *v=new vector<double>(genobeg);return v;}
inline vector<double>*getGenoEnd(){vector<double> *v=new vector<double>(genoend);return v;}
vector<double>*getRhoOverTheta();
vector<double>*getRoverM(ParamQt*param);
vector<double>*getRhoPerSite();
vector<double>*getThetaPerSite();
vector<double>*getPosteriors();
vector<double>*getTMRCA() {vector<double> *v=new vector<double>(tmrcas);return v;}
vector<double>*getTTotal() {vector<double> *v=new vector<double>(ttotals);return v;}
inline bool isinitialised(){return(outputinitialised);}
void countVectors();
inline QString getFileName() {return file[0]->fileName();}
inline QString getComment(){return(comment);}
void readNames(QString str);
inline QStringList getNames(){return(names);};
void makeCF(ParamQt*param);
inline void addRegions(QString str){
QStringList strl=str.split(",");
for(unsigned int i=0;i<strl.size();i++) regions.push_back(strl[i].toInt());
}// adds to the list of regions, keeping the list sorted and unique
inline vector<int> getRegions(){
return(regions);
}
inline void addBlocks(QString tmpBlocks,int i){
previousL.push_back(getL());
if (i==0) blocks=tmpBlocks; else {
int L=getL();
QStringList qstrl=tmpBlocks.split(",");
for (int j=1;j<qstrl.size();j++) blocks.append(",").append(QString::number(L+qstrl[j].toInt()));
blocks.append("\n");
};
}
protected:
bool outputinitialised;
QString comment;
vector<QFile*>file;
vector<QXmlStreamReader*> xml;
QString blocks;
int currentIteration;
vector<int> previousL;
vector<double>thetas;
vector<double>rhos;
vector<double>deltas;
vector<double>likelihoods;
vector<double>priors;
vector<double>numrecedges;
vector<double>genorec;
vector<double>relgenorec;
vector<double>genobeg;
vector<double>genoend;
vector<double>tmrcas;
vector<double>ttotals;
vector<int> regions;
QStringList names;
std::string getStdoutFromCommand(std::string cmd);
};
#endif
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