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#ifndef PARAMQT_H
#define PARAMQT_H
//
#include <QtXml>
#include <QtGui>
#include "gsl/gsl_math.h"
#include "../warg/src/param.h"
//
using namespace weakarg;
using namespace std;
class ParamQt :public QObject, public Param {
Q_OBJECT
public:
ParamQt();
~ParamQt();
virtual void display(QPaintDevice * qpd);
void getXY(vector<double>**xx,vector<double>**yy);
void makeYforLeaves(vector<double> * v,Node * cur,int *x);
void displayTree(QPainter *painter,vector<double>*x,vector<double>*y);
void displayEdges(QPainter *painter,vector<double>*x,vector<double>*y);
inline void setGene(int g) {gene=g;}
inline int getGene() {return gene;}
void setBlocks(QString qstr);
inline void setTreeData(RecTree * t,QString strblocks) {
delete(rectree);
rectree=t;
if (data==NULL) {
vector<int> blocks;
QStringList qsl=strblocks.split(",");
for (int i=0;i<qsl.size();i++) blocks.push_back(qsl.at(i).toInt());
data=new Data(rectree->getN(),blocks);}
}///<Sets the tree
inline void clearTreeData(){
if(data==NULL) delete(data);
}
bool isCons;
virtual inline void incrTimeScale() {timeScale*=1.1;};
virtual inline void decrTimeScale() {timeScale/=1.1;};
inline void setTimeScale(double ts) {timeScale=ts;};
inline double getRateScale() {return rateScale;}
inline void setRateScale(double r) {rateScale=r;}
inline double getTimeScale() {return timeScale;}
double getRM();
//inline void clearConv() {convnames.clear();convdata.clear();}
inline void addConv(string name, double data){
for(unsigned int i=0;i<convnames.size();i++) {
if(name.compare(convnames.at(i))==0) {convdata[i]=data;return;}
}
convnames.push_back(name);
convdata.push_back(data);
}
inline string getConvName(int index){
if(index>=(int)convnames.size()){cerr<<"Error in paramqt: index "<<index<<" doesn't exist in convnames"<<endl;throw;};
return convnames.at(index);}
inline double getConvData(int index){
if(index>=(int)convdata.size()){cerr<<"Error in paramqt: index "<<index<<" doesn't exist in convdata"<<endl;throw;};
return convdata.at(index);}
inline int countConv(){return convdata.size();}
int getIdAt(int x,int y,QPaintDevice * qpd);
inline void setDisplayTree(RecTree *intree,bool isnew=false){
displaytree=intree;
if(isnew) displayset=true;
}///*Sets the tree that will be displayed
inline void newDisplayTree(RecTree *intree,bool forceages=false){
if(displayset) delete(displaytree);
//displaytree=new RecTree(intree,intree->newick(64),false,forceages);
displaytree=new RecTree(*intree);
displayset=true;
}///*Sets the tree that will be displayed to a new tree copied from intree
inline RecTree * getDisplayTree(){
return(displaytree);
}///*Gets the tree that will be displayed
inline void unsetDisplayTree(){
if(displayset) delete(displaytree);
displayset=false;
}///*removes the display tree
inline bool displaySet(){
return(displayset);
}///*returns whether the tree is set
inline void setNumber(long i){
iteration=i;
}///* Sets the iteration we are on
inline long getNumber(){
return(iteration);
}///* Sets the iteration we are on
inline void toggleRecView(){
recview++;
if(recview>=3) recview=0;
}
inline void setNameType(int i){
nametype=i;
}
inline void setRecView(int i){if(i>=0 &&i<3) recview=i;}
inline int getRecView(){return(recview);}
RecTree *displaytree;
int displayset;
double rateScale;
double timeScale;
long iteration;
int recview;
int labview;
int nametype;
vector<double> convdata;// convergence diagnostics
vector<string> convnames;// convergence diagnostics
QStringList labels;
QStringList names;
inline QString isolateName(int i){
if(i>=names.size() || i<0 || nametype<0) { return(QString::number(i));
}else {
if(nametype==1) {
QStringList tmp=names[i].split("+");
tmp.erase(tmp.begin());
return(tmp.join(" "));
}else if(nametype==2) {
QStringList tmp=names[i].split("+");
tmp.erase(tmp.begin());
tmp=tmp.join(" ").split(".");
tmp.erase(tmp.begin()+tmp.size()-1);
return(tmp.join(" "));
}
return(names[i]);
}
}
inline QString nodeLabel(int i){
if(i>=labels.size() || i<0) { return(QString(""));
}else return(labels[i]);
}
void setNames(QStringList qn){
names=qn;
}
void setLabels(QStringList qn){
labels=qn;
}
void makeCF(vector <vector<double> > *v);///<Accounts for clonal frame proportions in v
void setCF(vector <vector<double> > *v,int count);///< Sets the ClonalFrame proportions as labels
int gene;//Which gene to show; -1 for all
int lastCommonAncestor(int s1, int s2);///< Returns the last common ancestor between two individuals
vector<int> consistentAgeList(vector<double> *res);///< Returns a list of node ordersthat is consistent if -f option is used, and puts their ages in res
double pairwiseDistance(int s1, int s2);///<Returns the pairwise distance between sequence s1 and s2
vector<double> pairwiseDistanceList();///<List of the unique pairwise distances i9n order for(c1=0..N-1 for(c2=c1+1..N-1)).
vector<vector<double> > pairwiseDistanceMatrix(bool print=false);///< returns a pairwise distance matrix for the current tree
int recCount(int s1, int s2);///< Gets the number of recombination events from s2 to s1 (or ancestors) before they coalesce
vector<vector<int> > recCountMatrix(bool print);///< Gets the pairwise count of recombination events
vector<vector<double> > recPriorMatrix();///< recombination prior matrix, pairwise
};
#endif
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