#include <iostream>
#include <fstream>
void distFromString(Vector& v, char *s, double& dist);
void matchPoint2String(Vector& v, int len, char *s, double& dist);
void updateFit(Vector& v, char *s1,
	       char *ss, double& dist);
void updateFit(Vector& v, char *s1, char *s2,
	       char *ss, double& dist);
void updateFit(Vector& v, char *s1, char *s2, char *s3,
	       char *ss, double& dist);
void updateFit(Vector& v, char *s1, char *s2, char *s3, char *s4,
	       char *ss, double& dist);
void rotateString2Front(Vector& v, char *s);
void distFromAnBn(Vector& pt, Vector& dist);
void advancePoint(Vector& pt1, double h);
void advancePoint2Section(Vector& pt1, double h);
void advancePoint2ANYSection(Vector& pt1, double h);
void shift2FirstPoint(Matrix& po, char *s);
void findFirstPoint(char *s, Vector& fpt);
double distFromFirstPoint(Vector& pt, char *s);
void distFromSBn(Vector& pt, char *s, char *tail, 
		 Vector& count, Vector& dist);
void distFromSAn(Vector& pt, char *s, char *tail, 
		 Vector& count, Vector& dist);

const int NF=5;
class FwdFit{
public:
  FwdFit(Vector& ptt, char *taill);
  FwdFit(Vector& ptt, char *headd, char *taill);
  void printfit(ostream& ofile = cout);
  void printallleaves(ostream& ofile = cout);
  void updatefit();
  void getBestFit(char *s, double& distance);
  ~FwdFit();
private:
  Vector pt;//length = 3
  char tail[50];
  char *ffit[NF];
  Vector dist;// length = (NF)
  char exchar;
  char *triffit[3*NF];
  Vector tridist; //length = (3*NF)
  char triexchar;
  void initialize(char *);
  void trifurcate();
  void trifurcateAt(int);
  void sorttrifits();
  void copytrifits();
};

void setRepeatMax(int n);

class ZeroFit{
public:
  ZeroFit(char *s, double error);
  ~ZeroFit();
  void updateFit();
  void getBestFit(char *s, double& error);
  void saveFit(int index);
  double returnDistance();
private:
  char sf[200];
  Matrix *po;
  double err;
  void nextstring();
  void findpo();
};