#include "vector.h"
#include "grid.h"
#include "simpstrg.h"

/* This file contains type defs and function declarations for ALL
   files with source code */

class peddata
{
public:
  // char ped[20];
  // int id, fid, mid, sex, aff_con;
  ivectors loci;
};

typedef vector<peddata> pedvector;

//declarations


//___________________________________________________________________________
// Function declarations

int readinput(char* datafile, char* pedfile, int debug,
      int &program_code, int &data_type, int &num_loci,
      int &numblanks, int &num_markers, ivector &markers, 
      int &map_type, int &map_size, dvector &map, 
      int &num_total_affecteds,
      int &num_indiv, ivector &indiv_list, int &hap_or_freq,
	      int &mkvorder, int &bayes,
      int &num_total_control, int &num_control,
      ivector &control_list, ivector &num_alleles,
      ivectors &allele_list, dvectors &allele_freq,
      dvector &mut_rates, int &est_p, double &p, double &max_res,
      int &map_res, int &max_cand, int &anc_hap_known,
      int &num_anc_hap_known, ivectors &anc_hap, 
      int &C_loc, int &C_all, int &E_int,
      simpstrg& resout, simpstrg& ancout, 
      simpstrg& maxout, simpstrg& oneout,      
      int &L_End, int &R_End,
      double &fixed_thresh, 
      double &var_thresh,
      pedvector &peds);
//int readinput(char* datafile, char* pedfile, int debug);
int get_next(ifstream& dfs, int& nextvar);
int get_next(ifstream& dfs, double& nextvar);
int get_next(ifstream& dfs, simpstrg& nextvar);
int skip_to_loci(ifstream& dfs, int numblanks);
void print_var(const char* varname, double varval, int index = -1);
void print_var(const char* varname, const simpstrg& varval, int index = -1);
void check_error(const char* checkvar);
int read_ped_file(const char* pedfile, int &numblanks, pedvector& peds);
//int read_ped_file(char* pedfile, int pedfile_type, pedvector& peds);

//___________________________________________________________________________

//declarations from makeobjectfunctions.C
void countallelesff(ivector &allelecounts, const dgrid &freqfreq);
void makedatafrompeds(igrid &data, const pedvector &peds, 
      const int &num_markers, const ivector &markers,
      const int &num_indiv, const ivector &indiv_list,
      const int &debug);
void makemap(dvector &y, const int &num_markers, const ivector &markers,
     const int &map_type, const int &map_size,
     const dvector &map,
     const int &debug);
void makeallelecountsff(ivector &allelecountsff, 
const int &num_markers, const ivector &markers,
const ivector &num_alleles,
const int &hap_or_freq,
const int &debug);
void makeindfreq(igrid &freqallele, dgrid &freqfreq,
const int &num_markers, const ivector &markers,
const ivector &num_alleles,
const ivectors &allele_list, const dvectors &allele_freq,
const int &hap_or_freq,
const int &debug);
void makeindjointfreq2(dgrid &jointfreq2, const ivector &allelecountsff,
       const dgrid &freqfreq, const int &num_markers,
       const int &debug);
void makejointfreq2C(dgrid &jointfreq2C, const ivector &allelecountsff,
     const dgrid &freqfreq, const int &C, 
     const int &debug);
void makejointfreq3(dvector &jointfreq3, const dgrid &freqfreq, 
    const ivector &allelecountsff,
    const int &C, const int &debug);
void makemut(dvector &mut_markers, const dvector &mut_rates,
     const ivector &markers, const int &debug);
void rescalemut(dvector &mut_markers_rescale, const dvector &mut_markers,
const ivector &allelecountsff, const int &C, 
const int &debug);
void jointfreq3reset(dvector &jointfreq3, const igrid &freqallele,
     const dgrid &freqfreq, const ivector &allelecounts,
     const int &callele, const int &loc,
     const int &debug);
void jointfreq2reset(dgrid &jointfreq2, const igrid &freqallele,
     const dgrid &freqfreq, const ivector &allelecounts,
     const int &callele, const int &loc,
     const int &debug);
void jointfreq2Creset(dgrid &jointfreq2C, const igrid &freqallele,
      const dgrid &freqfreq, const ivector &allelecounts,
      const int &callele, const int &loc,
      const int &debug);
void freqfreqreset(dgrid &freqfreq, const igrid &freqallele, 
   const int &callele, const int &loc,
   const int &debug);
void makecondfreq2l(dgrid &condfreq2l, const igrid &freqallele,
    const dgrid &freqfreq, const dgrid &jointfreq2,
    const ivector &allelecounts, const int &C,
    const int &debug);
void makecondfreq2r(dgrid &condfreq2r, const igrid &freqallele,
    const dgrid &freqfreq, const dgrid &jointfreq2,
    const ivector &allelecounts, const int &C,
    const int &debug);
void makecondfreq3l(dvector &condfreq3l, const dvector &jointfreq3,
    const dgrid &freqfreq,
    const ivector &allelecounts, const int &C,
    const int &debug);
void makecondfreq3r(dvector &condfreq3r, const dvector &jointfreq3,
    const dgrid &freqfreq,
    const ivector &allelecounts, const int &C,
    const int &debug);
void makecondfreq3F(dgrid &condfreq3F, const dvector &jointfreq3, 
    const dgrid &freqfreq,
    const ivector &allelecounts, const int &C, 
    const int &debug);
void makecondfreq2C(dgrid &condfreq2C, const dgrid &jointfreq2C, 
    const igrid &freqallele,
    const dgrid &freqfreq, const ivector &allelecounts,
    const int &loc,
    const int &debug);
void makex(const dvector &y, dvector &x, const int &C, const int &debug);
void makecontrolsfrompeds(igrid &controls, const pedvector &peds, 
  const int &num_markers, const ivector &markers,
  const int &num_control, const ivector &control_list,
  const int &debug);
void make_augy(dvector &augy, const dvector &y, const int &C,
       const int &sub, const int &num_sub, const int &debug);
void make_mody(dvector &mody, const dvector &y, const int &C,
       const int &sub, const int &num_sub, 
       const int &res, const int &map_res,
       const int &debug);
void makejointfreq3mkv(dvector &jointfreq3, const dgrid &jointfreq2,
       const dgrid &freqfreq,
       const ivector &allelecounts, const int &C,
       const int &debug);
void jointfreq2resetmkv(dgrid &jointfreq2, dvectors &h_freq_lists,
const ivectors &a_lists,
const int &callele, const int &loc,
const int &debug);
void makecondfreq2Cdt1(dgrid &condfreq2C, 
       const dgrid &freqfreq, const ivector &allelecounts,
       const int &loc,
       const int &debug);


//for source in mapfunctions.C
void augmentdata(const igrid& data, igrid& augdata, 
const igrid& freqallele, igrid& augfreqallele,
const dgrid& freqfreq, dgrid& augfreqfreq, 
const dgrid& jointfreq2, dgrid& augjointfreq2, 
//const dvector& y, dvector& augy, 
const ivector& allelecounts, ivector& augallelecounts,
const dvector& mut_markers, dvector& augmut_markers,
const int &C, const int &ctrall, 
const int &debug);
void makejointfreq3(dvector &jointfreq3, const dgrid &jointfreq2, 
    const int &C, const int &debug);
void make_auganc_hap(const int &C, const int &ctrall, 
     const int &anc_hap_known,
     const ivectors &anc_hap, ivector &auganc_hap,
     int &max_counter, const int &debug);
void updateanchapstore(ivectors &anchapstore, int &anchapcounter,
       const int &C_loc, const igrid &candanc,
       const int &debug);
int assignE(const ivector &maxlikCint, const dvector &maxlikCloc);
int pickmaxlikanc(const dvectors &resonetempstore);

//for source in routines.C
void onehap(dvector &resultsone, const int &C, int &LE, int &RE,
    const igrid &data,
    const ivector &anchap, const dvector &x, const dvector &y,
    const igrid &freqallele, const dgrid &freqfreq, 
    const dgrid &jointfreq2,
    const dgrid &condfreq2l, const dgrid &condfreq2r, 
    const dgrid &condfreq2C,
    const dvector &condfreq3l, const dvector &condfreq3r,
    const ivector &allelecounts, 
    dgrid &obsprobs, dgrid &obsprobsCnum,
    dgrid &obsprobsCden,
    const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
    dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
    dgrid &alpha, dgrid &beta, dgrid &gamma,
    dvector &cstar, dvector &cstarmut, dvector &loglikvec,
    const int &estp, const double &pinit, const double &m);

void maxhap(dvector &resultsmax, const int &ctrall,
    const igrid &allelelist,
    igrid &candanc, dgrid &candres, 
    const double &threshfix, const double &threshvar, 
    const int &mapest, const int &E,
    //onehapobjects
    dvector &resultsone, const int &C, int &LE, int &RE,
    const igrid &data,
    ivector &anchap, const dvector &x, const dvector &y,
    const igrid &freqallele, const dgrid &freqfreq, 
    const dgrid &jointfreq2,
    const dgrid &condfreq2l, const dgrid &condfreq2r, 
    const dgrid &condfreq2C,
    const dvector &condfreq3l, const dvector &condfreq3r,
    const ivector &allelecounts, 
    dgrid &obsprobs, dgrid &obsprobsCnum,
    dgrid &obsprobsCden,
    const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
    dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
    dgrid &alpha, dgrid &beta, dgrid &gamma,
    dvector &cstar, dvector &cstarmut, dvector &loglikvec,
    const int &estp, const double &pinit, const double &m);

void onegen(dvector &resultsone, const int &C, int &LE, int &RE,
    const igrid &data,
    const ivector &anchap, const dvector &x, const dvector &y,
    const igrid &freqallele, const dgrid &freqfreq, 
    const dgrid &jointfreq2,
    const dgrid &condfreq2l, const dgrid &condfreq2r, 
    const dgrid &condfreq2C,
    const dvector &condfreq3l, const dvector &condfreq3r,
    const ivector &allelecounts, 
    dgrid &obsprobs, dgrid &obsprobsCnum,
    dgrid &obsprobsCden,
    const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
    dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
    dgrid &alpha, dgrid &beta, dgrid &gamma,
    dvector &cstar, dvector &cstarmut, dvector &loglikvec,
    const int &estp, const double &pinit, const double &m,
    //extra objects for genotype code
    dvector &scratchvec, const dgrid &jointfreq2C,
    const dgrid &condfreq3F, 
    dvector &obsprobsCltRE, dgrid &nullprobs, 
    dgrid &nullprobsCnum, dgrid &nullprobsCden,
    dvector &nullprobsCltRE);
void onegenmkv2(dvector &resultsone, const int &C, int &LE, int &RE,
		const igrid &data,
		const ivector &anchap, const dvector &x, const dvector &y,
		const igrid &freqallele, const dgrid &freqfreq, 
		const dgrid &jointfreq2, const dgrid &jointfreq3, 
		const dgrid &jointfreq3f,
		const dgrid &jointfreq4, const dgrid &jointfreq4f,
		const ivector &allelecounts, 
		dgrid &obsprobs, dvectors &obsCnum, dvectors &obsCden,
		const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
		dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
		dgrid &alpha, dgrid &beta, dgrid &gamma,
		dvector &cstar, dvector &cstarmut, dvector &loglikvec,
		const int &estp, const double &pinit, const double &m,
		//extra objects for genotype code
		dvector &scratchvec, dgrid &nullprobs,
		dvectors &nullCnum, dvectors &nullCden, dvectors &gammaC);

void max(dvector &resultsmax, const int &ctrall,
const igrid &allelelist,
igrid &candanc, dgrid &candres, 
const double &threshfix, const double &threshvar, 
const int &mapest, const int &E, const int &data_type,
//onehapobjects
dvector &resultsone, const int &C, int &LE, int &RE,
const igrid &data,
ivector &anchap, const dvector &x, const dvector &y,
const igrid &freqallele, const dgrid &freqfreq, 
const dgrid &jointfreq2,
const dgrid &condfreq2l, const dgrid &condfreq2r, 
const dgrid &condfreq2C,
const dvector &condfreq3l, const dvector &condfreq3r,
const ivector &allelecounts, 
dgrid &obsprobs, dgrid &obsprobsCnum,
dgrid &obsprobsCden,
const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
dgrid &alpha, dgrid &beta, dgrid &gamma,
dvector &cstar, dvector &cstarmut, dvector &loglikvec,
const int &estp, const double &pinit, const double &m,
//extra objects for genotype code
dvector &scratchvec, const dgrid &jointfreq2C,
const dgrid &condfreq3F, 
dvector &obsprobsCltRE, dgrid &nullprobs, 
dgrid &nullprobsCnum, dgrid &nullprobsCden, 
dvector &nullprobsCltRE);
void onehapmkv2(dvector &resultsone, const int &C, int &LE, int &RE,
const igrid &data,
const ivector &anchap, const dvector &x, const dvector &y,
const igrid &freqallele, const dgrid &freqfreq, 
const dgrid &jointfreq2, const dgrid &jointfreq3mkv2, 
const dgrid &jointfreq3fmkv2,
const dgrid &jointfreq4mkv2,
const dgrid &jointfreq4fmkv2,
const dgrid &condfreq2l, const dgrid &condfreq2r,  
const dgrid &condfreq3fmkv2, const dgrid &condfreq3lmkv2, 
const dgrid &condfreq3rmkv2,
const ivector &allelecounts, 
dgrid &obsprobs, dvector &obsprobsAstore, 
const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
dgrid &alpha, dgrid &beta, dgrid &gamma,
dvector &cstar, dvector &cstarmut, dvector &loglikvec,
const int &estp, const double &pinit, const double &m);
void maxmkv2(dvector &resultsmax, const int &ctrall,
	     const igrid &allelelist,
	     igrid &candanc, dgrid &candres, 
	     const double &threshfix, const double &threshvar, 
	     const int &mapest, const int &E, const int &data_type,
	     //onehapobjects
	     dvector &resultsone, const int &C, int &LE, int &RE,
	     const igrid &data,
	     ivector &anchap, const dvector &x, const dvector &y,
	     const igrid &freqallele, const dgrid &freqfreq, 
	     const dgrid &jointfreq2,
	     const dgrid &condfreq2l, const dgrid &condfreq2r, 
	     const dgrid &condfreq2C,
	     const dvector &condfreq3l, const dvector &condfreq3r,
	     const ivector &allelecounts, 
	     dgrid &obsprobs, dgrid &obsprobsCnum,
	     dgrid &obsprobsCden,
	     const dvector &mut, dvector &mutmatch, dvector &mutnomatch, 
	     dgrid &initstore, dgrid &transstore, dgrid &transstoreC, 
	     dgrid &alpha, dgrid &beta, dgrid &gamma,
	     dvector &cstar, dvector &cstarmut, dvector &loglikvec,
	     const int &estp, const double &pinit, const double &m,
	     //extra objects for genotype code
	     dvector &scratchvec, const dgrid &jointfreq2C,
	     const dgrid &condfreq3F, 
	     dvector &obsprobsCltRE, dgrid &nullprobs, 
	     dgrid &nullprobsCnum, dgrid &nullprobsCden, 
	     dvector &nullprobsCltRE, 
	     //for onehapmkv2 
	     const dgrid &jointfreq3mkv2, const dgrid &jointfreq3fmkv2,
	     const dgrid &jointfreq4mkv2, const dgrid &jointfreq4fmkv2,
	     const dgrid &condfreq3fmkv2, const dgrid &condfreq3lmkv2,
	     const dgrid &condfreq3rmkv2, dvector &obsprobsAstore,
	     //for onegenmkv2
	     dvectors &obsCnum, dvectors &obsCden,
	     dvectors &nullCnum, dvectors &nullCden, dvectors &gammaC);


//for source in prefunctions.C
//declarations
void countalleles(ivector &allelecounts, const igrid &freqallele);
double getfreq(const igrid &freqallele, const dgrid &freqfreq, 
       const int &Lallele, const int &L);
double getcondfreq2C(const igrid &freqallele, const dgrid &condfreq2C, 
     const int &Lallele, const int &L);
double getjointfreq2C(const igrid &freqallele, const dgrid &jointfreq2C, 
      const int &Lallele, const int &L, const int &callele,
      const int &C);
double getjointfreq2(const igrid &freqallele, const ivector &allelecounts,
     const dgrid &jointfreq2, const int &ilocus, 
     const int &iallele, const int &jallele);
double getcondfreq2l(const igrid &freqallele, const ivector &allelecounts,
     const dgrid &condfreq2l, const int &ilocus, 
     const int &iallele, const int &jallele);
double getcondfreq2r(const igrid &freqallele, const ivector &allelecounts,
     const dgrid &condfreq2r, const int &ilocus, 
     const int &iallele, const int &jallele, const int &C);
double getjointfreq3(const igrid &freqallele, const ivector &allelecounts,
     const dvector &jointfreq3, const int &ilocus, 
     const int &iallele, const int &jallele, 
     const int &kallele);
double getcondfreq3F(const igrid &freqallele, const ivector &allelecounts,
     const dgrid &condfreq3F, const int &C, 
     const int &iallele, const int &kallele,
     const int &cond);
void makesmallerdataset(igrid &augdata, const igrid &data, 
const int &C_loc, const int &C_all,
const int &data_type, const int &debug);

//for source in estfunctions.C
void makenullshare(dgrid &obsprobs, const igrid &data,
   const igrid &freqallele, const dgrid &freqfreq, 
   const dgrid &condfreq2l, const dgrid &condfreq2r,
   const dgrid &condfreq2C,
   const ivector &allelecounts,
   const int &LE, const int &RE, const int &C);
void makenullshareCnum(dgrid &obsprobsCnum, const igrid &data,
       const igrid &freqallele, const dgrid &freqfreq,
       const ivector &allelecounts,
       const dgrid &jointfreq2, const dvector &condfreq3l,
       const dvector &condfreq3r, const int &C,
       const int &LE, const int &RE, 
       const double &m, const ivector &anchap);
void makenullshareCden(dgrid &obsprobsCden, const igrid &data, 
       const igrid &freqallele,
       const dgrid &freqfreq, const int &C, 
       const int &LE, const int &RE);
void makemutmatch(dvector &mutmatch, dvector &mutnomatch, 
  const dvector &mut,
  const ivector &allelecounts, const double &tau,
  const int &C);
void makemodlshare(dgrid &obsprobs, const igrid &data,
   const dvector &mutmatch, dvector &mutnomatch,
   const ivector &anchap, 
   const int &C, const int &RE, const int &LE);
void makemodlshareCnum(dgrid &obsprobsCnum, const igrid &data,
       const dgrid &obsprobs, const int &C,
       const int &LE, const int &RE);
void makemodlshareCden(dgrid &obsprobsCden, const igrid &data,
       const dgrid &obsprobs, 
       const int &C, 
       const int &LE, const int &RE);
void makeinit(dgrid &initstore, const dvector &x, const double &tau, 
      const double &p, const int &C, const int &LE, const int &RE);
void maketrans(dgrid &transstore, const dvector &x, 
       const double &tau, const double &p, 
       const int &C, const int &LE, const int &RE);
void maketransC(dgrid &transstoreC, const dvector &x, 
const double &tau, const double &p, 
const int &C, const int &LE, const int &RE);
void makealpha(dgrid &alpha, const dgrid &initstore, 
       const dgrid &transstore, const dgrid &transstoreC,
       const dgrid &obsprobs, const dgrid &obsprobsnum,
       const dgrid &obsprobsCden, 
       const int &C, const int &LE, const int &RE);
void makebeta(dgrid &beta, const dgrid &initstore, 
      const dgrid &transstore, const dgrid &transstoreC,
      const dgrid &obsprobs, const dgrid &obsprobsCnum,
      const dgrid &obsprobsCden, 
      const int &C, const int &LE, const int &RE);
void makegamma(dgrid &gamma, const dgrid &alpha, const dgrid &beta,
       const int &C, const int &LE, const int &RE);
void makecstar(dvector &cstar, const dgrid &gamma, 
       const int &C, const int &LE, const int &RE);
void makecstarmut(dvector &cstarmut, const dvector &cstar,
  const dgrid &gamma,
  const igrid &data, const ivector &anchap,
  const dvector &mutmatch,
  const int &C, const int &LE, const int &RE);
double bisecmle(const dvector &cstar, const dvector &cstarmut, 
const dvector &y, 
const dvector &x,
const int &C, const int &LE, const int &RE, 
const dvector &mut, const ivector &allelecounts,
const double &m);
double loglikder(double &tau, const dvector &y, const dvector &x,
const dvector &cstar, 
const int &C, const int &LE, const int &RE);
double mutloglikder(const double &tau, const dvector &mut,//mrescaled 
    const dvector &cstar, const dvector &cstarmut,
    const ivector &allelecounts, const int &C, 
    const int &LE, const int &RE);
double makep(const dvector &cstar, const int &numhap, const int &C);
void makeloglik(dvector &loglikvec, const dgrid &alpha, 
const dgrid &initstore,
const int &C, const int &RE);

//for code in step.C
void makeinitcandanc(igrid &candanc, const int &C, 
     const int &LE, const int &RE, const int &ctrall, 
     const igrid &allelelist, int &numcand);
void makecandanc(igrid &candanc, const igrid &allelelist, int &dirjump, 
int &numcand, int &numkeep, const int &C, int &LE, int &RE,
const int &ctrall);
void rowswitchint(igrid &candanc, const int &row, const int &row1);
void rowswitchdou(dgrid &candres, const int &row, const int &row1);
void sortcandancbylik(igrid &candanc, dgrid &candres, 
      const int &numcand, const int &loclik);  
int whichdir(const int &LE, const int &RE, const dvector &x);
int findnumkeep(const dgrid &candres, const int &dirjump, 
const double &threshfix, const double &threshvar, 
int &numcand);
void cleantemps(igrid &candanc, dgrid &candres, const int &numcand, 
const int &numkeep, const int &LE, const int &RE);
void correctlik(dgrid &candres, const int &numcand, const int &loclik);

//for source in genfunctions.C
void makenullsharegen(dgrid &nullprobs, const igrid &data,
      const igrid &freqallele, const dgrid &freqfreq,
      const dgrid &condfreq2l, const dgrid &condfreq2r,
      const dgrid &condfreq2C,
      const ivector &allelecounts,
      const int &LE, const int &RE, const int &C);
void makenullshareCnumgen(dgrid &nullprobsCnum, const igrid &data,
  const igrid &freqallele, const dgrid &freqfreq,
  const ivector &allelecounts,
  const dgrid &jointfreq2, const dgrid &condfreq2C,
  const dvector &condfreq3l,
  const dvector &condfreq3r, 
  const dgrid &condfreq3F,
  const int &C,
  const int &LE, const int &RE);
void makenullshareCdengen(dgrid &nullprobsCden, const igrid &data, 
  const igrid &freqallele,
  const dgrid &freqfreq, const int &C, 
  const int &LE, const int &RE);
void makenullshareCltREgen(dvector &nullprobsCltRE, const igrid &data,
   const igrid &freqallele, const dgrid &freqfreq,
   const ivector &allelecounts,
   const dgrid &jointfreq2C, 
   const int &C,
   const int &RE);
void makemodlsharegen(dgrid &obsprobs, const dgrid &nullprobs, 
      const igrid &data,
      const dvector &mutmatch, dvector &mutnomatch,
      const ivector &anchap, 
      const int &C, const int &LE, const int &RE);
void makemodlshareCnumgen(dgrid &obsprobsCnum, const dgrid &nullprobsCnum,
  const igrid &data, const ivector &anchap, 
  const dvector &mutmatch, const dvector &mutnomatch,
  const int &C, const int &LE, const int &RE);
void makemodlshareCdengen(dgrid &obsprobsCden, const dgrid &nullprobsCden,
  const igrid &data, const ivector &anchap, 
  const dvector &mutmatch, const dvector &mutnomatch,
  const int &C, const int &LE, const int &RE);
void makemodlshareCltREgen(dvector &obsprobsCltRE, 
   const dvector &nullprobsCltRE,
   const igrid &data, const ivector &anchap, 
   const dvector &mutmatch, const dvector &mutnomatch,
   const int &C, const int &RE);
void makeinitgen(dgrid &initstore, dvector &scratchvec,
const dvector &x, const double &tau, 
const double &p, const double &freqC,
const int &C, const int &LE, const int &RE);
void maketransgen(dgrid &transstore, dvector &scratchvec, const dvector &x, 
  const double &tau, const double &p, const double &freqC,
  const int &C, const int &LE, const int &RE);
void maketransCgen(dgrid &transstoreC, dvector &scratchvec,
   const dvector &x, 
   const double &tau, const double &p, 
   const int &C, const int &LE, const int &RE);
void makealphagen(dgrid &alpha, const dgrid &initstore, 
  const dgrid &transstore, const dgrid &transstoreC,
  const dgrid &obsprobs, const dgrid &obsprobsCnum,
  const dgrid &obsprobsCden, 
  const int &C, const int &LE, const int &RE);
void makebetagen(dgrid &beta, const dgrid &initstore, 
const dgrid &transstore, const dgrid &transstoreC,
const dgrid &obsprobs, const dgrid &obsprobsCnum,
const dgrid &obsprobsCden, const dvector &obsprobsCltRE,
const int &C, const int &LE, const int &RE);
void makegammagen(dgrid &gamma, const dgrid &alpha, const dgrid &beta,
  const int &C, const int &LE, const int &RE);
void makecstargen(dvector &cstar, const dgrid &gamma, 
  const int &C, const int &LE, const int &RE);
void makecstarmutgen(dvector &cstarmut, const dvector &cstar,
     const dgrid &gamma,
     const igrid &data, const ivector &anchap,
     const dvector &mutmatch,
     const int &C, const int &LE, const int &RE);
void makeloglikgen(dvector &loglikvec, const dgrid &alpha, 
   const dgrid &initstore,
   const int &C, const int &RE);

//for source in esthapfreq.C
void m2lochfr_Hcon(dvector &h_freq_list, const int &loci, const int &locj, 
   const ivector &c_allele_lists_i, 
   const ivector &c_allele_lists_j, 
   const igrid &controls, 
   const int &debug);
void m2lochfr_Gcon(dvector &h_freq_list, const int &loci, const int &locj, 
   const ivector &c_allele_lists_i, 
   const ivector &c_allele_lists_j, 
   const igrid &controls, 
   const int &debug);
void count_alleles(ivector &allelecounts, const igrid &controls, 
   const int &debug);
void make_c_allele_lists(ivectors &c_allele_lists, const igrid &controls, 
const int &debug);
void make_haplotype_exp_Hcon(dgrid &haplotype_exp, 
     const igrid &controls,
     const ivector &c_allele_lists_i, 
     const ivector &c_allele_lists_j, 
     const int &i, const int &j,
     ivector &scratch, const ivector &missing,
     const int &debug);
void make_haplotype_res_Gcon(igrid &haplotype_res, 
     const igrid &controls,
     const ivector &c_allele_lists_i, 
     const ivector &c_allele_lists_j, 
     const int &i, const int &j,
     ivector &scratch, const ivector &missing,
     const int &debug);
void do_expectation_step_gen(dgrid &genotype_res, const dvector &h_freq_list, 
     igrid &haplotype_res, const ivector &missing,
     const int &debug);
void do_maximization_step_gen(dvector &h_freq_list, const dgrid &genotype_res,
      const igrid &haplotype_res, 
      const ivector &missing,
      const int &debug);
void make_missing_Hcon(ivector &missing, int &is_missing, 
       const igrid &controls, 
       const int &loci, const int &locj, 
       const int &debug);
void make_missing_Gcon(ivector &missing, int &is_missing, 
       const igrid &controls, 
       const int &loci, const int &locj, 
       const int &debug);
void make_a_freq_lists(dvectors &a_freq_lists, const dvector &h_freq_list,
       const int &debug);
void mg_expectation_step_gen(dvectors &mg_genoteype_res, 
     const dvector &h_freq_list, 
     const dvectors &a_freq_lists,
     const ivector &c_allele_lists_i, 
     const ivector &c_allele_lists_j, 
     const igrid &controls,
     const ivector &missing,
     const int &loci, const int &locj, 
     const int &debug);
int getposinlist(const int &allele, const ivector &list);
void mg_maximization_step_gen(dvector &h_freq_list, 
      const dvectors &mg_genoteype_res,
      const ivector &missing,
      const int &debug);
void mh_expectation_step_hap(dgrid &haplotype_exp, 
     const dvector &h_freq_list, 
     const igrid &controls,
     const ivector &c_allele_lists_i, 
     const ivector &c_allele_lists_j, 
     const int &i, const int &j,
     const dvectors &a_freq_lists,
     ivector &scratch, const ivector &missing,
     const int &debug);
void maximization_step_hap(dvector &h_freq_list, 
   const dgrid &haplotype_exp, const int &debug);
void make_init_h_freq(dvector &h_freq_list, const int &debug);
void countadditionalalleles(ivector &additionalalleles, 
    const ivectors &c_allele_lists,
    const igrid &data, const int &debug);
void finish_allele_list(ivectors &allele_list, const ivectors &c_allele_lists,
const igrid &data,
const int &debug);
void makejf2(dgrid &jointfreq2, const dvectors &hap_freq, const int &debug);
void makefa(igrid &freqallele, const ivectors &allele_list, const int &debug);
void makeff(dgrid &freqfreq, const igrid &freqallele,
    const ivectors &allele_list, 
    const dgrid &jointfreq2, const int &debug);
//new hmm routine
void makehap2fr_hmm_Gcon(dvectors &h_freq_lists, 
const ivectors &a_lists, 
const igrid &controls, 
const int &debug);
void makeb_Gfr(dvectorss &b, const ivectors &a_lists,
       const igrid &controls, const int &debug);
void make_a_freq_lists_Gfr(dvectors &a_freq_lists, 
   const dvectors &h_freq_lists,
   const int &debug);
void maketrans_Gfr(dvectors &trans, const dvectors &a_freq_lists,
   const dvectors &h_freq_lists, const int &debug);
void makealpha_Gfr(dvectorss &alpha, const dvectors &a_freq_lists,
   const dvectors &trans, const dvectorss &b,
   const int &debug);
void makebeta_Gfr(dvectorss &beta, const dvectors &trans, const dvectorss &b,
  const int &debug);
void makexi_Gfr(dvectorss &xi, const dvectorss &alpha, const dvectorss &beta, 
const dvectors &trans, const dvectorss &b, 
const int &debug);
void make_h_freq_lists_Gfr(dvectors &h_freq_lists, dvectors &a_freq_lists,
   const dvectorss &xi, const int &debug);
//haplotype controls
void makehap2fr_hmm_Hcon(dvectors &h_freq_lists, 
const ivectors &a_lists, 
const igrid &controls, 
const int &debug);
void make_missing_Hfr(ivector &missing, int &is_missing, 
      const igrid &controls, 
      const int &debug);
void makexi_nomissing_Hfr(dvectorss &xi, const ivector &missing, 
  const ivectors &a_lists, 
  const igrid &controls, const int &debug);
void makeb_Hfr(dvectorss &b, const ivector &missing, const ivectors &a_lists,
       const igrid &controls, const int &debug);
void maketrans_Hfr(dvectors &trans, const dvectors &a_freq_lists,
   const dvectors &h_freq_lists, const int &debug);
void makealpha_Hfr(dvectorss &alpha, const ivector &missing,
   const dvectors &a_freq_lists,
   const dvectors &trans, const dvectorss &b,
   const int &debug);
void makebeta_Hfr(dvectorss &beta, const ivector &missing, 
  const dvectors &trans, const dvectorss &b,
  const int &debug);
void makexi_Hfr(dvectorss &xi, const ivector &missing, 
const dvectorss &alpha, const dvectorss &beta, 
const dvectors &trans, const dvectorss &b, 
const int &debug);
void make_h_freq_lists_Hfr(dvectors &h_freq_lists, 
   const dvectorss &xi, const int &debug);
void make_adj_to_hfreqlists(dvectors &h_freq_lists_adj, 
    const dvectors &h_freq_lists, 
    ivectors &a_lists, const double &e,
    const ivector &additionalalleles,
    const int &hap_or_freq,
    const igrid &controls,
    const int &debug);
void adjust_init(dvector &init, const double &e, 
const ivector &additionalalleles,
const igrid &controls,
const int &debug);
void adjust_trans(dvectors &trans, const dvector &init, const igrid &controls,
  const double &e, const double &zero,
  const ivectors &a_lists, dvectors &a_freq_lists,
  const ivector &additionalalleles,
  const int &hap_or_freq,
  const int &debug);
void make_a_freq_lists_fr_trans(dvectors &a_freq_lists, const dvector &init,
const dvectors &trans, 
const int &lastloc, const int &debug);
double makelik_Gfr(const dvectorss &alpha);
double make_null_lik_Gfr(igrid &controls, const ivectors &allele_list,
const dvectors &h_freq_lists);
double make_lik_Gfr_DIRECT(const igrid &controls, const ivectors &a_lists,
   const dvectors &h_freq_lists);
int check_a_freq_lists(const dvectors &a_freq_lists, 
       const dvectors &h_freq_lists);

//declarations for se.C
double smapprox(int n);
void cr(int npts, const dvector& d, const dvector& ll, double chip,
        ivector& edge, int& numedge);

//declarations for random.C
//float ran1(long *idum);

//declarations for makeobjectfunctionsmkv.C
void makejf3(dgrid &jointfreq3mkv2, const dgrid &jointfreq2, 
     const dgrid &freqfreq, const ivectors &allele_list,
     const int &debug);
void makejf3f(dgrid &jointfreq3fmkv2, const dgrid &jointfreq3mkv2, 
      const ivectors &allele_list,
      const int &debug);
void makeaugjointfreq4mkv2(dgrid &jointfreq4mkv2, const dgrid &jointfreq3mkv2,
   const int &C);
void makeaugjointfreq4fmkv2(dgrid &jointfreq4fmkv2, 
    const dgrid &jointfreq3fmkv2,
    const int &C);
void augmentdatamkv2(dgrid &augjointfreq3mkv2, const dgrid &jointfreq3mkv2,
     dgrid &augjointfreq3fmkv2, const dgrid &jointfreq3fmkv2,
     const dgrid &jointfreq2, const dgrid &freqfreq,
     const ivector &allelecounts,
     const int &C, const int &debug);
void makecondfreq3lmkv2(dgrid &condfreq3lmkv2, const igrid &freqallele,
const dgrid &jointfreq2,
const dgrid &jointfreq3mkv2,
const ivector &allelecounts, const int &C,
const int &debug);
void makecondfreq3rmkv2(dgrid &condfreq3rmkv2, const igrid &freqallele,
const dgrid &jointfreq2,
const dgrid &jointfreq3mkv2,
const ivector &allelecounts, const int &C,
const int &debug);
void makecondfreq3fmkv2(dgrid &condfreq3fmkv2, const dgrid &jointfreq3fmkv2,
const dgrid &freqfreq, const ivector &allelecounts,
const int &C, const int &debug);
void makenullsharemkv2(dgrid &obsprobs, const igrid &data,
       const igrid &freqallele, const dgrid &freqfreq,
       const dgrid &condfreq2l, const dgrid &condfreq2r,
       const dgrid &condfreq3fmkv2, 
       const dgrid &condfreq3lmkv2, 
       const dgrid &condfreq3rmkv2,
       const ivector &allelecounts,
       const int &LE, const int &RE, const int &C,
       const int &debug);
double getcondfreq3fmkv2(const igrid &freqallele, const ivector &allelecounts,
const dgrid &condfreq3fmkv2, const int &ilocus, 
const int &iallele, const int &jallele);
double getcondfreq3mkv2(const igrid &freqallele, const ivector &allelecounts,
const dgrid &condfreq3mkv2, const int &ilocus, 
const int &iallele, const int &jallele,
const int &kallele);
void makealphamkv2(dgrid &alpha, const dgrid &initstore, 
   const dgrid &transstore,
   const dgrid &obsprobs, const dvector &obsprobsAstore,
   const int &C, const int &LE, const int &RE);
void makebetamkv2(dgrid &beta, const dgrid &initstore, 
  const dgrid &transstore, const dgrid &transstoreC,
  const dgrid &obsprobs, const dvector &obsprobsAstore,
  const int &C, const int &LE, const int &RE);
void makeobsprobsAstore(dvector &obsprobsAstore, const igrid &data,
const ivector &allelecounts,
const igrid &freqallele, const dgrid &freqfreq,
const dgrid &jointfreq2,
const dgrid &jointfreq3mkv2, 
const dgrid &jointfreq3fmkv2,
const dgrid &jointfreq4mkv2,
const dgrid &jointfreq4fmkv2,
const int &LE, const int &RE, const int &C,
const int &debug);
double getjointfreq4fmkv2(const igrid &freqallele, const ivector &allelecounts,
  const dgrid &jointfreq4fmkv2, const int &ilocus, 
  const int &iallele, const int &jallele,
  const int &C);
double getjointfreq4mkv2(const igrid &freqallele, const ivector &allelecounts,
const dgrid &jointfreq4mkv2, const int &ilocus, 
const int &iallele, const int &jallele,
const int &kallele, const int &C);
double getcondfreq3fmkv2(const igrid &freqallele, const ivector &allelecounts,
const dgrid &condfreq3fmkv2, const int &ilocus, 
const int &iallele, const int &jallele);
double getcondfreq3mkv2(const igrid &freqallele, const ivector &allelecounts,
const dgrid &condfreq3mkv2, const int &ilocus, 
const int &iallele, const int &jallele,
const int &kallele);
double getfreqSMART(const igrid &freqallele, const dgrid &freqfreq,
    const int &allele, const int &locus);
double getcondfreq2lSMART(const igrid &freqallele, const dgrid &freqfreq,
  const ivector &allelecounts, 
  const dgrid &jointfreq2, const int &l, 
  const int &allelel, const int &allelelp1);
double getcondfreq2rSMART(const igrid &freqallele, const dgrid &freqfreq,
  const ivector &allelecounts, 
  const dgrid &jointfreq2, const int &l, 
  const int &allelel, const int &allelelp1);
double getcondfreq3lSMART(const igrid &freqallele, const dgrid &freqfreq,
  const ivector &allelecounts, 
  const dgrid &jointfreq2, 
  const dgrid &jointfreq3mkv2,
  const dgrid &jointfreq3fmkv2,
  const int &l, 
  const int &allelel, const int &allelelp1,
  const int &allelelp2);
double getcondfreq3rSMART(const igrid &freqallele, const dgrid &freqfreq,
  const ivector &allelecounts, 
  const dgrid &jointfreq2, 
  const dgrid &jointfreq3mkv2,
  const dgrid &jointfreq3fmkv2,
  const int &l, 
  const int &allelel, const int &allelelp1,
  const int &allelelp2);
double getcondfreq4lSMART(const igrid &freqallele, const dgrid &freqfreq,
  const ivector &allelecounts, 
  const dgrid &jointfreq2, 
  const dgrid &jointfreq3mkv2,
  const dgrid &jointfreq4mkv2,
  const dgrid &jointfreq4fmkv2, const int &l, 
  const int &allelel, const int &allelelp1,
  const int &allelelp2, const int &allelelp3,
  const int &C);
double getcondfreq4rSMART(const igrid &freqallele, const dgrid &freqfreq,
			  const ivector &allelecounts, 
			  const dgrid &jointfreq2, 
			  const dgrid &jointfreq3mkv2,
			  const dgrid &jointfreq4mkv2,
			  const dgrid &jointfreq4fmkv2, const int &l, 
			  const int &allelel, const int &allelelp1,
			  const int &allelelp2, const int &allelelp3,
			  const int &C);
void makejf3fromh3fl(dgrid &jointfreq3mkv2, const dvectors &h3_freq_lists,
		     const int &debug);
void makejf2fromjf3(dgrid &jointfreq2, const dgrid &jointfreq3mkv2,
		    ivectors &a_list, const int &debug);
void makeindjointfreq3(dgrid &jointfreq3, const ivector &allelecountsff,
		       const dgrid &freqfreq, const int &num_markers,
		       const int &debug);


//declarations for esthapfreqmkv2.C
void makehap3fr_hmm_Hcon(dvectors &h3_freq_lists, 
			 const ivectors &a_lists, 
			 const igrid &controls, 
			 const int &debug);
void makeximkv2_nomissing_Hfr(dvectorss &xi, const ivector &missing, 
			      const ivectors &a_lists, 
			      const igrid &controls, const int &debug);
void makebmkv2_Hfr(dvectorss &b, const ivector &missing, 
		   const ivectors &a_lists,
		   const igrid &controls, const int &debug);
void maketransmkv2_Hfr(dvectors &trans, const dvectors &h3_freq_lists,
		       const dvectors &h2_freq_lists,
		       const ivectors &a_lists, const int &debug);
void makealphamkv2_Hfr(dvectorss &alpha, const ivector &missing,
		       const ivectors &a_lists,
		       const dvector &init,
		       const dvectors &trans, const dvectorss &b,
		       const int &debug);
void makebetamkv2_Hfr(dvectorss &beta, const ivector &missing, 
		      const dvectors &trans, const dvectorss &b,
		      const int &debug);
void makeximkv2_Hfr(dvectorss &xi, const ivector &missing, 
		    const dvectorss &alpha, const dvectorss &beta, 
		    const dvectors &trans, const dvectorss &b, 
		    const int &debug);
void makeh3freqlistsHfrxi(dvectors &h3_freq_lists, 
			  const dvectorss &xi, 
			  const ivectors &a_lists, const int &debug);
void makeh3freqlistsmkv2(dvectors &h3_freq_lists, dvectors &h2_freq_lists,
			 const dvector &init,
			 const dvectors &trans,const ivectors &a_lists,
			 const int &debug);
void makeh2freqlistsmkv2(dvectors &h2_freq_lists,
			 const dvectors &h3_freq_lists, 
			 const ivectors &a_lists, const int &debug);
void adjustmkv2(dvectors &h3_freq_lists_adj, const dvectors &h3_freq_lists,
		dvectors &h2_freq_lists, const double &e,
		const ivectors &a_lists,const int &debug);
void makehap3fr_hmm_HconBAYES(dvectors &h3_freq_lists, 
			      const ivectors &a_lists, 
			      const igrid &controls, const int &bayes,
			      const int &debug);
void makealphamkv2_HfrBAYES(dvectorss &alpha, const ivector &missing,
			    const ivectors &a_lists,
			    const dvector &init,
			    const dvectors &trans, const dvectorss &b,
			    const int &debug);
void makebetamkv2_HfrBAYES(dvectorss &beta, const ivector &missing, 
			   const ivectors &a_lists,
			   const dvectors &trans, const dvectorss &b,
			   const int &debug);
void makeximkv2_HfrBAYES(dvectorss &xi, const ivector &missing, 
			 const ivectors &a_lists,
			 const dvectorss &alpha, const dvectorss &beta, 
			 const dvectors &trans, const dvectorss &b, 
			 const int &debug);
void makeh3countsHfrxi(dvectors &h3_freq_lists, 
		       const dvectorss &xi, 
		       const ivectors &a_lists, const int &debug);
//genotype functions
void makehap3fr_hmm_GconBAYES(dvectors &h3_freq_lists, 
			      const ivectors &a_lists, 
			      const igrid &controls,const int &bayes, 
			      const int &debug);
void makebmkv2_Gfr(dvectorss &b, 
		   const ivectors &a_lists,
		   const igrid &controls, const int &debug);
void makealphamkv2_Gfr(dvectorss &alpha, 
		       const ivectors &a_lists,
		       const dvector &init,
		       const dvectors &trans, const dvectorss &b,
		       const int &debug);
void makebetamkv2_Gfr(dvectorss &alpha, 
		      const ivectors &a_lists,
		      const dvectors &trans, const dvectorss &b,
		      const int &debug);
void makeximkv2_Gfr(dvectorss &xi, const ivectors &a_lists,
		    const dvectorss &alpha, const dvectorss &beta, 
		    const dvectors &trans, const dvectorss &b, 
		    const int &debug);
void makeh3countsGfrxi(dvectors &h3_freq_lists, 
		       const dvectorss &xi, 
		       const ivectors &a_lists, const int &debug);
void makeh2countsGmkv2(dvectors &h2_freq_lists, const int &numgen,
			 const dvectors &h3_freq_lists, 
		       const ivectors &a_lists, const int &debug);
void makeh3freqlistsGmkv2(dvectors &h3_freq_lists, dvectors &h2_freq_lists,
			  const dvector &init,
			  const dvectors &trans,const ivectors &a_lists,
			  const int &debug);
//hap mkv1 functions
void makehap2fr_hmm_HconBAYES(dvectors &h_freq_lists, const int &bayes,
			      const ivectors &a_lists, 
			      const igrid &controls, 
			      const int &debug);
void makealpha_HfrBAYES(dvectorss &alpha, const ivector &missing,
			const ivectors &a_lists,
			const dvector &init,
			const dvectors &trans, const dvectorss &b,
			const int &debug);
void makebeta_HfrBAYES(dvectorss &beta, const ivector &missing, 
		       const ivectors &a_lists,
		       const dvectors &trans, const dvectorss &b,
		       const int &debug);
void makeh2countsHfrxi(dvectors &h2_freq_lists, 
		       const dvectorss &xi, 
		       const ivectors &a_lists, const int &debug);
void make_a_freq_lists_HfrBAYES(dvectors &a_freq_lists, const int &numhap, 
				const dvectors &h_freq_lists,
				const int &debug);
void makeh2freqlistsH(dvectors &h2_freq_lists,
			 dvectors &a_freq_lists,
			 const dvector &init,
			 const dvectors &trans,const ivectors &a_lists,
		      const int &debug);
//Genotype Mkv1 functions
void makehap2fr_hmm_GconBAYES(dvectors &h_freq_lists, 
			      const ivectors &a_lists, 
			      const igrid &controls, const int &bayes,
			      const int &debug);
void makealpha_GfrBAYES(dvectorss &alpha, const dvectors &a_freq_lists,
			const dvector &init,
			const dvectors &trans, const dvectorss &b,
			const int &debug);
void makebeta_GfrBAYES(dvectorss &beta, 
		       const dvectors &a_freq_lists,
		       const dvectors &trans, 
		       const dvectorss &b,
		       const int &debug);
void makexi_GfrBAYES(dvectorss &xi, const dvectorss &alpha, 
		     const dvectorss &beta, 
		     const dvectors &trans, const dvectorss &b, 
		     const dvectors &a_freq_lists,
		     const int &debug);
void makeh2countsGfrxi(dvectors &h2_freq_lists, 
		       const dvectorss &xi, 
		       const dvectors &a_freq_lists, const int &debug);





//declarations for genfunctionsmkv2.C
void makenullsharegenmkv2(dgrid &nullprobs, const igrid &data,
			  const igrid &freqallele, const dgrid &freqfreq,
			  const dgrid &jointfreq2, const dgrid &jointfreq3,
			  const dgrid &jointfreq3f, 
			  const ivector &allelecounts,
			  const int &LE, const int &RE, const int &C,
			  const int &debug);
void makeobsgenmkv2(dgrid &obsprobs, const dgrid &nullprobs, 
		    const igrid &data,
		    const dvector &mutmatch, dvector &mutnomatch,
		    const ivector &anchap, 
		    const int &C, const int &LE, const int &RE,
		    const int &debug);
void makeinitgenmkv2(dgrid &initstore, dvector &scratchvec,
		     const dvector &x, const double &tau, 
		     const double &p, 
		     const int &C, const int &LE, const int &RE,
		     const int &debug);
void maketransgenmkv2(dgrid &transstore, dvector &scratchvec, 
		      const dvector &x, 
		      const double &tau, const double &p,
		      const int &C, const int &LE, const int &RE,
		      const int &debug);
void maketransCgenmkv2(dgrid &transstoreC, dvector &scratchvec, 
		       const dvector &y, 
		       const double &tau, const double &p,
		       const int &C, const int &LE, const int &RE,
		       const int &debug);
void makealphagenmkv2(dgrid &alpha, const dgrid &initstore, 
		      const dgrid &transstore, const dgrid &transstoreC,
		      const dgrid &obsprobs, const dvectors &obsCnum,
		      const dvectors &obsCden, 
		      const int &C, const int &LE, const int &RE);
void makebetagenmkv2(dgrid &beta, const dgrid &initstore, 
		     const dgrid &transstore, const dgrid &transstoreC,
		     const dgrid &obsprobs, const dvectors &obsCnum,
		     const dvectors &obsCden, dvector &scratch,
		     const int &C, const int &LE, const int &RE);
void makenullCdengenmkv2(dvectors &nullCden, const igrid &data, 
			 const igrid &freqallele, const dgrid &freqfreq,
			 const dgrid &jointfreq2, 
			 const ivector &allelecounts,
			 const int &LE, const int &RE, const int &C,
			 const int &debug);
void makeobsCdengenmkv2(dvectors &obsCden, const dvectors &nullCden,
			const igrid &data,
			const dvector &mutmatch, dvector &mutnomatch,
			const ivector &anchap, 
			const int &C, const int &LE, const int &RE,
			const int &debug);
void makenullCnumgenmkv2(dvectors &nullCnum, const igrid &data,
			 const igrid &freqallele, const dgrid &freqfreq,
			 const dgrid &jointfreq2, 
                         const dgrid &jointfreq3mkv2,
			 const dgrid &jointfreq3fmkv2,
 			 const dgrid &jointfreq4mkv2,
			 const dgrid &jointfreq4fmkv2,
			 const ivector &allelecounts,
			 const int &LE, const int &RE, const int &C,
			 const int &debug);
void makeobsCnumgenmkv2(dvectors &obsCnum, const dvectors &nullCnum,
			const igrid &data,
			const dvector &mutmatch, dvector &mutnomatch,
			const ivector &anchap, 
			const int &C, const int &LE, const int &RE,
			const int &debug);
void makeloglikgenmkv2(dvector &loglikvec, const dgrid &alpha, 
		       const dgrid &initstore, const dgrid &obsprobs,
		       const int &C, const int &RE);
void makegammagenmkv2(dgrid &gamma, const dgrid &alpha, const dgrid &beta,
		      const int &C, const int &LE, const int &RE, 
		      const dvectors &gammaC);
void makecstargenmkv2(dvector &cstar, const dgrid &gamma, 
		      const int &C, const int &LE, const int &RE);
void makecstarmutgenmkv2(dvector &cstarmut, const dvector &cstar,
			 const dgrid &gamma,
			 const igrid &data, const ivector &anchap,
			 const dvector &mutmatch,
			 const int &C, const int &LE, const int &RE);
void makegammaC(dvectors &gammaC, const dgrid &alpha, const dgrid &beta,
		const dgrid &obsprobs, const dvectors &obsCnum,
		const dvectors &obsCden, const dgrid &initstore,
		const dgrid &transstore,
		const dgrid &transstoreC, const int &C, const int &LE,
		const int &RE);