#ifndef __FILE_EMM_H_SEEN__
#define __FILE_EMM_H_SEEN__

/*-----------------------------------------------------------------------------

Copyright (C) 2004, 2005, 2006, 2007.

A. Ronald Gallant
Post Office Box 659
Chapel Hill NC 27514-0659
USA   

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

-----------------------------------------------------------------------------*/

#include "libsnp.h"
#include "libsmm.h"
#include "emm_base.h"
#include "emmusr.h"
#include "snp.h"

namespace emm {
    
  class emmparms {
  private:
    std::vector<std::string> history;
    estblock est_blk;
    datblock dat_blk;
    modblock mod_blk;
    objblock obj_blk;
    scl::realmat rho;
    scl::intvec rho_mask;
    scl::realmat rho_increment;
    scl::realmat prop_scale;
    libsmm::prop_def prop_groups; 
    std::vector<std::string> usrparms;
    std::vector<std::string> mod_alvec;
    std::vector<std::string> obj_alvec;
    std::vector<std::string> grouptxt;
    std::vector<std::string> parmrhs;
    std::vector<std::string> scalerhs;
    std::vector<std::string> incrhs;
  public:
    emmparms() {}
    bool read_parms(const char* filename, std::ostream& detail);
    bool set_parms(const std::vector<std::string>& pf, std::ostream& detail);
    bool write_parms(std::string parmfile, std::string prefix, 
      INT_32BIT seed, const scl::realmat& rho_last, 
      const scl::realmat& rho_mode, const scl::realmat& sig) const;
    void set_estblock(const estblock& eb);
    void set_rho(const scl::realmat& r);
    const estblock& get_estblock() const {return est_blk;}
    const datblock& get_datblock() const {return dat_blk;}
    const modblock& get_modblock() const {return mod_blk;}
    const objblock& get_objblock() const {return obj_blk;}
    const std::vector<std::string> get_mod_alvec() const {return mod_alvec;}
    const std::vector<std::string> get_obj_alvec() const {return obj_alvec;}
    const scl::realmat& get_rho() const {return rho;}
    const scl::intvec& get_rho_mask() const {return rho_mask;}
    const scl::realmat& get_rho_increment() const {return rho_increment;}
    const scl::realmat& get_prop_scale() const {return prop_scale;}
    const libsmm::prop_def& get_prop_groups() const {return prop_groups;}
    const std::vector<std::string>& get_usrparms() const {return usrparms;}
  };
  
  class emm_objfun : public libsmm::objfun_base {
  private:
    snp::trnfrm tr;
    snp::snpll ll;
    scl::realmat V;
    INTEGER iter;
    REAL    toler;
    scl::realmat mutable mean_score;
    scl::realmat rho_infmat;
  public:
    emm_objfun (const scl::realmat& data, 
      INTEGER num_mod_parms, INTEGER num_mod_funcs,
      const std::vector<std::string>& mod_pfvec,
      const std::vector<std::string>& mod_alvec,
      const std::vector<std::string>& obj_pfvec,
      const std::vector<std::string>& obj_alvec, 
      std::ostream& detail);
    emm_objfun();
    emm_objfun(const emm_objfun& obj);
    ~emm_objfun() { }
    emm_objfun& operator=(const emm_objfun& obj);
    void set_data(const scl::realmat& data); 
    void set_iter(INTEGER itr) {iter = itr;}
    void set_toler(REAL tol) {toler = tol;}
    REAL operator()(const scl::realmat& rho, 
      const scl::realmat& sim, const scl::realmat& stats) const;
    bool write_diagnostics(const char* filename) const;
    libsmm::objfun_base* new_objfun();
    void delete_objfun(libsmm::objfun_base* objfun_ptr);
  };

  class mle_objfun : public libsmm::objfun_base {
  private:
    mutable usrmod_type model;
  public:
    mle_objfun
      (const scl::realmat& dat, INTEGER len_mod_parm, INTEGER len_mod_func,
       const std::vector<std::string>& mod_pfvec,
       const std::vector<std::string>& mod_alvec,
       const std::vector<std::string>& obj_pfvec,
       const std::vector<std::string>& obj_alvec, 
       std::ostream& detail);
    mle_objfun(const mle_objfun& obj);
    ~mle_objfun() { }
    mle_objfun& operator=(const mle_objfun& obj);
    void set_data(const scl::realmat& dat) { model.set_data(dat); }
    REAL operator()(const scl::realmat& rho, 
      const scl::realmat& sim, const scl::realmat& stats) const;
    bool write_diagnostics(const char* filename) const;
    libsmm::objfun_base* new_objfun();
    void delete_objfun(libsmm::objfun_base* objfun_ptr);
  };
}

#endif