/***************************************************************************
                          rosedb.cpp  -  description
                             -------------------
    begin                : Tue Nov 18 01:45:35 2003
    copyright            : (C) 1999-2006 by Cavalli Andrea
    author               : : cavalli $
    date                 : : 2003/12/09 11:10:33 $
    id                   : : coor.h,v 1.1.2.2 2003/12/09 11:10:33 cavalli Exp $
    email                : cavalli@bioc.unizh.ch amc82@cam.ac.uk
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include <rose/rosedb.h>

namespace Almost {

  ostream & operator<<(ostream & out, const RoseDBProtein & p){
    int s = p.sequ.size();
    out<<s<<"\n";
    out<<p.name<<"\n";
    //  out<<sequ<<"\n";
    //  out<<ss<<"\n";
    for(int i=0;i<s;i++){
      out<<i+1<<"\t"
	 <<p.sequ[i]<<"\t"
	 <<p.ss[i]<<"\t"
	 <<p.ha[i]<<"\t"
	 <<p.h[i]<<"\t"
	 <<p.n[i]<<"\t"
	 <<p.ca[i]<<"\t"
	 <<p.cb[i]<<"\t"
	 <<p.c[i]<<"\t"
	 <<p.phi[i]<<"\t"
	 <<p.psi[i]<<"\t"
	 <<p.omega[i]<<"\n";
    }
    for(int i=0;i<s;i++){
      out<<i+1<<"\t";
      for(int aa=0;aa<20;aa++)
	out<<p.psi_blast[i][aa]<<"\t";
      out<<"\n";
    }
    return out;
  }

  istream & operator>>(istream & in, RoseDBProtein &p){
    int s;
    in>>s;
    p.resize(s);
    in>>p.name;
    for(int i=0;i<s;i++){
      int aa;
      char c;
      double d;
      in >> aa;
      in >> c; p.sequ[i] = c;
      in >> c; p.ss[i] = c;
      in >> d; p.ha[i] = d;
      in >> d; p.h[i]  = d;
      in >> d; p.n[i]  = d;
      in >> d; p.ca[i] = d;
      in >> d; p.cb[i] = d;
      in >> d; p.c[i]  = d;
      in >> d; p.phi[i] = d;
      in >> d; p.psi[i] = d;
      in >> d; p.omega[i] = d;
    }
    for(int i=0;i<s;i++){
      int q;
      in >> q;
      for(int aa=0;aa<20;aa++){
	double d;
	in >> d; p.psi_blast[i][aa] = d;
      }
    }
    return in;
  }


  void rose_db_protein_from_files(string mrg,
				  string prf,
				  RoseDBProtein & p
				  ){
    ifstream mrg_in, prf_in;
    mrg_in.open(mrg.c_str());
    vector<ResidueData>  res_data;
    {
      string name = mrg;
      istream_iterator<string> iter(mrg_in),end;
      int pos = name.rfind("/");
      string n;
      if(pos==string::npos) n = name;
      else n = string(name.begin()+pos+1,name.end());

      while(iter!=end){
	ResidueData rd;
	strcpy(rd.prot, n.c_str());
	rd.num = atoi((*iter).c_str()); ++iter;
	rd.name = (*iter)[0]; ++iter;
	rd.phi = atof((*iter).c_str()); ++iter;
	rd.psi = atof((*iter).c_str()); ++iter;
	rd.ome = atof((*iter).c_str()); ++iter;
	rd.ha = atof((*iter).c_str()); ++iter;
	rd.h = atof((*iter).c_str()); ++iter;
	rd.n = atof((*iter).c_str()); ++iter;
	rd.ca = atof((*iter).c_str()); ++iter;
	rd.cb = atof((*iter).c_str()); ++iter;
	rd.c = atof((*iter).c_str()); ++iter;
	rd.ss = (*iter)[0]; ++iter;
	res_data.push_back(rd);
      }  
    }

    vector<vector<double> > matx;
    {
      Utils::read_mtx(prf,matx);
    }

    //Merge data in p;
    p.resize(res_data.size());
    p.name = res_data[0].prot;
    for(int aa=0;aa<res_data.size();aa++){
      p.sequ[aa] = res_data[aa].name;
      p.ss[aa] = res_data[aa].ss;

      p.ha[aa] = res_data[aa].ha;
      p.h[aa]  = res_data[aa].h;
      p.n[aa]  = res_data[aa].n;
      p.ca[aa] = res_data[aa].ca;
      p.cb[aa] = res_data[aa].cb;
      p.c[aa]  = res_data[aa].c;

      p.phi[aa] = res_data[aa].phi;
      p.psi[aa] = res_data[aa].psi;
      p.omega[aa] = res_data[aa].ome;
      p.psi_blast[aa] =  matx[aa];
    }
  }


}
// Local Variables:
// mode:C++
// End: