/***************************************************************************
                          bmbr_mod.cpp  -  description
                             -------------------
    begin                : Thu Nov 23 15:06:49 2006
    copyright            : (C) 2002 by Cavalli Andrea
    email                : cavalli@bioc.unizh.ch
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   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 <zeta/module.h>
#include <zeta/class.h>
#include <zeta/zextclass.h>
#include <zeta/zobj.hpp>
#include <iterator>
#include <pdb.h>
using namespace Almost;
using namespace std;

class BMBR {
  int data_set;
  map<pair<string,int> , map<string,double> > data;

  bool cs_reference;
  bool cs_list;
public:
  BMBR(string file, string pdbfile){
    ifstream in; in.open(file.c_str());
    if(!in){
      string err = "File not found: "+file;
      throw err.c_str();
    }
    cs_reference = false;
    cs_list = false;
    parse(in);


    //Dump data
    map<int,string> seq;
    map<int,double> ha;
    map<int,double> h;
    map<int,double> n;
    map<int,double> ca;
    map<int,double> cb;
    map<int,double> c;

    map<pair<string,int> , map<string,double> >::iterator iter = data.begin(),
      end = data.end();
    while(iter!=end){
      int aa = iter->first.second;
      seq[aa] = iter->first.first;
      map<string,double>::iterator i1 = iter->second.begin(),
	e1 =  iter->second.end();
      while(i1!=e1){
	if(i1->first=="HA"||i1->first=="HA2")
	  ha[aa] = i1->second;
	if(i1->first=="H")
	  h[aa] = i1->second;
	if(i1->first=="N")
	  n[aa] = i1->second;
	if(i1->first=="CA")
	  ca[aa] = i1->second;
	if(i1->first=="CB")
	  cb[aa] = i1->second;
	if(i1->first=="C")
	  c[aa] = i1->second;
	++i1;
      }
      ++iter;
    }

    PDB pdb(pdbfile);
    vector<string> pdbseq = pdb[0][0].sequence(PDBSegment::ICODE);
    for(int i=0;i<pdbseq.size();i++) cout<<pdbseq[i]<<" ";
    cout<<endl;

    map<string,vector<double> > data;
    
    map<int,string>::iterator i1 = seq.begin(),e1 = seq.end();
    while(i1!=e1){
      char buff[256];
      int aa = i1->first;
      sprintf(buff,"%s_%i",
	      i1->second.c_str(),
	      i1->first);
      data[buff].push_back(ha[aa]);
      data[buff].push_back(h[aa]);
      data[buff].push_back(n[aa]);
      data[buff].push_back(ca[aa]);
      data[buff].push_back(cb[aa]);
      data[buff].push_back(c[aa]);;
      cerr<<i1->first<<" "
	  <<i1->second<<" "
	  <<ha[aa]<<" "
	  <<h[aa]<<" "
	  <<n[aa]<<" "
	  <<ca[aa]<<" "
	  <<cb[aa]<<" "
	  <<c[aa]<<" "
	  <<"\n";
      ++i1;
    }

    for(int i=0;i<pdbseq.size();i++){
      if(data.find(pdbseq[i])!=data.end())
	cout<<pdbseq[i]<<" "
	    <<data[pdbseq[i]][0]<<" "
	    <<data[pdbseq[i]][1]<<" "
	    <<data[pdbseq[i]][2]<<" "
	    <<data[pdbseq[i]][3]<<" "
	    <<data[pdbseq[i]][4]<<" "
	    <<data[pdbseq[i]][5]<<" "
	    <<endl;
      else 
	cout<<pdbseq[i]<<" "
	    <<0<<" "
	    <<0<<" "
	    <<0<<" "
	    <<0<<" "
	    <<0<<" "
	    <<0<<"\n";
    }
  }

private:
  void parse(ifstream & in){
    istream_iterator<string> iter(in),end;
    string tok;
    tok = *iter; ++iter;

    if(string(tok.begin(),tok.begin()+4)=="data"){
      data_set = atoi(string(tok.begin()+5,tok.end()).c_str());
      cerr<<"DEBUG data "<<data_set<<endl;
    }


    while(iter!=end){
      tok = *iter; ++iter;
      //Start with save_ stop with save
      while(string(tok.begin(),tok.begin()+5)!="save_"){
	++iter; tok = *iter;
      }
      process_frame(in,tok);
      ++iter;
    }
  }

  void process_frame(ifstream & in,string tok){
    cerr<<"DEBUG frame: "<<tok<<endl;

    if(tok=="save_entry_information"){     
      process_save_entry_information(in);
      return;
    }

    else if(tok=="save_chemical_shift_referencing"||
	    tok=="save_chemical_shift_reference"
	    ){
      process_chemical_shift_referencing(in);
    }
    else if(string(tok.begin(),tok.begin()+20)=="save_chem_shift_list"||
	    string(tok.begin(),tok.begin()+24)=="save_chemical_shift_list"||
	    string(tok.begin(),tok.begin()+23)=="save_chemical_shift_set"||
	    string(tok.begin(),tok.begin()+28)=="save_assigned_chemical_shift"
	    ){
      process_save_chem_shift_list(in);
      return;
    }



    in>>tok;
    while(tok!="save_") in>>tok;
    cerr<<"DEBUG end  : "<<tok<<endl;
  }

  void process_chemical_shift_referencing(ifstream & in){
    cerr<<"DEBUG process_chemical_shift_referencing"<<endl;
    string tok;
    in >> tok;
    in >> tok;

    in >> tok;
    if(tok!="loop_"){
      cerr<<"ERROR in chemical_shift_referencing frame"<<endl;
      exit(1);
    }
    vector<string> entry;
    in >> tok;

    while(tok[0]=='_'){
      entry.push_back(tok);
      in>>tok;
    }
    int count = 0;
    while(tok!="stop_"){
      cerr<<entry[count%entry.size()]<<" "<<tok<<endl;
      in >> tok;
      if(tok[0]=='\"'){
	string t;
	in >> t;
	tok +=" "+t;
	while(tok[tok.size()-1]!='\"'){
	  in >> t;
	  tok +=" "+t;
	}
      }
      ++count;
    }
    cs_reference = true;
  }

  void process_save_chem_shift_list(ifstream & in){
    cerr<<"DEBUG process_save_chem_shift_list\n";
    string tok;
    in >> tok;
    in >> tok;

    in >> tok;
    bool extra_loop = false;
    if(tok=="loop_"){
      in >> tok;
      if(tok=="_Experiment_label") extra_loop = true;
      while(tok!="stop_") in >> tok;
    }
    else {
      cerr<<"Unexpected token"<<endl;
      exit(1);
    }

    if(extra_loop){
      in >> tok;
      while(tok!="stop_") in >> tok;

    }

    in >> tok;
    while(tok!="loop_") in >> tok;

    if(tok=="loop_"){
      int count = 0;
      vector<string> content;
      in>>tok;
      while(tok[0]=='_'){
	++count;
	content.push_back(tok);
	in>>tok;
      }

      //Now lines
      vector<string> lines;
      lines.push_back(tok);
      
      in>>tok;
      while(tok!="stop_"){
	lines.push_back(tok);
	in >> tok;
      }

      pair<string,int> current;
      string atom;
      double shift;

      for(int i=0;i<lines.size();i++){
	if(content[i%count]=="_Residue_seq_code"){
	  current.second = atoi(lines[i].c_str());
	}

	if(content[i%count]=="_Residue_label"){
	  current.first = lines[i];
	}

	if(content[i%count]=="_Atom_name"){
	  atom = lines[i];
	}

	if(content[i%count]=="_Chem_shift_value"){
	  shift = atof(lines[i].c_str());
	}

	if((i+1)%count == 0){
	  data[current][atom] = shift;
	}
      }
      cs_list = true;      
      in>>tok;
    }
  }

  void process_save_entry_information(ifstream &in){
    cerr<<"DEBUG process_save_entry_information"<<endl;
    string tok;
    in>>tok;
    while(tok!="save_"){
      cerr<<tok<<endl;
      in>>tok;
    }
  }
};


inline string to_string(const BMBR & p){
  return "<bmbr>";
}
extern "C" {
  void init_bmbr(){
    //declarations here

    Module mod = Module("bmbr","Parse BMRB files (incomplete));

    Class<BMBR,ArgList2<string,string> >(mod.self(),"bmbr")
      ;

  }
}