/***************************************************************************
                          pdbsegment.cpp  -  description
                             -------------------
    begin                : Sun Jun  2 22:47:19 2002
    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 <pdb/pdbsegment.h>

using namespace Almost;

PDBSegment::PDBSegment(const PDBSegment & segment){
  _name = segment._name;
  _chainID = segment._chainID;
  for(size_t i=0;i<segment.fragment.size();i++)
    fragment.push_back(new PDBFragment(segment[i]));
}

PDBSegment PDBSegment::sub(int b,int e){
  PDBSegment res;
  if((b<1)||(e>fragment.size())) { 
    cout<<"\t>> Wrong PDBSegment boudarries\n";
    return res;
  }
  
  for(int i=b-1;i<e;i++){
    res.fragment.push_back(new PDBFragment(*fragment[i]));
  }
  return res;
}


void PDBSegment::fix_numbering(){
  if(size()==0) return;
  //Check dup
  set<int> tags;
  bool dup = false;
  for(int i=0; i<size();i++){
    if(tags.find(fragment[i]->fragSeq())!=tags.end()){
      dup = true; break;
    }
    else tags.insert(fragment[i]->fragSeq());
  }
  if(!dup) return;
  int b =  fragment[0]->fragSeq();

  if(size()==1) return;
  int msg = 0;
  for(int i=1; i<size();i++){
    if(fragment[i]->fragSeq()!=i+b){
      if(msg<5){
	cout<<"Warning renumbering fragment "<<fragment[i]->fragSeq()<<" to "
	    <<i+b<<"\n";
	++msg;
      }
      else if(msg==5){
	cout<<"Warning suppressed.\n";++msg;
      }
      fragment[i]->set_fragSeq(b+i);
    }
  }

}

void swap__frag(PDBFragment & frag, string a1, string a2){
  int ipos=-1,jpos=-1;
  for(int i=0;i<frag.size();i++){
    if(frag[i].name== a1)
      ipos = i;
    else if(frag[i].name== a2)
      jpos = i;
  }

  if((ipos>-1)&&(jpos>-1)){
    string t = frag[ipos].name;
    frag[ipos].name = frag[jpos].name;
    frag[jpos].name = t;
  }
}




void PDBSegment::swap_atom(string r1, string a1, string a2){
  bool num = false;
  PDBSegment & seg = *this;
  if(r1.find("_")!=string::npos)
    num = 1;
  for(int i=0;i<seg.size();i++){
    if(!num){
      if((seg[i].name()==r1)||(r1=="*")){
	swap__frag(seg[i],a1,a2);
      }
    }
    else {
      if((seg[i].name(PDBFragment::LONG)==r1)||(r1=="*")){
	swap__frag(seg[i],a1,a2);
      }
    }
  }
}


vector<string> PDBSegment::sequence(int TYPE) const {
  vector<string> sVect;
  if(TYPE==LONG){
    for(int i=0;i<fragment.size();i++){
      char buff[16];
      sprintf(buff,"%s_%i",fragment[i]->name().c_str(),
	      fragment[i]->fragSeq());
      sVect.push_back(buff);
    }
  }
  else if(TYPE==ICODE){
    for(int i=0;i<fragment.size();i++){
      char buff[16];
      sprintf(buff,"%s_%i",fragment[i]->name().c_str(),
	      fragment[i]->fragSeq());
      string b = buff;
      if(fragment[i]->iCode()!=' ') b += fragment[i]->iCode();
      sVect.push_back(b);
    }
  }
  else {
    for(int i=0;i<fragment.size();i++)
      sVect.push_back(fragment[i]->name());
  }
  
  return sVect;
}