/***************************************************************************
                          select.cpp  -  description
                             -------------------
    begin                : Thu Jul  3 01:42:38 2003
    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 <almost.h>
#include <select.h>
#include <molecules/molecules.h>
#include <alm_fnmatch.h>

Almost::NameSelection::NameSelection(const Molecules & molecules, 
				     string regexp){
  molecules_ =  &molecules;

  if(regexp.find("%T")==0){
    //do type pattern
    regexp =string(regexp.begin()+2,regexp.end());
    for(int i=0;i<molecules.atom_size();++i){
      string atom = molecules[i].type_name();
      if(alm_fnmatch(regexp.c_str(),atom.c_str(),ALM_FNM_EXTMATCH)==0){
	result_.insert(i);
      }
    }
  }
  else {
    //parse regexp
    string seg;
    string frag;
    string at;

    int pos = regexp.find("/");
    if(pos==string::npos){
      cout<<"ERROR: wrong regexp"<<endl;
      return;
    }
      
    seg = string(regexp.begin(),regexp.begin()+pos);
    regexp = string(regexp.begin()+pos+1,regexp.end());

    pos = regexp.find("/");
    if(pos==string::npos){
      cout<<"ERROR: wrong regexp"<<endl;
      return;
    }

    seg = string(regexp.begin(),regexp.begin()+pos);
    regexp = string(regexp.begin()+pos+1,regexp.end());
    pos = regexp.find("/");
    if(pos==string::npos){
      cout<<"ERROR: wrong regexp"<<endl;
      return;
    }
    frag = string(regexp.begin(),regexp.begin()+pos);
    regexp = string(regexp.begin()+pos+1,regexp.end());


    at = regexp;


    //simple parse
    if(seg=="") seg="*";
    if(frag=="") frag="*";
    if(at=="") at="*";

    regexp = "/"+seg+"/"+frag+"/"+at;
      
    for(int i=0;i<molecules.atom_size();++i){
      string atom = molecules.atom_name(i,Molecules::BASE);
      if(alm_fnmatch(regexp.c_str(),atom.c_str(),ALM_FNM_EXTMATCH)==0){
	result_.insert(i);
      }
    }
  }
}


Almost::NameSelection::NameSelection(const Molecules & molecules, 
				     int from, int to){
  molecules_ =  &molecules;
  int beg = max((int)1,from);
  beg = beg -1;
  int end = min((int)to,molecules.fragment_size());
  for(int i=beg;i<end;i++){
    vector<int> a = molecules.fragment_atoms(i);
    for(int q=0;q<a.size();q++) result_.insert(a[q]);
  }
}

void Almost::remove_atoms(Molecules & molecules, NameSelection & ns){
  set<int>::iterator iter = ns.result().begin(), 
    end = ns.result().end();
  int nrem = 0;
  while(iter!=end){
    molecules.remove_atom(*iter-nrem);
    ++iter; ++nrem;
  }
}