/*********************************
tercpp: an open-source Translation Edit Rate (TER) scorer tool for Machine Translation.

Copyright 2010-2013, Christophe Servan, LIUM, University of Le Mans, France
Contact: christophe.servan@lium.univ-lemans.fr

The tercpp tool and library are free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 2.1 of the licence, or
(at your option) any later version.

This program and library are 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 Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
**********************************/
//
// C++ Implementation: tercalc
//
// Description:
//
//
// Author:  <>, (C) 2010
//
// Copyright: See COPYING file that comes with this distribution
//
//
#include "tercalc.h"
using namespace std;
using namespace TERCPPNS_Tools;
namespace TERCPPNS_TERCpp
{

terCalc::terCalc()
{
  TAILLE_PERMUT_MAX = 10;
  NBR_PERMUT_MAX = 10;
  infinite = 99999.0;
  shift_cost = 1.0;
  insert_cost = 1.0;
  delete_cost = 1.0;
  substitute_cost = 1.0;
  match_cost = 0.0;
  NBR_SEGS_EVALUATED = 0;
  NBR_PERMUTS_CONSID = 0;
  NBR_BS_APPELS = 0;
  TAILLE_BEAM = 10;
  DIST_MAX_PERMUT = 25;
  PRINT_DEBUG = false;
  hypSpans.clear();
  refSpans.clear();
  CALL_TER_ALIGN=0;
  CALL_CALC_PERMUT=0;
  CALL_FIND_BSHIFT=0;
  MAX_LENGTH_SENTENCE=10;
  S = new vector < vector < double > >(MAX_LENGTH_SENTENCE, std::vector<double>(MAX_LENGTH_SENTENCE,0.0));
  P = new vector < vector < char > >(MAX_LENGTH_SENTENCE, std::vector<char>(MAX_LENGTH_SENTENCE,' '));
}

terCalc::~terCalc()
{
  delete(S);
  delete(P);
}


terAlignment terCalc::WERCalculation ( vector< string >& hyp , vector< string >& ref )
{

  return minimizeDistanceEdition ( hyp, ref, hypSpans );

}

terAlignment terCalc::TER ( vector< int >& hyp, vector< int >& ref )
{
  stringstream s;
  s.str ( "" );
  string stringRef ( "" );
  string stringHyp ( "" );
  for ( vector<int>::iterator l_it = ref.begin(); l_it != ref.end(); l_it++ ) {
    if ( l_it == ref.begin() ) {
      s << ( *l_it );
    } else {
      s << " " << ( *l_it );
    }
  }
  stringRef = s.str();
  s.str ( "" );
  for ( vector<int>::iterator l_itHyp = hyp.begin(); l_itHyp != hyp.end(); l_itHyp++ ) {
    if ( l_itHyp == hyp.begin() ) {
      s << ( *l_itHyp );
    } else {
      s << " " << ( *l_itHyp );
    }
  }
  stringHyp = s.str();
  s.str ( "" );
  vector<string> l_vref=stringToVector ( stringRef , " " );
  vector<string> l_vhyp=stringToVector ( stringHyp , " " );
  return TER ( l_vhyp , l_vref);
}


hashMapInfos terCalc::createConcordMots ( vector< string >& hyp, vector< string >& ref )
{
  hashMap tempHash;
  hashMapInfos retour;
  for ( int i = 0; i < ( int ) hyp.size(); i++ ) {
    tempHash.addHasher ( hyp.at ( i ), "" );
  }
  bool cor[ref.size() ];
  for ( int i = 0; i < ( int ) ref.size(); i++ ) {
    if ( tempHash.trouve ( ( string ) ref.at ( i ) ) ) {
      cor[i] = true;
    } else {
      cor[i] = false;
    }
  }
  for ( int start = 0; start < ( int ) ref.size(); start++ ) {
    if ( cor[start] ) {
      for ( int end = start; ( ( end < ( int ) ref.size() ) && ( end - start <= TAILLE_PERMUT_MAX ) && ( cor[end] ) ); end++ ) {
        vector<string> ajouter = subVector ( ref, start, end + 1 );
        string ajouterString = vectorToString ( ajouter );
        vector<int> values = retour.getValue ( ajouterString );
        values.push_back ( start );
        if ( values.size() > 1 ) {
          retour.setValue ( ajouterString, values );
        } else {
          retour.addValue ( ajouterString, values );
        }
      }
    }
  }
  return retour;
}

bool terCalc::trouverIntersection ( vecInt& refSpan, vecInt& hypSpan )
{
  if ( ( refSpan.at ( 1 ) >= hypSpan.at ( 0 ) ) && ( refSpan.at ( 0 ) <= hypSpan.at ( 1 ) ) ) {
    return true;
  }
  return false;
}


terAlignment terCalc::minimizeDistanceEdition ( vector< string >& hyp, vector< string >& ref, vector< vecInt >& curHypSpans )
{
  double current_best = infinite;
  double last_best = infinite;
  int first_good = 0;
  int current_first_good = 0;
  int last_good = -1;
  int cur_last_good = 0;
  int last_peak = 0;
  int cur_last_peak = 0;
  int i=0;
  int j=0;
  int ref_size=0 ;
  ref_size=( int ) ref.size();
  int hyp_size=0;
  hyp_size=( int ) hyp.size();
  double cost, icost, dcost;
  double score;
  delete(S);
  delete(P);
  S = new vector < vector < double > >(ref_size+1, std::vector<double>(hyp_size+1,-1.0));
  P = new vector < vector < char > >(ref_size+1, std::vector<char>(hyp_size+1,'0'));



  NBR_BS_APPELS++;
// 	cerr << "Appels : " << NBR_BS_APPELS << endl;

//         for ( i = 0; i <= ref_size; i++ )
//         {
//             for ( j = 0; j <= hyp_size; j++ )
//             {
//                 S->at(i).at(j) = -1.0;
//                 P->at(i).at(j) = '0';
//             }
//         }
  S->at(0).at(0) = 0.0;
  for ( j = 0; j <= hyp_size; j++ ) {
    last_best = current_best;
    current_best = infinite;
    first_good = current_first_good;
    current_first_good = -1;
    last_good = cur_last_good;
    cur_last_good = -1;
    last_peak = cur_last_peak;
    cur_last_peak = 0;
    for ( i = first_good; i <= ref_size; i++ ) {
      if ( i > last_good ) {
        break;
      }
      if ( S->at(i).at(j) < 0 ) {
        continue;
      }
      score = S->at(i).at(j);
      if ( ( j < hyp_size ) && ( score > last_best + TAILLE_BEAM ) ) {
        continue;
      }
      if ( current_first_good == -1 ) {
        current_first_good = i ;
      }
      if ( ( i < ref_size ) && ( j < hyp_size ) ) {
        if ( ( int ) refSpans.size() ==  0 || ( int ) hypSpans.size() ==  0 || trouverIntersection ( refSpans.at ( i ), curHypSpans.at ( j ) ) ) {
          if ( ( int ) ( ref.at ( i ).compare ( hyp.at ( j ) ) ) == 0 ) {
            cost = match_cost + score;
            if ( ( S->at(i+1).at(j+1) == -1 ) || ( cost < S->at(i+1).at(j+1) ) ) {
              S->at(i+1).at(j+1) = cost;
              P->at(i+1).at(j+1) = 'A';
            }
            if ( cost < current_best ) {
              current_best = cost;
            }
            if ( current_best == cost ) {
              cur_last_peak = i + 1;
            }
          } else {
            cost = substitute_cost + score;
            if ( ( S->at(i+1).at(j+1) < 0 ) || ( cost < S->at(i+1).at(j+1) ) ) {
              S->at(i+1).at(j+1) = cost;
              P->at(i+1).at(j+1) = 'S';
              if ( cost < current_best ) {
                current_best = cost;
              }
              if ( current_best == cost ) {
                cur_last_peak = i + 1 ;
              }
            }
          }
        }
      }
      cur_last_good = i + 1;
      if ( j < hyp_size ) {
        icost = score + insert_cost;
        if ( ( S->at(i).at(j+1) < 0 ) || ( S->at(i).at(j+1) > icost ) ) {
          S->at(i).at(j+1) = icost;
          P->at(i).at(j+1) = 'I';
          if ( ( cur_last_peak <  i ) && ( current_best ==  icost ) ) {
            cur_last_peak = i;
          }
        }
      }
      if ( i < ref_size ) {
        dcost =  score + delete_cost;
        if ( ( S->at(i+1).at(j) < 0.0 ) || ( S->at(i+1).at(j) > dcost ) ) {
          S->at(i+1).at(j) = dcost;
          P->at(i+1).at(j) = 'D';
          if ( i >= last_good ) {
            last_good = i + 1 ;
          }
        }
      }
    }
  }


  int tracelength = 0;
  i = ref.size();
  j = hyp.size();
  while ( ( i > 0 ) || ( j > 0 ) ) {
    tracelength++;
    if ( P->at(i).at(j) == 'A' ) {
      i--;
      j--;
    } else if ( P->at(i).at(j) == 'S' ) {
      i--;
      j--;
    } else if ( P->at(i).at(j) == 'D' ) {
      i--;
    } else if ( P->at(i).at(j) == 'I' ) {
      j--;
    } else {
      cerr << "ERROR : terCalc::minimizeDistanceEdition : Invalid path : " << P->at(i).at(j) << endl;
      exit ( -1 );
    }
  }
  vector<char> path ( tracelength );
  i = ref.size();
  j = hyp.size();
  while ( ( i > 0 ) || ( j > 0 ) ) {
    path[--tracelength] = P->at(i).at(j);
    if ( P->at(i).at(j) == 'A' ) {
      i--;
      j--;
    } else if ( P->at(i).at(j) == 'S' ) {
      i--;
      j--;
    } else if ( P->at(i).at(j) == 'D' ) {
      i--;
    } else if ( P->at(i).at(j) == 'I' ) {
      j--;
    }
  }
  terAlignment to_return;
  to_return.numWords = ref_size;
  to_return.alignment = path;
  to_return.numEdits = S->at(ref_size).at(hyp_size);
  to_return.hyp = hyp;
  to_return.ref = ref;
  to_return.averageWords = ref_size;
  if ( PRINT_DEBUG ) {
    cerr << "BEGIN DEBUG : terCalc::minimizeDistanceEdition : to_return :" << endl << to_return.toString() << endl << "END DEBUG" << endl;
  }
  return to_return;

}
void terCalc::minimizeDistanceEdition ( vector< string >& hyp, vector< string >& ref, vector< vecInt >& curHypSpans, terAlignment* to_return )
{
  double current_best = infinite;
  double last_best = infinite;
  int first_good = 0;
  int current_first_good = 0;
  int last_good = -1;
  int cur_last_good = 0;
  int last_peak = 0;
  int cur_last_peak = 0;
  int i=0;
  int j=0;
  int ref_size=0 ;
  ref_size=( int ) ref.size();
  int hyp_size=0;
  hyp_size=( int ) hyp.size();
  double cost, icost, dcost;
  double score;
  delete(S);
  delete(P);
  S = new vector < vector < double > >(ref_size+1, std::vector<double>(hyp_size+1,-1.0));
  P = new vector < vector < char > >(ref_size+1, std::vector<char>(hyp_size+1,'0'));

  NBR_BS_APPELS++;
// 	cerr << "Appels : " << NBR_BS_APPELS << endl;

//         for ( i = 0; i <= ref_size; i++ )
//         {
//             for ( j = 0; j <= hyp_size; j++ )
//             {
//                S->at(i).at(j) = -1.0;
//                P->at(i).at(j) = '0';
//             }
//         }
  S->at(0).at(0) = 0.0;
  for ( j = 0; j <= hyp_size; j++ ) {
    last_best = current_best;
    current_best = infinite;
    first_good = current_first_good;
    current_first_good = -1;
    last_good = cur_last_good;
    cur_last_good = -1;
    last_peak = cur_last_peak;
    cur_last_peak = 0;
    for ( i = first_good; i <= ref_size; i++ ) {
      if ( i > last_good ) {
        break;
      }
      if (S->at(i).at(j) < 0 ) {
        continue;
      }
      score = S->at(i).at(j);
      if ( ( j < hyp_size ) && ( score > last_best + TAILLE_BEAM ) ) {
        continue;
      }
      if ( current_first_good == -1 ) {
        current_first_good = i ;
      }
      if ( ( i < ref_size ) && ( j < hyp_size ) ) {
        if ( ( int ) refSpans.size() ==  0 || ( int ) hypSpans.size() ==  0 || trouverIntersection ( refSpans.at ( i ), curHypSpans.at ( j ) ) ) {
          if ( ( int ) ( ref.at ( i ).compare ( hyp.at ( j ) ) ) == 0 ) {
            cost = match_cost + score;
            if ( ( S->at(i+1).at(j+1) == -1 ) || ( cost < S->at(i+1).at(j+1) ) ) {
              S->at(i+1).at(j+1) = cost;
              P->at(i+1).at(j+1) = 'A';
            }
            if ( cost < current_best ) {
              current_best = cost;
            }
            if ( current_best == cost ) {
              cur_last_peak = i + 1;
            }
          } else {
            cost = substitute_cost + score;
            if ( ( S->at(i+1).at(j+1) < 0 ) || ( cost < S->at(i+1).at(j+1) ) ) {
              S->at(i+1).at(j+1) = cost;
              P->at(i+1).at(j+1) = 'S';
              if ( cost < current_best ) {
                current_best = cost;
              }
              if ( current_best == cost ) {
                cur_last_peak = i + 1 ;
              }
            }
          }
        }
      }
      cur_last_good = i + 1;
      if ( j < hyp_size ) {
        icost = score + insert_cost;
        if ( ( S->at(i).at(j+1) < 0 ) || ( S->at(i).at(j+1) > icost ) ) {
          S->at(i).at(j+1) = icost;
          P->at(i).at(j+1) = 'I';
          if ( ( cur_last_peak <  i ) && ( current_best ==  icost ) ) {
            cur_last_peak = i;
          }
        }
      }
      if ( i < ref_size ) {
        dcost =  score + delete_cost;
        if ( ( S->at(i+1).at(j) < 0.0 ) || ( S->at(i+1).at(j) > dcost ) ) {
          S->at(i+1).at(j) = dcost;
          P->at(i+1).at(j) = 'D';
          if ( i >= last_good ) {
            last_good = i + 1 ;
          }
        }
      }
    }
  }


  int tracelength = 0;
  i = ref_size;;
  j = hyp_size;
  while ( ( i > 0 ) || ( j > 0 ) ) {
    tracelength++;
    if (P->at(i).at(j) == 'A' ) {
      i--;
      j--;
    } else if (P->at(i).at(j) == 'S' ) {
      i--;
      j--;
    } else if (P->at(i).at(j) == 'D' ) {
      i--;
    } else if (P->at(i).at(j) == 'I' ) {
      j--;
    } else {
      cerr << "ERROR : terCalc::minimizeDistanceEdition : Invalid path : " <<P->at(i).at(j) << endl;
      exit ( -1 );
    }
  }
  vector<char> path ( tracelength );
  i = ref_size;
  j = hyp_size;
  while ( ( i > 0 ) || ( j > 0 ) ) {
    path[--tracelength] =P->at(i).at(j);
    if (P->at(i).at(j) == 'A' ) {
      i--;
      j--;
    } else if (P->at(i).at(j) == 'S' ) {
      i--;
      j--;
    } else if (P->at(i).at(j) == 'D' ) {
      i--;
    } else if (P->at(i).at(j) == 'I' ) {
      j--;
    }
  }
//         terAlignment to_return;
  to_return->numWords = ref_size;
  to_return->alignment = path;
  to_return->numEdits = S->at(ref_size).at(hyp_size);
  to_return->hyp = hyp;
  to_return->ref = ref;
  to_return->averageWords = ref_size;
  if ( PRINT_DEBUG ) {
    cerr << "BEGIN DEBUG : terCalc::minimizeDistanceEdition : to_return :" << endl << to_return->toString() << endl << "END DEBUG" << endl;
  }
//         return to_return;

}


terAlignment terCalc::TER ( vector<string>& hyp, vector<string>& ref )
{
  hashMapInfos rloc = createConcordMots ( hyp, ref );
  terAlignment cur_align = minimizeDistanceEdition ( hyp, ref, hypSpans );
  vector<string> cur = hyp;
  cur_align.hyp = hyp;
  cur_align.ref = ref;
  cur_align.aftershift = hyp;
  double edits = 0;
//         int numshifts = 0;

  vector<terShift> * allshifts=new vector<terShift>(0);
  bestShiftStruct * returns=new bestShiftStruct();

//     cerr << "Initial Alignment:" << endl << cur_align.toString() <<endl;
  if ( PRINT_DEBUG ) {
    cerr << "BEGIN DEBUG : terCalc::TER : cur_align :" << endl << cur_align.toString() << endl << "END DEBUG" << endl;
  }
  while ( true ) {

    returns=findBestShift ( cur, hyp, ref, rloc, cur_align );
//             cerr << "****************************************************************** " <<  returns->getEmpty() << endl;
    if ( returns->getEmpty()) {
      break;
    }
    terShift bestShift = (*(returns->m_best_shift));
    cur_align = (*(returns->m_best_align));
    edits += bestShift.cost;
    bestShift.alignment = cur_align.alignment;
    bestShift.aftershift = cur_align.aftershift;
    allshifts->push_back ( bestShift );
    cur = cur_align.aftershift;
    delete(returns);
  }
  if ( PRINT_DEBUG ) {
    cerr << "BEGIN DEBUG : terCalc::TER : Final to return :" << endl << cur_align.toString() << endl << "END DEBUG" << endl;
  }
  terAlignment to_return;
  to_return = cur_align;
  to_return.allshifts = (*(allshifts));
  to_return.numEdits += edits;
  NBR_SEGS_EVALUATED++;
  return to_return;
}
bestShiftStruct * terCalc::findBestShift ( vector<string>& cur, vector<string>& hyp, vector<string>& ref, hashMapInfos& rloc, terAlignment& med_align )
{
  CALL_FIND_BSHIFT++;
// 	cerr << "CALL_FIND_BSHIFT " << CALL_FIND_BSHIFT <<endl;
//        to_return->m_empty = new bool(false);
  bool anygain = false;
  vector <bool> * herr = new vector<bool>(( int ) hyp.size() + 1 );
  vector <bool> * rerr = new vector<bool>( ( int ) ref.size() + 1 );
  vector <int> * ralign = new vector<int>( ( int ) ref.size() + 1 );
  int l_i,i,j,s;
  for (i = 0 ; i< ( int ) hyp.size() + 1 ; i++) {
    herr->at(i)=false;
  }
  for (i = 0 ; i< ( int ) ref.size() + 1 ; i++) {
    rerr->at(i)=false;
    ralign->at(i)=-1;
  }
  calculateTerAlignment ( med_align, herr, rerr, ralign );
  vector<vecTerShift> * poss_shifts = new vector< vector<terShift> >(0) ;
  terAlignment * cur_best_align = new terAlignment();
  terShift * cur_best_shift = new terShift();
  double cur_best_shift_cost = 0.0;
  vector<string> shiftarr;
  vector<vecInt> curHypSpans;
  terShift * curshift = new terShift();
  alignmentStruct shiftReturns;
  terAlignment * curalign = new terAlignment() ;


  if ( PRINT_DEBUG ) {
    cerr << "BEGIN DEBUG : terCalc::findBestShift (after the calculateTerAlignment call) :" << endl;
    cerr << "indices: ";
    for (l_i=0; l_i < ( int ) ref.size() ; l_i++) {
      cerr << l_i << "\t";
    }
    cerr << endl;
    cerr << "hyp : \t"<<vectorToString(hyp ,"\t") << endl;
    cerr << "cur : \t"<<vectorToString(cur ,"\t") << endl;
    cerr << "ref : \t"<<vectorToString(ref ,"\t") << endl;
    cerr << "herr   : "<<vectorToString(herr,"\t",( int ) hyp.size()) << " | " << ( int ) hyp.size() <<endl;
    cerr << "rerr   : "<<vectorToString(rerr,"\t",( int ) ref.size()) << " | " << ( int ) ref.size() <<endl;
    cerr << "ralign : "<< vectorToString(ralign,"\t",( int ) ref.size()) << " | " << ( int ) ref.size() << endl;
    cerr << "END DEBUG " << endl;
  }
  poss_shifts = calculerPermutations ( cur, ref, rloc, med_align, herr, rerr, ralign  );
  double curerr = med_align.numEdits;
  if ( PRINT_DEBUG ) {
    cerr << "BEGIN DEBUG : terCalc::findBestShift :" << endl;
    cerr << "Possible Shifts:" << endl;
    for ( i = ( int ) poss_shifts->size() - 1; i >= 0; i-- ) {
      for ( j = 0; j < ( int ) ( poss_shifts->at ( i ) ).size(); j++ ) {
        cerr << " [" << i << "] " << ( ( poss_shifts->at ( i ) ).at ( j ) ).toString() << endl;
      }
    }
    cerr << endl;
    cerr << "END DEBUG " << endl;
  }
// 	exit(0);
  cur_best_align->set(med_align);
  for ( i = ( int ) poss_shifts->size() - 1; i >= 0; i-- ) {
    if ( PRINT_DEBUG ) {
      cerr << "BEGIN DEBUG : terCalc::findBestShift :" << endl;
      cerr << "Considering shift of length " << i << " (" << ( poss_shifts->at ( i ) ).size() << ")" << endl;
      cerr << "END DEBUG " << endl;
    }
    /* Consider shifts of length i+1 */
    double curfix = curerr - ( cur_best_shift_cost + cur_best_align->numEdits );
    double maxfix = ( 2 * ( 1 + i ) );
    if ( ( curfix > maxfix ) || ( ( cur_best_shift_cost != 0 ) && ( curfix == maxfix ) ) ) {
      break;
    } else {
      for ( s = 0; s < ( int ) ( poss_shifts->at ( i ) ).size(); s++ ) {
        curfix = curerr - ( cur_best_shift_cost + cur_best_align->numEdits );
        if ( ( curfix > maxfix ) || ( ( cur_best_shift_cost != 0 ) && ( curfix == maxfix ) ) ) {
          break;
        } else {
          curshift->set(( poss_shifts->at ( i ) ).at ( s ));
          if ( PRINT_DEBUG ) {
            cerr << "BEGIN DEBUG : terCalc::findBestShift :" << endl;
            cerr << "cur : "<< join(" ",cur) << endl;
            cerr << "shift size : "<< i << endl;
            cerr << "shift number : "<< s << endl;
            cerr << "size of shift size  : "<< ( int ) ( poss_shifts->at ( i ) ).size() << endl;
            cerr << "curshift : "<< curshift->toString() << endl;

          }
// 			alignmentStruct shiftReturns;
          shiftReturns.set(permuter ( cur, curshift ));
          shiftarr = shiftReturns.nwords;
          curHypSpans = shiftReturns.aftershift;

          if ( PRINT_DEBUG ) {
            cerr << "shiftarr : "<< join(" ",shiftarr) << endl;
            cerr << "curHypSpans size : "<< (int)curHypSpans.size() << endl;
            cerr << "END DEBUG " << endl;
          }
// 			terAlignment tmp=minimizeDistanceEdition ( shiftarr, ref, curHypSpans );
          minimizeDistanceEdition ( shiftarr, ref, curHypSpans, curalign );
// 			curalign->set(tmp);

          curalign->hyp = hyp;
          curalign->ref = ref;
          curalign->aftershift = shiftarr;


          double gain = ( cur_best_align->numEdits + cur_best_shift_cost ) - ( curalign->numEdits + curshift->cost );

          if ( PRINT_DEBUG ) {
            cerr << "BEGIN DEBUG : terCalc::findBestShift :" << endl;
            cerr << "Gain for " << curshift->toString() << " is " << gain << ". (result: [" << curalign->join ( " ", shiftarr ) << "]" << endl;
            cerr << "Details of gains : gain = ( cur_best_align->numEdits + cur_best_shift_cost ) - ( curalign->numEdits + curshift->cost )"<<endl;
            cerr << "Details of gains : gain = ("<<cur_best_align->numEdits << "+" << cur_best_shift_cost << ") - (" << curalign->numEdits << "+" <<  curshift->cost << ")"<<endl;
            cerr << "" << curalign->toString() << "\n" << endl;
            cerr << "END DEBUG " << endl;
          }

          if ( ( gain > 0 ) || ( ( cur_best_shift_cost == 0 ) && ( gain == 0 ) ) ) {
            anygain = true;
            cur_best_shift->set(curshift);
            cur_best_shift_cost = curshift->cost;
            cur_best_align->set(curalign);
            if ( PRINT_DEBUG ) {
              cerr << "BEGIN DEBUG : terCalc::findBestShift :" << endl;
              cerr << "Tmp Choosing shift: " << cur_best_shift->toString() << " gives:\n" << cur_best_align->toString()  << "\n" << endl;
              cerr << "END DEBUG " << endl;
            }
          }
        }
      }
    }
  }
  bestShiftStruct * to_return=new bestShiftStruct();
  if ( anygain ) {
    to_return->setEmpty(false);
    if ( PRINT_DEBUG ) {
      cerr << "BEGIN DEBUG : terCalc::findBestShift :" << endl;
      cerr << "Final shift chosen : " << cur_best_shift->toString() << " gives:\n" << cur_best_align->toString()  << "\n" << endl;
      cerr << "END DEBUG " << endl;
    }
    to_return->m_best_shift->set(cur_best_shift);
// 	    terAlignment tmp=cur_best_align;
// 	    cur_best_align->toString();
// 	    to_return.m_best_align.toString();
// 	    if ((int)cur_best_align->alignment.size() == 0)
// 	    {
// 		to_return.m_best_align = cur_best_align;
// 	    }
// 	    else
// 	    {
// 		cerr << "Warning: cur_best_align->alignment.size() = 0 !!!"<<endl;
//
// 	    }
    to_return->m_best_align->set(cur_best_align);
// 	    to_return.m_best_align.toString();
  } else {
    to_return->setEmpty(true);
  }
// // 		cerr << to_return->toString() << endl;
  delete(poss_shifts);
  delete(cur_best_align);
  delete(cur_best_shift);
  delete(curshift);
  delete(curalign) ;
  return to_return;
}

void terCalc::calculateTerAlignment ( terAlignment& align, vector<bool>* herr, vector<bool>* rerr, vector<int>* ralign )
{
  int hpos = -1;
  int rpos = -1;
  CALL_TER_ALIGN++;
// 	cerr << "CALL_TER_ALIGN " << CALL_TER_ALIGN << endl;
  if ( PRINT_DEBUG ) {

    cerr << "BEGIN DEBUG : terCalc::calculateTerAlignment : " << endl << align.toString() << endl;
    cerr << "END DEBUG " << endl;
  }
//         cerr << (int)herr->size() <<endl;
//         cerr << (int)rerr->size() <<endl;
//         cerr << ( int ) align.alignment.size() <<endl;
//         for ( int i = 0; i < ( int ) align.alignment.size(); i++ )
//         {
//                 herr->at(i) = false;
//                 rerr->at(i) = false;
//                 ralign->at(i) = -1;
// 	}
  for ( int i = 0; i < ( int ) align.alignment.size(); i++ ) {
    char sym = align.alignment.at(i);
    if ( sym == 'A' ) {
      hpos++;
      rpos++;
      herr->at(hpos) = false;
      rerr->at(rpos) = false;
      ralign->at(rpos) = hpos;
    } else if ( sym == 'S' ) {
      hpos++;
      rpos++;
      herr->at(hpos) = true;
      rerr->at(rpos) = true;
      ralign->at(rpos) = hpos;
    } else if ( sym == 'I' ) {
      hpos++;
      herr->at(hpos) = true;
    } else if ( sym == 'D' ) {
      rpos++;
      rerr->at(rpos) = true;
      ralign->at(rpos) = hpos+1;
    } else {
      cerr << "ERROR : terCalc::calculateTerAlignment : Invalid mini align sequence " << sym << " at pos " << i << endl;
      exit ( -1 );
    }
  }
}

vector<vecTerShift> * terCalc::calculerPermutations ( vector< string >& hyp, vector< string >& ref, hashMapInfos& rloc, TERCPPNS_TERCpp::terAlignment& align, vector<bool>* herr, vector<bool>* rerr, vector<int>* ralign )
{
  vector<vecTerShift> * allshifts = new vector<vecTerShift>(0);
// 	to_return.clear();
  CALL_CALC_PERMUT++;
// 	cerr << "CALL_CALC_PERMUT " << CALL_CALC_PERMUT << endl;
  if ( ( TAILLE_PERMUT_MAX <= 0 ) || ( DIST_MAX_PERMUT <= 0 ) ) {
    return allshifts;
  }
  allshifts = new vector<vecTerShift>( TAILLE_PERMUT_MAX + 1 );
  int start=0;
  int end=0;
  bool ok = false;
  vector<int> mtiVec(0);
  vector<int>::iterator mti;
  int moveto=0;
  vector<string> cand(0);
  bool any_herr = false;
  bool any_rerr = false;
  int i=0;
  int l_nbr_permuts=0;
// 	for (i=0; i< (int)ref.size() +1 ; i++) {cerr << " " << ralign[i] ;} cerr <<endl;
  vector<int> movetoitVec(0);
  string subVectorHypString="";
  terShift * topush;
  for ( start = 0; start < ( int ) hyp.size(); start++ ) {
    subVectorHypString = vectorToString ( subVector ( hyp, start, start + 1 ) );
    if ( ! rloc.trouve ( subVectorHypString ) ) {
      continue;
    }

    ok = false;
    mtiVec = rloc.getValue ( subVectorHypString );
    mti = mtiVec.begin();
    while ( mti != mtiVec.end() && ( ! ok ) ) {
      moveto = ( *mti );
      mti++;
      if ( ( start != ralign->at(moveto) ) && ( ( ralign->at(moveto) - start ) <= DIST_MAX_PERMUT ) && ( ( start - ralign->at(moveto) - 1 ) <= DIST_MAX_PERMUT ) ) {
        ok = true;
      }
    }
    if ( ! ok ) {
      continue;
    }
    ok = true;
    for ( end = start; ( ok && ( end < ( int ) hyp.size() ) && ( end < start + TAILLE_PERMUT_MAX ) ); end++ ) {
      /* check if cand is good if so, add it */
      cand = subVector ( hyp, start, end + 1 );
      ok = false;
      if ( ! ( rloc.trouve ( vectorToString ( cand ) ) ) ) {
        continue;
      }

      any_herr = false;

      for ( i = 0; ( ( i <= ( end - start ) ) && ( ! any_herr ) ); i++ ) {
        if ( herr->at(start+i) ) {
          any_herr = true;
        }
      }
      if ( any_herr == false ) {
        ok = true;
        continue;
      }

      movetoitVec = rloc.getValue ( ( string ) vectorToString ( cand ) );
// 		cerr << "CANDIDATE " << ( string ) vectorToString ( cand )  <<" PLACED : " << ( string ) vectorToString ( movetoitVec," ") << endl;
      vector<int>::iterator movetoit;
      movetoit = movetoitVec.begin();
      while ( movetoit != movetoitVec.end() ) {
        moveto = ( *movetoit );
        movetoit++;
        if ( ! ( ( ralign->at(moveto) != start ) && ( ( ralign->at(moveto) < start ) || ( ralign->at(moveto) > end ) ) && ( ( ralign->at(moveto) - start ) <= DIST_MAX_PERMUT ) && ( ( start - ralign->at(moveto) ) <= DIST_MAX_PERMUT ) ) ) {
          continue;
        }
        ok = true;

        /* check to see if there are any errors in either string
        (only move if this is the case!)
        */

        any_rerr = false;
        for ( int i = 0; ( i <= end - start ) && ( ! any_rerr ); i++ ) {
          if ( rerr->at(moveto+i) ) {
            any_rerr = true;
          }
        }
        if ( ! any_rerr ) {
          continue;
        }
        for ( int roff = -1; roff <= ( end - start ); roff++ ) {
          topush = new terShift();
          bool topushNull = true;
          if ( ( roff == -1 ) && ( moveto == 0 ) ) {
            if ( PRINT_DEBUG ) {

              cerr << "BEGIN DEBUG : terCalc::calculerPermutations 01 : " << endl << "Consider making " << start << "..." << end << " (" << vectorToString(cand," ")<< ") moveto: " << moveto << " roff: " << roff << " ralign[mt+roff]: -1" << endl << "END DEBUG" << endl;
            }
//                             terShift t01 ( start, end, -1, -1 );
//                             topush = t01;
            topush->start=start;
            topush->end=end;
            topush->moveto=-1;
            topush->newloc=-1;
            topushNull = false;
          } else if  ( ( start != ralign->at(moveto+roff) ) && ( ( roff == 0 ) || ( ralign->at(moveto+roff) != ralign->at(moveto) ) ) ) {
            int newloc = ralign->at(moveto+roff);
            if ( PRINT_DEBUG ) {

              cerr << "BEGIN DEBUG : terCalc::calculerPermutations 02 : " << endl << "Consider making " << start << "..." << end << " (" << vectorToString(cand," ")<< ") moveto: " << moveto << " roff: " << roff << " ralign[mt+roff]: " << newloc << endl << "END DEBUG" << endl;
            }
//                                 terShift t02 ( start, end, moveto + roff, newloc );
//                                 topush = t02;
            topush->start=start;
            topush->end=end;
            topush->moveto=moveto + roff;
            topush->newloc=newloc;
            topushNull = false;
          }
          if ( !topushNull ) {
            topush->shifted = cand;
            topush->cost  = shift_cost;
            l_nbr_permuts++;
            if ( PRINT_DEBUG ) {

              cerr << "BEGIN DEBUG : terCalc::calculerPermutations 02 : " << endl;
              cerr << "start : " << start << endl;
              cerr << "end : " << end << endl;
              cerr << "end - start : " << end - start << endl;
              cerr << "nbr Permutations added: " << l_nbr_permuts << endl;
              cerr << "END DEBUG " << endl;
            }
            if (l_nbr_permuts < NBR_PERMUT_MAX + 1) {
              ( allshifts->at ( end - start ) ).push_back ( (*(topush)) );
            }
// 			    else
// 			    {
// 				break;
// 			    }
          }
          delete(topush);
        }
      }
    }
  }
//         to_return.clear();
//         for ( int i = 0; i < TAILLE_PERMUT_MAX + 1; i++ )
//         {
//             to_return.push_back ( ( vecTerShift ) allshifts.at ( i ) );
//         }
  return allshifts;
}


alignmentStruct terCalc::permuter ( vector< string >& words, TERCPPNS_TERCpp::terShift& s )
{
  return permuter ( words, s.start, s.end, s.newloc );
}
alignmentStruct terCalc::permuter ( vector< string >& words, TERCPPNS_TERCpp::terShift* s )
{
  return permuter ( words, s->start, s->end, s->newloc );
}


alignmentStruct terCalc::permuter ( vector< string >& words, int start, int end, int newloc )
{
  int c = 0;
  vector<string> nwords ( words );
  vector<vecInt> spans ( ( int ) hypSpans.size() );
  alignmentStruct to_return;
  if ( PRINT_DEBUG ) {

    if ( ( int ) hypSpans.size() > 0 ) {
      cerr << "BEGIN DEBUG : terCalc::permuter :" << endl << "word length: " << ( int ) words.size() << " span length: " << ( int ) hypSpans.size() << endl ;
    } else {
      cerr << "BEGIN DEBUG : terCalc::permuter :" << endl << "word length: " << ( int ) words.size() << " span length: null" << endl ;
    }
    cerr << "BEGIN DEBUG : terCalc::permuter :" << endl << join(" ",words) << " start: " << start << " end: " << end << " newloc "<< newloc << endl << "END DEBUG " << endl;
  }
  if (newloc >=  ( int ) words.size()) {
    if ( PRINT_DEBUG ) {
      cerr << "WARNING: Relocation over the size of the hypothesis, replacing at the end of it."<<endl;
    }
    newloc =  ( int ) words.size()-1;
  }

// 		}

  if ( newloc == -1 ) {
    for ( int i = start; i <= end; i++ ) {
      nwords.at ( c++ ) = words.at ( i );
      if ( ( int ) hypSpans.size() > 0 ) {
        spans.at ( c - 1 ) = hypSpans.at ( i );
      }
    }
    for ( int i = 0; i <= start - 1; i++ ) {
      nwords.at ( c++ ) = words.at ( i );
      if ( ( int ) hypSpans.size() > 0 ) {
        spans.at ( c - 1 ) = hypSpans.at ( i );
      }
    }
    for ( int i = end + 1; i < ( int ) words.size(); i++ ) {
      nwords.at ( c++ ) = words.at ( i );
      if ( ( int ) hypSpans.size() > 0 ) {
        spans.at ( c - 1 ) = hypSpans.at ( i );
      }
    }
  } else {
    if ( newloc < start ) {

      for ( int i = 0; i < newloc; i++ ) {
        nwords.at ( c++ ) = words.at ( i );
        if ( ( int ) hypSpans.size() > 0 ) {
          spans.at ( c - 1 ) = hypSpans.at ( i );
        }
      }
      for ( int i = start; i <= end; i++ ) {
        nwords.at ( c++ ) = words.at ( i );
        if ( ( int ) hypSpans.size() > 0 ) {
          spans.at ( c - 1 ) = hypSpans.at ( i );
        }
      }
      for ( int i = newloc ; i < start ; i++ ) {
        nwords.at ( c++ ) = words.at ( i );
        if ( ( int ) hypSpans.size() > 0 ) {
          spans.at ( c - 1 ) = hypSpans.at ( i );
        }
      }
      for ( int i = end + 1; i < ( int ) words.size(); i++ ) {
        nwords.at ( c++ ) = words.at ( i );
        if ( ( int ) hypSpans.size() > 0 ) {
          spans.at ( c - 1 ) = hypSpans.at ( i );
        }
      }
    } else {
      if ( newloc > end ) {
        for ( int i = 0; i <= start - 1; i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
        for ( int i = end + 1; i <= newloc; i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
        for ( int i = start; i <= end; i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
        for ( int i = newloc + 1; i < ( int ) words.size(); i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
      } else {
        // we are moving inside of ourselves
        for ( int i = 0; i <= start - 1; i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
        for ( int i = end + 1; ( i < ( int ) words.size() ) && ( i <= ( end + ( newloc - start ) ) ); i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
        for ( int i = start; i <= end; i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
        for ( int i = ( end + ( newloc - start ) + 1 ); i < ( int ) words.size(); i++ ) {
          nwords.at ( c++ ) = words.at ( i );
          if ( ( int ) hypSpans.size() > 0 ) {
            spans.at ( c - 1 ) = hypSpans.at ( i );
          }
        }
      }
    }
  }
  NBR_PERMUTS_CONSID++;

  if ( PRINT_DEBUG ) {
    cerr << "nwords" << join(" ",nwords) << endl;
// 	    cerr << "spans" << spans. << endl;
  }

  to_return.nwords = nwords;
  to_return.aftershift = spans;
  return to_return;
}
void terCalc::setDebugMode ( bool b )
{
  PRINT_DEBUG = b;
}

}