From 2d3948b98bb9e8c7bad60f1acd99ff0b42b3ae30 Mon Sep 17 00:00:00 2001
From: Chris Dyer <cdyer@Chriss-MacBook-Air.local>
Date: Sun, 10 Nov 2013 00:58:44 -0500
Subject: guard against direct includes of tr1

---
 decoder/dwarf.cc | 3209 ------------------------------------------------------
 1 file changed, 3209 deletions(-)
 delete mode 100644 decoder/dwarf.cc

(limited to 'decoder/dwarf.cc')

diff --git a/decoder/dwarf.cc b/decoder/dwarf.cc
deleted file mode 100644
index fb0404a6..00000000
--- a/decoder/dwarf.cc
+++ /dev/null
@@ -1,3209 +0,0 @@
-#include "dwarf.h"
-#include "tdict.h"
-#include "wordid.h"
-#include "lattice.h"
-#include "ff_dwarf.h"
-#include <assert.h>
-#include <algorithm>
-#include <ostream>
-#include <sstream>
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <set>
-#include <boost/functional/hash.hpp>
-#include <tr1/unordered_map>
-#include <boost/tuple/tuple.hpp>
-
-using namespace std;
-using namespace std::tr1;
-using namespace boost::tuples;
-using namespace boost;
-
-Alignment::Alignment() {
-  //unordered_map<std::vector<WordID>,int> XX;
-  _I=0;
-  _J=0;
-  kSOS = TD::Convert("<s>");
-  kEOS = TD::Convert("</s>");
-  kUNK = TD::Convert("**UNKNOWN**");
-  SourceFWAntsIdxs = new int*[MAX_ARITY];
-  SourceFWAntsAbsIdxs = new int*[MAX_ARITY];
-  TargetFWAntsIdxs = new int*[MAX_ARITY];
-  SourceAntsIdxs = new int*[MAX_ARITY];
-  TargetAntsIdxs = new int*[MAX_ARITY];
-  AntsAl = new int*[MAX_ARITY];
-  for (int idx=0; idx<MAX_ARITY; idx++) {
-    SourceAntsIdxs[idx] = new int[40];
-    SourceFWAntsIdxs[idx] = new int[40];
-    SourceFWAntsAbsIdxs[idx] = new int[40];
-    TargetAntsIdxs[idx] = new int[40];
-    TargetFWAntsIdxs[idx] = new int[40];
-    AntsAl[idx] = new int[40];
-  }    
-  for (int j=0; j<MAX_WORDS; j++) 
-    for (int i=0; i<MAX_WORDS; i++) _matrix[j][i]=false; 
-  for (int j=0; j<MAX_WORDS; j++) {
-    _tSpan[j][0]=MINIMUM_INIT;
-    _sSpan[j][1]=MAXIMUM_INIT;
-  }
-  for (int i=0; i<MAX_WORDS; i++) {
-    _sSpan[i][0]=MINIMUM_INIT;
-    _sSpan[i][1]=MAXIMUM_INIT;
-  }
-  alpha_oris=0.1;
-  alpha_orit=0.1;
-  alpha_doms=0.1;
-  alpha_domt=0.1;
-  beta_oris=0.1;
-  beta_orit=0.1;
-  beta_doms=0.1;
-  beta_domt=0.1;
-}
-
-void Alignment::set(int j,int i) {
-// create a link between j and i, update their corresponding span accordingly
-  if (DEBUG) cerr << "set(" << j << "," << i << ")" << endl;
-  assert(0<=j && j<MAX_WORDS);
-  assert(0<=i && i<MAX_WORDS);
-  if (0<=j && j<MAX_WORDS && 0<=i && i<MAX_WORDS) {
-    _matrix[j][i] = true;
-    _tSpan[j][0]=least(i,_tSpan[j][0]);
-    _tSpan[j][1]=most(i,_tSpan[j][1]);
-    _sSpan[i][0]=least(j,_sSpan[i][0]);
-    _sSpan[i][1]=most(j,_sSpan[i][1]);
-  }
-  _J=most(j+1,_J);
-  _I=most(i+1,_I);
-}
-
-void Alignment::reset(int j,int i) { //probably won't be used, since the alignment is not dynamic
-// remove the link between j and i, update their corresponding span accordingly
-  if (DEBUG) cerr << "reset(" << j << "," << i << ")" << endl;
-  assert(0<=j && j<MAX_WORDS);
-  assert(0<=i && i<MAX_WORDS);
-  _matrix[j][i] = false;
-  if (j==_sSpan[i][0] || j==_sSpan[i][1]) {
-    int min=MINIMUM_INIT;
-    int max=MAXIMUM_INIT;
-    for (int idx=_sSpan[i][0]; idx<=_sSpan[i][1]; idx++) {
-      if (_matrix[idx][i]) {
-        min=least(min,idx);
-        max=most(max,idx);
-      }
-    }
-    _sSpan[i][0]=min;
-    _sSpan[i][1]=max;
-  }
-  if (i==_tSpan[j][0] || i==_tSpan[j][1]) {
-    int min=MINIMUM_INIT;
-    int max=MAXIMUM_INIT;
-    for (int idx=_tSpan[j][0]; idx<=_tSpan[j][1]; idx++) {
-      if (_matrix[j][idx]) {
-        min=least(min,idx);
-        max=most(max,idx);
-      }
-    }
-    _tSpan[j][0]=min;
-    _tSpan[j][1]=max;
-  }
-}
-
-int Alignment::targetOf(int j, int start) {
-  assert(j>=0);
-  if (start==-1) start = _tSpan[j][0];
-  if (_tSpan[j][0]==MINIMUM_INIT) return -1;
-  for (int idx=start; idx<=_tSpan[j][1]; idx++) {
-    if (_matrix[j][idx]) return idx;
-  }
-  return -1;
-}
-
-int Alignment::sourceOf(int i, int start) {
-  assert(i>=0);
-  if (start==-1) start = _sSpan[i][0];
-  if (_sSpan[i][0]==MINIMUM_INIT) return -1;
-  for (int idx=start; idx<=_sSpan[i][1]; idx++) {
-    if (_matrix[idx][i]) return idx;
-  }
-  return -1;
-}
-
-void Alignment::clearAls(int prevJ, int prevI) {
-  for (int j=0; j<=prevJ; j++) {
-    for (int i=0; i<prevI; i++) {
-      _matrix[j][i]=false;
-    }
-  }
-  for (int j=0; j<=prevJ; j++) {
-    _tSpan[j][0] = MINIMUM_INIT;
-    _tSpan[j][1] = MAXIMUM_INIT;
-  }
-  for (int i=0; i<=prevI; i++) {
-    _sSpan[i][0] = MINIMUM_INIT;
-    _sSpan[i][1] = MAXIMUM_INIT;
-  }
-  _J=0;
-  _I=0;
-}
-
-int Alignment::DominanceSource(int fw1, int fw2) {
-  // Dominance of fw1 and fw2 
-  // 0 -> neither, 1 -> leftFirst, 2 -> rightFirst, 3 -> dontCare
-  if (DEBUG) cerr << "DominanceSource(" << fw1 << "," << fw2 << ")" << endl;
-  //cerr << TD::Convert(_f[fw1]) << "," << TD::Convert(_f[fw2]) << endl; 
-  //cerr << AsString() << endl;
-  int dom = 0;
-  curr_al.push_back(fw1); curr_al.push_back(fw2);
-  if (doms_hash.find(curr_al)==doms_hash.end()) {
-    int* block = blockSource(fw1,fw2);
-    //cerr << "block = " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    if (block[0]==fw1) { 
-      int tfw10 = _tSpan[fw1][0];
-      int tfw11 = _tSpan[fw1][1];
-      //cerr << "tfw = " << tfw10 << "," << tfw11 << endl;
-      if (tfw11<0) { 
-        dom+=1;
-      } else {
-        if ((block[2]==tfw10 || block[3]==tfw11)) dom+=1;
-      }
-    }
-    if (block[1]==fw2) {
-      int tfw20 = _tSpan[fw2][0];
-      int tfw21 = _tSpan[fw2][1];
-      //cerr << "tfw = " << tfw20 << "," << tfw21 << endl;
-      if (tfw21<0) {
-        dom+=2;
-      } else {
-        if ((block[2]==tfw20 || block[3]==tfw21)) dom+=2;
-      }
-    }
-    delete block;
-    doms_hash.insert(pair<vector<int>,int>(curr_al,dom));
-  } else {
-    dom = doms_hash[curr_al];
-  }
-  if (DEBUG) cerr << "  dom = " << dom << endl;
-  curr_al.pop_back(); curr_al.pop_back();
-  return dom;
-}
-
-vector<int> Alignment::DominanceSource4Sampler(int fw1, int fw2) {
-  if (DEBUG) cerr << "DominanceSource4Sampler(" << fw1 << "," << fw2 << ")" << endl;
-  int dom = 0;
-  int* block = blockSource(fw1,fw2);
-  //cerr << "block = " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-  if (block[0]==fw1) {
-    int tfw10 = _tSpan[fw1][0];
-    int tfw11 = _tSpan[fw1][1];
-    //cerr << "tfw = " << tfw10 << "," << tfw11 << endl;
-    if (tfw11<0) {
-      dom+=1;
-    } else {
-      if ((block[2]==tfw10 || block[3]==tfw11)) dom+=1;
-    }
-  }
-  if (block[1]==fw2) {
-    int tfw20 = _tSpan[fw2][0];
-    int tfw21 = _tSpan[fw2][1];
-    //cerr << "tfw = " << tfw20 << "," << tfw21 << endl;
-    if (tfw21<0) {
-      dom+=2;
-    } else {
-      if ((block[2]==tfw20 || block[3]==tfw21)) dom+=2;
-    }
-  }
-  if (DEBUG) cerr << "doms = " << dom << endl;
-  vector<int> ret;
-  ret.push_back(dom); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-int Alignment::DominanceTarget(int fw1, int fw2) {
-  int dom = 0;
-  curr_al.push_back(fw1); curr_al.push_back(fw2);
-  if (domt_hash.find(curr_al)==domt_hash.end()) {
-    int* block = blockTarget(fw1,fw2);
-    if (block[2]==fw1) {
-      int sfw10 = _sSpan[fw1][0];
-      int sfw11 = _sSpan[fw1][1];
-      if (sfw11<0) {
-        dom+=1;
-      } else {
-        if (block[0]==sfw10 || block[1]==sfw11) dom+=1;
-      }
-    }
-    if (block[3]==fw2) {
-      int sfw20 = _sSpan[fw2][0];
-      int sfw21 = _sSpan[fw2][0];
-      if (sfw21<0) {
-        dom+=2;
-      } else {
-        if (block[0]==sfw20 || block[1]==sfw21) dom+=2;
-      }
-    }
-    delete block;
-    domt_hash.insert(pair<vector<int>,int>(curr_al,dom));
-  } else {
-    dom = domt_hash[curr_al];
-  }
-  curr_al.pop_back(); curr_al.pop_back();
-  return dom;
-}
-
-vector<int> Alignment::DominanceTarget4Sampler(int fw1, int fw2) {
-  int dom = 0;
-  int* block = blockTarget(fw1,fw2);
-  if (block[2]==fw1) {
-    int sfw10 = _sSpan[fw1][0];
-    int sfw11 = _sSpan[fw1][1];
-    if (sfw11<0) {
-      dom+=1;
-    } else {
-      if (block[0]==sfw10 || block[1]==sfw11) dom+=1;
-    }
-  }
-  if (block[3]==fw2) {
-    int sfw20 = _sSpan[fw2][0];
-    int sfw21 = _sSpan[fw2][0];
-    if (sfw21<0) {
-      dom+=2;
-    } else {
-      if (block[0]==sfw20 || block[1]==sfw21) dom+=2;
-    }
-  }
-  vector<int> ret;
-  ret.push_back(dom); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-void Alignment::OrientationSource(int fw, int* oril, int* orir, bool Lcompute, bool Rcompute) {
-  OrientationSource(fw,fw,oril,orir,Lcompute,Rcompute);
-}
-
-vector<int> Alignment::OrientationSourceLeft4Sampler(int fw) {
-  return OrientationSourceLeft4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationSourceLeft4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationSourceLeft4Sampler(" << fw0 << "," << fw1 << ")" << endl;
-  int oril = 0;
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minTSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_J) {
-    if (minTSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minTSpan(fw0)==MINIMUM_INIT && minTSpan(fw1)==MINIMUM_INIT) {
-    fw0 = N1; fw1 = N0;
-  }
-  if (DEBUG) cerr << "fw0=" << fw0 << ", fw1=" << fw1 << ", N0=" << N0 << ", N1=" << N1 << endl;
-  if (maxTSpan(N0)<minTSpan(fw0) || maxTSpan(fw0)<minTSpan(N0)) {
-    if (DEBUG) cerr << "N0=" << minTSpan(N0) << "-" << maxTSpan(N0);
-    if (DEBUG) cerr << "fw=" << minTSpan(fw0) << "-" << maxTSpan(fw0) << endl;
-    int *block = blockTarget(minTSpan(N0),maxTSpan(N0));
-    if (block[0]<=fw0 && fw0<=block[1]) oril=5;
-    delete block;
-    if (oril==0) {
-      block = blockTarget(minTSpan(fw0),maxTSpan(fw0));
-      if (block[0]<=N0 && N0<=block[1]) oril=5;
-      delete block;
-    }
-    if (oril==0) {
-      if (maxTSpan(N0)<minTSpan(fw0)) {// if N0 is monotone
-        oril=1;
-        block = blockTarget(maxTSpan(N0),minTSpan(fw0)-1);
-        if (block[0] <= fw0 && fw0 <= block[1]) oril+=2;
-        delete block;
-      } else { //if (maxTSpan(fw0)<minTSpan(N0)) { // if NO is non-monotone
-        oril=2;
-        block = blockTarget(maxTSpan(fw0)+1,minTSpan(N0));
-        if (block[0] <= fw0 && fw0 <= block[1]) oril+=2;
-        delete block;
-      }
-    }
-  } else {
-    oril=5;
-  }
-  if (DEBUG) cerr << "oril = " << oril << endl;
-  int* block = blockSource(N0,fw0);
-  if (DEBUG) {
-    for (int i=0; i<4; i++) cerr << "block[" << i << "]=" << block[i] << endl;
-  }
-  vector<int> ret;
-  ret.push_back(oril); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-vector<int> Alignment::OrientationSourceRight4Sampler(int fw) {
-  return OrientationSourceRight4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationSourceRight4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationSourceLeft4Sampler(" << fw0 << "," << fw1 << ")" << endl;
-  int orir = 0;
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minTSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_J) {
-    if (minTSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minTSpan(fw0)==MINIMUM_INIT && minTSpan(fw1)==MINIMUM_INIT) {
-    fw0 = N1; fw1 = N0;
-  }
-  if (DEBUG) cerr << "fw0=" << fw0 << ", fw1=" << fw1 << ", N0=" << N0 << ", N1=" << N1 << endl;
-  if (maxTSpan(N1)<minTSpan(fw1) || maxTSpan(fw1)<minTSpan(N1)) {
-    int* block = blockTarget(minTSpan(N1),maxTSpan(N1));
-    if (block[0]<=fw1 && fw1<=block[2]) orir=5;
-    delete block;
-    if (orir==0) {
-      block = blockTarget(minTSpan(fw1),maxTSpan(fw1));
-      if (block[0]<=N1 && N1 <=block[1]) orir=5;
-      delete block;
-    }
-    if (DEBUG) cerr << "N1=" << minTSpan(N1) << "-" << maxTSpan(N1);
-    if (DEBUG) cerr << "fw1=" << minTSpan(fw1) << "-" << maxTSpan(fw1) << endl;
-    if (orir==0) {
-      if (maxTSpan(fw1)<minTSpan(N1)) { // if N1 is monotone
-        orir = 1;
-        block = blockTarget(maxTSpan(fw1)+1,minTSpan(N1));
-        if (block[0] <= fw1 && fw1 <= block[1]) orir+=2;
-        delete block;
-      } else {// if (maxTSpan(N1)<minTSpan(fw1)) { // if N1 is non-monotone
-        orir = 2;
-        block = blockTarget(maxTSpan(N1),minTSpan(fw1)-1);
-        if (block[0] <= fw1 && fw1 <= block[1]) orir+=2;
-        delete block;
-      }
-    }
-  } else {
-    orir = 5;
-  }
-  if (DEBUG) cerr << "orir = " << orir << endl;
-  int* block = blockSource(fw1,N1);
-  vector<int> ret;
-  ret.push_back(orir); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-void Alignment::OrientationSource(int fw0, int fw1, int* oril, int* orir, bool Lcompute, bool Rcompute) {
-  // Orientation
-  // A bit tricky since fw can be 1) unaligned 2) aligned to many
-  // 1 -> MA, 2 -> RA, 3 -> MG, 4 -> RG, 5 -> Other
-  if (DEBUG) cerr << "OrientationSource(" << fw0 << "," << fw1 << ")" << endl;
-  if (!Lcompute && !Rcompute) return;
-  curr_al.push_back(fw0);
-  curr_al.push_back(fw1);
-  *oril=0;
-  *orir=0;
-  int lr=0;
-  if (oris_hash.find(curr_al)==oris_hash.end()) {
-    // Find first aligned word N0 to the left of fw
-    int N0=fw0-1;
-    while (N0>=0) {
-      if (minTSpan(N0)!=MINIMUM_INIT) break;
-      N0--;
-    }
-    int N1=fw1+1;
-    while (N1<_J) {
-      if (minTSpan(N1)!=MINIMUM_INIT) break;
-      N1++;
-    }
-    if (minTSpan(fw0)==MINIMUM_INIT && minTSpan(fw1)==MINIMUM_INIT) {
-      fw0 = N1; fw1 = N0;
-      //cerr << "minTSpan(fw)==MINIMUM_INIT, thus fw0=" << fw0 << ", fw1=" << fw1 << endl;
-    }
-    if (DEBUG) cerr << "fw0=" << fw0 << ", fw1=" << fw1 << ", N0=" << N0 << ", N1=" << N1 << endl;
-    if (maxTSpan(N0)<minTSpan(fw0) || maxTSpan(fw0)<minTSpan(N0)) {
-      if (DEBUG) cerr << "N0=" << minTSpan(N0) << "-" << maxTSpan(N0);
-      if (DEBUG) cerr << "fw=" << minTSpan(fw0) << "-" << maxTSpan(fw0) << endl;
-      int *block = blockTarget(minTSpan(N0),maxTSpan(N0));
-      if (block[0]<=fw0 && fw0<=block[1]) *oril=5;
-      delete block;
-      if (*oril==0) {
-        block = blockTarget(minTSpan(fw0),maxTSpan(fw0));
-        if (block[0]<=N0 && N0<=block[1]) *oril=5;
-        delete block;
-      }
-      if (*oril==0) {
-        if (maxTSpan(N0)<minTSpan(fw0)) {// if N0 is monotone
-          *oril=1;
-          block = blockTarget(maxTSpan(N0),minTSpan(fw0)-1);
-          if (block[0] <= fw0 && fw0 <= block[1]) *oril+=2;
-          delete block;
-        } else { //if (maxTSpan(fw0)<minTSpan(N0)) { // if NO is non-monotone
-          *oril=2;
-          block = blockTarget(maxTSpan(fw0)+1,minTSpan(N0));
-          if (block[0] <= fw0 && fw0 <= block[1]) *oril+=2;
-          delete block;
-        }
-      }
-    } else {
-      *oril=5;
-    }
-    if (DEBUG) cerr << "oril =" << *oril << endl;
-    // Right neighbor
-    if (maxTSpan(N1)<minTSpan(fw1) || maxTSpan(fw1)<minTSpan(N1)) {
-      int* block = blockTarget(minTSpan(N1),maxTSpan(N1));
-      if (block[0]<=fw1 && fw1<=block[2]) *orir=5;
-      delete block;
-      if (*orir==0) {
-        block = blockTarget(minTSpan(fw1),maxTSpan(fw1));
-        if (block[0]<=N1 && N1 <=block[1]) *orir=5;
-        delete block;
-      }
-      if (DEBUG) cerr << "N1=" << minTSpan(N1) << "-" << maxTSpan(N1);
-      if (DEBUG) cerr << "fw1=" << minTSpan(fw1) << "-" << maxTSpan(fw1) << endl;
-      if (*orir==0) {
-        if (maxTSpan(fw1)<minTSpan(N1)) { // if N1 is monotone
-          *orir = 1;
-          block = blockTarget(maxTSpan(fw1)+1,minTSpan(N1));
-          if (block[0] <= fw1 && fw1 <= block[1]) *orir+=2;
-          delete block;
-        } else {// if (maxTSpan(N1)<minTSpan(fw1)) { // if N1 is non-monotone
-          *orir = 2;
-          block = blockTarget(maxTSpan(N1),minTSpan(fw1)-1);
-          if (block[0] <= fw1 && fw1 <= block[1]) *orir+=2;
-          delete block;
-        }
-      }
-    } else {
-      *orir = 5;
-    }
-    if (DEBUG) cerr << "orir =" << *orir << endl;
-    lr = link(*oril,*orir);
-    oris_hash.insert(pair<vector<int>,int>(curr_al,lr));  
-  } else {
-    lr = oris_hash[curr_al];  
-  }
-  if (DEBUG) cerr << "Lcompute=" << Lcompute << ", Rcompute=" << Rcompute << endl;
-  if (Lcompute) *oril = source(lr);
-  if (Rcompute) *orir = target(lr);
-  curr_al.pop_back();
-  curr_al.pop_back();
-}
-
-int Alignment::OrientationSource(int* left, int* right) {
-  if (DEBUG) {
-    cerr << "      OrientationSource(";
-    cerr << "left="<<left[0]<<","<<left[1]<<","<<left[2]<<","<<left[3];
-    cerr << " right="<<right[0]<<","<<right[1]<<","<<right[2]<<","<<right[3];
-    cerr << ")" << endl;
-  } 
-  //if ((right[1]<=left[0]) return 5;
-  if (!(left[1]<right[0])) return 5;
-  int ori = 1;
-  if (right[3]<left[2]) ori=2;
-  int gapstart = left[3]+1; int gapend = right[2]-1;
-  if (ori==2) { gapstart = right[3]+1; gapend = left[2]-1; }
-  for (int j=gapstart; j<=gapend; j++) {
-    if (sourceOf(j)!=-1) {
-      ori+=2; break;
-    }
-  }
-  return ori;
-}
-
-void Alignment::OrientationTarget(int fw, int *oril, int *orir, bool Lcompute, bool Rcompute) {
-  OrientationTarget(fw,fw,oril,orir,Lcompute,Rcompute);
-}
-
-vector<int> Alignment::OrientationTargetLeft4Sampler(int fw) {
-  return OrientationTargetLeft4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationTargetLeft4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationTargetLeft4Sampler " << fw0 << "," << fw1 << endl;
-  int oril=0; 
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minSSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_I) {
-    if (minSSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minSSpan(fw0)==MINIMUM_INIT && minSSpan(fw1)==MINIMUM_INIT) {
-    fw0=N1; fw1=N0;
-  }
-  if (maxSSpan(N0)<minSSpan(fw0) || maxSSpan(fw0)<minSSpan(N0)) {
-    int *block = blockSource(minSSpan(N0),maxSSpan(N0));
-    if (DEBUG) cerr << "block1[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    if (block[2]<=fw0 && fw0<=block[3])  //source span of fw0 subsumes NO's or the other way around
-      oril=5;
-    delete block;
-    if (oril==0) {
-      block = blockSource(minSSpan(fw0), maxSSpan(fw0));
-      if (DEBUG) cerr << "block2[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-      if (block[2] <= N0 && N0 <= block[3]) oril=5;
-      delete block;
-    }
-    if (oril==0) {
-      if (maxSSpan(N0)<minSSpan(fw0)) {// if N0 is monotone
-        oril=1;
-        block = blockSource(maxSSpan(N0),minSSpan(fw0)-1);
-        if (DEBUG) cerr << "block3[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        if (block[2] <= fw0 && fw0 <= block[3]) oril+=2;
-        delete block;
-      } else { // (maxSSpan(fw0)<minSSpan(N0)) // if NO is non-monotone
-        oril=2;
-        block = blockSource(maxSSpan(fw0)+1,minSSpan(N0));
-        if (DEBUG) cerr << "block4[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        if (block[2] <= fw0 && fw0 <= block[3]) oril+=2;
-        delete block;
-      }
-    }
-  } else { //source span of fw0 subsumes NO's or the other way around
-    oril=5;
-  }
-  if (DEBUG) cerr << "oril = " << oril << endl;
-  int* block = blockSource(N0,fw0);
-  vector<int> ret;
-  ret.push_back(oril); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-}
-
-vector<int> Alignment::OrientationTargetRight4Sampler(int fw) {
-  return OrientationTargetRight4Sampler(fw,fw);
-}
-
-vector<int> Alignment::OrientationTargetRight4Sampler(int fw0, int fw1) {
-  if (DEBUG) cerr << "OrientationTargetRight4Sampler " << fw0 << "," << fw1 << endl;
-  int orir=0;
-  int N0=fw0-1;
-  while (N0>=0) {
-    if (minSSpan(N0)!=MINIMUM_INIT) break;
-    N0--;
-  }
-  int N1=fw1+1;
-  while (N1<_I) {
-    if (minSSpan(N1)!=MINIMUM_INIT) break;
-    N1++;
-  }
-  if (minSSpan(fw0)==MINIMUM_INIT && minSSpan(fw1)==MINIMUM_INIT) {
-    fw0=N1; fw1=N0;
-  }
-  if (maxSSpan(N1)<minSSpan(fw1) || maxSSpan(fw1)<minSSpan(N1)) {
-    int *block = blockSource(minSSpan(N1),maxSSpan(N1));
-    if (block[2]<=fw1 && fw1<=block[3]) orir=5;
-    delete block;
-    if (orir==0) {
-      block = blockSource(minSSpan(fw1),maxSSpan(fw1));
-      if (block[2] <= N1 && N1 <= block[3]) orir=5;
-      delete block;
-    }
-    if (orir==0) {
-      if (maxSSpan(fw1)<minSSpan(N1)) { // if N1 is monotone
-        orir=1;
-        block = blockSource(maxSSpan(fw1)+1,minSSpan(N1));
-        if (block[2] <= fw1 && fw1 <= block[3]) orir+=2;
-        delete block;
-      } else { //if (maxSSpan(N1)<minSSpan(fw1)) { // if N1 is non-monotone
-        orir=2;
-        block = blockSource(maxSSpan(N1),minSSpan(fw1)-1);
-        if (block[2] <= fw1 && fw1 <= block[3]) orir+=2;
-        delete block;
-      }
-    }
-  } else {
-    orir=5;
-  }
-  if (DEBUG) cerr << "orir = " << orir << endl;
-  int* block = blockSource(fw1,N1);
-  vector<int> ret;
-  ret.push_back(orir); ret.push_back(block[0]); ret.push_back(block[1]);
-  ret.push_back(block[2]); ret.push_back(block[3]);
-  delete block;
-  return ret;
-
-}
-
-void Alignment::OrientationTarget(int fw0, int fw1, int*oril, int*orir, bool Lcompute, bool Rcompute) {
-  if (DEBUG) cerr << "OrientationTarget " << fw0 << "," << fw1 << endl;
-  // Left Neighbor
-  if (!Lcompute && !Rcompute) return;
-  *oril=0;
-  *orir=0;
-  curr_al.push_back(fw0);
-  curr_al.push_back(fw1);
-  int lr = 0;
-  if (orit_hash.find(curr_al)==orit_hash.end()) {
-    // Find first aligned word N0 to the left of fw
-    //int fw0 = fw; int fw1 = fw;
-    int N0=fw0-1;
-    while (N0>=0) {
-      if (minSSpan(N0)!=MINIMUM_INIT) break;
-      N0--;
-    }
-    int N1=fw1+1;
-    while (N1<_I) {
-      if (minSSpan(N1)!=MINIMUM_INIT) break;
-      N1++;
-    }
-    if (minSSpan(fw0)==MINIMUM_INIT && minSSpan(fw1)==MINIMUM_INIT) {
-      fw0=N1; fw1=N0;
-    }
-    if (DEBUG) {
-      cerr << "fw0:" << fw0 << ", fw1:" << fw1 << ", N0:" << N0 << ", N1:" << N1 << endl ;
-      cerr << "minSSpan(N0)=" << minSSpan(N0) << " maxSSpan(N0)=" << maxSSpan(N0);
-      cerr << " minSSpan(fw0)="<< minSSpan(fw0) << " maxSSpan(fw0)=" << maxSSpan(fw0) << endl;
-      cerr << "minSSpan(fw1)=" << minSSpan(fw1) << " maxSSpan(fw1)=" << maxSSpan(fw1);
-      cerr << " minSSpan(N1)="<< minSSpan(N1) << " maxSSpan(N1)=" << maxSSpan(N1) << endl;
-    }
-    if (maxSSpan(N0)<minSSpan(fw0) || maxSSpan(fw0)<minSSpan(N0)) {
-      int *block = blockSource(minSSpan(N0),maxSSpan(N0));
-      if (DEBUG) cerr << "block1[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-      if (block[2]<=fw0 && fw0<=block[3])  //source span of fw0 subsumes NO's or the other way around
-        *oril=5;
-      delete block;
-      if (*oril==0) {
-        block = blockSource(minSSpan(fw0), maxSSpan(fw0));
-        if (DEBUG) cerr << "block2[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        if (block[2] <= N0 && N0 <= block[3]) *oril=5;
-        delete block;
-      }
-      if (*oril==0) {  
-        if (maxSSpan(N0)<minSSpan(fw0)) {// if N0 is monotone
-          *oril=1;
-          block = blockSource(maxSSpan(N0),minSSpan(fw0)-1);
-          if (DEBUG) cerr << "block3[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-          if (block[2] <= fw0 && fw0 <= block[3]) *oril+=2;
-          delete block;
-        } else { // (maxSSpan(fw0)<minSSpan(N0)) // if NO is non-monotone
-          *oril=2;
-          block = blockSource(maxSSpan(fw0)+1,minSSpan(N0));
-          if (DEBUG) cerr << "block4[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-          if (block[2] <= fw0 && fw0 <= block[3]) *oril+=2;
-          delete block;
-        }
-      }
-    } else { //source span of fw0 subsumes NO's or the other way around
-      *oril=5;
-    }
-    if (DEBUG) cerr << "oril = " << *oril << endl;
-    // Right Neighbor
-    if (maxSSpan(N1)<minSSpan(fw1) || maxSSpan(fw1)<minSSpan(N1)) {
-      int *block = blockSource(minSSpan(N1),maxSSpan(N1));
-      if (block[2]<=fw1 && fw1<=block[3]) *orir=5; 
-      delete block;
-      if (*orir==0) {
-        block = blockSource(minSSpan(fw1),maxSSpan(fw1));
-        if (block[2] <= N1 && N1 <= block[3]) *orir=5;
-        delete block;
-      }
-      if (*orir==0) {
-        if (maxSSpan(fw1)<minSSpan(N1)) { // if N1 is monotone
-          *orir=1;
-          block = blockSource(maxSSpan(fw1)+1,minSSpan(N1));
-          if (block[2] <= fw1 && fw1 <= block[3]) *orir+=2;
-          delete block;
-        } else { //if (maxSSpan(N1)<minSSpan(fw1)) { // if N1 is non-monotone
-          *orir=2;
-          block = blockSource(maxSSpan(N1),minSSpan(fw1)-1);
-          if (block[2] <= fw1 && fw1 <= block[3]) *orir+=2;
-          delete block;
-        }
-      }
-    } else {
-      *orir=5;
-    }
-    if (DEBUG) cerr << "orir = " << *orir << endl;
-    lr = link(*oril,*orir);
-    orit_hash.insert(pair<vector<int>,int>(curr_al,lr));
-  } else {
-    lr = orit_hash[curr_al];
-  }
-  if (DEBUG) cerr << "Lcompute=" << Lcompute << ", Rcompute=" << Rcompute << endl;
-  if (DEBUG) cerr << "lr=" << lr << ", l=" << source(lr) << ", r=" << target(lr) << endl;
-  if (Lcompute>0) *oril=source(lr);
-  if (Rcompute>0) *orir=target(lr);
-  curr_al.pop_back();
-  curr_al.pop_back();
-}
-
-int* Alignment::blockSource(int idx1, int idx2) {
-// outputs a minimal block [s1,s2,t1,t2] that contains idx1 and idx2, where idx1 <= idx2
-  if (DEBUG) cerr << "blockSource[" << idx1 << "," << idx2 << "]" << endl;
-  int *curr = new int[4];
-  curr[0]=idx1; curr[1]=idx2; curr[2]=MINIMUM_INIT; curr[3]=MAXIMUM_INIT;
-  for (int j=curr[0]; j<=curr[1]; j++) {
-    curr[2] = least(curr[2],_tSpan[j][0]);
-    curr[3] =  most(curr[3],_tSpan[j][1]);
-  }
-  int next[4];
-  next[0]=curr[0]; next[1]=curr[1];
-  for (int i=curr[2]; i<=curr[3]; i++) {
-    next[0] = least(next[0],_sSpan[i][0]);
-    next[1] =  most(next[1],_sSpan[i][1]);
-  } 
-  next[2] = curr[2]; next[3]= curr[3];
-  int idx=1;
-  do {
-    // update the current
-    for (int j=next[0]; j<curr[0]; j++) {
-      curr[2] = least(curr[2],_tSpan[j][0]);
-      curr[3] =  most(curr[3],_tSpan[j][1]);
-    }
-    for (int j=curr[1]+1; j<=next[1]; j++) {
-      curr[2] = least(curr[2],_tSpan[j][0]);
-      curr[3] =  most(curr[3],_tSpan[j][1]);
-    }
-    curr[0] = next[0]; curr[1] = next[1]; 
-    if (curr[2]==next[2] && curr[3]==next[3]) break;
-    // prepare for the next 
-    for (int i=curr[2]; i<next[2]; i++) {
-      next[0]= least(next[0],_sSpan[i][0]);
-      next[1]=  most(next[1],_sSpan[i][1]);
-    }
-    for (int i=next[3]+1; i<=curr[3]; i++) {
-      next[0] = least(next[0],_sSpan[i][0]);
-      next[1] =  most(next[1],_sSpan[i][1]);
-    }
-    next[2] = curr[2]; next[3]= curr[3];
-    idx++;
-  } while(1);
-  return curr;
-}
-
-int* Alignment::blockTarget(int idx1, int idx2) {
-// outputs a minimal [s1,s2,t1,t2] that contains idx1 and idx2, where idx1<=idx2
-  int *curr = new int[4];
-  curr[0]=MINIMUM_INIT; curr[1]=MAXIMUM_INIT; curr[2]=idx1; curr[3]=idx2;
-        for (int i=curr[2]; i<=curr[3]; i++) {
-                curr[0] = least(curr[0],_sSpan[i][0]);
-                curr[1] =  most(curr[1],_sSpan[i][1]);
-        }
-        int next[4];
-        next[2]=curr[2]; next[3]=curr[3];
-        for (int j=curr[0]; j<=curr[1]; j++) {
-                next[2] = least(next[2],_tSpan[j][0]);
-                next[3] =  most(next[3],_tSpan[j][1]);
-        }
-        next[0] = curr[0]; next[1]= curr[1];
-        int idx=1;
-        do {
-                // update the current
-                for (int i=next[2]; i<curr[2]; i++) {
-                        curr[0] = least(curr[0],_sSpan[i][0]);
-                        curr[1] =  most(curr[1],_sSpan[i][1]);
-                }
-                for (int i=curr[3]+1; i<=next[3]; i++) {
-                        curr[0] = least(curr[0],_sSpan[i][0]);
-                        curr[1] =  most(curr[1],_sSpan[i][1]);
-                }
-                curr[2] = next[2]; curr[3] = next[3];
-                if (curr[0]==next[0] && curr[1]==next[1]) break;
-                // prepare for the next
-                for (int j=curr[0]; j<next[0]; j++) {
-                        next[2]= least(next[2],_tSpan[j][0]);
-                        next[3]=  most(next[3],_tSpan[j][1]);
-                }
-                for (int j=next[1]+1; j<=curr[1]; j++) {
-                        next[2] = least(next[2],_tSpan[j][0]);
-                        next[3] =  most(next[3],_tSpan[j][1]);
-                }
-                next[0] = curr[0]; next[1]= curr[1];
-                idx++;
-        } while(1);
-  return curr;
-}
-
-int Alignment::firstSourceAligned(int start) {
-  for (int j=start; j<_J; j++) 
-    if (_tSpan[j][0]!=MINIMUM_INIT) return j;
-  return -1;
-}
-
-int Alignment::lastSourceAligned(int end) {
-  for (int j=end; j>=0; j--)
-    if (_tSpan[j][0]!=MINIMUM_INIT) return j;
-  return -1;
-}
-
-int Alignment::firstTargetAligned(int start) {
-  for (int i=start; i<_I; i++) 
-    if (_sSpan[i][0]!=MINIMUM_INIT) return i;
-  return -1;
-}
-
-int Alignment::lastTargetAligned(int end) {
-  for (int i=end; i>=0; i--) 
-    if (_sSpan[i][0]!=MINIMUM_INIT) return i;
-  return -1;
-}
-
-void Alignment::BorderingSFWsOnly() {
-// removes the record of all function word alignments, except those at the borders
-// the number of alignments kept may be more than two
-// i.e. where the leftmost / the rightmost alignments are unaligned. 
-// In such cases, this function continues keeping function word alignments until the 
-// first (or last) alignment words. 
-  if (SourceFWIdxs[0]>2) {
-    int firstCut = 1;
-    for (int j=2; j<=SourceFWIdxs[0]; j++) {
-      if (SourceFWIdxs[3*j-2]>fas) break;
-      firstCut=j;
-    }
-    int lastCut  = SourceFWIdxs[0];
-    for (int j=SourceFWIdxs[0]-1; j>=0; j--) {
-      if (SourceFWIdxs[3*j-2]<las) break;
-      lastCut=j;
-    }
-    if (firstCut>=lastCut) return;
-    int delta = 0;
-    for (int j=lastCut; j<=SourceFWIdxs[0]; j++) {
-      delta++;
-      SourceFWIdxs[3*(firstCut+delta)-2]=SourceFWIdxs[3*j-2];
-      SourceFWIdxs[3*(firstCut+delta)-1]=SourceFWIdxs[3*j-1];
-      SourceFWIdxs[3*(firstCut+delta)]  =SourceFWIdxs[3*j];
-    }
-    SourceFWIdxs[0]=firstCut+delta;
-  }
-}
-
-void Alignment::BorderingTFWsOnly() {
-// similar to BorderingSFWsOnly() except this looks at the source side.
-  if (TargetFWIdxs[0]>2) {
-    int firstCut = 1;
-    for (int j=2; j<=TargetFWIdxs[0]; j++) {
-      if (TargetFWIdxs[3*j-2]>fat) break;
-      firstCut=j;
-    }
-    int lastCut  = TargetFWIdxs[0];
-    for (int j=TargetFWIdxs[0]-1; j>=0; j--) {
-      if (TargetFWIdxs[3*j-2]<lat) break;
-      lastCut=j;
-    }
-    if (firstCut>=lastCut) return;
-    int delta = 0;
-    for (int j=lastCut; j<=TargetFWIdxs[0]; j++) {
-      delta++;
-      TargetFWIdxs[3*(firstCut+delta)-2]=TargetFWIdxs[3*j-2];
-      TargetFWIdxs[3*(firstCut+delta)-1]=TargetFWIdxs[3*j-1];
-      TargetFWIdxs[3*(firstCut+delta)]  =TargetFWIdxs[3*j];
-    }
-    TargetFWIdxs[0]=firstCut+delta;
-  }
-}
-
-void Alignment::FillFWIdxsState(int* state, int fas, int las, int fat, int lat) {
-  if (DEBUG) cerr << "FillFWIdxsState ("<< fas <<","<< las<<"," << fat <<"," << lat << ")" << endl;
-  if (fas==las) las+=1;
-  if (fat==lat) lat+=1;
-  for (int idx=0; idx<12; idx++) state[idx]=-1;
-  if (SourceFWIdxs[0]<=2) {
-    if (SourceFWIdxs[0]>=1) {state[0]=SourceFWIdxs[1]; state[1]=SourceFWIdxs[2]; state[2]=SourceFWIdxs[3];}
-    if (SourceFWIdxs[0]==2) {state[3]=SourceFWIdxs[4]; state[4]=SourceFWIdxs[5]; state[5]=SourceFWIdxs[6];}
-  } else {
-    if (SourceFWIdxs[1]>fas) {
-      state[0]=SourceFWIdxs[1]; state[1]=SourceFWIdxs[2]; state[2]=SourceFWIdxs[3];
-    } else {
-      ostringstream issf; ostringstream isse;
-      for (int idx=1; idx<=SourceFWIdxs[0]; idx++) {
-        if (SourceFWIdxs[3*idx-2]>las) break;
-        if (idx>1) { issf << " "; isse << " ";};
-        issf << TD::Convert(SourceFWIdxs[3*idx-1]);
-        isse << TD::Convert(SourceFWIdxs[3*idx]);
-        state[0]=SourceFWIdxs[3*idx-2];
-        if (state[0]>=fas) break;
-      }
-      if (state[0]>=0) {
-        state[1]=TD::Convert(issf.str())*-1; state[2]=TD::Convert(isse.str()); //multiplying source with -1 as marker
-      }
-    }
-    if (SourceFWIdxs[SourceFWIdxs[0]*3-2]==las) {
-      state[3]=SourceFWIdxs[SourceFWIdxs[0]*3-2];
-      state[4]=SourceFWIdxs[SourceFWIdxs[0]*3-1]; 
-      state[5]=SourceFWIdxs[SourceFWIdxs[0]*3];
-    } else {
-      int lastCut = SourceFWIdxs[0];
-      for (int j=lastCut-1; j>=state[0]+1; j--) {
-        if (SourceFWIdxs[3*j-2]==state[0]) break;
-        if (SourceFWIdxs[3*j-2]<las) break;
-        lastCut=j;
-      }
-      state[3]=SourceFWIdxs[3*lastCut-2];
-      ostringstream issf; ostringstream isse;
-      for (int idx=lastCut; idx<=SourceFWIdxs[0]; idx++) {
-        if (idx>lastCut) { issf << " "; isse << " ";};
-        issf << TD::Convert(SourceFWIdxs[3*idx-1]);
-        isse << TD::Convert(SourceFWIdxs[3*idx]);
-      }
-      if (state[3]>=0) {
-        //multiplying source with -1 as compound marker
-        state[4]=TD::Convert(issf.str())*-1; state[5]=TD::Convert(isse.str()); 
-      }
-    }
-  }
-  if (TargetFWIdxs[0]<=2) {
-    if (TargetFWIdxs[0]>=1) {state[6]=TargetFWIdxs[1]; state[7]=TargetFWIdxs[2]; state[8]=TargetFWIdxs[3];}
-    if (TargetFWIdxs[0]==2) {state[9]=TargetFWIdxs[4]; state[10]=TargetFWIdxs[5]; state[11]=TargetFWIdxs[6];}
-  } else {
-    if (TargetFWIdxs[1]>fat) { //shouldn't come here if SetTargetBorderingFW is invoked
-      state[6]=TargetFWIdxs[1]; state[7]=TargetFWIdxs[2]; state[8]=TargetFWIdxs[3];
-    } else {
-      ostringstream issf; ostringstream isse;
-      for (int idx=1; idx<=TargetFWIdxs[0]; idx++) {
-        if (TargetFWIdxs[3*idx-2]>fat) break;
-        if (idx>1) { issf << " "; isse << " ";};
-        issf << TD::Convert(TargetFWIdxs[3*idx-1]);
-        isse << TD::Convert(TargetFWIdxs[3*idx]);
-        state[6]=TargetFWIdxs[3*idx-2];
-      }
-      state[7]=TD::Convert(issf.str()); state[8]=TD::Convert(isse.str())*-1; 
-      //multiplying target with -1 as compound marker
-    }
-    if (TargetFWIdxs[TargetFWIdxs[0]*3-2]==lat) {
-      state[9]=TargetFWIdxs[TargetFWIdxs[0]*3-2];
-      state[10]=TargetFWIdxs[TargetFWIdxs[0]*3-1];
-      state[11]=TargetFWIdxs[TargetFWIdxs[0]*3];
-    } else {
-      int lastCut = TargetFWIdxs[0];
-      for (int j=lastCut-1; j>=1; j--) {
-        if (TargetFWIdxs[3*j-2]<=state[9]) break;
-        if (TargetFWIdxs[3*j-2]<lat) break;
-        lastCut=j;
-      }
-      state[9]=TargetFWIdxs[3*lastCut-2];
-      ostringstream issf; ostringstream isse;
-      for (int idx=lastCut; idx<=TargetFWIdxs[0]; idx++) {
-        if (idx>lastCut) issf << " "; isse << " ";;
-        issf << TD::Convert(TargetFWIdxs[3*idx-1]);
-        isse << TD::Convert(TargetFWIdxs[3*idx]);
-      }
-      state[10]=TD::Convert(issf.str()); state[11]=TD::Convert(isse.str())*-1; 
-    }
-  }
-}
-
-void Alignment::simplifyBackward(vector<int *>*blocks, int* block, const vector<int>& danglings) {
-// given a *block*, see whether its target span contains any index inside *danglings*. 
-// if yes, break it; otherwise, keep it. put the result(s) to *blocks*
-  if (DEBUG) cerr << "simplifyBackward[" << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << "]" << endl;
-  if (DEBUG) for (int i=0; i<danglings.size(); i++) cerr << "danglings[" << i << "] = " << danglings[i] << endl;
-  if (danglings.size()==0) {
-    blocks->push_back(block); 
-    if (DEBUG) cerr << "pushing(0) " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    return; 
-  }
-  int currIdx = block[2];
-  int i_dangling = 0;
-  while (block[2]>danglings[i_dangling])  {
-    if (i_dangling+1 >= danglings.size()) break;
-    i_dangling++;
-  }
-  while (danglings[i_dangling]==currIdx) {
-    i_dangling++;
-    currIdx++;
-  } 
-  /*if (i_dangling>=danglings.size() && currIdx) {
-    blocks->push_back(block); 
-    if (DEBUG) cerr << "pushing(1) " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    return;
-  }
-  if (block[3]<danglings[i_dangling]) {
-    blocks->push_back(block); 
-    if (DEBUG) cerr << "pushing(2) " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-    return;
-  }*/
-  if (DEBUG) cerr << "i_dangling = " << i_dangling << endl;
-  int anchorIdx = danglings[i_dangling];
-  if (i_dangling+1>=danglings.size() || anchorIdx>block[3]+1) anchorIdx=block[3]+1;
-  if (DEBUG) cerr << "anchorIdx = " << anchorIdx << ", currIdx = " << currIdx << endl;
-  do {
-    while(currIdx<anchorIdx) {
-      if (DEBUG) cerr << "currIdx = " << currIdx << ", anchorIdx = " << anchorIdx << endl;
-      bool isMoved = false;
-      for (int idx=anchorIdx-1; idx>=currIdx; idx--) {
-        int *nublock = blockTarget(currIdx,idx);
-        if (nublock[2]==currIdx && nublock[3]==idx) {
-          if (nublock[0]!=MINIMUM_INIT) {
-            blocks->push_back(nublock);
-            if (DEBUG) cerr << "pushing(3) " << nublock[0] << "," << nublock[1] << "," << nublock[2] << "," << nublock[3] << endl;
-          } else { 
-            delete nublock; 
-          }
-          isMoved = true;
-          currIdx=idx+1; break;
-        } else {
-          delete nublock;
-        }
-      }
-      if (DEBUG) cerr << "isMoved=" << isMoved << ", currIdx=" << currIdx << endl;
-      if (!isMoved) {
-        int source = sourceOf(currIdx);
-        while (source>=0) {
-          if (source >= block[0]) {
-            int* nublock = new int[4];
-            nublock[0]=source; nublock[1]=source; nublock[2]=currIdx; nublock[3]=currIdx;
-            blocks->push_back(nublock);
-            if (DEBUG) cerr << "pushing(4) " << nublock[0] << "," << nublock[1] << "," << nublock[2] << "," << nublock[3] << endl;
-          } 
-          source = sourceOf(currIdx,source+1);
-        }
-        currIdx++;
-      }
-    }
-    currIdx=anchorIdx+1;
-    anchorIdx=block[3]+1;
-    if (i_dangling+1<danglings.size()) anchorIdx=danglings[++i_dangling];
-  } while(currIdx<=block[3]);
-}
-
-void Alignment::simplify(int* ret) {
-  // the idea is to create blocks of maximal consistent alignment in between a pair of function words
-  // exceptional cases include: one to non-contiguous many (or vice versa) -> treat this as one alignment each
-  // record all function word alignments first, important because it may be unaligned
-  // return true if it's truly simple (no function word alignment involves); false, otherwise
-  if (DEBUG) cerr << "begin simplify" << endl;
-  reset(0,0); reset(_J-1,_I-1); // remove the phrase boundary alignments, NEED TO CHECK AGAIN !!!
-  if (SourceFWIdxs[0]+TargetFWIdxs[0]==0) { // return singleton
-    if (DEBUG) cerr << "no function words" << endl;
-    for (int idx=0; idx<12; idx++) ret[idx]=-1;
-    ret[12]=1; ret[13]=0; ret[14]=0; // 0-0
-    FillFWIdxsState(ret,0,0,0,0);  
-    return;
-  }
-  curr_al.insert(curr_al.begin(),curr_al.size());
-  curr_al.push_back(SourceFWIdxs[0]);
-  for (int i=1; i<=SourceFWIdxs[0]; i++) curr_al.push_back(SourceFWIdxs[3*i-2]);
-  curr_al.push_back(TargetFWIdxs[0]);
-  for (int i=1; i<=TargetFWIdxs[0]; i++) curr_al.push_back(TargetFWIdxs[3*i-2]);
-  vector<int> el;
-  if (simplify_hash.find(curr_al)==simplify_hash.end()) {
-    if (DEBUG) {
-      cerr << "SourceFWIdxs:" << SourceFWIdxs[0] << endl;
-      for (int i=1; i<=SourceFWIdxs[0]; i++)  
-        cerr << SourceFWIdxs[3*i-2] << "," <<  SourceFWIdxs[3*i-1] << "," << SourceFWIdxs[3*i] << endl;  
-      cerr << "TargetFWIdxs:" << TargetFWIdxs[0] << endl;
-      for (int i=1; i<=TargetFWIdxs[0]; i++) { 
-        cerr << TargetFWIdxs[3*i-2] << "," <<  TargetFWIdxs[3*i-1] << "," << TargetFWIdxs[3*i] << endl;  
-      }
-    }
-
-    vector< int* > blocks; // each element contains s1,s2,t1,t2
-    int currIdx = 1; // start from 1 to avoid considering phrase start
-    std::set<int> FWIdxs;
-    std::vector<int> DanglingTargetFWIdxs;
-    for (int i=1; i<= SourceFWIdxs[0]; i++) FWIdxs.insert(SourceFWIdxs[3*i-2]);
-    for (int i=1; i<= TargetFWIdxs[0]; i++) {
-      int source = sourceOf(TargetFWIdxs[3*i-2]);
-      if (source>=0) {
-        do {
-          FWIdxs.insert(source);
-          source = sourceOf(TargetFWIdxs[3*i-2],source+1);
-        } while(source >=0);
-      } else {
-        int *block = new int[4];
-        block[0]=-1; block[1]=-1; block[2]=TargetFWIdxs[3*i-2]; block[3]=TargetFWIdxs[3*i-2];
-        blocks.push_back(block);
-        if (DEBUG) cerr << "pushing[1] " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-        DanglingTargetFWIdxs.push_back(TargetFWIdxs[3*i-2]);  
-      }
-    }
-    if (DEBUG)
-      for (std::set<int>::const_iterator iter=FWIdxs.begin(); iter!=FWIdxs.end(); iter++) { 
-        cerr << "FWIdxs=" << *iter << endl;
-      }
-    std::set<int>::const_iterator currFWIdx  = FWIdxs.begin();
-    if (currFWIdx == FWIdxs.end()) {
-      int* block = new int[4];
-      block[0]=1; block[1]=_J-2; block[2]=1; block[3]=_I-2; // no need to consider phrase boundaries
-      simplifyBackward(&blocks,block,DanglingTargetFWIdxs);
-    } else {
-      int anchorIdx = *currFWIdx; // also used to denote _J+1
-      do {
-        // add alignments whose source from currIdx to currFWIdx-1
-        while (currIdx<anchorIdx) {
-          bool isMoved = false;
-          //cerr << "anchorIdx = " << anchorIdx << ", currIdx = " << currIdx << endl;
-          for (int idx=anchorIdx-1; idx>=currIdx; idx--) {
-            int* block = blockSource(currIdx,idx);
-            if (block[0]==currIdx&&block[1]==idx) {
-              if (block[2]!=MINIMUM_INIT) { // must be aligned
-                simplifyBackward(&blocks,block,DanglingTargetFWIdxs); 
-              } else {
-                delete block;
-              }
-              currIdx = idx+1; isMoved = true;
-              break;
-            } else {
-              delete block;
-            }
-          }
-          if (!isMoved) {
-            int target = targetOf(currIdx);
-            while (target>=0) {
-              int* block = new int[4];
-              block[0]=currIdx; block[1]=currIdx; block[2]=target; block[3]=target;
-              blocks.push_back(block);
-              if (DEBUG) cerr << "pushing[2] " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-              target = targetOf(currIdx,target+1);
-            }
-            currIdx++;
-          }
-        }    
-        // add function word alignments (anchorIdx)
-        if (anchorIdx==getJ()) break;
-        int target = targetOf(anchorIdx);
-        do {
-          int* block = new int[4];
-          block[0]=anchorIdx; block[1]=anchorIdx; block[2]=target; block[3]=target;
-          blocks.push_back(block);
-          if (DEBUG) cerr << "pushing[3] " << block[0] << "," << block[1] << "," << block[2] << "," << block[3] << endl;
-          if (target>=0) target = targetOf(anchorIdx,target+1);
-        } while (target>=0);
-        // advance indexes
-        currIdx   = anchorIdx+1;
-        anchorIdx = getJ()-1; // was minus 2
-        if (++currFWIdx!=FWIdxs.end()) anchorIdx = *currFWIdx;
-      } while (currIdx<=getJ()-2);
-    }  
-
-    
-    vector<int> source_block_mapper(getJ(),-1);
-    vector<int> target_block_mapper(getI(),-1);
-    for (int i = 0; i<blocks.size(); i++) {
-      if (DEBUG) cerr << "blocks[" << i << "]=" << blocks[i][0] << "," << blocks[i][1] << "," << blocks[i][2] << "," << blocks[i][3] << endl;
-      if (blocks[i][0]>=0) source_block_mapper[blocks[i][0]]=1;
-      if (blocks[i][2]>=0) target_block_mapper[blocks[i][2]]=1; 
-    }
-    int curr = 1;
-    int prev = -1;
-    for (int idx=0; idx<source_block_mapper.size(); idx++) {
-      if (source_block_mapper[idx]>0) {
-        source_block_mapper[idx]=curr++;
-        prev = curr;
-      } else {
-        source_block_mapper[idx]=prev;
-      }
-    }
-    curr = 1;
-    for (int idx=0; idx<target_block_mapper.size(); idx++) {
-      if (target_block_mapper[idx]>0) {
-        target_block_mapper[idx]=curr++;
-        prev = curr;
-      } else {
-        target_block_mapper[idx]=prev;
-      }
-    }
-    
-    //assert(blocks.size()<=50);
-    if (DEBUG) cerr << "resulting alignment:" << endl;
-    for (int i = 0; i<blocks.size(); i++) {
-      if (blocks[i][2]<0 || blocks[i][0]<0) continue;
-      int source = source_block_mapper[blocks[i][0]]-1;
-      int target = target_block_mapper[blocks[i][2]]-1;
-      el.push_back(link(source,target));
-      if (DEBUG) cerr << source << "-" << target << " ";
-    }
-    el.insert(el.begin(),el.size());
-    if (DEBUG) cerr << endl;
-    el.push_back(SourceFWIdxs[0]);
-    for (int idx=1; idx<=SourceFWIdxs[0]; idx++) {
-      if (DEBUG) cerr << "SourceFWIdxs[" << (3*idx-2) << "] from " << SourceFWIdxs[3*idx-2] << endl;
-      el.push_back(source_block_mapper[SourceFWIdxs[3*idx-2]]-1);
-    }
-    el.push_back(TargetFWIdxs[0]);
-    for (int idx=1; idx<=TargetFWIdxs[0]; idx++) {
-      if (DEBUG) cerr << "TargetFWIdxs[" << (3*idx-2) << "] from " << TargetFWIdxs[3*idx-2] << endl;
-      el.push_back(target_block_mapper[TargetFWIdxs[3*idx-2]]-1);
-    }
-    el.push_back(source_block_mapper[fas]-1); 
-    el.push_back(source_block_mapper[las]-1);
-    el.push_back(target_block_mapper[fat]-1);
-    el.push_back(target_block_mapper[lat]-1);
-    if (DEBUG) {
-      cerr << "insert key:el = ";
-      for (int ii=0; ii<el.size(); ii++) 
-        cerr << ii << "." << el[ii] << " ";
-      cerr << " || " << endl;
-    }
-    if (DEBUG) cerr << "trying to insertL " <<  endl;
-    if (DEBUG) {
-      cerr << "size=" << curr_al.size() << " ";
-      for (int ii=0; ii<curr_al.size(); ii++) cerr << "curr_al[" << ii << "]=" << curr_al[ii] << " ";
-      cerr << endl;
-    }
-    simplify_hash.insert(pair<vector<int>, vector<int> > (curr_al,el));
-    if (DEBUG) cerr << "inserted" << endl;
-  } else {
-    el = simplify_hash[curr_al];
-  }
-  if (DEBUG) {
-    cerr << "pull key:el = ";
-    for (int ii=0; ii<el.size(); ii++)
-      cerr << ii << "." << el[ii] << " ";
-    cerr << endl;
-  }
-  ret[12] = el[0];
-  for (int i=1; i<=el[0]; i++) ret[12+i] = el[i];
-  int istart = el[0]+1;
-  assert(el[istart]==SourceFWIdxs[0]);
-  for (int i=1; i<=el[istart]; i++) SourceFWIdxs[3*i-2]=el[istart+i];
-  istart += el[istart]+1;
-  assert(el[istart]==TargetFWIdxs[0]);
-  for (int i=1; i<=el[istart]; i++) TargetFWIdxs[3*i-2]=el[istart+i];
-  istart += el[istart]+1;
-  FillFWIdxsState(ret,el[istart],el[istart+1],el[istart+2],el[istart+3]);
-}
-
-void Alignment::simplify_nofw(int* ret) {
-  for (int i=0; i<12; i++) ret[i]=-1;  
-  ret[12]=1; ret[13]=0; 
-}
-
-void Alignment::sort(int* num) {
-  if (num[0]>1) quickSort(num,1,num[0]);
-}
-
-void Alignment::quickSort(int arr[], int left, int right) {
-  int i = left, j = right;
-  int tmp1,tmp2,tmp3;
-  int mid = (left + right) / 2;
-  int pivot = arr[3*mid-2];
- 
-  /* partition */
-  while (i <= j) {
-    while (arr[3*i-2] < pivot) i++;
-    while (arr[3*j-2] > pivot) j--;
-    if (i <= j) {
-      tmp1 = arr[3*i-2]; tmp2 = arr[3*i-1]; tmp3 = arr[3*i];
-      arr[3*i-2] = arr[3*j-2]; arr[3*i-1] = arr[3*j-1]; arr[3*i] = arr[3*j];
-      arr[3*j-2] = tmp1; arr[3*j-1] = tmp2; arr[3*j] = tmp3;
-      i++;
-      j--;
-    }
-  };
- 
-  /* recursion */
-  if (left < j) quickSort(arr, left, j);
-  if (i < right) quickSort(arr, i, right);
-}
-
-double Alignment::ScoreOrientation(const CountTable& table, int offset, int ori, WordID cond1, WordID cond2) {
-  string source = TD::Convert(cond1);
-  string sourceidx;
-  if (table.mode == 1) {
-    sourceidx = source; 
-    int slashidx = sourceidx.find_last_of("/");
-    source = sourceidx.substr(0,slashidx);
-    string idx = sourceidx.substr(slashidx+1);
-    if (DEBUG) cerr << "   sourceidx = " << sourceidx << ", idx = " << idx << endl;
-    if (idx == "X") {
-      if (DEBUG) cerr << "        idx == X, returning 0" << endl;
-      return 0;
-    }
-  }
-  string target = TD::Convert(cond2);
-  if (DEBUG) cerr << "sourceidx='" << sourceidx << "', source='" << source << "', target='" << target << "'" << endl;
-  double count = table.ultimate[offset+ori-1];
-  double total = table.ultimate[offset+5];   
-  double alpha = 0.1;
-  double prob = count/total;
-  if (DEBUG) cerr << "level0 " << count << "/" << total << "=" << prob << endl;
-  
-  WordID key_id = (table.mode!=1) ? cond1 : TD::Convert(source); 
-  map<WordID,int*>::const_iterator it = table.model.find(key_id);
-  bool stop = (it==table.model.end());
-  if (!stop) {
-    stop=true;
-    if (it->second[offset+5]>=0) {
-      count = it->second[offset+ori-1] + alpha * prob;
-      total = it->second[offset+5] + alpha;
-      prob = count/total;
-      stop = false;
-      if (DEBUG) cerr << "level1 " << count << "/" << total << "=" << prob << endl;
-    }
-  }
-  if (stop) return prob;
-
-  string key = source + " " + target;
-  it = table.model.find(TD::Convert(key));
-  stop = (it==table.model.end());
-  if (!stop) {
-    stop = true;
-    if (it->second[offset+5]>=0) {
-      count = it->second[offset+ori-1] + alpha * prob;
-      total = it->second[offset+5] + alpha;
-      prob = count/total;
-      stop = false;
-      if (DEBUG) cerr << "level2 " << count << "/" << total << "=" << prob << endl;
-    }
-  }
-
-  if (stop || table.mode!=1) return prob;
-  
-  key = sourceidx + " " + target;
-  it = table.model.find(TD::Convert(key));
-  if (it!=table.model.end()) {
-    if (it->second[offset+5]>=0) {
-      count = it->second[offset+ori-1] + alpha * prob;
-      total = it->second[offset+5] + alpha;
-      prob = count/total;
-      if (DEBUG) cerr << "level3 " << count << "/" << total << "=" << prob << endl;
-    }
-  }
-
-  return prob;
-}
- 
-void Alignment::ScoreOrientation(const CountTable& table, int offset, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus,
-  double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientation:" << TD::Convert(cond1) << "," << TD::Convert(cond2) << ", alpha1 = " << alpha1 << ", beta1 = " << beta1 << endl;
-  double ret = ScoreOrientation(table,offset,ori,cond1,cond2);
-  if (isBonus) {
-    if (table.mode == 0) *bonus += log(ret); else *bonus += ret;
-  } else {
-    if (table.mode == 0) *cost += log(ret); else *cost += ret;
-  }
-}
-
-double Alignment::ScoreOrientationLeft(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,0,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
-
-double Alignment::ScoreOrientationLeftBackward(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,12,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
- 
-double Alignment::ScoreOrientationRight(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,6,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
-
-double Alignment::ScoreOrientationRightBackward(const CountTable& table, int ori, WordID cond1, WordID cond2) {
-  double ret = ScoreOrientation(table,18,ori,cond1,cond2); 
-  if (table.mode == 0) return log(ret);
-  return ret;
-}
-
-void Alignment::ScoreOrientationLeft(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationLeft(" << isBonus << ")" << endl;
-  ScoreOrientation(table,0,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::ScoreOrientationLeftBackward(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationLeftBackward" << endl;
-  ScoreOrientation(table,12,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::ScoreOrientationRight(const CountTable& table, int ori, WordID cond1, WordID cond2, 
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationRight(" << isBonus << ")" << endl;
-  ScoreOrientation(table,6,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::ScoreOrientationRightBackward(const CountTable& table, int ori, WordID cond1, WordID cond2,
-  bool isBonus, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, double alpha1, double beta1) {
-  if (DEBUG) cerr << "ScoreOrientationRightBackward" << endl;
-  ScoreOrientation(table,18,ori,cond1,cond2,isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha1,beta1);
-}
-
-void Alignment::computeOrientationSourceBackwardPos(const CountTable& table, double *cost, double *bonus,
-                                                 double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2) {
-  if (DEBUG) cerr << "computeOrientationSourceBackward" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    if (!(SourceFWRuleAbsIdxs[idx]<=maxdepth1 || maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2)) continue;
-    int* fwblock = blockSource(SourceFWRuleIdxs[3*idx-2],SourceFWRuleIdxs[3*idx-2]);
-    bool aligned = (fwblock[2]!=MINIMUM_INIT);
-    if (aligned) {
-      OrientationTarget(fwblock[2],fwblock[3],&oril,&orir);
-    } else {
-      OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    }
-    if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if ((aligned && fwblock[2]<=fat)||
-        (!aligned && SourceFWRuleIdxs[3*idx-2]<=fas)) isBonus=true;
-    if (SourceFWRuleAbsIdxs[idx]<=maxdepth1) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << SourceFWRuleAbsIdxs[idx];
-      ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    isBonus = false;
-    if ((aligned && lat<=fwblock[3])||
-        (!aligned && las<=SourceFWRuleIdxs[3*idx-2])) isBonus=true;
-    if (SourceFWRuleAbsIdxs[idx]<=maxdepth1) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << SourceFWRuleAbsIdxs[idx];
-      ScoreOrientationRightBackward(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2) {
-      ostringstream nusource;
-      nusource << TD::Convert(SourceFWRuleIdxs[3*idx-1]) << "/" << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      ScoreOrientationRightBackward(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    delete fwblock;
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    // antfas -> first aligned source word antecedent-wise
-    // antlas -> last aligned source word antecedent-wise
-    int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-    int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-    int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-    int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-    assert(antfat <= antlat);
-    assert(antfas <= antlas);
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      if (!(SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1 || maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2)) continue;
-      int* fwblock = blockSource(SourceFWAntsIdxs[i_ant][3*idx-2],SourceFWAntsIdxs[i_ant][3*idx-2]);
-      //bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool aligned = (fwblock[2]!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if (DEBUG) {
-        cerr << " aligned = " << aligned << endl;
-        cerr << "  fwblock = " << fwblock[0] << "," << fwblock[1] << "," << fwblock[2] << "," << fwblock[3] << endl;
-        cerr << "   antfas=" << antfas << ", antlas=" << antlas << ", antfat=" << antfat << ", antlat=" << antlat << endl;
-      }
-      if (aligned) {
-        if (DEBUG) cerr << "laligned" << endl;
-        if (antfat<fwblock[2]) {
-          if (DEBUG) cerr << antfat << "<" << fwblock[2] << endl;
-          Lcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!laligned" << endl;
-        if (antfas<fwblock[0] && fwblock[1] < antlas) Lcompute=false;
-      }
-      if (aligned) {
-        if (DEBUG) cerr << "raligned" << endl;
-        if (fwblock[3]<antlat) {
-          if (DEBUG) cerr << fwblock[3] << "<" << antlat << endl;
-          Rcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!raligned" << endl;
-        if (fwblock[1]<antlas && fwblock[1] < antlas) Rcompute=false;
-      }
-      if (!Lcompute && !Rcompute) continue;
-      if (!aligned) {
-        OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute,Rcompute);
-      } else {
-        OrientationTarget(fwblock[2],fwblock[3],&oril,&orir,Lcompute,Rcompute);
-      }
-      if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-      bool isBonus = false;
-      if (Lcompute) {
-        if ((aligned && fwblock[3]<=fat) ||
-            (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas)) isBonus = true;
-        if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << SourceFWAntsAbsIdxs[i_ant][idx];
-          ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-        if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << (-1*(maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1));
-          ScoreOrientationLeftBackward(table,oril,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if ((aligned && lat<=fwblock[2]) ||
-            (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]))isBonus = true;
-        if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << SourceFWAntsAbsIdxs[i_ant][idx];
-          ScoreOrientationRightBackward(table,orir,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-        if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2) {
-          ostringstream nusource;
-          nusource << TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]) << "/" << (-1*(maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1));
-          ScoreOrientationRightBackward(table,orir,TD::Convert(nusource.str()),SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-      }
-      delete fwblock;
-    }
-  }
-}
-
-
-void Alignment::computeOrientationSourceBackward(const CountTable& table, double *cost, double *bonus, 
-                                                 double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  if (DEBUG) cerr << "computeOrientationSourceBackward" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    int* fwblock = blockSource(SourceFWRuleIdxs[3*idx-2],SourceFWRuleIdxs[3*idx-2]);
-    bool aligned = (fwblock[2]!=MINIMUM_INIT);
-    if (aligned) {
-      OrientationTarget(fwblock[2],fwblock[3],&oril,&orir);
-    } else {
-      OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    }
-    if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if ((aligned && fwblock[2]<=fat)||
-        (!aligned && SourceFWRuleIdxs[3*idx-2]<=fas)) isBonus=true;
-    ScoreOrientationLeftBackward(table,oril,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    isBonus = false;
-    if ((aligned && lat<=fwblock[3])||
-        (!aligned && las<=SourceFWRuleIdxs[3*idx-2])) isBonus=true;
-    ScoreOrientationRightBackward(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    delete fwblock;
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    // antfas -> first aligned source word antecedent-wise
-    // antlas -> last aligned source word antecedent-wise
-    int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-    int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-    int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-    int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-    assert(antfat <= antlat);
-    assert(antfas <= antlas);
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      int* fwblock = blockSource(SourceFWAntsIdxs[i_ant][3*idx-2],SourceFWAntsIdxs[i_ant][3*idx-2]);
-      //bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool aligned = (fwblock[2]!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if (DEBUG) {
-        cerr << " aligned = " << aligned << endl;
-        cerr << "  fwblock = " << fwblock[0] << "," << fwblock[1] << "," << fwblock[2] << "," << fwblock[3] << endl;
-        cerr << "   antfas=" << antfas << ", antlas=" << antlas << ", antfat=" << antfat << ", antlat=" << antlat << endl; 
-      }
-      if (aligned) {
-        if (DEBUG) cerr << "laligned" << endl;
-        if (antfat<fwblock[2]) { 
-          if (DEBUG) cerr << antfat << "<" << fwblock[2] << endl;
-          Lcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!laligned" << endl;
-        if (antfas<fwblock[0] && fwblock[1] < antlas) Lcompute=false;
-      }
-      if (aligned) { 
-        if (DEBUG) cerr << "raligned" << endl;
-        if (fwblock[3]<antlat) { 
-          if (DEBUG) cerr << fwblock[3] << "<" << antlat << endl;
-          Rcompute=false;
-        }
-      } else {
-        if (DEBUG) cerr << "!raligned" << endl;
-        if (fwblock[1]<antlas && fwblock[1] < antlas) Rcompute=false;
-      }
-      if (!Lcompute && !Rcompute) continue;
-      if (!aligned) {
-        OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute,Rcompute);
-      } else {
-        OrientationTarget(fwblock[2],fwblock[3],&oril,&orir,Lcompute,Rcompute);
-      }
-      if (DEBUG) cerr << "oril = " << oril << ", orir = " << orir << endl;
-      bool isBonus = false;
-      if (Lcompute) {
-        if ((aligned && fwblock[3]<=fat) ||
-            (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas)) isBonus = true;
-        ScoreOrientationLeftBackward(table,oril,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if ((aligned && lat<=fwblock[2]) ||
-            (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]))isBonus = true;
-        ScoreOrientationRightBackward(table,orir,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-      delete fwblock;
-    }
-  }
-}
-
-void Alignment::computeOrientationSourcePos(const CountTable& table, double *cost, double *bonus,
-                double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2) {
-  // This implementation is actually really bad, not reusing codes at all
-  if (DEBUG) cerr << "computeOrientationSourcePos(maxfwidx=" << maxfwidx << ",maxdepth=" << maxdepth1 << "," << maxdepth2 << ")" << endl;
-  if (maxdepth1+maxdepth2==0) return;
-  int oril, orir;
-  ostringstream oss;
-  WordID sourceID;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    //if (!((SourceFWRuleAbsIdxs[idx]<=maxdepth1) || (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2))) continue; 
-    string source = TD::Convert(SourceFWRuleIdxs[3*idx-1]);
-    OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if (SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (!isBonus) // this is unnecessary because fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (maxdepth1>0) {
-      oss << source << "/";
-      if (SourceFWRuleAbsIdxs[idx]<=maxdepth1) 
-        oss << SourceFWRuleAbsIdxs[idx];
-      else 
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationLeft(table,oril,sourceID,SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxdepth2>0) {
-      oss << source << "/";
-      if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2)
-        oss << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      else 
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationLeft(table,oril,sourceID,SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    } 
-    isBonus = false;
-    if (las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (!isBonus) // this is unnecessary becuase fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (maxdepth1>0) {
-      oss << source << "/";
-      if (SourceFWRuleAbsIdxs[idx]<=maxdepth1)
-        oss << SourceFWRuleAbsIdxs[idx];
-      else
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationRight(table,orir,sourceID,SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-    if (maxdepth2>0) {
-      oss << source << "/";
-      if (maxfwidx-SourceFWRuleAbsIdxs[idx]+1<=maxdepth2)
-        oss << ((maxfwidx-SourceFWRuleAbsIdxs[idx]+1)*-1);
-      else
-        oss << "X";
-      sourceID = TD::Convert(oss.str());
-      oss.str("");
-      ScoreOrientationRight(table,orir,sourceID,SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    }
-
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      //if (!((SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1)||(maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2))) continue;
-      // antfas -> first aligned source word antecedent-wise
-      // antlas -> last aligned source word antecedent-wise
-      int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-      int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-      if (DEBUG) cerr << " SourceFWAntsAbsIdxs[i_ant][3*idx-1]=" << SourceFWAntsAbsIdxs[i_ant][3*idx-1] << endl;
-      string source = TD::Convert(SourceFWAntsIdxs[i_ant][3*idx-1]); 
-      assert(antfas <= antlas);
-      bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true;bool Rcompute = true;
-      if ((aligned && antfas<SourceFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Lcompute=false;
-      if ((aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<antlas) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute, Rcompute);
-      bool isBonus = false;
-      if (Lcompute) {
-        if (SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus = true;
-        //if (!isBonus)  // this is unnecessary
-        //  if (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        if (maxdepth1>0) {
-          oss << source << "/";
-          if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1)
-            oss << SourceFWAntsAbsIdxs[i_ant][idx];
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationLeft(table,oril,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-        if (maxdepth2>0) {
-          oss << source << "/";
-          if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2)
-            oss << ((maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1)*-1);
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationLeft(table,oril,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus = true;
-        //if (!isBonus) // this is unnecessary
-        //  if (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus=true;
-        if (maxdepth1>0) {
-          oss << source << "/";
-          if (SourceFWAntsAbsIdxs[i_ant][idx]<=maxdepth1)
-            oss << SourceFWAntsAbsIdxs[i_ant][idx];
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationRight(table,orir,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }	
-       if (maxdepth2>0) {
-          oss << source << "/";
-          if (maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1<=maxdepth2)
-            oss << ((maxfwidx-SourceFWAntsAbsIdxs[i_ant][idx]+1)*-1);
-          else
-            oss << "X";
-          sourceID = TD::Convert(oss.str());
-          oss.str("");
-          ScoreOrientationRight(table,orir,sourceID,SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-        }	
-      }
-    }
-  }
-}
-
-void Alignment::computeOrientationSource(const CountTable& table, double *cost, double *bonus, 
-                                         double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-// a bit complex due to imperfect state (TO DO!!!)
-// 1. there are cases where function word alignments come from antecedents, which orientation 
-// (either its left or its right) has been computed earlier.   
-// 2. some orientation will go as bonus
-  if (DEBUG) cerr << "computeOrientationSource" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl; 
-    OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if (SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (!isBonus) // this is unnecessary because fas <= las assertion 
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    ScoreOrientationLeft(table,oril,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris); 
-    isBonus = false;
-    if (las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (!isBonus) // this is unnecessary becuase fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    ScoreOrientationRight(table,orir,SourceFWRuleIdxs[3*idx-1],SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      // antfas -> first aligned source word antecedent-wise
-      // antlas -> last aligned source word antecedent-wise
-      int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-      int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-      assert(antfas <= antlas);
-      bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true;bool Rcompute = true;
-      if ((aligned && antfas<SourceFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas)) 
-          Lcompute=false; 
-      if ((aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<antlas) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas)) 
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute, Rcompute);
-      bool isBonus = false;
-      if (Lcompute) {
-        if (SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus = true;
-        //if (!isBonus)  // this is unnecessary
-        //  if (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeft(table,oril,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris); 
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus = true;
-        //if (!isBonus) // this is unnecessary
-        //  if (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus=true;
-        ScoreOrientationRight(table,orir,SourceFWAntsIdxs[i_ant][3*idx-1],SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-    }
-  }
-}
-
-void Alignment::computeOrientationSourceGen(const CountTable& table, double *cost, double *bonus,
-                                         double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, const map<WordID,WordID>& tags) {
-  if (DEBUG) cerr << "computeOrientationSourceGen" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering SourceFWRuleIdxs[" << idx << "]: " << SourceFWRuleIdxs[3*idx-2] << endl;
-    OrientationSource(SourceFWRuleIdxs[3*idx-2],&oril,&orir);
-    bool isBonus = false; // fas -> first aligned source word, las -> last aligned source word
-    if (SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    if (!isBonus) // this is unnecessary because fas <= las assertion 
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    ScoreOrientationLeft(table,oril,generalize(SourceFWRuleIdxs[3*idx-1],tags),SourceFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-    isBonus = false;
-    if (las<=SourceFWRuleIdxs[3*idx-2]) isBonus=true;
-    if (!isBonus) // this is unnecessary becuase fas <= las assertion
-      if (minTSpan(SourceFWRuleIdxs[3*idx-2])==MINIMUM_INIT && SourceFWRuleIdxs[3*idx-2]<=fas) isBonus=true;
-    ScoreOrientationRight(table,orir,generalize(SourceFWRuleIdxs[3*idx-1],tags),SourceFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG)
-        cerr << "considering SourceFWAntsIdxs[" << i_ant << "][" << idx << "]: " << SourceFWAntsIdxs[i_ant][3*idx-2] << endl;
-      // antfas -> first aligned source word antecedent-wise
-      // antlas -> last aligned source word antecedent-wise
-      int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-      int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-      assert(antfas <= antlas);
-      bool aligned = (minTSpan(SourceFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true;bool Rcompute = true;
-      if ((aligned && antfas<SourceFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Lcompute=false;
-      if ((aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<antlas) ||
-          (!aligned && antfas < SourceFWAntsIdxs[i_ant][3*idx-2] && SourceFWAntsIdxs[i_ant][3*idx-2] < antlas))
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      OrientationSource(SourceFWAntsIdxs[i_ant][3*idx-2],&oril,&orir,Lcompute, Rcompute);
-      bool isBonus = false;
-      if (Lcompute) {
-        if (SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus = true;
-        //if (!isBonus)  // this is unnecessary
-       //  if (!aligned && las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeft(table,oril,generalize(SourceFWAntsIdxs[i_ant][3*idx-1],tags),SourceFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (las<=SourceFWAntsIdxs[i_ant][3*idx-2]) isBonus = true;
-        //if (!isBonus) // this is unnecessary
-        //  if (!aligned && SourceFWAntsIdxs[i_ant][3*idx-2]<=fas) isBonus=true;
-        ScoreOrientationRight(table,orir,generalize(SourceFWAntsIdxs[i_ant][3*idx-1],tags),SourceFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_oris,beta_oris);
-      }
-    }
-  }
-}
-void Alignment::computeOrientationTarget(const CountTable& table, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  if (DEBUG) cerr << "computeOrientationTarget" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering TargetFWRuleIdxs[" << idx << "]: " << TargetFWRuleIdxs[3*idx-2] << endl;
-    OrientationTarget(TargetFWRuleIdxs[3*idx-2],&oril,&orir);
-    // the second and the third parameters of ScoreOrientationLeft must be e and f (not f and then e) 
-    bool isBonus = false;
-    if (TargetFWRuleIdxs[3*idx-2]<=fat) isBonus = true;
-    if (!isBonus)
-      if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    ScoreOrientationLeft(table,oril,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit); 
-    isBonus = false;
-    if (lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    if (!isBonus)
-      if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && TargetFWRuleIdxs[3*idx-2]<=fat) isBonus=true;
-    ScoreOrientationRight(table,orir,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-  }
-
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) cerr << "considering TargetFWAntsIdxs[" << i_ant << "][" << idx << "]: " << TargetFWAntsIdxs[i_ant][3*idx-2] << endl; 
-      int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-      int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-      int aligned = (minSSpan( TargetFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if ((aligned && antfat<TargetFWAntsIdxs[i_ant][3*idx-2]) ||
-          (!aligned && antfat < TargetFWAntsIdxs[i_ant][3*idx-2] && TargetFWAntsIdxs[i_ant][3*idx-2] < antlat)) 
-          Lcompute=false;
-      if ((aligned && TargetFWAntsIdxs[i_ant][3*idx-2]<antlat) ||
-          (!aligned && antfat < TargetFWAntsIdxs[i_ant][3*idx-2] && TargetFWAntsIdxs[i_ant][3*idx-2] < antlat)) 
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      bool isBonus = false;
-      OrientationTarget(TargetFWAntsIdxs[i_ant][3*idx-2],&oril,&orir, Lcompute, Rcompute);
-      if (Lcompute) {
-        if (TargetFWAntsIdxs[i_ant][3*idx-2]<=fat) isBonus=true;
-        //if (!isBonus) 
-        //  if (!aligned && lat<=TargetFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeft(table,oril,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit); 
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if (lat<=TargetFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        if (!isBonus)
-          //if (!aligned && TargetFWAntsIdxs[i_ant][3*idx-2]<=fat) isBonus=true;
-        ScoreOrientationRight(table,orir,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-      }
-    }
-  }
-}
-
-void Alignment::computeOrientationTargetBackward(const CountTable& table, double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  if (DEBUG) cerr << "computeOrientationTargetBackward" << endl;
-  int oril, orir;
-  for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << "considering TargetFWRuleIdxs[" << idx << "]: " << TargetFWRuleIdxs[3*idx-2] << endl;
-    int* fwblock = blockSource(TargetFWRuleIdxs[3*idx-2],TargetFWRuleIdxs[3*idx-2]);
-    bool aligned = (fwblock[0] == MINIMUM_INIT);
-    if (aligned) {
-      OrientationSource(fwblock[0],fwblock[1],&oril,&orir);
-    } else {
-      OrientationTarget(TargetFWRuleIdxs[3*idx-2],&oril,&orir);
-    }
-    delete fwblock;
-    // the second and the third parameters of ScoreOrientationLeft must be e and f (not f and then e)
-    bool isBonus = false;
-    if (TargetFWRuleIdxs[3*idx-2]<=fat) isBonus = true;
-    //if (!isBonus)  // unnecessary
-      //if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    ScoreOrientationLeftBackward(table,oril,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                         isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-    isBonus = false;
-    if (lat<=TargetFWRuleIdxs[3*idx-2]) isBonus = true;
-    //if (!isBonus) // unnecessary
-      //if (minSSpan(TargetFWRuleIdxs[3*idx-2])==MINIMUM_INIT && TargetFWRuleIdxs[3*idx-2]<=fat) isBonus=true;
-    ScoreOrientationRightBackward(table,orir,TargetFWRuleIdxs[3*idx-1],TargetFWRuleIdxs[3*idx],
-                          isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-  }
-
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    int antfat = firstTargetAligned(TargetAntsIdxs[i_ant][1]);
-    int antlat = lastTargetAligned(TargetAntsIdxs[i_ant][TargetAntsIdxs[i_ant][0]]);
-    int antfas = firstSourceAligned(SourceAntsIdxs[i_ant][1]);
-    int antlas = lastSourceAligned(SourceAntsIdxs[i_ant][SourceAntsIdxs[i_ant][0]]);
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) cerr << "considering TargetFWAntsIdxs[" << i_ant << "][" << idx << "]: " << TargetFWAntsIdxs[i_ant][3*idx-2] << endl;
-      int* fwblock = blockTarget(TargetFWAntsIdxs[i_ant][3*idx-2],TargetFWAntsIdxs[i_ant][3*idx-2]);
-      bool aligned = (fwblock[0]!=MINIMUM_INIT);
-      //bool aligned = (minSSpan( TargetFWAntsIdxs[i_ant][3*idx-2])!=MINIMUM_INIT);
-      bool Lcompute = true; bool Rcompute = true;
-      if ((aligned && antfas<fwblock[0]) ||
-          (!aligned && antfat < fwblock[2]))
-          Lcompute=false;
-      if ((aligned && fwblock[0]<antlas) ||
-          (!aligned && fwblock[3] < antlat))
-          Rcompute=false;
-      if (!Lcompute && !Rcompute) continue;
-      bool isBonus = false;
-      if (aligned) {
-        OrientationSource(fwblock[0],fwblock[1],&oril,&orir,Lcompute,Rcompute);
-      } else { 
-        OrientationTarget(TargetFWAntsIdxs[i_ant][3*idx-2],&oril,&orir, Lcompute, Rcompute);
-      }
-      if (Lcompute) {
-        if ((aligned && fwblock[1]<=fas) ||
-            (!aligned && fwblock[3]<=fat))
-            isBonus=true;
-        //if (!isBonus)
-        //  if (!aligned && lat<=TargetFWAntsIdxs[i_ant][3*idx-2]) isBonus=true;
-        ScoreOrientationLeftBackward(table,oril,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                             isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-      }
-      isBonus = false;
-      if (Rcompute) {
-        if ((aligned && las<=fwblock[0]) ||
-            (!aligned && lat<=fwblock[2]))
-            isBonus=true;
-        if (!isBonus)
-          //if (!aligned && TargetFWAntsIdxs[i_ant][3*idx-2]<=fat) isBonus=true;
-        ScoreOrientationRightBackward(table,orir,TargetFWAntsIdxs[i_ant][3*idx-1],TargetFWAntsIdxs[i_ant][3*idx],
-                              isBonus,cost,bonus,bo1,bo1_bonus,bo2,bo2_bonus,alpha_orit,beta_orit);
-      }
-      delete fwblock;
-    }
-  }
-}
-
-bool Alignment::MemberOf(int* FWIdxs, int pos1, int pos2) {
-  for (int idx=2; idx<=FWIdxs[0]; idx++) { 
-    if (FWIdxs[3*(idx-1)-2]==pos1 && FWIdxs[3*idx-2]==pos2) return true;
-  }
-  return false;
-}
-
-void Alignment::computeDominanceSource(const CountTable& table, WordID lfw, WordID rfw, 
-     double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-  // no bonus yet
-  if (DEBUG) cerr << "computeDominanceSource" << endl;
-  if (DEBUG) cerr << " initial cost=" << *cost << ", initial bonus=" << *bonus << endl;
-  for (int idx=2; idx<=SourceFWIdxs[0]; idx++) {
-    if (DEBUG) { 
-      cerr << "PrevSourceFWIdxs :" << SourceFWIdxs[3*(idx-1)-2] << "," << SourceFWIdxs[3*(idx-1)-1] 
-           << "," << SourceFWIdxs[3*(idx-1)] << endl;
-      cerr << "CurrSourceFWIdxs :" << SourceFWIdxs[3*(idx)-2] << "," << SourceFWIdxs[3*(idx)-1] 
-           << "," << SourceFWIdxs[3*(idx)] << endl;
-    }
-    bool compute = true;
-    for (int i_ant=0; i_ant<_Arity && compute; i_ant++) {
-      if (MemberOf(SourceFWAntsIdxs[i_ant],SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*(idx)-2])) {
-        //cerr << "Skipping, they have been calculated in the  " << (i_ant+1) << "-th branch" << endl;
-        compute=false;
-      }
-    }
-    if (compute) {
-      int dom = DominanceSource(SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*idx-2]);
-      if (DEBUG) cerr << "dom = " << dom << endl;
-      ScoreDominance(table,dom,SourceFWIdxs[3*(idx-1)-1],SourceFWIdxs[3*idx-1],SourceFWIdxs[3*(idx-1)],SourceFWIdxs[3*idx],
-              cost,bo1,bo2,false,alpha_doms,beta_doms);
-      if (DEBUG) cerr << "cost now is " << *cost << endl;
-    }
-  }
-  if (SourceFWIdxs[0]>0) {
-    if (lfw>=0) {
-      int dom = DominanceSource(0,SourceFWIdxs[1]);
-      if (DEBUG) cerr << " --> lfw = " << lfw << "-" << TD::Convert(lfw) << endl;
-      if (DEBUG) cerr << " --> rfw = " << rfw << "-" << TD::Convert(rfw) << endl;
-      ScoreDominance(table,dom,lfw,SourceFWIdxs[2],lfw,SourceFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-    }
-    if (rfw>=0) {
-      int dom = DominanceSource(SourceFWIdxs[3*SourceFWIdxs[0]-2],_J-1);
-      ScoreDominance(table,dom,SourceFWIdxs[3*SourceFWIdxs[0]-1],rfw,SourceFWIdxs[3*SourceFWIdxs[0]],
-                     rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-    }
-  }
-}
-
-void Alignment::computeDominanceSourcePos(const CountTable& table, WordID lfw, WordID rfw,
-     double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus, int maxfwidx, int maxdepth1, int maxdepth2) {
-  if (DEBUG) cerr << "computeDominanceSourcePos" << endl;
-  if (DEBUG) cerr << " initial cost=" << *cost << ", initial bonus=" << *bonus << endl;
-  ostringstream oss;
-  for (int idx=2; idx<=SourceFWIdxs[0]; idx++) {
-    if (DEBUG) {
-      cerr << "PrevSourceFWIdxs :" << SourceFWIdxs[3*(idx-1)-2] << "," << SourceFWIdxs[3*(idx-1)-1]
-           << "," << SourceFWIdxs[3*(idx-1)] << endl;
-      cerr << "CurrSourceFWIdxs :" << SourceFWIdxs[3*(idx)-2] << "," << SourceFWIdxs[3*(idx)-1]
-           << "," << SourceFWIdxs[3*(idx)] << endl;
-    }
-    //if (!((SourceFWAbsIdxs[3*(idx-1)-2]<=maxdepth1 && SourceFWAbsIdxs[3*idx-2]<=maxdepth1) ||
-    //      (maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1<=maxdepth2 && maxfwidx-SourceFWAbsIdxs[3*idx-2]+1<=maxdepth2))) continue;
-    bool compute = true;
-    for (int i_ant=0; i_ant<_Arity && compute; i_ant++) {
-      if (MemberOf(SourceFWAntsIdxs[i_ant],SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*(idx)-2])) {
-        //cerr << "Skipping, they have been calculated in the  " << (i_ant+1) << "-th branch" << endl;
-        compute=false;
-      }
-    }
-    if (compute) {
-      int dom = DominanceSource(SourceFWIdxs[3*(idx-1)-2],SourceFWIdxs[3*idx-2]);
-      if (DEBUG) cerr << "dom = " << dom << endl;
-      if (maxdepth1+maxdepth2>0) {
-        string source1 = TD::Convert(SourceFWIdxs[3*(idx-1)-1]);
-        string source2 = TD::Convert(SourceFWIdxs[3*(idx)-1]);
-        if (maxdepth1>0) {
-          oss << source1 << "/";
-          if (SourceFWAbsIdxs[3*(idx-1)-2]<=maxdepth1) 
-            oss << SourceFWAbsIdxs[3*(idx-1)-2];
-          else 
-            oss << "X";
-          WordID source1id = TD::Convert(oss.str());
-          oss.str("");
-          oss << source2 << "/";
-          if (SourceFWAbsIdxs[3*idx-2]<=maxdepth1)
-            oss << SourceFWAbsIdxs[3*idx-2];
-          else
-            oss << "X";
-          WordID source2id = TD::Convert(oss.str());
-          oss.str("");    
-          ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*(idx-1)],SourceFWIdxs[3*idx],
-              cost,bo1,bo2,false,alpha_doms,beta_doms);
-        }  
-        if (maxdepth2>0) {
-          oss << source1 << "/";
-          if (maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1<=maxdepth2) 
-            oss << ((maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1)*-1);
-          else
-            oss << "X";
-          WordID source1id = TD::Convert(oss.str());
-          oss.str("");
-          oss << source2 << "/";
-          if (maxfwidx-SourceFWAbsIdxs[3*idx-2]+1<=maxdepth2) 
-            oss << ((maxfwidx-SourceFWAbsIdxs[3*(idx-1)-2]+1)*-1);
-          else
-            oss << "X";
-          WordID source2id = TD::Convert(oss.str());
-          oss.str("");
-          ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*(idx-1)],SourceFWIdxs[3*idx],
-              cost,bo1,bo2,false,alpha_doms,beta_doms);
-        }
-      }
-    }
-  }
-  if (SourceFWIdxs[0]>0) {
-    if (lfw>=0) {
-      int dom = DominanceSource(0,SourceFWIdxs[1]);
-      string source1 = TD::Convert(lfw);
-      string source2 = TD::Convert(SourceFWIdxs[2]);
-      if (maxdepth1>0) {
-        oss << source1 << "/";
-        if (SourceFWAbsIdxs[1]-1<=maxdepth1) 
-          oss << (SourceFWAbsIdxs[1]-1);
-        else
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (SourceFWAbsIdxs[1]<=maxdepth1)
-          oss << SourceFWAbsIdxs[1];
-        else
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        oss.str("");
-        ScoreDominance(table,dom,source1id,source2id,lfw,SourceFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-      if (maxdepth2>0) { 
-        oss << source1 << "/";
-        if (maxfwidx-(SourceFWAbsIdxs[1]-1)+1<=maxdepth2) 
-          oss << ((maxfwidx-(SourceFWAbsIdxs[1]-1)+1)*-1);
-        else 
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (maxfwidx-SourceFWAbsIdxs[1]+1<=maxdepth2) 
-          oss << ((maxfwidx-SourceFWAbsIdxs[1]+1)*-1);
-        else 
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        oss.str("");
-        ScoreDominance(table,dom,source1id,source2id,lfw,SourceFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-    }
-    if (rfw>=0) {
-      int dom = DominanceSource(SourceFWIdxs[3*SourceFWIdxs[0]-2],_J-1);
-      string source1 = TD::Convert(SourceFWIdxs[3*SourceFWIdxs[0]-1]);
-      string source2 = TD::Convert(rfw);
-      if (maxdepth1>0) {
-        oss << source1 << "/";
-        if (SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]<=maxdepth1)
-          oss << SourceFWAbsIdxs[3*SourceFWIdxs[0]-2];
-        else
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1<=maxdepth1)
-          oss << (SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1);
-        else 
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*SourceFWIdxs[0]],
-                     rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-      if (maxdepth2>0) {
-        oss << source1 << "/";
-        if (maxfwidx-SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1<=maxdepth2) 
-          oss << ((maxfwidx-SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1)*-1);
-        else 
-          oss << "X";
-        WordID source1id = TD::Convert(oss.str());
-        oss.str("");
-        oss << source2 << "/";
-        if (maxfwidx-(SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1)+1<=maxdepth2) 
-          oss << ((maxfwidx-(SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]+1)+1)*-1);
-        else 
-          oss << "X";
-        WordID source2id = TD::Convert(oss.str());
-        oss.str("");
-        ScoreDominance(table,dom,source1id,source2id,SourceFWIdxs[3*SourceFWIdxs[0]],
-                     rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_doms,beta_doms);
-      }
-    }
-  }
-}
-
-
-void Alignment::computeDominanceTarget(const CountTable& table, WordID lfw, WordID rfw,
-     double *cost, double *bonus, double *bo1, double *bo1_bonus, double *bo2, double *bo2_bonus) {
-   if (DEBUG) cerr << "computeDominanceTarget" << endl;
-  for (int idx=2; idx<=TargetFWIdxs[0]; idx++) {
-    if (DEBUG) cerr << "PrevTargetFWIdxs :" << TargetFWIdxs[3*(idx-1)-2] << "," << TargetFWIdxs[3*(idx-1)-1] << "," <<TargetFWIdxs[3*(idx-1)] << endl;
-    if (DEBUG) cerr << "CurrTargetFWIdxs :" << TargetFWIdxs[3*(idx)-2] << "," << TargetFWIdxs[3*(idx)-1] << "," <<TargetFWIdxs[3*(idx)] << endl;
-    bool compute = true;
-    for (int i_ant=0; i_ant <_Arity && compute; i_ant++) {
-      if (MemberOf(TargetFWAntsIdxs[i_ant],TargetFWIdxs[3*(idx-1)-2],TargetFWIdxs[3*idx-2])) {
-        if (DEBUG) cerr << "Skipping, they have been calculated in the " << (i_ant+1) << "-th branch" << endl;
-        compute = false;
-      }
-    }
-    if (compute) {
-      int dom = DominanceTarget(TargetFWIdxs[3*(idx-1)-2],TargetFWIdxs[3*idx-2]);
-      //cerr << (3*(idx-1)) << "," << (3*idx) << "," << (3*(idx-1)-1) << "," << (3*idx-1) << endl;
-      if (DEBUG) cerr << "dom target = " << dom << endl;
-      ScoreDominance(table,dom,TargetFWIdxs[3*(idx-1)],TargetFWIdxs[3*idx],TargetFWIdxs[3*(idx-1)-1],TargetFWIdxs[3*idx-1],
-              cost,bo1,bo2,false,alpha_domt,beta_domt);
-    }
-  }
-  if (TargetFWIdxs[0]>0) {
-    if (DEBUG) cerr << "backoff dominance " << endl;
-    if (lfw>=0) {
-      int dom = DominanceTarget(0,TargetFWIdxs[1]);
-      if (DEBUG) cerr << "dom target (with left) = " << dom << endl;
-      ScoreDominance(table,dom,lfw,lfw,TargetFWIdxs[2],TargetFWIdxs[3],bonus,bo1_bonus,bo2_bonus,true,alpha_domt,beta_domt);
-    }
-    if (rfw>=0) {
-      int dom = DominanceTarget(TargetFWIdxs[3*TargetFWIdxs[0]-2],_I-1);
-      if (DEBUG) cerr << "dom target (with right) = " << dom << endl;
-      ScoreDominance(table,dom,TargetFWIdxs[3*TargetFWIdxs[0]-1],TargetFWIdxs[3*TargetFWIdxs[0]],
-                     rfw,rfw,bonus,bo1_bonus,bo2_bonus,true,alpha_domt,beta_domt);
-    }
-  }
-
-  //cerr << "END of computeDominanceTarget" << endl;
-}
-
-double Alignment::ScoreDominance(const CountTable& table, int dom, WordID source1, WordID source2, WordID target1, WordID target2) {
-  if (DEBUG) {
-     cerr << "ScoreDominance(source1=" << TD::Convert(source1) << ",source2=" << TD::Convert(source2)
-          << ",target1=" << TD::Convert(target1) << ",target2=" << TD::Convert(target2) << ", dom=" << dom << endl;
-  }
-  string _source1 = TD::Convert(source1);
-  string _source2 = TD::Convert(source2);
-  string _source1idx; string _source2idx;
-  if (table.mode==1) {
-    _source1idx = _source1; _source2idx = _source2;
-    _source1 = _source1idx.substr(0,_source1idx.find_last_of("/"));
-    _source2 = _source2idx.substr(0,_source2idx.find_last_of("/"));
-  }
-  string _target1 = TD::Convert(target1);
-  string _target2 = TD::Convert(target2);
-
-  double count = table.ultimate[dom];
-  double total = table.ultimate[4];
-  double prob = count/total;
-  if (DEBUG) cerr << "level0 " << count << "/" << total << "=" << prob << endl;
-  double alpha = 0.1;
-  
-  string key = _source1 + " " + _source2;
-  WordID key_id = TD::Convert(key);
-  map<WordID,int*>::const_iterator it = table.model.find(key_id); 
-  bool stop = (it==table.model.end());
-  if (!stop) {
-    stop = true;
-    if (it->second[4]>=0) {
-      count = it->second[dom] + alpha*prob;
-      total = it->second[4]   + alpha;
-      prob = count/total;
-      if (DEBUG) cerr << "level1 " << count << "/" << total << "=" << prob << endl;
-      stop = false;
-    }
-  } 
-  if (stop) return prob;
- 
-  key = _source1 + " " + _source2 + " " + _target1 + " " + _target2; 
-  key_id = TD::Convert(key);  
-  it = table.model.find(key_id);
-  stop = (it==table.model.end());
-  if (!stop) {
-    stop = true;
-    if (it->second[4]>=0) {
-      count = it->second[dom] + alpha*prob;
-      total = it->second[4]   + alpha;
-      prob = count/total;
-      if (DEBUG) cerr << "level2 " << count << "/" << total << "=" << prob << endl;
-      stop = false;
-    }
-  } 
- 
-  if (table.mode!=1 || stop) return prob;
-  key = _source1 + " " + _source2 + " " + _target1 + " " + _target2;
-  key_id = TD::Convert(key);
-  it = table.model.find(key_id);
-  if (it!=table.model.end()) {
-    if (it->second[4]>=0) {
-      count = it->second[dom] + alpha*prob;
-      total = it->second[4]   + alpha;
-      if (DEBUG) cerr << "level3 " << count << "/" << total << "=" << prob << endl;
-      prob = count/total;
-    }
-  }
-
-  return prob;
-}
-
-void Alignment::ScoreDominance(const CountTable& table, int dom, WordID source1, WordID source2, WordID target1, WordID target2, double *cost, double *bo1, double *bo2, bool isBonus, double alpha2, double beta2) {
-  if (DEBUG) 
-    cerr << "ScoreDominance(source1=" << TD::Convert(source1) << ",source2=" << TD::Convert(source2) 
-         << ",target1=" << TD::Convert(target1) << ",target2=" << TD::Convert(target2) << ",isBonus=" << isBonus << ", alpha2 = " << alpha2 << ", beta2 = " << beta2 << endl;
-  if (DEBUG) cerr << "    BEFORE=" << *cost << endl;
-  *cost += ScoreDominance(table,dom,source1,source2,target1,target2);
-  if (DEBUG) cerr << "    AFTER=" << *cost << endl;
-}
-
-WordID Alignment::F2EProjectionFromExternal(int idx, const vector<AlignmentPoint>& als, const string& delimiter) {
-  if (DEBUG) {
-    cerr << "F2EProjectionFromExternal=" << idx << endl;
-    for (int i=0; i< als.size(); i++) cerr << "als[" << i << "]=" << als[i] << " ";
-    cerr << endl;
-  }
-  vector<int> alignedTo;
-  for (int i=0; i<als.size(); i++) {
-    if (DEBUG) cerr << als[i] << " ";
-    if (als[i].s_==idx) 
-      alignedTo.push_back(als[i].t_);
-  }
-  if (DEBUG) {
-    cerr << endl;
-    cerr << "alignedTo = ";
-    for (int i=0; i<alignedTo.size(); i++) cerr << alignedTo[i] << " ";
-    cerr << endl;
-  }
-  if (alignedTo.size()==0) {
-    if (DEBUG) cerr << "returns [NULL] : " << TD::Convert("NULL") << endl;
-    return TD::Convert("NULL");
-  } else if (alignedTo.size()==1) {
-    if (DEBUG) cerr << "returns [" << TD::Convert(_e[alignedTo[0]]) << "] : " << _e[alignedTo[0]] << endl;
-    return _e[alignedTo[0]]; // if not aligned to many, why bother continuing
-  } else {
-    ostringstream projection;
-    for (int i=0; i<alignedTo.size(); i++) {
-      if (i>0) projection << delimiter;
-      projection << TD::Convert(_e[alignedTo[i]]);
-    }
-    if (DEBUG) {
-      cerr << "projection = " << projection.str() << endl;
-      cerr << "returns = " << TD::Convert(projection.str()) << endl;
-    }
-    return TD::Convert(projection.str());
-  }
-}
-
-WordID Alignment::E2FProjectionFromExternal(int idx, const vector<AlignmentPoint>& als, const string& delimiter) {
-  vector<int> alignedTo;
-  for (int i=0; i<als.size(); i++)
-    if (als[i].t_==idx) alignedTo.push_back(als[i].s_);
-  if (alignedTo.size()==0) {
-    return TD::Convert("NULL");
-  } else if (alignedTo.size()==1) {
-    return _f[alignedTo[0]]; // if not aligned to many, why bother continuing
-  } else {
-    ostringstream projection;
-    for (int i=0; i<alignedTo.size(); i++) {
-      if (i>0) projection << delimiter;
-      projection << TD::Convert(_f[alignedTo[i]]);
-    }
-    return TD::Convert(projection.str());
-  }
-}
-
-
-WordID Alignment::F2EProjection(int idx, const string& delimiter) {
-  if (DEBUG) cerr << "F2EProjection(" << idx << ")" << endl;
-  int e = targetOf(idx);
-  if (e<0) {
-    if (DEBUG) cerr << "projection = NULL" << endl;
-    return TD::Convert("NULL");
-  } else {
-    if (targetOf(idx,e+1)<0) {
-      if (DEBUG) cerr << "e-1=" << (e-1) << ", size=" << _e.size() << endl;
-      return getE(e-1); // if not aligned to many, why bother continuing
-    }
-    ostringstream projection;
-    bool firstTime = true;
-    do {
-      if (!firstTime) projection << delimiter; 
-      projection << TD::Convert(_e[e-1]); // transform space
-      firstTime = false;
-      e = targetOf(idx,e+1);
-      //if (DEBUG) cerr << "projection = " << projection.str() << endl;
-    } while(e>=0);
-    return TD::Convert(projection.str());
-  }
-}
-
-WordID Alignment::E2FProjection(int idx, const string& delimiter) {
-  //cerr << "E2FProjection(" << idx << ")" << endl;
-  //cerr << "i" << endl;
-  int f = sourceOf(idx);
-  //cerr << "j, f=" << f << endl;
-  if (f<0) {
-    //cerr << "projection = NULL" << endl;
-    return TD::Convert("NULL");
-  } else {
-    if (sourceOf(idx,f+1)<0) return getF(f-1);
-    bool firstTime = true;
-    ostringstream projection(ostringstream::out);
-    do {
-      if (!firstTime) projection << delimiter;
-      projection << TD::Convert(_f[f-1]); //transform space
-      firstTime = false;
-      f = sourceOf(idx,f+1);
-      //cerr << "projection = " << projection.str() << endl;
-    } while(f>=0);
-    return TD::Convert(projection.str());
-  }
-}
-void Alignment::computeBorderDominanceSource(const CountTable& table, double *cost, double *bonus, double *state_mono, 
-        double *state_nonmono, TRule &rule, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw) {
-  // HACK: GOAL is assumed to always be "S"
-  if (DEBUG) cerr << "computeBorderDominanceSource" << endl;
-  std::vector<WordID> f = rule.f();
-  std::vector<WordID> e = rule.e();
-  int nt_index[f.size()];
-  int nt_count=0;
-  for (int i=0; i<f.size(); i++) nt_index[i] = (f[i]<0)? ++nt_count : 0;
-  if (DEBUG) {
-    cerr << "f = ";
-    for (int i=0; i<f.size(); i++) cerr << i << "." << "[" << f[i] << "] ";
-    cerr << endl;
-    cerr << "e = ";
-    for (int i=0; i<e.size(); i++) cerr << i << "." << "[" << e[i] << "] ";
-    cerr << endl;
-  }
-  bool flag[f.size()]; 
-  for (int idx=0; idx<f.size(); idx++) flag[idx]=false;
-  //collect alignments
-  vector<int> als;
-  for (std::vector<AlignmentPoint>::const_iterator i = rule.als().begin(); i != rule.als().end(); ++i) {
-    int s = i->s_; int t = i->t_;
-    als.push_back(link(t,s));
-  }
-  if (DEBUG) cerr << "rule.Arity=" << rule.Arity() << endl;
-  if (rule.Arity()>0) {
-    int ntc=0;
-    for (int s=0; s<f.size(); s++) {
-      if (f[s]<=0) {
-        if (DEBUG) cerr << "f[s]=" << f[s] << "+" << s << " - ";
-        for (int t=0; t<e.size(); t++) {
-          if (e[t]==ntc) {
-            if (DEBUG) cerr << "e[t]=" << e[t] << "+" << t <<endl;
-            als.push_back(link(t,s));
-            ntc--;  break;
-          }
-        }
-      } 
-    }
-  }
-  if (DEBUG) {
-    cerr << "unsorted alignments (nonterminals and terminals)" << endl;
-    for (int i=0; i<als.size(); i++)
-      cerr << source(als[i]) << "-" << target(als[i]) << " ";
-    cerr << endl;
-  }
-  // sort alignments according to target
-  std::sort(als.begin(),als.end());
-  if (DEBUG) {
-    cerr << "sorted alignments (nonterminals and terminals)" << endl;
-    for (int i=0; i<als.size(); i++) 
-      cerr << source(als[i]) << "-" << target(als[i]) << " ";
-    cerr << endl;
-  }
-  // 0 -> neither, 1 -> leftFirst, 2 -> rightFirst, 3 -> dontCare
-  // ScoreDominance(const CountTable& table, int dom, WordID source1, WordID source2, WordID target1, WordID target2)
-  int prevs = 0;
-  for (int i=0; i<als.size(); i++) {
-    int currs = target(als[i]); //int currt = source(als[i]);
-    if (DEBUG) cerr << "prevs=" << prevs << ", currs=" << currs << endl << endl;
-    if (currs<prevs) {
-      if (DEBUG) cerr << "currs<prevs" << endl;
-      for (int s = currs; s <= prevs; s++) {
-        if (sfw.find(f[s])!=sfw.end()) {
-          WordID target = F2EProjectionFromExternal(s,rule.a_,"_SEP_");
-          if (DEBUG) cerr<<"  f[s]="<<TD::Convert(f[s])<<" is a function word, target="<<TD::Convert(target)<<endl;
-          //*cost += ScoreDominance(table,1,kSOS,f[s],kSOS,target) + ScoreDominance(table,2,f[s],kEOS,target,kEOS);
-          *cost += ScoreDominance(table,1,kSOS,f[s],kUNK,kUNK) + ScoreDominance(table,2,f[s],kEOS,kUNK,kUNK);
-          if (DEBUG) cerr << "  resulting cost="<< *cost << endl;
-        } else if (f[s]<=0) {
-          if (DEBUG) cerr << "  f[s]= is a nonterminal" << endl;
-          const int* ants = reinterpret_cast<const int *>(ant_contexts[nt_index[s]-1]);
-          *cost += Dwarf::IntegerToDouble(ants[51]); // 50->mono, 51->non-mono 
-          if (DEBUG) cerr << "  adding "<< Dwarf::IntegerToDouble(ants[51]) << " into cost, resulting = " << *cost << endl;
-        } 
-        flag[s] = true;
-      }
-    }
-    prevs = currs;
-  } 
-  if (DEBUG) cerr << "bonus and state matter" << endl;
-  for (int s=0; s<rule.f().size(); s++) {
-    if (!flag[s]) {
-      if (sfw.find(f[s])!=sfw.end()) {
-        WordID target = F2EProjectionFromExternal(s,rule.a_,"_SEP_");
-        if (DEBUG) cerr<<"  f[s]="<<TD::Convert(f[s])<<" is a function word, target="<<TD::Convert(target)<<endl;
-        //double indbonus = ScoreDominance(table,3,kSOS,f[s],kSOS,target) + ScoreDominance(table,3,f[s],kEOS,target,kEOS);
-        double indbonus = ScoreDominance(table,3,kSOS,f[s],kUNK,kUNK) + ScoreDominance(table,3,f[s],kEOS,kUNK,kUNK);
-        *bonus += indbonus;
-        *state_mono += indbonus;
-        //*state_nonmono += ScoreDominance(table,1,kSOS,f[s],kSOS,target) + ScoreDominance(table,2,f[s],kEOS,target,kEOS);
-        *state_nonmono += ScoreDominance(table,1,kSOS,f[s],kUNK,kUNK) + ScoreDominance(table,2,f[s],kEOS,kUNK,kUNK);
-        if (DEBUG) cerr<<"  new bonus="<<*bonus<<", new state="<<*state_mono<<","<<*state_nonmono<<endl;
-      } else if (f[s]<=0) {
-        if (DEBUG) cerr << "  f[s]="<< f[s] <<" is a nonterminal" << endl;
-        const int* ants = reinterpret_cast<const int *>(ant_contexts[nt_index[s]-1]);
-        double indbonus = Dwarf::IntegerToDouble(ants[50]);
-        *bonus += indbonus;
-        *state_mono += indbonus;
-        *state_nonmono += Dwarf::IntegerToDouble(ants[51]);
-        if (DEBUG) cerr << "  propagating state=" << *state_mono <<","<< *state_nonmono<< endl;
-      }
-    }
-  }
-  if (DEBUG) cerr << "LHS:" << rule.GetLHS() << ":" << TD::Convert(rule.GetLHS()*-1) <<endl;
-  if (rule.GetLHS()*-1==TD::Convert("S")) {
-    *state_mono = 0;
-    *state_nonmono = 0;
-    for (int i=0; i<rule.Arity(); i++) { 
-      const int* ants = reinterpret_cast<const int *>(ant_contexts[i]);
-      *cost += Dwarf::IntegerToDouble(ants[50]);
-    }
-    *bonus = 0;
-  }
-  if (DEBUG) cerr << "-->>>> cost="<<*cost<<", bonus="<<*bonus<<", state_mono="<<*state_mono<<", state_nonmono="<<*state_nonmono<<endl;
-}
-
-bool Alignment::prepare(TRule& rule, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw, const map<WordID,int>& tfw,const Lattice& sourcelattice, int spanstart, int spanend) {  
-  if (DEBUG) cerr << "===Rule===" << rule.AsString() << endl;
-  _f = rule.f();
-  _e = rule.e();
-  _Arity = rule.Arity();
-  if (DEBUG) {
-    cerr << "F: ";
-    for (int idx=0; idx<_f.size(); idx++) cerr << _f[idx] << " ";
-    cerr << endl;
-    cerr << "F': ";
-    for (int idx=0; idx<_f.size(); idx++) 
-      if (_f[idx]>=0) {
-        cerr << TD::Convert(_f[idx]) << " "; 
-      } else {
-        cerr << TD::Convert(_f[idx]*-1);
-      }
-    cerr << endl;
-    cerr << "E: ";
-    for (int idx=0; idx<_e.size(); idx++) 
-      cerr << _e[idx] << " ";
-    cerr << endl;
-    cerr << "E': ";
-    for (int idx=0; idx<_e.size(); idx++) 
-      if (_e[idx]>0) {
-        cerr << TD::Convert(_e[idx]) << " "; 
-      } else {
-        cerr << "[NT]" << " ";
-      }
-    cerr << endl;
-  }
-
-  SourceFWRuleIdxs[0]=0;
-  SourceFWRuleAbsIdxs[0]=0;
-  for (int idx=1; idx<=_f.size(); idx++) { // in transformed space
-    if (sfw.find(_f[idx-1])!=sfw.end()) {
-      SourceFWRuleIdxs[0]++;
-      SourceFWRuleAbsIdxs[++SourceFWRuleAbsIdxs[0]]=GetFWGlobalIdx(idx,sourcelattice,_f,spanstart,spanend,ant_contexts,sfw);
-      SourceFWRuleIdxs[3*SourceFWRuleIdxs[0]-2]=idx;
-      SourceFWRuleIdxs[3*SourceFWRuleIdxs[0]-1]=_f[idx-1];
-      SourceFWRuleIdxs[3*SourceFWRuleIdxs[0]]  =F2EProjectionFromExternal(idx-1,rule.a_,"_SEP_");
-    }
-  }
-  TargetFWRuleIdxs[0]=0;
-  for (int idx=1; idx<=_e.size(); idx++) { // in transformed space
-    if (tfw.find(_e[idx-1])!=tfw.end()) {
-      TargetFWRuleIdxs[0]++;
-      TargetFWRuleIdxs[3*TargetFWRuleIdxs[0]-2]=idx;
-      TargetFWRuleIdxs[3*TargetFWRuleIdxs[0]-1]=E2FProjectionFromExternal(idx-1,rule.a_,"_SEP_");
-      TargetFWRuleIdxs[3*TargetFWRuleIdxs[0]]  =_e[idx-1];
-    }
-  }
-
-  if (DEBUG) {
-    cerr << "SourceFWRuleIdxs[" << SourceFWRuleIdxs[0] << "]:";
-    for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-      cerr << " idx:" << SourceFWRuleIdxs[3*idx-2];
-      cerr << " absidx:" << SourceFWRuleAbsIdxs[idx];
-      cerr << " F:" << SourceFWRuleIdxs[3*idx-1];
-      cerr << " E:" << SourceFWRuleIdxs[3*idx];
-      cerr << "; ";
-    }
-    cerr << endl;
-    cerr << "TargetFWRuleIdxs[" << TargetFWRuleIdxs[0] << "]:";
-    for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-      cerr << " idx:" << TargetFWRuleIdxs[3*idx-2];
-      cerr << " F:" << TargetFWRuleIdxs[3*idx-1];
-      cerr << " E:" << TargetFWRuleIdxs[3*idx];
-    }
-    cerr << endl;
-  }
-  if (SourceFWRuleIdxs[0]+TargetFWRuleIdxs[0]==0) {
-    bool nofw = true;
-    for (int i_ant=0; i_ant<_Arity && nofw; i_ant++) { 
-      const int* ants = reinterpret_cast<const int *>(ant_contexts[i_ant]);
-      if (ants[0]>=0||ants[3]>=0||ants[6]>=0||ants[9]>=0) nofw=false;
-    } 
-    if (nofw) return true;
-  }
-  //cerr << "clearing als first" << endl;
-  clearAls(_J,_I);
-
-  if (DEBUG) cerr << "A["<< rule.a_.size() << "]: " ;
-  RuleAl[0]=0;
-  // add phrase start boundary
-  RuleAl[0]++; RuleAl[RuleAl[0]*2-1]=0; RuleAl[RuleAl[0]*2]=0;
-  if (DEBUG) cerr << RuleAl[RuleAl[0]*2-1] << "-" << RuleAl[RuleAl[0]*2] << " ";
-  for (int idx=0; idx<rule.a_.size(); idx++) {
-    RuleAl[0]++;
-    RuleAl[RuleAl[0]*2-1]=rule.a_[idx].s_+1;
-    RuleAl[RuleAl[0]*2]  =rule.a_[idx].t_+1;
-    if (DEBUG) cerr << RuleAl[RuleAl[0]*2-1] << "-" << RuleAl[RuleAl[0]*2] << " ";
-  }
-  // add phrase end boundary
-  RuleAl[0]++; RuleAl[RuleAl[0]*2-1]=_f.size()+1; RuleAl[RuleAl[0]*2]=_e.size()+1;
-  if (DEBUG) cerr << RuleAl[RuleAl[0]*2-1] << "-" << RuleAl[RuleAl[0]*2] << " ";
-  if (DEBUG) cerr << endl;
-
-  SourceRuleIdxs[0] = _f.size()+2; // +2 (phrase boundaries)
-  TargetRuleIdxs[0] = _e.size()+2; 
-  int ntidx=-1;
-  for (int idx=0; idx<_f.size()+2; idx++) { // idx in transformed space
-    SourceRuleIdxs[idx+1]=idx;
-    if (0<idx && idx<=_f.size()) if (_f[idx-1]<0) SourceRuleIdxs[idx+1]=ntidx--;
-  }
-  for (int idx=0; idx<_e.size()+2; idx++) {
-    TargetRuleIdxs[idx+1]=idx;
-    if (0<idx && idx<=_e.size()) {
-      //cerr << "_e[" <<(idx-1)<< "]=" << _e[idx-1] << endl;
-      if (_e[idx-1]<=0) TargetRuleIdxs[idx+1]=_e[idx-1]-1;
-    }
-  }
-  if (DEBUG) {
-    cerr << "SourceRuleIdxs:";
-    for (int idx=0; idx<SourceRuleIdxs[0]+1; idx++) 
-      cerr << " " << SourceRuleIdxs[idx];
-    cerr << endl;
-    cerr << "TargetRuleIdxs:";
-    for (int idx=0; idx<TargetRuleIdxs[0]+1; idx++) 
-      cerr << " " << TargetRuleIdxs[idx];
-    cerr << endl;
-  }
-
-  // sloppy, the integrity of anstates is assumed
-  // total = 50 bytes
-  // first 3 ints for leftmost source function words (1 for index, 4 for source WordID and 4 for target WordI
-  // second 3 for rightmost source function words
-  // third 3 for leftmost target function words
-  // fourth 3 for rightmost target function words
-  // the next 1 int for the number of alignments
-  // the remaining 37 ints for alignments (source then target)
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    const int* ants = reinterpret_cast<const int *>(ant_contexts[i_ant]);
-    int span = ants[Dwarf::STATE_SIZE-1];
-    if (DEBUG) {
-      cerr << "antcontexts[" << i_ant << "] ";
-      for (int idx=0; idx<Dwarf::STATE_SIZE; idx++) cerr << idx << "." << ants[idx] << " ";
-      cerr << endl;
-      cerr << "i,j = " << source(ants[Dwarf::STATE_SIZE-1]) << "," << target(ants[Dwarf::STATE_SIZE-1]) << endl;
-    }
-    SourceFWAntsIdxs[i_ant][0]=0;
-    SourceFWAntsAbsIdxs[i_ant][0]=0;
-    if (ants[0]>=0) {
-      // Given a span, give the index of the first function word
-      int firstfwidx = GetFirstFWIdx(source(span),target(span),sourcelattice,sfw);
-      if (DEBUG) cerr << "  firstfwidx = " << firstfwidx << endl;
-      int fwcount = 0;
-      if (ants[1]>=0) { // one function word
-        SourceFWAntsIdxs[i_ant][0]++; SourceFWAntsIdxs[i_ant][1]=ants[0];
-        SourceFWAntsIdxs[i_ant][2]=ants[1]; SourceFWAntsIdxs[i_ant][3]=ants[2]; 
-        fwcount++;
-      } else { // if ants[1] < 0 then compound fws
-        //cerr << "ants[1]<0" << endl;
-        istringstream ossf(TD::Convert(ants[1]*-1)); string ffw;
-        istringstream osse(TD::Convert(ants[2])); string efw; //projection would be mostly NULL
-        int delta=ants[0];
-        while (osse >> efw && ossf >> ffw) {
-          SourceFWAntsIdxs[i_ant][0]++; 
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-2]=ants[0]-(delta--);
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);  
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-          fwcount++;
-        }
-      }
-      if (DEBUG) cerr << " fwcount=" << fwcount << endl;
-      SourceFWAntsAbsIdxs[i_ant][0]=fwcount;
-      for (int i=1; i<=fwcount; i++) SourceFWAntsAbsIdxs[i_ant][i]=firstfwidx++;
-    }
-    if (ants[3]>=0) {
-      int lastfwidx = GetLastFWIdx(source(span),target(span),sourcelattice,sfw);
-      if (DEBUG) cerr << "  lastfwidx = " << lastfwidx << endl;
-      int fwcount=0;
-      if (ants[4]>=0) {
-        fwcount++;
-        SourceFWAntsIdxs[i_ant][0]++; 
-        SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-2]=ants[3]; 
-        SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-1]=ants[4]; 
-        SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3]  =ants[5];
-      } else { // if ants[4] < 0 then compound fws
-        //cerr << "ants[4]<0" << endl;
-        istringstream ossf(TD::Convert(ants[4]*-1)); string ffw;
-        istringstream osse(TD::Convert(ants[5]));    string efw;
-        int delta=0;
-        while (osse >> efw && ossf >> ffw) {
-          fwcount++;
-          SourceFWAntsIdxs[i_ant][0]++;
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-2]=ants[3]+(delta++);
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);
-          SourceFWAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-        }
-      }
-      if (DEBUG) cerr << " fwcount=" << fwcount << endl;
-      for (int i=1; i<=fwcount; i++) SourceFWAntsAbsIdxs[i_ant][SourceFWAntsAbsIdxs[i_ant][0]+i]=lastfwidx-fwcount+i;
-      SourceFWAntsAbsIdxs[i_ant][0]+=fwcount;
-    }
-    TargetFWAntsIdxs[i_ant][0]=0;
-    if (ants[6]>=0) {
-      if (ants[8]>=0) { // check the e part 
-        TargetFWAntsIdxs[i_ant][0]++; 
-        TargetFWAntsIdxs[i_ant][1]=ants[6];
-        TargetFWAntsIdxs[i_ant][2]=ants[7]; 
-        TargetFWAntsIdxs[i_ant][3]=ants[8];
-      } else { // if ants[8] < 0 then compound fws
-        //cerr << "ants[8]<0" << endl;
-        //cerr << "ants[7]=" << TD::Convert(ants[7]) << endl;
-        //cerr << "ants[8]=" << TD::Convert(ants[8]*-1) << endl;
-        istringstream ossf(TD::Convert(ants[7]));    string ffw;
-        istringstream osse(TD::Convert(ants[8]*-1)); string efw;
-        int delta=ants[6];
-        while (osse >> efw && ossf >> ffw) {
-          //cerr << "efw="<< efw << ",ffw=" << ffw << endl;
-          TargetFWAntsIdxs[i_ant][0]++;
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-2]=ants[6]-(delta--);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-        }
-      }
-    }
-    if (ants[9]>=0) {
-      if (ants[11]>=0) {
-        TargetFWAntsIdxs[i_ant][0]++; 
-        TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-2]=ants[9];
-        TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-1]=ants[10];
-        TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3]  =ants[11];
-      } else {
-        //cerr << "ants[11]<0" << endl;
-        //cerr << "ants[10]=" << TD::Convert(ants[10]) << endl;
-        //cerr << "ants[11]=" << TD::Convert(ants[11]*-1) << endl;
-        istringstream ossf(TD::Convert(ants[10]));    string ffw;
-        istringstream osse(TD::Convert(ants[11]*-1)); string efw;
-        int delta = 0;
-        while (osse >> efw && ossf >> ffw) {
-          //cerr << "efw="<< efw << ",ffw=" << ffw << endl;
-          TargetFWAntsIdxs[i_ant][0]++;
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-2]=ants[9]+(delta++);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3-1]=TD::Convert(ffw);
-          TargetFWAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][0]*3]  =TD::Convert(efw);
-        }
-      }
-    }
-    AntsAl[i_ant][0]=ants[12];//number of alignments
-    for (int idx=1; idx<=AntsAl[i_ant][0]; idx++) {
-      AntsAl[i_ant][idx*2-1] = source(ants[12+idx]);
-      AntsAl[i_ant][idx*2]   = target(ants[12+idx]);
-    }
-  }
-
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    int length = AntsAl[i_ant][0];
-    int maxs = -1000;
-    int maxt = -1000;
-    for (int idx=0; idx<length; idx++) {
-      if (maxs<AntsAl[i_ant][2*idx+1]) maxs = AntsAl[i_ant][2*idx+1];
-      if (maxt<AntsAl[i_ant][2*idx+2]) maxt = AntsAl[i_ant][2*idx+2];
-    }
-    if (DEBUG) cerr << "SourceFWAntsIdxs[" <<i_ant<<"][0]=" << SourceFWAntsIdxs[i_ant][0] << endl;
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) {
-        cerr << "SourceFWAntsIdxs["<<i_ant<<"]["<<(3*idx-2)<<"]="<<SourceFWAntsIdxs[i_ant][3*idx-2];
-        cerr << ","<<SourceFWAntsIdxs[i_ant][3*idx-1]<<","<<SourceFWAntsIdxs[i_ant][3*idx]<<endl;
-        cerr << "SourceFWAntsAbsIdxs["<<i_ant<<"]["<<idx<<"]="<<SourceFWAntsAbsIdxs[i_ant][idx] << endl;
-      }
-      if (maxs<SourceFWAntsIdxs[i_ant][3*idx-2]) maxs=SourceFWAntsIdxs[i_ant][3*idx-2];
-    }
-    if (DEBUG) cerr << "TargetFWAntsIdxs[" <<i_ant<<"][0]=" << TargetFWAntsIdxs[i_ant][0] << endl;
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) {
-        cerr << "TargetFWAntsIdxs["<<i_ant<<"]["<<(3*idx-2)<<"]="<<TargetFWAntsIdxs[i_ant][3*idx-2];
-        cerr << ","<<TargetFWAntsIdxs[i_ant][3*idx-1]<<","<<TargetFWAntsIdxs[i_ant][3*idx]<<endl;
-      }
-      if (maxt<TargetFWAntsIdxs[i_ant][3*idx-2]) maxt=TargetFWAntsIdxs[i_ant][3*idx-2];
-    }
-    SourceAntsIdxs[i_ant][0] = maxs+1;
-    if (DEBUG) cerr << "SourceAntsIdxs[" << i_ant << "][0]=" <<SourceAntsIdxs[i_ant][0] << endl;
-    for (int idx=0; idx<SourceAntsIdxs[i_ant][0]; idx++) SourceAntsIdxs[i_ant][idx+1]=idx;
-    TargetAntsIdxs[i_ant][0] = maxt+1;
-    if (DEBUG) cerr << "TargetAntsIdxs[" << i_ant << "][0]=" <<TargetAntsIdxs[i_ant][0] << endl;
-    for (int idx=0; idx<TargetAntsIdxs[i_ant][0]; idx++) TargetAntsIdxs[i_ant][idx+1]=idx;
-  }
-  int TotalSource = SourceRuleIdxs[0] - _Arity;
-  for (int idx=0; idx<_Arity; idx++) TotalSource += SourceAntsIdxs[idx][0];
-  int TotalTarget = TargetRuleIdxs[0] - _Arity;
-  for (int idx=0; idx<_Arity; idx++) TotalTarget += TargetAntsIdxs[idx][0];
-  if (DEBUG) cerr << "TotalSource = "<< TotalSource << ", TotalTarget = "<< TotalTarget << endl;
-  int curr = 0;
-  for (int idx=1; idx<=SourceRuleIdxs[0]; idx++) {
-    if (SourceRuleIdxs[idx]>=0) {
-      SourceRuleIdxs[idx]=curr++;
-    } else {
-      int i_ant = SourceRuleIdxs[idx]*-1-1;
-      if (DEBUG) cerr << "SourceAntsIdxs[" << i_ant << "]" << endl;
-      for (int idx2=1; idx2<=SourceAntsIdxs[i_ant][0]; idx2++) {
-        SourceAntsIdxs[i_ant][idx2]=curr++;
-        if (DEBUG) cerr << SourceAntsIdxs[i_ant][idx2] << " ";
-      }
-      if (DEBUG) cerr << endl;
-    }
-  }
-  if (DEBUG) {
-    cerr << "SourceRuleIdxs" << endl;
-    for (int idx=1; idx<=SourceRuleIdxs[0]; idx++) cerr << SourceRuleIdxs[idx] << " ";
-    cerr << endl;
-  }
-  curr = 0;
-  for (int idx=1; idx<=TargetRuleIdxs[0]; idx++) {
-    if (TargetRuleIdxs[idx]>=0) {
-      TargetRuleIdxs[idx]=curr++;
-    } else {
-      int i_ant = TargetRuleIdxs[idx]*-1-1;
-      if (DEBUG) cerr << "TargetRuleIdxs[" << i_ant << "]" << endl;
-      for (int idx2=1; idx2<=TargetAntsIdxs[i_ant][0]; idx2++) {
-        TargetAntsIdxs[i_ant][idx2]=curr++;
-        if (DEBUG) cerr << TargetAntsIdxs[i_ant][idx2] << " ";
-      }
-      if (DEBUG) cerr << endl;
-    }
-  }
-  if (DEBUG) {
-    cerr << "TargetRuleIdxs" << endl;
-    for (int idx=1; idx<=TargetRuleIdxs[0]; idx++) cerr << TargetRuleIdxs[idx] << " ";
-    cerr << endl;
-  }
-  for (int idx=1; idx<=RuleAl[0]; idx++) {
-    if (DEBUG) {
-      cerr << RuleAl[idx*2-1] << " - " << RuleAl[idx*2] << " to ";
-      cerr << SourceRuleIdxs[RuleAl[idx*2-1]+1] << " - " << TargetRuleIdxs[RuleAl[idx*2]+1] << endl;
-    }
-    set(SourceRuleIdxs[RuleAl[idx*2-1]+1],TargetRuleIdxs[RuleAl[idx*2]+1]);
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    for (int idx=1; idx<=AntsAl[i_ant][0]; idx++) {
-      if (DEBUG) {
-        cerr << AntsAl[i_ant][2*idx-1] << " - " << AntsAl[i_ant][2*idx] << " to ";
-        cerr << SourceAntsIdxs[i_ant][AntsAl[i_ant][2*idx-1]+1] << " - ";
-        cerr << TargetAntsIdxs[i_ant][AntsAl[i_ant][2*idx]+1] << endl;
-      }
-      set(SourceAntsIdxs[i_ant][AntsAl[i_ant][2*idx-1]+1],TargetAntsIdxs[i_ant][AntsAl[i_ant][2*idx]+1]);
-    }
-  }
-  SourceFWIdxs[0]=0;
-  SourceFWAbsIdxs[0]=0;
-  if (DEBUG) cerr << "SourceFWRuleIdxs:" << endl;
-  for (int idx=1; idx<=SourceFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << SourceFWRuleIdxs[3*idx-2] << " to " << SourceRuleIdxs[SourceFWRuleIdxs[3*idx-2]+1] << endl;
-    SourceFWRuleIdxs[3*idx-2] = SourceRuleIdxs[SourceFWRuleIdxs[3*idx-2]+1];
-    SourceFWAbsIdxs[0]++;
-    SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]=SourceFWRuleAbsIdxs[idx];
-    SourceFWIdxs[0]++;
-    SourceFWIdxs[3*SourceFWIdxs[0]-2]=SourceFWRuleIdxs[3*idx-2];
-    SourceFWIdxs[3*SourceFWIdxs[0]-1]=SourceFWRuleIdxs[3*idx-1];
-    SourceFWIdxs[3*SourceFWIdxs[0]]  =SourceFWRuleIdxs[3*idx];
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    if (DEBUG) cerr << "SourceFWAntsIdxs[" << i_ant << "]" << endl;
-    for (int idx=1; idx<=SourceFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) 
-        cerr << SourceFWAntsIdxs[i_ant][3*idx-2] << " to " << SourceAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][3*idx-2]+1] << endl;
-      SourceFWAntsIdxs[i_ant][3*idx-2] = SourceAntsIdxs[i_ant][SourceFWAntsIdxs[i_ant][3*idx-2]+1];
-      SourceFWAbsIdxs[0]++;
-      SourceFWAbsIdxs[3*SourceFWAbsIdxs[0]-2]=SourceFWAntsAbsIdxs[i_ant][idx];
-      SourceFWIdxs[0]++;
-      SourceFWIdxs[3*SourceFWIdxs[0]-2]=SourceFWAntsIdxs[i_ant][3*idx-2];
-      SourceFWIdxs[3*SourceFWIdxs[0]-1]=SourceFWAntsIdxs[i_ant][3*idx-1];
-      SourceFWIdxs[3*SourceFWIdxs[0]]  =SourceFWAntsIdxs[i_ant][3*idx];
-    }
-  }
-  sort(SourceFWIdxs);
-  sort(SourceFWAbsIdxs);
-  if (DEBUG) {
-    cerr << "SourceFWIdxs : ";
-    for (int idx=1; idx<=SourceFWIdxs[0]; idx++) {
-      cerr << "idx:" << SourceFWIdxs[3*idx-2] << ",";
-      cerr << "F:" << SourceFWIdxs[3*idx-1] << ",";
-      cerr << "E:" << SourceFWIdxs[3*idx] << " ";
-    }
-    cerr << endl;
-  }
-  TargetFWIdxs[0]=0;
-  if (DEBUG) cerr << "TargetFWRuleIdxs:" << endl;
-  for (int idx=1; idx<=TargetFWRuleIdxs[0]; idx++) {
-    if (DEBUG) cerr << TargetFWRuleIdxs[3*idx-2] << " to " << TargetRuleIdxs[TargetFWRuleIdxs[3*idx-2]+1] << endl;
-    TargetFWRuleIdxs[3*idx-2] = TargetRuleIdxs[TargetFWRuleIdxs[3*idx-2]+1];
-    TargetFWIdxs[0]++;    
-    TargetFWIdxs[3*TargetFWIdxs[0]-2]=TargetFWRuleIdxs[3*idx-2];
-    TargetFWIdxs[3*TargetFWIdxs[0]-1]=TargetFWRuleIdxs[3*idx-1];
-    TargetFWIdxs[3*TargetFWIdxs[0]]  =TargetFWRuleIdxs[3*idx];
-  }
-  for (int i_ant=0; i_ant<_Arity; i_ant++) {
-    if (DEBUG) cerr << "TargetFWAntsIdxs[" << i_ant << "]" << endl;
-    for (int idx=1; idx<=TargetFWAntsIdxs[i_ant][0]; idx++) {
-      if (DEBUG) cerr << TargetFWAntsIdxs[i_ant][3*idx-2] << " to " << TargetAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][3*idx-2]+1] << endl;
-      TargetFWAntsIdxs[i_ant][3*idx-2] = TargetAntsIdxs[i_ant][TargetFWAntsIdxs[i_ant][3*idx-2]+1];
-      TargetFWIdxs[0]++;
-      TargetFWIdxs[3*TargetFWIdxs[0]-2]=TargetFWAntsIdxs[i_ant][3*idx-2];
-      TargetFWIdxs[3*TargetFWIdxs[0]-1]=TargetFWAntsIdxs[i_ant][3*idx-1];
-      TargetFWIdxs[3*TargetFWIdxs[0]]  =TargetFWAntsIdxs[i_ant][3*idx];
-    }
-  }
-  sort(TargetFWIdxs);
-  if (DEBUG) {
-    cerr << "TargetFWIdxs : ";
-    for (int idx=1; idx<=TargetFWIdxs[0]; idx++) {
-      cerr << "idx:" << TargetFWIdxs[3*idx-2]<< ",";
-      cerr << "E:" << TargetFWIdxs[3*idx-1]<< ",";
-      cerr << "F:" << TargetFWIdxs[3*idx]<< " ";
-    }
-    cerr << endl;
-    cerr << AsString() << endl;
-  }
-  fas = firstSourceAligned(1); las = lastSourceAligned(_J-2);
-  fat = firstTargetAligned(1); lat = lastTargetAligned(_I-2); 
-  if (DEBUG) cerr << "fas=" << fas << ", las=" << las << ", fat=" << fat << ", lat=" << lat << endl;
-  assert(fas<=las);
-  assert(fat<=lat);
-  SetCurrAlVector();
-  if (DEBUG) cerr << "end prepare" << endl;
-  return false;
-}      
-
-string Alignment::AsStringSimple() {
-  ostringstream stream;
-  for (int j=0; j<getJ(); j++) {
-    int t = targetOf(j,minTSpan(j));
-    while (t>=0) {
-      stream << " " << j << "-" << t;
-      t = targetOf(j,t+1);
-    }
-  }
-  return stream.str();
-};
-
-
-string Alignment::AsString() {
-  ostringstream stream;
-  stream << "J:" << getJ() << " I:" << getI();
-  for (int j=0; j<getJ(); j++) {
-    int t = targetOf(j,minTSpan(j));
-    while (t>=0) {
-      stream << " " << j << "-" << t;
-      t = targetOf(j,t+1);
-    }
-  }
-  stream << " TargetSpan:";
-  for (int j=0; j<getJ(); j++)
-    if (minTSpan(j)!=MINIMUM_INIT)
-      stream << " " << j << "[" << minTSpan(j) << "," << maxTSpan(j) << "]";
-    else
-      stream << " " << j << "[-,-]";
-  stream << " SourceSpan:";
-  for (int i=0; i<getI(); i++)
-    if (minSSpan(i)!=MINIMUM_INIT)
-      stream << " " << i << "[" << minSSpan(i) << "," << maxSSpan(i) << "]";
-    else
-      stream << " " << i << "[-,-]";
-  return stream.str();
-};
-
-void Alignment::SetCurrAlVector() {
-  curr_al.clear();
-  for (int j=0; j<_J; j++) {
-    int i = targetOf(j);
-    while (i>=0) {
-      curr_al.push_back(link(j,i));
-      i = targetOf(j,i+1);
-    }
-  }
-}
-
-void CountTable::print() const {
-  cerr << "+++ Model +++" << endl;
-  for (map<WordID,int*>::const_iterator iter=model.begin(); iter!=model.end(); iter++) {
-    cerr << TD::Convert(iter->first) << " ";
-    for (int i=0; i<numColumn; i++) cerr << iter->second[i] << " ";
-    cerr << endl;
-  }
-  cerr << "+++ Ultimate +++" << endl;
-  for (int i=0; i<numColumn; i++) cerr << ultimate[i] << " ";
-  cerr << endl;
-}
-
-void Alignment::ToArrayInt(vector<int>* ret) {
-  ret->clear();
-  for (int i=0; i<_J; i++) {
-    int t = targetOf(i);
-    while (t>=0) {
-      ret->push_back(link(i,t));
-      t = targetOf(i,t+1);
-    }
-  }
-}
-
-int Alignment::GetFWGlobalIdx(int idx, const Lattice& sourcelattice, vector<WordID>& sources, int spanstart, int spanend, const std::vector<const void*>& ant_contexts, const map<WordID,int>& sfw) {
-  // get the index of the function word in the lattice
-  if (DEBUG) cerr << "   GetFWGlobalIdx(" << idx << "," << spanstart << "," << spanend << ")" << endl;
-  int curr = spanstart; int i_ant = 0;
-  for (int i=1; i<sources.size() && i<idx; i++) { // sources contain <s> and </s> 
-    if (sources[i]<0) {
-      const int* ants = reinterpret_cast<const int *>(ant_contexts[i_ant++]);
-      int antstate = ants[Dwarf::STATE_SIZE-1];
-      if (DEBUG) cerr << "    found NT[" << target(antstate) << "," << source(antstate) << "]" << endl;
-      curr += target(antstate)-source(antstate);
-    } else {
-      curr++;
-    }
-  }
-  if (DEBUG) cerr << "    curr = " << curr << endl;
-  //compute the fw index
-  int ret = 1;
-  for (int i=0; i<curr; i++) {
-    if (sfw.find(sourcelattice[i][0].label)!=sfw.end()) ret++;
-  }
-  if (DEBUG) cerr << "    ret = " << ret << endl;
-  return ret;
-}
-
-int Alignment::GetFirstFWIdx(int spanstart,int spanend, const Lattice& sourcelattice, const map<WordID,int>& sfw) {
-  if (DEBUG) cerr << "   GetFirstFWIdx(" << spanstart << "," << spanend << ")" << endl;  
-  int curr=0;
-  for (int i=0; i<spanend; i++) {
-    if (sfw.find(sourcelattice[i][0].label)!=sfw.end()) {
-      curr++;
-      if (i>=spanstart) return curr;
-    } 
-  }
-//  assert(0);
-  return curr;
-}
-
-int Alignment::GetLastFWIdx(int spanstart,int spanend, const Lattice& sourcelattice, const map<WordID,int>& sfw) {
-  if (DEBUG) cerr << "   GetLastFWIdx(" << spanstart << "," << spanend << ")" << endl;
-  int curr=0;
-  for (int i=0; i<spanend; i++) {
-    if (sfw.find(sourcelattice[i][0].label)!=sfw.end()) {
-      curr++;
-    } 
-  }
-  return curr;
-}
-
-WordID Alignment::generalize(WordID original, const map<WordID,WordID>& tags, bool pos) {
-  if (!pos) {
-    map<WordID,WordID>::const_iterator it = tags.find(original);
-    if (it!=tags.end()) {
-      return it->second;
-    }
-  } else {
-    string key,idx;
-    Dwarf::stripIndex(TD::Convert(original),&key,&idx);
-    map<WordID,WordID>::const_iterator it = tags.find(TD::Convert(key)); 
-    if (it!=tags.end()) {
-      ostringstream oss;
-      oss << TD::Convert(it->second) << "/" << idx;
-      return TD::Convert(oss.str());   
-    }
-  }
-  return original;
-}
-
-int* Alignment::SOS() {
-  int* neighbor = new int[4];
-  neighbor[0]=0; neighbor[1]=0;
-  neighbor[2]=0; neighbor[3]=0;
-  return neighbor;
-}
-
-int* Alignment::EOS() {
-  int* neighbor = new int[4];
-  neighbor[0]=getJ()-1; neighbor[1]=neighbor[0];
-  neighbor[2]=getI()-1; neighbor[3]=neighbor[2];
-  return neighbor;
-}
-
-int* Alignment::neighborLeft(int startidx, int endidx, bool* getit) {
-  if (DEBUG) cerr << "   neighborLeft("<<startidx<<","<<endidx<<")"<<endl;
-  int lborder = startidx;
-  int* ret;
-  while(lborder<=endidx) {
-    ret = blockSource(lborder,endidx);
-    if (ret[0]==lborder && ret[1]==endidx && ret[2]!=MINIMUM_INIT) {
-      *getit = true;
-      return ret;
-    } else {
-      delete[] ret;
-      lborder++;
-    }
-  }
-  ret = new int[4];
-  ret[0]=-1; ret[1]=-1; ret[2]=-1; ret[3]=-1;
-  *getit = false;
-  return ret;
-}
-
-int* Alignment:: neighborRight(int startidx, int endidx, bool* getit) {
-  if (DEBUG) cerr << "   neighborRight("<<startidx<<","<<endidx<<")"<<endl;
-  int rborder = endidx;
-  int* ret;
-  while(startidx<=rborder) {
-    ret = blockSource(startidx,rborder);
-    if (ret[0]==startidx && ret[1]==rborder && ret[2]!=MINIMUM_INIT) {
-      *getit = true;
-      return ret;
-    } else {
-      delete[] ret;
-      rborder--;
-    }
-  }
-  ret = new int[4];
-  ret[0]=-1; ret[1]=-1; ret[2]=-1; ret[3]=-1;
-  *getit = false;
-  return ret;
-}
-- 
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