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diff --git a/v0.6.4/src/MoveSwapMatrix.cpp b/v0.6.4/src/MoveSwapMatrix.cpp
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+/*
+
+Copyright (C) 1999,2000,2001 Franz Josef Och (RWTH Aachen - Lehrstuhl fuer Informatik VI)
+
+This file is part of GIZA++ ( extension of GIZA ).
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
+USA.
+
+*/
+#include "MoveSwapMatrix.h"
+
+template<class TRANSPAIR>
+MoveSwapMatrix<TRANSPAIR>::MoveSwapMatrix(const TRANSPAIR&_ef, const alignment&_a)
+ : alignment(_a), ef(_ef), l(ef.get_l()), m(ef.get_m()), _cmove(l+1, m+1), _cswap(m+1, m+1),
+ delmove(l+1, m+1,0),delswap(m+1, m+1,0),changed(l+2, 0), changedCounter(1),
+ modelnr(_ef.modelnr()),lazyEvaluation(0),centerDeleted(0)
+{
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ if( lazyEvaluation==0)
+ for(WordIndex j=1;j<=m;j++)updateJ(j, 0,thisValue);
+}
+
+template<class TRANSPAIR>
+void MoveSwapMatrix<TRANSPAIR>::updateJ(WordIndex j, bool useChanged,double thisValue)
+{
+ massert( lazyEvaluation==0 );
+ for(WordIndex i=0;i<=l;i++)
+ if( (useChanged==0||changed[i]!=changedCounter) )
+ if( get_al(j)!=i )
+ _cmove(i, j)=ef.scoreOfMove((*this), i, j,thisValue);
+ else
+ _cmove(i, j)=1.0;
+ for(WordIndex j2=j+1;j2<=m;j2++)
+ if( get_al(j)!=get_al(j2) )
+ _cswap(j, j2)=ef.scoreOfSwap((*this), j, j2,thisValue);
+ else
+ _cswap(j, j2)=1.0;
+ for(WordIndex j2=1;j2<j;j2++)
+ if( get_al(j)!=get_al(j2) )
+ _cswap(j2, j)=ef.scoreOfSwap((*this), j2, j,thisValue);
+ else
+ _cswap(j2, j)=1.0;
+}
+template<class TRANSPAIR>
+void MoveSwapMatrix<TRANSPAIR>::updateI(WordIndex i,double thisValue)
+{
+ massert( lazyEvaluation==0);
+ for(WordIndex j=1;j<=m;j++)
+ if( get_al(j)!=i )
+ _cmove(i, j)=ef.scoreOfMove((*this), i, j,thisValue);
+ else
+ _cmove(i, j)=1.0;
+}
+
+template<class TRANSPAIR>
+void MoveSwapMatrix<TRANSPAIR>::printWrongs()const{
+ for(WordIndex i=0;i<=l;i++)
+ {
+ for(WordIndex j=1;j<=m;j++)
+ if( get_al(j)==i)
+ cout << "A";
+ else
+ {
+ LogProb real=_cmove(i, j), wanted=ef.scoreOfMove((*this), i, j);
+ if( fabs(1.0-real/wanted)>1e-3 )
+ cout << 'b';
+ else if(fabs(1.0-real/wanted)>1e-10 )
+ cout << 'e';
+ else if(real!=wanted)
+ cout << 'E';
+ else
+ cout << ' ';
+ }
+ cout << endl;
+ }
+ cout << endl;
+ for(WordIndex j=1;j<=m;j++)
+ {
+ for(WordIndex j1=1;j1<=m;j1++)
+ if( j1>j )
+ {
+ if( get_al(j)==get_al(j1) )
+ cout << 'A';
+ else
+ cout << (_cswap(j, j1)==ef.scoreOfSwap((*this), j, j1));
+ }
+ else
+ cout << ' ';
+ cout << endl;
+ }
+ massert(0);
+}
+template<class TRANSPAIR>
+bool MoveSwapMatrix<TRANSPAIR>::isRight()const{
+ if( lazyEvaluation )
+ return 1;
+ for(WordIndex i=0;i<=l;i++)
+ for(WordIndex j=1;j<=m;j++)
+ if( get_al(j)!=i && (!(doubleEqual(_cmove(i, j), ef.scoreOfMove((*this), i, j)))) )
+ {
+ cerr << "DIFF: " << i << " " << j << " " << _cmove(i, j) << " " << ef.scoreOfMove((*this), i, j) << endl;
+ return 0;
+ }
+ for(WordIndex j=1;j<=m;j++)
+ for(WordIndex j1=1;j1<=m;j1++)
+ if( j1>j&&get_al(j)!=get_al(j1)&&(!doubleEqual(_cswap(j, j1), ef.scoreOfSwap((*this), j, j1))) )
+ {
+ cerr << "DIFFERENT: " << j << " " << j1 << " " << _cswap(j, j1) << " " << ef.scoreOfSwap((*this), j, j1) << endl;
+ return 0;
+ }
+ return 1;
+}
+
+template<class TRANSPAIR>
+void MoveSwapMatrix<TRANSPAIR>::doMove(WordIndex _i, WordIndex _j)
+{
+ WordIndex old_i=get_al(_j);
+ if( lazyEvaluation )
+ set(_j,_i);
+ else
+ {
+ if ( modelnr==5||modelnr==6 )
+ {
+ set(_j, _i);
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ for(WordIndex j=1;j<=m;j++)updateJ(j, 0,thisValue);
+ }
+ else if ( modelnr==4 )
+ {
+ changedCounter++;
+ for(unsigned int k=prev_cept(old_i);k<=next_cept(old_i);++k)changed[k]=changedCounter;
+ for(unsigned int k=prev_cept(_i);k<=next_cept(_i);++k)changed[k]=changedCounter;
+ set(_j, _i);
+ for(unsigned int k=prev_cept(old_i);k<=next_cept(old_i);++k)changed[k]=changedCounter;
+ for(unsigned int k=prev_cept(_i);k<=next_cept(_i);++k)changed[k]=changedCounter;
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ for(unsigned int i=0;i<=l;i++)
+ if(changed[i]==changedCounter)
+ updateI(i,thisValue);
+ for(unsigned int j=1;j<=m;j++)
+ if( changed[get_al(j)]==changedCounter )
+ updateJ(j, 1,thisValue);
+ }
+ else
+ {
+ assert(modelnr==3);
+ set(_j, _i);
+ changedCounter++;
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ updateI(old_i,thisValue);
+ changed[old_i]=changedCounter;
+ updateI(_i,thisValue);
+ changed[_i]=changedCounter;
+ for(WordIndex j=1;j<=m;j++)
+ if( get_al(j)==_i || get_al(j)==old_i )
+ updateJ(j, 1,thisValue);
+ }
+ }
+}
+template<class TRANSPAIR>
+void MoveSwapMatrix<TRANSPAIR>::doSwap(WordIndex _j1, WordIndex _j2)
+{
+ assert( cswap(_j1, _j2)>1 );
+ WordIndex i1=get_al(_j1), i2=get_al(_j2);
+ if( lazyEvaluation==1 )
+ {
+ set(_j1, i2);
+ set(_j2, i1);
+ }
+ else
+ {
+ if ( modelnr==5||modelnr==6 )
+ {
+ set(_j1, i2);
+ set(_j2, i1);
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ for(WordIndex j=1;j<=m;j++)updateJ(j, 0,thisValue);
+ }
+ else if( modelnr==4 )
+ {
+ changedCounter++;
+ for(unsigned int k=prev_cept(i1);k<=next_cept(i1);++k)changed[k]=changedCounter;
+ for(unsigned int k=prev_cept(i2);k<=next_cept(i2);++k)changed[k]=changedCounter;
+ set(_j1, i2);
+ set(_j2, i1);
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ for(unsigned int i=0;i<=l;i++)
+ if(changed[i]==changedCounter)
+ updateI(i,thisValue);
+ for(unsigned int j=1;j<=m;j++)
+ if( changed[get_al(j)]==changedCounter )
+ updateJ(j, 1,thisValue);
+ }
+ else
+ {
+ assert(modelnr==3);
+ set(_j1, i2);
+ set(_j2, i1);
+ changedCounter++;
+ double thisValue=ef.scoreOfAlignmentForChange((*this));
+ updateI(i1,thisValue);
+ changed[i1]=changedCounter;
+ updateI(i2,thisValue);
+ changed[i2]=changedCounter;
+ updateJ(_j1, 1,thisValue);
+ updateJ(_j2, 1,thisValue);
+ }
+ }
+}
+
+#include "transpair_model3.h"
+#include "transpair_model4.h"
+#include "transpair_model5.h"
+#include "transpair_modelhmm.h"
+template class MoveSwapMatrix<transpair_model3>;
+template class MoveSwapMatrix<transpair_model4>;
+template class MoveSwapMatrix<transpair_model5>;
+template class MoveSwapMatrix<transpair_modelhmm>;
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