void convert(const map< pair<int,int>,char >&reference,alignment&x) { int l=x.get_l(); int m=x.get_m(); for(map< pair<int,int>,char >::const_iterator i=reference.begin();i!=reference.end();++i) { if( i->first.first+1>int(m) ) { cerr << "ERROR m to big: " << i->first.first << " " << i->first.second+1 << " " << l << " " << m << " is wrong.\n"; continue; } if( i->first.second+1>int(l) ) { cerr << "ERROR l to big: " << i->first.first << " " << i->first.second+1 << " " << l << " " << m << " is wrong.\n"; continue; } if( x(i->first.first+1)!=0 ) cerr << "ERROR: position " << i->first.first+1 << " already set\n"; x.set(i->first.first+1,i->first.second+1); } }