long trie_recurse( DFA<N_AMINOACIDS> &A, IDFA<int> &Apep,
IDFAState<int> *pep,
vector<int> &pre,
const double thr_pos, int i ){
//cerr << i << " " << pre.size() << endl;
if( i == pre.size() ){
IDFA<int> A2;
vector<int> pre2( pre );
long snew = add_strings_near( A2, A, 0, A.pureAccepting(),
pre, pre2, thr_pos, max_energy(pre), min_energy(pre), 0 );
if( snew > 0 ){
/*cout << "1st guy: " << endl;
A.printDebug();
cout << "2nd guy: " << endl;
DFA<N_AMINOACIDS>(A2).printDebug();*/
A = A.join( DFA<N_AMINOACIDS>(A2) ).minimize();
}
//cerr << snew << endl;
return snew;
}
long r = 0;
float max_of_minima = 0.0;
vector<int> dominated(N_AMINOACIDS,0);
for( int j = 0 ; j < N_AMINOACIDS ; j ++ ){
if( IDFAState<int> * tgt = pep->next(aa_by_min_energy[j]) ){
pre[i] = aa_by_min_energy[j];
if( pep -> fanOut() > 1 ){
if( dominated[pre[i]] ){
continue;
}
for( int k = 0 ; k < N_AMINOACIDS ; k ++ ){
if( pre[i] != k && mj_domination[pre[i]][k] && ( tgt == pep->next(k) ) ){
/*cerr << aminoacids[pre[i]] << " (" << pre[i] << ") dom. " <<
aminoacids[k] << " (" << k << ")" << endl;*/
dominated[k]=1;
}
}
}
r += trie_recurse( A, Apep, tgt, pre, thr_pos, i+1 );
}
}
return r;
}
void CubeCreature::restore_energy(unsigned num){
energy+=num;
if(energy>max_energy())energy=max_energy();
}
