void CompNovoIdentificationBase::permute_(String prefix, String s, set<String> & permutations)
{
if (s.size() <= 1)
{
permutations.insert(prefix + s);
}
else
{
for (String::Iterator p = s.begin(); p < s.end(); p++)
{
char c = *p;
p = s.erase(p);
permute_(prefix + c, s, permutations);
s.insert(p, c);
}
}
}
// divide and conquer algorithm of the sequencing
void CompNovoIdentificationCID::getDecompositionsDAC_(set<String> & sequences, Size left, Size right, double peptide_weight, const PeakSpectrum & CID_spec, Map<double, CompNovoIonScoringCID::IonScore> & ion_scores)
{
static double oxonium_mass = EmpiricalFormula("H2O+").getMonoWeight();
double offset_suffix(CID_spec[left].getPosition()[0] - oxonium_mass);
double offset_prefix(peptide_weight - CID_spec[right].getPosition()[0]);
#ifdef DAC_DEBUG
static Int depth_(0);
++depth_;
String tabs_(depth_, '\t');
cerr << tabs_ << "void getDecompositionsDAC(sequences[" << sequences.size() << "], " << left << ", " << right << ") ";
cerr << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << " diff=";
#endif
double diff = CID_spec[right].getPosition()[0] - CID_spec[left].getPosition()[0];
#ifdef DAC_DEBUG
cerr << diff << endl;
cerr << "offset_prefix=" << offset_prefix << ", offset_suffix=" << offset_suffix << endl;
#endif
if (subspec_to_sequences_.has(left) && subspec_to_sequences_[left].has(right))
{
sequences = subspec_to_sequences_[left][right];
#ifdef DAC_DEBUG
depth_--;
cerr << tabs_ << "from cache DAC: " << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << " " << sequences.size() << " " << left << " " << right << endl;
#endif
return;
}
// no further solutions possible?
if (diff < min_aa_weight_)
{
#ifdef DAC_DEBUG
depth_--;
#endif
return;
}
// no further division needed?
if (diff <= max_decomp_weight_)
{
vector<MassDecomposition> decomps;
// if we are at the C-terminus use precursor_mass_tolerance_
if (offset_prefix < precursor_mass_tolerance_)
{
Param decomp_param(mass_decomp_algorithm_.getParameters());
decomp_param.setValue("tolerance", precursor_mass_tolerance_);
mass_decomp_algorithm_.setParameters(decomp_param);
getDecompositions_(decomps, diff);
decomp_param.setValue("tolerance", fragment_mass_tolerance_);
mass_decomp_algorithm_.setParameters(decomp_param);
}
else
{
getDecompositions_(decomps, diff);
}
//filterDecomps_(decomps);
#ifdef DAC_DEBUG
cerr << tabs_ << "Found " << decomps.size() << " decomps" << endl;
cerr << tabs_ << "Permuting...";
#endif
//static Map<String, set<String> > permute_cache;
for (vector<MassDecomposition>::const_iterator it = decomps.begin(); it != decomps.end(); ++it)
{
#ifdef DAC_DEBUG
cerr << it->toString() << endl;
#endif
String exp_string = it->toExpandedString();
if (!permute_cache_.has(exp_string))
{
permute_("", exp_string, sequences);
permute_cache_[exp_string] = sequences;
}
else
{
sequences = permute_cache_[exp_string];
}
}
#ifdef DAC_DEBUG
cerr << tabs_ << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << " " << peptide_weight << endl;
if (sequences.size() > max_subscore_number_)
{
cerr << tabs_ << "Reducing #sequences from " << sequences.size() << " to " << max_subscore_number_ << "(prefix=" << offset_prefix << ", suffix=" << offset_suffix << ")...";
}
#endif
// C-terminus
if (offset_suffix <= precursor_mass_tolerance_)
{
filterPermuts_(sequences);
}
// reduce the sequences
reducePermuts_(sequences, CID_spec, offset_prefix, offset_suffix);
#ifdef DAC_DEBUG
cerr << "Writing to cache " << left << " " << right << endl;
#endif
subspec_to_sequences_[left][right] = sequences;
#ifdef DAC_DEBUG
cerr << "ended" << endl;
cerr << tabs_ << "DAC: " << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << " " << sequences.size() << endl;
depth_--;
#endif
return;
}
// select suitable pivot peaks
vector<Size> pivots;
if (offset_suffix < precursor_mass_tolerance_ && offset_prefix < precursor_mass_tolerance_)
{
selectPivotIons_(pivots, left, right, ion_scores, CID_spec, peptide_weight, true);
}
else
{
selectPivotIons_(pivots, left, right, ion_scores, CID_spec, peptide_weight, false);
}
// run divide step
#ifdef DAC_DEBUG
cerr << tabs_ << "Selected " << pivots.size() << " pivot ions: ";
for (vector<Size>::const_iterator it = pivots.begin(); it != pivots.end(); ++it)
{
cerr << *it << "(" << CID_spec[*it].getPosition()[0] << ") ";
}
cerr << endl;
#endif
for (vector<Size>::const_iterator it = pivots.begin(); it != pivots.end(); ++it)
{
set<String> seq1, seq2, new_sequences;
// the smaller the 'gap' the greater the chance of not finding anything
// so we we compute the smaller gap first
double diff1(CID_spec[*it].getPosition()[0] - CID_spec[left].getPosition()[0]);
double diff2(CID_spec[right].getPosition()[0] - CID_spec[*it].getPosition()[0]);
if (diff1 < diff2)
{
getDecompositionsDAC_(seq1, left, *it, peptide_weight, CID_spec, ion_scores);
if (seq1.empty())
{
#ifdef DAC_DEBUG
cerr << tabs_ << "first call produced 0 candidates (" << diff1 << ")" << endl;
#endif
continue;
}
getDecompositionsDAC_(seq2, *it, right, peptide_weight, CID_spec, ion_scores);
}
else
{
getDecompositionsDAC_(seq2, *it, right, peptide_weight, CID_spec, ion_scores);
if (seq2.empty())
{
#ifdef DAC_DEBUG
cerr << tabs_ << "second call produced 0 candidates (" << diff2 << ")" << endl;
#endif
continue;
}
getDecompositionsDAC_(seq1, left, *it, peptide_weight, CID_spec, ion_scores);
}
#ifdef DAC_DEBUG
cerr << tabs_ << "Found " << seq1.size() << " solutions (1) " << diff1 << endl;
cerr << tabs_ << "Found " << seq2.size() << " solutions (2) " << diff2 << endl;
cerr << tabs_ << "inserting " << seq1.size() * seq2.size() << " sequences" << endl;
#endif
// C-terminus
if (offset_suffix <= fragment_mass_tolerance_)
{
filterPermuts_(seq1);
}
// test if we found enough sequence candidates
if (seq1.empty() || seq2.empty())
{
continue;
}
for (set<String>::const_iterator it1 = seq1.begin(); it1 != seq1.end(); ++it1)
{
for (set<String>::const_iterator it2 = seq2.begin(); it2 != seq2.end(); ++it2)
{
new_sequences.insert(*it2 + *it1);
}
}
if (seq1.size() * seq2.size() > max_subscore_number_ /* && (offset_prefix > fragment_mass_tolerance_ || offset_suffix > fragment_mass_tolerance_)*/)
{
#ifdef DAC_DEBUG
cerr << tabs_ << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << " " << peptide_weight << endl;
cerr << tabs_ << "Reducing #sequences from " << new_sequences.size() << " to " << max_subscore_number_ << "(prefix=" << offset_prefix << ", suffix=" << offset_suffix << ")...";
#endif
if (offset_prefix > precursor_mass_tolerance_ || offset_suffix > precursor_mass_tolerance_)
{
reducePermuts_(new_sequences, CID_spec, offset_prefix, offset_suffix);
}
#ifdef DAC_DEBUG
for (set<String>::const_iterator it1 = new_sequences.begin(); it1 != new_sequences.end(); ++it1)
{
cerr << tabs_ << *it1 << endl;
}
cerr << endl;
#endif
}
for (set<String>::const_iterator sit = new_sequences.begin(); sit != new_sequences.end(); ++sit)
{
sequences.insert(*sit);
}
}
#ifdef DAC_DEBUG
cerr << tabs_ << "Found sequences for " << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << endl;
for (set<String>::const_iterator sit = sequences.begin(); sit != sequences.end(); ++sit)
{
cerr << tabs_ << *sit << endl;
}
#endif
// reduce the permuts once again to reduce complexity
if (offset_prefix > precursor_mass_tolerance_ || offset_suffix > precursor_mass_tolerance_)
{
reducePermuts_(sequences, CID_spec, offset_prefix, offset_suffix);
}
#ifdef DAC_DEBUG
cerr << "Writing to cache " << left << " " << right << endl;
#endif
subspec_to_sequences_[left][right] = sequences;
#ifdef DAC_DEBUG
depth_--;
cerr << tabs_ << "DAC: " << CID_spec[left].getPosition()[0] << " " << CID_spec[right].getPosition()[0] << " " << sequences.size() << endl;
#endif
return;
}
