// 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;
}
void CompNovoIdentificationBase::updateMembers_()
{
// init residue mass table
String residue_set(param_.getValue("residue_set"));
set<const Residue *> residues = ResidueDB::getInstance()->getResidues(residue_set);
for (set<const Residue *>::const_iterator it = residues.begin(); it != residues.end(); ++it)
{
aa_to_weight_[(*it)->getOneLetterCode()[0]] = (*it)->getMonoWeight(Residue::Internal);
}
max_number_aa_per_decomp_ = param_.getValue("max_number_aa_per_decomp");
tryptic_only_ = param_.getValue("tryptic_only").toBool();
fragment_mass_tolerance_ = (DoubleReal)param_.getValue("fragment_mass_tolerance");
max_number_pivot_ = param_.getValue("max_number_pivot");
decomp_weights_precision_ = (DoubleReal)param_.getValue("decomp_weights_precision");
min_mz_ = (DoubleReal)param_.getValue("min_mz");
max_mz_ = (DoubleReal)param_.getValue("max_mz");
max_decomp_weight_ = (DoubleReal)param_.getValue("max_decomp_weight");
max_subscore_number_ = param_.getValue("max_subscore_number");
max_isotope_ = param_.getValue("max_isotope");
name_to_residue_.clear();
residue_to_name_.clear();
// now handle the modifications
ModificationDefinitionsSet mod_set((StringList)param_.getValue("fixed_modifications"), (StringList)param_.getValue("variable_modifications"));
set<ModificationDefinition> fixed_mods = mod_set.getFixedModifications();
for (set<ModificationDefinition>::const_iterator it = fixed_mods.begin(); it != fixed_mods.end(); ++it)
{
ResidueModification mod = ModificationsDB::getInstance()->getModification(it->getModification());
char aa = ' ';
if (mod.getOrigin().size() != 1 || mod.getOrigin() == "X")
{
cerr << "Warning: cannot handle modification " << it->getModification() << ", because aa is ambiguous (" << mod.getOrigin() << "), ignoring modification!" << endl;
continue;
}
else
{
aa = mod.getOrigin()[0];
}
if (mod.getMonoMass() != 0)
{
aa_to_weight_[aa] = mod.getMonoMass();
}
else
{
if (mod.getDiffMonoMass() != 0)
{
aa_to_weight_[aa] += mod.getDiffMonoMass();
}
else
{
cerr << "Warning: cannot handle modification " << it->getModification() << ", because no monoisotopic mass value was found! Ignoring modification!" << endl;
continue;
}
}
//cerr << "Setting fixed modification " << it->getModification() << " of amino acid '" << aa << "'; weight = " << aa_to_weight_[aa] << endl;
const Residue * res = ResidueDB::getInstance()->getModifiedResidue(it->getModification());
name_to_residue_[aa] = res;
residue_to_name_[res] = aa;
}
const StringList mod_names(StringList::create("a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z"));
vector<String>::const_iterator actual_mod_name = mod_names.begin();
set<ModificationDefinition> var_mods = mod_set.getVariableModifications();
for (set<ModificationDefinition>::const_iterator it = var_mods.begin(); it != var_mods.end(); ++it)
{
ResidueModification mod = ModificationsDB::getInstance()->getModification(it->getModification());
char aa = (*actual_mod_name)[0];
char origin_aa = ' ';
++actual_mod_name;
if (mod.getOrigin().size() != 1 || mod.getOrigin() == "X")
{
cerr << "CompNovoIdentificationBase: Warning: cannot handle modification " << it->getModification() << ", because aa is ambiguous (" << mod.getOrigin() << "), ignoring modification!" << endl;
continue;
}
else
{
origin_aa = mod.getOrigin()[0];
}
if (mod.getMonoMass() != 0)
{
aa_to_weight_[aa] = mod.getMonoMass();
}
else
{
if (mod.getDiffMonoMass() != 0)
{
aa_to_weight_[aa] = aa_to_weight_[origin_aa] + mod.getDiffMonoMass();
}
else
{
cerr << "CompNovoIdentificationBase: Warning: cannot handle modification " << it->getModification() << ", because no monoisotopic mass value was found! Ignoring modification!" << endl;
continue;
}
}
//cerr << "Mapping variable modification " << it->getModification() << " to letter '" << aa << "' (@" << origin_aa << "); weight = " << aa_to_weight_[aa] << endl;
const Residue * res = ResidueDB::getInstance()->getModifiedResidue(it->getModification());
name_to_residue_[aa] = res;
residue_to_name_[res] = aa;
}
/*
cerr << "Following masses are used for identification: " << endl;
for (Map<char, DoubleReal>::const_iterator it = aa_to_weight_.begin(); it != aa_to_weight_.end(); ++it)
{
cerr << it->first << " " << precisionWrapper(it->second) << endl;
}*/
initIsotopeDistributions_();
Param decomp_param(mass_decomp_algorithm_.getParameters());
decomp_param.setValue("tolerance", fragment_mass_tolerance_);
decomp_param.setValue("fixed_modifications", (StringList)param_.getValue("fixed_modifications"));
decomp_param.setValue("variable_modifications", (StringList)param_.getValue("variable_modifications"));
mass_decomp_algorithm_.setParameters(decomp_param);
min_aa_weight_ = numeric_limits<DoubleReal>::max();
for (Map<char, DoubleReal>::const_iterator it = aa_to_weight_.begin(); it != aa_to_weight_.end(); ++it)
{
if (min_aa_weight_ > it->second)
{
min_aa_weight_ = it->second;
}
}
return;
}
