void IDFilter::filterIdentificationsByRTPValues(const PeptideIdentification& identification,
PeptideIdentification& filtered_identification,
DoubleReal p_value)
{
DoubleReal border = 1 - p_value;
vector<PeptideHit> filtered_peptide_hits;
PeptideHit temp_peptide_hit;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
Size missing_meta_value = 0;
for (Size i = 0; i < identification.getHits().size(); i++)
{
if (identification.getHits()[i].metaValueExists("predicted_RT_p_value"))
{
if ((DoubleReal)(identification.getHits()[i].getMetaValue("predicted_RT_p_value")) <= border)
{
filtered_peptide_hits.push_back(identification.getHits()[i]);
}
}
else
++missing_meta_value;
}
if (missing_meta_value > 0)
LOG_WARN << "Filtering identifications by p-value did not work on " << missing_meta_value << " of " << identification.getHits().size() << " hits. Your data is missing a meta-value ('predicted_RT_p_value') from RTPredict!\n";
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
void IDFilter::filterIdentificationsByCharge(const PeptideIdentification& identification,
Int min_charge,
PeptideIdentification& filtered_identification)
{
vector<Size> new_peptide_indices;
vector<PeptideHit> filtered_peptide_hits;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
const vector<PeptideHit>& temp_peptide_hits = identification.getHits();
for (Size i = 0; i < temp_peptide_hits.size(); i++)
{
if (temp_peptide_hits[i].getCharge() >= min_charge)
{
new_peptide_indices.push_back(i);
}
}
for (Size i = 0; i < new_peptide_indices.size(); i++)
{
filtered_peptide_hits.push_back(identification.getHits()[new_peptide_indices[i]]);
}
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
void IDFilter::filterIdentificationsByExclusionPeptides(const PeptideIdentification& identification,
const set<String>& peptides,
PeptideIdentification& filtered_identification)
{
String protein_sequences;
String accession_sequences;
vector<PeptideHit> filtered_peptide_hits;
PeptideHit temp_peptide_hit;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
for (Size i = 0; i < identification.getHits().size(); i++)
{
if (find(peptides.begin(), peptides.end(), identification.getHits()[i].getSequence().toString()) == peptides.end())
{
filtered_peptide_hits.push_back(identification.getHits()[i]);
}
}
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
//Visualizing PeptideIdentification object
void MetaDataBrowser::visualize_(PeptideIdentification & meta, QTreeWidgetItem * parent)
{
PeptideIdentificationVisualizer * visualizer = new PeptideIdentificationVisualizer(isEditable(), this, this);
QStringList labels;
int id = ws_->addWidget(visualizer);
labels << QString("PeptideIdentification %1").arg(meta.getScoreType().c_str()) << QString::number(id);
visualizer->load(meta, id);
QTreeWidgetItem * item;
if (parent == nullptr)
{
item = new QTreeWidgetItem(treeview_, labels);
}
else
{
item = new QTreeWidgetItem(parent, labels);
}
//check for proteins and peptides hits
meta.assignRanks();
//list all peptides hits in the tree
for (Size i = 0; i < meta.getHits().size(); ++i)
{
visualize_(const_cast<PeptideHit &>(meta.getHits()[i]), item);
}
visualize_(dynamic_cast<MetaInfoInterface &>(meta), item);
connectVisualizer_(visualizer);
}
void IDFilter::filterIdentificationsByProteins(const PeptideIdentification& identification,
const vector<FASTAFile::FASTAEntry>& proteins,
PeptideIdentification& filtered_identification,
bool no_protein_identifiers)
{
// TODO: this is highly inefficient! the Protein-Index should be build once for all peptide-identifications instead of
// doing this once for every ID. Furthermore the index itself is inefficient (use seqan instead)
String protein_sequences;
String accession_sequences;
vector<PeptideHit> filtered_peptide_hits;
PeptideHit temp_peptide_hit;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
for (Size i = 0; i < proteins.size(); i++)
{
if (proteins[i].identifier != "")
{
accession_sequences.append("*" + proteins[i].identifier);
}
if (proteins[i].sequence != "")
{
protein_sequences.append("*" + proteins[i].sequence);
}
}
accession_sequences.append("*");
protein_sequences.append("*");
for (Size i = 0; i < identification.getHits().size(); i++)
{
if (no_protein_identifiers || accession_sequences == "*") // filter by sequence alone if no protein accesssions are available
{
if (protein_sequences.find(identification.getHits()[i].getSequence().toUnmodifiedString()) != String::npos)
{
filtered_peptide_hits.push_back(identification.getHits()[i]);
}
}
else // filter by protein accessions
{
for (vector<String>::const_iterator ac_it = identification.getHits()[i].getProteinAccessions().begin();
ac_it != identification.getHits()[i].getProteinAccessions().end();
++ac_it)
{
if (accession_sequences.find("*" + *ac_it) != String::npos)
{
filtered_peptide_hits.push_back(identification.getHits()[i]);
break; // we found a matching protein, the peptide is valid -> exit
}
}
}
}
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
void IDFilter::filterIdentificationsByBestHits(const PeptideIdentification& identification,
PeptideIdentification& filtered_identification,
bool strict)
{
vector<PeptideHit> filtered_peptide_hits;
PeptideHit temp_peptide_hit;
vector<Size> new_peptide_indices;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
if (!identification.getHits().empty())
{
Real optimal_value = identification.getHits()[0].getScore();
new_peptide_indices.push_back(0);
// searching for peptide(s) with maximal score
for (Size i = 1; i < identification.getHits().size(); i++)
{
Real temp_score = identification.getHits()[i].getScore();
bool new_leader = false;
if ((identification.isHigherScoreBetter() && (temp_score > optimal_value))
|| (!identification.isHigherScoreBetter() && (temp_score < optimal_value)))
new_leader = true;
if (new_leader)
{
optimal_value = temp_score;
new_peptide_indices.clear();
new_peptide_indices.push_back(i);
}
else if (temp_score == optimal_value)
{
new_peptide_indices.push_back(i);
}
}
if (!strict || new_peptide_indices.size() == 1)
{
for (Size i = 0; i < new_peptide_indices.size(); i++)
{
filtered_peptide_hits.push_back(identification.getHits()[new_peptide_indices[i]]);
}
}
}
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
void IDFilter::filterIdentificationsByCharge(const PeptideIdentification& identification,
Int min_charge,
PeptideIdentification& filtered_identification)
{
filtered_identification = identification;
const vector<PeptideHit>& temp_peptide_hits = identification.getHits();
vector<PeptideHit> filtered_peptide_hits;
for (Size i = 0; i < temp_peptide_hits.size(); ++i)
{
if (temp_peptide_hits[i].getCharge() >= min_charge)
{
filtered_peptide_hits.push_back(temp_peptide_hits[i]);
}
}
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
void IDFilter::filterIdentificationsByLength(const PeptideIdentification& identification,
PeptideIdentification& filtered_identification,
Size min_length,
Size max_length)
{
vector<Size> new_peptide_indices;
vector<PeptideHit> filtered_peptide_hits;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
Size ml = max_length;
if (max_length < min_length)
{
ml = UINT_MAX;
}
const vector<PeptideHit>& temp_peptide_hits = identification.getHits();
for (Size i = 0; i < temp_peptide_hits.size(); i++)
{
if (temp_peptide_hits[i].getSequence().size() >= min_length && temp_peptide_hits[i].getSequence().size() <= ml)
{
new_peptide_indices.push_back(i);
}
}
for (Size i = 0; i < new_peptide_indices.size(); i++)
{
filtered_peptide_hits.push_back(identification.getHits()[new_peptide_indices[i]]);
}
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
void IDFilter::filterIdentificationsByExclusionPeptides(const PeptideIdentification& identification,
const set<String>& peptides,
bool ignore_modifications,
PeptideIdentification& filtered_identification)
{
vector<PeptideHit> filtered_peptide_hits;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
for (Size i = 0; i < identification.getHits().size(); i++)
{
String query = ignore_modifications ? identification.getHits()[i].getSequence().toUnmodifiedString() : identification.getHits()[i].getSequence().toString();
if (find(peptides.begin(), peptides.end(), query) == peptides.end())
{
filtered_peptide_hits.push_back(identification.getHits()[i]);
}
}
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
void IDFilter::filterIdentificationsByLength(const PeptideIdentification& identification,
PeptideIdentification& filtered_identification,
Size min_length,
Size max_length)
{
filtered_identification = identification;
if (max_length < min_length)
{
max_length = UINT_MAX;
}
const vector<PeptideHit>& temp_peptide_hits = identification.getHits();
vector<PeptideHit> filtered_peptide_hits;
for (Size i = 0; i < temp_peptide_hits.size(); ++i)
{
if (min_length <= temp_peptide_hits[i].getSequence().size() && temp_peptide_hits[i].getSequence().size() <= max_length)
{
filtered_peptide_hits.push_back(temp_peptide_hits[i]);
}
}
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
void IDFilter::filterIdentificationsByVariableModifications(const PeptideIdentification& identification,
const vector<String>& fixed_modifications,
PeptideIdentification& filtered_identification)
{
vector<Size> new_peptide_indices;
vector<PeptideHit> filtered_peptide_hits;
filtered_identification = identification;
filtered_identification.setHits(vector<PeptideHit>());
const vector<PeptideHit>& temp_peptide_hits = identification.getHits();
for (Size i = 0; i < temp_peptide_hits.size(); i++)
{
const AASequence& aa_seq = temp_peptide_hits[i].getSequence();
/*
TODO: check these cases
// check terminal modifications
if (aa_seq.hasNTerminalModification())
{
String unimod_name = aa_seq.getNTerminalModification();
if (find(fixed_modifications.begin(), fixed_modifications.end(), unimod_name) == fixed_modifications.end())
{
new_peptide_indices.push_back(i);
continue;
}
}
if (aa_seq.hasCTerminalModification())
{
String unimod_name = aa_seq.getCTerminalModification();
if (find(fixed_modifications.begin(), fixed_modifications.end(), unimod_name) == fixed_modifications.end())
{
new_peptide_indices.push_back(i);
continue;
}
}
*/
// check internal modifications
for (Size j = 0; j != aa_seq.size(); ++j)
{
if (aa_seq[j].isModified())
{
String unimod_name = aa_seq[j].getModification() + " (" + aa_seq[j].getOneLetterCode() + ")";
if (find(fixed_modifications.begin(), fixed_modifications.end(), unimod_name) == fixed_modifications.end())
{
new_peptide_indices.push_back(i);
continue;
}
}
}
}
for (Size i = 0; i < new_peptide_indices.size(); i++)
{
const PeptideHit& ph = temp_peptide_hits[new_peptide_indices[i]];
filtered_peptide_hits.push_back(ph);
}
if (!filtered_peptide_hits.empty())
{
filtered_identification.setHits(filtered_peptide_hits);
filtered_identification.assignRanks();
}
}
void CompNovoIdentificationCID::getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec)
{
//if (CID_spec.getPrecursors().begin()->getMZ() > 1000.0)
//{
//cerr << "Weight of precursor has been estimated to exceed 2000.0 Da which is the current limit" << endl;
//return;
//}
PeakSpectrum new_CID_spec(CID_spec);
windowMower_(new_CID_spec, 0.3, 1);
Param zhang_param;
zhang_param = zhang_.getParameters();
zhang_param.setValue("tolerance", fragment_mass_tolerance_);
zhang_param.setValue("use_gaussian_factor", "true");
zhang_param.setValue("use_linear_factor", "false");
zhang_.setParameters(zhang_param);
Normalizer normalizer;
Param n_param(normalizer.getParameters());
n_param.setValue("method", "to_one");
normalizer.setParameters(n_param);
normalizer.filterSpectrum(new_CID_spec);
Size charge(2);
double precursor_weight(0); // [M+H]+
if (!CID_spec.getPrecursors().empty())
{
// believe charge of spectrum?
if (CID_spec.getPrecursors().begin()->getCharge() != 0)
{
charge = CID_spec.getPrecursors().begin()->getCharge();
}
else
{
// TODO estimate charge state
}
precursor_weight = CID_spec.getPrecursors().begin()->getMZ() * charge - ((charge - 1) * Constants::PROTON_MASS_U);
}
//cerr << "charge=" << charge << ", [M+H]=" << precursor_weight << endl;
// now delete all peaks that are right of the estimated precursor weight
Size peak_counter(0);
for (PeakSpectrum::ConstIterator it = new_CID_spec.begin(); it != new_CID_spec.end(); ++it, ++peak_counter)
{
if (it->getPosition()[0] > precursor_weight)
{
break;
}
}
if (peak_counter < new_CID_spec.size())
{
new_CID_spec.resize(peak_counter);
}
static double oxonium_mass = EmpiricalFormula("H2O+").getMonoWeight();
Peak1D p;
p.setIntensity(1);
p.setPosition(oxonium_mass);
new_CID_spec.push_back(p);
p.setPosition(precursor_weight);
new_CID_spec.push_back(p);
// add complement to spectrum
/*
for (PeakSpectrum::ConstIterator it1 = CID_spec.begin(); it1 != CID_spec.end(); ++it1)
{
// get m/z of complement
double mz_comp = precursor_weight - it1->getPosition()[0] + Constants::PROTON_MASS_U;
// search if peaks are available that have similar m/z values
Size count(0);
bool found(false);
for (PeakSpectrum::ConstIterator it2 = CID_spec.begin(); it2 != CID_spec.end(); ++it2, ++count)
{
if (fabs(mz_comp - it2->getPosition()[0]) < fragment_mass_tolerance)
{
// add peak intensity to corresponding peak in new_CID_spec
new_CID_spec[count].setIntensity(new_CID_spec[count].getIntensity());
}
}
if (!found)
{
// infer this peak
Peak1D p;
p.setIntensity(it1->getIntensity());
p.setPosition(mz_comp);
new_CID_spec.push_back(p);
}
}*/
CompNovoIonScoringCID ion_scoring;
Param ion_scoring_param(ion_scoring.getParameters());
ion_scoring_param.setValue("fragment_mass_tolerance", fragment_mass_tolerance_);
ion_scoring_param.setValue("precursor_mass_tolerance", precursor_mass_tolerance_);
ion_scoring_param.setValue("decomp_weights_precision", decomp_weights_precision_);
ion_scoring_param.setValue("double_charged_iso_threshold", (double)param_.getValue("double_charged_iso_threshold"));
ion_scoring_param.setValue("max_isotope_to_score", param_.getValue("max_isotope_to_score"));
ion_scoring_param.setValue("max_isotope", max_isotope_);
ion_scoring.setParameters(ion_scoring_param);
Map<double, IonScore> ion_scores;
ion_scoring.scoreSpectrum(ion_scores, new_CID_spec, precursor_weight, charge);
new_CID_spec.sortByPosition();
/*
cerr << "Size of ion_scores " << ion_scores.size() << endl;
for (Map<double, IonScore>::const_iterator it = ion_scores.begin(); it != ion_scores.end(); ++it)
{
cerr << it->first << " " << it->second.score << endl;
}*/
#ifdef WRITE_SCORED_SPEC
PeakSpectrum filtered_spec(new_CID_spec);
filtered_spec.clear();
for (Map<double, CompNovoIonScoringCID::IonScore>::const_iterator it = ion_scores.begin(); it != ion_scores.end(); ++it)
{
Peak1D p;
p.setIntensity(it->second.score);
p.setPosition(it->first);
filtered_spec.push_back(p);
}
DTAFile().store("spec_scored.dta", filtered_spec);
#endif
set<String> sequences;
getDecompositionsDAC_(sequences, 0, new_CID_spec.size() - 1, precursor_weight, new_CID_spec, ion_scores);
#ifdef SPIKE_IN
sequences.insert("AFCVDGEGR");
sequences.insert("APEFAAPWPDFVPR");
sequences.insert("AVKQFEESQGR");
sequences.insert("CCTESLVNR");
sequences.insert("DAFLGSFLYEYSR");
sequences.insert("DAIPENLPPLTADFAEDK");
sequences.insert("DDNKVEDIWSFLSK");
sequences.insert("DDPHACYSTVFDK");
sequences.insert("DEYELLCLDGSR");
sequences.insert("DGAESYKELSVLLPNR");
sequences.insert("DGASCWCVDADGR");
sequences.insert("DLFIPTCLETGEFAR");
sequences.insert("DTHKSEIAHR");
sequences.insert("DVCKNYQEAK");
sequences.insert("EACFAVEGPK");
sequences.insert("ECCHGDLLECADDR");
sequences.insert("EFLGDKFYTVISSLK");
sequences.insert("EFTPVLQADFQK");
sequences.insert("ELFLDSGIFQPMLQGR");
sequences.insert("ETYGDMADCCEK");
sequences.insert("EVGCPSSSVQEMVSCLR");
sequences.insert("EYEATLEECCAK");
sequences.insert("FADLIQSGTFQLHLDSK");
sequences.insert("FFSASCVPGATIEQK");
sequences.insert("FLANVSTVLTSK");
sequences.insert("FLSGSDYAIR");
sequences.insert("FTASCPPSIK");
sequences.insert("GAIEWEGIESGSVEQAVAK");
sequences.insert("GDVAFIQHSTVEENTGGK");
sequences.insert("GEPPSCAEDQSCPSER");
sequences.insert("GEYVPTSLTAR");
sequences.insert("GQEFTITGQKR");
sequences.insert("GTFAALSELHCDK");
sequences.insert("HLVDEPQNLIK");
sequences.insert("HQDCLVTTLQTQPGAVR");
sequences.insert("HTTVNENAPDQK");
sequences.insert("ILDCGSPDTEVR");
sequences.insert("KCPSPCQLQAER");
sequences.insert("KGTEFTVNDLQGK");
sequences.insert("KQTALVELLK");
sequences.insert("KVPQVSTPTLVEVSR");
sequences.insert("LALQFTTNAKR");
sequences.insert("LCVLHEKTPVSEK");
sequences.insert("LFTFHADICTLPDTEK");
sequences.insert("LGEYGFQNALIVR");
sequences.insert("LHVDPENFK");
sequences.insert("LKECCDKPLLEK");
sequences.insert("LKHLVDEPQNLIK");
sequences.insert("LKPDPNTLCDEFK");
sequences.insert("LLGNVLVVVLAR");
sequences.insert("LLVVYPWTQR");
sequences.insert("LRVDPVNFK");
sequences.insert("LTDEELAFPPLSPSR");
sequences.insert("LVNELTEFAK");
sequences.insert("MFLSFPTTK");
sequences.insert("MPCTEDYLSLILNR");
sequences.insert("NAPYSGYSGAFHCLK");
sequences.insert("NECFLSHKDDSPDLPK");
sequences.insert("NEPNKVPACPGSCEEVK");
sequences.insert("NLQMDDFELLCTDGR");
sequences.insert("QAGVQAEPSPK");
sequences.insert("RAPEFAAPWPDFVPR");
sequences.insert("RHPEYAVSVLLR");
sequences.insert("RPCFSALTPDETYVPK");
sequences.insert("RSLLLAPEEGPVSQR");
sequences.insert("SAFPPEPLLCSVQR");
sequences.insert("SAGWNIPIGTLLHR");
sequences.insert("SCWCVDEAGQK");
sequences.insert("SGNPNYPHEFSR");
sequences.insert("SHCIAEVEK");
sequences.insert("SISSGFFECER");
sequences.insert("SKYLASASTMDHAR");
sequences.insert("SLHTLFGDELCK");
sequences.insert("SLLLAPEEGPVSQR");
sequences.insert("SPPQCSPDGAFRPVQCK");
sequences.insert("SREGDPLAVYLK");
sequences.insert("SRQIPQCPTSCER");
sequences.insert("TAGTPVSIPVCDDSSVK");
sequences.insert("TCVADESHAGCEK");
sequences.insert("TQFGCLEGFGR");
sequences.insert("TVMENFVAFVDK");
sequences.insert("TYFPHFDLSHGSAQVK");
sequences.insert("TYMLAFDVNDEK");
sequences.insert("VDEVGGEALGR");
sequences.insert("VDLLIGSSQDDGLINR");
sequences.insert("VEDIWSFLSK");
sequences.insert("VGGHAAEYGAEALER");
sequences.insert("VGTRCCTKPESER");
sequences.insert("VKVDEVGGEALGR");
sequences.insert("VKVDLLIGSSQDDGLINR");
sequences.insert("VLDSFSNGMK");
sequences.insert("VLSAADKGNVK");
sequences.insert("VPQVSTPTLVEVSR");
sequences.insert("VTKCCTESLVNR");
sequences.insert("VVAASDASQDALGCVK");
sequences.insert("VVAGVANALAHR");
sequences.insert("YICDNQDTISSK");
sequences.insert("YLASASTMDHAR");
sequences.insert("YNGVFQECCQAEDK");
#endif
SpectrumAlignmentScore spectra_zhang;
spectra_zhang.setParameters(zhang_param);
vector<PeptideHit> hits;
Size missed_cleavages = param_.getValue("missed_cleavages");
for (set<String>::const_iterator it = sequences.begin(); it != sequences.end(); ++it)
{
Size num_missed = countMissedCleavagesTryptic_(*it);
if (missed_cleavages < num_missed)
{
//cerr << "Two many missed cleavages: " << *it << ", found " << num_missed << ", allowed " << missed_cleavages << endl;
continue;
}
PeakSpectrum CID_sim_spec;
getCIDSpectrum_(CID_sim_spec, *it, charge);
//normalizer.filterSpectrum(CID_sim_spec);
double cid_score = zhang_(CID_sim_spec, CID_spec);
PeptideHit hit;
hit.setScore(cid_score);
hit.setSequence(getModifiedAASequence_(*it));
hit.setCharge((Int)charge); //TODO unify charge interface: int or size?
hits.push_back(hit);
//cerr << getModifiedAASequence_(*it) << " " << cid_score << " " << endl;
}
// rescore the top hits
id.setHits(hits);
id.assignRanks();
hits = id.getHits();
SpectrumAlignmentScore alignment_score;
Param align_param(alignment_score.getParameters());
align_param.setValue("tolerance", fragment_mass_tolerance_);
align_param.setValue("use_linear_factor", "true");
alignment_score.setParameters(align_param);
for (vector<PeptideHit>::iterator it = hits.begin(); it != hits.end(); ++it)
{
//cerr << "Pre: " << it->getRank() << " " << it->getSequence() << " " << it->getScore() << " " << endl;
}
Size number_of_prescoring_hits = param_.getValue("number_of_prescoring_hits");
if (hits.size() > number_of_prescoring_hits)
{
hits.resize(number_of_prescoring_hits);
}
for (vector<PeptideHit>::iterator it = hits.begin(); it != hits.end(); ++it)
{
PeakSpectrum CID_sim_spec;
getCIDSpectrum_(CID_sim_spec, getModifiedStringFromAASequence_(it->getSequence()), charge);
normalizer.filterSpectrum(CID_sim_spec);
//DTAFile().store("sim_specs/" + it->getSequence().toUnmodifiedString() + "_sim_CID.dta", CID_sim_spec);
//double cid_score = spectra_zhang(CID_sim_spec, CID_spec);
double cid_score = alignment_score(CID_sim_spec, CID_spec);
//cerr << "Final: " << it->getSequence() << " " << cid_score << endl;
it->setScore(cid_score);
}
id.setHits(hits);
id.assignRanks();
hits = id.getHits();
for (vector<PeptideHit>::iterator it = hits.begin(); it != hits.end(); ++it)
{
//cerr << "Fin: " << it->getRank() << " " << it->getSequence() << " " << it->getScore() << " " << endl;
}
Size number_of_hits = param_.getValue("number_of_hits");
if (id.getHits().size() > number_of_hits)
{
hits.resize(number_of_hits);
}
id.setHits(hits);
id.assignRanks();
return;
}