ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
StringList in = getStringList_("in");
String edta = getStringOption_("pos");
String out = getStringOption_("out");
String out_sep = getStringOption_("out_separator");
String out_TIC_debug = getStringOption_("auto_rt:out_debug_TIC");
StringList in_header = getStringList_("in_header");
// number of out_debug_TIC files and input files must be identical
/*if (out_TIC_debug.size() > 0 && in.size() != out_TIC_debug.size())
{
LOG_FATAL_ERROR << "Error: number of input file 'in' and auto_rt:out_debug_TIC files must be identical!" << std::endl;
return ILLEGAL_PARAMETERS;
}*/
// number of header files and input files must be identical
if (in_header.size() > 0 && in.size() != in_header.size())
{
LOG_FATAL_ERROR << "Error: number of input file 'in' and 'in_header' files must be identical!" << std::endl;
return ILLEGAL_PARAMETERS;
}
if (!getFlag_("auto_rt:enabled") && !out_TIC_debug.empty())
{
LOG_FATAL_ERROR << "Error: TIC output file requested, but auto_rt is not enabled! Either do not request the file or switch on 'auto_rt:enabled'." << std::endl;
return ILLEGAL_PARAMETERS;
}
double rttol = getDoubleOption_("rt_tol");
double mztol = getDoubleOption_("mz_tol");
Size rt_collect = getIntOption_("rt_collect");
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mzml_file;
mzml_file.setLogType(log_type_);
MSExperiment<Peak1D> exp, exp_pp;
EDTAFile ed;
ConsensusMap cm;
ed.load(edta, cm);
StringList tf_single_header0, tf_single_header1, tf_single_header2; // header content, for each column
std::vector<String> vec_single; // one line for each compound, multiple columns per experiment
vec_single.resize(cm.size());
for (Size fi = 0; fi < in.size(); ++fi)
{
// load raw data
mzml_file.load(in[fi], exp);
exp.sortSpectra(true);
if (exp.empty())
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry." << std::endl;
return INCOMPATIBLE_INPUT_DATA;
}
// try to detect RT peaks (only for the first input file -- all others should align!)
// cm.size() might change in here...
if (getFlag_("auto_rt:enabled") && fi == 0)
{
ConsensusMap cm_local = cm; // we might have different RT peaks for each map if 'auto_rt' is enabled
cm.clear(false); // reset global list (about to be filled)
// compute TIC
MSChromatogram<> tic = exp.getTIC();
MSSpectrum<> tics, tic_gf, tics_pp, tics_sn;
for (Size ic = 0; ic < tic.size(); ++ic)
{ // rewrite Chromatogram to MSSpectrum (GaussFilter requires it)
Peak1D peak;
peak.setMZ(tic[ic].getRT());
peak.setIntensity(tic[ic].getIntensity());
tics.push_back(peak);
}
// smooth (no PP_CWT here due to efficiency reasons -- large FWHM take longer!)
double fwhm = getDoubleOption_("auto_rt:FHWM");
GaussFilter gf;
Param p = gf.getParameters();
p.setValue("gaussian_width", fwhm * 2); // wider than FWHM, just to be sure we have a fully smoothed peak. Merging two peaks is unlikely
p.setValue("use_ppm_tolerance", "false");
gf.setParameters(p);
tic_gf = tics;
gf.filter(tic_gf);
// pick peaks
PeakPickerHiRes pp;
p = pp.getParameters();
p.setValue("signal_to_noise", getDoubleOption_("auto_rt:SNThreshold"));
pp.setParameters(p);
pp.pick(tic_gf, tics_pp);
if (tics_pp.size())
{
LOG_INFO << "Found " << tics_pp.size() << " auto-rt peaks at: ";
for (Size ipp = 0; ipp != tics_pp.size(); ++ipp) LOG_INFO << " " << tics_pp[ipp].getMZ();
}
else
{
LOG_INFO << "Found no auto-rt peaks. Change threshold parameters!";
}
LOG_INFO << std::endl;
if (!out_TIC_debug.empty()) // if debug file was given
{ // store intermediate steps for debug
MSExperiment<> out_debug;
out_debug.addChromatogram(toChromatogram(tics));
out_debug.addChromatogram(toChromatogram(tic_gf));
SignalToNoiseEstimatorMedian<MSSpectrum<> > snt;
snt.init(tics);
for (Size is = 0; is < tics.size(); ++is)
{
Peak1D peak;
peak.setMZ(tic[is].getMZ());
peak.setIntensity(snt.getSignalToNoise(tics[is]));
tics_sn.push_back(peak);
}
out_debug.addChromatogram(toChromatogram(tics_sn));
out_debug.addChromatogram(toChromatogram(tics_pp));
// get rid of "native-id" missing warning
for (Size id = 0; id < out_debug.size(); ++id) out_debug[id].setNativeID(String("spectrum=") + id);
mzml_file.store(out_TIC_debug, out_debug);
LOG_DEBUG << "Storing debug AUTO-RT: " << out_TIC_debug << std::endl;
}
// add target EICs: for each m/z with no/negative RT, add all combinations of that m/z with auto-RTs
// duplicate m/z entries will be ignored!
// all other lines with positive RT values are copied unaffected
//do not allow doubles
std::set<double> mz_doubles;
for (ConsensusMap::Iterator cit = cm_local.begin(); cit != cm_local.end(); ++cit)
{
if (cit->getRT() < 0)
{
if (mz_doubles.find(cit->getMZ()) == mz_doubles.end())
{
mz_doubles.insert(cit->getMZ());
}
else
{
LOG_INFO << "Found duplicate m/z entry (" << cit->getMZ() << ") for auto-rt. Skipping ..." << std::endl;
continue;
}
ConsensusMap cm_RT_multiplex;
for (MSSpectrum<>::ConstIterator itp = tics_pp.begin(); itp != tics_pp.end(); ++itp)
{
ConsensusFeature f = *cit;
f.setRT(itp->getMZ());
cm.push_back(f);
}
}
else
{ // default feature with no auto-rt
LOG_INFO << "copying feature with RT " << cit->getRT() << std::endl;
cm.push_back(*cit);
}
}
// resize, since we have more positions now
vec_single.resize(cm.size());
}
// search for each EIC and add up
Int not_found(0);
Map<Size, double> quant;
String description;
if (fi < in_header.size())
{
HeaderInfo info(in_header[fi]);
description = info.header_description;
}
if (fi == 0)
{ // two additional columns for first file (theoretical RT and m/z)
tf_single_header0 << "" << "";
tf_single_header1 << "" << "";
tf_single_header2 << "RT" << "mz";
}
// 5 entries for each input file
tf_single_header0 << File::basename(in[fi]) << "" << "" << "" << "";
tf_single_header1 << description << "" << "" << "" << "";
tf_single_header2 << "RTobs" << "dRT" << "mzobs" << "dppm" << "intensity";
for (Size i = 0; i < cm.size(); ++i)
{
//std::cerr << "Rt" << cm[i].getRT() << " mz: " << cm[i].getMZ() << " R " << cm[i].getMetaValue("rank") << "\n";
double mz_da = mztol * cm[i].getMZ() / 1e6; // mz tolerance in Dalton
MSExperiment<>::ConstAreaIterator it = exp.areaBeginConst(cm[i].getRT() - rttol / 2,
cm[i].getRT() + rttol / 2,
cm[i].getMZ() - mz_da,
cm[i].getMZ() + mz_da);
Peak2D max_peak;
max_peak.setIntensity(0);
max_peak.setRT(cm[i].getRT());
max_peak.setMZ(cm[i].getMZ());
for (; it != exp.areaEndConst(); ++it)
{
if (max_peak.getIntensity() < it->getIntensity())
{
max_peak.setIntensity(it->getIntensity());
max_peak.setRT(it.getRT());
max_peak.setMZ(it->getMZ());
}
}
double ppm = 0; // observed m/z offset
if (max_peak.getIntensity() == 0)
{
++not_found;
}
else
{
// take median for m/z found
std::vector<double> mz;
MSExperiment<>::Iterator itm = exp.RTBegin(max_peak.getRT());
SignedSize low = std::min<SignedSize>(std::distance(exp.begin(), itm), rt_collect);
SignedSize high = std::min<SignedSize>(std::distance(itm, exp.end()) - 1, rt_collect);
MSExperiment<>::AreaIterator itt = exp.areaBegin((itm - low)->getRT() - 0.01, (itm + high)->getRT() + 0.01, cm[i].getMZ() - mz_da, cm[i].getMZ() + mz_da);
for (; itt != exp.areaEnd(); ++itt)
{
mz.push_back(itt->getMZ());
//std::cerr << "ppm: " << itt.getRT() << " " << itt->getMZ() << " " << itt->getIntensity() << std::endl;
}
if ((SignedSize)mz.size() > (low + high + 1)) LOG_WARN << "Compound " << i << " has overlapping peaks [" << mz.size() << "/" << low + high + 1 << "]" << std::endl;
if (!mz.empty())
{
double avg_mz = std::accumulate(mz.begin(), mz.end(), 0.0) / double(mz.size());
//std::cerr << "avg: " << avg_mz << "\n";
ppm = (avg_mz - cm[i].getMZ()) / cm[i].getMZ() * 1e6;
}
}
// appending the second column set requires separator
String append_sep = (fi == 0 ? "" : out_sep);
vec_single[i] += append_sep; // new line
if (fi == 0)
{
vec_single[i] += String(cm[i].getRT()) + out_sep +
String(cm[i].getMZ()) + out_sep;
}
vec_single[i] += String(max_peak.getRT()) + out_sep +
String(max_peak.getRT() - cm[i].getRT()) + out_sep +
String(max_peak.getMZ()) + out_sep +
String(ppm) + out_sep +
String(max_peak.getIntensity());
}
if (not_found) LOG_INFO << "Missing peaks for " << not_found << " compounds in file '" << in[fi] << "'.\n";
}
//-------------------------------------------------------------
// create header
//-------------------------------------------------------------
vec_single.insert(vec_single.begin(), ListUtils::concatenate(tf_single_header2, out_sep));
vec_single.insert(vec_single.begin(), ListUtils::concatenate(tf_single_header1, out_sep));
vec_single.insert(vec_single.begin(), ListUtils::concatenate(tf_single_header0, out_sep));
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
TextFile tf;
for (std::vector<String>::iterator v_it = vec_single.begin(); v_it != vec_single.end(); ++v_it)
{
tf.addLine(*v_it);
}
tf.store(out);
return EXECUTION_OK;
}
void IsobaricChannelExtractor::extractChannels(const MSExperiment<Peak1D>& ms_exp_data, ConsensusMap& consensus_map)
{
if (ms_exp_data.empty())
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.\n";
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Experiment has no scans!");
}
// clear the output map
consensus_map.clear(false);
consensus_map.setExperimentType("labeled_MS2");
// create predicate for spectrum checking
LOG_INFO << "Selecting scans with activation mode: " << (selected_activation_ == "" ? "any" : selected_activation_) << "\n";
HasActivationMethod<MSExperiment<Peak1D>::SpectrumType> activation_predicate(StringList::create(selected_activation_));
// now we have picked data
// --> assign peaks to channels
UInt64 element_index(0);
// remember the current precusor spectrum
MSExperiment<Peak1D>::ConstIterator prec_spec = ms_exp_data.end();
for (MSExperiment<Peak1D>::ConstIterator it = ms_exp_data.begin(); it != ms_exp_data.end(); ++it)
{
// remember the last MS1 spectra as we assume it to be the precursor spectrum
if (it->getMSLevel() == 1) prec_spec = it;
if (selected_activation_ == "" || activation_predicate(*it))
{
// check if precursor is available
if (it->getPrecursors().empty())
{
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, String("No precursor information given for scan native ID ") + it->getNativeID() + " with RT " + String(it->getRT()));
}
// check precursor constraints
if (!isValidPrecursor_(it->getPrecursors()[0]))
{
LOG_DEBUG << "Skip spectrum " << it->getNativeID() << ": Precursor doesn't fulfill all constraints." << std::endl;
continue;
}
// check precursor purity if we have a valid precursor ..
if (prec_spec != ms_exp_data.end())
{
const DoubleReal purity = computePrecursorPurity_(it, prec_spec);
if (purity < min_precursor_purity_)
{
LOG_DEBUG << "Skip spectrum " << it->getNativeID() << ": Precursor purity is below the threshold. [purity = " << purity << "]" << std::endl;
continue;
}
}
else
{
LOG_INFO << "No precursor available for spectrum: " << it->getNativeID() << std::endl;
}
if (!(prec_spec == ms_exp_data.end()) && computePrecursorPurity_(it, prec_spec) < min_precursor_purity_)
{
LOG_DEBUG << "Skip spectrum " << it->getNativeID() << ": Precursor purity is below the threshold." << std::endl;
continue;
}
// store RT&MZ of parent ion as centroid of ConsensusFeature
ConsensusFeature cf;
cf.setUniqueId();
cf.setRT(it->getRT());
cf.setMZ(it->getPrecursors()[0].getMZ());
Peak2D channel_value;
channel_value.setRT(it->getRT());
// for each each channel
UInt64 map_index = 0;
Peak2D::IntensityType overall_intensity = 0;
for (IsobaricQuantitationMethod::IsobaricChannelList::const_iterator cl_it = quant_method_->getChannelInformation().begin();
cl_it != quant_method_->getChannelInformation().end();
++cl_it)
{
// set mz-position of channel
channel_value.setMZ(cl_it->center);
// reset intensity
channel_value.setIntensity(0);
// as every evaluation requires time, we cache the MZEnd iterator
const MSExperiment<Peak1D>::SpectrumType::ConstIterator mz_end = it->MZEnd(cl_it->center + reporter_mass_shift_);
// add up all signals
for (MSExperiment<Peak1D>::SpectrumType::ConstIterator mz_it = it->MZBegin(cl_it->center - reporter_mass_shift_);
mz_it != mz_end;
++mz_it)
{
channel_value.setIntensity(channel_value.getIntensity() + mz_it->getIntensity());
}
// discard contribution of this channel as it is below the required intensity threshold
if (channel_value.getIntensity() < min_reporter_intensity_)
{
channel_value.setIntensity(0);
}
overall_intensity += channel_value.getIntensity();
// add channel to ConsensusFeature
cf.insert(map_index++, channel_value, element_index);
} // ! channel_iterator
// check if we keep this feature or if it contains low-intensity quantifications
if (remove_low_intensity_quantifications_ && hasLowIntensityReporter_(cf))
{
continue;
}
// check featureHandles are not empty
if (overall_intensity == 0)
{
cf.setMetaValue("all_empty", String("true"));
}
cf.setIntensity(overall_intensity);
consensus_map.push_back(cf);
// the tandem-scan in the order they appear in the experiment
++element_index;
}
} // ! Experiment iterator
/// add meta information to the map
registerChannelsInOutputMap_(consensus_map);
}
/// @brief extracts the iTRAQ channels from the MS data and stores intensity values in a consensus map
///
/// @param ms_exp_data Raw data to read
/// @param consensus_map Output each MS² scan as a consensus feature
/// @throws Exception::MissingInformation if no scans present or MS² scan has no precursor
void ItraqChannelExtractor::run(const MSExperiment<Peak1D>& ms_exp_data, ConsensusMap& consensus_map)
{
if (ms_exp_data.empty())
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Experiment has no scans!");
}
MSExperiment<> ms_exp_MS2;
String mode = (String) param_.getValue("select_activation");
std::cout << "Selecting scans with activation mode: " << (mode == "" ? "any" : mode) << "\n";
HasActivationMethod<MSExperiment<Peak1D>::SpectrumType> activation_predicate(ListUtils::create<String>(mode));
for (size_t idx = 0; idx < ms_exp_data.size(); ++idx)
{
if (ms_exp_data[idx].getMSLevel() == 2)
{
if (mode == "" || activation_predicate(ms_exp_data[idx]))
{
// copy only MS² scans
ms_exp_MS2.addSpectrum(ms_exp_data[idx]);
}
else
{
//std::cout << "deleting spectrum # " << idx << " with RT: " << ms_exp_data[idx].getRT() << "\n";
}
}
}
#ifdef ITRAQ_DEBUG
std::cout << "we have " << ms_exp_MS2.size() << " scans left of level " << ms_exp_MS2[0].getMSLevel() << std::endl;
std::cout << "run: channel_map_ has " << channel_map_.size() << " entries!" << std::endl;
#endif
consensus_map.clear(false);
// set <mapList> header
Int index_cnt = 0;
for (ChannelMapType::const_iterator cm_it = channel_map_.begin(); cm_it != channel_map_.end(); ++cm_it)
{
// structure of Map cm_it
// first == channel-name as Int e.g. 114
// second == ChannelInfo struct
ConsensusMap::FileDescription channel_as_map;
// label is the channel + description provided in the Params
if (itraq_type_ != TMT_SIXPLEX)
channel_as_map.label = "iTRAQ_" + String(cm_it->second.name) + "_" + String(cm_it->second.description);
else
channel_as_map.label = "TMT_" + String(cm_it->second.name) + "_" + String(cm_it->second.description);
channel_as_map.size = ms_exp_MS2.size();
//TODO what about .filename? leave empty?
// add some more MetaInfo
channel_as_map.setMetaValue("channel_name", cm_it->second.name);
channel_as_map.setMetaValue("channel_id", cm_it->second.id);
channel_as_map.setMetaValue("channel_description", cm_it->second.description);
channel_as_map.setMetaValue("channel_center", cm_it->second.center);
channel_as_map.setMetaValue("channel_active", String(cm_it->second.active ? "true" : "false"));
consensus_map.getFileDescriptions()[index_cnt++] = channel_as_map;
}
// create consensusElements
Peak2D::CoordinateType allowed_deviation = (Peak2D::CoordinateType) param_.getValue("reporter_mass_shift");
// now we have picked data
// --> assign peaks to channels
UInt element_index(0);
for (MSExperiment<>::ConstIterator it = ms_exp_MS2.begin(); it != ms_exp_MS2.end(); ++it)
{
// store RT&MZ of parent ion as centroid of ConsensusFeature
ConsensusFeature cf;
cf.setUniqueId();
cf.setRT(it->getRT());
if (it->getPrecursors().size() >= 1)
{
cf.setMZ(it->getPrecursors()[0].getMZ());
}
else
{
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, String("No precursor information given for scan native ID ") + String(it->getNativeID()) + " with RT " + String(it->getRT()));
}
Peak2D channel_value;
channel_value.setRT(it->getRT());
// for each each channel
Int index = 0;
Peak2D::IntensityType overall_intensity = 0;
for (ChannelMapType::const_iterator cm_it = channel_map_.begin(); cm_it != channel_map_.end(); ++cm_it)
{
// set mz-position of channel
channel_value.setMZ(cm_it->second.center);
// reset intensity
channel_value.setIntensity(0);
//add up all signals
for (MSExperiment<>::SpectrumType::ConstIterator mz_it =
it->MZBegin(cm_it->second.center - allowed_deviation)
; mz_it != it->MZEnd(cm_it->second.center + allowed_deviation)
; ++mz_it
)
{
channel_value.setIntensity(channel_value.getIntensity() + mz_it->getIntensity());
}
overall_intensity += channel_value.getIntensity();
// add channel to ConsensusFeature
cf.insert(index++, channel_value, element_index);
} // ! channel_iterator
// check featureHandles are not empty
if (overall_intensity == 0)
{
cf.setMetaValue("all_empty", String("true"));
}
cf.setIntensity(overall_intensity);
consensus_map.push_back(cf);
// the tandem-scan in the order they appear in the experiment
++element_index;
} // ! Experiment iterator
#ifdef ITRAQ_DEBUG
std::cout << "processed " << element_index << " scans" << std::endl;
#endif
consensus_map.setExperimentType("itraq");
return;
}
void StablePairFinder::run(const std::vector<ConsensusMap>& input_maps,
ConsensusMap& result_map)
{
// empty output destination:
result_map.clear(false);
// sanity checks:
if (input_maps.size() != 2)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"exactly two input maps required");
}
checkIds_(input_maps);
// set up the distance functor:
double max_intensity = max(input_maps[0].getMaxInt(),
input_maps[1].getMaxInt());
Param distance_params = param_.copy("");
distance_params.remove("use_identifications");
distance_params.remove("second_nearest_gap");
FeatureDistance feature_distance(max_intensity, false);
feature_distance.setParameters(distance_params);
// keep track of pairing:
std::vector<bool> is_singleton[2];
is_singleton[0].resize(input_maps[0].size(), true);
is_singleton[1].resize(input_maps[1].size(), true);
typedef pair<double, double> DoublePair;
DoublePair init = make_pair(FeatureDistance::infinity,
FeatureDistance::infinity);
// for every element in map 0:
// - index of nearest neighbor in map 1:
vector<UInt> nn_index_0(input_maps[0].size(), UInt(-1));
// - distances to nearest and second-nearest neighbors in map 1:
vector<DoublePair> nn_distance_0(input_maps[0].size(), init);
// for every element in map 1:
// - index of nearest neighbor in map 0:
vector<UInt> nn_index_1(input_maps[1].size(), UInt(-1));
// - distances to nearest and second-nearest neighbors in map 0:
vector<DoublePair> nn_distance_1(input_maps[1].size(), init);
// iterate over all feature pairs, find nearest neighbors:
// TODO: iterate over SENSIBLE RT (and m/z) window -- sort the maps beforehand
// to save a lot of processing time...
// Once done, remove the warning in the description of the 'use_identifications' parameter
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
const ConsensusFeature& feat0 = input_maps[0][fi0];
for (UInt fi1 = 0; fi1 < input_maps[1].size(); ++fi1)
{
const ConsensusFeature& feat1 = input_maps[1][fi1];
if (use_IDs_ && !compatibleIDs_(feat0, feat1)) // check peptide IDs
{
continue; // mismatch
}
pair<bool, double> result = feature_distance(feat0, feat1);
double distance = result.second;
// we only care if distance constraints are satisfied for "best
// matches", not for second-best; this means that second-best distances
// can become smaller than best distances
// (e.g. the RT is larger than allowed (->invalid pair), but m/z is perfect and has the most weight --> better score!)
bool valid = result.first;
// update entries for map 0:
if (distance < nn_distance_0[fi0].second)
{
if (valid && (distance < nn_distance_0[fi0].first))
{
nn_distance_0[fi0].second = nn_distance_0[fi0].first;
nn_distance_0[fi0].first = distance;
nn_index_0[fi0] = fi1;
}
else
{
nn_distance_0[fi0].second = distance;
}
}
// update entries for map 1:
if (distance < nn_distance_1[fi1].second)
{
if (valid && (distance < nn_distance_1[fi1].first))
{
nn_distance_1[fi1].second = nn_distance_1[fi1].first;
nn_distance_1[fi1].first = distance;
nn_index_1[fi1] = fi0;
}
else
{
nn_distance_1[fi1].second = distance;
}
}
}
}
// if features from the two maps are nearest neighbors of each other, they
// can become a pair:
for (UInt fi0 = 0; fi0 < input_maps[0].size(); ++fi0)
{
UInt fi1 = nn_index_0[fi0]; // nearest neighbor of "fi0" in map 1
// cout << "index: " << fi0 << ", RT: " << input_maps[0][fi0].getRT()
// << ", MZ: " << input_maps[0][fi0].getMZ() << endl
// << "neighbor: " << fi1 << ", RT: " << input_maps[1][fi1].getRT()
// << ", MZ: " << input_maps[1][fi1].getMZ() << endl
// << "d(i,j): " << nn_distance_0[fi0].first << endl
// << "d2(i): " << nn_distance_0[fi0].second << endl
// << "d2(j): " << nn_distance_1[fi1].second << endl;
// criteria set by the parameters must be fulfilled:
if ((nn_distance_0[fi0].first < FeatureDistance::infinity) &&
(nn_distance_0[fi0].first * second_nearest_gap_ <= nn_distance_0[fi0].second))
{
// "fi0" satisfies constraints...
if ((nn_index_1[fi1] == fi0) &&
(nn_distance_1[fi1].first * second_nearest_gap_ <= nn_distance_1[fi1].second))
{
// ...nearest neighbor of "fi0" also satisfies constraints (yay!)
// cout << "match!" << endl;
result_map.push_back(ConsensusFeature());
ConsensusFeature& f = result_map.back();
f.insert(input_maps[0][fi0]);
f.getPeptideIdentifications().insert(f.getPeptideIdentifications().end(),
input_maps[0][fi0].getPeptideIdentifications().begin(),
input_maps[0][fi0].getPeptideIdentifications().end());
f.insert(input_maps[1][fi1]);
f.getPeptideIdentifications().insert(f.getPeptideIdentifications().end(),
input_maps[1][fi1].getPeptideIdentifications().begin(),
input_maps[1][fi1].getPeptideIdentifications().end());
f.computeConsensus();
double quality = 1.0 - nn_distance_0[fi0].first;
double quality0 = 1.0 - nn_distance_0[fi0].first * second_nearest_gap_ / nn_distance_0[fi0].second;
double quality1 = 1.0 - nn_distance_1[fi1].first * second_nearest_gap_ / nn_distance_1[fi1].second;
quality = quality * quality0 * quality1; // TODO other formula?
// incorporate existing quality values:
Size size0 = max(input_maps[0][fi0].size(), size_t(1));
Size size1 = max(input_maps[1][fi1].size(), size_t(1));
// quality contribution from first map:
quality0 = input_maps[0][fi0].getQuality() * (size0 - 1);
// quality contribution from second map:
quality1 = input_maps[1][fi1].getQuality() * (size1 - 1);
f.setQuality((quality + quality0 + quality1) / (size0 + size1 - 1));
is_singleton[0][fi0] = false;
is_singleton[1][fi1] = false;
}
}
}
// write out unmatched consensus features
for (UInt input = 0; input <= 1; ++input)
{
for (UInt index = 0; index < input_maps[input].size(); ++index)
{
if (is_singleton[input][index])
{
result_map.push_back(input_maps[input][index]);
if (result_map.back().size() < 2) // singleton consensus feature
{
result_map.back().setQuality(0.0);
}
}
}
}
// canonical ordering for checking the results, and the ids have no real meaning anyway
result_map.sortByMZ();
// protein IDs and unassigned peptide IDs are added to the result by the
// FeatureGroupingAlgorithm!
}
void LabeledPairFinder::run(const vector<ConsensusMap>& input_maps, ConsensusMap& result_map)
{
if (input_maps.size() != 1)
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "exactly one input map required");
if (result_map.getFileDescriptions().size() != 2)
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "two file descriptions required");
if (result_map.getFileDescriptions().begin()->second.filename != result_map.getFileDescriptions().rbegin()->second.filename)
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "the two file descriptions have to contain the same file name");
checkIds_(input_maps);
//look up the light and heavy index
Size light_index = numeric_limits<Size>::max();
Size heavy_index = numeric_limits<Size>::max();
for (ConsensusMap::FileDescriptions::const_iterator it = result_map.getFileDescriptions().begin();
it != result_map.getFileDescriptions().end();
++it)
{
if (it->second.label == "heavy")
{
heavy_index = it->first;
}
else if (it->second.label == "light")
{
light_index = it->first;
}
}
if (light_index == numeric_limits<Size>::max() || heavy_index == numeric_limits<Size>::max())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "the input maps have to be labeled 'light' and 'heavy'");
}
result_map.clear(false);
// sort consensus features by RT (and MZ) to speed up searching afterwards
typedef ConstRefVector<ConsensusMap> RefMap;
RefMap model_ref(input_maps[0].begin(), input_maps[0].end());
model_ref.sortByPosition();
//calculate matches
ConsensusMap matches;
//settings
double rt_pair_dist = param_.getValue("rt_pair_dist");
double rt_dev_low = param_.getValue("rt_dev_low");
double rt_dev_high = param_.getValue("rt_dev_high");
double mz_dev = param_.getValue("mz_dev");
DoubleList mz_pair_dists = param_.getValue("mz_pair_dists");
bool mrm = param_.getValue("mrm").toBool();
//estimate RT parameters
if (param_.getValue("rt_estimate") == "true")
{
//find all possible RT distances of features with the same charge and a good m/z distance
vector<double> dists;
dists.reserve(model_ref.size());
for (RefMap::const_iterator it = model_ref.begin(); it != model_ref.end(); ++it)
{
for (RefMap::const_iterator it2 = model_ref.begin(); it2 != model_ref.end(); ++it2)
{
for (DoubleList::const_iterator dist_it = mz_pair_dists.begin(); dist_it != mz_pair_dists.end(); ++dist_it)
{
double mz_pair_dist = *dist_it;
if (it2->getCharge() == it->getCharge()
&& it2->getMZ() >= it->getMZ() + mz_pair_dist / it->getCharge() - mz_dev
&& it2->getMZ() <= it->getMZ() + mz_pair_dist / it->getCharge() + mz_dev)
{
dists.push_back(it2->getRT() - it->getRT());
}
}
}
}
if (dists.empty())
{
cout << "Warning: Could not find pairs for RT distance estimation. The manual settings are used!" << endl;
}
else
{
if (dists.size() < 50)
{
cout << "Warning: Found only " << dists.size() << " pairs. The estimated shift and std deviation are probably not reliable!" << endl;
}
//--------------------------- estimate initial parameters of fit ---------------------------
GaussFitter::GaussFitResult result(-1, -1, -1);
//first estimate of the optimal shift: median of the distances
sort(dists.begin(), dists.end());
Size median_index = dists.size() / 2;
result.x0 = dists[median_index];
//create histogram of distances
//consider only the maximum of pairs, centered around the optimal shift
Size max_pairs = model_ref.size() / 2;
Size start_index = (Size) max((SignedSize)0, (SignedSize)(median_index - max_pairs / 2));
Size end_index = (Size) min((SignedSize)(dists.size() - 1), (SignedSize)(median_index + max_pairs / 2));
double start_value = dists[start_index];
double end_value = dists[end_index];
double bin_step = fabs(end_value - start_value) / 99.999; //ensure that we have 100 bins
Math::Histogram<> hist(start_value, end_value, bin_step);
//std::cout << "HIST from " << start_value << " to " << end_value << " (bin size " << bin_step << ")" << endl;
for (Size i = start_index; i <= end_index; ++i)
{
hist.inc(dists[i]);
}
//cout << hist << endl;
dists.clear();
//determine median of bins (uniform background distribution)
vector<Size> bins(hist.begin(), hist.end());
sort(bins.begin(), bins.end());
Size bin_median = bins[bins.size() / 2];
bins.clear();
//estimate scale A: maximum of the histogram
Size max_value = hist.maxValue();
result.A = max_value - bin_median;
//overwrite estimate of x0 with the position of the highest bin
for (Size i = 0; i < hist.size(); ++i)
{
if (hist[i] == max_value)
{
result.x0 = hist.centerOfBin(i);
break;
}
}
//estimate sigma: first time the count is less or equal the median count in the histogram
double pos = result.x0;
while (pos > start_value && hist.binValue(pos) > bin_median)
{
pos -= bin_step;
}
double sigma_low = result.x0 - pos;
pos = result.x0;
while (pos<end_value&& hist.binValue(pos)> bin_median)
{
pos += bin_step;
}
double sigma_high = pos - result.x0;
result.sigma = (sigma_high + sigma_low) / 6.0;
//cout << "estimated optimal RT distance (before fit): " << result.x0 << endl;
//cout << "estimated allowed deviation (before fit): " << result.sigma*3.0 << endl;
//--------------------------- do gauss fit ---------------------------
vector<DPosition<2> > points(hist.size());
for (Size i = 0; i < hist.size(); ++i)
{
points[i][0] = hist.centerOfBin(i);
points[i][1] = max(0u, hist[i]);
}
GaussFitter fitter;
fitter.setInitialParameters(result);
result = fitter.fit(points);
cout << "estimated optimal RT distance: " << result.x0 << endl;
cout << "estimated allowed deviation: " << fabs(result.sigma) * 3.0 << endl;
rt_pair_dist = result.x0;
rt_dev_low = fabs(result.sigma) * 3.0;
rt_dev_high = fabs(result.sigma) * 3.0;
}
}
// check each feature
for (RefMap::const_iterator it = model_ref.begin(); it != model_ref.end(); ++it)
{
for (DoubleList::const_iterator dist_it = mz_pair_dists.begin(); dist_it != mz_pair_dists.end(); ++dist_it)
{
double mz_pair_dist = *dist_it;
RefMap::const_iterator it2 = lower_bound(model_ref.begin(), model_ref.end(), it->getRT() + rt_pair_dist - rt_dev_low, ConsensusFeature::RTLess());
while (it2 != model_ref.end() && it2->getRT() <= it->getRT() + rt_pair_dist + rt_dev_high)
{
// if in mrm mode, we need to compare precursor mass difference and fragment mass difference, charge remains the same
double prec_mz_diff(0);
if (mrm)
{
prec_mz_diff = fabs((double)it2->getMetaValue("MZ") - (double)it->getMetaValue("MZ"));
if (it->getCharge() != 0)
{
prec_mz_diff = fabs(prec_mz_diff - mz_pair_dist / it->getCharge());
}
else
{
prec_mz_diff = fabs(prec_mz_diff - mz_pair_dist);
}
}
bool mrm_correct_dist(false);
double frag_mz_diff = fabs(it->getMZ() - it2->getMZ());
//cerr << it->getRT() << " charge1=" << it->getCharge() << ", charge2=" << it2->getCharge() << ", prec_diff=" << prec_mz_diff << ", frag_diff=" << frag_mz_diff << endl;
if (mrm &&
it2->getCharge() == it->getCharge() &&
prec_mz_diff < mz_dev &&
(frag_mz_diff < mz_dev || fabs(frag_mz_diff - mz_pair_dist) < mz_dev))
{
mrm_correct_dist = true;
//cerr << "mrm_correct_dist" << endl;
}
if ((mrm && mrm_correct_dist) || (!mrm &&
it2->getCharge() == it->getCharge() &&
it2->getMZ() >= it->getMZ() + mz_pair_dist / it->getCharge() - mz_dev &&
it2->getMZ() <= it->getMZ() + mz_pair_dist / it->getCharge() + mz_dev
))
{
//cerr << "dist correct" << endl;
double score = sqrt(
PValue_(it2->getMZ() - it->getMZ(), mz_pair_dist / it->getCharge(), mz_dev, mz_dev) *
PValue_(it2->getRT() - it->getRT(), rt_pair_dist, rt_dev_low, rt_dev_high)
);
// Note: we used to copy the id from the light feature here, but that strategy does not generalize to more than two labels.
// We might want to report consensus features where the light one is missing but more than one heavier variant was found.
// Also, the old strategy is inconsistent with what was done in the unlabeled case. Thus now we assign a new unique id here.
matches.push_back(ConsensusFeature());
matches.back().setUniqueId();
matches.back().insert(light_index, *it);
matches.back().clearMetaInfo();
matches.back().insert(heavy_index, *it2);
matches.back().setQuality(score);
matches.back().setCharge(it->getCharge());
matches.back().computeMonoisotopicConsensus();
}
++it2;
}
}
}
//compute best pairs
// - sort matches by quality
// - take highest-quality matches first (greedy) and mark them as used
set<Size> used_features;
matches.sortByQuality(true);
for (ConsensusMap::const_iterator match = matches.begin(); match != matches.end(); ++match)
{
//check if features are not used yet
if (used_features.find(match->begin()->getUniqueId()) == used_features.end() &&
used_features.find(match->rbegin()->getUniqueId()) == used_features.end()
)
{
//if unused, add it to the final set of elements
result_map.push_back(*match);
used_features.insert(match->begin()->getUniqueId());
used_features.insert(match->rbegin()->getUniqueId());
}
}
//Add protein identifications to result map
for (Size i = 0; i < input_maps.size(); ++i)
{
result_map.getProteinIdentifications().insert(result_map.getProteinIdentifications().end(), input_maps[i].getProteinIdentifications().begin(), input_maps[i].getProteinIdentifications().end());
}
//Add unassigned peptide identifications to result map
for (Size i = 0; i < input_maps.size(); ++i)
{
result_map.getUnassignedPeptideIdentifications().insert(result_map.getUnassignedPeptideIdentifications().end(), input_maps[i].getUnassignedPeptideIdentifications().begin(), input_maps[i].getUnassignedPeptideIdentifications().end());
}
// Very useful for checking the results, and the ids have no real meaning anyway
result_map.sortByMZ();
}
void QTClusterFinder::run_(const vector<MapType> & input_maps,
ConsensusMap & result_map)
{
num_maps_ = input_maps.size();
if (num_maps_ < 2)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"At least two input maps required");
}
// set up the distance functor (and set other parameters):
DoubleReal max_intensity = input_maps[0].getMaxInt();
DoubleReal max_mz = input_maps[0].getMax()[1];
for (Size map_index = 1; map_index < num_maps_; ++map_index)
{
max_intensity = max(max_intensity, input_maps[map_index].getMaxInt());
max_mz = max(max_mz, input_maps[map_index].getMax()[0]);
}
setParameters_(max_intensity, max_mz);
// create the hash grid and fill it with features:
//cout << "Hashing..." << endl;
list<GridFeature> grid_features;
Grid grid(Grid::ClusterCenter(max_diff_rt_, max_diff_mz_));
for (Size map_index = 0; map_index < num_maps_; ++map_index)
{
for (Size feature_index = 0; feature_index < input_maps[map_index].size();
++feature_index)
{
grid_features.push_back(
GridFeature(input_maps[map_index][feature_index], map_index,
feature_index));
GridFeature & gfeature = grid_features.back();
// sort peptide hits once now, instead of multiple times later:
BaseFeature & feature = const_cast<BaseFeature &>(
grid_features.back().getFeature());
for (vector<PeptideIdentification>::iterator pep_it =
feature.getPeptideIdentifications().begin(); pep_it !=
feature.getPeptideIdentifications().end(); ++pep_it)
{
pep_it->sort();
}
grid.insert(std::make_pair(Grid::ClusterCenter(gfeature.getRT(), gfeature.getMZ()), &gfeature));
}
}
// compute QT clustering:
//cout << "Clustering..." << endl;
list<QTCluster> clustering;
computeClustering_(grid, clustering);
// number of clusters == number of data points:
Size size = clustering.size();
// Create a temporary map where we store which GridFeatures are next to which Clusters
OpenMSBoost::unordered_map<GridFeature *, std::vector< QTCluster * > > element_mapping;
for (list<QTCluster>::iterator it = clustering.begin(); it != clustering.end(); ++it)
{
OpenMSBoost::unordered_map<Size, GridFeature *> elements;
typedef std::multimap<DoubleReal, GridFeature *> InnerNeighborMap;
typedef OpenMSBoost::unordered_map<Size, InnerNeighborMap > NeighborMap;
NeighborMap neigh = it->getNeighbors();
for (NeighborMap::iterator n_it = neigh.begin(); n_it != neigh.end(); ++n_it)
{
for (InnerNeighborMap::iterator i_it = n_it->second.begin(); i_it != n_it->second.end(); ++i_it)
{
element_mapping[i_it->second].push_back( &(*it) );
}
}
}
ProgressLogger logger;
logger.setLogType(ProgressLogger::CMD);
logger.startProgress(0, size, "linking features");
Size progress = 0;
result_map.clear(false);
while (!clustering.empty())
{
// cout << "Clusters: " << clustering.size() << endl;
ConsensusFeature consensus_feature;
makeConsensusFeature_(clustering, consensus_feature, element_mapping);
if (!clustering.empty())
{
result_map.push_back(consensus_feature);
}
logger.setProgress(progress++);
}
logger.endProgress();
}