void MapAlignmentAlgorithmPoseClustering::align(const ConsensusMap & map, TransformationDescription & trafo)
{
// TODO: move this to updateMembers_? (if consensusMap prevails)
// TODO: why does superimposer work on consensus map???
const ConsensusMap & map_model = reference_;
ConsensusMap map_scene = map;
// run superimposer to find the global transformation
TransformationDescription si_trafo;
superimposer_.run(map_model, map_scene, si_trafo);
// apply transformation to consensus features and contained feature
// handles
for (Size j = 0; j < map_scene.size(); ++j)
{
//Calculate new RT
double rt = map_scene[j].getRT();
rt = si_trafo.apply(rt);
//Set RT of consensus feature centroid
map_scene[j].setRT(rt);
//Set RT of consensus feature handles
map_scene[j].begin()->asMutable().setRT(rt);
}
//run pairfinder to find pairs
ConsensusMap result;
//TODO: add another 2map interface to pairfinder?
std::vector<ConsensusMap> input(2);
input[0] = map_model;
input[1] = map_scene;
pairfinder_.run(input, result);
// calculate the local transformation
si_trafo.invert(); // to undo the transformation applied above
TransformationDescription::DataPoints data;
for (ConsensusMap::Iterator it = result.begin(); it != result.end();
++it)
{
if (it->size() == 2) // two matching features
{
ConsensusFeature::iterator feat_it = it->begin();
double y = feat_it->getRT();
double x = si_trafo.apply((++feat_it)->getRT());
// one feature should be from the reference map:
if (feat_it->getMapIndex() != 0)
{
data.push_back(make_pair(x, y));
}
else
{
data.push_back(make_pair(y, x));
}
}
}
trafo = TransformationDescription(data);
trafo.fitModel("linear");
}
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in"), out = getStringOption_("out");
TransformationDescription trafo_in;
TransformationXMLFile().load(in, trafo_in);
TransformationDescription::DataPoints data;
DoubleReal min = getDoubleOption_("min"), max = getDoubleOption_("max"),
step = getDoubleOption_("step");
if (max <= min)
{
data = trafo_in.getDataPoints();
sort(data.begin(), data.end());
max = data.back().first;
DoubleReal magnitude = floor(log10(max));
max = Math::ceilDecimal(max, magnitude - 1);
if (max <= min)
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "'min' must be lower than 'max'");
}
}
data.clear();
for (DoubleReal value = min; value <= max; value += step)
{
DoubleReal transformed = trafo_in.apply(value);
if (out.empty())
{
cout << value << '\t' << transformed << endl;
}
else data.push_back(make_pair(value, transformed));
}
if (!out.empty())
{
TransformationDescription trafo_out(trafo_in);
trafo_out.setDataPoints(data);
TransformationXMLFile().store(out, trafo_out);
}
return EXECUTION_OK;
}
void InternalCalibration::makeLinearRegression_(std::vector<DoubleReal> & observed_masses, std::vector<DoubleReal> & theoretical_masses)
{
if (observed_masses.size() != theoretical_masses.size())
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Number of observed and theoretical masses must agree.");
}
#ifdef DEBUG_CALIBRATION
std::ofstream out("calibration_regression.txt");
std::vector<DoubleReal> rel_errors(observed_masses.size(), 0.);
// determine rel error in ppm for the two reference masses
for (Size ref_peak = 0; ref_peak < observed_masses.size(); ++ref_peak)
{
rel_errors[ref_peak] = (theoretical_masses[ref_peak] - observed_masses[ref_peak]) / theoretical_masses[ref_peak] * 1e6;
out << observed_masses[ref_peak] << "\t" << rel_errors[ref_peak] << "\n";
std::cout << observed_masses[ref_peak] << " " << theoretical_masses[ref_peak] << std::endl;
// std::cout << observed_masses[ref_peak]<<"\t"<<rel_errors[ref_peak]<<std::endl;
}
#endif
TransformationDescription::DataPoints data;
for (Size i = 0; i < observed_masses.size(); ++i)
{
data.push_back(std::make_pair(observed_masses[i],
theoretical_masses[i]));
}
trafo_ = TransformationDescription(data);
trafo_.fitModel("linear", Param());
#ifdef DEBUG_CALIBRATION
// std::cout <<"\n\n---------------------------------\n\n"<< "after calibration "<<std::endl;
for (Size i = 0; i < observed_masses.size(); ++i)
{
DoubleReal new_mass = trafo_.apply(observed_masses[i]);
DoubleReal rel_error = (theoretical_masses[i] - (new_mass)) / theoretical_masses[i] * 1e6;
std::cout << observed_masses[i] << "\t" << rel_error << std::endl;
}
#endif
}
void MapAlignmentAlgorithmIdentification::computeTransformations_(
vector<SeqToList>& rt_data, vector<TransformationDescription>& transforms,
bool sorted)
{
Int size = rt_data.size(); // not Size because we compare to Ints later
transforms.clear();
// filter RT data (remove peptides that elute in several fractions):
// TODO
// compute RT medians:
LOG_DEBUG << "Computing RT medians..." << endl;
vector<SeqToValue> medians_per_run(size);
for (Int i = 0; i < size; ++i)
{
computeMedians_(rt_data[i], medians_per_run[i], sorted);
}
SeqToList medians_per_seq;
for (vector<SeqToValue>::iterator run_it = medians_per_run.begin();
run_it != medians_per_run.end(); ++run_it)
{
for (SeqToValue::iterator med_it = run_it->begin();
med_it != run_it->end(); ++med_it)
{
medians_per_seq[med_it->first].push_back(med_it->second);
}
}
// get reference retention time scale: either directly from reference file,
// or compute consensus time scale
bool reference_given = !reference_.empty(); // reference file given
if (reference_given)
{
// remove peptides that don't occur in enough runs:
LOG_DEBUG << "Removing peptides that occur in too few runs..." << endl;
SeqToValue temp;
for (SeqToValue::iterator ref_it = reference_.begin();
ref_it != reference_.end(); ++ref_it)
{
SeqToList::iterator med_it = medians_per_seq.find(ref_it->first);
if ((med_it != medians_per_seq.end()) &&
(med_it->second.size() + 1 >= min_run_occur_))
{
temp.insert(temp.end(), *ref_it); // new items should go at the end
}
}
LOG_DEBUG << "Removed " << reference_.size() - temp.size() << " of "
<< reference_.size() << " peptides." << endl;
temp.swap(reference_);
}
else // compute overall RT median per sequence (median of medians per run)
{
LOG_DEBUG << "Computing overall RT medians per sequence..." << endl;
// remove peptides that don't occur in enough runs (at least two):
LOG_DEBUG << "Removing peptides that occur in too few runs..." << endl;
SeqToList temp;
for (SeqToList::iterator med_it = medians_per_seq.begin();
med_it != medians_per_seq.end(); ++med_it)
{
if (med_it->second.size() >= min_run_occur_)
{
temp.insert(temp.end(), *med_it);
}
}
LOG_DEBUG << "Removed " << medians_per_seq.size() - temp.size() << " of "
<< medians_per_seq.size() << " peptides." << endl;
temp.swap(medians_per_seq);
computeMedians_(medians_per_seq, reference_);
}
if (reference_.empty())
{
throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "No reference RT information left after filtering");
}
double max_rt_shift = param_.getValue("max_rt_shift");
if (max_rt_shift <= 1)
{
// compute max. allowed shift from overall retention time range:
double rt_min = numeric_limits<double>::infinity(), rt_max = -rt_min;
for (SeqToValue::iterator it = reference_.begin(); it != reference_.end();
++it)
{
rt_min = min(rt_min, it->second);
rt_max = max(rt_max, it->second);
}
double rt_range = rt_max - rt_min;
max_rt_shift *= rt_range;
// in the degenerate case of only one reference point, "max_rt_shift"
// should be zero (because "rt_range" is zero) - this is covered below
}
if (max_rt_shift == 0)
{
max_rt_shift = numeric_limits<double>::max();
}
LOG_DEBUG << "Max. allowed RT shift (in seconds): " << max_rt_shift << endl;
// generate RT transformations:
LOG_DEBUG << "Generating RT transformations..." << endl;
LOG_INFO << "\nAlignment based on:" << endl; // diagnostic output
Size offset = 0; // offset in case of internal reference
for (Int i = 0; i < size + 1; ++i)
{
if (i == reference_index_)
{
// if one of the input maps was used as reference, it has been skipped
// so far - now we have to consider it again:
TransformationDescription trafo;
trafo.fitModel("identity");
transforms.push_back(trafo);
LOG_INFO << "- " << reference_.size() << " data points for sample "
<< i + 1 << " (reference)\n";
offset = 1;
}
if (i >= size) break;
// to be useful for the alignment, a peptide sequence has to occur in the
// current run ("medians_per_run[i]"), but also in at least one other run
// ("medians_overall"):
TransformationDescription::DataPoints data;
Size n_outliers = 0;
for (SeqToValue::iterator med_it = medians_per_run[i].begin();
med_it != medians_per_run[i].end(); ++med_it)
{
SeqToValue::const_iterator pos = reference_.find(med_it->first);
if (pos != reference_.end())
{
if (abs(med_it->second - pos->second) <= max_rt_shift)
{ // found, and satisfies "max_rt_shift" condition!
TransformationDescription::DataPoint point(med_it->second,
pos->second, pos->first);
data.push_back(point);
}
else
{
n_outliers++;
}
}
}
transforms.push_back(TransformationDescription(data));
LOG_INFO << "- " << data.size() << " data points for sample "
<< i + offset + 1;
if (n_outliers) LOG_INFO << " (" << n_outliers << " outliers removed)";
LOG_INFO << "\n";
}
LOG_INFO << endl;
// delete temporary reference
if (!reference_given) reference_.clear();
}
void MapAlignmentAlgorithmIdentification::computeTransformations_(
vector<SeqToList> & rt_data, vector<TransformationDescription> & transforms,
bool sorted)
{
Size size = rt_data.size();
transforms.clear();
// filter RT data (remove peptides that elute in several fractions):
// TODO
// compute RT medians:
LOG_DEBUG << "Computing RT medians..." << endl;
vector<SeqToValue> medians_per_run(size);
for (Size i = 0; i < size; ++i)
{
computeMedians_(rt_data[i], medians_per_run[i], sorted);
}
SeqToList medians_per_seq;
for (vector<SeqToValue>::iterator run_it = medians_per_run.begin();
run_it != medians_per_run.end(); ++run_it)
{
for (SeqToValue::iterator med_it = run_it->begin();
med_it != run_it->end(); ++med_it)
{
medians_per_seq[med_it->first] << med_it->second;
}
}
// get reference retention time scale: either directly from reference file,
// or compute consensus time scale
bool reference_given = !reference_.empty(); // reference file given
if (reference_given)
{
// remove peptides that don't occur in enough runs:
LOG_DEBUG << "Removing peptides that occur in too few runs..." << endl;
SeqToValue temp;
SeqToValue::iterator pos = temp.begin(); // to prevent segfault below
for (SeqToValue::iterator ref_it = reference_.begin();
ref_it != reference_.end(); ++ref_it)
{
SeqToList::iterator med_it = medians_per_seq.find(ref_it->first);
if ((med_it != medians_per_seq.end()) &&
(med_it->second.size() + 1 >= min_run_occur_))
{
temp.insert(pos, *ref_it);
pos = --temp.end(); // would cause segfault if "temp" was empty
}
}
temp.swap(reference_);
}
else // compute overall RT median per sequence (median of medians per run)
{
LOG_DEBUG << "Computing overall RT medians per sequence..." << endl;
// remove peptides that don't occur in enough runs (at least two):
LOG_DEBUG << "Removing peptides that occur in too few runs..." << endl;
SeqToList temp;
SeqToList::iterator pos = temp.begin(); // to prevent segfault below
for (SeqToList::iterator med_it = medians_per_seq.begin();
med_it != medians_per_seq.end(); ++med_it)
{
if (med_it->second.size() >= min_run_occur_)
{
temp.insert(pos, *med_it);
pos = --temp.end(); // would cause segfault if "temp" was empty
}
}
temp.swap(medians_per_seq);
computeMedians_(medians_per_seq, reference_);
}
DoubleReal max_rt_shift = param_.getValue("max_rt_shift");
if (max_rt_shift == 0)
{
max_rt_shift = numeric_limits<DoubleReal>::max();
}
else if (max_rt_shift <= 1) // compute max. allowed shift from overall retention time range:
{
DoubleReal rt_range, rt_min = reference_.begin()->second,
rt_max = rt_min;
for (SeqToValue::iterator it = ++reference_.begin();
it != reference_.end(); ++it)
{
rt_min = min(rt_min, it->second);
rt_max = max(rt_max, it->second);
}
rt_range = rt_max - rt_min;
max_rt_shift *= rt_range;
}
LOG_DEBUG << "Max. allowed RT shift (in seconds): " << max_rt_shift << endl;
// generate RT transformations:
LOG_DEBUG << "Generating RT transformations..." << endl;
LOG_INFO << "\nAlignment based on:" << endl; // diagnostic output
for (Size i = 0, offset = 0; i < size + 1; ++i)
{
if (i == reference_index_ - 1)
{
// if one of the input maps was used as reference, it has been skipped
// so far - now we have to consider it again:
TransformationDescription trafo;
trafo.fitModel("identity");
transforms.push_back(trafo);
LOG_INFO << "- 0 data points for sample " << i + 1 << " (reference)\n";
offset = 1;
}
if (i >= size)
break;
// to be useful for the alignment, a peptide sequence has to occur in the
// current run ("medians_per_run[i]"), but also in at least one other run
// ("medians_overall"):
TransformationDescription::DataPoints data;
for (SeqToValue::iterator med_it = medians_per_run[i].begin();
med_it != medians_per_run[i].end(); ++med_it)
{
SeqToValue::const_iterator pos = reference_.find(med_it->first);
if ((pos != reference_.end()) &&
(fabs(med_it->second - pos->second) <= max_rt_shift))
{ // found, and satisfies "max_rt_shift" condition!
data.push_back(make_pair(med_it->second, pos->second));
}
}
transforms.push_back(TransformationDescription(data));
LOG_INFO << "- " << data.size() << " data points for sample "
<< i + offset + 1 << "\n";
}
LOG_INFO << endl;
// delete temporary reference
if (!reference_given)
reference_.clear();
}