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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
using namespace OpenMS;
using namespace OpenMS::Math;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_LabeledEval LabeledEval
@brief Evaluation tool for isotope-labeled quantitation experiments.
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_LabeledEval.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_LabeledEval.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPLabeledEval :
public TOPPBase
{
public:
TOPPLabeledEval() :
TOPPBase("LabeledEval", " Evaluation tool for isotope-labeled quantitation experiments.", false)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Feature result file");
setValidFormats_("in", StringList::create("featureXML"));
registerInputFile_("truth", "<file>", "", "Expected result file.");
setValidFormats_("truth", StringList::create("consensusXML"));
registerDoubleOption_("rt_tol", "<tol>", 20.0, "Maximum allowed retention time deviation", false);
registerDoubleOption_("mz_tol", "<tol>", 0.25, "Maximum allowed m/z deviation (divided by charge)", false);
}
String fiveNumbers(vector<DoubleReal> a, UInt decimal_places)
{
sort(a.begin(), a.end());
return String::number(a[0], decimal_places) + " " + String::number(a[a.size() / 4], decimal_places) + " " + String::number(a[a.size() / 2], decimal_places) + " " + String::number(a[(3 * a.size()) / 4], decimal_places) + " " + String::number(a.back(), decimal_places);
}
String fiveNumberQuotients(vector<DoubleReal> a, vector<DoubleReal> b, UInt decimal_places)
{
vector<DoubleReal> errors;
for (Size i = 0; i < a.size(); ++i) errors.push_back(a[i] / b[i]);
return fiveNumbers(errors, decimal_places);
}
ExitCodes main_(int, const char **)
{
//load input features
FeatureMap<> input;
FeatureXMLFile().load(getStringOption_("in"), input);
//load truth consensusXML
ConsensusMap truth;
ConsensusXMLFile().load(getStringOption_("truth"), truth);
//parameters
DoubleReal mz_tol = getDoubleOption_("mz_tol");
DoubleReal rt_tol = getDoubleOption_("rt_tol");
//seek manual feature in automatic feature map
UInt matched_pairs = 0;
UInt half_matched_pairs = 0;
vector<DoubleReal> t_ratio, i_ratio, rt_diffs, mz_diffs;
for (Size t = 0; t < truth.size(); ++t)
{
if (truth[t].size() != 2)
{
cerr << "Error: consensus feature must contain exactly two elements!" << endl;
continue;
}
vector<Feature> best_matches(2);
vector<UInt> match_counts(2, 0);
vector<Peak2D> elements(2);
elements[0] = *(truth[t].getFeatures().begin());
elements[1] = *(++(truth[t].getFeatures().begin()));
DoubleReal mz_tol_charged = mz_tol / truth[t].getCharge();
for (Size e = 0; e < 2; ++e)
{
DoubleReal best_score = 0.0;
for (Size i = 0; i < input.size(); ++i)
{
const Feature & f_i = input[i];
if (fabs(f_i.getRT() - elements[e].getRT()) < rt_tol
&& fabs(f_i.getMZ() - elements[e].getMZ()) < mz_tol_charged)
{
++match_counts[e];
DoubleReal score = (1.0 - fabs(f_i.getMZ() - elements[e].getMZ()) / mz_tol_charged) * (1.0 - fabs(f_i.getRT() - elements[e].getRT()) / rt_tol);
if (score > best_score)
{
best_score = score;
best_matches[e] = f_i;
}
}
}
}
//not matched
if (match_counts[0] == 0 && match_counts[1] == 0)
{
}
//half matched
else if ((match_counts[0] > 0 && match_counts[1] == 0) || (match_counts[0] == 0 && match_counts[1] > 0))
{
++half_matched_pairs;
}
//matched
else
{
++matched_pairs;
DoubleReal a_r = best_matches[0].getIntensity() / best_matches[1].getIntensity();
t_ratio.push_back(a_r);
DoubleReal m_r = elements[0].getIntensity() / elements[1].getIntensity();
i_ratio.push_back(m_r);
rt_diffs.push_back(best_matches[1].getRT() - best_matches[0].getRT());
mz_diffs.push_back((best_matches[1].getMZ() - best_matches[0].getMZ()) * truth[t].getCharge());
}
}
cout << endl;
cout << "pair detection statistics:" << endl;
cout << "==========================" << endl;
cout << "truth pairs: " << truth.size() << endl;
cout << "input features: " << input.size() << endl;
cout << endl;
cout << "found: " << matched_pairs << " (" << String::number(100.0 * matched_pairs / truth.size(), 2) << "%)" << endl;
cout << "half found : " << half_matched_pairs << " (" << String::number(100.0 * half_matched_pairs / truth.size(), 2) << "%)" << endl;
cout << "not found : " << truth.size() - (matched_pairs + half_matched_pairs) << " (" << String::number(100.0 - 100.0 * (matched_pairs + half_matched_pairs) / truth.size(), 2) << "%)" << endl;
cout << endl;
cout << "relative pair ratios: " << fiveNumberQuotients(i_ratio, t_ratio, 3) << endl;
cout << "pair distance RT : " << fiveNumbers(rt_diffs, 2) << endl;
cout << "pair distance m/z: " << fiveNumbers(mz_diffs, 2) << endl;
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPLabeledEval tool;
return tool.main(argc, argv);
}
/// @endcond
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