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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: Clemens Groepl, Chris Bielow $
// $Authors: Katharina Albers $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentEvaluationAlgorithm.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_MapAlignmentEvaluation MapAlignmentEvaluation
@brief Evaluates alignment results against a ground truth.
<CENTER>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ MapAlignmentEvaluationAlgorithm \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_FeatureLinkerUnlabeled or @n @ref TOPP_FeatureLinkerUnlabeledQT </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> none (text output)</td>
</tr>
</table>
</CENTER>
This tool implements the evaluation measures published in\n
"Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements",\n
Eva Lange, Ralf Tautenhahn, Steffen Neumann, Clemens Groepl. BMC Bioinformatics 2008, 9:375.\n
doi:10.1186/1471-2105-9-375.\n
Input is a ground truth file as described on the CAAP web page\n
Output is a recall- or a precision-value.\n
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_MapAlignmentEvaluation.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_MapAlignmentEvaluation.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPMapAlignmentEvaluation :
public TOPPBase
{
public:
TOPPMapAlignmentEvaluation() :
TOPPBase("MapAlignmentEvaluation", "Evaluates alignment results against a ground truth.", false)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "input file: tool", true);
setValidFormats_("in", StringList::create("consensusXML"));
registerInputFile_("gt", "<file>", "", "input file: ground truth", true);
setValidFormats_("gt", StringList::create("consensusXML"));
registerStringOption_("type", "<name>", "", "Caap Evaluation type", true);
StringList types = Factory<MapAlignmentEvaluationAlgorithm>::registeredProducts();
types.push_back("F1");
setValidStrings_("type", types);
registerDoubleOption_("rt_dev", "<double>", 0.1, "Maximum allowed deviation of the retention time", false);
registerDoubleOption_("mz_dev", "<double>", 0.1, "Maximum allowed deviation of m/z", false);
registerDoubleOption_("int_dev", "<double>", 100, "Maximum allowed deviation of Intensity", false);
registerFlag_("use_charge", "Use charge criterion when assesing if two features are identical.", false);
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String gt = getStringOption_("gt");
String type = getStringOption_("type");
DoubleReal rt_dev = getDoubleOption_("rt_dev");
DoubleReal mz_dev = getDoubleOption_("mz_dev");
DoubleReal int_dev = getDoubleOption_("int_dev");
bool use_charge = getFlag_("use_charge");
//-------------------------------------------------------------
// check for valid input
//-------------------------------------------------------------
//check if both input files have the correct type
if (FileHandler::getType(in) != FileTypes::CONSENSUSXML)
{
writeLog_("Error: The input file must be of type consensusXML!");
return ILLEGAL_PARAMETERS;
}
if (FileHandler::getType(gt) != FileTypes::CONSENSUSXML)
{
writeLog_("Error: The groundtruth file must be of type consensusXML!");
return ILLEGAL_PARAMETERS;
}
//-------------------------------------------------------------
// read input files
//-------------------------------------------------------------
// reader
ConsensusXMLFile consensus_xml_file_in;
consensus_xml_file_in.setLogType(log_type_);
// tool -> consensus_map_in
ConsensusMap consensus_map_in;
consensus_xml_file_in.load(in, consensus_map_in);
// gt -> consensus_map_gt
ConsensusMap consensus_map_gt;
consensus_xml_file_in.load(gt, consensus_map_gt);
//-------------------------------------------------------------
// set up algorithm
//-------------------------------------------------------------
if (type == "F1")
{
MapAlignmentEvaluationAlgorithm * algorithm_p = Factory<MapAlignmentEvaluationAlgorithm>::create("precision");
MapAlignmentEvaluationAlgorithm * algorithm_r = Factory<MapAlignmentEvaluationAlgorithm>::create("recall");
DoubleReal precision = 0;
DoubleReal recall = 0;
//evaluate
algorithm_p->evaluate(consensus_map_in, consensus_map_gt, rt_dev, mz_dev, int_dev, use_charge, precision);
algorithm_r->evaluate(consensus_map_in, consensus_map_gt, rt_dev, mz_dev, int_dev, use_charge, recall);
//write output
cout << "precision" << ": " << precision << "\n";
cout << " recall" << ": " << recall << "\n";
cout << "--> F1" << ": " << (2 * precision * recall) / (precision + recall) << " (2*precision*recall)/(precision+recall)\n";
}
else
{
MapAlignmentEvaluationAlgorithm * algorithm = Factory<MapAlignmentEvaluationAlgorithm>::create(type);
DoubleReal result = 0;
//evaluate
algorithm->evaluate(consensus_map_in, consensus_map_gt, rt_dev, mz_dev, int_dev, use_charge, result);
//write output
cout << type << ": " << result << "\n";
}
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPMapAlignmentEvaluation tool;
return tool.main(argc, argv);
}
/// @endcond
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