/usr/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h is in libopenms-dev 1.11.1-3.
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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 $
// $Authors: Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------
#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderDefs.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
namespace OpenMS
{
/**@brief The main feature finder class.
- Stores the flags for (indices of) data points ("used", "unused")
- The algorithm itself is a factory product (derived from FeatureFinderAlgorithm)
- The main method is run(), which is a template so that we can deal with different types of input and output
- The run() method takes five arguments: algorithm_name, input_map, output, parameters, seeds
.
@ingroup FeatureFinder
*/
class OPENMS_DLLAPI FeatureFinder :
public ProgressLogger,
public FeatureFinderDefs
{
public:
/// Default constructor.
FeatureFinder();
/// Destructor
virtual ~FeatureFinder();
/**
@brief Executes the FeatureFinder using the given algorithm
There are several constraints for the @p input_map. They are tested before
the algorithm starts. It must only contain MS 1 level scans and you
have to call updateRanges() before passing it to this method.
The input map is sorted by RT & m/z if thats not the case.
Furthermore we throw an Exception if the data contains negative m/z values,
as this will disturb most algorithms.
@param algorithm_name Name of the feature finding algorithm to use
@param input_map Input peak map
@param features Output feature map
@param param Algorithm parameters
@param seeds List of seeds to use
Implemented in FeatureFinder_impl.h
*/
template <class PeakType, class FeatureType>
void run(const String & algorithm_name, MSExperiment<PeakType> & input_map, FeatureMap<FeatureType> & features, const Param & param, const FeatureMap<FeatureType> & seeds);
/// Returns a non-mutable reference to a peak flag
const Flag & getPeakFlag(const IndexPair & index) const
{
return flags_[index.first][index.second];
}
/// Returns mutable reference to a peak flag
Flag & getPeakFlag(const IndexPair & index)
{
return flags_[index.first][index.second];
}
/// Returns the default parameters for the algorithm with name @p algorithm_name
Param getParameters(const String & algorithm_name) const;
protected:
/// Container for flags attached to input data
std::vector<std::vector<Flag> > flags_;
}; // class FeatureFinder
} // namespace OpenMS
#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H
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