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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: Stephan Aiche $
// $Authors: Stephan Aiche $
// --------------------------------------------------------------------------
#include <map>
#include <vector>
#include <OpenMS/SIMULATION/LABELING/LabelFreeLabeler.h>
#include <OpenMS/METADATA/ProteinHit.h>
using std::map;
using std::vector;
namespace OpenMS
{
LabelFreeLabeler::LabelFreeLabeler() :
BaseLabeler()
{
}
LabelFreeLabeler::~LabelFreeLabeler()
{
}
void LabelFreeLabeler::preCheck(Param & /* param */) const
{
// no specific requirements
}
// merge all channels into the first one
// no further influence of the simulation process needed
void LabelFreeLabeler::setUpHook(FeatureMapSimVector & features)
{
if (features.size() == 1)
return;
else
{
LOG_INFO << "Merging input FASTA files into one. Intensities will be summed up if duplicates occur.";
FeatureMapSim final_map = mergeProteinIdentificationsMaps_(features);
features.clear();
features.push_back(final_map);
}
}
/// Labeling between digestion and rt simulation
void LabelFreeLabeler::postDigestHook(FeatureMapSimVector & /* features_to_simulate */)
{
}
/// Labeling between RT and Detectability
void LabelFreeLabeler::postRTHook(FeatureMapSimVector & /* features_to_simulate */)
{
}
/// Labeling between Detectability and Ionization
void LabelFreeLabeler::postDetectabilityHook(FeatureMapSimVector & /* features_to_simulate */)
{
}
/// Labeling between Ionization and RawMS
void LabelFreeLabeler::postIonizationHook(FeatureMapSimVector & /* features_to_simulate */)
{
}
/// Labeling after RawMS
void LabelFreeLabeler::postRawMSHook(FeatureMapSimVector & /* features_to_simulate */)
{
}
void LabelFreeLabeler::postRawTandemMSHook(FeatureMapSimVector &, MSSimExperiment &)
{
}
} // namespace OpenMS
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