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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 $
// $Authors: Stephan Aiche$
// --------------------------------------------------------------------------
#ifndef OPENMS_SIMULATION_LABELING_SILACLABELER_H
#define OPENMS_SIMULATION_LABELING_SILACLABELER_H
#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
namespace OpenMS
{
/**
@brief Simulate SILAC experiments
Add modified features to MS1 scans.
@htmlinclude OpenMS_SILACLabeler.parameters
*/
class OPENMS_DLLAPI SILACLabeler :
public BaseLabeler
{
public:
/// default constructor
SILACLabeler();
/// destructor
virtual ~SILACLabeler();
/// create new object (needed by Factory)
static BaseLabeler* create()
{
return new SILACLabeler();
}
/// name of the model (needed by Factory)
static const String getProductName()
{
return "SILAC";
}
// redeclaration of virtual methods
void preCheck(Param& /* param */) const;
void setUpHook(FeatureMapSimVector& /* channels */);
void postDigestHook(FeatureMapSimVector& /* features_to_simulate */);
void postRTHook(FeatureMapSimVector& /* features_to_simulate */);
void postDetectabilityHook(FeatureMapSimVector& /* features_to_simulate */);
void postIonizationHook(FeatureMapSimVector& /* features_to_simulate */);
void postRawMSHook(FeatureMapSimVector& /* features_to_simulate */);
void postRawTandemMSHook(FeatureMapSimVector& /* features_to_simulate */, MSSimExperiment& /* simulated map */);
protected:
void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
Feature mergeFeatures_(Feature& labeled_channel_feature, const String& unmodified_sequence, Map<String, Feature>& unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const;
Feature mergeAllChannelFeatures_(Feature& heavy_channel_feature, const String& unmodified_feature_sequence, Map<String, Feature>& light_channel_feature_index, Map<String, Feature>& medium_channel_feature_index) const;
String medium_channel_lysine_label_;
String medium_channel_arginine_label_;
String heavy_channel_lysine_label_;
String heavy_channel_arginine_label_;
bool canModificationBeApplied_(const String& modification_id, const String& aa) const;
void applyLabelToProteinHit_(FeatureMapSim& protein_hit, const String& arginine_label, const String& lysine_label) const;
void updateMembers_();
String getUnmodifiedSequence_(const Feature& feature, const String& arginine_label, const String& lysine_label) const;
private:
/// Map ID for the light/unlabeled channel
static const int LIGHT_FEATURE_MAPID_;
/// Map ID for the medium labeled channel
static const int MEDIUM_FEATURE_MAPID_;
/// Map ID for the heavy labeled channel
static const int HEAVY_FEATURE_MAPID_;
};
} // namespace OpenMS
#endif //#ifndef OPENMS_SIMULATION_LABELING_SILACLABELER_H
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