/usr/include/OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationCID.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,
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Sandro Andreotti $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATIONCID_H
#define OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATIONCID_H
// OpenMS includes
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h>
// stl includes
#include <vector>
namespace OpenMS
{
/**
@brief run with CompNovoIdentificationCID
@htmlinclude OpenMS_CompNovoIdentificationCID.parameters
@ingroup Analysis_ID
*/
class OPENMS_DLLAPI CompNovoIdentificationCID :
public CompNovoIdentificationBase
{
public:
/** @name constructors and destructors
*/
//@{
/// default constructor
CompNovoIdentificationCID();
/// copy constructor
CompNovoIdentificationCID(const CompNovoIdentificationCID & source);
/// destructor
virtual ~CompNovoIdentificationCID();
//@}
///
CompNovoIdentificationCID & operator=(const CompNovoIdentificationCID & source);
/** @name Accessors
*/
//@{
/// performs an ProteinIdentification run on a PeakMap
void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp);
/// performs an ProteinIdentification run on a PeakSpectrum
void getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec);
//@}
typedef CompNovoIonScoringBase::IsotopeType IsotopeType;
typedef CompNovoIonScoringBase::IonScore IonScore;
typedef CompNovoIdentificationBase::Permut Permut;
protected:
/// call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences
void getDecompositionsDAC_(std::set<String> & sequences, Size left, Size right, DoubleReal peptide_weight, const PeakSpectrum & CID_orig_spec, Map<DoubleReal, IonScore> & CID_nodes);
/// reduces the given number of permuts by scoring the perumtations to the CID and ETD spec
void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, DoubleReal prefix, DoubleReal suffix);
void updateMembers_();
DoubleReal precursor_mass_tolerance_;
};
}
#endif
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