/usr/include/OpenMS/ANALYSIS/OPENSWATH/DIAHelper.h is in libopenms-dev 1.11.1-5.
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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;
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// $Maintainer: Witold Wolski, Hannes Roest $
// $Authors: Witold Wolski, Hannes Roest $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H
#define OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H
#include <vector>
#include <OpenMS/CHEMISTRY/AASequence.h>
namespace OpenMS
{
namespace DIAHelpers
{
/**
@brief Helper functions for the DIA scoring of OpenSWATH
*/
///@{
/// compute the b and y series masses for a given AASequence
OPENMS_DLLAPI void getBYSeries(AASequence& a,
std::vector<double>& bseries, std::vector<double>& yseries, UInt charge = 1u);
/// for SWATH -- get the theoretical b and y series masses for a sequence
OPENMS_DLLAPI void getTheorMasses(AASequence& a, std::vector<double>& masses, UInt charge = 1u);
/// get averagine distribution given mass
OPENMS_DLLAPI void getAveragineIsotopeDistribution(double product_mz,
std::vector<std::pair<double, double> >& isotopesSpec,
double charge = 1.,
int nr_isotopes = 4,
double mannmass = 1.00048);
/// simulate spectrum from AASequence
OPENMS_DLLAPI void simulateSpectrumFromAASequence(AASequence& aa,
std::vector<double>& firstIsotopeMasses, //[out]
std::vector<std::pair<double, double> >& isotopeMasses, //[out]
double charge = 1.);
/// modify masses by charge
OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses, //![in]
std::vector<std::pair<double, double> >& modmass, //!< [out]
double charge = 1.);
/// add negative preisotope weights to spectrum
OPENMS_DLLAPI void addPreisotopeWeights(const std::vector<double>& firstIsotopeMasses,
std::vector<std::pair<double, double> >& isotopeSpec, // output
UInt nrpeaks = 2, //nr of preisotope peaks
double preIsotopePeaksWeight = -0.5, // weight of preisotope peaks
double mannmass = 1.000482, //
double charge = 1.);
/// given an experimental spectrum add isotope pattern.
OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec,
std::vector<std::pair<double, double> >& isotopeMasses, //[out]
double charge = 1.);
/// sorts vector of pairs by first
OPENMS_DLLAPI void sortByFirst(std::vector<std::pair<double, double> >& tmp);
/// extract first from vector of pairs
OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
/// extract second from vector of pairs
OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
///}@
}
}
#endif
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