xiccoord.h
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/**
* \file pappsomspp/msrun/xiccoord/xiccoord.h
* \date 22/04/2021
* \author Olivier Langella
* \brief XIC coordinate in MSrun
*/
/*******************************************************************************
* Copyright (c) 2021 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include "../../exportinmportconfig.h"
#include "../../mzrange.h"
#include "../../xic/xic.h"
#include <memory>
namespace pappso
{
struct XicCoord;
typedef std::shared_ptr<XicCoord> XicCoordSPtr;
/** @brief coordinates of the XIC to extract and the resulting XIC after
* extraction
*
* to extract a XIC, we need basically the mass to extract it
* this structure is meant to extact a XIC quickly and not to maintain
* information about it : no peptide, no scan number, no retention time...
*
*/
struct PMSPP_LIB_DECL XicCoord
{
/**
* Default constructor
*/
XicCoord();
/**
* Copy constructor
*
* @param other TODO
*/
XicCoord(const XicCoord &other);
/**
* Destructor
*/
virtual ~XicCoord();
/** @brief intialize the XIC and make a deep copy of object
*/
virtual XicCoordSPtr initializeAndClone() const;
/** @brief compute a new XIC coord as the sum of the given one
*/
virtual XicCoordSPtr addition(XicCoordSPtr &to_add) const;
/** @brief compute a new xic coord as a product by
*/
virtual XicCoordSPtr multiplyBy(double number) const;
/** @brief compute a new xic coord as a division by
*/
virtual XicCoordSPtr divideBy(double number) const;
/** @brief reset to zero
*/
virtual void reset();
/** @brief get a description of the XIC coordinate in a string
*/
virtual QString toString() const;
/** @brief the mass to extract
* */
MzRange mzRange;
/** @brief the targeted retention time to extract around
* intended in seconds, and related to one msrun. This is not a reference,
* just to save memory and cpu usage when extracting xic
*/
double rtTarget = 0;
/** @brief extracted xic
*/
XicSPtr xicSptr = nullptr;
};
} // namespace pappso
pappso::MzRange
Definition: mzrange.h:46
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition: exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::XicSPtr
std::shared_ptr< Xic > XicSPtr
Definition: xic.h:39
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41
pappso::XicCoord
coordinates of the XIC to extract and the resulting XIC after extraction
Definition: xiccoord.h:54
pappso::XicCoord::mzRange
MzRange mzRange
the mass to extract
Definition: xiccoord.h:103