libpappsomspp
Library for mass spectrometry
msrunxicextractor.h
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1 /**
2  * \file pappsomspp/xicextractor/private/msrunxicextractorpwiz.h
3  * \date 07/05/2018
4  * \author Olivier Langella
5  * \brief simple proteowizard based XIC extractor
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 #pragma once
32 
33 #include "../msrunxicextractorinterface.h"
34 
35 class MsRunXicExtractorFactory;
36 
37 namespace pappso
38 {
39 
40 
42 {
44 
45  public:
47  virtual ~MsRunXicExtractor();
48  virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range,
49  pappso::pappso_double rt_begin,
50  pappso::pappso_double rt_end) override;
51 
52  virtual std::vector<XicCstSPtr>
53  getXicCstSPtrList(const std::vector<MzRange> &mz_range_list) override;
54 
55  protected:
56  MsRunXicExtractor(MsRunReaderSPtr &msrun_reader);
57 
58  virtual void
59  getXicFromPwizMSDataFile(std::vector<Xic *> &xic_list,
60  const std::vector<MzRange> &mass_range_list,
61  pappso::pappso_double rt_begin,
62  pappso::pappso_double rt_end);
63 
64  protected:
65  std::vector<MsRunXicExtractorPoints> m_msrun_points;
66 };
67 
68 
69 } // namespace pappso
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:69
pappso::MsRunXicExtractor::MsRunXicExtractor
MsRunXicExtractor(const MsRunXicExtractor &other)
Definition: msrunxicextractor.cpp:85
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:172
pappso::MsRunXicExtractorInterface
Definition: msrunxicextractorinterface.h:64
pappso::MzRange
Definition: mzrange.h:67
pappso::XicCstSPtr
std::shared_ptr< const Xic > XicCstSPtr
Definition: xic.h:58
pappso::MsRunXicExtractor::getXicCstSPtr
virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override
get a XIC on this MsRun at the given mass range
Definition: msrunxicextractor.cpp:92
pappso::MsRunXicExtractor::getXicCstSPtrList
virtual std::vector< XicCstSPtr > getXicCstSPtrList(const std::vector< MzRange > &mz_range_list) override
extract a list of XIC given a list of mass to extract
Definition: msrunxicextractor.cpp:149
pappso::MsRunXicExtractor::MsRunXicExtractorFactory
friend MsRunXicExtractorFactory
Definition: msrunxicextractor.h:43
pappso::MsRunXicExtractor::~MsRunXicExtractor
virtual ~MsRunXicExtractor()
Definition: msrunxicextractor.cpp:80
pappso::MsRunXicExtractor
Definition: msrunxicextractor.h:42
pappso::MsRunXicExtractor::getXicFromPwizMSDataFile
virtual void getXicFromPwizMSDataFile(std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end)
Definition: msrunxicextractor.cpp:170
pappso::MsRunXicExtractor::m_msrun_points
std::vector< MsRunXicExtractorPoints > m_msrun_points
Definition: msrunxicextractor.h:65