libpappsomspp
Library for mass spectrometry
msrunxicextractorinterface.cpp
Go to the documentation of this file.
1 /**
2  * \file pappsomspp/xicextractor/msrunxicextractor.cpp
3  * \date 07/05/2018
4  * \author Olivier Langella
5  * \brief base interface to build XICs on an MsRun file
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 
32 
33 namespace pappso
34 {
35 
36 
38  MsRunReaderSPtr &msrun_reader)
39  : msp_msrun_reader(msrun_reader)
40 {
41 }
42 
43 
45  const MsRunXicExtractorInterface &other)
46  : msp_msrun_reader(other.msp_msrun_reader)
47 {
49 }
50 
52 {
53 }
54 
57 {
58  return getXicCstSPtr(mz_range, 0, 100000000);
59 }
60 
61 void
63 {
64  m_xicExtractMethod = method;
65 }
66 const MsRunIdCstSPtr &
68 {
69  return msp_msrun_reader.get()->getMsRunId();
70 }
71 } // namespace pappso
void setXicExtractMethod(XicExtractMethod method)
set the XIC extraction method
const MsRunIdCstSPtr & getMsRunId() const
virtual XicCstSPtr getXicCstSPtr(const MzRange &mz_range) final
get a XIC on this MsRun at the given mass range
MsRunXicExtractorInterface(MsRunReaderSPtr &msrun_reader)
constructor is private, use the MsRunXicExtractorFactory
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:151
std::shared_ptr< const Xic > XicCstSPtr
Definition: xic.h:37
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition: msrunid.h:44
XicExtractMethod
Definition: types.h:200