libpappsomspp
Library for mass spectrometry
timsmsrunreaderms2selected.h
Go to the documentation of this file.
1
/**
2
* \file pappsomspp/msrun/private/timsmsrunreaderms2.h
3
* \date 10/09/2019
4
* \author Olivier Langella
5
* \brief MSrun file reader for native Bruker TimsTOF specialized for MS2
6
* purpose
7
*/
8
9
/*******************************************************************************
10
* Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
11
*
12
* This file is part of the PAPPSOms++ library.
13
*
14
* PAPPSOms++ is free software: you can redistribute it and/or modify
15
* it under the terms of the GNU General Public License as published by
16
* the Free Software Foundation, either version 3 of the License, or
17
* (at your option) any later version.
18
*
19
* PAPPSOms++ is distributed in the hope that it will be useful,
20
* but WITHOUT ANY WARRANTY; without even the implied warranty of
21
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22
* GNU General Public License for more details.
23
*
24
* You should have received a copy of the GNU General Public License
25
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26
*
27
******************************************************************************/
28
29
30
#pragma once
31
32
#include "
timsmsrunreaderms2.h
"
33
#include "../../types.h"
34
#include "../../msfile/msfileaccessor.h"
35
#include "../../msfile/msfilereader.h"
36
#include "../../vendors/tims/timsdata.h"
37
38
namespace
pappso
39
{
40
41
class
PMSPP_LIB_DECL
TimsMsRunReaderMs2Selected
:
public
TimsMsRunReaderMs2
42
{
43
friend
class
MsFileAccessor
;
44
/**
45
* @todo write docs
46
*/
47
public
:
48
TimsMsRunReaderMs2Selected
(
MsRunIdCstSPtr
&msrun_id_csp);
49
virtual
~
TimsMsRunReaderMs2Selected
();
50
51
virtual
MassSpectrumSPtr
52
massSpectrumSPtr(std::size_t spectrum_index)
override
;
53
virtual
MassSpectrumCstSPtr
54
massSpectrumCstSPtr(std::size_t spectrum_index)
override
;
55
56
virtual
QualifiedMassSpectrum
57
qualifiedMassSpectrum(std::size_t spectrum_index,
58
bool
want_binary_data =
true
)
const override
;
59
60
virtual
void
61
readSpectrumCollection(
SpectrumCollectionHandlerInterface
&handler)
override
;
62
63
virtual
std::size_t spectrumListSize()
const override
;
64
65
virtual
bool
hasScanNumbers()
const override
;
66
67
void
setMs2FilterCstSPtr(
pappso::FilterInterfaceCstSPtr
filter);
68
void
setMs1FilterCstSPtr(
pappso::FilterInterfaceCstSPtr
filter);
69
70
protected
:
71
virtual
void
initialize()
override
;
72
virtual
bool
accept(
const
QString &file_name)
const override
;
73
74
private
:
75
TimsData
*mpa_timsData =
nullptr
;
76
};
77
78
79
}
// namespace pappso
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition:
massspectrum.h:55
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::FilterInterfaceCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
Definition:
filterinterface.h:47
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition:
msrunid.h:44
pappso::TimsData
Definition:
timsdata.h:71
pappso::MsFileAccessor
Definition:
msfileaccessor.h:35
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition:
qualifiedmassspectrum.h:85
pappso::TimsMsRunReaderMs2
Definition:
timsmsrunreaderms2.h:41
pappso::TimsMsRunReaderMs2Selected
Definition:
timsmsrunreaderms2selected.h:42
timsmsrunreaderms2.h
MSrun file reader for native Bruker TimsTOF specialized for MS2 purpose.
pappso::SpectrumCollectionHandlerInterface
interface to collect spectrums from the MsRunReader class
Definition:
msrunreader.h:59
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition:
massspectrum.h:54
pappsomspp
msrun
private
timsmsrunreaderms2selected.h
Generated on Fri Jan 8 2021 14:38:15 for libpappsomspp by
1.8.20