libpappsomspp
Library for mass spectrometry
msrunxicextractorfactory.h
Go to the documentation of this file.
1
/**
2
* \file pappsomspp/xicextractor/msrunxicextractorfactory.h
3
* \date 07/05/2018
4
* \author Olivier Langella
5
* \brief factory to build XIC extractor 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
31
#pragma once
32
33
#include "
msrunxicextractorinterface.h
"
34
35
36
namespace
pappso
37
{
38
/** @brief factory to build different kinds of XIC extractors
39
*/
40
class
PMSPP_LIB_DECL
MsRunXicExtractorFactory
41
{
42
private
:
43
static
MsRunXicExtractorFactory
m_instance
;
44
QString
m_tmpDirName
;
45
46
MsRunXicExtractorFactory
();
47
virtual
~
MsRunXicExtractorFactory
();
48
49
public
:
50
/** @brief singleton to get the only instance of the factory
51
*/
52
static
MsRunXicExtractorFactory
&getInstance();
53
54
/** @brief build a simple XIC extractor that directly uses Proeowizard library
55
* to read and extract XICs building the xic extractor is fast, but extracting
56
* each XIC is slow
57
* @param msrun_reader the MsRun reader on which the XIC extractor will run
58
*/
59
MsRunXicExtractorInterfaceSp
60
buildMsRunXicExtractorSp(
MsRunReaderSPtr
&msrun_reader)
const
;
61
62
/** @brief build Xic extractor that first read the whole MsRun, put it on disk
63
* and extract XICs more quickly This needs some space on disk to store slices
64
* (1 dalton each) building the XIC extractor is slow extracting XIC from
65
* slices is a very quick operation
66
* @param msrun_reader the MsRun reader on which the XIC extractor will run
67
*/
68
MsRunXicExtractorInterfaceSp
69
buildMsRunXicExtractorDiskSp(
MsRunReaderSPtr
&msrun_reader)
const
;
70
71
/** @brief build Xic extractor that first read the whole MsRun, put it on disk
72
* using a write cache and extract XICs more quickly This needs some space on
73
* disk to store slices (1 dalton each) building the XIC extractor is slower
74
* than buildMsRunXicExtractorPwizSp, but faster than
75
* buildMsRunXicExtractorDiskSp extracting XIC from slices is a very quick
76
* operation
77
* @param msrun_reader the MsRun reader on which the XIC extractor will run
78
*/
79
MsRunXicExtractorInterfaceSp
80
buildMsRunXicExtractorDiskBufferSp(
MsRunReaderSPtr
&msrun_reader)
const
;
81
82
/// set the temporary working directory
83
void
setTmpDir(
const
QString &dir_name);
84
};
85
86
}
// namespace pappso
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::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition:
msrunreader.h:151
pappso::MsRunXicExtractorFactory::m_tmpDirName
QString m_tmpDirName
Definition:
msrunxicextractorfactory.h:44
msrunxicextractorinterface.h
pappso::MsRunXicExtractorFactory::m_instance
static MsRunXicExtractorFactory m_instance
Definition:
msrunxicextractorfactory.h:43
pappso::MsRunXicExtractorFactory
factory to build different kinds of XIC extractors
Definition:
msrunxicextractorfactory.h:41
pappso::MsRunXicExtractorInterfaceSp
std::shared_ptr< MsRunXicExtractorInterface > MsRunXicExtractorInterfaceSp
Definition:
msrunxicextractorinterface.h:41
pappsomspp
xicextractor
msrunxicextractorfactory.h
Generated on Wed Oct 21 2020 12:29:32 for libpappsomspp by
1.8.20