libpappsomspp
Library for mass spectrometry
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msrunxicextractorinterface.h
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1/**
2 * \file pappsomspp/xicextractor/msrunxicextractor.h
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 ******************************************************************************/
27
28#pragma once
29
30
31#include "../msrun/msrunreader.h"
32#include <memory>
33#include <vector>
34#include <limits>
35#include <iterator>
36#include "../mzrange.h"
37#include "../xic/xic.h"
38#include "../processing/uimonitor/uimonitorinterface.h"
39
40
41namespace pappso
42{
43
44class MsRunXicExtractorInterface;
45typedef std::shared_ptr<MsRunXicExtractorInterface>
47
49{
50
51 public:
52 /** @brief set the XIC extraction method
53 */
54 void setXicExtractMethod(XicExtractMethod method); // sum or max
55
56 /** @brief set the retention time range in seconds around the target rt
57 *
58 * only the interesting part of the xic will be extracted, form the rt target
59 * - range_in_seconds to rt target + range in seconds by default, all the LC
60 * run time is extracted
61 *
62 * @param range_in_seconds range in seconds
63 */
64 void setRetentionTimeAroundTarget(double range_in_seconds);
65
66
67 /** @brief extract a list of XIC given a list of xic coordinates to extract
68 *
69 * XicCoord is a vessel containing the xic to fill and coordinates of this XIC
70 * in the MS run
71 *
72 * @param monitor process monitoring
73 * @param xic_coord_list list of xic coordinates to extract. The order of xic
74 * coordinates may change.
75 */
76 virtual void
77 extractXicCoordSPtrList(UiMonitorInterface &monitor,
78 std::vector<XicCoordSPtr> &xic_coord_list) final;
79
80
81 /** @brief multithreaded XIC extraction
82 *
83 * divide xic_coord_list and run extractXicCoordSPtrList separated threads
84 *
85 * @param monitor process monitoring
86 * @param xic_coord_list list of xic coordinates to extract. The order of xic
87 * coordinates may change.
88 */
89 virtual void extractXicCoordSPtrListParallelized(
90 UiMonitorInterface &monitor,
91 std::vector<XicCoordSPtr> &xic_coord_list) final;
92
93 const MsRunIdCstSPtr &getMsRunId() const;
94
95 /** @brief get the msrunreader currently used for XIC extraction
96 */
97 const MsRunReaderSPtr &getMsRunReaderSPtr() const;
98
99 /** @brief filter interface to apply just after XIC extration on each trace
100 */
101 void
102 setPostExtractionTraceFilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter);
103
104
105 protected:
106 /** @brief constructor is private, use the MsRunXicExtractorFactory
107 */
111
112 /** @brief possible post extraction process, eventually trace filters
113 */
114 virtual void postExtractionProcess(
115 UiMonitorInterface &monitor,
116 std::vector<XicCoordSPtr>::iterator it_xic_coord_list_begin,
117 std::vector<XicCoordSPtr>::iterator it_xic_coord_list_end);
118
120 UiMonitorInterface &monitor,
121 std::vector<XicCoordSPtr>::iterator it_xic_coord_list_begin,
122 std::vector<XicCoordSPtr>::iterator it_xic_coord_list_end) = 0;
123
124
125 protected:
127 XicExtractMethod m_xicExtractMethod = XicExtractMethod::max;
128 double m_retentionTimeAroundTarget = std::numeric_limits<double>::max();
129 pappso::FilterInterfaceCstSPtr mcsp_postExtractionTraceFilter = nullptr;
130};
131
132
133} // namespace pappso
virtual void protectedExtractXicCoordSPtrList(UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)=0
#define PMSPP_LIB_DECL
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:56
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition msrunid.h:46
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< MsRunXicExtractorInterface > MsRunXicExtractorInterfaceSp
XicExtractMethod
Definition types.h:240