libpappsomspp
Library for mass spectrometry
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specxtractinterface.h
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1/**
2 * \file pappsomspp/processing/spectree/specxtractinterface.h
3 * \date 11/12/2023
4 * \author Olivier Langella
5 * \brief Matthieu David's SpecTree structure
6 *
7 * C++ implementation of algorithm already described in :
8 * 1. David, M., Fertin, G., Rogniaux, H. & Tessier, D. SpecOMS: A Full Open
9 * Modification Search Method Performing All-to-All Spectra Comparisons within
10 * Minutes. J. Proteome Res. 16, 3030–3038 (2017).
11 *
12 * https://www.theses.fr/2019NANT4092
13 */
14
15
16/*
17 * SpecTree
18 * Copyright (C) 2023 Olivier Langella
19 * <olivier.langella@universite-paris-saclay.fr>
20 *
21 * This program is free software: you can redistribute ipetide to spectrum
22 * alignmentt and/or modify it under the terms of the GNU General Public License
23 * as published by the Free Software Foundation, either version 3 of the
24 * License, or (at your option) any later version.
25 *
26 * This program is distributed in the hope that it will be useful,
27 * but WITHOUT ANY WARRANTY; without even the implied warranty of
28 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29 * GNU General Public License for more details.
30 *
31 * You should have received a copy of the GNU General Public License
32 * along with this program. If not, see <http://www.gnu.org/licenses/>.
33 *
34 */
35
36#pragma once
37
38#include <map>
40
41namespace pappso
42{
43namespace spectree
44{
45
46/**
47 * @brief yield similarities between pairs of ItemCart
48 *
49 * The best thing is to implement this interface to process similarity at the
50 * time of the spectree extraction
51 */
53{
54 public:
55 /**
56 * Default constructor
57 */
59
60 /**
61 * Destructor
62 */
63 virtual ~SpecXtractInterface();
64
65 virtual void beginItemCartExtraction(std::size_t cart_id_a);
66 virtual void reportSimilarity(std::size_t cart_id_a,
67 std::size_t cart_id_b,
68 std::size_t similarity) = 0;
69 virtual void endItemCartExtraction(std::size_t cart_id_a);
70};
71
72/** @brief store all similarities in vectors an map : very costly for memory and
73 * CPU
74 *
75 * only for testing purpose
76 */
78{
79
80 public:
81 /**
82 * Default constructor
83 */
85
86 /**
87 * Destructor
88 */
89 virtual ~SpecXtractMap();
90
91 void reportSimilarity(std::size_t cart_id_a,
92 std::size_t cart_id_b,
93 std::size_t similarity) override;
94
95 const std::map<std::size_t, std::map<std::size_t, std::size_t>> &
96 getMapSimilarities() const;
97
98 void clear();
99
100 private:
101 std::map<std::size_t, std::map<std::size_t, std::size_t>> m_mapSimilarities;
102};
103
104} // namespace spectree
105} // namespace pappso
yield similarities between pairs of ItemCart
virtual void reportSimilarity(std::size_t cart_id_a, std::size_t cart_id_b, std::size_t similarity)=0
store all similarities in vectors an map : very costly for memory and CPU
void reportSimilarity(std::size_t cart_id_a, std::size_t cart_id_b, std::size_t similarity) override
std::map< std::size_t, std::map< std::size_t, std::size_t > > m_mapSimilarities
const std::map< std::size_t, std::map< std::size_t, std::size_t > > & getMapSimilarities() const
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39