libpappsomspp
Library for mass spectrometry
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itemcart.h
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1/**
2 * \file pappsomspp/processing/spectree/itemcart.h
3 * \date 13/12/2023
4 * \author Olivier Langella
5 * \brief basic object to study using spectree
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 th^e 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 <vector>
40
41namespace pappso
42{
43namespace spectree
44{
45/**
46 * @brief container for spectree items
47 *
48 * ItemCart is the basic container to use SpecTree algorithm
49 * each cart has an id (long integer) and a list of items (list of integers)
50 *
51 * SpecTree will be able to quickly count common items between every cart
52 */
53
55{
56 public:
57 /**
58 * Default constructor
59 */
60 ItemCart();
61
62 ItemCart(std::size_t id, const std::vector<std::size_t> &item_list);
63
64 /**
65 * Copy constructor
66 *
67 * @param other TODO
68 */
69 ItemCart(const ItemCart &other);
70
71 /**
72 * Destructor
73 */
74 virtual ~ItemCart();
75
76 const std::vector<std::size_t> &getItemList() const;
77
78 std::size_t getId() const;
79
80 ItemCart &operator=(const ItemCart &other);
81
82 protected:
83 std::size_t m_id;
84 std::vector<std::size_t> m_itemList;
85};
86} // namespace spectree
87} // namespace pappso
container for spectree items
Definition itemcart.h:55
std::vector< std::size_t > m_itemList
Definition itemcart.h:84
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39