libpappsomspp
Library for mass spectrometry
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grpprotein.cpp
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1
2/*******************************************************************************
3 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
4 *
5 * This file is part of the PAPPSOms++ library.
6 *
7 * PAPPSOms++ is free software: you can redistribute it and/or modify
8 * it under the terms of the GNU General Public License as published by
9 * the Free Software Foundation, either version 3 of the License, or
10 * (at your option) any later version.
11 *
12 * PAPPSOms++ is distributed in the hope that it will be useful,
13 * but WITHOUT ANY WARRANTY; without even the implied warranty of
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 * GNU General Public License for more details.
16 *
17 * You should have received a copy of the GNU General Public License
18 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
19 *
20 * Contributors:
21 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
22 *implementation
23 ******************************************************************************/
24
25#include "grpprotein.h"
26
27
28#include "grpexperiment.h"
29#include "grppeptide.h"
30#include "../utils.h"
31
32using namespace pappso;
33GrpProtein::GrpProtein(const QString &accession, const QString &description)
34 : m_accession(accession.simplified()), m_description(description.simplified())
35{
36}
37
38
40 : m_grpPeptidePtrList(other.m_grpPeptidePtrList),
41 m_accession(other.m_accession),
42 m_description(other.m_description)
43
44{
45
48 m_rank = other.m_rank;
49 m_count = other.m_count;
50}
51
55
58{
59 return m_grpPeptidePtrList.begin();
60}
63{
64 return m_grpPeptidePtrList.end();
65}
66
67unsigned int
69{
70 return m_count;
71}
72void
77void
79{
81}
82
83unsigned int
85{
86 return m_groupNumber;
87}
88
89unsigned int
94unsigned int
96{
97 return m_rank;
98}
99const QString
101{
102 if(m_groupNumber == 0)
103 {
104 return "";
105 }
106 return QString("%1.%2.%3")
110}
111bool
113{
114 return (m_accession == other.m_accession);
115}
116
117
118const QString &
120{
121 return m_accession;
122}
123const QString &
125{
126 return m_description;
127}
128void
130{
131 // p_grpPeptide->push_back(this);
132 m_grpPeptidePtrList.push_back(p_grpPeptide);
133}
134
135void
137{
138 qDebug() << "GrpProtein::strip begin " << this->m_accession;
139 // m_grpPeptidePtrList.sort();
140 std::sort(m_grpPeptidePtrList.begin(), m_grpPeptidePtrList.end());
141 // m_grpPeptidePtrList.unique();
143 std::unique(m_grpPeptidePtrList.begin(), m_grpPeptidePtrList.end()),
144 m_grpPeptidePtrList.end());
145 qDebug() << "GrpProtein::strip end";
146}
147
148void
149GrpProtein::setRank(unsigned int i)
150{
151 m_rank = i;
152}
153void
155{
156 m_groupNumber = i;
157}
const QString m_accession
Definition grpprotein.h:80
const QString m_description
Definition grpprotein.h:81
unsigned int m_rank
Definition grpprotein.h:84
std::vector< GrpPeptide * > m_grpPeptidePtrList
Definition grpprotein.h:77
GrpProtein(const GrpProtein &other)
unsigned int getGroupNumber() const
bool operator==(const GrpProtein &other) const
void setRank(unsigned int i)
unsigned int m_groupNumber
Definition grpprotein.h:82
const QString & getAccession() const
void push_back(GrpPeptide *p_grpPeptide)
void strip()
ensure that each peptide in peptide list is unique and sorted by pointer adress
std::vector< GrpPeptide * >::const_iterator const_iterator
Definition grpprotein.h:54
const QString getGroupingId() const
unsigned int getSubGroupNumber() const
unsigned int m_subGroupNumber
Definition grpprotein.h:83
void setGroupNumber(unsigned int i)
unsigned int m_count
Definition grpprotein.h:85
const QString & getDescription() const
unsigned int getCount() const
unsigned int getRank() const
const_iterator end() const
void setSubGroupNumber(unsigned int i)
const_iterator begin() const
static const QString getLexicalOrderedString(unsigned int num)
Definition utils.cpp:52
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39