libpappsomspp
Library for mass spectrometry
xic.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 MassChroqPRM.
6  * *
7  * * MassChroqPRM 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  * * MassChroqPRM 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 MassChroqPRM. 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 <QDebug>
26 #include "xic.h"
27 #include <algorithm>
28 #include <cmath>
29 #include "../exception/exceptionoutofrange.h"
30 
31 namespace pappso
32 {
33 
34 
36 {
37  qDebug() << "Xic::Xic begin";
38  qDebug() << "Xic::Xic end";
39 }
40 
41 Xic::Xic(const Trace &other) : Trace(other)
42 {
43 }
44 
46 {
47 }
48 
49 
52 {
53  return std::make_shared<const Xic>(*this);
54 }
55 
56 XicSPtr
58 {
59  return std::make_shared<Xic>(*this);
60 }
61 
62 void
64 {
65  for(auto &&peak : *this)
66  {
67  qDebug() << "rt = " << peak.x << ", int = " << peak.y;
68  }
69 }
70 
71 const DataPoint &
73 {
74  for(auto &&peak : *this)
75  {
76  if(peak.y == rt)
77  return peak;
78  }
79  throw ExceptionOutOfRange(
80  QObject::tr("no intensity for this retention time"));
81 }
82 
83 unsigned int
85 {
86  if(rt_first > rt_second)
87  {
88  std::swap(rt_first, rt_second);
89  }
90  unsigned int distance = 0;
91  auto it = this->begin();
92  auto itend = this->end();
93 
94  while((it->x < rt_first) && (it != itend))
95  {
96  it++;
97  }
98  while((rt_second > it->x) && (it != itend))
99  {
100  qDebug() << "Xic::getMsPointDistance " << rt_first << " it->rt " << it->x
101  << " rt_second " << rt_second << distance;
102  distance++;
103  it++;
104  }
105 
106 
107  return distance;
108 }
109 
110 void
112 {
113  sortX();
114 }
115 
116 } // namespace pappso
A simple container of DataPoint instances.
Definition: trace.h:147
void sortX()
Definition: trace.cpp:936
const DataPoint & atRetentionTime(pappso_double rt) const
get the DataPoint at the given retention time
Definition: xic.cpp:72
void sortByRetentionTime()
sort peaks by retention time
Definition: xic.cpp:111
XicCstSPtr makeXicCstSPtr() const
Definition: xic.cpp:51
void debugPrintValues() const
Definition: xic.cpp:63
unsigned int getMsPointDistance(pappso_double rt, pappso_double rt_other) const
get the number of MS measurement between 2 retention times on this xic
Definition: xic.cpp:84
XicSPtr makeXicSPtr() const
Definition: xic.cpp:57
virtual ~Xic()
Definition: xic.cpp:45
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const Xic > XicCstSPtr
Definition: xic.h:37
double pappso_double
A type definition for doubles.
Definition: types.h:48
std::shared_ptr< Xic > XicSPtr
Definition: xic.h:39
@ rt
Retention time.