libpappsomspp
Library for mass spectrometry
filterexclusionmz.cpp
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1 /**
2  * \file pappsomspp/processing/filters/filterexclusionmz.cpp
3  * \date 09/02/2021
4  * \author Thomas Renne
5  * \brief Delete small peaks in the exclusion range
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2021 Thomas Renne <thomas.renne@e.email>.
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 #include "filterexclusionmz.h"
29 #include <QDebug>
30 #include "../../exception/exceptionnotrecognized.h"
31 
32 using namespace pappso;
33 
34 FilterMzExclusion::FilterMzExclusion(const QString &strBuildParams)
35 {
36  buildFilterFromString(strBuildParams);
37 }
38 
40  : m_exclusionPrecision(precision_ptr)
41 {
42 }
43 
45  : m_exclusionPrecision(other.m_exclusionPrecision)
46 {
47 }
48 
50 {
51 }
52 
53 void
55 {
56  qDebug();
57  if(strBuildParams.startsWith("mzExclusion|"))
58  {
59  QStringList params =
60  strBuildParams.split("|").back().split(";", Qt::SkipEmptyParts);
61 
62  QString precision = params.at(0);
63  m_exclusionPrecision =
64  PrecisionFactory::fromString(precision.replace("dalton", " dalton")
65  .replace("ppm", " ppm")
66  .replace("res", " res"));
67  }
68  else
69  {
71  QString("building mzExclusion from string %1 is not possible")
72  .arg(strBuildParams));
73  }
74  qDebug();
75 }
76 
79 {
80  qDebug();
81  qDebug() << "before" << data_points.size();
82  data_points.sortY();
83 
84  Trace new_trace = removeTraceInExclusionMargin(data_points);
85  new_trace.sortX();
86  data_points = std::move(new_trace);
87  qDebug() << "after" << data_points.size();
88  qDebug();
89  return data_points;
90 }
91 
92 QString
94 {
95  return "mzExclusion";
96 }
97 
98 
99 QString
101 {
102  QString strCode =
103  QString("%1|%2").arg(name()).arg(m_exclusionPrecision->toString());
104 
105  strCode.replace(" ", "");
106 
107  return strCode;
108 }
109 
112  pappso::Trace &points) const
113 {
114  Trace new_trace;
115  std::vector<MzRange> excluded_ranges;
116 
117  for(auto &data_point : points)
118  {
119  auto exclude_index = excluded_ranges.begin(), end = excluded_ranges.end();
120 
121  exclude_index =
122  std::find_if(exclude_index, end, [&data_point](MzRange range) {
123  return (data_point.x >= range.lower() &&
124  data_point.x <= range.upper());
125  });
126  if(exclude_index == end)
127  {
128  new_trace.push_back(data_point);
129  MzRange new_range(data_point.x, m_exclusionPrecision);
130  excluded_ranges.push_back(new_range);
131  }
132  }
133 
134  return new_trace;
135 }
excetion to use when an item type is not recognized
void buildFilterFromString(const QString &strBuildParams) override
build this filter using a string
QString toString() const override
Trace & filter(Trace &data_points) const override
get all the datapoints and remove different isotope and add their intensity and change to charge = 1 ...
Trace removeTraceInExclusionMargin(Trace &points) const
FilterMzExclusion(PrecisionPtr precision_ptr)
QString name() const override
pappso_double lower() const
Definition: mzrange.h:71
pappso_double upper() const
Definition: mzrange.h:77
static PrecisionPtr fromString(const QString &str)
get a precision pointer from a string
Definition: precision.cpp:72
A simple container of DataPoint instances.
Definition: trace.h:148
void sortY()
Definition: trace.cpp:964
void sortX()
Definition: trace.cpp:956
Delete small peaks in the exclusion range.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39