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
32using namespace pappso;
33
34FilterMzExclusion::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
53void
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(SortOrder::descending);
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
92QString
94{
95 return "mzExclusion";
96}
97
98
99QString
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 sortX(SortOrder sort_order=SortOrder::ascending)
Definition: trace.cpp:1086
void sortY(SortOrder sort_order=SortOrder::ascending)
Definition: trace.cpp:1100
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