libpappsomspp
Library for mass spectrometry
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pappso::FilterMzExclusion Class Reference

#include <filterexclusionmz.h>

Inheritance diagram for pappso::FilterMzExclusion:
pappso::FilterNameInterface pappso::FilterInterface

Public Member Functions

 FilterMzExclusion (PrecisionPtr precision_ptr)
 
 FilterMzExclusion (const QString &strBuildParams)
 
 FilterMzExclusion (const FilterMzExclusion &other)
 
virtual ~FilterMzExclusion ()
 
QString name () const override
 
QString toString () const override
 
Tracefilter (Trace &data_points) const override
 get all the datapoints and remove different isotope and add their intensity and change to charge = 1 when the charge is known
 
- Public Member Functions inherited from pappso::FilterNameInterface
virtual ~FilterNameInterface ()
 
- Public Member Functions inherited from pappso::FilterInterface
virtual ~FilterInterface ()
 

Private Member Functions

void buildFilterFromString (const QString &strBuildParams) override
 build this filter using a string
 
Trace removeTraceInExclusionMargin (Trace &points) const
 

Private Attributes

PrecisionPtr m_exclusionPrecision
 

Additional Inherited Members

- Protected Member Functions inherited from pappso::FilterNameInterface

Detailed Description

Definition at line 36 of file filterexclusionmz.h.

Constructor & Destructor Documentation

◆ FilterMzExclusion() [1/3]

FilterMzExclusion::FilterMzExclusion ( pappso::PrecisionPtr precision_ptr)

Default constructor

Definition at line 39 of file filterexclusionmz.cpp.

40 : m_exclusionPrecision(precision_ptr)
41{
42}

◆ FilterMzExclusion() [2/3]

FilterMzExclusion::FilterMzExclusion ( const QString & strBuildParams)
Parameters
strBuildParamsstring to build the filter "mzExclusion|0.02dalton"

Definition at line 34 of file filterexclusionmz.cpp.

35{
36 buildFilterFromString(strBuildParams);
37}
void buildFilterFromString(const QString &strBuildParams) override
build this filter using a string

References buildFilterFromString().

◆ FilterMzExclusion() [3/3]

FilterMzExclusion::FilterMzExclusion ( const FilterMzExclusion & other)

Copy constructor

Parameters
otherTODO

Definition at line 44 of file filterexclusionmz.cpp.

◆ ~FilterMzExclusion()

FilterMzExclusion::~FilterMzExclusion ( )
virtual

Destructor

Definition at line 49 of file filterexclusionmz.cpp.

50{
51}

Member Function Documentation

◆ buildFilterFromString()

void pappso::FilterMzExclusion::buildFilterFromString ( const QString & strBuildParams)
overrideprivatevirtual

build this filter using a string

Parameters
strBuildParamsa string coding the filter and its parameters "filterName|param1;param2;param3"

Implements pappso::FilterNameInterface.

Definition at line 54 of file filterexclusionmz.cpp.

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);
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}
excetion to use when an item type is not recognized
static PrecisionPtr fromString(const QString &str)
get a precision pointer from a string
Definition precision.cpp:72

References pappso::PrecisionFactory::fromString().

Referenced by FilterMzExclusion().

◆ filter()

pappso::Trace & pappso::FilterMzExclusion::filter ( pappso::Trace & data_points) const
overridevirtual

get all the datapoints and remove different isotope and add their intensity and change to charge = 1 when the charge is known

Returns
a list of datapoint

Implements pappso::FilterInterface.

Definition at line 78 of file filterexclusionmz.cpp.

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}
Trace removeTraceInExclusionMargin(Trace &points) const
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

References pappso::descending, pappso::Trace::sortX(), and pappso::Trace::sortY().

◆ name()

QString pappso::FilterMzExclusion::name ( ) const
overridevirtual

Implements pappso::FilterNameInterface.

Definition at line 93 of file filterexclusionmz.cpp.

94{
95 return "mzExclusion";
96}

◆ removeTraceInExclusionMargin()

pappso::Trace pappso::FilterMzExclusion::removeTraceInExclusionMargin ( pappso::Trace & points) const
private

Definition at line 111 of file filterexclusionmz.cpp.

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}
pappso_double lower() const
Definition mzrange.h:71
pappso_double upper() const
Definition mzrange.h:77

References pappso::MzRange::lower(), and pappso::MzRange::upper().

◆ toString()

QString pappso::FilterMzExclusion::toString ( ) const
overridevirtual

Implements pappso::FilterNameInterface.

Definition at line 100 of file filterexclusionmz.cpp.

101{
102 QString strCode =
103 QString("%1|%2").arg(name()).arg(m_exclusionPrecision->toString());
104
105 strCode.replace(" ", "");
106
107 return strCode;
108}
QString name() const override
virtual QString toString() const =0

Member Data Documentation

◆ m_exclusionPrecision

PrecisionPtr pappso::FilterMzExclusion::m_exclusionPrecision
private

Definition at line 79 of file filterexclusionmz.h.


The documentation for this class was generated from the following files: