libpappsomspp
Library for mass spectrometry
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 More...
 
- 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 More...
 
Trace removeTraceInExclusionMargin (Trace &points) const
 

Private Attributes

PrecisionPtr m_exclusionPrecision
 

Additional Inherited Members

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.

46 {
47 }

◆ ~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();
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 sortY()
Definition: trace.cpp:964
void sortX()
Definition: trace.cpp:956

References 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: