libpappsomspp
Library for mass spectrometry
pappso::XicCoordTims Struct Reference

coordinates of the XIC to extract and the resulting XIC after extraction More...

#include <xiccoordtims.h>

Inheritance diagram for pappso::XicCoordTims:
pappso::XicCoord

Public Member Functions

 XicCoordTims ()
 
 XicCoordTims (const XicCoordTims &other)
 
virtual ~XicCoordTims ()
 
virtual XicCoordSPtr initializeAndClone () const override
 intialize the XIC and make a deep copy of object More...
 
virtual XicCoordSPtr addition (XicCoordSPtr &to_add) const override
 compute a new XIC coord as the sum of the given one More...
 
virtual XicCoordSPtr multiplyBy (double number) const override
 compute a new xic coord as a product by More...
 
virtual XicCoordSPtr divideBy (double number) const override
 compute a new xic coord as a division by More...
 
virtual void reset () override
 reset to zero More...
 
virtual QString toString () const override
 get a description of the XIC coordinate in a string More...
 
- Public Member Functions inherited from pappso::XicCoord
 XicCoord ()
 
 XicCoord (const XicCoord &other)
 
virtual ~XicCoord ()
 
virtual XicCoordSPtr initializeAndClone () const
 intialize the XIC and make a deep copy of object More...
 
virtual XicCoordSPtr addition (XicCoordSPtr &to_add) const
 compute a new XIC coord as the sum of the given one More...
 
virtual XicCoordSPtr multiplyBy (double number) const
 compute a new xic coord as a product by More...
 
virtual XicCoordSPtr divideBy (double number) const
 compute a new xic coord as a division by More...
 
virtual void reset ()
 reset to zero More...
 
virtual QString toString () const
 get a description of the XIC coordinate in a string More...
 

Public Attributes

std::size_t scanNumBegin
 mobility index begin More...
 
std::size_t scanNumEnd
 mobility index end More...
 
- Public Attributes inherited from pappso::XicCoord
MzRange mzRange
 the mass to extract More...
 
double rtTarget = 0
 the targeted retention time to extract around intended in seconds, and related to one msrun. This is not a reference, just to save memory and cpu usage when extracting xic More...
 
XicSPtr xicSptr = nullptr
 extracted xic More...
 

Detailed Description

coordinates of the XIC to extract and the resulting XIC after extraction

to extract a XIC, we need basically the mass to extract it this structure is meant to extact a XIC quickly and not to maintain information about it : no peptide, no scan number, no retention time...

Definition at line 50 of file xiccoordtims.h.

Constructor & Destructor Documentation

◆ XicCoordTims() [1/2]

pappso::XicCoordTims::XicCoordTims ( )
inline

Default constructor

Definition at line 55 of file xiccoordtims.h.

55: XicCoord(){};

◆ XicCoordTims() [2/2]

pappso::XicCoordTims::XicCoordTims ( const XicCoordTims other)

Copy constructor

Parameters
otherTODO

Definition at line 38 of file xiccoordtims.cpp.

38 : XicCoord(other)
39{
40 scanNumBegin = other.scanNumBegin;
41 scanNumEnd = other.scanNumEnd;
42}
std::size_t scanNumEnd
mobility index end
Definition: xiccoordtims.h:91
std::size_t scanNumBegin
mobility index begin
Definition: xiccoordtims.h:87

References scanNumBegin, and scanNumEnd.

◆ ~XicCoordTims()

pappso::XicCoordTims::~XicCoordTims ( )
virtual

Destructor

Definition at line 45 of file xiccoordtims.cpp.

46{
47}

Member Function Documentation

◆ addition()

XicCoordSPtr pappso::XicCoordTims::addition ( XicCoordSPtr to_add) const
overridevirtual

compute a new XIC coord as the sum of the given one

Reimplemented from pappso::XicCoord.

Definition at line 63 of file xiccoordtims.cpp.

64{
65 XicCoordTimsSPtr xic_coord_sp = std::make_shared<XicCoordTims>(*this);
66
67 XicCoordTims *toadd = dynamic_cast<XicCoordTims *>(to_add.get());
68
69 if(toadd == nullptr)
70 {
71 throw ExceptionNotPossible(
72 QObject::tr("XicCoord to add is of a different type"));
73 }
74
75 // xic_coord_sp.get()->xicSptr = xic_coord_sp.get()->xicSptr;
76
77 xic_coord_sp.get()->mzRange += to_add.get()->mzRange;
78 xic_coord_sp.get()->rtTarget += to_add.get()->rtTarget;
79 xic_coord_sp.get()->scanNumBegin += toadd->scanNumBegin;
80 xic_coord_sp.get()->scanNumEnd += toadd->scanNumEnd;
81
82 qDebug() << "xic_coord_sp.get()->scanNumBegin="
83 << xic_coord_sp.get()->scanNumBegin;
84 qDebug() << "xic_coord_sp.get()->scanNumEnd="
85 << xic_coord_sp.get()->scanNumEnd;
86 return xic_coord_sp;
87}
std::shared_ptr< XicCoordTims > XicCoordTimsSPtr
Definition: xiccoordtims.h:40

References scanNumBegin, and scanNumEnd.

◆ divideBy()

XicCoordSPtr pappso::XicCoordTims::divideBy ( double  number) const
overridevirtual

compute a new xic coord as a division by

Reimplemented from pappso::XicCoord.

Definition at line 107 of file xiccoordtims.cpp.

108{
109
110 XicCoordTimsSPtr xic_coord_sp = std::make_shared<XicCoordTims>(*this);
111
112 // xic_coord_sp.get()->xicSptr = nullptr;
113
114 xic_coord_sp.get()->rtTarget /= number;
115 xic_coord_sp.get()->mzRange *= (double)((double)1 / number);
116
117 xic_coord_sp.get()->scanNumBegin /= number;
118 xic_coord_sp.get()->scanNumEnd /= number;
119
120 qDebug() << "xic_coord_sp.get()->scanNumBegin="
121 << xic_coord_sp.get()->scanNumBegin;
122 qDebug() << "xic_coord_sp.get()->scanNumEnd="
123 << xic_coord_sp.get()->scanNumEnd;
124 return xic_coord_sp;
125}

◆ initializeAndClone()

XicCoordSPtr pappso::XicCoordTims::initializeAndClone ( ) const
overridevirtual

intialize the XIC and make a deep copy of object

Reimplemented from pappso::XicCoord.

Definition at line 51 of file xiccoordtims.cpp.

52{
53
54 XicCoordTimsSPtr xic_coord_sp = std::make_shared<XicCoordTims>(*this);
55
56 xic_coord_sp.get()->xicSptr = std::make_shared<Xic>();
57
58 return xic_coord_sp;
59}

◆ multiplyBy()

XicCoordSPtr pappso::XicCoordTims::multiplyBy ( double  number) const
overridevirtual

compute a new xic coord as a product by

Reimplemented from pappso::XicCoord.

Definition at line 91 of file xiccoordtims.cpp.

92{
93 XicCoordTimsSPtr xic_coord_sp = std::make_shared<XicCoordTims>(*this);
94
95 // xic_coord_sp.get()->xicSptr = nullptr;
96
97 xic_coord_sp.get()->rtTarget *= number;
98 xic_coord_sp.get()->mzRange *= number;
99
100 xic_coord_sp.get()->scanNumBegin *= number;
101 xic_coord_sp.get()->scanNumEnd *= number;
102
103 return xic_coord_sp;
104}

◆ reset()

void pappso::XicCoordTims::reset ( )
overridevirtual

reset to zero

Reimplemented from pappso::XicCoord.

Definition at line 129 of file xiccoordtims.cpp.

130{
131
132 xicSptr = nullptr;
133
134 rtTarget = 0;
135 mzRange = MzRange(0.0, 0.0);
136 scanNumBegin = 0;
137 scanNumEnd = 0;
138}
XicSPtr xicSptr
extracted xic
Definition: xiccoord.h:113
double rtTarget
the targeted retention time to extract around intended in seconds, and related to one msrun....
Definition: xiccoord.h:109
MzRange mzRange
the mass to extract
Definition: xiccoord.h:103

References pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, scanNumBegin, scanNumEnd, and pappso::XicCoord::xicSptr.

◆ toString()

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

get a description of the XIC coordinate in a string

Reimplemented from pappso::XicCoord.

Definition at line 141 of file xiccoordtims.cpp.

142{
143 return QString("%1 begin=%2 end=%3")
144 .arg(XicCoord::toString())
145 .arg(scanNumBegin)
146 .arg(scanNumEnd);
147}
virtual QString toString() const
get a description of the XIC coordinate in a string
Definition: xiccoord.cpp:115

References scanNumBegin, scanNumEnd, and pappso::XicCoord::toString().

Member Data Documentation

◆ scanNumBegin

std::size_t pappso::XicCoordTims::scanNumBegin

◆ scanNumEnd

std::size_t pappso::XicCoordTims::scanNumEnd

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