pappso::XicCoord Struct Reference

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

#include <xiccoord.h>

Inheritance diagram for pappso::XicCoord:

Public Member Functions
	XicCoord ()
	XicCoord (const XicCoord &other)
virtual	~XicCoord ()
virtual XicCoordSPtr	initializeAndClone () const
	intialize the XIC and make a deep copy of object
virtual XicCoordSPtr	addition (XicCoordSPtr &to_add) const
	compute a new XIC coord as the sum of the given one
virtual XicCoordSPtr	multiplyBy (double number) const
	compute a new xic coord as a product by
virtual XicCoordSPtr	divideBy (double number) const
	compute a new xic coord as a division by
virtual void	reset ()
	reset to zero
virtual QString	toString () const
	get a description of the XIC coordinate in a string
virtual const QVariant	getParam (XicCoordParam param) const
	get a specific XIC coordinate parameter

Public Attributes
MzRange	mzRange
	the mass to extract
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
XicSPtr	xicSptr = nullptr
	extracted xic

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 66 of file xiccoord.h.

Constructor & Destructor Documentation

XicCoord() [1/2]

pappso::XicCoord::XicCoord

(

)

Default constructor

Definition at line 36 of file xiccoord.cpp.

  : mzRange(pappso_double(1), PrecisionFactory::getPpmInstance(10.0)),
    rtTarget(0)
{
}

XicCoord() [2/2]

XicCoord::XicCoord

(

const XicCoord &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 43 of file xiccoord.cpp.

  : mzRange(other.mzRange), rtTarget(other.rtTarget)
{
  xicSptr = other.xicSptr;
}

References xicSptr.

~XicCoord()

XicCoord::~XicCoord ( )

virtual

Destructor

Definition at line 49 of file xiccoord.cpp.

{
}

Member Function Documentation

addition()

pappso::XicCoordSPtr pappso::XicCoord::addition ( XicCoordSPtr &  to_add ) const

virtual

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

Reimplemented in pappso::XicCoordTims.

Definition at line 65 of file xiccoord.cpp.

{
  XicCoordSPtr xic_coord_sp = std::make_shared<XicCoord>(*this);
 
  // xic_coord_sp.get()->xicSptr = nullptr;
 
  xic_coord_sp.get()->rtTarget += to_add.get()->rtTarget;
 
  xic_coord_sp.get()->mzRange += to_add.get()->mzRange;
 
  return xic_coord_sp;
}

divideBy()

pappso::XicCoordSPtr pappso::XicCoord::divideBy ( double  number ) const

virtual

compute a new xic coord as a division by

Reimplemented in pappso::XicCoordTims.

Definition at line 92 of file xiccoord.cpp.

{
  XicCoordSPtr xic_coord_sp = std::make_shared<XicCoord>(*this);
 
  // xic_coord_sp.get()->xicSptr = nullptr;
 
  xic_coord_sp.get()->rtTarget /= number;
  xic_coord_sp.get()->mzRange *= (double)((double)1 / number);
 
  return xic_coord_sp;
}

getParam()

const QVariant pappso::XicCoord::getParam ( XicCoordParam  param ) const

virtual

get a specific XIC coordinate parameter

Reimplemented in pappso::XicCoordTims.

Definition at line 123 of file xiccoord.cpp.

{
  return QVariant();
}

Referenced by pappso::IonMobilityGrid::storeObservedIdentityBetween().

initializeAndClone()

pappso::XicCoordSPtr pappso::XicCoord::initializeAndClone ( ) const

virtual

intialize the XIC and make a deep copy of object

Reimplemented in pappso::XicCoordTims.

Definition at line 54 of file xiccoord.cpp.

{
  XicCoordSPtr xic_coord_sp = std::make_shared<XicCoord>(*this);
 
  xic_coord_sp.get()->xicSptr = std::make_shared<Xic>();
 
  return xic_coord_sp;
}

Referenced by pappso::IonMobilityGrid::translateXicCoordFromTo().

multiplyBy()

XicCoordSPtr XicCoord::multiplyBy ( double  number ) const

virtual

compute a new xic coord as a product by

Reimplemented in pappso::XicCoordTims.

Definition at line 79 of file xiccoord.cpp.

{
  XicCoordSPtr xic_coord_sp = std::make_shared<XicCoord>(*this);
 
  // xic_coord_sp.get()->xicSptr = nullptr;
 
  xic_coord_sp.get()->rtTarget *= number;
  xic_coord_sp.get()->mzRange *= number;
 
  return xic_coord_sp;
}

reset()

void pappso::XicCoord::reset ( )

virtual

reset to zero

Reimplemented in pappso::XicCoordTims.

Definition at line 106 of file xiccoord.cpp.

{
 
  xicSptr = nullptr;
 
  rtTarget = 0;
  mzRange  = MzRange(0.0, 0.0);
}

toString()

QString pappso::XicCoord::toString ( ) const

virtual

get a description of the XIC coordinate in a string

Reimplemented in pappso::XicCoordTims.

Definition at line 116 of file xiccoord.cpp.

{
  return QString("mz=%1 rt=%2").arg(mzRange.toString()).arg(rtTarget);
}

Referenced by pappso::XicCoordTims::toString().

Member Data Documentation

mzRange

MzRange pappso::XicCoord::mzRange

the mass to extract

Definition at line 120 of file xiccoord.h.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsData::getXicCoordTimsFromPrecursorId(), and pappso::XicCoordTims::reset().

rtTarget

double pappso::XicCoord::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

Definition at line 126 of file xiccoord.h.

Referenced by pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsData::getXicCoordTimsFromPrecursorId(), and pappso::XicCoordTims::reset().

xicSptr

XicSPtr pappso::XicCoord::xicSptr = nullptr

extracted xic

Definition at line 130 of file xiccoord.h.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), XicCoord(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsData::getXicCoordTimsFromPrecursorId(), and pappso::XicCoordTims::reset().

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

• pappsomspp/msrun/xiccoord/xiccoord.h
• pappsomspp/msrun/xiccoord/xiccoord.cpp