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 (const 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

virtual void	writeCborStream (QCborStreamWriter &cbor_writer) const
	writes xic coordinates in a cbor stream

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 67 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)
{
}

References mzRange, and rtTarget.

Referenced by XicCoord(), pappso::XicCoordTims::XicCoordTims(), and pappso::XicCoordTims::XicCoordTims().

◆ XicCoord() [2/2]

XicCoord::XicCoord ( const XicCoord & other )

Copy constructor

Parameters

other TODO

Definition at line 42 of file xiccoord.cpp.

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

References XicCoord(), mzRange, rtTarget, and xicSptr.

◆ ~XicCoord()

XicCoord::~XicCoord ( )

virtual

Destructor

Definition at line 47 of file xiccoord.cpp.

48{

49}

Member Function Documentation

◆ addition()

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

virtual

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

Reimplemented in pappso::XicCoordTims.

Definition at line 63 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;
}

References mzRange, and rtTarget.

◆ 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 90 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;
}

References mzRange, and rtTarget.

◆ getParam()

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

virtual

get a specific XIC coordinate parameter

Reimplemented in pappso::XicCoordTims.

Definition at line 121 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 52 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;
}

References xicSptr.

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 77 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;
}

References mzRange, and rtTarget.

◆ reset()

void pappso::XicCoord::reset ( )

virtual

reset to zero

Reimplemented in pappso::XicCoordTims.

Definition at line 104 of file xiccoord.cpp.

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

References mzRange, rtTarget, and xicSptr.

◆ toString()

QString pappso::XicCoord::toString ( ) const

virtual

get a description of the XIC coordinate in a string

Reimplemented in pappso::XicCoordTims.

Definition at line 114 of file xiccoord.cpp.

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

References mzRange, and rtTarget.

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

◆ writeCborStream()

void pappso::XicCoord::writeCborStream ( QCborStreamWriter & cbor_writer ) const

virtual

writes xic coordinates in a cbor stream

Reimplemented in pappso::XicCoordTims.

Definition at line 127 of file xiccoord.cpp.

{
  cbor_writer.append(QLatin1String("xic_coord"));
  cbor_writer.startMap(2);
  cbor_writer.append(QLatin1String("mz_range"));
  cbor_writer.startArray(2);
  cbor_writer.append(mzRange.lower());
  cbor_writer.append(mzRange.upper());
  cbor_writer.endArray();
 
  cbor_writer.append(QLatin1String("rt"));
  cbor_writer.append(rtTarget);
 
  cbor_writer.endMap();
}

References mzRange, and rtTarget.

Member Data Documentation

◆ mzRange

MzRange pappso::XicCoord::mzRange

the mass to extract

Definition at line 125 of file xiccoord.h.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), XicCoord(), XicCoord(), addition(), divideBy(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId(), multiplyBy(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex(), reset(), pappso::XicCoordTims::reset(), toString(), writeCborStream(), and pappso::XicCoordTims::writeCborStream().

◆ 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 131 of file xiccoord.h.

Referenced by XicCoord(), XicCoord(), addition(), divideBy(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId(), multiplyBy(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex(), reset(), pappso::XicCoordTims::reset(), toString(), writeCborStream(), and pappso::XicCoordTims::writeCborStream().

◆ xicSptr

XicSPtr pappso::XicCoord::xicSptr = nullptr

extracted xic

Definition at line 135 of file xiccoord.h.

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

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

pappsomspp/core/msrun/xiccoord/xiccoord.h
pappsomspp/core/msrun/xiccoord/xiccoord.cpp

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XicCoord() [1/2]

◆ XicCoord() [2/2]

◆ ~XicCoord()

Member Function Documentation

◆ addition()

◆ divideBy()

◆ getParam()

◆ initializeAndClone()

◆ multiplyBy()

◆ reset()

◆ toString()

◆ writeCborStream()

Member Data Documentation

◆ mzRange

◆ rtTarget

◆ xicSptr