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:

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
virtual XicCoordSPtr	addition (const XicCoordSPtr &to_add) const override
	compute a new XIC coord as the sum of the given one
virtual XicCoordSPtr	multiplyBy (double number) const override
	compute a new xic coord as a product by
virtual XicCoordSPtr	divideBy (double number) const override
	compute a new xic coord as a division by
virtual void	reset () override
	reset to zero
virtual QString	toString () const override
	get a description of the XIC coordinate in a string
virtual const QVariant	getParam (XicCoordParam param) const override
	get a specific XIC coordinate parameter
virtual void	writeCborStream (QCborStreamWriter &cbor_writer) const override
	writes xic coordinates in a cbor stream
void	scanNumBeginRangeCorrection (long start_dev, long stop_dev)
	apply scan num correction on xic coordinate
Public Member Functions inherited from pappso::XicCoord
	XicCoord ()
	XicCoord (const XicCoord &other)
virtual	~XicCoord ()

Public Attributes
std::size_t	scanNumBegin
	mobility index begin
std::size_t	scanNumEnd
	mobility index end
Public Attributes inherited from pappso::XicCoord
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 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.

: XicCoord(){};

References pappso::XicCoord::XicCoord().

Referenced by XicCoordTims(), and addition().

XicCoordTims() [2/2]

pappso::XicCoordTims::XicCoordTims

(

const XicCoordTims &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 41 of file xiccoordtims.cpp.

                                                    : XicCoord(other)
{
  scanNumBegin = other.scanNumBegin;
  scanNumEnd   = other.scanNumEnd;
}

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

~XicCoordTims()

pappso::XicCoordTims::~XicCoordTims ( )

virtual

Destructor

Definition at line 48 of file xiccoordtims.cpp.

{
}

Member Function Documentation

addition()

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

overridevirtual

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

Reimplemented from pappso::XicCoord.

Definition at line 66 of file xiccoordtims.cpp.

{
  XicCoordTimsSPtr xic_coord_sp = std::make_shared<XicCoordTims>(*this);
 
  XicCoordTims *toadd = dynamic_cast<XicCoordTims *>(to_add.get());
 
  if(toadd == nullptr)
    {
      throw ExceptionNotPossible(QObject::tr("XicCoord to add is of a different type"));
    }
 
  // xic_coord_sp.get()->xicSptr = xic_coord_sp.get()->xicSptr;
 
  xic_coord_sp.get()->mzRange += to_add.get()->mzRange;
  xic_coord_sp.get()->rtTarget += to_add.get()->rtTarget;
  xic_coord_sp.get()->scanNumBegin += toadd->scanNumBegin;
  xic_coord_sp.get()->scanNumEnd += toadd->scanNumEnd;
 
  qDebug() << "xic_coord_sp.get()->scanNumBegin=" << xic_coord_sp.get()->scanNumBegin;
  qDebug() << "xic_coord_sp.get()->scanNumEnd=" << xic_coord_sp.get()->scanNumEnd;
  return xic_coord_sp;
}

References XicCoordTims(), 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.

{
 
  XicCoordTimsSPtr xic_coord_sp = std::make_shared<XicCoordTims>(*this);
 
  // xic_coord_sp.get()->xicSptr = nullptr;
 
  xic_coord_sp.get()->rtTarget /= number;
  xic_coord_sp.get()->mzRange *= (double)((double)1 / number);
 
  xic_coord_sp.get()->scanNumBegin /= number;
  xic_coord_sp.get()->scanNumEnd /= number;
 
  qDebug() << "xic_coord_sp.get()->scanNumBegin=" << xic_coord_sp.get()->scanNumBegin;
  qDebug() << "xic_coord_sp.get()->scanNumEnd=" << xic_coord_sp.get()->scanNumEnd;
  return xic_coord_sp;
}

getParam()

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

overridevirtual

get a specific XIC coordinate parameter

Reimplemented from pappso::XicCoord.

Definition at line 146 of file xiccoordtims.cpp.

{
  switch(param)
    {
      case XicCoordParam::TimsTofIonMobilityScanNumberStart:
        return QVariant((quint64)scanNumBegin);
        break;
      case XicCoordParam::TimsTofIonMobilityScanNumberStop:
        return QVariant((quint64)scanNumEnd);
        break;
      default:
        return QVariant();
    }
}

References scanNumBegin, scanNumEnd, pappso::TimsTofIonMobilityScanNumberStart, and pappso::TimsTofIonMobilityScanNumberStop.

initializeAndClone()

XicCoordSPtr pappso::XicCoordTims::initializeAndClone ( ) const

overridevirtual

intialize the XIC and make a deep copy of object

Reimplemented from pappso::XicCoord.

Definition at line 54 of file xiccoordtims.cpp.

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

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.

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

reset()

void pappso::XicCoordTims::reset ( )

overridevirtual

reset to zero

Reimplemented from pappso::XicCoord.

Definition at line 127 of file xiccoordtims.cpp.

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

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

scanNumBeginRangeCorrection()

void pappso::XicCoordTims::scanNumBeginRangeCorrection	(	long	start_dev,
		long	stop_dev )

apply scan num correction on xic coordinate

Definition at line 161 of file xiccoordtims.cpp.

{
  long begin = scanNumBegin + start_dev;
  long end   = scanNumEnd + stop_dev;
  if(begin < 0)
    scanNumBegin = 0;
  else
    scanNumBegin = begin;
  if(end < 0)
    scanNumEnd = 0;
  else
    scanNumEnd = end;
}

References scanNumBegin, and scanNumEnd.

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

toString()

QString pappso::XicCoordTims::toString ( ) const

overridevirtual

get a description of the XIC coordinate in a string

Reimplemented from pappso::XicCoord.

Definition at line 139 of file xiccoordtims.cpp.

{
  return QString("%1 begin=%2 end=%3").arg(XicCoord::toString()).arg(scanNumBegin).arg(scanNumEnd);
}

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

writeCborStream()

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

overridevirtual

writes xic coordinates in a cbor stream

Reimplemented from pappso::XicCoord.

Definition at line 178 of file xiccoordtims.cpp.

{
  cbor_writer.append(QLatin1String("xic_coord"));
  cbor_writer.startMap(3);
  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.append(QLatin1String("tim_im_range"));
  cbor_writer.startArray(2);
  cbor_writer.append((quint64)scanNumBegin);
  cbor_writer.append((quint64)scanNumEnd);
  cbor_writer.endArray();
  cbor_writer.endMap();
}

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

Member Data Documentation

scanNumBegin

std::size_t pappso::XicCoordTims::scanNumBegin

mobility index begin

Definition at line 97 of file xiccoordtims.h.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), XicCoordTims(), addition(), getParam(), pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex(), reset(), scanNumBeginRangeCorrection(), toString(), and writeCborStream().

scanNumEnd

std::size_t pappso::XicCoordTims::scanNumEnd

mobility index end

Definition at line 101 of file xiccoordtims.h.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), XicCoordTims(), addition(), getParam(), pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex(), reset(), scanNumBeginRangeCorrection(), toString(), and writeCborStream().

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

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