pappso::TimsFrameType1 Class Reference

#include <timsframetype1.h>

Inheritance diagram for pappso::TimsFrameType1:

Public Member Functions
	TimsFrameType1 (std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
	TimsFrameType1 (const TimsFrameType1 &other)
virtual	~TimsFrameType1 ()
virtual std::size_t	getScanPeakCount (std::size_t scanNum) const override
	get the number of peaks in this spectrum need the binary file
virtual std::vector< quint32 >	getScanTofIndexList (std::size_t scanNum) const override
	get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
virtual std::vector< quint32 >	getScanIntensityList (std::size_t scanNum) const override
	get raw intensities without transformation from one scan it needs intensity normalization
virtual pappso::MassSpectrumSPtr	getMassSpectrumSPtr (std::size_t scanNum) const override
	get the mass spectrum corresponding to a scan number
Public Member Functions inherited from pappso::TimsFrame
	TimsFrame (std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
	TimsFrame (const TimsFrame &other)
virtual	~TimsFrame ()
virtual Trace	cumulateScansToTrace (std::size_t scanIndexBegin, std::size_t scanIndexEnd) const override
	cumulate scan list into a trace
virtual Trace	combineScansToTraceWithDowngradedMzResolution (std::size_t mzindex_merge_window, std::size_t scanNumBegin, std::size_t scanNumEnd, quint32 &mz_minimum_index, quint32 &mz_maximum_index) const override
	cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution
virtual Trace	combineScansToTraceWithDowngradedMzResolution2 (std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, std::size_t mobility_scan_begin, std::size_t mobility_scan_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const override
	cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution
void	combineScansInTofIndexIntensityMap (TimsDataFastMap &rawSpectrum, std::size_t scan_index_begin, std::size_t scan_index_end) const override
	cumulate scan list into a trace into a raw spectrum map
virtual void	combineScansInTofIndexIntensityMap (TimsDataFastMap &tof_index_intensity_map, std::size_t scan_index_begin, std::size_t scan_index_end, quint32 tof_index_begin, quint32 tof_index_end) const override
	cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time
virtual Trace	getMobilityScan (std::size_t scanNum, std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const override
	get a single mobility scan m/z + intensities
virtual quint64	cumulateScanIntensities (std::size_t scanNum) const override
virtual quint64	cumulateScanRangeIntensities (std::size_t scanNumBegin, std::size_t scanNumEnd) const override
	...
Public Member Functions inherited from pappso::TimsFrameBase
	TimsFrameBase (std::size_t frameId, quint32 scanCount)
	constructor for binary independant tims frame
	TimsFrameBase (const TimsFrameBase &other)
virtual	~TimsFrameBase ()
virtual bool	hasSameCalibrationData (const TimsFrameBase &other) const
	tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled between frames
virtual std::size_t	getTotalNumberOfScans () const
	get the number of scans contained in this frame each scan represents an ion mobility slice
virtual quint32	getMaximumRawMassIndex () const
	get the maximum raw mass index contained in this frame
virtual pappso::MassSpectrumCstSPtr	getMassSpectrumCstSPtr (std::size_t scan_index) const final
	get the mass spectrum corresponding to a scan index
bool	checkScanNum (std::size_t scanNum) const
	check that this scan number exists
void	setAcqDurationInMilliseconds (double acquisition_duration_ms)
void	setMzCalibration (double T1_frame, double T2_frame, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3, double C4, double T1_ref, double T2_ref, double dC1, double dC2)
void	setTimsCalibration (int tims_model_type, double C0, double C1, double C2, double C3, double C4, double C5, double C6, double C7, double C8, double C9)
void	setRtInSeconds (double time)
void	setMsMsType (quint8 type)
unsigned int	getMsLevel () const
double	getRtInSeconds () const
std::size_t	getId () const
double	getDriftTimeInMilliseconds (std::size_t scan_index) const
	get drift time of a scan number in milliseconds
double	getOneOverK0Transformation (std::size_t scan_index) const
	get 1/K0 value of a given scan (mobility value)
std::size_t	getScanIndexFromOneOverK0 (double one_over_k0) const
	get the scan number from a given 1/Ko mobility value
double	getVoltageTransformation (std::size_t scanNum) const
	get voltage for a given scan number
pappso::Trace	getTraceFromTofIndexIntensityMap (TimsDataFastMap &accumulated_scans) const
	transform accumulation of raw scans into a real mass spectrum
virtual const MzCalibrationInterfaceSPtr &	getMzCalibrationInterfaceSPtr () const final
	get the MzCalibration model to compute mz and TOF for this frame
void	setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration)
virtual Trace	getIonMobilityTraceByTofIndexRange (std::size_t tof_index_begin, std::size_t tof_index_end, Enums::XicExtractMethod method, std::size_t scan_index_begin, std::size_t scan_index_end) const
	get a mobility trace cumulating intensities inside the given mass index range

Protected Member Functions
virtual void	cumulateScan (std::size_t scanNum, TimsDataFastMap &accumulate_into) const override
	cumulate a scan into a map
virtual void	cumulateScan2 (std::size_t scanNum, TimsDataFastMap &accumulate_into, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const override
virtual pappso::TraceSPtr	getRawTraceSPtr (std::size_t scanNum) const override
	get the raw index tof_index and intensities (normalized)
virtual std::vector< TofIndexIntensityPair >	getRawValuePairList (std::size_t scanNum, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const override
	get the raw index tof_index and intensities (normalized)
Protected Member Functions inherited from pappso::TimsFrame
	TimsFrame (std::size_t timsId, quint32 scanNum)
	constructor for binary independant tims frame
void	extractTimsXicListInRtRange (std::vector< XicCoordTims * >::iterator &itXicListbegin, std::vector< XicCoordTims * >::iterator &itXicListend, Enums::XicExtractMethod method) const
Protected Member Functions inherited from pappso::TimsFrameBase
virtual std::vector< TofIndexIntensityPair > &	downgradeResolutionOfTofIndexIntensityPairList (std::size_t tof_index_merge_window, std::vector< TofIndexIntensityPair > &spectrum) const
	Downgrade the TOF index resolution to lower the number of real m/z computations.

Private Member Functions
void	copyAndLzfDecompress (const char *src, std::size_t len)
	copy buffer header and lzf decompress each scan for tims compression type 1
unsigned int	lzfDecompressScan (const char *src, unsigned int src_len, char *dest, unsigned int dest_len)
	decompress a single LZF compressed scan buffer

Private Attributes
std::vector< std::size_t >	m_scanOffsetList
std::vector< std::size_t >	m_scanSizeList

Additional Inherited Members
Protected Attributes inherited from pappso::TimsFrame
QByteArray	m_binaryData
Protected Attributes inherited from pappso::TimsFrameBase
quint32	m_scanCount
	total number of scans contained in this frame
std::size_t	m_frameId
	Tims frame database id (the SQL identifier of this frame)
double	m_acqDurationInMilliseconds = 0
	acquisition duration in milliseconds
quint8	m_msMsType = 0
double	m_rtInSeconds = 0
	retention time
double	m_timsDvStart = 0
double	m_timsSlope
double	m_timsTtrans = 0
double	m_timsNdelay = 0
double	m_timsVmin = 0
double	m_timsVmax = 0
double	m_timsC6 = 0
double	m_timsC7 = 0
MzCalibrationInterfaceSPtr	msp_mzCalibration = nullptr

Detailed Description

Todo

write docs

Definition at line 38 of file timsframetype1.h.

Constructor & Destructor Documentation

TimsFrameType1() [1/2]

pappso::TimsFrameType1::TimsFrameType1	(	std::size_t	timsId,
		quint32	scanNum,
		char *	p_bytes,
		std::size_t	len )

Parameters

timsId	tims frame id
scanNum	total number of scans in this frame
p_bytes	pointer on the decompressed binary buffer
len	size of the decompressed binary buffer

Definition at line 41 of file timsframetype1.cpp.

  : TimsFrame(timsId, scanNum)
{
  qDebug() << timsId;
  m_binaryData.resize(len * 2);
 
  if(p_bytes != nullptr)
    {
      qDebug() << timsId;
      copyAndLzfDecompress(p_bytes, len);
      qDebug() << timsId;
    }
  else
    {
      if(m_scanCount == 0)
        {
 
          throw pappso::PappsoException(
            QObject::tr(
              "TimsFrameType1::TimsFrameType1(%1,%2,nullptr,%3) FAILED")
              .arg(m_frameId)
              .arg(m_scanCount)
              .arg(len));
        }
    }
}

References pappso::TimsFrame::TimsFrame(), copyAndLzfDecompress(), pappso::TimsFrame::m_binaryData, pappso::TimsFrameBase::m_frameId, and pappso::TimsFrameBase::m_scanCount.

Referenced by TimsFrameType1().

TimsFrameType1() [2/2]

pappso::TimsFrameType1::TimsFrameType1

(

const TimsFrameType1 &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 71 of file timsframetype1.cpp.

                                                          : TimsFrame(other)
{
}

References pappso::TimsFrame::TimsFrame(), and TimsFrameType1().

~TimsFrameType1()

pappso::TimsFrameType1::~TimsFrameType1 ( )

virtual

Destructor

Definition at line 75 of file timsframetype1.cpp.

{
}

Member Function Documentation

copyAndLzfDecompress()

void pappso::TimsFrameType1::copyAndLzfDecompress ( const char * src, std::size_t len )

private

copy buffer header and lzf decompress each scan for tims compression type 1

Parameters

src	raw data buffer containing scan offsets and LZF compressed scans
len	length of the data buffer

Definition at line 81 of file timsframetype1.cpp.

{
 
  qDebug() << " m_scanNumber=" << m_scanCount << " len=" << len;
  // the start position offset for each scan and the length of the last scan
  // copy first m_scanNumber*4 bytes in qbyte array
  std::size_t count = (m_scanCount + 2) * 4;
 
  qDebug() << " count=" << count;
  if(m_binaryData.size() < (long)(count + count))
    {
      qDebug() << " m_timsDataFrame.size()=" << m_binaryData.size();
      m_binaryData.resize(count + count);
    }
 
  /*
    std::size_t decompressed_size =
      lzfDecompressScan(src + 3687 - 8,
                        9,
                        m_timsDataFrame.data() + 3660,
                        m_timsDataFrame.size() - 3660);
 
    qDebug() << "decompressed_size=" << decompressed_size;
    */
  // memcpy(m_timsDataFrame.data(), src, count);
 
  qDebug() << "offset begin at last :" << count + 4;
 
  // std::vector<std::size_t> compressed_len_list;
  std::size_t offset;
  std::size_t previous_offset = (*(quint32 *)(src));
  qDebug() << "first offset= " << previous_offset;
  std::size_t cumul_decompressed_size = 0;
 
 
  for(quint32 i = 1; i <= m_scanCount; i++)
    {
      offset = (*(quint32 *)(src + (i * 4)));
 
      std::size_t compressed_size = offset - previous_offset;
 
      qDebug() << "scan i=" << i << " previous_offset=" << previous_offset
               << " offset=" << offset << " length=" << compressed_size;
      // compressed_len_list.push_back(offset - previous_offset);
      std::size_t remaining_size = m_binaryData.size();
 
      if(cumul_decompressed_size < remaining_size)
        {
          remaining_size = remaining_size - cumul_decompressed_size;
        }
      else
        {
          remaining_size = 0;
        }
      qDebug() << " remaining_size=" << remaining_size;
      std::size_t decompressed_size =
        lzfDecompressScan(src + previous_offset - 8,
                          compressed_size,
                          m_binaryData.data() + cumul_decompressed_size,
                          remaining_size);
 
 
      m_scanOffsetList.push_back(cumul_decompressed_size);
      m_scanSizeList.push_back(decompressed_size / 4);
      cumul_decompressed_size += decompressed_size;
      qDebug() << " decompressed_size=" << decompressed_size;
 
 
      previous_offset = offset;
    }
  /*
    std::size_t last_offset = (*(quint32 *)(src + (m_scanNumber * 4)));
    qDebug() << "last scan length :" << last_offset;
 
    qDebug() << "last scan length bonus:"
             << (*(quint32 *)(src + (m_scanNumber + 1 * 4)));
 
    qDebug() << " m_scanOffsetList.size()=" << m_scanOffsetList.size()
             << " m_scanNumber=" << m_scanNumber;
             */
  /*
    throw PappsoException(
      QObject::tr("ERROR reading TimsFrameType1 ").arg(m_timsId));
      */
}

References lzfDecompressScan(), pappso::TimsFrame::m_binaryData, pappso::TimsFrameBase::m_scanCount, m_scanOffsetList, and m_scanSizeList.

Referenced by TimsFrameType1().

cumulateScan()

void pappso::TimsFrameType1::cumulateScan ( std::size_t scanNum, TimsDataFastMap & accumulate_into ) const

overrideprotectedvirtual

cumulate a scan into a map

Parameters

scanNum

scan number 0 to (m_scanNumber-1)

Reimplemented from pappso::TimsFrame.

Definition at line 219 of file timsframetype1.cpp.

{
  if(m_binaryData.size() == 0)
    return;
  // checkScanNum(scanNum);
 
 
  std::size_t size = m_scanSizeList[scanNum];
 
  std::size_t offset = m_scanOffsetList[scanNum];
 
  // qDebug() << "begin offset=" << offset << " size=" << size;
  qint32 value     = 0;
  qint32 tof_index = 0;
  for(std::size_t i = 0; i < size; i++)
    {
      value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
      // qDebug() << " i=" << i << " value=" << value;
 
      if(value < 0)
        {
          tof_index += -1 * value;
        }
      else
        {
 
          quint32 x = tof_index;
          quint32 y = value;
 
          accumulate_into.accumulateIntensity(x, y);
 
          tof_index++;
        }
    }
  qDebug() << "end";
}

References pappso::TimsDataFastMap::accumulateIntensity(), pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, pappso::x, and pappso::y.

cumulateScan2()

void pappso::TimsFrameType1::cumulateScan2 ( std::size_t scanNum, TimsDataFastMap & accumulate_into, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end ) const

overrideprotectedvirtual

Reimplemented from pappso::TimsFrame.

Definition at line 259 of file timsframetype1.cpp.

{
  if(m_binaryData.size() == 0)
    return;
  // checkScanNum(scanNum);
 
 
  std::size_t size = m_scanSizeList[scanNum];
 
  std::size_t offset = m_scanOffsetList[scanNum];
 
  // qDebug() << "begin offset=" << offset << " size=" << size;
  qint32 value     = 0;
  qint32 tof_index = 0;
  for(std::size_t i = 0; i < size; i++)
    {
      value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
      // qDebug() << " i=" << i << " value=" << value;
 
      if(value < 0)
        {
          tof_index += -1 * value;
        }
      else
        {
 
          quint32 x = tof_index;
          quint32 y = value;
 
 
          if(x < accepted_tof_index_range_begin)
            {
              tof_index++;
              continue;
            }
          if(x > accepted_tof_index_range_end)
            {
              break;
            }
          accumulate_into.accumulateIntensity(x, y);
 
          tof_index++;
        }
    }
  qDebug() << "end";
}

References pappso::TimsDataFastMap::accumulateIntensity(), pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, pappso::x, and pappso::y.

getMassSpectrumSPtr()

pappso::MassSpectrumSPtr pappso::TimsFrameType1::getMassSpectrumSPtr ( std::size_t scanNum ) const

overridevirtual

get the mass spectrum corresponding to a scan number

Parameters

scanNum

the scan number to retrieve

Reimplemented from pappso::TimsFrame.

Definition at line 430 of file timsframetype1.cpp.

{
 
  qDebug() << " scanNum=" << scanNum;
 
  checkScanNum(scanNum);
 
  try
    {
      qDebug();
 
      pappso::MassSpectrumSPtr mass_spectrum_sptr =
        std::make_shared<pappso::MassSpectrum>();
      // std::vector<DataPoint>
 
      if(m_binaryData.size() == 0)
        return mass_spectrum_sptr;
      qDebug();
 
      std::size_t size = m_scanSizeList[scanNum];
 
      std::size_t offset = m_scanOffsetList[scanNum];
 
      qDebug() << " offset=" << offset << " size=" << size;
      if(size == 0)
        return mass_spectrum_sptr;
 
 
      MzCalibrationInterface *mz_calibration_p =
        getMzCalibrationInterfaceSPtr().get();
 
 
      qint32 value     = 0;
      qint32 tof_index = 0;
      // std::vector<quint32> index_list;
      DataPoint data_point;
      for(std::size_t i = 0; i < size; i++)
        {
          value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
 
          if(value < 0)
            {
              tof_index += -1 * value;
            }
          else
            {
              data_point.y = value;
 
              // intensity normalization
              data_point.y *= 100.0 / m_acqDurationInMilliseconds;
 
 
              // mz calibration
              data_point.x = mz_calibration_p->getMzFromTofIndex(tof_index);
              mass_spectrum_sptr.get()->push_back(data_point);
              tof_index++;
            }
        }
 
 
      qDebug() << mass_spectrum_sptr.get()->toString();
      return mass_spectrum_sptr;
    }
  catch(PappsoException &error)
    {
      throw pappso::PappsoException(
        QObject::tr("Error TimsFrameType1::getMassSpectrumSPtr frameId=%1 "
                    "scanNum=%2 :\n%3")
          .arg(getId())
          .arg(scanNum)
          .arg(error.qwhat()));
    }
}

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::getId(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, pappso::PappsoException::qwhat(), pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by getScanPeakCount().

getRawTraceSPtr()

pappso::TraceSPtr pappso::TimsFrameType1::getRawTraceSPtr ( std::size_t scanNum ) const

overrideprotectedvirtual

get the raw index tof_index and intensities (normalized)

Parameters

scanNum

the scan number to extract

Returns

trace vector

Reimplemented from pappso::TimsFrame.

Definition at line 506 of file timsframetype1.cpp.

{
 
  // qDebug();
 
  pappso::TraceSPtr trace_sptr = std::make_shared<pappso::Trace>();
  // std::vector<DataPoint>
 
  if(m_binaryData.size() == 0)
    return trace_sptr;
  qDebug();
 
  std::size_t size = m_scanSizeList[scanNum];
 
  std::size_t offset = m_scanOffsetList[scanNum];
 
  qDebug() << " offset=" << offset << " size=" << size;
  if(size == 0)
    return trace_sptr;
 
  // qDebug();
  qint32 value     = 0;
  qint32 tof_index = 0;
 
  // std::vector<quint32> index_list;
  DataPoint data_point;
  for(std::size_t i = 0; i < size; i++)
    {
      value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
 
      if(value < 0)
        {
          tof_index += -1 * value;
        }
      else
        {
          data_point.y = value;
 
          // intensity normalization
          data_point.y *= 100.0 / m_acqDurationInMilliseconds;
 
 
          // mz calibration
          data_point.x = tof_index;
          trace_sptr.get()->push_back(data_point);
          tof_index++;
        }
    }
 
 
  // qDebug();
  return trace_sptr;
}

References pappso::TimsFrameBase::m_acqDurationInMilliseconds, pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, pappso::DataPoint::x, and pappso::DataPoint::y.

getRawValuePairList()

std::vector< TimsFrameType1::TofIndexIntensityPair > pappso::TimsFrameType1::getRawValuePairList ( std::size_t scanNum, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end ) const

overrideprotectedvirtual

get the raw index tof_index and intensities (normalized)

Parameters

scanNum	the scan number to extract
accepted_tof_index_range_begin	mz index begin
accepted_tof_index_range_end	mz index end

Returns

vector of RawValuePair

Reimplemented from pappso::TimsFrame.

Definition at line 562 of file timsframetype1.cpp.

{
 
  // qDebug();
 
  std::vector<TimsFrame::TofIndexIntensityPair> trace_sptr;
  // std::vector<DataPoint>
 
  if(m_binaryData.size() == 0)
    return trace_sptr;
  qDebug();
 
  std::size_t size = m_scanSizeList[scanNum];
 
  std::size_t offset = m_scanOffsetList[scanNum];
 
  qDebug() << " offset=" << offset << " size=" << size;
  if(size == 0)
    return trace_sptr;
 
  // qDebug();
  qint32 value     = 0;
  qint32 tof_index = 0;
 
  // std::vector<quint32> index_list;
  TimsFrame::TofIndexIntensityPair data_point;
  for(std::size_t i = 0; i < size; i++)
    {
      value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
 
      if(value < 0)
        {
          tof_index += -1 * value;
        }
      else
        {
          data_point.intensity_index = value;
 
          if(data_point.intensity_index < accepted_tof_index_range_begin)
            {
              tof_index++;
              continue;
            }
          if(data_point.intensity_index > accepted_tof_index_range_end)
            {
              break;
            }
          // intensity normalization
          data_point.intensity_index *= 100.0 / m_acqDurationInMilliseconds;
 
 
          // mz calibration
          data_point.tof_index = tof_index;
          trace_sptr.push_back(data_point);
          tof_index++;
        }
    }
 
 
  // qDebug();
  return trace_sptr;
}

References pappso::TimsFrameBase::TofIndexIntensityPair::intensity_index, pappso::TimsFrameBase::m_acqDurationInMilliseconds, pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, and pappso::TimsFrameBase::TofIndexIntensityPair::tof_index.

getScanIntensityList()

std::vector< quint32 > pappso::TimsFrameType1::getScanIntensityList ( std::size_t scanNum ) const

overridevirtual

get raw intensities without transformation from one scan it needs intensity normalization

Reimplemented from pappso::TimsFrame.

Definition at line 369 of file timsframetype1.cpp.

{
 
 
  qDebug() << " scanNum=" << scanNum;
 
  checkScanNum(scanNum);
 
  std::vector<quint32> int_values;
 
  try
    {
      qDebug();
 
 
      if(m_binaryData.size() == 0)
        return int_values;
      qDebug();
 
      std::size_t size = m_scanSizeList[scanNum];
 
      std::size_t offset = m_scanOffsetList[scanNum];
 
      qDebug() << " offset=" << offset << " size=" << size;
      if(size == 0)
        return int_values;
 
      qint32 value     = 0;
      qint32 tof_index = 0;
      // std::vector<quint32> index_list;
      for(std::size_t i = 0; i < size; i++)
        {
          value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
 
          if(value < 0)
            {
              tof_index += -1 * value;
            }
          else
            {
              int_values.push_back(value);
              tof_index++;
            }
        }
 
 
      qDebug();
      return int_values;
    }
  catch(PappsoException &error)
    {
      throw pappso::PappsoException(QObject::tr("Error %1 frameId=%2 "
                                                "scanNum=%3 :\n%4")
                                      .arg(__FUNCTION__)
                                      .arg(getId())
                                      .arg(scanNum)
                                      .arg(error.qwhat()));
    }
}

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::getId(), pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, and pappso::PappsoException::qwhat().

getScanPeakCount()

std::size_t pappso::TimsFrameType1::getScanPeakCount ( std::size_t scanIndex ) const

overridevirtual

get the number of peaks in this spectrum need the binary file

Parameters

scanIndex

scan index in the frame in the order it lies in frame's binary data, from 0 to N-1

Reimplemented from pappso::TimsFrame.

Definition at line 211 of file timsframetype1.cpp.

{
  pappso::MassSpectrumSPtr mass_spectrum_sptr = getMassSpectrumSPtr(scanNum);
  return mass_spectrum_sptr.get()->size();
}

References getMassSpectrumSPtr().

getScanTofIndexList()

std::vector< quint32 > pappso::TimsFrameType1::getScanTofIndexList ( std::size_t scanNum ) const

overridevirtual

get raw index list for one given scan index are not TOF nor m/z, just index on digitizer

Reimplemented from pappso::TimsFrame.

Definition at line 310 of file timsframetype1.cpp.

{
  qDebug();
  checkScanNum(scanNum);
 
  std::vector<quint32> mzindex_values;
 
  try
    {
      qDebug();
 
 
      if(m_binaryData.size() == 0)
        return mzindex_values;
      qDebug();
 
      std::size_t size = m_scanSizeList[scanNum];
 
      std::size_t offset = m_scanOffsetList[scanNum];
 
      qDebug() << " offset=" << offset << " size=" << size;
      if(size == 0)
        return mzindex_values;
 
      qint32 value     = 0;
      qint32 tof_index = 0;
      // std::vector<quint32> index_list;
      for(std::size_t i = 0; i < size; i++)
        {
          value = (*(qint32 *)(m_binaryData.constData() + offset + (i * 4)));
 
          if(value < 0)
            {
              tof_index += -1 * value;
            }
          else
            {
              mzindex_values.push_back(tof_index);
              tof_index++;
            }
        }
 
 
      qDebug();
      return mzindex_values;
    }
  catch(PappsoException &error)
    {
      throw pappso::PappsoException(QObject::tr("Error %1 frameId=%2 "
                                                "scanNum=%3 :\n%4")
                                      .arg(__FUNCTION__)
                                      .arg(getId())
                                      .arg(scanNum)
                                      .arg(error.qwhat()));
    }
  qDebug();
}

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::getId(), pappso::TimsFrame::m_binaryData, m_scanOffsetList, m_scanSizeList, and pappso::PappsoException::qwhat().

lzfDecompressScan()

unsigned int pappso::TimsFrameType1::lzfDecompressScan ( const char * src, unsigned int src_len, char * dest, unsigned int dest_len )

private

decompress a single LZF compressed scan buffer

Parameters

src	pointer on the LZF compressed buffer
src_len	length of the source buffer
dest	pointer to the destination buffer (in the qbyte array)
dest_len	length of the destination buffer (max possible in the qbytearray)

Returns

scan decompressed size

Definition at line 169 of file timsframetype1.cpp.

{
  qDebug() << "src=" << src << " src_len=" << src_len
           << " dest_len=" << dest_len;
  if(src_len == 0)
    return 0;
  unsigned int decompressed_size;
  unsigned int more_space = src_len * 2;
  decompressed_size       = lzf_decompress(src, src_len, dest, dest_len);
  while(decompressed_size == 0)
    {
      qDebug() << "dest_len=" << dest_len;
      qDebug() << "decompressed_size=" << decompressed_size;
 
      if(errno == EINVAL)
        {
          throw PappsoException(
            QObject::tr("ERROR reading TimsFrameType1 %1 TIMS binary file %2: "
                        "LZF decompression error EINVAL")
              .arg(m_frameId));
        }
      else if(errno == E2BIG)
        {
          qDebug() << " m_timsDataFrame.size()=" << m_binaryData.size()
                   << " more_space=" << more_space;
          m_binaryData.resize(m_binaryData.size() + more_space);
          dest_len += more_space;
          qDebug();
          decompressed_size = lzf_decompress(src, src_len, dest, dest_len);
        }
      else
        {
          break;
        }
    }
  return decompressed_size;
}

References pappso::TimsFrame::m_binaryData, and pappso::TimsFrameBase::m_frameId.

Referenced by copyAndLzfDecompress().

Member Data Documentation

m_scanOffsetList

std::vector<std::size_t> pappso::TimsFrameType1::m_scanOffsetList

private

Definition at line 146 of file timsframetype1.h.

Referenced by copyAndLzfDecompress(), cumulateScan(), cumulateScan2(), getMassSpectrumSPtr(), getRawTraceSPtr(), getRawValuePairList(), getScanIntensityList(), and getScanTofIndexList().

m_scanSizeList

std::vector<std::size_t> pappso::TimsFrameType1::m_scanSizeList

private

Definition at line 147 of file timsframetype1.h.

Referenced by copyAndLzfDecompress(), cumulateScan(), cumulateScan2(), getMassSpectrumSPtr(), getRawTraceSPtr(), getRawValuePairList(), getScanIntensityList(), and getScanTofIndexList().

---

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

• pappsomspp/core/vendors/tims/timsframetype1.h
• pappsomspp/core/vendors/tims/timsframetype1.cpp