#include <mzcborspectrumcollectionreader.h>

Inheritance diagram for pappso::cbor::mzcbor::MzcborSpectrumCollectionReader:

Public Member Functions
	MzcborSpectrumCollectionReader (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)
virtual	~MzcborSpectrumCollectionReader ()
void	setMsRunId (const MsRunIdCstSPtr &msrun_id)
void	setNativeId2SpectrumIndexMapPtr (const std::map< QString, std::size_t > *nativeId2SpectrumIndexMap)
Public Member Functions inherited from pappso::cbor::mzcbor::MzcborReaderBase
	MzcborReaderBase ()
virtual	~MzcborReaderBase ()
virtual void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
	read mzCBOR file
virtual void	readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
	read mzCBOR from any device (memory buffer or else)
virtual void	close ()
	convenient function to clean pointer before leaving
bool	isMzcbor () const
const QStringList &	getMsrunIdList () const
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
	CborStreamReaderInterface ()
virtual	~CborStreamReaderInterface ()

Protected Member Functions
virtual void	readMsrun () override
	read only the targeted msrun
void	readSpectrumListAndLeave ()
	only the spectrum list of targeted msrun, then stop parsing
void	readSpectrum (std::size_t index_count, bool want_binary_data)
	read each spectrum in the targeted msrun (msrunId)
std::map< QString, CvParam >	readScan ()
Protected Member Functions inherited from pappso::cbor::mzcbor::MzcborReaderBase
void	readRoot (pappso::UiMonitorInterface &monitor)
virtual void	readReferenceableParamGroupList ()
std::map< QString, CvParam >	getCvParamsMap ()
	read the array containing cvParams to give accessions and values
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool	getExpectedString ()
void	initCborReader (QFile *pcborfile)
void	initCborReader (QIODevice *pcborfile)

Private Attributes
const MsRunReadConfig &	m_msRunReadConfig
SpectrumCollectionHandlerInterface &	m_SpectrumCollectionHandlerInterface
MsRunIdCstSPtr	mcsp_msRunId
QString	m_xmlMzMlRunId
const std::map< QString, std::size_t > *	mp_nativeId2SpectrumIndexMap = nullptr

Additional Inherited Members
Protected Attributes inherited from pappso::cbor::mzcbor::MzcborReaderBase
bool	m_stopParsing = false
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader *	mpa_cborReader = nullptr
QString	m_expectedString
QByteArray	m_data

Detailed Description

Todo: write docs

Definition at line 45 of file mzcborspectrumcollectionreader.h.

Constructor & Destructor Documentation

◆ MzcborSpectrumCollectionReader()

pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::MzcborSpectrumCollectionReader	(	const MsRunReadConfig &	config,
		SpectrumCollectionHandlerInterface &	handler )

Default constructor

Definition at line 37 of file mzcborspectrumcollectionreader.cpp.

  : m_msRunReadConfig(m_msRunReadConfig),
    m_SpectrumCollectionHandlerInterface(m_SpectrumCollectionHandlerInterface)
{
}

References m_msRunReadConfig, and m_SpectrumCollectionHandlerInterface.

◆ ~MzcborSpectrumCollectionReader()

pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::~MzcborSpectrumCollectionReader ( )

virtual

Destructor

Definition at line 45 of file mzcborspectrumcollectionreader.cpp.

46{

47}

Member Function Documentation

◆ readMsrun()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readMsrun ( )

overrideprotectedvirtual

read only the targeted msrun

Reimplemented from pappso::cbor::mzcbor::MzcborReaderBase.

Definition at line 65 of file mzcborspectrumcollectionreader.cpp.

{
  // qDebug();
 
  mpa_cborReader->enterContainer();
  bool ms_run_to_read = false;
 
  while(getExpectedString())
    {
      if(m_expectedString == "id")
        {
          getExpectedString();
 
          if((m_expectedString == m_xmlMzMlRunId) || (m_xmlMzMlRunId.isEmpty()))
            {
              ms_run_to_read = true;
            }
        }
      else if(m_expectedString == "spectrumList")
        {
          if(ms_run_to_read)
            {
              readSpectrumListAndLeave();
            }
          else
            {
              mpa_cborReader->next();
            }
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
  mpa_cborReader->leaveContainer();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_xmlMzMlRunId, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readSpectrumListAndLeave().

◆ readScan()

std::map< QString, pappso::cbor::mzcbor::CvParam > pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readScan ( )

protected

Definition at line 416 of file mzcborspectrumcollectionreader.cpp.

{
  std::map<QString, CvParam> cv_params;
  mpa_cborReader->enterContainer();
  while(getExpectedString())
    {
      qDebug() << m_expectedString;
      if(m_expectedString == "cvParam")
        {
          cv_params = getCvParamsMap();
        }
      else
        {
          mpa_cborReader->next();
        }
    }
  mpa_cborReader->leaveContainer();
  return cv_params;
}

References pappso::cbor::mzcbor::MzcborReaderBase::getCvParamsMap(), pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

◆ readSpectrum()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum	(	std::size_t	index_count,
		bool	want_binary_data )

protected

read each spectrum in the targeted msrun (msrunId)

Definition at line 182 of file mzcborspectrumcollectionreader.cpp.

{
 
  qDebug() << index_count << " " << want_binary_data;
  try
    {
      Spectrum cbor_spectrum;
      cbor_spectrum.fromCbor(*mpa_cborReader, want_binary_data);
      //<spectrum id="controllerType=0 controllerNumber=1 scan=1" index="0"
      // defaultArrayLength="1552">
 
 
      // Now, with or without the peak list, we have to craft a qualified mass
      // spectrum that will hold all the metadata about the data potentially
      // found in it.
      QualifiedMassSpectrum qualified_mass_spectrum;
 
      MassSpectrumId spectrum_id(mcsp_msRunId, cbor_spectrum.index);
      spectrum_id.setNativeId(cbor_spectrum.id);
 
      spectrum_id.setSpectrumIndex(cbor_spectrum.index);
 
      qualified_mass_spectrum.setMassSpectrumId(spectrum_id);
      qualified_mass_spectrum.setRtInSeconds(cbor_spectrum.getRtInSeconds());
 
 
      if(cbor_spectrum.precursorList.size() > 0)
        {
          qualified_mass_spectrum.setPrecursorNativeId(
            cbor_spectrum.precursorList.at(0).spectrumRef);
          if(mp_nativeId2SpectrumIndexMap != nullptr)
            {
              auto it =
                mp_nativeId2SpectrumIndexMap->find(cbor_spectrum.precursorList.at(0).spectrumRef);
              if(it != mp_nativeId2SpectrumIndexMap->end())
                {
                  qualified_mass_spectrum.setPrecursorSpectrumIndex(it->second);
                }
            }
 
          for(auto &precursor : cbor_spectrum.precursorList)
            {
              // *****************************************************
              // get isolation window (very simplified)
              // *****************************************************
 
              try
                {
                  // qWarning() << "pappso::MzcborMsRunReader::qualifiedMassSpectrum";
                  qualified_mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::IsolationWindowTargetMz,
                    precursor.isolationWindow.getTargetMz());
 
 
                  auto it = precursor.isolationWindow.cvParamMap.find("MS:1000828");
 
                  if(it == precursor.isolationWindow.cvParamMap.end())
                    {
                      throw pappso::ExceptionNotFound(QObject::tr(
                        "isolation window lower offset MS:1000828 not found in cvParam map"));
                    }
                  qualified_mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::IsolationWindowLowerOffset,
                    it->second.valueDouble);
 
 
                  it = precursor.isolationWindow.cvParamMap.find("MS:1000829");
 
                  if(it == precursor.isolationWindow.cvParamMap.end())
                    {
                      throw pappso::ExceptionNotFound(QObject::tr(
                        "isolation window upper offset MS:1000829 not found in cvParam map"));
                    }
 
                  qualified_mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::IsolationWindowUpperOffset,
                    it->second.valueDouble);
                }
              catch(const pappso::ExceptionNotFound &not_found)
                {
                  // isolation window not available
                  // throw not_found;
                }
              // *****************************************************
              // end get isolation window (very simplified)
              // *****************************************************
 
              PrecursorIonData ion_data;
              ion_data.mz = precursor.isolationWindow.getTargetMz();
              for(auto &selected_ion : precursor.selectedIonList)
                {
                  ion_data.charge = selected_ion.getChargeState();
 
                  bool is_ok;
                  ion_data.intensity = selected_ion.getIntensity(&is_ok);
                  ion_data.mz        = selected_ion.getMz();
 
                  qualified_mass_spectrum.appendPrecursorIonData(ion_data);
                }
            }
        }
 
      qDebug();
      qualified_mass_spectrum.setMsLevel(cbor_spectrum.getMsLevel());
 
      qDebug();
      qualified_mass_spectrum.setEmptyMassSpectrum(!cbor_spectrum.defaultArrayLength);
 
      if(cbor_spectrum.binaryDataArrayList.size() == 2)
        {
          qDebug();
          MassSpectrumSPtr mass_spectrum_sp = std::make_shared<MassSpectrum>();
          qDebug();
          cbor_spectrum.decodeTrace(*(mass_spectrum_sp.get()));
          qDebug();
          qualified_mass_spectrum.setMassSpectrumSPtr(mass_spectrum_sp);
          qDebug();
        }
 
      qDebug() << "spectrum_id.getNativeId()=" << spectrum_id.getNativeId();
      qDebug() << "rt=" << qualified_mass_spectrum.getRtInSeconds();
      qDebug() << "mslevel=" << qualified_mass_spectrum.getMsLevel();
 
      if(m_msRunReadConfig.acceptMsLevel(qualified_mass_spectrum.getMsLevel()))
        {
          if(m_msRunReadConfig.acceptRetentionTimeInSeconds(
               qualified_mass_spectrum.getRtInSeconds()))
            {
 
              if(qualified_mass_spectrum.getMassSpectrumId().getSpectrumIndex() ==
                 std::numeric_limits<std::size_t>::max())
                {
                  throw pappso::PappsoException(
                    QObject::tr("ERROR in %1 spectrum index not initialised").arg(__FUNCTION__));
                }
              m_SpectrumCollectionHandlerInterface.setQualifiedMassSpectrum(
                qualified_mass_spectrum);
            }
        }
 
      /*
       *
            <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" />
            <cvParam cvRef="MS" accession="MS:1000130" value="" name="positive scan" />
            <cvParam cvRef="MS" accession="MS:1000285" value="17377980" name="total ion current" />
            <cvParam cvRef="MS" accession="MS:1000127" value="" name="centroid spectrum" />
            <cvParam cvRef="MS" accession="MS:1000504" value="519.138854980469" name="base peak m/z"
       unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
       <cvParam cvRef="MS"
       accession="MS:1000505" value="1702482.375" name="base peak intensity"
       unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS" /> <cvParam
       cvRef="MS" accession="MS:1000528" value="400.153411865234" name="lowest observed m/z"
       unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" /> <cvParam cvRef="MS"
       accession="MS:1000527" value="1013.12335205078" name="highest observed m/z"
       unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" /> <scanList count="1"> <cvParam
       cvRef="MS" accession="MS:1000795" value="" name="no combination" /> <scan
       instrumentConfigurationRef="IC1"> <cvParam cvRef="MS" accession="MS:1000016"
       value="0.0048758833" name="scan start time" unitAccession="UO:0000031" unitName="minute"
       unitCvRef="UO" /> <cvParam cvRef="MS" accession="MS:1000512" value="FTMS + p NSI Full lock ms
       [400.00-1400.00]" name="filter string" /> <cvParam cvRef="MS" accession="MS:1000927"
       value="250" name="ion injection time" unitAccession="UO:0000028" unitName="millisecond"
       unitCvRef="UO" /> <scanWindowList count="1"> <scanWindow> <cvParam cvRef="MS"
       accession="MS:1000501" value="400" name="scan window lower limit" unitAccession="MS:1000040"
       unitName="m/z" unitCvRef="MS" /> <cvParam cvRef="MS" accession="MS:1000500" value="1400"
       name="scan window upper limit" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
                  </scanWindow>
                </scanWindowList>
              </scan>
            </scanList>
            <binaryDataArrayList count="2">
            */
 
      // qDebug();
      // Get the native pwiz-spectrum from the spectrum list.
      // Note that this pointer is a shared pointer from pwiz.
      /*
        pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp =
          getPwizSpectrumPtr(spectrum_list_p.get(), iter, want_binary_data);
        // qDebug();
 
        // Instantiate the mass spectrum id that will hold critical information
        // like the the native id string and the spectrum index.
 
        MassSpectrumId massSpectrumId(mcsp_msRunId, iter);
 
        // qDebug();
        // Get the spectrum native id as a QString to store it in the mass
        // spectrum id class. This is will allow later to refer to the same
        // spectrum starting back from the file.
 
        QString native_id = QString::fromStdString(native_pwiz_spectrum_sp->id);
        massSpectrumId.setNativeId(native_id);
 
        // Finally, instantiate the qualified mass spectrum with its id. This
        // function will continue performing pappso-spectrum detailed
        // qualification.
 
        bool ok = false;
 
        QualifiedMassSpectrum qualified_mass_spectrum = qualifiedMassSpectrumFromPwizSpectrumPtr(
          massSpectrumId, native_pwiz_spectrum_sp.get(), want_binary_data, ok);
 
        if(!ok)
          {
            // qDebug() << "Encountered a mass spectrum for which the returned "
            //"status is bad.";
            continue;
          }
 
        // qDebug();
        // Before handing the mass spectrum out to the m_SpectrumCollectionHandlerInterface, see if
        // the native mass spectrum was empty or not.
 
        // if(!native_pwiz_spectrum_sp->defaultArrayLength)
        // qDebug() << "The mass spectrum has not defaultArrayLength";
 
        qualified_mass_spectrum.setEmptyMassSpectrum(!native_pwiz_spectrum_sp->defaultArrayLength);
 
        // The m_SpectrumCollectionHandlerInterface will receive the index of the mass spectrum in
        the
        // current run via the mass spectrum id member datum.
 
        // qDebug();
      */
    }
  catch(pappso::PappsoException &error)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR reading spectrum index %1 :\%2").arg(index_count).arg(error.qwhat()));
    }
}

Referenced by readSpectrumListAndLeave().

◆ readSpectrumListAndLeave()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrumListAndLeave ( )

protected

only the spectrum list of targeted msrun, then stop parsing

Definition at line 104 of file mzcborspectrumcollectionreader.cpp.

{
  mpa_cborReader->enterContainer();
  // We want to iterate in the pwiz-spectrum-list and for each pwiz-spectrum
  // create a pappso-spectrum (QualifiedMassSpectrum). Once the pappso mass
  // spectrum has been fully qualified (that is, the member data have been
  // set), it is transferred to the m_SpectrumCollectionHandlerInterface passed as parameter to this
  // function for the consumer to do what it wants with it.
 
  // Does the m_SpectrumCollectionHandlerInterface consuming the mass spectra read from file want
  // these mass spectra to hold the binary data arrays (mz/i vectors)?
 
  const bool want_binary_data = m_msRunReadConfig.needPeakList();
 
 
  // qDebug();
 
  // We'll need it to perform the looping in the spectrum list.
  std::size_t spectrum_list_size = 0;
 
  // qDebug() << "The spectrum list has size:" << spectrum_list_size;
 
  while(getExpectedString())
    {
 
      qDebug() << m_expectedString;
      if(m_expectedString == "count")
        {
          if(mpa_cborReader->isUnsignedInteger())
            {
              spectrum_list_size = mpa_cborReader->toUnsignedInteger();
              mpa_cborReader->next();
              qDebug() << "spectrum count=" << spectrum_list_size;
            }
 
          // Inform the m_SpectrumCollectionHandlerInterface of the spectrum list so that it can
          // handle feedback to the user.
          m_SpectrumCollectionHandlerInterface.spectrumListHasSize(spectrum_list_size);
        }
      else if(m_expectedString == "spectrum")
        {
 
          mpa_cborReader->enterContainer(); // start array
 
          std::size_t index_count = 0;
          while(mpa_cborReader->hasNext())
            {
              // If the user of this reader instance wants to stop reading the
              // spectra, then break this loop.
              if(m_SpectrumCollectionHandlerInterface.shouldStop())
                {
                  qDebug() << "The operation was cancelled. Breaking the loop.";
                  m_stopParsing = true;
                  return;
                }
 
              readSpectrum(index_count, want_binary_data);
              index_count++;
            }
 
          mpa_cborReader->leaveContainer(); // stop array
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
 
  qDebug() << "Loading ended";
  m_SpectrumCollectionHandlerInterface.loadingEnded();
 
  mpa_cborReader->leaveContainer();
  m_stopParsing = true;
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_msRunReadConfig, m_SpectrumCollectionHandlerInterface, pappso::cbor::mzcbor::MzcborReaderBase::m_stopParsing, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readSpectrum().

Referenced by readMsrun().

◆ setMsRunId()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::setMsRunId ( const MsRunIdCstSPtr & msrun_id )

Definition at line 50 of file mzcborspectrumcollectionreader.cpp.

{
  mcsp_msRunId   = msrun_id;
  m_xmlMzMlRunId = mcsp_msRunId.get()->getRunId();
}

References m_xmlMzMlRunId, and mcsp_msRunId.

Referenced by pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

◆ setNativeId2SpectrumIndexMapPtr()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::setNativeId2SpectrumIndexMapPtr ( const std::map< QString, std::size_t > * nativeId2SpectrumIndexMap )

Definition at line 57 of file mzcborspectrumcollectionreader.cpp.

{
  mp_nativeId2SpectrumIndexMap = nativeId2SpectrumIndexMap;
}

References mp_nativeId2SpectrumIndexMap.

Referenced by pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

Member Data Documentation

◆ m_msRunReadConfig

const MsRunReadConfig& pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_msRunReadConfig

private

Definition at line 81 of file mzcborspectrumcollectionreader.h.

Referenced by MzcborSpectrumCollectionReader(), readSpectrum(), and readSpectrumListAndLeave().

◆ m_SpectrumCollectionHandlerInterface

SpectrumCollectionHandlerInterface& pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_SpectrumCollectionHandlerInterface

private

Definition at line 82 of file mzcborspectrumcollectionreader.h.

Referenced by MzcborSpectrumCollectionReader(), readSpectrum(), and readSpectrumListAndLeave().

◆ m_xmlMzMlRunId

QString pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_xmlMzMlRunId

private

Definition at line 84 of file mzcborspectrumcollectionreader.h.

Referenced by readMsrun(), and setMsRunId().

◆ mcsp_msRunId

MsRunIdCstSPtr pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::mcsp_msRunId

private

Definition at line 83 of file mzcborspectrumcollectionreader.h.

Referenced by readSpectrum(), and setMsRunId().

◆ mp_nativeId2SpectrumIndexMap

const std::map<QString, std::size_t>* pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::mp_nativeId2SpectrumIndexMap = nullptr

private

Definition at line 86 of file mzcborspectrumcollectionreader.h.

Referenced by readSpectrum(), and setNativeId2SpectrumIndexMapPtr().

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

pappsomspp/core/processing/cbor/mzcbor/mzcborspectrumcollectionreader.h
pappsomspp/core/processing/cbor/mzcbor/mzcborspectrumcollectionreader.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzcborSpectrumCollectionReader()

◆ ~MzcborSpectrumCollectionReader()

Member Function Documentation

◆ readMsrun()

◆ readScan()

◆ readSpectrum()

◆ readSpectrumListAndLeave()

◆ setMsRunId()

◆ setNativeId2SpectrumIndexMapPtr()

Member Data Documentation

◆ m_msRunReadConfig

◆ m_SpectrumCollectionHandlerInterface

◆ m_xmlMzMlRunId

◆ mcsp_msRunId

◆ mp_nativeId2SpectrumIndexMap