pappso::cbor::mzcbor::MzmlConvert Class Reference

#include <mzmlconvert.h>

Inheritance diagram for pappso::cbor::mzcbor::MzmlConvert:

Public Member Functions
	MzmlConvert (pappso::UiMonitorInterface *p_monitor, pappso::cbor::CborStreamWriter *p_output)
virtual	~MzmlConvert ()
void	writeMzcborIndex (pappso::cbor::CborStreamWriter *writer) const
const std::vector< QString > &	getRunIdList () const
const std::vector< std::vector< qint64 > > &	getRunAndSpectrumOffsetList () const
const std::vector< std::vector< QString > > &	getRunAndSpectrumIdList () const
Public Member Functions inherited from pappso::XmlStreamReaderInterface
	XmlStreamReaderInterface ()
virtual	~XmlStreamReaderInterface ()
virtual bool	readFile (const QString &fileName)
bool	read (QIODevice *device)
bool	read (const QString &xml_content)
QString	errorString () const

Protected Member Functions
virtual void	readStream () override
Protected Member Functions inherited from pappso::XmlStreamReaderInterface
void	cloneStartElement (QXmlStreamWriter &output) const
void	cloneElement (QXmlStreamWriter &output)
void	cloneNode (QXmlStreamWriter &output)

Private Member Functions
void	attributeListToCbor (const QXmlStreamAttributes &xml_attributes)
void	attributeValueToCbor (const QStringView &value_str)
void	insideElement (QString &last_element, bool &array_started)
void	getCurrentSpectrumSize ()
void	readBinaryDataArrayList ()
QString	readBinaryDataArray (QVector< double > &double_array)

Private Attributes
pappso::UiMonitorInterface *	mp_monitor
pappso::cbor::CborStreamWriter *	mp_cborWriter
std::vector< QString >	m_elementStash
QStringList	m_elementToStoreInArray
std::size_t	m_currentSpectrumSize = 0
QVector< double >	m_doubleArray
std::vector< QString >	m_runIdList
std::vector< std::vector< qint64 > >	m_runAndSpectrumOffsetList
std::vector< std::vector< QString > >	m_runAndSpectrumIdList
std::vector< std::vector< qint64 > >	m_runAndSpectrumTotalIonCountList
std::vector< std::vector< std::uint8_t > >	m_runAndSpectrumMsLevelList
std::vector< std::vector< double > >	m_runAndSpectrumRtList
QString	m_uuid

Additional Inherited Members
Protected Attributes inherited from pappso::XmlStreamReaderInterface
QXmlStreamReader	m_qxmlStreamReader

Detailed Description

Todo

write docs

Definition at line 47 of file mzmlconvert.h.

Constructor & Destructor Documentation

MzmlConvert()

pappso::cbor::mzcbor::MzmlConvert::MzmlConvert	(	pappso::UiMonitorInterface *	p_monitor,
		pappso::cbor::CborStreamWriter *	p_output )

Default constructor

Definition at line 39 of file mzmlconvert.cpp.

  : mp_monitor(p_monitor), mp_cborWriter(p_output)
{
  m_elementToStoreInArray.clear();
  m_elementToStoreInArray << "cv" << "userParam" << "cvParam" << "binaryDataArray" << "spectrum"
                          << "sourceFile"
                          << "referenceableParamGroup" << "software" << "instrumentConfiguration"
                          << "processingMethod" << "dataProcessing" << "scan" << "scanWindow"
                          << "precursor" << "selectedIon";
 
 
  m_elementStash.clear();
  m_currentSpectrumSize = 0;
  m_doubleArray.clear();
  m_runIdList.clear();
  m_runAndSpectrumOffsetList.clear();
  m_runAndSpectrumIdList.clear();
}

References m_currentSpectrumSize, m_doubleArray, m_elementStash, m_elementToStoreInArray, m_runAndSpectrumIdList, m_runAndSpectrumOffsetList, m_runIdList, mp_cborWriter, and mp_monitor.

~MzmlConvert()

pappso::cbor::mzcbor::MzmlConvert::~MzmlConvert ( )

virtual

Destructor

Definition at line 59 of file mzmlconvert.cpp.

{
}

Member Function Documentation

attributeListToCbor()

void pappso::cbor::mzcbor::MzmlConvert::attributeListToCbor ( const QXmlStreamAttributes & xml_attributes )

private

Definition at line 460 of file mzmlconvert.cpp.

{
  for(auto &xml_attribute : xml_attributes)
    {
      qDebug() << xml_attribute.name() << " " << xml_attribute.value();
      mp_cborWriter->append(xml_attribute.name());
      attributeValueToCbor(xml_attribute.value());
 
      if((m_elementStash.size() > 0) && (m_elementStash.back() == "run") &&
         (xml_attribute.name() == "id"))
        {
          m_runAndSpectrumOffsetList.push_back(std::vector<qint64>());
          m_runAndSpectrumIdList.push_back(std::vector<QString>());
          m_runAndSpectrumMsLevelList.push_back(std::vector<std::uint8_t>());
          m_runAndSpectrumRtList.push_back(std::vector<double>());
          m_runAndSpectrumTotalIonCountList.push_back(std::vector<qint64>());
          m_runIdList.push_back(xml_attribute.value().toString());
        }
    }
}

References attributeValueToCbor(), m_elementStash, m_runAndSpectrumIdList, m_runAndSpectrumMsLevelList, m_runAndSpectrumOffsetList, m_runAndSpectrumRtList, m_runAndSpectrumTotalIonCountList, m_runIdList, and mp_cborWriter.

Referenced by insideElement(), and readStream().

attributeValueToCbor()

void pappso::cbor::mzcbor::MzmlConvert::attributeValueToCbor ( const QStringView & value_str )

private

Definition at line 433 of file mzmlconvert.cpp.

{
  bool ok(false);
  double d = value_str.toDouble(&ok);
  if(ok)
    {
      if(value_str.contains('.'))
        {
          mp_cborWriter->append(d);
        }
      else
        {
          qint64 bigint = value_str.toLongLong(&ok);
          if(ok)
            {
              mp_cborWriter->append(bigint);
            }
        }
    }
  else
    {
      mp_cborWriter->append(value_str);
    }
}

References mp_cborWriter.

Referenced by attributeListToCbor().

getCurrentSpectrumSize()

void pappso::cbor::mzcbor::MzmlConvert::getCurrentSpectrumSize ( )

private

Definition at line 224 of file mzmlconvert.cpp.

{
  // defaultArrayLength 1552
 
  m_currentSpectrumSize = m_qxmlStreamReader.attributes().value("defaultArrayLength").toULongLong();
}

References m_currentSpectrumSize, and pappso::XmlStreamReaderInterface::m_qxmlStreamReader.

Referenced by insideElement().

getRunAndSpectrumIdList()

const std::vector< std::vector< QString > > & pappso::cbor::mzcbor::MzmlConvert::getRunAndSpectrumIdList

(

)

const

Definition at line 495 of file mzmlconvert.cpp.

{
  return m_runAndSpectrumIdList;
}

References m_runAndSpectrumIdList.

getRunAndSpectrumOffsetList()

const std::vector< std::vector< qint64 > > & pappso::cbor::mzcbor::MzmlConvert::getRunAndSpectrumOffsetList

(

)

const

Definition at line 489 of file mzmlconvert.cpp.

{
  return m_runAndSpectrumOffsetList;
}

References m_runAndSpectrumOffsetList.

getRunIdList()

const std::vector< QString > & pappso::cbor::mzcbor::MzmlConvert::getRunIdList

(

)

const

Definition at line 482 of file mzmlconvert.cpp.

{
 
  return m_runIdList;
}

References m_runIdList.

insideElement()

void pappso::cbor::mzcbor::MzmlConvert::insideElement ( QString & last_element, bool & array_started )

private

Definition at line 265 of file mzmlconvert.cpp.

{
  m_elementStash.push_back(m_qxmlStreamReader.name().toString());
 
 
  qDebug() << m_qxmlStreamReader.name();
 
  if(m_elementStash.back() == "spectrum")
    {
      // qDebug() << m_qxmlStreamReader.attributes().value("id").toString();
      m_runAndSpectrumIdList.back().push_back(
        m_qxmlStreamReader.attributes().value("id").toString());
      getCurrentSpectrumSize();
      // qFatal();
    }
 
 
  // stop an array ?
  qDebug() << "current element=" << m_elementStash.back();
  qDebug() << "last_element=" << last_element_in;
  if(array_started_in && (last_element_in != m_qxmlStreamReader.name().toString()))
    {
      mp_cborWriter->endArray();
      qDebug() << "mp_cborWriter->endArray()";
      array_started_in = false;
    }
  if(m_elementStash.back() == "binaryDataArrayList")
    {
      qDebug() << "readBinaryDataArrayList()";
      readBinaryDataArrayList();
    }
 
  else
    {
 
 
      // start an array ?
      if(m_elementToStoreInArray.contains(m_elementStash.back()))
        {
          // start an array ?
          if((!array_started_in) && (last_element_in != m_elementStash.back()))
            {
              mp_cborWriter->append(m_elementStash.back());
              mp_cborWriter->startArray();
 
              qDebug() << "mp_cborWriter->startArray()";
              array_started_in = true;
            }
        }
 
      if(m_elementStash.back() == "spectrum")
        {
          if(mp_cborWriter->device() != nullptr)
            m_runAndSpectrumOffsetList.back().push_back(mp_cborWriter->device()->pos());
        }
 
 
      if(!array_started_in)
        mp_cborWriter->append(m_elementStash.back());
 
      bool array_started = false;
 
 
      if(m_elementStash.back() == "cvParam")
        {
 
          // *********** special treatment for cvParam **********
          if(!array_started_in)
            {
              throw pappso::PappsoException(
                QObject::tr("unable to write cvParam outside CBOR array"));
            }
          // array_started = true;
          qDebug() << m_qxmlStreamReader.name() << " "
                   << m_elementStash.at(m_elementStash.size() - 2);
          CvParam cv_param;
          cv_param.fromMzml(m_qxmlStreamReader);
          cv_param.toCbor(*mp_cborWriter);
          qDebug() << cv_param.name;
 
          if(m_elementStash.at(m_elementStash.size() - 2) == "spectrum")
            {
              qDebug() << "cvparam in spectrum";
              if(cv_param.accession == "MS:1000511")
                {
                  m_runAndSpectrumMsLevelList.back().push_back(cv_param.getExpectedUint8());
                  qDebug() << m_runAndSpectrumMsLevelList.back().back();
                }
              else if(cv_param.accession == "MS:1000285")
                { // TIC
                  m_runAndSpectrumTotalIonCountList.back().push_back(cv_param.getExpectedDouble());
                }
            }
          else if(m_elementStash.at(m_elementStash.size() - 2) == "scan")
            {
              if(cv_param.accession == "MS:1000016")
                { // rt
                  double rt = cv_param.getExpectedDouble();
 
                  if(cv_param.unitAccession == "UO:0000031")
                    {
                      // // minutes
                      rt = rt * 60;
                    }
                  m_runAndSpectrumRtList.back().push_back(rt);
                }
            }
          qDebug();
          // *********** special treatment for cvParam **********
          //
          qDebug() << "finish cvParam " << cv_param.accession;
        }
      else
        {
 
          mp_cborWriter->startMap();
          attributeListToCbor(m_qxmlStreamReader.attributes());
 
          QString last_element;
 
          while(m_qxmlStreamReader.readNext() && !m_qxmlStreamReader.isEndElement())
            {
              qDebug() << m_qxmlStreamReader.name();
              if(m_qxmlStreamReader.isCharacters())
                {
                  // clean content:
                  QStringView content = m_qxmlStreamReader.text().trimmed();
                  if((m_qxmlStreamReader.text().toString() == "\n") ||
                     (m_qxmlStreamReader.text().toString() == "\n\t"))
                    {
                    }
                  else
                    {
                      // text node
                      if(!content.isEmpty())
                        {
                          qDebug() << "text isCharacters" << content.mid(0, 10);
                          mp_cborWriter->append("@text@");
                          mp_cborWriter->append(content);
                        }
                    }
                }
              else if(m_qxmlStreamReader.isStartElement())
                {
                  QString tmp_element = m_qxmlStreamReader.name().toString();
                  qDebug() << tmp_element;
                  insideElement(last_element, array_started);
                  last_element = tmp_element;
                }
            }
 
          if(array_started)
            {
              mp_cborWriter->endArray();
            }
 
          mp_cborWriter->endMap();
 
          qDebug() << m_qxmlStreamReader.name();
        }
    }
 
  qDebug() << m_elementStash.back();
  m_elementStash.pop_back();
}

References pappso::cbor::mzcbor::CvParam::accession, attributeListToCbor(), pappso::cbor::mzcbor::CvParam::fromMzml(), getCurrentSpectrumSize(), pappso::cbor::mzcbor::CvParam::getExpectedDouble(), pappso::cbor::mzcbor::CvParam::getExpectedUint8(), insideElement(), m_elementStash, m_elementToStoreInArray, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_runAndSpectrumIdList, m_runAndSpectrumMsLevelList, m_runAndSpectrumOffsetList, m_runAndSpectrumRtList, m_runAndSpectrumTotalIonCountList, mp_cborWriter, pappso::cbor::mzcbor::CvParam::name, readBinaryDataArrayList(), pappso::cbor::mzcbor::CvParam::toCbor(), and pappso::cbor::mzcbor::CvParam::unitAccession.

Referenced by insideElement(), and readStream().

readBinaryDataArray()

QString pappso::cbor::mzcbor::MzmlConvert::readBinaryDataArray ( QVector< double > & double_array )

private

readBinaryDataArrayList()

void pappso::cbor::mzcbor::MzmlConvert::readBinaryDataArrayList ( )

private

Definition at line 233 of file mzmlconvert.cpp.

{
 
  qDebug() << m_qxmlStreamReader.name();
  // m_qxmlStreamReader.skipCurrentElement();
  /*
   *
          <binaryDataArray encodedLength="9092">
            <cvParam cvRef="MS" accession="MS:1000515" value="" name="intensity array"
   unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS" /> <cvParam cvRef="MS"
   accession="MS:1000523" value="" name="64-bit float" /> <cvParam cvRef="MS" accession="MS:1000574"
   value="" name="zlib compression" /> <binary>*/
  std::size_t count = m_qxmlStreamReader.attributes().value("count").toULongLong();
 
  mp_cborWriter->append("binaryDataArray");
  mp_cborWriter->startArray(count);
  while(m_qxmlStreamReader.readNext() && !m_qxmlStreamReader.isEndElement())
    {
      if(m_qxmlStreamReader.isStartElement())
        {
          BinaryDataArray binary_data_array;
          binary_data_array.fromMzml(m_qxmlStreamReader);
          binary_data_array.toCbor(*mp_cborWriter);
          // writeZlibDataArray();
        }
    }
  mp_cborWriter->endArray();
  qDebug() << m_qxmlStreamReader.name();
}

References pappso::cbor::mzcbor::BinaryDataArray::fromMzml(), pappso::XmlStreamReaderInterface::m_qxmlStreamReader, mp_cborWriter, and pappso::cbor::mzcbor::BinaryDataArray::toCbor().

Referenced by insideElement().

readStream()

void pappso::cbor::mzcbor::MzmlConvert::readStream ( )

overrideprotectedvirtual

Implements pappso::XmlStreamReaderInterface.

Definition at line 169 of file mzmlconvert.cpp.

{
  mp_cborWriter->startMap();
  if(m_qxmlStreamReader.readNextStartElement())
    {
      qDebug() << m_qxmlStreamReader.name().toString();
      if(m_qxmlStreamReader.name().toString() == "indexedmzML")
        {
          m_qxmlStreamReader.readNextStartElement();
        }
      if(m_qxmlStreamReader.name().toString() == "mzML")
        {
          // write mzCBOR header
          mp_cborWriter->append("mzCBOR");
          mp_cborWriter->startMap();
 
          mp_cborWriter->append("mode");
          mp_cborWriter->append(0);
 
          mp_cborWriter->writeInformations(
            PAPPSOMSPP_NAME, PAPPSOMSPP_VERSION, "mzCBOR", "mzMLconvert");
 
          m_uuid = mp_cborWriter->getUuid();
          mp_cborWriter->endMap();
 
          mp_cborWriter->append(m_qxmlStreamReader.name().toString());
 
          mp_cborWriter->startMap();
          mp_cborWriter->append("xmlns");
          mp_cborWriter->append(m_qxmlStreamReader.namespaceUri());
          attributeListToCbor(m_qxmlStreamReader.attributes());
          mp_cborWriter->endMap();
 
 
          bool array_started = false;
          QString last_element;
          while(m_qxmlStreamReader.readNextStartElement())
            {
              qDebug();
              insideElement(last_element, array_started);
              last_element = m_qxmlStreamReader.name().toString();
              qDebug();
            }
        }
      else
        {
          m_qxmlStreamReader.raiseError(QObject::tr("Not an mzML input file"));
          m_qxmlStreamReader.skipCurrentElement();
        }
    }
  mp_cborWriter->endMap();
}

References attributeListToCbor(), insideElement(), pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_uuid, mp_cborWriter, PAPPSOMSPP_NAME, and PAPPSOMSPP_VERSION.

writeMzcborIndex()

void pappso::cbor::mzcbor::MzmlConvert::writeMzcborIndex

(

pappso::cbor::CborStreamWriter *

writer

)

const

Definition at line 65 of file mzmlconvert.cpp.

{
  writer->startMap();
 
  writer->writeInformations(PAPPSOMSPP_NAME, PAPPSOMSPP_VERSION, "mzCBORindex", "mzMLconvert");
 
  writer->append("from");
  writer->append(m_uuid);
 
  writer->append("runIdList");
  writer->writeArray(m_runIdList);
 
 
  std::vector<std::size_t> msrun_size;
 
 
  writer->append("runSpectrumIndexList");
  writer->startArray(m_runAndSpectrumOffsetList.size());
  for(auto &spectrum_offset_list : m_runAndSpectrumOffsetList)
    {
      msrun_size.push_back(spectrum_offset_list.size());
      writer->writeArray(spectrum_offset_list);
    }
  writer->endArray();
 
 
  writer->append("runSpectrumNativeIdList");
  writer->startArray(m_runAndSpectrumIdList.size());
  for(auto &spectrum_id_list : m_runAndSpectrumIdList)
    {
      writer->writeArray(spectrum_id_list);
    }
  writer->endArray();
 
  // TIC
  bool size_ok = true;
  for(std::size_t i = 0; i < msrun_size.size(); i++)
    {
      if(m_runAndSpectrumTotalIonCountList.at(i).size() != msrun_size.at(i))
        {
          size_ok = false;
        }
    }
  if(size_ok)
    {
      writer->append("runSpectrumTotalIonCountList");
      writer->startArray(m_runAndSpectrumIdList.size());
      for(auto &spectrum_tic_list : m_runAndSpectrumTotalIonCountList)
        {
          writer->writeArray(spectrum_tic_list);
        }
      writer->endArray();
    }
 
  // retention time
  size_ok = true;
  for(std::size_t i = 0; i < msrun_size.size(); i++)
    {
      if(m_runAndSpectrumRtList.at(i).size() != msrun_size.at(i))
        {
          size_ok = false;
        }
    }
  if(size_ok)
    {
 
      writer->append("runSpectrumRtList");
      writer->startArray(m_runAndSpectrumRtList.size());
      for(auto &spectrum_rt_list : m_runAndSpectrumRtList)
        {
          writer->writeArray(spectrum_rt_list);
        }
      writer->endArray();
    }
  else
    {
      // qFatal() << "wrong size";
    }
 
  // MS Level
  size_ok = true;
  for(std::size_t i = 0; i < msrun_size.size(); i++)
    {
      if(m_runAndSpectrumMsLevelList.at(i).size() != msrun_size.at(i))
        {
          size_ok = false;
        }
    }
  if(size_ok)
    {
      writer->append("runSpectrumMsLevelList");
      writer->startArray(m_runAndSpectrumMsLevelList.size());
      for(auto &spectrum_mslevel_list : m_runAndSpectrumMsLevelList)
        {
          writer->writeArray(spectrum_mslevel_list);
        }
      writer->endArray();
    }
 
  writer->endMap();
}

References m_runAndSpectrumIdList, m_runAndSpectrumMsLevelList, m_runAndSpectrumOffsetList, m_runAndSpectrumRtList, m_runAndSpectrumTotalIonCountList, m_runIdList, m_uuid, PAPPSOMSPP_NAME, PAPPSOMSPP_VERSION, pappso::cbor::CborStreamWriter::writeArray(), and pappso::cbor::CborStreamWriter::writeInformations().

Member Data Documentation

m_currentSpectrumSize

std::size_t pappso::cbor::mzcbor::MzmlConvert::m_currentSpectrumSize = 0

private

Definition at line 87 of file mzmlconvert.h.

Referenced by MzmlConvert(), and getCurrentSpectrumSize().

m_doubleArray

QVector<double> pappso::cbor::mzcbor::MzmlConvert::m_doubleArray

private

Definition at line 89 of file mzmlconvert.h.

Referenced by MzmlConvert().

m_elementStash

std::vector<QString> pappso::cbor::mzcbor::MzmlConvert::m_elementStash

private

Definition at line 84 of file mzmlconvert.h.

Referenced by MzmlConvert(), attributeListToCbor(), and insideElement().

m_elementToStoreInArray

QStringList pappso::cbor::mzcbor::MzmlConvert::m_elementToStoreInArray

private

Definition at line 85 of file mzmlconvert.h.

Referenced by MzmlConvert(), and insideElement().

m_runAndSpectrumIdList

std::vector<std::vector<QString> > pappso::cbor::mzcbor::MzmlConvert::m_runAndSpectrumIdList

private

Definition at line 93 of file mzmlconvert.h.

Referenced by MzmlConvert(), attributeListToCbor(), getRunAndSpectrumIdList(), insideElement(), and writeMzcborIndex().

m_runAndSpectrumMsLevelList

std::vector<std::vector<std::uint8_t> > pappso::cbor::mzcbor::MzmlConvert::m_runAndSpectrumMsLevelList

private

Definition at line 95 of file mzmlconvert.h.

Referenced by attributeListToCbor(), insideElement(), and writeMzcborIndex().

m_runAndSpectrumOffsetList

std::vector<std::vector<qint64> > pappso::cbor::mzcbor::MzmlConvert::m_runAndSpectrumOffsetList

private

Definition at line 92 of file mzmlconvert.h.

Referenced by MzmlConvert(), attributeListToCbor(), getRunAndSpectrumOffsetList(), insideElement(), and writeMzcborIndex().

m_runAndSpectrumRtList

std::vector<std::vector<double> > pappso::cbor::mzcbor::MzmlConvert::m_runAndSpectrumRtList

private

Definition at line 96 of file mzmlconvert.h.

Referenced by attributeListToCbor(), insideElement(), and writeMzcborIndex().

m_runAndSpectrumTotalIonCountList

std::vector<std::vector<qint64> > pappso::cbor::mzcbor::MzmlConvert::m_runAndSpectrumTotalIonCountList

private

Definition at line 94 of file mzmlconvert.h.

Referenced by attributeListToCbor(), insideElement(), and writeMzcborIndex().

m_runIdList

std::vector<QString> pappso::cbor::mzcbor::MzmlConvert::m_runIdList

private

Definition at line 91 of file mzmlconvert.h.

Referenced by MzmlConvert(), attributeListToCbor(), getRunIdList(), and writeMzcborIndex().

m_uuid

QString pappso::cbor::mzcbor::MzmlConvert::m_uuid

private

Definition at line 97 of file mzmlconvert.h.

Referenced by readStream(), and writeMzcborIndex().

mp_cborWriter

pappso::cbor::CborStreamWriter* pappso::cbor::mzcbor::MzmlConvert::mp_cborWriter

private

Definition at line 82 of file mzmlconvert.h.

Referenced by MzmlConvert(), attributeListToCbor(), attributeValueToCbor(), insideElement(), readBinaryDataArrayList(), and readStream().

mp_monitor

pappso::UiMonitorInterface* pappso::cbor::mzcbor::MzmlConvert::mp_monitor

private

Definition at line 81 of file mzmlconvert.h.

Referenced by MzmlConvert().

---

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

• pappsomspp/core/processing/cbor/mzcbor/mzmlconvert.h
• pappsomspp/core/processing/cbor/mzcbor/mzmlconvert.cpp