#include <spectrum.h>

Public Member Functions
void	fromCbor (CborStreamReader &reader, bool want_binary_data)
	fill the structure reading data from a CBOR stream
QJsonObject	toJsonObject () const
	write the structure to a JSON object This is a simplified representation for easy JSON data handling binary arrays are decoded in simple traces
void	toMgf (QTextStream &output, MsRunIdCstSPtr msrun_id_csptr) const
	write spectrum in MGF text format
void	decodeTrace (pappso::Trace &trace) const
uint	getMsLevel () const
double	getRtInSeconds () const
qint64	getTotalIonCount () const

Static Public Member Functions
static std::map< QString, pappso::cbor::mzcbor::CvParam >	readScanCvParams (CborStreamReader &reader)

Public Attributes
QString	id
std::size_t	index
std::size_t	defaultArrayLength
CvParamMap	cvParamMap
CvParamMap	scanListCvParamMap
CvParamMap	precursorListCvParamMap
std::vector< Scan >	scanList
std::vector< Precursor >	precursorList
std::vector< BinaryDataArray >	binaryDataArrayList

Detailed Description

Todo: write docs

Definition at line 50 of file spectrum.h.

Member Function Documentation

◆ decodeTrace()

void pappso::cbor::mzcbor::Spectrum::decodeTrace ( pappso::Trace & trace ) const

Definition at line 356 of file spectrum.cpp.

{
  qDebug();
  std::vector<pappso_double> xVector;
  std::vector<pappso_double> yVector;
  for(auto &binary_array : binaryDataArrayList)
    {
      qDebug();
      if(binary_array.isIntensity())
        {
          qDebug();
          binary_array.decodeVector(defaultArrayLength, yVector);
        }
      else if(binary_array.isMz())
        {
          qDebug();
          binary_array.decodeVector(defaultArrayLength, xVector);
        }
      else
        {
 
          throw pappso::ExceptionNotFound(QObject::tr(
            "error in pappso::cbor::mzcbor::Spectrum::decodeTrace: binary vector type not found"));
        }
      qDebug();
    }
 
  qDebug();
  trace.initialize(xVector, yVector);
  qDebug();
}

References binaryDataArrayList, defaultArrayLength, and pappso::Trace::initialize().

Referenced by pappso::MzcborMsRunReader::massSpectrumSPtr(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), toJsonObject(), and toMgf().

◆ fromCbor()

void pappso::cbor::mzcbor::Spectrum::fromCbor	(	CborStreamReader &	reader,
		bool	want_binary_data )

fill the structure reading data from a CBOR stream

Parameters

reader	CBOR stream
want_binary_data	if true, stores also binary data array list

Definition at line 43 of file spectrum.cpp.

{
  QString txt_value;
  // cborBinaryDataArray.clear();
  precursorList.clear();
  defaultArrayLength = 0;
  index              = 0;
  cvParamMap.clear();
  scanListCvParamMap.clear();
  scanList.clear();
  id.clear();
  qDebug();
 
  if(reader.isInvalid())
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR in Spectrum::fromCbor :\ncbor is not valid"));
    }
  if(reader.enterContainer())
    {
      while(reader.hasNext() && (!reader.isInvalid()))
        {
          if(reader.isString())
            {
              reader.decodeString(txt_value);
              qDebug() << txt_value;
              if(txt_value == "id")
                {
                  reader.decodeString(txt_value);
                  qDebug() << txt_value;
                  id = txt_value;
                }
              else if(txt_value == "index")
                {
                  index = reader.toUnsignedInteger();
                  reader.next();
                }
              else if(txt_value == "defaultArrayLength")
                {
                  defaultArrayLength = reader.toUnsignedInteger();
                  reader.next();
                }
              else if(txt_value == "cvParam")
                {
                  cvParamMap.fromCbor(reader);
                }
              else if(txt_value == "scanList")
                {
                  // mpa_cborReader->next();
                  reader.enterContainer();
 
                  while(reader.hasNext() && (!reader.isInvalid()))
                    {
                      if(reader.isString())
                        {
                          if(reader.decodeString(txt_value))
                            {
                              qDebug() << txt_value;
                              if(txt_value == "cvParam")
                                {
                                  scanListCvParamMap.fromCbor(reader);
                                }
                              else if(txt_value == "scan")
                                {
                                  // scan array
                                  reader.enterContainer();
 
                                  while(reader.hasNext() && (!reader.isInvalid()))
                                    {
                                      // scan array
                                      Scan scan;
                                      scan.fromCbor(reader);
                                      scanList.emplace_back(scan);
                                    }
                                  reader.leaveContainer();
                                }
                            }
                          else
                            {
                              reader.next();
                            }
                        }
                      else
                        {
                          reader.next();
                        }
                    }
                  reader.leaveContainer();
                }
              else if(txt_value == "precursorList")
                {
 
                  reader.enterContainer();
 
                  while(reader.hasNext() && (!reader.isInvalid()))
                    {
                      if(reader.isString())
                        {
                          if(reader.decodeString(txt_value))
                            {
                              qDebug() << txt_value;
 
                              if(txt_value == "cvParam")
                                {
                                  precursorListCvParamMap.fromCbor(reader);
                                }
                              else if(txt_value == "precursor")
                                {
 
                                  reader
                                    .enterContainer(); //                                     array
 
                                  while(reader.hasNext() && (!reader.isInvalid()))
                                    {
                                      // scan array
                                      Precursor precursor;
                                      precursor.fromCbor(reader);
                                      precursorList.emplace_back(precursor);
                                    }
                                  reader
                                    .leaveContainer(); //                                     array
 
                                  // reader.next();
                                }
                              else
                                {
                                  reader.next();
                                }
                            }
                          else
                            {
                              reader.next();
                            }
                        }
                      else
                        {
                          reader.next();
                        }
                    }
                  reader.leaveContainer();
                }
              else if(txt_value == "binaryDataArray")
                {
                  if(want_binary_data)
                    {
 
                      reader.enterContainer(); // start array
 
                      while(reader.hasNext())
                        {
 
                          BinaryDataArray data_array;
                          data_array.fromCbor(reader);
                          binaryDataArrayList.emplace_back(data_array);
                        }
 
                      reader.leaveContainer(); // end array
                    }
                  else
                    {
                      reader.next();
                    }
                }
              else
                {
                  reader.next();
                }
            }
          // reader.next();
        }
 
      reader.leaveContainer();
    }
  else
    {
      throw pappso::PappsoException(QObject::tr("ERROR in Spectrum::fromCbor : no container"));
    }
 
 
  if(reader.lastError() != QCborError::NoError)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR in Spectrum::fromCbor :\n%1").arg(reader.lastError().toString()));
    }
}

References binaryDataArrayList, cvParamMap, pappso::cbor::CborStreamReader::decodeString(), defaultArrayLength, pappso::cbor::mzcbor::BinaryDataArray::fromCbor(), pappso::cbor::mzcbor::Precursor::fromCbor(), pappso::cbor::mzcbor::Scan::fromCbor(), index, precursorList, precursorListCvParamMap, scanList, and scanListCvParamMap.

Referenced by pappso::MzcborMsRunReader::fillMzcborSpectrum(), and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum().

◆ getMsLevel()

uint pappso::cbor::mzcbor::Spectrum::getMsLevel ( ) const

Definition at line 328 of file spectrum.cpp.

{
  //        <cvParam cvRef="MS" accession="MS:1000511" value="1" name="ms level" />
 
  auto it = cvParamMap.find("MS:1000511");
  if(it == cvParamMap.end())
    {
      throw pappso::ExceptionNotFound(QObject::tr("MS level not found in cvParam map"));
    }
  qDebug() << it->first << " " << it->second.valueInt;
  return it->second.valueInt;
}

References cvParamMap.

Referenced by pappso::MzcborMsRunReader::qualifiedMassSpectrum(), and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum().

◆ getRtInSeconds()

double pappso::cbor::mzcbor::Spectrum::getRtInSeconds ( ) const

Definition at line 342 of file spectrum.cpp.

{
  if(scanList.size() == 0)
    {
      throw pappso::ExceptionNotFound(QObject::tr("scan list is empty in spectrum"));
    }
  if(scanList.size() > 1)
    {
      throw pappso::ExceptionNotFound(QObject::tr("too many scans in spectrum"));
    }
  return scanList.front().getRtInSeconds();
}

References scanList.

Referenced by pappso::MzcborMsRunReader::newXicCoordSPtrFromSpectrumIndex(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum().

◆ getTotalIonCount()

qint64 pappso::cbor::mzcbor::Spectrum::getTotalIonCount ( ) const

Definition at line 313 of file spectrum.cpp.

{
  //   <cvParam cvRef="MS" accession="MS:1000285" value="17377980" name="total ion current" />
 
  auto it = cvParamMap.find("MS:1000285");
  if(it == cvParamMap.end())
    {
      throw pappso::ExceptionNotFound(QObject::tr("total ion count not found in cvParam map"));
    }
  qDebug() << it->first << " " << it->second.valueInt;
  return it->second.valueInt;
}

References cvParamMap.

◆ readScanCvParams()

std::map< QString, pappso::cbor::mzcbor::CvParam > pappso::cbor::mzcbor::Spectrum::readScanCvParams ( CborStreamReader & reader )

static

Definition at line 278 of file spectrum.cpp.

{
  CvParamMap cv_params;
  reader.enterContainer();
  QString txt_value;
 
  while(reader.hasNext() && (!reader.isInvalid()))
    {
      if(reader.isString())
        {
          if(reader.decodeString(txt_value))
            {
              qDebug() << txt_value;
              if(txt_value == "cvParam")
                {
                  cv_params.fromCbor(reader);
                }
              else
                {
                  reader.next();
                }
            }
        }
      else
        {
          reader.next();
        }
    }
 
  reader.leaveContainer();
  return cv_params;
}

References pappso::cbor::CborStreamReader::decodeString(), and pappso::cbor::mzcbor::CvParamMap::fromCbor().

◆ toJsonObject()

QJsonObject pappso::cbor::mzcbor::Spectrum::toJsonObject ( ) const

write the structure to a JSON object This is a simplified representation for easy JSON data handling binary arrays are decoded in simple traces

Returns: QJsonObject

Definition at line 231 of file spectrum.cpp.

{
  QJsonObject spectrum_json;
  spectrum_json.insert("id", id);
  spectrum_json.insert("index", (qint64)index);
  spectrum_json.insert("defaultArrayLength", (qint64)defaultArrayLength);
  spectrum_json.insert("cvParam", cvParamMap.toJsonArray());
 
  QJsonObject scan_list;
  // QJsonObject scan_list_cvparam;
  scan_list.insert("cvParam", scanListCvParamMap.toJsonArray());
  QJsonArray scan_array;
  for(auto &scan : scanList)
    {
      scan_array.append(scan.toJsonObject());
    }
  scan_list.insert("scan", scan_array);
  spectrum_json.insert("scanList", scan_list);
 
  if(!precursorList.empty())
    {
      QJsonObject precursor_list;
      // QJsonObject scan_list_cvparam;
      precursor_list.insert("cvParam", precursorListCvParamMap.toJsonArray());
      QJsonArray precursor_array;
      for(auto &precursor : precursorList)
        {
          precursor_array.append(precursor.toJsonObject());
        }
      precursor_list.insert("precursor", precursor_array);
      spectrum_json.insert("precursorList", precursor_list);
    }
 
  if(!binaryDataArrayList.empty())
    {
      Trace trace;
 
      decodeTrace(trace);
 
 
      spectrum_json.insert("spectrum", trace.toJsonObject());
    }
 
  return spectrum_json;
}

References binaryDataArrayList, cvParamMap, decodeTrace(), defaultArrayLength, index, precursorList, precursorListCvParamMap, scanList, scanListCvParamMap, and pappso::Trace::toJsonObject().

◆ toMgf()

void pappso::cbor::mzcbor::Spectrum::toMgf	(	QTextStream &	output,
		MsRunIdCstSPtr	msrun_id_csptr ) const

write spectrum in MGF text format

Definition at line 389 of file spectrum.cpp.

{
  // BEGIN IONS
  // TITLE=20120906_balliau_extract_1_A01_urnb-1.2016.2016.3
  // RTINSECONDS=679.467
  // PEPMASS=417.210251631473 92010.6328125
  // CHARGE=3+
  // 88.03964233 1132.5438232422
  // 91.05783844 1945.9479980469
  // 93.03697968 6423.5581054688
  // 93.8877182 949.33984375
  output << "BEGIN IONS" << Qt::endl;
  QString title;
  if(msrun_id_csptr.get() != nullptr)
    {
      title = msrun_id_csptr.get()->getSampleName();
    }
 
  output << "TITLE=" << title << "." << index << Qt::endl;
  output << "RTINSECONDS=" << QString::number(scanList.front().getRtInSeconds(), 'f', 4)
         << Qt::endl;
  bool is_ok;
  double intensity = precursorList.front().selectedIonList.front().getIntensity(&is_ok);
  if(is_ok)
    {
      output << "PEPMASS="
             << QString::number(precursorList.front().selectedIonList.front().getMz(), 'f', 8)
             << " " << QString::number(intensity, 'g', 10) << Qt::endl;
    }
  else
    {
      output << "PEPMASS="
             << QString::number(precursorList.front().selectedIonList.front().getMz(), 'f', 8)
             << Qt::endl;
    }
  output << "CHARGE=" << precursorList.front().selectedIonList.front().getChargeState() << "+"
         << Qt::endl;
 
  Trace trace;
  decodeTrace(trace);
 
  for(const pappso::DataPoint &one_point : trace)
    {
      output << QString::number(one_point.x, 'f', 8) << " " << QString::number(one_point.y, 'f', 8)
             << Qt::endl;
    }
  output << "END IONS" << Qt::endl;
}