libpappsomspp
Library for mass spectrometry
pappso::MzxmlOutput Class Reference

#include <mzxmloutput.h>

Classes

class  Translater
 

Public Member Functions

 MzxmlOutput (UiMonitorInterface &monitor, QIODevice *p_output_device)
 
 ~MzxmlOutput ()
 
void write (MsRunReader *p_msrunreader)
 
void close ()
 
void maskMs1 (bool mask_ms1)
 
void setReadAhead (bool read_ahead)
 

Private Member Functions

void writeHeader (MsRunReader *p_msrunreader)
 
void writeQualifiedMassSpectrum (const QualifiedMassSpectrum &spectrum)
 
std::size_t getScanNumber (const QualifiedMassSpectrum &spectrum) const
 
std::size_t getPrecursorScanNumber (const QualifiedMassSpectrum &spectrum) const
 
std::size_t getScanNumberFromNativeId (const QString &native_id) const
 

Private Attributes

UiMonitorInterfacem_monitor
 
QXmlStreamWriter * mpa_outputStream
 
bool m_isReadAhead = false
 
bool m_ms1IsMasked = false
 

Detailed Description

Todo:
use msrunreader as input and writes all peaks into an mzXML output stream

Definition at line 43 of file mzxmloutput.h.

Constructor & Destructor Documentation

◆ MzxmlOutput()

MzxmlOutput::MzxmlOutput ( UiMonitorInterface monitor,
QIODevice *  p_output_device 
)

Default constructor

Definition at line 75 of file mzxmloutput.cpp.

77  : m_monitor(monitor)
78 {
79 
80  mpa_outputStream = new QXmlStreamWriter(p_output_device);
81  mpa_outputStream->setAutoFormatting(true);
82 
83  mpa_outputStream->writeStartDocument("1.0");
84 }
UiMonitorInterface & m_monitor
Definition: mzxmloutput.h:90
QXmlStreamWriter * mpa_outputStream
Definition: mzxmloutput.h:91

References mpa_outputStream.

◆ ~MzxmlOutput()

MzxmlOutput::~MzxmlOutput ( )

Destructor

Definition at line 86 of file mzxmloutput.cpp.

87 {
88  close();
89  delete mpa_outputStream;
90 }

References close(), and mpa_outputStream.

Member Function Documentation

◆ close()

void MzxmlOutput::close ( )

Definition at line 221 of file mzxmloutput.cpp.

222 {
223  mpa_outputStream->writeEndDocument();
224 }

References mpa_outputStream.

Referenced by ~MzxmlOutput(), and pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ getPrecursorScanNumber()

std::size_t MzxmlOutput::getPrecursorScanNumber ( const QualifiedMassSpectrum spectrum) const
private

Definition at line 254 of file mzxmloutput.cpp.

255 {
256 
257  std::size_t scan_number =
259  if(scan_number == std::numeric_limits<std::size_t>::max())
260  {
261  scan_number = spectrum.getPrecursorSpectrumIndex() + 1;
262  }
263  return scan_number;
264 }
std::size_t getScanNumberFromNativeId(const QString &native_id) const
const QString & getPrecursorNativeId() const
std::size_t getPrecursorSpectrumIndex() const
Get the scan number of the precursor ion.

References pappso::QualifiedMassSpectrum::getPrecursorNativeId(), pappso::QualifiedMassSpectrum::getPrecursorSpectrumIndex(), and getScanNumberFromNativeId().

Referenced by writeQualifiedMassSpectrum().

◆ getScanNumber()

std::size_t MzxmlOutput::getScanNumber ( const QualifiedMassSpectrum spectrum) const
private

Definition at line 242 of file mzxmloutput.cpp.

243 {
244  std::size_t scan_number =
246  if(scan_number == std::numeric_limits<std::size_t>::max())
247  {
248  scan_number = spectrum.getMassSpectrumId().getSpectrumIndex() + 1;
249  }
250  return scan_number;
251 }
std::size_t getSpectrumIndex() const
const QString & getNativeId() const
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getNativeId(), getScanNumberFromNativeId(), and pappso::MassSpectrumId::getSpectrumIndex().

Referenced by writeQualifiedMassSpectrum().

◆ getScanNumberFromNativeId()

std::size_t MzxmlOutput::getScanNumberFromNativeId ( const QString &  native_id) const
private

Definition at line 228 of file mzxmloutput.cpp.

229 {
230  QStringList native_id_list = native_id.split("=");
231  if(native_id_list.size() < 2)
232  {
233  }
234  else
235  {
236  return native_id_list.back().toULong();
237  }
238  return std::numeric_limits<std::size_t>::max();
239 }

Referenced by getPrecursorScanNumber(), and getScanNumber().

◆ maskMs1()

void MzxmlOutput::maskMs1 ( bool  mask_ms1)

Definition at line 388 of file mzxmloutput.cpp.

389 {
390  m_ms1IsMasked = mask_ms1;
391 }

References m_ms1IsMasked.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ setReadAhead()

void MzxmlOutput::setReadAhead ( bool  read_ahead)

Definition at line 93 of file mzxmloutput.cpp.

94 {
95  m_isReadAhead = isReadAhead;
96 }

References m_isReadAhead.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ write()

void MzxmlOutput::write ( MsRunReader p_msrunreader)

Definition at line 98 of file mzxmloutput.cpp.

99 {
100  qDebug();
101  m_monitor.setTotalSteps(p_msrunreader->spectrumListSize());
102  writeHeader(p_msrunreader);
103 
104  Translater translater(this);
105 
106  translater.setReadAhead(m_isReadAhead);
107 
108  translater.setNeedMsLevelPeakList(1, !m_ms1IsMasked);
109  // translater.setNeedMsLevelPeakList(1, false);
110  // translater.setNeedMsLevelPeakList(2, false);
111  p_msrunreader->readSpectrumCollection(translater);
112 
114  qDebug();
115 }
virtual std::size_t spectrumListSize() const =0
get the totat number of spectrum conained in the MSrun data file
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler)=0
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
void writeHeader(MsRunReader *p_msrunreader)
virtual void setTotalSteps(std::size_t total_number_of_steps)
use it if the number of steps is known in an algorithm the total number of steps is usefull to report...

References m_isReadAhead, m_monitor, m_ms1IsMasked, pappso::MsRunReader::readSpectrumCollection(), pappso::SpectrumCollectionHandlerInterface::setNeedMsLevelPeakList(), pappso::SpectrumCollectionHandlerInterface::setReadAhead(), pappso::UiMonitorInterface::setTotalSteps(), pappso::MsRunReader::spectrumListSize(), and writeHeader().

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ writeHeader()

void MzxmlOutput::writeHeader ( MsRunReader p_msrunreader)
private

Definition at line 118 of file mzxmloutput.cpp.

119 {
120 
121  mpa_outputStream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
122  "xsi");
123  // xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.0"
124  // xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.0
125  // http://sashimi.sourceforge.net/schema_revision/mzXML_2.0/mzXML_idx_2.0.xsd"
126  /*
127 114 writer.setPrefix("xsi", xmlnsxsi);
128 115 writer.setDefaultNamespace(namespaceURI);
129 mpa_outputStream->writeStartElement("mzXML");
130 117 writer.writeNamespace("xsi", xmlnsxsi);
131 118 writer.writeDefaultNamespace(namespaceURI);
132 119
133 120 writer.writeAttribute(xmlnsxsi, "schemaLocation",
134 xsischemaLocation); 121 */
135  mpa_outputStream->writeStartElement("mzXML");
136  mpa_outputStream->writeAttribute(
137  "xmlns", "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2");
138  mpa_outputStream->writeAttribute(
139  "xsi:schemaLocation",
140  "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 "
141  "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/"
142  "mzXML_idx_3.2.xsd");
143 
144  mpa_outputStream->writeStartElement("msRun");
145  mpa_outputStream->writeAttribute(
146  "scanCount", QString("%1").arg(p_msrunreader->spectrumListSize()));
147  //<msRun scanCount="16576" startTime="PT0.292553S" endTime="PT3000.34S">
148  // writer.writeAttribute("scanCount",
149  // ms_run.getSpectrumCount(this.controller).toString());
150 
151  /*
152  * # < parentFile fileName = #
153  * "file://SEQUEST1/raw/vidal/20060411_VIDAL_JEAN_1_PEPCR1_42140.RAW" #
154  * fileType = "RAWData" fileSha1 = #
155  * "23c1620d4ad3f4f0103b0141b7caec1e8b7eebf5" / >
156  */
157  mpa_outputStream->writeStartElement("parentFile");
158  mpa_outputStream->writeAttribute("fileName",
159  p_msrunreader->getMsRunId()->getFileName());
160  mpa_outputStream->writeAttribute("fileType", "RAWData");
161  mpa_outputStream->writeEndElement();
162  /*
163 144
164 145 MsInstrumentList instrument_list =
165 ms_run.getMsInstruments(controller); 146 for (MsInstrument
166 instrument : instrument_list) { 147 this.write(instrument); 148 }
167 */
168 
169  mpa_outputStream->writeStartElement("msInstrument");
170  mpa_outputStream->writeAttribute("msInstrumentID", "1");
171  //<msManufacturer category="msManufacturer" value="Thermo Scientific"/>
172  mpa_outputStream->writeStartElement("msManufacturer");
173  mpa_outputStream->writeAttribute("category", "msManufacturer");
174  mpa_outputStream->writeAttribute("value", "unknown");
175  mpa_outputStream->writeEndElement();
176  //<msModel category="msModel" value="Q Exactive"/>
177  // <msIonisation category="msIonisation" value="nanoelectrospray"/>
178  // <msMassAnalyzer category="msMassAnalyzer" value="quadrupole"/>
179  // <msDetector category="msDetector" value="inductive detector"/>
180  // <software type="acquisition" name="Xcalibur"
181  // version="2.1-152001/2.1.0.1520"/>
182  mpa_outputStream->writeEndElement();
183  /*
184 149
185 150 // #< dataProcessing centroided ="1" >
186 151 // my $ref_data_processings =
187 $ms_run_description->dataProcessing(); 152 MsDataProcessingList
188 dataProcList = ms_run.getMsDataProcessings(controller); 153 for
189 (MsDataProcessing msDataProc : dataProcList) { 154 this.write(msDataProc); 155 }
190 */
191  mpa_outputStream->writeStartElement("dataProcessing");
192  //<dataProcessing centroided="1">
193  mpa_outputStream->writeAttribute("centroided", "1");
194  // <software type="conversion" name="ProteoWizard" version="3.0.3706"/>
195  mpa_outputStream->writeStartElement("software");
196  mpa_outputStream->writeAttribute("type", "conversion");
197  mpa_outputStream->writeAttribute("name", PAPPSOMSPP_NAME);
198  mpa_outputStream->writeAttribute("version", PAPPSOMSPP_VERSION);
199  mpa_outputStream->writeEndElement();
200  //<processingOperation name="Conversion to mzML"/>
201  mpa_outputStream->writeStartElement("processingOperation");
202  mpa_outputStream->writeAttribute("name", "Conversion to mzXML");
203  //<software type="processing" name="ProteoWizard" version="3.0.3706"/>
204  mpa_outputStream->writeStartElement("software");
205  mpa_outputStream->writeAttribute("type", "processing");
206  mpa_outputStream->writeAttribute("name", PAPPSOMSPP_NAME);
207  mpa_outputStream->writeAttribute("version", PAPPSOMSPP_VERSION);
208  mpa_outputStream->writeEndElement();
209  //<comment>Thermo/Xcalibur peak picking</comment>
210  mpa_outputStream->writeStartElement("comment");
211  mpa_outputStream->writeCharacters("pappso::MzxmlOutput");
212  mpa_outputStream->writeEndElement();
213  //</dataProcessing>
214  mpa_outputStream->writeEndElement();
215  mpa_outputStream->writeEndElement();
216  // Peaks
217 }
const MsRunIdCstSPtr & getMsRunId() const
#define PAPPSOMSPP_VERSION
Definition: config.h:4
#define PAPPSOMSPP_NAME
Definition: config.h:3

References pappso::MsRunReader::getMsRunId(), mpa_outputStream, PAPPSOMSPP_NAME, PAPPSOMSPP_VERSION, and pappso::MsRunReader::spectrumListSize().

Referenced by write().

◆ writeQualifiedMassSpectrum()

void MzxmlOutput::writeQualifiedMassSpectrum ( const QualifiedMassSpectrum spectrum)
private

Definition at line 267 of file mzxmloutput.cpp.

269 {
270  qDebug();
271  mpa_outputStream->writeStartElement("scan");
272  /*
273  <scan num="1"
274  scanType="Full"
275  centroided="1"
276  msLevel="1"
277  peaksCount="1552"
278  polarity="+"
279  retentionTime="PT0.292553S"
280  lowMz="400.153411865234"
281  highMz="1013.123352050781"
282  basePeakMz="445.12003"
283  basePeakIntensity="2.0422125e06"
284  totIonCurrent="1.737798e07">*/
285  mpa_outputStream->writeAttribute("num",
286  QString("%1").arg(getScanNumber(spectrum)));
287  mpa_outputStream->writeAttribute("centroided", QString("1"));
288  mpa_outputStream->writeAttribute("msLevel",
289  QString("%1").arg(spectrum.getMsLevel()));
290  if(spectrum.getMassSpectrumCstSPtr().get() == nullptr)
291  {
292  mpa_outputStream->writeAttribute("peaksCount", "0");
293  }
294  else
295  {
296  mpa_outputStream->writeAttribute("peaksCount",
297  QString("%1").arg(spectrum.size()));
298 
299  if(spectrum.size() > 0)
300  {
301  mpa_outputStream->writeAttribute(
302  "lowMz",
303  QString::number(
304  spectrum.getMassSpectrumCstSPtr().get()->front().x, 'f', 12));
305 
306  mpa_outputStream->writeAttribute(
307  "highMz",
308  QString::number(
309  spectrum.getMassSpectrumCstSPtr().get()->back().x, 'f', 12));
310  // mpa_outputStream->writeAttribute("highMz",
311  // QString::number(spectrum.getMassSpectrumCstSPtr().get()->back().x,
312  // 'f', 10)); basePeakMz="245.1271988"
313  // basePeakIntensity="5810.7739"
314  // totIonCurrent="57803.815999999999">
315  }
316  }
317  mpa_outputStream->writeAttribute("polarity", "+");
318  mpa_outputStream->writeAttribute(
319  "retentionTime",
320  QString("PT%1S").arg(QString::number(spectrum.getRtInSeconds(), 'f', 2)));
321 
322  if(spectrum.getMsLevel() > 1)
323  {
324 
325  //<precursorMz precursorScanNum="16574"
326  // precursorIntensity="58403.04296875" precursorCharge="2"
327  ////activationMethod="HCD">994.690619901808</precursorMz>
328  mpa_outputStream->writeStartElement("precursorMz");
329  mpa_outputStream->writeAttribute(
330  "precursorScanNum",
331  QString("%1").arg(getPrecursorScanNumber(spectrum)));
332  mpa_outputStream->writeAttribute(
333  "precursorIntensity",
334  QString::number(spectrum.getPrecursorIntensity(), 'f', 4));
335  mpa_outputStream->writeAttribute(
336  "precursorCharge", QString("%1").arg(spectrum.getPrecursorCharge()));
337  mpa_outputStream->writeCharacters(
338  QString::number(spectrum.getPrecursorMz(), 'f', 12));
339  mpa_outputStream->writeEndElement();
340  }
341 
342  /*<peaks compressionType="none"
343  compressedLen="0"
344  precision="64"
345  byteOrder="network"
346  contentType="m/z-int"></peaks>*/
347 
348  mpa_outputStream->writeStartElement("peaks");
349  mpa_outputStream->writeAttribute("compressionType", "none");
350  mpa_outputStream->writeAttribute("compressedLen", "0");
351  mpa_outputStream->writeAttribute("precision", "64");
352  mpa_outputStream->writeAttribute("byteOrder", "network");
353  mpa_outputStream->writeAttribute("contentType", "m/z-int");
354 
355  if(spectrum.getMassSpectrumCstSPtr().get() != nullptr)
356  {
357  QByteArray byte_array;
358  if(QSysInfo::ByteOrder == QSysInfo::LittleEndian)
359  {
360  for(const DataPoint &peak :
361  *(spectrum.getMassSpectrumCstSPtr().get()))
362  {
363  double swap = change_endian(peak.x);
364  byte_array.append((char *)&swap, 8);
365  swap = change_endian(peak.y);
366  byte_array.append((char *)&swap, 8);
367  }
368  }
369  else
370  {
371  for(const DataPoint &peak :
372  *(spectrum.getMassSpectrumCstSPtr().get()))
373  {
374  byte_array.append((char *)&peak.x, 8);
375  byte_array.append((char *)&peak.y, 8);
376  }
377  }
378  mpa_outputStream->writeCharacters(byte_array.toBase64());
379  }
380  mpa_outputStream->writeEndElement();
381 
382  // scan
383  mpa_outputStream->writeEndElement();
384  qDebug();
385 }
std::size_t getScanNumber(const QualifiedMassSpectrum &spectrum) const
std::size_t getPrecursorScanNumber(const QualifiedMassSpectrum &spectrum) const
uint getMsLevel() const
Get the mass spectrum level.
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
uint getPrecursorCharge(bool *ok=nullptr) const
Get the precursor charge.
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
Get the intensity of the precursor ion.
pappso_double getPrecursorMz(bool *ok=nullptr) const
Get the precursor m/z ratio.
pappso_double getRtInSeconds() const
Get the retention time in seconds.
T change_endian(T in)
Definition: mzxmloutput.cpp:43

References change_endian(), pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getMsLevel(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getPrecursorMz(), getPrecursorScanNumber(), pappso::QualifiedMassSpectrum::getRtInSeconds(), getScanNumber(), mpa_outputStream, and pappso::QualifiedMassSpectrum::size().

Member Data Documentation

◆ m_isReadAhead

bool pappso::MzxmlOutput::m_isReadAhead = false
private

Definition at line 92 of file mzxmloutput.h.

Referenced by setReadAhead(), and write().

◆ m_monitor

UiMonitorInterface& pappso::MzxmlOutput::m_monitor
private

Definition at line 90 of file mzxmloutput.h.

Referenced by write().

◆ m_ms1IsMasked

bool pappso::MzxmlOutput::m_ms1IsMasked = false
private

Definition at line 93 of file mzxmloutput.h.

Referenced by maskMs1(), and write().

◆ mpa_outputStream

QXmlStreamWriter* pappso::MzxmlOutput::mpa_outputStream
private

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