libpappsomspp
Library for mass spectrometry
pappso::MzxmlOutput Class Reference

#include <mzxmloutput.h>

Classes

class  Translater
 

Public Member Functions

 MzxmlOutput (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

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 42 of file mzxmloutput.h.

Constructor & Destructor Documentation

◆ MzxmlOutput()

MzxmlOutput::MzxmlOutput ( QIODevice *  p_output_device)

Default constructor

Definition at line 74 of file mzxmloutput.cpp.

75 {
76 
77  mpa_outputStream = new QXmlStreamWriter(p_output_device);
78  mpa_outputStream->setAutoFormatting(true);
79 
80  mpa_outputStream->writeStartDocument("1.0");
81 }
QXmlStreamWriter * mpa_outputStream
Definition: mzxmloutput.h:89

References mpa_outputStream.

◆ ~MzxmlOutput()

MzxmlOutput::~MzxmlOutput ( )

Destructor

Definition at line 83 of file mzxmloutput.cpp.

84 {
85  close();
86  delete mpa_outputStream;
87 }

References close(), and mpa_outputStream.

Member Function Documentation

◆ close()

void MzxmlOutput::close ( )

Definition at line 215 of file mzxmloutput.cpp.

216 {
217  mpa_outputStream->writeEndDocument();
218 }

References mpa_outputStream.

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

◆ getPrecursorScanNumber()

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

Definition at line 248 of file mzxmloutput.cpp.

249 {
250 
251  std::size_t scan_number =
253  if(scan_number == std::numeric_limits<std::size_t>::max())
254  {
255  scan_number = spectrum.getPrecursorSpectrumIndex() + 1;
256  }
257  return scan_number;
258 }
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 236 of file mzxmloutput.cpp.

237 {
238  std::size_t scan_number =
240  if(scan_number == std::numeric_limits<std::size_t>::max())
241  {
242  scan_number = spectrum.getMassSpectrumId().getSpectrumIndex() + 1;
243  }
244  return scan_number;
245 }
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 222 of file mzxmloutput.cpp.

223 {
224  QStringList native_id_list = native_id.split("=");
225  if(native_id_list.size() < 2)
226  {
227  }
228  else
229  {
230  return native_id_list.back().toULong();
231  }
232  return std::numeric_limits<std::size_t>::max();
233 }

Referenced by getPrecursorScanNumber(), and getScanNumber().

◆ maskMs1()

void MzxmlOutput::maskMs1 ( bool  mask_ms1)

Definition at line 382 of file mzxmloutput.cpp.

383 {
384  m_ms1IsMasked = mask_ms1;
385 }

References m_ms1IsMasked.

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

◆ setReadAhead()

void MzxmlOutput::setReadAhead ( bool  read_ahead)

Definition at line 90 of file mzxmloutput.cpp.

91 {
92  m_isReadAhead = isReadAhead;
93 }

References m_isReadAhead.

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

◆ write()

void MzxmlOutput::write ( MsRunReader p_msrunreader)

Definition at line 95 of file mzxmloutput.cpp.

96 {
97  qDebug();
98  writeHeader(p_msrunreader);
99 
100  Translater translater(this);
101 
102  translater.setReadAhead(m_isReadAhead);
103 
104  translater.setNeedMsLevelPeakList(1, !m_ms1IsMasked);
105  // translater.setNeedMsLevelPeakList(1, false);
106  // translater.setNeedMsLevelPeakList(2, false);
107  p_msrunreader->readSpectrumCollection(translater);
108  qDebug();
109 }
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)

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

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

◆ writeHeader()

void MzxmlOutput::writeHeader ( MsRunReader p_msrunreader)
private

Definition at line 112 of file mzxmloutput.cpp.

113 {
114 
115  mpa_outputStream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
116  "xsi");
117  // xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.0"
118  // xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.0
119  // http://sashimi.sourceforge.net/schema_revision/mzXML_2.0/mzXML_idx_2.0.xsd"
120  /*
121 114 writer.setPrefix("xsi", xmlnsxsi);
122 115 writer.setDefaultNamespace(namespaceURI);
123 mpa_outputStream->writeStartElement("mzXML");
124 117 writer.writeNamespace("xsi", xmlnsxsi);
125 118 writer.writeDefaultNamespace(namespaceURI);
126 119
127 120 writer.writeAttribute(xmlnsxsi, "schemaLocation",
128 xsischemaLocation); 121 */
129  mpa_outputStream->writeStartElement("mzXML");
130  mpa_outputStream->writeAttribute(
131  "xmlns", "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2");
132  mpa_outputStream->writeAttribute(
133  "xsi:schemaLocation",
134  "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 "
135  "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/"
136  "mzXML_idx_3.2.xsd");
137 
138  mpa_outputStream->writeStartElement("msRun");
139  mpa_outputStream->writeAttribute(
140  "scanCount", QString("%1").arg(p_msrunreader->spectrumListSize()));
141  //<msRun scanCount="16576" startTime="PT0.292553S" endTime="PT3000.34S">
142  // writer.writeAttribute("scanCount",
143  // ms_run.getSpectrumCount(this.controller).toString());
144 
145  /*
146  * # < parentFile fileName = #
147  * "file://SEQUEST1/raw/vidal/20060411_VIDAL_JEAN_1_PEPCR1_42140.RAW" #
148  * fileType = "RAWData" fileSha1 = #
149  * "23c1620d4ad3f4f0103b0141b7caec1e8b7eebf5" / >
150  */
151  mpa_outputStream->writeStartElement("parentFile");
152  mpa_outputStream->writeAttribute("fileName",
153  p_msrunreader->getMsRunId()->getFileName());
154  mpa_outputStream->writeAttribute("fileType", "RAWData");
155  mpa_outputStream->writeEndElement();
156  /*
157 144
158 145 MsInstrumentList instrument_list =
159 ms_run.getMsInstruments(controller); 146 for (MsInstrument
160 instrument : instrument_list) { 147 this.write(instrument); 148 }
161 */
162 
163  mpa_outputStream->writeStartElement("msInstrument");
164  mpa_outputStream->writeAttribute("msInstrumentID", "1");
165  //<msManufacturer category="msManufacturer" value="Thermo Scientific"/>
166  mpa_outputStream->writeStartElement("msManufacturer");
167  mpa_outputStream->writeAttribute("category", "msManufacturer");
168  mpa_outputStream->writeAttribute("value", "unknown");
169  mpa_outputStream->writeEndElement();
170  //<msModel category="msModel" value="Q Exactive"/>
171  // <msIonisation category="msIonisation" value="nanoelectrospray"/>
172  // <msMassAnalyzer category="msMassAnalyzer" value="quadrupole"/>
173  // <msDetector category="msDetector" value="inductive detector"/>
174  // <software type="acquisition" name="Xcalibur"
175  // version="2.1-152001/2.1.0.1520"/>
176  mpa_outputStream->writeEndElement();
177  /*
178 149
179 150 // #< dataProcessing centroided ="1" >
180 151 // my $ref_data_processings =
181 $ms_run_description->dataProcessing(); 152 MsDataProcessingList
182 dataProcList = ms_run.getMsDataProcessings(controller); 153 for
183 (MsDataProcessing msDataProc : dataProcList) { 154 this.write(msDataProc); 155 }
184 */
185  mpa_outputStream->writeStartElement("dataProcessing");
186  //<dataProcessing centroided="1">
187  mpa_outputStream->writeAttribute("centroided", "1");
188  // <software type="conversion" name="ProteoWizard" version="3.0.3706"/>
189  mpa_outputStream->writeStartElement("software");
190  mpa_outputStream->writeAttribute("type", "conversion");
191  mpa_outputStream->writeAttribute("name", PAPPSOMSPP_NAME);
192  mpa_outputStream->writeAttribute("version", PAPPSOMSPP_VERSION);
193  mpa_outputStream->writeEndElement();
194  //<processingOperation name="Conversion to mzML"/>
195  mpa_outputStream->writeStartElement("processingOperation");
196  mpa_outputStream->writeAttribute("name", "Conversion to mzXML");
197  //<software type="processing" name="ProteoWizard" version="3.0.3706"/>
198  mpa_outputStream->writeStartElement("software");
199  mpa_outputStream->writeAttribute("type", "processing");
200  mpa_outputStream->writeAttribute("name", PAPPSOMSPP_NAME);
201  mpa_outputStream->writeAttribute("version", PAPPSOMSPP_VERSION);
202  mpa_outputStream->writeEndElement();
203  //<comment>Thermo/Xcalibur peak picking</comment>
204  mpa_outputStream->writeStartElement("comment");
205  mpa_outputStream->writeCharacters("pappso::MzxmlOutput");
206  mpa_outputStream->writeEndElement();
207  //</dataProcessing>
208  mpa_outputStream->writeEndElement();
209  mpa_outputStream->writeEndElement();
210  // Peaks
211 }
virtual std::size_t spectrumListSize() const =0
get the totat number of spectrum conained in the MSrun data file
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 261 of file mzxmloutput.cpp.

263 {
264  qDebug();
265  mpa_outputStream->writeStartElement("scan");
266  /*
267  <scan num="1"
268  scanType="Full"
269  centroided="1"
270  msLevel="1"
271  peaksCount="1552"
272  polarity="+"
273  retentionTime="PT0.292553S"
274  lowMz="400.153411865234"
275  highMz="1013.123352050781"
276  basePeakMz="445.12003"
277  basePeakIntensity="2.0422125e06"
278  totIonCurrent="1.737798e07">*/
279  mpa_outputStream->writeAttribute("num",
280  QString("%1").arg(getScanNumber(spectrum)));
281  mpa_outputStream->writeAttribute("centroided", QString("1"));
282  mpa_outputStream->writeAttribute("msLevel",
283  QString("%1").arg(spectrum.getMsLevel()));
284  if(spectrum.getMassSpectrumCstSPtr().get() == nullptr)
285  {
286  mpa_outputStream->writeAttribute("peaksCount", "0");
287  }
288  else
289  {
290  mpa_outputStream->writeAttribute("peaksCount",
291  QString("%1").arg(spectrum.size()));
292 
293  if(spectrum.size() > 0)
294  {
295  mpa_outputStream->writeAttribute(
296  "lowMz",
297  QString::number(
298  spectrum.getMassSpectrumCstSPtr().get()->front().x, 'f', 12));
299 
300  mpa_outputStream->writeAttribute(
301  "highMz",
302  QString::number(
303  spectrum.getMassSpectrumCstSPtr().get()->back().x, 'f', 12));
304  // mpa_outputStream->writeAttribute("highMz",
305  // QString::number(spectrum.getMassSpectrumCstSPtr().get()->back().x,
306  // 'f', 10)); basePeakMz="245.1271988"
307  // basePeakIntensity="5810.7739"
308  // totIonCurrent="57803.815999999999">
309  }
310  }
311  mpa_outputStream->writeAttribute("polarity", "+");
312  mpa_outputStream->writeAttribute(
313  "retentionTime",
314  QString("PT%1S").arg(QString::number(spectrum.getRtInSeconds(), 'f', 2)));
315 
316  if(spectrum.getMsLevel() > 1)
317  {
318 
319  //<precursorMz precursorScanNum="16574"
320  // precursorIntensity="58403.04296875" precursorCharge="2"
321  ////activationMethod="HCD">994.690619901808</precursorMz>
322  mpa_outputStream->writeStartElement("precursorMz");
323  mpa_outputStream->writeAttribute(
324  "precursorScanNum",
325  QString("%1").arg(getPrecursorScanNumber(spectrum)));
326  mpa_outputStream->writeAttribute(
327  "precursorIntensity",
328  QString::number(spectrum.getPrecursorIntensity(), 'f', 4));
329  mpa_outputStream->writeAttribute(
330  "precursorCharge", QString("%1").arg(spectrum.getPrecursorCharge()));
331  mpa_outputStream->writeCharacters(
332  QString::number(spectrum.getPrecursorMz(), 'f', 12));
333  mpa_outputStream->writeEndElement();
334  }
335 
336  /*<peaks compressionType="none"
337  compressedLen="0"
338  precision="64"
339  byteOrder="network"
340  contentType="m/z-int"></peaks>*/
341 
342  mpa_outputStream->writeStartElement("peaks");
343  mpa_outputStream->writeAttribute("compressionType", "none");
344  mpa_outputStream->writeAttribute("compressedLen", "0");
345  mpa_outputStream->writeAttribute("precision", "64");
346  mpa_outputStream->writeAttribute("byteOrder", "network");
347  mpa_outputStream->writeAttribute("contentType", "m/z-int");
348 
349  if(spectrum.getMassSpectrumCstSPtr().get() != nullptr)
350  {
351  QByteArray byte_array;
352  if(QSysInfo::ByteOrder == QSysInfo::LittleEndian)
353  {
354  for(const DataPoint &peak :
355  *(spectrum.getMassSpectrumCstSPtr().get()))
356  {
357  double swap = change_endian(peak.x);
358  byte_array.append((char *)&swap, 8);
359  swap = change_endian(peak.y);
360  byte_array.append((char *)&swap, 8);
361  }
362  }
363  else
364  {
365  for(const DataPoint &peak :
366  *(spectrum.getMassSpectrumCstSPtr().get()))
367  {
368  byte_array.append((char *)&peak.x, 8);
369  byte_array.append((char *)&peak.y, 8);
370  }
371  }
372  mpa_outputStream->writeCharacters(byte_array.toBase64());
373  }
374  mpa_outputStream->writeEndElement();
375 
376  // scan
377  mpa_outputStream->writeEndElement();
378  qDebug();
379 }
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 90 of file mzxmloutput.h.

Referenced by setReadAhead(), and write().

◆ m_ms1IsMasked

bool pappso::MzxmlOutput::m_ms1IsMasked = false
private

Definition at line 91 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: