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 /*
127114 writer.setPrefix("xsi", xmlnsxsi);
128115 writer.setDefaultNamespace(namespaceURI);
129mpa_outputStream->writeStartElement("mzXML");
130117 writer.writeNamespace("xsi", xmlnsxsi);
131118 writer.writeDefaultNamespace(namespaceURI);
132119
133120 writer.writeAttribute(xmlnsxsi, "schemaLocation",
134xsischemaLocation); 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 /*
163144
164145 MsInstrumentList instrument_list =
165ms_run.getMsInstruments(controller); 146 for (MsInstrument
166instrument : 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 /*
184149
185150 // #< dataProcessing centroided ="1" >
186151 // my $ref_data_processings =
187$ms_run_description->dataProcessing(); 152 MsDataProcessingList
188dataProcList = 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
Definition: msrunreader.cpp:56
#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: