libpappsomspp
Library for mass spectrometry
Loading...
Searching...
No Matches
Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
pappso::cbor::mzcbor::Spectrum Struct Reference

#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.

357{
358 qDebug();
359 std::vector<pappso_double> xVector;
360 std::vector<pappso_double> yVector;
361 for(auto &binary_array : binaryDataArrayList)
362 {
363 qDebug();
364 if(binary_array.isIntensity())
365 {
366 qDebug();
367 binary_array.decodeVector(defaultArrayLength, yVector);
368 }
369 else if(binary_array.isMz())
370 {
371 qDebug();
372 binary_array.decodeVector(defaultArrayLength, xVector);
373 }
374 else
375 {
376
377 throw pappso::ExceptionNotFound(QObject::tr(
378 "error in pappso::cbor::mzcbor::Spectrum::decodeTrace: binary vector type not found"));
379 }
380 qDebug();
381 }
382
383 qDebug();
384 trace.initialize(xVector, yVector);
385 qDebug();
386}
pappso::Trace::initialize
size_t initialize(const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector)
Definition trace.cpp:597
pappso::cbor::mzcbor::Spectrum::binaryDataArrayList
std::vector< BinaryDataArray > binaryDataArrayList
Definition spectrum.h:90

References pappso::Trace::initialize().

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

◆ fromCbor()

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

fill the structure reading data from a CBOR stream

Parameters
readerCBOR stream
want_binary_dataif true, stores also binary data array list

Definition at line 43 of file spectrum.cpp.

44{
45 QString txt_value;
46 // cborBinaryDataArray.clear();
47 precursorList.clear();
48 defaultArrayLength = 0;
49 index = 0;
50 cvParamMap.clear();
51 scanListCvParamMap.clear();
52 scanList.clear();
53 id.clear();
54 qDebug();
55
56 if(reader.isInvalid())
57 {
58 throw pappso::PappsoException(
59 QObject::tr("ERROR in Spectrum::fromCbor :\ncbor is not valid"));
60 }
61 if(reader.enterContainer())
62 {
63 while(reader.hasNext() && (!reader.isInvalid()))
64 {
65 if(reader.isString())
66 {
67 reader.decodeString(txt_value);
68 qDebug() << txt_value;
69 if(txt_value == "id")
70 {
71 reader.decodeString(txt_value);
72 qDebug() << txt_value;
73 id = txt_value;
74 }
75 else if(txt_value == "index")
76 {
77 index = reader.toUnsignedInteger();
78 reader.next();
79 }
80 else if(txt_value == "defaultArrayLength")
81 {
82 defaultArrayLength = reader.toUnsignedInteger();
83 reader.next();
84 }
85 else if(txt_value == "cvParam")
86 {
87 cvParamMap.fromCbor(reader);
88 }
89 else if(txt_value == "scanList")
90 {
91 // mpa_cborReader->next();
92 reader.enterContainer();
93
94 while(reader.hasNext() && (!reader.isInvalid()))
95 {
96 if(reader.isString())
97 {
98 if(reader.decodeString(txt_value))
99 {
100 qDebug() << txt_value;
101 if(txt_value == "cvParam")
102 {
103 scanListCvParamMap.fromCbor(reader);
104 }
105 else if(txt_value == "scan")
106 {
107 // scan array
108 reader.enterContainer();
109
110 while(reader.hasNext() && (!reader.isInvalid()))
111 {
112 // scan array
113 Scan scan;
114 scan.fromCbor(reader);
115 scanList.emplace_back(scan);
116 }
117 reader.leaveContainer();
118 }
119 }
120 else
121 {
122 reader.next();
123 }
124 }
125 else
126 {
127 reader.next();
128 }
129 }
130 reader.leaveContainer();
131 }
132 else if(txt_value == "precursorList")
133 {
134
135 reader.enterContainer();
136
137 while(reader.hasNext() && (!reader.isInvalid()))
138 {
139 if(reader.isString())
140 {
141 if(reader.decodeString(txt_value))
142 {
143 qDebug() << txt_value;
144
145 if(txt_value == "cvParam")
146 {
147 precursorListCvParamMap.fromCbor(reader);
148 }
149 else if(txt_value == "precursor")
150 {
151
152 reader
153 .enterContainer(); // array
154
155 while(reader.hasNext() && (!reader.isInvalid()))
156 {
157 // scan array
158 Precursor precursor;
159 precursor.fromCbor(reader);
160 precursorList.emplace_back(precursor);
161 }
162 reader
163 .leaveContainer(); // array
164
165 // reader.next();
166 }
167 else
168 {
169 reader.next();
170 }
171 }
172 else
173 {
174 reader.next();
175 }
176 }
177 else
178 {
179 reader.next();
180 }
181 }
182 reader.leaveContainer();
183 }
184 else if(txt_value == "binaryDataArray")
185 {
186 if(want_binary_data)
187 {
188
189 reader.enterContainer(); // start array
190
191 while(reader.hasNext())
192 {
193
194 BinaryDataArray data_array;
195 data_array.fromCbor(reader);
196 binaryDataArrayList.emplace_back(data_array);
197 }
198
199 reader.leaveContainer(); // end array
200 }
201 else
202 {
203 reader.next();
204 }
205 }
206 else
207 {
208 reader.next();
209 }
210 }
211 // reader.next();
212 }
213
214 reader.leaveContainer();
215 }
216 else
217 {
218 throw pappso::PappsoException(QObject::tr("ERROR in Spectrum::fromCbor : no container"));
219 }
220
221
222 if(reader.lastError() != QCborError::NoError)
223 {
224 throw pappso::PappsoException(
225 QObject::tr("ERROR in Spectrum::fromCbor :\n%1").arg(reader.lastError().toString()));
226 }
227}
pappso::cbor::mzcbor::CvParamMap::fromCbor
void fromCbor(CborStreamReader &reader)
fill the structure reading data from a CBOR stream
Definition cvparammap.cpp:33
pappso::cbor::mzcbor::Spectrum::precursorList
std::vector< Precursor > precursorList
Definition spectrum.h:89
pappso::cbor::mzcbor::Spectrum::scanList
std::vector< Scan > scanList
Definition spectrum.h:88

References binaryDataArrayList, cvParamMap, pappso::cbor::CborStreamReader::decodeString(), defaultArrayLength, pappso::cbor::mzcbor::BinaryDataArray::fromCbor(), pappso::cbor::mzcbor::CvParamMap::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.

329{
330 // <cvParam cvRef="MS" accession="MS:1000511" value="1" name="ms level" />
331
332 auto it = cvParamMap.find("MS:1000511");
333 if(it == cvParamMap.end())
334 {
335 throw pappso::ExceptionNotFound(QObject::tr("MS level not found in cvParam map"));
336 }
337 qDebug() << it->first << " " << it->second.valueInt;
338 return it->second.valueInt;
339}

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.

343{
344 if(scanList.size() == 0)
345 {
346 throw pappso::ExceptionNotFound(QObject::tr("scan list is empty in spectrum"));
347 }
348 if(scanList.size() > 1)
349 {
350 throw pappso::ExceptionNotFound(QObject::tr("too many scans in spectrum"));
351 }
352 return scanList.front().getRtInSeconds();
353}

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.

314{
315 // <cvParam cvRef="MS" accession="MS:1000285" value="17377980" name="total ion current" />
316
317 auto it = cvParamMap.find("MS:1000285");
318 if(it == cvParamMap.end())
319 {
320 throw pappso::ExceptionNotFound(QObject::tr("total ion count not found in cvParam map"));
321 }
322 qDebug() << it->first << " " << it->second.valueInt;
323 return it->second.valueInt;
324}

◆ readScanCvParams()

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

Definition at line 278 of file spectrum.cpp.

279{
280 CvParamMap cv_params;
281 reader.enterContainer();
282 QString txt_value;
283
284 while(reader.hasNext() && (!reader.isInvalid()))
285 {
286 if(reader.isString())
287 {
288 if(reader.decodeString(txt_value))
289 {
290 qDebug() << txt_value;
291 if(txt_value == "cvParam")
292 {
293 cv_params.fromCbor(reader);
294 }
295 else
296 {
297 reader.next();
298 }
299 }
300 }
301 else
302 {
303 reader.next();
304 }
305 }
306
307 reader.leaveContainer();
308 return cv_params;
309}

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.

232{
233 QJsonObject spectrum_json;
234 spectrum_json.insert("id", id);
235 spectrum_json.insert("index", (qint64)index);
236 spectrum_json.insert("defaultArrayLength", (qint64)defaultArrayLength);
237 spectrum_json.insert("cvParam", cvParamMap.toJsonArray());
238
239 QJsonObject scan_list;
240 // QJsonObject scan_list_cvparam;
241 scan_list.insert("cvParam", scanListCvParamMap.toJsonArray());
242 QJsonArray scan_array;
243 for(auto &scan : scanList)
244 {
245 scan_array.append(scan.toJsonObject());
246 }
247 scan_list.insert("scan", scan_array);
248 spectrum_json.insert("scanList", scan_list);
249
250 if(!precursorList.empty())
251 {
252 QJsonObject precursor_list;
253 // QJsonObject scan_list_cvparam;
254 precursor_list.insert("cvParam", precursorListCvParamMap.toJsonArray());
255 QJsonArray precursor_array;
256 for(auto &precursor : precursorList)
257 {
258 precursor_array.append(precursor.toJsonObject());
259 }
260 precursor_list.insert("precursor", precursor_array);
261 spectrum_json.insert("precursorList", precursor_list);
262 }
263
264 if(!binaryDataArrayList.empty())
265 {
266 Trace trace;
267
268 decodeTrace(trace);
269
270
271 spectrum_json.insert("spectrum", trace.toJsonObject());
272 }
273
274 return spectrum_json;
275}
pappso::cbor::mzcbor::CvParamMap::toJsonArray
QJsonArray toJsonArray() const
write the structure to a JSON array
Definition cvparammap.cpp:59
pappso::cbor::mzcbor::Spectrum::decodeTrace
void decodeTrace(pappso::Trace &trace) const
Definition spectrum.cpp:356

References 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.

390{
391 // BEGIN IONS
392 // TITLE=20120906_balliau_extract_1_A01_urnb-1.2016.2016.3
393 // RTINSECONDS=679.467
394 // PEPMASS=417.210251631473 92010.6328125
395 // CHARGE=3+
396 // 88.03964233 1132.5438232422
397 // 91.05783844 1945.9479980469
398 // 93.03697968 6423.5581054688
399 // 93.8877182 949.33984375
400 output << "BEGIN IONS" << Qt::endl;
401 QString title;
402 if(msrun_id_csptr.get() != nullptr)
403 {
404 title = msrun_id_csptr.get()->getSampleName();
405 }
406
407 output << "TITLE=" << title << "." << index << Qt::endl;
408 output << "RTINSECONDS=" << QString::number(scanList.front().getRtInSeconds(), 'f', 4)
409 << Qt::endl;
410 bool is_ok;
411 double intensity = precursorList.front().selectedIonList.front().getIntensity(&is_ok);
412 if(is_ok)
413 {
414 output << "PEPMASS="
415 << QString::number(precursorList.front().selectedIonList.front().getMz(), 'f', 8)
416 << " " << QString::number(intensity, 'g', 10) << Qt::endl;
417 }
418 else
419 {
420 output << "PEPMASS="
421 << QString::number(precursorList.front().selectedIonList.front().getMz(), 'f', 8)
422 << Qt::endl;
423 }
424 output << "CHARGE=" << precursorList.front().selectedIonList.front().getChargeState() << "+"
425 << Qt::endl;
426
427 Trace trace;
428 decodeTrace(trace);
429
430 for(const pappso::DataPoint &one_point : trace)
431 {
432 output << QString::number(one_point.x, 'f', 8) << " " << QString::number(one_point.y, 'f', 8)
433 << Qt::endl;
434 }
435 output << "END IONS" << Qt::endl;
436}

Member Data Documentation

◆ binaryDataArrayList

std::vector<BinaryDataArray> pappso::cbor::mzcbor::Spectrum::binaryDataArrayList

Definition at line 90 of file spectrum.h.

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

◆ cvParamMap

CvParamMap pappso::cbor::mzcbor::Spectrum::cvParamMap

Definition at line 84 of file spectrum.h.

Referenced by fromCbor().

◆ defaultArrayLength

std::size_t pappso::cbor::mzcbor::Spectrum::defaultArrayLength

Definition at line 82 of file spectrum.h.

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

◆ id

QString pappso::cbor::mzcbor::Spectrum::id

Definition at line 80 of file spectrum.h.

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

◆ index

std::size_t pappso::cbor::mzcbor::Spectrum::index

Definition at line 81 of file spectrum.h.

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

◆ precursorList

std::vector<Precursor> pappso::cbor::mzcbor::Spectrum::precursorList

Definition at line 89 of file spectrum.h.

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

◆ precursorListCvParamMap

CvParamMap pappso::cbor::mzcbor::Spectrum::precursorListCvParamMap

Definition at line 86 of file spectrum.h.

Referenced by fromCbor().

◆ scanList

std::vector<Scan> pappso::cbor::mzcbor::Spectrum::scanList

Definition at line 88 of file spectrum.h.

Referenced by fromCbor().

◆ scanListCvParamMap

CvParamMap pappso::cbor::mzcbor::Spectrum::scanListCvParamMap

Definition at line 85 of file spectrum.h.

Referenced by fromCbor().

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