libpappsomspp
Library for mass spectrometry
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pappso::cbor::mzcbor::Spectrum Struct Reference

#include <spectrum.h>

Public Member Functions

void fromCbor (CborStreamReader &reader, bool want_binary_data)
void decodeTrace (pappso::Trace &trace)
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
std::map< QString, pappso::cbor::mzcbor::CvParam > cvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > scanListCvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > scanCvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > precursorListCvParamMap
QCborMap cborScanList
std::vector< Precursor > precursorList
std::vector< BinaryDataArray > binaryDataArrayList
QCborMap cborBinaryDataArray

Detailed Description

Todo
write docs

Definition at line 46 of file spectrum.h.

Member Function Documentation

◆ decodeTrace()

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

Definition at line 306 of file spectrum.cpp.

307{
308 std::vector<pappso_double> xVector;
309 std::vector<pappso_double> yVector;
310 for(auto &binary_array : binaryDataArrayList)
311 {
312 if(binary_array.isIntensity())
313 {
314 binary_array.decodeVector(defaultArrayLength, yVector);
315 }
316 else if(binary_array.isMz())
317 {
318 binary_array.decodeVector(defaultArrayLength, xVector);
319 }
320 else
321 {
322
323 throw pappso::ExceptionNotFound(QObject::tr(
324 "error in pappso::cbor::mzcbor::Spectrum::decodeTrace: binary vector type not found"));
325 }
326 }
327
328 trace.initialize(xVector, yVector);
329}
pappso::Trace::initialize
size_t initialize(const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector)
Definition trace.cpp:564
pappso::cbor::mzcbor::Spectrum::binaryDataArrayList
std::vector< BinaryDataArray > binaryDataArrayList
Definition spectrum.h:68

References binaryDataArrayList, defaultArrayLength, and 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 )

Definition at line 34 of file spectrum.cpp.

35{
36 QString txt_value;
37 cborBinaryDataArray.clear();
38 precursorList.clear();
39 defaultArrayLength = 0;
40 index = 0;
41 cvParamMap.clear();
42 scanListCvParamMap.clear();
43 scanCvParamMap.clear();
44 id.clear();
45 qDebug();
46
47 if(reader.isInvalid())
48 {
49 throw pappso::PappsoException(
50 QObject::tr("ERROR in Spectrum::fromCbor :\ncbor is not valid"));
51 }
52 if(reader.enterContainer())
53 {
54 while(reader.hasNext() && (!reader.isInvalid()))
55 {
56 if(reader.isString())
57 {
58 reader.decodeString(txt_value);
59 qDebug() << txt_value;
60 if(txt_value == "id")
61 {
62 reader.decodeString(txt_value);
63 qDebug() << txt_value;
64 id = txt_value;
65 }
66 else if(txt_value == "index")
67 {
68 index = reader.toUnsignedInteger();
69 reader.next();
70 }
71 else if(txt_value == "defaultArrayLength")
72 {
73 defaultArrayLength = reader.toUnsignedInteger();
74 reader.next();
75 }
76 else if(txt_value == "cvParam")
77 {
78 cvParamMap = CvParam::getCvParamsMapFromCbor(reader);
79 }
80 else if(txt_value == "scanList")
81 {
82 // mpa_cborReader->next();
83 reader.enterContainer();
84
85 while(reader.hasNext() && (!reader.isInvalid()))
86 {
87 if(reader.isString())
88 {
89 if(reader.decodeString(txt_value))
90 {
91 qDebug() << txt_value;
92 if(txt_value == "cvParam")
93 {
94 scanListCvParamMap = CvParam::getCvParamsMapFromCbor(reader);
95 }
96 else if(txt_value == "scan")
97 {
98 // scan array
99 reader.enterContainer();
100 while(reader.hasNext())
101 {
102 auto new_cv = readScanCvParams(reader);
103 scanCvParamMap.insert(new_cv.begin(), new_cv.end());
104 }
105 reader.leaveContainer();
106 }
107 }
108 else
109 {
110 reader.next();
111 }
112 }
113 else
114 {
115 reader.next();
116 }
117 }
118 reader.leaveContainer();
119 }
120 else if(txt_value == "precursorList")
121 {
122
123 reader.enterContainer();
124
125 while(reader.hasNext() && (!reader.isInvalid()))
126 {
127 if(reader.isString())
128 {
129 if(reader.decodeString(txt_value))
130 {
131 qDebug() << txt_value;
132
133 if(txt_value == "cvParam")
134 {
135 precursorListCvParamMap = CvParam::getCvParamsMapFromCbor(reader);
136 }
137 else if(txt_value == "precursor")
138 {
139
140 reader
141 .enterContainer(); // array
142
143 while(reader.hasNext() && (!reader.isInvalid()))
144 {
145 // scan array
146 Precursor precursor;
147 precursor.fromCbor(reader);
148 precursorList.emplace_back(precursor);
149 }
150 reader
151 .leaveContainer(); // array
152
153 // reader.next();
154 }
155 else
156 {
157 reader.next();
158 }
159 }
160 else
161 {
162 reader.next();
163 }
164 }
165 else
166 {
167 reader.next();
168 }
169 }
170 reader.leaveContainer();
171 }
172 else if(txt_value == "binaryDataArray")
173 {
174 if(want_binary_data)
175 {
176
177 reader.enterContainer(); // start array
178
179 while(reader.hasNext())
180 {
181
182 BinaryDataArray data_array;
183 data_array.fromCbor(reader);
184 binaryDataArrayList.emplace_back(data_array);
185 }
186
187 reader.leaveContainer(); // end array
188 }
189 else
190 {
191 reader.next();
192 }
193 }
194 else
195 {
196 reader.next();
197 }
198 }
199 // reader.next();
200 }
201
202 reader.leaveContainer();
203 }
204 else
205 {
206 throw pappso::PappsoException(QObject::tr("ERROR in Spectrum::fromCbor : no container"));
207 }
208
209
210 if(reader.lastError() != QCborError::NoError)
211 {
212 throw pappso::PappsoException(
213 QObject::tr("ERROR in Spectrum::fromCbor :\n%1").arg(reader.lastError()));
214 }
215}
pappso::cbor::mzcbor::CvParam::getCvParamsMapFromCbor
static std::map< QString, pappso::cbor::mzcbor::CvParam > getCvParamsMapFromCbor(CborStreamReader &reader)
Definition cvparam.cpp:182
pappso::cbor::mzcbor::Spectrum::cvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > cvParamMap
Definition spectrum.h:62
pappso::cbor::mzcbor::Spectrum::readScanCvParams
static std::map< QString, pappso::cbor::mzcbor::CvParam > readScanCvParams(CborStreamReader &reader)
Definition spectrum.cpp:219
pappso::cbor::mzcbor::Spectrum::precursorList
std::vector< Precursor > precursorList
Definition spectrum.h:67
pappso::cbor::mzcbor::Spectrum::scanListCvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > scanListCvParamMap
Definition spectrum.h:63
pappso::cbor::mzcbor::Spectrum::scanCvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > scanCvParamMap
Definition spectrum.h:64
pappso::cbor::mzcbor::Spectrum::precursorListCvParamMap
std::map< QString, pappso::cbor::mzcbor::CvParam > precursorListCvParamMap
Definition spectrum.h:65

References binaryDataArrayList, cborBinaryDataArray, cvParamMap, pappso::cbor::CborStreamReader::decodeString(), defaultArrayLength, pappso::cbor::mzcbor::BinaryDataArray::fromCbor(), pappso::cbor::mzcbor::Precursor::fromCbor(), pappso::cbor::mzcbor::CvParam::getCvParamsMapFromCbor(), index, precursorList, precursorListCvParamMap, readScanCvParams(), scanCvParamMap, and scanListCvParamMap.

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

◆ getMsLevel()

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

Definition at line 269 of file spectrum.cpp.

270{
271 // <cvParam cvRef="MS" accession="MS:1000511" value="1" name="ms level" />
272
273 auto it = cvParamMap.find("MS:1000511");
274 if(it == cvParamMap.end())
275 {
276 throw pappso::ExceptionNotFound(QObject::tr("MS level not found in cvParam map"));
277 }
278 qDebug() << it->first << " " << it->second.valueInt;
279 return it->second.valueInt;
280}

References cvParamMap.

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

◆ getRtInSeconds()

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

Definition at line 283 of file spectrum.cpp.

284{
285 // <cvParam cvRef="MS" accession="MS:1000016" value="0.0048758833" name="scan start
286 // time" unitAccession="UO:0000031" unitName="minute" unitCvRef="UO" />
287
288 auto it = scanCvParamMap.find("MS:1000016");
289 if(it == scanCvParamMap.end())
290 {
291 throw pappso::ExceptionNotFound(QObject::tr("retention time not found in cvParam map"));
292 }
293 double rt_seconds = it->second.valueDouble;
294 if(it->second.unitAccession == "UO:0000031")
295 {
296 // // minutes
297 rt_seconds = rt_seconds * 60;
298 }
299
300 // <cvParam cvRef="MS" accession="MS:1000016" value="0" name="scan start time"
301 // unitAccession="UO:0000031" unitName="minute" unitCvRef="UO" />
302 return rt_seconds;
303}

References scanCvParamMap.

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 254 of file spectrum.cpp.

255{
256 // <cvParam cvRef="MS" accession="MS:1000285" value="17377980" name="total ion current" />
257
258 auto it = cvParamMap.find("MS:1000285");
259 if(it == cvParamMap.end())
260 {
261 throw pappso::ExceptionNotFound(QObject::tr("total ion count not found in cvParam map"));
262 }
263 qDebug() << it->first << " " << it->second.valueInt;
264 return it->second.valueInt;
265}

References cvParamMap.

◆ readScanCvParams()

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

Definition at line 219 of file spectrum.cpp.

220{
221 std::map<QString, CvParam> cv_params;
222 reader.enterContainer();
223 QString txt_value;
224
225 while(reader.hasNext() && (!reader.isInvalid()))
226 {
227 if(reader.isString())
228 {
229 if(reader.decodeString(txt_value))
230 {
231 qDebug() << txt_value;
232 if(txt_value == "cvParam")
233 {
234 cv_params = CvParam::getCvParamsMapFromCbor(reader);
235 }
236 else
237 {
238 reader.next();
239 }
240 }
241 }
242 else
243 {
244 reader.next();
245 }
246 }
247
248 reader.leaveContainer();
249 return cv_params;
250}

References pappso::cbor::CborStreamReader::decodeString(), and pappso::cbor::mzcbor::CvParam::getCvParamsMapFromCbor().

Referenced by fromCbor().

Member Data Documentation

◆ binaryDataArrayList

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

Definition at line 68 of file spectrum.h.

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

◆ cborBinaryDataArray

QCborMap pappso::cbor::mzcbor::Spectrum::cborBinaryDataArray

Definition at line 69 of file spectrum.h.

Referenced by fromCbor().

◆ cborScanList

QCborMap pappso::cbor::mzcbor::Spectrum::cborScanList

Definition at line 66 of file spectrum.h.

◆ cvParamMap

std::map<QString, pappso::cbor::mzcbor::CvParam> pappso::cbor::mzcbor::Spectrum::cvParamMap

Definition at line 62 of file spectrum.h.

Referenced by fromCbor(), getMsLevel(), and getTotalIonCount().

◆ defaultArrayLength

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

Definition at line 60 of file spectrum.h.

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

◆ id

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

Definition at line 58 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 59 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 67 of file spectrum.h.

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

◆ precursorListCvParamMap

std::map<QString, pappso::cbor::mzcbor::CvParam> pappso::cbor::mzcbor::Spectrum::precursorListCvParamMap

Definition at line 65 of file spectrum.h.

Referenced by fromCbor().

◆ scanCvParamMap

std::map<QString, pappso::cbor::mzcbor::CvParam> pappso::cbor::mzcbor::Spectrum::scanCvParamMap

Definition at line 64 of file spectrum.h.

Referenced by fromCbor(), and getRtInSeconds().

◆ scanListCvParamMap

std::map<QString, pappso::cbor::mzcbor::CvParam> pappso::cbor::mzcbor::Spectrum::scanListCvParamMap

Definition at line 63 of file spectrum.h.

Referenced by fromCbor().

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