libpappsomspp
Library for mass spectrometry
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pappso::Utils Class Reference

#include <utils.h>

Static Public Member Functions

static const QString getLexicalOrderedString (unsigned int num)
 
static void writeLexicalOrderedString (QTextStream *p_out, unsigned int num)
 
static int zeroDecimalsInValue (pappso_double value)
 0.11 would return 0 (no empty decimal) 2.001 would return 2 1000.0001254 would return 3
 
static pappso_double roundToDecimals (pappso_double value, int decimal_places)
 
static long long int roundToDecimal32bitsAsLongLongInt (pappso::pappso_double input)
 
static std::string toUtf8StandardString (const QString &text)
 
static bool writeToFile (const QString &text, const QString &file_name)
 
static bool appendToFile (const QString &text, const QString &file_name)
 
static std::size_t extractScanNumberFromMzmlNativeId (const QString &spectrum_native_id)
 
static QString pointerToString (const void *const pointer)
 
static bool almostEqual (double value1, double value2, int decimalPlaces=10)
 
static double nearestGreater (double value)
 
static QString chronoTimePointDebugString (const QString &msg, std::chrono::system_clock::time_point chrono_time=std::chrono::system_clock::now())
 
static QString chronoIntervalDebugString (const QString &msg, std::chrono::system_clock::time_point chrono_start, std::chrono::system_clock::time_point chrono_finish=std::chrono::system_clock::now())
 
static std::vector< double > splitMzStringToDoubleVectorWithSpaces (const QString &text, std::size_t &error_count)
 
static std::vector< std::size_t > splitSizetStringToSizetVectorWithSpaces (const QString &text, std::size_t &error_count)
 
static QString booleanToString (bool value)
 convenient function to transform a boolean to QString "TRUE" or "FALSE" QString returned is readable by R
 
static QString mzFormatAsString (MzFormat mz_format)
 Convenience function to return a string describing the MzFormat of a file.
 
static QString fileReaderTypeAsString (FileReaderType file_reader_type)
 
static QString toString (specglob::SpectralAlignmentType type)
 Convenience function to return a string describing the specglob alingment type.
 
static QString toString (specglob::ExperimentalSpectrumDataPointType type)
 Convenience function to return a string describing the specglob experimental spectrum data point.
 

Static Public Attributes

static QRegularExpression xyMassDataFormatRegExp
 
static QRegularExpression mzListDataFormatRegExp
 Regular expression matching <m/z value><non-numerical*>
 
static QRegularExpression sizetListDataFormatRegExp
 Regular expression matching <size_t><non-numerical*>
 
static QRegularExpression endOfLineRegExp = QRegularExpression("^\\s+$")
 Regular expression that tracks the end of line in text files.
 

Detailed Description

Definition at line 49 of file utils.h.

Member Function Documentation

◆ almostEqual()

bool pappso::Utils::almostEqual ( double  value1,
double  value2,
int  decimalPlaces = 10 
)
static

Tell if both double values, are equal within the double representation capabilities of the platform.

Definition at line 261 of file utils.cpp.

262{
263 // QString value1String = QString("%1").arg(value1,
264 // 0, 'f', 60);
265 // QString value2String = QString("%1").arg(value2,
266 // 0, 'f', 60);
267
268 // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
269 //<< "value1:" << value1String << "value2:" << value2String;
270
271 // The machine epsilon has to be scaled to the magnitude of the values used
272 // and multiplied by the desired precision in ULPs (units in the last place)
273 // (decimal places).
274
275 double valueSum = std::abs(value1 + value2);
276 // QString valueSumString = QString("%1").arg(valueSum,
277 // 0, 'f', 60);
278
279 double valueDiff = std::abs(value1 - value2);
280 // QString valueDiffString = QString("%1").arg(valueDiff,
281 // 0, 'f', 60);
282
283 double epsilon = std::numeric_limits<double>::epsilon();
284 // QString epsilonString = QString("%1").arg(epsilon,
285 // 0, 'f', 60);
286
287 double scaleFactor = epsilon * valueSum * decimalPlaces;
288 // QString scaleFactorString = QString("%1").arg(scaleFactor,
289 // 0, 'f', 60);
290
291 // qWarning() << "valueDiff:" << valueDiffString << "valueSum:" <<
292 // valueSumString <<
293 //"epsilon:" << epsilonString << "scaleFactor:" << scaleFactorString;
294
295 bool res = valueDiff < scaleFactor
296 // unless the result is subnormal:
297 || valueDiff < std::numeric_limits<double>::min();
298
299 // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
300 //<< "returning res:" << res;
301
302 return res;
303}

References pappso::res.

Referenced by pappso::Trace::removeZeroYDataPoints().

◆ appendToFile()

bool pappso::Utils::appendToFile ( const QString &  text,
const QString &  file_name 
)
static

Definition at line 195 of file utils.cpp.

196{
197
198 QFile file(file_name);
199
200 if(file.open(QFile::WriteOnly | QFile::Append))
201 {
202
203 QTextStream out(&file);
204
205 out << text;
206
207 out.flush();
208 file.close();
209
210 return true;
211 }
212
213 return false;
214}

◆ booleanToString()

QString pappso::Utils::booleanToString ( bool  value)
static

convenient function to transform a boolean to QString "TRUE" or "FALSE" QString returned is readable by R

Returns
QString "TRUE" or "FALSE"

Definition at line 424 of file utils.cpp.

425{
426 if(value)
427 return "TRUE";
428 return "FALSE";
429}

◆ chronoIntervalDebugString()

QString pappso::Utils::chronoIntervalDebugString ( const QString &  msg,
std::chrono::system_clock::time_point  chrono_start,
std::chrono::system_clock::time_point  chrono_finish = std::chrono::system_clock::now() 
)
static

Definition at line 330 of file utils.cpp.

334{
335 QString debug_text =
336 QString(
337 "%1 %2 min = %3 s = %4 ms = %5 "
338 "µs\n")
339 .arg(msg)
340 .arg(std::chrono::duration_cast<std::chrono::minutes>(chrono_finish -
341 chrono_start)
342 .count())
343 .arg(std::chrono::duration_cast<std::chrono::seconds>(chrono_finish -
344 chrono_start)
345 .count())
346 .arg(std::chrono::duration_cast<std::chrono::milliseconds>(chrono_finish -
347 chrono_start)
348 .count())
349 .arg(std::chrono::duration_cast<std::chrono::microseconds>(chrono_finish -
350 chrono_start)
351 .count());
352
353 return debug_text;
354}

◆ chronoTimePointDebugString()

QString pappso::Utils::chronoTimePointDebugString ( const QString &  msg,
std::chrono::system_clock::time_point  chrono_time = std::chrono::system_clock::now() 
)
static

Definition at line 314 of file utils.cpp.

316{
317
318 time_t tt;
319
320 tt = std::chrono::system_clock::to_time_t(chrono_time);
321
322 QString debug_text =
323 QString("%1 - %2\n").arg(msg).arg(QString::fromLatin1(ctime(&tt)));
324
325 return debug_text;
326}

◆ extractScanNumberFromMzmlNativeId()

std::size_t pappso::Utils::extractScanNumberFromMzmlNativeId ( const QString &  spectrum_native_id)
static

TODO activate this in a future release to ensure scan number for(auto i = 0; i < native_id_list.size(); i += 2) { if(native_id_list[i] == "scan") { return native_id_list[i + 1].toULong(); } }

throw ExceptionNotFound( QObject::tr("scan number not found in mzML native id %1") .arg(spectrum_native_id));

Definition at line 218 of file utils.cpp.

219{
220 qDebug() << " " << spectrum_native_id;
221 QStringList native_id_list = spectrum_native_id.split("=");
222 if(native_id_list.size() < 2)
223 {
224 throw ExceptionNotFound(
225 QObject::tr("scan number not found in mzML native id %1")
226 .arg(spectrum_native_id));
227 }
228 else
229 {
230 /** TODO activate this in a future release to ensure scan number
231 for(auto i = 0; i < native_id_list.size(); i += 2)
232 {
233 if(native_id_list[i] == "scan")
234 {
235 return native_id_list[i + 1].toULong();
236 }
237 }
238
239 throw ExceptionNotFound(
240 QObject::tr("scan number not found in mzML native id %1")
241 .arg(spectrum_native_id));
242
243*/
244 return native_id_list.back().toULong();
245 }
246 return 0;
247}

◆ fileReaderTypeAsString()

QString pappso::Utils::fileReaderTypeAsString ( FileReaderType  file_reader_type)
static

Definition at line 473 of file utils.cpp.

474{
475
476 if(file_reader_type == FileReaderType::pwiz)
477 return "pwiz";
478 else if(file_reader_type == FileReaderType::xy)
479 return "xy";
480 else if(file_reader_type == FileReaderType::tims)
481 return "tims";
482 else if(file_reader_type == FileReaderType::tims_frames)
483 return "tims_frames";
484 else
485 return "unknown";
486}

References pappso::pwiz, pappso::tims, pappso::tims_frames, and pappso::xy.

◆ getLexicalOrderedString()

const QString pappso::Utils::getLexicalOrderedString ( unsigned int  num)
static

Definition at line 52 of file utils.cpp.

53{
54 int size = log10(num);
55 size += 97;
56 QLatin1Char latin1_char(size);
57 QString base(latin1_char);
58 base.append(QString().setNum(num));
59 return (base);
60}

References pappso::log10.

Referenced by pappso::GrpGroup::getGroupingId(), pappso::GrpPeptide::getGroupingId(), pappso::GrpProtein::getGroupingId(), pappso::GrpSubGroup::getGroupingId(), pappso::PwizMsFileReader::getMsRunIds(), and pappso::XyMsFileReader::getMsRunIds().

◆ mzFormatAsString()

QString pappso::Utils::mzFormatAsString ( MzFormat  mz_format)
static

Convenience function to return a string describing the MzFormat of a file.

 

Returns
QString like "brukerTims" for enum value MzFormat::brukerTims.

Definition at line 432 of file utils.cpp.

433{
434
435 if(mz_format == MzFormat::mzML)
436 return "mzML";
437 else if(mz_format == MzFormat::mzXML)
438 return "mzXML";
439 else if(mz_format == MzFormat::MGF)
440 return "MGF";
441 else if(mz_format == MzFormat::SQLite3)
442 return "SQLite3";
443 else if(mz_format == MzFormat::xy)
444 return "xy";
445 else if(mz_format == MzFormat::mz5)
446 return "mz5";
447 else if(mz_format == MzFormat::msn)
448 return "msn";
449 else if(mz_format == MzFormat::abSciexWiff)
450 return "abSciexWiff";
451 else if(mz_format == MzFormat::abSciexT2D)
452 return "abSciexT2D";
453 else if(mz_format == MzFormat::agilentMassHunter)
454 return "agilentMassHunter";
455 else if(mz_format == MzFormat::thermoRaw)
456 return "thermoRaw";
457 else if(mz_format == MzFormat::watersRaw)
458 return "watersRaw";
459 else if(mz_format == MzFormat::brukerFid)
460 return "brukerFid";
461 else if(mz_format == MzFormat::brukerYep)
462 return "brukerYep";
463 else if(mz_format == MzFormat::brukerBaf)
464 return "brukerBaf";
465 else if(mz_format == MzFormat::brukerTims)
466 return "brukerTims";
467 else
468 return "unknown";
469}
@ xy
(x,y) format
@ SQLite3
SQLite3 format.
@ MGF
Mascot format.

References pappso::abSciexT2D, pappso::abSciexWiff, pappso::agilentMassHunter, pappso::brukerBaf, pappso::brukerFid, pappso::brukerTims, pappso::brukerYep, pappso::MGF, pappso::msn, pappso::mz5, pappso::mzML, pappso::mzXML, pappso::SQLite3, pappso::thermoRaw, pappso::watersRaw, and pappso::xy.

◆ nearestGreater()

double pappso::Utils::nearestGreater ( double  value)
static

Definition at line 307 of file utils.cpp.

308{
309 return std::nextafter(value, value + 1);
310}

◆ pointerToString()

QString pappso::Utils::pointerToString ( const void *const  pointer)
static

Definition at line 251 of file utils.cpp.

252{
253 return QString("%1").arg(
254 (quintptr)pointer, QT_POINTER_SIZE * 2, 16, QChar('0'));
255}

Referenced by pappso::QualifiedMassSpectrum::toString(), and pappso::MsRunDataSetTreeNode::toString().

◆ roundToDecimal32bitsAsLongLongInt()

long long int pappso::Utils::roundToDecimal32bitsAsLongLongInt ( pappso::pappso_double  input)
static

Definition at line 131 of file utils.cpp.

132{
133 pappso::pappso_double test_decimal = 100000000000;
134 if(sizeof(int *) == 4)
135 { // 32bits
136 test_decimal = 100000000;
137 }
138 return (floor(input * test_decimal));
139}
double pappso_double
A type definition for doubles.
Definition types.h:50

◆ roundToDecimals()

pappso_double pappso::Utils::roundToDecimals ( pappso_double  value,
int  decimal_places 
)
static

Definition at line 120 of file utils.cpp.

121{
122 if(decimal_places < 0)
123 return value;
124
125 return ceil((value * pow(10, decimal_places)) - 0.49) /
126 pow(10, decimal_places);
127}

Referenced by pappso::MassSpectrumMinusCombiner::combine(), pappso::MassSpectrumPlusCombiner::combine(), pappso::TraceMinusCombiner::combine(), and pappso::TracePlusCombiner::combine().

◆ splitMzStringToDoubleVectorWithSpaces()

std::vector< double > pappso::Utils::splitMzStringToDoubleVectorWithSpaces ( const QString &  text,
std::size_t &  error_count 
)
static

Definition at line 358 of file utils.cpp.

360{
361
362 QStringList string_list =
363 text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts);
364
365 // qDebug() << "string list:" << string_list;
366
367 std::vector<double> double_vector;
368
369 for(int iter = 0; iter < string_list.size(); ++iter)
370 {
371 QString current_string = string_list.at(iter);
372
373 bool ok = false;
374
375 double current_double = current_string.toDouble(&ok);
376
377 if(!current_double && !ok)
378 {
379 ++error_count;
380 continue;
381 }
382
383 double_vector.push_back(current_double);
384 }
385
386 return double_vector;
387}

◆ splitSizetStringToSizetVectorWithSpaces()

std::vector< std::size_t > pappso::Utils::splitSizetStringToSizetVectorWithSpaces ( const QString &  text,
std::size_t &  error_count 
)
static

Definition at line 391 of file utils.cpp.

393{
394 // qDebug() << "Parsing text:" << text;
395
396 QStringList string_list =
397 text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts);
398
399 // qDebug() << "string list size:" << string_list.size()
400 //<< "values:" << string_list;
401
402 std::vector<std::size_t> sizet_vector;
403
404 for(int iter = 0; iter < string_list.size(); ++iter)
405 {
406 QString current_string = string_list.at(iter);
407
408 bool ok = false;
409
410 std::size_t current_sizet = current_string.toUInt(&ok);
411
412 if(!current_sizet && !ok)
413 {
414 ++error_count;
415 continue;
416 }
417
418 sizet_vector.push_back(current_sizet);
419 }
420
421 return sizet_vector;
422}

◆ toString() [1/2]

QString pappso::Utils::toString ( specglob::ExperimentalSpectrumDataPointType  type)
static

Convenience function to return a string describing the specglob experimental spectrum data point.

Returns
QString

Definition at line 508 of file utils.cpp.

509{
510 switch(type)
511 {
513 return "both";
514 break;
516 return "native";
517 break;
519 return "symetric";
520 break;
521 default:
522 return "synthetic";
523 }
524}
@ symetric
new peak : computed symetric mass from a corresponding native peak
@ both
both, the ion and the complement exists in the original spectrum

References pappso::specglob::both, pappso::specglob::native, and pappso::specglob::symetric.

◆ toString() [2/2]

QString pappso::Utils::toString ( specglob::SpectralAlignmentType  type)
static

Convenience function to return a string describing the specglob alingment type.

Returns
QString

Definition at line 489 of file utils.cpp.

490{
491 switch(type)
492 {
494 return "AL";
495 break;
497 return "NA";
498 break;
500 return "RA";
501 break;
502 default:
503 return "ER";
504 }
505}
@ nonAlign
the type of alignment to put in origin matrix NON Alignment (0 - NA)

References pappso::specglob::align, pappso::specglob::nonAlign, and pappso::specglob::reAlign.

Referenced by pappso::specglob::PeptideModel::toProForma(), and pappso::specglob::PeptideModel::toString().

◆ toUtf8StandardString()

std::string pappso::Utils::toUtf8StandardString ( const QString &  text)
static

Definition at line 143 of file utils.cpp.

144{
145 std::string env_backup = setlocale(LC_ALL, "");
146
147 // struct lconv *lc_backup = localeconv();
148 // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
149 //<< "env_backup=" << env_backup.c_str() << "lc_backup->decimal_point"
150 //<< lc_backup->decimal_point;
151
152 // Force locale to be "C".
153 setlocale(LC_ALL, "C");
154
155 // Now perform the conversion.
156 QByteArray byte_array = text.toUtf8();
157 std::string stdText = "";
158
159 for(char c : byte_array)
160 {
161 stdText += c;
162 }
163
164 // Set back the locale to the backed-up one.
165 setlocale(LC_ALL, env_backup.c_str());
166
167 return stdText;
168}

References pappso::c.

Referenced by pappso::PwizMsFileReader::initialize(), and pappso::PwizMsRunReader::initialize().

◆ writeLexicalOrderedString()

void pappso::Utils::writeLexicalOrderedString ( QTextStream *  p_out,
unsigned int  num 
)
static

Definition at line 64 of file utils.cpp.

65{
66 *p_out << (char)(log10(num) + 97) << num;
67}

References pappso::log10.

◆ writeToFile()

bool pappso::Utils::writeToFile ( const QString &  text,
const QString &  file_name 
)
static

Definition at line 172 of file utils.cpp.

173{
174
175 QFile file(file_name);
176
177 if(file.open(QFile::WriteOnly | QFile::Truncate))
178 {
179
180 QTextStream out(&file);
181
182 out << text;
183
184 out.flush();
185 file.close();
186
187 return true;
188 }
189
190 return false;
191}

◆ zeroDecimalsInValue()

int pappso::Utils::zeroDecimalsInValue ( pappso_double  value)
static

0.11 would return 0 (no empty decimal) 2.001 would return 2 1000.0001254 would return 3

Determine the number of zero decimals between the decimal point and the first non-zero decimal.

Parameters
valuethe value to be analyzed
Returns
the number of '0' decimals between the decimal separator '.' and the first non-0 decimal

Definition at line 82 of file utils.cpp.

83{
84 // qDebug() << qSetRealNumberPrecision(10) << "Double value: " << value;
85
86 int intPart = static_cast<int>(value);
87
88 // qDebug() << "int part:" << intPart;
89
90 double decimalPart = value - intPart;
91
92 // qDebug() << qSetRealNumberPrecision(10) << "decimal part: " << decimalPart;
93
94 int count = 0;
95
96 while(decimalPart > 0)
97 {
98 ++count;
99
100 decimalPart *= 10;
101
102 // qDebug() << "Iteration " << count << "decimal part:" << decimalPart;
103
104 if(decimalPart >= 1)
105 {
106 // qDebug() << "Because decimal part " << decimalPart
107 //<< "is >= 1, breaking loop while count is " << count << ".";
108
109 break;
110 }
111 }
112
113 // qDebug() << "Returning count:" << count - 1;
114
115 return count - 1;
116}

Referenced by pappso::MzIntegrationParams::createArbitraryBins(), and pappso::BasePlotWidget::drawXDeltaFeatures().

Member Data Documentation

◆ endOfLineRegExp

QRegularExpression pappso::Utils::endOfLineRegExp = QRegularExpression("^\\s+$")
static

Regular expression that tracks the end of line in text files.

Definition at line 63 of file utils.h.

Referenced by pappso::XyMsRunReader::accept(), pappso::XyMsFileReader::initialize(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().

◆ mzListDataFormatRegExp

QRegularExpression pappso::Utils::mzListDataFormatRegExp
static

Regular expression matching <m/z value><non-numerical*>

Definition at line 57 of file utils.h.

◆ sizetListDataFormatRegExp

QRegularExpression pappso::Utils::sizetListDataFormatRegExp
static

Regular expression matching <size_t><non-numerical*>

Definition at line 60 of file utils.h.

◆ xyMassDataFormatRegExp

QRegularExpression pappso::Utils::xyMassDataFormatRegExp
static
Initial value:
=
QRegularExpression("^(\\d*\\.?\\d+)([^\\d^\\.^-]+)(-?\\d*\\.?\\d*[e-]?\\d*)")

Regular expression matching <numerical value><non-numerical*><numerical value>

Definition at line 54 of file utils.h.

Referenced by pappso::XyMsRunReader::accept(), pappso::XyMsFileReader::initialize(), pappso::DataPoint::initialize(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().


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