libpappsomspp
Library for mass spectrometry
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 More...
 
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 More...
 

Static Public Attributes

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

Detailed Description

Definition at line 48 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 260 of file utils.cpp.

261{
262 // QString value1String = QString("%1").arg(value1,
263 // 0, 'f', 60);
264 // QString value2String = QString("%1").arg(value2,
265 // 0, 'f', 60);
266
267 // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
268 //<< "value1:" << value1String << "value2:" << value2String;
269
270 // The machine epsilon has to be scaled to the magnitude of the values used
271 // and multiplied by the desired precision in ULPs (units in the last place)
272 // (decimal places).
273
274 double valueSum = std::abs(value1 + value2);
275 // QString valueSumString = QString("%1").arg(valueSum,
276 // 0, 'f', 60);
277
278 double valueDiff = std::abs(value1 - value2);
279 // QString valueDiffString = QString("%1").arg(valueDiff,
280 // 0, 'f', 60);
281
282 double epsilon = std::numeric_limits<double>::epsilon();
283 // QString epsilonString = QString("%1").arg(epsilon,
284 // 0, 'f', 60);
285
286 double scaleFactor = epsilon * valueSum * decimalPlaces;
287 // QString scaleFactorString = QString("%1").arg(scaleFactor,
288 // 0, 'f', 60);
289
290 // qWarning() << "valueDiff:" << valueDiffString << "valueSum:" <<
291 // valueSumString <<
292 //"epsilon:" << epsilonString << "scaleFactor:" << scaleFactorString;
293
294 bool res = valueDiff < scaleFactor
295 // unless the result is subnormal:
296 || valueDiff < std::numeric_limits<double>::min();
297
298 // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
299 //<< "returning res:" << res;
300
301 return res;
302}

References pappso::res.

◆ appendToFile()

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

Definition at line 194 of file utils.cpp.

195{
196
197 QFile file(file_name);
198
199 if(file.open(QFile::WriteOnly | QFile::Append))
200 {
201
202 QTextStream out(&file);
203
204 out << text;
205
206 out.flush();
207 file.close();
208
209 return true;
210 }
211
212 return false;
213}

◆ 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 423 of file utils.cpp.

424{
425 if(value)
426 return "TRUE";
427 return "FALSE";
428}

◆ 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 329 of file utils.cpp.

333{
334 QString debug_text =
335 QString(
336 "%1 %2 min = %3 s = %4 ms = %5 "
337 "µs\n")
338 .arg(msg)
339 .arg(std::chrono::duration_cast<std::chrono::minutes>(chrono_finish -
340 chrono_start)
341 .count())
342 .arg(std::chrono::duration_cast<std::chrono::seconds>(chrono_finish -
343 chrono_start)
344 .count())
345 .arg(std::chrono::duration_cast<std::chrono::milliseconds>(chrono_finish -
346 chrono_start)
347 .count())
348 .arg(std::chrono::duration_cast<std::chrono::microseconds>(chrono_finish -
349 chrono_start)
350 .count());
351
352 return debug_text;
353}

◆ 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 313 of file utils.cpp.

315{
316
317 time_t tt;
318
319 tt = std::chrono::system_clock::to_time_t(chrono_time);
320
321 QString debug_text =
322 QString("%1 - %2\n").arg(msg).arg(QString::fromLatin1(ctime(&tt)));
323
324 return debug_text;
325}

◆ 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 217 of file utils.cpp.

218{
219 qDebug() << " " << spectrum_native_id;
220 QStringList native_id_list = spectrum_native_id.split("=");
221 if(native_id_list.size() < 2)
222 {
223 throw ExceptionNotFound(
224 QObject::tr("scan number not found in mzML native id %1")
225 .arg(spectrum_native_id));
226 }
227 else
228 {
229 /** TODO activate this in a future release to ensure scan number
230 for(auto i = 0; i < native_id_list.size(); i += 2)
231 {
232 if(native_id_list[i] == "scan")
233 {
234 return native_id_list[i + 1].toULong();
235 }
236 }
237
238 throw ExceptionNotFound(
239 QObject::tr("scan number not found in mzML native id %1")
240 .arg(spectrum_native_id));
241
242*/
243 return native_id_list.back().toULong();
244 }
245 return 0;
246}

◆ 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 QString base(size);
57 base.append(QString().setNum(num));
58 return (base);
59}

References pappso::log10.

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

◆ nearestGreater()

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

Definition at line 306 of file utils.cpp.

307{
308 return std::nextafter(value, value + 1);
309}

◆ pointerToString()

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

Definition at line 250 of file utils.cpp.

251{
252 return QString("%1").arg(
253 (quintptr)pointer, QT_POINTER_SIZE * 2, 16, QChar('0'));
254}

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

◆ roundToDecimal32bitsAsLongLongInt()

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

Definition at line 130 of file utils.cpp.

131{
132 pappso::pappso_double test_decimal = 100000000000;
133 if(sizeof(int *) == 4)
134 { // 32bits
135 test_decimal = 100000000;
136 }
137 return (floor(input * test_decimal));
138}
double pappso_double
A type definition for doubles.
Definition: types.h:48

◆ roundToDecimals()

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

Definition at line 119 of file utils.cpp.

120{
121 if(decimal_places < 0)
122 return value;
123
124 return ceil((value * pow(10, decimal_places)) - 0.49) /
125 pow(10, decimal_places);
126}

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 357 of file utils.cpp.

359{
360
361 QStringList string_list =
362 text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts);
363
364 // qDebug() << "string list:" << string_list;
365
366 std::vector<double> double_vector;
367
368 for(int iter = 0; iter < string_list.size(); ++iter)
369 {
370 QString current_string = string_list.at(iter);
371
372 bool ok = false;
373
374 double current_double = current_string.toDouble(&ok);
375
376 if(!current_double && !ok)
377 {
378 ++error_count;
379 continue;
380 }
381
382 double_vector.push_back(current_double);
383 }
384
385 return double_vector;
386}

◆ splitSizetStringToSizetVectorWithSpaces()

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

Definition at line 390 of file utils.cpp.

392{
393 // qDebug() << "Parsing text:" << text;
394
395 QStringList string_list =
396 text.split(QRegularExpression("[\\s]+"), Qt::SkipEmptyParts);
397
398 // qDebug() << "string list size:" << string_list.size()
399 //<< "values:" << string_list;
400
401 std::vector<std::size_t> sizet_vector;
402
403 for(int iter = 0; iter < string_list.size(); ++iter)
404 {
405 QString current_string = string_list.at(iter);
406
407 bool ok = false;
408
409 std::size_t current_sizet = current_string.toUInt(&ok);
410
411 if(!current_sizet && !ok)
412 {
413 ++error_count;
414 continue;
415 }
416
417 sizet_vector.push_back(current_sizet);
418 }
419
420 return sizet_vector;
421}

◆ toUtf8StandardString()

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

Definition at line 142 of file utils.cpp.

143{
144 std::string env_backup = setlocale(LC_ALL, "");
145
146 // struct lconv *lc_backup = localeconv();
147 // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
148 //<< "env_backup=" << env_backup.c_str() << "lc_backup->decimal_point"
149 //<< lc_backup->decimal_point;
150
151 // Force locale to be "C".
152 setlocale(LC_ALL, "C");
153
154 // Now perform the conversion.
155 QByteArray byte_array = text.toUtf8();
156 std::string stdText = "";
157
158 for(char c : byte_array)
159 {
160 stdText += c;
161 }
162
163 // Set back the locale to the backed-up one.
164 setlocale(LC_ALL, env_backup.c_str());
165
166 return stdText;
167}

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 63 of file utils.cpp.

64{
65 *p_out << (char)(log10(num) + 97) << num;
66}

References pappso::log10.

◆ writeToFile()

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

Definition at line 171 of file utils.cpp.

172{
173
174 QFile file(file_name);
175
176 if(file.open(QFile::WriteOnly | QFile::Truncate))
177 {
178
179 QTextStream out(&file);
180
181 out << text;
182
183 out.flush();
184 file.close();
185
186 return true;
187 }
188
189 return false;
190}

◆ 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 81 of file utils.cpp.

82{
83 //qDebug() << qSetRealNumberPrecision(10) << "Double value: " << value;
84
85 int intPart = static_cast<int>(value);
86
87 //qDebug() << "int part:" << intPart;
88
89 double decimalPart = value - intPart;
90
91 //qDebug() << qSetRealNumberPrecision(10) << "decimal part: " << decimalPart;
92
93 int count = 0;
94
95 while(decimalPart > 0)
96 {
97 ++count;
98
99 decimalPart *= 10;
100
101 //qDebug() << "Iteration " << count << "decimal part:" << decimalPart;
102
103 if(decimalPart >= 1)
104 {
105 //qDebug() << "Because decimal part " << decimalPart
106 //<< "is >= 1, breaking loop while count is " << count << ".";
107
108 break;
109 }
110 }
111
112 //qDebug() << "Returning count:" << count;
113
114 return count;
115}

Referenced by pappso::MzIntegrationParams::createArbitraryBins().

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 62 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 56 of file utils.h.

◆ sizetListDataFormatRegExp

QRegularExpression pappso::Utils::sizetListDataFormatRegExp
static

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

Definition at line 59 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 53 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: