#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 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 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 233 of file utils.cpp.

 {
   // QString value1String = QString("%1").arg(value1,
   // 0, 'f', 60);
   // QString value2String = QString("%1").arg(value2,
   // 0, 'f', 60);
  
   // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
   //<< "value1:" << value1String << "value2:" << value2String;
  
   // The machine epsilon has to be scaled to the magnitude of the values used
   // and multiplied by the desired precision in ULPs (units in the last place)
   // (decimal places).
  
   double valueSum = std::abs(value1 + value2);
   // QString valueSumString = QString("%1").arg(valueSum,
   // 0, 'f', 60);
  
   double valueDiff = std::abs(value1 - value2);
   // QString valueDiffString = QString("%1").arg(valueDiff,
   // 0, 'f', 60);
  
   double epsilon = std::numeric_limits<double>::epsilon();
   // QString epsilonString = QString("%1").arg(epsilon,
   // 0, 'f', 60);
  
   double scaleFactor = epsilon * valueSum * decimalPlaces;
   // QString scaleFactorString = QString("%1").arg(scaleFactor,
   // 0, 'f', 60);
  
   // qWarning() << "valueDiff:" << valueDiffString << "valueSum:" <<
   // valueSumString <<
   //"epsilon:" << epsilonString << "scaleFactor:" << scaleFactorString;
  
   bool res = valueDiff < scaleFactor
              // unless the result is subnormal:
              || valueDiff < std::numeric_limits<double>::min();
  
   // qWarning() << __FILE__ << __LINE__ << __FUNCTION__
   //<< "returning res:" << res;
  
   return res;
 }

References pappso::res.

◆ appendToFile()

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

static

Definition at line 167 of file utils.cpp.

 {
  
   QFile file(file_name);
  
   if(file.open(QFile::WriteOnly | QFile::Append))
     {
  
       QTextStream out(&file);
  
       out << text;
  
       out.flush();
       file.close();
  
       return true;
     }
  
   return false;
 }

◆ 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 302 of file utils.cpp.

 {
   QString debug_text =
     QString(
       "%1 %2 min = %3 s = %4 ms = %5 "
       "µs\n")
       .arg(msg)
       .arg(std::chrono::duration_cast<std::chrono::minutes>(chrono_finish -
                                                             chrono_start)
              .count())
       .arg(std::chrono::duration_cast<std::chrono::seconds>(chrono_finish -
                                                             chrono_start)
              .count())
       .arg(std::chrono::duration_cast<std::chrono::milliseconds>(chrono_finish -
                                                                  chrono_start)
              .count())
       .arg(std::chrono::duration_cast<std::chrono::microseconds>(chrono_finish -
                                                                  chrono_start)
              .count());
  
   return debug_text;
 }

◆ 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 286 of file utils.cpp.

 {
  
   time_t tt;
  
   tt = std::chrono::system_clock::to_time_t(chrono_time);
  
   QString debug_text =
     QString("%1 - %2\n").arg(msg).arg(QString::fromLatin1(ctime(&tt)));
  
   return debug_text;
 }

◆ 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 190 of file utils.cpp.

 {
   qDebug() << " " << spectrum_native_id;
   QStringList native_id_list = spectrum_native_id.split("=");
   if(native_id_list.size() < 2)
     {
       throw ExceptionNotFound(
         QObject::tr("scan number not found in mzML native id %1")
           .arg(spectrum_native_id));
     }
   else
     {
       /** 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));
  
 */
       return native_id_list.back().toULong();
     }
   return 0;
 }

◆ getLexicalOrderedString()

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

static

Definition at line 52 of file utils.cpp.

 {
   int size = log10(num);
   size += 97;
   QString base(size);
   base.append(QString().setNum(num));
   return (base);
 }

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 279 of file utils.cpp.

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

◆ pointerToString()

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

static

Definition at line 223 of file utils.cpp.

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

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

◆ roundToDecimals()

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

static

Definition at line 104 of file utils.cpp.

 {
   if(decimal_places < 0)
     return value;
  
   return ceil((value * pow(10, decimal_places)) - 0.49) /
          pow(10, decimal_places);
 }

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 330 of file utils.cpp.

 {
  
   QStringList string_list =
     text.split(QRegularExpression("[\\s]+"), QString::SkipEmptyParts);
  
   // qDebug() << "string list:" << string_list;
  
   std::vector<double> double_vector;
  
   for(int iter = 0; iter < string_list.size(); ++iter)
     {
       QString current_string = string_list.at(iter);
  
       bool ok = false;
  
       double current_double = current_string.toDouble(&ok);
  
       if(!current_double && !ok)
         {
           ++error_count;
           continue;
         }
  
       double_vector.push_back(current_double);
     }
  
   return double_vector;
 }

◆ splitSizetStringToSizetVectorWithSpaces()

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

static

Definition at line 363 of file utils.cpp.

 {
   // qDebug() << "Parsing text:" << text;
  
   QStringList string_list =
     text.split(QRegularExpression("[\\s]+"), QString::SkipEmptyParts);
  
   // qDebug() << "string list size:" << string_list.size()
   //<< "values:" << string_list;
  
   std::vector<std::size_t> sizet_vector;
  
   for(int iter = 0; iter < string_list.size(); ++iter)
     {
       QString current_string = string_list.at(iter);
  
       bool ok = false;
  
       std::size_t current_sizet = current_string.toUInt(&ok);
  
       if(!current_sizet && !ok)
         {
           ++error_count;
           continue;
         }
  
       sizet_vector.push_back(current_sizet);
     }
  
   return sizet_vector;
 }

◆ toUtf8StandardString()

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

static

Definition at line 115 of file utils.cpp.

 {
   std::string env_backup = setlocale(LC_ALL, "");
  
   // struct lconv *lc_backup = localeconv();
   // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
   //<< "env_backup=" << env_backup.c_str() << "lc_backup->decimal_point"
   //<< lc_backup->decimal_point;
  
   // Force locale to be "C".
   setlocale(LC_ALL, "C");
  
   // Now perform the conversion.
   QByteArray byte_array = text.toUtf8();
   std::string stdText   = "";
  
   for(char c : byte_array)
     {
       stdText += c;
     }
  
   // Set back the locale to the backed-up one.
   setlocale(LC_ALL, env_backup.c_str());
  
   return stdText;
 }

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.

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

References pappso::log10.

◆ writeToFile()

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

static

Definition at line 144 of file utils.cpp.

 {
  
   QFile file(file_name);
  
   if(file.open(QFile::WriteOnly | QFile::Truncate))
     {
  
       QTextStream out(&file);
  
       out << text;
  
       out.flush();
       file.close();
  
       return true;
     }
  
   return false;
 }

◆ 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

value the 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.

 {
   int intPart = static_cast<int>(value);
  
   double decimalPart = value - intPart;
  
   int count = -1;
  
   while(1)
     {
       ++count;
  
       decimalPart *= 10;
  
       if(decimalPart > 1)
         return count;
     }
  
   return count;
 }

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:

pappsomspp/utils.h
pappsomspp/utils.cpp

Static Public Member Functions

Static Public Attributes

Detailed Description

Member Function Documentation

◆ almostEqual()

◆ appendToFile()

◆ chronoIntervalDebugString()

◆ chronoTimePointDebugString()

◆ extractScanNumberFromMzmlNativeId()

◆ getLexicalOrderedString()

◆ nearestGreater()

◆ pointerToString()

◆ roundToDecimals()

◆ splitMzStringToDoubleVectorWithSpaces()

◆ splitSizetStringToSizetVectorWithSpaces()

◆ toUtf8StandardString()

◆ writeLexicalOrderedString()

◆ writeToFile()

◆ zeroDecimalsInValue()

Member Data Documentation

◆ endOfLineRegExp

◆ mzListDataFormatRegExp

◆ sizetListDataFormatRegExp

◆ xyMassDataFormatRegExp