pappso::Utils Class Reference

#include <utils.h>

Static Public Member Functions
static QString	getVersion ()
static const QString	getLexicalOrderedString (unsigned int num)
static void	writeLexicalOrderedString (QTextStream *p_out, unsigned int num)
static int	zeroDecimalsInValue (pappso_double value)
	Determine the number of zero decimals between the decimal point and the first non-zero decimal.
static pappso_double	roundToDecimals (pappso_double value, int decimal_places)
static long long int	roundToDecimal32bitsAsLongLongInt (pappso_double input)
static std::string	toUtf8StandardString (const QString &text)
static bool	writeToFile (const QString &text, const QString &file_name)
static bool	writeToFile (const std::vector< double > &data, int decimals, 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)
	Tell if both double values, are equal within the double representation capabilities of the platform.
static double	roundValueToDecimalPlaces (double value, int decimal_places, bool round_up=true)
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	msDataFormatAsString (Enums::MsDataFormat mz_format)
	Convenience function to return a string describing the MzFormat of a file.
static QString	fileReaderTypeAsString (Enums::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 QString	toString (Enums::PrecisionUnit precision_unit)
	Convenience function to return a string naming the precision.
static QString	toString (Enums::PeptideIon m_ionType)
	Convenience function to return a string describing the ion type.
static AaModificationP	guessAaModificationPbyMonoisotopicMassDelta (Enums::AminoAcidChar aa, pappso_double mass, QChar position=' ')
	get the most suitable modification given an amino acid, a mass and a position
static bool	isAminoAcidChar (Enums::AminoAcidChar x)
static AaModificationP	translateAaModificationFromUnimod (const QString &unimod_accession)
static QJsonArray	toJson (const std::vector< double > &myVec)
	convert vector of double into json array

Static Public Attributes
static QRegularExpression	unsignedDoubleNumberNoExponentialRegExp
static QRegularExpression	anythingButDigitDotDash = QRegularExpression("[^\\d^\\.^-]+")
static QRegularExpression	signedDoubleNumberExponentialRegExp
static QRegularExpression	xyMassDataFormatRegExp
	Regular expression matching <numerical value><non-numerical*><numerical value>.
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 50 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 327 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;
}

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

appendToFile()

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

static

Definition at line 263 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;
}

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 497 of file utils.cpp.

{
  if(value)
    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 414 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 399 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 286 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;
}

Referenced by pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum().

fileReaderTypeAsString()

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

static

Definition at line 548 of file utils.cpp.

{
 
  if(file_reader_type == Enums::FileReaderType::pwiz)
    return "pwiz";
  else if(file_reader_type == Enums::FileReaderType::xy)
    return "xy";
  else if(file_reader_type == Enums::FileReaderType::tims)
    return "tims";
  else if(file_reader_type == Enums::FileReaderType::tims_frames)
    return "tims_frames";
  else
    return "unknown";
}

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

getLexicalOrderedString()

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

static

Definition at line 73 of file utils.cpp.

{
  int size = log10(num);
  size += 97;
  QLatin1Char latin1_char(size);
  QString base(latin1_char);
  base.append(QString().setNum(num));
  return (base);
}

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

getVersion()

QString pappso::Utils::getVersion ( )

static

Definition at line 670 of file utils.cpp.

{
  QString version(PAPPSOMSPP_VERSION);
  return version;
}

References PAPPSOMSPP_VERSION.

Referenced by pappso::cbor::psm::MzIdentMlReader::MzIdentMlReader(), pappso::cbor::psm::SageFileReader::SageFileReader(), pappso::cbor::psm::PsmFileScanProcessAndCopy::informationsReady(), pappso::cbor::mzcbor::MzcborCopyReplaceBase::readCbor(), and pappso::cbor::CborStreamWriter::writeInformations().

guessAaModificationPbyMonoisotopicMassDelta()

pappso::AaModificationP pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta ( Enums::AminoAcidChar aa, pappso::pappso_double mass, QChar position = ' ' )

static

get the most suitable modification given an amino acid, a mass and a position

@aa amino acid @mass float m/z @position protein or peptide position in ['^','$', '[', ']'], default is a space

Definition at line 678 of file utils.cpp.

{
  if((position != '[') && (!Utils::isAminoAcidChar(aa)))
    {
      throw pappso::PappsoException(
        QObject::tr("Utils::guessAaModificationPbyMonoisotopicMassDelta => "
                    "not an amino acid %1")
          .arg((char)aa));
    }
  pappso::PrecisionPtr precision = pappso::PrecisionFactory::getDaltonInstance(0.01);
 
  pappso::AaModificationP oxidation =
    pappso::AaModification::getInstance("MOD:00425"); // MOD:00425 15.994915
  if((aa == pappso::Enums::AminoAcidChar::methionine) &&
     pappso::MzRange(oxidation->getMass(), precision).contains(mass))
    {
      return oxidation;
    }
  pappso::AaModificationP iodoacetamide =
    pappso::AaModification::getInstance("MOD:00397"); // 57.021465
  if(pappso::MzRange(iodoacetamide->getMass(), precision).contains(mass))
    {
      return iodoacetamide;
    }
  pappso::AaModificationP acetylated =
    pappso::AaModification::getInstance("MOD:00408"); // 42.010567
  if(pappso::MzRange(acetylated->getMass(), precision).contains(mass))
    {
      return acetylated;
    }
  pappso::AaModificationP phosphorylated =
    pappso::AaModification::getInstance("MOD:00696"); // 79.96633
  if(pappso::MzRange(phosphorylated->getMass(), precision).contains(mass))
    {
      return phosphorylated;
    }
  pappso::AaModificationP ammonia = pappso::AaModification::getInstance("MOD:01160"); //-17.026548
  if(pappso::MzRange(ammonia->getMass(), precision).contains(mass))
    {
      return ammonia;
    }
  pappso::AaModificationP dehydrated =
    pappso::AaModification::getInstance("MOD:00704"); //-18.010565
  pappso::AaModificationP glu_pyroglu =
    pappso::AaModification::getInstance("MOD:00420"); // Glu->pyro-Glu
  if(pappso::MzRange(dehydrated->getMass(), precision).contains(mass))
    {
      if((aa == Enums::AminoAcidChar::glutamic_acid) && (position == '^'))
        {
          return glu_pyroglu;
        }
      else
        {
          return dehydrated;
        }
    }
  pappso::AaModificationP dimethylated =
    pappso::AaModification::getInstance("MOD:00429"); // 28.0313
  if(pappso::MzRange(dimethylated->getMass(), precision).contains(mass))
    {
      return dimethylated;
    }
 
  pappso::AaModificationP dimethylated_medium = pappso::AaModification::getInstance("MOD:00552");
  if(pappso::MzRange(dimethylated_medium->getMass(), precision).contains(mass))
    {
      return dimethylated_medium;
    }
 
  pappso::AaModificationP dimethylated_heavy = pappso::AaModification::getInstance("MOD:00638");
  if(pappso::MzRange(dimethylated_heavy->getMass(), precision).contains(mass))
    {
      return dimethylated_heavy;
    }
  pappso::AaModificationP DimethylpyrroleAdduct = pappso::AaModification::getInstance("MOD:00628");
  if(pappso::MzRange(DimethylpyrroleAdduct->getMass(), precision).contains(mass))
    {
      return DimethylpyrroleAdduct;
    }
 
  // modification not found, creating customized mod :
  return pappso::AaModification::getInstanceCustomizedMod(mass);
 
  throw pappso::ExceptionNotFound(
    QObject::tr("Utils::guessAaModificationPbyMonoisotopicMassDelta => "
                "modification not found for mass %1")
      .arg(mass));
}

References pappso::MzRange::contains(), pappso::PrecisionFactory::getDaltonInstance(), pappso::AaModification::getInstance(), pappso::AaModification::getInstanceCustomizedMod(), pappso::AaModification::getMass(), pappso::Enums::glutamic_acid, isAminoAcidChar(), and pappso::Enums::methionine.

Referenced by pappso::cbor::psm::SageReader::getStaticModificationList(), pappso::cbor::psm::SageReader::getVariableModificationList(), pappso::PeptideProFormaParser::parseStringToPeptide(), and pappso::cbor::psm::MzIdentMlReader::readPeptide().

isAminoAcidChar()

bool pappso::Utils::isAminoAcidChar ( Enums::AminoAcidChar x )

static

Definition at line 822 of file utils.cpp.

{
  switch(x)
    {
      case Enums::AminoAcidChar::alanine:
      case Enums::AminoAcidChar::cysteine:
      case Enums::AminoAcidChar::aspartic_acid:
      case Enums::AminoAcidChar::glutamic_acid:
      case Enums::AminoAcidChar::phenylalanine:
      case Enums::AminoAcidChar::glycine:
      case Enums::AminoAcidChar::histidine:
      case Enums::AminoAcidChar::isoleucine:
      case Enums::AminoAcidChar::lysine:
      case Enums::AminoAcidChar::leucine:
      case Enums::AminoAcidChar::methionine:
      case Enums::AminoAcidChar::asparagine:
      case Enums::AminoAcidChar::proline:
      case Enums::AminoAcidChar::glutamine:
      case Enums::AminoAcidChar::arginine:
      case Enums::AminoAcidChar::serine:
      case Enums::AminoAcidChar::threonine:
      case Enums::AminoAcidChar::valine:
      case Enums::AminoAcidChar::tryptophan:
      case Enums::AminoAcidChar::tyrosine:
      case Enums::AminoAcidChar::selenocysteine:
      case Enums::AminoAcidChar::pyrrolysine:
        return true;
 
      default:
        return false;
    }
}

References pappso::Enums::alanine, pappso::Enums::arginine, pappso::Enums::asparagine, pappso::Enums::aspartic_acid, pappso::Enums::cysteine, pappso::Enums::glutamic_acid, pappso::Enums::glutamine, pappso::Enums::glycine, pappso::Enums::histidine, pappso::Enums::isoleucine, pappso::Enums::leucine, pappso::Enums::lysine, pappso::Enums::methionine, pappso::Enums::phenylalanine, pappso::Enums::proline, pappso::Enums::pyrrolysine, pappso::Enums::selenocysteine, pappso::Enums::serine, pappso::Enums::threonine, pappso::Enums::tryptophan, pappso::Enums::tyrosine, pappso::Enums::valine, and pappso::x.

Referenced by pappso::cbor::psm::SageReader::getVariableModificationList(), and guessAaModificationPbyMonoisotopicMassDelta().

msDataFormatAsString()

QString pappso::Utils::msDataFormatAsString ( Enums::MsDataFormat 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 505 of file utils.cpp.

{
 
  if(mz_format == Enums::MsDataFormat::mzML)
    return "mzML";
  else if(mz_format == Enums::MsDataFormat::mzXML)
    return "mzXML";
  else if(mz_format == Enums::MsDataFormat::MGF)
    return "MGF";
  else if(mz_format == Enums::MsDataFormat::SQLite3)
    return "SQLite3";
  else if(mz_format == Enums::MsDataFormat::xy)
    return "xy";
  else if(mz_format == Enums::MsDataFormat::mz5)
    return "mz5";
  else if(mz_format == Enums::MsDataFormat::msn)
    return "msn";
  else if(mz_format == Enums::MsDataFormat::abSciexWiff)
    return "abSciexWiff";
  else if(mz_format == Enums::MsDataFormat::abSciexT2D)
    return "abSciexT2D";
  else if(mz_format == Enums::MsDataFormat::agilentMassHunter)
    return "agilentMassHunter";
  else if(mz_format == Enums::MsDataFormat::thermoRaw)
    return "thermoRaw";
  else if(mz_format == Enums::MsDataFormat::watersRaw)
    return "watersRaw";
  else if(mz_format == Enums::MsDataFormat::brukerFid)
    return "brukerFid";
  else if(mz_format == Enums::MsDataFormat::brukerYep)
    return "brukerYep";
  else if(mz_format == Enums::MsDataFormat::brukerBaf)
    return "brukerBaf";
  else if(mz_format == Enums::MsDataFormat::brukerTims)
    return "brukerTims";
  else if(mz_format == Enums::MsDataFormat::brukerBafAscii)
    return "brukerBafAscii";
  else
    return "unknown";
}

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

nearestGreater()

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

static

Definition at line 392 of file utils.cpp.

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

pointerToString()

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

static

Definition at line 318 of file utils.cpp.

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

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

roundToDecimal32bitsAsLongLongInt()

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

static

Definition at line 151 of file utils.cpp.

{
  pappso::pappso_double test_decimal = 100000000000;
  if(sizeof(int *) == 4)
    { // 32bits
      test_decimal = 100000000;
    }
  return (floor(input * test_decimal));
}

roundToDecimals()

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

static

Definition at line 141 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::TraceMinusCombiner::combine(), and pappso::TracePlusCombiner::combine().

roundValueToDecimalPlaces()

double pappso::Utils::roundValueToDecimalPlaces ( double value, int decimal_places, bool round_up = true )

static

Definition at line 372 of file utils.cpp.

{
  if(decimal_places < 0)
    return value;
 
  double multiplier = std::pow(10.0, decimal_places);
 
  if(round_up)
    {
      // Strict ceiling: round UP.
      return std::ceil(value * multiplier) / multiplier;
    }
  else
    {
      // Add a tiny epsilon (1e-9) to counteract the "1.005" floating-point trap
      return std::round(value * multiplier + 1e-9) / multiplier;
    }
}

Referenced by pappso::MzIntegrationParams::createArbitraryBins(), and pappso::MzIntegrationParams::createDataBasedBins().

splitMzStringToDoubleVectorWithSpaces()

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

static

Definition at line 435 of file utils.cpp.

{
 
  QStringList string_list = text.split(QRegularExpression("[\\s]+"), Qt::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 466 of file utils.cpp.

{
  // qDebug() << "Parsing text:" << text;
 
  QStringList string_list = text.split(QRegularExpression("[\\s]+"), Qt::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;
}

toJson()

QJsonArray pappso::Utils::toJson ( const std::vector< double > & myVec )

static

convert vector of double into json array

Definition at line 811 of file utils.cpp.

{
  QJsonArray result;
  for(auto i = myVec.begin(); i != myVec.end(); i++)
    {
      result.push_back((*i));
    }
  return result;
}

Referenced by pappso::MassSpectrumWidget::getJsonPsmIsotope().

toString() [1/4]

QString pappso::Utils::toString ( Enums::PeptideIon m_ionType )

static

Convenience function to return a string describing the ion type.

Returns

QString

Definition at line 584 of file utils.cpp.

{
  switch(m_ionType)
    {
      case Enums::PeptideIon::y:
        return "y";
        break;
      case Enums::PeptideIon::yp:
        return "yP";
        break;
      case Enums::PeptideIon::ystar:
        return "y*";
        break;
      case Enums::PeptideIon::yo:
        return "yO";
        break;
      case Enums::PeptideIon::bstar:
        return "b*";
        break;
      case Enums::PeptideIon::bo:
        return "bO";
        break;
      case Enums::PeptideIon::a:
        return "a";
        break;
      case Enums::PeptideIon::astar:
        return "a*";
        break;
      case Enums::PeptideIon::ao:
        return "aO";
        break;
      case Enums::PeptideIon::c:
        return "c";
        break;
        // SvgIon.moxygen - mN
      case Enums::PeptideIon::z:
        return "z";
        break;
      case Enums::PeptideIon::b:
        return "b";
        break;
      case Enums::PeptideIon::bp:
        return "bP";
        break;
      case Enums::PeptideIon::x:
        return "x";
        break;
      default:
        throw PappsoException(QString("Enums::PeptideIon name not implemented"));
        break;
    }
}

References pappso::Enums::a, pappso::Enums::ao, pappso::Enums::astar, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::c, pappso::Enums::x, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, pappso::Enums::ystar, and pappso::Enums::z.

toString() [2/4]

QString pappso::Utils::toString ( Enums::PrecisionUnit precision_unit )

static

Convenience function to return a string naming the precision.

Returns

QString

Definition at line 658 of file utils.cpp.

{
  auto it = precisionUnitMap.find(precision_unit);
  if(it != precisionUnitMap.end())
    {
      return it->second;
    }
 
  throw pappso::ExceptionNotFound(QObject::tr("precision unit not found in precisionUnitMap"));
}

References pappso::precisionUnitMap.

toString() [3/4]

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 639 of file utils.cpp.

{
  switch(type)
    {
      case specglob::ExperimentalSpectrumDataPointType::both:
        return "both";
        break;
      case specglob::ExperimentalSpectrumDataPointType::native:
        return "native";
        break;
      case specglob::ExperimentalSpectrumDataPointType::symmetric:
        return "symmetric";
        break;
      default:
        return "synthetic";
    }
}

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

toString() [4/4]

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

static

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

Returns

QString

Definition at line 564 of file utils.cpp.

{
  switch(type)
    {
      case specglob::SpectralAlignmentType::align:
        return "AL";
        break;
      case specglob::SpectralAlignmentType::nonAlign:
        return "NA";
        break;
      case specglob::SpectralAlignmentType::reAlign:
        return "RA";
        break;
      default:
        return "ER";
    }
}

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

Referenced by pappso::MassSpectrumWidget::getJsonPsmIsotope(), pappso::Peptide::getMassIonSerie(), pappso::cbor::psm::PsmFeatures::parameterMapReady(), pappso::cbor::psm::PsmIonSeries::parameterMapReady(), pappso::cbor::psm::PsmIonSeriesScan::process(), pappso::specglob::PeptideModel::toProForma(), and pappso::specglob::PeptideModel::toString().

toUtf8StandardString()

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

static

Definition at line 167 of file utils.cpp.

{
  std::string env_backup;
  try
    {
#ifdef MXE
      // std::locale::global(std::locale("C")); // set locale to default locale
      env_backup = std::setlocale(LC_ALL, nullptr);
      std::setlocale(LC_ALL, "C");
#else
      std::locale::global(std::locale("C")); // set locale to default locale
#endif
    }
  catch(std::exception &error)
    {
      throw pappso::PappsoException(
        QObject::tr("Error trying to set local to C : %1").arg(error.what()));
    }
  // Now perform the conversion.
  QByteArray byte_array = text.toUtf8();
  std::string stdText   = "";
 
  for(char c : byte_array)
    {
      stdText += c;
    }
 
  try
    {
#ifdef MXE
      // std::locale::global(std::locale("C")); // set locale to default locale
      std::setlocale(LC_ALL, env_backup.c_str());
#else // Set back the locale to the backed-up one.
      std::locale::global(std::locale("")); // sets locale according to OS environment
#endif
    }
  catch(std::exception &error)
    {
 
      throw pappso::PappsoException(
        QObject::tr("Error trying to set local to original system one %1 : %2")
          .arg(env_backup.c_str())
          .arg(error.what()));
    }
 
  return stdText;
}

References pappso::c.

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

translateAaModificationFromUnimod()

pappso::AaModificationP pappso::Utils::translateAaModificationFromUnimod ( const QString & unimod_accession )

static

Definition at line 771 of file utils.cpp.

{
  if(unimod_accession == "UNIMOD:1")
    {
 
      return pappso::AaModification::getInstance("MOD:00394");
    }
  if(unimod_accession == "UNIMOD:4")
    {
 
      return pappso::AaModification::getInstance("MOD:00397");
    }
  if(unimod_accession == "UNIMOD:7")
    {
 
      return pappso::AaModification::getInstance("MOD:00400");
    }
  if(unimod_accession == "UNIMOD:27")
    {
 
      return pappso::AaModification::getInstance("MOD:00420");
    }
  // UNIMOD:28 => MOD:00040
  if(unimod_accession == "UNIMOD:28")
    {
 
      return pappso::AaModification::getInstance("MOD:00040");
    }
 
  if(unimod_accession == "UNIMOD:35")
    {
 
      return pappso::AaModification::getInstance("MOD:00425");
    }
  qInfo() << "unimod_accession:" << unimod_accession << " not found";
  return nullptr;
}

References pappso::AaModification::getInstance().

Referenced by pappso::cbor::psm::MzIdentMlReader::readPeptide().

writeLexicalOrderedString()

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

static

Definition at line 85 of file utils.cpp.

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

writeToFile() [1/2]

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

static

Definition at line 217 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;
}

Referenced by pappso::MzIntegrationParams::createArbitraryBins(), and pappso::MzIntegrationParams::createDataBasedBins().

writeToFile() [2/2]

bool pappso::Utils::writeToFile ( const std::vector< double > & data, int decimals, const QString & file_name )

static

Definition at line 240 of file utils.cpp.

{
  QFile file(file_name);
 
  if(file.open(QFile::WriteOnly | QFile::Append))
    {
      file.open(QIODevice::WriteOnly);
 
      QTextStream fileStream(&file);
 
      for(auto &&value : data)
        fileStream << QString("%1\n").arg(value, 0, 'f', decimals);
 
      fileStream.flush();
      file.close();
 
      return true;
    }
 
  return false;
}

zeroDecimalsInValue()

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

static

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

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

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 103 of file utils.cpp.

{
  // qDebug() << qSetRealNumberPrecision(10) << "Double value: " << value;
 
  int intPart = static_cast<int>(value);
 
  // qDebug() << "int part:" << intPart;
 
  double decimalPart = value - intPart;
 
  // qDebug() << qSetRealNumberPrecision(10) << "decimal part: " << decimalPart;
 
  int count = 0;
 
  while(decimalPart > 0)
    {
      ++count;
 
      decimalPart *= 10;
 
      // qDebug() << "Iteration " << count << "decimal part:" << decimalPart;
 
      if(decimalPart >= 1)
        {
          // qDebug() << "Because decimal part " << decimalPart
          //<< "is >= 1, breaking loop while count is " << count << ".";
 
          break;
        }
    }
 
  // qDebug() << "Returning count:" << count - 1;
 
  return count - 1;
}

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

Member Data Documentation

anythingButDigitDotDash

QRegularExpression pappso::Utils::anythingButDigitDotDash = QRegularExpression("[^\\d^\\.^-]+")

static

Definition at line 55 of file utils.h.

endOfLineRegExp

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

static

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

Definition at line 69 of file utils.h.

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

mzListDataFormatRegExp

QRegularExpression pappso::Utils::mzListDataFormatRegExp

static

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

Definition at line 63 of file utils.h.

signedDoubleNumberExponentialRegExp

QRegularExpression pappso::Utils::signedDoubleNumberExponentialRegExp

static

Initial value:

                                                            =
QRegularExpression("-?\\d*\\.?\\d*[e-]?\\d*")

Definition at line 56 of file utils.h.

sizetListDataFormatRegExp

QRegularExpression pappso::Utils::sizetListDataFormatRegExp

static

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

Definition at line 66 of file utils.h.

unsignedDoubleNumberNoExponentialRegExp

QRegularExpression pappso::Utils::unsignedDoubleNumberNoExponentialRegExp

static

Initial value:

                                                                =
QRegularExpression("\\d*\\.?\\d+")

Definition at line 54 of file utils.h.

Referenced by pappso::BafAsciiMsRunReader::craftLineParserRegExpPattern(), and pappso::BafAsciiFileReader::initialize().

xyMassDataFormatRegExp

QRegularExpression pappso::Utils::xyMassDataFormatRegExp

static

Initial value:

                                               =
 
QRegularExpression(QString("^(%1)(%2)(%3)")
                     .arg(Utils::unsignedDoubleNumberNoExponentialRegExp.pattern())
                     .arg(Utils::anythingButDigitDotDash.pattern())
                     .arg(Utils::signedDoubleNumberExponentialRegExp.pattern()))

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

Definition at line 60 of file utils.h.

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

---

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

• pappsomspp/core/utils.h
• pappsomspp/core/utils.cpp