47#include "../../utils.h"
48#include "../../massspectrum/massspectrum.h"
56 qRegisterMetaType<pappso::MzIntegrationParams>(
"pappso::MzIntegrationParams");
58 qRegisterMetaType<pappso::MzIntegrationParams *>(
59 "pappso::MzIntegrationParams *");
86 bool removeZeroValDataPoints)
87 : m_smallestMz(minMz),
89 m_binningType(binningType),
90 m_decimalPlaces(decimalPlaces),
91 mp_precision(precisionPtr),
92 m_binSizeDivisor(binSizeDivisor),
93 m_removeZeroValDataPoints(removeZeroValDataPoints)
103 : m_smallestMz(other.m_smallestMz),
104 m_greatestMz(other.m_greatestMz),
105 m_binningType(other.m_binningType),
106 m_decimalPlaces(other.m_decimalPlaces),
107 mp_precision(other.mp_precision),
108 m_binSizeDivisor(other.m_binSizeDivisor),
109 m_removeZeroValDataPoints(other.m_removeZeroValDataPoints)
290 errors += (
m_smallestMz == std::numeric_limits<double>::max() ? 1 : 0);
295 errors += (
m_greatestMz == std::numeric_limits<double>::min() ? 1 : 0);
306 <<
"The m/z integration parameters are not valid or do not apply...";
316 return (
m_smallestMz != std::numeric_limits<double>::max()) &&
327 std::vector<double> bins;
343 qFatal(
"Programming error.");
356 std::vector<double> bins;
436 double first_mz = ceil((min_mz * std::pow(10,
m_decimalPlaces)) - 0.49) /
448 std::vector<pappso::pappso_double> bins;
461 bins.push_back(previous_mz_bin);
470 while(previous_mz_bin <= last_mz)
490 current_mz = previous_mz_bin +
503 double current_rounded_mz =
517 if(current_rounded_mz == previous_mz_bin)
530 bins.push_back(current_rounded_mz);
533 previous_mz_bin = current_rounded_mz;
539 QString fileName =
"/tmp/massSpecArbitraryBins.txt-at-" +
540 QDateTime::currentDateTime().toString(
"yyyyMMdd-HH-mm-ss");
542 qDebug() <<
"Writing the list of bins setup in the "
543 "mass spectrum in file "
546 QFile file(fileName);
547 file.open(QIODevice::WriteOnly);
549 QTextStream fileStream(&file);
551 for(
auto &&bin : bins)
552 fileStream << QString(
"%1\n").arg(bin, 0,
'f', 10);
578 std::vector<pappso::pappso_double> bins;
580 if(mass_spectrum_csp->size() < 2)
587 local_mass_spectrum.
sortMz();
608 std::vector<pappso::DataPoint>::const_iterator it =
609 local_mass_spectrum.begin();
619 while(it != local_mass_spectrum.end())
628 end_mz_out = start_mz_in + step;
639 bins.push_back(start_mz_in);
642 start_mz_in = end_mz_out;
653 QString fileName =
"/tmp/massSpecDataBasedBins.txt";
655 qDebug() <<
"Writing the list of bins setup in the "
656 "mass spectrum in file "
659 QFile file(fileName);
660 file.open(QIODevice::WriteOnly);
662 QTextStream fileStream(&file);
664 for(
auto &&bin : m_bins)
665 fileStream << QString(
"[%1-%2]\n")
666 .arg(bin.startMzIn, 0,
'f', 10)
667 .arg(bin.endMzOut, 0,
'f', 10);
672 qDebug() <<
"elements."
673 <<
"starting with mz" << m_bins.front().startMzIn <<
"ending with mz"
674 << m_bins.back().endMzOut;
687 for(
int iter = 0; iter < offset; ++iter)
691 text +=
"m/z integration parameters:\n";
697 QString::asprintf(
"Smallest (first) m/z: %.6f\n",
m_smallestMz));
702 text.append(QString::asprintf(
"Greatest (last) m/z: %.6f\n",
m_greatestMz));
708 std::map<BinningType, QString>::iterator it;
712 qFatal(
"Programming error.");
716 text.append(QString(
"Binning type: %1\n").arg(it->second.toLatin1().data()));
725 text.append(QString(
"Bin nominal size: %1\n")
731 text.append(QString(
"Bin size: %2\n")
744 text += QString(
"Remove 0-val data points: %1\n")
Class to represent a mass spectrum.
void sortMz()
Sort the DataPoint instances of this spectrum.
The MzIntegrationParams class provides the parameters definining how m/z !
Q_INVOKABLE BinningType getBinningType() const
Q_INVOKABLE int getDecimalPlaces() const
pappso::pappso_double getSmallestMz() const
pappso::pappso_double m_smallestMz
MzIntegrationParams & operator=(const MzIntegrationParams &other)
int getBinSizeDivisor() const
BinningType m_binningType
Q_INVOKABLE pappso::pappso_double getGreatestMz() const
pappso::pappso_double m_greatestMz
Q_INVOKABLE MzIntegrationParams()
Q_INVOKABLE pappso::PrecisionPtr getPrecision() const
void setBinSizeDivisor(int divisor)
std::vector< double > createArbitraryBins()
Q_INVOKABLE void setPrecision(pappso::PrecisionPtr precisionPtr)
Q_INVOKABLE void updateSmallestMz(pappso::pappso_double value)
Q_INVOKABLE void updateGreatestMz(pappso::pappso_double value)
Q_INVOKABLE bool isRemoveZeroValDataPoints() const
Q_INVOKABLE bool isValid() const
Q_INVOKABLE bool hasValidMzRange() const
Q_INVOKABLE QString toString(int offset=0, const QString &spacer=QString()) const
pappso::PrecisionPtr mp_precision
Q_INVOKABLE void setSmallestMz(pappso::pappso_double value)
bool m_removeZeroValDataPoints
Q_INVOKABLE void setBinningType(BinningType binningType)
Q_INVOKABLE void reset()
Reset the instance to default values.
std::vector< double > createDataBasedBins(pappso::MassSpectrumCstSPtr massSpectrum)
Q_INVOKABLE void setDecimalPlaces(int decimal_places)
Q_INVOKABLE std::vector< pappso::pappso_double > createBins()
Q_INVOKABLE void setRemoveZeroValDataPoints(bool removeOrNot=true)
virtual ~MzIntegrationParams()
Q_INVOKABLE void setGreatestMz(pappso::pappso_double value)
virtual QString toString() const =0
virtual pappso_double getNominal() const final
virtual pappso_double delta(pappso_double value) const =0
virtual PrecisionUnit unit() const =0
static PrecisionPtr getResInstance(pappso_double value)
get a resolution precision pointer
static PrecisionPtr getPpmInstance(pappso_double value)
get a ppm precision pointer
static PrecisionPtr getDaltonInstance(pappso_double value)
get a Dalton precision pointer
static int zeroDecimalsInValue(pappso_double value)
0.11 would return 0 (no empty decimal) 2.001 would return 2 1000.0001254 would return 3
int mzIntegrationParamsMetaTypeId
int mzIntegrationParamsPtrMetaTypeId
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
BinningType
Type of binning when performing integrations to a mass spectrum.
@ DATA_BASED
binning based on mass spectral data
@ ARBITRARY
binning based on arbitrary bin size value
double pappso_double
A type definition for doubles.
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::map< BinningType, QString > binningTypeMap
Map relating the BinningType to a textual representation.