libpappsomspp
Library for mass spectrometry
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tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge More...
Namespaces | |
namespace | specglob |
namespace | specself |
namespace | spectree |
Classes | |
class | Aa |
class | AaBase |
class | AaCode |
collection of integer code for each amino acid 0 => null 1 to 20 => amino acid sorted by there mass (lower to higher). Leucine is replaced by Isoleucine More... | |
class | AaModification |
class | AaStringCodec |
code and decode amino acid string sequence to unique integer More... | |
class | AaStringCodeMassMatching |
convert a list of mass to amino acid string codes More... | |
class | AtomNumberInterface |
class | BafAsciiFileReader |
class | BafAsciiMsRunReader |
class | BaseColorMapPlotWidget |
class | BasePlotContext |
class | BasePlotWidget |
class | BaseTracePlotWidget |
struct | CodeToMass |
struct | ColorMapPlotConfig |
class | CosineSimilarity |
class | DaltonPrecision |
struct | DataPoint |
class | DeepProtEnumStr |
class | DriftSpecMassSpecColorMapPlotWidget |
class | DriftSpecTracePlotWidget |
class | Enzyme |
class | EnzymeProductInterface |
class | ExceptionInterrupted |
class | ExceptionNotFound |
class | ExceptionNotImplemented |
class | ExceptionNotPossible |
class | ExceptionNotRecognized |
excetion to use when an item type is not recognized More... | |
class | ExceptionOutOfRange |
class | FastaFileIndexer |
class | FastaFileIndexerInterface |
class | FastaHandlerInterface |
class | FastaOutputStream |
class | FastaReader |
class | FastaSeqHandler |
class | FastaWriterInterface |
class | FilterCeilingAmplitudePercentage |
Redefines the ceiling intensity of the Trace. More... | |
class | FilterChargeDeconvolution |
class | FilterComplementIonEnhancer |
try to detect complementary ions and assign maximum intensity of both elements More... | |
class | FilterFloorAmplitudePercentage |
Redefines the floor intensity of the Trace. More... | |
class | FilterFloorY |
apply std::floor (round to lowest integer) to all Y values More... | |
class | FilterGreatestY |
keep N datapoints form the greatest intensities to the lowest More... | |
class | FilterGreatestYperWindow |
keep N datapoints form the greatest intensities to the lowest within a mass range in dalton More... | |
class | FilterHighPass |
remove datapoints below a given Y value (intensity) More... | |
class | FilterHighPassPercentage |
remove datapoints below a given intensity percentage (ratio) of the maximum intensity More... | |
class | FilterInterface |
generic interface to apply a filter on a trace More... | |
class | FilterLocalMaximum |
finds all local maxima, i.e. any point that has a greater y value than both of its neighboring points and only keep those points More... | |
class | FilterLowIntensitySignalRemoval |
Redefines the floor intensity of the Trace. More... | |
class | FilterLowPass |
remove datapoints higher than a given Y value (intensity) More... | |
class | FilterMorphoAntiSpike |
anti spike filter set to zero alone values inside the window More... | |
class | FilterMorphoBackground |
compute background of a trace compute background noise on a trace More... | |
class | FilterMorphoMax |
transform the trace into its maximum over a window More... | |
class | FilterMorphoMaxMin |
transform the trace with the maximum of the minimum equivalent of the erode filter for pictures More... | |
class | FilterMorphoMean |
mean filter apply mean of y values inside the window : this results in a kind of smoothing More... | |
class | FilterMorphoMedian |
median filter apply median of y values inside the window More... | |
class | FilterMorphoMin |
transform the trace into its minimum over a window More... | |
class | FilterMorphoMinMax |
transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures More... | |
class | FilterMorphoSum |
test purpose More... | |
class | FilterMorphoWindowBase |
base class that apply a signal treatment based on a window More... | |
class | FilterMzExclusion |
class | FilterNameInterface |
Interface that allows to build filter objects from strings. More... | |
class | FilterNormalizeIntensities |
Sets the maximum intensity of the trace to the provided value. More... | |
class | FilterOboPsiModSink |
class | FilterOboPsiModTermAccession |
class | FilterOboPsiModTermDiffMono |
class | FilterOboPsiModTermLabel |
class | FilterOboPsiModTermName |
class | FilterPeakDelta |
class | FilterQuantileBasedRemoveY |
removes a value found by quantile to all Y values More... | |
class | FilterRemoveC13 |
class | FilterRemoveY |
removes a value to all Y values More... | |
class | FilterResampleKeepGreater |
class | FilterResampleKeepPointInPolygon |
class | FilterResampleKeepSmaller |
class | FilterResampleKeepXRange |
class | FilterResampleRemoveXRange |
class | FilterRescaleY |
rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored More... | |
class | FilterRoundY |
apply std::round (round to nearest integer) to all Y values More... | |
class | FilterSavitzkyGolay |
uses Savitsky-Golay filter on trace More... | |
class | FilterScaleFactorY |
rescales Y values given a tranformation factor More... | |
class | FilterSuite |
apply a suite of filters from a vector More... | |
class | FilterSuiteString |
class | FilterTandemDeisotope |
Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests: More... | |
class | FilterTriangle |
struct | FrameIdDescr |
class | GrpExperiment |
class | GrpGroup |
class | GrpGroupingMonitor |
class | GrpGroupingMonitorInterface |
class | GrpMapPeptideToGroup |
class | GrpMapPeptideToSubGroupSet |
class | GrpPeptide |
class | GrpPeptideSet |
class | GrpProtein |
class | GrpSubGroup |
class | GrpSubGroupSet |
class | HttpButton |
class | IntegrationScope |
class | IntegrationScopeBase |
class | IntegrationScopeRect |
class | IntegrationScopeRhomb |
struct | IntegrationScopeSpec |
class | Ion |
class | IonIsotopeRatioScore |
class | IonMobilityGrid |
class | LinearRegression |
class | MapTrace |
class | MassDataCombinerInterface |
class | MassSpecTracePlotContext |
class | MassSpecTracePlotWidget |
class | MassSpectrum |
Class to represent a mass spectrum. More... | |
class | MassSpectrumCombiner |
class | MassSpectrumFilterGreatestItensities |
class | MassSpectrumFilterInterface |
generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface, but some filter are only relevant if they are used on MassSpectrum using this interface means the filter can only be applied on MassSpectrum and not on Trace More... | |
class | MassSpectrumFilterResampleKeepMzRange |
class | MassSpectrumFilterResampleRemoveMzRange |
class | MassSpectrumId |
struct | MassSpectrumLineData |
class | MassSpectrumMinusCombiner |
class | MassSpectrumPlusCombiner |
class | MassSpectrumWidget |
class | MgfOutput |
class | MorpheusScore |
class | MsDataFormatEnumStr |
static functions to convert mz file formats More... | |
class | MsFileAccessor |
class | MsFileReader |
class | MsRunAlignment |
class | MsRunDataSetTree |
class | MsRunDataSetTreeNode |
class | MsRunDataSetTreeNodeVisitorInterface |
class | MsRunId |
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL) More... | |
class | MsRunQualifiedSpectrumLoader |
Load all qualified spectrum into a vector. More... | |
class | MsRunReadConfig |
class | MsRunReader |
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More... | |
class | MsRunReaderRetentionTimeLine |
collect retention times along MS run More... | |
class | MsRunReaderScanNumberMultiMap |
provides a multimap to find quickly spectrum index from scan number More... | |
class | MsRunReaderTicChromatogram |
calculate a TIC chromatogram More... | |
class | MsRunRetentionTime |
struct | MsRunRetentionTimeSeamarkPoint |
class | MsRunSimpleStatistics |
example of interface to count MS levels of all spectrum in an MSrun More... | |
class | MsRunSlice |
class | MsRunXicExtractor |
class | MsRunXicExtractorDisk |
class | MsRunXicExtractorDiskBuffer |
class | MsRunXicExtractorFactory |
factory to build different kinds of XIC extractors More... | |
class | MsRunXicExtractorInterface |
class | MzCalibrationInterface |
class | MzCalibrationModel1 |
class | MzCalibrationModel1Cached |
class | MzCalibrationStore |
class | MzIdentMlWriter |
class | MzIntegrationParams |
The MzIntegrationParams class provides the parameters definining how m/z ! More... | |
class | MzRange |
class | MzxmlOutput |
class | OboChooserWidget |
class | OboListModel |
class | OboListProxyModel |
class | OboListWidget |
class | OboPsiMod |
class | OboPsiModHandlerInterface |
class | OboPsiModTerm |
class | OboTermForm |
class | PappsoException |
class | PeakIonIsotopeMatch |
class | PeakIonMatch |
class | Peptide |
class | PeptideBuilder |
builds a peptide shared pointer from peptide string and adds fixed modifications More... | |
class | PeptideFixedModificationBuilder |
class | PeptideFragment |
class | PeptideFragmentIon |
class | PeptideFragmentIonListBase |
class | PeptideInterface |
class | PeptideIsotopeSpectrumMatch |
class | PeptideMethioninRemove |
potential remove Nter Methionin More... | |
class | PeptideModificatorBase |
class | PeptideModificatorInterface |
class | PeptideModificatorPipeline |
class | PeptideModificatorTee |
class | PeptideNaturalIsotope |
class | PeptideNaturalIsotopeAverage |
class | PeptideNaturalIsotopeList |
class | PeptideProFormaParser |
class | PeptideRawFragmentMasses |
class | PeptideSemiEnzyme |
cut a regular peptide obtained with an enzyme at any position from Nter or Cter More... | |
class | PeptideSinkInterface |
class | PeptideSizeFilter |
filter peptide string by size More... | |
class | PeptideSpectrumMatch |
class | PeptideSpSinkInterface |
class | PeptideStrParser |
class | PeptideVariableModificationBuilder |
Modify a peptide shared pointer with a variable modification on one AA. More... | |
class | PeptideVariableModificationReplacement |
class | PpmPrecision |
class | PrecisionBase |
class | PrecisionFactory |
class | PrecisionWidget |
struct | PrecursorIonData |
class | Protein |
class | ProteinIntegerCode |
class | ProteinPresenceAbsenceMatrix |
class | PsmFeatures |
class | PwizMsFileReader |
class | PwizMsRunReader |
class | QCPSpectrum |
class | QCPXic |
class | QualifiedMassSpectrum |
Class representing a fully specified mass spectrum. More... | |
class | QualifiedXic |
class | ResPrecision |
struct | SavGolParams |
Parameters for the Savitzky-Golay filter. More... | |
class | SelectionPolygon |
struct | SelectionPolygonSpec |
struct | SimplePeakIonMatch |
class | SpectrumCollectionHandlerInterface |
interface to collect spectrums from the MsRunReader class More... | |
class | SwitchWidget |
class | TandemWrapperRun |
class | TicXicChromDriftSpecColorMapPlotWidget |
class | TicXicChromMassSpecColorMapPlotWidget |
class | TicXicChromTracePlotWidget |
class | TimsBinDec |
class | TimsData |
class | TimsDataFastMap |
replacement for std::map More... | |
class | TimsDdaPrecursors |
class | TimsDiaSlices |
class | TimsDirectXicExtractor |
class | TimsFrame |
class | TimsFrameBase |
class | TimsFrameMobilityTraces |
class | TimsFrameRawDataChunck |
struct | TimsFrameRecord |
class | TimsFramesMsRunReader |
class | TimsFrameType1 |
class | TimsMs2CentroidFilter |
class | TimsMsFileReader |
class | TimsMsRunReader |
class | TimsMsRunReaderBase |
class | TimsMsRunReaderDia |
class | TimsMsRunReaderMs2 |
class | TimsMsRunReaderMs2Selected |
class | TimsXicExtractorInterface |
class | Trace |
A simple container of DataPoint instances. More... | |
class | TraceCombiner |
class | TraceDetectionInterface |
class | TraceDetectionMoulon |
class | TraceDetectionSinkInterface |
class | TraceDetectionZivy |
class | TraceMinusCombiner |
class | TracePeak |
class | TracePeakList |
class | TracePlusCombiner |
class | UiMonitorInterface |
class | UiMonitorText |
class | UiMonitorTextPercent |
class | UiMonitorVoid |
class | Utils |
class | WrapTandemInput |
class | WrapTandemResults |
class | Xic |
struct | XicCoord |
coordinates of the XIC to extract and the resulting XIC after extraction More... | |
struct | XicCoordTims |
coordinates of the XIC to extract and the resulting XIC after extraction More... | |
class | XicPeptideFragmentIon |
class | XicPeptideFragmentIonNaturalIsotope |
class | XicPeptideInterface |
class | XicWidget |
class | XmlStreamReaderInterface |
convenient xml reader helper More... | |
class | XtandemError |
class | XtandemHyperscore |
class | XtandemHyperscoreBis |
class | XtandemPresetReader |
class | XtandemSpectrumProcess |
class | XyMsFileReader |
class | XyMsRunReader |
Enumerations | |
enum class | QualifiedMassSpectrumParameter { IonMobOneOverK0 , IonMobOneOverK0Begin , IonMobOneOverK0End , TimsIonMobScanIndex , TimsFrameIonMobScanIndexBegin , TimsFrameIonMobScanIndexEnd , IsolationMz , IsolationMzWidth , CollisionEnergy , BrukerPrecursorIndex , TimsFrameScansCount , TimsFrameMzIndexBegin , TimsFrameMzIndexEnd , ScanNumber , last } |
enum class | MsRunReadConfigParameter { TimsFrameIonMobScanIndexBegin , TimsFrameIonMobScanIndexEnd , TimsFrameIonMobOneOverK0Begin , TimsFrameIonMobOneOverK0End , MzRangeBegin , MzRangeEnd , TimsFrameMzIndexMergeWindow } |
enum class | XicCoordParam : std::int8_t { TimsTofIonMobilityScanNumberStart , TimsTofIonMobilityScanNumberStop } |
enum class | PeptideDirection : std::int8_t { Nter = 0 , Cter = 1 } |
enum class | PeptideIonNter { b , bstar , bo , a , astar , ao , bp , c } |
enum class | PeptideIonCter { y , ystar , yo , z , yp , x } |
enum class | AtomIsotope { C , H , O , N , S } |
enum class | RawFragmentationMode : std::int8_t { full = 0 , proline_effect = 1 } |
enum | IntegrationScopeFeatures { FAILURE = 0x0000 , SUCCESS = 1 << 1 , FLAT_ON_X_AXIS = 1 << 2 , FLAT_ON_Y_AXIS = 1 << 3 , RHOMBOID_VERTICAL = 1 << 4 , RHOMBOID_HORIZONTAL = 1 << 5 , NOT_PRINTABLE = 1 << 6 , FLAT_ON_ANY_AXIS = (FLAT_ON_X_AXIS | FLAT_ON_Y_AXIS) } |
enum class | BinningType { NONE = 0 , DATA_BASED , ARBITRARY , LAST } |
Type of binning when performing integrations to a mass spectrum. More... | |
enum class | PointSpec { TOP_LEFT_POINT = 0 , TOP_RIGHT_POINT = 1 , BOTTOM_RIGHT_POINT = 2 , BOTTOM_LEFT_POINT = 3 , ENUM_LAST = 4 } |
enum class | DataDimension { NOT_SET = 0 , HORIZONTAL , VERTICAL } |
enum class | DeepProtMatchType : std::uint8_t { uncategorized = 0 , ZeroMassDelta = 1 , ZeroMassDeltaMissedCleavage , ZeroMassDeltaSemiTryptic , DeltaPosition = 4 , NoDeltaPosition = 5 , last = 6 } |
definition of different class of PSMs used by DeepProt More... | |
enum class | DeepProtPeptideCandidateStatus : std::uint8_t { unmodified = 0 , ZeroMassDelta = 1 , CterRemoval = 2 , NterRemoval = 3 , MissedCleavage = 4 , DeltaPosition = 5 , NoDeltaPosition = 6 , last = 7 } |
definition of different status for potential peptide candidates on the same spectrum More... | |
enum class | TimeUnit { none , s , min , h } |
enum class | PrecisionUnit { none , dalton , ppm , res , mz , last } |
enum class | AtomIsotopeSurvey : std::int8_t { C , H , O , N , S , last } |
enum class | Isotope { C13 , H2 , O17 , O18 , N15 , S33 , S34 , S36 } |
enum class | MsDataFormat : std::int8_t { unknown = 0 , mzML = 1 , mzXML = 2 , MGF = 3 , SQLite3 = 4 , xy = 5 , mz5 = 6 , msn = 7 , abSciexWiff = 8 , abSciexT2D = 9 , agilentMassHunter = 10 , thermoRaw = 11 , watersRaw = 12 , brukerFid = 13 , brukerYep = 14 , brukerBaf = 15 , brukerTims = 16 , brukerBafAscii = 17 , last = 18 } |
enum class | FileReaderType { pwiz , xy , bafascii , tims , tims_frames , tims_ms2 , tims_dia } |
enum class | AminoAcidChar : char { alanine = 'A' , cysteine = 'C' , aspartic_acid = 'D' , glutamic_acid = 'E' , phenylalanine = 'F' , glycine = 'G' , histidine = 'H' , isoleucine = 'I' , lysine = 'K' , leucine = 'L' , methionine = 'M' , asparagine = 'N' , proline = 'P' , glutamine = 'Q' , arginine = 'R' , serine = 'S' , threonine = 'T' , valine = 'V' , tryptophan = 'W' , tyrosine = 'Y' , selenocysteine = 'U' , pyrrolysine = 'O' } |
enum class | SortType : std::int8_t { no_sort = 0 , x = 1 , y = 2 } |
enum class | SortOrder : std::int8_t { ascending = 0 , descending = 1 } |
enum class | DataCompression : std::int8_t { unset = -1 , none = 0 , zlib = 1 } |
enum class | DataKind : std::int8_t { unset = -1 , rt = 0 , dt = 1 , mz = 2 } |
enum class | Axis : std::int8_t { unset = 0x000 , x = 1 << 0 , y = 1 << 1 , z = 1 << 2 } |
enum class | AxisScale : std::int8_t { unset = 0 , orig = 1 , log10 = 2 } |
enum class | XicExtractMethod : std::int8_t { sum = 1 , max = 2 } |
enum class | PeptideIon : std::int8_t { b = 0 , bstar = 1 , bo = 2 , a = 3 , astar = 4 , ao = 5 , bp = 6 , c = 7 , y = 8 , ystar = 9 , yo = 10 , z = 11 , yp = 12 , x = 13 } |
PeptideIon enum defines all types of ions (Nter or Cter) More... | |
enum class | DragDirections { NOT_SET = 0x0000 , LEFT_TO_RIGHT = 1 << 0 , RIGHT_TO_LEFT = 1 << 1 , TOP_TO_BOTTOM = 1 << 2 , BOTTOM_TO_TOP = 1 << 3 } |
enum class | SelectionDrawingLines { NOT_SET = 0x0000 , TOP_LINE = 1 << 0 , BOTTOM_LINE = 1 << 1 , HORIZONTAL_LINES = (TOP_LINE | BOTTOM_LINE) , RIGHT_LINE = 1 << 2 , LEFT_LINE = 1 << 3 , VERTICAL_LINES = (RIGHT_LINE | LEFT_LINE) , FULL_POLYGON = (HORIZONTAL_LINES | VERTICAL_LINES) } |
enum class | RangeType { outermost = 1 , innermost = 2 } |
enum class | MsRunXicExtractorFactoryType : std::int8_t { nose = 0 , direct = 1 , disk = 2 , diskbuffer } |
Functions | |
bool | operator== (Aa const &l, Aa const &r) |
bool | operator< (Aa const &l, Aa const &r) |
QDataStream & | operator<< (QDataStream &outstream, const MassSpectrum &massSpectrum) |
QDataStream & | operator>> (QDataStream &instream, MassSpectrum &massSpectrum) |
bool | peptideIonTypeIsComplement (PeptideIon ion_type_ref, PeptideIon ion_type) |
tells if an ion type is the complement ion of the other | |
bool | peptideIonIsNter (PeptideIon ion_type) |
tells if an ion is Nter | |
PeptideDirection | getPeptideIonDirection (PeptideIon ion_type) |
get the direction of a peptide ion | |
uint64_t | Combinations (unsigned int n, unsigned int k) |
pappso_double | isotopem_ratio (pappso_double abundance, unsigned int total, unsigned int heavy) |
pappso_double | isotopem_ratio_cache (Isotope isotope, unsigned int total, unsigned int heavy) |
std::vector< PeptideNaturalIsotopeAverageSp > | getByIntensityRatioByIsotopeNumber (const PeptideInterfaceSp &peptide, unsigned int charge, PrecisionPtr precision, unsigned int isotopeNumber, pappso_double minimumIntensity) |
PMSPP_LIB_DECL std::vector< TracePeak >::iterator | findBestTracePeakGivenRtList (std::vector< TracePeak >::iterator begin, std::vector< TracePeak >::iterator end, const std::vector< double > &rt_list, std::size_t &nb_peaks) |
find the best peak matching a list of retention times | |
PMSPP_LIB_DECL std::vector< TracePeak >::iterator | findTracePeakGivenRt (std::vector< TracePeak >::iterator begin, std::vector< TracePeak >::iterator end, double rt) |
find the peak matching a retention time | |
std::vector< PeakIonIsotopeMatch >::iterator | findComplementIonType (std::vector< PeakIonIsotopeMatch >::iterator begin, std::vector< PeakIonIsotopeMatch >::iterator end, const PeakIonIsotopeMatch &peak_ion, std::size_t peptide_size) |
find the first element containing the complementary ion complementary ion of y1 is b(n-1) for instance | |
unsigned int | factorial (unsigned int n) |
QDataStream & | operator<< (QDataStream &out, const DataPoint &dataPoint) |
QDataStream & | operator>> (QDataStream &in, DataPoint &dataPoint) |
QDataStream & | operator<< (QDataStream &out, const Trace &trace) |
QDataStream & | operator>> (QDataStream &out, Trace &trace) |
std::vector< DataPoint >::iterator | findFirstEqualOrGreaterX (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value) |
find the first element in which X is equal or greater than the value searched important : it implies that Trace is sorted by X | |
std::vector< DataPoint >::const_iterator | findFirstEqualOrGreaterX (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, const double &value) |
std::vector< DataPoint >::iterator | findFirstGreaterX (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value) |
find the first element in which X is greater than the value searched important : it implies that Trace is sorted by X | |
std::vector< DataPoint >::const_iterator | findFirstGreaterX (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, const double &value) |
std::vector< DataPoint >::iterator | findDifferentYvalue (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &y_value) |
find the first element in which Y is different of value | |
std::vector< DataPoint >::const_iterator | findDifferentYvalue (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, const double &y_value) |
std::vector< DataPoint >::const_iterator | minYDataPoint (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
std::vector< DataPoint >::iterator | minYDataPoint (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end) |
find the element with the smallest Y value (intensity) | |
std::vector< DataPoint >::const_iterator | maxYDataPoint (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
std::vector< DataPoint >::iterator | maxYDataPoint (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end) |
find the element with the greatest Y value (intensity) | |
std::vector< DataPoint >::const_iterator | moveLowerYRigthDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin) |
Move right to the lower value. | |
std::vector< DataPoint >::const_iterator | moveLowerYLeftDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin) |
Move left to the lower value. | |
double | sumYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init) |
calculate the sum of y value of a trace | |
double | meanYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
calculate the mean of y value of a trace | |
double | quantileYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double quantile) |
calculate the quantile of y value of a trace | |
double | medianYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
calculate the median of y value of a trace | |
double | areaTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
calculate the area of a trace | |
Trace | flooredLocalMaxima (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double y_floor) |
const pappso_double | MHPLUS (1.007276466879) |
const pappso_double | MPROTON (1.007276466879) |
const pappso_double | MPROTIUM (1.007825032241) |
const pappso_double | ONEMILLION (1000000) |
const pappso_double | MASSOXYGEN (15.99491461956) |
const pappso_double | MASSCARBON (12) |
const pappso_double | MASSH2O ((MPROTIUM *2)+MASSOXYGEN) |
const pappso_double | MASSNITROGEN (14.0030740048) |
const pappso_double | MASSNH3 ((MPROTIUM *3)+MASSNITROGEN) |
const pappso_double | MASSCO (MASSCARBON+MASSOXYGEN) |
const pappso_double | MASSPHOSPHORUS (30.973761998) |
const pappso_double | MASSSULFUR (31.9720711741) |
const pappso_double | MASSPHOSPHORYLATEDR (MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS) |
const pappso_double | MASSSELENIUM (79.916520) |
const pappso_double | DIFFC12C13 (1.0033548378) |
const pappso_double | DIFFS32S33 (32.9714589101 - MASSSULFUR) |
const pappso_double | DIFFS32S34 (33.9678670300 - MASSSULFUR) |
const pappso_double | DIFFS32S36 (35.9670812000 - MASSSULFUR) |
const pappso_double | DIFFH1H2 (2.0141017778 - MPROTIUM) |
const pappso_double | DIFFO16O18 (17.9991610 - MASSOXYGEN) |
const pappso_double | DIFFO16O17 (16.99913150 - MASSOXYGEN) |
const pappso_double | DIFFN14N15 (15.0001088982 - MASSNITROGEN) |
const pappso_double | ABUNDANCEH2 (0.00011570983569203332000374651045149221317842602729797363281250) |
const pappso_double | ABUNDANCEN15 (0.00364198543205827118818262988497735932469367980957031250000000) |
const pappso_double | ABUNDANCEO17 (0.00038099847600609595965615028489992255344986915588378906250000) |
const pappso_double | ABUNDANCEO18 (0.00205139179443282221315669744399201590567827224731445312500000) |
const pappso_double | ABUNDANCEC13 (0.01078805814953308406245469086570665240287780761718750000000000) |
const pappso_double | ABUNDANCEC12 (0.98921194185046687152862432412803173065185546875000000000000000) |
const pappso_double | ABUNDANCES33 (0.00751939844812414937003097747947322204709053039550781250000000) |
const pappso_double | ABUNDANCES34 (0.04252059835213182203972337447339668869972229003906250000000000) |
const pappso_double | ABUNDANCES36 (0.00010999120070394368536836893213148869108408689498901367187500) |
QDataStream & | operator>> (QDataStream &instream, MsRunSlice &slice) |
Variables | |
static const std::size_t | CHECKED_LINES_COUNT = 10 |
constexpr std::size_t | MAX_MS_LEVELS = 12 |
class PMSPP_LIB_DECL | MsRunReader |
uint64_t | combinations_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioC13_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioN15_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioS36_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioS34_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioS33_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioO17_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioO18_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
pappso_double | ratioH2_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
std::map< BinningType, QString > | binningTypeMap |
Map relating the BinningType to a textual representation. | |
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
first sort peaks by decreasing intensities, then keep most intense ones and avoid any peaks in possible C13 windows after
typedef const AaModification* pappso::AaModificationP |
Definition at line 52 of file aamodification.h.
typedef std::unique_ptr<const AaModification> pappso::AaModificationUp |
Definition at line 51 of file aamodification.h.
typedef std::shared_ptr<const AaStringCodec> pappso::AaStringCodecSp |
shared pointer on a Protein object
Definition at line 41 of file aastringcodec.h.
typedef std::shared_ptr<const BaseColorMapPlotWidget> pappso::BaseColorMapPlotWidgetCstSPtr |
Definition at line 61 of file basecolormapplotwidget.h.
typedef std::shared_ptr<BaseColorMapPlotWidget> pappso::BaseColorMapPlotWidgetSPtr |
Definition at line 59 of file basecolormapplotwidget.h.
typedef std::shared_ptr<const BasePlotWidget> pappso::BasePlotWidgetCstSPtr |
Definition at line 81 of file baseplotwidget.h.
typedef std::shared_ptr<BasePlotWidget> pappso::BasePlotWidgetSPtr |
Definition at line 80 of file baseplotwidget.h.
typedef std::shared_ptr<const BaseTracePlotWidget> pappso::BaseTracePlotWidgetCstSPtr |
Definition at line 57 of file basetraceplotwidget.h.
typedef std::shared_ptr<BaseTracePlotWidget> pappso::BaseTracePlotWidgetSPtr |
Definition at line 56 of file basetraceplotwidget.h.
typedef std::shared_ptr<const DataPoint> pappso::DataPointCstSPtr |
Definition at line 18 of file datapoint.h.
typedef std::shared_ptr<FastaFileIndexer> pappso::FastaFileIndexerSPtr |
Definition at line 49 of file fastafileindexer.h.
typedef std::shared_ptr<const FilterCeilingAmplitudePercentage> pappso::FilterCeilingAmplitudePercentageCstSPtr |
Definition at line 53 of file filterceilingamplitudepercentage.h.
typedef std::shared_ptr<FilterCeilingAmplitudePercentage> pappso::FilterCeilingAmplitudePercentageSPtr |
Definition at line 51 of file filterceilingamplitudepercentage.h.
typedef std::shared_ptr<const FilterFloorAmplitudePercentage> pappso::FilterFloorAmplitudePercentageCstSPtr |
Definition at line 53 of file filterflooramplitudepercentage.h.
typedef std::shared_ptr<FilterFloorAmplitudePercentage> pappso::FilterFloorAmplitudePercentageSPtr |
Definition at line 51 of file filterflooramplitudepercentage.h.
typedef std::shared_ptr<const FilterInterface> pappso::FilterInterfaceCstSPtr |
Definition at line 47 of file filterinterface.h.
typedef std::shared_ptr<FilterInterface> pappso::FilterInterfaceSPtr |
Definition at line 46 of file filterinterface.h.
typedef std::shared_ptr<const FilterLowIntensitySignalRemoval> pappso::FilterLowIntensitySignalRemovalCstSPtr |
Definition at line 53 of file filterlowintensitysignalremoval.h.
typedef std::shared_ptr<FilterLowIntensitySignalRemoval> pappso::FilterLowIntensitySignalRemovalSPtr |
Definition at line 51 of file filterlowintensitysignalremoval.h.
typedef std::shared_ptr<const FilterNameInterface> pappso::FilterNameInterfaceCstSPtr |
Definition at line 60 of file filternameinterface.h.
typedef std::shared_ptr<FilterNameInterface> pappso::FilterNameInterfaceSPtr |
Definition at line 59 of file filternameinterface.h.
typedef std::shared_ptr<const FilterNormalizeIntensities> pappso::FilterNormalizeIntensitiesCstSPtr |
Definition at line 53 of file filternormalizeintensities.h.
typedef std::shared_ptr<FilterNormalizeIntensities> pappso::FilterNormalizeIntensitiesSPtr |
Definition at line 51 of file filternormalizeintensities.h.
typedef std::shared_ptr<const FilterSavitzkyGolay> pappso::FilterSavitzkyGolayCstSPtr |
Definition at line 137 of file savgolfilter.h.
typedef std::shared_ptr<FilterSavitzkyGolay> pappso::FilterSavitzkyGolaySPtr |
Definition at line 136 of file savgolfilter.h.
typedef std::shared_ptr<FilterSuiteString> pappso::FilterSuiteStringSPtr |
Definition at line 77 of file filtersuitestring.h.
typedef std::shared_ptr<GrpGroup> pappso::GrpGroupSp |
Definition at line 39 of file grpgroup.h.
typedef std::shared_ptr<const GrpGroup> pappso::GrpGroupSpConst |
Definition at line 40 of file grpgroup.h.
typedef std::shared_ptr<GrpPeptide> pappso::GrpPeptideSp |
Definition at line 40 of file grppeptide.h.
typedef std::shared_ptr<const GrpPeptide> pappso::GrpPeptideSpConst |
Definition at line 39 of file grppeptide.h.
typedef std::shared_ptr<GrpProtein> pappso::GrpProteinSp |
Definition at line 37 of file grpprotein.h.
typedef std::shared_ptr<const GrpProtein> pappso::GrpProteinSpConst |
Definition at line 36 of file grpprotein.h.
typedef std::shared_ptr<GrpSubGroup> pappso::GrpSubGroupSp |
Definition at line 39 of file grpsubgroup.h.
typedef std::shared_ptr<const GrpSubGroup> pappso::GrpSubGroupSpConst |
Definition at line 38 of file grpsubgroup.h.
typedef std::shared_ptr<const IntegrationScopeBase> pappso::IntegrationScopeBaseCstSPtr |
Definition at line 120 of file integrationscopebase.h.
typedef std::shared_ptr<IntegrationScopeBase> pappso::IntegrationScopeBaseSPtr |
Definition at line 119 of file integrationscopebase.h.
typedef std::shared_ptr<const IntegrationScope> pappso::IntegrationScopeCstSPtr |
Definition at line 89 of file integrationscope.h.
typedef std::shared_ptr<const IntegrationScopeRect> pappso::IntegrationScopeRectCstSPtr |
Definition at line 94 of file integrationscoperect.h.
typedef std::shared_ptr<IntegrationScopeRect> pappso::IntegrationScopeRectSPtr |
Definition at line 93 of file integrationscoperect.h.
typedef std::shared_ptr<const IntegrationScopeRhomb> pappso::IntegrationScopeRhombCstSPtr |
Definition at line 149 of file integrationscoperhomb.h.
typedef std::shared_ptr<IntegrationScopeRhomb> pappso::IntegrationScopeRhombSPtr |
Definition at line 147 of file integrationscoperhomb.h.
typedef std::shared_ptr<const IntegrationScopeSpec> pappso::IntegrationScopeSpecCstSPtr |
Definition at line 178 of file integrationscopebase.h.
typedef std::shared_ptr<IntegrationScopeSpec> pappso::IntegrationScopeSpecSPtr |
Definition at line 177 of file integrationscopebase.h.
using pappso::IntegrationScopeSpecVector = typedef std::vector<IntegrationScopeSpec> |
Definition at line 105 of file filterresample.h.
typedef std::shared_ptr<IntegrationScope> pappso::IntegrationScopeSPtr |
Definition at line 88 of file integrationscope.h.
typedef std::shared_ptr<const MapTrace> pappso::MapTraceCstSPtr |
Definition at line 27 of file maptrace.h.
typedef std::shared_ptr<MapTrace> pappso::MapTraceSPtr |
Definition at line 26 of file maptrace.h.
typedef std::shared_ptr<const MassSpectrumCombiner> pappso::MassSpectrumCombinerCstSPtr |
Definition at line 24 of file massspectrumcombiner.h.
typedef std::shared_ptr<MassSpectrumCombiner> pappso::MassSpectrumCombinerSPtr |
Definition at line 25 of file massspectrumcombiner.h.
typedef std::shared_ptr<const MassSpectrum> pappso::MassSpectrumCstSPtr |
Definition at line 57 of file massspectrum.h.
typedef std::shared_ptr<const MassSpectrumMinusCombiner> pappso::MassSpectrumMinusCombinerCstSPtr |
Definition at line 20 of file massspectrumminuscombiner.h.
typedef std::shared_ptr<MassSpectrumMinusCombiner> pappso::MassSpectrumMinusCombinerSPtr |
Definition at line 22 of file massspectrumminuscombiner.h.
typedef std::shared_ptr<const MassSpectrumPlusCombiner> pappso::MassSpectrumPlusCombinerCstSPtr |
Definition at line 19 of file massspectrumpluscombiner.h.
typedef std::shared_ptr<MassSpectrumPlusCombiner> pappso::MassSpectrumPlusCombinerSPtr |
Definition at line 21 of file massspectrumpluscombiner.h.
typedef std::shared_ptr<MassSpectrum> pappso::MassSpectrumSPtr |
Definition at line 56 of file massspectrum.h.
typedef std::shared_ptr<const MsFileAccessor> pappso::MsFileAccessorCstSPtr |
Definition at line 128 of file msfileaccessor.h.
typedef std::shared_ptr<MsFileAccessor> pappso::MsFileAccessorSPtr |
Definition at line 127 of file msfileaccessor.h.
typedef std::shared_ptr<const MsRunDataSetTree> pappso::MsRunDataSetTreeCstSPtr |
Definition at line 26 of file msrundatasettree.h.
typedef std::shared_ptr<const MsRunDataSetTreeNode> pappso::MsRunDataSetTreeNodeCstSPtr |
Definition at line 30 of file msrundatasettreenode.h.
typedef std::shared_ptr<MsRunDataSetTreeNode> pappso::MsRunDataSetTreeNodeSPtr |
Definition at line 29 of file msrundatasettreenode.h.
typedef std::shared_ptr<MsRunDataSetTree> pappso::MsRunDataSetTreeSPtr |
Definition at line 25 of file msrundatasettree.h.
typedef std::shared_ptr<const MsRunId> pappso::MsRunIdCstSPtr |
typedef std::shared_ptr<MsRunId> pappso::MsRunIdSPtr |
typedef std::shared_ptr<const MsRunReader> pappso::MsRunReaderCstSPtr |
Definition at line 57 of file msrunreader.h.
typedef std::shared_ptr<MsRunReader> pappso::MsRunReaderSPtr |
Definition at line 56 of file msrunreader.h.
typedef std::shared_ptr<const MsRunSlice> pappso::MsRunSliceSPtr |
Definition at line 40 of file msrunslice.h.
typedef std::shared_ptr<MsRunXicExtractorInterface> pappso::MsRunXicExtractorInterfaceSp |
Definition at line 46 of file msrunxicextractorinterface.h.
typedef std::shared_ptr<MzCalibrationInterface> pappso::MzCalibrationInterfaceSPtr |
Definition at line 38 of file mzcalibrationinterface.h.
typedef std::shared_ptr<Peptide> pappso::NoConstPeptideSp |
typedef double pappso::pappso_double |
typedef float pappso::pappso_float |
typedef std::shared_ptr<const PeakIonIsotopeMatch> pappso::PeakIonIsotopeMatchCstSPtr |
Definition at line 34 of file peakionisotopematch.h.
typedef std::shared_ptr<const PeptideFragmentIonListBase> pappso::PeptideFragmentIonListBaseSp |
Definition at line 43 of file peptidefragmentionlistbase.h.
typedef std::shared_ptr<const PeptideFragmentIon> pappso::PeptideFragmentIonSp |
Definition at line 46 of file peptidefragmention.h.
typedef std::shared_ptr<const PeptideFragment> pappso::PeptideFragmentSp |
Definition at line 45 of file peptidefragment.h.
typedef std::shared_ptr<const PeptideInterface> pappso::PeptideInterfaceSp |
Definition at line 39 of file peptideinterface.h.
typedef std::shared_ptr<const PeptideNaturalIsotopeAverage> pappso::PeptideNaturalIsotopeAverageSp |
Definition at line 40 of file peptidenaturalisotopeaverage.h.
typedef std::shared_ptr<const PeptideNaturalIsotopeList> pappso::PeptideNaturalIsotopeListSp |
Definition at line 45 of file peptidenaturalisotopelist.h.
typedef std::shared_ptr<const PeptideNaturalIsotope> pappso::PeptideNaturalIsotopeSp |
Definition at line 43 of file peptidenaturalisotope.h.
typedef std::shared_ptr< const Peptide > pappso::PeptideSp |
Definition at line 48 of file aamodification.h.
typedef QString pappso::PeptideStr |
typedef const PrecisionBase* pappso::PrecisionPtr |
Definition at line 122 of file precision.h.
typedef std::shared_ptr<const Protein> pappso::ProteinSp |
typedef std::shared_ptr<const QualifiedMassSpectrum> pappso::QualifiedMassSpectrumCstSPtr |
Definition at line 45 of file qualifiedmassspectrum.h.
typedef std::shared_ptr<QualifiedMassSpectrum> pappso::QualifiedMassSpectrumSPtr |
Definition at line 43 of file qualifiedmassspectrum.h.
typedef std::shared_ptr<Xic> pappso::QualifiedXicSp |
Definition at line 42 of file qualifiedxic.h.
typedef std::shared_ptr<TimsData> pappso::TimsDataSp |
shared pointer on a TimsData object
Definition at line 52 of file timsdata.h.
typedef std::shared_ptr<const TimsFrameBase> pappso::TimsFrameBaseCstSPtr |
Definition at line 42 of file timsframebase.h.
typedef std::shared_ptr<TimsFrameBase> pappso::TimsFrameBaseSPtr |
Definition at line 41 of file timsframebase.h.
typedef std::shared_ptr<const TimsFrame> pappso::TimsFrameCstSPtr |
Definition at line 43 of file timsframe.h.
typedef std::shared_ptr<const TimsFramesMsRunReader> pappso::TimsFramesMsRunReaderCstSPtr |
Definition at line 85 of file timsframesmsrunreader.h.
typedef std::shared_ptr<TimsFramesMsRunReader> pappso::TimsFramesMsRunReaderSPtr |
Definition at line 83 of file timsframesmsrunreader.h.
typedef std::shared_ptr<TimsFrame> pappso::TimsFrameSPtr |
Definition at line 42 of file timsframe.h.
typedef std::shared_ptr<TimsMsRunReaderMs2> pappso::TimsMsRunReaderMs2SPtr |
Definition at line 19 of file msfileaccessor.h.
typedef std::shared_ptr<const TraceCombiner> pappso::TraceCombinerCstSPtr |
Definition at line 23 of file tracecombiner.h.
typedef std::shared_ptr<TraceCombiner> pappso::TraceCombinerSPtr |
Definition at line 24 of file tracecombiner.h.
typedef std::shared_ptr<const Trace> pappso::TraceCstSPtr |
typedef std::shared_ptr<const TraceDetectionInterface> pappso::TraceDetectionInterfaceCstSPtr |
Definition at line 35 of file tracedetectioninterface.h.
typedef std::shared_ptr<TraceDetectionInterface> pappso::TraceDetectionInterfaceSPtr |
Definition at line 33 of file tracedetectioninterface.h.
typedef std::shared_ptr<const TraceMinusCombiner> pappso::TraceMinusCombinerCstSPtr |
Definition at line 22 of file traceminuscombiner.h.
typedef std::shared_ptr<TraceMinusCombiner> pappso::TraceMinusCombinerSPtr |
Definition at line 23 of file traceminuscombiner.h.
typedef std::shared_ptr<const TracePeak> pappso::TracePeakCstSPtr |
Definition at line 35 of file tracepeak.h.
typedef std::shared_ptr<const TracePlusCombiner> pappso::TracePlusCombinerCstSPtr |
Definition at line 22 of file tracepluscombiner.h.
typedef std::shared_ptr<TracePlusCombiner> pappso::TracePlusCombinerSPtr |
Definition at line 23 of file tracepluscombiner.h.
typedef std::shared_ptr<Trace> pappso::TraceSPtr |
typedef unsigned int pappso::uint |
typedef std::shared_ptr<XicCoord> pappso::XicCoordSPtr |
Definition at line 43 of file xiccoord.h.
typedef std::shared_ptr<XicCoordTims> pappso::XicCoordTimsSPtr |
Definition at line 40 of file xiccoordtims.h.
typedef std::shared_ptr<const Xic> pappso::XicCstSPtr |
typedef std::shared_ptr<Xic> pappso::XicSPtr |
typedef std::vector<std::pair<XicCstSPtr, TracePeakCstSPtr> > pappso::XicXicPeakPairList |
Definition at line 45 of file xicwidget.h.
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Definition at line 165 of file types.h.
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Type of binning when performing integrations to a mass spectrum.
Enumerator | |
---|---|
NONE | < no binning |
DATA_BASED | binning based on mass spectral data |
ARBITRARY | binning based on arbitrary bin size value |
LAST |
Definition at line 47 of file mzintegrationparams.h.
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Enumerator | |
---|---|
NOT_SET | |
HORIZONTAL | |
VERTICAL |
Definition at line 34 of file selectionpolygon.h.
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definition of different class of PSMs used by DeepProt
Definition at line 41 of file deepprotenum.h.
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definition of different status for potential peptide candidates on the same spectrum
Enumerator | |
---|---|
unmodified | precursor mass was not compared |
ZeroMassDelta | |
CterRemoval | |
NterRemoval | |
MissedCleavage | |
DeltaPosition | |
NoDeltaPosition | |
last |
Definition at line 60 of file deepprotenum.h.
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Enumerator | |
---|---|
NOT_SET | |
LEFT_TO_RIGHT | |
RIGHT_TO_LEFT | |
TOP_TO_BOTTOM | |
BOTTOM_TO_TOP |
Definition at line 26 of file baseplotcontext.h.
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Enumerator | |
---|---|
pwiz | using libpwizlite |
xy | |
bafascii | |
tims | TimsMsRunReader : each scan is returned as a mass spectrum. |
tims_frames | TimsFramesMsRunReader : the whole frame is merged in a single spectrum |
tims_ms2 | TimsMsRunReaderMs2 : Spectrum are delivered for each precursor (MS1 or MS2) |
tims_dia | TimsMsRunReaderDia : Spectrum are delivered for DIA window (slice) |
Enumerator | |
---|---|
FAILURE | |
SUCCESS | |
FLAT_ON_X_AXIS | |
FLAT_ON_Y_AXIS | |
RHOMBOID_VERTICAL | |
RHOMBOID_HORIZONTAL | |
NOT_PRINTABLE | |
FLAT_ON_ANY_AXIS |
Definition at line 45 of file integrationscopebase.h.
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Definition at line 119 of file types.h.
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Enumerator | |
---|---|
TimsFrameIonMobScanIndexBegin | |
TimsFrameIonMobScanIndexEnd | |
TimsFrameIonMobOneOverK0Begin | |
TimsFrameIonMobOneOverK0End | |
MzRangeBegin | |
MzRangeEnd | |
TimsFrameMzIndexMergeWindow |
Definition at line 35 of file msrunreadconfig.h.
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Enumerator | |
---|---|
nose | default factory |
direct | build a simple XIC extractor that directly uses Proeowizard library to read and extract XICs building the xic extractor is fast, but extracting each XIC is slow |
disk | build Xic extractor that first read the whole MsRun, put it on disk and extract XICs more quickly This needs some space on disk to store slices (1 dalton each) building the XIC extractor is slow extracting XIC from slices is a very quick operation |
diskbuffer | build Xic extractor that first read the whole MsRun, put it on disk using a write cache and extract XICs more quickly This needs some space on disk to store slices (1 dalton each) building the XIC extractor is slower than buildMsRunXicExtractorPwizSp, but faster than buildMsRunXicExtractorDiskSp extracting XIC from slices is a very quick operation |
Definition at line 45 of file msrunxicextractorfactory.h.
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PeptideIon enum defines all types of ions (Nter or Cter)
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Enumerator | |
---|---|
TOP_LEFT_POINT | |
TOP_RIGHT_POINT | |
BOTTOM_RIGHT_POINT | |
BOTTOM_LEFT_POINT | |
ENUM_LAST |
Definition at line 23 of file selectionpolygon.h.
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Definition at line 47 of file qualifiedmassspectrum.h.
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Enumerator | |
---|---|
outermost | |
innermost |
Definition at line 72 of file baseplotwidget.h.
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Enumerator | |
---|---|
full | |
proline_effect |
Definition at line 42 of file peptiderawfragmentmasses.h.
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Enumerator | |
---|---|
NOT_SET | |
TOP_LINE | |
BOTTOM_LINE | |
HORIZONTAL_LINES | |
RIGHT_LINE | |
LEFT_LINE | |
VERTICAL_LINES | |
FULL_POLYGON |
Definition at line 55 of file baseplotwidget.h.
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Enumerator | |
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ascending | |
descending |
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Enumerator | |
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TimsTofIonMobilityScanNumberStart | TimsTOF specific ion mobility start range |
TimsTofIonMobilityScanNumberStop | TimsTOF specific ion mobility stop range |
Definition at line 49 of file xiccoord.h.
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const pappso_double pappso::ABUNDANCEC12 | ( | 0. | 98921194185046687152862432412803173065185546875000000000000000 | ) |
const pappso_double pappso::ABUNDANCEC13 | ( | 0. | 01078805814953308406245469086570665240287780761718750000000000 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEH2 | ( | 0. | 00011570983569203332000374651045149221317842602729797363281250 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEN15 | ( | 0. | 00364198543205827118818262988497735932469367980957031250000000 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEO17 | ( | 0. | 00038099847600609595965615028489992255344986915588378906250000 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEO18 | ( | 0. | 00205139179443282221315669744399201590567827224731445312500000 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCES33 | ( | 0. | 00751939844812414937003097747947322204709053039550781250000000 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCES34 | ( | 0. | 04252059835213182203972337447339668869972229003906250000000000 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCES36 | ( | 0. | 00010999120070394368536836893213148869108408689498901367187500 | ) |
Referenced by isotopem_ratio_cache().
PMSPP_LIB_DECL double pappso::areaTrace | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end | ||
) |
calculate the area of a trace
Definition at line 309 of file trace.cpp.
Referenced by pappso::TracePeak::TracePeak(), and pappso::TracePeak::TracePeak().
uint64_t pappso::Combinations | ( | unsigned int | n, |
unsigned int | k | ||
) |
Definition at line 47 of file peptidenaturalisotope.cpp.
References CACHE_ARRAY_SIZE, and combinations_cache.
Referenced by isotopem_ratio().
const pappso_double pappso::DIFFC12C13 | ( | 1. | 0033548378 | ) |
Referenced by pappso::FilterChargeDeconvolution::FilterChargeDeconvolution(), pappso::FilterChargeDeconvolution::FilterChargeDeconvolution(), pappso::FilterRemoveC13::FilterRemoveC13(), pappso::FilterRemoveC13::FilterRemoveC13(), pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(), pappso::FilterChargeDeconvolution::buildFilterFromString(), pappso::AaModification::calculateMassFromChemicalComponents(), and pappso::QCPSpectrum::highlightPrecursorPeaks().
const pappso_double pappso::DIFFH1H2 | ( | 2.0141017778 - | MPROTIUM | ) |
const pappso_double pappso::DIFFN14N15 | ( | 15.0001088982 - | MASSNITROGEN | ) |
const pappso_double pappso::DIFFO16O17 | ( | 16.99913150 - | MASSOXYGEN | ) |
const pappso_double pappso::DIFFO16O18 | ( | 17.9991610 - | MASSOXYGEN | ) |
const pappso_double pappso::DIFFS32S33 | ( | 32.9714589101 - | MASSSULFUR | ) |
const pappso_double pappso::DIFFS32S34 | ( | 33.9678670300 - | MASSSULFUR | ) |
const pappso_double pappso::DIFFS32S36 | ( | 35.9670812000 - | MASSSULFUR | ) |
unsigned int pappso::factorial | ( | unsigned int | n | ) |
Definition at line 43 of file xtandemhyperscore.cpp.
Referenced by pappso::XtandemHyperscore::XtandemHyperscore(), and pappso::XtandemHyperscoreBis::computeXtandemHyperscore().
std::vector< TracePeak >::iterator pappso::findBestTracePeakGivenRtList | ( | std::vector< TracePeak >::iterator | begin, |
std::vector< TracePeak >::iterator | end, | ||
const std::vector< double > & | rt_list, | ||
std::size_t & | nb_peaks | ||
) |
find the best peak matching a list of retention times
begin | begin iterator |
end | end iterator |
rt_list | retention time list in seconds |
nb_peaks | retrieve the number of detected peaks concerned by the retention times |
Definition at line 55 of file tracepeaklist.cpp.
PMSPP_LIB_DECL std::vector< PeakIonIsotopeMatch >::iterator pappso::findComplementIonType | ( | std::vector< PeakIonIsotopeMatch >::iterator | begin, |
std::vector< PeakIonIsotopeMatch >::iterator | end, | ||
const PeakIonIsotopeMatch & | peak_ion, | ||
std::size_t | peptide_size | ||
) |
find the first element containing the complementary ion complementary ion of y1 is b(n-1) for instance
Definition at line 30 of file peakionisotopematch.cpp.
References pappso::PeakIonMatch::getCharge().
Referenced by pappso::PsmFeatures::findComplementIonPairs().
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::findDifferentYvalue | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
const double & | y_value | ||
) |
Definition at line 142 of file trace.cpp.
References pappso::DataPoint::y.
PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::findDifferentYvalue | ( | std::vector< DataPoint >::iterator | begin, |
std::vector< DataPoint >::iterator | end, | ||
const double & | y_value | ||
) |
find the first element in which Y is different of value
Definition at line 127 of file trace.cpp.
References pappso::DataPoint::y.
Referenced by pappso::FilterMorphoAntiSpike::filter().
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::findFirstEqualOrGreaterX | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
const double & | value | ||
) |
Definition at line 85 of file trace.cpp.
References pappso::DataPoint::x.
PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::findFirstEqualOrGreaterX | ( | std::vector< DataPoint >::iterator | begin, |
std::vector< DataPoint >::iterator | end, | ||
const double & | value | ||
) |
find the first element in which X is equal or greater than the value searched important : it implies that Trace is sorted by X
Definition at line 71 of file trace.cpp.
References pappso::DataPoint::x.
Referenced by pappso::TraceDetectionZivy::detect(), pappso::FilterResampleKeepSmaller::filter(), pappso::FilterResampleRemoveXRange::filter(), pappso::FilterResampleKeepXRange::filter(), pappso::specglob::ExperimentalSpectrum::findMz(), pappso::Trace::maxY(), and pappso::Trace::sumY().
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::findFirstGreaterX | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
const double & | value | ||
) |
Definition at line 113 of file trace.cpp.
References pappso::DataPoint::x.
PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::findFirstGreaterX | ( | std::vector< DataPoint >::iterator | begin, |
std::vector< DataPoint >::iterator | end, | ||
const double & | value | ||
) |
find the first element in which X is greater than the value searched important : it implies that Trace is sorted by X
Definition at line 99 of file trace.cpp.
References pappso::DataPoint::x.
Referenced by pappso::FilterResampleKeepGreater::filter(), pappso::FilterResampleRemoveXRange::filter(), pappso::FilterResampleKeepXRange::filter(), pappso::Trace::maxY(), and pappso::Trace::sumY().
std::vector< TracePeak >::iterator pappso::findTracePeakGivenRt | ( | std::vector< TracePeak >::iterator | begin, |
std::vector< TracePeak >::iterator | end, | ||
double | rt | ||
) |
find the peak matching a retention time
begin | begin iterator |
end | end iterator |
rt | retention time in seconds |
Definition at line 81 of file tracepeaklist.cpp.
PMSPP_LIB_DECL Trace pappso::flooredLocalMaxima | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
double | y_floor | ||
) |
Definition at line 329 of file trace.cpp.
References pappso::Trace::maxYDataPoint(), and pappso::DataPoint::y.
std::vector< PeptideNaturalIsotopeAverageSp > pappso::getByIntensityRatioByIsotopeNumber | ( | const PeptideInterfaceSp & | peptide, |
unsigned int | charge, | ||
PrecisionPtr | precision, | ||
unsigned int | isotopeNumber, | ||
pappso_double | minimumIntensity | ||
) |
/brief get a sorted (by expected intensity) vector of natural isotope average by isotope number
Definition at line 351 of file peptidenaturalisotopelist.cpp.
References pappso::PeptideNaturalIsotopeAverage::getIsotopeRank(), pappso::PeptideNaturalIsotopeAverage::isEmpty(), and pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp().
PMSPP_LIB_DECL PeptideDirection pappso::getPeptideIonDirection | ( | PeptideIon | ion_type | ) |
get the direction of a peptide ion
ion_type | the ion to test |
Definition at line 70 of file peptide.cpp.
References Cter, Nter, and peptideIonIsNter().
Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon(), and pappso::PeptideFragmentIon::getPeptideIonDirection().
pappso_double pappso::isotopem_ratio | ( | pappso_double | abundance, |
unsigned int | total, | ||
unsigned int | heavy | ||
) |
Definition at line 79 of file peptidenaturalisotope.cpp.
References Combinations().
Referenced by isotopem_ratio_cache().
pappso_double pappso::isotopem_ratio_cache | ( | Isotope | isotope, |
unsigned int | total, | ||
unsigned int | heavy | ||
) |
Definition at line 95 of file peptidenaturalisotope.cpp.
References ABUNDANCEC13(), ABUNDANCEH2(), ABUNDANCEN15(), ABUNDANCEO17(), ABUNDANCEO18(), ABUNDANCES33(), ABUNDANCES34(), ABUNDANCES36(), C13, CACHE_ARRAY_SIZE, H2, isotopem_ratio(), N15, O17, O18, ratioC13_cache, ratioH2_cache, ratioN15_cache, ratioO17_cache, ratioO18_cache, ratioS33_cache, ratioS34_cache, ratioS36_cache, S33, S34, and S36.
Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::PeptideNaturalIsotope::getIntensityRatio().
const pappso_double pappso::MASSCARBON | ( | 12 | ) |
const pappso_double pappso::MASSCO | ( | MASSCARBON+ | MASSOXYGEN | ) |
const pappso_double pappso::MASSH2O | ( | (MPROTIUM *2)+ | MASSOXYGEN | ) |
const pappso_double pappso::MASSNH3 | ( | (MPROTIUM *3)+ | MASSNITROGEN | ) |
const pappso_double pappso::MASSNITROGEN | ( | 14. | 0030740048 | ) |
const pappso_double pappso::MASSOXYGEN | ( | 15. | 99491461956 | ) |
const pappso_double pappso::MASSPHOSPHORUS | ( | 30. | 973761998 | ) |
const pappso_double pappso::MASSPHOSPHORYLATEDR | ( | MPROTIUM+(MASSOXYGEN *3)+ | MASSPHOSPHORUS | ) |
Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon().
const pappso_double pappso::MASSSELENIUM | ( | 79. | 916520 | ) |
const pappso_double pappso::MASSSULFUR | ( | 31. | 9720711741 | ) |
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::maxYDataPoint | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end | ||
) |
Definition at line 180 of file trace.cpp.
Referenced by pappso::TracePeak::TracePeak(), pappso::TracePeak::TracePeak(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::FilterCeilingAmplitudePercentage::filter(), pappso::FilterFloorAmplitudePercentage::filter(), pappso::FilterLocalMaximum::filter(), pappso::FilterNormalizeIntensities::filter(), pappso::FilterHighPassPercentage::filter(), pappso::FilterRescaleY::filter(), pappso::FilterTriangle::filter(), pappso::LinearRegression::getNrmsd(), and pappso::FilterMorphoMax::getWindowValue().
PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::maxYDataPoint | ( | std::vector< DataPoint >::iterator | begin, |
std::vector< DataPoint >::iterator | end | ||
) |
PMSPP_LIB_DECL double pappso::meanYTrace | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end | ||
) |
calculate the mean of y value of a trace
Definition at line 253 of file trace.cpp.
References sumYTrace().
Referenced by pappso::LinearRegression::getCoefficientOfDetermination(), and pappso::FilterMorphoMean::getWindowValue().
PMSPP_LIB_DECL double pappso::medianYTrace | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end | ||
) |
calculate the median of y value of a trace
Definition at line 291 of file trace.cpp.
Referenced by pappso::FilterMorphoMedian::getWindowValue().
const pappso_double pappso::MHPLUS | ( | 1. | 007276466879 | ) |
Referenced by pappso::specglob::PeptideSpectrum::PeptideSpectrum(), pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), pappso::specself::SelfSpectrumDataPoint::fillAntiSpectrumDataPoint(), pappso::specglob::PeptideModel::generateTheoreticalPeaks(), pappso::PsmFeatures::getIonPairPrecursorMassDelta(), pappso::specglob::PeptideModel::getMz(), pappso::Ion::getMz(), pappso::QualifiedMassSpectrum::getPrecursorMass(), pappso::PeptideInterface::matchPeak(), pappso::XtandemSpectrumProcess::process(), pappso::PeptideRawFragmentMasses::pushBackIonMz(), and pappso::FilterChargeDeconvolution::transformToMonoChargedForAllDataPoint().
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::minYDataPoint | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end | ||
) |
Definition at line 158 of file trace.cpp.
Referenced by pappso::FilterCeilingAmplitudePercentage::filter(), pappso::FilterFloorAmplitudePercentage::filter(), pappso::FilterGreatestYperWindow::filter(), pappso::LinearRegression::getNrmsd(), and pappso::FilterMorphoMin::getWindowValue().
PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::minYDataPoint | ( | std::vector< DataPoint >::iterator | begin, |
std::vector< DataPoint >::iterator | end | ||
) |
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::moveLowerYLeftDataPoint | ( | const Trace & | trace, |
std::vector< DataPoint >::const_iterator | begin | ||
) |
Move left to the lower value.
Definition at line 223 of file trace.cpp.
Referenced by pappso::TraceDetectionZivy::detect().
PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::moveLowerYRigthDataPoint | ( | const Trace & | trace, |
std::vector< DataPoint >::const_iterator | begin | ||
) |
Move right to the lower value.
Definition at line 205 of file trace.cpp.
Referenced by pappso::TraceDetectionZivy::detect().
const pappso_double pappso::MPROTIUM | ( | 1. | 007825032241 | ) |
const pappso_double pappso::MPROTON | ( | 1. | 007276466879 | ) |
const pappso_double pappso::ONEMILLION | ( | 1000000 | ) |
Referenced by pappso::PpmPrecision::delta().
Definition at line 347 of file aa.cpp.
References pappso::Aa::isLesser().
PMSPP_LIB_DECL QDataStream & pappso::operator<< | ( | QDataStream & | out, |
const DataPoint & | dataPoint | ||
) |
Definition at line 156 of file datapoint.cpp.
References pappso::DataPoint::x, and pappso::DataPoint::y.
PMSPP_LIB_DECL QDataStream & pappso::operator<< | ( | QDataStream & | out, |
const Trace & | trace | ||
) |
PMSPP_LIB_DECL QDataStream & pappso::operator<< | ( | QDataStream & | outstream, |
const MassSpectrum & | massSpectrum | ||
) |
Definition at line 345 of file massspectrum.cpp.
Definition at line 342 of file aa.cpp.
References pappso::Aa::isAaEqual().
PMSPP_LIB_DECL QDataStream & pappso::operator>> | ( | QDataStream & | in, |
DataPoint & | dataPoint | ||
) |
Definition at line 167 of file datapoint.cpp.
References pappso::DataPoint::x, and pappso::DataPoint::y.
PMSPP_LIB_DECL QDataStream & pappso::operator>> | ( | QDataStream & | instream, |
MassSpectrum & | massSpectrum | ||
) |
Definition at line 360 of file massspectrum.cpp.
QDataStream & pappso::operator>> | ( | QDataStream & | instream, |
MsRunSlice & | slice | ||
) |
Definition at line 158 of file msrunslice.cpp.
References pappso::PappsoException::qwhat(), pappso::MsRunSlice::setSize(), pappso::MsRunSlice::setSliceNumber(), pappso::MsRunSlice::setSpectrum(), and pappso::MsRunSlice::size().
PMSPP_LIB_DECL QDataStream & pappso::operator>> | ( | QDataStream & | out, |
Trace & | trace | ||
) |
Definition at line 50 of file trace.cpp.
PMSPP_LIB_DECL bool pappso::peptideIonIsNter | ( | PeptideIon | ion_type | ) |
tells if an ion is Nter
ion_type | the ion to test |
Definition at line 60 of file peptide.cpp.
Referenced by pappso::PsmFeatures::findComplementIonPairs(), getPeptideIonDirection(), pappso::XtandemHyperscoreBis::getXtandemPredictedIonIntensityFactor(), peptideIonTypeIsComplement(), pappso::PeptideRawFragmentMasses::pushBackIonMasses(), and pappso::PeptideRawFragmentMasses::pushBackIonMz().
PMSPP_LIB_DECL bool pappso::peptideIonTypeIsComplement | ( | PeptideIon | ion_type_ref, |
PeptideIon | ion_type | ||
) |
tells if an ion type is the complement ion of the other
ion_type_ref | the ion type reference |
ion_type | the ion to test |
Definition at line 43 of file peptide.cpp.
References ao, b, bstar, peptideIonIsNter(), y, yo, and ystar.
PMSPP_LIB_DECL double pappso::quantileYTrace | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
double | quantile | ||
) |
calculate the quantile of y value of a trace
begin | begin iterator |
end | end iterator |
quantile | the quantile value between 0 and 1 |
Definition at line 265 of file trace.cpp.
Referenced by pappso::FilterQuantileBasedRemoveY::filter().
PMSPP_LIB_DECL double pappso::sumYTrace | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
double | init | ||
) |
calculate the sum of y value of a trace
Definition at line 244 of file trace.cpp.
Referenced by pappso::LinearRegression::LinearRegression(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::FilterMorphoSum::getWindowValue(), meanYTrace(), and pappso::Trace::sumY().
std::map< BinningType, QString > pappso::binningTypeMap |
Map relating the BinningType to a textual representation.
Definition at line 67 of file mzintegrationparams.cpp.
Referenced by pappso::MzIntegrationParams::toString().
|
static |
Definition at line 27 of file bafasciifilereader.cpp.
Referenced by pappso::BafAsciiFileReader::initialize().
uint64_t pappso::combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
|
constexpr |
Definition at line 59 of file msrunreadconfig.h.
Referenced by pappso::MsRunReadConfig::MsRunReadConfig(), pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::getMsLevelsAsString(), pappso::MsRunReadConfig::operator=(), pappso::MsRunReadConfig::reset(), pappso::MsRunReadConfig::setMsLevels(), and pappso::MsRunReadConfig::toString().
Definition at line 55 of file msrunreader.h.
pappso_double pappso::ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 85 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 92 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 86 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 90 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 91 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 89 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 88 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().
pappso_double pappso::ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 87 of file peptidenaturalisotope.cpp.
Referenced by isotopem_ratio_cache().