libpappsomspp
Library for mass spectrometry
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tries to keep as much as possible monoisotopes, removing any possible C13 peaks More...
Classes | |
class | Aa |
class | AaBase |
class | AaModification |
class | AtomNumberInterface |
class | BaseColorMapPlotWidget |
struct | BasePlotContext |
class | BasePlotWidget |
class | BaseTracePlotWidget |
struct | ColorMapPlotConfig |
class | DaltonPrecision |
struct | DataPoint |
class | DriftSpecMassSpecColorMapPlotWidget |
class | DriftSpecTracePlotWidget |
class | Enzyme |
class | EnzymeProductInterface |
class | ExceptionNotFound |
class | ExceptionNotImplemented |
class | ExceptionNotPossible |
class | ExceptionOutOfRange |
class | FastaFileIndexer |
class | FastaFileIndexerInterface |
class | FastaHandlerInterface |
class | FastaOutputStream |
class | FastaReader |
class | FastaWriterInterface |
class | FilterComplementIonEnhancer |
try to detect complementary ions and assign maximum intensity of both elements 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 | 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 | FilterOboPsiModSink |
class | FilterOboPsiModTermAccession |
class | FilterOboPsiModTermDiffMono |
class | FilterOboPsiModTermLabel |
class | FilterOboPsiModTermName |
class | FilterPseudoCentroid |
class | FilterRemoveC13 |
class | FilterResampleKeepGreater |
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 | 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 |
class | GrpExperiment |
class | GrpGroup |
class | GrpGroupingMonitor |
class | GrpGroupingMonitorInterface |
class | GrpMapPeptideToGroup |
class | GrpMapPeptideToSubGroupSet |
class | GrpPeptide |
class | GrpPeptideSet |
class | GrpProtein |
class | GrpSubGroup |
class | GrpSubGroupSet |
class | Ion |
class | IonIsotopeRatioScore |
class | LinearRegression |
class | MapTrace |
class | MassDataCombinerInterface |
struct | MassSpecTracePlotContext |
class | MassSpecTracePlotWidget |
class | MassSpectrum |
Class to represent a mass spectrum. More... | |
class | MassSpectrumCombiner |
class | MassSpectrumCombinerFactory |
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 |
class | MassSpectrumMinusCombiner |
class | MassSpectrumPlusCombiner |
class | MassSpectrumWidget |
class | MgfOutput |
class | MorpheusScore |
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 | MsRunReader |
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More... | |
class | MsRunReaderScanNumberMultiMap |
provides a multimap to find quickly spectrum index from scan number 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 | MzPrecision |
class | MzRange |
class | MzxmlOutput |
class | OboPsiMod |
class | OboPsiModHandlerInterface |
class | OboPsiModTerm |
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 | 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 | PwizMsFileReader |
class | PwizMsRunReader |
class | QCPSpectrum |
class | QCPXic |
class | QualifiedMassSpectrum |
Class representing a fully specified mass spectrum. More... | |
class | QualifiedXic |
class | ResPrecision |
struct | RtPoint |
struct | SavGolParams |
Parameters for the Savitzky-Golay filter. More... | |
struct | SimplePeakIonMatch |
class | SpectrumCollectionHandlerInterface |
interface to collect spectrums from the MsRunReader class More... | |
class | TandemWrapperRun |
class | TicXicChromDriftSpecColorMapPlotWidget |
class | TicXicChromMassSpecColorMapPlotWidget |
class | TicXicChromTracePlotWidget |
class | TimsBinDec |
class | TimsData |
class | TimsDirectXicExtractor |
class | TimsFrame |
class | TimsFrameBase |
class | TimsMs2CentroidFilter |
class | TimsMsFileReader |
class | TimsMsRunReader |
class | TimsMsRunReaderMs2 |
class | TimsMsRunReaderMs2Selected |
class | TimsXicExtractorInterface |
struct | TimsXicStructure |
structure needed to extract XIC from Tims data More... | |
class | Trace |
A simple container of DataPoint instances. More... | |
class | TraceCombiner |
class | TraceDetectionInterface |
class | TraceDetectionMoulon |
class | TraceDetectionSinkInterface |
class | TraceDetectionZivy |
class | TraceMinusCombiner |
class | TracePeak |
class | TracePlusCombiner |
class | Utils |
class | Xic |
class | XicPeptideFragmentIon |
class | XicPeptideFragmentIonNaturalIsotope |
class | XicPeptideInterface |
class | XicWidget |
class | XtandemHyperscore |
class | XtandemHyperscoreBis |
class | XtandemInputSaxHandler |
class | XtandemOutputSaxHandler |
class | XtandemPresetSaxHandler |
class | XtandemSpectrumProcess |
class | XyMsFileReader |
class | XyMsRunReader |
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 | peptideIonIsNter (PeptideIon ion_type) |
tells if an ion is Nter More... | |
PeptideDirection | getPeptideIonDirection (PeptideIon ion_type) |
get the direction of a peptide ion More... | |
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) |
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 More... | |
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 More... | |
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 More... | |
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) More... | |
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) More... | |
std::vector< DataPoint >::const_iterator | moveLowerYRigthDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin) |
Move right to the lower value. More... | |
std::vector< DataPoint >::const_iterator | moveLowerYLeftDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin) |
Move left to the lower value. More... | |
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 More... | |
double | meanYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
calculate the mean of y value of a trace More... | |
double | medianYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
calculate the median of y value of a trace More... | |
double | areaTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) |
calculate the area of a trace More... | |
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 (31.97207100) |
const pappso_double | MASSPHOSPHORYLATEDR (MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS) |
const pappso_double | MASSSELENIUM (79.916520) |
const pappso_double | DIFFC12C13 (1.0033548378) |
const pappso_double | DIFFS32S33 (32.97145876 - MASSSULFUR) |
const pappso_double | DIFFS32S34 (33.96786690 - MASSSULFUR) |
const pappso_double | DIFFS32S36 (35.96708076 - 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 (0.00015574) |
const pappso_double | ABUNDANCEN15 (0.003663) |
const pappso_double | ABUNDANCEO17 (0.000372) |
const pappso_double | ABUNDANCEO18 (0.0020004) |
const pappso_double | ABUNDANCEC13 (0.011078) |
const pappso_double | ABUNDANCEC12 (0.988922) |
const pappso_double | ABUNDANCES33 (0.00750) |
const pappso_double | ABUNDANCES34 (0.04215) |
const pappso_double | ABUNDANCES36 (0.00020) |
QDataStream & | operator>> (QDataStream &instream, MsRunSlice &slice) |
Variables | |
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} |
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 BaseColorMapPlotWidget> pappso::BaseColorMapPlotWidgetCstSPtr |
Definition at line 59 of file basecolormapplotwidget.h.
typedef std::shared_ptr<BaseColorMapPlotWidget> pappso::BaseColorMapPlotWidgetSPtr |
Definition at line 57 of file basecolormapplotwidget.h.
typedef std::shared_ptr<const BasePlotWidget> pappso::BasePlotWidgetCstSPtr |
Definition at line 133 of file baseplotwidget.h.
typedef std::shared_ptr<BasePlotWidget> pappso::BasePlotWidgetSPtr |
Definition at line 132 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 17 of file datapoint.h.
typedef std::shared_ptr<FastaFileIndexer> pappso::FastaFileIndexerSPtr |
Definition at line 49 of file fastafileindexer.h.
typedef std::shared_ptr<const FilterInterface> pappso::FilterInterfaceCstSPtr |
Definition at line 46 of file filterinterface.h.
typedef std::shared_ptr<FilterInterface> pappso::FilterInterfaceSPtr |
Definition at line 45 of file filterinterface.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 MapTrace> pappso::MapTraceCstSPtr |
Definition at line 26 of file maptrace.h.
typedef std::shared_ptr<MapTrace> pappso::MapTraceSPtr |
Definition at line 25 of file maptrace.h.
typedef std::shared_ptr<const MassSpectrumCombiner> pappso::MassSpectrumCombinerCstSPtr |
Definition at line 25 of file massspectrumcombiner.h.
typedef std::shared_ptr<MassSpectrumCombiner> pappso::MassSpectrumCombinerSPtr |
Definition at line 26 of file massspectrumcombiner.h.
typedef std::shared_ptr<const MassSpectrum> pappso::MassSpectrumCstSPtr |
Definition at line 55 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 54 of file massspectrum.h.
typedef std::shared_ptr<const MsRunDataSetTree> pappso::MsRunDataSetTreeCstSPtr |
Definition at line 28 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 27 of file msrundatasettree.h.
typedef std::shared_ptr<const MsRunId> pappso::MsRunIdCstSPtr |
typedef std::shared_ptr<const MsRunReader> pappso::MsRunReaderCstSPtr |
Definition at line 152 of file msrunreader.h.
typedef std::shared_ptr<MsRunReader> pappso::MsRunReaderSPtr |
Definition at line 151 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 43 of file msrunxicextractorinterface.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<const TimsFrameBase> pappso::TimsFrameBaseCstSPtr |
Definition at line 40 of file timsframebase.h.
typedef std::shared_ptr<TimsFrameBase> pappso::TimsFrameBaseSPtr |
Definition at line 39 of file timsframebase.h.
typedef std::shared_ptr<const TimsFrame> pappso::TimsFrameCstSPtr |
Definition at line 42 of file timsframe.h.
typedef std::shared_ptr<TimsFrame> pappso::TimsFrameSPtr |
Definition at line 41 of file timsframe.h.
typedef std::shared_ptr<TimsMsRunReaderMs2> pappso::TimsMsRunReaderMs2SPtr |
Definition at line 18 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<const Xic> pappso::XicCstSPtr |
typedef std::shared_ptr<Xic> pappso::XicSPtr |
typedef std::vector<std::pair<XicCstSPtr, TracePeakCstSPtr> > pappso::XicXicPeakPairList |
Definition at line 44 of file xicwidget.h.
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H | |
O | |
N | |
S |
Definition at line 69 of file peptidenaturalisotope.cpp.
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pwiz | |
xy | |
tims | |
tims_ms2 |
Definition at line 20 of file msfileaccessor.h.
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PeptideIon enum defines all types of ions (Nter or Cter)
Definition at line 333 of file types.h.
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x_axis | |
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both |
Definition at line 53 of file baseplotwidget.h.
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Definition at line 47 of file qualifiedmassspectrum.h.
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Definition at line 62 of file baseplotwidget.h.
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proline_effect |
Definition at line 42 of file peptiderawfragmentmasses.h.
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const pappso_double pappso::ABUNDANCEC12 | ( | 0. | 988922 | ) |
const pappso_double pappso::ABUNDANCEC13 | ( | 0. | 011078 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEH2 | ( | 0. | 00015574 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEN15 | ( | 0. | 003663 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEO17 | ( | 0. | 000372 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCEO18 | ( | 0. | 0020004 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCES33 | ( | 0. | 00750 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCES34 | ( | 0. | 04215 | ) |
Referenced by isotopem_ratio_cache().
const pappso_double pappso::ABUNDANCES36 | ( | 0. | 00020 | ) |
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 240 of file trace.cpp.
Referenced by 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 | ) |
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 | ( | 32.97145876 - | MASSSULFUR | ) |
const pappso_double pappso::DIFFS32S34 | ( | 33.96786690 - | MASSSULFUR | ) |
const pappso_double pappso::DIFFS32S36 | ( | 35.96708076 - | 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().
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 | ||
) |
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 87 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 | ||
) |
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 31 of file trace.cpp.
References pappso::DataPoint::x.
Referenced by pappso::TraceDetectionZivy::detect(), pappso::FilterResampleKeepSmaller::filter(), pappso::FilterResampleRemoveXRange::filter(), pappso::FilterResampleKeepXRange::filter(), 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 | ||
) |
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 59 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().
PMSPP_LIB_DECL Trace pappso::flooredLocalMaxima | ( | std::vector< DataPoint >::const_iterator | begin, |
std::vector< DataPoint >::const_iterator | end, | ||
double | y_floor | ||
) |
Definition at line 260 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().
PeptideDirection pappso::getPeptideIonDirection | ( | PeptideIon | ion_type | ) |
get the direction of a peptide ion
ion_type | the ion to test |
Definition at line 54 of file peptide.cpp.
References 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(), CACHE_ARRAY_SIZE, isotopem_ratio(), ratioC13_cache, ratioH2_cache, ratioN15_cache, ratioO17_cache, ratioO18_cache, ratioS33_cache, ratioS34_cache, and ratioS36_cache.
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 | ) |
Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon().
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. | 97207100 | ) |
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 138 of file trace.cpp.
References pappso::DataPoint::y.
Referenced by pappso::TracePeak::TracePeak(), pappso::FilterLocalMaximum::filter(), pappso::FilterHighPassPercentage::filter(), pappso::FilterRescaleY::filter(), pappso::FilterTriangle::filter(), pappso::LinearRegression::getNrmsd(), pappso::FilterMorphoMax::getWindowValue(), and pappso::MsRunXicExtractor::getXicCstSPtr().
PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::maxYDataPoint | ( | std::vector< DataPoint >::iterator | begin, |
std::vector< DataPoint >::iterator | end | ||
) |
find the element with the greatest Y value (intensity)
Definition at line 149 of file trace.cpp.
References pappso::DataPoint::y.
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 211 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 222 of file trace.cpp.
Referenced by pappso::FilterMorphoMedian::getWindowValue().
const pappso_double pappso::MHPLUS | ( | 1. | 007276466879 | ) |
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 116 of file trace.cpp.
References pappso::DataPoint::y.
Referenced by 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 | ||
) |
find the element with the smallest Y value (intensity)
Definition at line 127 of file trace.cpp.
References pappso::DataPoint::y.
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 181 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 163 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 285 of file aa.cpp.
References pappso::Aa::isLesser().
QDataStream & pappso::operator<< | ( | QDataStream & | out, |
const DataPoint & | dataPoint | ||
) |
Definition at line 152 of file datapoint.cpp.
References pappso::DataPoint::x, and pappso::DataPoint::y.
QDataStream & pappso::operator<< | ( | QDataStream & | out, |
const Trace & | trace | ||
) |
QDataStream & pappso::operator<< | ( | QDataStream & | outstream, |
const MassSpectrum & | massSpectrum | ||
) |
Definition at line 342 of file massspectrum.cpp.
Definition at line 280 of file aa.cpp.
References pappso::Aa::isAaEqual().
QDataStream & pappso::operator>> | ( | QDataStream & | in, |
DataPoint & | dataPoint | ||
) |
Definition at line 163 of file datapoint.cpp.
References pappso::DataPoint::x, and pappso::DataPoint::y.
QDataStream & pappso::operator>> | ( | QDataStream & | instream, |
MassSpectrum & | massSpectrum | ||
) |
Definition at line 357 of file massspectrum.cpp.
QDataStream & pappso::operator>> | ( | QDataStream & | instream, |
MsRunSlice & | slice | ||
) |
Definition at line 156 of file msrunslice.cpp.
References pappso::PappsoException::qwhat(), pappso::MsRunSlice::setSize(), pappso::MsRunSlice::setSliceNumber(), pappso::MsRunSlice::setSpectrum(), and pappso::MsRunSlice::size().
QDataStream & pappso::operator>> | ( | QDataStream & | out, |
Trace & | trace | ||
) |
bool pappso::peptideIonIsNter | ( | PeptideIon | ion_type | ) |
tells if an ion is Nter
ion_type | the ion to test |
Definition at line 44 of file peptide.cpp.
Referenced by getPeptideIonDirection(), pappso::XtandemHyperscoreBis::getXtandemPredictedIonIntensityFactor(), pappso::PeptideRawFragmentMasses::pushBackIonMasses(), and pappso::PeptideRawFragmentMasses::pushBackIonMz().
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 202 of file trace.cpp.
References pappso::DataPoint::y.
Referenced by pappso::LinearRegression::LinearRegression(), pappso::FilterMorphoSum::getWindowValue(), pappso::MsRunXicExtractor::getXicCstSPtr(), meanYTrace(), and pappso::Trace::sumY().
uint64_t pappso::combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0} |
Definition at line 44 of file peptidenaturalisotope.cpp.
Referenced by Combinations().
Definition at line 236 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().