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# libpappsomspp

Todo List

## Namespaces

### Namespace List

#### pappso

##### specglob

###### AminoAcidModel

alignment_type

amino_acid

bracket

mass_difference

remove

###### ExperimentalSpectrum

ExperimentalSpectrum

ExperimentalSpectrum

~ExperimentalSpectrum

createSymetricPeakList

findMz

getMassList

getMassList

getPrecursorMass

getQualifiedMassSpectrum

getSymetricMz

getTargetMzSum

reverseFindDiffMz

toString

m_precisionPtr

m_precursorMass

m_qualifiedMassSpectrum

m_targetMzSum

###### ExperimentalSpectrumDataPoint

indice

symmetric_mz

type

###### PeptideModel

PeptideModel

PeptideModel

PeptideModel

~PeptideModel

assignResidualMass2Cter

checkForAaModification

checkForAaModificationP

checkForMutation

checkForMutations

copyDeep

eliminateComplementaryDelta

eliminateNegativeOffset

generateTheoreticalPeaks

getCountSharedPeaks

getIntensityExperimentalPeaks

getIntensitySharedPeaks

getMass

getMassDelta

getMz

getTheoreticalIonMassList

getTheoreticalPeakDataPointList

getTheoreticalPeakDataPointListToString

hasRemoval

ltrimOnRemoval

matchExperimentalPeaks

modifCount

operator=

removeBracketsForAlignedAA

setBeginMassDelta

toProForma

toString

m_beginMassDelta

m_countSharedPeaks

m_cterModification

m_experimentalPrecursorMass

m_intensityExperimentalPeaks

m_intensitySharedPeaks

m_nterModification

m_theoreticalPeakList

mcsp_peakList

###### PeptideSpectrum

PeptideSpectrum

PeptideSpectrum

~PeptideSpectrum

getMassList

getPeptideSp

msp_peptide

###### PeptideSpectrumDataPoint

diff_mz

mz

###### PostTreatment

PostTreatment

~PostTreatment

findBetterPeptideModel

findReplaceMutations

getBetterPeptideModel

getOriginalPeptideModel

tryBetterPositionOffsets

tryToCumulateOffSets

tryToRemoveOffsets

m_betterPeptideModel

m_originalPeptideModel

m_precision

###### ScoreValues

ScoreValues

ScoreValues

~ScoreValues

get

operator=

set

m_scoreTable

###### SpectralAlignment

SpectralAlignment

~SpectralAlignment

align

backTrack

buildPeptideModel

fillMassDelta

fillMatricesWithScores

getBestRealignScore

getExperimentalSpectrumCsp

getExperimentalSpectrumDataPoint

getMatrix

getMaxPosIterator

getMaxScore

getPeptideSpectraCsp

getPrecursorMzDelta

getScoreRow

rtrim

m_BETTER_END_RA

m_itPosMax

m_matrix

m_maxScore

m_precisionPtr

m_precursorMassDelta

m_scoreValues

mcsp_experimentalSpectrum

mcsp_peptideSpectrum

###### SpectralAlignmentDataPoint

alignment_type

mass_difference

origin_column_indices

score

###### TheoreticalPeakDataPoint

aa_indice

it_experimental_peak_match

mz_range

ExperimentalSpectrumCsp

PeptideSpectraCsp

###### ExperimentalSpectrumDataPointType

native

symmetric

both

synthetic

###### ScoreValueType

scoreNonAlign

scoreReAlignNative

scoreReAlignSym

scoreReAlignBoth

scoreAlignNative

scoreAlignSym

scoreAlignBoth

scoreReAlignNativeNO

scoreReAlignSymNO

scoreReAlignBothNO

###### SpectralAlignmentType

nonAlign

reAlign

align

##### specself

###### SelfSpectrum

SelfSpectrum

~SelfSpectrum

getMatrix

getTrace

setPrecursorMass

setVariableModification

m_matrix

m_trace

###### SelfSpectrumDataPoint

fillAntiSpectrumDataPoint

fillSelfSpectrumDataPoint

setVariableModification

aaCodeList

antiAaCodeList

antiMassDelta

m_isComplement

massDelta

SelfSpectrumMatrix

##### spectree

###### Bucket

Bucket

Bucket

back

front

getCartList

getId

operator<

push_back

size

m_cartList

m_itemId

###### BucketClustering

BucketClustering

addItemCart

asSortedList

getItemCartCount

removeBucketsWithinCartIdRange

size

m_bucketMap

m_itemCartCount

###### ItemCart

ItemCart

ItemCart

ItemCart

~ItemCart

getId

getItemList

operator=

m_id

m_itemList

###### SpecTree

###### MapSimilarityCount

aboveThreshold

keys

map_id_count

###### MapSimilarityCountElement

aboveThreshold

count

lastWitness

###### SpecTreeNode

count

nextIndex

parentIndex

value

SpecTree

~SpecTree

addNewNode

extractSpectrumPairSimilarityCount

extractSpectrumSimilarityCount

getSpectrumFirstNodeIndex

manageSideAccess

toString

walkBackInBranchFromNode

walkBackInBranchFromNodeToTarget

xtract

index_not_defined

m_nodeList

m_spectrumFirstNodeIndex

###### SpecXtractInterface

SpecXtractInterface

~SpecXtractInterface

beginItemCartExtraction

endItemCartExtraction

reportSimilarity

###### SpecXtractMap

SpecXtractMap

~SpecXtractMap

clear

getMapSimilarities

reportSimilarity

m_mapSimilarities

erase_if

##### Aa

Aa

Aa

Aa

Aa

~Aa

addAaModification

getInternalCterModification

getInternalNterModification

getMass

getModificationList

getNumberOfAtom

getNumberOfIsotope

getNumberOfModification

getTotalModificationMass

isAaEqual

isLesser

operator=

removeAaModification

removeAllButInternalModification

removeInternalCterModification

removeInternalNterModification

replaceAaModification

toAbsoluteString

toProForma

toString

m_listMod

##### AaBase

AaIntMap

AaMassMap

AminoAcidCharList

AaBase

AaBase

AaBase

~AaBase

getAaMass

getAminoAcidChar

getAminoAcidCharList

getLetter

getMass

getNumberOfAtom

getNumberOfIsotope

replaceLeucineIsoleucine

AaModification

m_aaLetter

m_aaMassMap

m_aaNumberOfCarbonMap

m_aaNumberOfHydrogenMap

m_aaNumberOfNitrogenMap

m_aaNumberOfOxygenMap

m_aaNumberOfSulfurMap

m_aminoAcidCharList

##### AaCode

AaCode

AaCode

~AaCode

addAaModification

getAa

getAa

getAaCode

getMass

getSize

updateMass

updateNumbers

m_aaCollection

m_asciiTable

m_massCollection

##### AaModification

MapAccessionModifications

AaModification

~AaModification

AaModification

calculateMassFromChemicalComponents

createInstance

createInstance

createInstanceC13N15LabelledAminoAcid

createInstanceMutation

getAccession

getInstance

getInstance

getInstanceCustomizedMod

getInstanceInsertionAccessionByAaLetter

getInstanceMutation

getInstanceRemovalAccessionByAaLetter

getInstanceXtandemMod

getMass

getName

getNumberOfAtom

getNumberOfIsotope

getXrefOrigin

isInternal

setDiffFormula

setXrefOrigin

toProForma

m_accession

m_atomCount

m_mapAccessionModifications

m_mapIsotope

m_mass

m_mutex

m_name

m_origin

##### AaStringCodec

AaStringCodec

AaStringCodec

~AaStringCodec

code

codeLlc

codeLlc

codeOnlyContains

decode

decode

generateCodeMassFromModel

generateLlcCodeListByMaxPeptideSize

generateLlcCodeListUpToMaxPeptideSize

getAaCode

getLimitMax

getMass

recGenerateModel

uniqueCodeContainsAminoAcid

m_aaCode

m_base

m_units

##### AaStringCodeMassMatching

###### aaCodeAndMassRange

code

mz

mz_range_low

mz_range_up

AaStringCodeMassMatching

AaStringCodeMassMatching

~AaStringCodeMassMatching

filterCodeList

getAaCodeFromMass

getAaCodeFromMassList

getAaCodeFromMassWearingModification

getPrecisionPtr

m_aaCode

m_aaCodec

m_base

m_codeMassList

m_precision

##### AtomNumberInterface

getNumberOfAtom

getNumberOfIsotope

##### BafAsciiFileReader

BafAsciiFileReader

~BafAsciiFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### BafAsciiMsRunReader

BafAsciiMsRunReader

~BafAsciiMsRunReader

accept

acquireDevice

craftLineParserRegExp

craftLineParserRegExpPattern

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

parseMassSpectrumLine

qualifiedMassSpectrum

qualifiedMassSpectrumFromBafAsciiMSDataFile

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

spectrumListSize

MsFileAccessor

m_fileName

m_spectrumCount

##### BaseColorMapPlotWidget

BaseColorMapPlotWidget

BaseColorMapPlotWidget

~BaseColorMapPlotWidget

addColorMap

addColorMap

axisScale

currentXaxisRangeIndices

currentYaxisRangeIndices

dataTo3ColString

dataToMatrixString

getColorMapPlotConfig

getOrigColorMapPlotConfig

getPlottingColor

setColorMapPlotConfig

setPlottingColor

transposeAxes

xAxisDataKind

xAxisScale

yAxisDataKind

yAxisScale

zAxisDataResetToOriginal

zAxisFilterHighPassPercentage

zAxisFilterLowPassPercentage

zAxisFilterLowPassThreshold

zAxisScale

zAxisScaleToLog10

m_colorMapPlotConfig

mpa_origColorMapData

mpa_origColorMapPlotConfig

##### BasePlotContext

BasePlotContext

BasePlotContext

~BasePlotContext

operator=

recordDragDirections

toString

updateIntegrationScope

updateIntegrationScopeRect

updateIntegrationScopeRhomb

updateIntegrationScopeRhombHorizontal

updateIntegrationScopeRhombVertical

m_currentDragPoint

m_dataKind

m_dragDirections

m_integrationScopeRhombHeight

m_integrationScopeRhombWidth

m_isKeyBoardDragging

m_isLeftPseudoButtonKeyPressed

m_isMeasuringDistance

m_isMouseDragging

m_isRightPseudoButtonKeyPressed

m_keyboardModifiers

m_lastCursorHoveredPoint

m_lastPressedMouseButton

m_lastReleasedMouseButton

m_mouseButtonsAtMousePress

m_mouseButtonsAtMouseRelease

m_pressedKeyCode

m_pressedMouseButtons

m_releasedKeyCode

m_selectionPolygon

m_startDragPoint

m_wasClickOnXAxis

m_wasClickOnYAxis

m_wasMouseDragging

m_wassKeyBoardDragging

m_xDelta

m_xRange

m_xRegionRangeEnd

m_xRegionRangeStart

m_yDelta

m_yRange

m_yRegionRangeEnd

m_yRegionRangeStart

msp_integrationScope

##### BasePlotWidget

BasePlotWidget

BasePlotWidget

~BasePlotWidget

allLayerNamesToString

axisDoubleClickHandler

axisPan

axisReframe

axisRescale

axisZoom

calculateDragDeltas

createAllAncillaryItems

directionKeyPressEvent

directionKeyReleaseEvent

dragDirection

drawSelectionRectangleAndPrepareZoom

drawXScopeSpanFeatures

drawYScopeSpanFeatures

getContext

getInnermostRangeX

getInnermostRangeY

getOutermostRangeX

getOutermostRangeY

getPen

getPlottingColor

getPlottingColor

getRange

getRangeX

getRangeY

hideAllPlotItems

hideSelectionRectangle

hideTracers

horizontalGetGraphCoordNewPointCountPixels

horizontalMoveMouseCursorCountPixels

integrationRequestedSignal

isClickOntoXAxis

isClickOntoYAxis

isSelectionRectangleVisible

isVerticalDisplacementAboveThreshold

keyPressEvent

keyPressEventSignal

keyReleaseEvent

keyReleaseEventSignal

lastCursorHoveredPointSignal

layerableLayerIndex

layerableLayerName

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerLeftButtonDraggingCursor

mouseMoveHandlerNotDraggingCursor

mouseMoveHandlerRightButtonDraggingCursor

mousePressHandler

mousePseudoButtonKeyPressEvent

mousePseudoButtonKeyReleaseEvent

mouseReleaseEventSignal

mouseReleaseHandler

mouseReleaseHandlerLeftButton

mouseReleaseHandlerRightButton

mouseWheelEventSignal

mouseWheelHandler

moveMouseCursorGraphCoordToGlobal

moveMouseCursorPixelCoordToGlobal

plotRangesChangedSignal

plottableDestructionRequestedSignal

plottableSelectionChangedSignal

redrawPlotBackground

replotWithAxesRanges

replotWithAxisRangeX

replotWithAxisRangeY

resetAxesRangeHistory

resetSelectionRectangle

restoreAxesRangeHistory

restorePreviousAxesRangeHistory

setAxisLabelX

setAxisLabelY

setFocus

setFocusSignal

setPen

setPlottingColor

setPlottingColor

setupWidget

showTracers

spaceKeyReleaseEvent

updateAxesRangeHistory

updateContextXandYAxisRanges

updateIntegrationScope

updateIntegrationScopeDrawing

updateIntegrationScopeHorizontalRhomb

updateIntegrationScopeRect

updateIntegrationScopeRhomb

updateIntegrationScopeVerticalRhomb

verticalGetGraphCoordNewPointCountPixels

verticalMoveMouseCursorCountPixels

whatIsVisibleOfTheSelectionRectangle

xAxisMeasurementSignal

yMinMaxOnXAxisCurrentRange

yMinMaxOnXAxisCurrentRange

m_axisLabelX

m_axisLabelY

m_context

m_desc

m_fileName

m_focusedBrush

m_focusedColor

m_lastAxisRangeHistoryIndex

m_leftMousePseudoButtonKey

m_mouseMoveHandlerSkipAmount

m_mouseMoveHandlerSkipCount

m_name

m_pen

m_rightMousePseudoButtonKey

m_shouldTracersBeVisible

m_unfocusedBrush

m_unfocusedColor

m_xAxisRangeHistory

m_yAxisRangeHistory

mp_hPosTracerItem

mp_selectionRectangeLine1

mp_selectionRectangeLine2

mp_selectionRectangeLine3

mp_selectionRectangeLine4

mp_vEndTracerItem

mp_vPosTracerItem

mp_vStartTracerItem

mp_xDeltaTextItem

mp_yDeltaTextItem

##### BaseTracePlotWidget

BaseTracePlotWidget

BaseTracePlotWidget

~BaseTracePlotWidget

addTrace

axisDoubleClickHandler

axisPan

axisReframe

axisRescale

axisZoom

clearGraphData

findIntegrationLowerRangeForKey

getValueRangeOnKeyRange

getValueRangeOnKeyRange

getValuesX

getValuesY

getYatX

getYatX

setGraphData

setGraphData

toTrace

toTrace

toTrace

toTrace

##### CodeToMass

code

mass

##### ColorMapPlotConfig

ColorMapPlotConfig

ColorMapPlotConfig

ColorMapPlotConfig

operator=

setOrigAndLastMaxZValue

setOrigAndLastMinZValue

setOrigMaxZValue

setOrigMinZValue

toString

keyCellCount

lastMaxZFilterThresholdPercentage

lastMaxZValue

lastMinZFilterThresholdPercentage

lastMinZValue

maxKeyValue

maxMzValue

minKeyValue

minMzValue

mzCellCount

origMaxZValue

origMinZValue

xAxisDataKind

xAxisScale

yAxisDataKind

yAxisScale

zAxisScale

##### CosineSimilarity

CosineSimilarity

CosineSimilarity

~CosineSimilarity

similarity

mp_precision

msp_filterExclusion

##### DaltonPrecision

DaltonPrecision

~DaltonPrecision

delta

toString

unit

PrecisionFactory

##### DataPoint

DataPoint

DataPoint

DataPoint

DataPoint

DataPoint

incrementX

incrementY

initialize

initialize

initialize

isValid

makeDataPointCstSPtr

operator=

operator==

reset

toString

toString

x

y

##### DeepProtEnumStr

DeepProtMatchTypeFromString

DeepProtPeptideCandidateStatusFromString

toString

toString

##### DriftSpecMassSpecColorMapPlotWidget

DriftSpecMassSpecColorMapPlotWidget

~DriftSpecMassSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### DriftSpecTracePlotWidget

DriftSpecTracePlotWidget

~DriftSpecTracePlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### Enzyme

Enzyme

Enzyme

~Enzyme

eat

getMiscleavage

getQRegExpRecognitionSite

replaceWildcards

sanityCheck

setMaxPeptideVariantListSize

setMiscleavage

setTakeOnlyFirstWildcard

m_maxPeptideVariantListSize

m_miscleavage

m_recognitionSite

m_takeOnlyFirstWildcard

m_wildCardB

m_wildCardX

m_wildCardZ

##### EnzymeProductInterface

setPeptide

##### ExceptionInterrupted

ExceptionInterrupted

clone

##### ExceptionNotFound

ExceptionNotFound

clone

##### ExceptionNotImplemented

ExceptionNotImplemented

clone

##### ExceptionNotPossible

ExceptionNotPossible

clone

##### ExceptionNotRecognized

ExceptionNotRecognized

clone

##### ExceptionOutOfRange

ExceptionOutOfRange

clone

##### FastaFileIndexer

FastaFileIndexer

FastaFileIndexer

~FastaFileIndexer

close

getSequenceByIndex

makeFastaFileIndexerSPtr

open

parseFastaFile

size

m_fasta_file

m_indexArray

mpa_sequenceTxtIn

##### FastaFileIndexerInterface

close

getSequenceByIndex

open

##### FastaHandlerInterface

setSequence

##### FastaOutputStream

FastaOutputStream

~FastaOutputStream

writeProtein

m_ofastastream

##### FastaReader

FastaReader

~FastaReader

parse

parse

parseOnlyOne

FastaFileIndexer

m_handler

##### FastaSeqHandler

getDescription

getSequence

setSequence

description

sequence

##### FastaWriterInterface

writeProtein

##### FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

~FilterCeilingAmplitudePercentage

buildFilterFromString

filter

getPercentage

name

operator=

toString

m_percentage

##### FilterChargeDeconvolution

###### DataPointInfo

data_point

new_mono_charge_data_point

parent

z1_range

z1_vect

z2_range

z2_vect

z_charge

DataPointInfoSp

FilterChargeDeconvolution

FilterChargeDeconvolution

FilterChargeDeconvolution

~FilterChargeDeconvolution

addDataPointRefByExclusion

addDataPointToList

buildFilterFromString

computeBestChargeOfDataPoint

computeIsotopeDeconvolution

filter

name

toString

transformToMonoChargedForAllDataPoint

m_diffC12C13_z1

m_diffC12C13_z2

m_precisionPtrZ1

m_precisionPtrZ2

##### FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

~FilterComplementIonEnhancer

buildFilterFromString

enhanceComplementMassInRange

filter

name

toString

m_precisionPtr

m_targetMzSum

##### FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

~FilterFloorAmplitudePercentage

buildFilterFromString

filter

getPercentage

name

operator=

toString

m_percentage

##### FilterFloorY

FilterFloorY

FilterFloorY

~FilterFloorY

filter

operator=

##### FilterGreatestY

FilterGreatestY

FilterGreatestY

~FilterGreatestY

filter

getNumberOfPoints

operator=

m_numberOfPoints

##### FilterGreatestYperWindow

FilterGreatestYperWindow

FilterGreatestYperWindow

~FilterGreatestYperWindow

filter

getNumberOfPoints

operator=

m_numberOfPoints

m_xWindowRange

##### FilterHighPass

FilterHighPass

FilterHighPass

~FilterHighPass

filter

operator=

m_passY

##### FilterHighPassPercentage

FilterHighPassPercentage

FilterHighPassPercentage

~FilterHighPassPercentage

filter

operator=

m_ratioPassY

##### FilterInterface

~FilterInterface

filter

##### FilterLocalMaximum

FilterLocalMaximum

FilterLocalMaximum

~FilterLocalMaximum

filter

getHalfWindowSize

m_halfWindowSize

##### FilterLowIntensitySignalRemoval

ApicesSPtr

ClusterApices

TraceCIter

FilterLowIntensitySignalRemoval

FilterLowIntensitySignalRemoval

FilterLowIntensitySignalRemoval

~FilterLowIntensitySignalRemoval

backwardFindApex

buildFilterFromString

detectClusterApices

filter

forwardFindApex

getThreshold

name

nonConstFilter

operator=

reconstructTrace

toString

INTRA_CLUSTER_INTER_PEAK_DISTANCE

m_clusters

m_curApex

m_curIter

m_max

m_min

m_minIntPointCount

m_minIntStdDevFactor

m_minMean

m_minStdDev

m_noiseLevel

m_noiseMean

m_noiseStdDev

m_prevApex

m_prevIter

m_seen_upward_phase

m_threshold

nan

##### FilterLowPass

FilterLowPass

FilterLowPass

~FilterLowPass

filter

operator=

m_passY

##### FilterMorphoAntiSpike

FilterMorphoAntiSpike

FilterMorphoAntiSpike

FilterMorphoAntiSpike

~FilterMorphoAntiSpike

buildFilterFromString

filter

getHalfWindowSize

name

operator=

toString

m_halfWindowSize

##### FilterMorphoBackground

FilterMorphoBackground

FilterMorphoBackground

~FilterMorphoBackground

filter

getFilterMorphoMedian

getFilterMorphoMinMax

operator=

m_filterMorphoMedian

m_filterMorphoMinMax

##### FilterMorphoMax

FilterMorphoMax

FilterMorphoMax

~FilterMorphoMax

getMaxHalfEdgeWindows

getWindowValue

operator=

##### FilterMorphoMaxMin

FilterMorphoMaxMin

FilterMorphoMaxMin

~FilterMorphoMaxMin

filter

getMaxMinHalfEdgeWindows

operator=

m_filterMax

m_filterMin

##### FilterMorphoMean

FilterMorphoMean

FilterMorphoMean

~FilterMorphoMean

getMeanHalfEdgeWindows

getWindowValue

operator=

##### FilterMorphoMedian

FilterMorphoMedian

FilterMorphoMedian

~FilterMorphoMedian

getWindowValue

operator=

##### FilterMorphoMin

FilterMorphoMin

FilterMorphoMin

~FilterMorphoMin

getMinHalfEdgeWindows

getWindowValue

operator=

##### FilterMorphoMinMax

FilterMorphoMinMax

FilterMorphoMinMax

~FilterMorphoMinMax

filter

getMinMaxHalfEdgeWindows

operator=

m_filterMax

m_filterMin

##### FilterMorphoSum

FilterMorphoSum

FilterMorphoSum

~FilterMorphoSum

getWindowValue

operator=

##### FilterMorphoWindowBase

FilterMorphoWindowBase

FilterMorphoWindowBase

~FilterMorphoWindowBase

filter

getHalfWindowSize

getWindowValue

operator=

m_halfWindowSize

##### FilterMzExclusion

FilterMzExclusion

FilterMzExclusion

FilterMzExclusion

~FilterMzExclusion

buildFilterFromString

filter

name

removeTraceInExclusionMargin

toString

m_exclusionPrecision

##### FilterNameInterface

~FilterNameInterface

buildFilterFromString

name

toString

##### FilterNormalizeIntensities

FilterNormalizeIntensities

FilterNormalizeIntensities

FilterNormalizeIntensities

~FilterNormalizeIntensities

buildFilterFromString

filter

name

operator=

toString

m_newYMax

nan

##### FilterOboPsiModSink

FilterOboPsiModSink

~FilterOboPsiModSink

getFirst

getOboPsiModTermList

getOne

setOboPsiModTerm

size

m_oboPsiModTermList

##### FilterOboPsiModTermAccession

FilterOboPsiModTermAccession

~FilterOboPsiModTermAccession

setOboPsiModTerm

m_accession

m_sink

##### FilterOboPsiModTermDiffMono

FilterOboPsiModTermDiffMono

~FilterOboPsiModTermDiffMono

setOboPsiModTerm

m_massRange

m_sink

##### FilterOboPsiModTermLabel

FilterOboPsiModTermLabel

FilterOboPsiModTermLabel

~FilterOboPsiModTermLabel

setOboPsiModTerm

m_labelMatch

m_sink

##### FilterOboPsiModTermName

FilterOboPsiModTermName

~FilterOboPsiModTermName

setOboPsiModTerm

m_nameMatch

m_sink

##### FilterPeakDelta

FilterPeakDelta

FilterPeakDelta

~FilterPeakDelta

filter

##### FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

~FilterQuantileBasedRemoveY

buildFilterFromString

filter

getQuantileThreshold

name

operator=

toString

m_quantile

##### FilterRemoveC13

FilterRemoveC13

FilterRemoveC13

~FilterRemoveC13

addExclusionMap

filter

notExcluded

m_diffC12C13_z1

m_diffC12C13_z2

m_precisionPtr

##### FilterRemoveY

FilterRemoveY

FilterRemoveY

~FilterRemoveY

filter

getValue

operator=

m_valueToRemove

##### FilterResampleKeepGreater

FilterResampleKeepGreater

FilterResampleKeepGreater

~FilterResampleKeepGreater

filter

getThresholdX

operator=

m_value

##### FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

~FilterResampleKeepPointInPolygon

filter

filter

filter

newSelectionPolygonSpec

operator=

m_greatestMz

m_integrationScopeSpecs

m_lowestMz

##### FilterResampleKeepSmaller

FilterResampleKeepSmaller

FilterResampleKeepSmaller

~FilterResampleKeepSmaller

filter

m_value

##### FilterResampleKeepXRange

FilterResampleKeepXRange

FilterResampleKeepXRange

~FilterResampleKeepXRange

filter

operator=

m_maxX

m_minX

##### FilterResampleRemoveXRange

FilterResampleRemoveXRange

FilterResampleRemoveXRange

~FilterResampleRemoveXRange

filter

operator=

m_maxX

m_minX

##### FilterRescaleY

FilterRescaleY

FilterRescaleY

~FilterRescaleY

filter

getDynamicRange

operator=

m_dynamic

##### FilterRoundY

FilterRoundY

FilterRoundY

~FilterRoundY

filter

operator=

##### FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

~FilterSavitzkyGolay

buildFilterFromString

convlv

dmatrix

dvector

filter

filteredData

four1

free_dmatrix

free_dvector

free_ivector

getParameters

ivector

lubksb

ludcmp

name

operator=

realft

runFilter

sgcoeff

toString

twofft

m_params

m_x

m_yf

m_yr

##### FilterScaleFactorY

FilterScaleFactorY

FilterScaleFactorY

~FilterScaleFactorY

filter

getScaleFactorY

operator=

m_factor

##### FilterSuite

FilterSuite

FilterSuite

filter

##### FilterSuiteString

FilterNameType

FilterSuiteString

~FilterSuiteString

addFilterFromString

begin

buildFilterFromString

end

filter

name

toString

m_filterVector

##### FilterTandemDeisotope

FilterTandemDeisotope

FilterTandemDeisotope

filter

m_arbitrary_minimum_mz

m_arbitrary_range_between_isotopes

##### FilterTriangle

FilterTriangle

FilterTriangle

~FilterTriangle

filter

setTriangleSlope

sumAndRemove

m_maxMzRange

m_triangleSlope

##### FrameIdDescr

m_frameId

m_globalScanIndex

m_scanCount

##### GrpExperiment

GrpExperiment

~GrpExperiment

addPostGroupingGrpProteinSpRemoval

addPreGroupingGrpProteinSpRemoval

addSubGroupSp

getGrpGroupSpList

getGrpProteinSp

getGrpProteinSpList

numbering

removeNonInformativeSubGroups

setGrpPeptide

setRemoveNonInformativeSubgroups

startGrouping

m_grpGroupSpList

m_grpPeptideList

m_grpPostGroupingProteinListRemoval

m_grpPreGroupingProteinListRemoval

m_grpProteinList

m_isGroupingStarted

m_isRemoveNonInformativeSubgroups

m_mapPeptides

m_mapProteins

m_remainingGrpProteinList

mp_monitor

##### GrpGroup

GrpGroup

GrpGroup

~GrpGroup

addGroup

addSubGroupSp

check

containsAny

getGroupingId

getGroupNumber

getGrpPeptideSet

getGrpSubGroupSpList

getSubGroupSpList

makeGrpGroupSp

numbering

operator<

removeFirstNonInformativeSubGroup

removeNonInformativeSubGroups

setGroupNumber

GrpExperiment

m_groupNumber

m_mapPeptideToSubGroupSet

m_peptideSet

m_subGroupList

##### GrpGroupingMonitor

GrpGroupingMonitor

~GrpGroupingMonitor

groupingProtein

removingNonInformativeSubGroupsInGroup

startGrouping

startNumberingAllGroups

startRemovingNonInformativeSubGroupsInAllGroups

stopGrouping

stopRemovingNonInformativeSubGroupsInAllGroups

m_currentProtein

m_totalNumberPeptide

m_totalNumberProtein

mp_outStream

##### GrpGroupingMonitorInterface

~GrpGroupingMonitorInterface

groupingProtein

removingNonInformativeSubGroupsInGroup

startGrouping

startNumberingAllGroups

startRemovingNonInformativeSubGroupsInAllGroups

stopGrouping

stopRemovingNonInformativeSubGroupsInAllGroups

##### GrpMapPeptideToGroup

GrpMapPeptideToGroup

GrpMapPeptideToGroup

~GrpMapPeptideToGroup

clear

getGroupList

set

m_mapPeptideToGroup

##### GrpMapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet

~GrpMapPeptideToSubGroupSet

add

check

getSubGroupSet

hasSpecificPeptide

printInfos

remove

size

m_mapPeptideToSubGroupSet

##### GrpPeptide

GrpPeptide

~GrpPeptide

getGroupingId

getGroupNumber

getRank

getSequence

operator<

setGroupNumber

setRank

GrpExperiment

m_groupNumber

m_mass

m_rank

m_sequence

##### GrpPeptideSet

GrpPeptideSet

GrpPeptideSet

GrpPeptideSet

~GrpPeptideSet

addAll

biggerAndContainsAll

contains

containsAll

containsAny

getGrpPeptideList

numbering

operator=

operator==

printInfos

privContainsAll

setGroupNumber

size

GrpMapPeptideToGroup

GrpMapPeptideToSubGroupSet

m_peptidePtrList

##### GrpProtein

const_iterator

GrpProtein

~GrpProtein

GrpProtein

begin

countPlus

end

getAccession

getCount

getDescription

getGroupingId

getGroupNumber

getRank

getSubGroupNumber

operator==

push_back

setGroupNumber

setRank

setSubGroupNumber

strip

GrpExperiment

m_accession

m_count

m_description

m_groupNumber

m_grpPeptidePtrList

m_rank

m_subGroupNumber

##### GrpSubGroup

GrpSubGroup

GrpSubGroup

~GrpSubGroup

getFirstAccession

getGroupingId

getGroupNumber

getGrpProteinList

getPeptideSet

getSubGroupNumber

includes

makeGrpSubGroupSp

maxCount

merge

numbering

operator<

peptideListSize

setGroupNumber

setSubGroupNumber

m_groupNumber

m_grpProteinPtrList

m_peptidePtrList

m_subGroupNumber

##### GrpSubGroupSet

GrpSubGroupSet

GrpSubGroupSet

~GrpSubGroupSet

add

addAll

begin

contains

end

erase

printInfos

remove

size

GrpGroup

m_grpSubGroupPtrList

##### HttpButton

HttpButton

~HttpButton

getChEBIUrl

getOlsUrl

getPubMedUrl

getRESIDUrl

getUnimodUrl

mousePressEvent

setText

##### IntegrationScope

IntegrationScope

IntegrationScope

IntegrationScope

IntegrationScope

~IntegrationScope

contains

getBottomMostPoint

getDataKindX

getLeftMostPoint

getPoint

getRightMostPoint

getTopMostPoint

getWidth

is1D

is2D

isRectangle

isRhomboid

operator=

range

reset

setDataKindX

setPoint

setWidth

toString

transpose

update

m_dataKindX

m_point

m_width

##### IntegrationScopeBase

IntegrationScopeBase

IntegrationScopeBase

~IntegrationScopeBase

contains

getBottomMostPoint

getBottomMostPoints

getDataKindX

getDataKindY

getHeight

getLeftMostBottomPoint

getLeftMostPoint

getLeftMostPoints

getLeftMostTopPoint

getPoint

getPoints

getRhombHorizontalSize

getRhombVerticalSize

getRightMostBottomPoint

getRightMostPoint

getRightMostPoints

getRightMostTopPoint

getTopMostPoint

getTopMostPoints

getWidth

is1D

is2D

isRectangle

isRhomboid

range

reset

setDataKindX

setDataKindY

toString

transpose

##### IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

~IntegrationScopeRect

contains

getBottomMostPoint

getDataKindX

getDataKindY

getHeight

getTopMostPoint

is1D

is2D

isRectangle

isRhomboid

operator=

operator=

range

reset

setDataKindX

setDataKindY

setHeight

toString

transpose

update

update

m_dataKindY

m_height

##### IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

~IntegrationScopeRhomb

addPoint

contains

getBottomMostPoint

getBottomMostPoints

getDataKindX

getDataKindY

getHeight

getLeftMostBottomPoint

getLeftMostPoint

getLeftMostPoints

getLeftMostTopPoint

getPoint

getPoints

getRhombHorizontalSize

getRhombVerticalSize

getRightMostBottomPoint

getRightMostPoint

getRightMostPoints

getRightMostTopPoint

getTopMostPoint

getTopMostPoints

getWidth

is1D

is2D

isRectangle

isRhomboid

operator=

range

reset

setDataKindX

setDataKindY

toString

transpose

m_dataKindX

m_dataKindY

m_points

##### IntegrationScopeSpec

IntegrationScopeSpec

IntegrationScopeSpec

IntegrationScopeSpec

operator=

toString

dataKind

integrationScopeSPtr

##### Ion

Ion

~Ion

getMass

getMz

##### IonIsotopeRatioScore

IonIsotopeRatioScore

~IonIsotopeRatioScore

getIonIsotopeRatioScore

m_ionIsotopeRatioScore

##### IonMobilityGrid

IonMobilityGrid

~IonMobilityGrid

computeCorrections

getMapCorrectionsStart

getMapDiferrencesStart

storeObservedIdentityBetween

translateXicCoordFromTo

m_mapCorrectionsStart

m_mapCorrectionsStop

m_mapDiferrencesStart

m_mapDiferrencesStop

##### LinearRegression

LinearRegression

LinearRegression

getCoefficientOfDetermination

getIntercept

getNrmsd

getRmsd

getSize

getSlope

getYfromX

m_data

m_intercept

m_slope

##### MapTrace

MapTrace

MapTrace

MapTrace

MapTrace

MapTrace

~MapTrace

initialize

initialize

insertOrUpdate

insertOrUpdate

makeMapTraceCstSPtr

makeMapTraceSPtr

operator=

toString

toTrace

xValues

yValues

##### MassDataCombinerInterface

Iterator

MassDataCombinerInterface

~MassDataCombinerInterface

combine

combine

combine

getDecimalPlaces

setDecimalPlaces

m_decimalPlaces

##### MassSpecTracePlotContext

MassSpecTracePlotContext

MassSpecTracePlotContext

~MassSpecTracePlotContext

operator=

operator=

toString

m_lastMr

m_lastMz

m_lastResolvingPower

m_lastTicIntensity

m_lastZ

##### MassSpecTracePlotWidget

MassSpecTracePlotWidget

MassSpecTracePlotWidget

~MassSpecTracePlotWidget

computeResolvingPower

deconvolute

deconvoluteChargedState

deconvoluteIsotopicCluster

getChargeMinimalFractionalPart

getChargeStateEnvelopePeakSpan

keyPressEvent

keyPressEventSignal

keyReleaseEvent

massDeconvolutionSignal

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseEventSignal

mouseReleaseHandler

refreshBaseContext

resolvingPowerComputationSignal

setChargeMinimalFractionalPart

setChargeStateEnvelopePeakSpan

m_chargeMinimalFractionalPart

m_chargeStateEnvelopePeakSpan

m_context

##### MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

~MassSpectrum

debugPrintValues

equals

filterSum

makeMassSpectrumCstSPtr

makeMassSpectrumSPtr

massSpectrumFilter

maxIntensityDataPoint

minIntensityDataPoint

operator=

operator=

operator=

operator=

sortMz

tic

tic

totalIonCurrent

##### MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

~MassSpectrumCombiner

binCount

binsAsString

findBin

getBins

setBins

m_bins

##### MassSpectrumFilterGreatestItensities

MassSpectrumFilterGreatestItensities

MassSpectrumFilterGreatestItensities

~MassSpectrumFilterGreatestItensities

filter

operator=

m_filterGreatestY

##### MassSpectrumFilterInterface

~MassSpectrumFilterInterface

filter

##### MassSpectrumFilterResampleKeepMzRange

MassSpectrumFilterResampleKeepMzRange

MassSpectrumFilterResampleKeepMzRange

~MassSpectrumFilterResampleKeepMzRange

filter

m_filterRange

##### MassSpectrumFilterResampleRemoveMzRange

MassSpectrumFilterResampleRemoveMzRange

MassSpectrumFilterResampleRemoveMzRange

~MassSpectrumFilterResampleRemoveMzRange

filter

m_filterRange

##### MassSpectrumId

MassSpectrumId

MassSpectrumId

MassSpectrumId

MassSpectrumId

~MassSpectrumId

getMsRunIdCstSPtr

getNativeId

getSpectrumIndex

isValid

operator=

operator==

setMsRunId

setNativeId

setSpectrumIndex

toString

m_nativeId

m_spectrumIndex

mcsp_msRunId

##### MassSpectrumLineData

dash

ionizationMode

ionSourceType

msLevel

mz_range

peakCount

peakList

peakShapeType

retentionTime

##### MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

~MassSpectrumMinusCombiner

combine

combine

operator=

##### MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

~MassSpectrumPlusCombiner

combine

combine

operator=

##### MassSpectrumWidget

MassSpectrumWidget

~MassSpectrumWidget

clearData

computeIsotopeMassList

highlightPrecursorPeaks

ionChanged

mzChanged

mzChangeEvent

peakChanged

peakChangeEvent

peptideAnnotate

plot

rescale

savePdf

setIonList

setMassSpectrumCstSPtr

setMaximumIsotopeNumber

setMaximumIsotopeRank

setMs1Precision

setMs2Precision

setMsLevel

setPeptideCharge

setPeptideSp

setQualifiedMassSpectrum

setVisibleMassDelta

toQPaintDevice

QCPSpectrum

_custom_plot

_ion_list

_is_visible_mass_delta

_isotope_mass_list

_max_isotope_number

_max_isotope_rank

_ms_level

_p_mouse_peak

_p_ms1_precision

_p_ms2_precision

_peak_ion_isotope_match_list

_peptide_charge

_peptide_sp

_spectrum_sp

_tag_nmost_intense

##### MgfOutput

MgfOutput

~MgfOutput

close

write

mpa_outputStream

##### MorpheusScore

MorpheusScore

~MorpheusScore

getMorpheusScore

_morpheus_score

##### MsDataFormatEnumStr

toString

##### MsFileAccessor

MsFileAccessor

MsFileAccessor

~MsFileAccessor

buildMsRunReaderSPtr

buildMsRunReaderSPtr

buildTimsMsRunReaderMs2SPtr

getFileFormat

getFileName

getFileReaderType

getMsRunIds

getMsRunReaderSPtrByRunId

getOboPsiModTermFileFormat

getOboPsiModTermNativeIDFormat

getpreferredFileReaderType

getSelectedMsRunId

msRunReaderSPtr

msRunReaderSPtr

msRunReaderSPtrForSelectedMsRunId

setPreferredFileReaderType

setSelectedMsRunId

m_fileFormat

m_fileName

m_fileReaderType

m_oboPsiModTermNativeIDFormat

m_preferredFileReaderTypeMap

m_xmlPrefix

mcsp_selectedMsRunId

##### MsFileReader

MsFileReader

~MsFileReader

getFileFormat

getMsRunIds

m_fileFormat

m_fileName

MsRunAlignment

##### MsRunDataSetTree

DoubleNodeVectorMap

NodeVector

QualMassSpectraVector

MsRunDataSetTree

~MsRunDataSetTree

accept

accept

addDataSetQualMassSpectraInsideDtRtRange

addDataSetTreeNodesInsideDtRtRange

addMassSpectrum

addMassSpectrum

addMassSpectrum

depth

documentNodeInDtRtMap

findNode

findNode

flattenedView

flattenedViewMsLevel

getIndexNodeMap

getRootNodes

getSpectrumCount

indexNodeMapSize

massSpectrumIndex

massSpectrumIndex

precursorNodeByProductSpectrumIndex

precursorNodesByPrecursorMz

productNodesByPrecursorSpectrumIndex

removeDataSetQualMassSpectraOutsideDtRtRange

removeDataSetTreeNodesOutsideDtRtRange

size

m_dtDoubleNodeVectorMap

m_indexNodeMap

m_rootNodes

m_rtDoubleNodeVectorMap

m_spectrumCount

mcsp_msRunId

##### MsRunDataSetTreeNode

MsRunDataSetTreeNode

MsRunDataSetTreeNode

MsRunDataSetTreeNode

~MsRunDataSetTreeNode

accept

depth

findNode

findNode

flattenedView

flattenedViewChildrenOnly

flattenedViewMsLevelNodes

getParent

getQualifiedMassSpectrum

hasParent

operator=

precursorIonNodesByPrecursorMz

productNodesByPrecursorMz

setParent

setQualifiedMassSpectrum

size

toString

MsRunDataSetTree

m_children

mcsp_massSpectrum

mp_parent

##### MsRunDataSetTreeNodeVisitorInterface

setNodesToProcessCount

shouldStop

visit

##### MsRunId

MsRunId

MsRunId

MsRunId

MsRunId

~MsRunId

getFileName

getMsDataFormat

getRunId

getSampleName

getXmlId

isValid

operator=

operator==

setFileName

setMsDataFormat

setRunId

setSampleName

setXmlId

toString

m_fileName

m_mzFormat

m_runId

m_sampleName

m_xmlId

##### MsRunQualifiedSpectrumLoader

MsRunQualifiedSpectrumLoader

~MsRunQualifiedSpectrumLoader

clear

getQualifiedMassSpectrumList

needPeakList

setQualifiedMassSpectrum

spectrumListHasSize

m_qualifiedSpectrumList

##### MsRunReadConfig

MsRunReadConfig

MsRunReadConfig

~MsRunReadConfig

acceptMsLevel

acceptRetentionTimeInSeconds

getMsLevels

getMsLevelsAsString

getParameterValue

getRetentionTimeEndInSeconds

getRetentionTimeStartInSeconds

needPeakList

operator=

reset

setMsLevels

setNeedPeakList

setParameterValue

setRetentionTimeEndInSeconds

setRetentionTimeStartInSeconds

toString

m_isPeakListNeeded

m_msLevels

m_paramsMap

m_retentionTimeEndSeconds

m_retentionTimeStartSeconds

##### MsRunReader

MsRunReader

MsRunReader

~MsRunReader

accept

acquireDevice

getMsRunId

getRetentionTimeLine

getTicChromatogram

hasScanNumbers

initialize

isMonoThread

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

scanNumber2SpectrumIndex

setMonoThread

spectrumListSize

MsFileAccessor

m_isMonoThread

mcsp_msRunId

mpa_multiMapScanNumber

##### MsRunReaderRetentionTimeLine

MsRunReaderRetentionTimeLine

~MsRunReaderRetentionTimeLine

getRetentionTimeLine

needPeakList

setQualifiedMassSpectrum

m_retention_time_list

##### MsRunReaderScanNumberMultiMap

MsRunReaderScanNumberMultiMap

~MsRunReaderScanNumberMultiMap

getSpectrumIndexFromScanNumber

needPeakList

setQualifiedMassSpectrum

m_mmap_scan2index

##### MsRunReaderTicChromatogram

MsRunReaderTicChromatogram

~MsRunReaderTicChromatogram

getTicChromatogram

needPeakList

setQualifiedMassSpectrum

m_ticChromMapTrace

##### MsRunRetentionTime

###### PeptideMs2Point

entityHash

precursorIntensity

retentionTime

###### ComputeRetentionTimeReference

maximum_intensity

weighted_intensity

last

MsRunRetentionTime

MsRunRetentionTime

~MsRunRetentionTime

addPeptideAsSeamark

addPeptideAsSeamark

align

computeSeamarks

correctNewTimeValues

getAlignedRetentionTimeVector

getBackRetentionTimeReference

getCommonDeltaRt

getCommonDeltaRt

getCommonSeamarksDeltaRt

getFrontRetentionTimeReference

getMs1MeanFilter

getMs1RetentionTimeVector

getMs2MeanFilter

getMs2MedianFilter

getMsRunId

getMsRunReaderSPtr

getNumberOfCorrectedValues

getSeamarks

getSeamarksReferences

isAligned

linearRegressionMs2toMs1

setAlignedRetentionTimeVector

setMs1MeanFilter

setMs2MeanFilter

setMs2MedianFilter

translateAligned2OriginalRetentionTime

translateOriginal2AlignedRetentionTime

m_alignedRetentionTimeVector

m_allMs2Points

m_ms1MeanFilter

m_ms1RetentionTimeVector

m_ms2MeanFilter

m_ms2MedianFilter

m_retentionTimeReferenceMethod

m_seamarks

m_valuesCorrected

mcsp_msrunId

msp_msrunReader

##### MsRunRetentionTimeSeamarkPoint

entityHash

intensity

retentionTime

##### MsRunSimpleStatistics

getMsLevelCount

getTotalCount

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_countMsLevelSpectrum

##### MsRunSlice

MsRunSlice

MsRunSlice

~MsRunSlice

appendToStream

clear

getSliceNumber

getSpectrum

getSpectrum

makeMsRunSliceSp

setSize

setSliceNumber

setSpectrum

size

m_sliceNumber

m_spectrumList

##### MsRunXicExtractor

###### MsRunXicExtractorPoints

rt

spectrum_index

###### MsRunXicExtractorReadPoints

MsRunXicExtractorReadPoints

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_msrun_points

MsRunXicExtractor

~MsRunXicExtractor

MsRunXicExtractor

extractOneXicCoord

getXicFromPwizMSDataFile

protectedExtractXicCoordSPtrList

m_msrun_points

MsRunXicExtractorFactory

##### MsRunXicExtractorDisk

MsRunXicExtractorDisk

MsRunXicExtractorDisk

~MsRunXicExtractorDisk

MsRunXicExtractorDisk

acquireSlices

appendSliceOnDisk

endPwizRead

extractOneXicCoord

prepareExtractor

protectedExtractXicCoordSPtrList

serializeMsRun

storeSlices

unserializeSlice

m_maxMz

m_minMz

m_msRunSliceListCache

m_mutex

m_retentionTimeList

m_rtSize

m_temporaryDirectory

mpa_temporaryDirectory

MsRunXicExtractorFactory

##### MsRunXicExtractorDiskBuffer

MsRunXicExtractorDiskBuffer

~MsRunXicExtractorDiskBuffer

MsRunXicExtractorDiskBuffer

appendSliceInBuffer

endPwizRead

flushBufferOnDisk

storeSlices

m_bufferMaxSize

m_bufferSize

m_sliceBufferMap

MsRunXicExtractorFactory

##### MsRunXicExtractorFactory

MsRunXicExtractorFactory

~MsRunXicExtractorFactory

buildMsRunXicExtractorSp

getInstance

setMsRunXicExtractorFactoryType

setTmpDir

m_instance

m_tmpDirName

m_type

##### MsRunXicExtractorInterface

MsRunXicExtractorInterface

MsRunXicExtractorInterface

~MsRunXicExtractorInterface

extractXicCoordSPtrList

extractXicCoordSPtrListParallelized

getMsRunId

getMsRunReaderSPtr

postExtractionProcess

protectedExtractXicCoordSPtrList

setPostExtractionTraceFilterCstSPtr

setRetentionTimeAroundTarget

setXicExtractMethod

m_retentionTimeAroundTarget

m_xicExtractMethod

mcsp_postExtractionTraceFilter

msp_msrun_reader

##### MzCalibrationInterface

MzCalibrationInterface

~MzCalibrationInterface

getMzFromTofIndex

getTofFromTofIndex

getTofFromTofIndex

getTofIndexFromMz

operator=

operator==

m_digitizerDelay

m_digitizerTimebase

m_mzCalibrationArr

##### MzCalibrationModel1

MzCalibrationModel1

~MzCalibrationModel1

getMzFromTofIndex

getTofIndexFromMz

##### MzCalibrationModel1Cached

MzCalibrationModel1Cached

~MzCalibrationModel1Cached

getMzFromTofIndex

m_arrMasses

m_max

##### MzCalibrationStore

MzCalibrationStore

~MzCalibrationStore

getInstance

m_mapMzCalibrationSPtr

##### MzIdentMlWriter

MzIdentMlWriter

~MzIdentMlWriter

toXmlDouble

toXmlMass

toXmlMassDelta

writeCvList

writeCvParam

writeCvParam

writeCvParam

writeCvParamUo

writeCvParamUo

writeDBSequence

writeDBSequence

writeStartMzIdentMlDocument

writeUserParam

writeUserParam

writeUserParam

writeUserParam

##### MzIntegrationParams

MzIntegrationParams

MzIntegrationParams

MzIntegrationParams

~MzIntegrationParams

createArbitraryBins

createBins

createBins

createDataBasedBins

getBinningType

getBinSizeDivisor

getDecimalPlaces

getGreatestMz

getPrecision

getSmallestMz

hasValidMzRange

isRemoveZeroValDataPoints

isValid

operator=

reset

setBinningType

setBinSizeDivisor

setDecimalPlaces

setGreatestMz

setPrecision

setRemoveZeroValDataPoints

setSmallestMz

toString

updateGreatestMz

updateSmallestMz

m_binningType

m_binSizeDivisor

m_decimalPlaces

m_greatestMz

m_removeZeroValDataPoints

m_smallestMz

mp_precision

##### MzRange

MzRange

MzRange

MzRange

MzRange

~MzRange

contains

getMz

lower

operator*=

operator+=

operator=

toString

upper

m_delta

m_mz

##### MzxmlOutput

###### Translater

Translater

~Translater

needPeakList

setQualifiedMassSpectrum

mp_output

MzxmlOutput

~MzxmlOutput

close

getPrecursorScanNumber

getScanNumber

getScanNumberFromNativeId

maskMs1

setReadAhead

write

write

writeHeader

writeQualifiedMassSpectrum

m_isReadAhead

m_monitor

m_ms1IsMasked

mpa_outputStream

##### OboChooserWidget

OboChooserWidget

~OboChooserWidget

getOboPsiModTermSelected

isOboTermSelected

setMzTarget

setPrecision

ui

##### OboListModel

###### OboPsiModHandler

OboPsiModHandler

~OboPsiModHandler

setOboPsiModTerm

mp_parent

OboListModel

~OboListModel

data

getOboPsiModTerm

loadPsiMod

rowCount

m_oboPsiModTermList

##### OboListProxyModel

OboListProxyModel

~OboListProxyModel

filterAcceptsRow

filterMzPrecision

lessThan

m_mzTarget

m_precisionPtr

mp_sourceModel

##### OboListWidget

OboListWidget

~OboListWidget

filterMzPrecision

getMzTarget

getPrecisionPtr

oboTermChanged

onFilterChanged

onFilterChanged

onFilterChanged

onSelectionChanged

mpa_oboListModel

mpa_oboListProxyModel

ui

##### OboPsiMod

OboPsiMod

~OboPsiMod

parse

m_handler

m_term

##### OboPsiModHandlerInterface

setOboPsiModTerm

##### OboPsiModTerm

OboPsiModTerm

~OboPsiModTerm

OboPsiModTerm

clearTerm

isA

isValid

operator=

parseLine

m_accession

m_definition

m_diffFormula

m_diffMono

m_findExactPsiModLabel

m_findRelatedPsiMsLabel

m_firstParse

m_formula

m_isA

m_massMono

m_name

m_origin

m_psiModLabel

m_psiMsLabel

OboPsiMod

##### OboTermForm

OboTermForm

~OboTermForm

displayOboTerm

getOboPsiModTerm

isOboTerm

parseDefinitionLabel

m_findExternalLinks

m_oboPsiModTerm

ui

##### PappsoException

PappsoException

PappsoException

~PappsoException

clone

qwhat

raise

what

m_message

m_stdMessage

##### PeakIonIsotopeMatch

PeakIonIsotopeMatch

PeakIonIsotopeMatch

PeakIonIsotopeMatch

~PeakIonIsotopeMatch

getPeptideNaturalIsotopeAverageSp

operator=

toString

_naturalIsotopeAverageSp

##### PeakIonMatch

PeakIonMatch

PeakIonMatch

PeakIonMatch

~PeakIonMatch

getCharge

getPeak

getPeptideFragmentIonSp

getPeptideIonDirection

getPeptideIonType

operator=

toString

_charge

_ion_sp

_peak

##### Peptide

Peptide

~Peptide

Peptide

Peptide

addAaModification

addAaModificationOnAllAminoAcid

begin

begin

countModificationOnAa

end

end

getAa

getAaPositionList

getAaPositionList

getConstAa

getInternalCterModification

getInternalNterModification

getLiAbsoluteString

getMass

getMass

getModificationPositionList

getModificationPositionList

getNumberOfAtom

getNumberOfIsotope

getNumberOfModification

getSequence

isPalindrome

makeNoConstPeptideSp

makePeptideSp

rbegin

removeAaModification

removeCterAminoAcid

removeInternalCterModification

removeInternalNterModification

removeNterAminoAcid

rend

replaceAaModification

replaceLeucineIsoleucine

reverse

rotate

setInternalCterModification

setInternalNterModification

size

toAbsoluteString

toProForma

toString

operator<

operator==

PeptideProFormaParser

m_aaVec

m_proxyMass

##### PeptideBuilder

PeptideBuilder

~PeptideBuilder

addFixedAaModification

setPeptide

setSink

m_fixedModificationList

m_sink

##### PeptideFixedModificationBuilder

PeptideFixedModificationBuilder

~PeptideFixedModificationBuilder

addAa

setPeptideSp

setProtCter

setProtElse

setProtNter

setSink

m_aaModificationList

m_isProtCterMod

m_isProtElseMod

m_isProtNterMod

m_sink

mp_mod

##### PeptideFragment

PeptideFragment

PeptideFragment

PeptideFragment

~PeptideFragment

getMass

getNumberOfAtom

getNumberOfIsotope

getPeptideIonDirection

getPeptideIonDirectionName

getPeptideSp

getSequence

isPalindrome

size

m_direction

m_mass

m_nterCterCleavage

m_size

msp_peptide

##### PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

~PeptideFragmentIon

getCompletePeptideIonName

getMass

getName

getNumberOfAtom

getNumberOfIsotope

getNumberOfNeutralPhosphoLoss

getPeptideFragmentSp

getPeptideIonColor

getPeptideIonDirection

getPeptideIonDirection

getPeptideIonName

getPeptideIonName

getPeptideIonType

getSequence

isPalindrome

makePeptideFragmentIonSp

size

m_ionType

m_mass

m_neutralPhosphoLossNumber

msp_fragment

##### PeptideFragmentIonListBase

IonList

PeptideFragmentIonListBase

PeptideFragmentIonListBase

~PeptideFragmentIonListBase

begin

end

getCIDionList

getETDionList

getIonList

getPeptideFragmentIonList

getPeptideFragmentIonSp

getPeptideFragmentIonSp

getPeptideFragmentIonSp

getPeptideFragmentList

getPeptideSp

getPhosphorylationNumber

makePeptideFragmentIonListBaseSp

size

m_ionList

m_phosphorylationNumber

msp_peptide

msp_peptide_fragment_ion_list

##### PeptideInterface

getFormula

getName

getSequence

getSequenceLi

isPalindrome

matchPeak

size

##### PeptideIsotopeSpectrumMatch

const_iterator

PeptideIsotopeSpectrumMatch

PeptideIsotopeSpectrumMatch

PeptideIsotopeSpectrumMatch

~PeptideIsotopeSpectrumMatch

begin

dropPeaksLackingMonoisotope

end

getBestPeakIterator

getPeakIonIsotopeMatchList

size

_peak_ion_match_list

_precision

##### PeptideMethioninRemove

PeptideMethioninRemove

~PeptideMethioninRemove

setPeptide

setSink

m_isPotential

m_sink

##### PeptideModificatorBase

PeptideModificatorBase

~PeptideModificatorBase

getModificationPositionList

getModificationPositionList

setModificationPattern

m_pattern

##### PeptideModificatorInterface

~PeptideModificatorInterface

setPeptideSp

##### PeptideModificatorPipeline

PeptideModificatorPipeline

PeptideModificatorPipeline

~PeptideModificatorPipeline

addFixedCterModificationString

addFixedModificationString

addFixedNterModificationString

addLabeledModificationString

addPotentialCterModificationString

addPotentialModificationString

addPotentialNterModificationString

parseFixedModification

parseLabeledModification

parsePotentialModification

privAddFixedModificationString

privAddPotentialModificationString

setPeptide

setPeptideSp

setSink

m_pepModificatorPtrList

m_sink

mp_firstModificator

mp_lastPeptideSinkInterface

mp_peptideModificatorTee

##### PeptideModificatorTee

PeptideModificatorTee

PeptideModificatorTee

~PeptideModificatorTee

addModificator

setPeptideSp

m_peptideModPtrList

##### PeptideNaturalIsotope

PeptideNaturalIsotope

PeptideNaturalIsotope

~PeptideNaturalIsotope

getIntensityRatio

getIsotopeMap

getIsotopeNumber

getMass

getNumberOfAtom

getNumberOfIsotope

getSequence

isPalindrome

size

m_mapIsotope

m_mass

m_peptide

m_ratio

##### PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

~PeptideNaturalIsotopeAverage

getCharge

getComponents

getIntensityRatio

getIsotopeNumber

getIsotopeRank

getMz

getPeptideInterfaceSp

getPrecision

isEmpty

makePeptideNaturalIsotopeAverageSp

matchPeak

recursiveDepletion

toString

m_abundanceRatio

m_averageMz

m_isotopeLevel

m_isotopeRank

m_peptideNaturalIsotopeSpList

m_z

mcsp_peptideSp

mp_precision

##### PeptideNaturalIsotopeList

const_iterator

PeptideNaturalIsotopeList

PeptideNaturalIsotopeList

~PeptideNaturalIsotopeList

begin

end

getByIntensityRatio

getByIsotopeNumber

getIntensityRatioPerIsotopeNumber

getPeptideInterfaceSp

makePeptideNaturalIsotopeListSp

size

msp_peptide

msp_peptide_natural_isotope_list

##### PeptideProFormaParser

parseNoConstString

parseString

parseStringToPeptide

_rx_modmass

_rx_psimod

##### PeptideRawFragmentMasses

ionDeltatMzMassMap

PeptideRawFragmentMasses

~PeptideRawFragmentMasses

getDeltaMass

pushBackIonMasses

pushBackIonMz

pushBackMatchSpectrum

m_cumulativeCterMasses

m_cumulativeNterMasses

m_ionDeltaMz

##### PeptideSemiEnzyme

PeptideSemiEnzyme

~PeptideSemiEnzyme

setPeptide

setSink

m_sink

##### PeptideSinkInterface

setSink

##### PeptideSizeFilter

PeptideSizeFilter

~PeptideSizeFilter

setPeptide

setSink

m_maxSize

m_minSize

m_sink

##### PeptideSpectrumMatch

const_iterator

PeptideSpectrumMatch

PeptideSpectrumMatch

PeptideSpectrumMatch

PeptideSpectrumMatch

~PeptideSpectrumMatch

begin

contains

countTotalMatchedIons

end

getBestPeakIterator

getIonTypeCountArray

privMatchIonList

size

_ion_type_count

_peak_ion_match_list

_precision

##### PeptideSpSinkInterface

setSink

##### PeptideStrParser

parseNoConstString

parseString

parseStringToPeptide

_mod_parser

_rx_modmass

_rx_psimod

##### PeptideVariableModificationBuilder

PeptideVariableModificationBuilder

~PeptideVariableModificationBuilder

addAa

next_combination

setMaxNumberMod

setMinNumberMod

setModificationCounter

setPeptideSp

setProtCter

setProtElse

setProtNter

setSink

m_aaModificationList

m_isProtCterMod

m_isProtElseMod

m_isProtNterMod

m_maxNumberMod

m_minNumberMod

m_modificationCount

m_sink

mp_mod

##### PeptideVariableModificationReplacement

PeptideVariableModificationReplacement

~PeptideVariableModificationReplacement

replaceModificationsAtPosition

setPeptideSp

mp_modAfter

##### PpmPrecision

PpmPrecision

~PpmPrecision

delta

toString

unit

PrecisionFactory

##### PrecisionBase

PrecisionBase

delta

getNominal

toString

unit

m_nominal

##### PrecisionFactory

MapDaltonPrecision

MapPpmPrecision

MapResPrecision

fromString

getDaltonInstance

getPpmInstance

getPrecisionPtrFractionInstance

getPrecisionPtrInstance

getResInstance

m_mapDalton

m_mapPpm

m_mapRes

##### PrecisionWidget

PrecisionWidget

~PrecisionWidget

getPrecision

precisionChanged

setCurrentIndex

setDaltonValueChanged

setPpmValueChanged

setPrecision

setResValueChanged

m_oldIndex

mp_daltonValueSpinBox

mp_ppmValueSpinBox

mp_precisionDalton

mp_precisionPpm

mp_precisionRes

mp_resValueSpinBox

mp_unitComboBox

##### PrecursorIonData

PrecursorIonData

charge

intensity

mz

##### Protein

Protein

Protein

Protein

~Protein

getAccession

getDescription

getMass

getSequence

makeProteinSp

operator==

removeTranslationStop

reverse

setAccession

setDescription

setSequence

size

m_accession

m_description

m_length

m_removeTranslationStopRegExp

m_sequence

##### ProteinIntegerCode

ProteinIntegerCode

ProteinIntegerCode

~ProteinIntegerCode

computePeptideCodeFragments

convolution

convolutionKernel

getPeptideCodedFragment

getProteinSp

getSeqAaCode

match

m_peptideCodedFragments

m_seqAaCode

msp_protein

##### ProteinPresenceAbsenceMatrix

###### ProteinPresenceAbsenceMatrixElement

absent

present

ProteinPresenceAbsenceMatrix

ProteinPresenceAbsenceMatrix

~ProteinPresenceAbsenceMatrix

convolution

convolutionKernel

fillMatrix

getPresenceAbsenceMatrix

getScore

operator=

m_presenceAbsenceMatrix

##### PsmFeatures

PsmFeatures

~PsmFeatures

countMatchedIonComplementPairs

findComplementIonPairs

getAaSequenceCoverage

getComplementPairsAaSequenceCoverage

getIntensityOfMatchedIon

getIonIsotopeLinearRegression

getIonPairPrecursorMassDelta

getMatchedMzDiffMean

getMatchedMzDiffSd

getMaxConsecutiveIon

getMaxIntensityMatchedIonComplementPairPrecursorMassDelta

getMaxIntensityPeakIonMatch

getNumberOfMatchedIons

getPeakIonPairs

getTotalIntensity

getTotalIntensityOfMatchedIonComplementPairs

getTotalIntensityOfMatchedIons

setPeptideSpectrumCharge

m_ionList

m_matchedMzDiffMean

m_matchedMzDiffMedian

m_matchedMzDiffSd

m_ms2precision

m_parentCharge

m_peakIonPairs

m_precursorTheoreticalMass

m_precursorTheoreticalMz

m_spectrumSumIntensity

msp_filterChargeDeconvolution

msp_filterKeepGreater

msp_filterMzExclusion

msp_peptide

msp_peptideSpectrumMatch

##### PwizMsFileReader

PwizMsFileReader

~PwizMsFileReader

getFileFormat

getMsRunIds

initialize

m_msDataPtrVector

##### PwizMsRunReader

PwizMsRunReader

~PwizMsRunReader

accept

acquireDevice

getOboPsiModTermNativeIDFormat

getPwizSpectrumPtr

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

processDriftTime

processRetentionTime

qualifiedMassSpectrum

qualifiedMassSpectrumFromPwizMSData

qualifiedMassSpectrumFromPwizSpectrumPtr

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

readSpectrumCollectionWithMsrunReadConfig

releaseDevice

setGlobalLocaleToCurrentOs

setGlobalLocaleToEnglish

spectrumListSize

MsFileAccessor

m_hasScanNumbers

m_mutex

msp_msData

##### QCPSpectrum

QCPSpectrum

~QCPSpectrum

addMassDelta

addMs1IsotopePattern

addPeakIonIsotopeMatch

clearData

getMostIntensePeakBetween

getNearestPeakBetween

highlightPrecursorPeaks

keyPressEvent

keyReleaseEvent

mouseMoveEvent

mousePressEvent

mouseReleaseEvent

rescale

setMzRangeChanged

setSpectrumP

MassSpectrumWidget

_bar_width

_click

_control_key

_intensity_range

_map_ion_type_bars

_mass_delta_range

_mz_range

_old_x

_old_y

_p_delta_axis_rect

_p_delta_graph

_p_peak_bars

_p_peak_bars_isotope

_p_spectrum

_parent

mp_peak_bars_precursor

##### QCPXic

QCPXic

~QCPXic

addMsMsEvent

addXicP

addXicPeakList

clear

clearXicPeakBorders

drawXicPeakBorders

getRetentionTimeFromSecondsToLocal

keyPressEvent

keyReleaseEvent

mouseMoveEvent

mousePressEvent

mouseReleaseEvent

rescale

setName

setRtRangeChanged

xAxisToSeconds

XicWidget

_click

_colours

_control_key

_current_ms2_event

_graph_color

_graph_peak_border_list

_graph_peak_surface_list

_intensity_range

_map_xic_graph

_mouse_move

_old_x

_old_y

_parent

_rt_range

##### QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

~QualifiedMassSpectrum

appendPrecursorIonData

cloneMassSpectrumSPtr

getDtInMilliSeconds

getMassSpectrumCstSPtr

getMassSpectrumId

getMassSpectrumId

getMassSpectrumSPtr

getMsLevel

getMzSortedPrecursorDataChargeValuesAsString

getMzSortedPrecursorDataMzValuesAsString

getParameterValue

getPrecursorCharge

getPrecursorDataChargeValuesAsString

getPrecursorDataChargeValuesAsString

getPrecursorDataMzValuesAsString

getPrecursorDataMzValuesAsString

getPrecursorIntensity

getPrecursorIonData

getPrecursorIonDataSortedWithMz

getPrecursorMass

getPrecursorMz

getPrecursorNativeId

getPrecursorSpectrumIndex

getRtInMinutes

getRtInSeconds

isEmptyMassSpectrum

makeQualifiedMassSpectrumCstSPtr

makeQualifiedMassSpectrumSPtr

operator=

setDtInMilliSeconds

setEmptyMassSpectrum

setMassSpectrumId

setMassSpectrumSPtr

setMsLevel

setParameterValue

setPrecursorNativeId

setPrecursorSpectrumIndex

setRtInSeconds

size

toString

m_dt

m_isEmptyMassSpectrum

m_massSpectrumId

m_msLevel

m_paramsMap

m_precursorIonData

m_precursorNativeId

m_precursorSpectrumIndex

m_rt

msp_massSpectrum

##### QualifiedXic

QualifiedXic

~QualifiedXic

QualifiedXic

getMz

getXicCstSPtr

getXicSPtr

m_msRunId

m_mz

mp_precision

msp_xic

##### ResPrecision

ResPrecision

~ResPrecision

delta

toString

unit

PrecisionFactory

##### SavGolParams

SavGolParams

SavGolParams

SavGolParams

initialize

initialize

initialize

toString

convolveWithNr

lD

m

nL

nR

##### SelectionPolygon

SelectionPolygon

SelectionPolygon

SelectionPolygon

SelectionPolygon

~SelectionPolygon

computeMinMaxCoordinates

computeMinMaxCoordinates

contains

contains

convertTo1D

copyPoint

debugAlgorithm

getBottomMostPoint

getLeftMostPoint

getPoint

getPoints

getRightMostPoint

getTopMostPoint

height

is1D

is2D

isRectangle

operator=

range

rangeX

rangeY

resetPoints

set1D

set2D

setPoint

setPoint

toShort4PointsString

toString

transpose

width

m_maxX

m_maxY

m_minX

m_minY

m_points

##### SelectionPolygonSpec

SelectionPolygonSpec

SelectionPolygonSpec

SelectionPolygonSpec

operator=

toString

dataKind

selectionPolygon

##### SimplePeakIonMatch

ion_charge

ion_mz

ion_size

ion_type

peak

##### SpectrumCollectionHandlerInterface

isReadAhead

loadingEnded

needMsLevelPeakList

needPeakList

setNeedMsLevelPeakList

setQualifiedMassSpectrum

setReadAhead

shouldStop

spectrumListHasSize

m_isReadAhead

m_needPeakListByMsLevel

##### SwitchWidget

SwitchWidget

~SwitchWidget

getSwitchValue

setSwitchValue

updateSwitchValue

m_switchButtonValue

##### TandemWrapperRun

TandemWrapperRun

~TandemWrapperRun

checkXtandemVersion

convertOrginalMsData2mzXmlData

getMs2FilterSuiteString

readTandemPresetFile

readyReadStandardError

readyReadStandardOutput

run

runTandem

setTandemBinaryPath

tandemProgressMessage

wrapTandemInputFile

writeFinalTandemOutput

m_conversionTime

m_convertMzDataUsingSpectrumIndex

m_maxTandemRunTimeMs

m_mzFormat

m_tandemBinary

m_tandemVersion

m_tmpDir

m_xtProcess

mp_monitor

mpa_temporaryDirectory

msp_ms2FilterSuiteString

##### TicXicChromDriftSpecColorMapPlotWidget

TicXicChromDriftSpecColorMapPlotWidget

~TicXicChromDriftSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### TicXicChromMassSpecColorMapPlotWidget

TicXicChromMassSpecColorMapPlotWidget

~TicXicChromMassSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### TicXicChromTracePlotWidget

TicXicChromTracePlotWidget

~TicXicChromTracePlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### TimsBinDec

TimsBinDec

TimsBinDec

~TimsBinDec

closeLinearRead

getQfileLinear

getQfileRandom

getTimsFrameFromRawDataChunck

getTimsFrameSPtrByOffset

moveLinearReadForward

startLinearRead

m_decompressMemoryBufferSize

m_firstFrameId

m_lastFrameId

m_linearAccessRawDataChunckDequeSize

m_linearAccessRawDataChunckList

m_linearForwardThreshold

m_randemAccessFrameRawDataChunck

m_timsBinFile

m_timsCompressionType

mp_fileLinear

mp_fileRandom

mpa_decompressMemoryBuffer

##### TimsData

TimsData

TimsData

~TimsData

fillFrameIdDescrList

getFrameCount

getFrameIdDescrList

getGlobalScanIndexByScanCoordinates

getMassSpectrumCstSPtr

getMassSpectrumCstSPtrByGlobalScanIndex

getMassSpectrumCstSPtrByRawIndex

getMsLevelByGlobalScanIndex

getMsLevelBySpectrumIndex

getQualifiedMassSpectrumByGlobalScanIndex

getQualifiedMassSpectrumByRawIndex

getRawIndexFromCoordinate

getRawMsBySpectrumIndex

getRetentionTimeLine

getRetentionTimeLineInSeconds

getScanByGlobalScanIndex

getScanCoordinateFromRawIndex

getScanCoordinatesByGlobalScanIndex

getTicChromatogram

getTimsBinDecPtr

getTimsDataDirectory

getTimsDdaPrecursorsPtr

getTimsDiaSlicesPtr

getTimsFrameBaseCstSPtr

getTimsFrameBaseCstSPtrCached

getTimsFrameCstSPtr

getTimsFrameCstSPtrCached

getTimsFrameRecordList

getTimsMS1FrameIdsInRtRange

getTimsMS2FrameIdsInRtRange

getTotalNumberOfFrames

getTotalNumberOfScans

getTotalScanCount

isDdaRun

isDiaRun

openDatabaseConnection

m_cacheSize

m_frameCount

m_frameIdDescrList

m_mapFramesRecord

m_mapMzCalibrationRecord

m_mapTimsCalibrationRecord

m_mutex

m_someoneIsLoadingFrameId

m_thousandIndexToFrameIdDescrListIndex

m_timsDataDirectory

m_timsFrameBaseCache

m_timsFrameCache

m_totalScanCount

mpa_mzCalibrationStore

mpa_timsBinDec

mpa_timsDdaPrecursors

mpa_timsDiaSlices

TimsDdaPrecursors

TimsDiaSlices

##### TimsDataFastMap

###### TimsDataFastMapElement

count

first_access

TimsDataFastMap

accumulateIntensity

builtInCentroid

clear

downsizeMzRawMap

getTimsDataFastMapInstance

getTofIndexList

readIntensity

removeArtefactualSpike

m_preAllocatedFastMapPerThread

mapTofIndexIntensity

tofIndexList

##### TimsDdaPrecursors

###### SpectrumDescr

collisionEnergy

isolationMz

isolationWidth

ms1_index

ms2_index

parent_frame

precursor_id

precursor_ion_data

scan_mobility_end

scan_mobility_start

tims_frame_list

TimsDdaPrecursors

~TimsDdaPrecursors

fillSpectrumDescriptionWithSqlRecord

getClosestPrecursorIdByMz

getCombinedMs2ScansByPrecursorId

getMatchPrecursorIdByKo

getMs2BuiltinCentroid

getPrecursorsByMzRtCharge

getQualifiedMs1MassSpectrumBySpectrumDescr

getQualifiedMs2MassSpectrumBySpectrumDescr

getSpectrumDescrListByFrameId

getSpectrumDescrWithPrecursorId

getSpectrumDescrWithScanCoordinates

getTotalPrecursorCount

getXicCoordTimsFromPrecursorId

ms2ReaderGenerateMS1MS2Spectrum

ms2ReaderSpectrumCollectionByMsLevel

rawReaderSpectrumCollectionByMsLevel

setMonoThread

setMs1FilterCstSPtr

setMs2BuiltinCentroid

setMs2FilterCstSPtr

m_builtinMs2Centroid

m_isMonoThread

m_mapXicCoordRecord

m_mutex

m_totalPrecursorCount

mcsp_ms1Filter

mcsp_ms2Filter

mp_timsDataOrigin

TimsData

##### TimsDiaSlices

###### FrameSliceRange

begin_global_slice_index

end_global_slice_index

frame_id

###### MsMsWindow

isMzInRange

CollisionEnergy

IsolationMz

IsolationWidth

ScanNumBegin

ScanNumEnd

SliceIndex

WindowGroup

###### MsMsWindowGroup

WindowGroup

###### MsMsWindowGroupList

~MsMsWindowGroupList

addInGroup

getWindowGroupPtrByGroupId

TimsDiaSlices

~TimsDiaSlices

getCombinedMs2ScansByGlobalSliceIndex

getFrameIdByGlobalSliceIndex

getFrameSliceRangeByGlobalSliceIndex

getGlobalSliceIndexBeginByFrameId

getLastMs1FrameIdByMs2FrameId

getMapFrame2WindowGroupPtr

getMs1QualifiedSpectrumByGlobalSliceIndex

getMs2QualifiedSpectrumByGlobalSliceIndex

getMsMsWindowByGlobalSliceIndex

getMsMsWindowGroupList

getTotalSlicesCount

m_builtinMs2Centroid

m_frameId2GlobalSliceIndexBegin

m_frameSliceRangeList

m_mapFrame2WindowGroupPtr

m_ms1frameIdList

m_ms2frameId2Ms1FrameId

m_msMsWindowGroupList

m_totalSlicesCount

mp_timsDataOrigin

##### TimsDirectXicExtractor

TimsDirectXicExtractor

~TimsDirectXicExtractor

protectedExtractXicCoordSPtrList

##### TimsFrame

###### XicComputeStructure

XicComputeStructure

mobilityIndexBegin

mobilityIndexEnd

mzIndexLowerBound

mzIndexUpperBound

tmpIntensity

xic_ptr

TimsFrame

TimsFrame

~TimsFrame

TimsFrame

combineScansInTofIndexIntensityMap

combineScansInTofIndexIntensityMap

combineScansToTraceWithDowngradedMzResolution

combineScansToTraceWithDowngradedMzResolution2

cumulateScan

cumulateScan2

cumulateScanIntensities

cumulateScanRangeIntensities

cumulateScansToTrace

extractTimsXicListInRtRange

getMassSpectrumSPtr

getMobilityScan

getRawTraceSPtr

getRawValuePairList

getScanIntensityList

getScanOffset

getScanPeakCount

getScanTofIndexList

unshufflePacket

m_binaryData

TimsDirectXicExtractor

##### TimsFrameBase

###### TofIndexIntensityPair

intensity_index

tof_index

TimsFrameBase

TimsFrameBase

~TimsFrameBase

checkScanNum

combineScansInTofIndexIntensityMap

combineScansInTofIndexIntensityMap

combineScansToTraceWithDowngradedMzResolution

combineScansToTraceWithDowngradedMzResolution2

cumulateScanIntensities

cumulateScanRangeIntensities

cumulateScansToTrace

downgradeResolutionOfTofIndexIntensityPairList

getDriftTimeInMilliseconds

getId

getIonMobilityTraceByTofIndexRange

getMassSpectrumCstSPtr

getMassSpectrumSPtr

getMaximumRawMassIndex

getMobilityScan

getMsLevel

getMzCalibrationInterfaceSPtr

getOneOverK0Transformation

getRtInSeconds

getScanIndexFromOneOverK0

getScanIntensityList

getScanPeakCount

getScanTofIndexList

getTotalNumberOfScans

getTraceFromTofIndexIntensityMap

getVoltageTransformation

hasSameCalibrationData

setAcqDurationInMilliseconds

setMsMsType

setMzCalibration

setMzCalibrationInterfaceSPtr

setRtInSeconds

setTimsCalibration

m_acqDurationInMilliseconds

m_frameId

m_msMsType

m_rtInSeconds

m_scanCount

m_timsC6

m_timsC7

m_timsDvStart

m_timsNdelay

m_timsSlope

m_timsTtrans

m_timsVmax

m_timsVmin

msp_mzCalibration

##### TimsFrameMobilityTraces

TimsFrameMobilityTraces

TimsFrameMobilityTraces

~TimsFrameMobilityTraces

extractMobilityTraces

getIonMobTraceList

getMzList

getScanIndexList

getTofIndexList

m_ionMobTraceList

m_scanIndexList

m_tofIndexList

mcsp_timsFrameCstSPtr

##### TimsFrameRawDataChunck

TimsFrameRawDataChunck

~TimsFrameRawDataChunck

getCompressedSize

getFrameId

getFrameLength

getFrameNumberOfScans

getMemoryBuffer

readTimsFrame

m_frameId

m_frameLength

m_frameNumberOfScans

m_memoryBufferSize

mpa_memoryBuffer

##### TimsFrameRecord

accumulation_time

frame_id

frame_t1

frame_t2

frame_time

msms_type

mz_calibration_id

tims_calibration_id

tims_offset

##### TimsFramesMsRunReader

TimsFramesMsRunReader

~TimsFramesMsRunReader

computeTicChromatogram

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

##### TimsFrameType1

TimsFrameType1

TimsFrameType1

~TimsFrameType1

copyAndLzfDecompress

cumulateScan

cumulateScan2

getMassSpectrumSPtr

getRawTraceSPtr

getRawValuePairList

getScanIntensityList

getScanPeakCount

getScanTofIndexList

lzfDecompressScan

m_scanOffsetList

m_scanSizeList

##### TimsMs2CentroidFilter

TimsMs2CentroidFilter

TimsMs2CentroidFilter

~TimsMs2CentroidFilter

filter

##### TimsMsFileReader

TimsMsFileReader

~TimsMsFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### TimsMsRunReader

TimsMsRunReader

TimsMsRunReader

~TimsMsRunReader

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

##### TimsMsRunReaderBase

TimsMsRunReaderBase

TimsMsRunReaderBase

~TimsMsRunReaderBase

accept

acquireDevice

getRetentionTimeLine

getTicChromatogram

getTimsDataSPtr

hasScanNumbers

initialize

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

releaseDevice

MsFileAccessor

msp_timsData

##### TimsMsRunReaderDia

TimsMsRunReaderDia

TimsMsRunReaderDia

~TimsMsRunReaderDia

acquireDevice

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

mp_timsDiaSlices

##### TimsMsRunReaderMs2

TimsMsRunReaderMs2

TimsMsRunReaderMs2

~TimsMsRunReaderMs2

accept

acquireDevice

getPrecursorsIDFromMzRt

getRetentionTimeLine

getTicChromatogram

getTimsDataSPtr

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

setMs1FilterCstSPtr

setMs2BuiltinCentroid

setMs2FilterCstSPtr

spectrumListSize

MsFileAccessor

m_builtinMs2Centroid

mp_timsDdaPrecursors

msp_ms1Filter

msp_ms2Filter

msp_timsData

##### TimsMsRunReaderMs2Selected

TimsMsRunReaderMs2Selected

~TimsMsRunReaderMs2Selected

accept

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

setMs1FilterCstSPtr

setMs2FilterCstSPtr

spectrumListSize

MsFileAccessor

mpa_timsData

##### TimsXicExtractorInterface

TimsXicExtractorInterface

~TimsXicExtractorInterface

mp_timsData

TimsData

##### Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

~Trace

append

containsX

dataPointCstIteratorWithX

dataPointIndexWithX

dataPointIteratorWithX

filter

initialize

initialize

initialize

initialize

initialize

makeTraceCstSPtr

makeTraceSPtr

maxX

maxXDataPoint

maxY

maxY

maxYDataPoint

minX

minXDataPoint

minY

minYDataPoint

operator=

operator=

removeZeroYDataPoints

sort

sortX

sortY

sumY

sumY

toMap

toString

unique

xAsBase64Encoded

xValues

yAsBase64Encoded

yValues

MassSpectrumCombinerInterface

TraceCombiner

TraceMinusCombiner

TracePlusCombiner

##### TraceCombiner

TraceCombiner

TraceCombiner

TraceCombiner

TraceCombiner

~TraceCombiner

##### TraceDetectionInterface

detect

##### TraceDetectionMoulon

TraceDetectionMoulon

TraceDetectionMoulon

~TraceDetectionMoulon

detect

getSmoothingHalfEdgeWindows

getTicStart

getTicStop

setFilterMorphoMean

setTicStart

setTicStop

m_ticStart

m_ticStop

m_xicFilterSmoothing

##### TraceDetectionSinkInterface

setTracePeak

##### TraceDetectionZivy

TraceDetectionZivy

~TraceDetectionZivy

detect

getDetectionThresholdOnMaxmin

getDetectionThresholdOnMinmax

getMaxMinHalfEdgeWindows

getMinMaxHalfEdgeWindows

getSmoothingHalfEdgeWindows

setDetectionThresholdOnMaxmin

setDetectionThresholdOnMinmax

setFilterMorphoMaxMin

setFilterMorphoMean

setFilterMorphoMinMax

m_detectionThresholdOnMaxMin

m_detectionThresholdOnMinMax

m_maxMin

m_minMax

m_smooth

##### TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

~TraceMinusCombiner

combine

combine

MassSpectrumMinusCombiner

##### TracePeak

TracePeak

TracePeak

TracePeak

TracePeak

~TracePeak

containsRt

getArea

getLeftBoundary

getLeftBoundary

getMaxXicElement

getMaxXicElement

getRightBoundary

getRightBoundary

makeTracePeakCstSPtr

operator=

operator==

setArea

setLeftBoundary

setMaxXicElement

setRightBoundary

m_area

m_left

m_max

m_right

##### TracePeakList

TracePeakList

TracePeakList

~TracePeakList

setTracePeak

##### TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

~TracePlusCombiner

combine

combine

MassSpectrumPlusCombiner

##### UiMonitorInterface

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

m_totalSteps

##### UiMonitorText

UiMonitorText

~UiMonitorText

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

m_count

m_outputStream

##### UiMonitorTextPercent

UiMonitorTextPercent

~UiMonitorTextPercent

count

setTotalSteps

m_unit

##### UiMonitorVoid

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

##### Utils

almostEqual

appendToFile

booleanToString

chronoIntervalDebugString

chronoTimePointDebugString

extractScanNumberFromMzmlNativeId

fileReaderTypeAsString

getLexicalOrderedString

getVersion

msDataFormatAsString

nearestGreater

pointerToString

roundToDecimal32bitsAsLongLongInt

roundToDecimals

splitMzStringToDoubleVectorWithSpaces

splitSizetStringToSizetVectorWithSpaces

toString

toString

toUtf8StandardString

writeLexicalOrderedString

writeToFile

zeroDecimalsInValue

anythingButDigitDotDash

endOfLineRegExp

mzListDataFormatRegExp

signedDoubleNumberExponentialRegExp

sizetListDataFormatRegExp

unsignedDoubleNumberNoExponentialRegExp

xyMassDataFormatRegExp

##### WrapTandemInput

WrapTandemInput

~WrapTandemInput

getOriginalMsDataFileName

getOriginalTandemOutputFileName

getOriginalTandemPresetFileName

readStream

m_destinationMzXmlFileName

m_destinationTandemInputFile

m_destinationTandemInputFileName

m_destinationTandemOutputFileName

m_originMzDataFileName

m_originTandemOutpuFileName

m_originTandemPresetFileName

m_writerXmlTandemInput

##### WrapTandemResults

WrapTandemResults

~WrapTandemResults

process_group_note

readStream

setInputParameters

m_destinationTandemOutputFile

m_mapTandemInputParameters

m_originalMsDataFileName

m_writerXmlTandemOutput

##### Xic

Xic

Xic

~Xic

atRetentionTime

debugPrintValues

getMsPointDistance

makeXicCstSPtr

makeXicSPtr

operator=

operator=

sortByRetentionTime

##### XicCoord

XicCoord

XicCoord

~XicCoord

addition

divideBy

getParam

initializeAndClone

multiplyBy

reset

toString

mzRange

rtTarget

xicSptr

##### XicCoordTims

XicCoordTims

XicCoordTims

~XicCoordTims

addition

divideBy

getParam

initializeAndClone

multiplyBy

reset

scanNumBeginRangeCorrection

toString

scanNumBegin

scanNumEnd

##### XicPeptideFragmentIon

XicPeptideFragmentIon

XicPeptideFragmentIon

~XicPeptideFragmentIon

getPeptideFragmentIonSp

msp_peptideFragmentIon

##### XicPeptideFragmentIonNaturalIsotope

XicPeptideFragmentIonNaturalIsotope

XicPeptideFragmentIonNaturalIsotope

~XicPeptideFragmentIonNaturalIsotope

getCharge

getPeptideFragmentIonSp

getPeptideNaturalIsotopeAverageSp

msp_naturalIsotopeAverage

msp_peptideFragmentIon

##### XicPeptideInterface

XicPeptideInterface

~XicPeptideInterface

getCharge

m_z

msp_peptideInterface

##### XicWidget

XicWidget

~XicWidget

addMsMsEvent

addXicPeakList

addXicSp

clear

clearXicPeakBorders

clicked

drawXicPeakBorders

getIntensityAxisP

getName

getRtAxisP

getXicCstSPtr

operateNewRange

plot

replotAll

rescale

rescaleOneRange

rtChanged

rtChangeEvent

setName

setRetentionTimeInMinutes

setRetentionTimeInSeconds

toQPaintDevice

xicClickEvent

xicPeakListChanged

QCPXic

_map_xic_msms_event

_map_xic_name

_qcp_xic

_rt_in_seconds

_xic_peak_sp_list

_xic_sp_list

##### XmlStreamReaderInterface

XmlStreamReaderInterface

~XmlStreamReaderInterface

cloneElement

cloneNode

cloneStartElement

errorString

read

read

readFile

readStream

m_qxmlStreamReader

##### XtandemError

XtandemError

clone

##### XtandemHyperscore

AaFactorMap

XtandemHyperscore

XtandemHyperscore

~XtandemHyperscore

getHyperscore

getMatchedIons

getXtandemPredictedIonIntensityFactor

_aa_ion_factor_b

_aa_ion_factor_y

_ion_count

_proto_hyperscore

_refine_spectrum_synthesis

##### XtandemHyperscoreBis

AaFactorMap

XtandemHyperscoreBis

~XtandemHyperscoreBis

computeXtandemHyperscore

getHyperscore

getMatchedIons

getTotalMatchedIons

getXtandemPredictedIonIntensityFactor

reset

m_aaIonFactorBb

m_aaIonFactorY

m_ionCount

m_ionList

m_isRefineSpectrumSynthesis

m_protoHyperscore

m_totalMatchedIons

mp_precision

##### XtandemPresetReader

XtandemPresetReader

~XtandemPresetReader

getCountNote

getMs2FiltersOptions

getNumberOfThreads

read_note

readStream

m_countNote

m_ms2precisionUnit

m_ms2precisionValue

m_threads

##### XtandemSpectrumProcess

XtandemSpectrumProcess

XtandemSpectrumProcess

~XtandemSpectrumProcess

getDynamicRange

getExcludeParent

getExcludeParentNeutralLoss

getIonScore

getMinimumMz

getNeutralLossMass

getNeutralLossWindowDalton

getNmostIntense

getRefineSpectrumModel

getRemoveIsotope

process

setDynamicRange

setExcludeParent

setExcludeParentNeutralLoss

setIonScore

setMinimumMz

setNeutralLossMass

setNeutralLossWindowDalton

setNmostIntense

setRefineSpectrumModel

setRemoveIsotope

_a_ions

_ao_ions

_astar_ions

_b_ions

_bo_ions

_bstar_ions

_c_ions

_x_ions

_y_ions

_yo_ions

_ystar_ions

_z_ions

m_filter_floor

m_filter_highpass

m_filter_keep_greater

m_filter_remove_c13

m_filter_rescale

m_isExcludeParent

m_isExcludeParent_lower_dalton

m_isExcludeParent_neutral_loss

m_isExcludeParent_upper_dalton

m_isRefineSpectrumModel

m_isRemoveIsotope

m_n_most_intense

m_neutralLossMass

m_neutralLossWindowDalton

##### XyMsFileReader

XyMsFileReader

~XyMsFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### XyMsRunReader

XyMsRunReader

~XyMsRunReader

accept

acquireDevice

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

qualifiedMassSpectrumFromXyMSDataFile

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

spectrumListSize

MsFileAccessor

m_fileName

AaModificationP

AaModificationUp

AaStringCodecSp

BaseColorMapPlotWidgetCstSPtr

BaseColorMapPlotWidgetSPtr

BasePlotWidgetCstSPtr

BasePlotWidgetSPtr

BaseTracePlotWidgetCstSPtr

BaseTracePlotWidgetSPtr

DataPointCstSPtr

FastaFileIndexerSPtr

FilterCeilingAmplitudePercentageCstSPtr

FilterCeilingAmplitudePercentageSPtr

FilterFloorAmplitudePercentageCstSPtr

FilterFloorAmplitudePercentageSPtr

FilterInterfaceCstSPtr

FilterInterfaceSPtr

FilterLowIntensitySignalRemovalCstSPtr

FilterLowIntensitySignalRemovalSPtr

FilterNameInterfaceCstSPtr

FilterNameInterfaceSPtr

FilterNormalizeIntensitiesCstSPtr

FilterNormalizeIntensitiesSPtr

FilterSavitzkyGolayCstSPtr

FilterSavitzkyGolaySPtr

FilterSuiteStringSPtr

GrpGroupSp

GrpGroupSpConst

GrpPeptideSp

GrpPeptideSpConst

GrpProteinSp

GrpProteinSpConst

GrpSubGroupSp

GrpSubGroupSpConst

IntegrationScopeBaseCstSPtr

IntegrationScopeBaseSPtr

IntegrationScopeCstSPtr

IntegrationScopeRectCstSPtr

IntegrationScopeRectSPtr

IntegrationScopeRhombCstSPtr

IntegrationScopeRhombSPtr

IntegrationScopeSpecCstSPtr

IntegrationScopeSpecSPtr

IntegrationScopeSpecVector

IntegrationScopeSPtr

MapTraceCstSPtr

MapTraceSPtr

MassSpectrumCombinerCstSPtr

MassSpectrumCombinerSPtr

MassSpectrumCstSPtr

MassSpectrumMinusCombinerCstSPtr

MassSpectrumMinusCombinerSPtr

MassSpectrumPlusCombinerCstSPtr

MassSpectrumPlusCombinerSPtr

MassSpectrumSPtr

MsFileAccessorCstSPtr

MsFileAccessorSPtr

MsRunDataSetTreeCstSPtr

MsRunDataSetTreeNodeCstSPtr

MsRunDataSetTreeNodeSPtr

MsRunDataSetTreeSPtr

MsRunIdCstSPtr

MsRunIdSPtr

MsRunReaderCstSPtr

MsRunReaderSPtr

MsRunSliceSPtr

MsRunXicExtractorInterfaceSp

MzCalibrationInterfaceSPtr

NoConstPeptideSp

pappso_double

pappso_float

PeakIonIsotopeMatchCstSPtr

PeptideFragmentIonListBaseSp

PeptideFragmentIonSp

PeptideFragmentSp

PeptideInterfaceSp

PeptideNaturalIsotopeAverageSp

PeptideNaturalIsotopeListSp

PeptideNaturalIsotopeSp

PeptideSp

PeptideStr

PrecisionPtr

ProteinSp

QualifiedMassSpectrumCstSPtr

QualifiedMassSpectrumSPtr

QualifiedXicSp

TimsDataSp

TimsFrameBaseCstSPtr

TimsFrameBaseSPtr

TimsFrameCstSPtr

TimsFramesMsRunReaderCstSPtr

TimsFramesMsRunReaderSPtr

TimsFrameSPtr

TimsMsRunReaderMs2SPtr

TraceCombinerCstSPtr

TraceCombinerSPtr

TraceCstSPtr

TraceDetectionInterfaceCstSPtr

TraceDetectionInterfaceSPtr

TraceMinusCombinerCstSPtr

TraceMinusCombinerSPtr

TracePeakCstSPtr

TracePlusCombinerCstSPtr

TracePlusCombinerSPtr

TraceSPtr

uint

XicCoordSPtr

XicCoordTimsSPtr

XicCstSPtr

XicSPtr

XicXicPeakPairList

##### AminoAcidChar

alanine

cysteine

aspartic_acid

glutamic_acid

phenylalanine

glycine

histidine

isoleucine

lysine

leucine

methionine

asparagine

proline

glutamine

arginine

serine

threonine

valine

tryptophan

tyrosine

selenocysteine

pyrrolysine

##### AtomIsotope

C

H

O

N

S

##### AtomIsotopeSurvey

C

H

O

N

S

last

##### Axis

unset

x

y

z

##### AxisScale

unset

orig

log10

##### BinningType

NONE

DATA_BASED

ARBITRARY

LAST

##### DataCompression

unset

none

zlib

##### DataDimension

NOT_SET

HORIZONTAL

VERTICAL

##### DataKind

unset

rt

dt

mz

##### DeepProtMatchType

uncategorized

ZeroMassDelta

ZeroMassDeltaMissedCleavage

ZeroMassDeltaSemiTryptic

DeltaPosition

NoDeltaPosition

last

##### DeepProtPeptideCandidateStatus

unmodified

ZeroMassDelta

CterRemoval

NterRemoval

MissedCleavage

DeltaPosition

NoDeltaPosition

last

##### DragDirections

NOT_SET

LEFT_TO_RIGHT

RIGHT_TO_LEFT

TOP_TO_BOTTOM

BOTTOM_TO_TOP

##### FileReaderType

pwiz

xy

bafascii

tims

tims_frames

tims_ms2

tims_dia

##### IntegrationScopeFeatures

FAILURE

SUCCESS

FLAT_ON_X_AXIS

FLAT_ON_Y_AXIS

RHOMBOID_VERTICAL

RHOMBOID_HORIZONTAL

NOT_PRINTABLE

FLAT_ON_ANY_AXIS

##### Isotope

C13

H2

O17

O18

N15

S33

S34

S36

##### MsDataFormat

unknown

mzML

mzXML

MGF

SQLite3

xy

mz5

msn

abSciexWiff

abSciexT2D

agilentMassHunter

thermoRaw

watersRaw

brukerFid

brukerYep

brukerBaf

brukerTims

brukerBafAscii

last

##### MsRunReadConfigParameter

TimsFrameIonMobScanIndexBegin

TimsFrameIonMobScanIndexEnd

TimsFrameIonMobOneOverK0Begin

TimsFrameIonMobOneOverK0End

MzRangeBegin

MzRangeEnd

TimsFrameMzIndexMergeWindow

##### MsRunXicExtractorFactoryType

nose

direct

disk

diskbuffer

##### PeptideDirection

Nter

Cter

##### PeptideIon

b

bstar

bo

a

astar

ao

bp

c

y

ystar

yo

z

yp

x

##### PeptideIonCter

y

ystar

yo

z

yp

x

##### PeptideIonNter

b

bstar

bo

a

astar

ao

bp

c

##### PointSpec

TOP_LEFT_POINT

TOP_RIGHT_POINT

BOTTOM_RIGHT_POINT

BOTTOM_LEFT_POINT

ENUM_LAST

##### PrecisionUnit

none

dalton

ppm

res

mz

last

##### QualifiedMassSpectrumParameter

IonMobOneOverK0

IonMobOneOverK0Begin

IonMobOneOverK0End

TimsIonMobScanIndex

TimsFrameIonMobScanIndexBegin

TimsFrameIonMobScanIndexEnd

IsolationMz

IsolationMzWidth

CollisionEnergy

BrukerPrecursorIndex

TimsFrameScansCount

TimsFrameMzIndexBegin

TimsFrameMzIndexEnd

ScanNumber

last

##### RangeType

outermost

innermost

##### RawFragmentationMode

full

proline_effect

##### SelectionDrawingLines

NOT_SET

TOP_LINE

BOTTOM_LINE

HORIZONTAL_LINES

RIGHT_LINE

LEFT_LINE

VERTICAL_LINES

FULL_POLYGON

##### SortOrder

ascending

descending

##### SortType

no_sort

x

y

##### TimeUnit

none

s

min

h

##### XicCoordParam

TimsTofIonMobilityScanNumberStart

TimsTofIonMobilityScanNumberStop

##### XicExtractMethod

sum

max

ABUNDANCEC12

ABUNDANCEC13

ABUNDANCEH2

ABUNDANCEN15

ABUNDANCEO17

ABUNDANCEO18

ABUNDANCES33

ABUNDANCES34

ABUNDANCES36

areaTrace

Combinations

DIFFC12C13

DIFFH1H2

DIFFN14N15

DIFFO16O17

DIFFO16O18

DIFFS32S33

DIFFS32S34

DIFFS32S36

factorial

findBestTracePeakGivenRtList

findComplementIonType

findDifferentYvalue

findDifferentYvalue

findFirstEqualOrGreaterX

findFirstEqualOrGreaterX

findFirstGreaterX

findFirstGreaterX

findTracePeakGivenRt

flooredLocalMaxima

getByIntensityRatioByIsotopeNumber

getPeptideIonDirection

isotopem_ratio

isotopem_ratio_cache

MASSCARBON

MASSCO

MASSH2O

MASSNH3

MASSNITROGEN

MASSOXYGEN

MASSPHOSPHORUS

MASSPHOSPHORYLATEDR

MASSSELENIUM

MASSSULFUR

maxYDataPoint

maxYDataPoint

meanYTrace

medianYTrace

MHPLUS

minYDataPoint

minYDataPoint

moveLowerYLeftDataPoint

moveLowerYRigthDataPoint

MPROTIUM

MPROTON

ONEMILLION

operator<

operator<<

operator<<

operator<<

operator==

operator>>

operator>>

operator>>

operator>>

peptideIonIsNter

peptideIonTypeIsComplement

quantileYTrace

sumYTrace

binningTypeMap

CHECKED_LINES_COUNT

combinations_cache

MAX_MS_LEVELS

MsRunReader

ratioC13_cache

ratioH2_cache

ratioN15_cache

ratioO17_cache

ratioO18_cache

ratioS33_cache

ratioS34_cache

ratioS36_cache

Ui

### Namespace Members

#### All

a

b

c

d

e

f

g

i

m

n

o

p

q

r

s

t

u

x

Functions

Variables

Typedefs

Enumerations

Enumerator

## Classes

### Class List

#### pappso

##### specglob

###### AminoAcidModel

alignment_type

amino_acid

bracket

mass_difference

remove

###### ExperimentalSpectrum

ExperimentalSpectrum

ExperimentalSpectrum

~ExperimentalSpectrum

createSymetricPeakList

findMz

getMassList

getMassList

getPrecursorMass

getQualifiedMassSpectrum

getSymetricMz

getTargetMzSum

reverseFindDiffMz

toString

m_precisionPtr

m_precursorMass

m_qualifiedMassSpectrum

m_targetMzSum

###### ExperimentalSpectrumDataPoint

indice

symmetric_mz

type

###### PeptideModel

PeptideModel

PeptideModel

PeptideModel

~PeptideModel

assignResidualMass2Cter

checkForAaModification

checkForAaModificationP

checkForMutation

checkForMutations

copyDeep

eliminateComplementaryDelta

eliminateNegativeOffset

generateTheoreticalPeaks

getCountSharedPeaks

getIntensityExperimentalPeaks

getIntensitySharedPeaks

getMass

getMassDelta

getMz

getTheoreticalIonMassList

getTheoreticalPeakDataPointList

getTheoreticalPeakDataPointListToString

hasRemoval

ltrimOnRemoval

matchExperimentalPeaks

modifCount

operator=

removeBracketsForAlignedAA

setBeginMassDelta

toProForma

toString

m_beginMassDelta

m_countSharedPeaks

m_cterModification

m_experimentalPrecursorMass

m_intensityExperimentalPeaks

m_intensitySharedPeaks

m_nterModification

m_theoreticalPeakList

mcsp_peakList

###### PeptideSpectrum

PeptideSpectrum

PeptideSpectrum

~PeptideSpectrum

getMassList

getPeptideSp

msp_peptide

###### PeptideSpectrumDataPoint

diff_mz

mz

###### PostTreatment

PostTreatment

~PostTreatment

findBetterPeptideModel

findReplaceMutations

getBetterPeptideModel

getOriginalPeptideModel

tryBetterPositionOffsets

tryToCumulateOffSets

tryToRemoveOffsets

m_betterPeptideModel

m_originalPeptideModel

m_precision

###### ScoreValues

ScoreValues

ScoreValues

~ScoreValues

get

operator=

set

m_scoreTable

###### SpectralAlignment

SpectralAlignment

~SpectralAlignment

align

backTrack

buildPeptideModel

fillMassDelta

fillMatricesWithScores

getBestRealignScore

getExperimentalSpectrumCsp

getExperimentalSpectrumDataPoint

getMatrix

getMaxPosIterator

getMaxScore

getPeptideSpectraCsp

getPrecursorMzDelta

getScoreRow

rtrim

m_BETTER_END_RA

m_itPosMax

m_matrix

m_maxScore

m_precisionPtr

m_precursorMassDelta

m_scoreValues

mcsp_experimentalSpectrum

mcsp_peptideSpectrum

###### SpectralAlignmentDataPoint

alignment_type

mass_difference

origin_column_indices

score

###### TheoreticalPeakDataPoint

aa_indice

it_experimental_peak_match

mz_range

##### specself

###### SelfSpectrum

SelfSpectrum

~SelfSpectrum

getMatrix

getTrace

setPrecursorMass

setVariableModification

m_matrix

m_trace

###### SelfSpectrumDataPoint

fillAntiSpectrumDataPoint

fillSelfSpectrumDataPoint

setVariableModification

aaCodeList

antiAaCodeList

antiMassDelta

m_isComplement

massDelta

##### spectree

###### Bucket

Bucket

Bucket

back

front

getCartList

getId

operator<

push_back

size

m_cartList

m_itemId

###### BucketClustering

BucketClustering

addItemCart

asSortedList

getItemCartCount

removeBucketsWithinCartIdRange

size

m_bucketMap

m_itemCartCount

###### ItemCart

ItemCart

ItemCart

ItemCart

~ItemCart

getId

getItemList

operator=

m_id

m_itemList

###### SpecTree

###### MapSimilarityCount

aboveThreshold

keys

map_id_count

###### MapSimilarityCountElement

aboveThreshold

count

lastWitness

###### SpecTreeNode

count

nextIndex

parentIndex

value

SpecTree

~SpecTree

addNewNode

extractSpectrumPairSimilarityCount

extractSpectrumSimilarityCount

getSpectrumFirstNodeIndex

manageSideAccess

toString

walkBackInBranchFromNode

walkBackInBranchFromNodeToTarget

xtract

index_not_defined

m_nodeList

m_spectrumFirstNodeIndex

###### SpecXtractInterface

SpecXtractInterface

~SpecXtractInterface

beginItemCartExtraction

endItemCartExtraction

reportSimilarity

###### SpecXtractMap

SpecXtractMap

~SpecXtractMap

clear

getMapSimilarities

reportSimilarity

m_mapSimilarities

##### Aa

Aa

Aa

Aa

Aa

~Aa

addAaModification

getInternalCterModification

getInternalNterModification

getMass

getModificationList

getNumberOfAtom

getNumberOfIsotope

getNumberOfModification

getTotalModificationMass

isAaEqual

isLesser

operator=

removeAaModification

removeAllButInternalModification

removeInternalCterModification

removeInternalNterModification

replaceAaModification

toAbsoluteString

toProForma

toString

m_listMod

##### AaBase

AaIntMap

AaMassMap

AminoAcidCharList

AaBase

AaBase

AaBase

~AaBase

getAaMass

getAminoAcidChar

getAminoAcidCharList

getLetter

getMass

getNumberOfAtom

getNumberOfIsotope

replaceLeucineIsoleucine

AaModification

m_aaLetter

m_aaMassMap

m_aaNumberOfCarbonMap

m_aaNumberOfHydrogenMap

m_aaNumberOfNitrogenMap

m_aaNumberOfOxygenMap

m_aaNumberOfSulfurMap

m_aminoAcidCharList

##### AaCode

AaCode

AaCode

~AaCode

addAaModification

getAa

getAa

getAaCode

getMass

getSize

updateMass

updateNumbers

m_aaCollection

m_asciiTable

m_massCollection

##### AaModification

MapAccessionModifications

AaModification

~AaModification

AaModification

calculateMassFromChemicalComponents

createInstance

createInstance

createInstanceC13N15LabelledAminoAcid

createInstanceMutation

getAccession

getInstance

getInstance

getInstanceCustomizedMod

getInstanceInsertionAccessionByAaLetter

getInstanceMutation

getInstanceRemovalAccessionByAaLetter

getInstanceXtandemMod

getMass

getName

getNumberOfAtom

getNumberOfIsotope

getXrefOrigin

isInternal

setDiffFormula

setXrefOrigin

toProForma

m_accession

m_atomCount

m_mapAccessionModifications

m_mapIsotope

m_mass

m_mutex

m_name

m_origin

##### AaStringCodec

AaStringCodec

AaStringCodec

~AaStringCodec

code

codeLlc

codeLlc

codeOnlyContains

decode

decode

generateCodeMassFromModel

generateLlcCodeListByMaxPeptideSize

generateLlcCodeListUpToMaxPeptideSize

getAaCode

getLimitMax

getMass

recGenerateModel

uniqueCodeContainsAminoAcid

m_aaCode

m_base

m_units

##### AaStringCodeMassMatching

###### aaCodeAndMassRange

code

mz

mz_range_low

mz_range_up

AaStringCodeMassMatching

AaStringCodeMassMatching

~AaStringCodeMassMatching

filterCodeList

getAaCodeFromMass

getAaCodeFromMassList

getAaCodeFromMassWearingModification

getPrecisionPtr

m_aaCode

m_aaCodec

m_base

m_codeMassList

m_precision

##### AtomNumberInterface

getNumberOfAtom

getNumberOfIsotope

##### BafAsciiFileReader

BafAsciiFileReader

~BafAsciiFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### BafAsciiMsRunReader

BafAsciiMsRunReader

~BafAsciiMsRunReader

accept

acquireDevice

craftLineParserRegExp

craftLineParserRegExpPattern

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

parseMassSpectrumLine

qualifiedMassSpectrum

qualifiedMassSpectrumFromBafAsciiMSDataFile

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

spectrumListSize

MsFileAccessor

m_fileName

m_spectrumCount

##### BaseColorMapPlotWidget

BaseColorMapPlotWidget

BaseColorMapPlotWidget

~BaseColorMapPlotWidget

addColorMap

addColorMap

axisScale

currentXaxisRangeIndices

currentYaxisRangeIndices

dataTo3ColString

dataToMatrixString

getColorMapPlotConfig

getOrigColorMapPlotConfig

getPlottingColor

setColorMapPlotConfig

setPlottingColor

transposeAxes

xAxisDataKind

xAxisScale

yAxisDataKind

yAxisScale

zAxisDataResetToOriginal

zAxisFilterHighPassPercentage

zAxisFilterLowPassPercentage

zAxisFilterLowPassThreshold

zAxisScale

zAxisScaleToLog10

m_colorMapPlotConfig

mpa_origColorMapData

mpa_origColorMapPlotConfig

##### BasePlotContext

BasePlotContext

BasePlotContext

~BasePlotContext

operator=

recordDragDirections

toString

updateIntegrationScope

updateIntegrationScopeRect

updateIntegrationScopeRhomb

updateIntegrationScopeRhombHorizontal

updateIntegrationScopeRhombVertical

m_currentDragPoint

m_dataKind

m_dragDirections

m_integrationScopeRhombHeight

m_integrationScopeRhombWidth

m_isKeyBoardDragging

m_isLeftPseudoButtonKeyPressed

m_isMeasuringDistance

m_isMouseDragging

m_isRightPseudoButtonKeyPressed

m_keyboardModifiers

m_lastCursorHoveredPoint

m_lastPressedMouseButton

m_lastReleasedMouseButton

m_mouseButtonsAtMousePress

m_mouseButtonsAtMouseRelease

m_pressedKeyCode

m_pressedMouseButtons

m_releasedKeyCode

m_selectionPolygon

m_startDragPoint

m_wasClickOnXAxis

m_wasClickOnYAxis

m_wasMouseDragging

m_wassKeyBoardDragging

m_xDelta

m_xRange

m_xRegionRangeEnd

m_xRegionRangeStart

m_yDelta

m_yRange

m_yRegionRangeEnd

m_yRegionRangeStart

msp_integrationScope

##### BasePlotWidget

BasePlotWidget

BasePlotWidget

~BasePlotWidget

allLayerNamesToString

axisDoubleClickHandler

axisPan

axisReframe

axisRescale

axisZoom

calculateDragDeltas

createAllAncillaryItems

directionKeyPressEvent

directionKeyReleaseEvent

dragDirection

drawSelectionRectangleAndPrepareZoom

drawXScopeSpanFeatures

drawYScopeSpanFeatures

getContext

getInnermostRangeX

getInnermostRangeY

getOutermostRangeX

getOutermostRangeY

getPen

getPlottingColor

getPlottingColor

getRange

getRangeX

getRangeY

hideAllPlotItems

hideSelectionRectangle

hideTracers

horizontalGetGraphCoordNewPointCountPixels

horizontalMoveMouseCursorCountPixels

integrationRequestedSignal

isClickOntoXAxis

isClickOntoYAxis

isSelectionRectangleVisible

isVerticalDisplacementAboveThreshold

keyPressEvent

keyPressEventSignal

keyReleaseEvent

keyReleaseEventSignal

lastCursorHoveredPointSignal

layerableLayerIndex

layerableLayerName

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerLeftButtonDraggingCursor

mouseMoveHandlerNotDraggingCursor

mouseMoveHandlerRightButtonDraggingCursor

mousePressHandler

mousePseudoButtonKeyPressEvent

mousePseudoButtonKeyReleaseEvent

mouseReleaseEventSignal

mouseReleaseHandler

mouseReleaseHandlerLeftButton

mouseReleaseHandlerRightButton

mouseWheelEventSignal

mouseWheelHandler

moveMouseCursorGraphCoordToGlobal

moveMouseCursorPixelCoordToGlobal

plotRangesChangedSignal

plottableDestructionRequestedSignal

plottableSelectionChangedSignal

redrawPlotBackground

replotWithAxesRanges

replotWithAxisRangeX

replotWithAxisRangeY

resetAxesRangeHistory

resetSelectionRectangle

restoreAxesRangeHistory

restorePreviousAxesRangeHistory

setAxisLabelX

setAxisLabelY

setFocus

setFocusSignal

setPen

setPlottingColor

setPlottingColor

setupWidget

showTracers

spaceKeyReleaseEvent

updateAxesRangeHistory

updateContextXandYAxisRanges

updateIntegrationScope

updateIntegrationScopeDrawing

updateIntegrationScopeHorizontalRhomb

updateIntegrationScopeRect

updateIntegrationScopeRhomb

updateIntegrationScopeVerticalRhomb

verticalGetGraphCoordNewPointCountPixels

verticalMoveMouseCursorCountPixels

whatIsVisibleOfTheSelectionRectangle

xAxisMeasurementSignal

yMinMaxOnXAxisCurrentRange

yMinMaxOnXAxisCurrentRange

m_axisLabelX

m_axisLabelY

m_context

m_desc

m_fileName

m_focusedBrush

m_focusedColor

m_lastAxisRangeHistoryIndex

m_leftMousePseudoButtonKey

m_mouseMoveHandlerSkipAmount

m_mouseMoveHandlerSkipCount

m_name

m_pen

m_rightMousePseudoButtonKey

m_shouldTracersBeVisible

m_unfocusedBrush

m_unfocusedColor

m_xAxisRangeHistory

m_yAxisRangeHistory

mp_hPosTracerItem

mp_selectionRectangeLine1

mp_selectionRectangeLine2

mp_selectionRectangeLine3

mp_selectionRectangeLine4

mp_vEndTracerItem

mp_vPosTracerItem

mp_vStartTracerItem

mp_xDeltaTextItem

mp_yDeltaTextItem

##### BaseTracePlotWidget

BaseTracePlotWidget

BaseTracePlotWidget

~BaseTracePlotWidget

addTrace

axisDoubleClickHandler

axisPan

axisReframe

axisRescale

axisZoom

clearGraphData

findIntegrationLowerRangeForKey

getValueRangeOnKeyRange

getValueRangeOnKeyRange

getValuesX

getValuesY

getYatX

getYatX

setGraphData

setGraphData

toTrace

toTrace

toTrace

toTrace

##### CodeToMass

code

mass

##### ColorMapPlotConfig

ColorMapPlotConfig

ColorMapPlotConfig

ColorMapPlotConfig

operator=

setOrigAndLastMaxZValue

setOrigAndLastMinZValue

setOrigMaxZValue

setOrigMinZValue

toString

keyCellCount

lastMaxZFilterThresholdPercentage

lastMaxZValue

lastMinZFilterThresholdPercentage

lastMinZValue

maxKeyValue

maxMzValue

minKeyValue

minMzValue

mzCellCount

origMaxZValue

origMinZValue

xAxisDataKind

xAxisScale

yAxisDataKind

yAxisScale

zAxisScale

##### CosineSimilarity

CosineSimilarity

CosineSimilarity

~CosineSimilarity

similarity

mp_precision

msp_filterExclusion

##### DaltonPrecision

DaltonPrecision

~DaltonPrecision

delta

toString

unit

PrecisionFactory

##### DataPoint

DataPoint

DataPoint

DataPoint

DataPoint

DataPoint

incrementX

incrementY

initialize

initialize

initialize

isValid

makeDataPointCstSPtr

operator=

operator==

reset

toString

toString

x

y

##### DeepProtEnumStr

DeepProtMatchTypeFromString

DeepProtPeptideCandidateStatusFromString

toString

toString

##### DriftSpecMassSpecColorMapPlotWidget

DriftSpecMassSpecColorMapPlotWidget

~DriftSpecMassSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### DriftSpecTracePlotWidget

DriftSpecTracePlotWidget

~DriftSpecTracePlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### Enzyme

Enzyme

Enzyme

~Enzyme

eat

getMiscleavage

getQRegExpRecognitionSite

replaceWildcards

sanityCheck

setMaxPeptideVariantListSize

setMiscleavage

setTakeOnlyFirstWildcard

m_maxPeptideVariantListSize

m_miscleavage

m_recognitionSite

m_takeOnlyFirstWildcard

m_wildCardB

m_wildCardX

m_wildCardZ

##### EnzymeProductInterface

setPeptide

##### ExceptionInterrupted

ExceptionInterrupted

clone

##### ExceptionNotFound

ExceptionNotFound

clone

##### ExceptionNotImplemented

ExceptionNotImplemented

clone

##### ExceptionNotPossible

ExceptionNotPossible

clone

##### ExceptionNotRecognized

ExceptionNotRecognized

clone

##### ExceptionOutOfRange

ExceptionOutOfRange

clone

##### FastaFileIndexer

FastaFileIndexer

FastaFileIndexer

~FastaFileIndexer

close

getSequenceByIndex

makeFastaFileIndexerSPtr

open

parseFastaFile

size

m_fasta_file

m_indexArray

mpa_sequenceTxtIn

##### FastaFileIndexerInterface

close

getSequenceByIndex

open

##### FastaHandlerInterface

setSequence

##### FastaOutputStream

FastaOutputStream

~FastaOutputStream

writeProtein

m_ofastastream

##### FastaReader

FastaReader

~FastaReader

parse

parse

parseOnlyOne

FastaFileIndexer

m_handler

##### FastaSeqHandler

getDescription

getSequence

setSequence

description

sequence

##### FastaWriterInterface

writeProtein

##### FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

~FilterCeilingAmplitudePercentage

buildFilterFromString

filter

getPercentage

name

operator=

toString

m_percentage

##### FilterChargeDeconvolution

###### DataPointInfo

data_point

new_mono_charge_data_point

parent

z1_range

z1_vect

z2_range

z2_vect

z_charge

DataPointInfoSp

FilterChargeDeconvolution

FilterChargeDeconvolution

FilterChargeDeconvolution

~FilterChargeDeconvolution

addDataPointRefByExclusion

addDataPointToList

buildFilterFromString

computeBestChargeOfDataPoint

computeIsotopeDeconvolution

filter

name

toString

transformToMonoChargedForAllDataPoint

m_diffC12C13_z1

m_diffC12C13_z2

m_precisionPtrZ1

m_precisionPtrZ2

##### FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

~FilterComplementIonEnhancer

buildFilterFromString

enhanceComplementMassInRange

filter

name

toString

m_precisionPtr

m_targetMzSum

##### FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

~FilterFloorAmplitudePercentage

buildFilterFromString

filter

getPercentage

name

operator=

toString

m_percentage

##### FilterFloorY

FilterFloorY

FilterFloorY

~FilterFloorY

filter

operator=

##### FilterGreatestY

FilterGreatestY

FilterGreatestY

~FilterGreatestY

filter

getNumberOfPoints

operator=

m_numberOfPoints

##### FilterGreatestYperWindow

FilterGreatestYperWindow

FilterGreatestYperWindow

~FilterGreatestYperWindow

filter

getNumberOfPoints

operator=

m_numberOfPoints

m_xWindowRange

##### FilterHighPass

FilterHighPass

FilterHighPass

~FilterHighPass

filter

operator=

m_passY

##### FilterHighPassPercentage

FilterHighPassPercentage

FilterHighPassPercentage

~FilterHighPassPercentage

filter

operator=

m_ratioPassY

##### FilterInterface

~FilterInterface

filter

##### FilterLocalMaximum

FilterLocalMaximum

FilterLocalMaximum

~FilterLocalMaximum

filter

getHalfWindowSize

m_halfWindowSize

##### FilterLowIntensitySignalRemoval

ApicesSPtr

ClusterApices

TraceCIter

FilterLowIntensitySignalRemoval

FilterLowIntensitySignalRemoval

FilterLowIntensitySignalRemoval

~FilterLowIntensitySignalRemoval

backwardFindApex

buildFilterFromString

detectClusterApices

filter

forwardFindApex

getThreshold

name

nonConstFilter

operator=

reconstructTrace

toString

INTRA_CLUSTER_INTER_PEAK_DISTANCE

m_clusters

m_curApex

m_curIter

m_max

m_min

m_minIntPointCount

m_minIntStdDevFactor

m_minMean

m_minStdDev

m_noiseLevel

m_noiseMean

m_noiseStdDev

m_prevApex

m_prevIter

m_seen_upward_phase

m_threshold

nan

##### FilterLowPass

FilterLowPass

FilterLowPass

~FilterLowPass

filter

operator=

m_passY

##### FilterMorphoAntiSpike

FilterMorphoAntiSpike

FilterMorphoAntiSpike

FilterMorphoAntiSpike

~FilterMorphoAntiSpike

buildFilterFromString

filter

getHalfWindowSize

name

operator=

toString

m_halfWindowSize

##### FilterMorphoBackground

FilterMorphoBackground

FilterMorphoBackground

~FilterMorphoBackground

filter

getFilterMorphoMedian

getFilterMorphoMinMax

operator=

m_filterMorphoMedian

m_filterMorphoMinMax

##### FilterMorphoMax

FilterMorphoMax

FilterMorphoMax

~FilterMorphoMax

getMaxHalfEdgeWindows

getWindowValue

operator=

##### FilterMorphoMaxMin

FilterMorphoMaxMin

FilterMorphoMaxMin

~FilterMorphoMaxMin

filter

getMaxMinHalfEdgeWindows

operator=

m_filterMax

m_filterMin

##### FilterMorphoMean

FilterMorphoMean

FilterMorphoMean

~FilterMorphoMean

getMeanHalfEdgeWindows

getWindowValue

operator=

##### FilterMorphoMedian

FilterMorphoMedian

FilterMorphoMedian

~FilterMorphoMedian

getWindowValue

operator=

##### FilterMorphoMin

FilterMorphoMin

FilterMorphoMin

~FilterMorphoMin

getMinHalfEdgeWindows

getWindowValue

operator=

##### FilterMorphoMinMax

FilterMorphoMinMax

FilterMorphoMinMax

~FilterMorphoMinMax

filter

getMinMaxHalfEdgeWindows

operator=

m_filterMax

m_filterMin

##### FilterMorphoSum

FilterMorphoSum

FilterMorphoSum

~FilterMorphoSum

getWindowValue

operator=

##### FilterMorphoWindowBase

FilterMorphoWindowBase

FilterMorphoWindowBase

~FilterMorphoWindowBase

filter

getHalfWindowSize

getWindowValue

operator=

m_halfWindowSize

##### FilterMzExclusion

FilterMzExclusion

FilterMzExclusion

FilterMzExclusion

~FilterMzExclusion

buildFilterFromString

filter

name

removeTraceInExclusionMargin

toString

m_exclusionPrecision

##### FilterNameInterface

~FilterNameInterface

buildFilterFromString

name

toString

##### FilterNormalizeIntensities

FilterNormalizeIntensities

FilterNormalizeIntensities

FilterNormalizeIntensities

~FilterNormalizeIntensities

buildFilterFromString

filter

name

operator=

toString

m_newYMax

nan

##### FilterOboPsiModSink

FilterOboPsiModSink

~FilterOboPsiModSink

getFirst

getOboPsiModTermList

getOne

setOboPsiModTerm

size

m_oboPsiModTermList

##### FilterOboPsiModTermAccession

FilterOboPsiModTermAccession

~FilterOboPsiModTermAccession

setOboPsiModTerm

m_accession

m_sink

##### FilterOboPsiModTermDiffMono

FilterOboPsiModTermDiffMono

~FilterOboPsiModTermDiffMono

setOboPsiModTerm

m_massRange

m_sink

##### FilterOboPsiModTermLabel

FilterOboPsiModTermLabel

FilterOboPsiModTermLabel

~FilterOboPsiModTermLabel

setOboPsiModTerm

m_labelMatch

m_sink

##### FilterOboPsiModTermName

FilterOboPsiModTermName

~FilterOboPsiModTermName

setOboPsiModTerm

m_nameMatch

m_sink

##### FilterPeakDelta

FilterPeakDelta

FilterPeakDelta

~FilterPeakDelta

filter

##### FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

~FilterQuantileBasedRemoveY

buildFilterFromString

filter

getQuantileThreshold

name

operator=

toString

m_quantile

##### FilterRemoveC13

FilterRemoveC13

FilterRemoveC13

~FilterRemoveC13

addExclusionMap

filter

notExcluded

m_diffC12C13_z1

m_diffC12C13_z2

m_precisionPtr

##### FilterRemoveY

FilterRemoveY

FilterRemoveY

~FilterRemoveY

filter

getValue

operator=

m_valueToRemove

##### FilterResampleKeepGreater

FilterResampleKeepGreater

FilterResampleKeepGreater

~FilterResampleKeepGreater

filter

getThresholdX

operator=

m_value

##### FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

~FilterResampleKeepPointInPolygon

filter

filter

filter

newSelectionPolygonSpec

operator=

m_greatestMz

m_integrationScopeSpecs

m_lowestMz

##### FilterResampleKeepSmaller

FilterResampleKeepSmaller

FilterResampleKeepSmaller

~FilterResampleKeepSmaller

filter

m_value

##### FilterResampleKeepXRange

FilterResampleKeepXRange

FilterResampleKeepXRange

~FilterResampleKeepXRange

filter

operator=

m_maxX

m_minX

##### FilterResampleRemoveXRange

FilterResampleRemoveXRange

FilterResampleRemoveXRange

~FilterResampleRemoveXRange

filter

operator=

m_maxX

m_minX

##### FilterRescaleY

FilterRescaleY

FilterRescaleY

~FilterRescaleY

filter

getDynamicRange

operator=

m_dynamic

##### FilterRoundY

FilterRoundY

FilterRoundY

~FilterRoundY

filter

operator=

##### FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

~FilterSavitzkyGolay

buildFilterFromString

convlv

dmatrix

dvector

filter

filteredData

four1

free_dmatrix

free_dvector

free_ivector

getParameters

ivector

lubksb

ludcmp

name

operator=

realft

runFilter

sgcoeff

toString

twofft

m_params

m_x

m_yf

m_yr

##### FilterScaleFactorY

FilterScaleFactorY

FilterScaleFactorY

~FilterScaleFactorY

filter

getScaleFactorY

operator=

m_factor

##### FilterSuite

FilterSuite

FilterSuite

filter

##### FilterSuiteString

FilterNameType

FilterSuiteString

~FilterSuiteString

addFilterFromString

begin

buildFilterFromString

end

filter

name

toString

m_filterVector

##### FilterTandemDeisotope

FilterTandemDeisotope

FilterTandemDeisotope

filter

m_arbitrary_minimum_mz

m_arbitrary_range_between_isotopes

##### FilterTriangle

FilterTriangle

FilterTriangle

~FilterTriangle

filter

setTriangleSlope

sumAndRemove

m_maxMzRange

m_triangleSlope

##### FrameIdDescr

m_frameId

m_globalScanIndex

m_scanCount

##### GrpExperiment

GrpExperiment

~GrpExperiment

addPostGroupingGrpProteinSpRemoval

addPreGroupingGrpProteinSpRemoval

addSubGroupSp

getGrpGroupSpList

getGrpProteinSp

getGrpProteinSpList

numbering

removeNonInformativeSubGroups

setGrpPeptide

setRemoveNonInformativeSubgroups

startGrouping

m_grpGroupSpList

m_grpPeptideList

m_grpPostGroupingProteinListRemoval

m_grpPreGroupingProteinListRemoval

m_grpProteinList

m_isGroupingStarted

m_isRemoveNonInformativeSubgroups

m_mapPeptides

m_mapProteins

m_remainingGrpProteinList

mp_monitor

##### GrpGroup

GrpGroup

GrpGroup

~GrpGroup

addGroup

addSubGroupSp

check

containsAny

getGroupingId

getGroupNumber

getGrpPeptideSet

getGrpSubGroupSpList

getSubGroupSpList

makeGrpGroupSp

numbering

operator<

removeFirstNonInformativeSubGroup

removeNonInformativeSubGroups

setGroupNumber

GrpExperiment

m_groupNumber

m_mapPeptideToSubGroupSet

m_peptideSet

m_subGroupList

##### GrpGroupingMonitor

GrpGroupingMonitor

~GrpGroupingMonitor

groupingProtein

removingNonInformativeSubGroupsInGroup

startGrouping

startNumberingAllGroups

startRemovingNonInformativeSubGroupsInAllGroups

stopGrouping

stopRemovingNonInformativeSubGroupsInAllGroups

m_currentProtein

m_totalNumberPeptide

m_totalNumberProtein

mp_outStream

##### GrpGroupingMonitorInterface

~GrpGroupingMonitorInterface

groupingProtein

removingNonInformativeSubGroupsInGroup

startGrouping

startNumberingAllGroups

startRemovingNonInformativeSubGroupsInAllGroups

stopGrouping

stopRemovingNonInformativeSubGroupsInAllGroups

##### GrpMapPeptideToGroup

GrpMapPeptideToGroup

GrpMapPeptideToGroup

~GrpMapPeptideToGroup

clear

getGroupList

set

m_mapPeptideToGroup

##### GrpMapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet

~GrpMapPeptideToSubGroupSet

add

check

getSubGroupSet

hasSpecificPeptide

printInfos

remove

size

m_mapPeptideToSubGroupSet

##### GrpPeptide

GrpPeptide

~GrpPeptide

getGroupingId

getGroupNumber

getRank

getSequence

operator<

setGroupNumber

setRank

GrpExperiment

m_groupNumber

m_mass

m_rank

m_sequence

##### GrpPeptideSet

GrpPeptideSet

GrpPeptideSet

GrpPeptideSet

~GrpPeptideSet

addAll

biggerAndContainsAll

contains

containsAll

containsAny

getGrpPeptideList

numbering

operator=

operator==

printInfos

privContainsAll

setGroupNumber

size

GrpMapPeptideToGroup

GrpMapPeptideToSubGroupSet

m_peptidePtrList

##### GrpProtein

const_iterator

GrpProtein

~GrpProtein

GrpProtein

begin

countPlus

end

getAccession

getCount

getDescription

getGroupingId

getGroupNumber

getRank

getSubGroupNumber

operator==

push_back

setGroupNumber

setRank

setSubGroupNumber

strip

GrpExperiment

m_accession

m_count

m_description

m_groupNumber

m_grpPeptidePtrList

m_rank

m_subGroupNumber

##### GrpSubGroup

GrpSubGroup

GrpSubGroup

~GrpSubGroup

getFirstAccession

getGroupingId

getGroupNumber

getGrpProteinList

getPeptideSet

getSubGroupNumber

includes

makeGrpSubGroupSp

maxCount

merge

numbering

operator<

peptideListSize

setGroupNumber

setSubGroupNumber

m_groupNumber

m_grpProteinPtrList

m_peptidePtrList

m_subGroupNumber

##### GrpSubGroupSet

GrpSubGroupSet

GrpSubGroupSet

~GrpSubGroupSet

add

addAll

begin

contains

end

erase

printInfos

remove

size

GrpGroup

m_grpSubGroupPtrList

##### HttpButton

HttpButton

~HttpButton

getChEBIUrl

getOlsUrl

getPubMedUrl

getRESIDUrl

getUnimodUrl

mousePressEvent

setText

##### IntegrationScope

IntegrationScope

IntegrationScope

IntegrationScope

IntegrationScope

~IntegrationScope

contains

getBottomMostPoint

getDataKindX

getLeftMostPoint

getPoint

getRightMostPoint

getTopMostPoint

getWidth

is1D

is2D

isRectangle

isRhomboid

operator=

range

reset

setDataKindX

setPoint

setWidth

toString

transpose

update

m_dataKindX

m_point

m_width

##### IntegrationScopeBase

IntegrationScopeBase

IntegrationScopeBase

~IntegrationScopeBase

contains

getBottomMostPoint

getBottomMostPoints

getDataKindX

getDataKindY

getHeight

getLeftMostBottomPoint

getLeftMostPoint

getLeftMostPoints

getLeftMostTopPoint

getPoint

getPoints

getRhombHorizontalSize

getRhombVerticalSize

getRightMostBottomPoint

getRightMostPoint

getRightMostPoints

getRightMostTopPoint

getTopMostPoint

getTopMostPoints

getWidth

is1D

is2D

isRectangle

isRhomboid

range

reset

setDataKindX

setDataKindY

toString

transpose

##### IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

~IntegrationScopeRect

contains

getBottomMostPoint

getDataKindX

getDataKindY

getHeight

getTopMostPoint

is1D

is2D

isRectangle

isRhomboid

operator=

operator=

range

reset

setDataKindX

setDataKindY

setHeight

toString

transpose

update

update

m_dataKindY

m_height

##### IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

~IntegrationScopeRhomb

addPoint

contains

getBottomMostPoint

getBottomMostPoints

getDataKindX

getDataKindY

getHeight

getLeftMostBottomPoint

getLeftMostPoint

getLeftMostPoints

getLeftMostTopPoint

getPoint

getPoints

getRhombHorizontalSize

getRhombVerticalSize

getRightMostBottomPoint

getRightMostPoint

getRightMostPoints

getRightMostTopPoint

getTopMostPoint

getTopMostPoints

getWidth

is1D

is2D

isRectangle

isRhomboid

operator=

range

reset

setDataKindX

setDataKindY

toString

transpose

m_dataKindX

m_dataKindY

m_points

##### IntegrationScopeSpec

IntegrationScopeSpec

IntegrationScopeSpec

IntegrationScopeSpec

operator=

toString

dataKind

integrationScopeSPtr

##### Ion

Ion

~Ion

getMass

getMz

##### IonIsotopeRatioScore

IonIsotopeRatioScore

~IonIsotopeRatioScore

getIonIsotopeRatioScore

m_ionIsotopeRatioScore

##### IonMobilityGrid

IonMobilityGrid

~IonMobilityGrid

computeCorrections

getMapCorrectionsStart

getMapDiferrencesStart

storeObservedIdentityBetween

translateXicCoordFromTo

m_mapCorrectionsStart

m_mapCorrectionsStop

m_mapDiferrencesStart

m_mapDiferrencesStop

##### LinearRegression

LinearRegression

LinearRegression

getCoefficientOfDetermination

getIntercept

getNrmsd

getRmsd

getSize

getSlope

getYfromX

m_data

m_intercept

m_slope

##### MapTrace

MapTrace

MapTrace

MapTrace

MapTrace

MapTrace

~MapTrace

initialize

initialize

insertOrUpdate

insertOrUpdate

makeMapTraceCstSPtr

makeMapTraceSPtr

operator=

toString

toTrace

xValues

yValues

##### MassDataCombinerInterface

Iterator

MassDataCombinerInterface

~MassDataCombinerInterface

combine

combine

combine

getDecimalPlaces

setDecimalPlaces

m_decimalPlaces

##### MassSpecTracePlotContext

MassSpecTracePlotContext

MassSpecTracePlotContext

~MassSpecTracePlotContext

operator=

operator=

toString

m_lastMr

m_lastMz

m_lastResolvingPower

m_lastTicIntensity

m_lastZ

##### MassSpecTracePlotWidget

MassSpecTracePlotWidget

MassSpecTracePlotWidget

~MassSpecTracePlotWidget

computeResolvingPower

deconvolute

deconvoluteChargedState

deconvoluteIsotopicCluster

getChargeMinimalFractionalPart

getChargeStateEnvelopePeakSpan

keyPressEvent

keyPressEventSignal

keyReleaseEvent

massDeconvolutionSignal

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseEventSignal

mouseReleaseHandler

refreshBaseContext

resolvingPowerComputationSignal

setChargeMinimalFractionalPart

setChargeStateEnvelopePeakSpan

m_chargeMinimalFractionalPart

m_chargeStateEnvelopePeakSpan

m_context

##### MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

~MassSpectrum

debugPrintValues

equals

filterSum

makeMassSpectrumCstSPtr

makeMassSpectrumSPtr

massSpectrumFilter

maxIntensityDataPoint

minIntensityDataPoint

operator=

operator=

operator=

operator=

sortMz

tic

tic

totalIonCurrent

##### MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

~MassSpectrumCombiner

binCount

binsAsString

findBin

getBins

setBins

m_bins

##### MassSpectrumFilterGreatestItensities

MassSpectrumFilterGreatestItensities

MassSpectrumFilterGreatestItensities

~MassSpectrumFilterGreatestItensities

filter

operator=

m_filterGreatestY

##### MassSpectrumFilterInterface

~MassSpectrumFilterInterface

filter

##### MassSpectrumFilterResampleKeepMzRange

MassSpectrumFilterResampleKeepMzRange

MassSpectrumFilterResampleKeepMzRange

~MassSpectrumFilterResampleKeepMzRange

filter

m_filterRange

##### MassSpectrumFilterResampleRemoveMzRange

MassSpectrumFilterResampleRemoveMzRange

MassSpectrumFilterResampleRemoveMzRange

~MassSpectrumFilterResampleRemoveMzRange

filter

m_filterRange

##### MassSpectrumId

MassSpectrumId

MassSpectrumId

MassSpectrumId

MassSpectrumId

~MassSpectrumId

getMsRunIdCstSPtr

getNativeId

getSpectrumIndex

isValid

operator=

operator==

setMsRunId

setNativeId

setSpectrumIndex

toString

m_nativeId

m_spectrumIndex

mcsp_msRunId

##### MassSpectrumLineData

dash

ionizationMode

ionSourceType

msLevel

mz_range

peakCount

peakList

peakShapeType

retentionTime

##### MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

~MassSpectrumMinusCombiner

combine

combine

operator=

##### MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

~MassSpectrumPlusCombiner

combine

combine

operator=

##### MassSpectrumWidget

MassSpectrumWidget

~MassSpectrumWidget

clearData

computeIsotopeMassList

highlightPrecursorPeaks

ionChanged

mzChanged

mzChangeEvent

peakChanged

peakChangeEvent

peptideAnnotate

plot

rescale

savePdf

setIonList

setMassSpectrumCstSPtr

setMaximumIsotopeNumber

setMaximumIsotopeRank

setMs1Precision

setMs2Precision

setMsLevel

setPeptideCharge

setPeptideSp

setQualifiedMassSpectrum

setVisibleMassDelta

toQPaintDevice

QCPSpectrum

_custom_plot

_ion_list

_is_visible_mass_delta

_isotope_mass_list

_max_isotope_number

_max_isotope_rank

_ms_level

_p_mouse_peak

_p_ms1_precision

_p_ms2_precision

_peak_ion_isotope_match_list

_peptide_charge

_peptide_sp

_spectrum_sp

_tag_nmost_intense

##### MgfOutput

MgfOutput

~MgfOutput

close

write

mpa_outputStream

##### MorpheusScore

MorpheusScore

~MorpheusScore

getMorpheusScore

_morpheus_score

##### MsDataFormatEnumStr

toString

##### MsFileAccessor

MsFileAccessor

MsFileAccessor

~MsFileAccessor

buildMsRunReaderSPtr

buildMsRunReaderSPtr

buildTimsMsRunReaderMs2SPtr

getFileFormat

getFileName

getFileReaderType

getMsRunIds

getMsRunReaderSPtrByRunId

getOboPsiModTermFileFormat

getOboPsiModTermNativeIDFormat

getpreferredFileReaderType

getSelectedMsRunId

msRunReaderSPtr

msRunReaderSPtr

msRunReaderSPtrForSelectedMsRunId

setPreferredFileReaderType

setSelectedMsRunId

m_fileFormat

m_fileName

m_fileReaderType

m_oboPsiModTermNativeIDFormat

m_preferredFileReaderTypeMap

m_xmlPrefix

mcsp_selectedMsRunId

##### MsFileReader

MsFileReader

~MsFileReader

getFileFormat

getMsRunIds

m_fileFormat

m_fileName

MsRunAlignment

##### MsRunDataSetTree

DoubleNodeVectorMap

NodeVector

QualMassSpectraVector

MsRunDataSetTree

~MsRunDataSetTree

accept

accept

addDataSetQualMassSpectraInsideDtRtRange

addDataSetTreeNodesInsideDtRtRange

addMassSpectrum

addMassSpectrum

addMassSpectrum

depth

documentNodeInDtRtMap

findNode

findNode

flattenedView

flattenedViewMsLevel

getIndexNodeMap

getRootNodes

getSpectrumCount

indexNodeMapSize

massSpectrumIndex

massSpectrumIndex

precursorNodeByProductSpectrumIndex

precursorNodesByPrecursorMz

productNodesByPrecursorSpectrumIndex

removeDataSetQualMassSpectraOutsideDtRtRange

removeDataSetTreeNodesOutsideDtRtRange

size

m_dtDoubleNodeVectorMap

m_indexNodeMap

m_rootNodes

m_rtDoubleNodeVectorMap

m_spectrumCount

mcsp_msRunId

##### MsRunDataSetTreeNode

MsRunDataSetTreeNode

MsRunDataSetTreeNode

MsRunDataSetTreeNode

~MsRunDataSetTreeNode

accept

depth

findNode

findNode

flattenedView

flattenedViewChildrenOnly

flattenedViewMsLevelNodes

getParent

getQualifiedMassSpectrum

hasParent

operator=

precursorIonNodesByPrecursorMz

productNodesByPrecursorMz

setParent

setQualifiedMassSpectrum

size

toString

MsRunDataSetTree

m_children

mcsp_massSpectrum

mp_parent

##### MsRunDataSetTreeNodeVisitorInterface

setNodesToProcessCount

shouldStop

visit

##### MsRunId

MsRunId

MsRunId

MsRunId

MsRunId

~MsRunId

getFileName

getMsDataFormat

getRunId

getSampleName

getXmlId

isValid

operator=

operator==

setFileName

setMsDataFormat

setRunId

setSampleName

setXmlId

toString

m_fileName

m_mzFormat

m_runId

m_sampleName

m_xmlId

##### MsRunQualifiedSpectrumLoader

MsRunQualifiedSpectrumLoader

~MsRunQualifiedSpectrumLoader

clear

getQualifiedMassSpectrumList

needPeakList

setQualifiedMassSpectrum

spectrumListHasSize

m_qualifiedSpectrumList

##### MsRunReadConfig

MsRunReadConfig

MsRunReadConfig

~MsRunReadConfig

acceptMsLevel

acceptRetentionTimeInSeconds

getMsLevels

getMsLevelsAsString

getParameterValue

getRetentionTimeEndInSeconds

getRetentionTimeStartInSeconds

needPeakList

operator=

reset

setMsLevels

setNeedPeakList

setParameterValue

setRetentionTimeEndInSeconds

setRetentionTimeStartInSeconds

toString

m_isPeakListNeeded

m_msLevels

m_paramsMap

m_retentionTimeEndSeconds

m_retentionTimeStartSeconds

##### MsRunReader

MsRunReader

MsRunReader

~MsRunReader

accept

acquireDevice

getMsRunId

getRetentionTimeLine

getTicChromatogram

hasScanNumbers

initialize

isMonoThread

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

scanNumber2SpectrumIndex

setMonoThread

spectrumListSize

MsFileAccessor

m_isMonoThread

mcsp_msRunId

mpa_multiMapScanNumber

##### MsRunReaderRetentionTimeLine

MsRunReaderRetentionTimeLine

~MsRunReaderRetentionTimeLine

getRetentionTimeLine

needPeakList

setQualifiedMassSpectrum

m_retention_time_list

##### MsRunReaderScanNumberMultiMap

MsRunReaderScanNumberMultiMap

~MsRunReaderScanNumberMultiMap

getSpectrumIndexFromScanNumber

needPeakList

setQualifiedMassSpectrum

m_mmap_scan2index

##### MsRunReaderTicChromatogram

MsRunReaderTicChromatogram

~MsRunReaderTicChromatogram

getTicChromatogram

needPeakList

setQualifiedMassSpectrum

m_ticChromMapTrace

##### MsRunRetentionTime

###### PeptideMs2Point

entityHash

precursorIntensity

retentionTime

###### ComputeRetentionTimeReference

maximum_intensity

weighted_intensity

last

MsRunRetentionTime

MsRunRetentionTime

~MsRunRetentionTime

addPeptideAsSeamark

addPeptideAsSeamark

align

computeSeamarks

correctNewTimeValues

getAlignedRetentionTimeVector

getBackRetentionTimeReference

getCommonDeltaRt

getCommonDeltaRt

getCommonSeamarksDeltaRt

getFrontRetentionTimeReference

getMs1MeanFilter

getMs1RetentionTimeVector

getMs2MeanFilter

getMs2MedianFilter

getMsRunId

getMsRunReaderSPtr

getNumberOfCorrectedValues

getSeamarks

getSeamarksReferences

isAligned

linearRegressionMs2toMs1

setAlignedRetentionTimeVector

setMs1MeanFilter

setMs2MeanFilter

setMs2MedianFilter

translateAligned2OriginalRetentionTime

translateOriginal2AlignedRetentionTime

m_alignedRetentionTimeVector

m_allMs2Points

m_ms1MeanFilter

m_ms1RetentionTimeVector

m_ms2MeanFilter

m_ms2MedianFilter

m_retentionTimeReferenceMethod

m_seamarks

m_valuesCorrected

mcsp_msrunId

msp_msrunReader

##### MsRunRetentionTimeSeamarkPoint

entityHash

intensity

retentionTime

##### MsRunSimpleStatistics

getMsLevelCount

getTotalCount

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_countMsLevelSpectrum

##### MsRunSlice

MsRunSlice

MsRunSlice

~MsRunSlice

appendToStream

clear

getSliceNumber

getSpectrum

getSpectrum

makeMsRunSliceSp

setSize

setSliceNumber

setSpectrum

size

m_sliceNumber

m_spectrumList

##### MsRunXicExtractor

###### MsRunXicExtractorPoints

rt

spectrum_index

###### MsRunXicExtractorReadPoints

MsRunXicExtractorReadPoints

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_msrun_points

MsRunXicExtractor

~MsRunXicExtractor

MsRunXicExtractor

extractOneXicCoord

getXicFromPwizMSDataFile

protectedExtractXicCoordSPtrList

m_msrun_points

MsRunXicExtractorFactory

##### MsRunXicExtractorDisk

MsRunXicExtractorDisk

MsRunXicExtractorDisk

~MsRunXicExtractorDisk

MsRunXicExtractorDisk

acquireSlices

appendSliceOnDisk

endPwizRead

extractOneXicCoord

prepareExtractor

protectedExtractXicCoordSPtrList

serializeMsRun

storeSlices

unserializeSlice

m_maxMz

m_minMz

m_msRunSliceListCache

m_mutex

m_retentionTimeList

m_rtSize

m_temporaryDirectory

mpa_temporaryDirectory

MsRunXicExtractorFactory

##### MsRunXicExtractorDiskBuffer

MsRunXicExtractorDiskBuffer

~MsRunXicExtractorDiskBuffer

MsRunXicExtractorDiskBuffer

appendSliceInBuffer

endPwizRead

flushBufferOnDisk

storeSlices

m_bufferMaxSize

m_bufferSize

m_sliceBufferMap

MsRunXicExtractorFactory

##### MsRunXicExtractorFactory

MsRunXicExtractorFactory

~MsRunXicExtractorFactory

buildMsRunXicExtractorSp

getInstance

setMsRunXicExtractorFactoryType

setTmpDir

m_instance

m_tmpDirName

m_type

##### MsRunXicExtractorInterface

MsRunXicExtractorInterface

MsRunXicExtractorInterface

~MsRunXicExtractorInterface

extractXicCoordSPtrList

extractXicCoordSPtrListParallelized

getMsRunId

getMsRunReaderSPtr

postExtractionProcess

protectedExtractXicCoordSPtrList

setPostExtractionTraceFilterCstSPtr

setRetentionTimeAroundTarget

setXicExtractMethod

m_retentionTimeAroundTarget

m_xicExtractMethod

mcsp_postExtractionTraceFilter

msp_msrun_reader

##### MzCalibrationInterface

MzCalibrationInterface

~MzCalibrationInterface

getMzFromTofIndex

getTofFromTofIndex

getTofFromTofIndex

getTofIndexFromMz

operator=

operator==

m_digitizerDelay

m_digitizerTimebase

m_mzCalibrationArr

##### MzCalibrationModel1

MzCalibrationModel1

~MzCalibrationModel1

getMzFromTofIndex

getTofIndexFromMz

##### MzCalibrationModel1Cached

MzCalibrationModel1Cached

~MzCalibrationModel1Cached

getMzFromTofIndex

m_arrMasses

m_max

##### MzCalibrationStore

MzCalibrationStore

~MzCalibrationStore

getInstance

m_mapMzCalibrationSPtr

##### MzIdentMlWriter

MzIdentMlWriter

~MzIdentMlWriter

toXmlDouble

toXmlMass

toXmlMassDelta

writeCvList

writeCvParam

writeCvParam

writeCvParam

writeCvParamUo

writeCvParamUo

writeDBSequence

writeDBSequence

writeStartMzIdentMlDocument

writeUserParam

writeUserParam

writeUserParam

writeUserParam

##### MzIntegrationParams

MzIntegrationParams

MzIntegrationParams

MzIntegrationParams

~MzIntegrationParams

createArbitraryBins

createBins

createBins

createDataBasedBins

getBinningType

getBinSizeDivisor

getDecimalPlaces

getGreatestMz

getPrecision

getSmallestMz

hasValidMzRange

isRemoveZeroValDataPoints

isValid

operator=

reset

setBinningType

setBinSizeDivisor

setDecimalPlaces

setGreatestMz

setPrecision

setRemoveZeroValDataPoints

setSmallestMz

toString

updateGreatestMz

updateSmallestMz

m_binningType

m_binSizeDivisor

m_decimalPlaces

m_greatestMz

m_removeZeroValDataPoints

m_smallestMz

mp_precision

##### MzRange

MzRange

MzRange

MzRange

MzRange

~MzRange

contains

getMz

lower

operator*=

operator+=

operator=

toString

upper

m_delta

m_mz

##### MzxmlOutput

###### Translater

Translater

~Translater

needPeakList

setQualifiedMassSpectrum

mp_output

MzxmlOutput

~MzxmlOutput

close

getPrecursorScanNumber

getScanNumber

getScanNumberFromNativeId

maskMs1

setReadAhead

write

write

writeHeader

writeQualifiedMassSpectrum

m_isReadAhead

m_monitor

m_ms1IsMasked

mpa_outputStream

##### OboChooserWidget

OboChooserWidget

~OboChooserWidget

getOboPsiModTermSelected

isOboTermSelected

setMzTarget

setPrecision

ui

##### OboListModel

###### OboPsiModHandler

OboPsiModHandler

~OboPsiModHandler

setOboPsiModTerm

mp_parent

OboListModel

~OboListModel

data

getOboPsiModTerm

loadPsiMod

rowCount

m_oboPsiModTermList

##### OboListProxyModel

OboListProxyModel

~OboListProxyModel

filterAcceptsRow

filterMzPrecision

lessThan

m_mzTarget

m_precisionPtr

mp_sourceModel

##### OboListWidget

OboListWidget

~OboListWidget

filterMzPrecision

getMzTarget

getPrecisionPtr

oboTermChanged

onFilterChanged

onFilterChanged

onFilterChanged

onSelectionChanged

mpa_oboListModel

mpa_oboListProxyModel

ui

##### OboPsiMod

OboPsiMod

~OboPsiMod

parse

m_handler

m_term

##### OboPsiModHandlerInterface

setOboPsiModTerm

##### OboPsiModTerm

OboPsiModTerm

~OboPsiModTerm

OboPsiModTerm

clearTerm

isA

isValid

operator=

parseLine

m_accession

m_definition

m_diffFormula

m_diffMono

m_findExactPsiModLabel

m_findRelatedPsiMsLabel

m_firstParse

m_formula

m_isA

m_massMono

m_name

m_origin

m_psiModLabel

m_psiMsLabel

OboPsiMod

##### OboTermForm

OboTermForm

~OboTermForm

displayOboTerm

getOboPsiModTerm

isOboTerm

parseDefinitionLabel

m_findExternalLinks

m_oboPsiModTerm

ui

##### PappsoException

PappsoException

PappsoException

~PappsoException

clone

qwhat

raise

what

m_message

m_stdMessage

##### PeakIonIsotopeMatch

PeakIonIsotopeMatch

PeakIonIsotopeMatch

PeakIonIsotopeMatch

~PeakIonIsotopeMatch

getPeptideNaturalIsotopeAverageSp

operator=

toString

_naturalIsotopeAverageSp

##### PeakIonMatch

PeakIonMatch

PeakIonMatch

PeakIonMatch

~PeakIonMatch

getCharge

getPeak

getPeptideFragmentIonSp

getPeptideIonDirection

getPeptideIonType

operator=

toString

_charge

_ion_sp

_peak

##### Peptide

Peptide

~Peptide

Peptide

Peptide

addAaModification

addAaModificationOnAllAminoAcid

begin

begin

countModificationOnAa

end

end

getAa

getAaPositionList

getAaPositionList

getConstAa

getInternalCterModification

getInternalNterModification

getLiAbsoluteString

getMass

getMass

getModificationPositionList

getModificationPositionList

getNumberOfAtom

getNumberOfIsotope

getNumberOfModification

getSequence

isPalindrome

makeNoConstPeptideSp

makePeptideSp

rbegin

removeAaModification

removeCterAminoAcid

removeInternalCterModification

removeInternalNterModification

removeNterAminoAcid

rend

replaceAaModification

replaceLeucineIsoleucine

reverse

rotate

setInternalCterModification

setInternalNterModification

size

toAbsoluteString

toProForma

toString

operator<

operator==

PeptideProFormaParser

m_aaVec

m_proxyMass

##### PeptideBuilder

PeptideBuilder

~PeptideBuilder

addFixedAaModification

setPeptide

setSink

m_fixedModificationList

m_sink

##### PeptideFixedModificationBuilder

PeptideFixedModificationBuilder

~PeptideFixedModificationBuilder

addAa

setPeptideSp

setProtCter

setProtElse

setProtNter

setSink

m_aaModificationList

m_isProtCterMod

m_isProtElseMod

m_isProtNterMod

m_sink

mp_mod

##### PeptideFragment

PeptideFragment

PeptideFragment

PeptideFragment

~PeptideFragment

getMass

getNumberOfAtom

getNumberOfIsotope

getPeptideIonDirection

getPeptideIonDirectionName

getPeptideSp

getSequence

isPalindrome

size

m_direction

m_mass

m_nterCterCleavage

m_size

msp_peptide

##### PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

~PeptideFragmentIon

getCompletePeptideIonName

getMass

getName

getNumberOfAtom

getNumberOfIsotope

getNumberOfNeutralPhosphoLoss

getPeptideFragmentSp

getPeptideIonColor

getPeptideIonDirection

getPeptideIonDirection

getPeptideIonName

getPeptideIonName

getPeptideIonType

getSequence

isPalindrome

makePeptideFragmentIonSp

size

m_ionType

m_mass

m_neutralPhosphoLossNumber

msp_fragment

##### PeptideFragmentIonListBase

IonList

PeptideFragmentIonListBase

PeptideFragmentIonListBase

~PeptideFragmentIonListBase

begin

end

getCIDionList

getETDionList

getIonList

getPeptideFragmentIonList

getPeptideFragmentIonSp

getPeptideFragmentIonSp

getPeptideFragmentIonSp

getPeptideFragmentList

getPeptideSp

getPhosphorylationNumber

makePeptideFragmentIonListBaseSp

size

m_ionList

m_phosphorylationNumber

msp_peptide

msp_peptide_fragment_ion_list

##### PeptideInterface

getFormula

getName

getSequence

getSequenceLi

isPalindrome

matchPeak

size

##### PeptideIsotopeSpectrumMatch

const_iterator

PeptideIsotopeSpectrumMatch

PeptideIsotopeSpectrumMatch

PeptideIsotopeSpectrumMatch

~PeptideIsotopeSpectrumMatch

begin

dropPeaksLackingMonoisotope

end

getBestPeakIterator

getPeakIonIsotopeMatchList

size

_peak_ion_match_list

_precision

##### PeptideMethioninRemove

PeptideMethioninRemove

~PeptideMethioninRemove

setPeptide

setSink

m_isPotential

m_sink

##### PeptideModificatorBase

PeptideModificatorBase

~PeptideModificatorBase

getModificationPositionList

getModificationPositionList

setModificationPattern

m_pattern

##### PeptideModificatorInterface

~PeptideModificatorInterface

setPeptideSp

##### PeptideModificatorPipeline

PeptideModificatorPipeline

PeptideModificatorPipeline

~PeptideModificatorPipeline

addFixedCterModificationString

addFixedModificationString

addFixedNterModificationString

addLabeledModificationString

addPotentialCterModificationString

addPotentialModificationString

addPotentialNterModificationString

parseFixedModification

parseLabeledModification

parsePotentialModification

privAddFixedModificationString

privAddPotentialModificationString

setPeptide

setPeptideSp

setSink

m_pepModificatorPtrList

m_sink

mp_firstModificator

mp_lastPeptideSinkInterface

mp_peptideModificatorTee

##### PeptideModificatorTee

PeptideModificatorTee

PeptideModificatorTee

~PeptideModificatorTee

addModificator

setPeptideSp

m_peptideModPtrList

##### PeptideNaturalIsotope

PeptideNaturalIsotope

PeptideNaturalIsotope

~PeptideNaturalIsotope

getIntensityRatio

getIsotopeMap

getIsotopeNumber

getMass

getNumberOfAtom

getNumberOfIsotope

getSequence

isPalindrome

size

m_mapIsotope

m_mass

m_peptide

m_ratio

##### PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

~PeptideNaturalIsotopeAverage

getCharge

getComponents

getIntensityRatio

getIsotopeNumber

getIsotopeRank

getMz

getPeptideInterfaceSp

getPrecision

isEmpty

makePeptideNaturalIsotopeAverageSp

matchPeak

recursiveDepletion

toString

m_abundanceRatio

m_averageMz

m_isotopeLevel

m_isotopeRank

m_peptideNaturalIsotopeSpList

m_z

mcsp_peptideSp

mp_precision

##### PeptideNaturalIsotopeList

const_iterator

PeptideNaturalIsotopeList

PeptideNaturalIsotopeList

~PeptideNaturalIsotopeList

begin

end

getByIntensityRatio

getByIsotopeNumber

getIntensityRatioPerIsotopeNumber

getPeptideInterfaceSp

makePeptideNaturalIsotopeListSp

size

msp_peptide

msp_peptide_natural_isotope_list

##### PeptideProFormaParser

parseNoConstString

parseString

parseStringToPeptide

_rx_modmass

_rx_psimod

##### PeptideRawFragmentMasses

ionDeltatMzMassMap

PeptideRawFragmentMasses

~PeptideRawFragmentMasses

getDeltaMass

pushBackIonMasses

pushBackIonMz

pushBackMatchSpectrum

m_cumulativeCterMasses

m_cumulativeNterMasses

m_ionDeltaMz

##### PeptideSemiEnzyme

PeptideSemiEnzyme

~PeptideSemiEnzyme

setPeptide

setSink

m_sink

##### PeptideSinkInterface

setSink

##### PeptideSizeFilter

PeptideSizeFilter

~PeptideSizeFilter

setPeptide

setSink

m_maxSize

m_minSize

m_sink

##### PeptideSpectrumMatch

const_iterator

PeptideSpectrumMatch

PeptideSpectrumMatch

PeptideSpectrumMatch

PeptideSpectrumMatch

~PeptideSpectrumMatch

begin

contains

countTotalMatchedIons

end

getBestPeakIterator

getIonTypeCountArray

privMatchIonList

size

_ion_type_count

_peak_ion_match_list

_precision

##### PeptideSpSinkInterface

setSink

##### PeptideStrParser

parseNoConstString

parseString

parseStringToPeptide

_mod_parser

_rx_modmass

_rx_psimod

##### PeptideVariableModificationBuilder

PeptideVariableModificationBuilder

~PeptideVariableModificationBuilder

addAa

next_combination

setMaxNumberMod

setMinNumberMod

setModificationCounter

setPeptideSp

setProtCter

setProtElse

setProtNter

setSink

m_aaModificationList

m_isProtCterMod

m_isProtElseMod

m_isProtNterMod

m_maxNumberMod

m_minNumberMod

m_modificationCount

m_sink

mp_mod

##### PeptideVariableModificationReplacement

PeptideVariableModificationReplacement

~PeptideVariableModificationReplacement

replaceModificationsAtPosition

setPeptideSp

mp_modAfter

##### PpmPrecision

PpmPrecision

~PpmPrecision

delta

toString

unit

PrecisionFactory

##### PrecisionBase

PrecisionBase

delta

getNominal

toString

unit

m_nominal

##### PrecisionFactory

MapDaltonPrecision

MapPpmPrecision

MapResPrecision

fromString

getDaltonInstance

getPpmInstance

getPrecisionPtrFractionInstance

getPrecisionPtrInstance

getResInstance

m_mapDalton

m_mapPpm

m_mapRes

##### PrecisionWidget

PrecisionWidget

~PrecisionWidget

getPrecision

precisionChanged

setCurrentIndex

setDaltonValueChanged

setPpmValueChanged

setPrecision

setResValueChanged

m_oldIndex

mp_daltonValueSpinBox

mp_ppmValueSpinBox

mp_precisionDalton

mp_precisionPpm

mp_precisionRes

mp_resValueSpinBox

mp_unitComboBox

##### PrecursorIonData

PrecursorIonData

charge

intensity

mz

##### Protein

Protein

Protein

Protein

~Protein

getAccession

getDescription

getMass

getSequence

makeProteinSp

operator==

removeTranslationStop

reverse

setAccession

setDescription

setSequence

size

m_accession

m_description

m_length

m_removeTranslationStopRegExp

m_sequence

##### ProteinIntegerCode

ProteinIntegerCode

ProteinIntegerCode

~ProteinIntegerCode

computePeptideCodeFragments

convolution

convolutionKernel

getPeptideCodedFragment

getProteinSp

getSeqAaCode

match

m_peptideCodedFragments

m_seqAaCode

msp_protein

##### ProteinPresenceAbsenceMatrix

###### ProteinPresenceAbsenceMatrixElement

absent

present

ProteinPresenceAbsenceMatrix

ProteinPresenceAbsenceMatrix

~ProteinPresenceAbsenceMatrix

convolution

convolutionKernel

fillMatrix

getPresenceAbsenceMatrix

getScore

operator=

m_presenceAbsenceMatrix

##### PsmFeatures

PsmFeatures

~PsmFeatures

countMatchedIonComplementPairs

findComplementIonPairs

getAaSequenceCoverage

getComplementPairsAaSequenceCoverage

getIntensityOfMatchedIon

getIonIsotopeLinearRegression

getIonPairPrecursorMassDelta

getMatchedMzDiffMean

getMatchedMzDiffSd

getMaxConsecutiveIon

getMaxIntensityMatchedIonComplementPairPrecursorMassDelta

getMaxIntensityPeakIonMatch

getNumberOfMatchedIons

getPeakIonPairs

getTotalIntensity

getTotalIntensityOfMatchedIonComplementPairs

getTotalIntensityOfMatchedIons

setPeptideSpectrumCharge

m_ionList

m_matchedMzDiffMean

m_matchedMzDiffMedian

m_matchedMzDiffSd

m_ms2precision

m_parentCharge

m_peakIonPairs

m_precursorTheoreticalMass

m_precursorTheoreticalMz

m_spectrumSumIntensity

msp_filterChargeDeconvolution

msp_filterKeepGreater

msp_filterMzExclusion

msp_peptide

msp_peptideSpectrumMatch

##### PwizMsFileReader

PwizMsFileReader

~PwizMsFileReader

getFileFormat

getMsRunIds

initialize

m_msDataPtrVector

##### PwizMsRunReader

PwizMsRunReader

~PwizMsRunReader

accept

acquireDevice

getOboPsiModTermNativeIDFormat

getPwizSpectrumPtr

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

processDriftTime

processRetentionTime

qualifiedMassSpectrum

qualifiedMassSpectrumFromPwizMSData

qualifiedMassSpectrumFromPwizSpectrumPtr

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

readSpectrumCollectionWithMsrunReadConfig

releaseDevice

setGlobalLocaleToCurrentOs

setGlobalLocaleToEnglish

spectrumListSize

MsFileAccessor

m_hasScanNumbers

m_mutex

msp_msData

##### QCPSpectrum

QCPSpectrum

~QCPSpectrum

addMassDelta

addMs1IsotopePattern

addPeakIonIsotopeMatch

clearData

getMostIntensePeakBetween

getNearestPeakBetween

highlightPrecursorPeaks

keyPressEvent

keyReleaseEvent

mouseMoveEvent

mousePressEvent

mouseReleaseEvent

rescale

setMzRangeChanged

setSpectrumP

MassSpectrumWidget

_bar_width

_click

_control_key

_intensity_range

_map_ion_type_bars

_mass_delta_range

_mz_range

_old_x

_old_y

_p_delta_axis_rect

_p_delta_graph

_p_peak_bars

_p_peak_bars_isotope

_p_spectrum

_parent

mp_peak_bars_precursor

##### QCPXic

QCPXic

~QCPXic

addMsMsEvent

addXicP

addXicPeakList

clear

clearXicPeakBorders

drawXicPeakBorders

getRetentionTimeFromSecondsToLocal

keyPressEvent

keyReleaseEvent

mouseMoveEvent

mousePressEvent

mouseReleaseEvent

rescale

setName

setRtRangeChanged

xAxisToSeconds

XicWidget

_click

_colours

_control_key

_current_ms2_event

_graph_color

_graph_peak_border_list

_graph_peak_surface_list

_intensity_range

_map_xic_graph

_mouse_move

_old_x

_old_y

_parent

_rt_range

##### QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

~QualifiedMassSpectrum

appendPrecursorIonData

cloneMassSpectrumSPtr

getDtInMilliSeconds

getMassSpectrumCstSPtr

getMassSpectrumId

getMassSpectrumId

getMassSpectrumSPtr

getMsLevel

getMzSortedPrecursorDataChargeValuesAsString

getMzSortedPrecursorDataMzValuesAsString

getParameterValue

getPrecursorCharge

getPrecursorDataChargeValuesAsString

getPrecursorDataChargeValuesAsString

getPrecursorDataMzValuesAsString

getPrecursorDataMzValuesAsString

getPrecursorIntensity

getPrecursorIonData

getPrecursorIonDataSortedWithMz

getPrecursorMass

getPrecursorMz

getPrecursorNativeId

getPrecursorSpectrumIndex

getRtInMinutes

getRtInSeconds

isEmptyMassSpectrum

makeQualifiedMassSpectrumCstSPtr

makeQualifiedMassSpectrumSPtr

operator=

setDtInMilliSeconds

setEmptyMassSpectrum

setMassSpectrumId

setMassSpectrumSPtr

setMsLevel

setParameterValue

setPrecursorNativeId

setPrecursorSpectrumIndex

setRtInSeconds

size

toString

m_dt

m_isEmptyMassSpectrum

m_massSpectrumId

m_msLevel

m_paramsMap

m_precursorIonData

m_precursorNativeId

m_precursorSpectrumIndex

m_rt

msp_massSpectrum

##### QualifiedXic

QualifiedXic

~QualifiedXic

QualifiedXic

getMz

getXicCstSPtr

getXicSPtr

m_msRunId

m_mz

mp_precision

msp_xic

##### ResPrecision

ResPrecision

~ResPrecision

delta

toString

unit

PrecisionFactory

##### SavGolParams

SavGolParams

SavGolParams

SavGolParams

initialize

initialize

initialize

toString

convolveWithNr

lD

m

nL

nR

##### SelectionPolygon

SelectionPolygon

SelectionPolygon

SelectionPolygon

SelectionPolygon

~SelectionPolygon

computeMinMaxCoordinates

computeMinMaxCoordinates

contains

contains

convertTo1D

copyPoint

debugAlgorithm

getBottomMostPoint

getLeftMostPoint

getPoint

getPoints

getRightMostPoint

getTopMostPoint

height

is1D

is2D

isRectangle

operator=

range

rangeX

rangeY

resetPoints

set1D

set2D

setPoint

setPoint

toShort4PointsString

toString

transpose

width

m_maxX

m_maxY

m_minX

m_minY

m_points

##### SelectionPolygonSpec

SelectionPolygonSpec

SelectionPolygonSpec

SelectionPolygonSpec

operator=

toString

dataKind

selectionPolygon

##### SimplePeakIonMatch

ion_charge

ion_mz

ion_size

ion_type

peak

##### SpectrumCollectionHandlerInterface

isReadAhead

loadingEnded

needMsLevelPeakList

needPeakList

setNeedMsLevelPeakList

setQualifiedMassSpectrum

setReadAhead

shouldStop

spectrumListHasSize

m_isReadAhead

m_needPeakListByMsLevel

##### SwitchWidget

SwitchWidget

~SwitchWidget

getSwitchValue

setSwitchValue

updateSwitchValue

m_switchButtonValue

##### TandemWrapperRun

TandemWrapperRun

~TandemWrapperRun

checkXtandemVersion

convertOrginalMsData2mzXmlData

getMs2FilterSuiteString

readTandemPresetFile

readyReadStandardError

readyReadStandardOutput

run

runTandem

setTandemBinaryPath

tandemProgressMessage

wrapTandemInputFile

writeFinalTandemOutput

m_conversionTime

m_convertMzDataUsingSpectrumIndex

m_maxTandemRunTimeMs

m_mzFormat

m_tandemBinary

m_tandemVersion

m_tmpDir

m_xtProcess

mp_monitor

mpa_temporaryDirectory

msp_ms2FilterSuiteString

##### TicXicChromDriftSpecColorMapPlotWidget

TicXicChromDriftSpecColorMapPlotWidget

~TicXicChromDriftSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### TicXicChromMassSpecColorMapPlotWidget

TicXicChromMassSpecColorMapPlotWidget

~TicXicChromMassSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### TicXicChromTracePlotWidget

TicXicChromTracePlotWidget

~TicXicChromTracePlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

##### TimsBinDec

TimsBinDec

TimsBinDec

~TimsBinDec

closeLinearRead

getQfileLinear

getQfileRandom

getTimsFrameFromRawDataChunck

getTimsFrameSPtrByOffset

moveLinearReadForward

startLinearRead

m_decompressMemoryBufferSize

m_firstFrameId

m_lastFrameId

m_linearAccessRawDataChunckDequeSize

m_linearAccessRawDataChunckList

m_linearForwardThreshold

m_randemAccessFrameRawDataChunck

m_timsBinFile

m_timsCompressionType

mp_fileLinear

mp_fileRandom

mpa_decompressMemoryBuffer

##### TimsData

TimsData

TimsData

~TimsData

fillFrameIdDescrList

getFrameCount

getFrameIdDescrList

getGlobalScanIndexByScanCoordinates

getMassSpectrumCstSPtr

getMassSpectrumCstSPtrByGlobalScanIndex

getMassSpectrumCstSPtrByRawIndex

getMsLevelByGlobalScanIndex

getMsLevelBySpectrumIndex

getQualifiedMassSpectrumByGlobalScanIndex

getQualifiedMassSpectrumByRawIndex

getRawIndexFromCoordinate

getRawMsBySpectrumIndex

getRetentionTimeLine

getRetentionTimeLineInSeconds

getScanByGlobalScanIndex

getScanCoordinateFromRawIndex

getScanCoordinatesByGlobalScanIndex

getTicChromatogram

getTimsBinDecPtr

getTimsDataDirectory

getTimsDdaPrecursorsPtr

getTimsDiaSlicesPtr

getTimsFrameBaseCstSPtr

getTimsFrameBaseCstSPtrCached

getTimsFrameCstSPtr

getTimsFrameCstSPtrCached

getTimsFrameRecordList

getTimsMS1FrameIdsInRtRange

getTimsMS2FrameIdsInRtRange

getTotalNumberOfFrames

getTotalNumberOfScans

getTotalScanCount

isDdaRun

isDiaRun

openDatabaseConnection

m_cacheSize

m_frameCount

m_frameIdDescrList

m_mapFramesRecord

m_mapMzCalibrationRecord

m_mapTimsCalibrationRecord

m_mutex

m_someoneIsLoadingFrameId

m_thousandIndexToFrameIdDescrListIndex

m_timsDataDirectory

m_timsFrameBaseCache

m_timsFrameCache

m_totalScanCount

mpa_mzCalibrationStore

mpa_timsBinDec

mpa_timsDdaPrecursors

mpa_timsDiaSlices

TimsDdaPrecursors

TimsDiaSlices

##### TimsDataFastMap

###### TimsDataFastMapElement

count

first_access

TimsDataFastMap

accumulateIntensity

builtInCentroid

clear

downsizeMzRawMap

getTimsDataFastMapInstance

getTofIndexList

readIntensity

removeArtefactualSpike

m_preAllocatedFastMapPerThread

mapTofIndexIntensity

tofIndexList

##### TimsDdaPrecursors

###### SpectrumDescr

collisionEnergy

isolationMz

isolationWidth

ms1_index

ms2_index

parent_frame

precursor_id

precursor_ion_data

scan_mobility_end

scan_mobility_start

tims_frame_list

TimsDdaPrecursors

~TimsDdaPrecursors

fillSpectrumDescriptionWithSqlRecord

getClosestPrecursorIdByMz

getCombinedMs2ScansByPrecursorId

getMatchPrecursorIdByKo

getMs2BuiltinCentroid

getPrecursorsByMzRtCharge

getQualifiedMs1MassSpectrumBySpectrumDescr

getQualifiedMs2MassSpectrumBySpectrumDescr

getSpectrumDescrListByFrameId

getSpectrumDescrWithPrecursorId

getSpectrumDescrWithScanCoordinates

getTotalPrecursorCount

getXicCoordTimsFromPrecursorId

ms2ReaderGenerateMS1MS2Spectrum

ms2ReaderSpectrumCollectionByMsLevel

rawReaderSpectrumCollectionByMsLevel

setMonoThread

setMs1FilterCstSPtr

setMs2BuiltinCentroid

setMs2FilterCstSPtr

m_builtinMs2Centroid

m_isMonoThread

m_mapXicCoordRecord

m_mutex

m_totalPrecursorCount

mcsp_ms1Filter

mcsp_ms2Filter

mp_timsDataOrigin

TimsData

##### TimsDiaSlices

###### FrameSliceRange

begin_global_slice_index

end_global_slice_index

frame_id

###### MsMsWindow

isMzInRange

CollisionEnergy

IsolationMz

IsolationWidth

ScanNumBegin

ScanNumEnd

SliceIndex

WindowGroup

###### MsMsWindowGroup

WindowGroup

###### MsMsWindowGroupList

~MsMsWindowGroupList

addInGroup

getWindowGroupPtrByGroupId

TimsDiaSlices

~TimsDiaSlices

getCombinedMs2ScansByGlobalSliceIndex

getFrameIdByGlobalSliceIndex

getFrameSliceRangeByGlobalSliceIndex

getGlobalSliceIndexBeginByFrameId

getLastMs1FrameIdByMs2FrameId

getMapFrame2WindowGroupPtr

getMs1QualifiedSpectrumByGlobalSliceIndex

getMs2QualifiedSpectrumByGlobalSliceIndex

getMsMsWindowByGlobalSliceIndex

getMsMsWindowGroupList

getTotalSlicesCount

m_builtinMs2Centroid

m_frameId2GlobalSliceIndexBegin

m_frameSliceRangeList

m_mapFrame2WindowGroupPtr

m_ms1frameIdList

m_ms2frameId2Ms1FrameId

m_msMsWindowGroupList

m_totalSlicesCount

mp_timsDataOrigin

##### TimsDirectXicExtractor

TimsDirectXicExtractor

~TimsDirectXicExtractor

protectedExtractXicCoordSPtrList

##### TimsFrame

###### XicComputeStructure

XicComputeStructure

mobilityIndexBegin

mobilityIndexEnd

mzIndexLowerBound

mzIndexUpperBound

tmpIntensity

xic_ptr

TimsFrame

TimsFrame

~TimsFrame

TimsFrame

combineScansInTofIndexIntensityMap

combineScansInTofIndexIntensityMap

combineScansToTraceWithDowngradedMzResolution

combineScansToTraceWithDowngradedMzResolution2

cumulateScan

cumulateScan2

cumulateScanIntensities

cumulateScanRangeIntensities

cumulateScansToTrace

extractTimsXicListInRtRange

getMassSpectrumSPtr

getMobilityScan

getRawTraceSPtr

getRawValuePairList

getScanIntensityList

getScanOffset

getScanPeakCount

getScanTofIndexList

unshufflePacket

m_binaryData

TimsDirectXicExtractor

##### TimsFrameBase

###### TofIndexIntensityPair

intensity_index

tof_index

TimsFrameBase

TimsFrameBase

~TimsFrameBase

checkScanNum

combineScansInTofIndexIntensityMap

combineScansInTofIndexIntensityMap

combineScansToTraceWithDowngradedMzResolution

combineScansToTraceWithDowngradedMzResolution2

cumulateScanIntensities

cumulateScanRangeIntensities

cumulateScansToTrace

downgradeResolutionOfTofIndexIntensityPairList

getDriftTimeInMilliseconds

getId

getIonMobilityTraceByTofIndexRange

getMassSpectrumCstSPtr

getMassSpectrumSPtr

getMaximumRawMassIndex

getMobilityScan

getMsLevel

getMzCalibrationInterfaceSPtr

getOneOverK0Transformation

getRtInSeconds

getScanIndexFromOneOverK0

getScanIntensityList

getScanPeakCount

getScanTofIndexList

getTotalNumberOfScans

getTraceFromTofIndexIntensityMap

getVoltageTransformation

hasSameCalibrationData

setAcqDurationInMilliseconds

setMsMsType

setMzCalibration

setMzCalibrationInterfaceSPtr

setRtInSeconds

setTimsCalibration

m_acqDurationInMilliseconds

m_frameId

m_msMsType

m_rtInSeconds

m_scanCount

m_timsC6

m_timsC7

m_timsDvStart

m_timsNdelay

m_timsSlope

m_timsTtrans

m_timsVmax

m_timsVmin

msp_mzCalibration

##### TimsFrameMobilityTraces

TimsFrameMobilityTraces

TimsFrameMobilityTraces

~TimsFrameMobilityTraces

extractMobilityTraces

getIonMobTraceList

getMzList

getScanIndexList

getTofIndexList

m_ionMobTraceList

m_scanIndexList

m_tofIndexList

mcsp_timsFrameCstSPtr

##### TimsFrameRawDataChunck

TimsFrameRawDataChunck

~TimsFrameRawDataChunck

getCompressedSize

getFrameId

getFrameLength

getFrameNumberOfScans

getMemoryBuffer

readTimsFrame

m_frameId

m_frameLength

m_frameNumberOfScans

m_memoryBufferSize

mpa_memoryBuffer

##### TimsFrameRecord

accumulation_time

frame_id

frame_t1

frame_t2

frame_time

msms_type

mz_calibration_id

tims_calibration_id

tims_offset

##### TimsFramesMsRunReader

TimsFramesMsRunReader

~TimsFramesMsRunReader

computeTicChromatogram

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

##### TimsFrameType1

TimsFrameType1

TimsFrameType1

~TimsFrameType1

copyAndLzfDecompress

cumulateScan

cumulateScan2

getMassSpectrumSPtr

getRawTraceSPtr

getRawValuePairList

getScanIntensityList

getScanPeakCount

getScanTofIndexList

lzfDecompressScan

m_scanOffsetList

m_scanSizeList

##### TimsMs2CentroidFilter

TimsMs2CentroidFilter

TimsMs2CentroidFilter

~TimsMs2CentroidFilter

filter

##### TimsMsFileReader

TimsMsFileReader

~TimsMsFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### TimsMsRunReader

TimsMsRunReader

TimsMsRunReader

~TimsMsRunReader

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

##### TimsMsRunReaderBase

TimsMsRunReaderBase

TimsMsRunReaderBase

~TimsMsRunReaderBase

accept

acquireDevice

getRetentionTimeLine

getTicChromatogram

getTimsDataSPtr

hasScanNumbers

initialize

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

releaseDevice

MsFileAccessor

msp_timsData

##### TimsMsRunReaderDia

TimsMsRunReaderDia

TimsMsRunReaderDia

~TimsMsRunReaderDia

acquireDevice

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

mp_timsDiaSlices

##### TimsMsRunReaderMs2

TimsMsRunReaderMs2

TimsMsRunReaderMs2

~TimsMsRunReaderMs2

accept

acquireDevice

getPrecursorsIDFromMzRt

getRetentionTimeLine

getTicChromatogram

getTimsDataSPtr

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

setMs1FilterCstSPtr

setMs2BuiltinCentroid

setMs2FilterCstSPtr

spectrumListSize

MsFileAccessor

m_builtinMs2Centroid

mp_timsDdaPrecursors

msp_ms1Filter

msp_ms2Filter

msp_timsData

##### TimsMsRunReaderMs2Selected

TimsMsRunReaderMs2Selected

~TimsMsRunReaderMs2Selected

accept

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

setMs1FilterCstSPtr

setMs2FilterCstSPtr

spectrumListSize

MsFileAccessor

mpa_timsData

##### TimsXicExtractorInterface

TimsXicExtractorInterface

~TimsXicExtractorInterface

mp_timsData

TimsData

##### Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

~Trace

append

containsX

dataPointCstIteratorWithX

dataPointIndexWithX

dataPointIteratorWithX

filter

initialize

initialize

initialize

initialize

initialize

makeTraceCstSPtr

makeTraceSPtr

maxX

maxXDataPoint

maxY

maxY

maxYDataPoint

minX

minXDataPoint

minY

minYDataPoint

operator=

operator=

removeZeroYDataPoints

sort

sortX

sortY

sumY

sumY

toMap

toString

unique

xAsBase64Encoded

xValues

yAsBase64Encoded

yValues

MassSpectrumCombinerInterface

TraceCombiner

TraceMinusCombiner

TracePlusCombiner

##### TraceCombiner

TraceCombiner

TraceCombiner

TraceCombiner

TraceCombiner

~TraceCombiner

##### TraceDetectionInterface

detect

##### TraceDetectionMoulon

TraceDetectionMoulon

TraceDetectionMoulon

~TraceDetectionMoulon

detect

getSmoothingHalfEdgeWindows

getTicStart

getTicStop

setFilterMorphoMean

setTicStart

setTicStop

m_ticStart

m_ticStop

m_xicFilterSmoothing

##### TraceDetectionSinkInterface

setTracePeak

##### TraceDetectionZivy

TraceDetectionZivy

~TraceDetectionZivy

detect

getDetectionThresholdOnMaxmin

getDetectionThresholdOnMinmax

getMaxMinHalfEdgeWindows

getMinMaxHalfEdgeWindows

getSmoothingHalfEdgeWindows

setDetectionThresholdOnMaxmin

setDetectionThresholdOnMinmax

setFilterMorphoMaxMin

setFilterMorphoMean

setFilterMorphoMinMax

m_detectionThresholdOnMaxMin

m_detectionThresholdOnMinMax

m_maxMin

m_minMax

m_smooth

##### TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

~TraceMinusCombiner

combine

combine

MassSpectrumMinusCombiner

##### TracePeak

TracePeak

TracePeak

TracePeak

TracePeak

~TracePeak

containsRt

getArea

getLeftBoundary

getLeftBoundary

getMaxXicElement

getMaxXicElement

getRightBoundary

getRightBoundary

makeTracePeakCstSPtr

operator=

operator==

setArea

setLeftBoundary

setMaxXicElement

setRightBoundary

m_area

m_left

m_max

m_right

##### TracePeakList

TracePeakList

TracePeakList

~TracePeakList

setTracePeak

##### TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

~TracePlusCombiner

combine

combine

MassSpectrumPlusCombiner

##### UiMonitorInterface

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

m_totalSteps

##### UiMonitorText

UiMonitorText

~UiMonitorText

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

m_count

m_outputStream

##### UiMonitorTextPercent

UiMonitorTextPercent

~UiMonitorTextPercent

count

setTotalSteps

m_unit

##### UiMonitorVoid

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

##### Utils

almostEqual

appendToFile

booleanToString

chronoIntervalDebugString

chronoTimePointDebugString

extractScanNumberFromMzmlNativeId

fileReaderTypeAsString

getLexicalOrderedString

getVersion

msDataFormatAsString

nearestGreater

pointerToString

roundToDecimal32bitsAsLongLongInt

roundToDecimals

splitMzStringToDoubleVectorWithSpaces

splitSizetStringToSizetVectorWithSpaces

toString

toString

toUtf8StandardString

writeLexicalOrderedString

writeToFile

zeroDecimalsInValue

anythingButDigitDotDash

endOfLineRegExp

mzListDataFormatRegExp

signedDoubleNumberExponentialRegExp

sizetListDataFormatRegExp

unsignedDoubleNumberNoExponentialRegExp

xyMassDataFormatRegExp

##### WrapTandemInput

WrapTandemInput

~WrapTandemInput

getOriginalMsDataFileName

getOriginalTandemOutputFileName

getOriginalTandemPresetFileName

readStream

m_destinationMzXmlFileName

m_destinationTandemInputFile

m_destinationTandemInputFileName

m_destinationTandemOutputFileName

m_originMzDataFileName

m_originTandemOutpuFileName

m_originTandemPresetFileName

m_writerXmlTandemInput

##### WrapTandemResults

WrapTandemResults

~WrapTandemResults

process_group_note

readStream

setInputParameters

m_destinationTandemOutputFile

m_mapTandemInputParameters

m_originalMsDataFileName

m_writerXmlTandemOutput

##### Xic

Xic

Xic

~Xic

atRetentionTime

debugPrintValues

getMsPointDistance

makeXicCstSPtr

makeXicSPtr

operator=

operator=

sortByRetentionTime

##### XicCoord

XicCoord

XicCoord

~XicCoord

addition

divideBy

getParam

initializeAndClone

multiplyBy

reset

toString

mzRange

rtTarget

xicSptr

##### XicCoordTims

XicCoordTims

XicCoordTims

~XicCoordTims

addition

divideBy

getParam

initializeAndClone

multiplyBy

reset

scanNumBeginRangeCorrection

toString

scanNumBegin

scanNumEnd

##### XicPeptideFragmentIon

XicPeptideFragmentIon

XicPeptideFragmentIon

~XicPeptideFragmentIon

getPeptideFragmentIonSp

msp_peptideFragmentIon

##### XicPeptideFragmentIonNaturalIsotope

XicPeptideFragmentIonNaturalIsotope

XicPeptideFragmentIonNaturalIsotope

~XicPeptideFragmentIonNaturalIsotope

getCharge

getPeptideFragmentIonSp

getPeptideNaturalIsotopeAverageSp

msp_naturalIsotopeAverage

msp_peptideFragmentIon

##### XicPeptideInterface

XicPeptideInterface

~XicPeptideInterface

getCharge

m_z

msp_peptideInterface

##### XicWidget

XicWidget

~XicWidget

addMsMsEvent

addXicPeakList

addXicSp

clear

clearXicPeakBorders

clicked

drawXicPeakBorders

getIntensityAxisP

getName

getRtAxisP

getXicCstSPtr

operateNewRange

plot

replotAll

rescale

rescaleOneRange

rtChanged

rtChangeEvent

setName

setRetentionTimeInMinutes

setRetentionTimeInSeconds

toQPaintDevice

xicClickEvent

xicPeakListChanged

QCPXic

_map_xic_msms_event

_map_xic_name

_qcp_xic

_rt_in_seconds

_xic_peak_sp_list

_xic_sp_list

##### XmlStreamReaderInterface

XmlStreamReaderInterface

~XmlStreamReaderInterface

cloneElement

cloneNode

cloneStartElement

errorString

read

read

readFile

readStream

m_qxmlStreamReader

##### XtandemError

XtandemError

clone

##### XtandemHyperscore

AaFactorMap

XtandemHyperscore

XtandemHyperscore

~XtandemHyperscore

getHyperscore

getMatchedIons

getXtandemPredictedIonIntensityFactor

_aa_ion_factor_b

_aa_ion_factor_y

_ion_count

_proto_hyperscore

_refine_spectrum_synthesis

##### XtandemHyperscoreBis

AaFactorMap

XtandemHyperscoreBis

~XtandemHyperscoreBis

computeXtandemHyperscore

getHyperscore

getMatchedIons

getTotalMatchedIons

getXtandemPredictedIonIntensityFactor

reset

m_aaIonFactorBb

m_aaIonFactorY

m_ionCount

m_ionList

m_isRefineSpectrumSynthesis

m_protoHyperscore

m_totalMatchedIons

mp_precision

##### XtandemPresetReader

XtandemPresetReader

~XtandemPresetReader

getCountNote

getMs2FiltersOptions

getNumberOfThreads

read_note

readStream

m_countNote

m_ms2precisionUnit

m_ms2precisionValue

m_threads

##### XtandemSpectrumProcess

XtandemSpectrumProcess

XtandemSpectrumProcess

~XtandemSpectrumProcess

getDynamicRange

getExcludeParent

getExcludeParentNeutralLoss

getIonScore

getMinimumMz

getNeutralLossMass

getNeutralLossWindowDalton

getNmostIntense

getRefineSpectrumModel

getRemoveIsotope

process

setDynamicRange

setExcludeParent

setExcludeParentNeutralLoss

setIonScore

setMinimumMz

setNeutralLossMass

setNeutralLossWindowDalton

setNmostIntense

setRefineSpectrumModel

setRemoveIsotope

_a_ions

_ao_ions

_astar_ions

_b_ions

_bo_ions

_bstar_ions

_c_ions

_x_ions

_y_ions

_yo_ions

_ystar_ions

_z_ions

m_filter_floor

m_filter_highpass

m_filter_keep_greater

m_filter_remove_c13

m_filter_rescale

m_isExcludeParent

m_isExcludeParent_lower_dalton

m_isExcludeParent_neutral_loss

m_isExcludeParent_upper_dalton

m_isRefineSpectrumModel

m_isRemoveIsotope

m_n_most_intense

m_neutralLossMass

m_neutralLossWindowDalton

##### XyMsFileReader

XyMsFileReader

~XyMsFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### XyMsRunReader

XyMsRunReader

~XyMsRunReader

accept

acquireDevice

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

qualifiedMassSpectrumFromXyMSDataFile

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

spectrumListSize

MsFileAccessor

m_fileName

#### ContainsAny

result_type

ContainsAny

operator()

_peptide_set

#### GraphicDeviceWidget

GraphicDeviceWidget

~GraphicDeviceWidget

toQPaintDevice

toSvgFile

#### InHousePolynomialSolverResult

type

x1

x2

x3

#### ProteinPeptideList

ProteinPeptideList

~ProteinPeptideList

Class Index

### Class Hierarchy

pappso::AaCode

pappso::AaStringCodeMassMatching::aaCodeAndMassRange

pappso::AaStringCodec

pappso::AaStringCodeMassMatching

pappso::specglob::AminoAcidModel

#### pappso::AtomNumberInterface

##### pappso::AaBase

pappso::Aa

pappso::AaModification

##### pappso::PeptideInterface

pappso::Peptide

pappso::PeptideFragment

pappso::PeptideFragmentIon

pappso::PeptideNaturalIsotope

#### pappso::BasePlotContext

pappso::MassSpecTracePlotContext

pappso::spectree::Bucket

pappso::spectree::BucketClustering

pappso::CodeToMass

pappso::ColorMapPlotConfig

ContainsAny

pappso::CosineSimilarity

pappso::DataPoint

pappso::FilterChargeDeconvolution::DataPointInfo

pappso::DeepProtEnumStr

pappso::Enzyme

#### pappso::EnzymeProductInterface

pappso::PeptideBuilder

pappso::PeptideMethioninRemove

pappso::PeptideModificatorPipeline

pappso::PeptideSemiEnzyme

pappso::PeptideSizeFilter

pappso::specglob::ExperimentalSpectrumDataPoint

#### pappso::FastaFileIndexerInterface

pappso::FastaFileIndexer

#### pappso::FastaHandlerInterface

pappso::FastaSeqHandler

pappso::FastaReader

#### pappso::FastaWriterInterface

pappso::FastaOutputStream

#### pappso::FilterInterface

pappso::FilterFloorY

pappso::FilterGreatestY

pappso::FilterGreatestYperWindow

pappso::FilterHighPass

pappso::FilterHighPassPercentage

pappso::FilterLocalMaximum

pappso::FilterLowPass

pappso::FilterMorphoBackground

pappso::FilterMorphoMaxMin

pappso::FilterMorphoMinMax

##### pappso::FilterMorphoWindowBase

pappso::FilterMorphoMax

pappso::FilterMorphoMean

pappso::FilterMorphoMedian

pappso::FilterMorphoMin

pappso::FilterMorphoSum

##### pappso::FilterNameInterface

pappso::FilterCeilingAmplitudePercentage

pappso::FilterChargeDeconvolution

pappso::FilterComplementIonEnhancer

pappso::FilterFloorAmplitudePercentage

pappso::FilterLowIntensitySignalRemoval

pappso::FilterMorphoAntiSpike

pappso::FilterMzExclusion

pappso::FilterNormalizeIntensities

pappso::FilterQuantileBasedRemoveY

pappso::FilterSavitzkyGolay

pappso::FilterSuiteString

pappso::FilterPeakDelta

pappso::FilterRemoveC13

pappso::FilterRemoveY

pappso::FilterResampleKeepGreater

pappso::FilterResampleKeepPointInPolygon

pappso::FilterResampleKeepSmaller

pappso::FilterResampleKeepXRange

pappso::FilterResampleRemoveXRange

pappso::FilterRescaleY

pappso::FilterRoundY

pappso::FilterScaleFactorY

pappso::FilterSuite

pappso::FilterTriangle

pappso::FrameIdDescr

pappso::TimsDiaSlices::FrameSliceRange

pappso::GrpExperiment

pappso::GrpGroup

#### pappso::GrpGroupingMonitorInterface

pappso::GrpGroupingMonitor

pappso::GrpMapPeptideToGroup

pappso::GrpMapPeptideToSubGroupSet

pappso::GrpPeptide

pappso::GrpPeptideSet

pappso::GrpProtein

pappso::GrpSubGroup

pappso::GrpSubGroupSet

InHousePolynomialSolverResult

#### pappso::IntegrationScopeBase

##### pappso::IntegrationScope

pappso::IntegrationScopeRect

pappso::IntegrationScopeRhomb

pappso::IntegrationScopeSpec

#### pappso::Ion

pappso::PeptideInterface

pappso::IonIsotopeRatioScore

pappso::IonMobilityGrid

pappso::spectree::ItemCart

pappso::LinearRegression

#### std::map< K, T >

pappso::MapTrace

pappso::spectree::SpecTree::MapSimilarityCount

pappso::spectree::SpecTree::MapSimilarityCountElement

#### pappso::MassDataCombinerInterface

##### pappso::MassSpectrumCombiner

pappso::MassSpectrumMinusCombiner

pappso::MassSpectrumPlusCombiner

##### pappso::TraceCombiner

pappso::TraceMinusCombiner

pappso::TracePlusCombiner

#### pappso::MassSpectrumFilterInterface

pappso::FilterTandemDeisotope

pappso::MassSpectrumFilterGreatestItensities

pappso::MassSpectrumFilterResampleKeepMzRange

pappso::MassSpectrumFilterResampleRemoveMzRange

pappso::TimsMs2CentroidFilter

pappso::MassSpectrumId

pappso::MassSpectrumLineData

pappso::MgfOutput

pappso::MorpheusScore

pappso::MsDataFormatEnumStr

pappso::MsFileAccessor

#### pappso::MsFileReader

pappso::BafAsciiFileReader

pappso::PwizMsFileReader

pappso::TimsMsFileReader

pappso::XyMsFileReader

pappso::TimsDiaSlices::MsMsWindow

pappso::MsRunAlignment

pappso::MsRunDataSetTree

pappso::MsRunDataSetTreeNode

pappso::MsRunDataSetTreeNodeVisitorInterface

pappso::MsRunId

pappso::MsRunReadConfig

#### pappso::MsRunReader

pappso::BafAsciiMsRunReader

pappso::PwizMsRunReader

##### pappso::TimsMsRunReaderBase

pappso::TimsFramesMsRunReader

pappso::TimsMsRunReader

pappso::TimsMsRunReaderDia

###### pappso::TimsMsRunReaderMs2

pappso::TimsMsRunReaderMs2Selected

pappso::XyMsRunReader

pappso::MsRunRetentionTime< T >

pappso::MsRunRetentionTimeSeamarkPoint< T >

pappso::MsRunSlice

pappso::MsRunXicExtractorFactory

#### pappso::MsRunXicExtractorInterface

##### pappso::MsRunXicExtractor

###### pappso::MsRunXicExtractorDisk

pappso::MsRunXicExtractorDiskBuffer

##### pappso::TimsXicExtractorInterface

pappso::TimsDirectXicExtractor

pappso::MsRunXicExtractor::MsRunXicExtractorPoints

#### pappso::MzCalibrationInterface

##### pappso::MzCalibrationModel1

pappso::MzCalibrationModel1Cached

pappso::MzCalibrationStore

pappso::MzIntegrationParams

pappso::MzRange

pappso::MzxmlOutput

pappso::OboPsiMod

#### pappso::OboPsiModHandlerInterface

pappso::FilterOboPsiModSink

pappso::FilterOboPsiModTermAccession

pappso::FilterOboPsiModTermDiffMono

pappso::FilterOboPsiModTermLabel

pappso::FilterOboPsiModTermName

pappso::OboListModel::OboPsiModHandler

pappso::OboPsiModTerm

#### pappso::PeakIonMatch

pappso::PeakIonIsotopeMatch

pappso::PeptideFragmentIonListBase

pappso::PeptideIsotopeSpectrumMatch

#### pappso::PeptideModificatorInterface

##### pappso::PeptideModificatorBase

pappso::PeptideFixedModificationBuilder

###### pappso::PeptideVariableModificationBuilder

pappso::PeptideVariableModificationReplacement

pappso::PeptideModificatorPipeline

pappso::PeptideModificatorTee

pappso::MsRunRetentionTime< T >::PeptideMs2Point

pappso::PeptideNaturalIsotopeAverage

pappso::PeptideNaturalIsotopeList

pappso::PeptideProFormaParser

pappso::PeptideRawFragmentMasses

#### pappso::PeptideSinkInterface

pappso::PeptideMethioninRemove

pappso::PeptideSemiEnzyme

pappso::PeptideSizeFilter

pappso::specglob::PeptideSpectrumDataPoint

pappso::PeptideSpectrumMatch

#### pappso::PeptideSpSinkInterface

pappso::PeptideBuilder

pappso::PeptideModificatorBase

pappso::PeptideModificatorPipeline

pappso::PeptideStrParser

pappso::specglob::PostTreatment

#### pappso::PrecisionBase

pappso::DaltonPrecision

pappso::PpmPrecision

pappso::ResPrecision

pappso::PrecisionFactory

pappso::PrecursorIonData

pappso::Protein

pappso::ProteinIntegerCode

ProteinPeptideList

pappso::ProteinPresenceAbsenceMatrix

pappso::PsmFeatures

#### QCustomPlot

##### pappso::BasePlotWidget

###### pappso::BaseColorMapPlotWidget

pappso::DriftSpecMassSpecColorMapPlotWidget

pappso::TicXicChromDriftSpecColorMapPlotWidget

pappso::TicXicChromMassSpecColorMapPlotWidget

###### pappso::BaseTracePlotWidget

pappso::DriftSpecTracePlotWidget

pappso::MassSpecTracePlotWidget

pappso::TicXicChromTracePlotWidget

pappso::QCPSpectrum

pappso::QCPXic

#### QException

##### pappso::PappsoException

pappso::ExceptionInterrupted

pappso::ExceptionNotFound

pappso::ExceptionNotImplemented

pappso::ExceptionNotPossible

pappso::ExceptionNotRecognized

pappso::ExceptionOutOfRange

pappso::XtandemError

#### QObject

pappso::TandemWrapperRun

#### QPushButton

pappso::HttpButton

pappso::SwitchWidget

#### QSortFilterProxyModel

pappso::OboListProxyModel

#### QStringListModel

pappso::OboListModel

pappso::QualifiedMassSpectrum

#### pappso::QualifiedXic

pappso::XicPeptideFragmentIonNaturalIsotope

##### pappso::XicPeptideInterface

pappso::XicPeptideFragmentIon

#### QWidget

##### GraphicDeviceWidget

pappso::MassSpectrumWidget

pappso::XicWidget

pappso::OboChooserWidget

pappso::OboListWidget

pappso::OboTermForm

pappso::PrecisionWidget

#### QXmlStreamWriter

pappso::MzIdentMlWriter

pappso::SavGolParams

pappso::specglob::ScoreValues

pappso::SelectionPolygon

pappso::SelectionPolygonSpec

pappso::specself::SelfSpectrum

pappso::specself::SelfSpectrumDataPoint

pappso::SimplePeakIonMatch

pappso::specglob::SpectralAlignment

pappso::specglob::SpectralAlignmentDataPoint

pappso::spectree::SpecTree

pappso::spectree::SpecTree::SpecTreeNode

#### pappso::SpectrumCollectionHandlerInterface

pappso::MsRunQualifiedSpectrumLoader

pappso::MsRunReaderRetentionTimeLine

pappso::MsRunReaderScanNumberMultiMap

pappso::MsRunReaderTicChromatogram

pappso::MsRunSimpleStatistics

pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints

pappso::MzxmlOutput::Translater

pappso::TimsDdaPrecursors::SpectrumDescr

#### pappso::spectree::SpecXtractInterface

pappso::spectree::SpecXtractMap

pappso::specglob::TheoreticalPeakDataPoint

pappso::TimsBinDec

pappso::TimsData

pappso::TimsDataFastMap

pappso::TimsDataFastMap::TimsDataFastMapElement

pappso::TimsDdaPrecursors

pappso::TimsDiaSlices

#### pappso::TimsFrameBase

##### pappso::TimsFrame

pappso::TimsFrameType1

pappso::TimsFrameMobilityTraces

pappso::TimsFrameRawDataChunck

pappso::TimsFrameRecord

pappso::TimsFrameBase::TofIndexIntensityPair

#### pappso::TraceDetectionInterface

pappso::TraceDetectionMoulon

pappso::TraceDetectionZivy

#### pappso::TraceDetectionSinkInterface

pappso::TracePeakList

pappso::TracePeak

#### pappso::UiMonitorInterface

##### pappso::UiMonitorText

pappso::UiMonitorTextPercent

pappso::UiMonitorVoid

pappso::Utils

#### std::vector< T >

pappso::FilterSuite

pappso::TimsDiaSlices::MsMsWindowGroup

pappso::TimsDiaSlices::MsMsWindowGroupList

##### pappso::Trace

pappso::MassSpectrum

pappso::Xic

pappso::TracePeakList

pappso::specglob::ExperimentalSpectrum

pappso::specglob::PeptideModel

pappso::specglob::PeptideSpectrum

pappso::TimsFrame::XicComputeStructure

#### pappso::XicCoord

pappso::XicCoordTims

#### pappso::XmlStreamReaderInterface

pappso::WrapTandemInput

pappso::WrapTandemResults

pappso::XtandemPresetReader

pappso::XtandemHyperscore

pappso::XtandemHyperscoreBis

pappso::XtandemSpectrumProcess

### Class Members

#### All

_

a

b

c

d

e

f

g

h

i

k

l

m

n

o

p

q

r

s

t

u

v

w

x

y

z

~

#### Functions

a

b

c

d

e

f

g

h

i

k

l

m

n

o

p

q

r

s

t

u

v

w

x

y

z

~

#### Variables

_

a

b

c

d

e

f

g

i

k

l

m

n

o

p

r

s

t

u

v

w

x

y

z

Typedefs

Enumerations

Related Symbols

## Files

### File List

#### pappsomspp

##### amino_acid

###### aa.cpp

operator<

operator==

###### aa.h

###### pappso::Aa

Aa

Aa

Aa

Aa

~Aa

addAaModification

getInternalCterModification

getInternalNterModification

getMass

getModificationList

getNumberOfAtom

getNumberOfIsotope

getNumberOfModification

getTotalModificationMass

isAaEqual

isLesser

operator=

removeAaModification

removeAllButInternalModification

removeInternalCterModification

removeInternalNterModification

replaceAaModification

toAbsoluteString

toProForma

toString

m_listMod

operator<

operator==

aabase.cpp

###### aabase.h

###### pappso::AaBase

AaIntMap

AaMassMap

AminoAcidCharList

AaBase

AaBase

AaBase

~AaBase

getAaMass

getAminoAcidChar

getAminoAcidCharList

getLetter

getMass

getNumberOfAtom

getNumberOfIsotope

replaceLeucineIsoleucine

AaModification

m_aaLetter

m_aaMassMap

m_aaNumberOfCarbonMap

m_aaNumberOfHydrogenMap

m_aaNumberOfNitrogenMap

m_aaNumberOfOxygenMap

m_aaNumberOfSulfurMap

m_aminoAcidCharList

aacode.cpp

###### aacode.h

###### pappso::AaCode

AaCode

AaCode

~AaCode

addAaModification

getAa

getAa

getAaCode

getMass

getSize

updateMass

updateNumbers

m_aaCollection

m_asciiTable

m_massCollection

aamodification.cpp

###### aamodification.h

###### pappso::AaModification

MapAccessionModifications

AaModification

~AaModification

AaModification

calculateMassFromChemicalComponents

createInstance

createInstance

createInstanceC13N15LabelledAminoAcid

createInstanceMutation

getAccession

getInstance

getInstance

getInstanceCustomizedMod

getInstanceInsertionAccessionByAaLetter

getInstanceMutation

getInstanceRemovalAccessionByAaLetter

getInstanceXtandemMod

getMass

getName

getNumberOfAtom

getNumberOfIsotope

getXrefOrigin

isInternal

setDiffFormula

setXrefOrigin

toProForma

m_accession

m_atomCount

m_mapAccessionModifications

m_mapIsotope

m_mass

m_mutex

m_name

m_origin

AaModificationP

AaModificationUp

PeptideSp

aastringcodec.cpp

###### aastringcodec.h

###### pappso::CodeToMass

code

mass

###### pappso::AaStringCodec

AaStringCodec

AaStringCodec

~AaStringCodec

code

codeLlc

codeLlc

codeOnlyContains

decode

decode

generateCodeMassFromModel

generateLlcCodeListByMaxPeptideSize

generateLlcCodeListUpToMaxPeptideSize

getAaCode

getLimitMax

getMass

recGenerateModel

uniqueCodeContainsAminoAcid

m_aaCode

m_base

m_units

AaStringCodecSp

aastringcodemassmatching.cpp

###### aastringcodemassmatching.h

###### pappso::AaStringCodeMassMatching

###### aaCodeAndMassRange

code

mz

mz_range_low

mz_range_up

AaStringCodeMassMatching

AaStringCodeMassMatching

~AaStringCodeMassMatching

filterCodeList

getAaCodeFromMass

getAaCodeFromMassList

getAaCodeFromMassWearingModification

getPrecisionPtr

m_aaCode

m_aaCodec

m_base

m_codeMassList

m_precision

###### pappso::AaStringCodeMassMatching::aaCodeAndMassRange

code

mz

mz_range_low

mz_range_up

###### atomnumberinterface.h

###### pappso::AtomNumberInterface

getNumberOfAtom

getNumberOfIsotope

##### exception

###### exceptioninterrupted.h

###### pappso::ExceptionInterrupted

ExceptionInterrupted

clone

###### exceptionnotfound.h

###### pappso::ExceptionNotFound

ExceptionNotFound

clone

###### exceptionnotimplemented.h

###### pappso::ExceptionNotImplemented

ExceptionNotImplemented

clone

###### exceptionnotpossible.h

###### pappso::ExceptionNotPossible

ExceptionNotPossible

clone

###### exceptionnotrecognized.h

###### pappso::ExceptionNotRecognized

ExceptionNotRecognized

clone

###### exceptionoutofrange.h

###### pappso::ExceptionOutOfRange

ExceptionOutOfRange

clone

##### fasta

fastafileindexer.cpp

###### fastafileindexer.h

###### pappso::FastaFileIndexerInterface

close

getSequenceByIndex

open

###### pappso::FastaFileIndexer

FastaFileIndexer

FastaFileIndexer

~FastaFileIndexer

close

getSequenceByIndex

makeFastaFileIndexerSPtr

open

parseFastaFile

size

m_fasta_file

m_indexArray

mpa_sequenceTxtIn

FastaFileIndexerSPtr

###### fastahandlerinterface.h

###### pappso::FastaHandlerInterface

setSequence

###### pappso::FastaSeqHandler

getDescription

getSequence

setSequence

description

sequence

fastaoutputstream.cpp

###### fastaoutputstream.h

###### pappso::FastaOutputStream

FastaOutputStream

~FastaOutputStream

writeProtein

m_ofastastream

fastareader.cpp

###### fastareader.h

###### pappso::FastaReader

FastaReader

~FastaReader

parse

parse

parseOnlyOne

FastaFileIndexer

m_handler

###### fastawriterinterface.h

###### pappso::FastaWriterInterface

writeProtein

##### grouping

###### grpexperiment.cpp

###### ContainsAny

result_type

ContainsAny

operator()

_peptide_set

###### grpexperiment.h

###### pappso::GrpExperiment

GrpExperiment

~GrpExperiment

addPostGroupingGrpProteinSpRemoval

addPreGroupingGrpProteinSpRemoval

addSubGroupSp

getGrpGroupSpList

getGrpProteinSp

getGrpProteinSpList

numbering

removeNonInformativeSubGroups

setGrpPeptide

setRemoveNonInformativeSubgroups

startGrouping

m_grpGroupSpList

m_grpPeptideList

m_grpPostGroupingProteinListRemoval

m_grpPreGroupingProteinListRemoval

m_grpProteinList

m_isGroupingStarted

m_isRemoveNonInformativeSubgroups

m_mapPeptides

m_mapProteins

m_remainingGrpProteinList

mp_monitor

grpgroup.cpp

###### grpgroup.h

###### pappso::GrpGroup

GrpGroup

GrpGroup

~GrpGroup

addGroup

addSubGroupSp

check

containsAny

getGroupingId

getGroupNumber

getGrpPeptideSet

getGrpSubGroupSpList

getSubGroupSpList

makeGrpGroupSp

numbering

operator<

removeFirstNonInformativeSubGroup

removeNonInformativeSubGroups

setGroupNumber

GrpExperiment

m_groupNumber

m_mapPeptideToSubGroupSet

m_peptideSet

m_subGroupList

GrpGroupSp

GrpGroupSpConst

grpgroupingmonitor.cpp

###### grpgroupingmonitor.h

###### pappso::GrpGroupingMonitorInterface

~GrpGroupingMonitorInterface

groupingProtein

removingNonInformativeSubGroupsInGroup

startGrouping

startNumberingAllGroups

startRemovingNonInformativeSubGroupsInAllGroups

stopGrouping

stopRemovingNonInformativeSubGroupsInAllGroups

###### pappso::GrpGroupingMonitor

GrpGroupingMonitor

~GrpGroupingMonitor

groupingProtein

removingNonInformativeSubGroupsInGroup

startGrouping

startNumberingAllGroups

startRemovingNonInformativeSubGroupsInAllGroups

stopGrouping

stopRemovingNonInformativeSubGroupsInAllGroups

m_currentProtein

m_totalNumberPeptide

m_totalNumberProtein

mp_outStream

grpmappeptidetogroup.cpp

###### grpmappeptidetogroup.h

###### pappso::GrpMapPeptideToGroup

GrpMapPeptideToGroup

GrpMapPeptideToGroup

~GrpMapPeptideToGroup

clear

getGroupList

set

m_mapPeptideToGroup

grpmappeptidetosubgroupset.cpp

###### grpmappeptidetosubgroupset.h

###### pappso::GrpMapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet

~GrpMapPeptideToSubGroupSet

add

check

getSubGroupSet

hasSpecificPeptide

printInfos

remove

size

m_mapPeptideToSubGroupSet

grppeptide.cpp

###### grppeptide.h

###### pappso::GrpPeptide

GrpPeptide

~GrpPeptide

getGroupingId

getGroupNumber

getRank

getSequence

operator<

setGroupNumber

setRank

GrpExperiment

m_groupNumber

m_mass

m_rank

m_sequence

GrpPeptideSp

GrpPeptideSpConst

grppeptideset.cpp

###### grppeptideset.h

###### pappso::GrpPeptideSet

GrpPeptideSet

GrpPeptideSet

GrpPeptideSet

~GrpPeptideSet

addAll

biggerAndContainsAll

contains

containsAll

containsAny

getGrpPeptideList

numbering

operator=

operator==

printInfos

privContainsAll

setGroupNumber

size

GrpMapPeptideToGroup

GrpMapPeptideToSubGroupSet

m_peptidePtrList

grpprotein.cpp

###### grpprotein.h

###### pappso::GrpProtein

const_iterator

GrpProtein

~GrpProtein

GrpProtein

begin

countPlus

end

getAccession

getCount

getDescription

getGroupingId

getGroupNumber

getRank

getSubGroupNumber

operator==

push_back

setGroupNumber

setRank

setSubGroupNumber

strip

GrpExperiment

m_accession

m_count

m_description

m_groupNumber

m_grpPeptidePtrList

m_rank

m_subGroupNumber

GrpProteinSp

GrpProteinSpConst

grpsubgroup.cpp

###### grpsubgroup.h

###### pappso::GrpSubGroup

GrpSubGroup

GrpSubGroup

~GrpSubGroup

getFirstAccession

getGroupingId

getGroupNumber

getGrpProteinList

getPeptideSet

getSubGroupNumber

includes

makeGrpSubGroupSp

maxCount

merge

numbering

operator<

peptideListSize

setGroupNumber

setSubGroupNumber

m_groupNumber

m_grpProteinPtrList

m_peptidePtrList

m_subGroupNumber

GrpSubGroupSp

GrpSubGroupSpConst

grpsubgroupset.cpp

###### grpsubgroupset.h

###### pappso::GrpSubGroupSet

GrpSubGroupSet

GrpSubGroupSet

~GrpSubGroupSet

add

addAll

begin

contains

end

erase

printInfos

remove

size

GrpGroup

m_grpSubGroupPtrList

##### massspectrum

###### massspectrum.cpp

operator<<

operator>>

massSpectrumMetaTypeId

massSpectrumPtrMetaTypeId

###### massspectrum.h

###### pappso::MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

MassSpectrum

~MassSpectrum

debugPrintValues

equals

filterSum

makeMassSpectrumCstSPtr

makeMassSpectrumSPtr

massSpectrumFilter

maxIntensityDataPoint

minIntensityDataPoint

operator=

operator=

operator=

operator=

sortMz

tic

tic

totalIonCurrent

MassSpectrumCstSPtr

MassSpectrumSPtr

operator<<

operator>>

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

massSpectrumMetaTypeId

massSpectrumPtrMetaTypeId

massspectrumid.cpp

###### massspectrumid.h

###### pappso::MassSpectrumId

MassSpectrumId

MassSpectrumId

MassSpectrumId

MassSpectrumId

~MassSpectrumId

getMsRunIdCstSPtr

getNativeId

getSpectrumIndex

isValid

operator=

operator==

setMsRunId

setNativeId

setSpectrumIndex

toString

m_nativeId

m_spectrumIndex

mcsp_msRunId

qualifiedmassspectrum.cpp

###### qualifiedmassspectrum.h

###### pappso::PrecursorIonData

PrecursorIonData

charge

intensity

mz

###### pappso::QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

QualifiedMassSpectrum

~QualifiedMassSpectrum

appendPrecursorIonData

cloneMassSpectrumSPtr

getDtInMilliSeconds

getMassSpectrumCstSPtr

getMassSpectrumId

getMassSpectrumId

getMassSpectrumSPtr

getMsLevel

getMzSortedPrecursorDataChargeValuesAsString

getMzSortedPrecursorDataMzValuesAsString

getParameterValue

getPrecursorCharge

getPrecursorDataChargeValuesAsString

getPrecursorDataChargeValuesAsString

getPrecursorDataMzValuesAsString

getPrecursorDataMzValuesAsString

getPrecursorIntensity

getPrecursorIonData

getPrecursorIonDataSortedWithMz

getPrecursorMass

getPrecursorMz

getPrecursorNativeId

getPrecursorSpectrumIndex

getRtInMinutes

getRtInSeconds

isEmptyMassSpectrum

makeQualifiedMassSpectrumCstSPtr

makeQualifiedMassSpectrumSPtr

operator=

setDtInMilliSeconds

setEmptyMassSpectrum

setMassSpectrumId

setMassSpectrumSPtr

setMsLevel

setParameterValue

setPrecursorNativeId

setPrecursorSpectrumIndex

setRtInSeconds

size

toString

m_dt

m_isEmptyMassSpectrum

m_massSpectrumId

m_msLevel

m_paramsMap

m_precursorIonData

m_precursorNativeId

m_precursorSpectrumIndex

m_rt

msp_massSpectrum

QualifiedMassSpectrumCstSPtr

QualifiedMassSpectrumSPtr

###### QualifiedMassSpectrumParameter

IonMobOneOverK0

IonMobOneOverK0Begin

IonMobOneOverK0End

TimsIonMobScanIndex

TimsFrameIonMobScanIndexBegin

TimsFrameIonMobScanIndexEnd

IsolationMz

IsolationMzWidth

CollisionEnergy

BrukerPrecursorIndex

TimsFrameScansCount

TimsFrameMzIndexBegin

TimsFrameMzIndexEnd

ScanNumber

last

##### msfile

###### bafasciifilereader.cpp

CHECKED_LINES_COUNT

###### bafasciifilereader.h

###### pappso::BafAsciiFileReader

BafAsciiFileReader

~BafAsciiFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

msfileaccessor.cpp

###### msfileaccessor.h

###### pappso::MsFileAccessor

MsFileAccessor

MsFileAccessor

~MsFileAccessor

buildMsRunReaderSPtr

buildMsRunReaderSPtr

buildTimsMsRunReaderMs2SPtr

getFileFormat

getFileName

getFileReaderType

getMsRunIds

getMsRunReaderSPtrByRunId

getOboPsiModTermFileFormat

getOboPsiModTermNativeIDFormat

getpreferredFileReaderType

getSelectedMsRunId

msRunReaderSPtr

msRunReaderSPtr

msRunReaderSPtrForSelectedMsRunId

setPreferredFileReaderType

setSelectedMsRunId

m_fileFormat

m_fileName

m_fileReaderType

m_oboPsiModTermNativeIDFormat

m_preferredFileReaderTypeMap

m_xmlPrefix

mcsp_selectedMsRunId

MsFileAccessorCstSPtr

MsFileAccessorSPtr

TimsMsRunReaderMs2SPtr

msfilereader.cpp

###### msfilereader.h

###### pappso::MsFileReader

MsFileReader

~MsFileReader

getFileFormat

getMsRunIds

m_fileFormat

m_fileName

mzformatenumstr.cpp

###### mzformatenumstr.h

###### pappso::MsDataFormatEnumStr

toString

pwizmsfilereader.cpp

###### pwizmsfilereader.h

###### pappso::PwizMsFileReader

PwizMsFileReader

~PwizMsFileReader

getFileFormat

getMsRunIds

initialize

m_msDataPtrVector

timsmsfilereader.cpp

###### timsmsfilereader.h

###### pappso::TimsMsFileReader

TimsMsFileReader

~TimsMsFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

xymsfilereader.cpp

###### xymsfilereader.h

###### pappso::XyMsFileReader

XyMsFileReader

~XyMsFileReader

getFileFormat

getMsRunIds

initialize

selectMsRunReader

##### msrun

###### alignment

msrunalignment.cpp

###### msrunalignment.h

pappso::MsRunAlignment

msrunretentiontime.cpp

###### msrunretentiontime.h

###### pappso::MsRunRetentionTimeSeamarkPoint< T >

entityHash

intensity

retentionTime

###### pappso::MsRunRetentionTime< T >

###### PeptideMs2Point

entityHash

precursorIntensity

retentionTime

###### ComputeRetentionTimeReference

maximum_intensity

weighted_intensity

last

MsRunRetentionTime

MsRunRetentionTime

~MsRunRetentionTime

addPeptideAsSeamark

addPeptideAsSeamark

align

computeSeamarks

correctNewTimeValues

getAlignedRetentionTimeVector

getBackRetentionTimeReference

getCommonDeltaRt

getCommonDeltaRt

getCommonSeamarksDeltaRt

getFrontRetentionTimeReference

getMs1MeanFilter

getMs1RetentionTimeVector

getMs2MeanFilter

getMs2MedianFilter

getMsRunId

getMsRunReaderSPtr

getNumberOfCorrectedValues

getSeamarks

getSeamarksReferences

isAligned

linearRegressionMs2toMs1

setAlignedRetentionTimeVector

setMs1MeanFilter

setMs2MeanFilter

setMs2MedianFilter

translateAligned2OriginalRetentionTime

translateOriginal2AlignedRetentionTime

m_alignedRetentionTimeVector

m_allMs2Points

m_ms1MeanFilter

m_ms1RetentionTimeVector

m_ms2MeanFilter

m_ms2MedianFilter

m_retentionTimeReferenceMethod

m_seamarks

m_valuesCorrected

mcsp_msrunId

msp_msrunReader

###### pappso::MsRunRetentionTime< T >::PeptideMs2Point

entityHash

precursorIntensity

retentionTime

template.cpp

###### output

mgfoutput.cpp

###### mgfoutput.h

###### pappso::MgfOutput

MgfOutput

~MgfOutput

close

write

mpa_outputStream

###### mzxmloutput.cpp

change_endian

###### mzxmloutput.h

###### pappso::MzxmlOutput

###### Translater

Translater

~Translater

needPeakList

setQualifiedMassSpectrum

mp_output

MzxmlOutput

~MzxmlOutput

close

getPrecursorScanNumber

getScanNumber

getScanNumberFromNativeId

maskMs1

setReadAhead

write

write

writeHeader

writeQualifiedMassSpectrum

m_isReadAhead

m_monitor

m_ms1IsMasked

mpa_outputStream

###### pappso::MzxmlOutput::Translater

Translater

~Translater

needPeakList

setQualifiedMassSpectrum

mp_output

###### private

pwizmsrunreader.cpp

###### pwizmsrunreader.h

###### pappso::PwizMsRunReader

PwizMsRunReader

~PwizMsRunReader

accept

acquireDevice

getOboPsiModTermNativeIDFormat

getPwizSpectrumPtr

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

processDriftTime

processRetentionTime

qualifiedMassSpectrum

qualifiedMassSpectrumFromPwizMSData

qualifiedMassSpectrumFromPwizSpectrumPtr

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

readSpectrumCollectionWithMsrunReadConfig

releaseDevice

setGlobalLocaleToCurrentOs

setGlobalLocaleToEnglish

spectrumListSize

MsFileAccessor

m_hasScanNumbers

m_mutex

msp_msData

timsframesmsrunreader.cpp

###### timsframesmsrunreader.h

###### pappso::TimsFramesMsRunReader

TimsFramesMsRunReader

~TimsFramesMsRunReader

computeTicChromatogram

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

TimsFramesMsRunReaderCstSPtr

TimsFramesMsRunReaderSPtr

timsmsrunreader.cpp

###### timsmsrunreader.h

###### pappso::TimsMsRunReader

TimsMsRunReader

TimsMsRunReader

~TimsMsRunReader

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

timsmsrunreaderbase.cpp

###### timsmsrunreaderbase.h

###### pappso::TimsMsRunReaderBase

TimsMsRunReaderBase

TimsMsRunReaderBase

~TimsMsRunReaderBase

accept

acquireDevice

getRetentionTimeLine

getTicChromatogram

getTimsDataSPtr

hasScanNumbers

initialize

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

releaseDevice

MsFileAccessor

msp_timsData

timsmsrunreaderdia.cpp

###### timsmsrunreaderdia.h

###### pappso::TimsMsRunReaderDia

TimsMsRunReaderDia

TimsMsRunReaderDia

~TimsMsRunReaderDia

acquireDevice

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

spectrumListSize

MsFileAccessor

mp_timsDiaSlices

timsmsrunreaderms2.cpp

###### timsmsrunreaderms2.h

###### pappso::TimsMsRunReaderMs2

TimsMsRunReaderMs2

TimsMsRunReaderMs2

~TimsMsRunReaderMs2

accept

acquireDevice

getPrecursorsIDFromMzRt

getRetentionTimeLine

getTicChromatogram

getTimsDataSPtr

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

setMs1FilterCstSPtr

setMs2BuiltinCentroid

setMs2FilterCstSPtr

spectrumListSize

MsFileAccessor

m_builtinMs2Centroid

mp_timsDdaPrecursors

msp_ms1Filter

msp_ms2Filter

msp_timsData

timsmsrunreaderms2selected.cpp

###### timsmsrunreaderms2selected.h

###### pappso::TimsMsRunReaderMs2Selected

TimsMsRunReaderMs2Selected

~TimsMsRunReaderMs2Selected

accept

hasScanNumbers

initialize

massSpectrumCstSPtr

massSpectrumSPtr

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

setMs1FilterCstSPtr

setMs2FilterCstSPtr

spectrumListSize

MsFileAccessor

mpa_timsData

###### xiccoord

ionmobilitygrid.cpp

###### ionmobilitygrid.h

###### pappso::IonMobilityGrid

IonMobilityGrid

~IonMobilityGrid

computeCorrections

getMapCorrectionsStart

getMapDiferrencesStart

storeObservedIdentityBetween

translateXicCoordFromTo

m_mapCorrectionsStart

m_mapCorrectionsStop

m_mapDiferrencesStart

m_mapDiferrencesStop

xiccoord.cpp

###### xiccoord.h

###### pappso::XicCoord

XicCoord

XicCoord

~XicCoord

addition

divideBy

getParam

initializeAndClone

multiplyBy

reset

toString

mzRange

rtTarget

xicSptr

XicCoordSPtr

###### XicCoordParam

TimsTofIonMobilityScanNumberStart

TimsTofIonMobilityScanNumberStop

xiccoordtims.cpp

###### xiccoordtims.h

###### pappso::XicCoordTims

XicCoordTims

XicCoordTims

~XicCoordTims

addition

divideBy

getParam

initializeAndClone

multiplyBy

reset

scanNumBeginRangeCorrection

toString

scanNumBegin

scanNumEnd

XicCoordTimsSPtr

bafasciimsrunreader.cpp

###### bafasciimsrunreader.h

###### pappso::MassSpectrumLineData

dash

ionizationMode

ionSourceType

msLevel

mz_range

peakCount

peakList

peakShapeType

retentionTime

###### pappso::BafAsciiMsRunReader

BafAsciiMsRunReader

~BafAsciiMsRunReader

accept

acquireDevice

craftLineParserRegExp

craftLineParserRegExpPattern

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

parseMassSpectrumLine

qualifiedMassSpectrum

qualifiedMassSpectrumFromBafAsciiMSDataFile

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

spectrumListSize

MsFileAccessor

m_fileName

m_spectrumCount

msrundatasettree.cpp

###### msrundatasettree.h

###### pappso::MsRunDataSetTree

DoubleNodeVectorMap

NodeVector

QualMassSpectraVector

MsRunDataSetTree

~MsRunDataSetTree

accept

accept

addDataSetQualMassSpectraInsideDtRtRange

addDataSetTreeNodesInsideDtRtRange

addMassSpectrum

addMassSpectrum

addMassSpectrum

depth

documentNodeInDtRtMap

findNode

findNode

flattenedView

flattenedViewMsLevel

getIndexNodeMap

getRootNodes

getSpectrumCount

indexNodeMapSize

massSpectrumIndex

massSpectrumIndex

precursorNodeByProductSpectrumIndex

precursorNodesByPrecursorMz

productNodesByPrecursorSpectrumIndex

removeDataSetQualMassSpectraOutsideDtRtRange

removeDataSetTreeNodesOutsideDtRtRange

size

m_dtDoubleNodeVectorMap

m_indexNodeMap

m_rootNodes

m_rtDoubleNodeVectorMap

m_spectrumCount

mcsp_msRunId

MsRunDataSetTreeCstSPtr

MsRunDataSetTreeSPtr

msrundatasettreenode.cpp

###### msrundatasettreenode.h

###### pappso::MsRunDataSetTreeNode

MsRunDataSetTreeNode

MsRunDataSetTreeNode

MsRunDataSetTreeNode

~MsRunDataSetTreeNode

accept

depth

findNode

findNode

flattenedView

flattenedViewChildrenOnly

flattenedViewMsLevelNodes

getParent

getQualifiedMassSpectrum

hasParent

operator=

precursorIonNodesByPrecursorMz

productNodesByPrecursorMz

setParent

setQualifiedMassSpectrum

size

toString

MsRunDataSetTree

m_children

mcsp_massSpectrum

mp_parent

MsRunDataSetTreeNodeCstSPtr

MsRunDataSetTreeNodeSPtr

###### msrundatasettreevisitor.h

###### pappso::MsRunDataSetTreeNodeVisitorInterface

setNodesToProcessCount

shouldStop

visit

###### msrunid.cpp

msRunIdCstSPtrMetaTypeId

msRunIdMetaTypeId

###### msrunid.h

###### pappso::MsRunId

MsRunId

MsRunId

MsRunId

MsRunId

~MsRunId

getFileName

getMsDataFormat

getRunId

getSampleName

getXmlId

isValid

operator=

operator==

setFileName

setMsDataFormat

setRunId

setSampleName

setXmlId

toString

m_fileName

m_mzFormat

m_runId

m_sampleName

m_xmlId

MsRunIdCstSPtr

MsRunIdSPtr

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

msRunIdCstSPtrMetaTypeId

msRunIdMetaTypeId

msrunreadconfig.cpp

###### msrunreadconfig.h

###### pappso::MsRunReadConfig

MsRunReadConfig

MsRunReadConfig

~MsRunReadConfig

acceptMsLevel

acceptRetentionTimeInSeconds

getMsLevels

getMsLevelsAsString

getParameterValue

getRetentionTimeEndInSeconds

getRetentionTimeStartInSeconds

needPeakList

operator=

reset

setMsLevels

setNeedPeakList

setParameterValue

setRetentionTimeEndInSeconds

setRetentionTimeStartInSeconds

toString

m_isPeakListNeeded

m_msLevels

m_paramsMap

m_retentionTimeEndSeconds

m_retentionTimeStartSeconds

###### MsRunReadConfigParameter

TimsFrameIonMobScanIndexBegin

TimsFrameIonMobScanIndexEnd

TimsFrameIonMobOneOverK0Begin

TimsFrameIonMobOneOverK0End

MzRangeBegin

MzRangeEnd

TimsFrameMzIndexMergeWindow

MAX_MS_LEVELS

###### msrunreader.cpp

msRunReaderSPtrMetaTypeId

###### msrunreader.h

###### pappso::MsRunReader

MsRunReader

MsRunReader

~MsRunReader

accept

acquireDevice

getMsRunId

getRetentionTimeLine

getTicChromatogram

hasScanNumbers

initialize

isMonoThread

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

scanNumber2SpectrumIndex

setMonoThread

spectrumListSize

MsFileAccessor

m_isMonoThread

mcsp_msRunId

mpa_multiMapScanNumber

MsRunReaderCstSPtr

MsRunReaderSPtr

Q_DECLARE_METATYPE

MsRunReader

msRunReaderSPtrMetaTypeId

spectrumcollectionhandlerinterface.cpp

###### spectrumcollectionhandlerinterface.h

###### pappso::SpectrumCollectionHandlerInterface

isReadAhead

loadingEnded

needMsLevelPeakList

needPeakList

setNeedMsLevelPeakList

setQualifiedMassSpectrum

setReadAhead

shouldStop

spectrumListHasSize

m_isReadAhead

m_needPeakListByMsLevel

###### pappso::MsRunSimpleStatistics

getMsLevelCount

getTotalCount

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_countMsLevelSpectrum

###### pappso::MsRunReaderScanNumberMultiMap

MsRunReaderScanNumberMultiMap

~MsRunReaderScanNumberMultiMap

getSpectrumIndexFromScanNumber

needPeakList

setQualifiedMassSpectrum

m_mmap_scan2index

###### pappso::MsRunReaderRetentionTimeLine

MsRunReaderRetentionTimeLine

~MsRunReaderRetentionTimeLine

getRetentionTimeLine

needPeakList

setQualifiedMassSpectrum

m_retention_time_list

###### pappso::MsRunReaderTicChromatogram

MsRunReaderTicChromatogram

~MsRunReaderTicChromatogram

getTicChromatogram

needPeakList

setQualifiedMassSpectrum

m_ticChromMapTrace

###### pappso::MsRunQualifiedSpectrumLoader

MsRunQualifiedSpectrumLoader

~MsRunQualifiedSpectrumLoader

clear

getQualifiedMassSpectrumList

needPeakList

setQualifiedMassSpectrum

spectrumListHasSize

m_qualifiedSpectrumList

xymsrunreader.cpp

###### xymsrunreader.h

###### pappso::XyMsRunReader

XyMsRunReader

~XyMsRunReader

accept

acquireDevice

initialize

massSpectrumCstSPtr

massSpectrumSPtr

newXicCoordSPtrFromQualifiedMassSpectrum

newXicCoordSPtrFromSpectrumIndex

qualifiedMassSpectrum

qualifiedMassSpectrumFromXyMSDataFile

readSpectrumCollection

readSpectrumCollection2

readSpectrumCollectionByMsLevel

releaseDevice

spectrumListSize

MsFileAccessor

m_fileName

##### obo

filterobopsimodsink.cpp

###### filterobopsimodsink.h

###### pappso::FilterOboPsiModSink

FilterOboPsiModSink

~FilterOboPsiModSink

getFirst

getOboPsiModTermList

getOne

setOboPsiModTerm

size

m_oboPsiModTermList

filterobopsimodtermaccession.cpp

###### filterobopsimodtermaccession.h

###### pappso::FilterOboPsiModTermAccession

FilterOboPsiModTermAccession

~FilterOboPsiModTermAccession

setOboPsiModTerm

m_accession

m_sink

filterobopsimodtermdiffmono.cpp

###### filterobopsimodtermdiffmono.h

###### pappso::FilterOboPsiModTermDiffMono

FilterOboPsiModTermDiffMono

~FilterOboPsiModTermDiffMono

setOboPsiModTerm

m_massRange

m_sink

filterobopsimodtermlabel.cpp

###### filterobopsimodtermlabel.h

###### pappso::FilterOboPsiModTermLabel

FilterOboPsiModTermLabel

FilterOboPsiModTermLabel

~FilterOboPsiModTermLabel

setOboPsiModTerm

m_labelMatch

m_sink

filterobopsimodtermname.cpp

###### filterobopsimodtermname.h

###### pappso::FilterOboPsiModTermName

FilterOboPsiModTermName

~FilterOboPsiModTermName

setOboPsiModTerm

m_nameMatch

m_sink

###### obopsimod.cpp

initMyResource

###### obopsimod.h

###### pappso::OboPsiMod

OboPsiMod

~OboPsiMod

parse

m_handler

m_term

###### obopsimodhandlerinterface.h

###### pappso::OboPsiModHandlerInterface

setOboPsiModTerm

###### obopsimodterm.cpp

initMyResource

oboPsiModTermMetaTypeId

###### obopsimodterm.h

###### pappso::OboPsiModTerm

OboPsiModTerm

~OboPsiModTerm

OboPsiModTerm

clearTerm

isA

isValid

operator=

parseLine

m_accession

m_definition

m_diffFormula

m_diffMono

m_findExactPsiModLabel

m_findRelatedPsiMsLabel

m_firstParse

m_formula

m_isA

m_massMono

m_name

m_origin

m_psiModLabel

m_psiMsLabel

OboPsiMod

oboPsiModTermMetaTypeId

##### peptide

ion.cpp

###### ion.h

###### pappso::Ion

Ion

~Ion

getMass

getMz

###### peptide.cpp

getPeptideIonDirection

peptideIonIsNter

peptideIonTypeIsComplement

###### peptide.h

###### pappso::Peptide

Peptide

~Peptide

Peptide

Peptide

addAaModification

addAaModificationOnAllAminoAcid

begin

begin

countModificationOnAa

end

end

getAa

getAaPositionList

getAaPositionList

getConstAa

getInternalCterModification

getInternalNterModification

getLiAbsoluteString

getMass

getMass

getModificationPositionList

getModificationPositionList

getNumberOfAtom

getNumberOfIsotope

getNumberOfModification

getSequence

isPalindrome

makeNoConstPeptideSp

makePeptideSp

rbegin

removeAaModification

removeCterAminoAcid

removeInternalCterModification

removeInternalNterModification

removeNterAminoAcid

rend

replaceAaModification

replaceLeucineIsoleucine

reverse

rotate

setInternalCterModification

setInternalNterModification

size

toAbsoluteString

toProForma

toString

operator<

operator==

PeptideProFormaParser

m_aaVec

m_proxyMass

NoConstPeptideSp

###### PeptideDirection

Nter

Cter

###### PeptideIonCter

y

ystar

yo

z

yp

x

###### PeptideIonNter

b

bstar

bo

a

astar

ao

bp

c

getPeptideIonDirection

peptideIonIsNter

peptideIonTypeIsComplement

peptidefragment.cpp

###### peptidefragment.h

###### pappso::PeptideFragment

PeptideFragment

PeptideFragment

PeptideFragment

~PeptideFragment

getMass

getNumberOfAtom

getNumberOfIsotope

getPeptideIonDirection

getPeptideIonDirectionName

getPeptideSp

getSequence

isPalindrome

size

m_direction

m_mass

m_nterCterCleavage

m_size

msp_peptide

PeptideFragmentSp

peptidefragmention.cpp

###### peptidefragmention.h

###### pappso::PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

PeptideFragmentIon

~PeptideFragmentIon

getCompletePeptideIonName

getMass

getName

getNumberOfAtom

getNumberOfIsotope

getNumberOfNeutralPhosphoLoss

getPeptideFragmentSp

getPeptideIonColor

getPeptideIonDirection

getPeptideIonDirection

getPeptideIonName

getPeptideIonName

getPeptideIonType

getSequence

isPalindrome

makePeptideFragmentIonSp

size

m_ionType

m_mass

m_neutralPhosphoLossNumber

msp_fragment

PeptideFragmentIonSp

peptidefragmentionlistbase.cpp

###### peptidefragmentionlistbase.h

###### pappso::PeptideFragmentIonListBase

IonList

PeptideFragmentIonListBase

PeptideFragmentIonListBase

~PeptideFragmentIonListBase

begin

end

getCIDionList

getETDionList

getIonList

getPeptideFragmentIonList

getPeptideFragmentIonSp

getPeptideFragmentIonSp

getPeptideFragmentIonSp

getPeptideFragmentList

getPeptideSp

getPhosphorylationNumber

makePeptideFragmentIonListBaseSp

size

m_ionList

m_phosphorylationNumber

msp_peptide

msp_peptide_fragment_ion_list

PeptideFragmentIonListBaseSp

peptideinterface.cpp

###### peptideinterface.h

###### pappso::PeptideInterface

getFormula

getName

getSequence

getSequenceLi

isPalindrome

matchPeak

size

PeptideInterfaceSp

###### peptidenaturalisotope.cpp

CACHE_ARRAY_SIZE

###### AtomIsotope

C

H

O

N

S

Combinations

isotopem_ratio

isotopem_ratio_cache

combinations_cache

ratioC13_cache

ratioH2_cache

ratioN15_cache

ratioO17_cache

ratioO18_cache

ratioS33_cache

ratioS34_cache

ratioS36_cache

###### peptidenaturalisotope.h

###### pappso::PeptideNaturalIsotope

PeptideNaturalIsotope

PeptideNaturalIsotope

~PeptideNaturalIsotope

getIntensityRatio

getIsotopeMap

getIsotopeNumber

getMass

getNumberOfAtom

getNumberOfIsotope

getSequence

isPalindrome

size

m_mapIsotope

m_mass

m_peptide

m_ratio

PeptideNaturalIsotopeSp

peptidenaturalisotopeaverage.cpp

###### peptidenaturalisotopeaverage.h

###### pappso::PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

PeptideNaturalIsotopeAverage

~PeptideNaturalIsotopeAverage

getCharge

getComponents

getIntensityRatio

getIsotopeNumber

getIsotopeRank

getMz

getPeptideInterfaceSp

getPrecision

isEmpty

makePeptideNaturalIsotopeAverageSp

matchPeak

recursiveDepletion

toString

m_abundanceRatio

m_averageMz

m_isotopeLevel

m_isotopeRank

m_peptideNaturalIsotopeSpList

m_z

mcsp_peptideSp

mp_precision

PeptideNaturalIsotopeAverageSp

###### peptidenaturalisotopelist.cpp

getByIntensityRatioByIsotopeNumber

###### peptidenaturalisotopelist.h

###### pappso::PeptideNaturalIsotopeList

const_iterator

PeptideNaturalIsotopeList

PeptideNaturalIsotopeList

~PeptideNaturalIsotopeList

begin

end

getByIntensityRatio

getByIsotopeNumber

getIntensityRatioPerIsotopeNumber

getPeptideInterfaceSp

makePeptideNaturalIsotopeListSp

size

msp_peptide

msp_peptide_natural_isotope_list

PeptideNaturalIsotopeListSp

peptideproformaparser.cpp

###### peptideproformaparser.h

###### pappso::PeptideProFormaParser

parseNoConstString

parseString

parseStringToPeptide

_rx_modmass

_rx_psimod

peptiderawfragmentmasses.cpp

###### peptiderawfragmentmasses.h

###### pappso::SimplePeakIonMatch

ion_charge

ion_mz

ion_size

ion_type

peak

###### pappso::PeptideRawFragmentMasses

ionDeltatMzMassMap

PeptideRawFragmentMasses

~PeptideRawFragmentMasses

getDeltaMass

pushBackIonMasses

pushBackIonMz

pushBackMatchSpectrum

m_cumulativeCterMasses

m_cumulativeNterMasses

m_ionDeltaMz

###### RawFragmentationMode

full

proline_effect

peptidestrparser.cpp

###### peptidestrparser.h

###### pappso::PeptideStrParser

parseNoConstString

parseString

parseStringToPeptide

_mod_parser

_rx_modmass

_rx_psimod

##### processing

###### combiners

integrationscope.cpp

###### integrationscope.h

###### pappso::IntegrationScope

IntegrationScope

IntegrationScope

IntegrationScope

IntegrationScope

~IntegrationScope

contains

getBottomMostPoint

getDataKindX

getLeftMostPoint

getPoint

getRightMostPoint

getTopMostPoint

getWidth

is1D

is2D

isRectangle

isRhomboid

operator=

range

reset

setDataKindX

setPoint

setWidth

toString

transpose

update

m_dataKindX

m_point

m_width

IntegrationScopeCstSPtr

IntegrationScopeSPtr

integrationscopebase.cpp

###### integrationscopebase.h

###### pappso::IntegrationScopeBase

IntegrationScopeBase

IntegrationScopeBase

~IntegrationScopeBase

contains

getBottomMostPoint

getBottomMostPoints

getDataKindX

getDataKindY

getHeight

getLeftMostBottomPoint

getLeftMostPoint

getLeftMostPoints

getLeftMostTopPoint

getPoint

getPoints

getRhombHorizontalSize

getRhombVerticalSize

getRightMostBottomPoint

getRightMostPoint

getRightMostPoints

getRightMostTopPoint

getTopMostPoint

getTopMostPoints

getWidth

is1D

is2D

isRectangle

isRhomboid

range

reset

setDataKindX

setDataKindY

toString

transpose

###### pappso::IntegrationScopeSpec

IntegrationScopeSpec

IntegrationScopeSpec

IntegrationScopeSpec

operator=

toString

dataKind

integrationScopeSPtr

IntegrationScopeBaseCstSPtr

IntegrationScopeBaseSPtr

IntegrationScopeSpecCstSPtr

IntegrationScopeSpecSPtr

###### IntegrationScopeFeatures

FAILURE

SUCCESS

FLAT_ON_X_AXIS

FLAT_ON_Y_AXIS

RHOMBOID_VERTICAL

RHOMBOID_HORIZONTAL

NOT_PRINTABLE

FLAT_ON_ANY_AXIS

integrationscoperect.cpp

###### integrationscoperect.h

###### pappso::IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

IntegrationScopeRect

~IntegrationScopeRect

contains

getBottomMostPoint

getDataKindX

getDataKindY

getHeight

getTopMostPoint

is1D

is2D

isRectangle

isRhomboid

operator=

operator=

range

reset

setDataKindX

setDataKindY

setHeight

toString

transpose

update

update

m_dataKindY

m_height

IntegrationScopeRectCstSPtr

IntegrationScopeRectSPtr

integrationscoperhomb.cpp

###### integrationscoperhomb.h

###### pappso::IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

IntegrationScopeRhomb

~IntegrationScopeRhomb

addPoint

contains

getBottomMostPoint

getBottomMostPoints

getDataKindX

getDataKindY

getHeight

getLeftMostBottomPoint

getLeftMostPoint

getLeftMostPoints

getLeftMostTopPoint

getPoint

getPoints

getRhombHorizontalSize

getRhombVerticalSize

getRightMostBottomPoint

getRightMostPoint

getRightMostPoints

getRightMostTopPoint

getTopMostPoint

getTopMostPoints

getWidth

is1D

is2D

isRectangle

isRhomboid

operator=

range

reset

setDataKindX

setDataKindY

toString

transpose

m_dataKindX

m_dataKindY

m_points

IntegrationScopeRhombCstSPtr

IntegrationScopeRhombSPtr

massdatacombinerinterface.cpp

###### massdatacombinerinterface.h

###### pappso::MassDataCombinerInterface

Iterator

MassDataCombinerInterface

~MassDataCombinerInterface

combine

combine

combine

getDecimalPlaces

setDecimalPlaces

m_decimalPlaces

massspectrumcombiner.cpp

###### massspectrumcombiner.h

###### pappso::MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

MassSpectrumCombiner

~MassSpectrumCombiner

binCount

binsAsString

findBin

getBins

setBins

m_bins

MassSpectrumCombinerCstSPtr

MassSpectrumCombinerSPtr

massspectrumminuscombiner.cpp

###### massspectrumminuscombiner.h

###### pappso::MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

MassSpectrumMinusCombiner

~MassSpectrumMinusCombiner

combine

combine

operator=

MassSpectrumMinusCombinerCstSPtr

MassSpectrumMinusCombinerSPtr

massspectrumpluscombiner.cpp

###### massspectrumpluscombiner.h

###### pappso::MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

MassSpectrumPlusCombiner

~MassSpectrumPlusCombiner

combine

combine

operator=

MassSpectrumPlusCombinerCstSPtr

MassSpectrumPlusCombinerSPtr

###### mzintegrationparams.cpp

binningTypeMap

mzIntegrationParamsMetaTypeId

mzIntegrationParamsPtrMetaTypeId

###### mzintegrationparams.h

###### pappso::MzIntegrationParams

MzIntegrationParams

MzIntegrationParams

MzIntegrationParams

~MzIntegrationParams

createArbitraryBins

createBins

createBins

createDataBasedBins

getBinningType

getBinSizeDivisor

getDecimalPlaces

getGreatestMz

getPrecision

getSmallestMz

hasValidMzRange

isRemoveZeroValDataPoints

isValid

operator=

reset

setBinningType

setBinSizeDivisor

setDecimalPlaces

setGreatestMz

setPrecision

setRemoveZeroValDataPoints

setSmallestMz

toString

updateGreatestMz

updateSmallestMz

m_binningType

m_binSizeDivisor

m_decimalPlaces

m_greatestMz

m_removeZeroValDataPoints

m_smallestMz

mp_precision

###### BinningType

NONE

DATA_BASED

ARBITRARY

LAST

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

mzIntegrationParamsMetaTypeId

mzIntegrationParamsPtrMetaTypeId

selectionpolygon.cpp

###### selectionpolygon.h

###### pappso::SelectionPolygon

SelectionPolygon

SelectionPolygon

SelectionPolygon

SelectionPolygon

~SelectionPolygon

computeMinMaxCoordinates

computeMinMaxCoordinates

contains

contains

convertTo1D

copyPoint

debugAlgorithm

getBottomMostPoint

getLeftMostPoint

getPoint

getPoints

getRightMostPoint

getTopMostPoint

height

is1D

is2D

isRectangle

operator=

range

rangeX

rangeY

resetPoints

set1D

set2D

setPoint

setPoint

toShort4PointsString

toString

transpose

width

m_maxX

m_maxY

m_minX

m_minY

m_points

###### pappso::SelectionPolygonSpec

SelectionPolygonSpec

SelectionPolygonSpec

SelectionPolygonSpec

operator=

toString

dataKind

selectionPolygon

###### DataDimension

NOT_SET

HORIZONTAL

VERTICAL

###### PointSpec

TOP_LEFT_POINT

TOP_RIGHT_POINT

BOTTOM_RIGHT_POINT

BOTTOM_LEFT_POINT

ENUM_LAST

tracecombiner.cpp

###### tracecombiner.h

###### pappso::TraceCombiner

TraceCombiner

TraceCombiner

TraceCombiner

TraceCombiner

~TraceCombiner

TraceCombinerCstSPtr

TraceCombinerSPtr

traceminuscombiner.cpp

###### traceminuscombiner.h

###### pappso::TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

TraceMinusCombiner

~TraceMinusCombiner

combine

combine

MassSpectrumMinusCombiner

TraceMinusCombinerCstSPtr

TraceMinusCombinerSPtr

tracepluscombiner.cpp

###### tracepluscombiner.h

###### pappso::TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

TracePlusCombiner

~TracePlusCombiner

combine

combine

MassSpectrumPlusCombiner

TracePlusCombinerCstSPtr

TracePlusCombinerSPtr

###### compartraces

cosinesimilarity.cpp

###### cosinesimilarity.h

###### pappso::CosineSimilarity

CosineSimilarity

CosineSimilarity

~CosineSimilarity

similarity

mp_precision

msp_filterExclusion

###### detection

###### tracedetectioninterface.h

###### pappso::TraceDetectionSinkInterface

setTracePeak

###### pappso::TraceDetectionInterface

detect

TraceDetectionInterfaceCstSPtr

TraceDetectionInterfaceSPtr

tracedetectionmoulon.cpp

###### tracedetectionmoulon.h

###### pappso::TraceDetectionMoulon

TraceDetectionMoulon

TraceDetectionMoulon

~TraceDetectionMoulon

detect

getSmoothingHalfEdgeWindows

getTicStart

getTicStop

setFilterMorphoMean

setTicStart

setTicStop

m_ticStart

m_ticStop

m_xicFilterSmoothing

tracedetectionzivy.cpp

###### tracedetectionzivy.h

###### pappso::TraceDetectionZivy

TraceDetectionZivy

~TraceDetectionZivy

detect

getDetectionThresholdOnMaxmin

getDetectionThresholdOnMinmax

getMaxMinHalfEdgeWindows

getMinMaxHalfEdgeWindows

getSmoothingHalfEdgeWindows

setDetectionThresholdOnMaxmin

setDetectionThresholdOnMinmax

setFilterMorphoMaxMin

setFilterMorphoMean

setFilterMorphoMinMax

m_detectionThresholdOnMaxMin

m_detectionThresholdOnMinMax

m_maxMin

m_minMax

m_smooth

tracepeak.cpp

###### tracepeak.h

###### pappso::TracePeak

TracePeak

TracePeak

TracePeak

TracePeak

~TracePeak

containsRt

getArea

getLeftBoundary

getLeftBoundary

getMaxXicElement

getMaxXicElement

getRightBoundary

getRightBoundary

makeTracePeakCstSPtr

operator=

operator==

setArea

setLeftBoundary

setMaxXicElement

setRightBoundary

m_area

m_left

m_max

m_right

TracePeakCstSPtr

tracepeaklist.cpp

###### tracepeaklist.h

###### pappso::TracePeakList

TracePeakList

TracePeakList

~TracePeakList

setTracePeak

findBestTracePeakGivenRtList

findTracePeakGivenRt

###### filters

filterceilingamplitudepercentage.cpp

###### filterceilingamplitudepercentage.h

###### pappso::FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

FilterCeilingAmplitudePercentage

~FilterCeilingAmplitudePercentage

buildFilterFromString

filter

getPercentage

name

operator=

toString

m_percentage

FilterCeilingAmplitudePercentageCstSPtr

FilterCeilingAmplitudePercentageSPtr

filterchargedeconvolution.cpp

###### filterchargedeconvolution.h

###### pappso::FilterChargeDeconvolution

###### DataPointInfo

data_point

new_mono_charge_data_point

parent

z1_range

z1_vect

z2_range

z2_vect

z_charge

DataPointInfoSp

FilterChargeDeconvolution

FilterChargeDeconvolution

FilterChargeDeconvolution

~FilterChargeDeconvolution

addDataPointRefByExclusion

addDataPointToList

buildFilterFromString

computeBestChargeOfDataPoint

computeIsotopeDeconvolution

filter

name

toString

transformToMonoChargedForAllDataPoint

m_diffC12C13_z1

m_diffC12C13_z2

m_precisionPtrZ1

m_precisionPtrZ2

###### pappso::FilterChargeDeconvolution::DataPointInfo

data_point

new_mono_charge_data_point

parent

z1_range

z1_vect

z2_range

z2_vect

z_charge

filtercomplementionenhancer.cpp

###### filtercomplementionenhancer.h

###### pappso::FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

FilterComplementIonEnhancer

~FilterComplementIonEnhancer

buildFilterFromString

enhanceComplementMassInRange

filter

name

toString

m_precisionPtr

m_targetMzSum

filterexclusionmz.cpp

###### filterexclusionmz.h

###### pappso::FilterMzExclusion

FilterMzExclusion

FilterMzExclusion

FilterMzExclusion

~FilterMzExclusion

buildFilterFromString

filter

name

removeTraceInExclusionMargin

toString

m_exclusionPrecision

filterflooramplitudepercentage.cpp

###### filterflooramplitudepercentage.h

###### pappso::FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

FilterFloorAmplitudePercentage

~FilterFloorAmplitudePercentage

buildFilterFromString

filter

getPercentage

name

operator=

toString

m_percentage

FilterFloorAmplitudePercentageCstSPtr

FilterFloorAmplitudePercentageSPtr

###### filterinterface.h

###### pappso::FilterInterface

~FilterInterface

filter

###### pappso::MassSpectrumFilterInterface

~MassSpectrumFilterInterface

filter

FilterInterfaceCstSPtr

FilterInterfaceSPtr

filterlocalmaximum.cpp

###### filterlocalmaximum.h

###### pappso::FilterLocalMaximum

FilterLocalMaximum

FilterLocalMaximum

~FilterLocalMaximum

filter

getHalfWindowSize

m_halfWindowSize

filterlowintensitysignalremoval.cpp

###### filterlowintensitysignalremoval.h

###### pappso::FilterLowIntensitySignalRemoval

ApicesSPtr

ClusterApices

TraceCIter

FilterLowIntensitySignalRemoval

FilterLowIntensitySignalRemoval

FilterLowIntensitySignalRemoval

~FilterLowIntensitySignalRemoval

backwardFindApex

buildFilterFromString

detectClusterApices

filter

forwardFindApex

getThreshold

name

nonConstFilter

operator=

reconstructTrace

toString

INTRA_CLUSTER_INTER_PEAK_DISTANCE

m_clusters

m_curApex

m_curIter

m_max

m_min

m_minIntPointCount

m_minIntStdDevFactor

m_minMean

m_minStdDev

m_noiseLevel

m_noiseMean

m_noiseStdDev

m_prevApex

m_prevIter

m_seen_upward_phase

m_threshold

nan

FilterLowIntensitySignalRemovalCstSPtr

FilterLowIntensitySignalRemovalSPtr

filtermorpho.cpp

###### filtermorpho.h

###### pappso::FilterMorphoWindowBase

FilterMorphoWindowBase

FilterMorphoWindowBase

~FilterMorphoWindowBase

filter

getHalfWindowSize

getWindowValue

operator=

m_halfWindowSize

###### pappso::FilterMorphoSum

FilterMorphoSum

FilterMorphoSum

~FilterMorphoSum

getWindowValue

operator=

###### pappso::FilterMorphoMax

FilterMorphoMax

FilterMorphoMax

~FilterMorphoMax

getMaxHalfEdgeWindows

getWindowValue

operator=

###### pappso::FilterMorphoMin

FilterMorphoMin

FilterMorphoMin

~FilterMorphoMin

getMinHalfEdgeWindows

getWindowValue

operator=

###### pappso::FilterMorphoMinMax

FilterMorphoMinMax

FilterMorphoMinMax

~FilterMorphoMinMax

filter

getMinMaxHalfEdgeWindows

operator=

m_filterMax

m_filterMin

###### pappso::FilterMorphoMaxMin

FilterMorphoMaxMin

FilterMorphoMaxMin

~FilterMorphoMaxMin

filter

getMaxMinHalfEdgeWindows

operator=

m_filterMax

m_filterMin

###### pappso::FilterMorphoAntiSpike

FilterMorphoAntiSpike

FilterMorphoAntiSpike

FilterMorphoAntiSpike

~FilterMorphoAntiSpike

buildFilterFromString

filter

getHalfWindowSize

name

operator=

toString

m_halfWindowSize

###### pappso::FilterMorphoMedian

FilterMorphoMedian

FilterMorphoMedian

~FilterMorphoMedian

getWindowValue

operator=

###### pappso::FilterMorphoMean

FilterMorphoMean

FilterMorphoMean

~FilterMorphoMean

getMeanHalfEdgeWindows

getWindowValue

operator=

###### pappso::FilterMorphoBackground

FilterMorphoBackground

FilterMorphoBackground

~FilterMorphoBackground

filter

getFilterMorphoMedian

getFilterMorphoMinMax

operator=

m_filterMorphoMedian

m_filterMorphoMinMax

filternameinterface.cpp

###### filternameinterface.h

###### pappso::FilterNameInterface

~FilterNameInterface

buildFilterFromString

name

toString

FilterNameInterfaceCstSPtr

FilterNameInterfaceSPtr

filternormalizeintensities.cpp

###### filternormalizeintensities.h

###### pappso::FilterNormalizeIntensities

FilterNormalizeIntensities

FilterNormalizeIntensities

FilterNormalizeIntensities

~FilterNormalizeIntensities

buildFilterFromString

filter

name

operator=

toString

m_newYMax

nan

FilterNormalizeIntensitiesCstSPtr

FilterNormalizeIntensitiesSPtr

filterpass.cpp

###### filterpass.h

###### pappso::FilterLowPass

FilterLowPass

FilterLowPass

~FilterLowPass

filter

operator=

m_passY

###### pappso::FilterHighPass

FilterHighPass

FilterHighPass

~FilterHighPass

filter

operator=

m_passY

###### pappso::FilterHighPassPercentage

FilterHighPassPercentage

FilterHighPassPercentage

~FilterHighPassPercentage

filter

operator=

m_ratioPassY

###### pappso::FilterGreatestY

FilterGreatestY

FilterGreatestY

~FilterGreatestY

filter

getNumberOfPoints

operator=

m_numberOfPoints

###### pappso::FilterGreatestYperWindow

FilterGreatestYperWindow

FilterGreatestYperWindow

~FilterGreatestYperWindow

filter

getNumberOfPoints

operator=

m_numberOfPoints

m_xWindowRange

###### pappso::MassSpectrumFilterGreatestItensities

MassSpectrumFilterGreatestItensities

MassSpectrumFilterGreatestItensities

~MassSpectrumFilterGreatestItensities

filter

operator=

m_filterGreatestY

###### pappso::FilterFloorY

FilterFloorY

FilterFloorY

~FilterFloorY

filter

operator=

###### pappso::FilterRoundY

FilterRoundY

FilterRoundY

~FilterRoundY

filter

operator=

###### pappso::FilterRescaleY

FilterRescaleY

FilterRescaleY

~FilterRescaleY

filter

getDynamicRange

operator=

m_dynamic

###### pappso::FilterScaleFactorY

FilterScaleFactorY

FilterScaleFactorY

~FilterScaleFactorY

filter

getScaleFactorY

operator=

m_factor

###### pappso::FilterRemoveY

FilterRemoveY

FilterRemoveY

~FilterRemoveY

filter

getValue

operator=

m_valueToRemove

###### pappso::FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

FilterQuantileBasedRemoveY

~FilterQuantileBasedRemoveY

buildFilterFromString

filter

getQuantileThreshold

name

operator=

toString

m_quantile

filterpeakdelta.cpp

###### filterpeakdelta.h

###### pappso::FilterPeakDelta

FilterPeakDelta

FilterPeakDelta

~FilterPeakDelta

filter

filterremovec13.cpp

###### filterremovec13.h

###### pappso::FilterRemoveC13

FilterRemoveC13

FilterRemoveC13

~FilterRemoveC13

addExclusionMap

filter

notExcluded

m_diffC12C13_z1

m_diffC12C13_z2

m_precisionPtr

filterresample.cpp

###### filterresample.h

###### pappso::FilterResampleKeepSmaller

FilterResampleKeepSmaller

FilterResampleKeepSmaller

~FilterResampleKeepSmaller

filter

m_value

###### pappso::FilterResampleKeepGreater

FilterResampleKeepGreater

FilterResampleKeepGreater

~FilterResampleKeepGreater

filter

getThresholdX

operator=

m_value

###### pappso::FilterResampleRemoveXRange

FilterResampleRemoveXRange

FilterResampleRemoveXRange

~FilterResampleRemoveXRange

filter

operator=

m_maxX

m_minX

###### pappso::FilterResampleKeepXRange

FilterResampleKeepXRange

FilterResampleKeepXRange

~FilterResampleKeepXRange

filter

operator=

m_maxX

m_minX

###### pappso::FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

FilterResampleKeepPointInPolygon

~FilterResampleKeepPointInPolygon

filter

filter

filter

newSelectionPolygonSpec

operator=

m_greatestMz

m_integrationScopeSpecs

m_lowestMz

###### pappso::MassSpectrumFilterResampleRemoveMzRange

MassSpectrumFilterResampleRemoveMzRange

MassSpectrumFilterResampleRemoveMzRange

~MassSpectrumFilterResampleRemoveMzRange

filter

m_filterRange

###### pappso::MassSpectrumFilterResampleKeepMzRange

MassSpectrumFilterResampleKeepMzRange

MassSpectrumFilterResampleKeepMzRange

~MassSpectrumFilterResampleKeepMzRange

filter

m_filterRange

IntegrationScopeSpecVector

filtersuite.cpp

###### filtersuite.h

###### pappso::FilterSuite

FilterSuite

FilterSuite

filter

filtersuitestring.cpp

###### filtersuitestring.h

###### pappso::FilterSuiteString

FilterNameType

FilterSuiteString

~FilterSuiteString

addFilterFromString

begin

buildFilterFromString

end

filter

name

toString

m_filterVector

FilterSuiteStringSPtr

filtertandemremovec13.cpp

###### filtertandemremovec13.h

###### pappso::FilterTandemDeisotope

FilterTandemDeisotope

FilterTandemDeisotope

filter

m_arbitrary_minimum_mz

m_arbitrary_range_between_isotopes

filtertriangle.cpp

###### filtertriangle.h

###### pappso::FilterTriangle

FilterTriangle

FilterTriangle

~FilterTriangle

filter

setTriangleSlope

sumAndRemove

m_maxMzRange

m_triangleSlope

###### savgolfilter.cpp

SWAP

###### savgolfilter.h

###### pappso::SavGolParams

SavGolParams

SavGolParams

SavGolParams

initialize

initialize

initialize

toString

convolveWithNr

lD

m

nL

nR

###### pappso::FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

FilterSavitzkyGolay

~FilterSavitzkyGolay

buildFilterFromString

convlv

dmatrix

dvector

filter

filteredData

four1

free_dmatrix

free_dvector

free_ivector

getParameters

ivector

lubksb

ludcmp

name

operator=

realft

runFilter

sgcoeff

toString

twofft

m_params

m_x

m_yf

m_yr

FilterSavitzkyGolayCstSPtr

FilterSavitzkyGolaySPtr

###### specglob

experimentalspectrum.cpp

###### experimentalspectrum.h

###### pappso::specglob::ExperimentalSpectrumDataPoint

indice

symmetric_mz

type

###### pappso::specglob::ExperimentalSpectrum

ExperimentalSpectrum

ExperimentalSpectrum

~ExperimentalSpectrum

createSymetricPeakList

findMz

getMassList

getMassList

getPrecursorMass

getQualifiedMassSpectrum

getSymetricMz

getTargetMzSum

reverseFindDiffMz

toString

m_precisionPtr

m_precursorMass

m_qualifiedMassSpectrum

m_targetMzSum

ExperimentalSpectrumCsp

peptidemodel.cpp

###### peptidemodel.h

###### pappso::specglob::AminoAcidModel

alignment_type

amino_acid

bracket

mass_difference

remove

###### pappso::specglob::TheoreticalPeakDataPoint

aa_indice

it_experimental_peak_match

mz_range

###### pappso::specglob::PeptideModel

PeptideModel

PeptideModel

PeptideModel

~PeptideModel

assignResidualMass2Cter

checkForAaModification

checkForAaModificationP

checkForMutation

checkForMutations

copyDeep

eliminateComplementaryDelta

eliminateNegativeOffset

generateTheoreticalPeaks

getCountSharedPeaks

getIntensityExperimentalPeaks

getIntensitySharedPeaks

getMass

getMassDelta

getMz

getTheoreticalIonMassList

getTheoreticalPeakDataPointList

getTheoreticalPeakDataPointListToString

hasRemoval

ltrimOnRemoval

matchExperimentalPeaks

modifCount

operator=

removeBracketsForAlignedAA

setBeginMassDelta

toProForma

toString

m_beginMassDelta

m_countSharedPeaks

m_cterModification

m_experimentalPrecursorMass

m_intensityExperimentalPeaks

m_intensitySharedPeaks

m_nterModification

m_theoreticalPeakList

mcsp_peakList

peptidespectrum.cpp

###### peptidespectrum.h

###### pappso::specglob::PeptideSpectrumDataPoint

diff_mz

mz

###### pappso::specglob::PeptideSpectrum

PeptideSpectrum

PeptideSpectrum

~PeptideSpectrum

getMassList

getPeptideSp

msp_peptide

PeptideSpectraCsp

posttreatment.cpp

###### posttreatment.h

###### pappso::specglob::PostTreatment

PostTreatment

~PostTreatment

findBetterPeptideModel

findReplaceMutations

getBetterPeptideModel

getOriginalPeptideModel

tryBetterPositionOffsets

tryToCumulateOffSets

tryToRemoveOffsets

m_betterPeptideModel

m_originalPeptideModel

m_precision

scorevalues.cpp

###### scorevalues.h

###### pappso::specglob::ScoreValues

ScoreValues

ScoreValues

~ScoreValues

get

operator=

set

m_scoreTable

spectralalignment.cpp

###### spectralalignment.h

###### pappso::specglob::SpectralAlignmentDataPoint

alignment_type

mass_difference

origin_column_indices

score

###### pappso::specglob::SpectralAlignment

SpectralAlignment

~SpectralAlignment

align

backTrack

buildPeptideModel

fillMassDelta

fillMatricesWithScores

getBestRealignScore

getExperimentalSpectrumCsp

getExperimentalSpectrumDataPoint

getMatrix

getMaxPosIterator

getMaxScore

getPeptideSpectraCsp

getPrecursorMzDelta

getScoreRow

rtrim

m_BETTER_END_RA

m_itPosMax

m_matrix

m_maxScore

m_precisionPtr

m_precursorMassDelta

m_scoreValues

mcsp_experimentalSpectrum

mcsp_peptideSpectrum

###### types.h

###### ExperimentalSpectrumDataPointType

native

symmetric

both

synthetic

###### ScoreValueType

scoreNonAlign

scoreReAlignNative

scoreReAlignSym

scoreReAlignBoth

scoreAlignNative

scoreAlignSym

scoreAlignBoth

scoreReAlignNativeNO

scoreReAlignSymNO

scoreReAlignBothNO

###### SpectralAlignmentType

nonAlign

reAlign

align

###### specself

selfspectrum.cpp

###### selfspectrum.h

###### pappso::specself::SelfSpectrum

SelfSpectrum

~SelfSpectrum

getMatrix

getTrace

setPrecursorMass

setVariableModification

m_matrix

m_trace

SelfSpectrumMatrix

selfspectrumdatapoint.cpp

###### selfspectrumdatapoint.h

###### pappso::specself::SelfSpectrumDataPoint

fillAntiSpectrumDataPoint

fillSelfSpectrumDataPoint

setVariableModification

aaCodeList

antiAaCodeList

antiMassDelta

m_isComplement

massDelta

###### spectree

bucket.cpp

###### bucket.h

###### pappso::spectree::Bucket

Bucket

Bucket

back

front

getCartList

getId

operator<

push_back

size

m_cartList

m_itemId

###### bucketclustering.cpp

erase_if

###### bucketclustering.h

###### pappso::spectree::BucketClustering

BucketClustering

addItemCart

asSortedList

getItemCartCount

removeBucketsWithinCartIdRange

size

m_bucketMap

m_itemCartCount

itemcart.cpp

###### itemcart.h

###### pappso::spectree::ItemCart

ItemCart

ItemCart

ItemCart

~ItemCart

getId

getItemList

operator=

m_id

m_itemList

spectree.cpp

###### spectree.h

###### pappso::spectree::SpecTree

###### MapSimilarityCount

aboveThreshold

keys

map_id_count

###### MapSimilarityCountElement

aboveThreshold

count

lastWitness

###### SpecTreeNode

count

nextIndex

parentIndex

value

SpecTree

~SpecTree

addNewNode

extractSpectrumPairSimilarityCount

extractSpectrumSimilarityCount

getSpectrumFirstNodeIndex

manageSideAccess

toString

walkBackInBranchFromNode

walkBackInBranchFromNodeToTarget

xtract

index_not_defined

m_nodeList

m_spectrumFirstNodeIndex

###### pappso::spectree::SpecTree::SpecTreeNode

count

nextIndex

parentIndex

value

###### pappso::spectree::SpecTree::MapSimilarityCountElement

aboveThreshold

count

lastWitness

###### pappso::spectree::SpecTree::MapSimilarityCount

aboveThreshold

keys

map_id_count

specxtractinterface.cpp

###### specxtractinterface.h

###### pappso::spectree::SpecXtractInterface

SpecXtractInterface

~SpecXtractInterface

beginItemCartExtraction

endItemCartExtraction

reportSimilarity

###### pappso::spectree::SpecXtractMap

SpecXtractMap

~SpecXtractMap

clear

getMapSimilarities

reportSimilarity

m_mapSimilarities

###### tandemwrapper

tandemwrapperrun.cpp

###### tandemwrapperrun.h

###### pappso::XtandemError

XtandemError

clone

###### pappso::TandemWrapperRun

TandemWrapperRun

~TandemWrapperRun

checkXtandemVersion

convertOrginalMsData2mzXmlData

getMs2FilterSuiteString

readTandemPresetFile

readyReadStandardError

readyReadStandardOutput

run

runTandem

setTandemBinaryPath

tandemProgressMessage

wrapTandemInputFile

writeFinalTandemOutput

m_conversionTime

m_convertMzDataUsingSpectrumIndex

m_maxTandemRunTimeMs

m_mzFormat

m_tandemBinary

m_tandemVersion

m_tmpDir

m_xtProcess

mp_monitor

mpa_temporaryDirectory

msp_ms2FilterSuiteString

wraptandeminput.cpp

###### wraptandeminput.h

###### pappso::WrapTandemInput

WrapTandemInput

~WrapTandemInput

getOriginalMsDataFileName

getOriginalTandemOutputFileName

getOriginalTandemPresetFileName

readStream

m_destinationMzXmlFileName

m_destinationTandemInputFile

m_destinationTandemInputFileName

m_destinationTandemOutputFileName

m_originMzDataFileName

m_originTandemOutpuFileName

m_originTandemPresetFileName

m_writerXmlTandemInput

wraptandemresults.cpp

###### wraptandemresults.h

###### pappso::WrapTandemResults

WrapTandemResults

~WrapTandemResults

process_group_note

readStream

setInputParameters

m_destinationTandemOutputFile

m_mapTandemInputParameters

m_originalMsDataFileName

m_writerXmlTandemOutput

xtandempresetreader.cpp

###### xtandempresetreader.h

###### pappso::XtandemPresetReader

XtandemPresetReader

~XtandemPresetReader

getCountNote

getMs2FiltersOptions

getNumberOfThreads

read_note

readStream

m_countNote

m_ms2precisionUnit

m_ms2precisionValue

m_threads

###### uimonitor

###### uimonitorinterface.h

###### pappso::UiMonitorInterface

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

m_totalSteps

uimonitortext.cpp

###### uimonitortext.h

###### pappso::UiMonitorText

UiMonitorText

~UiMonitorText

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

m_count

m_outputStream

uimonitortextpercent.cpp

###### uimonitortextpercent.h

###### pappso::UiMonitorTextPercent

UiMonitorTextPercent

~UiMonitorTextPercent

count

setTotalSteps

m_unit

###### uimonitorvoid.h

###### pappso::UiMonitorVoid

appendText

count

setStatus

setTitle

setTotalSteps

shouldIstop

###### xml

mzidentmlwriter.cpp

###### mzidentmlwriter.h

###### pappso::MzIdentMlWriter

MzIdentMlWriter

~MzIdentMlWriter

toXmlDouble

toXmlMass

toXmlMassDelta

writeCvList

writeCvParam

writeCvParam

writeCvParam

writeCvParamUo

writeCvParamUo

writeDBSequence

writeDBSequence

writeStartMzIdentMlDocument

writeUserParam

writeUserParam

writeUserParam

writeUserParam

xmlstreamreaderinterface.cpp

###### xmlstreamreaderinterface.h

###### pappso::XmlStreamReaderInterface

XmlStreamReaderInterface

~XmlStreamReaderInterface

cloneElement

cloneNode

cloneStartElement

errorString

read

read

readFile

readStream

m_qxmlStreamReader

##### protein

enzyme.cpp

###### enzyme.h

###### pappso::Enzyme

Enzyme

Enzyme

~Enzyme

eat

getMiscleavage

getQRegExpRecognitionSite

replaceWildcards

sanityCheck

setMaxPeptideVariantListSize

setMiscleavage

setTakeOnlyFirstWildcard

m_maxPeptideVariantListSize

m_miscleavage

m_recognitionSite

m_takeOnlyFirstWildcard

m_wildCardB

m_wildCardX

m_wildCardZ

###### enzymeproductinterface.h

###### pappso::EnzymeProductInterface

setPeptide

###### pappso::PeptideModificatorInterface

~PeptideModificatorInterface

setPeptideSp

###### pappso::PeptideSinkInterface

setSink

###### pappso::PeptideSpSinkInterface

setSink

peptidebuilder.cpp

###### peptidebuilder.h

###### pappso::PeptideBuilder

PeptideBuilder

~PeptideBuilder

addFixedAaModification

setPeptide

setSink

m_fixedModificationList

m_sink

peptidefixedmodificationbuilder.cpp

###### peptidefixedmodificationbuilder.h

###### pappso::PeptideFixedModificationBuilder

PeptideFixedModificationBuilder

~PeptideFixedModificationBuilder

addAa

setPeptideSp

setProtCter

setProtElse

setProtNter

setSink

m_aaModificationList

m_isProtCterMod

m_isProtElseMod

m_isProtNterMod

m_sink

mp_mod

peptidemethioninremove.cpp

###### peptidemethioninremove.h

###### pappso::PeptideMethioninRemove

PeptideMethioninRemove

~PeptideMethioninRemove

setPeptide

setSink

m_isPotential

m_sink

peptidemodificatorbase.cpp

###### peptidemodificatorbase.h

###### pappso::PeptideModificatorBase

PeptideModificatorBase

~PeptideModificatorBase

getModificationPositionList

getModificationPositionList

setModificationPattern

m_pattern

peptidemodificatorpipeline.cpp

###### peptidemodificatorpipeline.h

###### pappso::PeptideModificatorPipeline

PeptideModificatorPipeline

PeptideModificatorPipeline

~PeptideModificatorPipeline

addFixedCterModificationString

addFixedModificationString

addFixedNterModificationString

addLabeledModificationString

addPotentialCterModificationString

addPotentialModificationString

addPotentialNterModificationString

parseFixedModification

parseLabeledModification

parsePotentialModification

privAddFixedModificationString

privAddPotentialModificationString

setPeptide

setPeptideSp

setSink

m_pepModificatorPtrList

m_sink

mp_firstModificator

mp_lastPeptideSinkInterface

mp_peptideModificatorTee

peptidemodificatortee.cpp

###### peptidemodificatortee.h

###### pappso::PeptideModificatorTee

PeptideModificatorTee

PeptideModificatorTee

~PeptideModificatorTee

addModificator

setPeptideSp

m_peptideModPtrList

peptidesemienzyme.cpp

###### peptidesemienzyme.h

###### pappso::PeptideSemiEnzyme

PeptideSemiEnzyme

~PeptideSemiEnzyme

setPeptide

setSink

m_sink

peptidesizefilter.cpp

###### peptidesizefilter.h

###### pappso::PeptideSizeFilter

PeptideSizeFilter

~PeptideSizeFilter

setPeptide

setSink

m_maxSize

m_minSize

m_sink

peptidevariablemodificationbuilder.cpp

###### peptidevariablemodificationbuilder.h

###### pappso::PeptideVariableModificationBuilder

PeptideVariableModificationBuilder

~PeptideVariableModificationBuilder

addAa

next_combination

setMaxNumberMod

setMinNumberMod

setModificationCounter

setPeptideSp

setProtCter

setProtElse

setProtNter

setSink

m_aaModificationList

m_isProtCterMod

m_isProtElseMod

m_isProtNterMod

m_maxNumberMod

m_minNumberMod

m_modificationCount

m_sink

mp_mod

peptidevariablemodificationreplacement.cpp

###### peptidevariablemodificationreplacement.h

###### pappso::PeptideVariableModificationReplacement

PeptideVariableModificationReplacement

~PeptideVariableModificationReplacement

replaceModificationsAtPosition

setPeptideSp

mp_modAfter

protein.cpp

###### protein.h

###### pappso::Protein

Protein

Protein

Protein

~Protein

getAccession

getDescription

getMass

getSequence

makeProteinSp

operator==

removeTranslationStop

reverse

setAccession

setDescription

setSequence

size

m_accession

m_description

m_length

m_removeTranslationStopRegExp

m_sequence

ProteinSp

proteinintegercode.cpp

###### proteinintegercode.h

###### pappso::ProteinIntegerCode

ProteinIntegerCode

ProteinIntegerCode

~ProteinIntegerCode

computePeptideCodeFragments

convolution

convolutionKernel

getPeptideCodedFragment

getProteinSp

getSeqAaCode

match

m_peptideCodedFragments

m_seqAaCode

msp_protein

proteinpeptidelist.cpp

###### proteinpeptidelist.h

###### ProteinPeptideList

ProteinPeptideList

~ProteinPeptideList

proteinpresenceabsencematrix.cpp

###### proteinpresenceabsencematrix.h

###### pappso::ProteinPresenceAbsenceMatrix

###### ProteinPresenceAbsenceMatrixElement

absent

present

ProteinPresenceAbsenceMatrix

ProteinPresenceAbsenceMatrix

~ProteinPresenceAbsenceMatrix

convolution

convolutionKernel

fillMatrix

getPresenceAbsenceMatrix

getScore

operator=

m_presenceAbsenceMatrix

##### psm

###### deepprot

deepprotenum.cpp

###### deepprotenum.h

###### pappso::DeepProtEnumStr

DeepProtMatchTypeFromString

DeepProtPeptideCandidateStatusFromString

toString

toString

###### DeepProtMatchType

uncategorized

ZeroMassDelta

ZeroMassDeltaMissedCleavage

ZeroMassDeltaSemiTryptic

DeltaPosition

NoDeltaPosition

last

###### DeepProtPeptideCandidateStatus

unmodified

ZeroMassDelta

CterRemoval

NterRemoval

MissedCleavage

DeltaPosition

NoDeltaPosition

last

###### experimental

ionisotoperatioscore.cpp

###### ionisotoperatioscore.h

###### pappso::IonIsotopeRatioScore

IonIsotopeRatioScore

~IonIsotopeRatioScore

getIonIsotopeRatioScore

m_ionIsotopeRatioScore

###### features

psmfeatures.cpp

###### psmfeatures.h

###### pappso::PsmFeatures

PsmFeatures

~PsmFeatures

countMatchedIonComplementPairs

findComplementIonPairs

getAaSequenceCoverage

getComplementPairsAaSequenceCoverage

getIntensityOfMatchedIon

getIonIsotopeLinearRegression

getIonPairPrecursorMassDelta

getMatchedMzDiffMean

getMatchedMzDiffSd

getMaxConsecutiveIon

getMaxIntensityMatchedIonComplementPairPrecursorMassDelta

getMaxIntensityPeakIonMatch

getNumberOfMatchedIons

getPeakIonPairs

getTotalIntensity

getTotalIntensityOfMatchedIonComplementPairs

getTotalIntensityOfMatchedIons

setPeptideSpectrumCharge

m_ionList

m_matchedMzDiffMean

m_matchedMzDiffMedian

m_matchedMzDiffSd

m_ms2precision

m_parentCharge

m_peakIonPairs

m_precursorTheoreticalMass

m_precursorTheoreticalMz

m_spectrumSumIntensity

msp_filterChargeDeconvolution

msp_filterKeepGreater

msp_filterMzExclusion

msp_peptide

msp_peptideSpectrumMatch

###### morpheus

morpheusscore.cpp

###### morpheusscore.h

###### pappso::MorpheusScore

MorpheusScore

~MorpheusScore

getMorpheusScore

_morpheus_score

###### xtandem

###### xtandemhyperscore.cpp

factorial

###### xtandemhyperscore.h

###### pappso::XtandemHyperscore

AaFactorMap

XtandemHyperscore

XtandemHyperscore

~XtandemHyperscore

getHyperscore

getMatchedIons

getXtandemPredictedIonIntensityFactor

_aa_ion_factor_b

_aa_ion_factor_y

_ion_count

_proto_hyperscore

_refine_spectrum_synthesis

###### xtandemhyperscorebis.cpp

factorial

###### xtandemhyperscorebis.h

###### pappso::XtandemHyperscoreBis

AaFactorMap

XtandemHyperscoreBis

~XtandemHyperscoreBis

computeXtandemHyperscore

getHyperscore

getMatchedIons

getTotalMatchedIons

getXtandemPredictedIonIntensityFactor

reset

m_aaIonFactorBb

m_aaIonFactorY

m_ionCount

m_ionList

m_isRefineSpectrumSynthesis

m_protoHyperscore

m_totalMatchedIons

mp_precision

xtandemspectrumprocess.cpp

###### xtandemspectrumprocess.h

###### pappso::XtandemSpectrumProcess

XtandemSpectrumProcess

XtandemSpectrumProcess

~XtandemSpectrumProcess

getDynamicRange

getExcludeParent

getExcludeParentNeutralLoss

getIonScore

getMinimumMz

getNeutralLossMass

getNeutralLossWindowDalton

getNmostIntense

getRefineSpectrumModel

getRemoveIsotope

process

setDynamicRange

setExcludeParent

setExcludeParentNeutralLoss

setIonScore

setMinimumMz

setNeutralLossMass

setNeutralLossWindowDalton

setNmostIntense

setRefineSpectrumModel

setRemoveIsotope

_a_ions

_ao_ions

_astar_ions

_b_ions

_bo_ions

_bstar_ions

_c_ions

_x_ions

_y_ions

_yo_ions

_ystar_ions

_z_ions

m_filter_floor

m_filter_highpass

m_filter_keep_greater

m_filter_remove_c13

m_filter_rescale

m_isExcludeParent

m_isExcludeParent_lower_dalton

m_isExcludeParent_neutral_loss

m_isExcludeParent_upper_dalton

m_isRefineSpectrumModel

m_isRemoveIsotope

m_n_most_intense

m_neutralLossMass

m_neutralLossWindowDalton

###### peakionisotopematch.cpp

findComplementIonType

###### peakionisotopematch.h

###### pappso::PeakIonIsotopeMatch

PeakIonIsotopeMatch

PeakIonIsotopeMatch

PeakIonIsotopeMatch

~PeakIonIsotopeMatch

getPeptideNaturalIsotopeAverageSp

operator=

toString

_naturalIsotopeAverageSp

PeakIonIsotopeMatchCstSPtr

findComplementIonType

Q_DECLARE_METATYPE

peakionmatch.cpp

###### peakionmatch.h

###### pappso::PeakIonMatch

PeakIonMatch

PeakIonMatch

PeakIonMatch

~PeakIonMatch

getCharge

getPeak

getPeptideFragmentIonSp

getPeptideIonDirection

getPeptideIonType

operator=

toString

_charge

_ion_sp

_peak

peptideisotopespectrummatch.cpp

###### peptideisotopespectrummatch.h

###### pappso::PeptideIsotopeSpectrumMatch

const_iterator

PeptideIsotopeSpectrumMatch

PeptideIsotopeSpectrumMatch

PeptideIsotopeSpectrumMatch

~PeptideIsotopeSpectrumMatch

begin

dropPeaksLackingMonoisotope

end

getBestPeakIterator

getPeakIonIsotopeMatchList

size

_peak_ion_match_list

_precision

peptidespectrummatch.cpp

###### peptidespectrummatch.h

###### pappso::PeptideSpectrumMatch

const_iterator

PeptideSpectrumMatch

PeptideSpectrumMatch

PeptideSpectrumMatch

PeptideSpectrumMatch

~PeptideSpectrumMatch

begin

contains

countTotalMatchedIons

end

getBestPeakIterator

getIonTypeCountArray

privMatchIonList

size

_ion_type_count

_peak_ion_match_list

_precision

##### trace

###### datapoint.cpp

operator<<

operator>>

dataPointCstSPtrMetaTypeId

dataPointMetaTypeId

###### datapoint.h

###### pappso::DataPoint

DataPoint

DataPoint

DataPoint

DataPoint

DataPoint

incrementX

incrementY

initialize

initialize

initialize

isValid

makeDataPointCstSPtr

operator=

operator==

reset

toString

toString

x

y

DataPointCstSPtr

operator<<

operator>>

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

dataPointCstSPtrMetaTypeId

dataPointMetaTypeId

linearregression.cpp

###### linearregression.h

###### pappso::LinearRegression

LinearRegression

LinearRegression

getCoefficientOfDetermination

getIntercept

getNrmsd

getRmsd

getSize

getSlope

getYfromX

m_data

m_intercept

m_slope

###### maptrace.cpp

mapTraceMetaTypeId

mapTracePtrMetaTypeId

###### maptrace.h

###### pappso::MapTrace

MapTrace

MapTrace

MapTrace

MapTrace

MapTrace

~MapTrace

initialize

initialize

insertOrUpdate

insertOrUpdate

makeMapTraceCstSPtr

makeMapTraceSPtr

operator=

toString

toTrace

xValues

yValues

MapTraceCstSPtr

MapTraceSPtr

operator<<

operator>>

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

mapTraceMetaTypeId

mapTracePtrMetaTypeId

###### trace.cpp

areaTrace

findDifferentYvalue

findDifferentYvalue

findFirstEqualOrGreaterX

findFirstEqualOrGreaterX

findFirstGreaterX

findFirstGreaterX

flooredLocalMaxima

maxYDataPoint

maxYDataPoint

meanYTrace

medianYTrace

minYDataPoint

minYDataPoint

moveLowerYLeftDataPoint

moveLowerYRigthDataPoint

operator<<

operator>>

quantileYTrace

sumYTrace

traceMetaTypeId

tracePtrMetaTypeId

###### trace.h

###### pappso::Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

Trace

~Trace

append

containsX

dataPointCstIteratorWithX

dataPointIndexWithX

dataPointIteratorWithX

filter

initialize

initialize

initialize

initialize

initialize

makeTraceCstSPtr

makeTraceSPtr

maxX

maxXDataPoint

maxY

maxY

maxYDataPoint

minX

minXDataPoint

minY

minYDataPoint

operator=

operator=

removeZeroYDataPoints

sort

sortX

sortY

sumY

sumY

toMap

toString

unique

xAsBase64Encoded

xValues

yAsBase64Encoded

yValues

MassSpectrumCombinerInterface

TraceCombiner

TraceMinusCombiner

TracePlusCombiner

TraceCstSPtr

TraceSPtr

areaTrace

findDifferentYvalue

findDifferentYvalue

findFirstEqualOrGreaterX

findFirstEqualOrGreaterX

findFirstGreaterX

findFirstGreaterX

flooredLocalMaxima

maxYDataPoint

maxYDataPoint

meanYTrace

medianYTrace

minYDataPoint

minYDataPoint

moveLowerYLeftDataPoint

moveLowerYRigthDataPoint

operator<<

operator>>

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

quantileYTrace

sumYTrace

traceMetaTypeId

tracePtrMetaTypeId

##### vendors

###### tims

###### mobilitytraces

timsframemobilitytraces.cpp

###### timsframemobilitytraces.h

###### pappso::TimsFrameMobilityTraces

TimsFrameMobilityTraces

TimsFrameMobilityTraces

~TimsFrameMobilityTraces

extractMobilityTraces

getIonMobTraceList

getMzList

getScanIndexList

getTofIndexList

m_ionMobTraceList

m_scanIndexList

m_tofIndexList

mcsp_timsFrameCstSPtr

###### mzcalibration

###### cardano.cpp

cubic_solver

inHousePolynomialSolve

BUFFER_inv27

BUFFER_pow11

BUFFER_SQRT3

###### cardano.h

###### InHousePolynomialSolverResult

type

x1

x2

x3

###### CardanoResultCase

notvalid

zerod

negatived

positived

quadratic

line

inHousePolynomialSolve

mzcalibrationinterface.cpp

###### mzcalibrationinterface.h

###### pappso::MzCalibrationInterface

MzCalibrationInterface

~MzCalibrationInterface

getMzFromTofIndex

getTofFromTofIndex

getTofFromTofIndex

getTofIndexFromMz

operator=

operator==

m_digitizerDelay

m_digitizerTimebase

m_mzCalibrationArr

MzCalibrationInterfaceSPtr

mzcalibrationmodel1.cpp

###### mzcalibrationmodel1.h

###### pappso::MzCalibrationModel1

MzCalibrationModel1

~MzCalibrationModel1

getMzFromTofIndex

getTofIndexFromMz

###### pappso::MzCalibrationModel1Cached

MzCalibrationModel1Cached

~MzCalibrationModel1Cached

getMzFromTofIndex

m_arrMasses

m_max

mzcalibrationstore.cpp

###### mzcalibrationstore.h

###### pappso::MzCalibrationStore

MzCalibrationStore

~MzCalibrationStore

getInstance

m_mapMzCalibrationSPtr

###### xicextractor

timsdirectxicextractor.cpp

###### timsdirectxicextractor.h

###### pappso::TimsDirectXicExtractor

TimsDirectXicExtractor

~TimsDirectXicExtractor

protectedExtractXicCoordSPtrList

timsxicextractorinterface.cpp

###### timsxicextractorinterface.h

###### pappso::TimsXicExtractorInterface

TimsXicExtractorInterface

~TimsXicExtractorInterface

mp_timsData

TimsData

timsbindec.cpp

###### timsbindec.h

###### pappso::TimsBinDec

TimsBinDec

TimsBinDec

~TimsBinDec

closeLinearRead

getQfileLinear

getQfileRandom

getTimsFrameFromRawDataChunck

getTimsFrameSPtrByOffset

moveLinearReadForward

startLinearRead

m_decompressMemoryBufferSize

m_firstFrameId

m_lastFrameId

m_linearAccessRawDataChunckDequeSize

m_linearAccessRawDataChunckList

m_linearForwardThreshold

m_randemAccessFrameRawDataChunck

m_timsBinFile

m_timsCompressionType

mp_fileLinear

mp_fileRandom

mpa_decompressMemoryBuffer

timsdata.cpp

###### timsdata.h

###### pappso::FrameIdDescr

m_frameId

m_globalScanIndex

m_scanCount

###### pappso::TimsData

TimsData

TimsData

~TimsData

fillFrameIdDescrList

getFrameCount

getFrameIdDescrList

getGlobalScanIndexByScanCoordinates

getMassSpectrumCstSPtr

getMassSpectrumCstSPtrByGlobalScanIndex

getMassSpectrumCstSPtrByRawIndex

getMsLevelByGlobalScanIndex

getMsLevelBySpectrumIndex

getQualifiedMassSpectrumByGlobalScanIndex

getQualifiedMassSpectrumByRawIndex

getRawIndexFromCoordinate

getRawMsBySpectrumIndex

getRetentionTimeLine

getRetentionTimeLineInSeconds

getScanByGlobalScanIndex

getScanCoordinateFromRawIndex

getScanCoordinatesByGlobalScanIndex

getTicChromatogram

getTimsBinDecPtr

getTimsDataDirectory

getTimsDdaPrecursorsPtr

getTimsDiaSlicesPtr

getTimsFrameBaseCstSPtr

getTimsFrameBaseCstSPtrCached

getTimsFrameCstSPtr

getTimsFrameCstSPtrCached

getTimsFrameRecordList

getTimsMS1FrameIdsInRtRange

getTimsMS2FrameIdsInRtRange

getTotalNumberOfFrames

getTotalNumberOfScans

getTotalScanCount

isDdaRun

isDiaRun

openDatabaseConnection

m_cacheSize

m_frameCount

m_frameIdDescrList

m_mapFramesRecord

m_mapMzCalibrationRecord

m_mapTimsCalibrationRecord

m_mutex

m_someoneIsLoadingFrameId

m_thousandIndexToFrameIdDescrListIndex

m_timsDataDirectory

m_timsFrameBaseCache

m_timsFrameCache

m_totalScanCount

mpa_mzCalibrationStore

mpa_timsBinDec

mpa_timsDdaPrecursors

mpa_timsDiaSlices

TimsDdaPrecursors

TimsDiaSlices

TimsDataSp

timsdatafastmap.cpp

###### timsdatafastmap.h

###### pappso::TimsDataFastMap

###### TimsDataFastMapElement

count

first_access

TimsDataFastMap

accumulateIntensity

builtInCentroid

clear

downsizeMzRawMap

getTimsDataFastMapInstance

getTofIndexList

readIntensity

removeArtefactualSpike

m_preAllocatedFastMapPerThread

mapTofIndexIntensity

tofIndexList

###### pappso::TimsDataFastMap::TimsDataFastMapElement

count

first_access

timsddaprecursors.cpp

###### timsddaprecursors.h

###### pappso::TimsDdaPrecursors

###### SpectrumDescr

collisionEnergy

isolationMz

isolationWidth

ms1_index

ms2_index

parent_frame

precursor_id

precursor_ion_data

scan_mobility_end

scan_mobility_start

tims_frame_list

TimsDdaPrecursors

~TimsDdaPrecursors

fillSpectrumDescriptionWithSqlRecord

getClosestPrecursorIdByMz

getCombinedMs2ScansByPrecursorId

getMatchPrecursorIdByKo

getMs2BuiltinCentroid

getPrecursorsByMzRtCharge

getQualifiedMs1MassSpectrumBySpectrumDescr

getQualifiedMs2MassSpectrumBySpectrumDescr

getSpectrumDescrListByFrameId

getSpectrumDescrWithPrecursorId

getSpectrumDescrWithScanCoordinates

getTotalPrecursorCount

getXicCoordTimsFromPrecursorId

ms2ReaderGenerateMS1MS2Spectrum

ms2ReaderSpectrumCollectionByMsLevel

rawReaderSpectrumCollectionByMsLevel

setMonoThread

setMs1FilterCstSPtr

setMs2BuiltinCentroid

setMs2FilterCstSPtr

m_builtinMs2Centroid

m_isMonoThread

m_mapXicCoordRecord

m_mutex

m_totalPrecursorCount

mcsp_ms1Filter

mcsp_ms2Filter

mp_timsDataOrigin

TimsData

###### pappso::TimsDdaPrecursors::SpectrumDescr

collisionEnergy

isolationMz

isolationWidth

ms1_index

ms2_index

parent_frame

precursor_id

precursor_ion_data

scan_mobility_end

scan_mobility_start

tims_frame_list

timsdiaslices.cpp

###### timsdiaslices.h

###### pappso::TimsDiaSlices

###### FrameSliceRange

begin_global_slice_index

end_global_slice_index

frame_id

###### MsMsWindow

isMzInRange

CollisionEnergy

IsolationMz

IsolationWidth

ScanNumBegin

ScanNumEnd

SliceIndex

WindowGroup

###### MsMsWindowGroup

WindowGroup

###### MsMsWindowGroupList

~MsMsWindowGroupList

addInGroup

getWindowGroupPtrByGroupId

TimsDiaSlices

~TimsDiaSlices

getCombinedMs2ScansByGlobalSliceIndex

getFrameIdByGlobalSliceIndex

getFrameSliceRangeByGlobalSliceIndex

getGlobalSliceIndexBeginByFrameId

getLastMs1FrameIdByMs2FrameId

getMapFrame2WindowGroupPtr

getMs1QualifiedSpectrumByGlobalSliceIndex

getMs2QualifiedSpectrumByGlobalSliceIndex

getMsMsWindowByGlobalSliceIndex

getMsMsWindowGroupList

getTotalSlicesCount

m_builtinMs2Centroid

m_frameId2GlobalSliceIndexBegin

m_frameSliceRangeList

m_mapFrame2WindowGroupPtr

m_ms1frameIdList

m_ms2frameId2Ms1FrameId

m_msMsWindowGroupList

m_totalSlicesCount

mp_timsDataOrigin

###### pappso::TimsDiaSlices::MsMsWindow

isMzInRange

CollisionEnergy

IsolationMz

IsolationWidth

ScanNumBegin

ScanNumEnd

SliceIndex

WindowGroup

###### pappso::TimsDiaSlices::MsMsWindowGroup

WindowGroup

###### pappso::TimsDiaSlices::MsMsWindowGroupList

~MsMsWindowGroupList

addInGroup

getWindowGroupPtrByGroupId

###### pappso::TimsDiaSlices::FrameSliceRange

begin_global_slice_index

end_global_slice_index

frame_id

timsframe.cpp

###### timsframe.h

###### pappso::TimsFrame

###### XicComputeStructure

XicComputeStructure

mobilityIndexBegin

mobilityIndexEnd

mzIndexLowerBound

mzIndexUpperBound

tmpIntensity

xic_ptr

TimsFrame

TimsFrame

~TimsFrame

TimsFrame

combineScansInTofIndexIntensityMap

combineScansInTofIndexIntensityMap

combineScansToTraceWithDowngradedMzResolution

combineScansToTraceWithDowngradedMzResolution2

cumulateScan

cumulateScan2

cumulateScanIntensities

cumulateScanRangeIntensities

cumulateScansToTrace

extractTimsXicListInRtRange

getMassSpectrumSPtr

getMobilityScan

getRawTraceSPtr

getRawValuePairList

getScanIntensityList

getScanOffset

getScanPeakCount

getScanTofIndexList

unshufflePacket

m_binaryData

TimsDirectXicExtractor

###### pappso::TimsFrame::XicComputeStructure

XicComputeStructure

mobilityIndexBegin

mobilityIndexEnd

mzIndexLowerBound

mzIndexUpperBound

tmpIntensity

xic_ptr

TimsFrameCstSPtr

TimsFrameSPtr

timsframebase.cpp

###### timsframebase.h

###### pappso::TimsFrameBase

###### TofIndexIntensityPair

intensity_index

tof_index

TimsFrameBase

TimsFrameBase

~TimsFrameBase

checkScanNum

combineScansInTofIndexIntensityMap

combineScansInTofIndexIntensityMap

combineScansToTraceWithDowngradedMzResolution

combineScansToTraceWithDowngradedMzResolution2

cumulateScanIntensities

cumulateScanRangeIntensities

cumulateScansToTrace

downgradeResolutionOfTofIndexIntensityPairList

getDriftTimeInMilliseconds

getId

getIonMobilityTraceByTofIndexRange

getMassSpectrumCstSPtr

getMassSpectrumSPtr

getMaximumRawMassIndex

getMobilityScan

getMsLevel

getMzCalibrationInterfaceSPtr

getOneOverK0Transformation

getRtInSeconds

getScanIndexFromOneOverK0

getScanIntensityList

getScanPeakCount

getScanTofIndexList

getTotalNumberOfScans

getTraceFromTofIndexIntensityMap

getVoltageTransformation

hasSameCalibrationData

setAcqDurationInMilliseconds

setMsMsType

setMzCalibration

setMzCalibrationInterfaceSPtr

setRtInSeconds

setTimsCalibration

m_acqDurationInMilliseconds

m_frameId

m_msMsType

m_rtInSeconds

m_scanCount

m_timsC6

m_timsC7

m_timsDvStart

m_timsNdelay

m_timsSlope

m_timsTtrans

m_timsVmax

m_timsVmin

msp_mzCalibration

###### pappso::TimsFrameBase::TofIndexIntensityPair

intensity_index

tof_index

TimsFrameBaseCstSPtr

TimsFrameBaseSPtr

timsframerawdatachunck.cpp

###### timsframerawdatachunck.h

###### pappso::TimsFrameRawDataChunck

TimsFrameRawDataChunck

~TimsFrameRawDataChunck

getCompressedSize

getFrameId

getFrameLength

getFrameNumberOfScans

getMemoryBuffer

readTimsFrame

m_frameId

m_frameLength

m_frameNumberOfScans

m_memoryBufferSize

mpa_memoryBuffer

###### timsframerecord.h

###### pappso::TimsFrameRecord

accumulation_time

frame_id

frame_t1

frame_t2

frame_time

msms_type

mz_calibration_id

tims_calibration_id

tims_offset

timsframetype1.cpp

###### timsframetype1.h

###### pappso::TimsFrameType1

TimsFrameType1

TimsFrameType1

~TimsFrameType1

copyAndLzfDecompress

cumulateScan

cumulateScan2

getMassSpectrumSPtr

getRawTraceSPtr

getRawValuePairList

getScanIntensityList

getScanPeakCount

getScanTofIndexList

lzfDecompressScan

m_scanOffsetList

m_scanSizeList

timsms2centroidfilter.cpp

###### timsms2centroidfilter.h

###### pappso::TimsMs2CentroidFilter

TimsMs2CentroidFilter

TimsMs2CentroidFilter

~TimsMs2CentroidFilter

filter

##### widget

###### httpbutton

httpbutton.cpp

###### httpbutton.h

###### pappso::HttpButton

HttpButton

~HttpButton

getChEBIUrl

getOlsUrl

getPubMedUrl

getRESIDUrl

getUnimodUrl

mousePressEvent

setText

###### massspectrumwidget

massspectrumwidget.cpp

###### massspectrumwidget.h

###### pappso::MassSpectrumWidget

MassSpectrumWidget

~MassSpectrumWidget

clearData

computeIsotopeMassList

highlightPrecursorPeaks

ionChanged

mzChanged

mzChangeEvent

peakChanged

peakChangeEvent

peptideAnnotate

plot

rescale

savePdf

setIonList

setMassSpectrumCstSPtr

setMaximumIsotopeNumber

setMaximumIsotopeRank

setMs1Precision

setMs2Precision

setMsLevel

setPeptideCharge

setPeptideSp

setQualifiedMassSpectrum

setVisibleMassDelta

toQPaintDevice

QCPSpectrum

_custom_plot

_ion_list

_is_visible_mass_delta

_isotope_mass_list

_max_isotope_number

_max_isotope_rank

_ms_level

_p_mouse_peak

_p_ms1_precision

_p_ms2_precision

_peak_ion_isotope_match_list

_peptide_charge

_peptide_sp

_spectrum_sp

_tag_nmost_intense

qcpspectrum.cpp

###### qcpspectrum.h

###### pappso::QCPSpectrum

QCPSpectrum

~QCPSpectrum

addMassDelta

addMs1IsotopePattern

addPeakIonIsotopeMatch

clearData

getMostIntensePeakBetween

getNearestPeakBetween

highlightPrecursorPeaks

keyPressEvent

keyReleaseEvent

mouseMoveEvent

mousePressEvent

mouseReleaseEvent

rescale

setMzRangeChanged

setSpectrumP

MassSpectrumWidget

_bar_width

_click

_control_key

_intensity_range

_map_ion_type_bars

_mass_delta_range

_mz_range

_old_x

_old_y

_p_delta_axis_rect

_p_delta_graph

_p_peak_bars

_p_peak_bars_isotope

_p_spectrum

_parent

mp_peak_bars_precursor

###### obo

###### obochooserwidget

obochooserwidget.cpp

###### obochooserwidget.h

###### pappso::OboChooserWidget

OboChooserWidget

~OboChooserWidget

getOboPsiModTermSelected

isOboTermSelected

setMzTarget

setPrecision

ui

###### obolistwidget

obolistmodel.cpp

###### obolistmodel.h

###### pappso::OboListModel

###### OboPsiModHandler

OboPsiModHandler

~OboPsiModHandler

setOboPsiModTerm

mp_parent

OboListModel

~OboListModel

data

getOboPsiModTerm

loadPsiMod

rowCount

m_oboPsiModTermList

###### pappso::OboListModel::OboPsiModHandler

OboPsiModHandler

~OboPsiModHandler

setOboPsiModTerm

mp_parent

obolistproxymodel.cpp

###### obolistproxymodel.h

###### pappso::OboListProxyModel

OboListProxyModel

~OboListProxyModel

filterAcceptsRow

filterMzPrecision

lessThan

m_mzTarget

m_precisionPtr

mp_sourceModel

obolistwidget.cpp

###### obolistwidget.h

###### pappso::OboListWidget

OboListWidget

~OboListWidget

filterMzPrecision

getMzTarget

getPrecisionPtr

oboTermChanged

onFilterChanged

onFilterChanged

onFilterChanged

onSelectionChanged

mpa_oboListModel

mpa_oboListProxyModel

ui

Q_DECLARE_METATYPE

###### obotermform

obotermform.cpp

###### obotermform.h

###### pappso::OboTermForm

OboTermForm

~OboTermForm

displayOboTerm

getOboPsiModTerm

isOboTerm

parseDefinitionLabel

m_findExternalLinks

m_oboPsiModTerm

ui

###### plotwidget

basecolormapplotwidget.cpp

###### basecolormapplotwidget.h

###### pappso::BaseColorMapPlotWidget

BaseColorMapPlotWidget

BaseColorMapPlotWidget

~BaseColorMapPlotWidget

addColorMap

addColorMap

axisScale

currentXaxisRangeIndices

currentYaxisRangeIndices

dataTo3ColString

dataToMatrixString

getColorMapPlotConfig

getOrigColorMapPlotConfig

getPlottingColor

setColorMapPlotConfig

setPlottingColor

transposeAxes

xAxisDataKind

xAxisScale

yAxisDataKind

yAxisScale

zAxisDataResetToOriginal

zAxisFilterHighPassPercentage

zAxisFilterLowPassPercentage

zAxisFilterLowPassThreshold

zAxisScale

zAxisScaleToLog10

m_colorMapPlotConfig

mpa_origColorMapData

mpa_origColorMapPlotConfig

BaseColorMapPlotWidgetCstSPtr

BaseColorMapPlotWidgetSPtr

baseplotcontext.cpp

###### baseplotcontext.h

###### pappso::BasePlotContext

BasePlotContext

BasePlotContext

~BasePlotContext

operator=

recordDragDirections

toString

updateIntegrationScope

updateIntegrationScopeRect

updateIntegrationScopeRhomb

updateIntegrationScopeRhombHorizontal

updateIntegrationScopeRhombVertical

m_currentDragPoint

m_dataKind

m_dragDirections

m_integrationScopeRhombHeight

m_integrationScopeRhombWidth

m_isKeyBoardDragging

m_isLeftPseudoButtonKeyPressed

m_isMeasuringDistance

m_isMouseDragging

m_isRightPseudoButtonKeyPressed

m_keyboardModifiers

m_lastCursorHoveredPoint

m_lastPressedMouseButton

m_lastReleasedMouseButton

m_mouseButtonsAtMousePress

m_mouseButtonsAtMouseRelease

m_pressedKeyCode

m_pressedMouseButtons

m_releasedKeyCode

m_selectionPolygon

m_startDragPoint

m_wasClickOnXAxis

m_wasClickOnYAxis

m_wasMouseDragging

m_wassKeyBoardDragging

m_xDelta

m_xRange

m_xRegionRangeEnd

m_xRegionRangeStart

m_yDelta

m_yRange

m_yRegionRangeEnd

m_yRegionRangeStart

msp_integrationScope

###### DragDirections

NOT_SET

LEFT_TO_RIGHT

RIGHT_TO_LEFT

TOP_TO_BOTTOM

BOTTOM_TO_TOP

###### baseplotwidget.cpp

basePlotContextMetaTypeId

basePlotContextPtrMetaTypeId

###### baseplotwidget.h

###### pappso::BasePlotWidget

BasePlotWidget

BasePlotWidget

~BasePlotWidget

allLayerNamesToString

axisDoubleClickHandler

axisPan

axisReframe

axisRescale

axisZoom

calculateDragDeltas

createAllAncillaryItems

directionKeyPressEvent

directionKeyReleaseEvent

dragDirection

drawSelectionRectangleAndPrepareZoom

drawXScopeSpanFeatures

drawYScopeSpanFeatures

getContext

getInnermostRangeX

getInnermostRangeY

getOutermostRangeX

getOutermostRangeY

getPen

getPlottingColor

getPlottingColor

getRange

getRangeX

getRangeY

hideAllPlotItems

hideSelectionRectangle

hideTracers

horizontalGetGraphCoordNewPointCountPixels

horizontalMoveMouseCursorCountPixels

integrationRequestedSignal

isClickOntoXAxis

isClickOntoYAxis

isSelectionRectangleVisible

isVerticalDisplacementAboveThreshold

keyPressEvent

keyPressEventSignal

keyReleaseEvent

keyReleaseEventSignal

lastCursorHoveredPointSignal

layerableLayerIndex

layerableLayerName

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerLeftButtonDraggingCursor

mouseMoveHandlerNotDraggingCursor

mouseMoveHandlerRightButtonDraggingCursor

mousePressHandler

mousePseudoButtonKeyPressEvent

mousePseudoButtonKeyReleaseEvent

mouseReleaseEventSignal

mouseReleaseHandler

mouseReleaseHandlerLeftButton

mouseReleaseHandlerRightButton

mouseWheelEventSignal

mouseWheelHandler

moveMouseCursorGraphCoordToGlobal

moveMouseCursorPixelCoordToGlobal

plotRangesChangedSignal

plottableDestructionRequestedSignal

plottableSelectionChangedSignal

redrawPlotBackground

replotWithAxesRanges

replotWithAxisRangeX

replotWithAxisRangeY

resetAxesRangeHistory

resetSelectionRectangle

restoreAxesRangeHistory

restorePreviousAxesRangeHistory

setAxisLabelX

setAxisLabelY

setFocus

setFocusSignal

setPen

setPlottingColor

setPlottingColor

setupWidget

showTracers

spaceKeyReleaseEvent

updateAxesRangeHistory

updateContextXandYAxisRanges

updateIntegrationScope

updateIntegrationScopeDrawing

updateIntegrationScopeHorizontalRhomb

updateIntegrationScopeRect

updateIntegrationScopeRhomb

updateIntegrationScopeVerticalRhomb

verticalGetGraphCoordNewPointCountPixels

verticalMoveMouseCursorCountPixels

whatIsVisibleOfTheSelectionRectangle

xAxisMeasurementSignal

yMinMaxOnXAxisCurrentRange

yMinMaxOnXAxisCurrentRange

m_axisLabelX

m_axisLabelY

m_context

m_desc

m_fileName

m_focusedBrush

m_focusedColor

m_lastAxisRangeHistoryIndex

m_leftMousePseudoButtonKey

m_mouseMoveHandlerSkipAmount

m_mouseMoveHandlerSkipCount

m_name

m_pen

m_rightMousePseudoButtonKey

m_shouldTracersBeVisible

m_unfocusedBrush

m_unfocusedColor

m_xAxisRangeHistory

m_yAxisRangeHistory

mp_hPosTracerItem

mp_selectionRectangeLine1

mp_selectionRectangeLine2

mp_selectionRectangeLine3

mp_selectionRectangeLine4

mp_vEndTracerItem

mp_vPosTracerItem

mp_vStartTracerItem

mp_xDeltaTextItem

mp_yDeltaTextItem

BasePlotWidgetCstSPtr

BasePlotWidgetSPtr

###### RangeType

outermost

innermost

###### SelectionDrawingLines

NOT_SET

TOP_LINE

BOTTOM_LINE

HORIZONTAL_LINES

RIGHT_LINE

LEFT_LINE

VERTICAL_LINES

FULL_POLYGON

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

basePlotContextMetaTypeId

basePlotContextPtrMetaTypeId

basetraceplotwidget.cpp

###### basetraceplotwidget.h

###### pappso::BaseTracePlotWidget

BaseTracePlotWidget

BaseTracePlotWidget

~BaseTracePlotWidget

addTrace

axisDoubleClickHandler

axisPan

axisReframe

axisRescale

axisZoom

clearGraphData

findIntegrationLowerRangeForKey

getValueRangeOnKeyRange

getValueRangeOnKeyRange

getValuesX

getValuesY

getYatX

getYatX

setGraphData

setGraphData

toTrace

toTrace

toTrace

toTrace

BaseTracePlotWidgetCstSPtr

BaseTracePlotWidgetSPtr

colormapplotconfig.cpp

###### colormapplotconfig.h

###### pappso::ColorMapPlotConfig

ColorMapPlotConfig

ColorMapPlotConfig

ColorMapPlotConfig

operator=

setOrigAndLastMaxZValue

setOrigAndLastMinZValue

setOrigMaxZValue

setOrigMinZValue

toString

keyCellCount

lastMaxZFilterThresholdPercentage

lastMaxZValue

lastMinZFilterThresholdPercentage

lastMinZValue

maxKeyValue

maxMzValue

minKeyValue

minMzValue

mzCellCount

origMaxZValue

origMinZValue

xAxisDataKind

xAxisScale

yAxisDataKind

yAxisScale

zAxisScale

driftspecmassspeccolormapplotwidget.cpp

###### driftspecmassspeccolormapplotwidget.h

###### pappso::DriftSpecMassSpecColorMapPlotWidget

DriftSpecMassSpecColorMapPlotWidget

~DriftSpecMassSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

driftspectraceplotwidget.cpp

###### driftspectraceplotwidget.h

###### pappso::DriftSpecTracePlotWidget

DriftSpecTracePlotWidget

~DriftSpecTracePlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

massspectraceplotcontext.cpp

###### massspectraceplotcontext.h

###### pappso::MassSpecTracePlotContext

MassSpecTracePlotContext

MassSpecTracePlotContext

~MassSpecTracePlotContext

operator=

operator=

toString

m_lastMr

m_lastMz

m_lastResolvingPower

m_lastTicIntensity

m_lastZ

###### massspectraceplotwidget.cpp

massSpecTracePlotContextMetaTypeId

massSpecTracePlotContextPtrMetaTypeId

###### massspectraceplotwidget.h

###### pappso::MassSpecTracePlotWidget

MassSpecTracePlotWidget

MassSpecTracePlotWidget

~MassSpecTracePlotWidget

computeResolvingPower

deconvolute

deconvoluteChargedState

deconvoluteIsotopicCluster

getChargeMinimalFractionalPart

getChargeStateEnvelopePeakSpan

keyPressEvent

keyPressEventSignal

keyReleaseEvent

massDeconvolutionSignal

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseEventSignal

mouseReleaseHandler

refreshBaseContext

resolvingPowerComputationSignal

setChargeMinimalFractionalPart

setChargeStateEnvelopePeakSpan

m_chargeMinimalFractionalPart

m_chargeStateEnvelopePeakSpan

m_context

Q_DECLARE_METATYPE

Q_DECLARE_METATYPE

massSpecTracePlotContextMetaTypeId

massSpecTracePlotContextPtrMetaTypeId

ticxicchromdriftspeccolormapplotwidget.cpp

###### ticxicchromdriftspeccolormapplotwidget.h

###### pappso::TicXicChromDriftSpecColorMapPlotWidget

TicXicChromDriftSpecColorMapPlotWidget

~TicXicChromDriftSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

ticxicchrommassspeccolormapplotwidget.cpp

###### ticxicchrommassspeccolormapplotwidget.h

###### pappso::TicXicChromMassSpecColorMapPlotWidget

TicXicChromMassSpecColorMapPlotWidget

~TicXicChromMassSpecColorMapPlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

ticxicchromtraceplotwidget.cpp

###### ticxicchromtraceplotwidget.h

###### pappso::TicXicChromTracePlotWidget

TicXicChromTracePlotWidget

~TicXicChromTracePlotWidget

keyPressEvent

keyReleaseEvent

mouseMoveHandler

mouseMoveHandlerDraggingCursor

mouseMoveHandlerNotDraggingCursor

mousePressHandler

mouseReleaseHandler

###### precisionwidget

precisionwidget.cpp

###### precisionwidget.h

###### pappso::PrecisionWidget

PrecisionWidget

~PrecisionWidget

getPrecision

precisionChanged

setCurrentIndex

setDaltonValueChanged

setPpmValueChanged

setPrecision

setResValueChanged

m_oldIndex

mp_daltonValueSpinBox

mp_ppmValueSpinBox

mp_precisionDalton

mp_precisionPpm

mp_precisionRes

mp_resValueSpinBox

mp_unitComboBox

###### switchbuttonwidget

switchbuttonwidget.cpp

###### switchbuttonwidget.h

###### pappso::SwitchWidget

SwitchWidget

~SwitchWidget

getSwitchValue

setSwitchValue

updateSwitchValue

m_switchButtonValue

###### xicwidget

qcpxic.cpp

###### qcpxic.h

###### pappso::QCPXic

QCPXic

~QCPXic

addMsMsEvent

addXicP

addXicPeakList

clear

clearXicPeakBorders

drawXicPeakBorders

getRetentionTimeFromSecondsToLocal

keyPressEvent

keyReleaseEvent

mouseMoveEvent

mousePressEvent

mouseReleaseEvent

rescale

setName

setRtRangeChanged

xAxisToSeconds

XicWidget

_click

_colours

_control_key

_current_ms2_event

_graph_color

_graph_peak_border_list

_graph_peak_surface_list

_intensity_range

_map_xic_graph

_mouse_move

_old_x

_old_y

_parent

_rt_range

xicwidget.cpp

###### xicwidget.h

###### pappso::XicWidget

XicWidget

~XicWidget

addMsMsEvent

addXicPeakList

addXicSp

clear

clearXicPeakBorders

clicked

drawXicPeakBorders

getIntensityAxisP

getName

getRtAxisP

getXicCstSPtr

operateNewRange

plot

replotAll

rescale

rescaleOneRange

rtChanged

rtChangeEvent

setName

setRetentionTimeInMinutes

setRetentionTimeInSeconds

toQPaintDevice

xicClickEvent

xicPeakListChanged

QCPXic

_map_xic_msms_event

_map_xic_name

_qcp_xic

_rt_in_seconds

_xic_peak_sp_list

_xic_sp_list

XicXicPeakPairList

graphicdevicewidget.cpp

###### graphicdevicewidget.h

###### GraphicDeviceWidget

GraphicDeviceWidget

~GraphicDeviceWidget

toQPaintDevice

toSvgFile

##### xic

qualifiedxic.cpp

###### qualifiedxic.h

###### pappso::QualifiedXic

QualifiedXic

~QualifiedXic

QualifiedXic

getMz

getXicCstSPtr

getXicSPtr

m_msRunId

m_mz

mp_precision

msp_xic

QualifiedXicSp

xic.cpp

###### xic.h

###### pappso::Xic

Xic

Xic

~Xic

atRetentionTime

debugPrintValues

getMsPointDistance

makeXicCstSPtr

makeXicSPtr

operator=

operator=

sortByRetentionTime

XicCstSPtr

XicSPtr

xicpeptidefragmention.cpp

###### xicpeptidefragmention.h

###### pappso::XicPeptideFragmentIon

XicPeptideFragmentIon

XicPeptideFragmentIon

~XicPeptideFragmentIon

getPeptideFragmentIonSp

msp_peptideFragmentIon

xicpeptidefragmentionnaturalisotope.cpp

###### xicpeptidefragmentionnaturalisotope.h

###### pappso::XicPeptideFragmentIonNaturalIsotope

XicPeptideFragmentIonNaturalIsotope

XicPeptideFragmentIonNaturalIsotope

~XicPeptideFragmentIonNaturalIsotope

getCharge

getPeptideFragmentIonSp

getPeptideNaturalIsotopeAverageSp

msp_naturalIsotopeAverage

msp_peptideFragmentIon

xicpeptideinterface.cpp

###### xicpeptideinterface.h

###### pappso::XicPeptideInterface

XicPeptideInterface

~XicPeptideInterface

getCharge

m_z

msp_peptideInterface

##### xicextractor

###### private

###### msrunslice.cpp

operator>>

###### msrunslice.h

###### pappso::MsRunSlice

MsRunSlice

MsRunSlice

~MsRunSlice

appendToStream

clear

getSliceNumber

getSpectrum

getSpectrum

makeMsRunSliceSp

setSize

setSliceNumber

setSpectrum

size

m_sliceNumber

m_spectrumList

MsRunSliceSPtr

operator>>

msrunxicextractor.cpp

###### msrunxicextractor.h

###### pappso::MsRunXicExtractor

###### MsRunXicExtractorPoints

rt

spectrum_index

###### MsRunXicExtractorReadPoints

MsRunXicExtractorReadPoints

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_msrun_points

MsRunXicExtractor

~MsRunXicExtractor

MsRunXicExtractor

extractOneXicCoord

getXicFromPwizMSDataFile

protectedExtractXicCoordSPtrList

m_msrun_points

MsRunXicExtractorFactory

###### pappso::MsRunXicExtractor::MsRunXicExtractorPoints

rt

spectrum_index

###### pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints

MsRunXicExtractorReadPoints

loadingEnded

needPeakList

setQualifiedMassSpectrum

m_msrun_points

msrunxicextractordisk.cpp

###### msrunxicextractordisk.h

###### pappso::MsRunXicExtractorDisk

MsRunXicExtractorDisk

MsRunXicExtractorDisk

~MsRunXicExtractorDisk

MsRunXicExtractorDisk

acquireSlices

appendSliceOnDisk

endPwizRead

extractOneXicCoord

prepareExtractor

protectedExtractXicCoordSPtrList

serializeMsRun

storeSlices

unserializeSlice

m_maxMz

m_minMz

m_msRunSliceListCache

m_mutex

m_retentionTimeList

m_rtSize

m_temporaryDirectory

mpa_temporaryDirectory

MsRunXicExtractorFactory

msrunxicextractordiskbuffer.cpp

###### msrunxicextractordiskbuffer.h

###### pappso::MsRunXicExtractorDiskBuffer

MsRunXicExtractorDiskBuffer

~MsRunXicExtractorDiskBuffer

MsRunXicExtractorDiskBuffer

appendSliceInBuffer

endPwizRead

flushBufferOnDisk

storeSlices

m_bufferMaxSize

m_bufferSize

m_sliceBufferMap

MsRunXicExtractorFactory

msrunxicextractorfactory.cpp

###### msrunxicextractorfactory.h

###### pappso::MsRunXicExtractorFactory

MsRunXicExtractorFactory

~MsRunXicExtractorFactory

buildMsRunXicExtractorSp

getInstance

setMsRunXicExtractorFactoryType

setTmpDir

m_instance

m_tmpDirName

m_type

###### MsRunXicExtractorFactoryType

nose

direct

disk

diskbuffer

msrunxicextractorinterface.cpp

###### msrunxicextractorinterface.h

###### pappso::MsRunXicExtractorInterface

MsRunXicExtractorInterface

MsRunXicExtractorInterface

~MsRunXicExtractorInterface

extractXicCoordSPtrList

extractXicCoordSPtrListParallelized

getMsRunId

getMsRunReaderSPtr

postExtractionProcess

protectedExtractXicCoordSPtrList

setPostExtractionTraceFilterCstSPtr

setRetentionTimeAroundTarget

setXicExtractMethod

m_retentionTimeAroundTarget

m_xicExtractMethod

mcsp_postExtractionTraceFilter

msp_msrun_reader

MsRunXicExtractorInterfaceSp

##### exportinmportconfig.h

PMSPP_LIB_DECL

mzrange.cpp

##### mzrange.h

###### pappso::MzRange

MzRange

MzRange

MzRange

MzRange

~MzRange

contains

getMz

lower

operator*=

operator+=

operator=

toString

upper

m_delta

m_mz

##### pappsoexception.h

###### pappso::PappsoException

PappsoException

PappsoException

~PappsoException

clone

qwhat

raise

what

m_message

m_stdMessage

precision.cpp

##### precision.h

###### pappso::PrecisionBase

PrecisionBase

delta

getNominal

toString

unit

m_nominal

###### pappso::DaltonPrecision

DaltonPrecision

~DaltonPrecision

delta

toString

unit

PrecisionFactory

###### pappso::PpmPrecision

PpmPrecision

~PpmPrecision

delta

toString

unit

PrecisionFactory

###### pappso::ResPrecision

ResPrecision

~ResPrecision

delta

toString

unit

PrecisionFactory

###### pappso::PrecisionFactory

MapDaltonPrecision

MapPpmPrecision

MapResPrecision

fromString

getDaltonInstance

getPpmInstance

getPrecisionPtrFractionInstance

getPrecisionPtrInstance

getResInstance

m_mapDalton

m_mapPpm

m_mapRes

PrecisionPtr

##### types.h

PEPTIDE_ION_TYPE_COUNT

pappso_double

pappso_float

PeptideStr

uint

###### AminoAcidChar

alanine

cysteine

aspartic_acid

glutamic_acid

phenylalanine

glycine

histidine

isoleucine

lysine

leucine

methionine

asparagine

proline

glutamine

arginine

serine

threonine

valine

tryptophan

tyrosine

selenocysteine

pyrrolysine

###### AtomIsotopeSurvey

C

H

O

N

S

last

###### Axis

unset

x

y

z

###### AxisScale

unset

orig

log10

###### DataCompression

unset

none

zlib

###### DataKind

unset

rt

dt

mz

###### FileReaderType

pwiz

xy

bafascii

tims

tims_frames

tims_ms2

tims_dia

###### Isotope

C13

H2

O17

O18

N15

S33

S34

S36

###### MsDataFormat

unknown

mzML

mzXML

MGF

SQLite3

xy

mz5

msn

abSciexWiff

abSciexT2D

agilentMassHunter

thermoRaw

watersRaw

brukerFid

brukerYep

brukerBaf

brukerTims

brukerBafAscii

last

###### PeptideIon

b

bstar

bo

a

astar

ao

bp

c

y

ystar

yo

z

yp

x

###### PrecisionUnit

none

dalton

ppm

res

mz

last

###### SortOrder

ascending

descending

###### SortType

no_sort

x

y

###### TimeUnit

none

s

min

h

###### XicExtractMethod

sum

max

ABUNDANCEC12

ABUNDANCEC13

ABUNDANCEH2

ABUNDANCEN15

ABUNDANCEO17

ABUNDANCEO18

ABUNDANCES33

ABUNDANCES34

ABUNDANCES36

DIFFC12C13

DIFFH1H2

DIFFN14N15

DIFFO16O17

DIFFO16O18

DIFFS32S33

DIFFS32S34

DIFFS32S36

MASSCARBON

MASSCO

MASSH2O

MASSNH3

MASSNITROGEN

MASSOXYGEN

MASSPHOSPHORUS

MASSPHOSPHORYLATEDR

MASSSELENIUM

MASSSULFUR

MHPLUS

MPROTIUM

MPROTON

ONEMILLION

utils.cpp

##### utils.h

###### pappso::Utils

almostEqual

appendToFile

booleanToString

chronoIntervalDebugString

chronoTimePointDebugString

extractScanNumberFromMzmlNativeId

fileReaderTypeAsString

getLexicalOrderedString

getVersion

msDataFormatAsString

nearestGreater

pointerToString

roundToDecimal32bitsAsLongLongInt

roundToDecimals

splitMzStringToDoubleVectorWithSpaces

splitSizetStringToSizetVectorWithSpaces

toString

toString

toUtf8StandardString

writeLexicalOrderedString

writeToFile

zeroDecimalsInValue

anythingButDigitDotDash

endOfLineRegExp

mzListDataFormatRegExp

signedDoubleNumberExponentialRegExp

sizetListDataFormatRegExp

unsignedDoubleNumberNoExponentialRegExp

xyMassDataFormatRegExp

### File Members

All

Functions

Variables

Enumerations

Macros

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