#
## All the words in this file will be ignored in the spellcheck
#

###################################
# Header {{{
###################################

ETH
Eberhard
Freie
Hoenggerberg
IMSB
Karls
Lund
MERCHANTABILITY
Redistributions
Tuebingen
Universitaet
# }}}

###################################
# Authors {{{
###################################

Aebersold
Aiche
Albers
Alexandra
Andreas
Andreotti
Anton
Axel
Bastian
Bauer
Belz
Bertsch
Bielow
Blank
Brauer
Chris
Clemens
Cornelia
Daniel
David
Demirev
Dimitri
Dominik
Erhan
Espona
Eva
Fabian
Florian
Franken
Frederic
Freidank
Friedle
George
Groarke
Groepl
Guillaume
Hannes
Helge
Hendrik
Heumos
Holger
Hussong
Immanuel
Ivar
Jameson
Jang
Jin
Johan
Johannes
Juliane
Julianus
Junker
Katharina
Kenar
Khalil
Knut
Kohlbacher
Kriegel
Kunszt
Kutuzova
Lange
Langwisch
Lankenau
Lars
Lehnert
Lennart
Liang
Lucia
Luhn
Lukas
Marc
Marcel
Markus
Martin
Mateusz
Mathias
McCloskeyt
Micha
Moritz
Mosthaf
Mueller
Musch
Nahnsen
Nico
Nicolai
Nikos
Nilse
Noske
Ole
Oliver
Patel
Patikos
Pervukhin
Peter
Pfeifer
Pfeuffer
Plattfaut
Ralf
Rausch
Reinert
Rene
Roest
Rosenberger
Rost
Rprop
Ruedi
Sachsenberg
Sandro
Sass
Schachmann
Scheil
Schilling
Schmachtenberg
Schmitz
Schulz
Schulz-Trieglaff
Startek
Steffen
Stephan
Sturm
Sven
Svetlana
Swenja
Thueringer
Timo
Tobias
Trieglaff
Valkenborg
Veit
Vipul
Volker
Walzer
Waschischeck
Wein
Weisser
Witold
Wojnar
Wolski
Xiao
Zeller
Zerck
Zimmermann
Zubarev
ącki
Łącki
# }}}

###################################
# More than 5 occurrences in the source code {{{
###################################

C'tor
DIA
Datastructures
DeNovo
Docu
Hiwi
Jacobian
MSVC
MapAlignment
Namespace
Quantitation
STL
SignalProcessing
SpectraPreprocessers
br
c'tor
datapoint
dataset
datastructures
de
dll
functor
functors
ifndef
ns
plex
quantitation
recomputation
reimplement
stl
todo
tt
workflow
xerces
# }}}

###################################
# More than 3 occurrences in the source code {{{
###################################

AA's
Accessor
AlphabetParser
AnalysisXML
C'Tor
Caap
ClusterMethod
Const
IMPL
Longman
PeakDetection
ProteinHits
RTs
TOPPASINPUTFILESDIALOG
XMass
Zhang
accessor
analysisXML
ansi
automagically
cdot
ctor
defgroup
frameSize
getter
gnuplot
lookup
lorentzian
lowpass
mapList
maxima
novo
stderr
subtree
typedefs
versa
# }}}

###################################
# Directory names and abbreviations {{{
###################################

ABI
AIP
Amol
BIGAUSSFITTER
BMC
CDATA
CHROMATOGRAMPEAK
CONFIDENCESCORING
CONSENSUSMAPNORMALIZERALGORITHMMEDIAN
CONSENSUSMAPNORMALIZERALGORITHMTHRESHOLD
CTD
Complife
DCT
DENOVOIDENTIFICATION
DRICHPEAK
ECCB
FEATUREFINDERALGORITHMPICKEDTRACEFITTERGAUSS
FEATUREGROUPINGALGORITHM
FEATUREGROUPINGALGORITHMIDENTIFICATION
FEATUREGROUPINGALGORITHMLABELED
FFT
FNs
FPs
FTMS
HCD
HIDDENSTUFF
HREF
ICAT
ISD
ISMB
ISOBARICNORMALIZER
ITRANSITION
ITRAQEIGHTPLEXQUANTITATIONMETHOD
ITRAQQUANTIFIER
IUPAC
JW
LABELEDPAIRFINDER
LCT
LDA
LLM
LMAISOTOPEFITTER
LOC
LOGCONFIGHANDLER
LSID
Lan
MAPALIGNMENTEVALUATIONALGORITHM
MAPMATCHER
MAXLIKELIFITTER
MDI
MIM
MIS
MSD
MSDB
Marr
NCCA
NIST
NONNEGATIVE
OFFLINEPRECURSORIONSELECTION
OMSSACSV
PEAKINTENSITYPREDICTOR
PEAKRT
PMF
POSECLUSTERINGAFFINESUPERIMPOSER
POSECLUSTERINGSHIFTSUPERIMPOSER
PRECURSORIONSELECTION
PSB
PSM
PSMs
PTMXML
PTMs
QA
QIT
QTCLUSTERFINDER
QTOF
RANGEUTILS
RBF
RGB
RMSE
RNGs
RNP
RRGGBB
RTFITTING
SAMPLENULL
SPECTRUMHELPERS
STABLEPAIRFINDER
STATSHELPERS
STREAMTYPE
SVC
SVG
SVR
TARGETEDEXPERIMENT
TARGETEDEXPERIMENTHELPER
TAc
TICs
TMP
TNVs
TOPPCLASSES
TPP
TPR
TPs
TRANSFORMATIONDESCRIPTION
TRANSFORMATIONMODEL
TRANSITIONEXPERIMENT
UTIL
UTILS
WEIGHTMODE's
WSDL
XCorr
mzid
qMZ
ttd
zlib's
# }}}

###################################
# Names and people {{{
###################################

ACM
AScore
Analysemethoden
Angeles
Backhaus
Beausoleil
Benno
Biotechnol
Boecker
Bougerel
Bruderer
Brusniak
Böcker
Choi
Cociorva
DL
Dayhoff
Dekker
Deutsch
Dunns
Epub
Erichson
Faires
Fohlman
GJ
Gambin
Giavalisco
Gobom
Golay
Graumann
Gropl
Grünberg
Gutenbrunner
HL
Hall
Heeren
Hengartner
Henner
Herk's
Herwig
Hildebrandt
Hookeun
Huettenhain
Hüsken
Igel
Jorgenson
Josuttis
Kalambet
Kozmin
Krafft
Ksenia
Kushnir
LONGMAN
Lalowski
Lehrach
Levenberg
Lippert
Lipták
Los
Luider
MJ
MSsim
MacCoss
Maciej
Mallick
Marquard
Marto
Martus
Mayr
Meena
Meinicke
Midani
Mikhailova
Modomics
Nagaev
Needleman
Newick
Nicolay
Nijenhuis
Orjan
Parag
Paulovich
Pavel
Pharmacopeia
Picotti
Plinke
Prakash
Prentice
Protoc
RG
Reiter
Rickard
Rijswijk
Rinner
Rockwood
Roepstoff
SQT
Sadygov
Savitzky
Scherbart
Schwikowski
Senko's
Shklov
Siccama
Sickmann
Siepen
Sillevis
Smitt
Spearman
Spectrometry
SteinScott
Sudek
Sylvain
TORTIOUS
Tabb
Teleman
Tholey
Tikhonov
Titulaer
Venable
Vidavsky
Voorhees
WABI
WH
Walzthoeni
Weiber
Wenger
Westin
Whiteaker
Wunsch
Zhou
Zinn
beineri
kinter
mProphet
nmeth
proteomic
sherman
williams
# }}}

###################################
# Classnames, functions and closely related {{{
###################################

###################################
# Classnames {{{
###################################

AAIndex
AASequence's
AASequences
AccurateMassSearch
AdapterBase
AlphabetTextParser
AnalysisResult
AnalysisResults
AnnotationItems
AutoMaxIntensity
AxisWidget
BasicGraph
BasisStatistic
BinaryTreeNodes
Bincontainer
BinnedSpectra
ByteArray
CVTerms
CachedMzMLConsumer
CachedMzMLConsumers
CarbonHydrogen
ChargeDifference
ChargePairs
ChromatogramList
ChromatogramPeaks
ClosedBoxes
CollisionEnergy
CompareFunctor
ConsensusElementLists
ConsensusMap
ConsensusMapNormalizer
ContentLengthHeader
CrossLinkDB
CrossLinkSpectrumMatches
CvMapping
DBSeq
DBSequenceElement
DBSuitabilityData
DCanvas
DFeature
DFitter
DOMErrorHandler
DOMHandler
DOMNodeListImpl
DSpectra
DWidget
DataArray
DataProcessingPtr
DataRepository
DataTime
DataValues
DatabaseFilters
DatabaseIO
DatabaseSuitability
DatabaseTranslation
DatabaseTranslations
DefaultParamHander
DefaultParamHandlerDocumenter
DividedByZero
DocumentID
DocumentIDs
DoubleReal
DoubleReals
Dpoints
DummyComparison
ElementNotFoundException
ElutionModel
EmpiricalFormula's
EnergyUnits
Enqueues
ExecutePipeline
ExtendedGraphClustered
ExtendedGraphClusteredWithRunInfo
FASTAEntries
FASTAHeader
FASTEEntry
FIAMSSchedule
FeatureFinderMetabo
FeatureFinderMultiplex
FeatureFinding
FeatureID
FeatureLinkerBase
FeatureUID
FeatureXMLs
FileConverter
FilledBinNumber
FinalizeAssay
FlexControlVersion
FragmentAnnotation
FragmentCharge
FragmentMassErrors
FragmentMz
FragmentNumber
FragmentSeriesNumber
FragmentType
FullId
FullIds
Functors
GUIProgressLoggerImpl
GlobalException
GraphML
GridSearch
HierarchicalClustering
HighRes
IDEvaluation
IDGraph
IDMerger
IDPool
IdentificationRun
IdentifyingTransition
Indices
Initializer
InputVertex
IntRealString
IntRealStringVector
IntermediateProduct
InvalidParameters
IonMatchError
IonName
IonNames
IonTypes
IsoSpecGeneratorWrapperSubclass
IsobaricAnalyzer
IsobaricQuantitation
IsolationWindowLow
IsolationWindowUp
IsotopeDisribution
IsotopeSpecies
KDTreeMaps
LabelType
LayerData
LessByInt
LessByReal
LessByString
LightPeptide
LocalClustering
LocalFileInputSource
LogCache
LogStreams
LossMasses
LowLevelComparator
LowRes
MRMFeatureFinder
MRMFeatures
MRMScoring
MSChromatograms
MSDGroups
MSDataConsumer
MSExperiments
MSSpectra
MapAligner
MapAlignerBase
MapAlignmentAlgorithm
MapAlignmentAlgorithms
MapAlignmentEvaluation
MassDifference
MathFunctionsMisc
MathFunctionsStatistics
MergerVertex
MessagePassers
MetaDataBrowser
MetaDataInterface
MetaInfoDescriptions
MetaInfodescriptions
MetaInformation
MetaInfos
MetaValueInterface
MetaboTargetAssay
MetaboTargetedAssays
Metafunction
MinReqElements
MissedCleavages
ModificationDB
ModifiedPeptideSequence
ModifiedSequence
MovingAverage
MsInspect
MultiplexPeakPattern
MutablePriorityQueue
MyDOMErrorHandler
MzDataHander
MzQuantML
MzTabCellType
MzTabDoubles
NormalizedRetentionTime
NucleicAcidSearchEngine
OPENSWATHALGO
OSWPeptidePrecursor's
OSWPeptidePrecursors
OnDiskExperiment
OpenBoxes
OpenSwathAlgoConfig
OpenXQuest
OutputFile
OutputNode
OutputVertex
PARSpectrumCountULAR
PILISSequenceDB
PSMExlpainedIonCurrent
ParamEditor
ParamNodes
ParamValues
ParameterHandler
PeakArray
PeakInfo
PeakMaps
PeakOptions
PeakSpektrum
PeptideGroupLabel
PeptideIdenfitication
PeptideIdentication
PeptideIdentifcation
PeptideIdentifications
PeptideIdentificationsPearsonDifference
PercentBackgroundInterference
PercolatorAdapter
PersistentObject
PlotCanvas
PlotWidget
PoolFile
PoseClustering
Preprocesses
ProcessingStep
ProductCharge
ProteinDetectionListElement
ProteinGroups
ProteinIdent
ProteinIdentication
ProteinIdentificationVisualizer
ProteinIndentification
ProteinProteinCrossLinks
ProteinQuantifier
ProteinsHits
QCFile
QEventLoop
QFile
QHttp
QMYSQL
QTClusters
QVariant
QualityControl
QuantifyingTransition
RNAMods
RTime
ReactionMonitoringTransitions
RelativeFragmentIntensity
ResMod
RetentionTimeCalculatorScore
RibonucleotideChainEnds
RichChromatogramPeak
RichPeakSpectrum
RunDescription
RunQuality
SILACAnalysis
SILACAnalyzer
SILACFilters
SavitzkyGolayQRFilter
SavitzkyGolaySVDFilter
ScanEventNumber
ScanFunction
SearchEngines
SearchParameter
SharedPtr
SignalToNoiseEstimatorRapid
SimplePeaks
SpecArray
SpectraFilePath
SpectraIDViewTab
SpectraSTPeakList
SpectrumAccess
SpectrumFragment
SpectrumGenerator
SpectrumList
SpectrumOpenGLCanvas
SqlOperation
StringConversion
StringLists
StringStream
StrippedSequence
TICWritingConsumer
TOPPSubsections
TSGXLMS
TandemScanningMethod
TargetedExperimentCompound
TargetedFileConverter
TermSpec
TerminusSpecificity
TextExporter
ToolDescriptor
ToolName
ToolVertex
TraMLs
TransformationDescriptions
TransformationXML
TransitionGroupId
TransitionGroupName
TransitionId
TransitionMap
TransitionName
UInts
UnderlyingIDStruc
UniprotID
XLPrecursors
ZhangSimilarityScoring
consensusfeaturehandler
datatypes
featureXML's
suggestedSize
# }}}

###################################
# Functions {{{
###################################

ConstChromatogramIterator
ConstSpectraIterator
Endianizes
MSGFtoPercolator
OptionalColumnNames
QtCore
Skellam
addFeatures
annotateInternalFragments
baseclass
beginChromatograms
beginSpectra
buildAnalysisSampleCollection
buildExtendedGraph
buildSynonyms
buildUIDfromAllPepIds
calculatedPI
checkCVTerms
clusteringmethod
compressBound
computeCombinedScore
computeFwhmAreaRobust
computeFwhmAreaSmoothRobust
convertTargetedPeptide
correctCVTermNames
countBasicResidues
createEmptyPeptideProbabilisticAdderFactor
currentAlphabetMass
dataReadProgress
dataSendProgress
distancemethod
encodeInt
encodeOligoBorder
encodings
endChromatograms
endSpectra
extractProteinAccessionSet
fillVectorsOfMessagePassersBruteForce
filterByProteinIDs
getAllDecomposition
getBestModificationByMonoMass
getChromatogam
getFWHMScansNum
getIDState
getInternalToYTerm
getLeftWidthParameter
getNeutralLosses
getNodeCount
getNodeName
getObjValue
getParamAs
getParameter
getParams
getProtonAffinity
getRightWidthParameter
getScoresFunctions
getSequenceDB
getSpecies
getSplineCount
getTaxonomyID
getTransforms
indistinguishableProteins
inferPosteriors
initLossModels
initMainModel
initModels
initPrecursorModel
inputFileWritable
isCorrupted
isLegalAveraginePattern
isoelectric
keepMatchingHits
loadTargets
massShift
minInputsPAF
newEnding
nextMove
nonZeros
peptideHit
peptideSiblings
regularData
removeDatabase
requestFinished
requestStarted
rescoreIncremental
resetDocumentPool
resolveConnectedComponentTargetsFirst
responseHeaderRecieved
sampleTheWavelet
scanSettingsRef
scanWindowList
scoreIntRatio
scoreTraceSim
searchModification
setBranchingMethod
setCoeffientLimits
setColumnUpper
setFWHMScansNum
setIDPoolFile
setNodeComparison
setParams
setScoresFunctions
setSequenceDB
shiftWindow
simulateSpectrumFromTransitions
sparseElement
sparseElements
sqlThrowingGetters
startElelement
stateChanged
streamtype
stringChecked
stringUnchecked
tminus
toLowercase
tplus
unassignedPeptideIDs
updateCRC
updateCombinedILPPeptideRule
updatePeptideHits
updateProteinHits
updateSpectraViewBar
writePeptideTable
writeProteinGroups
writeProteinTable
writeProteinsAndPeptidesmzTab
# }}}

###################################
# Closely related {{{
###################################

AAD
ApprLineFit
ArrowLeft
ArrowRight
AveragineModifications
BFS
BackbonePosition
BestCorr
CLP
CLion
CMake's
CVhandling
CalData
CalcMass
CbcBranchUserDecision
CbcCompareUser
CglFlowCover
CglProbing
ChargeFilter
ChargeStateIntensities
CoinCpuTime
ConnectedComponents
ConsensusElements
ConsensusID
CorrelationIntensity
DPACKAGE
DSEARCH
DTPrediction
DataCollection
DeNovoScore
DecoyDatabase
DetectingTransition
Elephas
ExitCode
ExpMass
FFid
FeatureId
FilteredGraph
FirstScan
FlowCover
GNUPlotFormula
GenBank
GeometricTools
IDConflictResolution
ILPwrapper
INCREMNTAL
ISDGraph
IdentificationRuns
InferenceEngine
InputFilesLists
IsoSpec's
JBC
KLinked
LNK
MSSpectrums
MSstatsTMT
MZTrafoModels
MaRaCluster
MapIndices
MeanError
Mobi
ModsDB
MultiplexFilterResult
MzTab's
NSIS
NightSky
NumOfScans
OPENPEPXLALGO
OPENPEPXLLFALGO
OddHole
OneLetterCode
OsiOslSolverInterface
PEPIons
PEPs
PILIS
PMFFactor
PPs
PRMNode
PTXQC
PepHit
PepID's
PeptideEvidences
PeptideID
PeptideIDs
PeptideIndexer
PercentInterference
PercentRSD
PrimaryRunPaths
ProtGroups
ProtID's
RTPrediction
SavitzkyGolay
ScanNr
ScoringMatrix
SequenceCollection
SpecId
SvgConfig
SwathWizard
Synon
TMPDIR
TopNoverRT
TrafoXMLs
TreeNode
Triqler
UltraModernUI
Widmagic
Wstring
XSValue
Xenial
absDeltaM
absFragMassError
absdm
bFact
bestForItsPeps
buildTheoreticalGraph
calculateSNident
cfd
cfg
checkExtremePSMScores
cmodel
concatMULTISEids
consensusElements
consensusFeatureId
consensusFeatureIdx
consensusfeaturemethod
correctedMZ
cstd
dScore
datadependent
deltaM
empFDR
enzC
enzInt
enzN
evaluateTransformationModel
extremum
featureIdx
featureIdxmaps
featureMap's
featureXMLs
featuredetection
fileformats
fileparameter
firstIsotopeMasses
firstprivate
fitTransformationModel
flowGen
fracIonsMatched
fragMassError
frequencyOld
gdebi
getNextPrecsSeq
getNumCols
getPValuesFromOutFiles
getScoresAndLabels
gfortran
gi
graphfile
groupID
img
initializeMap
innerVec
insertDependency
intMatched
intMatchedTot
isoDeltaM
kernelclasses
lastPackage
libHDF
libhdf
libicu
makensis
mapIdcs
mapaligment
markdownTable
markdownTableBodyLeft
markdownTableHead
markdownTableHeadCenter
markdownTableHeadLeft
markdownTableHeadNone
markdownTableHeadRight
masskey
maximus
maybeinliers
mergedpeps
mk
mmap
modus
movePepIDsAndRefProteinsToResult
multiplot
mySqrt
newIDRunIdx
newMergeIdxOffset
nrDiscarded
nsis
numResiduesof
oldMapIdx
oldProtRuns
ondisc
onelettercode
ostreams
outerVec
outputResults
passThreshold
passesWhitelist
peplen
peptideID
pkgs
postRaw
postacceleration
ppa
preIso
preIsotope
prePeaks
primaryMSRuns
primaryRunPaths
protGrp
protID
proteinSIP
proteindetectionprotocol
proteinsCollected
qTransform
qualityAttachments
qualityParameters
readChunk
readFeature
redundantCopy
relIntMatchedTot
removeExtremeValues
removeUnmatched
residuemod
resolveTies
rgbformula
rootProteinVtx
runIDToRunRef
runIDs
runQC
runinfo
seqCov
seqTable
setUsingObjective
spectradata
splitCC
tcharge
tempDigests
tempfile
threelettercode
tmpstructure
tmpvec
totInt
tracebackmatrix
tracematrix
transformationXMLs
trf
unassignedPeptideIdentifications
uncorrectedMZ
uniquePeps
unitAccession
unitName
unweight
usr
vcvars
winrt
xbase
xenial
xrefitem
xsize
yFact
zrange
# }}}

# }}}

###################################
# Doxygen {{{
###################################

Doxygen
ccc
cccc
cdots
dontinclude
emph
endcode
endverbatim
hideinitializer
ldots
ltnote
mathrm
relatesalso
textit
vdots
# }}}

###################################
# Common technical words {{{
###################################

AAcids
ABSciex
ADL
Accessors
Alanine
AmbAA's
Asn
BGCOLOR
BLOBs
Beavis
Bool
CMAKE
CMake
CMakeLists
CPUs
CRC
CVCollection
Carbamidomethyl
Checkbox
Chemometrics
ComboBox
DB's
DIMENSIONING
DLL
DOM
DefaultTag
Dotproduct
EBEBEB
EMG's
EOF
Enums
Exabyte
Exbibit
Exbibyte
FHWM
Failsafe
Fenyo
Fortran
FreeBSD
GCC
GLM
Google
HMM
Hydrogens
ID's
Javascript
Js
KiloBytes
LLVM
LOD
LOQ
MSVS
MacOS
MacOSX
Manhatten
Massdiff
Metabo
Metafunctions
MinGW
ModDB
Mutator
NDEBUG
NETLIB
NONPOSITIVE
NOP
NaN
Nm
NotStarted
OSX
Oxidations
Oxidiation
Oxygens
PIMPL
PRECRT
Phosphoruses
Prefractionation
Pubchemid
QNAN
Quantiles
RNAs
RNases
Rescale
SQL
SVMs
SciPy
SignalToNoise
SignificanceThreshold
SiteRegex
SomeType
Sortedness
Struct
Subfunction
Tabbar
ThermoFisher
Typedefs
UID's
Uncalibrated
Unselects
VC
VmRSS
VmSize
Werror
Wikipedia
Wnarrowing
acosine
alloverscore
allround
aminoacids
analysissummary
backsubstitution
badbit
basenames
bayes
bayesian
bitwise
boundings
boxplot
bruteforce
bufLen
caching's
chrono
classname
colspan
combobox
comboboxes
commandArgs
composable
consine
constness
coords
crc
crit
cvhandling
d'tors
dalton
datamatrices
datasets
deltaAbsError
deltaRelError
demangled
dereference
dereferences
dereferencing
destructors
discretized
docu
doi
downsample
endif
endlPointer
env
eol
equi
exe
executables
failbit
ffaa
ffff
fictious
filesystem
filtercoefficients
foldchange
fourier
gb's
gcc
gdb
getenv
getters
glutamate
goto
guanidine
gz
gzFile
gzerror
gzfile
halfbyte
halfbytes
handleable
hashmap
higherScoreBetter
highestscoring
hoc
hostname
hpp
html
https
hydrogens
hyperfine
hypersphere
hyperthreads
ifdef
iff
inCrc
inderdist
inlining
inputfiles
inputmatrix
inputvector
interdis
isopattern
isotopologue
isotopologues
iterable
jitter
li
libc
libf
libkdtree
libstdc
linebreak
linebreaks
linkable
linux
listelements
logfile
logscore
lossy
lvalue
mapcount
masse
maxpeak
medianize
medianized
mem
memFunc
memorycont
messagebox
messageboxes
metadataarrays
minima
misassignment
modpeptide
mol
multiclass
multiplet
multiplets
multithreaded
mutator
mutators
nRANSAC
nmer
nonisobaric
nonnull
nonrobust
noop
nucleobase
nullptrs
ol
ostringstream
osx
outstream
parallelization
parallelized
parameterization
parsable
peakintensity
peaklist
peakposition
pearson
peptidoform
php
plaintext
postcondition
postconditions
postdecrement
postfix
postorder
postprocess
powerset
preallocating
preorder
prepend
preprocessor
prettyprint
printf
propset
prote
pubmed
putativefeature
quantized
quantor
quartic
quartiles
rawfilegroup
readin
reannotated
reimplementation
reranked
resized
resizes
ribose
rowspan
rvalue
scatterplot
scrollbars
secan
secans
selfalignment
sigmoid
splitted
stdint
stdlib
stdout
stdv
sth
streambuffer
strtod
subdirectory
subelement
subfolders
subformulas
subfunctions
subnode
subnodes
subproblems
subscores
substring
subtest
subtool
subtools
svn
svnversion
tabData
tabbar
templating
threadsafe
timepoint's
tokenize
tokenizing
totalweight
tsv
tuples
typdefs
unary
ungrouped
unimodal
unix
unphosphorylated
untransformed
upto
urls
valgrind
vmRSS
vmSize
vtable
widgetstack
workflows
writeout
zeropadding
zoomselection
# }}}

###################################
# Common Mass spectrometry and OpenMS words {{{
###################################

AAAR
ANDI
Agilent
Askenazi
BiGaussian
Bioinformatics
Biomolecules
Bruker
CFs
CHNOPS
COOH
CRTP
CVTermList's
CVid
Carboxymethyl
Chauvenet's
CoarseIsotope
Compomer's
ComputeBuf
ConsensusFeatures
Contrib
Convolutes
DEFIANGR
DTT
DeltaScoreOther
Destructor
Destructors
DiffMonoMass
ECs
Electro
Elution
FAIM
FDA's
FFM
FIA
FTICR
FeatureGrouping
FeatureHandles
FileIO
FractionB
FractionY
FullUniModPeptideName
GC
HMMs
HSP
HUPO
HWHM
Histidin
Hydropathy
Hydrophobicity
Hydroxylation
IBSpectra
ICR
IDMAPPER
ILPS
IMSCORING
InsPecT
IsobaricLabelling
IsotopeDiffs
Isotopically
Kaatz
Kessner
LFQ
LOWESS
Labelgroup
Leucin
LibraryIntensity
Lys
MAAAR
MSData
MSLevels
MSPepHits
MSn
MSstats
MascotAdapter
MassHunter
MassTable
MedianPRMScore
MetaValue
Metadata
MonoMass
Monoisotopic
Myoglobin
Mz
MzData's
MzML
Nano
NanoFlow
NrModifications
OMSSA
OPENMP
OpenGL
OpenMP
OpenSWATH
PEPTLDE
PI's
PILISModel
PSM’s
PeakProcessing
PeakSpectra
PepNovo
PepXML
PeptideAveragine
PeptideHits
PeptidePrecursor
PeptideScores
Phenylalanin
PlotWidgets
Precomputing
Proc
ProteinAccession
ProteinIDRun
ProteinIdentifications
ProteinProphet
Proteome
Proteowizard
QTrap
QuantLayer
QuantLayers
RMSD
ROC
ROCCurves
RawMS
ReAdW
SCIEX
SNP
SSK
Sashimi
Savitski
SearchengineAdapters
Sequest
Sha
SpectraClustering
SpectraComparison
SpectraFilter
SpectraST
SpectrumIdentifications
SwathMaps
Sweetman
Swissprot
TAoCP
TOPPASWidgets
TOPPAdapter
TOPPTool
TOPPView
Thermo
TimsTOF
TotalPRMScore
TraML
Transcodes
TripleTOF
Trypsin
UnassignedPeptides
Unformatted
UniMod
VLSEEEIDDNFK
XIC
XTandem
XTandemXML
YEHR
aamasses
acquisitionSettings
aionseries
al
amidated
amu
arginines
autoionization
averageWeight
bern
bioml
bionseries
calibrant
chromsize
codon
colType
compomers
consensusXML
consensusmaps
cvParamType
cystein
dechargers
derivatization
dimers
dimethyl
eluting
endianness
et
fdrs
featuremaps
filestreams
getPrecursorModel
gma
gumbel
helperfunction
htmlinclude
hullpoints
hyperscore
iRT
iRTs
iTRAQ
idXML
idref
immonium
indexList
ingroup
ionizable
isotoped
isotopedistributions
isotopepeaks
isotoping
labelers
lazyload
lfq
loglevel
loglevels
logline
logstream
lysines
mQuest
markov
metavalues
microliter
mmu
monoisotope
monophosphate
msconvert
msdata
multimers
mw
mzIdentML
mzMLs
mzQuantML
mzTab's
mzmls
mzq
nRT
nativeIDs
nitrogens
noNamespaceSchemaLocation
noncentroided
nucleomics
obos
oligo
oligonucleotide’s
oligos
paramXML
peakMZ
peakdifference
peakgroup
peakpicker
pepID
pepXML
peptide’s
phosphorylated
phosphorylation
phosphorylations
ppConsumer
preallocate
prefractionation
protXML
proteases
proteotypic
protonated
pseudocounts
psidev
putbuffer
pwiz
pyroglutamic
rawfiles
rawfilesgroup
residuemasses
resolvers
retentional
sidechains
specsize
spectras
streambufs
subfeatures
subformulae
subsample
subspectrum
sulfoxide
timepoints
uncleaved
unfractionated
unfragmented
unitids
unphosporylated
userparams
yionseries
# }}}

###################################
# Common English words {{{
###################################

Artifcat
Dialogs
Eg
Emtpy
Glycan
Hyperfast
Precalculate
Precalculated
Prefetch
Reimplementation
Resamples
Rescaled
Rescales
SUBDIAGONAL
Scriptable
Smoothes
TRIANGULARIZED
UNKOWN
Unassign
abovementioned
advancedness
agglomerative
analyte
ascendingly
autoconversion
benchmarking
blazingly
booleans
calculcations
carbamidomethylation
chainable
clusterwise
cohesions
collisional
combinatorial
combinatoric
comperator
convolved
coverages
crosscorrelation
crosscorrelations
crosslinks
cumulate
customizable
decharges
deconvoluted
decos
dehydratase
deinstall
denoise
denoising
dereferenced
deterministically
deviancies
eluted
executability
experimentalist
findable
foldings
fractionation
fullfill
fullfilled
gapless
hithero
homolog
homologues
homonymous
identifaction
implicits
infos
inplace
interferences
invariants
lookahead
lookbehind
misassigned
misscleavage
monotonicity
multimodal
normalizable
normed
nucleosides
occurences
online
overdesigned
parallelizing
partite
passband
piecewise
postincrement
postprocessing
precalculate
precalculation
preceeding
precompute
predecessing
prefetched
preincrement
prepended
prepending
priori
proto
queuosine
quickselect
reassociating
rebalancing
recalibrated
recurse
referer
reflectable
reindexing
rerank
rescales
rescaling
resubstitute
rethrow
ribos
roundoff
seeked
silico
skipexists
smoothes
storable
subcomponents
sublist
subregion
subsampling
subsequence
suitabilities
superstrict
syncronicity
tRNA
templatization
thresholding
tradeoff
trimer
unapplicable
unasssigned
unclosed
unclustered
underflows
undistinguishable
unkowns
unpruned
unstorable
uptime
useable
vivo
writeable
# }}}

###################################
# Other words {{{
###################################

AATU
AQR
Abfrage
AnalysisSampleCollection
Anm
BTO
Bande
Bigl
Bigr
CHEMMOD
CHNOPSCl
DataProcessings
Decharges
Drosophila
FFFFFF
Finnigan
HCOOH
HH
Hashers
ICSC
JA
Leber
MMM
Moz
NICHT
OSM’s
OTT
PATO
ProteinDetection
SEs
SIGMOID
Senko
StudyVariables
TODOs
ToolX
UO
UU
Unweight
VLevels
Variablen
XLDB
Zustandssumme
abcdefghijklmnopq
abgeschaltet
afaik
akima
alleine
alles
anchorpunkte
auf
ausreichend
auswählt
autodetachment
bauen
benutzt
braucht
casted
cblabel
cbrange
cbtics
cleaveable
cleaveages
codebook
codebooks
combinatorically
compulsoriness
consensusHeaders
d'tor
dann
das
datasheet
dbx
ddd
decalibration
der
diese
doteq
einfluss
erstellen
featuremapper
featurewriter
fertig
firefox
floatdata
fpr
für
groupId
grouplabel
gruppe
guanidium
heterobifunctional
hier
homobifunctional
i's
indefinetly
indi
inf's
innerhalb
intensitaet
intensitaeten
intra
intvall
iteriere
iteriert
ith
jk
keine
lieber
liste
lokale
longrightarrow
looplinks
melanogaster
mers
multiSE
nan's
negs
newsection
nicht
nodename
oder
othermyname
paar
parametrize
peaks's
pepCluster
postRawHook
pragmas
reagens
referenceable
regularizer
repräsentiert
repulsions
rescale
rescaled
rescoring
reuseable
richtig
roundtrip
rstuvwxyz
setzen
sharedness
shitpile
sind
sonst
splot
subaligmnet
subcase
subfeature
submaps
summe
testweise
testworthiness
tis
toggable
tooltip
transitionID
ueber
uff
un
unallowed
uncalibrated
uniquify
unquantifiable
untestable
variadic
von
vorhanden
waren
wenn
wirklich
xattr
yay
yk
yz
z's
zu
zusammenrechnen
zweiter
# }}}

###################################
# Ignore for now (Need to be worked on mid-term) {{{
###################################

AXXA
IDEAK
PEPT
andsi
ci
datastructure
hh
le
psvi
seg
srsly
whitespace
# }}}

###################################
# Ignore words from doxygen {{{
###################################

ADDCXX
AnyException
BuildSystem
BuildSystems
CDASH
CGAL
CHANGELOG
CLI
CMakeCache
CRLF
CTRL
CUDA
CXX
ChangeLog
CodeBlocks
Cython
DBOOST
DBUILD
DCMAKE
DFPI
DINSTALL
DLL's
DMACRO
DVARIABLE
DVIPS
DependencyWalker's
DummyClasses
Ecoli
Elsevier
EmpiricalFormulas
Erhardt
FeatureFinders
GHOSTSCRIPT
GSL
Gaussians
Geer
Ghostscript
GitHub
HashSet
Herk
Homebrew
IDE's
IDEvalutator
JOM
JavaScriptCore
KDevelop
KNIME
Kohonen
LaTeX
LargeObject
Leinenbach
Logarithmize
MSDN
MYDIR
MacPorts
MacTeX
Makefiles
MapAligners
MascotAdapters
MathExtras
Mendeley
MikTeX
Miktex
MySQL
Myclass
NVIDIA
Nattkemper
NoiseFilters
NonPT
OMMSA
OpenMSInfo
OpenMSd
OpenSuse
PYOPENMS
PageDown
PageUp
PeakPickers
PeakPicking
QMAKE
QTDIR
QtGui
Quickstart
RangeManger
ReadMe
Repo
Ritter
SDK
SDK's
SGI
SimilarityComparators
Sourceforge
SpectrumMDIWindow
TELGFDPEAHFAIDDEVIAHTR
TOPPDocumenter
TRAC
TestLib
TextImporter
Timm
TopHatFilter
TortoiseSVN
TreeViewX
UAC
Ultraflex
VSE
VisualStudio
WILDMAGIC
WidgetTemplate
Wiebke
Wiki
WildMagic
WinXP
XSERVER
Xcode
Xmx
adminrepo
align'set
atstart
authentification
autoconf
automake
autowrap
bashrc
bdist
blackbox
bzlib
callgrind
cccccc
ccmake
cdef
cellpadding
cimport
clib
cmath
coinmp
coli
cond
consts
convolving
count'set
cppcheck
cppclass
cpplint
ctest
cython
debian
demangling
deref
devel
displaOne
dmg
dumpbin
eef
emacs
endhtmlonly
endlink
functionalities
galileo
getMember
github
glibtoolize
gnuwin
graphicssystem
gsl
gui
hardcoded
hardcoding
heatmaps
hotkeys
howto
htmlonly
iconized
instanciate
intensity'set
internet
iostream
isHeavy
jom
kcachegrind
ldd
libOpenMS
libboost
libbz
libcpp
libglpk
libgsl
libqt
libtool
libtoolize
libxerces
libzip
mainpage
memleaks
method'set
mkdir
mkspecs
moc
myClass
myNumber
myVec
myusername
nbsp
nmake
nogil
nomake
numpy
omssacl
opensource
operability
ouml
parallelize
pdflatex
pdfs
prebuild
precompiled
preprocessors
profiler
propedit
pxd
pxds
pyOpenMS
qmake
raw'set
rdparty
repo
roundf
rsync
runtimes
sed
setMember
setuptools
signbit
sln
someFunction
stdin
structs
stylesheets
subfolder
subpage
subproject
sudo
svnadmin
svnlook
svnroot
tabstop
tabwidth
testdata
testname
texlive
time'set
timeline
toolchain
toolset
tooltips
ubuntu
ulimit
uname
uncentroided
untabify
valign
verbinclude
webkit
wordpress
wtf
xargs
zypper
# }}}

###################################
# Ignore words (check in the future) {{{
###################################

###################################
# All of AASequence, ResidueDB and AAIndex {{{
###################################

AAKK
ABAR
AURR
AllNatural
AmbiguousWithoutX
Aust
BAEK
Biochem
Biopolymers
Charton
Cys
DFPIAM
DFPIAMGER
DFPIANGER
DNSTM
DNSTMGYMAAKK
EIVLTQSPGTL
Fauchere
Finkelstein
GIKTSEGTPGFRAPEVAR
HKMSYSGR
Hargrave
Hearn
JURD
KANM
KQYSAKAK
KRIW
KSKTLQYFA
KYTJ
Kanehisa
Kawashima
Khanarian
Kier
Kubota
LABAR
LRRK
MAXF
MEEJ
MGIKTSEGTPGFRAPEVAR
MLABAR
MSHHWGYGK
Manesh
Moosavi
Movahedi
NADH
Naderi
Nemethy
Ogata
Oobatake
Ooi
PEPC
PEPM
PEPR
PEPRc
PEPTIDER
PEPTX
PMID
PONP
PRS
Physicochemical
Pliska
Ptitsyn
QIAN
QKAAGSK
RDVEKFLSK
Rao
Sadeghi
Scheraga
SvmModelSet
Tyr
VINM
Verloop
Wilce
WithoutI
WithoutL
aminobutyric
asparagine
aspartate
basicitiy
glutamine
isoleucine
kj
leucine
ln
microstate
ndash
physico
protonation
selenocysteine
# }}}

###################################
# All of MapAlignmentAlgorithmSpectrumAlignment {{{
###################################

DebugRscript
Debugscoreheatmap
buffermatrix
debugRscript
debugflag
gnuplotScript
heatmap
highscore
innerclass
insertmatrix
insertscore
matchmatrix
matchscore
retentiontimes
scorefunction
# }}}

###################################
# MSInspectFile {{{
###################################

taccurateMZ
tbackground
tchargeStates
tdescription
tintensity
tkl
tmass
tmedian
tpeaks
tscanCount
tscanFirst
tscanLast
tsumSquaresDist
ttime
ttotalIntensity
# }}}

###################################
# ExternalProcess {{{
###################################

CLangs
ExternalProcessMBox
Gzipped
MaxQuant's
MaxQuants
MsgfplusReader
OpenEcho
PROSITE
ProteomeDiscoverer
QMessageBoxes
SQLLite
TurboSEQUEST
graphviz
iProphet
proteowizards
ptrs
pyProphet's
semver
texttt
xlinkPositionString
xlinkposition
# }}}

###################################
# Almost English words {{{
###################################

Acessors
Arithmethic
BinNumber
BinaryTreeNode's
Coeluting
Crossvalidated
INsensitive
Nedd
NotUsed
Superhack
Treesize
Uncharacterized
Uncomment
ahhh
alphabetMass
argh
arithmetics
bilinear
bilinearly
btw
channelunlabeled
choosingsimplepairfinderparams
choosingstablepairfinderparams
clusteringstep
clusteringsteps
clusterizable
clusterstep
coelutions
compat
console's
convolves
cspline
decharge
decharged
decomposers
dito
ein
einfach
elute
endline
fileclasses
gapped
gridvectors
gumble
i'th
id'd
identi
index'th
intensit
iterator's
linearMapping
lineedit
lipop
masserror
massmapping
maxscore
metabolomics
metas
myFileWatcher
myref
mytool
nName
ndend
negcharges
new'ed
nfactor
overdesigning
peakapex
peptidoforms
physicochemically
rty
savecookie
soooo
specificities
spline's
stend
stringify
subtag
synomys
templatized
tmpnam
useconds
viewport
# }}}

###################################
# Variable names and abbreviations {{{
###################################

AE
AMS
Appl
BPI
CCCs
CH's
CRHU
CV's
Cmpd
CompoundId
Cyazofamid
DAC
DSG
DSS
DTD
Deamidated
ECHGR
EDC
ELOOP
ELTS
EPD
EcoliMS
FFID
FME
FMEs
FMM
FullPeptideNames
Fxn
GN
HyperAlpha
HyperBeta
HyperBoth
HyperCommon
HyperXlink
IDMS
IDPEP
IDed
IZ
KRP
Lnx
MC's
MDV
MDVs
MTD
NIST's
NPP
NQ
NSETP
NTFS
Nreps
PDF
PEFF
PEPTIX
PEPTIXDE
PEPX
PIs
PMC
PearsonValue
Pfin
PnvScr
PrepDB
Probcorr
ProtIDRuns
QMIP
Qt's
RATFOR
RUND
SES
TBL
THRU
TIC's
TOPPs
Templated
Tf
Tfratio
TransitionIds
TransitionsIds
TreeIsotope
Vandermonde
XLMODS
XXXXX
abasicform
addedMass
adjacentEdges
aggr
alphacommon
alphaxlink
amax
ame
apriori
arctan
asc
avalue
betacommon
betaxlink
bgslope
bigauss
binom
bla
blabb
blabla
blubb
bp
bvalue
bz
c'tors
cf's
chargeRange
cilist
cleaveC
cns
colum
columnsfirst
conf
cutil
dNIC
dSize
dcn
ddThh
ddZ
debugbuffermatrix
debuginsertmatrix
debugscore
debugtracebackmatrix
dfs
diffmz
dscale
dueto
dx
enetz
epsabs
epsrel
errBuf
errHandler
errpr
evel
evtl
executablePath
exps
featureConcentrations
fgDOMErrorHandler
fileChecksum
fio
fiq
firstcolum
firstcolumn
fixup
fnds
ftnlen
fx
getA
gx
hasIMData
hasMandatoryMetaDataKeys
higherIsBetter
hy
ic
ifix
inpl
insertmaximum
io
ionintensity
iontag
iosconstructors
isocheck
ispectrum
itlow
itup
josie
jth
kim
lala
langwisc
leftMostPt
leftside
leq
lili
lma
lmagauss
logSN
loginbytes
lstsq
lu
lwidth
massC
massTable
massd
matchmaximum
minDistance
miscleavages
missingTheorDigests
modC
modtype
mths
mx
mxn
myDOMErrorHandler
myErrorHandler
mymeta
nbr
ncandidates
ncommonions
nd
nl
nonone
nph
nprimary
nrEdges
nrMessages
nrNodes
nrReplicates
numerics
nxlinkions
onerrdisplay
p'th
paul
peakApexPos
pepdep
pepevis
percolaror
piter
pkl
plugin
pmatch
posP
prf
protgrp
pushback
py
qVals
qcookie
querybytes
rankingScore
ratfor
refactored
refactoring
referenceableParamGroups
repr
rightside
robustifying
ru
rwidth
sapf
sar
sdats
sdid
sdst
secondcolum
semiSpecific
sfMaxCharge
sfMinCharge
sidlist
som
stree
subSectionDefaults
sufArray
sumdep
sumformulas
sx
terminalStateMap
tlast
tparam
unIDed
unassignedPepID
undef
uninitStructMember
userw
vigintile
wrt
wsfe
x's
xC
xcorrall
xf
xlinked
xxxxxx
xxxxxxx
zA
zs
# }}}

###################################
# Variable words {{{
###################################

AbstractBaseClass
AbstractBaseClassImpl
AdductCgf
Aicheler
Alka
Appleclang
ArchLinux
Aspartic
BOVIN
BaBI
BaP
BaRB
BaYI
Biocontainers
Blackbody
CHNH
CSI
CalibrationData's
Capitan
Carbamyl
CentOS
Chromeleon
ClassNameY
ClassnameWrapper
Colaianni
Comparators
ContactRole
CorrelateMassTraces
Csi
DBBa
DDA
DNUMBER
DOPENMS
DPYOPENMS
DPYTHON
Domenico
Dotbest
Dottheory
E-Values
EPEL
Ethofumesate
Eugen
Extensibility
FWHMs
FingerID
Formulary
FragmentAnnotations
GLS
Gitflow
Gln
Glu
Glus
Glutamic
Gly
Glycine
HeRB
HiResPrecursorMassCorrector
Histidine
HyRB
IDEs
ITMS
IdentificationClasses
Ile
IncompatibleBinning
InputParam
InputRead
JavaVM
JetBrains
Kernal
LIBS
Lennard
Leu
Lucent
MSBuild
MSFragger
MSGFPlus
MSRuns
Macromolecules
MagAlignerPoseClustering
McCloskey
MetboliteAdductDecharger
MyriMatch
NBaR
Naa
Netz
NewTool
OpenProXL
OpenSwathRTNormalizer
PEPTIDEAK
Phe
Phenylalanine
Photodissociation
Programme
Proline
Proteomics
PyPI
PyProphet
Pyl
Pyrrolysine
QApplication
QPA
QTCreator
QtByteArray
RHEL
Reimplemented
ResidueModifications
SCHPO
STRP
Selenocysteine
Ser
Serine
SimTandem
SiriusExport
SparseVectors
Specqual
Spectronaut
Springer
THIRDPARTY
TRFE
Thr
Threonine
TransitionGroupPicker
Trp
Tryptophan
Tyrosine
UBLH
UNambiguous
UUB
Uncompresses
Uncrustify
Untargeted
Valine
WIP
WindowsOS
addon
ammonium
analytes
analytical
binspread
biocontainers
bioinformaticians
boolean
bude
calibrants
carbonyl
centric
centroiding
centroids
chromatographic
conformational
constructable
covariances
css
cvLabel
cytochrome
daly
dataConsumer
dealloc
decharing
decomposable
decrementing
dep
desorption
detectability
differentially
dimensionality
disproportionally
dissociative
distro
distros
dlls
dnf
dockerfiles
eg
electronvolt
electrospray
elutes
epel
exactmass
experimentalists
extensibility
extrema
facto
fileorigins
fractionated
freetext
getWidgets
getWidgetsAsIntegers
gitter
gmake
groupinstall
humanA
humanB
humanC
humanD
humanE
humanF
humanG
iRprop
include
incrementing
indexListOffset
indexedmzML
initialises
installable
instantiation
instrumentConfiguration
instrumentConfigurationRef
interprophet
ionisation
iostreams
isSearchEngineSpecificScore
isolationWindow
isomassd
iteratively
lc
lexicographically
libcoinmp
libeigen
libs
libsqlite
libwildmagic
linkers
mAU
maxcpucount
microchannel
mmol
multiphoton
negativeInteger
nmc
nonNegativeInteger
nonPositiveInteger
normalisation
normalised
normalising
noroot
oligonucleotide's
omics
optimality
optimizations
ote
parallelizes
parsers
peakgroups
perl
photodiode
photoionization
plist
polylysine
positiveInteger
prebuilt
precomputed
precomputes
pyrolysis
qtbase
qtsvg
quartile
radiative
recalibration
redeclaration
redistributable
referenceableParamGroup
reionization
repolist
rightMostPt
searchable
serotransferrin
setptr
spectrometric
sptxt
standardisation
startmenu
stepwise
stoichiometry
subclasses
subdirectories
submodule
submodules
supDataArray
supDataArrayBinary
symlinks
testnameregex
thermospray
thirdparty
titin
translational
uiuiui
uncompresses
uncrustify
unlink
unweighted
vcredistXXXX
vcvarsall
venv
virtualenv
whitelisting
xFFFFFFFF
xe
# }}}

# }}}

