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

###################################
# 1. Header {{{
###################################
Redistributions
Tuebingen
Freie
Eberhard
Karls
ETH
Hoenggerberg
IMSB
Universitaet
Lund
MERCHANTABILITY
# }}}

###################################
# 2. Authors {{{
###################################
Julianus
Pfeuffer
Demirev
Zubarev
Liang
Xiao
Alexandra
Zerck
Andreas
Bertsch
Anton
Pervukhin
Bastian
Blank
Chris
Bauer
Chris
Bielow
Clemens
Groepl
Cornelia
Friedle
Daniel
Jameson
David
Wojnar
Dimitri
Schachmann
Erhan
Kenar
Eva
Lange
Fabian
Kriegel
Frederic
Lehnert
George
Rosenberger
Guillaume
Belz
Hannes
Roest
Hendrik
Brauer
Hendrik
Weisser
Holger
Franken
Holger
Plattfaut
Immanuel
Luhn
Johannes
Junker
Katharina
Albers
Knut
Reinert
Lars
Nilse
Lucia
Espona
Marc
Sturm
Marcel
Schilling
Martin
Langwisch
Mathias
Walzer
Nico
Pfeifer
Ole
Schulz-Trieglaff
Schulz
Trieglaff
Oliver
Kohlbacher
Rene
Hussong
Sandro
Andreotti
Steffen
Sass
Stephan
Aiche
Sven
Nahnsen
Timo
Sachsenberg
Vipul
Patel
Volker
Mosthaf
Lukas
Mueller
Markus
Mueller
Florian
Zeller
Peter
Kunszt
Johan
Helge
Lennart
Ralf
Nicolai
Ivar
Ruedi
Aebersold
Witold
Wolski
# }}}

###################################
# More than 5 occurrences in the source code {{{
###################################
workflow
xerces
de
DIA
dll
functors
MSVC
Quantitation
recomputation
datapoint
datastructures
Hiwi
MapAlignment
stl
tt
C'tor
dataset
DeNovo
Jacobian
Namespace
functor
ifndef
reimplement
SignalProcessing
SpectraPreprocessers
c'tor
plex
quantitation
br
ns
STL
Datastructures
todo
Docu
# }}}

###################################
# More than 3 occurrences in the source code {{{
###################################
Zhang
accessor
analysisXML
AnalysisXML
ansi
cdot
ClusterMethod
Const
C'Tor
gnuplot
getter
IMPL
Longman
lookup
subtree
TOPPASINPUTFILESDIALOG
typedefs
XMass
Accessor
ctor
defgroup
maxima
novo
PeakDetection
ProteinHits
RTs
stderr
AA's
AlphabetParser
automagically
Caap
frameSize
lorentzian
lowpass
mapList
versa

# }}}

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

###################################
# Names and people {{{
###################################
Hildebrandt
Needleman
Beausoleil
Wunsch
Henner
Josuttis
LONGMAN
Nicolay
TORTIOUS
Levenberg
Marquard
mProphet
AScore
Los
Angeles
Hengartner
Huettenhain
Picotti
Reiter
Rinner
Epub
Hall
Prentice
Vidavsky
Analysemethoden
Backhaus
Erichson
Plinke
Voorhees
Weiber
Dunns
Newick
Benno
Hookeun
Mallick
Parag
Paulovich
Prakash
Schwikowski
SteinScott
Whiteaker
Giavalisco
Gobom
Herwig
Lalowski
Lehrach
Maciej
Martus
Sickmann
MSsim
Gropl
Jorgenson
Dekker
Heeren
Luider
Rijswijk
Siccama
Sillevis
Smitt
Titulaer
Cociorva
DL
Graumann
MacCoss
MJ
proteomic
RG
Sadygov
SQT
Venable
WH
WABI
Lippert
Golay
Savitzky
ACM
Böcker
Lipták
Nijenhuis
Sudek
Boecker
Siepen
Teleman
Herk's
Brusniak
Meinicke
Scherbart
Tholey
Faires
Fohlman
Roepstoff
Gutenbrunner
Spectrometry
# }}}

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

# {{{Classnames
AAIndex
MapAlignmentAlgorithm
TargetedFileConverter
MultiplexPeakPattern
SILACAnalyzer
LowLevelComparator
AxisWidget
SpectrumCanvas
SpectrumWidget
CachedMzMLConsumer
LowLevelComparator
ParamEditor
SavitzkyGolayQRFilter
SavitzkyGolaySVDFilter
TICWritingConsumer
IsotopeWaveletFeatureFinder
MetaInfos
ChargePairs
ParamNodes
PeakInfo
FullIds
MergerVertex
Enqueues
ExecutePipeline
IonName
IntermediateProduct
MzQuantML
SILACAnalysis
DatabaseIO
QMYSQL
DefaultParamHandlerDocumenter
MapAligner
MapAlignerBase
PoseClustering
Metafunction
RichChromatogramPeak
MSExperiments
ConsensusMapNormalizer
MRMFeatureFinder
MRMFeatures
MSSpectra
ElementNotFoundException
LogStreams
MapAlignmentEvaluation
MapAlignmentAlgorithms
MSChromatograms
PeptideIdentifications
PeakArray
ConsensusElementLists
IntRealString
LessByInt
LessByReal
LessByString
MathFunctionsMisc
InvalidParameters
BasisStatistic
MathFunctionsStatistics
IsotopeWaveletFF
SpectrumGenerator
AutoMaxIntensity
MinReqElements
UInts
SILACFilters
CompareFunctor
Dpoints
DummyComparison
Bincontainer
BinaryTreeNodes
PeakSpektrum
ConsensusMap
IsobaricQuantitation
GlobalException
StringStream
MetaDataInterface
BinnedSpectra
Functors
ParameterHandler
ZhangSimilarityScoring
TransformationXML
PILISSequenceDB
GridSearch
GraphML
ProteinQuantifier
FilledBinNumber
DividedByZero
Preprocesses
IDPool
ToolName
TOPPSubsections
ElutionModel
MutablePriorityQueue
ClosedBoxes
FASTAHeader
HighRes
LowRes
OpenBoxes
IsolationWindowLow
IsolationWindowUp
DoubleReals
AASequences
ByteArray
MSDataConsumer
datatypes
MzTabCellType
CachedMzMLConsumers
MsInspect
ProteinGroups
SpecArray
RunQuality
CvMapping
ToolDescriptor
LocalFileInputSource
IDEvaluation
DataRepository
IntRealStringVector
FASTEEntry
CVTerms
RTime
Initializer
FlexControlVersion
QCFile
EnergyUnits
MetaInfodescriptions
MzDataHander
ScanFunction
TandemScanningMethod
DataTime
DataArray
OutputVertex
QFile
MetaInfoDescriptions
AnnotationItems
SharedPtr
SpectrumOpenGLCanvas
OutputNode
ToolVertex
InputVertex
TextExporter
FeatureFinding
DFeature
AASequence's
EmpiricalFormula's
IonTypes
ProteinsHits
AlphabetTextParser
DocumentID
DocumentIDs
IsotopeSpecies
IsotopeDisribution
StringLists
CarbonHydrogen
TermSpec
ProteinIndentification
DSpectra
DataValues
ChargeDifference
MassDifference
featureXML's
SpectrumAccess
OpenSwathAlgoConfig
consensusfeaturehandler
ChromatogramList
SpectrumList
DataProcessingPtr
FullId
Indices
FeatureFinderMetabo
MRMScoring
OPENSWATHALGO
DCanvas
PersistentObject
SignalToNoiseEstimatorRapid
PeptideIdentication
LabelType
MissedCleavages
PeptideGroupLabel
OnDiskExperiment
LocalClustering
MovingAverage
HierarchicalClustering
LocalClustering
SpectraIdentificationViewWidget
MetaValueInterface
ProteinIdentificationVisualizer

DWidget
MetaDataBrowser
#  }}}

# Functions {{{
computeFwhmAreaRobust
computeFwhmAreaSmoothRobust
encodeInt
encodings
updateCRC
loadTargets
regularData
sampleTheWavelet
getLeftWidthParameter
getRightWidthParameter
isoelectric
checkCVTerms
correctCVTermNames
setIDPoolFile
currentAlphabetMass
getAllDecomposition
updateSpectraViewBar
isCorrupted
countBasicResidues
compressBound
Endianizes
QtCore
updatePeptideHits
updateProteinHits
stringChecked
stringUnchecked
trypticCompressed
trypticSeqan
sparseElement
sparseElements
inputFileWritable
getParamAs
buildSynonyms
getProtonAffinity
getSequenceDB
setSequenceDB
initLossModels
initMainModel
initModels
initPrecursorModel
computeCombinedScore
streamtype
rescoreIncremental
setFWHMScansNum
getIDState
getTransforms
Skellam
beginChromatograms
beginSpectra
ConstChromatogramIterator
ConstSpectraIterator
endChromatograms
endSpectra
baseclass
clusteringmethod
distancemethod
dataReadProgress
dataSendProgress
requestFinished
requestStarted
responseHeaderRecieved
stateChanged
shiftWindow
isLegalAveraginePattern
scoreIntRatio
scoreTraceSim
tminus
tplus
peptideHit
writePeptideTable
writeProteinGroups
writeProteinsAndPeptidesmzTab
writeProteinTable
getParameter
encodeOligoBorder
indistinguishableProteins
massShift
removeDatabase
getChromatogam

#  }}}

AveragineModifications
FirstScan
NumOfScans

BFS
ConnectedComponents
PepHit
PeptideIDs
ProtGroups

JBC
PEPs
ScoringMatrix
PEPIons
PEPs
ConsensusID
PEPs

lastPackage
AAD
Elephas
GenBank
getPValuesFromOutFiles
gi
maximus

ApprLineFit
GeometricTools
DataCollection
IdentificationRuns
PeptideEvidences
SequenceCollection
spectradata
XSValue

PILIS
DecoyDatabase
PeptideIndexer
RTPredict
PeptideIndexer
passesWhitelist
SavitzkyGolay

# }}}

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

###################################
# common technical words {{{
###################################
Struct
Typedefs
FHWM
datasets
Fortran
NETLIB
nonrobust
LLVM
tokenize
Wikipedia
Exabyte
Exbibit
Exbibyte
subelement
subdirectory
NaN
peaklist
doi
pubmed
subproblems
acosine
tuples
hpp
fictious
SQL
Bool
DLL
exe
GCC
MinGW
MSVS
NDEBUG
stdlib
svnversion
VC
gdb
valgrind
postcondition
gcc
Js
mol
Nm
mem
memFunc
php
subtest
svn
endif
ifdef
analysissummary
linebreaks
docu
HMM
CMake
https
executables
CMakeLists
preprocessor
unix
CMAKE
Accessors
Beavis
destructors
Fenyo
tsv
GLM
vtable
stdv
mutators
postfix
dereferencing
demangled
hoc
rvalue
SomeType
stdint
postconditions
ADL
QNAN
getters
splitted
minima
highestscoring
Enums
hashmap
SVMs
dereference
outstream
discretized
ID's
UID's
d'tors
OPENMP
OpenMP
hostname
MacOS
scrollbars
workflows
constness
metadataarrays
classname
getenv
propset
secan
secans
zeropadding
prepend
noop
NOP
CRC
crc
MacOSX
bufLen
scatterplot
linux
subfunctions
inputfiles
Checkbox
widgetstack
listelements
ffaa
ffff
goto
messagebox
messageboxes
Tabbar
tabbar
tabData
iff
zoomselection
combobox
ComboBox
comboboxes
Unselects
Mutator
upto
gz
postorder
subnode
subnodes
parsable
mutator
preorder
postprocess
allround
postdecrement
resizes
coords
composable
gzerror
gzFile
gzfile
inCrc
badbit
failbit
ostringstream
strtod
Subfunction
halfbyte
halfbytes
handleable
lossy
memorycont
resized
maxpeak
boxplot
logfile
multiclass
substring
backsubstitution
filtercoefficients
Quantiles
Manhatten
Massdiff
Dotproduct
Sortedness
printf
stdout
li
libc
GSL
SciPy
colspan
html
inlining
iterable
eol
PIMPL
multiplet
multiplets
NotStarted
deltaAbsError
deltaRelError
higherScoreBetter
SignificanceThreshold
KiloBytes
pearson
rowspan
Google
ol
Javascript
BGCOLOR
EBEBEB
PRECRT
# }}}

###################################
# common Mass spectrometry and OpenMS words {{{
###################################
dimethyl
FTICR
MascotAdapter
Hydroxylation
Histidin
Leucin
Phenylalanin
PSM’s
pepID
Carboxymethyl
paramXML
TOPPASWidgets
Elution
nRT
ProteinProphet
pepXML
PepXML
Bruker
Monoisotopic
Trypsin
amu
mmu
Sequest
OMSSA
MSData
msdata
pwiz
Mz
Myoglobin
Superhirn
Bioinformatics
Destructor
Contrib
Lys
consensusmaps
userparams
rawfiles
CVTermList's
featuremaps
iTRAQ
htmlinclude
ingroup
XIC
TraML
getPrecursorModel
ConsensusFeatures
FeatureHandles
IDMAPPER
Precomputing
ProteinIdentifications
MetaValue
PeptideHits
PeptideScores
phosphorylated
phosphorylation
phosphorylations
FeatureGrouping
proteotypic
et
al
TAoCP
peakgroup
peakpicker
subfeatures
TOPPTool
loglevel
loglevels
logline
logstream
putbuffer
streambufs
subspectrum
FullUniModPeptideName
Labelgroup
LibraryIntensity
NrModifications
ReAdW
ECs
UnassignedPeptides
gumbel
ROC
ROCCurves
isotoped
isotoping
BiGaussian
ProductModels
QTrap
SCIEX
Kaatz
unfragmented
isotopedistributions
isotopepeaks
eluting
LOWESS
retentional
Electro
Nano
Thermo
microliter
nativeIDs
Sashimi
Sha
markov
fdrs
helperfunction
HMMs
pseudocounts
COOH
nitrogens
sidechains
SpectraST
OPENMP
OpenMP
aionseries
bionseries
Proteome
yionseries
InsPecT
Biomolecules
uncleaved
ionizable
labelers
Swissprot
protonated
subsample
unitids
chromsize
ppConsumer
specsize
filestreams
colType
CVid
calibrant
Convolutes
gma
endianness
metavalues
lazyload
indexList
Unformatted
ComputeBuf
bioml
rawfilesgroup
aamasses
peakdifference
residuemasses
bern
cvParamType
MzData's
noNamespaceSchemaLocation
acquisitionSettings
idref
msconvert
psidev
hullpoints
Compomer's
compomers
CHNOPS
Kessner
Proteowizard
mQuest
Hydropathy
protXML
Hydrophobicity
oligo
oligos
RMSD
Chauvenet's
iRT
hyperscore
Proc
SwathMaps
mzq
Isotopically
IBSpectra
timepoints
Transcodes
sulfoxide
codon
immonium
PepNovo
HUPO
OpenGL
PeakSpectra
XTandem
XTandemXML
mzIdentML
MzML
mzQuantML
SpectraClustering
SpectraFilter
UniMod
consensusXML
idXML
OpenSWATH
SpectrumWidgets
TOPPView
SpectraComparison
Metadata
FileIO
Destructors

Askenazi
Savitski
Sweetman

MAAAR
AAAR
PEPTLDE
SNP
YEHR
SSK
CRTP
VLSEEEIDDNFK
# }}}

###################################
# Common English words {{{
###################################
prepended
thresholding
vivo
silico
combinatoric
crosscorrelation
crosscorrelations
unclustered
seeked
online
precalculate
Precalculate
Precalculated
chainable
storable
deviancies
proto
cohesions
agglomerative
skipexists
smoothes
subregion
roundoff
Resamples
passband
Smoothes
sublist
postincrement
preincrement
ascendingly
syncronicity
homonymous
# }}}

###################################
# Other words {{{
###################################
d'tor
akima
VLevels
Senko
peaks's
doteq
dbx
codebook
codebooks
# }}}

###################################
# ignore for now {{{
# Need to be worked on mid-term   #
###################################
datastructure
whitespace
####}}}

###################################
# {{{ Ignore words from doxygen
operability
uncentroided
subpage
CHANGELOG
ChangeLog
verbinclude
PeakPickerRapid
AnyException
PeakPicking
CRLF
getMember
tabstop
untabify
tabwidth
setMember
SGI
DummyClasses
emacs
Erhardt
blackbox
testdata
bzlib
DependencyWalker's
QtGui
runtimes
SDK
SDK's
stdin
DLL's
Mendeley
Miktex
autowrap
bdist
cdef
cimport
clib
cppclass
Cython
cython
debian
deref
libcpp
libOpenMS
memleaks
myClass
nogil
numpy
pxd
pxds
pyOpenMS
setuptools
ubuntu
cccccc
ChangeLog
CLI

BuildSystem
CMakeCache
ctest
DLL's
DVIPS
Ghostscript
GHOSTSCRIPT
gnuwin
graphicssystem
HashSet
internet
JavaScriptCore
JOM
jom
libbz
MathExtras
MikTeX
nomake
OpenMSd
opensource
prebuild
precompiled
rdparty
roundf
signbit
sln
Sourceforge
subpage
toolchain
toolset
TortoiseSVN
UAC
VisualStudio
VSE
webkit
wtf
ccmake
CXX
dmg
Homebrew
MacPorts
MacTeX
MySQL
pdflatex
pdfs
PYOPENMS
QMAKE
qmake
Sourceforge
Xcode
WinXP
glibtoolize
libboost
libbz
libglpk
libgsl
libqt
libtool
libtoolize
libxerces
libzip
MySQL
OMMSA
OpenSuse
pdflatex
PYOPENMS
QMAKE
qmake
sudo
texlive
zypper
cmath
LargeObject
MSDN
Myclass
myNumber
myVec
someFunction
structs
VisualStudio
preprocessors
ADDCXX
DMACRO
howto
hotkeys
propedit
eef
mainpage
Quickstart
MapAligners
tooltips
autoconf
automake
bashrc
cellpadding
DBOOST
DBUILD
DCMAKE
devel
moc
LaTeX
adminrepo
atstart
BuildSystems
callgrind
CDASH
CodeBlocks
cppcheck
cpplint
demangling
dumpbin
galileo
hardcoded
hardcoding
iconized
IDE's
IDEvalutator
kcachegrind
KDevelop
KNIME
ldd
Makefiles
MYDIR
myusername
profiler
propedit
QTDIR
Repo
repo
rsync
sed
SpectrumMDIWindow
subproject
svnadmin
svnlook
svnroot
TestLib
timeline
TOPPDocumenter
TRAC
ulimit
uname
WidgetTemplate
Wiki
wordpress
xargs
Xmx
cond
DINSTALL
DVARIABLE

CGAL
DFPI
Elsevier
EmpiricalFormulas
FeatureFinders
heatmaps
Herk
Timm


stylesheets
TextImporter
MascotAdapters
subfolder
Gaussians
isHeavy
Leinenbach
NoiseFilters
NonPT
NVIDIA
TopHatFilter
TreeViewX
Ultraflex
Wiebke
iostream
Kohonen
Nattkemper
ouml
RangeManger
Ritter
Ecoli
Geer
parallelize
PeakPickers
SimilarityComparators
TELGFDPEAHFAIDDEVIAHTR
Logarithmize
instanciate
convolving
functionalities
authentification

GitHub
gui
mkdir
mkspecs
nmake
testname
WildMagic
coinmp
github
gsl
GSL
mkdir
valign
WildMagic
WILDMAGIC
WildMagic
XSERVER
endhtmlonly
endlink
htmlonly
coli
CTRL
omssacl
OpenMSInfo
consts
CUDA
nbsp
PageDown
PageUp
ReadMe

# }}}

###################################
# Ignore words (e.g. the rest of the words {{{
# These are words we find in the code and currently just ignore but they should
# be checked in the future
# Many of these are from commented out code and need to be looked at sometime
# in the future...
###################################

### all of AASequence, ResidueDB and AAIndex {{{
DFPIAM
DFPIAMGER
DFPIANGER
SvmModelSet
AllNatural
AmbiguousWithoutX
asparagine
aspartate
glutamine
isoleucine
leucine
selenocysteine
WithoutI
WithoutL
basicitiy
physico
aminobutyric
AURR
Aust
BAEK
Biochem
Biopolymers
Charton
Cys
Fauchere
Finkelstein
Hargrave
Hearn
JURD
Kanehisa
KANM
Kawashima
Khanarian
Kier
kj
KRIW
Kubota
KYTJ
ln
Manesh
MAXF
MEEJ
microstate
Moosavi
Movahedi
Naderi
NADH
ndash
Nemethy
Ogata
Oobatake
Ooi
Physicochemical
Pliska
PMID
PONP
protonation
Ptitsyn
QIAN
Rao
Sadeghi
Scheraga
Tyr
Verloop
VINM
Wilce
# }}}

# Superhirn stuff / commented out {{{
BaseInterScanDistance
debugDirectory
debugMonoIsoMassMax
debugMonoIsoMassMin
fMassTolDa
fMassTolPpm
fragmentMassScanLevels
getDebugMonoIsoMassMax
getDebugMonoIsoMassMin
getMonoIsoDebugging
IntensityApexPercentilCutoff
monoIsoDebugging
peakExtractionScanLevels
PeakProcessing
reportMonoPeaks
reportScanNumber
sfReportMonoPeaks
DebugMonoIsoMassMax
DebugMonoIsoMassMin
MonoIsoDebugging
sfIntensityFloor
sfMassTolDa
sfMassTolPpm
sfMinIntensity
lc
TRANSFORME
getParsedData
getParsedDataEmpty
LCelutionPeakDebugging
LCelutionPeakMassMax
LCelutionPeakMassMin
SearchedM
pkunszt
getDebugStream
getMassBounds
pDebug
pIdx
pIsotope
pLower
pStream
pUpper
sfDebug
fDetectableIsoFact
fIntensityCV
pTol
sfStream
printConsensIsotopPattern
printIsotopClusters
deconvoluted
sfCentroidWindowWidth
MODUS
percentil
processConsenusSpectraFragments
removeWaterLossRegion
fakeFeatureList
getDebug
getDistribution
isodist
setDebug
setDebugStream
# }}}

# All of MapAlignmentAlgorithmSpectrumAlignment {{{
buffermatrix
debugflag
debugRscript
DebugRscript
Debugscoreheatmap
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
# }}}

# Almost English words {{{
Coeluting
decharged
decharge
gapped
elute
coelutions
templatized
convolves
stringify
bilinear
bilinearly
clusterizable
clusterstep
clusteringsteps
fileclasses
endline
gridvectors
viewport
lineedit
BinNumber
Uncomment
Treesize
Arithmethic
arithmetics
clusteringstep
decomposers
specificities
massmapping
choosingsimplepairfinderparams

mytool
myFileWatcher
useconds
Acessors
choosingstablepairfinderparams
Crossvalidated
linearMapping
myref
iterator's
tmpnam
BinaryTreeNode's
console's
alphabetMass

Uncharacterized
lipop
cspline
overdesigning
peptidoforms
physicochemically
metabolomics
# }}}

# {{{ Variable names and abbreviations

refactoring
plugin
arctan
miscleavages
numerics
undef
amax
ifix
lstsq
RATFOR
ratfor
refactored
robustifying
Templated
userw
x's
Vandermonde
pushback

vigintile
cutil
sfMaxCharge
sfMinCharge
fixup
stree
avalue
bvalue
lwidth
rwidth
leftside
rightside
sufArray
tparam
tlast
PrepDB
bigauss

dscale
PnvScr
errpr
pkl
Appl
Fxn
piter
lmagauss
leq
DAC
ddThh
ddZ
lma
epsabs
epsrel
zs
wrt
cf's
nbr
repr
xf
exps
evtl
jth
zA
py
CV's
Qt's
TOPPs
bz
bla
blabla
getA
gx
hy
mx
mxn
NPP
NSETP
THRU
blabb
blubb
lala
lili
mymeta
josie
kim
paul

sapf
nd
xxxxxx
xxxxxxx
iosconstructors
nd
ame
IZ
evel
PDF
nl
Cmpd
Deamidated
NQ
dx
dfs
io
c'tors
XXXXX


#  }}}

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

}}}

# }}}


