Here is a list of all files with brief descriptions:

pappsomspp
core
amino_acid
aa.cpp
aa.h
aabase.cpp
aabase.h
aacode.cpp
aacode.h
aamodification.cpp
aamodification.h
aastringcodec.cpp
aastringcodec.h
aastringcodemassmatching.cpp
aastringcodemassmatching.h
atomnumberinterface.cpp
atomnumberinterface.h
chemicalformula.cpp
chemicalformula.h
exception
exceptioninterrupted.h
exceptionnotfound.h
exceptionnotimplemented.h
exceptionnotpossible.h
exceptionnotrecognized.h
exceptionoutofrange.h
fasta
fastafileindexer.cpp
fastafileindexer.h
fastahandlerinterface.h
fastaoutputstream.cpp
fastaoutputstream.h
fastareader.cpp
fastareader.h
fastawriterinterface.h
grouping
grpexperiment.cpp
grpexperiment.h
grpgroup.cpp
grpgroup.h
grpgroupingmonitor.cpp
grpgroupingmonitor.h
grpmappeptidetogroup.cpp
grpmappeptidetogroup.h
grpmappeptidetosubgroupset.cpp
grpmappeptidetosubgroupset.h
grppeptide.cpp
grppeptide.h
grppeptideset.cpp
grppeptideset.h
grpprotein.cpp
grpprotein.h
grpsubgroup.cpp
grpsubgroup.h
grpsubgroupset.cpp
grpsubgroupset.h
masschroq
input
jsoninput.cpp
jsoninput.h
precursorparser.cpp
precursorparser.h
output
cboroutputstream.cpp
cboroutputstream.h
alignmentmethod.cpp
alignmentmethod.h
mbrpeptidemeasurements.cpp
mbrpeptidemeasurements.h
msrun.cpp
msrun.h
msrungroup.cpp
msrungroup.h
msrunpeptidelist.cpp
msrunpeptidelist.h
peptide.cpp
peptide.h
peptidebase.cpp
peptidebase.h
peptidelabel.cpp
peptidelabel.h
peptidemeasurements.cpp
peptidemeasurements.h
peptidemeasurementsbase.cpp
peptidemeasurementsbase.h
peptideobservation.cpp
peptideobservation.h
precursor.cpp
precursor.h
protein.cpp
protein.h
quantificationmethod.cpp
quantificationmethod.h
types.h
utils.cpp
utils.h
massspectrum
massspectrum.cpp
massspectrum.h
massspectrumid.cpp
massspectrumid.h
qualifiedmassspectrum.cpp
qualifiedmassspectrum.h
msfile
bafasciifilereader.cpp
bafasciifilereader.h
msfileaccessor.cpp
msfileaccessor.h
msfilereader.cpp
msfilereader.h
mzcbormsfilereader.cpp
mzcbormsfilereader.h
mzformatenumstr.cpp
mzformatenumstr.h
pwizmsfilereader.cpp
pwizmsfilereader.h
timsmsfilereader.cpp
timsmsfilereader.h
xymsfilereader.cpp
xymsfilereader.h
msrun
alignment
msrunretentiontime.cpp
msrunretentiontime.h
template.cpp
output
mgfoutput.cpp
mgfoutput.h
mzxmloutput.cpp
mzxmloutput.h
private
mzcbormsrunreader.cpp	MSrun file reader for mzcbor
mzcbormsrunreader.h	MSrun file reader for mzcbor
pwizmsrunreader.cpp
pwizmsrunreader.h
timsframesmsrunreader.cpp
timsframesmsrunreader.h
timsmsrunreader.cpp
timsmsrunreader.h
timsmsrunreaderbase.cpp
timsmsrunreaderbase.h
timsmsrunreaderdia.cpp
timsmsrunreaderdia.h
timsmsrunreaderms2.cpp
timsmsrunreaderms2.h
timsmsrunreaderms2selected.cpp
timsmsrunreaderms2selected.h
xiccoord
ionmobilitygrid.cpp
ionmobilitygrid.h
xiccoord.cpp
xiccoord.h
xiccoordtims.cpp
xiccoordtims.h
bafasciimsrunreader.cpp
bafasciimsrunreader.h
msrundatasettree.cpp
msrundatasettree.h
msrundatasettreenode.cpp
msrundatasettreenode.h
msrundatasettreevisitor.h
msrunid.cpp
msrunid.h
msrunreadconfig.cpp
msrunreadconfig.h
msrunreader.cpp
msrunreader.h
spectrumcollectionhandlerinterface.cpp
spectrumcollectionhandlerinterface.h	Base interface to read MSrun files
xymsrunreader.cpp
xymsrunreader.h
obo
filterobopsimodmap.cpp
filterobopsimodmap.h
filterobopsimodsink.cpp
filterobopsimodsink.h
filterobopsimodtermaccession.cpp
filterobopsimodtermaccession.h
filterobopsimodtermdiffmono.cpp
filterobopsimodtermdiffmono.h
filterobopsimodtermlabel.cpp
filterobopsimodtermlabel.h
filterobopsimodtermname.cpp
filterobopsimodtermname.h
obopsimod.cpp
obopsimod.h
obopsimodhandlerinterface.h
obopsimodterm.cpp
obopsimodterm.h
obopsims.cpp
obopsims.h
obounimod.cpp
obounimod.h
peptide
ion.cpp
ion.h
peptide.cpp
peptide.h
peptidefragment.cpp
peptidefragment.h
peptidefragmention.cpp
peptidefragmention.h
peptidefragmentionlistbase.cpp
peptidefragmentionlistbase.h
peptideinterface.cpp
peptideinterface.h
peptidenaturalisotope.cpp
peptidenaturalisotope.h
peptidenaturalisotopeaverage.cpp
peptidenaturalisotopeaverage.h
peptidenaturalisotopelist.cpp
peptidenaturalisotopelist.h
peptideproformaparser.cpp
peptideproformaparser.h
peptiderawfragmentmasses.cpp
peptiderawfragmentmasses.h
peptidestrparser.cpp
peptidestrparser.h
processing
cbor
mzcbor
copyreplace
filtercomplement.cpp
filtercomplement.h
filterms1windowselection.cpp
filterms1windowselection.h
mzcborcopyreplacebase.cpp
mzcborcopyreplacebase.h
mzcborprecursorfinder.cpp	Read mzcbor stream or file, process it and write processed mzcbor output
mzcborprecursorfinder.h	Read mzcbor stream or file, process it and write processed mzcbor output
qcborspectrum.cpp	Low level CBOR map to store an mzCBOR Spectrum object
qcborspectrum.h	Low level CBOR map to store an mzCBOR Spectrum object
qcborspectrumprecursor.cpp	Low level CBOR map to store an mzCBOR Spectrum object
qcborspectrumprecursor.h	Low level CBOR map to store an mzCBOR Spectrum object
spectrumtube.cpp	Buffer to store a whole spectrum list
spectrumtube.h	Buffer to store a whole spectrum list
binarydataarray.cpp	PSI BinaryDataArray object for mzML/mzCBOR
binarydataarray.h	PSI BinaryDataArray object for mzML/mzCBOR
converttomzml.cpp
converttomzml.h
cvparam.cpp	PSI cvParam object for mzML/mzCBOR
cvparam.h	PSI cvParam object for mzML/mzCBOR
cvparammap.cpp	CvParam map
cvparammap.h	CvParam map
mzcborbuildindexreader.cpp	Read mzcbor to build an index
mzcborbuildindexreader.h	Read mzcbor to build an index
mzcborindexreader.cpp	Read mzcbor index file
mzcborindexreader.h	Read mzcbor index file
mzcborreaderbase.cpp	Read mzcbor stream or file, process it and write processed mzcbor output
mzcborreaderbase.h	Read mzcbor stream or file
mzcborspectrumcollectionreader.cpp	Read mzcbor for spectrum collection m_SpectrumCollectionHandlerInterface
mzcborspectrumcollectionreader.h	Read mzcbor for spectrum collection handler
mzmlconvert.cpp
mzmlconvert.h
precursor.cpp
precursor.h	PSI precursor object for mzML/mzCBOR
scan.cpp	PSI scan object for mzML/mzCBOR
scan.h	PSI scan object for mzML/mzCBOR
spectrum.cpp
spectrum.h	PSI spectrum object for mzML/mzCBOR
psm
evalscan
psmfeatures.cpp
psmfeatures.h
psmfeaturesscan.cpp
psmfeaturesscan.h
psmionseries.cpp
psmionseries.h
psmneweval.cpp
psmneweval.h
psmspecglob.cpp
psmspecglob.h
psmspecglobscan.cpp
psmspecglobscan.h
psmspecpeptidoms.cpp
psmspecpeptidoms.h
mzidentml
mzidentmlreader.cpp
mzidentmlreader.h
sage
sagefilereader.cpp
sagefilereader.h
sagereader.cpp
sagereader.h
sagetsvhandler.cpp
sagetsvhandler.h
cborscanmapbase.cpp
cborscanmapbase.h
psmcbor2json.cpp
psmcbor2json.h
psmcborutils.cpp
psmcborutils.h
psmfileappend.cpp
psmfileappend.h
psmfilereaderbase.cpp
psmfilereaderbase.h
psmfilescanprocess.cpp
psmfilescanprocess.h
psmfilescanprocessandcopy.cpp
psmfilescanprocessandcopy.h
psmproteinmap.cpp
psmproteinmap.h
cborstreamreader.cpp
cborstreamreader.h
cborstreamreaderinterface.cpp
cborstreamreaderinterface.h
cborstreamwriter.cpp
cborstreamwriter.h
jsonstreamwriter.cpp
jsonstreamwriter.h
combiners
integrationscope.cpp
integrationscope.h
integrationscopebase.cpp
integrationscopebase.h
integrationscoperect.cpp
integrationscoperect.h
integrationscoperhomb.cpp
integrationscoperhomb.h
massdatacombinerinterface.cpp
massdatacombinerinterface.h
massspectrumcombiner.cpp
massspectrumcombiner.h
massspectrumminuscombiner.cpp
massspectrumminuscombiner.h
massspectrumpluscombiner.cpp
massspectrumpluscombiner.h
mzintegrationparams.cpp
mzintegrationparams.h
selectionpolygon.cpp
selectionpolygon.h
tracecombiner.cpp
tracecombiner.h
traceminuscombiner.cpp
traceminuscombiner.h
tracepluscombiner.cpp
tracepluscombiner.h
compartraces
cosinesimilarity.cpp
cosinesimilarity.h
detection
cubicsplinemodel.cpp
cubicsplinemodel.h
highrespeakpicker.cpp
highrespeakpicker.h
localsignaltonoiseestimator.cpp
localsignaltonoiseestimator.h
signaltonoiseestimatormedian.cpp
tracedetectioninterface.h
tracedetectionmoulon.cpp
tracedetectionmoulon.h
tracedetectionzivy.cpp
tracedetectionzivy.h
tracepeak.cpp
tracepeak.h
tracepeaklist.cpp
tracepeaklist.h
filters
filterceilingamplitudepercentage.cpp
filterceilingamplitudepercentage.h
filterchargedeconvolution.cpp
filterchargedeconvolution.h
filtercomplementionenhancer.cpp
filtercomplementionenhancer.h
filterexclusionmz.cpp
filterexclusionmz.h
filterflooramplitudepercentage.cpp
filterflooramplitudepercentage.h
filterinterface.h
filterlocalmaximum.cpp
filterlocalmaximum.h
filterlowintensitysignalremoval.cpp
filterlowintensitysignalremoval.h
filtermorpho.cpp
filtermorpho.h
filternameinterface.cpp
filternameinterface.h
filternormalizeintensities.cpp
filternormalizeintensities.h
filterpass.cpp
filterpass.h
filterpeakdelta.cpp
filterpeakdelta.h
filterremovec13.cpp
filterremovec13.h
filterresample.cpp
filterresample.h
filtersuite.cpp
filtersuite.h
filtersuitestring.cpp
filtersuitestring.h
filtertandemremovec13.cpp
filtertandemremovec13.h
filtertriangle.cpp
filtertriangle.h
savgolfilter.cpp
savgolfilter.h
project
projectparameters.cpp
projectparameters.h
specglob
experimentalspectrum.cpp
experimentalspectrum.h
peptidemodel.cpp
peptidemodel.h
peptidespectrum.cpp
peptidespectrum.h
posttreatment.cpp
posttreatment.h
scorevalues.cpp
scorevalues.h
spectralalignment.cpp
spectralalignment.h
types.h
specpeptidoms
correctiontree.cpp
correctiontree.h
locationsaver.cpp
locationsaver.h
peptidemodel.cpp
peptidemodel.h
scenario.cpp
scenario.h
scorevalues.cpp
scorevalues.h
semiglobalalignment.cpp
semiglobalalignment.h
spomsprotein.cpp
spomsprotein.h
spomsspectrum.cpp
spomsspectrum.h
types.h
specself
selfspectrum.cpp
selfspectrum.h
selfspectrumdatapoint.cpp
selfspectrumdatapoint.h
spectree
bucket.cpp
bucket.h
bucketclustering.cpp
bucketclustering.h
itemcart.cpp
itemcart.h
spectree.cpp
spectree.h
specxtractinterface.cpp
specxtractinterface.h
tandemwrapper
tandemwrapperrun.cpp
tandemwrapperrun.h
wraptandeminput.cpp
wraptandeminput.h
wraptandemresults.cpp
wraptandemresults.h
xtandempresetreader.cpp
xtandempresetreader.h
uimonitor
uimonitorinterface.h
uimonitortext.cpp
uimonitortext.h
uimonitortextpercent.cpp
uimonitortextpercent.h
uimonitorvoid.h
xml
mzidentmlwriter.cpp	MzIdentML writer
mzidentmlwriter.h	MzIdentML writer
xmlstreamreaderinterface.cpp
xmlstreamreaderinterface.h
protein
enzyme.cpp
enzyme.h
enzymeproductinterface.h
peptidebuilder.cpp
peptidebuilder.h
peptidefixedmodificationbuilder.cpp
peptidefixedmodificationbuilder.h
peptidemethioninremove.cpp
peptidemethioninremove.h
peptidemodificatorbase.cpp
peptidemodificatorbase.h	Base class for all peptide modification builders
peptidemodificatorpipeline.cpp
peptidemodificatorpipeline.h
peptidemodificatortee.cpp
peptidemodificatortee.h
peptidesemienzyme.cpp
peptidesemienzyme.h
peptidesizefilter.cpp
peptidesizefilter.h
peptidevariablemodificationbuilder.cpp
peptidevariablemodificationbuilder.h
peptidevariablemodificationreplacement.cpp
peptidevariablemodificationreplacement.h	Potential replacement of a modification by an other
protein.cpp
protein.h
proteinintegercode.cpp	Transform protein amino acid sequence into vectors of amino acid codes
proteinintegercode.h	Transform protein amino acid sequence into vectors of amino acid codes
proteinpeptidelist.cpp
proteinpeptidelist.h
proteinpresenceabsencematrix.cpp	Presence/absence matrix of amino acid code along the protein sequence
proteinpresenceabsencematrix.h	Presence/absence matrix of amino acid code along the protein sequence
psm
deepprot
deepprotenum.cpp
deepprotenum.h
experimental
ionisotoperatioscore.cpp
ionisotoperatioscore.h
features
psmfeatures.cpp
psmfeatures.h
morpheus
morpheusscore.cpp
morpheusscore.h
xtandem
xtandemhyperscore.cpp
xtandemhyperscore.h
xtandemhyperscorebis.cpp
xtandemhyperscorebis.h
xtandemspectrumprocess.cpp
xtandemspectrumprocess.h
peakionisotopematch.cpp
peakionisotopematch.h
peakionmatch.cpp
peakionmatch.h
peptideisotopespectrummatch.cpp
peptideisotopespectrummatch.h
peptidespectrummatch.cpp
peptidespectrummatch.h
trace
datapoint.cpp
datapoint.h
linearregression.cpp	Compute linear regression
linearregression.h
maptrace.cpp
maptrace.h
trace.cpp
trace.h
vendors
tims
mobilitytraces
timsframemobilitytraces.cpp
timsframemobilitytraces.h
mzcalibration
cardano.cpp
cardano.h
mzcalibrationinterface.cpp
mzcalibrationinterface.h
mzcalibrationmodel1.cpp
mzcalibrationmodel1.h
mzcalibrationstore.cpp
mzcalibrationstore.h
xicextractor
timsdirectxicextractor.cpp
timsdirectxicextractor.h
timsxicextractorinterface.cpp
timsxicextractorinterface.h
timsbindec.cpp
timsbindec.h
timsdata.cpp
timsdata.h
timsdatafastmap.cpp
timsdatafastmap.h
timsddaprecursors.cpp
timsddaprecursors.h
timsdiaslices.cpp
timsdiaslices.h
timsframe.cpp
timsframe.h
timsframebase.cpp
timsframebase.h
timsframerawdatachunck.cpp
timsframerawdatachunck.h
timsframerecord.h
timsframetype1.cpp
timsframetype1.h
timsms2centroidfilter.cpp
timsms2centroidfilter.h
xic
qualifiedxic.cpp
qualifiedxic.h
xic.cpp
xic.h
xicpeptidefragmention.cpp
xicpeptidefragmention.h
xicpeptidefragmentionnaturalisotope.cpp
xicpeptidefragmentionnaturalisotope.h
xicpeptideinterface.cpp
xicpeptideinterface.h
xicextractor
private
msrunslice.cpp
msrunslice.h
msrunxicextractor.cpp
msrunxicextractor.h
msrunxicextractordisk.cpp
msrunxicextractordisk.h
msrunxicextractordiskbuffer.cpp
msrunxicextractordiskbuffer.h
msrunxicextractorfactory.cpp
msrunxicextractorfactory.h
msrunxicextractorinterface.cpp
msrunxicextractorinterface.h
mzrange.cpp
mzrange.h
pappsoexception.h
precision.cpp
precision.h
types.cpp
types.h
utils.cpp
utils.h
gui
httpbutton
httpbutton.cpp
httpbutton.h
massspectrumwidget
massspectrumwidget.cpp
massspectrumwidget.h
qcpspectrum.cpp
qcpspectrum.h
obo
obochooserwidget
obochooserwidget.cpp
obochooserwidget.h
obolistwidget
obolistmodel.cpp
obolistmodel.h
obolistproxymodel.cpp
obolistproxymodel.h
obolistwidget.cpp
obolistwidget.h
obotermform
obotermform.cpp
obotermform.h
plotwidget
basecolormapplotwidget.cpp
basecolormapplotwidget.h
baseplotcontext.cpp
baseplotcontext.h
baseplotwidget.cpp
baseplotwidget.h
basetraceplotwidget.cpp
basetraceplotwidget.h
colormapplotconfig.cpp
colormapplotconfig.h
driftspecmassspeccolormapplotwidget.cpp
driftspecmassspeccolormapplotwidget.h
driftspectraceplotwidget.cpp
driftspectraceplotwidget.h
massspectraceplotcontext.cpp
massspectraceplotcontext.h
massspectraceplotwidget.cpp
massspectraceplotwidget.h
ticxicchromdriftspeccolormapplotwidget.cpp
ticxicchromdriftspeccolormapplotwidget.h
ticxicchrommassspeccolormapplotwidget.cpp
ticxicchrommassspeccolormapplotwidget.h
ticxicchromtraceplotwidget.cpp
ticxicchromtraceplotwidget.h
precisionwidget
precisionwidget.cpp
precisionwidget.h
switchbuttonwidget
switchbuttonwidget.cpp
switchbuttonwidget.h
xicwidget
qcpxic.cpp
qcpxic.h
xicwidget.cpp
xicwidget.h
graphicdevicewidget.cpp
graphicdevicewidget.h
config.h
export-import-config.h