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File List
Here is a list of all files with brief descriptions:

pappsomspp |
amino_acid |
aa.cpp |
aa.h |
aabase.cpp |
aabase.h | Private amino acid model
aacode.cpp | Give an integer code to each amino acid
aacode.h | Give an integer code to each amino acid
aamodification.cpp |
aamodification.h | Amino acid modification model
aastringcodec.cpp | Code and decodefrom amino acid string to integer
aastringcodec.h | Code and decodefrom amino acid string to integer
aastringcodemassmatching.cpp | Convert mass list to amino acid string code list
aastringcodemassmatching.h | Convert mass list to amino acid string code list
atomnumberinterface.h |
exception |
exceptioninterrupted.h | Process interrupted exception
exceptionnotfound.h |
exceptionnotimplemented.h |
exceptionnotpossible.h |
exceptionnotrecognized.h | Excetion to use when an item type is not recognized (file format, object type...)
exceptionoutofrange.h |
fasta |
fastafileindexer.cpp | Quick random access to sequences in a fasta file using an index
fastafileindexer.h | Quick random access to sequences in a fasta file using an index
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 |
massspectrum |
massspectrum.cpp | Basic mass spectrum
massspectrum.h | Basic mass spectrum
massspectrumid.cpp |
massspectrumid.h |
qualifiedmassspectrum.cpp |
qualifiedmassspectrum.h |
msfile |
msfileaccessor.cpp |
msfileaccessor.h |
msfilereader.cpp |
msfilereader.h |
mzformatenumstr.cpp | Convert mzformat enumerations to strings
mzformatenumstr.h | Convert mzformat enumerations to strings
pwizmsfilereader.cpp |
pwizmsfilereader.h |
timsmsfilereader.cpp | MSrun file reader for native Bruker TimsTOF raw data
timsmsfilereader.h | MSrun file reader for native Bruker TimsTOF raw data
xymsfilereader.cpp |
xymsfilereader.h |
msrun |
alignment |
msrunalignment.cpp |
msrunalignment.h |
msrunretentiontime.cpp |
msrunretentiontime.h |
template.cpp |
output |
mgfoutput.cpp |
mgfoutput.h | Write msrun peaks into MGF output stream
mzxmloutput.cpp | Write msrun peaks into mzxml output stream
mzxmloutput.h | Write msrun peaks into mzxml output stream
private |
pwizmsrunreader.cpp | MSrun file reader base on proteowizard library
pwizmsrunreader.h | MSrun file reader base on proteowizard library
timsframesmsrunreader.cpp |
timsframesmsrunreader.h |
timsmsrunreader.cpp |
timsmsrunreader.h | MSrun file reader for native Bruker TimsTOF raw data
timsmsrunreaderms2.cpp | MSrun file reader for native Bruker TimsTOF specialized for MS2 purpose
timsmsrunreaderms2.h | MSrun file reader for native Bruker TimsTOF specialized for MS2 purpose
timsmsrunreaderms2selected.cpp |
timsmsrunreaderms2selected.h |
xiccoord |
ionmobilitygrid.cpp | Store observed ion mobility coordinates differences between MS runs
ionmobilitygrid.h | Store observed ion mobility coordinates differences between MS runs
xiccoord.cpp | XIC coordinate in MSrun
xiccoord.h | XIC coordinate in MSrun
xiccoordtims.cpp | XIC coordinate in a Tims MSrun
xiccoordtims.h | XIC coordinate in a Tims MSrun
msrundatasettree.cpp |
msrundatasettree.h |
msrundatasettreenode.cpp |
msrundatasettreenode.h |
msrundatasettreevisitor.h |
msrunid.cpp |
msrunid.h |
msrunreadconfig.cpp |
msrunreadconfig.h |
msrunreader.cpp | Base interface to read MSrun files
msrunreader.h | Base interface to read MSrun files
spectrumcollectionhandlerinterface.cpp |
spectrumcollectionhandlerinterface.h |
xymsrunreader.cpp |
xymsrunreader.h |
obo |
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 |
peptide |
ion.cpp | Ion interface
ion.h | Ion interface
peptide.cpp | Peptide model
peptide.h | Peptide model
peptidefragment.cpp |
peptidefragment.h | Peptide fragment model
peptidefragmention.cpp | Peptide ion model
peptidefragmention.h | Peptide ion model
peptidefragmentionlistbase.cpp | Fragmentation base object
peptidefragmentionlistbase.h | Fragmentation base object
peptideinterface.cpp |
peptideinterface.h |
peptidenaturalisotope.cpp | Peptide natural isotope model
peptidenaturalisotope.h | Peptide natural isotope model
peptidenaturalisotopeaverage.cpp |
peptidenaturalisotopeaverage.h |
peptidenaturalisotopelist.cpp | Peptide natural isotope model
peptidenaturalisotopelist.h | Peptide natural isotope model
peptideproformaparser.cpp | Parse peptide string in ProForma to pappso::Peptide
peptideproformaparser.h | Parse peptide string in ProForma to pappso::Peptide https://github.com/HUPO-PSI/ProForma/blob/master/README.md
peptiderawfragmentmasses.cpp | Class dedicated to raw mass computations of peptide products (fragments)
peptiderawfragmentmasses.h | Class dedicated to raw mass computations of peptide products (fragments)
peptidestrparser.cpp |
peptidestrparser.h |
processing |
combiners |
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 | Computes cosine similarity of 2 traces vector https://en.wikipedia.org/wiki/Cosine_similarity
cosinesimilarity.h | Computes cosine similarity of 2 traces vector https://en.wikipedia.org/wiki/Cosine_similarity
detection |
tracedetectioninterface.h |
tracedetectionmoulon.cpp |
tracedetectionmoulon.h |
tracedetectionzivy.cpp |
tracedetectionzivy.h |
tracepeak.cpp |
tracepeak.h |
tracepeaklist.cpp | Trace peak list
tracepeaklist.h | Trace peak list
filters |
filterceilingamplitudepercentage.cpp |
filterceilingamplitudepercentage.h |
filterchargedeconvolution.cpp |
filterchargedeconvolution.h | Sum peaks and transform mz to fit charge = 1
filtercomplementionenhancer.cpp | Enhance ion intensity of ion fragment complement
filtercomplementionenhancer.h | Enhance ion intensity of ion fragment complement
filterexclusionmz.cpp | Delete small peaks in the exclusion range
filterexclusionmz.h | Delete small peaks in the exclusion range
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 | Sum peaks under a triangle base
filterresample.cpp |
filterresample.h |
filtersuite.cpp |
filtersuite.h |
filtersuitestring.cpp |
filtersuitestring.h |
filtertandemremovec13.cpp |
filtertandemremovec13.h |
filtertriangle.cpp |
filtertriangle.h |
savgolfilter.cpp |
savgolfilter.h |
specglob |
experimentalspectrum.cpp | Transform a spectrum to SpecGlob spectra
experimentalspectrum.h | Transform a spectrum to SpecGlob spectra
peptidemodel.cpp |
peptidemodel.h | SpecGlobTool peptide model
peptidespectrum.cpp | Transform a peptide to SpecGlob spectrum
peptidespectrum.h | Transform a peptide to SpecGlob spectrum
posttreatment.cpp |
posttreatment.h |
scorevalues.cpp |
scorevalues.h | Scores to apply in comparisons
spectralalignment.cpp |
spectralalignment.h |
types.h | SpecGlobTool types definition
tandemwrapper |
tandemwrapperrun.cpp | Actually does really run tandem directly on Bruker's data
tandemwrapperrun.h | Actually does really run tandem directly on Bruker's data
wraptandeminput.cpp | Rewrites tandem xml input file with temporary files
wraptandeminput.h | Rewrites tandem xml input file with temporary files
wraptandemresults.cpp | Rewrites tandem xml output file with temporary files
wraptandemresults.h | Rewrites tandem xml output file with temporary files
xtandempresetreader.cpp | Read tandem preset file to get centroid parameters and number of threads
xtandempresetreader.h | Read tandem preset file to get centroid parameters and number of threads
uimonitor |
uimonitorinterface.h | Generic interface to monitor any long process A long process needs to be interrupted by the user and to report progress while running. This interface is used by long process in this library
uimonitortext.cpp | Simle text monitor implementation of the User Interface Monitor
uimonitortext.h | Simle text monitor implementation of the User Interface Monitor
uimonitortextpercent.cpp | Simle text monitor implementation of the User Interface Monitor displaying percent progression
uimonitortextpercent.h | Simle text monitor implementation of the User Interface Monitor displaying percent progression
uimonitorvoid.h | Simle monitor that does nothing
xml |
xmlstreamreaderinterface.cpp | Common interface to read all XML streams containing convenient functions
xmlstreamreaderinterface.h | Common interface to read all XML streams containing convenient functions
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 | Object to handle a protein
protein.h | Object to handle a protein
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 | Object to handle a peptide list linked to one protein
psm |
deepprot |
deepprotenum.cpp | Base type definition to use in DeepProt
deepprotenum.h | Base type definition to use in DeepProt
experimental |
ionisotoperatioscore.cpp | Psm score computed using ion isotopes
ionisotoperatioscore.h | Psm score computed using ion isotopes
features |
psmfeatures.cpp | Comutes various PSM (Peptide Spectrum Match) features
psmfeatures.h | Comutes various PSM (Peptide Spectrum Match) features
morpheus |
morpheusscore.cpp |
morpheusscore.h |
xtandem |
xtandemhyperscore.cpp | Process spectrum to compute X!Tandem hyperscore
xtandemhyperscore.h | Computation of the X!Tandem hyperscore
xtandemhyperscorebis.cpp | Computation of the X!Tandem hyperscore
xtandemhyperscorebis.h | Computation of the X!Tandem hyperscore
xtandemspectrumprocess.cpp |
xtandemspectrumprocess.h |
peakionisotopematch.cpp |
peakionisotopematch.h |
peakionmatch.cpp | Associate a peak and a peptide + charge
peakionmatch.h | Associate a peak and a peptide + charge
peptideisotopespectrummatch.cpp |
peptideisotopespectrummatch.h |
peptidespectrummatch.cpp | Find peaks matching between ions and spectrum
peptidespectrummatch.h | Find peaks matching between ions and spectrum
trace |
datapoint.cpp |
datapoint.h |
linearregression.cpp | Compute linear regression
linearregression.h |
maptrace.cpp |
maptrace.h |
trace.cpp |
trace.h |
vendors |
tims |
mzcalibration |
cardano.cpp | Cubic solver adapted from https://www.codeproject.com/articles/798474/to-solve-a-cubic-equation thanks to "Sergey Bochkanov" serge.nosp@m.y.bo.nosp@m.chkan.nosp@m.ov@a.nosp@m.lglib.nosp@m..net for his advise
cardano.h | Cubic solver adapted from https://www.codeproject.com/articles/798474/to-solve-a-cubic-equation thanks to "Sergey Bochkanov" serge.nosp@m.y.bo.nosp@m.chkan.nosp@m.ov@a.nosp@m.lglib.nosp@m..net for his advise
mzcalibrationinterface.cpp | Handles different ways to compute m/z using calibration parameters
mzcalibrationinterface.h | Handles different ways to compute m/z using calibration parameters
mzcalibrationmodel1.cpp | Implement Bruker's model type 1 formula to compute m/z
mzcalibrationmodel1.h | Implement Bruker's model type 1 formula to compute m/z
mzcalibrationstore.cpp |
mzcalibrationstore.h |
xicextractor |
timsdirectxicextractor.cpp | Minimum functions to extract XICs from Tims Data
timsdirectxicextractor.h | Minimum functions to extract XICs from Tims Data
timsxicextractorinterface.cpp | Minimum functions to extract XICs from Tims Data
timsxicextractorinterface.h | Minimum functions to extract XICs from Tims Data
timsbindec.cpp |
timsbindec.h | Binary file handler of Bruker's TimsTof raw data
timsdata.cpp | Main Tims data handler
timsdata.h | Main Tims data handler
timsframe.cpp | Handle a single Bruker's TimsTof frame
timsframe.h | Handle a single Bruker's TimsTof frame
timsframebase.cpp | Handle a single Bruker's TimsTof frame without binary data
timsframebase.h | Handle a single Bruker's TimsTof frame without binary data
timsframerawdatachunck.cpp | Stores raw binary tims frame
timsframerawdatachunck.h | Stores raw binary tims frame
timsframerecord.h | Simple structure to store SQL lite frame records
timsframetype1.cpp | Handle a single Bruker's TimsTof frame type 1 compression
timsframetype1.h | Handle a single Bruker's TimsTof frame type 1 compression
timsms2centroidfilter.cpp | Special process for tims MS2 spectrum (centroid like)
timsms2centroidfilter.h | Special process for tims MS2 spectrum (centroid like)
widget |
httpbutton |
httpbutton.cpp | Push button to trigger web browser on URL
httpbutton.h | Push button to trigger web browser on URL
massspectrumwidget |
massspectrumwidget.cpp |
massspectrumwidget.h |
qcpspectrum.cpp |
qcpspectrum.h |
obo |
obochooserwidget |
obochooserwidget.cpp | Display obo term list and choose items
obochooserwidget.h | Display obo term list and choose items
obolistwidget |
obolistmodel.cpp |
obolistmodel.h | MVC model of OBO term list
obolistproxymodel.cpp | MVC proxy model of OBO term list
obolistproxymodel.h | MVC proxy model of OBO term list
obolistwidget.cpp | Handles a list of obo term, select and click
obolistwidget.h | Handles a list of obo term, select and click
obotermform |
obotermform.cpp | Display an obo term form
obotermform.h | Display an obo term form
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 | Edit presicion in ppm or dalton
precisionwidget.h | Edit presicion in ppm or dalton
switchbuttonwidget |
switchbuttonwidget.cpp | Widget to transform a push button to a switch button
switchbuttonwidget.h | Widget to transform a push button to a switch button
xicwidget |
qcpxic.cpp | Custom plot XIC
qcpxic.h | Custom plot XIC
xicwidget.cpp |
xicwidget.h | Plot a XIC
graphicdevicewidget.cpp | Common graphic functions
graphicdevicewidget.h | Common graphic functions
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 | One mz slice (1 dalton) of an MsRun
msrunslice.h | One mz slice (1 dalton) of an MsRun
msrunxicextractor.cpp |
msrunxicextractor.h |
msrunxicextractordisk.cpp | Proteowizard based XIC extractor featuring disk cache
msrunxicextractordisk.h | MsRunReader based XIC extractor featuring disk cache
msrunxicextractordiskbuffer.cpp | Proteowizard based XIC extractor featuring disk cache + write buffer
msrunxicextractordiskbuffer.h | Proteowizard based XIC extractor featuring disk cache + write buffer
msrunxicextractorfactory.cpp | Factory to build XIC extractor on an MsRun file
msrunxicextractorfactory.h | Factory to build XIC extractor on an MsRun file
msrunxicextractorinterface.cpp |
msrunxicextractorinterface.h |
config.h |
exportinmportconfig.h |
mzrange.cpp |
mzrange.h |
pappsoexception.h |
precision.cpp |
precision.h |
types.h | This header contains all the type re-definitions and all the global variables definitions used in the PAPPSOms++ library
utils.cpp |
utils.h |