File List

Here is a list of all files with brief descriptions:

[detail level 12345]

▼ pappsomspp
► amino_acid
aa.cpp
aa.h
aabase.cpp
aabase.h	Private amino acid model
aamodification.cpp
aamodification.h	Amino acid modification model
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
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
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
msrunreader.cpp	Base interface to read MSrun files
msrunreader.h	Base interface to read MSrun files
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
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
► 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
filterpass.cpp
filterpass.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
► 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
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
► 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
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
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