
n = will probably not be wrapped (even though technically possible - most likely deprecated code, abstract base class or some other reason - 14 TOPP tools, 15 Utils)
x = cannot not be wrapped (too much code in TOPP tools; 32 TOPP tools, 16 Utils)
xx = is not yet wrapped, must be done (5 TOPP tools, no Utils)
ok = is done (42 TOPP tools out of 98 are currently ok, plus 8 utils)
?  = not yet clear (5 TOPP tools, 2 Utils)

Autwrap has wrapped 366 classes, 3794 methods and 62 enums



98 TOPP tools, 41 utils

In total, 153 classes are wrapped at the current moment.

ok   BaselineFilter.cpp # morph filter
ok   CompNovo.cpp
ok   CompNovoCID.cpp
ok   ConsensusID.cpp
ok   ConsensusMapNormalizer.cpp # all 3 algos
n    DBExporter.cpp
n    DBImporter.cpp
ok   Decharger.cpp
x    DTAExtractor.cpp # 134 lines
x    EICExtractor.cpp # 215 lines
n    ExecutePipeline.cpp
ok   FalseDiscoveryRate.cpp
ok   FeatureFinderCentroided.cpp
ok   FeatureFinderIsotopeWavelet.cpp
ok   FeatureFinderMetabo.cpp
n    FeatureFinderMRM.cpp
n    FeatureLinkerBase.cpp
?    FeatureLinkerLabeled.cpp
?    FeatureLinkerUnlabeled.cpp
ok   FeatureLinkerUnlabeledQT.cpp
n    FileConverter.cpp  # probably easier to just write in Python
n    FileFilter.cpp     # probably easier to just write in Python
x    FileInfo.cpp       # 1000+ lines
x    FileMerger.cpp     # 300 lines
n    GenericWrapper.cpp # not useful for Python
x    HighResPrecursorMassCorrector.cpp # 150 lines.PPHiRes is wrapped
x    IDConflictResolver.cpp  # ca 90 lines
x    IDFileConverter.cpp  # 300 lines
ok   IDFilter.cpp
ok   IDMapper.cpp
x    IDMerger.cpp         # 200 lines
x    IDPosteriorErrorProbability.cpp # 300 lines PosteriorErrorProbabilityModel is wrapped
xx   IDRipper.cpp         # TODO - not yet done on my side, needs hand-wrapping
x    IDRTCalibration.cpp # 100 lines
x    InclusionExclusionListCreator.cpp # TODO should we wrap this? 347 lines
x    InspectAdapter.cpp # 750 lines
ok   InternalCalibration.cpp
ok   MapAlignerIdentification.cpp
ok   MapAlignerPoseClustering.cpp
n    MapAlignerSpectrum.cpp
x    MapNormalizer.cpp  # 100 lines
?    MapRTTransformer.cpp # 150 lines, wrap MapRTTransformer
x    MapStatistics.cpp    # 400 lines
x    MascotAdapter.cpp  # 400 lines
x    MascotAdapterOnline.cpp # 200 lines
ok   MassTraceExtractor.cpp
ok   MRMMapper.cpp
x    MyriMatchAdapter.cpp  # 400 lines
?    MzTabExporter.cpp     # needs wrapping of depracated method in MzTabFile
ok   NoiseFilterGaussian.cpp
ok   NoiseFilterSGolay.cpp
x    OMSSAAdapter.cpp      # 700 lines
ok   OpenSwathAnalyzer.cpp
ok   OpenSwathChromatogramExtractor.cpp
ok   OpenSwathConfidenceScoring.cpp
?    OpenSwathDecoyGenerator.cpp
ok   OpenSwathFeatureXMLToTSV.cpp
ok   OpenSwathRTNormalizer.cpp
ok   PeakPickerHiRes.cpp
ok   PeakPickerWavelet.cpp
x    PepNovoAdapter.cpp   # 300 lines
x    PeptideIndexer.cpp   # 500 lines
xx   PhosphoScoring.cpp # AScore.pxd TODO , RichPeakSpectrum doesnt work
n    PrecursorIonSelector.cpp
x    PrecursorMassCorrector.cpp #Isotope Wavelet is wrapped, 200 lines
x    ProteinInference.cpp    # 200 lines
x    ProteinQuantifier.cpp # PeptideAndProteinQuant is wrapped, 600 lines
xx   ProteinResolver.cpp   # 500 lines, has a
x    PTModel.cpp  # 400 lines
x    PTPredict.cpp # 200 lines
ok   Resampler.cpp
x    RTModel.cpp   # 800 lines
x    RTPredict.cpp # 600 lines
xx   SeedListGenerator.cpp # TODO more work required overloading methods
x    SequestAdapter.cpp   # 1200 lines
x    SpecLibSearcher.cpp
ok   SpectraFilterBernNorm.cpp
ok   SpectraFilterMarkerMower.cpp
ok   SpectraFilterNLargest.cpp
ok   SpectraFilterNormalizer.cpp
ok   SpectraFilterParentPeakMower.cpp
ok   SpectraFilterScaler.cpp
ok   SpectraFilterSqrtMower.cpp
ok   SpectraFilterThresholdMower.cpp
ok   SpectraFilterWindowMower.cpp
ok   SpectraMerger.cpp
x    TextExporter.cpp   # 1000 lines
ok   TOFCalibration.cpp
x    XTandemAdapter.cpp  # 300 lines


UTILS

so far, 3 are wrapped

x    CVInspector.cpp   # 400 lines
x    DecoyDatabase.cpp # 200 lines
x    DeMeanderize.cpp  # 100 lines
ok   Digestor.cpp
ok   DigestorMotif.cpp
x    ERPairFinder.cpp   # 400 lines
ok   FeatureFinderSuperHirn.cpp
n    FFEval.cpp
n    FuzzyDiff.cpp
ok   IDDecoyProbability.cpp
x    IDExtractor.cpp  # 200 lines
n    IDMassAccuracy.cpp
n    IDSplitter.cpp
n    ImageCreator.cpp
n    INIUpdater.cpp
n    LabeledEval.cpp
n    MassCalculator.cpp
n    MRMPairFinder.cpp
?    MSSimulator.cpp  # 250 lines =
n    OpenMSInfo.cpp
n    OpenSwathDIAPreScoring.cpp
?    OpenSwathMzMLFileCacher.cpp
n    OpenSwathRewriteToFeatureXML.cpp
x    QCCalculator.cpp   # 600 lines
x    QCEmbedder.cpp     # 200 lines
x    QCExporter.cpp     # 100 lines
x    QCMerger.cpp       # 200 lines
x    QCShrinker.cpp     # 100 lines
x    RNPxl.cpp     # 1300 lines
x    RNPxlXICFilter.cpp # 200 lines
x    RTEvaluation.cpp  # 300 lines
ok   SemanticValidator.cpp
x    SequenceCoverageCalculator.cpp # 200 lines
x    SpecLibCreator.cpp # 200 lines
ok   SvmTheoreticalSpectrumGeneratorTrainer.cpp
n    TransformationEvaluation.cpp
x    XMLValidator.cpp # 80 lines


The TOPP tools are divided into several subgroups:

# In general, file handling is wrapped by FORMAT/ file handlers. Currently wrapped are the following formats:
- ConsensusXML
- FeatureXML
- IdXML
- ParamXML
- PepXML
- TransformationXML
- TraML
- MzData
- MzML
- MzQuantML
- MzXML

File Handling

x  DTAExtractor - Extracts spectra of an MS run file to several files in DTA format. # all in tool
x  FileConverter - Converts between different MS file formats. # all in tool
x  FileFilter - Extracts or manipulates portions of data from peak, feature or consensus feature files. # all in tool
x  FileInfo - Shows basic information about the file, such as data ranges and file type. # all in tool
x  FileMerger - Merges several MS files into one file. # all in tool
x  IDMerger - Merges several protein/peptide identification files into one file. # all in tool
x  IDFileConverter - Converts identification engine file formats. # all in tool
ok SpectraMerger - Merges spectra from an LC/MS map, either by precursor or by RT blocks # done
x  TextExporter - Exports various XML formats to a text file. # all in tool


Signal Processing and Preprocessing

ok  BaselineFilter - Removes the baseline from profile spectra using a top-hat filter. # morphological filter ok
ok  InternalCalibration - Applies an internal calibration.  # ok
x   MapNormalizer - Normalizes peak intensities in an MS run.               # all code in TOPP tool
ok  NoiseFilter - Removes noise from profile spectra by using different smoothing techniques. # both algos wrapped
ok  PeakPicker - Finds mass spectrometric peaks in profile mass spectra. # both algos wrapped
x   PrecursorMassCorrector - Correct the precursor entries of tandem MS scans. #mapped the FeatureFinder, rest of the code is in TOPP tool
ok  Resampler - Transforms an LC/MS map into an equally-spaced (in RT and m/z) map.
ok  SpectraFilter - Applies a filter to peak spectra. # done all 9...
ok  TOFCalibration - Applies time of flight calibration.


Quantitation

ok  Decharger - Decharges and merges different feature charge variants of the same chemical entity.
ok  FeatureFinder - Detects two-dimensional features in LC-MS data.
ok  ProteinQuantifier - Computes protein abundances from annotated feature/consensus maps # done with PeptideAndProteinQuant
x   SeedListGenerator - Generates seed lists for feature detection. # needs more work


Protein/Peptide Identification

ok  CompNovo - Performs a peptide/protein identification with the CompNovo engine.
x   InspectAdapter - Identifies MS/MS spectra using Inspect (external).
x   MascotAdapter - Identifies MS/MS spectra using Mascot (external).
x   MascotAdapterOnline - Identifies MS/MS spectra using Mascot (external).
x   OMSSAAdapter - Identifies MS/MS spectra using OMSSA (external).
x   PepNovoAdapter - Identifies MS/MS spectra using PepNovo (external).
x   XTandemAdapter - Identifies MS/MS spectra using XTandem (external).
x   SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. # too much code in TOPP tool


Protein/Peptide Processing

ok  ConsensusID - Computes a consensus identification from peptide identifications of several identification engines.
ok  FalseDiscoveryRate - Estimates the false discovery rate on peptide and protein level using decoy searches.
ok  IDDecoyProbability - Estimates peptide probabilities using a decoy search strategy. # UTILS tool wrapped
ok  IDFilter - Filters results from protein or peptide identification engines based on different criteria. # done
ok  IDMapper - Assigns protein/peptide identifications to feature or consensus features.
ok  IDPosteriorErrorProbability - Estimates posterior error probabilities using a mixture model.
x   IDRTCalibration - Can be used to calibrate RTs of peptide hits linearly to standards. # all in TOPP tool
x   PeptideIndexer - Refreshes the protein references for all peptide hits. # all in TOPP tool
x   ProteinInference - Infer proteins from a list of (high-confidence) peptides. # all in TOPP tool


Targeted Experiments

x   InclusionExclusionListCreator - Creates inclusion and/or exclusion lists for LC-MS/MS experiments. # most in TOPP tools except OfflinePrecursorSelection
x   PrecursorIonSelector - A tool for precursor ion selection based on identification results.


Peptide Property Prediction

x   PTModel - Trains a model for the prediction of proteotypic peptides from a training set. # most in TOPP tool
x   PTPredict - Predicts the likelihood of peptides to be proteotypic using a model trained by PTModel. # most in TOPP tool
x   RTModel - Trains a model for the retention time prediction of peptides from a training set. # most in TOPP tool
x   RTPredict - Predicts retention times for peptides using a model trained by RTModel. # most in TOPP tool


Map Alignment

ok  ConsensusMapNormalizer - Normalizes maps of one consensusXML file (after linking).
ok  MapAligner - Corrects retention time distortions between maps. # got 2 map aligners pose and id
ok  FeatureLinker - Groups corresponding features in one map or across maps (after alignment). # got featurelinking qt


## no wrapping of graphical tools
Graphical Tools

TOPPView - A viewer for mass spectrometry data.
TOPPAS - An assistant for GUI-driven TOPP workflow design.
INIFileEditor - An editor for OpenMS configuration files.


## no wrapping of generic tools
Misc

GenericWrapper - Allows the generic wrapping of external tools.
ExecutePipeline - Executes workflows created by TOPPAS.
