- Class ConsensusXMLFile  
- Take care that unique ids are assigned properly by TOPP tools before calling ConsensusXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers) 
- Class DBAdapter  
- Add DataProcessing to MetaInfoDescription (Hiwi, Mathias)  - Check if test is really complete (Hiwi, Mathias)  - Check that all values are quoted (Hiwi, Mathias)  - Implement StringDataArray and IntegerDataArray of spectrum (Hiwi, Mathias)  
- Class FalseDiscoveryRate  
- implement combined searches properly (Andreas)  
- Member FeatureFinder::run  (const String &algorithm_name, MSExperiment< PeakType > &input_map, FeatureMap< FeatureType > &features, const Param ¶m, const FeatureMap< FeatureType > &seeds)
- that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)  
- Class FeatureFinderAlgorithmPicked< PeakType, FeatureType >  
- Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc)  - Implement user-specified seed lists support (Marc)  
- Class FeatureXMLFile  
- Take care that unique ids are assigned properly by TOPP tools before calling FeatureXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers) 
- Page FileFilter  
- add tests for selecting modes (port remove modes) (Andreas)  
- Group FileIO  
- Implement reading of pepXML and protXML (Andreas)  - Allow reading of zipped XML files (David, Hiwi)  
- Class GaussTraceFitter< PeakType >  
- More docu  
- Class Identification  
- docu (Andreas) 
- Class IdentificationHit  
- docu (Andreas) 
- Class InclusionExclusionList  
- allow modifications (fixed?)  
- Page InspectAdapter  
- rewrite the Adapter! It uses old formats and coding style, e.g. mzData input allowed, no input restrictions, manual (unneccessary file checking of input files) etc... + the interface is not convenient, etc ... 
- Class InspectOutfile  
- Handle Modifications (Andreas) 
- Class IsotopeMarker  
- implement a real isotope marking here with isotopedistributions and fitting (Andreas) 
- Class LabeledPairFinder  
- Implement support for labled MRM experiments, Q1 m/z value and charges. (Andreas)  - Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)  
- Page MascotAdapter  
- This adapter is using antiquated internal methods and needs to be updated! E.g. use MascotGenericFile.h instead of MascotInfile.h....  
- Class ModelFitter< PeakType, FeatureType >  
- Fix problem with other peak types than Peak1D and enable the respective tests for FeatureFinderAlgorithmSimple, FeatureFinderAlgorithmSimplest, FeatureFinderAlgorithmWavelet (Clemens) 
- Class MzMLFile  
- Implement chromatograms (Andreas) 
- Class PeptideEvidence  
- implement CVParam 
- Page PILISIdentification  
- Check for missing precursors (Hiwi)  
- Class ProductModel< D >  
- This class provides new member functions, which makes Factory<BaseModel<2> >::create("ProductModel2D") pretty much useless! (Clemens) 
- Class ProteinIdentification  
- Add MetaInfoInterface to modifications => update IdXMLFile and ProteinIdentificationVisualizer (Andreas) 
- Class ProtXMLFile  
- Document which metavalues of Protein/PeptideHit are filled when reading ProtXML (Chris) 
- Member Residue::SizeOfResidueType  
- add c+1, z+1, z+2 ion types (Andreas)  
- Page RTPredict  
- This need serious clean up! Combining certain input and output options will result in strange behaviour, especially when using text output/input.  
- Page SequestAdapter  
- Check for missing precursors (Andreas) 
- Class SequestOutfile  
- Handle Modifications (Andreas)  - Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)  
- Class Spectrum1DCanvas  
- Use spectrum StringDataArray with name 'label' for peak annotations (Hiwi, Johannes) 
- Class SpectrumCanvas  
- Allow reordering the layer list by drag-and-drop (Hiwi, Johannes) 
- Class SpectrumIdentification  
- docu (Andreas) 
- Class SpectrumWidget  
- Add support to store the displayed data as SVG image (HiWi)  
- Class TOPPBase  
- : replace writeLog_, writeDebug_ with a logger concept we'd need something like -VLevels [LOGGERS] to specify which loggers shall print something the '-log' flag should clone all output to the log-file (maybe with custom [LOGGERS]), which can either be specified directly or is equal to '-out' (if present) with a ".log" suffix maybe a new LOGGER type (TOPP), which is only usable on TOPP level?  
- Class TOPPViewBase  
- Add TOPPView live-tutorial (Stephan, Marc) 
- Class TraceFitter< PeakType >  
- docu needs update 
- Member TraceFitter< PeakType >::getFeatureIntensityContribution  ()=0
- docu needs update  
- Class TwoDOptimization  
- Works only with defined types due to pointers to the data in the optimization namespace! Change that or remove templates (Alexandra)