- 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 FalseDiscoveryRate
- implement combined searches properly (Andreas)
- Class FeatureFinderAlgorithmPicked
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)
- Module FileIO
Implement reading of pepXML and protXML (Andreas)
Allow reading of zipped XML files (David, Hiwi)
- Class GaussTraceFitter
- 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 labeled 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....
- Member OpenMS::Internal::MapType
- replace hardcoded cv stuff with more flexible handling via obo r/w.
- 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)
- Page RTPredict
- This needs serious clean up! Combining certain input and output options will result in strange behaviour, especially when using text output/input.
- 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
- 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)