OpenMS: Todo List

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)

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)

Member FeatureFinder::run (const String &algorithm_name, MSExperiment< PeakType > &input_map, FeatureMap< FeatureType > &features, const Param &param, const FeatureMap< FeatureType > &seeds): that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)

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)

Implement reading of pepXML and protXML (Andreas)

Allow reading of zipped XML files (David, Hiwi)

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 IsotopeMarker: implement a real isotope marking here with isotopedistributions and fitting (Andreas)

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 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 need serious clean up! Combining certain input and output options will result in strange behaviour, especially when using text output/input.

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 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?

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)