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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)
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 &param, 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)

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5