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)

Writing of protXML is currently not supported

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 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)