add intensity-weighted average peak picker #4
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enable creation of distributions from LayerStatistics -- remove a lot of duplicate code in Canvas'
…mapping-is-mandatory CVInspector: the mapping_file argument is mandatory
* add rvalue reference setter to PId * Update src/openms/source/METADATA/PeptideIdentification.cpp Co-authored-by: Hannes Roest <[email protected]> * some rvalue reference versions * more fixes * tab * fix test * Update src/openms/source/KERNEL/MSExperiment.cpp Co-authored-by: Hannes Roest <[email protected]> * Update src/openms/source/KERNEL/ConsensusFeature.cpp Co-authored-by: Hannes Roest <[email protected]> * Update src/openms/source/KERNEL/MSExperiment.cpp * Apply suggestions from code review * Apply suggestions from code review * fixes * try to default in implementation file * clear experiment after move * Update IMDataConverter.cpp * fix test * Update src/openms/source/IONMOBILITY/IMDataConverter.cpp Co-authored-by: Hannes Roest <[email protected]>
Extend LayerStatistics
* test of cppcheck action * Update cppcheck.yml * Update cppcheck.yml * Update cppcheck.yml * Update cppcheck.yml * Update cppcheck.yml * exclude test folder
* [FIX] extract function * [FIX] also copy unit * Apply suggestions from code review * [FEATURE] move to cpp * [FIX] small fix * Update SpectrumHelper.cpp * Update SpectrumHelper.h * Update SpectrumHelper.h Co-authored-by: Timo Sachsenberg <[email protected]> Co-authored-by: Timo Sachsenberg <[email protected]>
[Feature] export MSExperiment to data frames for MassQL
* [FIX] adopt activation modes to new obo * [FIX] copy-paste error * Update MzMLHandler.cpp * fix some tests * fix test * fix missing activiation mode names * fix tests * Update src/openms/source/METADATA/Precursor.cpp * change BEAM to HCD for better usability * reviewer comments Co-authored-by: Hannes Roest <[email protected]>
…to layer_refactor
Co-authored-by: Timo Sachsenberg <[email protected]>
Layer refactor
…ta structures (incl. ProteomicsLFQ)
* function in DefaultParamHandler * meta values written in comet- & msgf+ adapter, test missing * forgot cpp ... * getToolPrefix function * parameter information written by all identification tools * changed most of the test files to have the new metavalues, added some of the metavalues to ctest whitelists * changed Novor test file to have spectrum index as int, resolves OpenMS#4878 * tests changed for Mascot and MascotOnline * updated Comet test files * added test for writeParametersToMeatValues in DefaultParamHandeler_test * fix crux test * re-change underscore to dash * fixed crux test error * minor PR changes * first functions for CometAdapter call in Suitability * working on corrected suitability functions * calculating correction factor with two id-searches * deNovo+database search, deNovo search done internally, database search given * DBSuitability test changed to test new functionalities by hand, will later be done correctly * corrected suitability changes done in TOPP tool - test not adjusted * no FDR filtering while correcting * correction with extrapolation - prob doesn't work * fixed brackets, correction should work * calculation fixed with Size to Int change * input parameters of suitability changed, also some docu * const & bug fixed, debug output * PR changes, new Exception 'InternalToolError' * exported regex construction for decoy string search into static funtions * add additional check for decoy strings to handle target+decoy hits * simpler version of correction factor calculation * docu changed accordingly * removed debug output * function to get xcorr if existing, return main score else * fixed linker error: static member in DecoyHelper now static function * topp docu up to date * multiple suitability outputs + force flag (still bugged) * multiple suitabilities output in topp tool, calculations working * Option to keep tmp files used or created by internal ID search * additional optional file & set seed for sampled fasta (needed for debugging) * wrong bool interpretation fixed * PR changes, boost regex not working * option to disable corrected suitability * testing non-corrected suitability * regex for decoy search fixed * fasta sampling done with getUniqueId() (instead of std::random_device) * fixed error case * correction factor written in output * removed redundant line * testing some private functions with friend class * topp test for DBSuitability - might not be stable * fixed error while checking for re-ranking * some decoy regex changes, PeptideIndexing test updated * change stl shuffle to OpenMS::Math::RandomShuffler * typos * looking at all hits for decoys instead of stopping after 10 hits * regex updated * smaller topp test files * [fix] reading no peak data while loading MzML for spectra map * multiple subsampling runs * median instead of mean * debug printing, will be removed later * docu & some bug fixes * LOG_WARN to LOG_DEBUG to avoid spam * [FIX] spectral quality with filtered novo ids, novo threshold as param * change DBSuit Topp output & test files for working spectral quality * small param description change * fixed build errprs * score matching FDR as threshold + docu, tests for private funtions * conversion operator for DataValue to ParamValue * FDR to 'conversion' score fixed * DataValue & ParamValue induced errors fixed * clear function for DatabaseSuitability:SuitabilityData * fixed DataValue test * fix test * Update DatabaseSuitability.cpp * avoid crash for empty ids Co-authored-by: Timo Sachsenberg <[email protected]> Co-authored-by: Chris Bielow <[email protected]> Co-authored-by: Timo Sachsenberg <[email protected]>
* Update GNPSExport.cpp I added a few more details on the proposed workflow (command examples) mainly - I think it would be great to add a link to an emptyfile.idXML at the IDMapper Requirements section "Even in untargeted metabolomics/proteomics, an empty idXML or mzid (peptide annotation format) file is needed as an input which can be found here link/to/emptyfile.idXML. * Update GNPSExport.cpp Small corrections * Update GNPSExport.cpp A few changes to make the text clearer Co-authored-by: Timo Sachsenberg <[email protected]>
…only; as historically supported)
[TEST] Mutual info test
A Painter1D class for Peaks
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Description
When ion mobility is present, use intensity-weighted average.