MSSimulator Erweiterung #123
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Bugfix MSFraggerAdapter
[FIX] pyopenms mac fix dependency order
…ata) (OpenMS#5744) * Prototyping of novel ID datastructure in accurate mass search * cleanup and todos * add basic id support AMS; add test template (comment) * fix AMS * backbone MzTab-M - not registered cmake * oms output * FIX tests * inital introduction mztab-m * CleanUp mztab-m data model * ADD class test MzTabM * [REFACTOR] MzTabBase * test * [TEST] OMS, mztab-m * ADD FileConverter OMS output * ADD FileConverter; ADD add parsing to CV; add to mztabmmeta * fill feature- , evidence section; resolve TODOs * [ADD] ProcessingAction; [RM] old MzTab code from AMS * [FIX] files * [ADD] DataProcessing, [ADD] evidence section * [ADD] debug info, [ADD] evidence section * [FIX] CleanUp AMS; CleanUp Evidence Section * [FIX] indent * [ADD] Summary Section; MzTaMFile * [FIX] featureXML output; [ADD] debug testing * [RM] paritally std:: cout; Revert to qint64 * rm debug info * Correction MzTabM; [ADD] generateMzTabMMetaDataSection_ to MzTabMFile * [ADD] MzTabFileHeader_1 * [ADD] First working version MzTabM and MzTabMFile * [ADD] mztabm and test to AMS * add opt columns feature, evidence section * additional changes, draft test * [FIX] Store OMS * rm debug output, add filter * add test, fix pipe op issue * small fixes, add python bindings * [FIX] tests * [FIX] tests, python bindings; [ADD] suggestions; [ADD] SME sorting * [FIX] python bindings; test properties * Update src/utils/AccurateMassSearch.cpp * [ADD] tests, suggestions, documentation; [FIX] Refactor * [FIX] suggestions, codefactor, test * [FIX] revert DataProcessing.pxd * [FIX] PyOpenMS ProcessingAction Co-authored-by: Timo Sachsenberg <sachsenb@informatik.uni-tuebingen.de> Co-authored-by: oliveralka <alka@informatik.uni-tuebingen.de> Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
seems like people change at will which one gets symlinked
* [PERFORMANCE] add index for peakannotations * add primary key to metainfo
* fix typo * fix OpenMS#5755 * revert wrong fix
* forward declare all svm types * add missing include * forward declare svm structs as structs not class
* compile fixes * Apply suggestions from code review Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de> Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>
This reverts commit c19574f.
…rnings Revert "compile fixes"
* make seqan private and move Wm5 dep to cpp * removed uneeded seqanwrapper include * move seqan back to get PR to build * Update CMakeLists.txt
…cessful test executions should be printed (OpenMS#5765) * expect OPENMS_TEST_VERBOSE_SUCCESS env variable set if output of successful test executions should be printed * fix cmake * Update src/tests/class_tests/openms/CMakeLists.txt Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>
Added a function to output a deisotoped MS1 spectrum containing only monoisotopic peaks.
Added a test for the createMonoisotopicExperiment() function.
Added an function to output a deisotoped MS1 spectrum, containing only monoisotopic peaks.
Added the header for the createMonoisotopicExperiment() function.
* disable output via OPENMS_TEST_SUPPRESS_SUCCESS * inverted logic * Update MorphologicalFilter_test.cpp
* replace boost with std variant * reduce output of MorphologicalFilter_test * use binary operators for std::variant compatibility * fix dll interface * Update AppliedProcessingStep.h * Update src/openms/source/METADATA/ID/IdentifiedMolecule.cpp
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Description
Extension of the MSSimulator class which allows it to output a mzml file which only contains monoisotopic peaks through the -out_mono parameter.
Also extended the MSSimulator_class_test to check the new function as well.
Checklist:
Note:
Hello Mr. Bielow,
after a lot of trouble at work i finally found the time to take a look at my code again and create this pull request.
Since a lot of class tests of classes i did not touch fail, even with a fresh version of OpenMS (without any changes) i am creating this pull request against your repository instead of creating one straight for the main OpenMS repository, like you mentioned in our last call, to see if this is maybe a problem of my computer.
Failed tests:
108:IdentificationDataConverter_test
157:FileHandler_test
184:MzMLFile_test
192:MzTabMFile_test
197:OMSFile_test
218:SwathMapMassCorrection_test
374:RNaseDigestion_test
379:RibonucleotideDB_test
395:AccurateMassSearchEngine_test
624:CachedMzML_test
625:CachedMzMLHandler_test
1590:TOPP_IDFileConverter_34_2
1591:TOPP_IDFileConverter_34_out
2315:TOPP_OMSSAAdapter_1
2316:TOPP_OMSSAAdapter_1_out
2319:TOPP_XTandemAdapter_1
2320:TOPP_XTandemAdapter_1_out
2321:TOPP_XTandemAdapter_2
2322:TOPP_XTandemAdapter_2_out
2323:TOPP_XTandemAdapter_3
2324:TOPP_XTandemAdapter_3_out
2346:TOPP_MaRaClusterAdapter_1
2347:TOPP_MaRaClusterAdapter_1_out_1
2348:TOPP_MaRaClusterAdapter_2
2349:TOPP_MaRaClusterAdapter_2_out_1
2370:TOPP_LuciphorAdapter_1
2371:TOPP_LuciphorAdapter_1_out1
2510:UTILS_QCCalculator_1
2511:UTILS_QCCalculator_1_out
2513:UTILS_QCCalculator_2_out
2515:Tutorial_AASequence
2516:Tutorial_Clustering
2517:Tutorial_DPosition
2518:Tutorial_DRange
2519:Tutorial_Element
2520:Tutorial_Enzyme
2521:Tutorial_EmpiricalFormula
2522:Tutorial_FeatureFinder
2523:Tutorial_FeatureMap
2524:Tutorial_FileIO
2525:Tutorial_FileIO_mzML
2526:Tutorial_FileIO_Consumer
2527:Tutorial_GaussFilter
2528:Tutorial_IdentificationClasses
2529:Tutorial_Labeled
2530:Tutorial_MSChromatogram
2531:Tutorial_MSExperiment
2532:Tutorial_MSSpectrum
2533:Tutorial_MapAlignment
2534:Tutorial_MetaInfo
2535:Tutorial_Param
2536:Tutorial_PeakPickerCWT
2537:Tutorial_Precursor
2538:Tutorial_RangeManager
2539:Tutorial_Residue
2540:Tutorial_ResidueModification
2541:Tutorial_SavitzkyGolayFilter
2542:Tutorial_TOFCalibration
2543:Tutorial_TheoreticalSpectrumGenerator
2544:Tutorial_MorphologicalFilter
2545:Tutorial_Unlabeled
2546:Tutorial_typeAsString
2547:Tutorial_PeakIntensityPredictor