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Created with Raphaël 2.2.012Feb1110985328Jan222120191815118619Dec181716149127Nov22Oct1413520Sep172129Aug24428Jul2423212019171614Jun4218May1716Apr31Mar24181Feb28Jan2721201919Dec18131285425Nov2413111023Oct222113715Sep822Jul720Jun1626May830Apr2927242322117627Mar262411107418Feb1711106527Jan14916Dec425Nov211328Oct242317144223Sep1916131211954229Aug282730Jul2419181512653227Jun1828May722Apr19171311109854326Mar212019151484127Feb26211823Jan141Oct7Sep328AugEliminated the _FORMULATAG workaround. Also, time for a version bump :)Thanks to https://github.com/lgatto/MSnbase/commit/3746a473aa0cdcc1eb7088812534efeb276fda53 polarity is now in Spectrum2 objects. Update to feed the data into there from the acquisition mode (note: even where present, data from mzR is unreliable and often -1)* Fixes in mb record generationMerge remote-tracking branch 'origin/master' into s4powerSupport for SMILES in RmbSpectraSetMore NULL-tolerance and independence during mbWorkflow. Fix for doublepeaks.Another selectPeaks fixremoved retrieval argument from findMsMsHRFixed fillback and additionalPeaks readditionRevamped mbWorkflow completely, cf #153:Fix selectPeaks methods again... (proper treatment of ... arguments)* Added fillback functionality: write results from reanalysis and peak filtering back into the spectrafixes #157Fixed bug that occurs under special conditions in workflow step 2Fixed some minor bugsMerge branch 'master' into s4power* moved precursor_types and ion_modes to package-level variables since they are reusedNow steps 4:8 will be skipped when processing only unknownsFix for unknowns - work faster but skipping steps 4:8 not possible yetFix missing @import for getSplash.R (the NAMESPACE is already correct :) )Moved s4power functionality into core RmbSpectrum2.Fix in findMz.formula so it works correctly for "special" cases like findMz.formula("", "mH")Fix in findMz.formula so it works correctly for "special" cases like findMz.formula("", "mH")Merge branch 'master' into s4powerfix: the ID read from the compiled record is not numericMerge remote-tracking branch 'ermueller/master'Merge remote-tracking branch 'origin/sneumann-patch-1'Useful fixes for writing mgf and for normalizationChanged it so that molfiles don't get generated when tentative or unknown, also no mention in list.tsvAdded new tentative and unknown functionality to RMassbankFixed minor bug related to double slashes in records with the parserPK integratedSet rtShift to 0.0 and use CC-BY in the default settings, closes #147sneumann-patch-…sneumann-patch-1 upstream/sneumann-patch-1removed now superfluous stuff in readWriteMgfData, added support for writing RmbSpectrum2Lists (without the parent).Merge remote-tracking branch 'origin/master' into s4powerVarious S4 improvements: selectPeaks for spectra, RmbSpectrum2Ext class for spectra with additional properties and corresponding S4 handling, MGF writing for RmbSpectraSet, stuff to merge spectra. Generics definition moved to separate file for inclusion order. DESCRIPTION inclusion order changed.Changed docs because of that bugBugfixTentative and unknown retrieval added - subject to changeMerge branch 'master' of https://github.com/sneumann/RMassBank