Latest Development Build

Commits

• e581c83: move gc in batch task to BatchTask#processQueueStep (SteffenHeu) #2386
• d1977bf: add used ram to StepTimeMeasurement (SteffenHeu) #2386
• b9277de: Merge pull request #2386 (Robin Schmid) #2386

mzmine 4.5.0

High-level changelog:

• Speed up spectral library matching up to ~20x
• Join aligner & GC aligner speed up (~2x) and memory improvements
• Improve timsTOF support: bbCID, tims autoMSMS, PASEF MS2 quality
• Harmonize mgf format exports: Spectra export, library export, SIRIUS export, GNPS/molecular networking export
• Harmonize spectral merging and fragment spectrum selection: Select by preset or use advanced setup for greater control
• 4D feature plot Kentrick plot highlight annotated features
• Fix support for Sciex wiff2 files (Sciex SDK in msconvert seems to produce issue)
• Improve message dialogs, checks, and warnings

What's Changed

• fix formula msms score not calculated in neg mode by @SteffenHeu in #2266
• add mz to kendrick tooltip by @SteffenHeu in #2265
• add ims tags to lib gen modules by @SteffenHeu in #2268
• add bbcid import for timstof files by @SteffenHeu in #2269
• highlight annotated rows in kendrick plot by @SteffenHeu in #2271
• fix npe by @SteffenHeu in #2272
• fix annotation pane in network overview not showing compound annotations by @SteffenHeu in #2274
• update usage of getNameParameterMap by @SteffenHeu in #2273
• Add logs to temp sparse file creation by @robinschmid in #2267
• Harmonize intensity in mgf export by @robinschmid in #2270
• fix selected mobilogram in ims overview by @SteffenHeu in #2275
• Fix memory mapping on exFAT by @robinschmid in #2278
• Add bin width ims raw overview, add flanking zeros to binned mobilograms by @SteffenHeu in #2277
• Add UniqueIdSupplier for stable ID for IO by @robinschmid in #2279
• refactor MZmineCore startup by @SteffenHeu in #2259
• Compact USI format as advanced parameter in library gen by @robinschmid in #2282
• cherry pick FileAndPathUtilTest fix by @SteffenHeu in #2288
• Remove onlinedb leftovers by @SteffenHeu in #2287
• add import for tims-autoMSMS acquisitions on timsTOF classic by @SteffenHeu in #2291
• Harmonize mgf export by using SpectralLibraryEntryFactory by @robinschmid in #2286
• fix import of wiff2 files by @SteffenHeu in #2296
• Improve PASEF MS2 quality by default by @SteffenHeu in #2263
• Use workspace by @SteffenHeu in #2281
• drop duplicate data points from other traces by @SteffenHeu in #2299
• Non sealed wizard workflow by @SteffenHeu in #2292
• Darkgrey by @SteffenHeu in #2298
• allow import of chromatograms with same x values but different y values by @SteffenHeu in #2313
• Spectral library search speed-up by @robinschmid in #2305
• Keep last caret position in DoubleParameter / Component after auto commit format by @robinschmid in #2302
• Export metadata file by default in wizard by @robinschmid in #2320
• csv tsv auto separator determination by @SteffenHeu in #2318
• Types for MRM processing by @SteffenHeu in #2293
• Charge type consensus non-null by @robinschmid in #2331
• display error message for failed batch param check by @SteffenHeu in #2332
• Mass detection param check by @SteffenHeu in #2333
• Mass calibration update by @SteffenHeu in #2328
• mrm review by @SteffenHeu in #2324
• Lock in TaksController for concurrency control by @robinschmid in #2338
• OptionalModuleParameter better layout by @robinschmid in #2334
• add ddamsmsinfo to extracted lcms pseudo spectra by @SteffenHeu in #2336
• fix alignment in lc library wizard not using rt tolerance by @SteffenHeu in #2340
• changes for mrm wizard by @SteffenHeu in #2339
• External (Waters) IMS Calibration permits negative T0 values by @AndrewDGillen in #2343
• push workflow filters into WorkflowWizardParameters.isApplicableToSteps by @robinschmid in #2345
• refine ion identity networking preconditions avoid error by @robinschmid in #2349
• MS2Deepscore task prefilter rows by @robinschmid in #2321
• Minimum height in InputTypeComponent otherwise error in wizard by @robinschmid in #2347
• Fix minimum size of embedded components by @robinschmid in #2344
• MS2 pairing in polarity switching files by @SteffenHeu in #2342
• Harmonize spectra merging and selection by @robinschmid in #2297
• fix wizard combobox selection when loading sequences by @robinschmid in #2346
• add exception handling to WrappedTask and to AbstractSimpleToolTask by @robinschmid in #2348
• mrm wizard by @SteffenHeu in #2353
• Add scan selection merging to DreaMS and MS2Deepscore by @robinschmid in #2354
• streamMsMsInfos check precursor mz in IMS Frames only by @robinschmid in #2351
• Fix rare racing condition in multi threaded peak finder by @robinschmid in #2352
• Improve chart generation in feature table by @SteffenHeu in #2360
• Option to log feature table filling by @robinschmid in #2358
• WrappedTask improve isWorkDone stability by @robinschmid in #2362
• fix mslevel filter loading and component by @SteffenHeu in #2359
• DoubleRangeType row bindings by @robinschmid in #2366
• Retain sorting of rows by @robinschmid in #2370
• Debugging module to compare contents of two feature lists by @robinschmid in #2367
• Files.lines in try with resources by @robinschmid in #2357
• message in Task.error is nullable because it is in exception.getErrorMessage by @robinschmid in #2363
• Faster file type detection on mzXML by @robinschmid in #2365
• Automatically save a batch file when the wizard is running by @SteffenHeu in #2361
• improve errors for local compound db search by @SteffenHeu in #2372
• add batch check for raw files and flist parameter setting by @SteffenHeu in #2371
• RowsFilterTask complete feature list cloning by @robinschmid in #2369

New Contributors

• @AndrewDGillen made their first contribution in #2343

Full Changelog: v4.4.3...v4.5.0

mzmine 4.4.3

What's Changed

• Fix NPE in terminal login by @robinschmid in #2261
• Fixes by @SteffenHeu in #2257
  • speed up ms2 pairing
  • deselect all in fragment dashboard
  • update ims expander parameter names
• fix exception if mzml chromatograms with 0 data points were imported by @SteffenHeu in #2264

Commits

• b6a0c99: Increment patch version (robinschmid)
• e067406: fix exception if mzml chromatograms with 0 data points were imported (SteffenHeu) #2264
• e607374: typo (SteffenHeu) #2264

Full Changelog: v4.4.0...Development-release

mzmine 4.4.0

High-level changelog:

• GC/EI-MS Interactive Molecular Networking
• MALDI Imaging co-localization and Interactive Molecular Networking
• Improved Lipid Annotation and new quality control tools including ECN models
• Metadata coloring
• Faster IMS data import from mzML
• Improved memory and storage management
• Bug fixes, usability enhancements

What's Changed

• Fix manual GC on memory bar and deduplicate by @robinschmid in #2081
• Update README.md linux install by @robinschmid in #2085
• Replace all double buffers by memory segments by @SteffenHeu in #2079
• Update jpackage plugin, build, actions by @robinschmid in #2083
• Enable thermo import via self-downloaded parser by @SteffenHeu in #2084
• Fix dev release name by @robinschmid in #2087
• Fix assertion error in file name pattern by @SteffenHeu in #2093
• fix edge table cell not clickable by @SteffenHeu in #2095
• save relative paths in projects by @SteffenHeu in #2092
• Option to run GC after each batch step by @robinschmid in #2076
• fix simsef imaging scheduler by @SteffenHeu in #2099
• change logging level in MemoryMapStorage by @SteffenHeu in #2103
• Sort raw data files in FeatureList by name by @robinschmid in #2101
• Use system proxies by @robinschmid in #2106
• Log batch step speed as TSV by @robinschmid in #2112
• Fix tests time out waiting for finished task by @robinschmid in #2109
• fix ElementsParameter with duplicate values in summary by @SteffenHeu in #2114
• add warning if wizard min samples is greater than number of files by @SteffenHeu in #2108
• Show MS2Deepscore edges in network visualizer by default by @robinschmid in #2111
• Improve logging of row relationships added and removed by @robinschmid in #2110
• Fix MiniTaskView minimum size when message label is too long by @robinschmid in #2116
• Error in metaCorr grouping if min samples filter is incorrectly set (too high) by @robinschmid in #2118
• Open tools directly by @robinschmid in #2135
• Fix PCA exception when changing feature lists or no selected sample types by @robinschmid in #2136
• Fix input selection in MSn tree visualizer by @robinschmid in #2137
• Fix NPE in StringParameter by @robinschmid in #2124
• PCA contributions as labels + resize stats dashboard for smaller display by @robinschmid in #2134
• Additional min samples filter warning by @robinschmid in #2115
• Handle empty json spectral libraries during import by @robinschmid in #2122
• add load + save support for merged spectra from lcms rns by @SteffenHeu in #2107
• Fix old projects not savable with mzmine 4.3 by @SteffenHeu in #2100
• Fix var args in DialogLoggerUtil by @robinschmid in #2144
• MenuBuilder example by @SteffenHeu in #2096
• Optimise IonTimeSeries.subSeries implementations by @SteffenHeu in #2016
• Improve memory mapping in data import by @robinschmid in #2153
• adding compound classification by @corinnabrungs in #2142
• Zenodo download: Allow full archive download or regex file filter by @robinschmid in #2120
• refactor baf dll to external folder by @SteffenHeu in #2141
• extend tooltips of some ims parameters by @SteffenHeu in #2148
• fix baseline correct unsupported operation in FeatureDataAccess by @robinschmid in #2126
• Small fixes by @SteffenHeu in #2171
• Add more logging and messages to data import by @robinschmid in #2154
• Add check in FeatureFullDataAccess by @robinschmid in #2177
• Sort scans after imzML import by @robinschmid in #2176
• Simplify Image correlation Task by @robinschmid in #2127
• Small improvements by @robinschmid in #2178
• Fix ecn scale by @ansgarkorf in #2181
• Zero copy Pearson correlation in MathUtils Similarity by @robinschmid in #2179
• Spectral library download added to FileNamesParameter by @robinschmid in #2121
• Chromatogram blank subtraction by @robinschmid in #2132
• Add documentation links by @ansgarkorf in #2185
• fix duplicate file warning showing erroneously by @SteffenHeu in #2184
• Improve baseline correction with feature resolver by @robinschmid in #2149
• Batch Library: adding scan number for merged spectra by @corinnabrungs in #2004
• Harmonize metadata IO and add more checks by @robinschmid in #2170
• Optimize panama: auto delete tmp files as soon as possible by @robinschmid in #2151
• Add message if specific spectral library is not imported by @robinschmid in #2155
• Apply preferences automatically after config.loadConfiguration by @robinschmid in #2186
• Small fixes by @SteffenHeu in #2187
• Image correlation avoid GC and precompute data, improve performance by @robinschmid in #2180
• Color samples, QC, Blanks by metadata by @robinschmid in #2190
• Metadata CLI argument by @robinschmid in #2173
• handling empty spectra in imported libraries, only problem if datapoints are: "peaks":[] not "peaks":[[]] by @corinnabrungs in #2182
• changing software name to mzmine instead of mzmine# by @corinnabrungs in #2183
• add types for uv support by @SteffenHeu in #2117
• Buffer charts in table by @robinschmid in #2192
• Add module category for other data visualisation by @SteffenHeu in #2205
• fix frame merging using mobility scans for frame spectrum by @SteffenHeu in #2202
• Fix internal CCS calibration for negative ion mode by @SteffenHeu in #2201
• Chart data export - include tooltips by @SteffenHeu in #2206
• New precursor mz search for spectral libraries by @robinschmid in #2158
• Import mrm traces from mzml by @SteffenHeu in #2199
• add methods for dummy flist by @SteffenHeu in #2207
• fix npe in MzMLChromatogram by @SteffenHeu in #2212
• Optimize gc decon preview by @ansgarkorf in #2208
• Add method to extract a Scan Id String from a Scan by @SteffenHeu in #2204
• Enable merged spectra import from mzml by @SteffenHeu in #2200
• fix npe in DoubleComponent by @SteffenHeu in #2214
• Add checks and annotations to DoubleComponent by @robinschmid in #2215
• Local min resolver update by @SteffenHeu in #2218
• Refactor local min resolver by @SteffenHeu in #2219
• change return types of subSeries and copyAndReplace by @SteffenHeu in #2221
• BaselineDataBuffer clearing fix by @SteffenHeu in #2224
• Improve logging in ms2deepscore by @robinschmid in #2226
• Fix npe in local libs by @robinschmid in #2227
• Local libs by @robinschmid in #2228
• update imaging wizard by @ansgarkorf in #2223
• Add online help to raw data import by @ansgarkorf in #2231
• adding export of compound_classes by @corinnabrungs in #2161
• Make metadata import more flexible by @robinschmid in #2232
• Add empty scan case to IonTimeSeriesUtils by @robinschmid in #2233
• Default Compo...

mzmine 4.3.0

What's Changed

• Use MSConvert for import of currently unsupported vendor files by @SteffenHeu in #1979
• Feature histogram by @robinschmid in #1959
• Handle original feature list in metaCorr grouping by @robinschmid in #1992
• Remove old histogram plot by @robinschmid in #1998
• allow TIMS-FT-ICR in wizard by @ansgarkorf in #1943
• fix mscovnert import if mzml file exists by @SteffenHeu in #1999
• FileDownloadTask and parameter to download external assets by @robinschmid in #1986
• Adjust local min edges by @SteffenHeu in #1977
• Add ms2deepscore - for finalization by @robinschmid in #1958
• Add MS2Deepscore to MZMine by @niekdejonge in #1737
• Replace ModuleComboParameter with ModuleOptionsEnumComboParameter by @robinschmid in #2005
• Fix floating point in MS2DeepscoreModelTest by @robinschmid in #2009
• fix resolver not using memory mapping for intensity + mz by @SteffenHeu in #2015
• Add docstrings for ms2deepscore module by @niekdejonge in #2014
• Add download of MS2Deepscore model by @robinschmid in #2008
• Feature preview dialog by @SteffenHeu in #2003
• fix resizing of raw data info pane by @SteffenHeu in #2021
• add missing FxCombobox method by @SteffenHeu in #2030
• option use msconvert for thermo import by @SteffenHeu in #2031
• Baseline correction by @SteffenHeu in #2010
• Waters msconvert by @SteffenHeu in #2048
• Fix project save by @SteffenHeu in #2051
• Gradle 8.10 by @robinschmid in #2058
• Fragmentation dashboard by @SteffenHeu in #2020
• Default parameters for formula prediction by @robinschmid in #2053
• Column factories with sorter by @robinschmid in #2063
• panama memory mapping by @SteffenHeu in #1678
• add method to return memory segment by @SteffenHeu in #2070
• Fix all MS2 in spectral networking by @robinschmid in #2075
• Update JVM memory options in build by @robinschmid in #2080

New Contributors

• @niekdejonge made their first contribution in #1737

Full Changelog: v4.2.0...v4.3.0

mzmine 4.2.0

What's Changed

• GC-MS spectral library search updated by @ansgarkorf in #1910
• Fix annotation in profile spectra by @SteffenHeu in #1919
• Spectral deconvolution preview @ansgarkorf in #1916
• Fix msms score by @ansgarkorf in #1920
• fix error if no ms2s or no ms2 chroms are present by @SteffenHeu in #1905
• Allow deletion of annotations from multiple rows. by @SteffenHeu in #1925
• Add sample type metadata column automatically detected from sample name, add to statistics dashboard by @SteffenHeu in #1914
• GC-EI-MS deconvolution and alignment update v2 by @ansgarkorf in #1930
• Speed up tdf import ~2.5x by @SteffenHeu in #1903
• Fix all MS/MS window only showing first or last file by @SteffenHeu in #1939
• Update to jdk 22 by @SteffenHeu in #1906
• Update rt normalization by @ansgarkorf in #1947
• Sort feature lists before alignment - first by name (NEW) then by number of rows (EXISTING) by @robinschmid in #1960
• Gradle 8.9 and toolchain for kotlin convention plugins by @robinschmid in #1961
• Remove x86 library by @ansgarkorf in #1963
• Import for Bruker .baf files by @SteffenHeu in #1913
• Add shortcut keys, refactor row deletion into module by @SteffenHeu in #1937
• Add link to spectral library docs by @SteffenHeu in #1976
• Manual compound annotation pane by @SteffenHeu in #1932
• Chromatogram builder wider MS2 grouping range by @robinschmid in #1981
• Biotransformer fix by @SteffenHeu in #1982
• Enable spectral mirror for GC data by @robinschmid in #1987

Full Changelog: v4.1.0...v4.2.0

mzmine 4.1.0

Summary

• mzwizard: ASTRAL support, MALDI spot analysis support (Bruker timsTOF-MS)
• Command-line CLI: User support via users file (-user) or login (-login)
• Fixed user login when proxy is used
• Library generation from other annotation tools: Generate libraries from spectral matches, lipid matches, local compound DB, ...
• Renamed Kendrick mass plot (KMD) to 4D feature plot (Kendrick)
• Polymers: 4D feature plot (Kendrick) now has repeating unit suggester and extraction of regions of interest (ROI)

Fixes

• Fix NIST search for GC-EI-MS data
• Better support for mzML IMS data

Quality of life features

• Command-line CLI & batch mode dialog: Change all output files at once (CLI: -output FULL PATH REFERENCE)
• Improve empty scan notification - many users were confused by its meaning and it showed up too often for correct data
• Notify user when processing polarity switching data without filtering for one polarity
• Search features in feature resolver preview

Full changelog

• Close zip inflater in MzMLPeaksDecoder by @robinschmid in #1822
• fix hgrow of ElementsCompositionRangeComponent by @SteffenHeu in #1830
• Fix resolver dialog by @SteffenHeu in #1803
• fix showing structure cell if no structure is there by @SteffenHeu in #1832
• add utility methods for ion calc by @SteffenHeu in #1833
• Fix NIST MS level bug by @kyrasolaris01 in #1834
• fix SortableFeatureComboBox by @SteffenHeu in #1841
• Make ListWithSubs.map public by @robinschmid in #1853
• Spot wizard by @SteffenHeu in #1839
• fix compile errors by @SteffenHeu in #1855
• Add tests for USI and GNPS lib ID by @robinschmid in #1829
• ScanPolarity to wizard and to raw data overview as quick control by @robinschmid in #1840
• Add NumberFormatType and change NumberType to T extends Number by @robinschmid in #1858
• Empty scan warning, DataType Default Visibility by @SteffenHeu in #1843
• Proxy update for login by @SteffenHeu in #1860
• Use annotation ion adduct charge for spectral lbirary building by @robinschmid in #1848
• IMS mzML import - memory map early and reduce memory overhead during import by @robinschmid in #1849
• Disable MassList check on IMS mzML file. No frames yet by @robinschmid in #1862
• Fix config save exception by @robinschmid in #1863
• add resilience try catch to config save by @robinschmid in #1864
• User proxy and CLI user argument by @robinschmid in #1865
• Add proxy settings to UsersView by @robinschmid in #1861
• add astral wizard icon and option by @SteffenHeu in #1866
• Set proxy via CLI argument by @robinschmid in #1869
• fix mass calibration previews by @SteffenHeu in #1873
• Polymers by @robinschmid in #1874
• Add RepeatingUnitSuggester by @kyrasolaris01 in #1831
• fix parsing of utf8 csv files if there is a bom by @SteffenHeu in #1872
• make MatchedLipid implement FeatureAnnotation by @SteffenHeu in #1871
• Design of FileNameSuffixExportParameter to automatically set all output files by @robinschmid in #1870
• Biotransformer fix by @SteffenHeu in #1875
• fix edit combo factory unreliable update on scroll by @SteffenHeu in #1886
• Region extraction for kendrick plot by @SteffenHeu in #1885
• Enable any polarity in ion identity networking by @robinschmid in #1888

Full Changelog: v4.0.8...v4.1.0

mzmine 4.0.8

What's Changed

• update more MZmine mentions to mzmine by @SteffenHeu in #1793
• Single users tab and fix for system clock offset by @robinschmid in #1809
• remove waters package by @SteffenHeu in #1808
• Directly select user after drag drop install by @robinschmid in #1810
• fix calibrant file parsing by @SteffenHeu in #1812
• Workshopfixes by @SteffenHeu in #1798
• move thermo parser extraction path, add to tmp file cleanup by @SteffenHeu in #1816
• Fix mzXML as ms1 scan closing tag is after MS2 scans by @robinschmid in #1814
• Easy parallel stream on pairs in a list by @robinschmid in #1804

Full Changelog: v4.0.3...v4.0.8

mzmine 4.0.3

What's Changed

• User on login by @robinschmid in #1791
  Full Changelog: v4.0.2...v4.0.3

Commits

• a18f4e2: disable more tests on mac (Robin Schmid)
• b0da2ea: Merge remote-tracking branch 'mzmine/master' into disable-test (Robin Schmid)
• 06fb40c: reset version (Robin Schmid)

What's Changed

• Fix polarity overwrite in lib generation by @robinschmid in #1482
• Add applied methods by @SteffenHeu in #1484
• fix FragmentScanSelection in case only merged ms2s are available. by @SteffenHeu in #1501
• fix intra feature sim by @SteffenHeu in #1500
• fix maldi charts for spots by @SteffenHeu in #1499
• remove mztab modules by @SteffenHeu in #1498
• add CCSBase export by @SteffenHeu in #1503
• Update README.md by @robinschmid in #1514
• fix formulae not sorted after flist prediction by @SteffenHeu in #1521
• Fix macOS build by @roman-bushuiev in #1547
• Fix black background by @kyrasolaris01 in #1550
• Add help for MSVoltammogram by @kyrasolaris01 in #1552
• change chart colors on theme change by @SteffenHeu in #1553
• Update transitive log4j dependencies to 2.22.0 by @robinschmid in #1539
• Kendrick plot fix by @kyrasolaris01 in #1516
• Pregenerate charts java21 by @SteffenHeu in #1511
• speed up gap filling, fix ims gap filling by @SteffenHeu in #1562
• [core] Binary search options by @robinschmid in #1568
• add project load integration test by @SteffenHeu in #1570
• [FeatureTable] Harmonize all Panes / Nodes that depend on FeatureList or FeatureTable by @robinschmid in #1567
• Fix mirror plot labels visibility by @robinschmid in #1573
• Fix networking of spectral libraries by @robinschmid in #1574
• JDK21 by @robinschmid in #1582
• Add unknown adducts for neutral losses/clusters by @robinschmid in #1533
• DataTypes.getAll(Class classes...) by @robinschmid in #1577
• add rt filter for biotransformer by @SteffenHeu in #1531
• Fix MSn tree, reduce to merged or individual scans by @robinschmid in #1572
• extension of the DatabaseIsotopeRefiner by @Sonja-analytik in #1507
• Add external networking edges import by @robinschmid in #1506
• Van krevelen diagram fix by @kyrasolaris01 in #1556
• Default StringParameter empty instead of null by @robinschmid in #586
• Update copyright by @robinschmid in #1588
• Remove classes as keys - memory leaks by @robinschmid in #1467
• Patch non null StringParameter by @robinschmid in #1589
• Batch - error on missing modules by @robinschmid in #1468
• [GC-EI] Make chromatograms optional in curve resolution by @robinschmid in #1211
• Fix imaging batch wizard by @kyrasolaris01 in #1537
• Remove netCDF from mass detection step by @robinschmid in #1141
• Simplify metacorr data usage by @robinschmid in #1590
• More fat features by @kyrasolaris01 in #1583
• Fix context menu by @kyrasolaris01 in #1603
• Test more data files by @robinschmid in #1604
• Add timstof spot dataset test by @robinschmid in #1605
• add keep annotated option to rows filter by @SteffenHeu in #1611
• Fix ccsbase export by @SteffenHeu in #1609
• Function to extract list of mz ranges into IonSeries by @robinschmid in #1595
• Dont allow multivariate curve resolution module on macos by @kyrasolaris01 in #1613
• Add timsTOF pasef data test by @robinschmid in #1612
• MassDetectors by @robinschmid in #1615
• add iintest ions, fix ion type in csv search by @SteffenHeu in #1610
• Add RowGroupSimple toString method by @robinschmid in #1623
• Invert listeners control from feature to FeatureList by @robinschmid in #1627
• mzML fix for special chars, Advanced import with MsProcessor to filter scans and apply processing during import by @robinschmid in #1619
• Use ThreadPool in TaskController by @robinschmid in #1628
• Improve TicPlot speed by @robinschmid in #1643
• Add all spectra to spectra plot by @robinschmid in #1648
• Use OpenCsv in CSVParsingUtils by @robinschmid in #1645
• factor of lowest signal mass detection for all data types by @corinnabrungs in #1651
• Fix metadata export by @SteffenHeu in #1649
• Add more columns to spectral library matches by @corinnabrungs in #1653
• Pdf export openpdf by @SteffenHeu in #1656
• Use Explained Intensity and deprecate MSMSScore by @kyrasolaris01 in #1660
• harmonise charge setting for sirius and gnps export by @SteffenHeu in #1666
• fix min data points not set in gap filling wizard by @SteffenHeu in #1670
• add interfaces for mvci controllers with feature, row, file selections by @SteffenHeu in #1667
• Add volcano plot by @SteffenHeu in #1661
• Online reactivity by @robinschmid in #1633
• Use volcano plot tab by @SteffenHeu in #1671
• Move lipids by @robinschmid in #1675
• Create modular project by @robinschmid in #1673
• Update test build GH action by @robinschmid in #1676
• remove gradle.properties by @robinschmid in #1677
• Update dependencies and clean up by @robinschmid in #1679
• Change paths in build to new system by @robinschmid in #1680
• Drop deprecated jlink option by @robinschmid in #1681
• log macos notarization by @robinschmid in #1683
• check if jar exists on macos by @robinschmid in #1684
• Modularize several parts by @robinschmid in #1687
• Fix charts after update of jfreechart by @robinschmid in #1688
• fix lipid score in restult tab by @kyrasolaris01 in #1693
• Fix some feature shapes not showing in feature table plots by @SteffenHeu in #1695
• Move components to framework module by @robinschmid in #1694
• Convention plugins in its own sub project by @robinschmid in #1696
• Fix jvmargs by @SteffenHeu in #1702
• revert jfreechart version by @SteffenHeu in #1699
• Delete src directory by @robinschmid in #1704
• Improve alignment scores by @robinschmid in #1701
• Remove auto update of TIC that causes lags by @robinschmid in #1703
• Patch MiniTaskView label update by @robinschmid in #1708
• Fix high priority thread pool rejection by @robinschmid in #1707
• Move local lib directory by @robinschmid in #1716
• add feature height to library export by @corinnabrungs in #1712
• change average height and area to maximum by @corinnabrungs in #1713
• Add PCA by @SteffenHeu in #1705
• Change modular build by @robinschmid in #1700
• add water loss as neutral loss option by @corinnabrungs in #1719
• Metadat...

MZmine 3.9.0

Version info

Version used at the 3rd Metabolomics Summer School in Copenhagen 2023

Commits

• 705ebd4: add mass detector option to wizard (robinschmid) #1475
• 0c15d65: handle wrong input, and add style (robinschmid) #1475
• 16d05fd: remove comments (robinschmid) #1475
• 7617763: copy value of wizard mass detector (robinschmid) #1475
• 979cab6: v3.9.0 (robinschmid) #1475
• 43cb25a: Merge remote-tracking branch 'mzmine/master' into scan_selection (robinschmid) #1475

What's Changed

• Fix quickstart using show instead of showAndWait by @robinschmid in #1471
• Add MS/MS scatter plot to raw data summary by @robinschmid in #1472
• Rename scan data types CENTROID to MASS_LIST by @robinschmid in #1473
• Better strings in raw summary data selection by @robinschmid in #1474
• Faster MS/MS scatter plot by binary search by @robinschmid in #1476
• Add mass detector options to wizard by @robinschmid in #1475

Full Changelog: v3.8.0...v3.9.0