Latest Development Build

Commits

• e693bf3: Increment patch version (SteffenHeu)
• 84ae3ac: Revert "for now do not notarize macOS build" (Steffen Heuckeroth)

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

MZmine 3.8.0

Commits

• b66225b: layout network parallel, like cytoscape (robinschmid) #1469
• 5ca4163: clean up parallel layout computation (robinschmid) #1469
• ece1fc7: Merge remote-tracking branch 'mzmine/master' into net_layout_parallel (robinschmid) #1469
• cd24c99: Increment patch version (robinschmid)
• 1df032f: add double shift key event open quick start (robinschmid) #1469
• 5ccb4a8: version 3.8.0 (robinschmid) #1469
• c5cb98d: Merge branch 'master' into net_layout_parallel (Robin Schmid) #1469
• 85b5935: version 3.8.0 (Robin Schmid)

What's Changed

• Update ims wizard by @SteffenHeu in #1442
• add selected scans to same range task by @SteffenHeu in #1444
• Add method for networking by @SteffenHeu in #1446
• imzml fix by @kyrasolaris01 in #1450
• Add speclib name by @SteffenHeu in #1447
• add batch export for all library matches to pdf by @SteffenHeu in #1445
• Increase score export format by @robinschmid in #1459
• update id export by @SteffenHeu in #1460
• Intra feature MS2 similarity by @robinschmid in #1458
• Fix mobilityscan selection by @corinnabrungs in #1461
• add IMS type to library building by @corinnabrungs in #1462
• Add graphics export to wizard by @robinschmid in #1451
• Add WeakListeners to decouple views automatically by @robinschmid in #1464
• Scan signal filter - remove mz ranges by @corinnabrungs in #1457
• Quick module search bar with CTRL F by @robinschmid in #1465
• Add spectral networking and graphml export to wizard by @robinschmid in #1463
• Hide empty annotation tabs in network visualizer by @robinschmid in #1466
• Network visualizer parallel layout in large networks by @robinschmid in #1469

New Contributors

• @kyrasolaris01 made their first contribution in #1450

Full Changelog: v3.7.2...v3.8.0

MZmine 3.7.2

What's Changed

• Fixed mz-ranges the massvoltammogram will be drawn in. by @WesMark in #1420
• Add missing ressource in network style by @robinschmid in #1436

Full Changelog: v3.7.0...Development-release

MZmine 3.7.0

Important notes

• This version might break project compatibility with earlier versions.

What's Changed

• Libexport log by @SteffenHeu in #1398
• Molecular networking by @robinschmid in #1397
• fix di wizard batch by @SteffenHeu in #1414
• Use GNPS2 for USI resolver by @robinschmid in #1406
• Refactor simsef sorting by @SteffenHeu in #1402
• fix temp file folder by @SteffenHeu in #1418
• Add quality export fix npe by @SteffenHeu in #1422
• Update build.gradle for mztab by @SteffenHeu in #1430
• check default and set temp dir on cleanup by @SteffenHeu in #1427
• MolNet visual overview by @robinschmid in #1417
• [GSOC'22 Project] Latest version of FeatureList Networking Visualization Module by @sanbit876 in #825
• Version 3.7.0 by @robinschmid in #1434

Full Changelog: v3.6.0...v3.7.0

MZmine 3.6.0

Commits

• d969c0a: Increment patch version (SteffenHeu)
• 22310e3: Version 3.6.0 (robinschmid)

What's Changed

• Update to JDK20 and gradle 8.1.1 by @robinschmid in #1361
• Isotope refinement for compound database search by @Sonja-analytik in #1042
• IIMN logo by @robinschmid in #1372
• Zoom into "Show isotope pattern" by @robinschmid in #1373
• Add small test batch file by @robinschmid in #1383
• fix removed files reappear issue, remove raw data renaming by @SteffenHeu in #1229
• Timstof by @SteffenHeu in #1144
• Add version and help cli arguments by @robinschmid in #1386
• fix illegal arg in ImsExpanderTask by @SteffenHeu in #1389
• Add conversion of existing library to GNPS batch library submission by @robinschmid in #1371
• Add threads and libraries cli arguments by @robinschmid in #1391
• Fix empty FileNameParameter by @robinschmid in #1394

Full Changelog: v3.5.0...v3.6.0

MZmine 3.5.0

What's Changed

• Updated README by @tomas-pluskal in #1323
• Fix GNPS GC-MS export by @robinschmid in #1334
• Add CLI argument to change files easily by @robinschmid in #1336
• .xlsx export for massvoltammograms by @WesMark in #1294
• Fixed bug reported by Sanchezillana by @christophuv in #1351
• Precursor Purity checker module by @robinschmid in #1342
• EC-MS annotation in mV instead of V by @WesMark in #1349
• add representation for multi charge iso pattern by @SteffenHeu in #1359
• add dia workflow wizard by @SteffenHeu in #1343
• tims maldi pressure recal by @SteffenHeu in #1147
• Fix elements parameter by @Sonja-analytik in #1363
• disable pressure compensation by @SteffenHeu in #1367
• use images as charts by @SteffenHeu in #1287
• Zoom to full chromatograms in feature table by @robinschmid in #1368
• release 3.5.0 by @robinschmid in #1369

Full Changelog: v3.4.27...v3.5.0