Commits

• 37e6745: Network with pie charts based on sample metadata (robinschmid) #3365
• 53b45e0: network pie legends (robinschmid) #3365
• cc6285c: metadata column instead of pie charts as label (robinschmid) #3365

High-level changelog

• Compound dashboard add another way to represent the feature finding results by grouping rows into compound rows. Run Compound grouper module and double click on feature list to see the new compound dashboard. Compound lists allow to reduce the number of rows in the Statistics dashboard and interactively links to other dashboards like the new Lipid dashboard.
• Lipid dashboard enables reviewing lipid annotations by ECN models and multiple lipid evidence models
• Improved lipid annotation with more lipid classes
• Sciex direct data support for wiff and wiff2 (Windows & Linux)
• Intensity normalization harmonized and streamlined in one module with new options to apply multiple normalization steps like sample metadata based normalization, standard compound normalization, sample batch normalization.
• Ion libraries definition for ion identity networking made easier
• Analog spectral library matching by modified cosine and by MS2Deepscore
• Interactive network visualizer now with analog spectral library matches to co-network library spectra. Added legend and more options.
• Wavelet feature resolver (experimental, subject of change and optimization) please provide feedback on your results.

What's Changed

• add codex skills for mvci and charts by @SteffenHeu in #3223
• Wavelet resolver (experimental) by @SteffenHeu in #2568
• Wizard advanced mode by @SteffenHeu in #3198
• Centralize module access by @robinschmid in #3230
• Fix loading of NIST MS search matches from projects by @robinschmid in #3238
• Export local csv example file by @robinschmid in #3236
• Proxy test without user by @robinschmid in #3237
• fix parsing of ccs reference list by @SteffenHeu in #3247
• sirius-api: update error message on duplicate id mapping by @SteffenHeu in #3243
• New Intensity normalization module by @SteffenHeu in #3231
• Fix sphingolipid chain bug by @ansgarkorf in #3252
• Centralize XML parser generation by @JonasLueb in #3253
• Add splash screen by @SteffenHeu in #3249
• Replace groupable list view with TreeView by @SteffenHeu in #3250
• Clear project sets all files and feature lists by @robinschmid in #3258
• hide advanced wizard toggle by @SteffenHeu in #3259
• Update external tools packaging by @SteffenHeu in #3248
• Add doc links by @SteffenHeu in #3264
• mzminetab: fix setTitle not setting title by @SteffenHeu in #3260
• Single row submission to spectral library by @SteffenHeu in #3274
• feature-table: fix npe when sorting the feature table after filtering by @SteffenHeu in #3273
• bruker: speed up maldi prm import, dont look for parent frame if id = 0 by @SteffenHeu in #3270
• update skills/gitignore by @SteffenHeu in #3267
• Single library submission, keep last selected by @robinschmid in #3276
• Intensity normalizer by @robinschmid in #3262
• Bugfix for extrapolation with RI calculation, now uses correct offset for large retention times by @wchu207 in #3261
• Correct textflow sizing inside dialog by @robinschmid in #3281
• update doc skill by @SteffenHeu in #3283
• fix message listing missing files by @SteffenHeu in #3284
• set initial size of parameter dialogs by @SteffenHeu in #3285
• Add more complex intensity normalizer tests by @robinschmid in #3282
• fix mirror chart export to clipboard by @SteffenHeu in #3291
• DoubleOrAuto parameter, Update other featre selection box by @SteffenHeu in #3289
• add export scans doc link by @SteffenHeu in #3299
• Allow override of csv database and project import in batch mode by @SteffenHeu in #3296
• update doc skill trigger by @SteffenHeu in #3302
• Rework IIN by @robinschmid in #3306
• GUI: fix percent format not rendered as % by @SteffenHeu in #3310
• Lipid dasboard by @SteffenHeu in #3308
• Analog search by @SteffenHeu in #3311
• Default less ions in wizard by @robinschmid in #3315
• Ion type parsing, handle and highlight parsing errors by @robinschmid in #3313
• Groupable treeview updates by @SteffenHeu in #3324
• mzmine PaintScale by @robinschmid in #3319
• Maximize new window on secondary screen by @robinschmid in #3325
• Auto update integration test results files if needed by @robinschmid in #3287
• charts: default visible for value marker by @SteffenHeu in #3327
• [on feature branch] Compound dashboard MVC + bind feature tables across dashboards by @robinschmid in #3316
• themes: change icons to vectors by @SteffenHeu in #3328
• Isotopic smiles structures by @SteffenHeu in #3330
• Chart logics respects plot orientation by @robinschmid in #3329
• WIFF2 support by @SteffenHeu in #3318
• Themes split by @SteffenHeu in #3309
• label unwrap by @robinschmid in #3335
• norm: add csv standard file to normalizer by @SteffenHeu in #3334
• Return parsed structure inchi, inchikey, smiles for spectral matches by @robinschmid in #3326
• isotopes: add fallback for isotope detection in ims data by @SteffenHeu in #3336
• Fix mzML import crash when optional scan-level CV params are missing or referenced by @david-cox-sciex in #3321
• Beta tags update by @robinschmid in #3339
• Analog search network visualizer by @SteffenHeu in #3322
• Compound dashboard in menu by @robinschmid in #3338
• [on feature] Compound dashboard all export modules by @robinschmid in #3331
• Compound dashboard annotation check param by @robinschmid in #3341
• analog: add to wizard by @SteffenHeu in #3340
• Compound dashbord by @robinschmid in #3342
• Preferred annotation in networking by @robinschmid in #3343
• CompoundRowBinding for max height and area on rows by @robinschmid in #3345
• sciex: copy wiff server to user dir by @SteffenHeu in #3344
• Update packages version v4.10 by @robinschmid in #3346

New Contributors

• @david-cox-sciex made their first contribution in #3321

Full Changelog: v4.9.14...Development-release

High-level changelog

• Fixes user login issues where the internal web view did not work. Now uses the OS trust store for SSL
• Allow project load in batch and allow merging of projects
• Improve labels in 4D feature plot (Kendrick & Van Krevelen)
• Separate release for older macs with intel cpu and for M series macs with Apple Silicon cpu

What's Changed

• Menu: add corr dashboard to visualisation menu, add rt corr to menu by @SteffenHeu in #3197
• Delete single db submit module by @SteffenHeu in #3203
• Fix-rsd-filter: correctly apply missing value tracking by @SteffenHeu in #3199
• Waters: fixes ms1 function not recognised with uv traces by @SteffenHeu in #3202
• Merge OS trust store by @robinschmid in #3212
• NistMS search: prevent class cast error in speclib after nistms search by @SteffenHeu in #3213
• Allow project load in batch by @SteffenHeu in #3192
• RT correction hide legend if too many datasets by @robinschmid in #3215
• Checkbox more visible by @robinschmid in #3219
• Add DefaultOffCustomParameter by @SteffenHeu in #3217
• No spectral matching if library import running by @robinschmid in #3218
• Add annotation lables to Kendrick and Van Krevelen by @ansgarkorf in #3210

Full Changelog: v4.9.0...v4.9.14

High level changelog

• Improved overall chart performance
• Feature table:
  o Drastically speed up load time
  o Increased chart quality
  o Added annotation quality widget
  o Added “Preferred annotation”
• Preferred annotations/Annotation quality summary
  o Preferred annotation column combines Spectral/Compound/Sirius/Lipid annotations
  o Annotation quality summary (AQS) for all annotation types
• Native Waters MassLynx data support
• Select data files by metadata groups (raw data files selection parameter)
• Export structure images to SVG
• Improve pdf export of spectral library matches
• Updated local max mass detector
• Update reporting
• Feature blank subtraction option to remove whole rows or each sample-specific feature below blank threshold
• Local compound database search:
  o Calculate most intense isotopic signal for compounds
  o Added optional charge filter
• Rows filter:
  o Fold-change filter also for single sample groups (significance requires at least 2 samples per group)

What's Changed

• FxCharts: Single delayed draw, FxXYPlotModel, table column fixed by @robinschmid in #2860
• ParameterUtils save and load parameters from xml by @robinschmid in #3026
• Copy of ScanSelectionParameter by @SteffenHeu in #3052
• Test utils by @SteffenHeu in #3050
• Waters Masslynx data import advanced by @SteffenHeu in #3049
• Report batch parameters by @SteffenHeu in #3056
• uv: add specific name to trace selection by @SteffenHeu in #3057
• rt-corr: improve rt correction on scans by @SteffenHeu in #3058
• Moving average by @robinschmid in #3061
• Update local max mass detector for tof data by @SteffenHeu in #3062
• Fx charts mobilogram by @SteffenHeu in #3068
• FxCharts @robinschmid in #2950
• Improve json string speclib parsing by @SteffenHeu in #3076 #3075
• Lipid chart hide in table if no matched fragments by @robinschmid in #3079
• Increase samples limit in feature shapes chart by @robinschmid in #3080
• Default width for ListTypes by @robinschmid in #3081
• MiniTaskView label update by @JonasLueb in #3086
• SimpleCharts: dont trigger ds update on non fx thread by @SteffenHeu in #3083
• Make SpectralDBAnnotation modular by @SteffenHeu in #3077
• feature-table: sub column visibility setting by @SteffenHeu in #3082
• Fix backbone formula for CAR by @ansgarkorf in #3087
• tdf: more descriptive error messages by @SteffenHeu in #3085
• Update download url by @SteffenHeu in #3095
• Keep specific feature list selection in clone by @robinschmid in #3097
• Filter tooltips by @JonasLueb in #3101
• Reporting: update main template, free text grow by @SteffenHeu in #3103
• Put proxy test into tab and log more info by @robinschmid in #3104
• Fix load of TDF with special chars in file path by @robinschmid in #3089
• Highlight grouped summary by @SteffenHeu in #3106
• Fix local max massdetector by @SteffenHeu in #3116
• Spectrum plot - auto select feature list by @SteffenHeu in #3114
• Report: add cost center by @SteffenHeu in #3107
• Default sorting of columns in CSV export by @robinschmid in #3112
• Use row charge in rows filter by @robinschmid in #3117
• Preset: add messages if presets are loaded from old parameters by @SteffenHeu in #3108
• Sort preferred annotations by @SteffenHeu in #3118
• Feature blank subtraction cleanup by @robinschmid in #3100
• Add export to SVG menu to Structure2DComponent by @robinschmid in #3124
• Combined annotation score by @robinschmid in #3128
• [on annotation-summary] Harmonize how subcolumn values are retrieved, CSV export: remove empty columns and duplicates by @robinschmid in #3111
• Exclude feature lists from batch last selection by @robinschmid in #3131
• OptionalParameter load from xml use defaultValue instead of false by @robinschmid in #3139
• Delayed update of rows in feature table by @robinschmid in #3130
• annotation-summary: change text color for annotations with bad scores by @SteffenHeu in #3137
• Select/exclude data files by metadata by @robinschmid in #3133
• Calculate most intense signal for compound db by @SteffenHeu in #3105
• Rows filter, significance p-value optional, require 1 or 2 samples by @robinschmid in #3138
• Annotation summary color indicator by @SteffenHeu in #3151
• Local compound DB search: Add strict charge filtering parameter by @SteffenHeu in #3141
• Check adduct formula most abundant isotope in compound DB search by @robinschmid in #3142
• Stable value isotope pattern caching of matched lipids by @robinschmid in #3152
• Fix raw file placeholder by @SteffenHeu in #3156
• Disable chart logger by @SteffenHeu in #3160
• Faster sorting of structure column by @robinschmid in #3164
• Mass detection preview in batch mode by @robinschmid in #3165
• Isotope pattern on demand, precompute all feature annotations when added to row by @robinschmid in #3155
• Rows filter keep with MS2 does not apply to GC-EI-MS by @robinschmid in #3136
• update annotation level name by @SteffenHeu in #3168
• Exclude isotope score from GC-EI by @robinschmid in #3173
• Darker tooltip by @robinschmid in #3176
• Set all DataType.getPrefColumnWidth to speed up feature table open by @robinschmid in #3171
• Harmonize copying of config and applied methods by @robinschmid in #3181
• Smaller ion, formula, comment, box plot columns by @robinschmid in #3183
• Overwrite default column visibility by @robinschmid in #3185
• Annotation summary by @robinschmid in #3110
• Tsf print error on open fail by @SteffenHeu in #3186
• Annotation summary fixes and feature table help by @SteffenHeu in #3188

Full Changelog: v4.8.30...v4.9.0

Highlights

• Formula prediction is faster and was added to the mzwizard
• RI delta shown for spectral library matches

Beta features

• Default presets for modules
• Reporting: Create features report pdf and html

Updates

• remove usage of javafx internals. by @JonasLueb in #2992
• Enable option for default presets for modules by @SteffenHeu in #3001
• Component wrapper layout by @robinschmid in #3015
• Fix advanced TSF import by @SteffenHeu in #3011
• Add Vendor import param by @SteffenHeu in #3013
• update timsfull integration test by @SteffenHeu in #3009
• Precision by @SteffenHeu in #3005
• allow multiple imported files for RawDataImportTask by @SteffenHeu in #3016
• Add RI delta by @SteffenHeu in #3008
• Reporting by @SteffenHeu in #2960
• Waters import by @SteffenHeu in #2970
• Cleanup Precision by @robinschmid in #3018
• Update java doc and annotations in task classes by @SteffenHeu in #3024
• Add dia ms2 builder with no correlation by @SteffenHeu in #2837
• rtcorr: fix error in scan rt correction if few standards are found by @SteffenHeu in #3029
• wizard: set gnps csv export type by @SteffenHeu in #3028
• disable ri by default in compound db search by @SteffenHeu in #3032
• Fix MultiChoiceComponent not displaying all checks by @SteffenHeu in #3033
• Add UV area to legacy export by @SteffenHeu in #3030
• Formula prediction from wizard by @SteffenHeu in #3031
• Background color for scene.root in css by @robinschmid in #3038
• More explicit error handling in tdf import by @SteffenHeu in #3040
• Update ims overview thresholds by @SteffenHeu in #3042
• Fix thermo CAD chromatograms having absorbance as unit by @SteffenHeu in #3044
• Fix row selection in feature table after sorting filtering by @robinschmid in #3046
• Scan processor: mass detection for MS2, update spectrum type by @SteffenHeu in #3048

Full Changelog: v4.8.0...v4.8.30

Highlights

• Bundled Thermo raw data support on macOS
• Faster formula prediction for feature lists (parallelized)
• Improve user login and webservices: Improved proxy configuration auto detection
• JDK25
• Improved logging of spectral library import results

Minor fixes

• Fix rerunning batch with Thermo raw files now detects the files were already imported. Previously in 4.8.0 an info dialog would pop up.

Updates

• Bugfix/thermo raw parser mac issue by @JonasLueb in #2907
• Add border to toggle button by @robinschmid in #2929
• wizard: implement equals in WizardMassDetectorNoiseLevels by @SteffenHeu in #2932
• DIA: fix unnecessary interpolation by @SteffenHeu in #2926
• jdk25 gradle 9.1 by @robinschmid in #2928
• Sirius api update by @SteffenHeu in #2936
• Update junit and mockito agent registration by @robinschmid in #2938
• ims: refactor frame ms2 info addition by @SteffenHeu in #2927
• Add merge aligner to batch by @SteffenHeu in #2949
• DIA trim corr points to overlap by @SteffenHeu in #2937
• Javafx24 by @robinschmid in #2951
• Handle missing feature data in cache by @robinschmid in #2948
• Better logging for spectral db parsing by @robinschmid in #2895
• Parallelized formula prediction by @SteffenHeu in #2961
• Batik: update usage of svg libraries by @SteffenHeu in #2966
• Improved proxy auto detect by @robinschmid in #2898
• Thermo Raw File Parser update. Also, make signing, notarization and stapling for MacOS great again. by @JonasLueb in #2968
• Skip already imported thermo raw files in batches by @robinschmid in #2979
• Gradle build cache by @robinschmid in #2862
• Modernize the build script with some lazy configuration by @robinschmid in #2985
• Add resolver test framework by @SteffenHeu in #2989

Full Changelog: v4.8.0...v4.8.5

Highlights

• Split feature list by metadata
• Native Thermo raw data support
• SIRIUS compound DB annotations
• Scan based RT correction
• Presets for all modules
• Merging of spectral libraries
• Spectral library parsing improved for various formats to cover more metadata and alternative formattings
• Flexible feature list row filters for comments, tags, substructures, lipids, formulas, and more (in the feature table and feature list rows filter module).
• Added new metadata-based filters to rows filter and wizard

Updates

• fix linebreak in binary of unifi mzmls by @SteffenHeu in #2695
• Add documentation links + readout script by @SteffenHeu in #2690
• Add Csv DB Q3 mass, allow mrm trimming by @SteffenHeu in #2713
• fix dia ms2 corr for exactly the same rt values by @SteffenHeu in #2706
• Baf fix by @SteffenHeu in #2719
• add correlated features filter by @SteffenHeu in #2710
• Other detector fixes by @SteffenHeu in #2709
• Add checkbox to pseudo spectrum pane by @SteffenHeu in #2705
• Mac test by @SteffenHeu in #2728
• Fix notarizing for Apple apps - on mactest branch by @JonasLueb in #2729
• Fix Syntax. Search every dependency for signing. by @JonasLueb in #2735
• fix null error by @JonasLueb in #2736
• fix file name not added in ScanUtils#extractScanIdString by @SteffenHeu in #2734
• Add new colors links by @robinschmid in #2739
• Add simple string mapper to DataType by @SteffenHeu in #2738
• add acquisition method type to spectral library by @SteffenHeu in #2745
• sign all libraries and sub-libraries. by @JonasLueb in #2748
• Comp DB Custom fields, refactoring by @SteffenHeu in #2743
• notarize dmgs, add background to dmg install. by @JonasLueb in #2750
• Use all annotation types for aligner on ID by @robinschmid in #2756
• Rt calibration by @SteffenHeu in #2476
• Redefine outputs now keeps previous file format and adds format automatically by @robinschmid in #2751
• Module to Merge spectral libraries while retaining metadata by @SteffenHeu in #2746
• use semicolon to separate multiple usis in export by @SteffenHeu in #2761
• Signing, notarization and stapling of mzmine-macOS-distribution by @JonasLueb in #2755
• Fix sorting of scores in formula results table by @robinschmid in #2752
• Add support for Uv spectra chromatogram building by @SteffenHeu in #2760
• Merge alignment scores after duplicate filter by @robinschmid in #2757
• Harmonize statistics by @robinschmid in #2716
• Update results for full integration tests by @robinschmid in #2764
• More options how to renumber IDs by @robinschmid in #2762
• Fix metadata reader for date columns by @robinschmid in #2763
• Retention time calibration adjustments by @robinschmid in #2759
• add documentation for uv modules by @SteffenHeu in #2768
• Auto update selected FeatureLists, RawDataFile, Libraries in components by @robinschmid in #2767
• Minimum samples filter also for metadata groups by @robinschmid in #2724
• merge modules for trimming, binning and shifting uv traces by @SteffenHeu in #2773
• Beta on BaselineCorrectionModule by @robinschmid in #2772
• fix feature values null in MsnTreeFeatureDetectionTask by @SteffenHeu in #2776
• Clean up rows filter in grouped dialog by @robinschmid in #2766
• Layout adjustments by @robinschmid in #2777
• Rename parameters in RowsFilterParameters by @robinschmid in #2774
• Remove HCA add DBScan by @robinschmid in #2680
• add toString, fix dia ms2 correlation threshold by @SteffenHeu in #2779
• Update MSe integration test to new results by @robinschmid in #2782
• Update mse project IntegrationTests by @robinschmid in #2783
• Add min samples in one group parameter by @robinschmid in #2771
• MSn tree feature builder documentation by @robinschmid in #2780
• Rename msn tree visualizer, easier to find by @robinschmid in #2781
• More filters in wizard by @robinschmid in #2775
• Different shapes in PCA scores by @robinschmid in #2784
• Dia pasef test by @SteffenHeu in #2785
• Precheck for RSD filter in RowsFilterTask by @robinschmid in #2786
• More checks in mzwizard by @robinschmid in #2787
• add uv wizard icon by @SteffenHeu in #2789
• harmonize icon sizes by @SteffenHeu in #2790
• All MS/MS visualizer in bounds by @robinschmid in #2794
• Feature list menu polarity applied by @robinschmid in #2793
• add dia correlation threshold as advanced parameter by @SteffenHeu in #2797
• manual annotation to only require one identifier by @SteffenHeu in #2798
• add cas, internal id, json to csv export by @SteffenHeu in #2806
• Add window position and size to preferences by @robinschmid in #2809
• Fix blank area on dialog screen change by @robinschmid in #2810
• Feature table rework + annotation filters by @robinschmid in #2805
• update dia pasef results by @SteffenHeu in #2816
• Batch mode docs by @robinschmid in #2819
• Imrove scan selection and other embedded parameters by @robinschmid in #2817
• Remove window settings from other parameters by @robinschmid in #2821
• Use own parameterset in feature table config by @robinschmid in #2818
• Presets for all modules by @robinschmid in #2813
• Scan selection use external parameter set by @robinschmid in #2823
• add maldi spot type to data from tsf by @SteffenHeu in #2827
• add correct polarity in PseudoSpectrumFeatureDataSetCalculationTask by @SteffenHeu in #2838
• fix npe in BioTransformerTask if annotation has no smiles by @SteffenHeu in #2840
• fix npe for rows filter by @SteffenHeu in #2847
• add split feature list module by @SteffenHeu in #2848
• Add dialog to ask if sample columns should be added for large datasets by @robinschmid in #2831
• Fix npe when using StringConverter and unmodifiable list in ComboBox by @robinschmid in #2857
• update dependencies by @SteffenHeu in #2849
• potential fix for concurrent modification exception for module parameters by @SteffenHeu in #2865
• fix polarity in msp export by @SteffenHeu in #2864
• fix spectral library search weak polarity check if spectral library is parsed as neutral by @SteffenHeu in #2863
• Simplify polarity check to isDefined by @robinschmid in #2873
• Copy files from FileNameParameter into mzmine project by @SteffenHeu in #2867
• Packaged thermo import by @SteffenHeu in #2870
• Parameters changed with delay by @robinschmid in #2829
• Introduce stricter Issue-Creation by @JonasLueb in #2875
• More flexible MSP reader by @robinschmid in #2872
• test: disable thermo test due to wrong working dir by default by @SteffenHeu in #2876
• csvdb: fix compound not loaded on case mismatch by @SteffenHeu in #2878
• Sirius via api by @SteffenHeu in https://github.c...

High level changelog:

Highlights

• Feature table row filters to search for substructures, lipids, formulas, etc in any annotation.
• (BETA FEATURE) Added presets system to all modules (save, load, and apply presets)
• (BETA FEATURE) Added presets for row filters (substructure search, formula ranges, lipid search etc.

Updates

• Feature table rework + row filters. by @robinschmid in #2805
• Add window position and size to preferences (define the screen and maximized state of mzmine on startup) by @robinschmid in #2809
• Feature list menu EIC plot polarity applied by @robinschmid in #2793
• Add DIA correlation threshold as advanced parameter by @SteffenHeu in #2797
• Improve manual annotation to only require one identifier by @SteffenHeu in #2798
• Add cas, internal id, json to csv export by @SteffenHeu in #2806
• Better resolution switching behavior for dialog screen change by @robinschmid in #2810
• Update DIA pasef results by @SteffenHeu in #2816
• Batch mode docs by @robinschmid in #2819
• Imrove scan selection and other embedded parameters by @robinschmid in #2817
• Use own parameterset in feature table config by @robinschmid in #2818
• Presets for all modules by @robinschmid in #2813

Full Changelog: v4.7.27...v4.7.28