- Using latest OpenMS modifications related to DDA implementation
- Added option to display only spectrogram data that contains convexhull (#545)
- Optimized commands creations (#543)
- prioritized the use of subordinate metadata when choosing between feature level and subordinate level (#544)
- update to feature map after call to targetedMatching (#544)
- added rawDataHandler member for Library (#544)
- matchSpectra requirements for msp (#544)
- changed getRequirements to getFilenameRequirements (#544)
- renamed library to spectra library (#544)
- updated RawDataHandler pointer logic for spectra_library (#544)
- Removed scan explorer window (#540)
- Fix StoreFeatureBackgroundEstimations and generalized export to other storing processors (#536)
- Fix/missing report metadata values (#541)
- DDA Implementation (#534)
- Added "LCMS DDA Transitions Library Construction" workflow
- Added "LCMS DDA Spectra Library Construction" workflow
- Added "LCMS DDA Spectra Library Matching" workflow
- PickMS1Features renamed Pick2DFeatures
- PickMS2Features renamed Pick3DFeatures
- Number of running threads is now an input on the Run Workflow Dialog (#529)
- Log messages improved (#528)
- Create output folder (#527)
- Fix loading and exporting for FeatureBackgroundEstimations, FeatureRSDEstimations, QuantitationMethods and StandardsConcentrations (#532)
- Fix inclusion/exclusion of points for multiple Calibration display (#531)
- Possibility to export Quantitations Methods (#522)
- Improving Calibration curve window: Possibility to exclude points, show chromatogram, editable parameters (WARNING: CALCULATE_CALIBRATION has been renamed OPTIMIZE_CALIBRATION) (#515)
- Show Inputs and Outputs in Workflow Step display (#520)
- Transformation_model_param_x_weight and transformation_model_param_y_weight do not accept empty values (replaced by 'x' and 'y') (#519)
- New Workflow Steps display (#517)
- Check missing or wrong columns for Quantitations Methods and Standards Concentrations files (#512)
- Check csv files BOM (#513)
- Improving Calibration curve display: show parameters, zooming, outlier points (#507)
- Improving logs: wrapping, auto scroll and line hovering (#509)
- Improving zooming on plots (#508)
- Using native system file picker (ImGui flavor still available as an option) (#505)
- Adding server building files (#496)
- Walkthrough : Non-targeted FIA-MS analysis with Thermo Orbitrap (#460)
- doc : Targeted flux analysis with LC-MS/MS Agilent Lipidomics (#473)
- Walkthrough: Targeted flux analysis with GC-MS full-scan Agilent (#476)
- Marking highest values in 2D Plots (#475)
- Report Doalog box now confirms success or error once the report is created (#480)
- Distributed Mode (#437)
- Fixed session error due to regex (#478)
- Fix some file picker don't popup when selecting file in the New Session dialog box (#479)
- upgrade CI macOS build to 13.1 (#472)
- ReadTheDocs Walkthrough : Targeted quantitation with HPLC data (#454)
- UI Splitting and Docking (#464)
- Support for small screens (#466)
- Enabled viewports (#467)
- Increased max points to be displayed to 10 millions (#470)
- Fixing SVG exports and deprecating HTML support (#458)
- Fixing FIAMS workflow and quantitationMethods.csv override (#461)
- Fixed Cancel button size for directory selection dialog box (#469)
- Save layout in session (#452)
- Read the Docs maintenance (#447)
- Display error in info panel when user select incorrect file for session file. (#456)
- Fix/fix sample group processing - processors can run into infinite loop. (#450)
- Enabled OpenMP for MacOS builds (fix crash when running multithreaded workflows) (#455)
- Modifying start menu title to include SmartPeakGUI version (#451)
- Fixed computation of merge injections (#434)
- Fix DDA parameters (#435)
- Statistics Widget: display message if no sample/transition is selected (#438)
- Min/Max zooming sliders issues (#440)
- Fixed export of PivotTable (#444)
- Fix export of Pivot Table (#445)
- Fix/select dilution (#446)
- "Select All" button when generating Report (#427)
- Added options to SmartPeakCLI (#429)
- --input-file (-f): Override input file.
- --parameter (-p): Override parameter.
- --mzml (-z): Overrides the default location for the mzML directory.
- --reports-out-dir (-ro): Overrides the default location for reports.
- --output-features (-o): Overrides the default location for output features.
- --input-features (-i): Overrides the default location for input features.
- Create Report: Pivotable and FeatureDB button to use FilePickerHandler (#431)
- Fixed number of transitions does not appear after loading (#430)
- Changed options to SmartPeakCLI (#429)
- --output (-o) is now replaced by either --output-features or --reports-out-dir
- --disable-progressbar short form has been replaced from -p to -pg
- --integrity short form has been replaced from -i to -t
- Implementation of user sessions (#423)
- Fixed some metadata not appearing in PivotTable (#424)
- Fixed failure to load featureQCComponents.csv when featureQCComponentGroups.csv is not provided (#423)
- SmartPeak support for exporting workflow results as plots (#412)
- Improving Feature Table (#385)
- Multithreading options for SequenceProcessor methods (#401)
- Fixed sorted data for Calibrator plot. (#413)
- Fixed Pivot table header with component name and groups (#410)
- Colouring logs (#406)
- Chromatogram's time-ranger in compact form (#397)
- CI: moved to python 3.7.2 to fix a change in typing module (#400)
- Enhancing issue filing usability (#403)
- Rework of Filenames class (#404)
- Fixed flooding of log when workflow fails to be loaded (#399)
- Fixed handling of windows separators in CLI. (#402)
- Fixed ProcessSequence Fails with SIGABRT (#398)
- DDA Workflow and Support for visualization of non-targeted LC-MS/MS data (#386)
- Automatic, accurate selection of data based on dilution and compound (#394)
- Added headless CLI to package (#391)
- Fixed show-back of log and info panel, once previously hidden. (#389)
- Display error if required column is missing in the parameters file. (#388)
- SmartPeak headless mode. (#365)
- Report error for invalid value in parameter.csv. (#387)
- Added support of NA keyword in the sequence file. (#376)
- Change testing framework to googletest (#374)
- Fixed display of native_id for scans in explorer view (#379)
- Removing trailing zeros in FilePicker (#377)
- Fixed MergeSpectra when spectrum has no peak (#382)
- Reworked FilePicker Handlers (#371)
- Display progress information (#367)
- Ability to export Sequence (#368)
- Advanced explorer views part 2 (#344)
- Adding search functionality to ParametersTable
- Sorting functionalities for ParametersTable
- Plot-Stepper for chromatograms and feature line plots
- Plot/Unplot All
- App wide tooltip info
- Adding quick help for various UI elements
- Fixing Crashes associated with getPathnameContent when starting GUI on macOS (#279)
- Fixed crash when updating parameters list (#369)
- Ability to export Parameters (#360)
- Compilation now uses C++17 standard.
- Fixed too much points to be displayed on Chromatograms (#358)
- Fixed crash on Linux when opening Transitions Tab (#364)
- Feat/aut722 Rework for a more modular GUI (#355)
- Moved Run Workflow window in its own widget
- Moved About dialog box in its own widget
- Moved Log into its own widget
- Added visible_ flag in Widget
- Moved SetWindowsize in Widget
- Made CalibratorsPlotWidget and LinePlot2DWidgets retainable.
- Report: removed draw_ and use Widget's visible_ instead
- RunworkflowWidget is resizable
- Fixed compilation with OpenMS, related with Parameters changes (#357)
- FIAMS_FullScan_Unknown_test.exe assertion failure (#348)
- Advanced Explorer Views 1 (#324)
- Advanced Explorer Views - adding sorting functionality and viewing of File Name
- Updated about popup [skip ci]
- Adding searching functionality
- Sorting and searching for injection/transition/feature tables
- Selective searching for tables with dropdown menu
- Disallow sorting for all-checked/all-unchecked columns
- Sorting and searching for various tables in main window
- Final enhancements to FilePicker, ExplorerTables and MainTables
- Preventing filenames from being appended twice when opening via button click
- Adding reusable table functions for searching/sorting
- Adding unittest for Widget
- Make parameters editable (#337)
- Enhancing FilePicker entries to be displayed in human readable format (#339)
- Added Statistics and more informations in the info panel (#341)
- Added SmartPeak documentation
- Adding working examples for calculating MDVs (#326)
- Refactor of Feature line and heatmap plots (#349)
- Fix formatting of changelog for emails and github releases (#340)
- Fixed crash when launching workflow with no injection (#332)
- Fixed Windows SmartPeak install: executable is not available from start menu (#338)
- Add cmake nsis configuration for creating application links
- Add icon to executable on windows
- Update cmake nsis config to include icon to installer and launch the application when installation complete
- Configure default CPACK_GENERATOR for windows
- Provide smartpeak tool python package for continuous integration. (#324)
- Peak picking for MS2 RawDataProcessor method. (#315)
- Include/Pass version tag to SmartPeak code. (#320)
- Add Utilities::getSmartPeakVersion() static method.
- Include version information in gui and logs.
- Description of the workflow steps displayed to the user. (#321)
- Description of the workflow steps displayed to the user.
- Disabled edition when workflow is running. Update application handler in main thread when workflow finished to run.
- Add getID, getName and getDescription to SequenceProcessor (#304)
- Ability to save and load previous workflows. (#307)
- Move commands to SequenceHandlers, remove the workflow modal dialog. Save/Load in menu.
- Remove unused format check.
- Improve error handling, avoid supplicate creations of commands.
- Use BuildCommandsFromNames, fixed const signed parameter.
- Implementation of SpectraPlotWidget, split Widgets in their own files.
- SmartPeak support for isotopic labeling experiments. (#283)
- Fix single entries not shown w/ file Picker.
- Parse isotopic_purity_values from a dedicated field.
- Add param for CalculateMDVAccuracies.
- Finalise SmartPeak support for isotopic labeling experiments.
- Update TRAML file with SumFormula.
- Update RawDataProcessor with modified OpenMS::IsotopeLabelingMDVs.
- Advanced plotting. (#298)
- Fix Sliders. Disable/Enable legend. Lines and scatter use same colors.
- More stability to display while running workflow.
- Sliders along with legend checkbox are now part of the chromatogram widget.
- Add compact view.
- Allow for resizing the GUI bottom, left and upper panes. (#297)
- Signing SmartPeak with DTU-issued certificate. (#296)
- Add exporter to GUI and remove previously generated sequences in examples data. (#288)
- Add Xcalibur writer to sequence parser.
- Add new application processor for XCalibur.
- Add makeSequenceFileMasshunter. (#287)
- Fix bug in directory and add to the gui export menu.
- Add method for making and writing an analyst sequence file along with tests. (#285)
- Add exporter to the GUI.
- Change member naming convention in SequenceProcessor classes.
- Change filenames to use an explicit param for the mzML filename using the filename member of the raw data metadata.
- Change sequenceParser to insert the injection name if no original filename value is provided.
- Update to SequenceParser to reflect change in filenaming semantics for mzML.
- Add addition of filename to featureMap when loading the featureMap. (#294)
- Switch to ImGui v1.81 Release. (#328)
- MergeFeatures (#295)
- Refactor SearchAccurateMass into two methods for searching the accurate mass and the other for making the consensus features from the individual adducts.
- Change weighted average to sum in MakeConsensusFeatures.
- Change FeatureMap creation step of Search accurate mass to make subordinates instead of features for compatibility with downstream quantitation and filtering.
- Rename MakeConsensusFeatures to MergeFeatures and updated the FIA-MS default workflow.
- Update MergeInjections to set the subordinate even merging at the Feature level.
- Migrate all ImGui::columns to ImGui::tables in the GUI. (#286)
- Switch to imgui v1.79, Boost to 1.73.
- Various adjustments to the current ImGui tables API.
- Resolve fatal error: reference is not a tree when checking out ImGui's specific commit.
- ImGui::Tables - removing inner borders in FilePicker.
- Update ImGui::Tables API. (#281)
- Append missing include for OpenSwathAlgo.
- Update GUI to latest ImGui API tables.
- Refresh parameters table only when parameters change. (#317)
- Refresh parameters table only when user parameters or workflow change
- Use notification to update the view.
- Move ParametersTableWidget to its own File.
- Move observers to sequenceHandlers.
- Refactor handling user parameters (#302)
- Parameter do not use anymore map/vectors/maps, but ParameterSet, container of FunctionParameter, containers of Parameter.
- It's still possible to initialize with the old structure of map/vector/map.
- Parameter can be initialized from an OpenMS Parameter (to create the schema).
- Parameter can be assigned to another Parameter, the schema, allowing validation.
- Commands return the list of Parameter they need to run (getParameterSchema()), allowing validation when setting up the workflow, not when running it.
- Parameter Panel show different colors: user overridden parameters, the default parameters (schema), and the unused (not appearing from the schema).
- Parameter Panel colors invalid values in red. Mouse over it shows some indication: constraint, expected Type.
- Fix Chromatogram stops updating after having selected all plots.
- Not specifying some user parameters will not prevent processors to run. (#329)
- Fix HPLC UV Unknowns preset. (#325)
- Log not written when GUI is launched from folder that requires Admin privileges to write to (#301)
- Add static method SmartPeak::Utilities::getLogFilepath() for dynamic path to log.
- Redirect logging path for GUI.
- Handle errors and log message to console.
- Fixed chromatogram and spectra range reset when selecting different components. (#314)
- File name not shown when selected. (#312)
- Displaying selected file name in the designated field & adding double-click-to-open feature.
- Add possibility to create new file from FilePicker.
- Extra warnings in FIA-MS workflow. (#311)
- Prioritize the use of subordinate metadata when choosing between feature level and subordinate level.
- Add extra logging to warn the user when the extract_spectra step for FIA-MS fails due to missing the RT that the spectra was acquired.
- Fixed Compilation issue with Commands, set LoadRawData parameter constraint to "ChromeleonFile" instead of "Chromeleon". (#308)
- Exception handling in QuantitationMethods. (#306)
- Add additional exception to catch misc OpenMS exceptions that interupt the workflow.
- Changed racked code to match ideosyncrocy in numbers less than 10.
- Replaced sample_name with injection_name in Analyst conversion.
- Bug in HPLC data processing (#284)
- Artificially scale the chromatograms when loading HPLC data derived from a .txt file.
- Small/minor aesthetic fix to tables. (#282)
- SequenceSegmentProcess exporters. (#280)
- Update Estimation methods to use filter templates as the template.
- Bad values copy in EstimateFeaturesRSD.
- Add extra debug info to SelectFeatures.
- Add sections in Filename for new store/load pairs in sequenceSegmentProcessor.
- Add new store/load pairs to sequenceSegmentProcessor for estimations of RSDs and Background.
- Update SharedProcessors with new sequenceSegmentProcessor store/load pairs.
- Bad GC-MS full scan workflow presets.
- Add views for filter and qc tables to the SessionHandler.
- Refactor initialization of shared pointers.
- Set FeatureMetadataSize dynamically.
- Update SessionHandler_test for the new entries in metadataToString and metadataToString.
- Update metadataToString and metadataToString with average_accuracy & absolute_difference.
- Add support for computing more accurate peak area metrics that will be used for downstream analysis and filtering in FIA-MS to pickms1features.
- Add consensus calculations to SearchAccurateMass.
- Add support for sample group handler in add sample to sequence.
- Add SampleGroupProcessor.
- Add MergeInjections with test for the case of subordinates.
- Add option to record the convex hull during PickMS1Features.
- Add hull points and best left/right widths to PickMS1Features.
- Add support for spectra explorer.
- Support for plotting spectra and additional support for defining the ranges of chromatograms and spectra as well as plotting features wtihout raw data and vice versa.
- Example data and preliminary code for FIA-MS workflow.
- Add documentation for ReadtheDocs with Sphinx/Doxygen.
- Working NSIS setup but it is missing all of the dependency libraries and executables.
- Implement SequenceProcessorMultithread.
- Top and bottom windows follow host's window resize.'
- Integrate recent changes from AppWindow to GUI: Changes to AppWindow were lost after the AppWindow files removal.
- Ask for pathnames before running workflow.
- Implement class `WorkflowManager`: workflow is copied back to the main app.
- Clear FilePicker's filter on entering a directory.
- Implement Info tab functionality, related to QuickInfo menu.
- Add widget Report to store a csv file with FeatureSummary or SequenceSummary.
- Update FIAMS parameters and TraML templates.
- Packaging for macOS (dmg), Linux (deb), Windows (exe), CI for macOS and CI for Windows.
- Add support for feature level feature table and matrix reporting along with optimization of feature table and feature matrix updating in the GUI.
- Update PickMS1Features and SearchAccurateMass so that all necessary feature metadata needed for downstream filtering, QC, and analytics is captured in the FeatureMap and saved to the FeatureMapHistory.
- Prioritize the use of subordinate metadata when choosing between feature level and subordinate level.
- Expand MergeInjections tests and isolated/corrected several bugs.
- Major bugs in SampleGroupProcessor; Add makeFeatureMapFromHistory for better handling of input FeatureXML files.
- Bug in UpdateFEatureMapHistory.
- Bug in mergeInjections where missing injection data caused the feature to be removed prematurely.
- Bug in FeatureMatrix.
- Bug in filtering by injection name or sequence segment name.
- Add options for running sequence processor with specified injections or segments.
- EMG processor and app state fixes.
- About window not using a popup/modal because it relies on hacks/workarounds.
- GUI can load a session from a sequence.
- Implement processor LoadSessionFromSequence.
- Add FilePicker
- Add AppStateProcessor logic to FilePicker
- getPathnameContent uses class Table, fetches name, size, type and date of entries
- File type filter.
- Navigate directories, show their content.
- Add AppState to AppWindow.
- Drag and Drop steps.
- Add Workflow widget to the application.
- Add processor class BuildCommandsFromIds to AppStateProcessor.
- Use single-pane navigation.
- Add "go up" directory button.
- Do not insert "." and ".." to folder content.
- Navigate directories, show their content.
- Add to gui: Report, Run workflow.
- Add validation check on Report checkboxes. At least one of both column should be selected.
- Add widget Report to store a csv file with FeatureSummary or SequenceSummary.
- Add Workflow widget to the application.
- Implement class GuiAppender.
- CLI and pivot export.
- Load files in a separate thread, and disable buttons until it's done.
- Add EMGProcessor.
- Add in features line and heatmap plots.
- Feature explorer pane.
- CLI can export integration start/end for FeatureSummary.csv and SequenceSummary.csv.
- Install dependency libboost-filesystem-dev apt package.
- Improve AppStateProcessor hierarchy, remove unnecessary structs, make them private methods.
- AppStateProcessor's methods become structs/classes.
- Separate CLI functionalities into AppState and AppStateProcessor.
- AppState does not keep info about selected metadata and sample types.
- Simplify CLI menu entries.
- Implicit conversion from char to plog::util::nstring.
- Indentation in AppWindow::HelpMarker().
- Avoid shadowing menu item with text below/under (level, z-index wise) it in workflow steps. Use Button instead of Text.
- FilePicker does not call OpenPopup at every frame.
- Add support for OpenMS shared data and removing fixed path names.
- Enable selecting all metadata in CLI app,
- Main arguments in GUI.
- Cmake configuration for OpenGL (Linux).
- CommandLine: reset fetures and raw data directories after loading a new sequence file.
First release of SmartPeak