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Peptides changelog

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  • Tests: The BDD scenario "Clicking a WebLogo glyph selects exactly the peptides carrying that monomer" waits a second after the selection before it clicks the column header. The table view shows a new selection in the context panel 100 ms after it unless the current object changed meanwhile, and a click on the header of the column already current is no change: a click within those 100 ms had the selection replace the column and the Peptides pane with it, and the scenario failed now and then in both modes ("no readings")
  • Tests: The Most Potent Residues and Logo Summary Table viewer categories load the package's components in before, as the other viewer categories do, so they pass when run on their own (they failed with "SeqHelper is not initialized")
  • Sequence Variability Map: Fixed the Mutation Cliffs mode switch being cut off by the left edge of a narrow viewer, where it could not be clicked
  • core#1146: SAR demo: subscribes to the grid's first draw at once instead of 50 ms later, so it no longer misses it and waits its 3 s cap
  • App: The landing header is u2's AppHeader (moved out of @datagrok-libraries/utils): the same icon, bullets and Learn more
  • core#1010: Logo Summary Table: Fixed WebLogo cells failing with "row counts differ" when the table is filtered and Web Logo Aggregation Type is not count
  • public#4226: Bio | Analyze | SAR is disabled until the current table has a macromolecule column, instead of warning
  • Tests: Added package tests for the invariant-map and mutation-cliff exports, the mutation-cliff counts and position chart on 200 peptides, and the MCL cluster counts with the Logo Summary Table statistics at thresholds 10, 75 and 96; they replace the counts and oracles of the export, mutation-cliffs and similarity-threshold BDD features
  • Settings: The Dendrogram box reads the tree that is actually shown: the tree is a grid neighbour, a sibling of the grid rather than a child, so its close button is looked for in the whole analysis view (the box stayed unchecked on reopen after GROK-20640's narrower lookup)
  • GROK-20640: Settings: Fixed the Dendrogram box reopening unchecked while the tree is shown, and unchecking it leaving the tree in place — the tree is attached beside the grid, not docked as a viewer
  • Tests: BDD suite closed its gaps against the TestTrack cases and the old Playwright specs: similarity thresholds 10-96, a launch at the default settings, the dock layout, selection after a project reopen, Mutation Cliffs glyphs, statistics after Manual Alignment; every feature states what it does not translate
  • 1930: Recalculate monomer-position stats and scaled-activity caches when rows are added or removed
  • 2304: Guard LogoSummaryTable.onPropertyChanged and render against a null dataFrame on a detached viewer
  • Manual Alignment: Fixed Apply writing the split monomers one position off and leaving the SAR statistics stale
  • Export Mutation Cliffs: Preserved the original double-precision activities and deltas
  • Viewers: Added automation surfaces (getWidgetStatus, isRenderPending, onRendered) and a peptides-sar-ready event; Command works as Control for multi-selection on macOS
  • Added BDD feature files translating the Playwright specs (bdd/)
  • Settings: Fixed the Sequence space checkbox warning "Embeddings columns are not initialized" instead of adding the viewer; unchecking it now removes the viewer and its columns

1.27.11 (2026-07-12)​

  • GROK-18695: Updated npm dependencies to clear reported vulnerabilities

1.27.10 (2026-07-08)​

Features​

  • Peptide Generation: New viewer that designs new candidate peptides from monomer-position statistics using an additive positional model, ranked by predicted activity (High/Low target) with per-peptide statistical support and novelty flags. Reuses the SAR viewers'/model's cached statistics when available, reacts to the dataframe filter, applies empirical-Bayes shrinkage to damp low-support noise, and carries an info icon explaining the model and its caveats. Appends per-position "basis" columns that render each chosen monomer (colored from the monomer library, width-fitted) with an effect circle (size = per-row-normalized effect magnitude, color = direction × significance: red raises, blue lowers, pale ≈ weak, grey = untestable) and the signed contribution value, with Most-Potent-Residues-style activity-distribution tooltips that explain the encoding. A header "+" button opens the generated peptides as a standalone table view, flattening the basis columns to "monomer, contribution, p-value" text. Not added to SAR analysis by default — add it manually from the viewers menu.

  • Moved the Peptides Playwright E2E suite into the package (playwright/); helpers from @datagrok-libraries/test/src/playwright

1.27.4 - 1.27.7 (2026-03-20)​

Features​

  • #3604: Migrated tags to roles
  • Variability Map: Added export functionality
  • SAR: Added extraction support
  • Multi Position Statistics: Introduced multi-position statistics viewer

Bug Fixes​

  • SAR: Absent monomers are now filtered out

1.27.3 (2025-11-12)​

  • Fix mutation cliffs viewer not updating on filter change
  • Fix mutation cliffs viewer not restoring selection on frame re-attach
  • Sequence variability map: filter out absent monomers from grid when filter is applied

1.27.0 (2025-11-10)​

  • Rework mutation cliffs and tooltips, shown information about sequence pairs and their statistics.

1.26.2 (2025-11-08)​

  • Add Current row tracking option to mutation cliffs viewer

1.26.1 (2025-11-07)​

  • Sequence mutation cliffs viewer: Initial release

1.26.0 (2025-11-05)​

  • Full filter reactivity for all panels, tooltips, aggregations and viewers
  • Corrected aggregate calculations, statistics and mean difference comparisons
  • Fix MCL viewer premature shutdown on loading

1.25.1 (2025-11-05)​

  • Fix distribution tooltips not showing on weblogo hover
  • Enable filter reactivity by default SAR viewers

1.25.0 (2025-11-04)​

  • Update dependencies
  • Enable filter reactivity for All Peptides Viewers (Invariant Map, Monomer-Position, Most Potent Residues, Logo Summary Table, WebLogo in header)
  • Got rid of target column for Peptides analysis
  • Add sum columns for Monomer-Position
  • Fix navigation bugs

1.23.14 (2025-06-17)​

  • Default selection grid for Peptides analysis

1.23.11 (2025-05-26)​

  • Fix model loading with empty cluster selection

1.23.10 (2025-05-15)​

  • Improved description for position statistics viewer

1.23.9 (2025-05-14)​

  • Reveerse events for Position statistics viewer

1.23.8 (2025-05-12)​

  • Performance improvements to Peptide viewers
  • LST white space reduction
  • Bug fixes
  • Position statistics viewer

1.23.6 (2025-04-30)​

  • Fix Peptides analysis not starting on data with existing position columns

1.23.5 (2025-04-22)​

  • Fix invisible Scroller in mutations cliffs

1.23.4 (2025-04-21)​

  • Fixes for selection table for DG null values
  • Correction of unselection for standalone viewers
  • Cosmetic corrections to null values in predictions

1.23.3 (2025-04-17)​

Selection widget: value retrieving fix

1.23.2 (2025-04-14)​

  • Manual setting of notation providers to tables

1.22.0 (2025-03-22)​

  • Fixed unhighlighting of header weblogo
  • Harmonization of selection and counts in monomer-position and MPR viewers
  • Added more comprehensive tooltips

1.21.7 (2025-03-17)​

  • Fixes and improvements of Selection panel

1.21.6 (2025-03-13)​

  • Fix demo and compatibility to older platform versions

1.21.5 (2025-03-12)​

  • Fix weblogo renderer with corrected colors and background corrections
  • Improved mutation cliffs preview window with horizontal splitter
  • Correct circle rendering in Monomer-Position viewer
  • Mutations groups column in mutation cliffs pairs panel

1.21.4 (2025-03-03)​

Fix SAR errors on nulling targets

1.21.3 (2025-02-28)​

MCL: Sparse matrix pruning to avoid browser crash

1.21.2 (2025-02-03)​

Correct Sizing of mutation cliff grids

1.21.1 (2025-01-10)​

LST: Fix flickering and incorrect rendering in some cases

1.21.0 (2025-01-06)​

Enable Project saving for SAR analysis

1.19.1 (2024-12-10)​

Fix JS-API related changes

1.19.0 (2024-11-01)​

Migrate to new seqHelper API

1.18.7 (2024-10-17)​

Fixes For GROK-16606, GROK-16609

1.18.6 (2024-10-08)​

MCL: Better layout for similar size clusters

1.18.5 (2024-10-07)​

Fix weblogo support

1.18.4 (2024-10-03)​

Use monomer tooltip from library

1.18.3 (2024-10-02)​

Add Monomer meta columns to the Monomer-Position viewer

1.18.2 (2024-09-22)​

Color monomer background in invariant map

1.18.1 (2024-09-18)​

Add monomer custom coloring

1.17.29 (2024-08-14)​

Update MCL implementation

1.17.28 (2024-08-08)​

  • Downgrade API version

1.17.27 (2024-08-08)​

  • Selection viewer restoring original grid sorting
  • MCL viewer limiting max intercluster lines
  • fix bugs with selections context panel

1.17.26 (2024-08-07)​

Rename monomer position viewer to sequence variability map

1.17.25 (2024-08-06)​

Update MCLalgorytm and Add params to starting menu

1.17.24 (2024-07-29)​

Fix invariant map values rendering

1.17.23 (2024-07-29)​

Added options to invariant map:

  • split selection for targets
  • coloring options via aggregation
  • value aggregation
  • tooltips
  • improved stability

1.17.22 (2024-07-22)​

Fix Active peptide selection viewer failing on frame attached.

1.17.21 (2024-07-12)​

Add support for string aggregation with pie chart viewer in LST viewer.

1.17.20 (2024-07-09)​

MCL: Reverse order of clusters

1.17.19 (2024-07-01)​

Fix dialog styles

1.17.18 (2024-05-27)​

Add inflation factor to MCL.

1.17.17 (2024-05-06)​

Add both annotations to the active peptide selection viewer.

1.17.16 (2024-04-29)​

Add thresholds to active peptide selection viewer.

1.17.15 (2024-04-17)​

Cluster max activity viewer working on level of cluster, not cluster size.

1.17.14 (2024-04-15)​

Fix display of the max activity vs cluster size viewer columns.

1.17.13 (2024-04-02)​

Features​

  • Add max activity vs cluster size viewer.

1.17.12 (2024-03-30)​

Features​

  • #2707: Add original and canonical to ISeqSplitted

1.17.11 (2024-03-12)​

  • Fix context panel issues with mutation cliff pairs.
  • Fix filter crashing app and never recovering.
  • Precompute mutation cliffs statistics for correct rendering.
  • Use mutation cliffs statistics for rendering (instead of invariant map data)
  • Use Count and mean difference for size and color of mutation cliffs table.
  • Correct tooltip for mutation cliffs table to use mutation cliffs stats.

1.17.10 (2024-02-29)​

Fix context panel crashing and never recovering

1.17.9 (2024-02-29)​

Fix Logo summary table not calculating for single clusters and not updating on filter.

1.17.8 (2024-02-22)​

Allow using qnum activity columns when running SAR analysis from top menu.

1.17.7 (2024-02-22)​

Allow using qnum activity columns.

1.17.6 (2024-02-20)​

Fix NW Distance function.

1.17.5 (2024-02-15)​

Added MCL clustering to peptide analysis.

1.17.3 (2024-02-01)​

  • Sequence space random seeding for reproducibility.
  • Use of generated clusters for summery web logo table.

1.17.2 (2023-12-26)​

  • Improved dimensionality reduction (sequence space).

1.17.0 (2023-11-29)​

Features​

  • Renamed activity column to Activity (previously: Scaled activity).
  • Improved input tooltip in the Mutation Cliffs pairs panel.
  • Autosize grids in the Mutation Cliffs pairs panel.
  • Hid sequence space embedding columns and axes selectors.
  • Saving context panels state.
  • Selected cells now have an orange thick border.
  • Distribution panel now shows distribution for (1) all activity values, (2) selected rows, (3) peptides selection from viewers if mismatched with the total selection.
  • Sequence space viewer now uses the Needleman-Wunsch algorithm to compute distances.
  • Linearization of helm format macromolecules before sequence space computation.
  • Improved rendering speed of invariant map (no lags).
  • Improved rendering speed upon selection/filtering.

Bug Fixes​

  • Fixed accordion wouldn't update after selection in table view.
  • Filtering dataframe causing most potent residues viewer and context panel to crash.
  • Filtering dataframe causing major lags.
  • Most potent residues viewer crashing on some data.
  • Weblogo viewer crashing or causing major lag on selection/filtering.

1.16.0 (2023-11-05)​

Features​

  • Added Select All and Deselect All functionality to all viewers.
  • Added Mean activity column for the Most Potent Residues viewer.
  • Added Mean activity to tooltips.
  • Added WebLogo to the Selection table.

Bug Fixes​

  • Fixed Logo Summary Table tooltip wouldn't show if the analysis table doesn't contain column name 'Cluster'.
  • Fixed tooltips would show irrelevant info.

1.15.3 (2023-10-26)​

Bug Fixes​

  • Fixed docking sequence space would completely remove the viewer.

1.15.2 (2023-10-26)​

Features​

  • Improved Sequence space default parameters (changed threshold similarity from 0.8 to 0.3)

1.15.1 (2023-10-19)​

Features​

  • Color-coding Sequence space by scaled activity.
  • Optimized Mutation Cliffs calculations to use workers.
  • Hid WebLogo positions in Logo Summary Table.

Bug Fixes​

  • Fixed Invariant Map color coding wouldn't change when changing the color column.

1.15.0 (2023-10-12)​

Features​

  • Added Sequence Space viewer.
  • Selection panel columns now inherit width from the main table.
  • Invariant Map cell values are now rendered with contrast color relative to the background.

Bug Fixes​

  • Fixed WebLogo in header margin width.
  • Widgets in Context panel will now fill all the available width.
  • Fixed LST rows are not resizable.
  • Fixed selection inconsistency.
  • Fixed Most Potent Residues keyboard navigation.
  • Fixed analysis not starting when there are columns of the same name.

1.14.1 (2023-09-28)​

Bug Fixes​

  • Fixed a bug when filtering single cluster would break Logo Summary Table.

1.14.0 (2023-09-28)​

Features​

  • Added keyboard navigation to Logo Summary Table, Monomer-Position, Most Potent Residues viewers and Mutation Cliff pairs panel.
  • Added icon to expand grids in property panel to fullscreen.

Bug Fixes​

  • Fixed Distribution panel labels.

1.13.3 (2023-09-20)​

Features​

  • WebLogo now reacts to filtering.

Bug Fixes​

  • Fixed distribution panel throwing error when selection matches filter.

1.13.2 (2023-09-14)​

Bug Fixes​

  • Downgraded datagrok-api dependency to version 1.16.4.

1.13.1 (2023-09-13)​

Bug Fixes​

  • Most Potent Residues: Fixed issue when the viewer failed to construct in some cases.

1.13.0 (2023-09-13)​

Features​

  • Monomer-Position and Most Potent Residues: Circle size is now based on the absolute value of mean difference.
  • Scaling default colors (blue for low values and red for high) in Monomer-Position viewer.
  • Highlight rows on mouse over Monomer-Position, Most Potent Residues, Logo Summary Table and WebLogo in the header.
  • Changed viewer interactivity to match the platform defaults. Learn more about viewer hotkeys here.
  • Accordion with actions, mutation cliffs pairs, distribution and selection panels now shows on any selection.
  • Removed steps from tutorial.
  • Ignore rows with missing values when starting the analysis.

Bug Fixes​

  • Logo Summary Table: Fixed interaction.

1.12.0 (2023-08-30)​

Features​

  • Added sequence identity and similairty functionality.
  • Peptides moved to Bio > Analyze > SAR.
  • Added tooltips for all inputs and buttons.
  • Added Selection panel which shows the current selection as a separate table.
  • UI/UX improvements.

Bug Fixes​

  • Fixed table view tooltips.
  • Fixed selection with WebLogo in the column header.
  • Fixed table view couldn't be filtered by monomer position columns.

1.11.0 (2023-08-03)​

This release introduces sequence identity functionality and some stability and usability improvements.

Features​

  • Added sequence identity functionality.
  • UI/UX improvements.
  • Added activity column choice in settings.

1.10.4 (2023-08-01)​

Features​

  • UI/UX improvements.

Bug Fixes​

  • Fixed Monomer-Position viewer not responding to selection correctly.

1.10.3 (2023-07-31)​

Bug Fixes​

  • Fixed wrong values in the invariant map.
  • Fixed Mutation Cliffs pair selection would still result in wrong sequences sometimes.

1.10.2 (2023-07-24)​

Bug Fixes​

  • Made invisible Mutation Cliffs pairs columns, containing sequence indexes in the original table view.

1.10.1 (2023-07-24)​

Features​

  • Invariant Map is now selecting sequences instead of filtering.
  • Minor UI/UX adjustments.

Bug Fixes​

  • Fixed mutation pair selection resulted in wrong unique sequences in the Mutation Cliffs bug.
  • Fixed position column labels not showing if the page was scaled.

1.10.0 (2023-07-19)​

This release focuses on improving analysis stability and usability.

Features​

  • Improved activity distribution plots to show selected vs. all.
  • Added position number in main table view column headers.
  • The Monomer-Position viewer in the Mutation Cliffs mode now shows the number of unique sequences that have monomer mutation at the selected position.
  • The Monomer-Position viewer in the Mutation Cliffs mode now selects unique sequences that have monomer mutation at the selected position.
  • The Mutation Cliffs panel now shows unique sequences and corresponding values from columns visible in the table view.

Bug Fixes​

  • Fixed bug when filter couldn't be applied to the original table after analysis started.