Code

Nightingale upgrade#820

Code

Merged

dlrice merged 192 commits intomainebi-uniprot/uniprot-website:mainfrom nightingaleebi-uniprot/uniprot-website:nightingaleCopy head branch name to clipboardDec 17, 2024

+14,942-8,407

Commits

Commits on May 29, 2024

• Add @floating-ui/dom package.

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• Add initial addTooltip function.

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• Add tooltip style.

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• Use tooltip in SubCellViz.

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• Remove tooltip on target click.

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Commits on May 31, 2024

• Add useEffect for tooltip display in useColumns.

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• Add div and tooltipOnHoverRef.

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• Tooltip wip.

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• Add data-column-name property to column label.

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• FeatureViewer tooltip wip.

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• Wip.

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Commits on Jun 10, 2024

• Don't ignore pointer events.

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• Refine showTooltip2 onClick logic.

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• Extract getUpdate and getTooltip fns.

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• Return cleanup function from addTooltip.

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Commits on Jun 11, 2024

• Remove tippy.js from package.json and webpack config.

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• Use timer to make sure tooltip sticks around. Various cleaning up.

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• Style tweak.

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• Fix isInTooltip selector.

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• Type fixes.

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• Remove protvista-tooltip.d.ts

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• Update snapshots.

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• Wait a bit before listening to click events in showTooltipAtCoordinates.

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• Remove old protvista tooltips from AlignmentView.

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• More cleaning up on unmount.

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• Update snapshots.

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• Import order fix.

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• Add tooltip titles.

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• Revert franklin version for now - will need updating.

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Commits on Jun 12, 2024

• Use useCapture rather than waiting for a frame.

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• Also need to specify useCapture in removeEventListener.

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• Pin exact version for @floating-ui/dom.

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Commits on Jun 14, 2024

• Forgot to add yarn.lock

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• Use useCallback for onProtvistaUniprotChange.

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Commits on Jul 31, 2024

• Add nightingale-track packge.

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• Add NightingaleTrack custom-element.

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• Install @nightingale-elements/nightingale-navigation and create custom-element component.

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• Install @nightingale-elements/nightingale-sequence and create custom-element component.

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• Install @nightingale-elements/nightingale-manager and create custom-element component.

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Commits on Aug 1, 2024

• Initial upgrade of Nightingale in VisualFeaturesView.

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• Attempt to use nightingale's Feature type; remove protvistaFeatureId in favor of accession.

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Commits on Aug 2, 2024

• More type fixes.

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• More type and test fixes.

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• Use NightingaleTrackComponent in AlignmentOverview.

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• Replace protvista in Overview component.

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• Replace protvista in Wrapped component.

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• Replace protvista in BlastResultTable.

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• Adjust stylesheets for nightingale.

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• Update getColorByType import.

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• Install @nightingale-elements/nightingale-variation and create custom-element component.

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Commits on Aug 6, 2024

• Fix Nightingale Manager reflected-attributes to be comma separated. Replace protvista-manager in VariationViewer.

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• Replace protvista with nightingale in VisualVariationView.

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• Update import.

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• Merge remote-tracking branch 'origin/floating-ui-tooltip' into nightingale

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• Regenerate yarn.lock file.

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• Import formatTooltip from protvista.

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Commits on Aug 7, 2024

• Update imports in AlignmentView.

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• Update package.json

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• Remove several protvista packages.

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• Remove several protvista type files; add TODO in nightingale-zoom-tool.scss.

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• Initial and messy UniProtKBFeaturesView table refactor.

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• Wip UniProtKBFeaturesView refactor.

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Commits on Aug 8, 2024

• UniProtKBFeaturesView table updates.

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Commits on Aug 12, 2024

• Move NightingaleManagerComponent from FeaturesView to VisualFeaturesView.

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• Initial UniProtKBFeatureColumnConfiguration

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Commits on Aug 13, 2024

• Add types to UniProtKBFeatureColumnConfiguration.

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• Initial TableFromData WIP.

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Commits on Aug 14, 2024

• Fix position column.

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• Get extraContent working.

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Commits on Aug 21, 2024

• Extract and use TableFromData.

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• Small fixes.

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• Convert uniProtKBFeatureColumnConfiguration to just an array of objects. Filter out columns based on screen size, show source etc rather doing so at the time of render.

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Commits on Aug 22, 2024

• Rely only on data to render each column.

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• Basic filtering.

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Commits on Aug 23, 2024

• Get highlight row working.

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• Reflect highlight in nightingale track.

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Commits on Aug 27, 2024

• Wire up nightingale coordinate changes.

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• CSS tweak.

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• Fix ID column rendering.

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• Be more restrictive in +/- button query selector. Restrict width of expanded sequence cards.

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• Style tweaking.

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• Add Aurel's comments to explain ↔.

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• Don't bother with destructuring feature table args.

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• Merge stylesheets; simplify logic.

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• Replace useReducer with useState; more cleanup.

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• Type fixes in UniProtKBFeatureColumnConfiguration.

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Commits on Aug 28, 2024

• Adding types, assorted fixes and TODOs.

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• More type fixes and tidying.

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  f9fad83

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• Attempting to fix custom event types.

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• Try to solve type issues with generics.

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Commits on Aug 29, 2024

• Copy logic for expandable/collapse logic to Table.

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• Create and use useExpandTable custom hook.

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• Show message when no filters selected.

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Commits on Aug 30, 2024

• Tooltip type fixes.

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• Refactor formatTooltip.

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Commits on Sep 2, 2024

• Make TableFromData more generic.

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• Attempting type fixes.

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• Attempting type fixes.

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• Cast feature type as string; make toggleAll conditional upon rowExtraContent.

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• Initial TableForData in interaction section.

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• Add filtering to interaction section TableForData.

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• Add initial Variation TableFromData.

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• Remove TableFromData out of NightingaleManagerComponent.

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• Wire up row/viz highlighting in VariationViewer.

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• Allow for noTranslateBody in TableFromData.

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• Tidy up VariationViewer.

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  c1a74d1

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• Fix extra content logic.

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  ca46fa0

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• Use Table in DiseaseInvolvementView.

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• Use Table for EMBLView.

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• Use Table in EMBLView.

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• Adapt DatatableWrapper tests for Table.

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• Remove DatatableWrapper tsx and scss.

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Commits on Sep 3, 2024

• Update NightingaleZoomTool and use within VisualFeaturesView.

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• Remove NightingaleZoomTool from FeatureViewer for now.

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• Update NightingaleZoomStyles and use in VisualVariationView.

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• Replace protvista-table with Table and adjust space between tables.

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• Adapt TableFromData for tables within search result pages.

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• Remove protvista-datatable references in various locations.

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• Remove protvista-datatable css variables (presently undefined in any case).

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• Remove protvista-datatable and protvista-feature-adapter.

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• Regenerate lock file.

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• Fix processFeaturesData args.

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• TableFromData in UniParcFeaturesView.

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• Fix getRowId.

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• Make primaryAccession optional in ProcessedFeature type.

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• TableFromData: condition upon number of rows before showing expand table.

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Commits on Oct 8, 2024

• Update nightingale and protvista-uniprot.

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Commits on Oct 9, 2024

• Ignore case for nightingale svg loader.

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Commits on Oct 10, 2024

• Move VARIANT_COUNT_LIMIT into shared limits config file. Update tooltip eventType casing.

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• Just redefine customElements.define to avoid duplicate define being called.

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• feature.begin --> feature.start

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• Add NightingaleFilter with lit/react; adjust filter logic for new nightingale approach.

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Commits on Oct 11, 2024

• eventtype --> eventType

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• Use formatTooltip from protvista-feature-adapter again.

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• Move mark border and background fns to nightingale utils file.

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• Add mark border and background to uniparc features view.

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Commits on Oct 16, 2024

• Fixes for alignment overview and variation viewer

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• Don't set the height of the track.

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• More attempts at fixing align overview.

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Commits on Oct 17, 2024

• Remove unused imports.

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• Move featureShapesMocks.json to ts.

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• Type fixes.

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• Type fixes in sequences utils.

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• More type fixes.

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  a1f32e8

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• Make FeaturesView generic.

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• Merge remote-tracking branch 'origin/main' into nightingale

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Commits on Oct 18, 2024

• Snapshot updates.

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• Get more tests to pass.

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• Mock @nightingale-elements/nightingale-navigation

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• Mock more nightingale elements in ProteinProcessingSection tests.

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• Code format change.

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• Add protvista-uniprot to transformIgnorePatterns.

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• Upgrade protvista-uniprot.

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• Remove yalc references.

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Commits on Oct 21, 2024

• Tidy up.

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Commits on Nov 7, 2024

• Make table header sticky

  Swaathik

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• replace sass variables with native css variable

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• Replace no-scroll with use-ctrl-to-zoom like protvista-uniprot

  Swaathik

  committed
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• Remove filter-scroll.

  dlrice

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Commits on Nov 8, 2024

• Upgrade to v5.3.0 of nightingale.

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Commits on Nov 11, 2024

• Update protvista-uniprot imports.

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• Use global custom properties for colors.

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• Adapt NightingaleZoomTool for protvista-uniprot.

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• Upgrade protvista-uniprot.

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• Remove all protvista packages; update import of getFeatureTooltip.

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Commits on Nov 12, 2024

• Update types for protvista-uniprot.

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• Upgrade protvista-uniprot.

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• Update ResizeObserver mock.

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• Update snapshots.

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• Upgrade nightingale.

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• Upgrade franklin.

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• Update snapshots.

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• Make border-collapse: collapse so border highlight works.

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Commits on Dec 3, 2024

• Add separator in the tooltip and improve styles

  Swaathik

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• update protvista-uniprot

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Commits on Dec 9, 2024

• Update franklin for sequence font size fix

  Swaathik

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Commits on Dec 12, 2024

• Initial scrolling behavior on feature click.

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• Make tooltip scrollable

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• Fix header border.

  dlrice

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• Refine scrolling to accomodate sticky header.

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• Extract scrolling logic into own hook.

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• Use useNightingaleFeatureTableScroll in VariantsViewer.

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• Simplify logic.

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• Merge remote-tracking branch 'origin/nightingale' into nightingale

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• Use uuid for uniparc features.

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• Update snapshots.

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Commits on Dec 13, 2024

• address comments

  Swaathik

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Commits on Dec 16, 2024

• rename tooltip handler function

  Swaathik

  committed
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• Merge remote-tracking branch 'origin/main' into nightingale

  dlrice

  committed
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• Merge remote-tracking branch 'origin/nightingale' into nightingale

  dlrice

  committed
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• Mock Math.random in VariationViewer unit tests.

  dlrice

  committed
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• Update react to latest 18 and adjust tsconfig to resolve type issues.

  dlrice

  committed
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