@jbrowse/plugin-linear-genome-view 5.0.0-beta.2 → 5.0.0-beta.20
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/esm/LinearGenomeView/afterAttach.d.ts +22 -5
- package/esm/LinearGenomeView/afterAttach.js +129 -106
- package/esm/LinearGenomeView/axisConfigSchema.d.ts +18 -0
- package/esm/LinearGenomeView/axisConfigSchema.js +22 -0
- package/esm/LinearGenomeView/components/CenterLine.js +10 -5
- package/esm/LinearGenomeView/components/ConnectedHoverHighlight.js +2 -3
- package/esm/LinearGenomeView/components/CrisprGuidePanel.js +3 -5
- package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts +9 -4
- package/esm/LinearGenomeView/components/ExportSvgDialog.js +45 -8
- package/esm/LinearGenomeView/components/GetSequenceDialog.js +2 -2
- package/esm/LinearGenomeView/components/Header.js +11 -1
- package/esm/LinearGenomeView/components/HeaderClearHighlightButton.js +2 -2
- package/esm/LinearGenomeView/components/HeaderPanControls.d.ts +3 -3
- package/esm/LinearGenomeView/components/HeaderPanControls.js +6 -3
- package/esm/LinearGenomeView/components/HeaderSearchBoxes.js +4 -1
- package/esm/LinearGenomeView/components/HeaderZoomControls.js +6 -35
- package/esm/LinearGenomeView/components/Highlight.js +27 -11
- package/esm/LinearGenomeView/components/HighlightBand.d.ts +11 -2
- package/esm/LinearGenomeView/components/HighlightBand.js +32 -13
- package/esm/LinearGenomeView/components/HighlightChip.d.ts +3 -3
- package/esm/LinearGenomeView/components/HighlightChip.js +13 -8
- package/esm/LinearGenomeView/components/HighlightLabelDialog.d.ts +6 -0
- package/esm/LinearGenomeView/components/HighlightLabelDialog.js +18 -0
- package/esm/LinearGenomeView/components/HoverPositionHighlight.js +3 -3
- package/esm/LinearGenomeView/components/ImportForm.js +7 -9
- package/esm/LinearGenomeView/components/LinearGenomeView.js +5 -12
- package/esm/LinearGenomeView/components/LinearGenomeViewContainer.js +13 -14
- package/esm/LinearGenomeView/components/MiniControls.js +11 -5
- package/esm/LinearGenomeView/components/OverviewHighlight.js +3 -3
- package/esm/LinearGenomeView/components/OverviewHighlightBand.d.ts +3 -2
- package/esm/LinearGenomeView/components/OverviewHighlightBand.js +6 -5
- package/esm/LinearGenomeView/components/OverviewRubberband.js +25 -48
- package/esm/LinearGenomeView/components/OverviewScalebar.js +4 -5
- package/esm/LinearGenomeView/components/OverviewScalebarPolygon.js +5 -3
- package/esm/LinearGenomeView/components/PaddingBlocks.js +3 -8
- package/esm/LinearGenomeView/components/RangeSelectOverlay.js +5 -6
- package/esm/LinearGenomeView/components/RegionWidthEditorDialog.d.ts +3 -2
- package/esm/LinearGenomeView/components/RegionWidthEditorDialog.js +4 -4
- package/esm/LinearGenomeView/components/ResizeAllTracksHandle.d.ts +5 -0
- package/esm/LinearGenomeView/components/ResizeAllTracksHandle.js +74 -0
- package/esm/LinearGenomeView/components/Rubberband.d.ts +1 -2
- package/esm/LinearGenomeView/components/Rubberband.js +3 -2
- package/esm/LinearGenomeView/components/SVGHighlightBand.d.ts +10 -1
- package/esm/LinearGenomeView/components/SVGHighlightBand.js +16 -5
- package/esm/LinearGenomeView/components/Scalebar.d.ts +2 -6
- package/esm/LinearGenomeView/components/Scalebar.js +8 -5
- package/esm/LinearGenomeView/components/ScalebarRefNameLabels.js +51 -36
- package/esm/LinearGenomeView/components/SearchBox.js +10 -16
- package/esm/LinearGenomeView/components/SearchPanelForm.d.ts +3 -2
- package/esm/LinearGenomeView/components/SearchPanelForm.js +4 -2
- package/esm/LinearGenomeView/components/SearchResultsDialog.d.ts +4 -8
- package/esm/LinearGenomeView/components/SearchResultsDialog.js +7 -4
- package/esm/LinearGenomeView/components/SearchResultsTable.d.ts +4 -7
- package/esm/LinearGenomeView/components/SearchResultsTable.js +25 -53
- package/esm/LinearGenomeView/components/SequenceFeatureHoverHighlight.js +2 -3
- package/esm/LinearGenomeView/components/SequenceSearchDialog.d.ts +2 -4
- package/esm/LinearGenomeView/components/StrandCheckboxes.d.ts +3 -2
- package/esm/LinearGenomeView/components/StrandCheckboxes.js +4 -2
- package/esm/LinearGenomeView/components/TrackContainer.d.ts +2 -3
- package/esm/LinearGenomeView/components/TrackContainer.js +63 -10
- package/esm/LinearGenomeView/components/TrackLabel.js +14 -4
- package/esm/LinearGenomeView/components/TrackLabelButtons.js +2 -2
- package/esm/LinearGenomeView/components/TrackLabelDragHandle.js +4 -5
- package/esm/LinearGenomeView/components/TrackLabelMenu.js +11 -14
- package/esm/LinearGenomeView/components/TrackLabelRefNameWarning.d.ts +3 -4
- package/esm/LinearGenomeView/components/TrackLabelRefNameWarning.js +23 -10
- package/esm/LinearGenomeView/components/TrackRenderingContainer.d.ts +6 -4
- package/esm/LinearGenomeView/components/TrackRenderingContainer.js +12 -24
- package/esm/LinearGenomeView/components/TracksContainer.js +11 -23
- package/esm/LinearGenomeView/components/VerticalGuide.d.ts +1 -2
- package/esm/LinearGenomeView/components/VerticalGuide.js +3 -16
- package/esm/LinearGenomeView/components/fetchSequence.d.ts +1 -2
- package/esm/LinearGenomeView/components/fetchSequence.js +15 -7
- package/esm/LinearGenomeView/components/recentLocationsMenu.js +10 -0
- package/esm/LinearGenomeView/components/useRangeSelect.d.ts +0 -3
- package/esm/LinearGenomeView/components/useRangeSelect.js +26 -61
- package/esm/LinearGenomeView/components/useSearchBoxPrefs.d.ts +3 -1
- package/esm/LinearGenomeView/components/useSearchBoxPrefs.js +4 -2
- package/esm/LinearGenomeView/components/useSideScroll.d.ts +17 -2
- package/esm/LinearGenomeView/components/useSideScroll.js +156 -102
- package/esm/LinearGenomeView/components/util.d.ts +4 -0
- package/esm/LinearGenomeView/components/util.js +4 -2
- package/esm/LinearGenomeView/consts.d.ts +2 -0
- package/esm/LinearGenomeView/consts.js +3 -1
- package/esm/LinearGenomeView/containingLgv.d.ts +21 -0
- package/esm/LinearGenomeView/containingLgv.js +23 -0
- package/esm/LinearGenomeView/headerFit.d.ts +4 -2
- package/esm/LinearGenomeView/headerFit.js +20 -7
- package/esm/LinearGenomeView/index.d.ts +2 -7
- package/esm/LinearGenomeView/index.js +5 -7
- package/esm/LinearGenomeView/keyboardHandler.d.ts +8 -7
- package/esm/LinearGenomeView/keyboardHandler.js +61 -23
- package/esm/LinearGenomeView/launchKeys.d.ts +1 -1
- package/esm/LinearGenomeView/launchKeys.js +11 -6
- package/esm/LinearGenomeView/lazyDialogs.d.ts +16 -3
- package/esm/LinearGenomeView/lazyDialogs.js +1 -0
- package/esm/LinearGenomeView/linkedViewSync.d.ts +3 -11
- package/esm/LinearGenomeView/linkedViewSync.js +27 -49
- package/esm/LinearGenomeView/menuItems.d.ts +16 -18
- package/esm/LinearGenomeView/menuItems.js +264 -164
- package/esm/LinearGenomeView/model.d.ts +1192 -560
- package/esm/LinearGenomeView/model.js +805 -590
- package/esm/LinearGenomeView/rExport/exportLinearView.d.ts +17 -0
- package/esm/LinearGenomeView/rExport/exportLinearView.js +117 -0
- package/esm/LinearGenomeView/rExport/rScript.d.ts +110 -0
- package/esm/LinearGenomeView/rExport/rScript.js +524 -0
- package/esm/LinearGenomeView/sharedScaleContainer.d.ts +1 -1
- package/esm/LinearGenomeView/sharedScaleContainer.js +2 -12
- package/esm/LinearGenomeView/showFiles.d.ts +2 -0
- package/esm/LinearGenomeView/showFiles.js +19 -0
- package/esm/LinearGenomeView/showRegionsWithUndo.d.ts +1 -1
- package/esm/LinearGenomeView/showRegionsWithUndo.js +13 -5
- package/esm/LinearGenomeView/stickyChrome.d.ts +5 -9
- package/esm/LinearGenomeView/stickyChrome.js +5 -9
- package/esm/LinearGenomeView/svgcomponents/SVGGridlines.js +4 -4
- package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts +4 -1
- package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +8 -21
- package/esm/LinearGenomeView/svgcomponents/SVGHighlights.d.ts +3 -1
- package/esm/LinearGenomeView/svgcomponents/SVGHighlights.js +9 -9
- package/esm/LinearGenomeView/svgcomponents/SVGHighlightsOverlay.d.ts +3 -1
- package/esm/LinearGenomeView/svgcomponents/SVGHighlightsOverlay.js +5 -5
- package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +13 -18
- package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.js +2 -5
- package/esm/LinearGenomeView/svgcomponents/SVGRowHeader.js +5 -6
- package/esm/LinearGenomeView/svgcomponents/SVGRuler.js +9 -10
- package/esm/LinearGenomeView/svgcomponents/SVGScalebar.js +3 -3
- package/esm/LinearGenomeView/svgcomponents/SVGStackedRow.d.ts +26 -0
- package/esm/LinearGenomeView/svgcomponents/SVGStackedRow.js +12 -0
- package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js +21 -13
- package/esm/LinearGenomeView/svgcomponents/SVGTracks.d.ts +4 -5
- package/esm/LinearGenomeView/svgcomponents/SVGTracks.js +7 -6
- package/esm/LinearGenomeView/svgcomponents/SVGView.d.ts +2 -3
- package/esm/LinearGenomeView/svgcomponents/SVGView.js +17 -3
- package/esm/LinearGenomeView/svgcomponents/renderViewTracks.d.ts +24 -20
- package/esm/LinearGenomeView/svgcomponents/renderViewTracks.js +42 -29
- package/esm/LinearGenomeView/svgcomponents/useViewSvgFigure.js +74 -77
- package/esm/LinearGenomeView/svgcomponents/util.d.ts +28 -12
- package/esm/LinearGenomeView/svgcomponents/util.js +41 -29
- package/esm/LinearGenomeView/types.d.ts +13 -10
- package/esm/LinearGenomeView/types.js +0 -1
- package/esm/LinearGenomeView/util.d.ts +103 -46
- package/esm/LinearGenomeView/util.js +222 -170
- package/esm/MultiLevelRubberband/MultiLevelRubberband.js +9 -6
- package/esm/MultiLevelRubberband/index.d.ts +2 -0
- package/esm/MultiLevelRubberband/index.js +2 -0
- package/esm/MultiLevelRubberband/menuItems.d.ts +34 -0
- package/esm/MultiLevelRubberband/menuItems.js +52 -0
- package/esm/MultiLevelRubberband/rowLabel.d.ts +22 -0
- package/esm/MultiLevelRubberband/rowLabel.js +27 -0
- package/esm/MultiLevelRubberband/types.d.ts +1 -0
- package/esm/MultiLevelRubberband/useRangeSelect.d.ts +2 -1
- package/esm/MultiLevelRubberband/useRangeSelect.js +45 -59
- package/esm/TrackModifiers/index.d.ts +83 -0
- package/esm/TrackModifiers/index.js +231 -0
- package/esm/displayKitTests/perRegionTestEnv.d.ts +244 -68
- package/esm/displayKitTests/perRegionTestEnv.js +30 -26
- package/esm/index.d.ts +21 -99
- package/esm/index.js +17 -38
- package/esm/searchUtils.d.ts +26 -10
- package/esm/searchUtils.js +137 -137
- package/esm/shared/RubberbandSpan.d.ts +3 -2
- package/esm/shared/RubberbandSpan.js +6 -3
- package/esm/shared/coordLabels.d.ts +11 -4
- package/esm/shared/coordLabels.js +20 -5
- package/esm/shared/useWindowDrag.d.ts +18 -0
- package/esm/shared/useWindowDrag.js +47 -0
- package/package.json +12 -11
- package/esm/FeatureTrack/configSchema.d.ts +0 -124
- package/esm/FeatureTrack/configSchema.js +0 -54
- package/esm/FeatureTrack/index.d.ts +0 -2
- package/esm/FeatureTrack/index.js +0 -13
- package/esm/LinearGenomeView/initKeys.d.ts +0 -12
- package/esm/LinearGenomeView/initKeys.js +0 -68
- package/esm/MultiLevelRubberband/VerticalGuide.d.ts +0 -6
- package/esm/MultiLevelRubberband/VerticalGuide.js +0 -21
- package/esm/lazyPluginExports.d.ts +0 -23
- package/esm/lazyPluginExports.js +0 -36
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import { rowLabels } from './rowLabel.js';
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/**
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* One row per genome row, each holding that row's own rubberband menu — Get
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* sequence, Copy range, Highlight region, and whatever a plugin contributes
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* under Launch.
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*
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* A drag on the multi-level strip commits offsets on EVERY row (see
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* `useRangeSelect`), so each row's `rubberBandMenuItems()` already describes a
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* real selection and was simply never offered: the stacked views' menu held
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* "Zoom to region(s)" and nothing else, while the same drag in a plain linear
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* genome view offered five actions. Per row rather than applied across rows
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* because each row is its own assembly — one sequence to fetch, one range to
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* copy, one highlight to place — so there is no "all rows" answer to give.
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*
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* Zoom is the exception and stays where each view already has it: zooming every
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* row at once is what the gesture means, and the synteny view holds its follow
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* anchor across the loop.
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*/
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export function multiLevelRowMenuItems(views) {
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return rowLabels(views).map((label, idx) => ({
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label,
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subMenu: views[idx].rubberBandMenuItems(),
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}));
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}
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/**
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* The same per-row rows for a bare CLICK on the strip rather than a drag — each
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* row's Center view here, Zoom to base level and Copy coordinate, at the base
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* that row paints under `px`.
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*
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* No all-rows row above them, unlike the drag's "Zoom to region(s)". A drag
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* names a span in pixels and every row can act on it; a click names a
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* COORDINATE, and the rows are different assemblies, so which genome's base the
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* pointer is over is the question the menu has to ask rather than answer.
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*
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* `px` rather than a resolved offset: each row maps the pixel through its own
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* `pxToBp`, so there is no one offset to pass.
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*/
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export function multiLevelRowClickMenuItems(views, px) {
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return rowLabels(views).flatMap((label, idx) => {
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const view = views[idx];
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// A row with no regions is dropped, because `pxToBp` THROWS on one rather
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// than answering an offset that names no base — so gating on the built
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// submenu being empty, which is what this did, was a guard that could never
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// fire in front of a call that had already thrown. Reachable: a row's
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// `initialized` is assembly readiness, and the stack mounts this strip once
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// ANY row is ready.
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if (!view.displayedRegions.length) {
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return [];
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}
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return [{ label, subMenu: view.rubberbandClickMenuItems(view.pxToBp(px)) }];
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});
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}
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/**
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* What to call each genome row, one label per row. The assembly name where
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* there is one, and the row's position where a row is still loading, so a label
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* stays true whatever the assemblies turn out to be called.
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*
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* A NAME THAT REPEATS PICKS UP ITS ROW NUMBER, because a stack can hold one
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* assembly twice — two loci of the same genome, a read against its own
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* reference — and there the bare name gives two menu rows that open different
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* things under identical text. Only the repeats pay for it: the ordinary
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* pairwise view still reads "hg38" and "mm39".
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*
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* One function over the whole list rather than one row at a time, since
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* uniqueness is a property of the list. Shared by every menu that names the
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* rows — the track selectors, the row menus, the follow anchors, the
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* rubberband — so they cannot drift into calling the same row two different
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* things one click apart. Here rather than in the synteny view because the
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* breakpoint split view is the same stack of rows and had been numbering them
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* itself.
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*/
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export declare function rowLabels(views: {
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assemblyNames: string[];
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}[]): string[];
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/**
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* What to call each genome row, one label per row. The assembly name where
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* there is one, and the row's position where a row is still loading, so a label
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* stays true whatever the assemblies turn out to be called.
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*
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* A NAME THAT REPEATS PICKS UP ITS ROW NUMBER, because a stack can hold one
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* assembly twice — two loci of the same genome, a read against its own
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* reference — and there the bare name gives two menu rows that open different
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* things under identical text. Only the repeats pay for it: the ordinary
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* pairwise view still reads "hg38" and "mm39".
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*
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* One function over the whole list rather than one row at a time, since
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* uniqueness is a property of the list. Shared by every menu that names the
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* rows — the track selectors, the row menus, the follow anchors, the
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* rubberband — so they cannot drift into calling the same row two different
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* things one click apart. Here rather than in the synteny view because the
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* breakpoint split view is the same stack of rows and had been numbering them
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* itself.
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*/
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export function rowLabels(views) {
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const names = views.map((view, idx) => view.assemblyNames[0] ?? `Row ${idx + 1}`);
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const counts = new Map();
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for (const name of names) {
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counts.set(name, (counts.get(name) ?? 0) + 1);
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}
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return names.map((name, idx) => counts.get(name) > 1 ? `${name} (row ${idx + 1})` : name);
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}
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clientX: number;
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clientY: number;
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isClick: boolean;
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}
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export declare function useRangeSelect(ref: React.RefObject<HTMLDivElement | null>, model: MultiLevelRubberbandModel): {
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isClick: boolean | undefined;
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rubberbandOn: boolean;
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guideX: number | undefined;
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anchorPosition: AnchorPosition | undefined;
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import { useCallback, useState } from 'react';
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import { getRelativeX } from '@jbrowse/core/util/getRelativeX';
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import { transaction } from 'mobx';
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import { useWindowDrag } from '../shared/useWindowDrag.js';
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export function useRangeSelect(ref, model) {
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const [startX, setStartX] = useState();
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// releases the committed offsets too, since mouseOut no longer does while the
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//
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// menu is open — dismissing the menu, by its backdrop or Escape, is the point
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//
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@@ -27,71 +35,48 @@ export function useRangeSelect(ref, model) {
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clearOffsets();
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function globalMouseMove(event) {
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setCurrentX(event.clientX - left);
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}
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function globalMouseUp(event) {
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if (startX === undefined) {
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useWindowDrag(ref, mouseDragging ? startX : undefined, {
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onMove: setCurrentX,
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onEnd: ({ startX, endX, isClick, clientX, clientY }) => {
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setAnchorPosition({ offsetX: endX, clientX, clientY, isClick });
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if (isClick) {
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// the click menu names a coordinate, not a span, so nothing is
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// committed; the guide stays at the click so the menu says where
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setGuideX(endX);
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return;
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}
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const
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handleClose();
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return;
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}
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setAnchorPosition({
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});
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const leftPx = Math.min(startX, offsetX);
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const rightPx = Math.max(startX, offsetX);
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const leftPx = Math.min(startX, endX);
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transaction(() => {
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view.setOffsets(view.pxToBp(leftPx), view.pxToBp(rightPx));
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setGuideX(undefined);
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}
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handleClose();
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}
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}
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window.addEventListener('mousemove', globalMouseMove);
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window.addEventListener('mouseup', globalMouseUp);
|
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window.addEventListener('keydown', globalKeyDown);
|
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return () => {
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window.removeEventListener('mousemove', globalMouseMove);
|
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window.removeEventListener('mouseup', globalMouseUp);
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window.removeEventListener('keydown', globalKeyDown);
|
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};
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}, [startX, mouseDragging, model, ref, handleClose]);
|
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+
},
|
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|
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onCancel: handleClose,
|
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});
|
|
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59
|
function mouseDown(event) {
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event.
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-
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|
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if (event.button === 0) {
|
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event.preventDefault();
|
|
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|
+
event.stopPropagation();
|
|
63
|
+
// clear any leftover menu/selection so a fresh drag isn't blocked by a
|
|
64
|
+
// stale anchorPosition keeping mouseDragging false
|
|
65
|
+
setAnchorPosition(undefined);
|
|
66
|
+
// the guide is what the pointer was showing up to now, and mouseMove
|
|
67
|
+
// won't touch it during the drag — leaving it set keeps the selection
|
|
68
|
+
// span from ever rendering, since the guide wins that either/or
|
|
69
|
+
setGuideX(undefined);
|
|
70
|
+
const relativeX = getRelativeX(event, ref.current);
|
|
71
|
+
setStartX(relativeX);
|
|
72
|
+
setCurrentX(relativeX);
|
|
73
|
+
}
|
|
91
74
|
}
|
|
92
75
|
function mouseMove(event) {
|
|
93
|
-
// Don't update guideX while
|
|
94
|
-
//
|
|
76
|
+
// Don't update guideX while a menu is open — the guide is what the click
|
|
77
|
+
// menu's rows refer to, so it stays at the click rather than following the
|
|
78
|
+
// pointer to the menu — or while a drag-selection is in progress (the
|
|
79
|
+
// rubberband should show, not the guide)
|
|
95
80
|
if (anchorPosition || mouseDragging) {
|
|
96
81
|
return;
|
|
97
82
|
}
|
|
@@ -112,13 +97,14 @@ export function useRangeSelect(ref, model) {
|
|
|
112
97
|
callback();
|
|
113
98
|
handleClose();
|
|
114
99
|
}
|
|
115
|
-
const
|
|
100
|
+
const isClick = anchorPosition?.isClick;
|
|
101
|
+
const rubberbandOn = startX !== undefined && !isClick;
|
|
116
102
|
const right = anchorPosition?.offsetX ?? currentX;
|
|
117
103
|
const left = rubberbandOn ? Math.min(right, startX) : 0;
|
|
118
104
|
const width = rubberbandOn ? Math.abs(right - startX) : 0;
|
|
119
105
|
const views = rubberbandOn ? model.views : [];
|
|
120
106
|
return {
|
|
121
|
-
|
|
107
|
+
isClick,
|
|
122
108
|
rubberbandOn,
|
|
123
109
|
guideX,
|
|
124
110
|
anchorPosition,
|
|
@@ -0,0 +1,83 @@
|
|
|
1
|
+
import type { FieldPredicate } from '@jbrowse/core/util/fieldPredicate';
|
|
2
|
+
import type { TrackInit } from '@jbrowse/core/util/tracks';
|
|
3
|
+
import type { DisplaySettings } from '@jbrowse/launch-args/displaySettings';
|
|
4
|
+
import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
|
|
5
|
+
/** The linear view a command line's tracks open in, as these helpers read it. */
|
|
6
|
+
export interface ModifierView {
|
|
7
|
+
centerLineInfo?: {
|
|
8
|
+
refName?: string;
|
|
9
|
+
offset: number;
|
|
10
|
+
start: number;
|
|
11
|
+
end: number;
|
|
12
|
+
reversed?: boolean;
|
|
13
|
+
oob?: boolean;
|
|
14
|
+
};
|
|
15
|
+
launchTrack: (trackId: string, trackSnapshot?: object, displaySnapshot?: object) => Promise<{
|
|
16
|
+
displays: unknown[];
|
|
17
|
+
} | undefined>;
|
|
18
|
+
showTrack: (trackId: string, trackSnapshot?: object, displaySnapshot?: object) => unknown;
|
|
19
|
+
tracks: {
|
|
20
|
+
configuration: {
|
|
21
|
+
trackId: string;
|
|
22
|
+
};
|
|
23
|
+
displays: unknown[];
|
|
24
|
+
activeDisplay: {
|
|
25
|
+
configuration: Record<string, unknown>;
|
|
26
|
+
};
|
|
27
|
+
}[];
|
|
28
|
+
}
|
|
29
|
+
/**
|
|
30
|
+
* `displayTypeOf` for a track the session holds, undefined for one it does
|
|
31
|
+
* not; `displayType` is the display the caller opens it as when no
|
|
32
|
+
* `display:` modifier names one.
|
|
33
|
+
*/
|
|
34
|
+
export declare function openedDisplayType(session: {
|
|
35
|
+
getTrackById: (trackId: string) => unknown;
|
|
36
|
+
}, trackId: string, modifiers: string[], displayType?: string): string | undefined;
|
|
37
|
+
/**
|
|
38
|
+
* Write the `filter` of `trackId`'s `settings` onto its display open in
|
|
39
|
+
* `view`, by field over the configured filter, as the track menu would.
|
|
40
|
+
* Returns the display's filter as written, which reopens the track as drawn,
|
|
41
|
+
* or undefined when the settings write no filter.
|
|
42
|
+
*/
|
|
43
|
+
export declare function writeFilter(view: Pick<ModifierView, 'tracks' | 'showTrack'>, trackId: string, settings: DisplaySettings): FieldPredicate[] | undefined;
|
|
44
|
+
/**
|
|
45
|
+
* @deprecated `writeFilter`, which every display category takes. This one
|
|
46
|
+
* writes an alignments `display`'s filter only.
|
|
47
|
+
*/
|
|
48
|
+
export declare function writeReadFilter(display: unknown, displayType: string | undefined, settings: DisplaySettings): FieldPredicate[] | undefined;
|
|
49
|
+
interface LaunchOptions {
|
|
50
|
+
/** the track entry's own display settings, which the modifiers write over */
|
|
51
|
+
displaySnapshot?: Record<string, unknown>;
|
|
52
|
+
trackSnapshot?: Record<string, unknown>;
|
|
53
|
+
/** changes the settings after the center-line sort resolves, before the open */
|
|
54
|
+
adjust?: (settings: DisplaySettings) => void;
|
|
55
|
+
warn?: (message: string) => void;
|
|
56
|
+
}
|
|
57
|
+
/**
|
|
58
|
+
* Open `trackId` in `view` with its command-line modifiers applied, and return
|
|
59
|
+
* the session-spec track entry that reopens it as drawn, or undefined when the
|
|
60
|
+
* open fails, which `launchTrack` reports to the session.
|
|
61
|
+
*/
|
|
62
|
+
export declare function launchTrackWithModifiers(view: ModifierView, trackId: string, displayType: string | undefined, modifiers: string[], { displaySnapshot, trackSnapshot, adjust, warn, }?: LaunchOptions): Promise<{
|
|
63
|
+
trackId: string;
|
|
64
|
+
filter?: FieldPredicate[] | undefined;
|
|
65
|
+
} | undefined>;
|
|
66
|
+
/**
|
|
67
|
+
* Open a session spec's track entry in a navigated `view`, its `modifiers`
|
|
68
|
+
* written over its display settings. When a modifier or the open fails, the
|
|
69
|
+
* session's snackbar says why and the track opens with its own settings.
|
|
70
|
+
*/
|
|
71
|
+
export declare function launchTrackInit(view: ModifierView & IAnyStateTreeNode, t: TrackInit): Promise<void>;
|
|
72
|
+
/**
|
|
73
|
+
* Write a track's `memberWrites` onto what its display in `view` already has,
|
|
74
|
+
* after every other modifier, so a member write keeps the rest of the setting
|
|
75
|
+
* whatever order the command line gives them in. A display replaces a color
|
|
76
|
+
* or facet object whole, which is why these cannot ride in on the launch
|
|
77
|
+
* snapshot. A keyed object (`rows`, ADR-257) seeds only its field and the
|
|
78
|
+
* objects written whole that the writes reach, such as `rows.color`: seeded
|
|
79
|
+
* whole it would restate the arrangement a field write must drop, and
|
|
80
|
+
* unseeded a spec holding the patch would lose the field and the channel.
|
|
81
|
+
*/
|
|
82
|
+
export declare function writeMembers(view: Pick<ModifierView, 'tracks' | 'showTrack'>, trackId: string, members: string[]): Record<string, unknown>;
|
|
83
|
+
export {};
|
|
@@ -0,0 +1,231 @@
|
|
|
1
|
+
import { keyedWritesAt, mergeConfSettings, writesWholeAt, } from '@jbrowse/core/configuration';
|
|
2
|
+
import { getEnv, getSession } from '@jbrowse/core/util';
|
|
3
|
+
import { basePaintedAt } from '@jbrowse/core/util/Base1DUtils';
|
|
4
|
+
import { predicatesOf, testsSomething, withFields, } from '@jbrowse/core/util/fieldPredicate';
|
|
5
|
+
import { normalizeTrackInit, trackDisplayType } from '@jbrowse/core/util/tracks';
|
|
6
|
+
import { buildDisplaySnapshot, displayCategory, memberPatch, memberWrites, mergeSettings, requestedDisplayType, } from '@jbrowse/launch-args/displaySettings';
|
|
7
|
+
import { getSnapshot, getType, isArrayType, isStateTreeNode, } from '@jbrowse/mobx-state-tree';
|
|
8
|
+
/**
|
|
9
|
+
* The display a linear view opens `conf` as, read off the display picker so it
|
|
10
|
+
* follows `display:` and the adapter rather than a list of track types.
|
|
11
|
+
*/
|
|
12
|
+
function displayTypeOf(pluginManager, conf, modifiers, displayType) {
|
|
13
|
+
return trackDisplayType(pluginManager, conf, 'LinearGenomeView', requestedDisplayType(modifiers) ?? displayType);
|
|
14
|
+
}
|
|
15
|
+
/**
|
|
16
|
+
* `displayTypeOf` for a track the session holds, undefined for one it does
|
|
17
|
+
* not; `displayType` is the display the caller opens it as when no
|
|
18
|
+
* `display:` modifier names one.
|
|
19
|
+
*/
|
|
20
|
+
export function openedDisplayType(session, trackId, modifiers, displayType) {
|
|
21
|
+
const conf = session.getTrackById(trackId);
|
|
22
|
+
return conf
|
|
23
|
+
? displayTypeOf(getEnv(session).pluginManager, (isStateTreeNode(conf) ? getSnapshot(conf) : conf), modifiers, displayType)
|
|
24
|
+
: undefined;
|
|
25
|
+
}
|
|
26
|
+
const consoleWarn = (message) => {
|
|
27
|
+
console.warn(`Warning: ${message}`);
|
|
28
|
+
};
|
|
29
|
+
function modifierLaunch(displayType, modifiers, warn = consoleWarn) {
|
|
30
|
+
return {
|
|
31
|
+
displayType,
|
|
32
|
+
settings: buildDisplaySnapshot(displayType, modifiers, warn),
|
|
33
|
+
members: memberWrites(displayType, modifiers),
|
|
34
|
+
};
|
|
35
|
+
}
|
|
36
|
+
// the entries grouped by field, as `setFilterFields` takes them: a field whose
|
|
37
|
+
// entries are all bare is `[]`, which clears it, defaults included
|
|
38
|
+
function filterPatch(entries) {
|
|
39
|
+
const patch = {};
|
|
40
|
+
for (const p of entries) {
|
|
41
|
+
patch[p.field] = [
|
|
42
|
+
...(patch[p.field] ?? []),
|
|
43
|
+
...(testsSomething(p) ? [p] : []),
|
|
44
|
+
];
|
|
45
|
+
}
|
|
46
|
+
return patch;
|
|
47
|
+
}
|
|
48
|
+
// the display snapshot a track opens with. `filter` stays out of it:
|
|
49
|
+
// `writeFilter` writes it once the track is open, since the list in a
|
|
50
|
+
// snapshot would replace the configured one
|
|
51
|
+
function launchSnapshot({ settings }) {
|
|
52
|
+
const { snap, displayType } = settings;
|
|
53
|
+
const { filter: _filter, ...unfiltered } = snap;
|
|
54
|
+
return {
|
|
55
|
+
...unfiltered,
|
|
56
|
+
...(displayType ? { type: displayType } : {}),
|
|
57
|
+
};
|
|
58
|
+
}
|
|
59
|
+
/**
|
|
60
|
+
* Write the `filter` of `trackId`'s `settings` onto its display open in
|
|
61
|
+
* `view`, by field over the configured filter, as the track menu would.
|
|
62
|
+
* Returns the display's filter as written, which reopens the track as drawn,
|
|
63
|
+
* or undefined when the settings write no filter.
|
|
64
|
+
*/
|
|
65
|
+
export function writeFilter(view, trackId, settings) {
|
|
66
|
+
const { filter } = settings.snap;
|
|
67
|
+
const track = view.tracks.find(t => t.configuration.trackId === trackId);
|
|
68
|
+
if (!filter || !track) {
|
|
69
|
+
return undefined;
|
|
70
|
+
}
|
|
71
|
+
const patch = filterPatch(filter);
|
|
72
|
+
const display = track.displays[0];
|
|
73
|
+
if (display?.setFilterFields) {
|
|
74
|
+
display.setFilterFields(patch);
|
|
75
|
+
return display.writtenFilter;
|
|
76
|
+
}
|
|
77
|
+
const written = withFields(predicatesOf(track.activeDisplay.configuration.filter), patch);
|
|
78
|
+
view.showTrack(trackId, {}, { filter: written });
|
|
79
|
+
return written;
|
|
80
|
+
}
|
|
81
|
+
/**
|
|
82
|
+
* @deprecated `writeFilter`, which every display category takes. This one
|
|
83
|
+
* writes an alignments `display`'s filter only.
|
|
84
|
+
*/
|
|
85
|
+
export function writeReadFilter(display, displayType, settings) {
|
|
86
|
+
const { filter } = settings.snap;
|
|
87
|
+
if (displayCategory(displayType) !== 'alignments' || !filter) {
|
|
88
|
+
return undefined;
|
|
89
|
+
}
|
|
90
|
+
const filterDisplay = display;
|
|
91
|
+
filterDisplay?.setFilterFields?.(filterPatch(filter));
|
|
92
|
+
return filterDisplay?.writtenFilter;
|
|
93
|
+
}
|
|
94
|
+
// the pivot is the base under the view's center, which a view has only once
|
|
95
|
+
// it shows a region
|
|
96
|
+
function centerSort(view, trackId, field, warn) {
|
|
97
|
+
const center = view.centerLineInfo;
|
|
98
|
+
if (center && !center.oob) {
|
|
99
|
+
return {
|
|
100
|
+
field,
|
|
101
|
+
pos: basePaintedAt(center, center.offset),
|
|
102
|
+
refName: center.refName ?? '',
|
|
103
|
+
};
|
|
104
|
+
}
|
|
105
|
+
else {
|
|
106
|
+
warn(`sort:${field} on "${trackId}" ignored — the view has no center position to sort at (pass --loc)`);
|
|
107
|
+
return undefined;
|
|
108
|
+
}
|
|
109
|
+
}
|
|
110
|
+
// The modifiers' settings written over the entry's own as a settings bag
|
|
111
|
+
// writes them (`mergeConfSettings`): a namespace such as `pileup` member by
|
|
112
|
+
// member, a bare value lifted first, and a channel such as `encoding.color`
|
|
113
|
+
// whole, so a `color:` modifier is not mixed into the entry's color by field.
|
|
114
|
+
// Plain JSON where no registered display type says which is which.
|
|
115
|
+
function overEntry(view, displayType, entry, over) {
|
|
116
|
+
const pluginManager = isStateTreeNode(view)
|
|
117
|
+
? getEnv(view).pluginManager
|
|
118
|
+
: undefined;
|
|
119
|
+
return displayType && pluginManager?.displayTypes.has(displayType)
|
|
120
|
+
? mergeConfSettings(pluginManager.getDisplayType(displayType).configSchema, entry, over)
|
|
121
|
+
: mergeSettings(structuredClone(entry), over);
|
|
122
|
+
}
|
|
123
|
+
/**
|
|
124
|
+
* Open `trackId` in `view` with its command-line modifiers applied, and return
|
|
125
|
+
* the session-spec track entry that reopens it as drawn, or undefined when the
|
|
126
|
+
* open fails, which `launchTrack` reports to the session.
|
|
127
|
+
*/
|
|
128
|
+
export async function launchTrackWithModifiers(view, trackId, displayType, modifiers, { displaySnapshot = {}, trackSnapshot = {}, adjust, warn = consoleWarn, } = {}) {
|
|
129
|
+
const launch = modifierLaunch(displayType, modifiers, warn);
|
|
130
|
+
const { snap, sort } = launch.settings;
|
|
131
|
+
const at = sort && centerSort(view, trackId, sort.field, warn);
|
|
132
|
+
if (at) {
|
|
133
|
+
snap.sort = at;
|
|
134
|
+
}
|
|
135
|
+
adjust?.(launch.settings);
|
|
136
|
+
const launched = overEntry(view, displayType, displaySnapshot, launchSnapshot(launch));
|
|
137
|
+
const opened = await view.launchTrack(trackId, trackSnapshot, launched);
|
|
138
|
+
if (!opened) {
|
|
139
|
+
return undefined;
|
|
140
|
+
}
|
|
141
|
+
const drawnFilter = writeFilter(view, trackId, launch.settings);
|
|
142
|
+
const members = writeMembers(view, trackId, launch.members);
|
|
143
|
+
return {
|
|
144
|
+
trackId,
|
|
145
|
+
...launched,
|
|
146
|
+
...(drawnFilter ? { filter: drawnFilter } : {}),
|
|
147
|
+
...members,
|
|
148
|
+
};
|
|
149
|
+
}
|
|
150
|
+
/**
|
|
151
|
+
* Open a session spec's track entry in a navigated `view`, its `modifiers`
|
|
152
|
+
* written over its display settings. When a modifier or the open fails, the
|
|
153
|
+
* session's snackbar says why and the track opens with its own settings.
|
|
154
|
+
*/
|
|
155
|
+
export async function launchTrackInit(view, t) {
|
|
156
|
+
const { trackId, trackSnapshot, displaySnapshot, modifiers } = normalizeTrackInit(t);
|
|
157
|
+
if (modifiers.length === 0) {
|
|
158
|
+
await view.launchTrack(trackId, trackSnapshot, displaySnapshot);
|
|
159
|
+
return;
|
|
160
|
+
}
|
|
161
|
+
const session = getSession(view);
|
|
162
|
+
const { type } = displaySnapshot;
|
|
163
|
+
const notes = [];
|
|
164
|
+
try {
|
|
165
|
+
await launchTrackWithModifiers(view, trackId, openedDisplayType(session, trackId, modifiers, typeof type === 'string' ? type : undefined), modifiers, {
|
|
166
|
+
trackSnapshot,
|
|
167
|
+
displaySnapshot,
|
|
168
|
+
warn: message => notes.push(message),
|
|
169
|
+
});
|
|
170
|
+
}
|
|
171
|
+
catch (e) {
|
|
172
|
+
console.error(e);
|
|
173
|
+
session.notifyError(`"${trackId}" ${modifiers.join(' ')}: ${e}`, e);
|
|
174
|
+
}
|
|
175
|
+
// launchTrack reports its own failure, such as a display:
|
|
176
|
+
// the track cannot open as
|
|
177
|
+
if (!view.tracks.some(t => t.configuration.trackId === trackId)) {
|
|
178
|
+
await view.launchTrack(trackId, trackSnapshot, displaySnapshot);
|
|
179
|
+
}
|
|
180
|
+
if (notes.length) {
|
|
181
|
+
session.notify(notes.join('; '), 'warning');
|
|
182
|
+
}
|
|
183
|
+
}
|
|
184
|
+
// the named members of a keyed object as configured, undefined when it
|
|
185
|
+
// states none of them
|
|
186
|
+
function keyedSeed(member, names) {
|
|
187
|
+
const configured = isStateTreeNode(member)
|
|
188
|
+
? getSnapshot(member)
|
|
189
|
+
: {};
|
|
190
|
+
const seed = Object.fromEntries(names.flatMap(name => configured[name] === undefined ? [] : [[name, configured[name]]]));
|
|
191
|
+
return Object.keys(seed).length > 0 ? seed : undefined;
|
|
192
|
+
}
|
|
193
|
+
/**
|
|
194
|
+
* Write a track's `memberWrites` onto what its display in `view` already has,
|
|
195
|
+
* after every other modifier, so a member write keeps the rest of the setting
|
|
196
|
+
* whatever order the command line gives them in. A display replaces a color
|
|
197
|
+
* or facet object whole, which is why these cannot ride in on the launch
|
|
198
|
+
* snapshot. A keyed object (`rows`, ADR-257) seeds only its field and the
|
|
199
|
+
* objects written whole that the writes reach, such as `rows.color`: seeded
|
|
200
|
+
* whole it would restate the arrangement a field write must drop, and
|
|
201
|
+
* unseeded a spec holding the patch would lose the field and the channel.
|
|
202
|
+
*/
|
|
203
|
+
export function writeMembers(view, trackId, members) {
|
|
204
|
+
if (members.length === 0) {
|
|
205
|
+
return {};
|
|
206
|
+
}
|
|
207
|
+
const track = view.tracks.find(t => t.configuration.trackId === trackId);
|
|
208
|
+
if (!track) {
|
|
209
|
+
throw new Error(`"${trackId}" is not open, so ${members.join(' ')} has nothing to write to`);
|
|
210
|
+
}
|
|
211
|
+
const { configuration } = track.activeDisplay;
|
|
212
|
+
const configured = getSnapshot(configuration);
|
|
213
|
+
const type = getType(configuration);
|
|
214
|
+
const patch = memberPatch(members, (root, reached) => {
|
|
215
|
+
// a list at a default the snapshot strips, Manhattan's marks, still seeds
|
|
216
|
+
// the write, so `marks.0.mark=bar` edits the mark drawn
|
|
217
|
+
const member = configuration[root];
|
|
218
|
+
const keyed = keyedWritesAt(type, [root]);
|
|
219
|
+
return keyed
|
|
220
|
+
? keyedSeed(member, [
|
|
221
|
+
keyed.keyedBy,
|
|
222
|
+
...reached.filter(m => writesWholeAt(type, [root, m])),
|
|
223
|
+
])
|
|
224
|
+
: (configured[root] ??
|
|
225
|
+
(isStateTreeNode(member) && isArrayType(getType(member))
|
|
226
|
+
? getSnapshot(member)
|
|
227
|
+
: undefined));
|
|
228
|
+
});
|
|
229
|
+
view.showTrack(trackId, {}, patch);
|
|
230
|
+
return patch;
|
|
231
|
+
}
|