@jbrowse/core 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/ReExports/workerNamespaceNames.js

@@ -1,275 +0,0 @@
-import { DATA_GRID_NAMES } from './MuiDataGridReExports.js';
-import { MUI_COMPONENT_NAMES } from './muiComponentNames.js';
-// Own-key names of each namespace-shaped UI module the RPC worker stubs.
-// workerModules.test.ts pins them to modules.ts; agent-docs/reference/EAGER_BUNDLE.md
-export const REACT_DOM_NAMES = [
-    '__DOM_INTERNALS_DO_NOT_USE_OR_WARN_USERS_THEY_CANNOT_UPGRADE',
-    'createPortal',
-    'default',
-    'flushSync',
-    'preconnect',
-    'prefetchDNS',
-    'preinit',
-    'preinitModule',
-    'preload',
-    'preloadModule',
-    'requestFormReset',
-    'unstable_batchedUpdates',
-    'useFormState',
-    'useFormStatus',
-    'version',
-];
-export const REACT_DOM_CLIENT_NAMES = [
-    'createRoot',
-    'default',
-    'hydrateRoot',
-    'version',
-];
-export const MOBX_REACT_NAMES = [
-    'Observer',
-    '_observerFinalizationRegistry',
-    'clearTimers',
-    'enableStaticRendering',
-    'isUsingStaticRendering',
-    'observer',
-    'useLocalObservable',
-];
-export const MUI_UTILS_NAMES = [
-    'capitalize',
-    'createChainedFunction',
-    'createSvgIcon',
-    'debounce',
-    'deprecatedPropType',
-    'getActiveElement',
-    'isMuiElement',
-    'mergeSlotProps',
-    'ownerDocument',
-    'ownerWindow',
-    'requirePropFactory',
-    'setRef',
-    'unstable_ClassNameGenerator',
-    'unstable_memoTheme',
-    'unstable_useEnhancedEffect',
-    'unstable_useId',
-    'unsupportedProp',
-    'useControlled',
-    'useEventCallback',
-    'useForkRef',
-];
-export const MUI_STYLES_NAMES = [
-    'CssVarsProvider',
-    'Experimental_CssVarsProvider',
-    'StyledEngineProvider',
-    'THEME_ID',
-    'ThemeProvider',
-    'adaptV4Theme',
-    'alpha',
-    'createColorScheme',
-    'createStyles',
-    'createTheme',
-    'css',
-    'darken',
-    'decomposeColor',
-    'duration',
-    'easing',
-    'emphasize',
-    'enhanceHighContrast',
-    'experimental_sx',
-    'extendTheme',
-    'getContrastRatio',
-    'getInitColorSchemeScript',
-    'getLuminance',
-    'getOverlayAlpha',
-    'hexToRgb',
-    'hslToRgb',
-    'keyframes',
-    'makeStyles',
-    'private_createTypography',
-    'private_excludeVariablesFromRoot',
-    'recomposeColor',
-    'responsiveFontSizes',
-    'rgbToHex',
-    'shouldSkipGeneratingVar',
-    'styled',
-    'unstable_createBreakpoints',
-    'unstable_createMuiStrictModeTheme',
-    'unstable_getUnit',
-    'unstable_toUnitless',
-    'useColorScheme',
-    'useTheme',
-    'useThemeProps',
-    'withStyles',
-    'withTheme',
-];
-export const TSS_REACT_NAMES = ['cx', 'keyframes', 'makeStyles'];
-export const MATERIAL_UI_LAB_NAMES = [
-    'Alert',
-    'Autocomplete',
-    'ToggleButton',
-    'ToggleButtonGroup',
-];
-export const MUI_MATERIAL_NAMES = [
-    ...MUI_COMPONENT_NAMES,
-    'alpha',
-    'createTheme',
-    'useTheme',
-];
-export const MATERIAL_UI_CORE_NAMES = [
-    ...MUI_COMPONENT_NAMES,
-    'alpha',
-    'makeStyles',
-    'useTheme',
-];
-export const CORE_UI_NAMES = [
-    'ActionLink',
-    'AssemblySelector',
-    'BaseExportSvgDialog',
-    'BaseTooltip',
-    'CONTEXT_MENU_Z_INDEX',
-    'CascadingMenu',
-    'CascadingMenuButton',
-    'ConfirmDialog',
-    'ContextMenu',
-    'CopyToClipboardButton',
-    'Crosshairs',
-    'Dialog',
-    'EditableTypography',
-    'ErrorBanner',
-    'ErrorBar',
-    'ErrorMessage',
-    'ErrorOverlay',
-    'ExportSvgDialog',
-    'ExternalLink',
-    'FatalErrorDialog',
-    'FileDropZone',
-    'FileSelector',
-    'GpuFallbackButton',
-    'INLINE_MENU_ROW_WIDTH',
-    'InfoDialog',
-    'JexlFilterDialog',
-    'LAUNCH_LABEL',
-    'LEGEND_ROW_HEIGHT',
-    'LEGEND_SVG_GUTTER_WIDTH',
-    'LEGEND_SWATCH',
-    'LabeledCheckbox',
-    'LegendSwatchGlyph',
-    'LoadingEllipses',
-    'LoadingOverlay',
-    'LoadingProgress',
-    'LogoFull',
-    'Logomark',
-    'MAX_LEGEND_ITEMS',
-    'Menu',
-    'MonospaceTextField',
-    'NumberTextField',
-    'PluggableComponent',
-    'PluggableComponents',
-    'PluggableElements',
-    'PrerenderedCanvas',
-    'ProgressChip',
-    'RefNameAutocomplete',
-    'RefNameAutocompleteEndAdornment',
-    'ReplaceCurrentViewButton',
-    'ResetToDefaultButton',
-    'ResizeHandle',
-    'SanitizedHTML',
-    'ScrollChrome',
-    'ScrollEdgeShadow',
-    'SettingsChangesTable',
-    'ShareLinkField',
-    'SingleSlider',
-    'SliderTooltip',
-    'StatusProgressBar',
-    'SubmitDialog',
-    'SubmitForm',
-    'SvgColorLegend',
-    'TOOLTIP_Z_INDEX',
-    'TagTextField',
-    'VIEW_HEADER_HEIGHT',
-    'VerticalScrollbar',
-    'ViewLoadingScreen',
-    'addExtensionElement',
-    'adornmentReservePx',
-    'checkboxItem',
-    'colorFwdStrand',
-    'colorInterchrom',
-    'colorLongInsert',
-    'colorLongreadInv',
-    'colorNeutralRead',
-    'colorPairLL',
-    'colorPairLR',
-    'colorPairLRDark',
-    'colorPairRL',
-    'colorPairRR',
-    'colorRevStrand',
-    'colorScaleIsEmpty',
-    'colorShortInsert',
-    'colorSplitReadInversion',
-    'colorSupplementary',
-    'colorUnmappedMate',
-    'colorUnmappedMateDark',
-    'createJBrowseBaseTheme',
-    'createJBrowseTheme',
-    'createJBrowseThemeFromArgs',
-    'defaultThemes',
-    'getInputWidth',
-    'hoverBoxStyle',
-    'launchTargetsMenuItem',
-    'legendEntries',
-    'legendIsReadable',
-    'legendSpecOf',
-    'legendSwatches',
-    'makeSizeMenu',
-    'makeSizeSubMenu',
-    'matchesTrackSelector',
-    'measureLegendText',
-    'methylated5hmC',
-    'methylated5mC',
-    'nonEmptyLegendSections',
-    'pushIntoSubMenu',
-    'pushLaunchViewMenuItem',
-    'radioItems',
-    'replaceViewAction',
-    'resolveSubMenu',
-    'sliderScale',
-    'staysOpenOnClick',
-    'tagColorPalette',
-    'unmethylated5mC',
-    'useAssemblySelection',
-    'useCopyToClipboard',
-    'useExportSvgPreference',
-    'useMouseState',
-    'useMouseTracking',
-    'useRecentLocations',
-    'wrapComponent',
-];
-const BASE_FEATURE_DETAIL_NAMES = [
-    'Attributes',
-    'BaseAttributes',
-    'BaseCard',
-    'BaseCoreDetails',
-    'FeatureDetails',
-    'FeatureWash',
-];
-export const WORKER_NAMESPACE_NAMES = {
-    'react-dom': REACT_DOM_NAMES,
-    'react-dom/client': REACT_DOM_CLIENT_NAMES,
-    'mobx-react': MOBX_REACT_NAMES,
-    '@mui/material/utils': MUI_UTILS_NAMES,
-    '@material-ui/core/utils': MUI_UTILS_NAMES,
-    'tss-react': TSS_REACT_NAMES,
-    'tss-react/mui': TSS_REACT_NAMES,
-    '@mui/material': MUI_MATERIAL_NAMES,
-    '@material-ui/core': MATERIAL_UI_CORE_NAMES,
-    '@mui/material/styles': MUI_STYLES_NAMES,
-    '@material-ui/core/styles': MUI_STYLES_NAMES,
-    '@material-ui/lab': MATERIAL_UI_LAB_NAMES,
-    '@mui/x-data-grid': DATA_GRID_NAMES,
-    '@jbrowse/core/ui': CORE_UI_NAMES,
-    // @mui/icons-material is NOT re-exported, so a plugin that wants an icon
-    // bundles icons-material, which reads `createSvgIcon` off this module. The
-    // main thread serves it (modules.ts) and the worker has to as well, or the
-    // plugin throws at module scope building its icons.
-    '@mui/material/SvgIcon': ['createSvgIcon'],
-    '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': BASE_FEATURE_DETAIL_NAMES,
-};

package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts

@@ -1,51 +0,0 @@
-import type { HighlightType } from '../../util/highlights.ts';
-/**
- * #stateModel HighlightsMixin
- * #category view
- *
- * The `view.highlight` band state shared verbatim by the LinearGenomeView and
- * DotplotView: an array of translucent highlight regions plus the
- * `showHighlightChips` toggle for their interactive chips. Both views compose
- * this so the props and actions stay identical by construction rather than by
- * two hand-kept copies. Visibility across all views is the session-wide
- * `highlightsVisible` flag (on BaseSession), not a prop here.
- */
-export default function HighlightsMixin(): import("@jbrowse/mobx-state-tree").IModelType<{
-    /**
-     * #property
-     * translucent highlight bands, seeded from URL params or session JSON and
-     * added interactively via the rubber-band menu
-     */
-    highlight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
-    /**
-     * #property
-     * pins the interactive highlight chip (link icon + context menu) to every
-     * highlight band; off by default, where a band instead reveals its chip
-     * while the pointer is in it. This is what a screenshot needs, since
-     * nothing hovers in one
-     */
-    showHighlightChips: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, {
-    /**
-     * #action
-     */
-    addToHighlights(highlight: HighlightType): void;
-    /**
-     * #action
-     */
-    setHighlight(highlight?: HighlightType[]): void;
-    /**
-     * #action
-     */
-    removeHighlight(highlight: HighlightType): void;
-    /**
-     * #action
-     */
-    updateHighlight(old: HighlightType, updates: Partial<HighlightType>): void;
-    /**
-     * #action
-     */
-    setShowHighlightChips(arg: boolean): void;
-} & {
-    afterAttach(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/pluggableElementTypes/models/HighlightsMixin.js

@@ -1,78 +0,0 @@
-import { cast, types } from '@jbrowse/mobx-state-tree';
-import { revealHighlightsOnGrowth } from '../../util/highlights.js';
-import { getSession } from '../../util/index.js';
-/**
- * #stateModel HighlightsMixin
- * #category view
- *
- * The `view.highlight` band state shared verbatim by the LinearGenomeView and
- * DotplotView: an array of translucent highlight regions plus the
- * `showHighlightChips` toggle for their interactive chips. Both views compose
- * this so the props and actions stay identical by construction rather than by
- * two hand-kept copies. Visibility across all views is the session-wide
- * `highlightsVisible` flag (on BaseSession), not a prop here.
- */
-export default function HighlightsMixin() {
-    return types
-        .model({
-        /**
-         * #property
-         * translucent highlight bands, seeded from URL params or session JSON and
-         * added interactively via the rubber-band menu
-         */
-        highlight: types.stripDefault(types.array(types.frozen()), []),
-        /**
-         * #property
-         * pins the interactive highlight chip (link icon + context menu) to every
-         * highlight band; off by default, where a band instead reveals its chip
-         * while the pointer is in it. This is what a screenshot needs, since
-         * nothing hovers in one
-         */
-        showHighlightChips: types.stripDefault(types.boolean, false),
-    })
-        .actions(self => ({
-        /**
-         * #action
-         */
-        addToHighlights(highlight) {
-            self.highlight.push(highlight);
-        },
-        /**
-         * #action
-         */
-        setHighlight(highlight) {
-            self.highlight = cast(highlight);
-        },
-        /**
-         * #action
-         */
-        removeHighlight(highlight) {
-            self.highlight.remove(highlight);
-        },
-        /**
-         * #action
-         */
-        updateHighlight(old, updates) {
-            const idx = self.highlight.indexOf(old);
-            if (idx !== -1) {
-                self.highlight[idx] = { ...old, ...updates };
-                // reachable from the highlight grid, which lists entries even with
-                // the bands off, so recoloring there would otherwise do nothing
-                // visible. Not a growth, so revealHighlightsOnGrowth can't see it
-                getSession(self).revealHighlights();
-            }
-        },
-        /**
-         * #action
-         */
-        setShowHighlightChips(arg) {
-            self.showHighlightChips = arg;
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            // covers the rubber-band menu, dotplot drag and URL init alike
-            revealHighlightsOnGrowth(self, () => self.highlight.length);
-        },
-    }));
-}

package/esm/ui/highlightChipReveal.d.ts

@@ -1,32 +0,0 @@
-import type { MouseTracker } from './useMouseTracking.ts';
-export declare const OverlayPointerProvider: import("react").Provider<MouseTracker | undefined>;
-/**
- * The stripe a band occupies: an x span across a full-height band, a y span
- * across a full-width one. The other axis is the whole overlay, which is why it
- * isn't here.
- */
-export type HighlightStripe = {
-    left: number;
-    width: number;
-} | {
-    top: number;
-    height: number;
-};
-/**
- * Whether a band should be drawing its chip, and the `setOpen` that keeps it
- * drawn while its menu is up.
- *
- * A band reveals its chip while the pointer is in its stripe, so the highlight's
- * menu is reachable where the highlight is rather than only from the view menu,
- * and a view full of bands is not also a view full of link icons. `persistent`
- * is the `showHighlightChips` pin, which a screenshot needs because nothing
- * hovers in one.
- *
- * The menu is the reason this owns state at all: it is portalled out of the
- * band, so opening it moves the pointer off the stripe that revealed it, and
- * unmounting the chip under an open menu takes the menu's own anchor with it.
- */
-export declare function useHighlightChip(stripe: HighlightStripe | undefined, persistent: boolean): {
-    chipVisible: boolean;
-    setMenuOpen: import("react").Dispatch<import("react").SetStateAction<boolean>>;
-};

package/esm/ui/highlightChipReveal.js

@@ -1,39 +0,0 @@
-import { createContext, use, useState } from 'react';
-import { useMouseSelector } from './useMouseTracking.js';
-/**
- * The pointer over the surface a view's highlight bands are positioned in — the
- * LinearGenomeView's tracks container, the DotplotView's plot area. Published by
- * whichever of those bound the handlers.
- *
- * A context rather than a prop because a band is often drawn by another plugin
- * through an extension point (grid-bookmark's bookmark bands), and those carry
- * only their `{ model }` props bag — the band families are siblings on screen
- * and would otherwise reach the pointer two different ways.
- */
-const OverlayPointerContext = createContext(undefined);
-export const OverlayPointerProvider = OverlayPointerContext.Provider;
-function pointerInStripe(stripe, state) {
-    return 'left' in stripe
-        ? state.x >= stripe.left && state.x < stripe.left + stripe.width
-        : state.y >= stripe.top && state.y < stripe.top + stripe.height;
-}
-/**
- * Whether a band should be drawing its chip, and the `setOpen` that keeps it
- * drawn while its menu is up.
- *
- * A band reveals its chip while the pointer is in its stripe, so the highlight's
- * menu is reachable where the highlight is rather than only from the view menu,
- * and a view full of bands is not also a view full of link icons. `persistent`
- * is the `showHighlightChips` pin, which a screenshot needs because nothing
- * hovers in one.
- *
- * The menu is the reason this owns state at all: it is portalled out of the
- * band, so opening it moves the pointer off the stripe that revealed it, and
- * unmounting the chip under an open menu takes the menu's own anchor with it.
- */
-export function useHighlightChip(stripe, persistent) {
-    const tracker = use(OverlayPointerContext);
-    const [menuOpen, setMenuOpen] = useState(false);
-    const hovered = useMouseSelector(tracker, state => !!state && !!stripe && pointerInStripe(stripe, state));
-    return { chipVisible: persistent || hovered || menuOpen, setMenuOpen };
-}

package/esm/util/adapterConfigKey.d.ts

@@ -1,12 +0,0 @@
-/**
- * The adapter-config axis of a fetch key: the config a fetch was issued
- * against, as one string. Every fetch that refetches on an adapter edit folds
- * this in — the comparative displays, the prerequisite reads, the density
- * tier, the global family's signature — so the axis is spelled once and cannot
- * drift between them.
- *
- * Not `adapterConfigCacheKey`: that one short-circuits on `adapterId`, which is
- * right for sharing one adapter instance and wrong for freshness, where an
- * edit to a config carrying an id still has to read as a different fetch.
- */
-export declare function adapterConfigKey(adapterConfig: Record<string, unknown>): string;

package/esm/util/adapterConfigKey.js

@@ -1,14 +0,0 @@
-/**
- * The adapter-config axis of a fetch key: the config a fetch was issued
- * against, as one string. Every fetch that refetches on an adapter edit folds
- * this in — the comparative displays, the prerequisite reads, the density
- * tier, the global family's signature — so the axis is spelled once and cannot
- * drift between them.
- *
- * Not `adapterConfigCacheKey`: that one short-circuits on `adapterId`, which is
- * right for sharing one adapter instance and wrong for freshness, where an
- * edit to a config carrying an id still has to read as a different fetch.
- */
-export function adapterConfigKey(adapterConfig) {
-    return JSON.stringify(adapterConfig);
-}