@jbrowse/plugin-circular-view 1.7.11 → 2.1.0

package/esm/BaseChordDisplay/models/BaseChordDisplayModel.d.ts

@@ -0,0 +1,99 @@
+import RendererType from '@jbrowse/core/pluggableElementTypes/renderers/RendererType';
+import { AnyReactComponentType } from '@jbrowse/core/util';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import React from 'react';
+export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    bezierRadiusRatio: import("mobx-state-tree").IType<number | undefined, number, number>;
+    assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: any;
+    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    filled: boolean;
+    reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    data: undefined;
+    message: string;
+    renderingComponent: AnyReactComponentType | undefined;
+    refNameMap: Record<string, string> | undefined;
+} & {
+    onChordClick(feature: Feature): void;
+} & {
+    readonly blockDefinitions: any;
+    renderProps(): any;
+    /**
+     * the pluggable element type object for this diplay's
+     * renderer
+     */
+    readonly rendererType: any;
+    isCompatibleWithRenderer(renderer: RendererType): boolean;
+    /**
+     * returns a string feature ID if the globally-selected object
+     * is probably a feature
+     */
+    readonly selectedFeatureId: string | undefined;
+} & {
+    renderStarted(): void;
+    renderSuccess({ message, data, reactElement, renderingComponent, }: {
+        message: string;
+        data: any;
+        reactElement: React.ReactElement;
+        renderingComponent: AnyReactComponentType;
+    }): void;
+    renderError(error: unknown): void;
+    setRefNameMap(refNameMap: Record<string, string>): void;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/BaseChordDisplay/models/BaseChordDisplayModel.js

@@ -0,0 +1,181 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
+import CircularChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
+import { getContainingView, getSession, makeAbortableReaction, } from '@jbrowse/core/util';
+import { isFeature } from '@jbrowse/core/util/simpleFeature';
+import { getParentRenderProps, getRpcSessionId, getTrackAssemblyNames, } from '@jbrowse/core/util/tracks';
+import { getParent, isAlive, types, getEnv } from 'mobx-state-tree';
+import renderReactionFactory from './renderReaction';
+export const BaseChordDisplayModel = types
+    .compose('BaseChordDisplay', BaseDisplay, types.model({
+    bezierRadiusRatio: 0.1,
+    assemblyName: types.maybe(types.string),
+}))
+    .volatile(() => {
+    return {
+        // NOTE: all this volatile stuff has to be filled in at once
+        // so that it stays consistent
+        filled: false,
+        reactElement: undefined,
+        data: undefined,
+        message: '',
+        renderingComponent: undefined,
+        refNameMap: undefined,
+    };
+})
+    .actions(self => {
+    const { pluginManager } = getEnv(self);
+    const track = self;
+    return {
+        onChordClick(feature) {
+            getConf(self, 'onChordClick', { feature, track, pluginManager });
+        },
+    };
+})
+    .views(self => ({
+    get blockDefinitions() {
+        const origSlices = getContainingView(self)
+            .staticSlices;
+        if (!self.refNameMap) {
+            return origSlices;
+        }
+        const slices = JSON.parse(JSON.stringify(origSlices));
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        slices.forEach((slice) => {
+            const regions = slice.region.elided
+                ? slice.region.regions
+                : [slice.region];
+            regions.forEach((region) => {
+                var _a;
+                const renamed = (_a = self.refNameMap) === null || _a === void 0 ? void 0 : _a[region.refName];
+                if (renamed && region.refName !== renamed) {
+                    region.refName = renamed;
+                }
+            });
+        });
+        return slices;
+    },
+    renderProps() {
+        const view = getContainingView(self);
+        return {
+            ...getParentRenderProps(self),
+            rpcDriverName: self.rpcDriverName,
+            displayModel: self,
+            bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+            radius: view.radiusPx,
+            blockDefinitions: this.blockDefinitions,
+            onChordClick: self.onChordClick,
+        };
+    },
+    /**
+     * the pluggable element type object for this diplay's
+     * renderer
+     */
+    get rendererType() {
+        const display = self;
+        const { pluginManager } = getEnv(self);
+        const ThisRendererType = pluginManager.getRendererType(self.rendererTypeName);
+        if (!ThisRendererType) {
+            throw new Error(`renderer "${display.rendererTypeName}" not found`);
+        }
+        if (!ThisRendererType.ReactComponent) {
+            throw new Error(`renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`);
+        }
+        return ThisRendererType;
+    },
+    isCompatibleWithRenderer(renderer) {
+        return !!(renderer instanceof CircularChordRendererType);
+    },
+    /**
+     * returns a string feature ID if the globally-selected object
+     * is probably a feature
+     */
+    get selectedFeatureId() {
+        if (!isAlive(self)) {
+            return undefined;
+        }
+        const session = getSession(self);
+        if (!session) {
+            return undefined;
+        }
+        const { selection } = session;
+        // does it quack like a feature?
+        if (isFeature(selection)) {
+            return selection.id();
+        }
+        return undefined;
+    },
+}))
+    .actions(self => ({
+    renderStarted() {
+        self.filled = false;
+        self.message = '';
+        self.reactElement = undefined;
+        self.data = undefined;
+        self.error = undefined;
+        self.renderingComponent = undefined;
+    },
+    renderSuccess({ message, data, reactElement, renderingComponent, }) {
+        if (message) {
+            self.filled = false;
+            self.message = message;
+            self.reactElement = undefined;
+            self.data = undefined;
+            self.error = undefined;
+            self.renderingComponent = undefined;
+        }
+        else {
+            self.filled = true;
+            self.message = '';
+            self.reactElement = reactElement;
+            self.data = data;
+            self.error = undefined;
+            self.renderingComponent = renderingComponent;
+        }
+    },
+    renderError(error) {
+        console.error(error);
+        // the rendering failed for some reason
+        self.filled = false;
+        self.message = '';
+        self.reactElement = undefined;
+        self.data = undefined;
+        self.error = error;
+        self.renderingComponent = undefined;
+    },
+    setRefNameMap(refNameMap) {
+        self.refNameMap = refNameMap;
+    },
+}))
+    .actions(self => {
+    const { pluginManager } = getEnv(self);
+    const { renderReactionData, renderReactionEffect } = pluginManager.jbrequire(renderReactionFactory);
+    return {
+        afterAttach() {
+            makeAbortableReaction(self, renderReactionData, renderReactionEffect, {
+                name: `${self.type} ${self.id} rendering`,
+                // delay: self.renderDelay || 300,
+                fireImmediately: true,
+            }, self.renderStarted, self.renderSuccess, self.renderError);
+            makeAbortableReaction(self, () => ({
+                assemblyNames: getTrackAssemblyNames(self.parentTrack),
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                adapter: getConf(getParent(self, 2), 'adapter'),
+                assemblyManager: getSession(self).assemblyManager,
+            }), 
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            async ({ assemblyNames, adapter, assemblyManager }, signal) => {
+                return assemblyManager.getRefNameMapForAdapter(adapter, assemblyNames[0], { signal, sessionId: getRpcSessionId(self) });
+            }, {
+                name: `${self.type} ${self.id} getting refNames`,
+                fireImmediately: true,
+            }, () => { }, refNameMap => {
+                self.setRefNameMap(refNameMap);
+            }, error => {
+                console.error(error);
+                self.setError(error);
+            });
+        },
+    };
+});
+//# sourceMappingURL=BaseChordDisplayModel.js.map

package/esm/BaseChordDisplay/models/BaseChordDisplayModel.js.map

@@ -0,0 +1 @@
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package/esm/BaseChordDisplay/models/baseChordDisplayConfig.d.ts

@@ -0,0 +1,2 @@
+declare const baseChordDisplayConfig: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export { baseChordDisplayConfig };

package/esm/BaseChordDisplay/models/baseChordDisplayConfig.js

@@ -0,0 +1,11 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+const baseChordDisplayConfig = ConfigurationSchema('BaseChordDisplay', {
+    onChordClick: {
+        type: 'boolean',
+        description: 'callback that should be run when a chord in the track is clicked',
+        defaultValue: false,
+        contextVariable: ['feature', 'track', 'pluginManager'],
+    },
+}, { explicitIdentifier: 'displayId' });
+export { baseChordDisplayConfig };
+//# sourceMappingURL=baseChordDisplayConfig.js.map

package/esm/BaseChordDisplay/models/baseChordDisplayConfig.js.map

@@ -0,0 +1 @@
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package/esm/BaseChordDisplay/models/renderReaction.d.ts

@@ -0,0 +1,30 @@
+declare function _default({ jbrequire }: {
+    jbrequire: any;
+}): {
+    renderReactionData: (self: any) => {
+        rendererType: any;
+        rpcManager: any;
+        renderProps: any;
+        renderArgs: {
+            assemblyName: any;
+            adapterConfig: any;
+            rendererType: any;
+            regions: any;
+            blockDefinitions: any;
+            sessionId: any;
+            timeout: number;
+        };
+    };
+    renderReactionEffect: (props: any, signal: any, self: any) => Promise<{
+        message: any;
+        html?: undefined;
+        data?: undefined;
+        renderingComponent?: undefined;
+    } | {
+        html: any;
+        data: any;
+        renderingComponent: any;
+        message?: undefined;
+    }>;
+};
+export default _default;

package/esm/BaseChordDisplay/models/renderReaction.js

@@ -0,0 +1,52 @@
+export default ({ jbrequire }) => {
+    const { getRpcSessionId } = jbrequire('@jbrowse/core/util/tracks');
+    const { getContainingView } = jbrequire('@jbrowse/core/util');
+    const { getSession } = jbrequire('@jbrowse/core/util');
+    function renderReactionData(self) {
+        var _a;
+        const view = getContainingView(self);
+        const { rendererType } = self;
+        const { rpcManager } = getSession(view);
+        return {
+            rendererType,
+            rpcManager,
+            renderProps: self.renderProps(),
+            renderArgs: {
+                assemblyName: (_a = view.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.assemblyName,
+                adapterConfig: JSON.parse(JSON.stringify(self.adapterConfig)),
+                rendererType: rendererType.name,
+                regions: JSON.parse(JSON.stringify(view.displayedRegions)),
+                blockDefinitions: self.blockDefinitions,
+                sessionId: getRpcSessionId(self),
+                timeout: 1000000,
+            },
+        };
+    }
+    async function renderReactionEffect(props, signal, self) {
+        if (!props) {
+            throw new Error('cannot render with no props');
+        }
+        const { rendererType, rpcManager, cannotBeRenderedReason, renderArgs, renderProps, } = props;
+        if (cannotBeRenderedReason) {
+            return { message: cannotBeRenderedReason };
+        }
+        // don't try to render 0 or NaN radius or no regions
+        if (!props.renderProps.radius ||
+            !props.renderArgs.regions ||
+            !props.renderArgs.regions.length) {
+            return { message: 'Skipping render' };
+        }
+        // check renderertype compatibility
+        if (!self.isCompatibleWithRenderer(rendererType)) {
+            throw new Error(`renderer ${rendererType.name} is not compatible with this display type`);
+        }
+        const { html, ...data } = await rendererType.renderInClient(rpcManager, {
+            ...renderArgs,
+            ...renderProps,
+            signal,
+        });
+        return { html, data, renderingComponent: rendererType.ReactComponent };
+    }
+    return { renderReactionData, renderReactionEffect };
+};
+//# sourceMappingURL=renderReaction.js.map

package/esm/BaseChordDisplay/models/renderReaction.js.map

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package/esm/CircularView/components/CircularView.d.ts

@@ -0,0 +1,4 @@
+export default CircularView;
+declare function CircularView({ model }: {
+    model: any;
+}): JSX.Element;

package/esm/CircularView/components/CircularView.js

@@ -0,0 +1,121 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { ResizeHandle, ErrorMessage } from '@jbrowse/core/ui';
+import { assembleLocString } from '@jbrowse/core/util';
+import { IconButton } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { grey } from '@mui/material/colors';
+// icons
+import ZoomOutIcon from '@mui/icons-material/ZoomOut';
+import ZoomInIcon from '@mui/icons-material/ZoomIn';
+import RotateLeftIcon from '@mui/icons-material/RotateLeft';
+import RotateRightIcon from '@mui/icons-material/RotateRight';
+import LockOpenIcon from '@mui/icons-material/LockOpen';
+import LockIcon from '@mui/icons-material/Lock';
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+// locals
+import Ruler from './Ruler';
+import ImportForm from './ImportForm';
+const dragHandleHeight = 3;
+const useStyles = makeStyles()(theme => ({
+    root: {
+        position: 'relative',
+        marginBottom: theme.spacing(1),
+        overflow: 'hidden',
+        background: 'white',
+    },
+    scroller: {
+        overflow: 'auto',
+    },
+    sliceRoot: {
+        background: 'none',
+        // background: theme.palette.background.paper,
+        boxSizing: 'content-box',
+        display: 'block',
+    },
+    iconButton: {
+        padding: '4px',
+        margin: '0 2px 0 2px',
+    },
+    controls: {
+        overflow: 'hidden',
+        whiteSpace: 'nowrap',
+        position: 'absolute',
+        background: grey[200],
+        boxSizing: 'border-box',
+        borderRight: '1px solid #a2a2a2',
+        borderBottom: '1px solid #a2a2a2',
+        left: 0,
+        top: 0,
+    },
+    importFormContainer: {
+        marginBottom: theme.spacing(4),
+    },
+}));
+const Slices = observer(({ model }) => {
+    return (React.createElement(React.Fragment, null,
+        model.staticSlices.map(slice => (React.createElement(Ruler, { key: assembleLocString(slice.region.elided ? slice.region.regions[0] : slice.region), model: model, slice: slice }))),
+        model.tracks.map(track => {
+            const display = track.displays[0];
+            return (React.createElement(display.RenderingComponent, { key: display.id, display: display, view: model }));
+        })));
+});
+const Controls = observer(({ model, showingFigure }) => {
+    const { classes } = useStyles();
+    return (React.createElement("div", { className: classes.controls },
+        React.createElement(IconButton, { onClick: model.zoomOutButton, className: classes.iconButton, title: model.lockedFitToWindow ? 'unlock to zoom out' : 'zoom out', disabled: !showingFigure || model.atMaxBpPerPx || model.lockedFitToWindow, color: "secondary" },
+            React.createElement(ZoomOutIcon, null)),
+        React.createElement(IconButton, { onClick: model.zoomInButton, className: classes.iconButton, title: "zoom in", disabled: !showingFigure || model.atMinBpPerPx, color: "secondary" },
+            React.createElement(ZoomInIcon, null)),
+        React.createElement(IconButton, { onClick: model.rotateCounterClockwiseButton, className: classes.iconButton, title: "rotate counter-clockwise", disabled: !showingFigure, color: "secondary" },
+            React.createElement(RotateLeftIcon, null)),
+        React.createElement(IconButton, { onClick: model.rotateClockwiseButton, className: classes.iconButton, title: "rotate clockwise", disabled: !showingFigure, color: "secondary" },
+            React.createElement(RotateRightIcon, null)),
+        React.createElement(IconButton, { onClick: model.toggleFitToWindowLock, className: classes.iconButton, title: model.lockedFitToWindow
+                ? 'locked model to window size'
+                : 'unlocked model to zoom further', disabled: model.tooSmallToLock, color: "secondary" }, model.lockedFitToWindow ? React.createElement(LockIcon, null) : React.createElement(LockOpenIcon, null)),
+        model.hideTrackSelectorButton ? null : (React.createElement(IconButton, { onClick: model.activateTrackSelector, title: "Open track selector", "data-testid": "circular_track_select", color: "secondary" },
+            React.createElement(TrackSelectorIcon, null)))));
+});
+const CircularView = observer(({ model }) => {
+    const { classes } = useStyles();
+    const initialized = !!model.displayedRegions.length && model.figureWidth && model.figureHeight;
+    const showImportForm = !initialized && !model.disableImportForm;
+    const showFigure = initialized && !showImportForm;
+    return (React.createElement("div", { className: classes.root, style: {
+            width: model.width,
+            height: model.height,
+        }, "data-testid": model.id }, model.error ? (React.createElement(ErrorMessage, { error: model.error })) : (React.createElement(React.Fragment, null,
+        showImportForm ? React.createElement(ImportForm, { model: model }) : null,
+        React.createElement(React.Fragment, null,
+            !showFigure ? null : (React.createElement("div", { className: classes.scroller, style: {
+                    width: model.width,
+                    height: model.height,
+                } },
+                React.createElement("div", { className: classes.rotator, style: {
+                        transform: [`rotate(${model.offsetRadians}rad)`].join(' '),
+                        transition: 'transform 0.5s',
+                        transformOrigin: model.centerXY
+                            .map(x => `${x}px`)
+                            .join(' '),
+                    } },
+                    React.createElement("svg", { style: {
+                            position: 'absolute',
+                            left: 0,
+                            top: 0,
+                        }, className: classes.sliceRoot, width: `${model.figureWidth}px`, height: `${model.figureHeight}px`, version: "1.1" },
+                        React.createElement("g", { transform: `translate(${model.centerXY})` },
+                            React.createElement(Slices, { model: model })))))),
+            React.createElement(Controls, { model: model, showingFigure: showFigure }),
+            model.hideVerticalResizeHandle ? null : (React.createElement(ResizeHandle, { onDrag: model.resizeHeight, style: {
+                    height: dragHandleHeight,
+                    position: 'absolute',
+                    bottom: 0,
+                    left: 0,
+                    background: '#ccc',
+                    boxSizing: 'border-box',
+                    borderTop: '1px solid #fafafa',
+                } })))))));
+});
+export default CircularView;
+//# sourceMappingURL=CircularView.js.map

package/esm/CircularView/components/CircularView.js.map

@@ -0,0 +1 @@
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package/esm/CircularView/components/ImportForm.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+declare const ImportForm: ({ model }: {
+    model: any;
+}) => JSX.Element;
+export default ImportForm;

package/esm/CircularView/components/ImportForm.js

@@ -0,0 +1,40 @@
+import React, { useState } from 'react';
+import { Button, Container, Grid } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
+const useStyles = makeStyles()(theme => ({
+    importFormContainer: {
+        marginBottom: theme.spacing(4),
+    },
+}));
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+const ImportForm = observer(({ model }) => {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { error: modelError } = model;
+    const { assemblyNames, assemblyManager } = session;
+    const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0]);
+    const [error, setError] = useState(modelError);
+    const assembly = assemblyManager.get(selectedAsm);
+    const assemblyError = assemblyNames.length
+        ? assembly === null || assembly === void 0 ? void 0 : assembly.error
+        : 'No configured assemblies';
+    const regions = (assembly === null || assembly === void 0 ? void 0 : assembly.regions) || [];
+    const err = assemblyError || error;
+    return (React.createElement(Container, { className: classes.importFormContainer },
+        err ? (React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
+            React.createElement(Grid, { item: true },
+                React.createElement(ErrorMessage, { error: err })))) : null,
+        React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
+            React.createElement(Grid, { item: true },
+                React.createElement(AssemblySelector, { onChange: val => {
+                        setError(undefined);
+                        setSelectedAsm(val);
+                    }, session: session, selected: selectedAsm })),
+            React.createElement(Grid, { item: true },
+                React.createElement(Button, { disabled: !(regions === null || regions === void 0 ? void 0 : regions.length), onClick: () => model.setDisplayedRegions(regions), variant: "contained", color: "primary" }, regions.length ? 'Open' : 'Loading…')))));
+});
+export default ImportForm;
+//# sourceMappingURL=ImportForm.js.map

package/esm/CircularView/components/ImportForm.js.map

@@ -0,0 +1 @@
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package/esm/CircularView/components/Ruler.d.ts

@@ -0,0 +1,5 @@
+export default CircularRuler;
+declare function CircularRuler({ model, slice }: {
+    model: any;
+    slice: any;
+}): JSX.Element;