@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.0

package/dist/LinearSyntenyDisplay/model.d.ts

@@ -1,291 +0,0 @@
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-import type { Instance } from 'mobx-state-tree';
-interface Pos {
-    offsetPx: number;
-}
-export interface FeatPos {
-    p11: Pos;
-    p12: Pos;
-    p21: Pos;
-    p22: Pos;
-    f: Feature;
-    cigar: string[];
-}
-declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): 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>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
-    configuration: AnyConfigurationSchemaType;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearSyntenyDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    colorBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-}, {
-    rendererTypeName: string;
-    error: unknown;
-    message: string | undefined;
-} & {
-    readonly RenderingComponent: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & 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;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: () => void;
-        blockState?: Record<string, any>;
-    }>;
-    readonly DisplayBlurb: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & 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;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
-    readonly adapterConfig: any;
-    readonly parentTrack: any;
-    renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): null;
-} & {
-    setMessage(arg?: string): void;
-    setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
-    reload(): void;
-} & {
-    renderInProgress: string | undefined;
-    features: Feature[] | undefined;
-    message: string | undefined;
-    loadingStatus: string | undefined;
-} & {
-    readonly level: number;
-    readonly height: number;
-    renderProps(): {
-        rpcDriverName: string | undefined;
-        displayModel: {
-            id: string;
-            type: "LinearComparativeDisplay";
-            rpcDriverName: string | undefined;
-            configuration: {
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                        [x: string]: any;
-                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-                } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & {
-            readonly RenderingComponent: React.FC<{
-                model: {
-                    id: string;
-                    type: string;
-                    rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string;
-                    error: unknown;
-                    message: string | undefined;
-                } & 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;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: () => void;
-                blockState?: Record<string, any>;
-            }>;
-            readonly DisplayBlurb: React.FC<{
-                model: {
-                    id: string;
-                    type: string;
-                    rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string;
-                    error: unknown;
-                    message: string | undefined;
-                } & 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;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-            }> | null;
-            readonly adapterConfig: any;
-            readonly parentTrack: any;
-            renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: undefined | React.FC<any>;
-            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-            regionCannotBeRendered(): null;
-        } & {
-            setMessage(arg?: string): void;
-            setError(error?: unknown): void;
-            setRpcDriverName(rpcDriverName: string): void;
-            reload(): void;
-        } & {
-            renderInProgress: string | undefined;
-            features: Feature[] | undefined;
-            message: string | undefined;
-            loadingStatus: string | undefined;
-        } & 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>>;
-        } & {
-            type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
-            configuration: AnyConfigurationSchemaType;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & {
-            readonly RenderingComponent: React.FC<{
-                model: {
-                    id: string;
-                    type: string;
-                    rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string;
-                    error: unknown;
-                    message: string | undefined;
-                } & 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;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: () => void;
-                blockState?: Record<string, any>;
-            }>;
-            readonly DisplayBlurb: React.FC<{
-                model: {
-                    id: string;
-                    type: string;
-                    rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    rendererTypeName: string;
-                    error: unknown;
-                    message: string | undefined;
-                } & 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;
-                    message: string | undefined;
-                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-            }> | null;
-            readonly adapterConfig: any;
-            readonly parentTrack: any;
-            renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: undefined | React.FC<any>;
-            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-            regionCannotBeRendered(): null;
-        } & {
-            setMessage(arg?: string): void;
-            setError(error?: unknown): void;
-            setRpcDriverName(rpcDriverName: string): void;
-            reload(): void;
-        } & {
-            renderInProgress: string | undefined;
-            features: Feature[] | undefined;
-            message: string | undefined;
-            loadingStatus: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        highResolutionScaling: number;
-    };
-} & {
-    setLoading(newStopToken: string): void;
-    setMessage(messageText: string): void;
-    setLoadingStatus(messageText: string): void;
-    setRendered(args?: {
-        features: Feature[];
-    }): void;
-    setError(error: unknown): void;
-} & {
-    afterAttach(): void;
-} & {
-    mainCanvas: HTMLCanvasElement | null;
-    clickMapCanvas: HTMLCanvasElement | null;
-    cigarClickMapCanvas: HTMLCanvasElement | null;
-    mouseoverCanvas: HTMLCanvasElement | null;
-    featPositions: FeatPos[];
-    mouseoverId: string | undefined;
-    clickId: string | undefined;
-    cigarMouseoverId: number;
-    alpha: number;
-    minAlignmentLength: number;
-} & {
-    setFeatPositions(arg: FeatPos[]): void;
-    setMainCanvasRef(ref: HTMLCanvasElement | null): void;
-    setClickMapCanvasRef(ref: HTMLCanvasElement | null): void;
-    setCigarClickMapCanvasRef(ref: HTMLCanvasElement | null): void;
-    setMouseoverCanvasRef(ref: HTMLCanvasElement | null): void;
-    setMouseoverId(arg?: string): void;
-    setCigarMouseoverId(arg: number): void;
-    setClickId(arg?: string): void;
-    setAlpha(value: number): void;
-    setMinAlignmentLength(value: number): void;
-    setColorBy(value: string): void;
-} & {
-    readonly adapterConfig: any;
-    readonly trackIds: string[];
-    readonly numFeats: number;
-    readonly ready: boolean;
-    readonly featMap: {
-        [k: string]: FeatPos;
-    };
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type LinearSyntenyDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export type LinearSyntenyDisplayModel = Instance<LinearSyntenyDisplayStateModel>;
-export default stateModelFactory;

package/dist/LinearSyntenyDisplay/model.js

@@ -1,133 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const stateModelFactory_1 = __importDefault(require("../LinearComparativeDisplay/stateModelFactory"));
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearSyntenyDisplay', (0, stateModelFactory_1.default)(configSchema), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearSyntenyDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        colorBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, 'default'),
-    }))
-        .volatile(() => ({
-        mainCanvas: null,
-        clickMapCanvas: null,
-        cigarClickMapCanvas: null,
-        mouseoverCanvas: null,
-        featPositions: [],
-        mouseoverId: undefined,
-        clickId: undefined,
-        cigarMouseoverId: -1,
-        alpha: 0.2,
-        minAlignmentLength: 0,
-    }))
-        .actions(self => ({
-        setFeatPositions(arg) {
-            self.featPositions = arg;
-        },
-        setMainCanvasRef(ref) {
-            self.mainCanvas = ref;
-        },
-        setClickMapCanvasRef(ref) {
-            self.clickMapCanvas = ref;
-        },
-        setCigarClickMapCanvasRef(ref) {
-            self.cigarClickMapCanvas = ref;
-        },
-        setMouseoverCanvasRef(ref) {
-            self.mouseoverCanvas = ref;
-        },
-        setMouseoverId(arg) {
-            self.mouseoverId = arg;
-        },
-        setCigarMouseoverId(arg) {
-            self.cigarMouseoverId = arg;
-        },
-        setClickId(arg) {
-            self.clickId = arg;
-        },
-        setAlpha(value) {
-            self.alpha = value;
-        },
-        setMinAlignmentLength(value) {
-            self.minAlignmentLength = value;
-        },
-        setColorBy(value) {
-            self.colorBy = value;
-        },
-    }))
-        .views(self => ({
-        get adapterConfig() {
-            return {
-                name: self.parentTrack.configuration.adapter.type,
-                assemblyNames: (0, configuration_1.getConf)(self, 'assemblyNames'),
-                ...(0, configuration_1.getConf)(self.parentTrack, 'adapter'),
-            };
-        },
-        get trackIds() {
-            return (0, configuration_1.getConf)(self, 'trackIds');
-        },
-        get numFeats() {
-            return self.featPositions.length;
-        },
-        get ready() {
-            return this.numFeats > 0;
-        },
-        get featMap() {
-            return Object.fromEntries(self.featPositions.map(f => [f.f.id(), f]));
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            ;
-            (async () => {
-                try {
-                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('./afterAttach')));
-                    doAfterAttach(self);
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            })();
-        },
-    }));
-}
-exports.default = stateModelFactory;

package/dist/LinearSyntenyView/components/DiagonalizationProgressDialog.d.ts

@@ -1,6 +0,0 @@
-import type { LinearSyntenyViewModel } from '../model';
-declare const DiagonalizationProgressDialog: ({ handleClose, model, }: {
-    handleClose: () => void;
-    model: LinearSyntenyViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default DiagonalizationProgressDialog;

package/dist/LinearSyntenyView/components/DiagonalizationProgressDialog.js

@@ -1,87 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mobx_1 = require("mobx");
-const mobx_react_1 = require("mobx-react");
-const diagonalize_1 = require("../util/diagonalize");
-const DiagonalizationProgressDialog = (0, mobx_react_1.observer)(function ({ handleClose, model, }) {
-    const [progress, setProgress] = (0, react_1.useState)(0);
-    const [message, setMessage] = (0, react_1.useState)('Initializing...');
-    const [error, setError] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        const runDiagonalization = async () => {
-            const session = (0, util_1.getSession)(model);
-            try {
-                if (model.views.length !== 2) {
-                    setError('Diagonalization requires exactly 2 views');
-                    setProgress(100);
-                    session.notify('Diagonalization requires exactly 2 views', 'warning');
-                    return;
-                }
-                const queryView = model.views[1];
-                setProgress(5);
-                setMessage('Collecting alignment data...');
-                const alignments = [];
-                for (const level of model.levels) {
-                    for (const track of level.tracks) {
-                        for (const display of track.displays) {
-                            const { featPositions } = display;
-                            for (const { f } of featPositions) {
-                                const mate = f.get('mate');
-                                alignments.push({
-                                    queryRefName: f.get('refName'),
-                                    refRefName: mate.refName,
-                                    queryStart: f.get('start'),
-                                    queryEnd: f.get('end'),
-                                    refStart: mate.start,
-                                    refEnd: mate.end,
-                                    strand: f.get('strand') || 1,
-                                });
-                            }
-                        }
-                    }
-                }
-                if (alignments.length === 0) {
-                    setError('No alignments found');
-                    setProgress(100);
-                    session.notify('No alignments found to diagonalize', 'warning');
-                    return;
-                }
-                const result = await (0, diagonalize_1.diagonalizeRegions)(alignments, queryView.displayedRegions, async (prog, msg) => {
-                    setProgress(prog);
-                    setMessage(msg);
-                });
-                if (result.newRegions.length > 0) {
-                    setProgress(95);
-                    setMessage('Applying new layout...');
-                    (0, mobx_1.transaction)(() => {
-                        queryView.setDisplayedRegions(result.newRegions);
-                    });
-                    setProgress(100);
-                    setMessage('Diagonalization complete');
-                    setTimeout(() => {
-                        handleClose();
-                    }, 1500);
-                }
-                else {
-                    setError('No regions to reorder');
-                    setProgress(100);
-                    session.notify('No query regions found to reorder', 'warning');
-                }
-            }
-            catch (err) {
-                console.error('Diagonalization error:', err);
-                setError(`Error: ${err}`);
-                setProgress(100);
-                session.notify(`Diagonalization failed: ${err}`, 'error');
-            }
-        };
-        runDiagonalization();
-    }, [model, handleClose]);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Diagonalizing", onClose: handleClose, children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { style: { minWidth: 400 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body1", gutterBottom: true, color: error ? 'error' : 'inherit', children: error || message }), (0, jsx_runtime_1.jsx)(material_1.LinearProgress, { variant: "determinate", value: progress, style: { marginTop: 16 }, color: error ? 'error' : 'primary' }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { variant: "caption", color: "textSecondary", style: { marginTop: 8, display: 'block' }, children: [Math.round(progress), "% complete"] })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: handleClose, color: "primary", disabled: progress < 100, children: progress < 100 ? 'Processing...' : 'Done' }) })] }));
-});
-exports.default = DiagonalizationProgressDialog;

package/dist/LinearSyntenyView/components/ExportSvgDialog.d.ts

@@ -1,7 +0,0 @@
-import type { ExportSvgOptions } from '../types';
-export default function ExportSvgDialog({ model, handleClose, }: {
-    model: {
-        exportSvg(opts: ExportSvgOptions): Promise<void>;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -1,58 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ExportSvgDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const TextField2_1 = __importDefault(require("./TextField2"));
-function LoadingMessage() {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }), (0, jsx_runtime_1.jsx)(material_1.Typography, { display: "inline", children: "Creating SVG" })] }));
-}
-function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
-}
-function ExportSvgDialog({ model, handleClose, }) {
-    const session = (0, util_1.getSession)(model);
-    const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
-    const [rasterizeLayers, setRasterizeLayers] = (0, react_1.useState)(offscreenCanvas);
-    const [loading, setLoading] = (0, react_1.useState)(false);
-    const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
-    const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
-    const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
-    const [error, setError] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(LoadingMessage, {})) : null, (0, jsx_runtime_1.jsx)(TextField2_1.default, { helperText: "filename", value: filename, onChange: event => {
-                            setFilename(event.target.value);
-                        } }), (0, jsx_runtime_1.jsxs)(TextField2_1.default, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => {
-                            setTrackLabels(event.target.value);
-                        }, children: [(0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "offset", children: "Offset" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "overlay", children: "Overlay" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "left", children: "Left" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "none", children: "None" })] }), (0, jsx_runtime_1.jsx)("br", {}), session.allThemes ? ((0, jsx_runtime_1.jsx)(TextField2_1.default, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
-                            setThemeName(event.target.value);
-                        }, children: Object.entries(session.allThemes()).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, offscreenCanvas ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
-                                setRasterizeLayers(val => !val);
-                            } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : ((0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Note: rasterizing layers not yet supported in this browser, so SVG size may be large" }))] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
-                            setLoading(true);
-                            setError(undefined);
-                            try {
-                                await model.exportSvg({
-                                    rasterizeLayers,
-                                    filename,
-                                    themeName,
-                                    trackLabels,
-                                });
-                                handleClose();
-                            }
-                            catch (e) {
-                                console.error(e);
-                                setError(e);
-                            }
-                            finally {
-                                setLoading(false);
-                            }
-                        }, children: "Submit" })] })] }));
-}

package/dist/LinearSyntenyView/components/Icons.d.ts

@@ -1,3 +0,0 @@
-import type { SvgIconProps } from '@mui/material';
-export declare function Curves(props: SvgIconProps): import("react/jsx-runtime").JSX.Element;
-export declare function StraightLines(props: SvgIconProps): import("react/jsx-runtime").JSX.Element;

package/dist/LinearSyntenyView/components/Icons.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Curves = Curves;
-exports.StraightLines = StraightLines;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const material_1 = require("@mui/material");
-function Curves(props) {
-    return ((0, jsx_runtime_1.jsx)(material_1.SvgIcon, { ...props, children: (0, jsx_runtime_1.jsx)("path", { fill: "currentColor", d: "M16.5,21C13.5,21 12.31,16.76 11.05,12.28C10.14,9.04 9,5 7.5,5C4.11,5 4,11.93 4,12H2C2,11.63 2.06,3 7.5,3C10.5,3 11.71,7.25 12.97,11.74C13.83,14.8 15,19 16.5,19C19.94,19 20.03,12.07 20.03,12H22.03C22.03,12.37 21.97,21 16.5,21Z" }) }));
-}
-function StraightLines(props) {
-    return ((0, jsx_runtime_1.jsx)(material_1.SvgIcon, { ...props, children: (0, jsx_runtime_1.jsx)("path", { fill: "currentColor", d: "M22 12L17 22L7.1 6.04L4.24 12H2L7 2L16.9 17.96L19.76 12H22Z" }) }));
-}

package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.d.ts

@@ -1,8 +0,0 @@
-import type { LinearSyntenyViewModel } from '../../model';
-declare const ImportSyntenyOpenCustomTrack: ({ model, assembly1, assembly2, selectedRow, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    selectedRow: number;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ImportSyntenyOpenCustomTrack;