@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LinearComparativeDisplay/index.js

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+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const configSchemaF_1 = __importDefault(require("./configSchemaF"));
+const stateModelFactory_1 = __importDefault(require("./stateModelFactory"));
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchemaF_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearComparativeDisplay',
+            configSchema,
+            stateModel: (0, stateModelFactory_1.default)(configSchema),
+            trackType: 'SyntenyTrack',
+            viewType: 'LinearComparativeView',
+            ReactComponent: () => {
+                return null;
+            },
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/LinearComparativeDisplay/index.js.map

@@ -0,0 +1 @@
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package/dist/LinearComparativeDisplay/stateModelFactory.d.ts

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+/// <reference types="react" />
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Instance } from 'mobx-state-tree';
+import { Feature } from '@jbrowse/core/util';
+/**
+ * #stateModel LinearComparativeDisplay
+ */
+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;
+    height: import("mobx-state-tree").IType<number | undefined, number, number>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    message: string | undefined;
+} & {
+    readonly RenderingComponent: import("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>>; /**
+             * #action
+             * controlled by a reaction
+             */
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string; /**
+             * #action
+             * controlled by a reaction
+             */
+            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: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    renderInProgress: AbortController | undefined;
+    features: Feature[] | undefined;
+    message: string | undefined;
+} & {
+    /**
+     * #getter
+     */
+    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: unknown): any;
+            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+            height: number;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & {
+            readonly RenderingComponent: import("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>>; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: Function | undefined;
+                blockState?: Record<string, any> | undefined;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                    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: import("react").FC<any> | undefined;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setMessage(arg?: string | undefined): void;
+            setError(error?: unknown): void;
+            setRpcDriverName(rpcDriverName: string): void;
+            reload(): void;
+        } & {
+            renderInProgress: AbortController | undefined;
+            features: Feature[] | undefined;
+            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>>;
+        } & {
+            type: import("mobx-state-tree").ISimpleType<"LinearComparativeDisplay">;
+            configuration: AnyConfigurationSchemaType;
+            height: import("mobx-state-tree").IType<number | undefined, number, number>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & {
+            readonly RenderingComponent: import("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>>; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    message: string | undefined;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: Function | undefined;
+                blockState?: Record<string, any> | undefined;
+            }>;
+            readonly DisplayBlurb: import("react").FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string; /**
+                     * #action
+                     * controlled by a reaction
+                     */
+                    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: import("react").FC<any> | undefined;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setMessage(arg?: string | undefined): void;
+            setError(error?: unknown): void;
+            setRpcDriverName(rpcDriverName: string): void;
+            reload(): void;
+        } & {
+            renderInProgress: AbortController | undefined;
+            features: Feature[] | undefined;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        highResolutionScaling: number;
+    };
+} & {
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setLoading(abortController: AbortController): void;
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setMessage(messageText: string): void;
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setRendered(args?: {
+        features: Feature[];
+    }): void;
+    /**
+     * #action
+     * controlled by a reaction
+     */
+    setError(error: unknown): void;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;
+export type LinearComparativeDisplayModel = ReturnType<typeof stateModelFactory>;
+export type LinearComparativeDisplay = Instance<LinearComparativeDisplayModel>;

package/dist/LinearComparativeDisplay/stateModelFactory.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+/**
+ * #stateModel LinearComparativeDisplay
+ */
+function stateModelFactory(configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearComparativeDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('LinearComparativeDisplay'),
+        /**
+         * #property
+         */
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+        /**
+         * #property
+         */
+        height: 100,
+    }))
+        .volatile(( /* self */) => ({
+        renderInProgress: undefined,
+        features: undefined,
+        message: undefined,
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        renderProps() {
+            return {
+                rpcDriverName: self.rpcDriverName,
+                displayModel: self,
+                highResolutionScaling: 2,
+            };
+        },
+    }))
+        .actions(self => {
+        let renderInProgress;
+        return {
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setLoading(abortController) {
+                self.message = undefined;
+                self.error = undefined;
+                renderInProgress = abortController;
+            },
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setMessage(messageText) {
+                if (renderInProgress && !renderInProgress.signal.aborted) {
+                    renderInProgress.abort();
+                }
+                self.message = messageText;
+                self.error = undefined;
+                renderInProgress = undefined;
+            },
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setRendered(args) {
+                if (!args) {
+                    return;
+                }
+                const { features } = args;
+                const existingFeatures = self.features || [];
+                const featIds = new Set(existingFeatures.map(f => f.id()) || []);
+                const newFeatIds = new Set((features === null || features === void 0 ? void 0 : features.map(f => f.id())) || []);
+                let foundNewFeatureNotInExistingMap = false;
+                let foundExistingFeatureNotInNewMap = false;
+                for (let i = 0; i < features.length; i++) {
+                    if (!featIds.has(features[i].id())) {
+                        foundNewFeatureNotInExistingMap = true;
+                        break;
+                    }
+                }
+                for (let i = 0; i < existingFeatures.length; i++) {
+                    if (!newFeatIds.has(existingFeatures[i].id())) {
+                        foundExistingFeatureNotInNewMap = true;
+                        break;
+                    }
+                }
+                self.message = undefined;
+                self.error = undefined;
+                renderInProgress = undefined;
+                if (foundNewFeatureNotInExistingMap ||
+                    foundExistingFeatureNotInNewMap ||
+                    !self.features) {
+                    self.features = features;
+                }
+            },
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setError(error) {
+                console.error(error);
+                if (renderInProgress && !renderInProgress.signal.aborted) {
+                    renderInProgress.abort();
+                }
+                // the rendering failed for some reason
+                self.message = undefined;
+                self.error = error;
+                renderInProgress = undefined;
+            },
+        };
+    })
+        .actions(self => ({
+        afterAttach() {
+            (0, util_1.makeAbortableReaction)(
+            // @ts-expect-error
+            self, renderBlockData, renderBlockEffect, {
+                name: `${self.type} ${self.id} rendering`,
+                delay: 1000,
+                fireImmediately: true,
+            }, self.setLoading, self.setRendered, self.setError);
+        },
+    }));
+}
+function renderBlockData(self) {
+    const { rpcManager } = (0, util_1.getSession)(self);
+    const display = self;
+    // Alternative to readConfObject(config) is below used because renderProps is
+    // something under our control.  Compare to serverSideRenderedBlock
+    (0, configuration_1.readConfObject)(self.configuration);
+    const { adapterConfig } = self;
+    const parent = (0, util_1.getContainingView)(self);
+    const sessionId = (0, tracks_1.getRpcSessionId)(self);
+    (0, mobx_state_tree_1.getSnapshot)(parent);
+    return parent.initialized
+        ? {
+            rpcManager,
+            renderProps: {
+                ...display.renderProps(),
+                view: parent,
+                adapterConfig,
+                sessionId,
+                timeout: 1000000,
+                self,
+            },
+        }
+        : undefined;
+}
+async function renderBlockEffect(props) {
+    if (!props) {
+        return;
+    }
+    const { rpcManager, renderProps } = props;
+    const { adapterConfig } = renderProps;
+    const view0 = renderProps.view.views[0];
+    const features = (await rpcManager.call('getFeats', 'CoreGetFeatures', {
+        regions: view0.staticBlocks.contentBlocks,
+        sessionId: 'getFeats',
+        adapterConfig,
+    }));
+    return {
+        features: (0, util_1.dedupe)(features, f => f.id()),
+    };
+}
+exports.default = stateModelFactory;
+//# sourceMappingURL=stateModelFactory.js.map

package/dist/LinearComparativeDisplay/stateModelFactory.js.map

@@ -0,0 +1 @@
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package/dist/LinearComparativeView/components/Header.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearComparativeViewModel } from '../model';
+type LCV = LinearComparativeViewModel;
+declare const Header: ({ model }: {
+    model: LCV;
+}) => React.JSX.Element;
+export default Header;

package/dist/LinearComparativeView/components/Header.js

@@ -0,0 +1,89 @@
+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_react_1 = require("mobx-react");
+const ui_1 = require("@jbrowse/core/ui");
+// icons
+const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
+const Icons_1 = require("@jbrowse/core/ui/Icons");
+const useStyles = (0, mui_1.makeStyles)()(() => ({
+    headerBar: {
+        gridArea: '1/1/auto/span 2',
+        display: 'flex',
+    },
+    spacer: {
+        flexGrow: 1,
+    },
+    iconButton: {
+        margin: 5,
+    },
+    bp: {
+        display: 'flex',
+        alignItems: 'center',
+        marginLeft: 10,
+    },
+    searchContainer: {
+        marginLeft: 5,
+    },
+    searchBox: {
+        display: 'flex',
+    },
+}));
+const TrackSelector = (0, mobx_react_1.observer)(({ model }) => {
+    return (react_1.default.createElement(material_1.IconButton, { onClick: model.activateTrackSelector, title: "Open track selector" },
+        react_1.default.createElement(Icons_1.TrackSelector, null)));
+});
+const Header = (0, mobx_react_1.observer)(function ({ model }) {
+    const { classes } = useStyles();
+    const [menuAnchorEl, setMenuAnchorEl] = (0, react_1.useState)();
+    const anyShowHeaders = model.views.some(view => !view.hideHeader);
+    return (react_1.default.createElement("div", { className: classes.headerBar },
+        react_1.default.createElement(TrackSelector, { model: model }),
+        react_1.default.createElement(material_1.IconButton, { onClick: event => setMenuAnchorEl(event.currentTarget), className: classes.iconButton },
+            react_1.default.createElement(MoreVert_1.default, null)),
+        !anyShowHeaders
+            ? model.views.map(view => (react_1.default.createElement("div", { key: view.id, className: classes.searchBox },
+                react_1.default.createElement("div", { className: classes.searchContainer },
+                    react_1.default.createElement(plugin_linear_genome_view_1.SearchBox, { model: view, showHelp: false })),
+                react_1.default.createElement("div", { className: classes.bp },
+                    react_1.default.createElement(material_1.Typography, { variant: "body2", color: "textSecondary", className: classes.bp },
+                        Math.round(view.coarseTotalBp).toLocaleString('en-US'),
+                        " bp")))))
+            : null,
+        react_1.default.createElement("div", { className: classes.spacer }),
+        menuAnchorEl ? (react_1.default.createElement(ui_1.Menu, { anchorEl: menuAnchorEl, open: true, onMenuItemClick: (_event, callback) => {
+                callback();
+                setMenuAnchorEl(undefined);
+            }, menuItems: model.headerMenuItems(), onClose: () => setMenuAnchorEl(undefined) })) : null));
+});
+exports.default = Header;
+//# sourceMappingURL=Header.js.map

package/dist/LinearComparativeView/components/Header.js.map

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package/dist/LinearComparativeView/components/LinearComparativeView.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearComparativeViewModel } from '../model';
+type LCV = LinearComparativeViewModel;
+declare const _default: (props: {
+    ExtraButtons?: React.ReactNode;
+    model: LCV;
+}) => React.JSX.Element;
+export default _default;