@jbrowse/plugin-linear-comparative-view 2.12.0 → 2.12.1

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LaunchSyntenyViewDialog;
 const react_1 = __importStar(require("react"));
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
@@ -66,4 +67,3 @@ function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
                 } }, "Submit"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
 }
-exports.default = LaunchSyntenyViewDialog;

package/dist/LGVSyntenyDisplay/components/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.navToSynteny = void 0;
+exports.navToSynteny = navToSynteny;
 const util_1 = require("@jbrowse/core/util");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 const mobx_1 = require("mobx");
@@ -108,4 +108,3 @@ async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip,
         view2.views[1].navToLocString(l2, mateAsm),
     ]);
 }
-exports.navToSynteny = navToSynteny;

package/dist/LGVSyntenyDisplay/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LGVSyntenyDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const model_1 = __importDefault(require("./model"));
@@ -21,4 +22,3 @@ function LGVSyntenyDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LGVSyntenyDisplayF;

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
  * #stateModel LGVSyntenyDisplay
@@ -36,7 +35,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -48,9 +47,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -61,7 +60,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -152,16 +151,14 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined; /**
-             * #method
-             */
+            rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
@@ -180,12 +177,12 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -198,8 +195,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -211,10 +208,10 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -223,8 +220,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -232,7 +229,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -245,8 +242,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -258,36 +255,38 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
+    featureUnderMouseVolatile: undefined | import("@jbrowse/core/util").Feature;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n: number): void;
-    setFeatureHeight(n?: number | undefined): void;
-    setNoSpacing(flag?: boolean | undefined): void;
+    setFeatureHeight(n?: number): void;
+    setNoSpacing(flag?: boolean): void;
     setColorScheme(colorScheme: {
         type: string;
-        tag?: string | undefined;
-        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
+        tag?: string;
+        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy;
     }): void;
     updateColorTagMap(uniqueTag: string[]): void;
-    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
+    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
-    setConfig(conf: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
+    setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared").IFilter): void;
     setJexlFilters(filters: string[]): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        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>;
 } & {
     readonly maxHeight: any;
@@ -314,8 +313,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
                 pos: number;
                 refName: number;
                 type: string;
-                tag?: string | undefined;
-            } | undefined;
+                tag?: string;
+            };
         };
     }) => import("react").JSX.Element | null;
     renderPropsPre(): any;

package/dist/LaunchLinearSyntenyView.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LaunchLinearSyntenyView;
 const mobx_1 = require("mobx");
 function LaunchLinearSyntenyView(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-LinearSyntenyView', 
@@ -45,7 +46,6 @@ function LaunchLinearSyntenyView(pluginManager) {
         }
     });
 }
-exports.default = LaunchLinearSyntenyView;
 function tryTrack(model, trackId, idsNotFound) {
     try {
         model.showTrack(trackId);

package/dist/LinearComparativeDisplay/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearComparativeDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const stateModelFactory_1 = __importDefault(require("./stateModelFactory"));
@@ -21,4 +22,3 @@ function LinearComparativeDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LinearComparativeDisplayF;

package/dist/LinearComparativeDisplay/stateModelFactory.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Instance } from 'mobx-state-tree';
 import { Feature } from '@jbrowse/core/util';
@@ -23,11 +22,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
-            type: string; /**
-             * #property
-             */
+            type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("mobx-state-tree/dist/internal" /**
+         * #property
+         */).NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
@@ -36,15 +35,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
-            rendererTypeName: 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;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -68,16 +64,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
-     * #action
-     * controlled by a reaction
-     */
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -98,7 +91,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             configuration: {
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
+                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>;
             height: number;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -109,11 +108,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly RenderingComponent: import("react").FC<{
                 model: {
                     id: string;
-                    type: string; /**
-                     * #property
-                     */
+                    type: string;
                     rpcDriverName: string | undefined;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                } & import("mobx-state-tree/dist/internal" /**
+                 * #property
+                 */).NonEmptyObject & {
                     rendererTypeName: string;
                     error: unknown;
                     message: string | undefined;
@@ -122,15 +121,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     type: import("mobx-state-tree").ISimpleType<string>;
                     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
                 }, {
-                    rendererTypeName: 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;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -154,16 +150,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
-             * #action
-             * controlled by a reaction
-             */
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -187,9 +180,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly RenderingComponent: import("react").FC<{
                 model: {
                     id: string;
-                    type: string; /**
-                     * #property
-                     */
+                    type: string;
                     rpcDriverName: string | undefined;
                 } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                     rendererTypeName: string;
@@ -200,15 +191,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     type: import("mobx-state-tree").ISimpleType<string>;
                     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
                 }, {
-                    rendererTypeName: 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;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -232,16 +220,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             readonly adapterConfig: any;
             readonly parentTrack: any;
             renderProps(): any;
-            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType; /**
-             * #action
-             * controlled by a reaction
-             */
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
             readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;

package/dist/LinearComparativeView/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearComparativeViewF;
 const react_1 = require("react");
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
 const model_1 = __importDefault(require("./model"));
@@ -39,4 +40,3 @@ function LinearComparativeViewF(pluginManager) {
         });
     });
 }
-exports.default = LinearComparativeViewF;