@jbrowse/plugin-linear-comparative-view 2.17.0 → 3.0.0

package/dist/LinearComparativeView/model.d.ts

@@ -1,12 +1,7 @@
-import { Instance, SnapshotIn } from 'mobx-state-tree';
-import { MenuItem } from '@jbrowse/core/ui';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-/**
- * #stateModel LinearComparativeView
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { MenuItem } from '@jbrowse/core/ui';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Instance, SnapshotIn } from 'mobx-state-tree';
 declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -16,7 +11,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactiveOverlay: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     levels: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -50,7 +46,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -71,8 +67,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -82,6 +78,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -118,12 +115,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -140,7 +137,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -162,7 +159,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -184,15 +181,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
-        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -247,7 +244,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;
@@ -261,81 +258,30 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     setWidth(newWidth: number): void;
     setMinimized(flag: boolean): void;
 } & {
-    /**
-     * #volatile
-     */
     width: number | undefined;
 } & {
-    /**
-     * #getter
-     */
     readonly initialized: boolean;
-    /**
-     * #getter
-     */
     readonly refNames: string[][];
-    /**
-     * #getter
-     */
     readonly assemblyNames: string[];
 } & {
+    afterAttach(): void;
     beforeDestroy(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
-    /**
-     * #action
-     */
     setWidth(newWidth: number): void;
-    /**
-     * #action
-     */
     setViews(views: SnapshotIn<LinearGenomeViewModel>[]): void;
-    /**
-     * #action
-     */
     removeView(view: LinearGenomeViewModel): void;
-    /**
-     * #action
-     */
     setLevelHeight(newHeight: number, level?: number): number;
-    /**
-     * #action
-     */
+    setLinkViews(arg: boolean): void;
     activateTrackSelector(level: number): import("@jbrowse/core/util").Widget;
-    /**
-     * #action
-     */
     toggleTrack(trackId: string, level?: number): void;
-    /**
-     * #action
-     */
     showTrack(trackId: string, level?: number, initialSnapshot?: {}): void;
-    /**
-     * #action
-     */
     hideTrack(trackId: string, level?: number): void;
-    /**
-     * #action
-     */
     squareView(): void;
-    /**
-     * #action
-     */
     clearView(): void;
 } & {
-    /**
-     * #method
-     * includes a subset of view menu options because the full list is a
-     * little overwhelming. overridden by subclasses
-     */
     headerMenuItems(): MenuItem[];
 } & {
-    /**
-     * #method
-     */
     menuItems(): MenuItem[];
-    /**
-     * #method
-     */
     rubberBandMenuItems(): {
         label: string;
         onClick: () => void;
@@ -351,7 +297,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactiveOverlay: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     levels: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -385,7 +332,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -406,8 +353,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -417,6 +364,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -453,12 +401,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -475,7 +423,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -497,7 +445,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -519,15 +467,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
-        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -582,7 +530,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;

package/dist/LinearComparativeView/model.js

@@ -15,111 +15,85 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
-// jbrowse
 const BaseViewModel_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/models/BaseViewModel"));
 const util_1 = require("@jbrowse/core/util");
 const mst_1 = require("@jbrowse/core/util/types/mst");
-// icons
 const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
-// lazies
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
-/**
- * #stateModel LinearComparativeView
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
 function stateModelFactory(pluginManager) {
     var _a;
     const LinearSyntenyViewHelper = (_a = pluginManager.getViewType('LinearSyntenyViewHelper')) === null || _a === void 0 ? void 0 : _a.stateModel;
     return mobx_state_tree_1.types
         .compose('LinearComparativeView', BaseViewModel_1.default, mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearComparativeView'),
-        /**
-         * #property
-         */
         trackSelectorType: 'hierarchical',
-        /**
-         * #property
-         */
         showIntraviewLinks: true,
-        /**
-         * #property
-         */
-        interactToggled: false,
-        /**
-         * #property
-         */
+        linkViews: false,
+        interactiveOverlay: false,
         levels: mobx_state_tree_1.types.array(LinearSyntenyViewHelper),
-        /**
-         * #property
-         * currently this is limited to an array of two
-         */
         views: mobx_state_tree_1.types.array(pluginManager.getViewType('LinearGenomeView')
             .stateModel),
-        /**
-         * #property
-         * this represents tracks specific to this view specifically used for
-         * read vs ref dotplots where this track would not really apply
-         * elsewhere
-         */
         viewTrackConfigs: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('track')),
     }))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         width: undefined,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get initialized() {
-            return (
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-            self.width !== undefined &&
+            return (self.width !== undefined &&
                 self.views.length > 0 &&
                 self.views.every(view => view.initialized));
         },
-        /**
-         * #getter
-         */
         get refNames() {
             return self.views.map(v => [
                 ...new Set(v.staticBlocks.map(m => m.refName)),
             ]);
         },
-        /**
-         * #getter
-         */
         get assemblyNames() {
             return [...new Set(self.views.flatMap(v => v.assemblyNames))];
         },
     }))
         .actions(self => ({
-        // automatically removes session assemblies associated with this view
-        // e.g. read vs ref
+        afterAttach() {
+            const actions = new Set([
+                'horizontalScroll',
+                'zoomTo',
+                'setScaleFactor',
+            ]);
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_state_tree_1.onAction)(self, param => {
+                if (self.linkViews) {
+                    const { name, path, args } = param;
+                    if (actions.has(name) && path) {
+                        this.onSubviewAction(name, path, args);
+                    }
+                }
+            }));
+        },
         beforeDestroy() {
             var _a;
             const session = (0, util_1.getSession)(self);
@@ -131,40 +105,27 @@ function stateModelFactory(pluginManager) {
             self.views.forEach(view => {
                 const ret = (0, mobx_state_tree_1.getPath)(view);
                 if (!ret.endsWith(path)) {
-                    // @ts-expect-error
                     view[actionName](args === null || args === void 0 ? void 0 : args[0]);
                 }
             });
         },
-        /**
-         * #action
-         */
         setWidth(newWidth) {
             self.width = newWidth;
         },
-        /**
-         * #action
-         */
         setViews(views) {
             self.views = (0, mobx_state_tree_1.cast)(views);
         },
-        /**
-         * #action
-         */
         removeView(view) {
             self.views.remove(view);
         },
-        /**
-         * #action
-         */
         setLevelHeight(newHeight, level = 0) {
             const l = self.levels[level];
             l.setHeight(newHeight);
             return l.height;
         },
-        /**
-         * #action
-         */
+        setLinkViews(arg) {
+            self.linkViews = arg;
+        },
         activateTrackSelector(level) {
             if (self.trackSelectorType === 'hierarchical') {
                 const session = (0, util_1.getSession)(self);
@@ -178,32 +139,20 @@ function stateModelFactory(pluginManager) {
             }
             throw new Error(`invalid track selector type ${self.trackSelectorType}`);
         },
-        /**
-         * #action
-         */
         toggleTrack(trackId, level = 0) {
             var _a;
             (_a = self.levels[level]) === null || _a === void 0 ? void 0 : _a.toggleTrack(trackId);
         },
-        /**
-         * #action
-         */
         showTrack(trackId, level = 0, initialSnapshot = {}) {
             if (!self.levels[level]) {
                 self.levels[level] = (0, mobx_state_tree_1.cast)({ level });
             }
             self.levels[level].showTrack(trackId, initialSnapshot);
         },
-        /**
-         * #action
-         */
         hideTrack(trackId, level = 0) {
             var _a;
             (_a = self.levels[level]) === null || _a === void 0 ? void 0 : _a.hideTrack(trackId);
         },
-        /**
-         * #action
-         */
         squareView() {
             const average = (0, util_1.avg)(self.views.map(v => v.bpPerPx));
             for (const view of self.views) {
@@ -214,28 +163,17 @@ function stateModelFactory(pluginManager) {
                 }
             }
         },
-        /**
-         * #action
-         */
         clearView() {
             self.views = (0, mobx_state_tree_1.cast)([]);
             self.levels = (0, mobx_state_tree_1.cast)([]);
         },
     }))
         .views(() => ({
-        /**
-         * #method
-         * includes a subset of view menu options because the full list is a
-         * little overwhelming. overridden by subclasses
-         */
         headerMenuItems() {
             return [];
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         menuItems() {
             return [
                 {
@@ -253,9 +191,6 @@ function stateModelFactory(pluginManager) {
                 },
             ];
         },
-        /**
-         * #method
-         */
         rubberBandMenuItems() {
             return [
                 {
@@ -284,8 +219,6 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .preProcessSnapshot(snap => {
-        // @ts-expect-error
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         const { tracks, levels = [{ tracks, level: 0 }], ...rest } = snap || {};
         return {
             ...rest,

package/dist/LinearReadVsRef/LinearReadVsRef.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 export default function ReadVsRefDialog({ track, feature: preFeature, handleClose, }: {
     feature: Feature;
     handleClose: () => void;
     track: any;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;