@jbrowse/plugin-linear-genome-view 2.2.0 → 2.2.2

package/dist/LinearGenomeView/model.js.map

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

@@ -1,9 +1,9 @@
 /// <reference types="react" />
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { BaseLinearDisplay, BaseLinearDisplayComponent, baseLinearDisplayConfigSchema, BlockModel } from './BaseLinearDisplay';
+import { BaseLinearDisplay, BaseLinearDisplayComponent, BlockModel, baseLinearDisplayConfigSchema } from './BaseLinearDisplay';
 import { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
-import { LinearGenomeViewModel, LinearGenomeViewStateModel, renderToSvg, RefNameAutocomplete, SearchBox } from './LinearGenomeView';
+import { renderToSvg, LinearGenomeViewModel, LinearGenomeViewStateModel, RefNameAutocomplete, SearchBox } from './LinearGenomeView';
 import { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory } from './LinearBasicDisplay';
 export default class LinearGenomeViewPlugin extends Plugin {
     name: string;
@@ -611,7 +611,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: {
                 id: string;
                 displayName: string | undefined;
-                type: "LinearGenomeView";
+                minimized: boolean;
+                type: string;
                 offsetPx: number;
                 bpPerPx: number;
                 displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
@@ -649,6 +650,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -808,9 +810,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & import("mobx-state-tree").IStateTreeNode<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>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             } & {
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -839,6 +842,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1001,7 +1005,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: {
                 id: string;
                 displayName: string | undefined;
-                type: "LinearGenomeView";
+                minimized: boolean;
+                type: string;
                 offsetPx: number;
                 bpPerPx: number;
                 displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
@@ -1039,6 +1044,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1198,9 +1204,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & import("mobx-state-tree").IStateTreeNode<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>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             } & {
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -1229,6 +1236,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1391,7 +1399,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: {
                 id: string;
                 displayName: string | undefined;
-                type: "LinearGenomeView";
+                minimized: boolean;
+                type: string;
                 offsetPx: number;
                 bpPerPx: number;
                 displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
@@ -1429,6 +1438,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1588,9 +1598,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & import("mobx-state-tree").IStateTreeNode<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>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             } & {
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -1619,6 +1630,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;

package/dist/index.js

@@ -27,28 +27,26 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SearchBox = exports.RefNameAutocomplete = exports.BaseLinearDisplay = exports.BaseLinearDisplayComponent = exports.renderToSvg = exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.linearBareDisplayConfigSchemaFactory = exports.baseLinearDisplayConfigSchema = void 0;
-const react_1 = require("react");
-const mobx_1 = require("mobx");
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
+// icons
 const LineStyle_1 = __importDefault(require("@mui/icons-material/LineStyle"));
 const BaseLinearDisplay_1 = require("./BaseLinearDisplay");
 Object.defineProperty(exports, "BaseLinearDisplay", { enumerable: true, get: function () { return BaseLinearDisplay_1.BaseLinearDisplay; } });
 Object.defineProperty(exports, "BaseLinearDisplayComponent", { enumerable: true, get: function () { return BaseLinearDisplay_1.BaseLinearDisplayComponent; } });
 Object.defineProperty(exports, "baseLinearDisplayConfigSchema", { enumerable: true, get: function () { return BaseLinearDisplay_1.baseLinearDisplayConfigSchema; } });
-const LinearBareDisplay_1 = require("./LinearBareDisplay");
+const LinearBareDisplay_1 = __importStar(require("./LinearBareDisplay"));
 Object.defineProperty(exports, "linearBareDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBareDisplay_1.configSchemaFactory; } });
-const LinearGenomeView_1 = require("./LinearGenomeView");
+const LinearGenomeView_1 = __importStar(require("./LinearGenomeView"));
 Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return LinearGenomeView_1.renderToSvg; } });
 Object.defineProperty(exports, "RefNameAutocomplete", { enumerable: true, get: function () { return LinearGenomeView_1.RefNameAutocomplete; } });
 Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function () { return LinearGenomeView_1.SearchBox; } });
-const LinearBasicDisplay_1 = require("./LinearBasicDisplay");
+const LinearBasicDisplay_1 = __importStar(require("./LinearBasicDisplay"));
 Object.defineProperty(exports, "linearBasicDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBasicDisplay_1.configSchema; } });
 Object.defineProperty(exports, "linearBasicDisplayModelFactory", { enumerable: true, get: function () { return LinearBasicDisplay_1.modelFactory; } });
 const FeatureTrack_1 = __importDefault(require("./FeatureTrack"));
 const BasicTrack_1 = __importDefault(require("./BasicTrack"));
+const LaunchLinearGenomeView_1 = __importDefault(require("./LaunchLinearGenomeView"));
 class LinearGenomeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -65,71 +63,10 @@ class LinearGenomeViewPlugin extends Plugin_1.default {
     install(pluginManager) {
         (0, FeatureTrack_1.default)(pluginManager);
         (0, BasicTrack_1.default)(pluginManager);
-        pluginManager.addDisplayType(() => {
-            const configSchema = (0, LinearBareDisplay_1.configSchemaFactory)(pluginManager);
-            return new DisplayType_1.default({
-                name: 'LinearBareDisplay',
-                configSchema,
-                stateModel: (0, LinearBareDisplay_1.stateModelFactory)(configSchema),
-                trackType: 'BasicTrack',
-                viewType: 'LinearGenomeView',
-                ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
-            });
-        });
-        pluginManager.addDisplayType(() => {
-            const configSchema = (0, LinearBasicDisplay_1.configSchema)(pluginManager);
-            return new DisplayType_1.default({
-                name: 'LinearBasicDisplay',
-                configSchema,
-                stateModel: (0, LinearBasicDisplay_1.modelFactory)(configSchema),
-                trackType: 'FeatureTrack',
-                viewType: 'LinearGenomeView',
-                ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
-            });
-        });
-        pluginManager.addViewType(() => new ViewType_1.default({
-            name: 'LinearGenomeView',
-            stateModel: (0, LinearGenomeView_1.stateModelFactory)(pluginManager),
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinearGenomeView/components/LinearGenomeView')))),
-        }));
-        pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
-        // @ts-ignore
-        async ({ session, assembly, loc, tracks = [], }) => {
-            try {
-                const { assemblyManager } = session;
-                const view = session.addView('LinearGenomeView', {});
-                await (0, mobx_1.when)(() => !!view.volatileWidth);
-                if (!assembly) {
-                    throw new Error('No assembly provided when launching linear genome view');
-                }
-                const asm = await assemblyManager.waitForAssembly(assembly);
-                if (!asm) {
-                    throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
-                }
-                view.navToLocString(loc, assembly);
-                const idsNotFound = [];
-                tracks.forEach(track => {
-                    try {
-                        view.showTrack(track);
-                    }
-                    catch (e) {
-                        if (`${e}`.match('Could not resolve identifier')) {
-                            idsNotFound.push(track);
-                        }
-                        else {
-                            throw e;
-                        }
-                    }
-                });
-                if (idsNotFound.length) {
-                    throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
-                }
-            }
-            catch (e) {
-                session.notify(`${e}`, 'error');
-                throw e;
-            }
-        });
+        (0, LinearBasicDisplay_1.default)(pluginManager);
+        (0, LinearGenomeView_1.default)(pluginManager);
+        (0, LinearBareDisplay_1.default)(pluginManager);
+        (0, LaunchLinearGenomeView_1.default)(pluginManager);
     }
     configure(pluginManager) {
         if ((0, util_1.isAbstractMenuManager)(pluginManager.rootModel)) {

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAEzC,6CAAgF;AAEhF,QAAQ;AACR,8EAAyD;AAEzD,2DAK4B;AA+D1B,kGAnEA,qCAAiB,OAmEA;AADjB,2GAjEA,8CAA0B,OAiEA;AAL1B,8GA1DA,iDAA6B,OA0DA;AAxD/B,yEAE4B;AAuD1B,qHAxDuB,uCAAoC,OAwDvB;AAtDtC,uEAQ2B;AAiDzB,4FAxDA,8BAAW,OAwDA;AAGX,oGAxDA,sCAAmB,OAwDA;AACnB,0FAxDA,4BAAS,OAwDA;AApDX,2EAG6B;AA2C3B,sHA7CgB,iCAAqC,OA6ChB;AACrC,+GA7CgB,iCAA8B,OA6ChB;AA1ChC,kEAA0C;AAC1C,8DAAsC;AACtC,sFAA8D;AAE9D,MAAqB,sBAAuB,SAAQ,gBAAM;IAA1D;;QACE,SAAI,GAAG,wBAAwB,CAAA;QAE/B,YAAO,GAAG;YACR,0BAA0B,EAA1B,8CAA0B;YAC1B,iBAAiB,EAAjB,qCAAiB;YACjB,6BAA6B,EAA7B,iDAA6B;YAC7B,SAAS,EAAT,4BAAS;YACT,YAAY,EAAZ,+BAAY;YACZ,gBAAgB,EAAhB,mCAAgB;SACjB,CAAA;IAsBH,CAAC;IApBC,OAAO,CAAC,aAA4B;QAClC,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QAC5B,IAAA,oBAAW,EAAC,aAAa,CAAC,CAAA;QAC1B,IAAA,4BAAmB,EAAC,aAAa,CAAC,CAAA;QAClC,IAAA,0BAAiB,EAAC,aAAa,CAAC,CAAA;QAChC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;IACxC,CAAC;IAED,SAAS,CAAC,aAA4B;QACpC,IAAI,IAAA,4BAAqB,EAAC,aAAa,CAAC,SAAS,CAAC,EAAE;YAClD,aAAa,CAAC,SAAS,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,KAAK,EAAE,oBAAoB;gBAC3B,IAAI,EAAE,mBAAa;gBACnB,OAAO,EAAE,CAAC,OAA6B,EAAE,EAAE;oBACzC,OAAO,CAAC,OAAO,CAAC,kBAAkB,EAAE,EAAE,CAAC,CAAA;gBACzC,CAAC;aACF,CAAC,CAAA;SACH;IACH,CAAC;CACF;AAhCD,yCAgCC"}

package/esm/BaseLinearDisplay/components/Tooltip.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { BaseLinearDisplayModel } from '../models/BaseLinearDisplayModel';
-declare type Coord = [number, number];
+type Coord = [number, number];
 declare const Tooltip: ({ model, clientMouseCoord, }: {
     model: BaseLinearDisplayModel;
     clientMouseCoord: Coord;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -14,7 +14,7 @@ export interface Layout {
     maxY: number;
     name: string;
 }
-declare type LayoutRecord = [number, number, number, number];
+type LayoutRecord = [number, number, number, number];
 export declare const BaseLinearDisplay: 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>;
@@ -369,6 +369,6 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 }>;
-export declare type BaseLinearDisplayStateModel = typeof BaseLinearDisplay;
-export declare type BaseLinearDisplayModel = Instance<BaseLinearDisplayStateModel>;
+export type BaseLinearDisplayStateModel = typeof BaseLinearDisplay;
+export type BaseLinearDisplayModel = Instance<BaseLinearDisplayStateModel>;
 export {};

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts

@@ -49,8 +49,8 @@ declare const blockState: import("mobx-state-tree").IModelType<{
     beforeDestroy(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default blockState;
-export declare type BlockStateModel = typeof blockState;
-export declare type BlockModel = Instance<BlockStateModel>;
+export type BlockStateModel = typeof blockState;
+export type BlockModel = Instance<BlockStateModel>;
 export declare function renderBlockData(self: BlockModel, optDisplay?: AbstractDisplayModel): {
     rendererType: any;
     rpcManager: import("@jbrowse/core/rpc/RpcManager").default;

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -131,7 +131,7 @@ const blockState = types
             const { rpcManager } = getSession(self);
             const { rendererType } = display;
             const { renderArgs } = renderBlockData(cast(self));
-            // renderArgs can be undefined if an error occured in this block
+            // renderArgs can be undefined if an error occurred in this block
             if (renderArgs) {
                 rendererType
                     .freeResourcesInClient(rpcManager, JSON.parse(JSON.stringify(renderArgs)))

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"serverSideRenderedBlock.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/serverSideRenderedBlock.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,OAAO,EAAE,IAAI,EAAY,MAAM,iBAAiB,CAAA;AAC3E,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EACL,iBAAiB,EACjB,UAAU,EACV,oBAAoB,EACpB,iBAAiB,EACjB,aAAa,EACb,qBAAqB,GAEtB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AACrD,OAAO,EAEL,gBAAgB,GACjB,MAAM,0BAA0B,CAAA;AAEjC,OAAO,EACL,qBAAqB,EACrB,eAAe,GAChB,MAAM,2BAA2B,CAAA;AAElC,OAAO,8BAA8B,MAAM,8CAA8C,CAAA;AAEzF,oEAAoE;AACpE,MAAM,UAAU,GAAG,KAAK;KACrB,KAAK,CAAC,YAAY,EAAE;IACnB,GAAG,EAAE,KAAK,CAAC,MAAM;IACjB,MAAM,EAAE,MAAM;IACd,UAAU,EAAE,CAAC;IACb,0BAA0B,EAAE,KAAK;IACjC,2BAA2B,EAAE,KAAK;CACnC,CAAC;IACF,yFAAyF;KACxF,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,gBAAgB,EAAE,SAAwC;IAC1D,MAAM,EAAE,KAAK;IACb,YAAY,EAAE,SAA2C;IACzD,QAAQ,EAAE,SAA6C;IACvD,MAAM,EAAE,SAAgB;IACxB,MAAM,EAAE,EAAE;IACV,KAAK,EAAE,SAAoB;IAC3B,OAAO,EAAE,SAA+B;IACxC,gBAAgB,EAAE,KAAK;IACvB,cAAc,EAAE,8BAA8B;IAC9C,WAAW,EAAE,SAAgB;CAC9B,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE;IACd,IAAI,gBAA6C,CAAA;IACjD,OAAO;QACL,QAAQ;YACN,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;QACvC,CAAC;QACD,WAAW;YACT,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,qBAAqB,CACnB,IAAW,EACX,eAAe,EACf,iBAAwB,EAAE,qCAAqC;YAC/D;gBACE,IAAI,EAAE,GAAG,OAAO,CAAC,EAAE,IAAI,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY;gBACjE,KAAK,EAAE,OAAO,CAAC,WAAW;gBAC1B,eAAe,EAAE,IAAI;aACtB,EACD,IAAI,CAAC,UAAU,EACf,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,QAAQ,CACd,CAAA;QACH,CAAC;QACD,SAAS,CAAC,OAAe;YACvB,IAAI,CAAC,MAAM,GAAG,OAAO,CAAA;QACvB,CAAC;QACD,UAAU,CAAC,eAAgC;YACzC,IAAI,gBAAgB,KAAK,SAAS,EAAE;gBAClC,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;oBACpC,gBAAgB,CAAC,KAAK,EAAE,CAAA;iBACzB;aACF;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,eAAe,CAAA;QACpC,CAAC;QACD,UAAU,CAAC,WAAmB;YAC5B,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,WAAW,CAAA;YAC1B,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,WAAW,CACT,KAQa;YAEb,IAAI,CAAC,KAAK,EAAE;gBACV,OAAM;aACP;YACD,MAAM,EACJ,YAAY,EACZ,QAAQ,EACR,MAAM,EACN,gBAAgB,EAChB,WAAW,GACZ,GAAG,KAAK,CAAA;YACT,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;YAChC,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YACxB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;YACpB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;YACxC,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;YAC9B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,QAAQ,CAAC,KAAsB;YAC7B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;YACpB,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,uCAAuC;YACvC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;YAClB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;YAC5B,IAAI,gBAAgB,CAAC,KAAc,CAAC,EAAE;gBACpC,IAAI,CAAC,MAAM,EAAE,CAAA;aACd;QACH,CAAC;QACD,MAAM;YACJ,IAAI,CAAC,gBAAgB,GAAG,SAAS,CAAA;YACjC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,cAAc,GAAG,8BAA8B,CAAA;YACpD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,SAAS,CAAM,IAAI,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;QAClC,CAAC;QACD,aAAa;YACX,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YACvC,MAAM,EAAE,YAAY,EAAE,GAAG,OAAO,CAAA;YAChC,MAAM,EAAE,UAAU,EAAE,GAAG,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;YAClD,iEAAiE;YACjE,IAAI,UAAU,EAAE;gBACd,YAAY;qBACT,qBAAqB,CACpB,UAAU,EACV,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CACvC;qBACA,KAAK,CAAC,CAAC,CAAQ,EAAE,EAAE;oBAClB,kEAAkE;oBAClE,OAAO,CAAC,IAAI,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;gBACjD,CAAC,CAAC,CAAA;aACL;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEJ,eAAe,UAAU,CAAA;AAIzB,2EAA2E;AAC3E,mDAAmD;AACnD,MAAM,UAAU,eAAe,CAC7B,IAAgB,EAChB,UAAiC;IAEjC,IAAI;QACF,MAAM,OAAO,GAAG,UAAU,IAAK,oBAAoB,CAAC,IAAI,CAAS,CAAA;QACjE,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,OAAO,CAAC,CAAA;QAC3D,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QACnE,MAAM,aAAa,GAAG,qBAAqB,CAAC,WAAW,CAAC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package/esm/BasicTrack/index.d.ts

@@ -1,3 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
+declare const _default: (pm: PluginManager) => void;
 export default _default;

package/esm/BasicTrack/index.js

@@ -1,12 +1,12 @@
 import { createBaseTrackModel, TrackType, } from '@jbrowse/core/pluggableElementTypes';
 import configSchemaF from './configSchema';
-export default (pluginManager) => {
-    pluginManager.addTrackType(() => {
-        const configSchema = configSchemaF(pluginManager);
+export default (pm) => {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
         return new TrackType({
             name: 'BasicTrack',
             configSchema,
-            stateModel: createBaseTrackModel(pluginManager, 'BasicTrack', configSchema),
+            stateModel: createBaseTrackModel(pm, 'BasicTrack', configSchema),
         });
     });
 };

package/esm/BasicTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BasicTrack/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,oBAAoB,EACpB,SAAS,GACV,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QAEjD,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,YAAY;YAClB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAC9B,aAAa,EACb,YAAY,EACZ,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BasicTrack/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,oBAAoB,EACpB,SAAS,GACV,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QAEtC,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,YAAY;YAClB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,YAAY,EAAE,YAAY,CAAC;SACjE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LaunchLinearGenomeView/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LaunchLinearGenomeView/index.js

@@ -0,0 +1,42 @@
+import { when } from '@jbrowse/core/util';
+export default (pluginManager) => {
+    pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
+    // @ts-ignore
+    async ({ session, assembly, loc, tracks = [], }) => {
+        try {
+            const { assemblyManager } = session;
+            const view = session.addView('LinearGenomeView', {});
+            await when(() => !!view.volatileWidth);
+            if (!assembly) {
+                throw new Error('No assembly provided when launching linear genome view');
+            }
+            const asm = await assemblyManager.waitForAssembly(assembly);
+            if (!asm) {
+                throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
+            }
+            await view.navToLocString(loc, assembly);
+            const idsNotFound = [];
+            tracks.forEach(track => {
+                try {
+                    view.showTrack(track);
+                }
+                catch (e) {
+                    if (`${e}`.match('Could not resolve identifier')) {
+                        idsNotFound.push(track);
+                    }
+                    else {
+                        throw e;
+                    }
+                }
+            });
+            if (idsNotFound.length) {
+                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+            }
+        }
+        catch (e) {
+            session.notify(`${e}`, 'error');
+            throw e;
+        }
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/LaunchLinearGenomeView/index.js.map

@@ -0,0 +1 @@
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package/esm/LinearBareDisplay/index.d.ts

@@ -1,2 +1,6 @@
-export { configSchemaFactory } from './configSchema';
-export { stateModelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { configSchemaFactory } from './configSchema';
+import { stateModelFactory } from './model';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { configSchemaFactory, stateModelFactory };

package/esm/LinearBareDisplay/index.js

@@ -1,3 +1,19 @@
-export { configSchemaFactory } from './configSchema';
-export { stateModelFactory } from './model';
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
+import { BaseLinearDisplayComponent } from '../BaseLinearDisplay';
+import { configSchemaFactory } from './configSchema';
+import { stateModelFactory } from './model';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'LinearBareDisplay',
+            configSchema,
+            stateModel: stateModelFactory(configSchema),
+            trackType: 'BasicTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        });
+    });
+};
+export { configSchemaFactory, stateModelFactory };
 //# sourceMappingURL=index.js.map

package/esm/LinearBareDisplay/index.js.map

@@ -1 +1 @@
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package/esm/LinearBasicDisplay/components/SetMaxHeight.js

@@ -1,18 +1,12 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, Typography, TextField, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Typography, TextField, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
 const useStyles = makeStyles()(theme => ({
     root: {
         width: 500,
     },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
     field: {
         margin: theme.spacing(2),
     },
@@ -21,11 +15,7 @@ function SetMaxHeightDlg({ model, handleClose, }) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = useState(`${maxHeight}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, "aria-labelledby": "alert-dialog-title", "aria-describedby": "alert-dialog-description" },
-        React.createElement(DialogTitle, { id: "alert-dialog-title" },
-            "Filter options",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose, size: "large" },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         React.createElement(DialogContent, { className: classes.root },
             React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
             React.createElement(TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" }),

package/esm/LinearBasicDisplay/components/SetMaxHeight.js.map

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package/esm/LinearBasicDisplay/index.d.ts

@@ -1,2 +1,6 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import configSchema from './configSchema';
+import modelFactory from './model';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { modelFactory, configSchema };

package/esm/LinearBasicDisplay/index.js

@@ -1,3 +1,20 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
+import { BaseLinearDisplayComponent } from '../BaseLinearDisplay';
+// locals
+import configSchema from './configSchema';
+import modelFactory from './model';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const config = configSchema(pluginManager);
+        return new DisplayType({
+            name: 'LinearBasicDisplay',
+            configSchema: config,
+            stateModel: modelFactory(config),
+            trackType: 'FeatureTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        });
+    });
+};
+export { modelFactory, configSchema };
 //# sourceMappingURL=index.js.map