@jbrowse/plugin-linear-genome-view 2.4.1 → 2.4.2

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map

@@ -1 +1 @@
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package/dist/BaseLinearDisplay/models/util.d.ts

@@ -1,3 +1,5 @@
+import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
 export interface RenderProps {
     rendererType: any;
     renderArgs: {
@@ -16,3 +18,5 @@ export interface ErrorProps {
     displayError: string;
 }
 export declare function getDisplayStr(totalBytes: number): string;
+export declare function getId(id: string, index: number): string;
+export declare function estimateRegionsStatsPre(self: IAnyStateTreeNode): Promise<Stats>;

package/dist/BaseLinearDisplay/models/util.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getDisplayStr = void 0;
+exports.estimateRegionsStatsPre = exports.getId = exports.getDisplayStr = void 0;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function getDisplayStr(totalBytes) {
     let displayBp;
     if (Math.floor(totalBytes / 1000000) > 0) {
@@ -15,4 +18,33 @@ function getDisplayStr(totalBytes) {
     return displayBp;
 }
 exports.getDisplayStr = getDisplayStr;
+// stabilize clipid under test for snapshot
+function getId(id, index) {
+    const isJest = typeof jest === 'undefined';
+    return `clip-${isJest ? id : 'jest'}-${index}`;
+}
+exports.getId = getId;
+async function estimateRegionsStatsPre(self) {
+    const view = (0, util_1.getContainingView)(self);
+    const regions = view.staticBlocks.contentBlocks;
+    const { rpcManager } = (0, util_1.getSession)(self);
+    const { adapterConfig } = self;
+    if (!adapterConfig) {
+        // A track extending the base track might not have an adapter config
+        // e.g. Apollo tracks don't use adapters
+        return {};
+    }
+    const sessionId = (0, tracks_1.getRpcSessionId)(self);
+    return rpcManager.call(sessionId, 'CoreEstimateRegionStats', {
+        sessionId,
+        regions,
+        adapterConfig,
+        statusCallback: (message) => {
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setMessage(message);
+            }
+        },
+    });
+}
+exports.estimateRegionsStatsPre = estimateRegionsStatsPre;
 //# sourceMappingURL=util.js.map

package/dist/BaseLinearDisplay/models/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/util.ts"],"names":[],"mappings":";;;AAaA,SAAgB,aAAa,CAAC,UAAkB;IAC9C,IAAI,SAAS,CAAA;IACb,IAAI,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE;QACxC,SAAS,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,UAAU,GAAG,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;KAC7E;SAAM,IAAI,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE;QAC5C,SAAS,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;KAC1E;SAAM;QACL,SAAS,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,QAAQ,CAAA;KAC9C;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAVD,sCAUC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/util.ts"],"names":[],"mappings":";;;AACA,6CAAkE;AAClE,sDAA2D;AAC3D,qDAA4D;AAgB5D,SAAgB,aAAa,CAAC,UAAkB;IAC9C,IAAI,SAAS,CAAA;IACb,IAAI,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE;QACxC,SAAS,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,UAAU,GAAG,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;KAC7E;SAAM,IAAI,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE;QAC5C,SAAS,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;KAC1E;SAAM;QACL,SAAS,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,QAAQ,CAAA;KAC9C;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAVD,sCAUC;AAED,2CAA2C;AAC3C,SAAgB,KAAK,CAAC,EAAU,EAAE,KAAa;IAC7C,MAAM,MAAM,GAAG,OAAO,IAAI,KAAK,WAAW,CAAA;IAC1C,OAAO,QAAQ,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,IAAI,KAAK,EAAE,CAAA;AAChD,CAAC;AAHD,sBAGC;AAEM,KAAK,UAAU,uBAAuB,CAAC,IAAuB;IACnE,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAA0B,CAAA;IAC7D,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,aAAa,CAAA;IAE/C,MAAM,EAAE,UAAU,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,IAAI,CAAC,aAAa,EAAE;QAClB,oEAAoE;QACpE,wCAAwC;QACxC,OAAO,EAAE,CAAA;KACV;IACD,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;IAEvC,OAAO,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,yBAAyB,EAAE;QAC3D,SAAS;QACT,OAAO;QACP,aAAa;QACb,cAAc,EAAE,CAAC,OAAe,EAAE,EAAE;YAClC,IAAI,IAAA,yBAAO,EAAC,IAAI,CAAC,EAAE;gBACjB,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAA;aACzB;QACH,CAAC;KACF,CAAmB,CAAA;AACtB,CAAC;AAvBD,0DAuBC"}

package/dist/LinearBareDisplay/index.js

@@ -12,6 +12,7 @@ exports.default = (pluginManager) => {
         return new pluggableElementTypes_1.DisplayType({
             name: 'LinearBareDisplay',
             configSchema,
+            displayName: 'Bare feature display',
             stateModel: (0, model_1.stateModelFactory)(configSchema),
             trackType: 'BasicTrack',
             viewType: 'LinearGenomeView',

package/dist/LinearBareDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":";;;AACA,+EAAiE;AAEjE,SAAS;AACT,iDAAoD;AACpD,mCAA2C;AAC3C,6DAAkE;AAElE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,kCAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,UAAU,EAAE,IAAA,yBAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,+CAAoD;AAA3C,mHAAA,mBAAmB,OAAA;AAC5B,iCAA2C;AAAlC,0GAAA,iBAAiB,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":";;;AACA,+EAAiE;AAEjE,SAAS;AACT,iDAAoD;AACpD,mCAA2C;AAC3C,6DAAkE;AAElE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,kCAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,WAAW,EAAE,sBAAsB;YACnC,UAAU,EAAE,IAAA,yBAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,+CAAoD;AAA3C,mHAAA,mBAAmB,OAAA;AAC5B,iCAA2C;AAAlC,0GAAA,iBAAiB,OAAA"}

package/dist/LinearBareDisplay/model.d.ts

@@ -125,8 +125,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -139,7 +139,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
@@ -149,19 +149,16 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
+    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionsStatsP(arg: any): void;
+    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionsStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
@@ -175,18 +172,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {

package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts

@@ -2,7 +2,7 @@
 declare function SetMaxHeightDlg({ model, handleClose, }: {
     model: {
         maxHeight?: number;
-        setMaxHeight: Function;
+        setMaxHeight: (arg?: number) => void;
     };
     handleClose: () => void;
 }): JSX.Element;

package/dist/LinearBasicDisplay/components/SetMaxHeight.js

@@ -28,14 +28,11 @@ const mobx_react_1 = require("mobx-react");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useStyles = (0, mui_1.makeStyles)()({
     root: {
         width: 500,
     },
-    field: {
-        margin: theme.spacing(2),
-    },
-}));
+});
 function SetMaxHeightDlg({ model, handleClose, }) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;

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

@@ -1 +1 @@
-{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearBasicDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,yCAAyC;AACzC,4CAMsB;AACtB,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;IAED,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,EACvB,KAAK,EACL,WAAW,GAOZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,iBAAiB,GAC7B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}
+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearBasicDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,yCAAyC;AACzC,4CAMsB;AACtB,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAA;AAEF,SAAS,eAAe,CAAC,EACvB,KAAK,EACL,WAAW,GAOZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,iBAAiB,GAC7B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}

package/dist/LinearBasicDisplay/index.js

@@ -14,7 +14,7 @@ exports.default = (pluginManager) => {
         const config = (0, configSchema_1.default)(pluginManager);
         return new pluggableElementTypes_1.DisplayType({
             name: 'LinearBasicDisplay',
-            displayName: 'Basic deature display',
+            displayName: 'Basic feature display',
             configSchema: config,
             stateModel: (0, model_1.default)(config),
             trackType: 'FeatureTrack',

package/dist/LinearBasicDisplay/model.d.ts

@@ -56,9 +56,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            /**
-             * #method
-             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -67,9 +64,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
-     * #action
-     */
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     /**
      * #property
@@ -144,9 +139,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    /**
-     * #method
-     */
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): undefined;
@@ -160,8 +152,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -174,7 +166,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
@@ -184,19 +176,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
+    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionsStatsP(arg: any): void;
+    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionsStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
@@ -210,18 +199,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
@@ -274,7 +258,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setMaxHeight(val: number): void;
+    setMaxHeight(val?: number): void;
 } & {
     /**
      * #method
@@ -341,9 +325,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            /**
-             * #method
-             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -352,9 +333,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
-     * #action
-     */
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
     id: string;

package/dist/LinearBasicDisplay/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/model.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA4B;AAC5B,+DAIoC;AACpC,6CAA+C;AAE/C,qDAAyD;AAEzD,QAAQ;AACR,gFAA2D;AAE3D,SAAS;AACT,4DAAwD;AAExD,MAAM,eAAe,GAAG,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,2BAA2B,GAAC,CAAC,CAAA;AAEvE;;;;GAIG;AACH,SAAS,iBAAiB,CAAC,YAAwC;IACjE,OAAO,uBAAK;SACT,OAAO,CACN,oBAAoB,EACpB,qCAAiB,EACjB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;QACzC;;WAEG;QACH,eAAe,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QAC3C;;WAEG;QACH,qBAAqB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QACjD;;WAEG;QACH,gBAAgB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QAC3C;;WAEG;QACH,cAAc,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QACzC;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAA;QAC5C,CAAC;QAED;;WAEG;QACH,IAAI,UAAU;;YACZ,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,YAAY,CAAC,CAAC,CAAA;QAC1E,CAAC;QAED;;WAEG;QACH,IAAI,gBAAgB;;YAClB,OAAO,CACL,MAAA,IAAI,CAAC,qBAAqB,mCAC1B,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,kBAAkB,CAAC,CAAC,CAChD,CAAA;QACH,CAAC;QAED;;WAEG;QACH,IAAI,SAAS;;YACX,OAAO,MAAA,IAAI,CAAC,cAAc,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,CAAA;QACxE,CAAC;QAED;;WAEG;QACH,IAAI,WAAW;;YACb,OAAO,CACL,MAAA,IAAI,CAAC,gBAAgB,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,aAAa,CAAC,CAAC,CACpE,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,cAAc;YAChB,MAAM,UAAU,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,CAAC,CAAC,IAAI,EAAE,CAAA;YACpD,MAAM,MAAM,GAAG,UAA6C,CAAA;YAE5D,OAAO,IAAI,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,CAC1C;gBACE,GAAG,MAAM;gBACT,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,WAAW,EAAE,IAAI,CAAC,WAAW;gBAC7B,SAAS,EAAE,IAAI,CAAC,SAAS;aAC1B,EACD,IAAA,wBAAM,EAAC,IAAI,CAAC,CACb,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SAEF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,gBAAgB;YACd,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,UAAU,CAAA;QACzC,CAAC;QACD;;WAEG;QACH,sBAAsB;YACpB,IAAI,CAAC,qBAAqB,GAAG,CAAC,IAAI,CAAC,gBAAgB,CAAA;QACrD,CAAC;QACD;;WAEG;QACH,cAAc,CAAC,GAAW;YACxB,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,GAAY;YACvB,IAAI,CAAC,cAAc,GAAG,GAAG,CAAA;QAC3B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EACJ,cAAc,EAAE,mBAAmB,EACnC,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QACR,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,MAAM,GAAG,IAAI,CAAC,cAAc,CAAA;gBAClC,MAAM,UAAU,GAAG,gBAAgB,EAAE,CAAA;gBACrC,MAAM,cAAc,GAAG,UAA6C,CAAA;gBACpE,OAAO;oBACL,GAAG,cAAc;oBACjB,MAAM;iBACP,CAAA;YACH,CAAC;YAED;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,aAAa;wBACpB,IAAI,EAAE,oBAAc;wBACpB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,UAAU;wBACxB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,gBAAgB,EAAE;qBACvC;oBACD;wBACE,KAAK,EAAE,mBAAmB;wBAC1B,IAAI,EAAE,oBAAc;wBACpB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,gBAAgB;wBAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,sBAAsB,EAAE;qBAC7C;oBACD;wBACE,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,oBAAc;wBACpB,OAAO,EAAE;4BACP,SAAS;4BACT,uBAAuB;4BACvB,QAAQ;4BACR,UAAU;yBACX,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;4BACZ,KAAK,EAAE,GAAG;4BACV,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC;yBACxC,CAAC,CAAC;qBACJ;oBACD;wBACE,KAAK,EAAE,gBAAgB;wBACvB,OAAO,EAAE,GAAG,EAAE;4BACZ,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC1C,eAAe;gCACf,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE;6BAC7B,CAAC,CAAA;wBACJ,CAAC;qBACF;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC;AAKD,kBAAe,iBAAiB,CAAA"}

package/dist/LinearGenomeView/components/RefNameAutocomplete.js

@@ -38,13 +38,12 @@ const Help_1 = __importDefault(require("@mui/icons-material/Help"));
 const HelpDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./HelpDialog'))));
 function aggregateResults(results) {
     const m = {};
-    for (let i = 0; i < results.length; i++) {
-        const r = results[i];
-        const d = r.getDisplayString();
-        if (!m[d]) {
-            m[d] = [];
+    for (const result of results) {
+        const displayString = result.getDisplayString();
+        if (!m[displayString]) {
+            m[displayString] = [];
         }
-        m[d].push(r);
+        m[displayString].push(result);
     }
     return m;
 }
@@ -66,11 +65,8 @@ function getDeduplicatedResult(results) {
 // because they do not have a matchedObject. the trix search results already
 // filter so don't need re-filtering
 function filterOptions(options, searchQuery) {
-    return options.filter(option => {
-        const { result } = option;
-        return (result.getLabel().toLowerCase().includes(searchQuery) ||
-            result.matchedObject);
-    });
+    return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
+        result.matchedObject);
 }
 function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
     const session = (0, util_1.getSession)(model);
@@ -84,15 +80,14 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
     const debouncedSearch = (0, util_1.useDebounce)(currentSearch, 300);
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    const regions = (assembly === null || assembly === void 0 ? void 0 : assembly.regions) || [];
-    const options = (0, react_1.useMemo)(() => regions.map(option => ({
+    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
+    const options = (0, react_1.useMemo)(() => (regions === null || regions === void 0 ? void 0 : regions.map(option => ({
         result: new BaseResults_1.RefSequenceResult({
             refName: option.refName,
             label: option.refName,
             matchedAttribute: 'refName',
         }),
-    })), [regions]);
+    }))) || [], [regions]);
     (0, react_1.useEffect)(() => {
         let active = true;
         (async () => {
@@ -121,8 +116,7 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + icon width + 50 accommodates help icon and search
     // icon
-    const w = (0, util_1.measureText)(inputBoxVal, 16) + 50;
-    const width = Math.min(Math.max(w, minWidth), maxWidth);
+    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 16) + 50, minWidth), maxWidth);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
     return (react_1.default.createElement(react_1.default.Fragment, null,

package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map

@@ -1 +1 @@
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