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

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -4,7 +4,7 @@ import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
 import { getConf } from '@jbrowse/core/configuration';
 import { isAbortException, getContainingView, getContainingTrack, getSession, getViewParams, isSelectionContainer, isSessionModelWithWidgets, isFeature, ReactRendering, } from '@jbrowse/core/util';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
-import { getParentRenderProps, getRpcSessionId, } from '@jbrowse/core/util/tracks';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
 import { autorun } from 'mobx';
 import { addDisposer, isAlive, types } from 'mobx-state-tree';
 // icons
@@ -12,24 +12,7 @@ import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import { Tooltip } from '../components/BaseLinearDisplay';
 import TooLargeMessage from '../components/TooLargeMessage';
 import BlockState, { renderBlockData } from './serverSideRenderedBlock';
-// stabilize clipid under test for snapshot
-function getId(id, index) {
-    const isJest = typeof jest === 'undefined';
-    return `clip-${isJest ? id : 'jest'}-${index}`;
-}
-function getDisplayStr(totalBytes) {
-    let displayBp;
-    if (Math.floor(totalBytes / 1000000) > 0) {
-        displayBp = `${Number.parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
-    }
-    else if (Math.floor(totalBytes / 1000) > 0) {
-        displayBp = `${Number.parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
-    }
-    else {
-        displayBp = `${Math.floor(totalBytes)} bytes`;
-    }
-    return displayBp;
-}
+import { getId, getDisplayStr, estimateRegionsStatsPre } from './util';
 const minDisplayHeight = 20;
 /**
  * #stateModel BaseLinearDisplay
@@ -62,8 +45,8 @@ function stateModelFactory() {
         message: '',
         featureIdUnderMouse: undefined,
         contextMenuFeature: undefined,
-        estimatedRegionStatsP: undefined,
-        estimatedRegionStats: undefined,
+        estimatedRegionsStatsP: undefined,
+        estimatedRegionsStats: undefined,
     }))
         .views(self => ({
         get height() {
@@ -136,7 +119,7 @@ function stateModelFactory() {
         get features() {
             const featureMaps = [];
             for (const block of self.blockState.values()) {
-                if (block && block.features) {
+                if (block === null || block === void 0 ? void 0 : block.features) {
                     featureMaps.push(block.features);
                 }
             }
@@ -182,7 +165,7 @@ function stateModelFactory() {
          */
         get currentBytesRequested() {
             var _a;
-            return ((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
+            return ((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
         },
         /**
          * #getter
@@ -190,7 +173,7 @@ function stateModelFactory() {
         get currentFeatureScreenDensity() {
             var _a;
             const view = getContainingView(self);
-            return (((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
+            return (((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
         },
         /**
          * #getter
@@ -202,7 +185,7 @@ function stateModelFactory() {
          * #getter
          */
         get estimatedStatsReady() {
-            return !!self.estimatedRegionStats;
+            return !!self.estimatedRegionsStats || !!self.userBpPerPxLimit;
         },
         /**
          * #getter
@@ -210,7 +193,7 @@ function stateModelFactory() {
         get maxAllowableBytes() {
             var _a;
             return (self.userByteSizeLimit ||
-                ((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
+                ((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
                 getConf(self, 'fetchSizeLimit'));
         },
     }))
@@ -221,11 +204,13 @@ function stateModelFactory() {
         setMessage(message) {
             self.message = message;
         },
+    }))
+        .actions(self => ({
         afterAttach() {
             // watch the parent's blocks to update our block state when they change,
             // then we recreate the blocks on our own model (creating and deleting to
             // match the parent blocks)
-            const blockWatchDisposer = autorun(() => {
+            addDisposer(self, autorun(() => {
                 const blocksPresent = {};
                 const view = getContainingView(self);
                 if (view.initialized) {
@@ -241,61 +226,38 @@ function stateModelFactory() {
                         }
                     });
                 }
-            });
-            addDisposer(self, blockWatchDisposer);
+            }));
         },
         /**
          * #action
          */
-        estimateRegionsStats(regions, opts) {
-            if (self.estimatedRegionStatsP) {
-                return self.estimatedRegionStatsP;
-            }
-            const { rpcManager } = 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 Promise.resolve({});
+        async estimateRegionsStats() {
+            if (!self.estimatedRegionsStatsP) {
+                self.estimatedRegionsStatsP = estimateRegionsStatsPre(self).catch(e => {
+                    this.setRegionsStatsP(undefined);
+                    throw e;
+                });
             }
-            const sessionId = getRpcSessionId(self);
-            const params = {
-                sessionId,
-                regions,
-                adapterConfig,
-                statusCallback: (message) => {
-                    if (isAlive(self)) {
-                        this.setMessage(message);
-                    }
-                },
-                ...opts,
-            };
-            self.estimatedRegionStatsP = rpcManager
-                .call(sessionId, 'CoreEstimateRegionStats', params)
-                .catch(e => {
-                this.setRegionStatsP(undefined);
-                throw e;
-            });
-            return self.estimatedRegionStatsP;
+            return self.estimatedRegionsStatsP;
         },
         /**
          * #action
          */
-        setRegionStatsP(p) {
-            self.estimatedRegionStatsP = p;
+        setRegionsStatsP(arg) {
+            self.estimatedRegionsStatsP = arg;
         },
         /**
          * #action
          */
-        setRegionStats(estimatedRegionStats) {
-            self.estimatedRegionStats = estimatedRegionStats;
+        setRegionsStats(estimatedRegionsStats) {
+            self.estimatedRegionsStats = estimatedRegionsStats;
         },
         /**
          * #action
          */
-        clearRegionStats() {
-            self.estimatedRegionStatsP = undefined;
-            self.estimatedRegionStats = undefined;
+        clearRegionsStats() {
+            self.estimatedRegionsStatsP = undefined;
+            self.estimatedRegionsStats = undefined;
         },
         /**
          * #action
@@ -324,7 +286,7 @@ function stateModelFactory() {
          */
         updateStatsLimit(stats) {
             const view = getContainingView(self);
-            if (stats.bytes) {
+            if (stats === null || stats === void 0 ? void 0 : stats.bytes) {
                 self.userByteSizeLimit = stats.bytes;
             }
             else {
@@ -409,11 +371,10 @@ function stateModelFactory() {
             if (!self.estimatedStatsReady || view.dynamicBlocks.totalBp < 20000) {
                 return false;
             }
-            const bpLimitOrDensity = self.userBpPerPxLimit
-                ? view.bpPerPx > self.userBpPerPxLimit
-                : self.currentFeatureScreenDensity > self.maxFeatureScreenDensity;
             return (self.currentBytesRequested > self.maxAllowableBytes ||
-                bpLimitOrDensity);
+                (self.userBpPerPxLimit
+                    ? view.bpPerPx > self.userBpPerPxLimit
+                    : self.currentFeatureScreenDensity > self.maxFeatureScreenDensity));
         },
         /**
          * #getter
@@ -436,7 +397,6 @@ function stateModelFactory() {
              */
             async reload() {
                 self.setError();
-                const aborter = new AbortController();
                 const view = getContainingView(self);
                 // extra check for contentBlocks.length
                 // https://github.com/GMOD/jbrowse-components/issues/2694
@@ -444,68 +404,63 @@ function stateModelFactory() {
                     return;
                 }
                 try {
-                    self.estimatedRegionStatsP = self.estimateRegionsStats(view.staticBlocks.contentBlocks, { signal: aborter.signal });
-                    const estimatedRegionStats = await self.estimatedRegionStatsP;
+                    const estimatedRegionsStats = await self.estimateRegionsStats();
                     if (isAlive(self)) {
-                        self.setRegionStats(estimatedRegionStats);
+                        self.setRegionsStats(estimatedRegionsStats);
                         superReload();
                     }
-                    else {
-                        return;
-                    }
                 }
                 catch (e) {
                     console.error(e);
                     self.setError(e);
                 }
             },
-            afterAttach() {
-                // this autorun performs stats estimation
-                //
-                // the chain of events calls estimateRegionsStats against the data
-                // adapter which by default uses featureDensity, but can also respond
-                // with a byte size estimate and fetch size limit (data adapter can
-                // define what is too much data)
-                addDisposer(self, autorun(async () => {
-                    var _a;
-                    try {
-                        const aborter = new AbortController();
-                        const view = getContainingView(self);
-                        // extra check for contentBlocks.length
-                        // https://github.com/GMOD/jbrowse-components/issues/2694
-                        if (!view.initialized ||
-                            !view.staticBlocks.contentBlocks.length) {
-                            return;
-                        }
-                        // don't re-estimate featureDensity even if zoom level changes,
-                        // jbrowse1-style assume it's sort of representative
-                        if (((_a = self.estimatedRegionStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
-                            self.setCurrBpPerPx(view.bpPerPx);
-                            return;
-                        }
-                        // we estimate stats once at a given zoom level
-                        if (view.bpPerPx === self.currBpPerPx) {
-                            return;
-                        }
-                        self.clearRegionStats();
+        };
+    })
+        .actions(self => ({
+        afterAttach() {
+            // this autorun performs stats estimation
+            //
+            // the chain of events calls estimateRegionsStats against the data
+            // adapter which by default uses featureDensity, but can also respond
+            // with a byte size estimate and fetch size limit (data adapter can
+            // define what is too much data)
+            addDisposer(self, autorun(async () => {
+                var _a;
+                try {
+                    const view = getContainingView(self);
+                    // extra check for contentBlocks.length
+                    // https://github.com/GMOD/jbrowse-components/issues/2694
+                    if (!view.initialized ||
+                        !view.staticBlocks.contentBlocks.length) {
+                        return;
+                    }
+                    // don't re-estimate featureDensity even if zoom level changes,
+                    // jbrowse1-style assume it's sort of representative
+                    if (((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
                         self.setCurrBpPerPx(view.bpPerPx);
-                        const statsP = self.estimateRegionsStats(view.staticBlocks.contentBlocks, { signal: aborter.signal });
-                        self.setRegionStatsP(statsP);
-                        const estimatedRegionStats = await statsP;
-                        if (isAlive(self)) {
-                            self.setRegionStats(estimatedRegionStats);
-                        }
+                        return;
                     }
-                    catch (e) {
-                        if (!isAbortException(e) && isAlive(self)) {
-                            console.error(e);
-                            self.setError(e);
-                        }
+                    // we estimate stats once at a given zoom level
+                    if (view.bpPerPx === self.currBpPerPx) {
+                        return;
                     }
-                }, { delay: 500 }));
-            },
-        };
-    })
+                    self.clearRegionsStats();
+                    self.setCurrBpPerPx(view.bpPerPx);
+                    const estimatedRegionsStats = await self.estimateRegionsStats();
+                    if (isAlive(self)) {
+                        self.setRegionsStats(estimatedRegionsStats);
+                    }
+                }
+                catch (e) {
+                    if (!isAbortException(e) && isAlive(self)) {
+                        console.error(e);
+                        self.setError(e);
+                    }
+                }
+            }));
+        },
+    }))
         .views(self => ({
         /**
          * #method
@@ -522,8 +477,7 @@ function stateModelFactory() {
          *  react node allows user to force load at current setting
          */
         regionCannotBeRendered(_region) {
-            const { regionTooLarge } = self;
-            return regionTooLarge ? React.createElement(TooLargeMessage, { model: self }) : null;
+            return self.regionTooLarge ? React.createElement(TooLargeMessage, { model: self }) : null;
         },
         /**
          * #method
@@ -535,19 +489,21 @@ function stateModelFactory() {
          * #method
          */
         contextMenuItems() {
-            return self.contextMenuFeature
-                ? [
-                    {
-                        label: 'Open feature details',
-                        icon: MenuOpenIcon,
-                        onClick: () => {
-                            if (self.contextMenuFeature) {
-                                self.selectFeature(self.contextMenuFeature);
-                            }
+            return [
+                ...(self.contextMenuFeature
+                    ? [
+                        {
+                            label: 'Open feature details',
+                            icon: MenuOpenIcon,
+                            onClick: () => {
+                                if (self.contextMenuFeature) {
+                                    self.selectFeature(self.contextMenuFeature);
+                                }
+                            },
                         },
-                    },
-                ]
-                : [];
+                    ]
+                    : []),
+            ];
         },
         /**
          * #method
@@ -556,7 +512,7 @@ function stateModelFactory() {
             const view = getContainingView(self);
             return {
                 ...getParentRenderProps(self),
-                notReady: self.currBpPerPx !== view.bpPerPx || !self.estimatedRegionStats,
+                notReady: self.currBpPerPx !== view.bpPerPx || !self.estimatedRegionsStats,
                 rpcDriverName: self.rpcDriverName,
                 displayModel: self,
                 onFeatureClick(_, featureId) {

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

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package/esm/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/esm/BaseLinearDisplay/models/util.js

@@ -1,3 +1,6 @@
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { isAlive } from 'mobx-state-tree';
 export function getDisplayStr(totalBytes) {
     let displayBp;
     if (Math.floor(totalBytes / 1000000) > 0) {
@@ -11,4 +14,31 @@ export function getDisplayStr(totalBytes) {
     }
     return displayBp;
 }
+// stabilize clipid under test for snapshot
+export function getId(id, index) {
+    const isJest = typeof jest === 'undefined';
+    return `clip-${isJest ? id : 'jest'}-${index}`;
+}
+export async function estimateRegionsStatsPre(self) {
+    const view = getContainingView(self);
+    const regions = view.staticBlocks.contentBlocks;
+    const { rpcManager } = 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 = getRpcSessionId(self);
+    return rpcManager.call(sessionId, 'CoreEstimateRegionStats', {
+        sessionId,
+        regions,
+        adapterConfig,
+        statusCallback: (message) => {
+            if (isAlive(self)) {
+                self.setMessage(message);
+            }
+        },
+    });
+}
 //# sourceMappingURL=util.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EAAqB,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAgB5D,MAAM,UAAU,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;AAED,2CAA2C;AAC3C,MAAM,UAAU,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;AAED,MAAM,CAAC,KAAK,UAAU,uBAAuB,CAAC,IAAuB;IACnE,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC7D,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,aAAa,CAAA;IAE/C,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,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,eAAe,CAAC,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,OAAO,CAAC,IAAI,CAAC,EAAE;gBACjB,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAA;aACzB;QACH,CAAC;KACF,CAAmB,CAAA;AACtB,CAAC"}

package/esm/LinearBareDisplay/index.js

@@ -9,6 +9,7 @@ export default (pluginManager) => {
         return new DisplayType({
             name: 'LinearBareDisplay',
             configSchema,
+            displayName: 'Bare feature display',
             stateModel: stateModelFactory(configSchema),
             trackType: 'BasicTrack',
             viewType: 'LinearGenomeView',

package/esm/LinearBareDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,SAAS;AACT,OAAO,EAAE,mBAAmB,EAAE,MAAM,gBAAgB,CAAA;AACpD,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAC3C,OAAO,EAAE,0BAA0B,EAAE,MAAM,uBAAuB,CAAA;AAElE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,WAAW,EAAE,sBAAsB;YACnC,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,OAAO,EAAE,mBAAmB,EAAE,MAAM,gBAAgB,CAAA;AACpD,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA"}

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

@@ -3,14 +3,11 @@ import { observer } from 'mobx-react';
 import { Dialog } from '@jbrowse/core/ui';
 import { Button, DialogActions, DialogContent, Typography, TextField, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
+const useStyles = makeStyles()({
     root: {
         width: 500,
     },
-    field: {
-        margin: theme.spacing(2),
-    },
-}));
+});
 function SetMaxHeightDlg({ model, handleClose, }) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;

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

@@ -1 +1 @@
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+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearBasicDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,UAAU,EACV,SAAS,GACV,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,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,QAAQ,CAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,UAAU,qHAGE;YACb,oBAAC,SAAS,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,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,oBAAC,MAAM,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,eAAe,QAAQ,CAAC,eAAe,CAAC,CAAA"}

package/esm/LinearBasicDisplay/index.js

@@ -8,7 +8,7 @@ export default (pluginManager) => {
         const config = configSchema(pluginManager);
         return new DisplayType({
             name: 'LinearBasicDisplay',
-            displayName: 'Basic deature display',
+            displayName: 'Basic feature display',
             configSchema: config,
             stateModel: modelFactory(config),
             trackType: 'FeatureTrack',