@jbrowse/plugin-linear-genome-view 4.0.3 → 4.1.1

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

@@ -8,6 +8,7 @@ export interface NonBlockCanvasDisplayModel {
     drawn: boolean;
     loading: boolean;
     lastDrawnOffsetPx?: number;
+    lastDrawnBpPerPx?: number;
     statusMessage?: string;
     showLegend?: boolean;
     legendItems?: () => LegendItem[];

package/esm/BaseLinearDisplay/components/NonBlockCanvasDisplayComponent.js

@@ -31,14 +31,18 @@ const NonBlockCanvasDisplayComponent = observer(function NonBlockCanvasDisplayCo
     return error ? (_jsx(BlockErrorMessage, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : (_jsx(DataDisplay, { model: model, children: children }));
 });
 const DataDisplay = observer(function DataDisplay({ model, children, }) {
-    const { drawn, loading, showLegend, legendItems } = model;
+    const { drawn, loading, showLegend, legendItems, lastDrawnBpPerPx } = model;
     const view = getContainingView(model);
     const items = legendItems?.() ?? [];
-    const calculatedLeft = (model.lastDrawnOffsetPx ?? 0) - view.offsetPx;
+    const hasZoomed = lastDrawnBpPerPx !== undefined && lastDrawnBpPerPx !== view.bpPerPx;
+    const calculatedLeft = hasZoomed
+        ? 0
+        : (model.lastDrawnOffsetPx ?? 0) - view.offsetPx;
     return (_jsxs("div", { "data-testid": `drawn-${drawn}`, children: [_jsx("div", { style: {
                     position: 'absolute',
                     left: calculatedLeft,
-                }, children: children }), showLegend && items.length > 0 ? _jsx(FloatingLegend, { items: items }) : null, calculatedLeft !== 0 || loading ? _jsx(LoadingBar, { model: model }) : null] }));
+                    visibility: hasZoomed ? 'hidden' : undefined,
+                }, children: children }), showLegend && items.length > 0 ? _jsx(FloatingLegend, { items: items }) : null, hasZoomed || calculatedLeft !== 0 || loading ? (_jsx(LoadingBar, { model: model })) : null] }));
 });
 const LoadingBar = observer(function LoadingBar({ model, }) {
     const { classes } = useStyles();

package/esm/BaseLinearDisplay/components/Tooltip.js

@@ -11,7 +11,7 @@ const Tooltip = observer(function Tooltip({ model, clientMouseCoord, }) {
     const { featureUnderMouse, featureIdUnderMouse, mouseoverExtraInformation } = model;
     const x = clientMouseCoord[0] + 15;
     const y = clientMouseCoord[1];
-    const contents = useMemo(() => featureUnderMouse || mouseoverExtraInformation
+    const contents = useMemo(() => featureUnderMouse && mouseoverExtraInformation
         ? getConf(model, 'mouseover', {
             feature: featureUnderMouse,
             mouseoverExtraInformation,

package/esm/BaseLinearDisplay/model.d.ts

@@ -139,6 +139,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -195,6 +196,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -248,6 +250,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -529,6 +532,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -585,6 +589,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -638,6 +643,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -864,6 +870,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -920,6 +927,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -973,6 +981,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/BaseLinearDisplay/model.js

@@ -10,13 +10,13 @@ import CloseFullscreenIcon from '@mui/icons-material/CloseFullscreen';
 import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import { autorun } from 'mobx';
+import { calculateSvgLegendWidth } from "./calculateSvgLegendWidth.js";
 import { deduplicateFeatureLabels } from "./components/util.js";
-import { calculateSvgLegendWidth } from "./index.js";
 import FeatureDensityMixin from "./models/FeatureDensityMixin.js";
 import TrackHeightMixin from "./models/TrackHeightMixin.js";
 import configSchema from "./models/configSchema.js";
 import BlockState from "./models/serverSideRenderedBlock.js";
-import { fetchFeatureByIdRpc, findSubfeatureById, getTranscripts, hasExonsOrCDS, } from "./util.js";
+import { fetchFeatureByIdRpc, findSubfeatureById, getTranscripts, hasIntrons, } from "./util.js";
 const Tooltip = lazy(() => import("./components/Tooltip.js"));
 const CollapseIntronsDialog = lazy(() => import("./components/CollapseIntronsDialog/CollapseIntronsDialog.js"));
 function stateModelFactory() {
@@ -321,7 +321,7 @@ function stateModelFactory() {
                             session.notify('Copied to clipboard', 'success');
                         },
                     },
-                    ...(hasExonsOrCDS(transcripts)
+                    ...(hasIntrons(transcripts)
                         ? [
                             {
                                 label: 'Collapse introns',
@@ -379,7 +379,7 @@ function stateModelFactory() {
         afterAttach() {
             addDisposer(self, autorun(function blockDefinitionsAutorun() {
                 try {
-                    if (!isAlive(self)) {
+                    if (!isAlive(self) || self.isMinimized) {
                         return;
                     }
                     const view = getContainingView(self);

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

@@ -2,19 +2,24 @@ import type { StopToken } from '@jbrowse/core/util/stopToken';
 export default function NonBlockCanvasDisplayMixin(): import("@jbrowse/mobx-state-tree").IModelType<{}, {
     loading: boolean;
     lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number | undefined;
     ref: HTMLCanvasElement | null;
     renderingImageData: ImageBitmap | undefined;
     renderingStopToken: StopToken | undefined;
     statusMessage: string | undefined;
+    canvasDrawn: boolean;
 } & {
     readonly drawn: boolean;
+    readonly fullyDrawn: boolean;
 } & {
     setLastDrawnOffsetPx(n: number): void;
+    setLastDrawnBpPerPx(n: number): void;
     setLoading(f: boolean): void;
     setRef(ref: HTMLCanvasElement | null): void;
     setRenderingImageData(imageData: ImageBitmap | undefined): void;
     setRenderingStopToken(token?: StopToken): void;
     setStatusMessage(msg?: string): void;
+    setCanvasDrawn(drawn: boolean): void;
 } & {
     beforeDestroy(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/BaseLinearDisplay/models/NonBlockCanvasDisplayMixin.js

@@ -6,20 +6,28 @@ export default function NonBlockCanvasDisplayMixin() {
         .volatile(() => ({
         loading: false,
         lastDrawnOffsetPx: undefined,
+        lastDrawnBpPerPx: undefined,
         ref: null,
         renderingImageData: undefined,
         renderingStopToken: undefined,
         statusMessage: undefined,
+        canvasDrawn: false,
     }))
         .views(self => ({
         get drawn() {
             return self.lastDrawnOffsetPx !== undefined;
         },
+        get fullyDrawn() {
+            return this.drawn && !self.loading && self.canvasDrawn;
+        },
     }))
         .actions(self => ({
         setLastDrawnOffsetPx(n) {
             self.lastDrawnOffsetPx = n;
         },
+        setLastDrawnBpPerPx(n) {
+            self.lastDrawnBpPerPx = n;
+        },
         setLoading(f) {
             self.loading = f;
         },
@@ -35,6 +43,9 @@ export default function NonBlockCanvasDisplayMixin() {
         setStatusMessage(msg) {
             self.statusMessage = msg;
         },
+        setCanvasDrawn(drawn) {
+            self.canvasDrawn = drawn;
+        },
     }))
         .actions(self => ({
         beforeDestroy() {

package/esm/BaseLinearDisplay/util.d.ts

@@ -11,5 +11,6 @@ export declare function fetchFeatureByIdRpc({ rpcManager, sessionId, trackId, re
 export declare function findSubfeatureById(feature: Feature, targetId: string): Feature | undefined;
 export declare function featureHasExonsOrCDS(feature: Feature): boolean;
 export declare function hasExonsOrCDS(transcripts: Feature[]): boolean;
+export declare function hasIntrons(transcripts: Feature[]): boolean;
 export declare function getTranscripts(feature?: Feature): Feature[];
 export declare function drawCanvasImageData(canvas: HTMLCanvasElement | null, imageData: ImageBitmap | undefined): boolean;

package/esm/BaseLinearDisplay/util.js

@@ -1,4 +1,4 @@
-import { SimpleFeature } from '@jbrowse/core/util';
+import { SimpleFeature, mergeIntervals } from '@jbrowse/core/util';
 export async function fetchFeatureByIdRpc({ rpcManager, sessionId, trackId, rendererType, featureId, parentFeatureId, }) {
     const lookupId = parentFeatureId || featureId;
     const { feature: featureData } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
@@ -38,6 +38,16 @@ export function featureHasExonsOrCDS(feature) {
 export function hasExonsOrCDS(transcripts) {
     return transcripts.some(t => featureHasExonsOrCDS(t));
 }
+export function hasIntrons(transcripts) {
+    const subs = transcripts.flatMap(transcript => transcript
+        .get('subfeatures')
+        ?.filter((f) => f.get('type') === 'exon' || f.get('type') === 'CDS') ?? []);
+    if (subs.length < 2) {
+        return false;
+    }
+    const merged = mergeIntervals(subs.map((f) => ({ start: f.get('start'), end: f.get('end') })), 0);
+    return merged.length > 1;
+}
 export function getTranscripts(feature) {
     if (!feature) {
         return [];

package/esm/LinearBareDisplay/model.d.ts

@@ -134,6 +134,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -190,6 +191,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -243,6 +245,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -524,6 +527,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -580,6 +584,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -633,6 +638,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -859,6 +865,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -915,6 +922,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -968,6 +976,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/LinearBasicDisplay/model.d.ts

@@ -1,5 +1,5 @@
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { MenuItem } from '@jbrowse/core/ui';
+import type { MenuItem, SubMenuItem } from '@jbrowse/core/ui';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -93,7 +93,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     trackDisplayMode: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     configuration: AnyConfigurationSchemaType;
-    jexlFilters: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
+    jexlFiltersSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 } & {
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
     trackGeneGlyphMode: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -147,6 +147,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -203,6 +204,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -256,6 +258,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -537,6 +540,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -593,6 +597,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -646,6 +651,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -872,6 +878,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -928,6 +935,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -981,6 +989,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1087,7 +1096,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
 } & {
-    readonly activeFilters: any;
+    activeFilters(): string[];
     readonly rendererTypeName: any;
     readonly sequenceAdapter: any;
     readonly showLabels: any;
@@ -1175,6 +1184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1228,11 +1238,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
+    filterMenuItems(): MenuItem[];
+} & {
     trackMenuItems(): MenuItem[];
+} & {
+    afterAttach(): void;
 } & {
     readonly geneGlyphMode: any;
     readonly subfeatureLabels: any;
@@ -1251,6 +1266,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setGeneGlyphMode(val: string): void;
     setSubfeatureLabels(val: string): void;
     toggleDisplayDirectionalChevrons(): void;
+} & {
+    filterMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | SubMenuItem | {
+        label: string;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+    })[];
 } & {
     trackMenuItems(): MenuItem[];
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
@@ -1345,7 +1367,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     trackDisplayMode: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     configuration: AnyConfigurationSchemaType;
-    jexlFilters: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
+    jexlFiltersSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 } & {
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
     trackGeneGlyphMode: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;

package/esm/LinearBasicDisplay/model.js

@@ -55,6 +55,31 @@ function stateModelFactory(configSchema) {
             self.trackDisplayDirectionalChevrons = !self.displayDirectionalChevrons;
         },
     }))
+        .views(self => {
+        const { filterMenuItems: superFilterMenuItems } = self;
+        return {
+            filterMenuItems() {
+                const filters = self.activeFilters();
+                return [
+                    {
+                        label: 'Show only genes',
+                        type: 'checkbox',
+                        checked: filters.includes("jexl:get(feature,'type')=='gene'"),
+                        onClick: () => {
+                            const geneFilter = "jexl:get(feature,'type')=='gene'";
+                            if (filters.includes(geneFilter)) {
+                                self.setJexlFilters(filters.filter(f => f !== geneFilter));
+                            }
+                            else {
+                                self.setJexlFilters([...filters, geneFilter]);
+                            }
+                        },
+                    },
+                    ...superFilterMenuItems(),
+                ];
+            },
+        };
+    })
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
@@ -109,27 +134,6 @@ function stateModelFactory(configSchema) {
                         },
                     ];
                 }
-                const filtersMenu = findSubMenu(items, 'Filters');
-                if (filtersMenu) {
-                    filtersMenu.subMenu = [
-                        {
-                            label: 'Show only genes',
-                            type: 'checkbox',
-                            checked: self.activeFilters.includes("jexl:get(feature,'type')=='gene'"),
-                            onClick: () => {
-                                const geneFilter = "jexl:get(feature,'type')=='gene'";
-                                const currentFilters = self.activeFilters;
-                                if (currentFilters.includes(geneFilter)) {
-                                    self.setJexlFilters(currentFilters.filter((f) => f !== geneFilter));
-                                }
-                                else {
-                                    self.setJexlFilters([...currentFilters, geneFilter]);
-                                }
-                            },
-                        },
-                        ...filtersMenu.subMenu,
-                    ];
-                }
                 return items;
             },
         };

package/esm/LinearFeatureDisplay/components/AddFiltersDialog.d.ts

@@ -1,7 +1,7 @@
 declare const AddFiltersDialog: ({ model, handleClose, }: {
     model: {
         jexlFilters?: string[];
-        activeFilters: string[];
+        activeFilters: () => string[];
         setJexlFilters: (arg?: string[]) => void;
     };
     handleClose: () => void;

package/esm/LinearFeatureDisplay/components/AddFiltersDialog.js

@@ -23,17 +23,16 @@ function checkJexl(code) {
 const AddFiltersDialog = observer(function AddFiltersDialog({ model, handleClose, }) {
     const { classes } = useStyles();
     const { activeFilters } = model;
-    const [data, setData] = useState(activeFilters.join('\n'));
+    const [data, setData] = useState(activeFilters().join('\n'));
     const [error, setError] = useState();
     useEffect(() => {
         try {
-            data
+            for (const line of data
                 .split('\n')
                 .map(line => line.trim())
-                .filter(line => !!line)
-                .map(line => {
-                checkJexl(line.trim());
-            });
+                .filter(line => !!line)) {
+                checkJexl(line);
+            }
             setError(undefined);
         }
         catch (e) {
@@ -41,7 +40,7 @@ const AddFiltersDialog = observer(function AddFiltersDialog({ model, handleClose
             setError(e);
         }
     }, [data]);
-    return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [_jsxs(DialogContent, { children: [_jsxs("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', _jsxs("ul", { children: [_jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'end') - get(feature,'start') < 1000000" }), ' ', "- show only features with length less than 1Mbp"] })] })] }), error ? _jsx("p", { className: classes.error, children: `${error}` }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
+    return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [_jsxs(DialogContent, { children: [_jsxs("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', _jsxs("ul", { children: [_jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:startsWith(get(feature,'name'),'PREFIX')" }), " - show only feature where the string 'PREFIX' is the prefix of feature name. endsWith also works"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:includes(get(feature,'name'),'PREFIX')" }), " - show only feature where the string 'PREFIX' is the prefix of feature name"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'end') - get(feature,'start') < 1000000" }), ' ', "- show only features with length less than 1Mbp"] })] }), _jsxs("p", { children: ["Please see", ' ', _jsx("a", { href: "https://jbrowse.org/jb2/docs/config_guides/jexl/", children: "Jexl" }), ' ', "documentation for more information"] })] }), error ? _jsx("p", { className: classes.error, children: `${error}` }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
                             setData(event.target.value);
                         }, slotProps: {
                             input: {