@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/LinearReadCloudDisplay/drawFeats.js.map

@@ -1 +1 @@
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+{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/drawFeats.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAKlE,OAAO,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAA;AACjD,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AAIzD,MAAM,UAAU,SAAS,CACvB,IAAiC,EACjC,GAA6B;IAE7B,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAA;IAC1B,IAAI,CAAC,SAAS,EAAE;QACd,OAAM;KACP;IACD,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;IAC3C,MAAM,YAAY,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAC1C,MAAM,GAAG,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAC7C,IAAI,CAAC,GAAG,EAAE;QACR,OAAM;KACP;IAED,MAAM,SAAS,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;IAE3C,IAAI,SAAS,EAAE;QACb,cAAc,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;KACpD;SAAM;QACL,kBAAkB,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;KACxD;AACH,CAAC"}

package/esm/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -0,0 +1,11 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { ChainData } from '../shared/fetchChains';
+import { LinearReadCloudDisplayModel } from './model';
+export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
+    ctx: CanvasRenderingContext2D;
+    self: LinearReadCloudDisplayModel;
+    chainData: ChainData;
+    view: LinearGenomeViewModel;
+    asm: Assembly;
+}): void;

package/esm/LinearReadCloudDisplay/drawLongReadChains.js

@@ -0,0 +1,65 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { max, min } from '@jbrowse/core/util';
+import { fillColor, strokeColor } from '../shared/color';
+import { fillRectCtx, strokeRectCtx } from './util';
+export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
+    var _a, _b, _c, _d, _e;
+    const distances = [];
+    const minXs = [];
+    const { chains } = chainData;
+    const { height } = self;
+    const featureHeight = getConf(self, 'featureHeight');
+    // get bounds on the 'distances' (pixel span that a particular split long
+    // read 'chain' would have in view)
+    for (const chain of chains) {
+        let minX = Number.MAX_VALUE;
+        let maxX = Number.MIN_VALUE;
+        for (const elt of chain) {
+            const refName = asm.getCanonicalRefName(elt.refName) || elt.refName;
+            const rs = (_a = view.bpToPx({ refName, coord: elt.start })) === null || _a === void 0 ? void 0 : _a.offsetPx;
+            const re = (_b = view.bpToPx({ refName, coord: elt.end })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+            if (rs !== undefined && re !== undefined) {
+                minX = Math.min(minX, rs);
+                maxX = Math.max(maxX, re);
+            }
+        }
+        const distance = Math.abs(maxX - minX);
+        distances.push(distance);
+        minXs.push(minX);
+    }
+    const maxD = Math.log(max(distances));
+    const minD = Math.max(Math.log(min(distances)) - 1, 0);
+    const scaler = (height - 20) / (maxD - minD);
+    const halfHeight = featureHeight / 2 - 0.5;
+    // draw split long read 'chains' as connected entities
+    for (let i = 0; i < chains.length; i++) {
+        const chain = chains[i];
+        const w = distances[i];
+        const top = (Math.log(w) - minD) * scaler;
+        const min = minXs[i];
+        fillRectCtx(min - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
+        const c1 = chain[0];
+        let primaryStrand;
+        if (!(c1.flags & 2048)) {
+            primaryStrand = c1.strand;
+        }
+        else {
+            const res = (_c = c1.SA) === null || _c === void 0 ? void 0 : _c.split(';')[0].split(',')[2];
+            primaryStrand = res === '-' ? -1 : 1;
+        }
+        for (const v0 of chain) {
+            const ra = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const rs = (_d = view.bpToPx({ refName: ra, coord: v0.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
+            const re = (_e = view.bpToPx({ refName: ra, coord: v0.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
+            if (rs !== undefined && re !== undefined) {
+                const w = Math.max(re - rs, 2);
+                const l = rs - view.offsetPx;
+                const effectiveStrand = v0.strand * primaryStrand;
+                const c = effectiveStrand === -1 ? 'color_rev_strand' : 'color_fwd_strand';
+                strokeRectCtx(l, top, w, featureHeight, ctx, strokeColor[c]);
+                fillRectCtx(l, top, w, featureHeight, ctx, fillColor[c]);
+            }
+        }
+    }
+}
+//# sourceMappingURL=drawLongReadChains.js.map

package/esm/LinearReadCloudDisplay/drawLongReadChains.js.map

@@ -0,0 +1 @@
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package/esm/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -0,0 +1,17 @@
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
+import { LinearReadCloudDisplayModel } from './model';
+export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
+    ctx: CanvasRenderingContext2D;
+    self: LinearReadCloudDisplayModel;
+    chainData: ChainData;
+    view: LinearGenomeViewModel;
+    asm: Assembly;
+}): void;
+export declare function getPairedColor({ type, v0, v1, stats, }: {
+    type: string;
+    v0: ReducedFeature;
+    v1: ReducedFeature;
+    stats?: ChainStats;
+}): readonly [string, string] | undefined;

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -0,0 +1,95 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { max, min } from '@jbrowse/core/util';
+import { fillRectCtx, strokeRectCtx } from './util';
+import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from '../shared/color';
+export function drawPairChains({ ctx, self, chainData, view, asm, }) {
+    var _a, _b, _c, _d, _e, _f, _g;
+    const coords = [];
+    const featureHeight = getConf(self, 'featureHeight');
+    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
+    const { chains, stats } = chainData;
+    for (const chain of chains) {
+        // if we're looking at a paired read (flag 1) then assume it is just
+        // two reads (some small cases may defy this assumption such as
+        // secondary alignments but this may be uncommon)
+        if (chain.length > 1) {
+            const v0 = chain[0];
+            const v1 = chain[1];
+            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
+            const r1s = (_b = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+            const r1e = (_c = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _c === void 0 ? void 0 : _c.offsetPx;
+            const r2s = (_d = view.bpToPx({ refName: ra2, coord: v1.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
+            const r2e = (_e = view.bpToPx({ refName: ra2, coord: v1.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
+            let distance = 0;
+            if (r1s !== undefined &&
+                r1e !== undefined &&
+                r2s !== undefined &&
+                r2e !== undefined) {
+                if (v0.refName === v1.refName) {
+                    const s = Math.min(v0.start, v1.start);
+                    const e = Math.max(v0.end, v1.end);
+                    distance = Math.abs(e - s);
+                }
+                coords.push({
+                    r1s,
+                    r1e,
+                    r2s,
+                    r2e,
+                    v0,
+                    v1,
+                    distance,
+                });
+            }
+        }
+        else if (self.drawSingletons) {
+            const v0 = chain[0];
+            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const r1s = (_f = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _f === void 0 ? void 0 : _f.offsetPx;
+            const r1e = (_g = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _g === void 0 ? void 0 : _g.offsetPx;
+            if (r1s !== undefined && r1e !== undefined) {
+                const w1 = Math.max(r1e - r1s, 2);
+                fillRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00');
+                strokeRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00');
+            }
+        }
+    }
+    const maxD = Math.log(max(coords.map(c => c.distance)));
+    const minD = Math.max(Math.log(min(coords.map(c => c.distance))) - 1, 0);
+    const scaler = (self.height - 20) / (maxD - minD);
+    for (let i = 0; i < coords.length; i++) {
+        const { r1e, r1s, r2e, r2s, distance, v0, v1 } = coords[i];
+        const w1 = Math.max(r1e - r1s, 2);
+        const w2 = Math.max(r2e - r2s, 2);
+        const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || [];
+        const top = (Math.log(distance) - minD) * scaler;
+        const halfHeight = featureHeight / 2 - 0.5;
+        const w = r2s - r1e;
+        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
+        strokeRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke);
+        strokeRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke);
+        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill);
+        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill);
+    }
+}
+export function getPairedColor({ type, v0, v1, stats, }) {
+    if (type === 'insertSizeAndOrientation') {
+        return getPairedInsertSizeAndOrientationColor(v0, v1, stats);
+    }
+    else if (type === 'orientation') {
+        return getPairedOrientationColor(v0);
+    }
+    else if (type === 'insertSize') {
+        return getPairedInsertSizeColor(v0, v1, stats);
+    }
+    else if (type === 'gradient') {
+        const s = Math.min(v0.start, v1.start);
+        const e = Math.max(v0.end, v1.end);
+        return [
+            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,
+            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,
+        ];
+    }
+    return undefined;
+}
+//# sourceMappingURL=drawPairChains.js.map

package/esm/LinearReadCloudDisplay/drawPairChains.js.map

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package/esm/LinearReadCloudDisplay/model.d.ts

@@ -13,7 +13,7 @@ interface Filter {
 }
 /**
  * #stateModel LinearReadCloudDisplay
- * extends `BaseLinearDisplay`
+ * extends `BaseDisplay`, it is not a block based track, hence not BaseLinearDisplay
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -21,70 +21,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }, {
-        renderInProgress: AbortController | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined; /**
-         * #action
-         */
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void; /**
-         * #action
-         */
-        setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        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>>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
-    /**
-     * #property
-     */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
-    /**
-     * #property
-     */
+    configuration: AnyConfigurationSchemaType;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -94,17 +36,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             value: import("mobx-state-tree").ISimpleType<string>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    /**
-     * #property
-     */
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         extra: import("mobx-state-tree").IType<any, any, any>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
@@ -114,6 +55,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<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>;
@@ -121,6 +63,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -133,13 +76,19 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<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>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             * internal, a reference to a HTMLCanvas because we use a autorun to draw
+             * the canvas
+             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -149,100 +98,66 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: import("@jbrowse/core/util").Feature | 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";
-    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly renderDelay: number;
-    readonly TooltipComponent: React.FC<any>;
-    readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+} & {
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
 } & {
-    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): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
-} & {
-    setMessage(message: string): void;
 } & {
     afterAttach(): 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 | undefined): void;
-    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    setCurrBpPerPx(n: number): void;
-    deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
-    reload(): void;
-    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+} & {
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void; /**
+     * #property
+     */
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
     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(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
-} & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {
     loading: boolean;
-    drawn: boolean;
     chainData: ChainData | undefined;
+    lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
-    lastDrawnOffsetPx: number;
 } & {
     /**
      * #action
-     * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
      */
-    reload(): void;
+    setDrawSingletons(f: boolean): void;
     /**
      * #action
      */
-    setRef(ref: HTMLCanvasElement | null): void;
-    setColorScheme(s: {
-        type: string;
-    }): void;
+    setLastDrawnOffsetPx(n: number): void;
     /**
      * #action
      */
-    setChainData(args: ChainData): void;
+    setLastDrawnBpPerPx(n: number): void;
     /**
      * #action
      */
@@ -250,31 +165,46 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setDrawn(f: boolean): void;
+    reload(): void;
     /**
      * #action
+     * internal, a reference to a HTMLCanvas because we use a autorun to draw
+     * the canvas
      */
-    setFilterBy(filter: Filter): void;
+    setRef(ref: HTMLCanvasElement | null): void;
+    setColorScheme(s: {
+        type: string;
+    }): void;
     /**
      * #action
      */
-    setLastDrawnOffsetPx(n: number): void;
-} & {
+    setChainData(args: ChainData): void;
     /**
-     * #getter
+     * #action
      */
-    readonly ready: boolean;
-    readonly rendererTypeName: string;
+    setFilterBy(filter: Filter): void;
+} & {
+    readonly drawn: boolean;
+} & {
     renderProps(): any;
     /**
      * #method
      */
     trackMenuItems(): (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 | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        icon?: undefined;
+        subMenu?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
         subMenu?: undefined;
     } | {
         label: string;
@@ -285,6 +215,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             label: string;
             onClick: () => void;
         }[];
+        type?: undefined;
+        checked?: undefined;
         onClick?: undefined;
     })[];
     /**
@@ -292,73 +224,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
-    }): Promise<JSX.Element | undefined>;
+    }): Promise<React.ReactNode>;
 } & {
     afterAttach(): void;
-}, {
-    type: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }, {
-        renderInProgress: AbortController | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        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>>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: string;
-    id: string;
-    rpcDriverName: string | undefined;
-    heightPreConfig: number | undefined;
-    userBpPerPxLimit: number | undefined;
-    userByteSizeLimit: number | undefined;
-} & import("mobx-state-tree")._NotCustomized>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type LinearReadCloudDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearReadCloudDisplayModel = Instance<LinearReadCloudDisplayStateModel>;
 export default stateModelFactory;