@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/LDRenderer/makeImageData.js

@@ -0,0 +1,157 @@
+import Flatbush from '@jbrowse/core/util/flatbush';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
+import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
+import { scaleSequential } from '@mui/x-charts-vendor/d3-scale';
+const colorSchemes = {
+    r2: interpolateRgbBasis([
+        'rgb(255, 255, 255)',
+        'rgb(255, 224, 224)',
+        'rgb(255, 192, 192)',
+        'rgb(255, 128, 128)',
+        'rgb(255, 64, 64)',
+        'rgb(255, 0, 0)',
+        'rgb(208, 0, 0)',
+        'rgb(160, 0, 0)',
+    ]),
+    dprime: interpolateRgbBasis([
+        'rgb(255, 255, 255)',
+        'rgb(224, 224, 255)',
+        'rgb(192, 192, 255)',
+        'rgb(128, 128, 255)',
+        'rgb(64, 64, 255)',
+        'rgb(0, 0, 255)',
+        'rgb(0, 0, 208)',
+        'rgb(0, 0, 160)',
+    ]),
+    rSigned: interpolateRgbBasis([
+        'rgb(0, 0, 160)',
+        'rgb(0, 0, 208)',
+        'rgb(0, 0, 255)',
+        'rgb(64, 64, 255)',
+        'rgb(128, 128, 255)',
+        'rgb(192, 192, 255)',
+        'rgb(224, 224, 255)',
+        'rgb(255, 255, 255)',
+        'rgb(255, 224, 224)',
+        'rgb(255, 192, 192)',
+        'rgb(255, 128, 128)',
+        'rgb(255, 64, 64)',
+        'rgb(255, 0, 0)',
+        'rgb(208, 0, 0)',
+        'rgb(160, 0, 0)',
+    ]),
+    dprimeSigned: interpolateRgbBasis([
+        'rgb(0, 100, 0)',
+        'rgb(0, 128, 0)',
+        'rgb(0, 160, 0)',
+        'rgb(64, 192, 64)',
+        'rgb(128, 224, 128)',
+        'rgb(192, 240, 192)',
+        'rgb(224, 248, 224)',
+        'rgb(255, 255, 255)',
+        'rgb(224, 224, 255)',
+        'rgb(192, 192, 255)',
+        'rgb(128, 128, 255)',
+        'rgb(64, 64, 255)',
+        'rgb(0, 0, 255)',
+        'rgb(0, 0, 208)',
+        'rgb(0, 0, 160)',
+    ]),
+};
+export function makeImageData(ctx, props) {
+    const { ldData, regions, bpPerPx, stopTokenCheck, yScalar, useGenomicPositions = false, signedLD = false, } = props;
+    const { snps, ldValues, metric } = ldData;
+    const n = snps.length;
+    if (n === 0) {
+        return undefined;
+    }
+    checkStopToken2(stopTokenCheck);
+    const region = regions[0];
+    if (!region) {
+        return undefined;
+    }
+    let colorInterpolator;
+    if (signedLD) {
+        colorInterpolator =
+            metric === 'dprime' ? colorSchemes.dprimeSigned : colorSchemes.rSigned;
+    }
+    else {
+        colorInterpolator =
+            metric === 'dprime' ? colorSchemes.dprime : colorSchemes.r2;
+    }
+    const scale = scaleSequential(colorInterpolator).domain(signedLD ? [-1, 1] : [0, 1]);
+    const viewWidthPx = (region.end - region.start) / bpPerPx;
+    const sqrt2 = Math.sqrt(2);
+    const uniformW = viewWidthPx / (n * sqrt2);
+    const boundaries = [];
+    if (useGenomicPositions) {
+        for (let i = 0; i < n; i++) {
+            const snpPos = snps[i].start;
+            const prevPos = i > 0 ? snps[i - 1].start : region.start;
+            const boundaryPos = (prevPos + snpPos) / 2;
+            const pixelPos = (boundaryPos - region.start) / bpPerPx / sqrt2;
+            boundaries.push(pixelPos);
+        }
+        const lastSnpPos = snps[n - 1].start;
+        const finalBoundary = lastSnpPos + 50 * bpPerPx;
+        boundaries.push((finalBoundary - region.start) / bpPerPx / sqrt2);
+    }
+    if (yScalar) {
+        ctx.scale(1, yScalar);
+    }
+    ctx.save();
+    ctx.rotate(-Math.PI / 4);
+    const coords = [];
+    const items = [];
+    let ldIdx = 0;
+    for (let i = 1; i < n; i++) {
+        for (let j = 0; j < i; j++) {
+            const ldVal = ldValues[ldIdx] ?? 0;
+            ctx.fillStyle = scale(ldVal);
+            let x;
+            let y;
+            let cellW;
+            let cellH;
+            if (useGenomicPositions) {
+                x = boundaries[j];
+                y = boundaries[i];
+                cellW = boundaries[j + 1] - x;
+                cellH = boundaries[i + 1] - y;
+            }
+            else {
+                x = j * uniformW;
+                y = i * uniformW;
+                cellW = uniformW;
+                cellH = uniformW;
+            }
+            ctx.fillRect(x, y, cellW, cellH);
+            coords.push(x, y, x + cellW, y + cellH);
+            items.push({
+                i,
+                j,
+                ldValue: ldVal,
+                snp1: snps[i],
+                snp2: snps[j],
+            });
+            ldIdx++;
+            checkStopToken2(stopTokenCheck);
+        }
+    }
+    ctx.restore();
+    const flatbush = new Flatbush(Math.max(items.length, 1));
+    if (coords.length) {
+        for (let k = 0; k < coords.length; k += 4) {
+            flatbush.add(coords[k], coords[k + 1], coords[k + 2], coords[k + 3]);
+        }
+    }
+    else {
+        flatbush.add(0, 0, 0, 0);
+    }
+    flatbush.finish();
+    return {
+        flatbush: flatbush.data,
+        items,
+        maxScore: signedLD ? 1 : 1,
+        w: uniformW,
+    };
+}

package/esm/LDRenderer/types.d.ts

@@ -0,0 +1,8 @@
+import type { LDMatrixResult } from '../VariantRPC/getLDMatrix.ts';
+export interface LDFlatbushItem {
+    i: number;
+    j: number;
+    ldValue: number;
+    snp1: LDMatrixResult['snps'][0];
+    snp2: LDMatrixResult['snps'][0];
+}

package/esm/LDRenderer/types.js

@@ -0,0 +1 @@
+export {};

package/esm/LDTrack/configSchema.d.ts

@@ -0,0 +1,85 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: (pluginManager: PluginManager) => import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+export default configSchema;

package/esm/LDTrack/configSchema.js

@@ -0,0 +1,7 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+function x() { }
+const configSchema = (pluginManager) => ConfigurationSchema('LDTrack', {}, {
+    baseConfiguration: createBaseTrackConfig(pluginManager),
+});
+export default configSchema;

package/esm/LDTrack/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function LDTrackF(pm: PluginManager): void;

package/esm/LDTrack/index.js

@@ -0,0 +1,14 @@
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import configSchemaF from "./configSchema.js";
+export default function LDTrackF(pm) {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
+        return new TrackType({
+            name: 'LDTrack',
+            displayName: 'LD track',
+            configSchema,
+            stateModel: createBaseTrackModel(pm, 'LDTrack', configSchema),
+        });
+    });
+}

package/esm/LinearVariantDisplay/model.d.ts

@@ -45,7 +45,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         setStatusMessage(message: string): void;
         setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
         setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
@@ -55,7 +55,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -82,7 +82,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
@@ -92,10 +92,11 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     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<"LinearVariantDisplay">;
     configuration: AnyConfigurationSchemaType;
+    minorAlleleFrequencyFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -327,11 +328,11 @@ export default 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;
     getFeatureById(featureId: string, parentFeatureId?: string): import("@jbrowse/core/util").Feature | undefined;
-    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord>;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord | undefined;
-    searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord | undefined;
-    readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util").FeatureLabelData>;
+    getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+    searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+    readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util.ts").FeatureLabelData>;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -395,7 +396,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 setStatusMessage(message: string): void;
                 setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
                 setMessage(messageText: string): void;
-                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
                 setError(error: unknown): void;
                 reload(): void;
                 setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
@@ -439,7 +440,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 setStatusMessage(message: string): void;
                 setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
                 setMessage(messageText: string): void;
-                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
                 setError(error: unknown): void;
                 reload(): void;
                 setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
@@ -459,7 +460,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                         [x: string]: any;
                     } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -486,7 +487,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
+            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
             showLegend: boolean | undefined;
             showTooltips: boolean | undefined;
         } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -720,11 +721,11 @@ export default 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;
             getFeatureById(featureId: string, parentFeatureId?: string): import("@jbrowse/core/util").Feature | undefined;
-            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord>;
+            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord>;
             getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-            getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord | undefined;
-            searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord | undefined;
-            readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util").FeatureLabelData>;
+            getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util.ts").FeatureLabelData>;
         } & {
             addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
             deleteBlock(key: string): void;
@@ -787,7 +788,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 setStatusMessage(message: string): void;
                 setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
                 setMessage(messageText: string): void;
-                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
                 setError(error: unknown): void;
                 reload(): void;
                 setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
@@ -797,7 +798,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -824,7 +825,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         }, {
@@ -1058,11 +1059,11 @@ export default 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;
             getFeatureById(featureId: string, parentFeatureId?: string): import("@jbrowse/core/util").Feature | undefined;
-            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord>;
+            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord>;
             getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-            getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord | undefined;
-            searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types").LayoutRecord | undefined;
-            readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util").FeatureLabelData>;
+            getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util.ts").FeatureLabelData>;
         } & {
             addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
             deleteBlock(key: string): void;
@@ -1092,7 +1093,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
 } & {
-    readonly activeFilters: string[];
+    activeFilters(): string[];
     readonly rendererTypeName: any;
     readonly sequenceAdapter: any;
     readonly showLabels: any;
@@ -1239,36 +1240,119 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
+    filterMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
     afterAttach(): void;
+} & {
+    readonly minorAlleleFrequencyFilter: any;
+} & {
+    setMafFilter(value: number): void;
 } & {
     readonly featureWidgetType: {
         type: string;
         id: string;
     };
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    id: string;
-    type: "LinearFeatureDisplay";
-    rpcDriverName: string | undefined;
-    heightPreConfig: number | undefined;
-    userBpPerPxLimit: number | undefined;
-    userByteSizeLimit: number | undefined;
-    blockState: import("mobx").IKeyValueMap<import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    activeFilters(): string[];
+    filterMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
         key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }>>;
-    configuration: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    showLegend: boolean | undefined;
-    showTooltips: boolean | undefined;
-    trackShowLabels: boolean | undefined;
-    trackShowDescriptions: boolean | undefined;
-    trackDisplayMode: string | undefined;
-    trackMaxHeight: number | undefined;
-    jexlFilters: string[] | undefined;
-} & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized>;
+    }, {
+        stopToken: import("@jbrowse/core/util").StopToken | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        blockStatusMessage: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message?: React.ReactNode;
+                statusMessage?: string;
+                reactElement?: React.ReactElement;
+                isRenderingPending?: boolean;
+            };
+        }) => import("react/jsx-runtime").JSX.Element;
+        renderProps: any;
+        renderArgs: Record<string, unknown> | undefined;
+        isRenderingPending: boolean;
+        cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
+    } & {
+        doReload(): void;
+        setStatusMessage(message: string): void;
+        setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
+        setMessage(messageText: string): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
+        beforeDestroy(): void;
+    } & {
+        readonly statusMessage: any;
+    } & {
+        afterAttach(): void;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearFeatureDisplay">;
+    trackShowLabels: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    trackShowDescriptions: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    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;
+    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<"LinearVariantDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    minorAlleleFrequencyFilterSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+}>>;
 export type LinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>;

package/esm/LinearVariantDisplay/model.js

@@ -1,18 +1,56 @@
-import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { types } from '@jbrowse/mobx-state-tree';
 import { linearFeatureDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view';
+import { createMAFFilterMenuItem } from "../shared/mafFilterUtils.js";
 export default function stateModelFactory(configSchema) {
     return types
         .compose('LinearVariantDisplay', linearFeatureDisplayModelFactory(configSchema), types.model({
         type: types.literal('LinearVariantDisplay'),
         configuration: ConfigurationReference(configSchema),
+        minorAlleleFrequencyFilterSetting: types.maybe(types.number),
     }))
-        .views(() => ({
-        get featureWidgetType() {
-            return {
-                type: 'VariantFeatureWidget',
-                id: 'variantFeature',
-            };
+        .views(self => ({
+        get minorAlleleFrequencyFilter() {
+            return (self.minorAlleleFrequencyFilterSetting ??
+                getConf(self, 'minorAlleleFrequencyFilter'));
         },
-    }));
+    }))
+        .actions(self => ({
+        setMafFilter(value) {
+            self.minorAlleleFrequencyFilterSetting = value;
+        },
+    }))
+        .views(self => {
+        const { activeFilters: superActiveFilters, filterMenuItems: superFilterMenuItems, } = self;
+        return {
+            get featureWidgetType() {
+                return {
+                    type: 'VariantFeatureWidget',
+                    id: 'variantFeature',
+                };
+            },
+            activeFilters() {
+                const filters = [...superActiveFilters()];
+                if (self.minorAlleleFrequencyFilter > 0) {
+                    filters.push(`jexl:maf(feature) >= ${self.minorAlleleFrequencyFilter}`);
+                }
+                return filters;
+            },
+            filterMenuItems() {
+                return [...superFilterMenuItems(), createMAFFilterMenuItem(self)];
+            },
+        };
+    })
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { minorAlleleFrequencyFilterSetting, ...rest } = snap;
+        return {
+            ...rest,
+            ...(minorAlleleFrequencyFilterSetting
+                ? { minorAlleleFrequencyFilterSetting }
+                : {}),
+        };
+    });
 }