@jbrowse/plugin-variants 2.4.2 → 2.6.1

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
@@ -11,33 +10,46 @@ const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeature
 const vcf_1 = require("@gmod/vcf");
 // locals
 const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
-const VariantCsqPanel_1 = __importDefault(require("./VariantCsqPanel"));
-const VariantAnnPanel_1 = __importDefault(require("./VariantAnnPanel"));
 const BreakendPanel_1 = __importDefault(require("./BreakendPanel"));
+const VariantAnnotationTable_1 = __importDefault(require("./VariantAnnotationTable"));
+const basicDescriptions = {
+    CHROM: 'chromosome: An identifier from the reference genome',
+    POS: 'position: The reference position, with the 1st base having position 1',
+    ID: 'identifier: Semi-colon separated list of unique identifiers where available',
+    REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
+    ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
+    QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
+    FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
+};
 function VariantFeatureDetails(props) {
     const { model } = props;
     const { featureData, descriptions } = model;
     const feat = JSON.parse(JSON.stringify(featureData));
     const { samples, ...rest } = feat;
-    const basicDescriptions = {
-        CHROM: 'chromosome: An identifier from the reference genome',
-        POS: 'position: The reference position, with the 1st base having position 1',
-        ID: 'identifier: Semi-colon separated list of unique identifiers where available',
-        REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
-        ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
-        QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
-        FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
-    };
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "variant-side-drawer" },
         react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
         react_1.default.createElement(material_1.Divider, null),
-        react_1.default.createElement(VariantCsqPanel_1.default, { feature: rest, descriptions: descriptions }),
+        react_1.default.createElement(CsqPanel, { feature: rest, descriptions: descriptions }),
         react_1.default.createElement(material_1.Divider, null),
-        react_1.default.createElement(VariantAnnPanel_1.default, { feature: rest, descriptions: descriptions }),
+        react_1.default.createElement(AnnPanel, { feature: rest, descriptions: descriptions }),
         react_1.default.createElement(material_1.Divider, null),
         feat.type === 'breakend' ? (react_1.default.createElement(BreakendPanel_1.default, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
         feat.type === 'translocation' ? (react_1.default.createElement(BreakendPanel_1.default, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
         react_1.default.createElement(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })));
 }
+function AnnPanel({ descriptions, feature, }) {
+    var _a, _b, _c, _d;
+    const annDesc = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description;
+    const annFields = ((_c = annDesc === null || annDesc === void 0 ? void 0 : annDesc.match(/.*Functional annotations:'(.*)'$/)) === null || _c === void 0 ? void 0 : _c[1].split('|')) || [];
+    const ann = ((_d = feature.INFO) === null || _d === void 0 ? void 0 : _d.ANN) || [];
+    return (react_1.default.createElement(VariantAnnotationTable_1.default, { fields: annFields, data: ann, title: "Variant ANN field" }));
+}
+function CsqPanel({ descriptions, feature, }) {
+    var _a, _b, _c, _d;
+    const csqDescription = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description;
+    const csqFields = ((_c = csqDescription === null || csqDescription === void 0 ? void 0 : csqDescription.match(/.*Format: (.*)/)) === null || _c === void 0 ? void 0 : _c[1].split('|')) || [];
+    const csq = ((_d = feature.INFO) === null || _d === void 0 ? void 0 : _d.CSQ) || [];
+    return (react_1.default.createElement(VariantAnnotationTable_1.default, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
+}
 exports.default = (0, mobx_react_1.observer)(VariantFeatureDetails);
 //# sourceMappingURL=VariantFeatureWidget.js.map

package/dist/VariantFeatureWidget/VariantFeatureWidget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VariantFeatureWidget.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/VariantFeatureWidget.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA8C;AAC9C,yFAAkF;AAClF,mCAAyC;AAEzC,SAAS;AACT,4EAAmD;AACnD,oEAA2C;AAC3C,sFAA6D;AAG7D,MAAM,iBAAiB,GAAG;IACxB,KAAK,EAAE,qDAAqD;IAC5D,GAAG,EAAE,uEAAuE;IAC5E,EAAE,EAAE,6EAA6E;IACjF,GAAG,EAAE,2EAA2E;IAChF,GAAG,EAAE,4EAA4E;IACjF,IAAI,EAAE,mEAAmE;IACzE,MAAM,EACJ,kIAAkI;CACrI,CAAA;AAED,SAAS,qBAAqB,CAAC,KAK9B;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC3C,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC,CAAA;IACpD,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;IAEjC,OAAO,CACL,8BAAC,gBAAK,mBAAa,qBAAqB;QACtC,8BAAC,kCAAc,IACb,OAAO,EAAE,IAAI,EACb,YAAY,EAAE,EAAE,GAAG,iBAAiB,EAAE,GAAG,YAAY,EAAE,KACnD,KAAK,GACT;QACF,8BAAC,kBAAO,OAAG;QACX,8BAAC,QAAQ,IAAC,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,YAAY,GAAI;QACvD,8BAAC,kBAAO,OAAG;QACX,8BAAC,QAAQ,IAAC,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,YAAY,GAAI;QACvD,8BAAC,kBAAO,OAAG;QACV,IAAI,CAAC,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,CAC1B,8BAAC,uBAAa,IACZ,OAAO,EAAE,IAAI,EACb,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,CACtB,CAAC,GAAW,EAAE,EAAE,WAAC,OAAA,CAAA,MAAA,IAAA,mBAAa,EAAC,GAAG,CAAC,0CAAE,YAAY,KAAI,EAAE,CAAA,EAAA,CACxD,EACD,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CAAC,CAAC,IAAI;QACP,IAAI,CAAC,IAAI,KAAK,eAAe,CAAC,CAAC,CAAC,CAC/B,8BAAC,uBAAa,IACZ,OAAO,EAAE,IAAI,EACb,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,GACrD,CACH,CAAC,CAAC,CAAC,IAAI;QACR,8BAAC,2BAAiB,IAChB,OAAO,EAAE,IAAI,KACT,KAAK,EACT,YAAY,EAAE,YAAY,GAC1B,CACI,CACT,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,YAAY,EACZ,OAAO,GAIR;;IACC,MAAM,OAAO,GAAG,MAAA,MAAA,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,IAAI,0CAAE,GAAG,0CAAE,WAAW,CAAA;IACpD,MAAM,SAAS,GACb,CAAA,MAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,KAAK,CAAC,kCAAkC,CAAC,0CAAG,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,KAAI,EAAE,CAAA;IAC1E,MAAM,GAAG,GAAG,CAAA,MAAA,OAAO,CAAC,IAAI,0CAAE,GAAG,KAAI,EAAE,CAAA;IACnC,OAAO,CACL,8BAAC,gCAAsB,IACrB,MAAM,EAAE,SAAS,EACjB,IAAI,EAAE,GAAG,EACT,KAAK,EAAC,mBAAmB,GACzB,CACH,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,YAAY,EACZ,OAAO,GAIR;;IACC,MAAM,cAAc,GAAG,MAAA,MAAA,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,IAAI,0CAAE,GAAG,0CAAE,WAAW,CAAA;IAC3D,MAAM,SAAS,GACb,CAAA,MAAA,cAAc,aAAd,cAAc,uBAAd,cAAc,CAAE,KAAK,CAAC,gBAAgB,CAAC,0CAAG,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,KAAI,EAAE,CAAA;IAC/D,MAAM,GAAG,GAAG,CAAA,MAAA,OAAO,CAAC,IAAI,0CAAE,GAAG,KAAI,EAAE,CAAA;IACnC,OAAO,CACL,8BAAC,gCAAsB,IACrB,MAAM,EAAE,SAAS,EACjB,IAAI,EAAE,GAAG,EACT,KAAK,EAAC,mBAAmB,GACzB,CACH,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,qBAAqB,CAAC,CAAA"}

package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,6 +1,12 @@
-/// <reference types="react" />
+import React from 'react';
 import { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;
-    descriptions: any;
-}): JSX.Element | null;
+    descriptions: {
+        FORMAT?: {
+            [key: string]: {
+                Description?: string;
+            };
+        };
+    };
+}): React.JSX.Element | null;

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -30,12 +30,9 @@ const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeature
 const util_1 = require("@jbrowse/core/util");
 const ResizeBar_1 = __importStar(require("@jbrowse/core/ui/ResizeBar"));
 function SampleFilters({ columns, filter, setFilter, }) {
-    const [showFilters, setShowFilters] = (0, react_1.useState)(false);
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
-        showFilters ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
-            columns.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null));
+        react_1.default.createElement(material_1.Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
+        columns.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) })))));
 }
 function VariantSamples(props) {
     var _a;
@@ -61,9 +58,10 @@ function VariantSamples(props) {
         })
             .filter(row => filters.length
             ? filters.every(key => {
-                const val = row[key];
                 const currFilter = filter[key];
-                return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
+                return currFilter
+                    ? row[key].match(new RegExp(currFilter, 'i'))
+                    : true;
             })
             : true);
     }
@@ -71,6 +69,7 @@ function VariantSamples(props) {
         error = e;
     }
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
+    const [checked, setChecked] = (0, react_1.useState)(false);
     const [widths, setWidths] = (0, react_1.useState)(keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e]))));
     const columns = keys.map((field, index) => {
         var _a, _b;
@@ -80,15 +79,17 @@ function VariantSamples(props) {
             width: widths[index],
         });
     });
-    // disableSelectionOnClick helps avoid
+    // disableRowSelectionOnClick helps avoid
     // https://github.com/mui-org/material-ui-x/issues/1197
     return !preFilteredRows.length ? null : (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Samples" },
         error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
-        react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter }),
+        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
+        checked ? (react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
         react_1.default.createElement("div", { ref: ref },
             react_1.default.createElement(ResizeBar_1.default, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
-            react_1.default.createElement("div", { ref: ref, style: { height: 600, width: '100%', overflow: 'auto' } },
-                react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
+            react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null }, slotProps: {
+                    toolbar: { printOptions: { disableToolbarButton: true } },
+                } }))));
 }
 exports.default = VariantSamples;
 //# sourceMappingURL=VariantSampleGrid.js.map

package/dist/VariantFeatureWidget/VariantSampleGrid.js.map

@@ -1 +1 @@
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package/dist/VariantFeatureWidget/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -14,10 +14,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, {

package/dist/VariantTrack/configSchema.d.ts

@@ -1,3 +1,75 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/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: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/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;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/dist/VcfAdapter/VcfAdapter.js

@@ -102,6 +102,6 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-exports.default = VcfAdapter;
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
+exports.default = VcfAdapter;
 //# sourceMappingURL=VcfAdapter.js.map

package/dist/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+DAAsC;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;kBADxC,UAAU"}

package/dist/VcfAdapter/configSchema.d.ts

@@ -1,2 +1,13 @@
-declare const VcfAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    vcfLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/dist/VcfTabixAdapter/configSchema.d.ts

@@ -1,2 +1,33 @@
-declare const VcfTabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    vcfGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;

package/esm/ChordVariantDisplay/models/configSchema.d.ts

@@ -1,3 +1,15 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    renderer: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IAnyModelType, [undefined]>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    onChordClick: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
 export default stateModelFactory;

package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts

@@ -12,6 +12,14 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
 } & {
     bezierRadiusRatio: import("mobx-state-tree").IType<number | undefined, number, number>;
     assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        onChordClick: {
+            type: string;
+            description: string;
+            defaultValue: boolean;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
      * #property
@@ -20,12 +28,13 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown; /**
      * #property
      */
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
@@ -34,7 +43,10 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
-            error: unknown;
+            error: unknown; /**
+             * #method
+             */
+            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>;
@@ -42,6 +54,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         }, {
             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;
@@ -54,6 +67,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         } & 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>;
@@ -61,6 +75,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -70,8 +85,9 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     readonly DisplayMessageComponent: import("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;
@@ -107,7 +123,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
 } & {
     renderSvg(opts: import("@jbrowse/plugin-circular-view/src/CircularView/models/CircularView").ExportSvgOptions & {
         theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    }): Promise<import("react").JSX.Element>;
 } & {
     /**
      * #getter

package/esm/LinearVariantDisplay/configSchema.d.ts

@@ -1,5 +1,29 @@
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").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[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
 export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;