@jbrowse/plugin-variants 2.11.2 → 2.12.1

package/dist/ChordVariantDisplay/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ChordVariantDisplayF;
 const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 // locals
@@ -23,4 +24,3 @@ function ChordVariantDisplayF(pluginManager) {
         });
     });
 }
-exports.default = ChordVariantDisplayF;

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 /**
@@ -53,8 +52,8 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -79,22 +78,22 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
     filled: boolean;
-    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+    reactElement: import("react").ReactElement | undefined;
     data: undefined;
     html: string | undefined;
     message: string;
-    renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
+    renderingComponent: undefined | import("@jbrowse/core/util").AnyReactComponentType;
     refNameMap: Record<string, string> | undefined;
 } & {
     onChordClick(feature: Feature): void;
@@ -102,7 +101,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): boolean;
+    isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): renderer is import("@jbrowse/core/pluggableElementTypes").CircularChordRendererType;
     readonly selectedFeatureId: string | undefined;
 } & {
     renderStarted(): void;
@@ -110,7 +109,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         message: string;
         data: any;
         html: string;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+        reactElement: import("react").ReactElement;
         renderingComponent: import("@jbrowse/core/util").AnyReactComponentType;
     }): void;
     renderError(error: unknown): void;

package/dist/LinearVariantDisplay/configSchema.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = configSchemaF;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 /**
@@ -18,4 +19,3 @@ function configSchemaF(pluginManager) {
         explicitlyTyped: true,
     });
 }
-exports.default = configSchemaF;

package/dist/LinearVariantDisplay/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearVariantDisplayF;
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const model_1 = __importDefault(require("./model"));
@@ -21,4 +22,3 @@ function LinearVariantDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LinearVariantDisplayF;

package/dist/LinearVariantDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Feature } from '@jbrowse/core/util';
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
@@ -37,7 +36,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -49,9 +48,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -62,7 +61,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -140,8 +139,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -166,12 +165,12 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -184,8 +183,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     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;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -197,10 +196,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -209,8 +208,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -218,7 +217,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -231,8 +230,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -253,20 +252,32 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
-    setJexlFilters(f?: string[] | undefined): void;
+    setJexlFilters(f?: string[]): void;
     toggleShowLabels(): void;
     toggleShowDescriptions(): void;
     setDisplayMode(val: string): void;
-    setMaxHeight(val?: number | undefined): void;
+    setMaxHeight(val?: number): void;
 } & {
     renderProps(): {
         config: {
             [x: string]: any;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: unknown): any;
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
         filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
     };

package/dist/LinearVariantDisplay/model.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = stateModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
@@ -50,4 +51,3 @@ function stateModelFactory(configSchema) {
         },
     }));
 }
-exports.default = stateModelFactory;

package/dist/StructuralVariantChordRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = StructuralVariantChordRendererF;
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
@@ -15,4 +16,3 @@ function StructuralVariantChordRendererF(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = StructuralVariantChordRendererF;

package/dist/VariantFeatureWidget/AnnotGrid.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantAnnotPanel;
 const react_1 = __importStar(require("react"));
 const x_data_grid_1 = require("@mui/x-data-grid");
 const material_1 = require("@mui/material");
@@ -34,4 +35,3 @@ function VariantAnnotPanel({ rows, columns, }) {
         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") }),
         react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null } }))) : null;
 }
-exports.default = VariantAnnotPanel;

package/dist/VariantFeatureWidget/BreakendPanel.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BreakendPanel;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
@@ -81,4 +82,3 @@ function BreakendPanel(props) {
         react_1.default.createElement(LocStringList, { model: model, locStrings: locStrings }),
         viewType ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, locStrings: locStrings, feature: feature })) : null));
 }
-exports.default = BreakendPanel;

package/dist/VariantFeatureWidget/VariantAnnotationTable.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantAnnotationTable;
 const react_1 = __importDefault(require("react"));
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
@@ -13,4 +14,3 @@ function VariantAnnotationTable({ data, fields, title, }) {
                 ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
             })) || [], columns: fields.map(c => ({ field: c })) }))) : null;
 }
-exports.default = VariantAnnotationTable;

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantSamples;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
@@ -87,4 +88,3 @@ function VariantSamples(props) {
                 toolbar: { printOptions: { disableToolbarButton: true } },
             } })));
 }
-exports.default = VariantSamples;

package/dist/VariantFeatureWidget/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantFeatureWidgetF;
 const react_1 = require("react");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 const stateModelFactory_1 = require("./stateModelFactory");
@@ -39,4 +40,3 @@ function VariantFeatureWidgetF(pluginManager) {
         ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantFeatureWidget')))),
     }));
 }
-exports.default = VariantFeatureWidgetF;

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -31,7 +44,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
+    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
     afterCreate(): void;
@@ -49,13 +62,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

package/dist/VariantFeatureWidget/stateModelFactory.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = void 0;
+exports.stateModelFactory = stateModelFactory;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
 function stateModelFactory(pluginManager) {
@@ -10,4 +10,3 @@ function stateModelFactory(pluginManager) {
         descriptions: mobx_state_tree_1.types.frozen(),
     }));
 }
-exports.stateModelFactory = stateModelFactory;

package/dist/VariantTrack/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantTrackF;
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = __importDefault(require("./configSchema"));
@@ -17,4 +18,3 @@ function VariantTrackF(pm) {
         });
     });
 }
-exports.default = VariantTrackF;

package/dist/VcfAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VcfAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function VcfAdapterF(pluginManager) {
@@ -36,4 +37,3 @@ function VcfAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfAdapter'))).then(r => r.default),
     }));
 }
-exports.default = VcfAdapterF;

package/dist/VcfFeature/util.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSOAndDescByExamination = exports.getSOAndDescFromAltDefs = exports.getSOTermAndDescription = void 0;
+exports.getSOTermAndDescription = getSOTermAndDescription;
+exports.getSOAndDescFromAltDefs = getSOAndDescFromAltDefs;
+exports.getSOAndDescByExamination = getSOAndDescByExamination;
 const vcf_1 = require("@gmod/vcf");
 const altTypeToSO = {
     DEL: 'deletion',
@@ -57,7 +59,6 @@ function getSOTermAndDescription(ref, alt, parser) {
     }
     return [];
 }
-exports.getSOTermAndDescription = getSOTermAndDescription;
 function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
@@ -79,7 +80,6 @@ function getSOAndDescFromAltDefs(alt, parser) {
     // no parent
     return [];
 }
-exports.getSOAndDescFromAltDefs = getSOAndDescFromAltDefs;
 // note: term SNV is used instead of SNP because SO definition of SNP says
 // abundance must be at least 1% in population, and can't be sure we meet
 // that
@@ -129,7 +129,6 @@ function getSOAndDescByExamination(ref, alt) {
     }
     return ['indel', makeDescriptionString('indel', ref, alt)];
 }
-exports.getSOAndDescByExamination = getSOAndDescByExamination;
 function makeDescriptionString(soTerm, ref, alt) {
     return `${soTerm} ${ref} -> ${alt}`;
 }

package/dist/VcfTabixAdapter/index.js

@@ -27,6 +27,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = void 0;
+exports.default = VcfTabixAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 var configSchema_2 = require("./configSchema");
@@ -39,4 +40,3 @@ function VcfTabixAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfTabixAdapter'))).then(r => r.default),
     }));
 }
-exports.default = VcfTabixAdapterF;

package/dist/extensionPoints.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ExtensionPointsF;
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
@@ -48,4 +49,3 @@ function ExtensionPointsF(pluginManager) {
         };
     });
 }
-exports.default = ExtensionPointsF;

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 /**
@@ -53,8 +52,8 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -79,22 +78,22 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
     filled: boolean;
-    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+    reactElement: import("react").ReactElement | undefined;
     data: undefined;
     html: string | undefined;
     message: string;
-    renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
+    renderingComponent: undefined | import("@jbrowse/core/util").AnyReactComponentType;
     refNameMap: Record<string, string> | undefined;
 } & {
     onChordClick(feature: Feature): void;
@@ -102,7 +101,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): boolean;
+    isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): renderer is import("@jbrowse/core/pluggableElementTypes").CircularChordRendererType;
     readonly selectedFeatureId: string | undefined;
 } & {
     renderStarted(): void;
@@ -110,7 +109,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         message: string;
         data: any;
         html: string;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+        reactElement: import("react").ReactElement;
         renderingComponent: import("@jbrowse/core/util").AnyReactComponentType;
     }): void;
     renderError(error: unknown): void;

package/esm/LinearVariantDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Feature } from '@jbrowse/core/util';
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
@@ -37,7 +36,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -49,9 +48,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -62,7 +61,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -140,8 +139,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -166,12 +165,12 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -184,8 +183,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     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;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -197,10 +196,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     afterAttach(): void;
 } & {
     setCurrStatsBpPerPx(n: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -209,8 +208,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -218,7 +217,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -231,8 +230,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -253,20 +252,32 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
-    setJexlFilters(f?: string[] | undefined): void;
+    setJexlFilters(f?: string[]): void;
     toggleShowLabels(): void;
     toggleShowDescriptions(): void;
     setDisplayMode(val: string): void;
-    setMaxHeight(val?: number | undefined): void;
+    setMaxHeight(val?: number): void;
 } & {
     renderProps(): {
         config: {
             [x: string]: any;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: unknown): any;
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
         filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
     };

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -12,13 +12,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -31,7 +44,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
+    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
     afterCreate(): void;
@@ -49,13 +62,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.11.2",
+  "version": "2.12.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -46,7 +46,6 @@
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
-    "@jbrowse/plugin-alignments": "^2.0.0",
     "@jbrowse/plugin-circular-view": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^5.0.0",
@@ -63,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
+  "gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
 }