@jbrowse/plugin-alignments 2.6.3 → 2.7.0

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-declare const _default: (props: {
+declare const AlignmentsFeatureDetails: (props: {
     model: IAnyStateTreeNode;
 }) => React.JSX.Element;
-export default _default;
+export default AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -120,7 +120,7 @@ function PairLink({ locString, model, }) {
             (0, util_1.navToLoc)(locString, model);
         }, href: "#" }, locString));
 }
-exports.default = (0, mobx_react_1.observer)(function AlignmentFeatureDetails(props) {
+const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const feat = (0, clone_1.default)(model.featureData);
     const SA = (0, util_1.getTag)('SA', feat);
@@ -131,3 +131,4 @@ exports.default = (0, mobx_react_1.observer)(function AlignmentFeatureDetails(pr
         SA ? react_1.default.createElement(AlignmentsFeatureSuppAligns_1.default, { model: model, tag: SA }) : null,
         feat.flags !== undefined ? (react_1.default.createElement(AlignmentsFeatureFlags_1.default, { feature: feat, ...props })) : null));
 });
+exports.default = AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/util.d.ts

@@ -1,8 +1,6 @@
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(tag: string, feat: {
-    tags?: {
-        [key: string]: unknown;
-    };
+    tags?: Record<string, unknown>;
     [key: string]: unknown;
 }): unknown;
 export declare function navToLoc(locString: string, model: IAnyStateTreeNode): Promise<void>;

package/dist/BamAdapter/BamAdapter.d.ts

@@ -2,6 +2,7 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
+import { IFilter } from '../shared';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -29,15 +30,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: {
-            flagInclude: number;
-            flagExclude: number;
-            tagFilter: {
-                tag: string;
-                value: unknown;
-            };
-            readName: string;
-        };
+        filterBy: IFilter;
     }): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -2,20 +2,12 @@ import { IndexedCramFile, CramRecord } from '@gmod/cram';
 import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region, Feature } from '@jbrowse/core/util';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+import { IFilter } from '../shared';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
     readGroups?: (string | undefined)[];
 }
-interface FilterBy {
-    flagInclude: number;
-    flagExclude: number;
-    tagFilter: {
-        tag: string;
-        value: unknown;
-    };
-    readName: string;
-}
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
@@ -30,7 +22,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         cram: IndexedCramFile;
         sequenceAdapter: BaseSequenceAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<string | undefined>;
+    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
     private setup;
@@ -41,7 +33,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: FilterBy;
+        filterBy: IFilter;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;

package/dist/CramAdapter/CramAdapter.js

@@ -10,6 +10,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
 const rxjs_2 = require("rxjs");
+// locals
 const CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
 class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -54,7 +55,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return this.configureP;
     }
-    async getHeader(opts) {
+    async getHeader(_opts) {
         const { cram } = await this.configure();
         return cram.cram.getHeaderText();
     }

package/dist/CramAdapter/util.js

@@ -11,9 +11,7 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
     let refPos = 0;
     let sublen = 0;
     let lastPos = start;
-    for (let i = 0; i < readFeatures.length; i++) {
-        const f = readFeatures[i];
-        const { code, pos, data, sub, ref } = f;
+    for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
         sublen = refPos - lastPos;
         lastPos = refPos;
         if (sublen && insLen > 0) {
@@ -25,7 +23,7 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
             insLen = 0;
         }
-        refPos = f.refPos - 1 - start;
+        refPos = p - 1 - start;
         if (code === 'X') {
             // substitution
             mismatches[j++] = {
@@ -134,8 +132,7 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     let sublen = 0;
     let insLen = 0;
     if (readFeatures !== undefined) {
-        for (let i = 0; i < readFeatures.length; i++) {
-            const { code, refPos, sub, data } = readFeatures[i];
+        for (const { code, refPos, sub, data } of readFeatures) {
             sublen = refPos - lastPos;
             seq += ref.slice(lastPos - refStart, refPos - refStart);
             lastPos = refPos;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,7 +1,6 @@
 import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
-declare function AlignmentsDisplay({ model }: {
+declare const AlignmentsDisplay: ({ model, }: {
     model: AlignmentsDisplayModel;
-}): React.JSX.Element | null;
-declare const _default: typeof AlignmentsDisplay;
-export default _default;
+}) => React.JSX.Element | null;
+export default AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -15,7 +15,7 @@ const useStyles = (0, mui_1.makeStyles)()({
         zIndex: 2,
     },
 });
-function AlignmentsDisplay({ model }) {
+const AlignmentsDisplay = (0, mobx_react_1.observer)(function AlignmentsDisplay({ model, }) {
     var _a;
     const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
@@ -35,5 +35,5 @@ function AlignmentsDisplay({ model }) {
                 top,
             } },
             react_1.default.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
-}
-exports.default = (0, mobx_react_1.observer)(AlignmentsDisplay);
+});
+exports.default = AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/models/model.d.ts

@@ -55,10 +55,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #property
-             * refers to LinearPileupDisplay sub-display model
-             */
+            message: string | undefined;
         } & 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>;
@@ -69,14 +66,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any; /**
-     * #stateModel LinearAlignmentsDisplay
-     * extends `BaseDisplay`
-     */
+    readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    readonly DisplayMessageComponent: React.FC<any> | undefined; /**
+     * #action
+     */
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): null;

package/dist/LinearAlignmentsDisplay/models/model.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 });
+/* eslint-disable react-refresh/only-export-components */
 const react_1 = __importDefault(require("react"));
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,17 +1,10 @@
 /// <reference types="react" />
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+import { IFilter } from '../shared';
 import { ExtraColorBy } from '../shared/color';
-export interface Filter {
-    flagInclude: number;
-    flagExclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value: string;
-    };
-}
 /**
  * #stateModel SharedLinearPileupDisplayMixin
  * #category display
@@ -61,17 +54,20 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #action
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            /**
+             * #action
+             */
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: unknown): void;
+        setError(error: unknown): void; /**
+         * #action
+         */
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -139,6 +135,10 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             value: import("mobx-state-tree").ISimpleType<string>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    /**
+     * #property
+     */
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -173,11 +173,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
+            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]>; /**
              * #property
              */
-        } & 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>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -233,9 +233,14 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     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;
+    featureIdUnderMouse: string | undefined; /**
+     * #property
+     */
     contextMenuFeature: Feature | undefined;
 } & {
+    /**
+     * #property
+     */
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -250,10 +255,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
-    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void; /**
-     * #action
-     * uses copy-to-clipboard and generates notification
-     */
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
@@ -323,7 +325,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     /**
      * #action
      */
-    setFilterBy(filter: Filter): void;
+    setFilterBy(filter: IFilter): void;
+    /**
+     * #action
+     */
+    setJexlFilters(filters: string[]): void;
 } & {
     /**
      * #getter
@@ -350,6 +356,10 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
      * #getter
      */
     renderReady(): boolean;
+    /**
+     * #getter
+     */
+    readonly filters: SerializableFilterChain;
 } & {
     /**
      * #getter
@@ -372,7 +382,16 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     /**
      * #getter
      */
-    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    readonly DisplayBlurb: ({ model, }: {
+        model: {
+            sortedBy?: {
+                pos: number;
+                refName: number;
+                type: string;
+                tag?: string | undefined;
+            } | undefined;
+        };
+    }) => import("react").JSX.Element | null;
     /**
      * #method
      */
@@ -444,17 +463,20 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #action
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            /**
+             * #action
+             */
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: unknown): void;
+        setError(error: unknown): void; /**
+         * #action
+         */
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -32,6 +32,7 @@ const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const configuration_1 = require("@jbrowse/core/configuration");
+const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
@@ -90,6 +91,10 @@ function SharedLinearPileupDisplayMixin(configSchema) {
          * #property
          */
         filterBy: mobx_state_tree_1.types.optional(shared_1.FilterModel, {}),
+        /**
+         * #property
+         */
+        jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
     }))
         .volatile(() => ({
         colorTagMap: mobx_1.observable.map({}),
@@ -204,6 +209,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         setFilterBy(filter) {
             self.filterBy = (0, mobx_state_tree_1.cast)(filter);
         },
+        /**
+         * #action
+         */
+        setJexlFilters(filters) {
+            self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
+        },
     }))
         .views(self => ({
         /**
@@ -247,6 +258,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         renderReady() {
             return self.tagsReady;
         },
+        /**
+         * #getter
+         */
+        get filters() {
+            return new serializableFilterChain_1.default({ filters: self.jexlFilters });
+        },
     }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
@@ -310,6 +327,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     displayModel: self,
                     colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,
                     filterBy: JSON.parse(JSON.stringify(filterBy)),
+                    filters: self.filters,
                     colorTagMap: Object.fromEntries(colorTagMap.toJSON()),
                     config: self.rendererConfig,
                     async onFeatureClick(_, featureId) {
@@ -479,9 +497,9 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                 if (!self.autorunReady) {
                     return;
                 }
-                const { colorBy } = self;
+                const { colorBy, tagsReady } = self;
                 const { staticBlocks } = view;
-                if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
+                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) && !tagsReady) {
                     const vals = await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks);
                     self.updateColorTagMap(vals);
                 }

package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { ObservableMap } from 'mobx';
-declare function ColorByTagDlg(props: {
+declare const ColorByModificationsDialog: ({ model, handleClose, }: {
     model: {
         setColorScheme: (arg: {
             type: string;
@@ -8,9 +8,8 @@ declare function ColorByTagDlg(props: {
         modificationTagMap: ObservableMap<string, string>;
         colorBy?: {
             type: string;
-        };
+        } | undefined;
     };
     handleClose: () => void;
-}): React.JSX.Element;
-declare const _default: typeof ColorByTagDlg;
-export default _default;
+}) => React.JSX.Element;
+export default ColorByModificationsDialog;

package/dist/LinearPileupDisplay/components/ColorByModifications.js

@@ -8,8 +8,7 @@ const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
 const ModificationsTable_1 = __importDefault(require("./ModificationsTable"));
-function ColorByTagDlg(props) {
-    const { model, handleClose } = props;
+const ColorByModificationsDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const { colorBy, modificationTagMap } = model;
     const modifications = [...modificationTagMap.entries()];
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
@@ -36,5 +35,5 @@ function ColorByTagDlg(props) {
                         handleClose();
                     } }, "Methylation"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
-}
-exports.default = (0, mobx_react_1.observer)(ColorByTagDlg);
+});
+exports.default = ColorByModificationsDialog;

package/dist/LinearPileupDisplay/components/ColorByTag.d.ts

@@ -1,9 +1,11 @@
 import React from 'react';
-declare function ColorByTagDlg(props: {
+declare const ColorByTagDialog: ({ model, handleClose, }: {
     model: {
-        setColorScheme: Function;
+        setColorScheme: (arg: {
+            type: string;
+            tag: string;
+        }) => void;
     };
     handleClose: () => void;
-}): React.JSX.Element;
-declare const _default: typeof ColorByTagDlg;
-export default _default;
+}) => React.JSX.Element;
+export default ColorByTagDialog;

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -27,22 +27,19 @@ const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
-function ColorByTagDlg(props) {
-    const { model, handleClose } = props;
+const ColorByTagDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const [tag, setTag] = (0, react_1.useState)('');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag" },
         react_1.default.createElement(material_1.DialogContent, { style: { overflowX: 'hidden' } },
             react_1.default.createElement(material_1.Typography, null, "Enter tag to color by: "),
             react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),
-            react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
-                    maxLength: 2,
-                }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off" }),
+            react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: { maxLength: 2 }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off" }),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
                         model.setColorScheme({ type: 'tag', tag });
                         handleClose();
                     }, disabled: !validTag }, "Submit"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));
-}
-exports.default = (0, mobx_react_1.observer)(ColorByTagDlg);
+});
+exports.default = ColorByTagDialog;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-export interface LinearPileupDisplayBlurbProps {
+declare const LinearPileupDisplayBlurb: ({ model, }: {
     model: {
         sortedBy?: {
             pos: number;
@@ -8,6 +8,5 @@ export interface LinearPileupDisplayBlurbProps {
             tag?: string;
         };
     };
-}
-declare const _default: (props: LinearPileupDisplayBlurbProps) => React.JSX.Element | null;
-export default _default;
+}) => React.JSX.Element | null;
+export default LinearPileupDisplayBlurb;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -6,12 +6,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-exports.default = (0, mobx_react_1.observer)(function LinearPileupDisplayBlurb(props) {
+const LinearPileupDisplayBlurb = (0, mobx_react_1.observer)(function ({ model, }) {
     var _a;
-    const { model } = props;
     const { sortedBy } = model;
     return sortedBy ? (react_1.default.createElement("div", { "data-testid": `blurb-${sortedBy}` },
         react_1.default.createElement(material_1.Typography, { color: "secondary", variant: "caption" }, sortedBy
             ? `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}`
             : null))) : null;
 });
+exports.default = LinearPileupDisplayBlurb;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -1,12 +1,11 @@
 import React from 'react';
-declare function SetFeatureHeightDlg(props: {
+declare const SetFeatureHeightDialog: (props: {
     model: {
         setFeatureHeight: (arg?: number) => void;
         setNoSpacing: (arg?: boolean) => void;
         featureHeightSetting: number;
-        noSpacing?: boolean;
+        noSpacing?: boolean | undefined;
     };
     handleClose: () => void;
-}): React.JSX.Element;
-declare const _default: typeof SetFeatureHeightDlg;
-export default _default;
+}) => React.JSX.Element;
+export default SetFeatureHeightDialog;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.js

@@ -27,7 +27,7 @@ const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
-function SetFeatureHeightDlg(props) {
+const SetFeatureHeightDialog = (0, mobx_react_1.observer)(function (props) {
     const { model, handleClose } = props;
     const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
     const [height, setHeight] = (0, react_1.useState)(`${featureHeightSetting}`);
@@ -45,5 +45,5 @@ function SetFeatureHeightDlg(props) {
                         handleClose();
                     } }, "Submit"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
-}
-exports.default = (0, mobx_react_1.observer)(SetFeatureHeightDlg);
+});
+exports.default = SetFeatureHeightDialog;

package/dist/LinearPileupDisplay/components/SetMaxHeight.d.ts

@@ -1,10 +1,9 @@
 import React from 'react';
-declare function SetMaxHeightDlg(props: {
+declare const SetMaxHeightDialog: (props: {
     model: {
         maxHeight?: number;
         setMaxHeight: Function;
     };
     handleClose: () => void;
-}): React.JSX.Element;
-declare const _default: typeof SetMaxHeightDlg;
-export default _default;
+}) => React.JSX.Element;
+export default SetMaxHeightDialog;

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -33,7 +33,7 @@ const useStyles = (0, mui_1.makeStyles)()({
         width: 500,
     },
 });
-function SetMaxHeightDlg(props) {
+const SetMaxHeightDialog = (0, mobx_react_1.observer)(function (props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
@@ -48,5 +48,5 @@ function SetMaxHeightDlg(props) {
                         handleClose();
                     } }, "Submit"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
-}
-exports.default = (0, mobx_react_1.observer)(SetMaxHeightDlg);
+});
+exports.default = SetMaxHeightDialog;

package/dist/LinearPileupDisplay/components/SortByTag.d.ts

@@ -1,9 +1,8 @@
 import React from 'react';
-declare function SortByTagDlg(props: {
+declare const SortByTagDialog: (props: {
     model: {
         setSortedBy: Function;
     };
     handleClose: () => void;
-}): React.JSX.Element;
-declare const _default: typeof SortByTagDlg;
-export default _default;
+}) => React.JSX.Element;
+export default SortByTagDialog;