@jbrowse/plugin-alignments 2.4.2 → 2.5.0

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function ColorByTagDlg(props: {
     model: {
         setColorScheme: Function;

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export interface LinearPileupDisplayBlurbProps {
     model: {
         sortedBy?: {

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SetFeatureHeightDlg(props: {
     model: {
         setFeatureHeight: (arg?: number) => void;

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SetMaxHeightDlg(props: {
     model: {
         maxHeight?: number;

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -28,11 +28,11 @@ const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
 const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useStyles = (0, mui_1.makeStyles)()({
     root: {
         width: 500,
     },
-}));
+});
 function SetMaxHeightDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
@@ -41,9 +41,7 @@ function SetMaxHeightDlg(props) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.root },
             react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
-            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => {
-                    setMax(event.target.value);
-                }, placeholder: "Enter max height for layout" }),
+            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max height for layout" }),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
                         model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);

package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAA;AAEF,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,6BAA6B,GACzC;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SortByTagDlg(props: {
     model: {
         setSortedBy: Function;

package/dist/LinearPileupDisplay/configSchema.d.ts

@@ -1,3 +1,59 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    colorScheme: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, 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 default configSchemaF;

package/dist/LinearPileupDisplay/model.d.ts

@@ -3,6 +3,15 @@ import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+export interface Filter {
+    flagInclude: number;
+    flagExclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 /**
  * #stateModel LinearPileupDisplay
  * extends `BaseLinearDisplay`
@@ -25,6 +34,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        /**
+         * #stateModel LinearPileupDisplay
+         * extends `BaseLinearDisplay`
+         */
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -34,15 +47,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
-        status: string; /**
-         * #property
-         */
+        status: string;
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
-        /**
-         * #property
-         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -52,13 +60,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #property
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #property
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -66,9 +78,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: 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">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -103,6 +138,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
+            /**
+             * #action
+             */
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -126,7 +164,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
-            error: unknown;
+            error: unknown; /**
+             * #action
+             */
         } & 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>;
@@ -154,8 +194,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -174,31 +214,34 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
 } & {
     afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
+    readonly regionTooLargeReason: string; /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
 } & {
     reload(): Promise<void>;
 } & {
@@ -286,30 +329,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setConfig(configuration: AnyConfigurationModel): void;
+    setConfig(conf: AnyConfigurationModel): void;
     /**
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
-    setFilterBy(filter: {
-        flagInclude: number;
-        flagExclude: number;
-        readName?: string;
-        tagFilter?: {
-            tag: string;
-            value: string;
-        };
-    }): void;
+    setFilterBy(filter: Filter): void;
 } & {
     /**
      * #action
      */
     reload(): void;
 } & {
-    /**
-     * #getter
-     */
-    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -318,6 +349,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    /**
+     * #getter
+     */
+    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -422,12 +458,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    /**
-     * #action
-     */
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
-     * #action
-     */
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -444,23 +475,21 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined; /**
-         * #action
-         */
+        renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined;
+        message: string | undefined; /**
+         * #getter
+         */
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
-        renderProps: any; /**
-         * #getter
-         */
+        renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
@@ -471,10 +500,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
-            maxHeightReached: boolean;
-            renderProps: any; /**
-             * #getter
+            maxHeightReached: boolean; /**
+             * #method
              */
+            renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -482,9 +511,37 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number; /**
+             * #getter
+             */
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number; /**
+             * #method
+             */
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
     id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;

package/dist/LinearPileupDisplay/model.js

@@ -219,7 +219,7 @@ function stateModelFactory(configSchema) {
                     const view = (0, util_1.getContainingView)(self);
                     const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
                     if (!view.initialized ||
-                        !self.estimatedStatsReady ||
+                        !self.featureDensityStatsReady ||
                         self.regionTooLarge) {
                         return;
                     }
@@ -291,9 +291,7 @@ function stateModelFactory(configSchema) {
                             // feature.id that was returned e.g. that the user hasn't
                             // moused over to a new position during the async operation
                             // above
-                            // @ts-expect-error
                             if (self.featureIdUnderMouse === feature.uniqueId) {
-                                // @ts-expect-error
                                 self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
                             }
                         }
@@ -347,8 +345,8 @@ function stateModelFactory(configSchema) {
         /**
          * #action
          */
-        setConfig(configuration) {
-            self.configuration = configuration;
+        setConfig(conf) {
+            self.configuration = conf;
         },
         /**
          * #action
@@ -390,41 +388,41 @@ function stateModelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #getter
-         */
-        get maxHeight() {
-            const conf = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-            return self.trackMaxHeight !== undefined
-                ? self.trackMaxHeight
-                : conf.maxHeight;
-        },
         /**
          * #getter
          */
         get rendererConfig() {
-            const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
+            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, } = self;
+            const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
-                height: self.featureHeight,
-                noSpacing: self.noSpacing,
-                maxHeight: this.maxHeight,
-                mismatchAlpha: self.mismatchAlpha,
+                ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+                ...(noSpacing !== undefined ? { noSpacing } : {}),
+                ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
+                ...(trackMaxHeight !== undefined
+                    ? { maxHeight: trackMaxHeight }
+                    : {}),
             }, (0, util_1.getEnv)(self));
         },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get maxHeight() {
+            return (0, configuration_1.readConfObject)(self.rendererConfig, 'maxHeight');
+        },
         /**
          * #getter
          */
         get featureHeightSetting() {
-            return (self.featureHeight || (0, configuration_1.readConfObject)(this.rendererConfig, 'height'));
+            return (0, configuration_1.readConfObject)(self.rendererConfig, 'height');
         },
         /**
          * #getter
          */
         get mismatchAlphaSetting() {
-            return self.mismatchAlpha !== undefined
-                ? self.mismatchAlpha
-                : (0, configuration_1.readConfObject)(this.rendererConfig, 'mismatchAlpha');
+            return (0, configuration_1.readConfObject)(self.rendererConfig, 'mismatchAlpha');
         },
         /**
          * #getter
@@ -521,7 +519,6 @@ function stateModelFactory(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (feature) {
-                                    // @ts-expect-error
                                     self.selectFeature(new util_1.SimpleFeature(feature));
                                 }
                             }

package/dist/LinearPileupDisplay/model.js.map

@@ -1 +1 @@
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package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearReadArcsDisplayModel } from '../model';
 declare const _default: ({ model, }: {
     model: LinearReadArcsDisplayModel;