@jbrowse/plugin-linear-genome-view 2.4.2 → 2.6.1

package/esm/LinearBasicDisplay/model.d.ts

@@ -4,6 +4,7 @@ import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
 /**
  * #stateModel LinearBasicDisplay
+ * #category display
  * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
  * etc.
  */
@@ -13,12 +14,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: 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<{
-            refName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #property
-             */
+            refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -32,9 +35,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         renderInProgress: AbortController | undefined;
-        filled: boolean; /**
-         * #property
-         */
+        filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
@@ -51,7 +52,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #method
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
@@ -63,8 +66,33 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         reload(): void;
         beforeDestroy(): void;
     }, 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;
+        }; /**
+         * #property
+         */
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string; /**
+             * #property
+             */
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     /**
      * #property
@@ -89,21 +117,23 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
+            rpcDriverName: string | undefined; /**
              * #property
              */
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -111,6 +141,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -123,17 +154,19 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
-            rendererTypeName: string;
+            rendererTypeName: string; /**
+             * #action
+             */
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null; /**
-     * #action
-     */
+    }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
@@ -141,21 +174,49 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    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;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): 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;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    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: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -169,49 +230,22 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: 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;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-    setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
-    reload(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
 } & {
-    afterAttach(): void;
-} & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): MenuItem[];
     contextMenuItems(): MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("../BaseLinearDisplay").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
 } & {
     /**
      * #getter
@@ -282,12 +316,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: 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<{
-            refName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #property
-             */
+            refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -301,9 +337,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         renderInProgress: AbortController | undefined;
-        filled: boolean; /**
-         * #property
-         */
+        filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
@@ -320,7 +354,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #method
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
@@ -332,11 +368,37 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         reload(): void;
         beforeDestroy(): void;
     }, 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;
+        }; /**
+         * #property
+         */
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string; /**
+             * #property
+             */
+            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/esm/LinearBasicDisplay/model.js

@@ -9,6 +9,7 @@ import { BaseLinearDisplay } from '../BaseLinearDisplay';
 const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
 /**
  * #stateModel LinearBasicDisplay
+ * #category display
  * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
  * etc.
  */

package/esm/LinearBasicDisplay/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,EACL,OAAO,EACP,sBAAsB,GAEvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,KAAK,EAAE,MAAM,EAAY,MAAM,iBAAiB,CAAA;AAEzD,QAAQ;AACR,OAAO,cAAc,MAAM,gCAAgC,CAAA;AAE3D,SAAS;AACT,OAAO,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAA;AAExD,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AAEvE;;;;;GAKG;AACH,SAAS,iBAAiB,CAAC,YAAwC;IACjE,OAAO,KAAK;SACT,OAAO,CACN,oBAAoB,EACpB,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;QACzC;;WAEG;QACH,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;QAC3C;;WAEG;QACH,qBAAqB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;QACjD;;WAEG;QACH,gBAAgB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC3C;;WAEG;QACH,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACzC;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAA;QAC5C,CAAC;QAED;;WAEG;QACH,IAAI,UAAU;;YACZ,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,YAAY,CAAC,CAAC,CAAA;QAC1E,CAAC;QAED;;WAEG;QACH,IAAI,gBAAgB;;YAClB,OAAO,CACL,MAAA,IAAI,CAAC,qBAAqB,mCAC1B,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,kBAAkB,CAAC,CAAC,CAChD,CAAA;QACH,CAAC;QAED;;WAEG;QACH,IAAI,SAAS;;YACX,OAAO,MAAA,IAAI,CAAC,cAAc,mCAAI,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,CAAA;QACxE,CAAC;QAED;;WAEG;QACH,IAAI,WAAW;;YACb,OAAO,CACL,MAAA,IAAI,CAAC,gBAAgB,mCAAI,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,aAAa,CAAC,CAAC,CACpE,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,cAAc;YAChB,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,CAAC,IAAI,EAAE,CAAA;YACpD,MAAM,MAAM,GAAG,UAA6C,CAAA;YAE5D,OAAO,IAAI,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,CAC1C;gBACE,GAAG,MAAM;gBACT,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,WAAW,EAAE,IAAI,CAAC,WAAW;gBAC7B,SAAS,EAAE,IAAI,CAAC,SAAS;aAC1B,EACD,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SAEF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,gBAAgB;YACd,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,UAAU,CAAA;QACzC,CAAC;QACD;;WAEG;QACH,sBAAsB;YACpB,IAAI,CAAC,qBAAqB,GAAG,CAAC,IAAI,CAAC,gBAAgB,CAAA;QACrD,CAAC;QACD;;WAEG;QACH,cAAc,CAAC,GAAW;YACxB,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,GAAY;YACvB,IAAI,CAAC,cAAc,GAAG,GAAG,CAAA;QAC3B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EACJ,cAAc,EAAE,mBAAmB,EACnC,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QACR,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,MAAM,GAAG,IAAI,CAAC,cAAc,CAAA;gBAClC,MAAM,UAAU,GAAG,gBAAgB,EAAE,CAAA;gBACrC,MAAM,cAAc,GAAG,UAA6C,CAAA;gBACpE,OAAO;oBACL,GAAG,cAAc;oBACjB,MAAM;iBACP,CAAA;YACH,CAAC;YAED;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,aAAa;wBACpB,IAAI,EAAE,cAAc;wBACpB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,UAAU;wBACxB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,gBAAgB,EAAE;qBACvC;oBACD;wBACE,KAAK,EAAE,mBAAmB;wBAC1B,IAAI,EAAE,cAAc;wBACpB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,gBAAgB;wBAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,sBAAsB,EAAE;qBAC7C;oBACD;wBACE,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,cAAc;wBACpB,OAAO,EAAE;4BACP,SAAS;4BACT,uBAAuB;4BACvB,QAAQ;4BACR,UAAU;yBACX,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;4BACZ,KAAK,EAAE,GAAG;4BACV,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,GAAG,CAAC;yBACxC,CAAC,CAAC;qBACJ;oBACD;wBACE,KAAK,EAAE,gBAAgB;wBACvB,OAAO,EAAE,GAAG,EAAE;4BACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC1C,eAAe;gCACf,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE;6BAC7B,CAAC,CAAA;wBACJ,CAAC;qBACF;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC;AAKD,eAAe,iBAAiB,CAAA"}

package/esm/LinearGenomeView/components/CenterLine.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function CenterLine({ model }: {
     model: LGV;
-}): JSX.Element | null;
+}): React.JSX.Element | null;
 declare const _default: typeof CenterLine;
 export default _default;

package/esm/LinearGenomeView/components/Cytobands.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
@@ -12,10 +12,10 @@ declare const _default: ({ overview, block, assembly, }: {
         loadingP: Promise<void> | undefined;
         volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("@jbrowse/core/util").Feature[] | undefined;
     } & {
@@ -29,12 +29,12 @@ declare const _default: ({ overview, block, assembly, }: {
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -42,21 +42,21 @@ declare const _default: ({ overview, block, assembly, }: {
         setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
@@ -66,10 +66,10 @@ declare const _default: ({ overview, block, assembly, }: {
         loadingP: Promise<void> | undefined;
         volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("@jbrowse/core/util").Feature[] | undefined;
     } & {
@@ -83,12 +83,12 @@ declare const _default: ({ overview, block, assembly, }: {
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -96,23 +96,23 @@ declare const _default: ({ overview, block, assembly, }: {
         setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { ExportSvgOptions } from '..';
 export default function ExportSvgDlg({ model, handleClose, }: {
     model: {
         exportSvg(opts: ExportSvgOptions): Promise<void>;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function SequenceDialog({ model, handleClose, }: {
     model: LGV;
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SequenceDialog;
 export default _default;

package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -1,4 +1,4 @@
-import React, { useEffect, useMemo, useState } from 'react';
+import React, { useEffect, useState } from 'react';
 import { makeStyles } from 'tss-react/mui';
 import { Button, Checkbox, CircularProgress, Container, DialogActions, DialogContent, FormGroup, FormControlLabel, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -56,24 +56,22 @@ function SequenceDialog({ model, handleClose, }) {
     const [comp, setComplement] = useState(false);
     const { leftOffset, rightOffset } = model;
     const loading = Boolean(sequenceChunks === undefined);
-    // avoid infinite looping of useEffect
-    // random note: the current selected region can't be a computed because it
-    // uses action on base1dview even though it's on the ephemeral base1dview
-    const regionsSelected = useMemo(() => model.getSelectedRegions(leftOffset, rightOffset), [model, leftOffset, rightOffset]);
     useEffect(() => {
         let active = true;
         const controller = new AbortController();
         (async () => {
             try {
-                if (regionsSelected.length > 0) {
-                    const chunks = await fetchSequence(model, regionsSelected, controller.signal);
-                    if (active) {
-                        setSequenceChunks(chunks);
-                    }
-                }
-                else {
+                // random note: the current selected region can't be a computed because
+                // it uses action on base1dview even though it's on the ephemeral
+                // base1dview
+                const selection = model.getSelectedRegions(leftOffset, rightOffset);
+                if (selection.length === 0) {
                     throw new Error('Selected region is out of bounds');
                 }
+                const chunks = await fetchSequence(model, selection, controller.signal);
+                if (active) {
+                    setSequenceChunks(chunks);
+                }
             }
             catch (e) {
                 console.error(e);
@@ -86,7 +84,7 @@ function SequenceDialog({ model, handleClose, }) {
             controller.abort();
             active = false;
         };
-    }, [model, session, regionsSelected]);
+    }, [model, session, leftOffset, rightOffset]);
     const sequence = sequenceChunks
         ? formatSeqFasta(sequenceChunks
             .filter(f => !!f)
@@ -95,9 +93,9 @@ function SequenceDialog({ model, handleClose, }) {
             const chunkRefName = chunk.get('refName');
             const chunkStart = chunk.get('start') + 1;
             const chunkEnd = chunk.get('end');
-            const chunkLocstring = `${chunkRefName}:${chunkStart}-${chunkEnd}`;
+            const loc = `${chunkRefName}:${chunkStart}-${chunkEnd}`;
             if ((chunkSeq === null || chunkSeq === void 0 ? void 0 : chunkSeq.length) !== chunkEnd - chunkStart + 1) {
-                throw new Error(`${chunkLocstring} returned ${chunkSeq.length.toLocaleString()} bases, but should have returned ${(chunkEnd - chunkStart).toLocaleString()}`);
+                throw new Error(`${loc} returned ${chunkSeq.length.toLocaleString()} bases, but should have returned ${(chunkEnd - chunkStart).toLocaleString()}`);
             }
             if (rev) {
                 chunkSeq = reverse(chunkSeq);
@@ -106,7 +104,7 @@ function SequenceDialog({ model, handleClose, }) {
                 chunkSeq = complement(chunkSeq);
             }
             return {
-                header: chunkLocstring + (rev ? '-rev' : '') + (comp ? '-comp' : ''),
+                header: loc + (rev ? '-rev' : '') + (comp ? '-comp' : ''),
                 seq: chunkSeq,
             };
         }))
@@ -114,7 +112,7 @@ function SequenceDialog({ model, handleClose, }) {
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
     return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
-            model.setOffsets(undefined, undefined);
+            model.setOffsets();
         }, title: "Reference sequence" },
         React.createElement(DialogContent, null,
             error ? (React.createElement(Typography, { color: "error" }, `${error}`)) : loading ? (React.createElement(Container, null,

package/esm/LinearGenomeView/components/GetSequenceDialog.js.map

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package/esm/LinearGenomeView/components/Gridlines.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function VerticalGuides({ model }: {
     model: LGV;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof VerticalGuides;
 export default _default;