npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.4.1 → 2.5.0 - Mend

@jbrowse/plugin-linear-genome-view 2.4.1 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (201) hide show

package/dist/LinearBasicDisplay/model.d.ts CHANGED Viewed

@@ -56,9 +56,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            /**
-             * #method
-             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -67,9 +64,37 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         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>>; /**
-     * #action
+    /**
+     * #getter
      */
+    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
@@ -94,7 +119,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #property
      */
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -144,9 +169,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    /**
-     * #method
-     */
     trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): undefined;
@@ -160,8 +182,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: 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";
@@ -174,35 +196,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    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 featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): 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): 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: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
@@ -210,18 +229,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     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(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
@@ -274,7 +288,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setMaxHeight(val: number): void;
+    setMaxHeight(val?: number): void;
 } & {
     /**
      * #method
@@ -341,9 +355,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            /**
-             * #method
-             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -352,12 +363,41 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         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>>; /**
-     * #action
+    /**
+     * #getter
      */
+    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/dist/LinearBasicDisplay/model.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/model.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA4B;AAC5B,+DAIoC;AACpC,6CAA+C;AAE/C,qDAAyD;AAEzD,QAAQ;AACR,gFAA2D;AAE3D,SAAS;AACT,4DAAwD;AAExD,MAAM,eAAe,GAAG,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,2BAA2B,GAAC,CAAC,CAAA;AAEvE;;;;GAIG;AACH,SAAS,iBAAiB,CAAC,YAAwC;IACjE,OAAO,uBAAK;SACT,OAAO,CACN,oBAAoB,EACpB,qCAAiB,EACjB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;QACzC;;WAEG;QACH,eAAe,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QAC3C;;WAEG;QACH,qBAAqB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,OAAO,CAAC;QACjD;;WAEG;QACH,gBAAgB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QAC3C;;WAEG;QACH,cAAc,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QACzC;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAA;QAC5C,CAAC;QAED;;WAEG;QACH,IAAI,UAAU;;YACZ,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,YAAY,CAAC,CAAC,CAAA;QAC1E,CAAC;QAED;;WAEG;QACH,IAAI,gBAAgB;;YAClB,OAAO,CACL,MAAA,IAAI,CAAC,qBAAqB,mCAC1B,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,kBAAkB,CAAC,CAAC,CAChD,CAAA;QACH,CAAC;QAED;;WAEG;QACH,IAAI,SAAS;;YACX,OAAO,MAAA,IAAI,CAAC,cAAc,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,CAAA;QACxE,CAAC;QAED;;WAEG;QACH,IAAI,WAAW;;YACb,OAAO,CACL,MAAA,IAAI,CAAC,gBAAgB,mCAAI,IAAA,uBAAO,EAAC,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,IAAA,uBAAO,EAAC,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,IAAA,wBAAM,EAAC,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,oBAAc;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,oBAAc;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,oBAAc;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,IAAA,iBAAU,EAAC,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,kBAAe,iBAAiB,CAAA"}

package/dist/LinearGenomeView/components/CenterLine.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function CenterLine({ model }: {

package/dist/LinearGenomeView/components/Cytobands.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
@@ -12,10 +11,10 @@ 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 +28,12 @@ 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 +41,21 @@ 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 +65,10 @@ 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 +82,12 @@ 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;
     } & {
@@ -96,21 +95,21 @@ 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")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;

package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { ExportSvgOptions } from '..';
 export default function ExportSvgDlg({ model, handleClose, }: {
     model: {

package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function SequenceDialog({ model, handleClose, }: {

package/dist/LinearGenomeView/components/GetSequenceDialog.js CHANGED Viewed

@@ -84,24 +84,22 @@ function SequenceDialog({ model, handleClose, }) {
     const [comp, setComplement] = (0, react_1.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 = (0, react_1.useMemo)(() => model.getSelectedRegions(leftOffset, rightOffset), [model, leftOffset, rightOffset]);
     (0, react_1.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);
@@ -114,7 +112,7 @@ function SequenceDialog({ model, handleClose, }) {
             controller.abort();
             active = false;
         };
-    }, [model, session, regionsSelected]);
+    }, [model, session, leftOffset, rightOffset]);
     const sequence = sequenceChunks
         ? (0, formatFastaStrings_1.formatSeqFasta)(sequenceChunks
             .filter(f => !!f)
@@ -123,9 +121,9 @@ 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 ${(chunkEnd - chunkStart).toLocaleString()}`);
             }
             if (rev) {
                 chunkSeq = (0, util_1.reverse)(chunkSeq);
@@ -134,7 +132,7 @@ function SequenceDialog({ model, handleClose, }) {
                 chunkSeq = (0, util_1.complement)(chunkSeq);
             }
             return {
-                header: chunkLocstring + (rev ? '-rev' : '') + (comp ? '-comp' : ''),
+                header: loc + (rev ? '-rev' : '') + (comp ? '-comp' : ''),
                 seq: chunkSeq,
             };
         }))
@@ -142,7 +140,7 @@ function SequenceDialog({ model, handleClose, }) {
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
     return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
-            model.setOffsets(undefined, undefined);
+            model.setOffsets();
         }, title: "Reference sequence" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : loading ? (react_1.default.createElement(material_1.Container, null,

package/dist/LinearGenomeView/components/GetSequenceDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/components/Gridlines.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function VerticalGuides({ model }: {

package/dist/LinearGenomeView/components/Header.d.ts CHANGED Viewed

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

package/dist/LinearGenomeView/components/HelpDialog.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export default function HelpDialog({ handleClose, }: {
     handleClose: () => void;
 }): JSX.Element;

package/dist/LinearGenomeView/components/ImportForm.d.ts CHANGED Viewed

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

package/dist/LinearGenomeView/components/ImportForm.js CHANGED Viewed

@@ -37,8 +37,6 @@ const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 // locals
 const RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
 const util_2 = require("./util");
-// lazies
-const SearchResultsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SearchResultsDialog'))));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     importFormContainer: {
         padding: theme.spacing(2),
@@ -55,7 +53,7 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { assemblyNames, assemblyManager, textSearchManager } = session;
-    const { rankSearchResults, isSearchDialogDisplayed, error } = model;
+    const { rankSearchResults, error } = model;
     const [selectedAsm, setSelectedAsm] = (0, react_1.useState)(assemblyNames[0]);
     const [option, setOption] = (0, react_1.useState)();
     const searchScope = model.searchScope(selectedAsm);
@@ -98,7 +96,7 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                 await navToOption(option);
             }
             else if ((_a = option === null || option === void 0 ? void 0 : option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                model.setSearchResults(option.results, option.getLabel());
+                model.setSearchResults(option.results, option.getLabel(), selectedAsm);
             }
             else {
                 const [ref, rest] = (0, util_2.splitLast)(input, ':');
@@ -117,7 +115,7 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                         assembly,
                     });
                     if (results.length > 1) {
-                        model.setSearchResults(results, input.toLowerCase());
+                        model.setSearchResults(results, input.toLowerCase(), selectedAsm);
                     }
                     else if (results.length === 1) {
                         await navToOption(results[0]);
@@ -168,7 +166,6 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                             react_1.default.createElement(material_1.Button, { disabled: !value, className: classes.button, onClick: () => {
                                     model.setError(undefined);
                                     model.showAllRegionsInAssembly(selectedAsm);
-                                }, variant: "contained", color: "secondary" }, "Show all regions in assembly")))))),
-        isSearchDialogDisplayed ? (react_1.default.createElement(SearchResultsDialog, { model: model, optAssemblyName: selectedAsm, handleClose: () => model.setSearchResults(undefined, undefined) })) : null));
+                                }, variant: "contained", color: "secondary" }, "Show all regions in assembly"))))))));
 });
 //# sourceMappingURL=ImportForm.js.map

package/dist/LinearGenomeView/components/ImportForm.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/LinearGenomeView/components/LinearGenomeView.d.ts CHANGED Viewed

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

package/dist/LinearGenomeView/components/LinearGenomeView.js CHANGED Viewed

@@ -12,8 +12,6 @@ const mobx_react_1 = require("mobx-react");
 const TrackContainer_1 = __importDefault(require("./TrackContainer"));
 const TracksContainer_1 = __importDefault(require("./TracksContainer"));
 const ImportForm_1 = __importDefault(require("./ImportForm"));
-const GetSequenceDialog_1 = __importDefault(require("./GetSequenceDialog"));
-const SearchResultsDialog_1 = __importDefault(require("./SearchResultsDialog"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     note: {
         textAlign: 'center',
@@ -33,8 +31,6 @@ const LinearGenomeView = (0, mobx_react_1.observer)(({ model }) => {
     const MiniControlsComponent = model.MiniControlsComponent();
     const HeaderComponent = model.HeaderComponent();
     return (react_1.default.createElement("div", { style: { position: 'relative' } },
-        model.seqDialogDisplayed ? (react_1.default.createElement(GetSequenceDialog_1.default, { model: model, handleClose: () => model.setGetSequenceDialogOpen(false) })) : null,
-        model.isSearchDialogDisplayed ? (react_1.default.createElement(SearchResultsDialog_1.default, { model: model, handleClose: () => model.setSearchResults(undefined, undefined) })) : null,
         react_1.default.createElement(HeaderComponent, { model: model }),
         react_1.default.createElement(MiniControlsComponent, { model: model }),
         react_1.default.createElement(TracksContainer_1.default, { model: model }, !tracks.length ? (react_1.default.createElement(material_1.Paper, { variant: "outlined", className: classes.note }, !model.hideNoTracksActive ? (react_1.default.createElement(react_1.default.Fragment, null,

package/dist/LinearGenomeView/components/LinearGenomeView.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/components/MiniControls.d.ts CHANGED Viewed

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

package/dist/LinearGenomeView/components/OverviewScalebar.js CHANGED Viewed

@@ -66,6 +66,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         position: 'relative',
     },
     overviewSvg: {
+        pointerEvents: 'none',
         width: '100%',
         position: 'absolute',
     },
@@ -124,7 +125,7 @@ const OverviewBox = (0, mobx_react_1.observer)(function ({ scale, model, block,
         react_1.default.createElement(material_1.Typography, { style: {
                 left: block.offsetPx + 3,
                 color: canDisplayCytobands
-                    ? theme.palette.primary.contrastText
+                    ? theme.palette.text.primary
                     : refNameColor,
             }, className: classes.scalebarRefName }, refName),
         react_1.default.createElement("div", { className: cx(classes.scalebarContig, canDisplayCytobands