@jbrowse/plugin-linear-genome-view 2.1.7 → 2.2.0

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

@@ -14,8 +14,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     assembly?: ({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: Error | undefined;
-        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -26,41 +28,35 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         readonly initialized: boolean;
         readonly name: string;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
-        readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        afterAttach(): 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<{
@@ -72,8 +68,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & 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>>;
     }, {
-        error: Error | undefined;
-        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -84,41 +82,35 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         readonly initialized: boolean;
         readonly name: string;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
-        readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        afterAttach(): 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<{

package/esm/LinearGenomeView/index.d.ts

@@ -24,6 +24,7 @@ export interface BpOffset {
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
+    Wrapper?: React.FC<any>;
 }
 export interface NavLocation {
     refName: string;
@@ -38,6 +39,9 @@ export declare const RESIZE_HANDLE_HEIGHT = 3;
 export declare const INTER_REGION_PADDING_WIDTH = 2;
 export declare const SPACING = 7;
 export declare const WIDGET_HEIGHT = 32;
+/**
+ * #stateModel LinearGenomeView
+ */
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -90,8 +94,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     searchQuery: string | undefined;
     seqDialogDisplayed: boolean;
 } & {
+    /**
+     * #getter
+     */
     readonly width: number;
+    /**
+     * #getter
+     */
     readonly interRegionPaddingWidth: number;
+    /**
+     * #getter
+     */
     readonly assemblyNames: string[];
 } & {
     MiniControlsComponent(): React.FC<any>;
@@ -124,31 +137,99 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]): void;
     readonly trackTypeActions: Map<string, MenuItem[]>;
 } & {
+    /**
+     * #action
+     */
     setShowCytobands(flag: boolean): void;
+    /**
+     * #action
+     */
     setWidth(newWidth: number): void;
+    /**
+     * #action
+     */
     setError(error: Error | undefined): void;
+    /**
+     * #action
+     */
     toggleHeader(): void;
+    /**
+     * #action
+     */
     toggleHeaderOverview(): void;
+    /**
+     * #action
+     */
     toggleNoTracksActive(): void;
+    /**
+     * #action
+     */
     toggleShowGridlines(): void;
+    /**
+     * #action
+     */
     scrollTo(offsetPx: number): number;
+    /**
+     * #action
+     */
     zoomTo(bpPerPx: number): number;
+    /**
+     * #action
+     * sets offsets used in the get sequence dialog
+     */
     setOffsets(left?: BpOffset, right?: BpOffset): void;
+    /**
+     * #action
+     */
     setSearchResults(results?: BaseResult[], query?: string): void;
+    /**
+     * #action
+     */
     setGetSequenceDialogOpen(open: boolean): void;
+    /**
+     * #action
+     */
     setNewView(bpPerPx: number, offsetPx: number): void;
+    /**
+     * #action
+     */
     horizontallyFlip(): void;
+    /**
+     * #action
+     */
     showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
     hideTrack(trackId: string): number;
 } & {
+    /**
+     * #action
+     */
     moveTrack(movingId: string, targetId: string): void;
+    /**
+     * #action
+     */
     closeView(): void;
+    /**
+     * #action
+     */
     toggleTrack(trackId: string): void;
+    /**
+     * #action
+     */
     setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    /**
+     * #action
+     */
     toggleCenterLine(): void;
+    /**
+     * #action
+     */
     setDisplayedRegions(regions: Region[]): void;
+    /**
+     * #action
+     */
     activateTrackSelector(): import("@jbrowse/core/util").Widget;
     /**
+     * #method
      * Helper method for the fetchSequence.
      * Retrieves the corresponding regions that were selected by the rubberband
      *
@@ -169,49 +250,118 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         variant?: string | undefined;
         isLeftEndOfDisplayedRegion?: boolean | undefined;
     }[];
+    /**
+     * #action
+     * schedule something to be run after the next time displayedRegions is set
+     */
     afterDisplayedRegionsSet(cb: Function): void;
+    /**
+     * #action
+     */
     horizontalScroll(distance: number): number;
+    /**
+     * #action
+     */
     center(): void;
+    /**
+     * #action
+     */
     showAllRegions(): void;
+    /**
+     * #action
+     */
     showAllRegionsInAssembly(assemblyName?: string): void;
+    /**
+     * #action
+     */
     setDraggingTrackId(idx?: string): void;
+    /**
+     * #action
+     */
     setScaleFactor(factor: number): void;
+    /**
+     * #action
+     * this "clears the view" and makes the view return to the import form
+     */
     clearView(): void;
+    /**
+     * #action
+     * creates an svg export and save using FileSaver
+     */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
 } & {
     slide: (viewWidths: number) => void;
 } & {
     zoom: (targetBpPerPx: number) => void;
 } & {
+    /**
+     * #getter
+     */
     readonly canShowCytobands: boolean;
+    /**
+     * #getter
+     */
     readonly showCytobands: boolean;
+    /**
+     * #getter
+     */
     readonly anyCytobandsExist: boolean;
+    /**
+     * #getter
+     * the cytoband is displayed to the right of the chromosome name,
+     * and that offset is calculated manually with this method
+     */
     readonly cytobandOffset: number;
 } & {
+    /**
+     * #method
+     * return the view menu items
+     */
     menuItems(): MenuItem[];
 } & {
+    /**
+     * #getter
+     * static blocks are an important concept jbrowse uses to avoid
+     * re-rendering when you scroll to the side. when you horizontally
+     * scroll to the right, old blocks to the left may be removed, and
+     * new blocks may be instantiated on the right. tracks may use the
+     * static blocks to render their data for the region represented by
+     * the block
+     */
     readonly staticBlocks: BlockSet;
+    /**
+     * #getter
+     * dynamic blocks represent the exact coordinates of the currently
+     * visible genome regions on the screen. they are similar to static
+     * blocks, but statcic blocks can go offscreen while dynamic blocks
+     * represent exactly what is on screen
+     */
     readonly dynamicBlocks: BlockSet;
-    readonly roundedDynamicBlocks: {
-        start: number;
-        end: number;
-        regionNumber?: number | undefined;
-        reversed?: boolean | undefined;
-        refName: string;
-        assemblyName: string;
-        key: string;
-        offsetPx: number;
-        widthPx: number;
-        variant?: string | undefined;
-        isLeftEndOfDisplayedRegion?: boolean | undefined;
-    }[];
+    /**
+     * #getter
+     * rounded dynamic blocks are dynamic blocks without fractions of bp
+     */
+    readonly roundedDynamicBlocks: BaseBlock[];
+    /**
+     * #getter
+     * a single "combo-locstring" representing all the regions visible
+     * on the screen
+     */
     readonly visibleLocStrings: string;
+    /**
+     * #getter
+     * same as visibleLocStrings, but only updated every 300ms
+     */
     readonly coarseVisibleLocStrings: string;
 } & {
+    /**
+     * #action
+     */
     setCoarseDynamicBlocks(blocks: BlockSet): void;
     afterAttach(): void;
 } & {
     /**
+     * #action
      * offset is the base-pair-offset in the displayed region, index is the index of the
      * displayed region in the linear genome view
      *
@@ -219,8 +369,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * @param end - object as `{start, end, offset, index}`
      */
     moveTo(start?: BpOffset, end?: BpOffset): void;
-    navToLocString(locString: string, optAssemblyName?: string): void;
     /**
+     * #action
+     * navigate to the given locstring
+     *
+     * @param locString - e.g. "chr1:1-100"
+     * @param optAssemblyName - (optional) the assembly name to use when navigating to the locstring
+     */
+    navToLocString(locString: string, optAssemblyName?: string): Promise<void>;
+    /**
+     * #action
      * Navigate to a location based on its refName and optionally start, end,
      * and assemblyName. Can handle if there are multiple displayedRegions
      * from same refName. Only navigates to a location if it is entirely
@@ -229,12 +387,21 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *
      * Throws an error if navigation was unsuccessful
      *
-     * @param location - a proposed location to navigate to
+     * @param query - a proposed location to navigate to
      */
     navTo(query: NavLocation): void;
+    /**
+     * #action
+     */
     navToMultiple(locations: NavLocation[]): void;
 } & {
+    /**
+     * #method
+     */
     rubberBandMenuItems(): MenuItem[];
+    /**
+     * #method
+     */
     bpToPx({ refName, coord, regionNumber, }: {
         refName: string;
         coord: number;
@@ -244,6 +411,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         offsetPx: number;
     } | undefined;
     /**
+     * #method
      * scrolls the view to center on the given bp. if that is not in any
      * of the displayed regions, does nothing
      * @param coord - basepair at which you want to center the view
@@ -251,6 +419,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * @param regionNumber - index of the displayedRegion
      */
     centerAt(coord: number, refName: string, regionNumber: number): void;
+    /**
+     * #method
+     */
     pxToBp(px: number): {
         coord: number;
         index: number;
@@ -262,6 +433,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         end: number;
         reversed: boolean;
     };
+    /**
+     * #getter
+     */
     readonly centerLineInfo: {
         coord: number;
         index: number;