@jbrowse/plugin-linear-genome-view 1.5.0 → 1.5.4

package/dist/BaseLinearDisplay/components/Block.d.ts

@@ -1,18 +1,15 @@
-import { BaseBlock } from '@jbrowse/core/util/blockTypes';
 import React from 'react';
-interface ContentBlockProps {
+import { BaseBlock } from '@jbrowse/core/util/blockTypes';
+declare const ContentBlock: ({ block, children }: {
     block: BaseBlock;
     children: React.ReactNode;
-}
-interface ElidedBlockProps {
+}) => JSX.Element;
+declare function ElidedBlock({ width }: {
     width: number;
-}
-interface InterRegionPaddingBlockProps {
+}): JSX.Element;
+declare function InterRegionPaddingBlock({ boundary, width, style, }: {
     boundary: boolean;
     width: number;
     style?: React.CSSProperties;
-}
-declare const ContentBlock: ({ block, children }: ContentBlockProps) => JSX.Element;
-declare function ElidedBlock({ width }: ElidedBlockProps): JSX.Element;
-declare function InterRegionPaddingBlock({ boundary, width, style, }: InterRegionPaddingBlockProps): JSX.Element;
+}): JSX.Element;
 export { ContentBlock, ElidedBlock, InterRegionPaddingBlock };

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

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export declare const useStyles: (props?: any) => Record<"closeButton", string>;
+export default function HelpDialog({ handleClose, }: {
+    handleClose: () => void;
+}): JSX.Element;

package/dist/LinearGenomeView/components/LinearGenomeView.d.ts

@@ -1,9 +1,7 @@
 /// <reference types="react" />
-import { Instance } from 'mobx-state-tree';
-import { LinearGenomeViewStateModel, ExportSvgOptions } from '..';
-declare type LGV = Instance<LinearGenomeViewStateModel>;
+import { LinearGenomeViewModel } from '..';
+declare type LGV = LinearGenomeViewModel;
 declare const LinearGenomeView: ({ model }: {
     model: LGV;
-}) => JSX.Element | null;
+}) => JSX.Element;
 export default LinearGenomeView;
-export declare function renderToSvg(model: LGV, opts: ExportSvgOptions): Promise<string>;

package/dist/LinearGenomeView/components/LinearGenomeViewSvg.d.ts

@@ -0,0 +1,4 @@
+import { LinearGenomeViewModel, ExportSvgOptions } from '..';
+declare type LGV = LinearGenomeViewModel;
+export declare function renderToSvg(model: LGV, opts: ExportSvgOptions): Promise<string>;
+export {};

package/dist/LinearGenomeView/components/OverviewRubberBand.d.ts

@@ -1,9 +1,8 @@
 import React from 'react';
-import { Instance } from 'mobx-state-tree';
 import ReactPropTypes from 'prop-types';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
-import { LinearGenomeViewStateModel } from '..';
-declare type LGV = Instance<LinearGenomeViewStateModel>;
+import { LinearGenomeViewModel } from '..';
+declare type LGV = LinearGenomeViewModel;
 declare function OverviewRubberBand({ model, overview, ControlComponent, }: {
     model: LGV;
     overview: Base1DViewModel;

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

@@ -1,10 +1,124 @@
 import React from 'react';
 import { Instance } from 'mobx-state-tree';
-import { LinearGenomeViewStateModel } from '..';
-declare type LGV = Instance<LinearGenomeViewStateModel>;
+import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+import { ContentBlock } from '@jbrowse/core/util/blockTypes';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { LinearGenomeViewModel } from '..';
+declare const Polygon: ({ model, overview, useOffset, }: {
+    model: LGV;
+    overview: Instance<Base1DViewModel>;
+    useOffset?: boolean | undefined;
+}) => JSX.Element | null;
+declare type LGV = LinearGenomeViewModel;
+declare const Cytobands: ({ overview, block, assembly, }: {
+    overview: Base1DViewModel;
+    assembly?: (import("mobx-state-tree").ModelInstanceTypeProps<{
+        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;
+        refNameAliases: {
+            [key: string]: string;
+        } | undefined;
+        cytobands: import("@jbrowse/core/util/simpleFeature").Feature[] | undefined;
+    } & {
+        readonly initialized: boolean;
+        readonly name: string;
+        readonly aliases: string[];
+        hasName(name: string): boolean;
+        readonly allAliases: string[];
+        readonly refNames: string[] | undefined;
+        readonly allRefNames: string[] | undefined;
+        readonly rpcManager: any;
+        readonly refNameColors: string[];
+    } & {
+        getCanonicalRefName(refName: string): string;
+        getRefNameColor(refName: string): string | undefined;
+        isValidRefName(refName: string): boolean;
+    } & {
+        setLoading(): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+            adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
+            refNameAliases: Record<string, string>;
+            cytobands: import("@jbrowse/core/util/simpleFeature").Feature[];
+        }): void;
+        setError(e: Error): void;
+        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setRefNameAliases(refNameAliases: Record<string, string>): void;
+        setCytobands(cytobands: import("@jbrowse/core/util/simpleFeature").Feature[]): void;
+        afterAttach(): void;
+    } & {
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+    } & 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;
+        refNameAliases: {
+            [key: string]: string;
+        } | undefined;
+        cytobands: import("@jbrowse/core/util/simpleFeature").Feature[] | undefined;
+    } & {
+        readonly initialized: boolean;
+        readonly name: string;
+        readonly aliases: string[];
+        hasName(name: string): boolean;
+        readonly allAliases: string[];
+        readonly refNames: string[] | undefined;
+        readonly allRefNames: string[] | undefined;
+        readonly rpcManager: any;
+        readonly refNameColors: string[];
+    } & {
+        getCanonicalRefName(refName: string): string;
+        getRefNameColor(refName: string): string | undefined;
+        isValidRefName(refName: string): boolean;
+    } & {
+        setLoading(): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
+            adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
+            refNameAliases: Record<string, string>;
+            cytobands: import("@jbrowse/core/util/simpleFeature").Feature[];
+        }): void;
+        setError(e: Error): void;
+        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setRefNameAliases(refNameAliases: Record<string, string>): void;
+        setCytobands(cytobands: import("@jbrowse/core/util/simpleFeature").Feature[]): void;
+        afterAttach(): void;
+    } & {
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    block: ContentBlock;
+}) => JSX.Element | null;
 declare function OverviewScaleBar({ model, children, }: {
     model: LGV;
     children: React.ReactNode;
 }): JSX.Element;
 declare const _default: typeof OverviewScaleBar;
 export default _default;
+export { Cytobands, Polygon };

package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts

@@ -6,12 +6,14 @@ export interface Option {
     group?: string;
     result: BaseResult;
 }
-declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, value, TextFieldProps, }: {
+declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, value, minWidth, TextFieldProps, }: {
     model: LinearGenomeViewModel;
     onSelect: (region: BaseResult) => void;
     assemblyName?: string;
     value?: string;
+    fetchResults: (query: string) => Promise<BaseResult[]>;
     style?: React.CSSProperties;
+    minWidth?: number;
     TextFieldProps?: TFP;
 }): JSX.Element;
 declare const _default: typeof RefNameAutocomplete;

package/dist/LinearGenomeView/components/ScaleBar.d.ts

@@ -24,6 +24,7 @@ declare const _default: React.ForwardRefExoticComponent<{
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
         trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
         showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }> & {
         width: number;
     } & {
@@ -111,6 +112,7 @@ declare const _default: React.ForwardRefExoticComponent<{
             assemblyName: string;
         } | undefined;
     } & {
+        setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
         setError(error: Error | undefined): void;
         toggleHeader(): void;
@@ -162,6 +164,11 @@ declare const _default: React.ForwardRefExoticComponent<{
         slide: (viewWidths: number) => void;
     } & {
         zoom: (targetBpPerPx: number) => void;
+    } & {
+        readonly canShowCytobands: boolean;
+        readonly showCytobands: boolean;
+        readonly anyCytobandsExist: boolean;
+        readonly cytobandOffset: number;
     } & {
         menuItems(): import("@jbrowse/core/ui").MenuItem[];
         readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -213,6 +220,7 @@ declare const _default: React.ForwardRefExoticComponent<{
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
         trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
         showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         width: number;
     } & {
@@ -300,6 +308,7 @@ declare const _default: React.ForwardRefExoticComponent<{
             assemblyName: string;
         } | undefined;
     } & {
+        setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
         setError(error: Error | undefined): void;
         toggleHeader(): void;
@@ -351,6 +360,11 @@ declare const _default: React.ForwardRefExoticComponent<{
         slide: (viewWidths: number) => void;
     } & {
         zoom: (targetBpPerPx: number) => void;
+    } & {
+        readonly canShowCytobands: boolean;
+        readonly showCytobands: boolean;
+        readonly anyCytobandsExist: boolean;
+        readonly cytobandOffset: number;
     } & {
         menuItems(): import("@jbrowse/core/ui").MenuItem[];
         readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;

package/dist/LinearGenomeView/components/util.d.ts

@@ -1,2 +1,2 @@
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-export declare function dedupe(results?: BaseResult[]): BaseResult[] | undefined;
+export declare function dedupe(results: BaseResult[] | undefined, cb: (result: BaseResult) => string): BaseResult[];

package/dist/LinearGenomeView/index.d.ts

@@ -4,9 +4,8 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { renderToSvg } from './components/LinearGenomeView';
+import { renderToSvg } from './components/LinearGenomeViewSvg';
 import RefNameAutocomplete from './components/RefNameAutocomplete';
-export { default as ReactComponent } from './components/LinearGenomeView';
 export interface BpOffset {
     refName?: string;
     index: number;
@@ -56,6 +55,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
     trackLabels: import("mobx-state-tree").IType<string | undefined, string, string>;
     showCenterLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showCytobandsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     width: number;
 } & {
@@ -155,6 +155,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         assemblyName: string;
     } | undefined;
 } & {
+    setShowCytobands(flag: boolean): void;
     setWidth(newWidth: number): void;
     setError(error: Error | undefined): void;
     toggleHeader(): void;
@@ -248,6 +249,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     slide: (viewWidths: number) => void;
 } & {
     zoom: (targetBpPerPx: number) => void;
+} & {
+    readonly canShowCytobands: boolean;
+    readonly showCytobands: boolean;
+    readonly anyCytobandsExist: boolean;
+    readonly cytobandOffset: number;
 } & {
     menuItems(): MenuItem[];
     readonly staticBlocks: BlockSet;
@@ -279,3 +285,4 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 export { renderToSvg, RefNameAutocomplete };
 export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
+export { default as ReactComponent } from './components/LinearGenomeView';