@jbrowse/plugin-linear-genome-view 1.3.4 → 1.5.0
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.
- package/dist/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +3 -2
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +20 -10
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +2 -2
- package/dist/LinearBareDisplay/model.d.ts +10 -9
- package/dist/LinearBasicDisplay/model.d.ts +13 -9
- package/dist/LinearGenomeView/components/Header.d.ts +2 -4
- package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts +1 -11
- package/dist/LinearGenomeView/components/ScaleBar.d.ts +46 -14
- package/dist/LinearGenomeView/components/util.d.ts +2 -0
- package/dist/LinearGenomeView/index.d.ts +13 -2
- package/dist/index.d.ts +47 -56
- package/dist/plugin-linear-genome-view.cjs.development.js +642 -423
- package/dist/plugin-linear-genome-view.cjs.development.js.map +1 -1
- package/dist/plugin-linear-genome-view.cjs.production.min.js +1 -1
- package/dist/plugin-linear-genome-view.cjs.production.min.js.map +1 -1
- package/dist/plugin-linear-genome-view.esm.js +652 -433
- package/dist/plugin-linear-genome-view.esm.js.map +1 -1
- package/package.json +4 -2
- package/src/BaseLinearDisplay/components/BaseLinearDisplay.tsx +100 -21
- package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +10 -10
- package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +15 -13
- package/src/LinearBasicDisplay/model.ts +25 -3
- package/src/LinearGenomeView/components/ExportSvgDialog.tsx +17 -8
- package/src/LinearGenomeView/components/Header.tsx +101 -104
- package/src/LinearGenomeView/components/ImportForm.tsx +146 -113
- package/src/LinearGenomeView/components/LinearGenomeView.test.js +6 -6
- package/src/LinearGenomeView/components/OverviewScaleBar.tsx +4 -1
- package/src/LinearGenomeView/components/RefNameAutocomplete.tsx +196 -169
- package/src/LinearGenomeView/components/SearchResultsDialog.tsx +1 -16
- package/src/LinearGenomeView/components/SequenceDialog.tsx +59 -58
- package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap +5 -177
- package/src/LinearGenomeView/components/util.ts +8 -0
- package/src/LinearGenomeView/index.tsx +39 -28
- package/src/index.ts +3 -1
package/dist/index.d.ts
CHANGED
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@@ -3,7 +3,7 @@ import Plugin from '@jbrowse/core/Plugin';
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import PluginManager from '@jbrowse/core/PluginManager';
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import { BaseLinearDisplay, BaseLinearDisplayComponent, baseLinearDisplayConfigSchema, BlockModel } from './BaseLinearDisplay';
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import { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
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-
import { LinearGenomeViewModel, LinearGenomeViewStateModel, renderToSvg } from './LinearGenomeView';
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import { LinearGenomeViewModel, LinearGenomeViewStateModel, renderToSvg, RefNameAutocomplete } from './LinearGenomeView';
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import { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory } from './LinearBasicDisplay';
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export default class LinearGenomeViewPlugin extends Plugin {
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name: string;
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@@ -37,7 +37,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
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features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
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layout: any;
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status: string;
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error:
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error: unknown;
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message: string | undefined;
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maxHeightReached: boolean;
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ReactComponent: ({ model, }: {
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@@ -57,14 +57,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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maxHeightReached: boolean;
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renderProps: any;
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} | undefined): void;
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setError(error:
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setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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}> & {
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rendererTypeName: string;
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error:
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error: unknown;
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} & {
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readonly RenderingComponent: import("react").FC<{
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model: import("mobx-state-tree").ModelInstanceTypeProps<{
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@@ -73,14 +73,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}> & {
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rendererTypeName: string;
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error:
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error: unknown;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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error:
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error: unknown;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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onHorizontalScroll?: Function | undefined;
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blockState?: Record<string, any> | undefined;
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@@ -92,33 +92,32 @@ export default class LinearGenomeViewPlugin extends Plugin {
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}> & {
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rendererTypeName: string;
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error:
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error: unknown;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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error:
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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}> | null;
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readonly adapterConfig: any;
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readonly parentTrack: any;
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renderProps(): any;
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readonly rendererType: any;
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readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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regionCannotBeRendered(): undefined;
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} & {
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setError(error?:
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setError(error?: unknown): void;
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setRpcDriverName(rpcDriverName: string): void;
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reload(): void;
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} & {
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message: string;
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featureIdUnderMouse: string | undefined;
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contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
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additionalContextMenuItemCallbacks: Function[];
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scrollTop: number;
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} & {
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readonly blockType: "staticBlocks" | "dynamicBlocks";
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@@ -133,7 +132,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
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readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util/simpleFeature").Feature>;
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readonly featureUnderMouse: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
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getFeatureOverlapping(blockKey: string, x: number, y: number): any;
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getFeatureByID(id: string): [number, number, number, number] | undefined;
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getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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searchFeatureByID(id: string): [number, number, number, number] | undefined;
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} & {
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afterAttach(): void;
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setHeight(displayHeight: number): number;
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@@ -147,20 +147,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
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clearFeatureSelection(): void;
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setFeatureIdUnderMouse(feature: string | undefined): void;
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reload(): void;
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addAdditionalContextMenuItemCallback(callback: Function): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
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} & {
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
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readonly contextMenuItems: {
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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contextMenuItems(): {
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label: string;
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icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
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onClick: () => void;
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}[];
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readonly renderProps: any;
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renderProps(): any;
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} & {
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renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
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overrideHeight: number;
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@@ -193,7 +190,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
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features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
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layout: any;
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status: string;
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error:
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error: unknown;
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message: string | undefined;
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maxHeightReached: boolean;
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ReactComponent: ({ model, }: {
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@@ -213,14 +210,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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maxHeightReached: boolean;
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renderProps: any;
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} | undefined): void;
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setError(error:
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setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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}, {
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rendererTypeName: string;
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} & {
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readonly RenderingComponent: import("react").FC<{
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model: import("mobx-state-tree").ModelInstanceTypeProps<{
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}> & {
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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onHorizontalScroll?: Function | undefined;
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blockState?: Record<string, any> | undefined;
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}> & {
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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error:
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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}> | null;
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readonly adapterConfig: any;
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readonly parentTrack: any;
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renderProps(): any;
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readonly rendererType: any;
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readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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regionCannotBeRendered(): undefined;
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} & {
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setError(error?: unknown): void;
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setRpcDriverName(rpcDriverName: string): void;
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reload(): void;
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} & {
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message: string;
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featureIdUnderMouse: string | undefined;
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contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
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additionalContextMenuItemCallbacks: Function[];
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scrollTop: number;
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} & {
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readonly blockType: "staticBlocks" | "dynamicBlocks";
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readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util/simpleFeature").Feature>;
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readonly featureUnderMouse: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
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getFeatureOverlapping(blockKey: string, x: number, y: number): any;
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getFeatureByID(id: string): [number, number, number, number] | undefined;
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getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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searchFeatureByID(id: string): [number, number, number, number] | undefined;
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} & {
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afterAttach(): void;
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setHeight(displayHeight: number): number;
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clearFeatureSelection(): void;
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setFeatureIdUnderMouse(feature: string | undefined): void;
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reload(): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
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} & {
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
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readonly contextMenuItems: {
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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contextMenuItems(): {
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label: string;
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icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
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onClick: () => void;
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}[];
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renderProps(): any;
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} & {
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renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
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overrideHeight: number;
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features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
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layout: any;
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status: string;
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error:
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error: unknown;
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message: string | undefined;
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maxHeightReached: boolean;
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ReactComponent: ({ model, }: {
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} | undefined): void;
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setError(error:
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setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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}, {
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rendererTypeName: string;
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error:
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error: unknown;
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} & {
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readonly RenderingComponent: import("react").FC<{
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model: import("mobx-state-tree").ModelInstanceTypeProps<{
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@@ -394,14 +388,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}> & {
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rendererTypeName: string;
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error:
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error: unknown;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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error:
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+
error: unknown;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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onHorizontalScroll?: Function | undefined;
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blockState?: Record<string, any> | undefined;
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@@ -413,33 +407,32 @@ export default class LinearGenomeViewPlugin extends Plugin {
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}> & {
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rendererTypeName: string;
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-
error:
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+
error: unknown;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
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type: import("mobx-state-tree").ISimpleType<string>;
|
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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error:
|
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+
error: unknown;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
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}> | null;
|
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readonly adapterConfig: any;
|
|
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|
readonly parentTrack: any;
|
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|
-
|
|
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|
+
renderProps(): any;
|
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|
readonly rendererType: any;
|
|
430
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|
readonly DisplayMessageComponent: import("react").FC<any> | undefined;
|
|
431
|
-
|
|
425
|
+
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
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426
|
readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
|
|
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|
regionCannotBeRendered(): undefined;
|
|
434
428
|
} & {
|
|
435
|
-
setError(error?:
|
|
429
|
+
setError(error?: unknown): void;
|
|
436
430
|
setRpcDriverName(rpcDriverName: string): void;
|
|
437
431
|
reload(): void;
|
|
438
432
|
} & {
|
|
439
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|
message: string;
|
|
440
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|
featureIdUnderMouse: string | undefined;
|
|
441
435
|
contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
|
|
442
|
-
additionalContextMenuItemCallbacks: Function[];
|
|
443
436
|
scrollTop: number;
|
|
444
437
|
} & {
|
|
445
438
|
readonly blockType: "staticBlocks" | "dynamicBlocks";
|
|
@@ -454,7 +447,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
|
|
|
454
447
|
readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util/simpleFeature").Feature>;
|
|
455
448
|
readonly featureUnderMouse: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
|
|
456
449
|
getFeatureOverlapping(blockKey: string, x: number, y: number): any;
|
|
457
|
-
getFeatureByID(id: string): [number, number, number, number] | undefined;
|
|
450
|
+
getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
|
|
451
|
+
searchFeatureByID(id: string): [number, number, number, number] | undefined;
|
|
458
452
|
} & {
|
|
459
453
|
afterAttach(): void;
|
|
460
454
|
setHeight(displayHeight: number): number;
|
|
@@ -468,20 +462,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
|
|
|
468
462
|
clearFeatureSelection(): void;
|
|
469
463
|
setFeatureIdUnderMouse(feature: string | undefined): void;
|
|
470
464
|
reload(): void;
|
|
471
|
-
addAdditionalContextMenuItemCallback(callback: Function): void;
|
|
472
465
|
setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
|
|
473
466
|
} & {
|
|
474
467
|
regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
|
|
475
468
|
regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
|
|
476
|
-
|
|
477
|
-
|
|
478
|
-
readonly contextMenuItems: {
|
|
469
|
+
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
470
|
+
contextMenuItems(): {
|
|
479
471
|
label: string;
|
|
480
472
|
icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
|
|
481
473
|
onClick: () => void;
|
|
482
474
|
}[];
|
|
483
|
-
|
|
484
|
-
readonly renderProps: any;
|
|
475
|
+
renderProps(): any;
|
|
485
476
|
} & {
|
|
486
477
|
renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
|
|
487
478
|
overrideHeight: number;
|
|
@@ -498,6 +489,6 @@ export default class LinearGenomeViewPlugin extends Plugin {
|
|
|
498
489
|
install(pluginManager: PluginManager): void;
|
|
499
490
|
configure(pluginManager: PluginManager): void;
|
|
500
491
|
}
|
|
501
|
-
export { BaseLinearDisplayComponent, BaseLinearDisplay, baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, };
|
|
492
|
+
export { BaseLinearDisplayComponent, BaseLinearDisplay, baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, RefNameAutocomplete, };
|
|
502
493
|
export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel };
|
|
503
494
|
export type { BaseLinearDisplayModel } from './BaseLinearDisplay';
|