@jbrowse/plugin-linear-genome-view 2.12.0 → 2.12.2
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/Block.js +3 -3
- package/dist/BaseLinearDisplay/components/BlockMsg.js +1 -1
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +22 -24
- package/dist/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +2 -2
- package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js +1 -1
- package/dist/BaseLinearDisplay/models/TrackHeightMixin.js +1 -1
- package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.js +1 -1
- package/dist/BaseLinearDisplay/models/renderSvg.js +1 -2
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +4 -4
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +1 -2
- package/dist/BaseLinearDisplay/models/util.js +3 -4
- package/dist/BasicTrack/index.js +1 -1
- package/dist/FeatureTrack/index.js +1 -1
- package/dist/LaunchLinearGenomeView/index.js +1 -1
- package/dist/LinearBareDisplay/configSchema.js +1 -2
- package/dist/LinearBareDisplay/index.js +1 -1
- package/dist/LinearBareDisplay/model.d.ts +26 -33
- package/dist/LinearBareDisplay/model.js +1 -2
- package/dist/LinearBasicDisplay/index.js +1 -1
- package/dist/LinearBasicDisplay/model.d.ts +52 -53
- package/dist/LinearGenomeView/components/ExportSvgDialog.js +1 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js +1 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +1 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.js +1 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete/util.js +3 -4
- package/dist/LinearGenomeView/components/RubberbandSpan.js +1 -1
- package/dist/LinearGenomeView/components/SearchResultsDialog.js +1 -1
- package/dist/LinearGenomeView/components/SearchResultsTable.js +1 -1
- package/dist/LinearGenomeView/components/hooks.d.ts +2 -2
- package/dist/LinearGenomeView/components/hooks.js +3 -4
- package/dist/LinearGenomeView/components/util.js +4 -5
- package/dist/LinearGenomeView/index.js +1 -1
- package/dist/LinearGenomeView/model.d.ts +10 -10
- package/dist/LinearGenomeView/model.js +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGBackground.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGHeader.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGRuler.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGTracks.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/util.js +1 -2
- package/dist/LinearGenomeView/util.d.ts +3 -3
- package/dist/LinearGenomeView/util.js +4 -5
- package/dist/index.d.ts +74 -2237
- package/dist/searchUtils.js +5 -6
- package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +22 -24
- package/esm/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +2 -2
- package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +4 -4
- package/esm/LinearBareDisplay/model.d.ts +26 -33
- package/esm/LinearBasicDisplay/model.d.ts +52 -53
- package/esm/LinearGenomeView/components/hooks.d.ts +2 -2
- package/esm/LinearGenomeView/model.d.ts +10 -10
- package/esm/LinearGenomeView/util.d.ts +3 -3
- package/esm/index.d.ts +74 -2237
- package/package.json +2 -2
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.
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exports.ContentBlock = void 0;
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exports.ElidedBlock = ElidedBlock;
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exports.InterRegionPaddingBlock = InterRegionPaddingBlock;
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const react_1 = __importDefault(require("react"));
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const mui_1 = require("tss-react/mui");
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const mobx_react_1 = require("mobx-react");
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const { classes } = useStyles();
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return react_1.default.createElement("div", { className: classes.elidedBlock, style: { width } });
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}
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exports.ElidedBlock = ElidedBlock;
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function InterRegionPaddingBlock({ boundary, width, style = {}, }) {
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const { classes } = useStyles();
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return (react_1.default.createElement("div", { style: {
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? classes.boundaryPaddingBlock
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: classes.interRegionPaddingBlock }));
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}
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exports.InterRegionPaddingBlock = InterRegionPaddingBlock;
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.default = BlockMsg;
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const react_1 = __importDefault(require("react"));
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const material_1 = require("@mui/material");
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const mui_1 = require("tss-react/mui");
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react_1.default.createElement(material_1.Tooltip, { title: message },
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react_1.default.createElement("div", null, message))));
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}
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exports.default = BlockMsg;
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}, {
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renderInProgress: AbortController | undefined;
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filled: boolean;
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reactElement: React.ReactElement
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reactElement: React.ReactElement | undefined;
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features: Map<string, Feature> | undefined;
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layout: any;
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status: string;
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error?: unknown;
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reload: () => void;
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message: React.ReactNode;
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filled?: boolean
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status?: string
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reactElement?: React.ReactElement
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filled?: boolean;
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status?: string;
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reactElement?: React.ReactElement;
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};
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}) => React.JSX.Element | undefined;
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renderProps: any;
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setLoading(abortController: AbortController): void;
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setMessage(messageText: string): void;
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setRendered(props: {
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reactElement: React.ReactElement
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reactElement: React.ReactElement;
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features: Map<string, Feature>;
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layout: any;
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maxHeightReached: boolean;
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error: unknown;
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message: string | undefined;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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onHorizontalScroll?: Function
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blockState?: Record<string, any
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onHorizontalScroll?: Function;
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blockState?: Record<string, any>;
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}>;
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readonly DisplayBlurb: React.FC<{
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model: {
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readonly parentTrack: any;
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renderProps(): any;
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readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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readonly DisplayMessageComponent: React.FC<any
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readonly DisplayMessageComponent: undefined | React.FC<any>;
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trackMenuItems(): MenuItem[];
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readonly viewMenuActions: MenuItem[];
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regionCannotBeRendered(): null;
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} & {
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setMessage(arg?: string
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setMessage(arg?: string): void;
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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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setHeight(displayHeight: number): number;
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resizeHeight(distance: number): number;
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} & {
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featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
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currStatsBpPerPx: number;
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} & {
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readonly currentBytesRequested: number;
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afterAttach(): void;
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} & {
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setCurrStatsBpPerPx(n: number): void;
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setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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setFeatureDensityStatsP(arg: any): void;
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setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
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setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
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clearFeatureDensityStats(): void;
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} & {
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readonly regionTooLarge: boolean;
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readonly regionTooLargeReason: string;
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} & {
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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* #action
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*/
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
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} & {
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featureIdUnderMouse:
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contextMenuFeature:
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featureIdUnderMouse: undefined | string;
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contextMenuFeature: undefined | Feature;
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} & {
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/**
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* #getter
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* if a display-level message should be displayed instead of the blocks,
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* make this return a react component
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*/
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readonly DisplayMessageComponent: React.FC<any
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readonly DisplayMessageComponent: undefined | React.FC<any>;
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* #getter
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}, {
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exports.renderBlockData =
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.
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exports.getDisplayStr = getDisplayStr;
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exports.getId = getId;
|
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exports.getDisplayStr = getDisplayStr;
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.filter(f => !!f)
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exports.getFeatureDensityStatsPre = getFeatureDensityStatsPre;
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CHANGED
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|
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|
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|
3
3
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|
|
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4
|
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|
|
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|
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|
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|
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|
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|
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exports.default = FeatureTrackF;
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@@ -1,5 +1,6 @@
|
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"use strict";
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exports.default = LaunchLinearGenomeViewF;
|
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|
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|
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@@ -1,6 +1,6 @@
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|
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|
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|
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|
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+
exports.default = LinearBareDisplayF;
|
|
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|
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|
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|
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@@ -1,4 +1,3 @@
|
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/// <reference types="react" />
|
|
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|
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|
|
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|
/**
|
|
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|
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|
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@@ -34,7 +33,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
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|
}, {
|
|
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34
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|
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|
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reactElement: import("react").ReactElement
|
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|
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layout: any;
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|
|
@@ -46,9 +45,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
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46
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|
error?: unknown;
|
|
47
46
|
reload: () => void;
|
|
48
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|
message: import("react").ReactNode;
|
|
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|
-
filled?: boolean
|
|
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|
-
status?: string
|
|
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|
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reactElement?: import("react").ReactElement
|
|
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|
+
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|
|
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|
+
status?: string;
|
|
50
|
+
reactElement?: import("react").ReactElement;
|
|
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51
|
};
|
|
53
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|
}) => import("react").JSX.Element | undefined;
|
|
54
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|
renderProps: any;
|
|
@@ -59,7 +58,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
59
58
|
setLoading(abortController: AbortController): void;
|
|
60
59
|
setMessage(messageText: string): void;
|
|
61
60
|
setRendered(props: {
|
|
62
|
-
reactElement: import("react").ReactElement
|
|
61
|
+
reactElement: import("react").ReactElement;
|
|
63
62
|
features: Map<string, import("@jbrowse/core/util").Feature>;
|
|
64
63
|
layout: any;
|
|
65
64
|
maxHeightReached: boolean;
|
|
@@ -77,9 +76,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
77
76
|
};
|
|
78
77
|
fetchSizeLimit: {
|
|
79
78
|
type: string;
|
|
80
|
-
defaultValue: number;
|
|
81
|
-
* #method
|
|
82
|
-
*/
|
|
79
|
+
defaultValue: number;
|
|
83
80
|
description: string;
|
|
84
81
|
};
|
|
85
82
|
height: {
|
|
@@ -131,8 +128,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
131
128
|
error: unknown;
|
|
132
129
|
message: string | undefined;
|
|
133
130
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
134
|
-
onHorizontalScroll?: Function
|
|
135
|
-
blockState?: Record<string, any
|
|
131
|
+
onHorizontalScroll?: Function;
|
|
132
|
+
blockState?: Record<string, any>;
|
|
136
133
|
}>;
|
|
137
134
|
readonly DisplayBlurb: import("react").FC<{
|
|
138
135
|
model: {
|
|
@@ -157,12 +154,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
157
154
|
readonly parentTrack: any;
|
|
158
155
|
renderProps(): any;
|
|
159
156
|
readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
|
|
160
|
-
readonly DisplayMessageComponent: import("react").FC<any
|
|
157
|
+
readonly DisplayMessageComponent: undefined | import("react").FC<any>;
|
|
161
158
|
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
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159
|
readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
|
|
163
160
|
regionCannotBeRendered(): null;
|
|
164
161
|
} & {
|
|
165
|
-
setMessage(arg?: string
|
|
162
|
+
setMessage(arg?: string): void;
|
|
166
163
|
setError(error?: unknown): void;
|
|
167
164
|
setRpcDriverName(rpcDriverName: string): void;
|
|
168
165
|
reload(): void;
|
|
@@ -171,14 +168,12 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
171
168
|
} & {
|
|
172
169
|
readonly height: number;
|
|
173
170
|
} & {
|
|
174
|
-
setScrollTop(scrollTop: number): void;
|
|
175
|
-
* #method
|
|
176
|
-
*/
|
|
171
|
+
setScrollTop(scrollTop: number): void;
|
|
177
172
|
setHeight(displayHeight: number): number;
|
|
178
173
|
resizeHeight(distance: number): number;
|
|
179
174
|
} & {
|
|
180
|
-
featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
181
|
-
featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
175
|
+
featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
|
|
176
|
+
featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
|
|
182
177
|
currStatsBpPerPx: number;
|
|
183
178
|
} & {
|
|
184
179
|
readonly currentBytesRequested: number;
|
|
@@ -190,10 +185,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
190
185
|
afterAttach(): void;
|
|
191
186
|
} & {
|
|
192
187
|
setCurrStatsBpPerPx(n: number): void;
|
|
193
|
-
setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
188
|
+
setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
|
|
194
189
|
getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
|
|
195
190
|
setFeatureDensityStatsP(arg: any): void;
|
|
196
|
-
setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats
|
|
191
|
+
setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
|
|
197
192
|
clearFeatureDensityStats(): void;
|
|
198
193
|
} & {
|
|
199
194
|
readonly regionTooLarge: boolean;
|
|
@@ -202,8 +197,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
202
197
|
regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
|
|
203
198
|
regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
|
|
204
199
|
} & {
|
|
205
|
-
featureIdUnderMouse:
|
|
206
|
-
contextMenuFeature: import("@jbrowse/core/util").Feature
|
|
200
|
+
featureIdUnderMouse: undefined | string;
|
|
201
|
+
contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
|
|
207
202
|
} & {
|
|
208
203
|
readonly blockType: "dynamicBlocks" | "staticBlocks";
|
|
209
204
|
readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
@@ -211,7 +206,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
211
206
|
readonly renderDelay: number;
|
|
212
207
|
readonly TooltipComponent: import("react").FC<any>;
|
|
213
208
|
readonly selectedFeatureId: string | undefined;
|
|
214
|
-
readonly DisplayMessageComponent: import("react").FC<any
|
|
209
|
+
readonly DisplayMessageComponent: undefined | import("react").FC<any>;
|
|
215
210
|
} & {
|
|
216
211
|
readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
|
|
217
212
|
readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
|
|
@@ -224,8 +219,8 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
224
219
|
selectFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
225
220
|
navToFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
226
221
|
clearFeatureSelection(): void;
|
|
227
|
-
setFeatureIdUnderMouse(feature?: string
|
|
228
|
-
setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature
|
|
222
|
+
setFeatureIdUnderMouse(feature?: string): void;
|
|
223
|
+
setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
|
|
229
224
|
} & {
|
|
230
225
|
reload(): Promise<void>;
|
|
231
226
|
} & {
|
|
@@ -274,7 +269,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
274
269
|
}, {
|
|
275
270
|
renderInProgress: AbortController | undefined;
|
|
276
271
|
filled: boolean;
|
|
277
|
-
reactElement: import("react").ReactElement
|
|
272
|
+
reactElement: import("react").ReactElement | undefined;
|
|
278
273
|
features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
|
|
279
274
|
layout: any;
|
|
280
275
|
status: string;
|
|
@@ -286,9 +281,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
286
281
|
error?: unknown;
|
|
287
282
|
reload: () => void;
|
|
288
283
|
message: import("react").ReactNode;
|
|
289
|
-
filled?: boolean
|
|
290
|
-
status?: string
|
|
291
|
-
reactElement?: import("react").ReactElement
|
|
284
|
+
filled?: boolean;
|
|
285
|
+
status?: string;
|
|
286
|
+
reactElement?: import("react").ReactElement;
|
|
292
287
|
};
|
|
293
288
|
}) => import("react").JSX.Element | undefined;
|
|
294
289
|
renderProps: any;
|
|
@@ -299,7 +294,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
299
294
|
setLoading(abortController: AbortController): void;
|
|
300
295
|
setMessage(messageText: string): void;
|
|
301
296
|
setRendered(props: {
|
|
302
|
-
reactElement: import("react").ReactElement
|
|
297
|
+
reactElement: import("react").ReactElement;
|
|
303
298
|
features: Map<string, import("@jbrowse/core/util").Feature>;
|
|
304
299
|
layout: any;
|
|
305
300
|
maxHeightReached: boolean;
|
|
@@ -317,9 +312,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
317
312
|
};
|
|
318
313
|
fetchSizeLimit: {
|
|
319
314
|
type: string;
|
|
320
|
-
defaultValue: number;
|
|
321
|
-
* #method
|
|
322
|
-
*/
|
|
315
|
+
defaultValue: number;
|
|
323
316
|
description: string;
|
|
324
317
|
};
|
|
325
318
|
height: {
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.stateModelFactory =
|
|
3
|
+
exports.stateModelFactory = stateModelFactory;
|
|
4
4
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
5
|
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
6
6
|
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
@@ -46,4 +46,3 @@ function stateModelFactory(configSchema) {
|
|
|
46
46
|
};
|
|
47
47
|
});
|
|
48
48
|
}
|
|
49
|
-
exports.stateModelFactory = stateModelFactory;
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|
@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.configSchema = exports.modelFactory = void 0;
|
|
7
|
+
exports.default = LinearBasicDisplay;
|
|
7
8
|
const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
|
|
8
9
|
const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
|
|
9
10
|
// locals
|
|
@@ -23,7 +24,6 @@ function LinearBasicDisplay(pluginManager) {
|
|
|
23
24
|
});
|
|
24
25
|
});
|
|
25
26
|
}
|
|
26
|
-
exports.default = LinearBasicDisplay;
|
|
27
27
|
var model_2 = require("./model");
|
|
28
28
|
Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
|
|
29
29
|
var configSchema_2 = require("./configSchema");
|