@jbrowse/plugin-breakpoint-split-view 2.11.2 → 2.12.1
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/BreakpointAlignmentsFeatureDetail/index.js +1 -1
- package/dist/BreakpointSplitView/components/ExportSvgDialog.js +1 -1
- package/dist/BreakpointSplitView/components/util.js +6 -7
- package/dist/BreakpointSplitView/index.js +1 -1
- package/dist/BreakpointSplitView/model.d.ts +23 -169
- package/dist/BreakpointSplitView/model.js +1 -1
- package/dist/BreakpointSplitView/svgcomponents/SVGBackground.js +1 -1
- package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js +1 -2
- package/dist/BreakpointSplitView/svgcomponents/util.js +2 -3
- package/dist/BreakpointSplitView/util.js +4 -4
- package/esm/BreakpointSplitView/model.d.ts +23 -169
- package/package.json +2 -2
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@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
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return result;
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.default = BreakpointAlignmentsFeatureDetailF;
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const react_1 = require("react");
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const configuration_1 = require("@jbrowse/core/configuration");
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const mst_1 = require("@jbrowse/core/util/types/mst");
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@@ -54,4 +55,3 @@ function BreakpointAlignmentsFeatureDetailF(pluginManager) {
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});
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});
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}
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exports.default = BreakpointAlignmentsFeatureDetailF;
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@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
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return result;
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.default = ExportSvgDialog;
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const react_1 = __importStar(require("react"));
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const material_1 = require("@mui/material");
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const ui_1 = require("@jbrowse/core/ui");
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@@ -85,4 +86,3 @@ function ExportSvgDialog({ model, handleClose, }) {
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}
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} }, "Submit"))));
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}
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exports.default = ExportSvgDialog;
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@@ -1,6 +1,11 @@
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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.getBadlyPairedAlignments = getBadlyPairedAlignments;
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exports.getMatchedAlignmentFeatures = getMatchedAlignmentFeatures;
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exports.hasPairedReads = hasPairedReads;
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exports.findMatchingAlt = findMatchingAlt;
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exports.getMatchedBreakendFeatures = getMatchedBreakendFeatures;
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exports.getMatchedTranslocationFeatures = getMatchedTranslocationFeatures;
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const util_1 = require("@jbrowse/core/util");
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const vcf_1 = require("@gmod/vcf");
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// this finds candidate alignment features, aimed at plotting split reads from
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}
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return [...candidates.values()].filter(v => v.length > 1);
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}
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exports.getBadlyPairedAlignments = getBadlyPairedAlignments;
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function getTag(f, tag) {
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const tags = f.get('tags');
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return tags ? tags[tag] : f.get(tag);
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}
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return [...candidates.values()].filter(v => v.length > 1);
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}
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exports.getMatchedAlignmentFeatures = getMatchedAlignmentFeatures;
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function hasPairedReads(features) {
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for (const f of features.values()) {
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if (f.get('flags') & 1) {
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}
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return false;
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}
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exports.hasPairedReads = hasPairedReads;
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function findMatchingAlt(feat1, feat2) {
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const alts = feat1.get('ALT');
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if (alts) {
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}
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return undefined;
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}
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exports.findMatchingAlt = findMatchingAlt;
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// Returns paired BND features across multiple views by inspecting the ALT
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// field to get exact coordinate matches
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function getMatchedBreakendFeatures(feats) {
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}
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return [...candidates.values()].filter(v => v.length > 1);
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}
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exports.getMatchedBreakendFeatures = getMatchedBreakendFeatures;
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// Getting "matched" TRA means just return all TRA
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function getMatchedTranslocationFeatures(feats) {
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const ret = [];
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}
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return ret;
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}
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exports.getMatchedTranslocationFeatures = getMatchedTranslocationFeatures;
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.default = BreakpointSplitViewF;
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const react_1 = require("react");
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// locals
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const BreakpointSplitView_1 = __importDefault(require("./BreakpointSplitView"));
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@@ -40,4 +41,3 @@ function BreakpointSplitViewF(pluginManager) {
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});
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});
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}
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exports.default = BreakpointSplitViewF;
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@@ -51,16 +51,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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type: import("mobx-state-tree").IType<string | undefined, string, string>;
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offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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displayedRegions: import("mobx-state-tree").
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refName: import("mobx-state-tree").ISimpleType<string>;
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start: import("mobx-state-tree").ISimpleType<number>;
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end: import("mobx-state-tree").ISimpleType<number>;
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reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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} & {
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assemblyName: import("mobx-state-tree").ISimpleType<string>;
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}, {
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setRefName(newRefName: string): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
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tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
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hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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} & {
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volatileWidth: number | undefined;
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minimumBlockWidth: number;
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draggingTrackId:
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draggingTrackId: undefined | string;
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volatileError: unknown;
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afterDisplayedRegionsSetCallbacks: Function[];
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scaleFactor: number;
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trackRefs: Record<string, HTMLDivElement>;
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coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
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coarseTotalBp: number;
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leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
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rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
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} & {
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readonly trackLabelsSetting: any;
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readonly width: number;
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removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
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scrollTo(offsetPx: number): number;
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zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
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setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string
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setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
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setNewView(bpPerPx: number, offsetPx: number): void;
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horizontallyFlip(): void;
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showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
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moveTrack(movingId: string, targetId: string): void;
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closeView(): void;
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toggleTrack(trackId: string): boolean;
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setTrackLabels(setting: "
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setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
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setShowCenterLine(b: boolean): void;
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setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
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activateTrackSelector(): import("@jbrowse/core/util").Widget;
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getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
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start: number;
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end: number;
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type: string;
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regionNumber?: number
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reversed?: boolean
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regionNumber?: number;
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reversed?: boolean;
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refName: string;
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assemblyName: string;
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key: string;
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offsetPx: number;
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widthPx: number;
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variant?: string
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isLeftEndOfDisplayedRegion?: boolean
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variant?: string;
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isLeftEndOfDisplayedRegion?: boolean;
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}[];
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afterDisplayedRegionsSet(cb: Function): void;
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horizontalScroll(distance: number): number;
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center(): void;
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showAllRegions(): void;
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showAllRegionsInAssembly(assemblyName?: string
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setDraggingTrackId(idx?: string
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showAllRegionsInAssembly(assemblyName?: string): void;
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setDraggingTrackId(idx?: string): void;
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setScaleFactor(factor: number): void;
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clearView(): void;
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exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
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setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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afterAttach(): void;
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} & {
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moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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navToLocString(input: string, optAssemblyName?: string
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moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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navToSearchString({ input, assembly, }: {
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input: string;
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assembly:
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configuration: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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error: unknown;
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loaded: boolean;
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loadingP: Promise<void> | undefined;
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volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: {
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} | undefined;
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lowerCaseRefNameAliases: {
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} | undefined;
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cytobands: Feature[] | undefined;
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} & {
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getConf(arg: string): any;
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} & {
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readonly initialized: boolean;
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readonly name: string;
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readonly aliases: string[];
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readonly displayName: string | undefined;
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hasName(name: string): boolean;
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readonly allAliases: string[];
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readonly allRefNames: string[] | undefined;
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readonly lowerCaseRefNames: string[] | undefined;
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readonly allRefNamesWithLowerCase: string[] | undefined;
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readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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readonly refNameColors: string[];
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} & {
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} & {
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getCanonicalRefName(refName: string): string | undefined;
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getRefNameColor(refName: string): string | undefined; /**
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* #property
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*/
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isValidRefName(refName: string): boolean;
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} & {
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setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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setError(e: unknown): void;
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setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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}, lcAliases: {
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setCytobands(cytobands: Feature[]): void;
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} & {
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getAdapterMapEntry(adapterConf: {
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}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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getRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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getReverseRefNameMapForAdapter(adapterConf: {
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}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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}>;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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}, {
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loadingP: Promise<void> | undefined;
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volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: {
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
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tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
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hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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@@ -307,4 +308,3 @@ function stateModelFactory(pluginManager) {
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exports.default = stateModelFactory;
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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+
exports.default = SVGBackground;
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const util_1 = require("@jbrowse/core/util");
|
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@@ -10,4 +11,3 @@ function SVGBackground({ width, height, shift, }) {
|
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|
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|
|
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}
|
|
13
|
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exports.default = SVGBackground;
|
|
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
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|
};
|
|
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|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
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exports.renderToSvg =
|
|
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|
+
exports.renderToSvg = renderToSvg;
|
|
7
7
|
const react_1 = __importDefault(require("react"));
|
|
8
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|
const mobx_1 = require("mobx");
|
|
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const util_1 = require("@jbrowse/core/util");
|
|
@@ -65,4 +65,3 @@ async function renderToSvg(model, opts) {
|
|
|
65
65
|
react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }))),
|
|
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|
react_1.default.createElement("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)" }, model.matchedTracks.map(track => (react_1.default.createElement(Overlay_1.default, { parentRef: { current: null }, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }))))))), createRootFn);
|
|
67
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|
}
|
|
68
|
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exports.renderToSvg = renderToSvg;
|
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.
|
|
3
|
+
exports.getTrackNameMaxLen = getTrackNameMaxLen;
|
|
4
|
+
exports.getTrackOffsets = getTrackOffsets;
|
|
4
5
|
const util_1 = require("@jbrowse/core/util");
|
|
5
6
|
// locals
|
|
6
7
|
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
7
8
|
function getTrackNameMaxLen(views, fontSize, session) {
|
|
8
9
|
return (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0);
|
|
9
10
|
}
|
|
10
|
-
exports.getTrackNameMaxLen = getTrackNameMaxLen;
|
|
11
11
|
function getTrackOffsets(view, textOffset, extra = 0) {
|
|
12
12
|
const offsets = {};
|
|
13
13
|
let curr = textOffset;
|
|
@@ -17,4 +17,3 @@ function getTrackOffsets(view, textOffset, extra = 0) {
|
|
|
17
17
|
}
|
|
18
18
|
return offsets;
|
|
19
19
|
}
|
|
20
|
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exports.getTrackOffsets = getTrackOffsets;
|
|
@@ -1,6 +1,9 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.
|
|
3
|
+
exports.useNextFrame = void 0;
|
|
4
|
+
exports.getPxFromCoordinate = getPxFromCoordinate;
|
|
5
|
+
exports.yPos = yPos;
|
|
6
|
+
exports.intersect = intersect;
|
|
4
7
|
const react_1 = require("react");
|
|
5
8
|
const util_1 = require("@jbrowse/core/util");
|
|
6
9
|
const [, TOP, , BOTTOM] = [0, 1, 2, 3];
|
|
@@ -17,7 +20,6 @@ function getPxFromCoordinate(view, refName, coord) {
|
|
|
17
20
|
var _a;
|
|
18
21
|
return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
|
|
19
22
|
}
|
|
20
|
-
exports.getPxFromCoordinate = getPxFromCoordinate;
|
|
21
23
|
// get's the yposition of a layout record in a track
|
|
22
24
|
function yPos(trackId, level, views, tracks, c, getYPosOverride) {
|
|
23
25
|
const display = tracks[level].displays[0];
|
|
@@ -33,7 +35,6 @@ function yPos(trackId, level, views, tracks, c, getYPosOverride) {
|
|
|
33
35
|
heightFromSpecificLevel(views, trackId, level, getYPosOverride) +
|
|
34
36
|
display.scrollTop);
|
|
35
37
|
}
|
|
36
|
-
exports.yPos = yPos;
|
|
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|
// we combo a useEffect and useState combo to force rerender on snap changing.
|
|
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39
|
// the setup of this being a useEffect+useState makes it re-render once the
|
|
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40
|
// useEffect is called, which is generally the "next frame". If we removed the
|
|
@@ -53,4 +54,3 @@ function intersect(cb, a1 = [], a2 = [], ...rest) {
|
|
|
53
54
|
const a12 = a1.filter(value => ids.has(cb(value)));
|
|
54
55
|
return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
|
|
55
56
|
}
|
|
56
|
-
exports.intersect = intersect;
|
|
@@ -51,16 +51,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
51
51
|
type: import("mobx-state-tree").IType<string | undefined, string, string>;
|
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52
|
offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
53
53
|
bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
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|
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displayedRegions: import("mobx-state-tree").
|
|
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|
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refName: import("mobx-state-tree").ISimpleType<string>;
|
|
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|
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start: import("mobx-state-tree").ISimpleType<number>;
|
|
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|
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end: import("mobx-state-tree").ISimpleType<number>;
|
|
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|
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reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
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|
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} & {
|
|
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|
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assemblyName: import("mobx-state-tree").ISimpleType<string>;
|
|
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|
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}, {
|
|
62
|
-
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|
|
63
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
54
|
+
displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
|
|
64
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|
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
|
|
65
56
|
hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
66
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|
hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
@@ -83,15 +74,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
83
74
|
} & {
|
|
84
75
|
volatileWidth: number | undefined;
|
|
85
76
|
minimumBlockWidth: number;
|
|
86
|
-
draggingTrackId:
|
|
77
|
+
draggingTrackId: undefined | string;
|
|
87
78
|
volatileError: unknown;
|
|
88
79
|
afterDisplayedRegionsSetCallbacks: Function[];
|
|
89
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|
scaleFactor: number;
|
|
90
81
|
trackRefs: Record<string, HTMLDivElement>;
|
|
91
82
|
coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
|
|
92
83
|
coarseTotalBp: number;
|
|
93
|
-
leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
|
|
94
|
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rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
|
|
84
|
+
leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
|
|
85
|
+
rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
|
|
95
86
|
} & {
|
|
96
87
|
readonly trackLabelsSetting: any;
|
|
97
88
|
readonly width: number;
|
|
@@ -140,8 +131,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
140
131
|
removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
|
|
141
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|
scrollTo(offsetPx: number): number;
|
|
142
133
|
zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
|
|
143
|
-
setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
|
|
144
|
-
setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string
|
|
134
|
+
setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
|
|
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|
+
setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
|
|
145
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|
setNewView(bpPerPx: number, offsetPx: number): void;
|
|
146
137
|
horizontallyFlip(): void;
|
|
147
138
|
showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
|
|
@@ -154,30 +145,30 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
154
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|
moveTrack(movingId: string, targetId: string): void;
|
|
155
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|
closeView(): void;
|
|
156
147
|
toggleTrack(trackId: string): boolean;
|
|
157
|
-
setTrackLabels(setting: "
|
|
148
|
+
setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
|
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setShowCenterLine(b: boolean): void;
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setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
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activateTrackSelector(): import("@jbrowse/core/util").Widget;
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getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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+
getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
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start: number;
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end: number;
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type: string;
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regionNumber?: number
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reversed?: boolean
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regionNumber?: number;
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reversed?: boolean;
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refName: string;
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assemblyName: string;
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key: string;
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offsetPx: number;
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widthPx: number;
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variant?: string
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isLeftEndOfDisplayedRegion?: boolean
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variant?: string;
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isLeftEndOfDisplayedRegion?: boolean;
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}[];
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afterDisplayedRegionsSet(cb: Function): void;
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horizontalScroll(distance: number): number;
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center(): void;
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showAllRegions(): void;
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-
showAllRegionsInAssembly(assemblyName?: string
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setDraggingTrackId(idx?: string
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showAllRegionsInAssembly(assemblyName?: string): void;
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setDraggingTrackId(idx?: string): void;
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setScaleFactor(factor: number): void;
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clearView(): void;
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exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
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@@ -202,141 +193,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
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afterAttach(): void;
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} & {
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moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset
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navToLocString(input: string, optAssemblyName?: string
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moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
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navToLocString(input: string, optAssemblyName?: string): Promise<void>;
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navToSearchString({ input, assembly, }: {
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input: string;
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assembly:
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configuration: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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error: unknown;
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loaded: boolean;
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loadingP: Promise<void> | undefined;
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volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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refNameAliases: {
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[x: string]: string | undefined;
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} | undefined;
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lowerCaseRefNameAliases: {
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[x: string]: string | undefined;
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} | undefined;
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cytobands: Feature[] | undefined;
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getConf(arg: string): any;
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readonly initialized: boolean;
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readonly name: string;
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readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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readonly aliases: string[];
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readonly displayName: string | undefined;
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hasName(name: string): boolean;
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readonly allAliases: string[];
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-
readonly allRefNames: string[] | undefined;
|
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readonly lowerCaseRefNames: string[] | undefined;
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readonly allRefNamesWithLowerCase: string[] | undefined;
|
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-
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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|
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readonly refNameColors: string[];
|
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-
} & {
|
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239
|
-
readonly refNames: string[] | undefined;
|
|
240
|
-
} & {
|
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241
|
-
getCanonicalRefName(refName: string): string | undefined;
|
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|
-
getRefNameColor(refName: string): string | undefined; /**
|
|
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|
-
* #property
|
|
244
|
-
*/
|
|
245
|
-
isValidRefName(refName: string): boolean;
|
|
246
|
-
} & {
|
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247
|
-
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
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|
-
setError(e: unknown): void;
|
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249
|
-
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
250
|
-
setRefNameAliases(aliases: {
|
|
251
|
-
[x: string]: string | undefined;
|
|
252
|
-
}, lcAliases: {
|
|
253
|
-
[x: string]: string | undefined;
|
|
254
|
-
}): void;
|
|
255
|
-
setCytobands(cytobands: Feature[]): void;
|
|
256
|
-
setLoadingP(p?: Promise<void> | undefined): void;
|
|
257
|
-
load(): Promise<void>;
|
|
258
|
-
loadPre(): Promise<void>;
|
|
259
|
-
} & {
|
|
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|
-
getAdapterMapEntry(adapterConf: {
|
|
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|
-
[x: string]: unknown;
|
|
262
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
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|
-
getRefNameMapForAdapter(adapterConf: {
|
|
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|
-
[x: string]: unknown;
|
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265
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
266
|
-
[x: string]: string | undefined;
|
|
267
|
-
}>;
|
|
268
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
269
|
-
[x: string]: unknown;
|
|
270
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
271
|
-
[x: string]: string | undefined;
|
|
272
|
-
}>;
|
|
273
|
-
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
274
|
-
configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
275
|
-
}, {
|
|
276
|
-
error: unknown;
|
|
277
|
-
loaded: boolean;
|
|
278
|
-
loadingP: Promise<void> | undefined;
|
|
279
|
-
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
280
|
-
refNameAliases: {
|
|
281
|
-
[x: string]: string | undefined;
|
|
282
|
-
} | undefined;
|
|
283
|
-
lowerCaseRefNameAliases: {
|
|
284
|
-
[x: string]: string | undefined;
|
|
285
|
-
} | undefined;
|
|
286
|
-
cytobands: Feature[] | undefined;
|
|
287
|
-
} & {
|
|
288
|
-
getConf(arg: string): any;
|
|
289
|
-
} & {
|
|
290
|
-
readonly initialized: boolean;
|
|
291
|
-
readonly name: string;
|
|
292
|
-
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
293
|
-
readonly aliases: string[];
|
|
294
|
-
readonly displayName: string | undefined;
|
|
295
|
-
hasName(name: string): boolean;
|
|
296
|
-
readonly allAliases: string[];
|
|
297
|
-
readonly allRefNames: string[] | undefined;
|
|
298
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
299
|
-
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
300
|
-
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
301
|
-
readonly refNameColors: string[];
|
|
302
|
-
} & {
|
|
303
|
-
readonly refNames: string[] | undefined;
|
|
304
|
-
} & {
|
|
305
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
306
|
-
getRefNameColor(refName: string): string | undefined; /**
|
|
307
|
-
* #property
|
|
308
|
-
*/
|
|
309
|
-
isValidRefName(refName: string): boolean;
|
|
310
|
-
} & {
|
|
311
|
-
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
312
|
-
setError(e: unknown): void;
|
|
313
|
-
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
314
|
-
setRefNameAliases(aliases: {
|
|
315
|
-
[x: string]: string | undefined;
|
|
316
|
-
}, lcAliases: {
|
|
317
|
-
[x: string]: string | undefined;
|
|
318
|
-
}): void;
|
|
319
|
-
setCytobands(cytobands: Feature[]): void;
|
|
320
|
-
setLoadingP(p?: Promise<void> | undefined): void;
|
|
321
|
-
load(): Promise<void>;
|
|
322
|
-
loadPre(): Promise<void>;
|
|
323
|
-
} & {
|
|
324
|
-
getAdapterMapEntry(adapterConf: {
|
|
325
|
-
[x: string]: unknown;
|
|
326
|
-
}, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
327
|
-
getRefNameMapForAdapter(adapterConf: {
|
|
328
|
-
[x: string]: unknown;
|
|
329
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
330
|
-
[x: string]: string | undefined;
|
|
331
|
-
}>;
|
|
332
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
333
|
-
[x: string]: unknown;
|
|
334
|
-
}, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
335
|
-
[x: string]: string | undefined;
|
|
336
|
-
}>;
|
|
337
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
200
|
+
assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
|
|
338
201
|
}): Promise<void>;
|
|
339
|
-
navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string
|
|
202
|
+
navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
|
|
340
203
|
navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
|
|
341
204
|
navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
|
|
342
205
|
} & {
|
|
@@ -344,12 +207,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
344
207
|
bpToPx({ refName, coord, regionNumber, }: {
|
|
345
208
|
refName: string;
|
|
346
209
|
coord: number;
|
|
347
|
-
regionNumber?: number
|
|
210
|
+
regionNumber?: number;
|
|
348
211
|
}): {
|
|
349
212
|
index: number;
|
|
350
213
|
offsetPx: number;
|
|
351
214
|
} | undefined;
|
|
352
|
-
centerAt(coord: number, refName: string, regionNumber?: number
|
|
215
|
+
centerAt(coord: number, refName: string, regionNumber?: number): void;
|
|
353
216
|
pxToBp(px: number): {
|
|
354
217
|
coord: number;
|
|
355
218
|
index: number;
|
|
@@ -359,7 +222,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
359
222
|
offset: number;
|
|
360
223
|
start: number;
|
|
361
224
|
end: number;
|
|
362
|
-
reversed
|
|
225
|
+
reversed?: boolean;
|
|
363
226
|
};
|
|
364
227
|
readonly centerLineInfo: {
|
|
365
228
|
coord: number;
|
|
@@ -370,7 +233,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
370
233
|
offset: number;
|
|
371
234
|
start: number;
|
|
372
235
|
end: number;
|
|
373
|
-
reversed
|
|
236
|
+
reversed?: boolean;
|
|
374
237
|
} | undefined;
|
|
375
238
|
} & {
|
|
376
239
|
afterCreate(): void;
|
|
@@ -383,16 +246,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
383
246
|
type: import("mobx-state-tree").IType<string | undefined, string, string>;
|
|
384
247
|
offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
385
248
|
bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
386
|
-
displayedRegions: import("mobx-state-tree").
|
|
387
|
-
refName: import("mobx-state-tree").ISimpleType<string>;
|
|
388
|
-
start: import("mobx-state-tree").ISimpleType<number>;
|
|
389
|
-
end: import("mobx-state-tree").ISimpleType<number>;
|
|
390
|
-
reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
391
|
-
} & {
|
|
392
|
-
assemblyName: import("mobx-state-tree").ISimpleType<string>;
|
|
393
|
-
}, {
|
|
394
|
-
setRefName(newRefName: string): void;
|
|
395
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
249
|
+
displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
|
|
396
250
|
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
|
|
397
251
|
hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
398
252
|
hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-breakpoint-split-view",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.12.1",
|
|
4
4
|
"description": "JBrowse 2 breakpoint detail split view",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -58,5 +58,5 @@
|
|
|
58
58
|
"publishConfig": {
|
|
59
59
|
"access": "public"
|
|
60
60
|
},
|
|
61
|
-
"gitHead": "
|
|
61
|
+
"gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
|
|
62
62
|
}
|