@jbrowse/plugin-breakpoint-split-view 2.7.2 → 2.9.0
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/BreakpointSplitView/BreakpointSplitView.d.ts +6 -5
- package/dist/BreakpointSplitView/BreakpointSplitView.js +5 -5
- package/dist/BreakpointSplitView/components/Breakends.js +5 -5
- package/dist/BreakpointSplitView/components/BreakpointSplitView.js +20 -61
- package/dist/BreakpointSplitView/components/BreakpointSplitViewOverlay.d.ts +6 -0
- package/dist/BreakpointSplitView/components/BreakpointSplitViewOverlay.js +61 -0
- package/dist/BreakpointSplitView/components/Translocations.js +4 -4
- package/dist/BreakpointSplitView/model.d.ts +124 -2
- package/esm/BreakpointSplitView/BreakpointSplitView.d.ts +6 -5
- package/esm/BreakpointSplitView/BreakpointSplitView.js +5 -5
- package/esm/BreakpointSplitView/components/Breakends.js +5 -5
- package/esm/BreakpointSplitView/components/BreakpointSplitView.js +20 -38
- package/esm/BreakpointSplitView/components/BreakpointSplitViewOverlay.d.ts +6 -0
- package/esm/BreakpointSplitView/components/BreakpointSplitViewOverlay.js +33 -0
- package/esm/BreakpointSplitView/components/Translocations.js +4 -4
- package/esm/BreakpointSplitView/model.d.ts +124 -2
- package/package.json +2 -2
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@@ -1,9 +1,10 @@
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-
import { Feature } from '@jbrowse/core/util';
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import { Feature, Region } from '@jbrowse/core/util';
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import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
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import {
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type LGV = LinearGenomeViewModel;
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import { IStateTreeNode } from 'mobx-state-tree';
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export default class BreakpointSplitViewType extends ViewType {
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snapshotFromBreakendFeature(feature: Feature, view:
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snapshotFromBreakendFeature(feature: Feature, view: {
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displayedRegions: Region[];
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} & IStateTreeNode): {
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type: string;
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views: {
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type: string;
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@@ -18,6 +19,6 @@ export default class BreakpointSplitViewType extends ViewType {
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offsetPx: number;
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}[];
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displayName: string;
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featureData: unknown;
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};
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}
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export {};
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@@ -24,8 +24,7 @@ class BreakpointSplitViewType extends ViewType_1.default {
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if (!assembly.regions) {
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throw new Error(`assembly ${assemblyName} regions not loaded`);
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}
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const
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const featureRefName = getCanonicalRefName(feature.get('refName'));
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const featureRefName = assembly.getCanonicalRefName(feature.get('refName'));
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const topRegion = assembly.regions.find(f => f.refName === featureRefName);
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let mateRefName;
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let startMod = 0;
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@@ -34,12 +33,12 @@ class BreakpointSplitViewType extends ViewType_1.default {
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if (alt === '<TRA>') {
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const INFO = feature.get('INFO');
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endPos = INFO.END[0] - 1;
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mateRefName = getCanonicalRefName(INFO.CHR2[0]);
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mateRefName = assembly.getCanonicalRefName(INFO.CHR2[0]);
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}
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else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
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const matePosition = bnd.MatePosition.split(':');
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endPos = +matePosition[1] - 1;
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mateRefName = getCanonicalRefName(matePosition[0]);
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mateRefName = assembly.getCanonicalRefName(matePosition[0]);
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if (bnd.Join === 'left') {
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startMod = -1;
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}
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@@ -50,7 +49,7 @@ class BreakpointSplitViewType extends ViewType_1.default {
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else if (feature.get('mate')) {
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// a generic 'mate' feature
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const mate = feature.get('mate');
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mateRefName = getCanonicalRefName(mate.refName);
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mateRefName = assembly.getCanonicalRefName(mate.refName);
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endPos = mate.start;
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}
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if (!mateRefName) {
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@@ -85,6 +84,7 @@ class BreakpointSplitViewType extends ViewType_1.default {
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},
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],
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displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
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featureData: undefined,
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};
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}
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}
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@@ -82,26 +82,26 @@ const Breakends = (0, mobx_react_1.observer)(function ({ model, trackId, parentR
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}
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else {
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const path = [
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'M',
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'M', // move to
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x1 -
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20 *
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(relevantAlt.Join === 'left' ? -1 : 1) *
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(reversed1 ? -1 : 1),
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y1,
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'L',
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'L', // line to
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x1,
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y1,
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'L',
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'L', // line to
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x2,
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y2,
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'L',
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'L', // line to
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x2 -
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20 *
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(relevantAlt.MateDirection === 'left' ? 1 : -1) *
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(reversed2 ? -1 : 1),
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y2,
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].join(' ');
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ret.push(react_1.default.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
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ret.push(react_1.default.createElement("path", { d: path, "data-testid": "r2", key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
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var _a, _b, _c;
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const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
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featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
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"use strict";
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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var desc = Object.getOwnPropertyDescriptor(m, k);
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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desc = { enumerable: true, get: function() { return m[k]; } };
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}
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Object.defineProperty(o, k2, desc);
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}) : (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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o[k2] = m[k];
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}));
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var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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Object.defineProperty(o, "default", { enumerable: true, value: v });
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}) : function(o, v) {
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o["default"] = v;
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});
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var __importStar = (this && this.__importStar) || function (mod) {
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if (mod && mod.__esModule) return mod;
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var result = {};
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if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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__setModuleDefault(result, mod);
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return result;
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};
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var __importDefault = (this && this.__importDefault) || function (mod) {
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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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const react_1 =
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const react_1 = __importDefault(require("react"));
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const mobx_react_1 = require("mobx-react");
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const mobx_state_tree_1 = require("mobx-state-tree");
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const mui_1 = require("tss-react/mui");
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const
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const BreakpointSplitViewOverlay_1 = __importDefault(require("./BreakpointSplitViewOverlay"));
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const useStyles = (0, mui_1.makeStyles)()(theme => ({
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viewDivider: {
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background: theme.palette.secondary.main,
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container: {
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display: 'grid',
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},
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overlay: {
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display: 'flex',
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width: '100%',
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gridArea: '1/1',
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'& path': {
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cursor: 'crosshair',
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fill: 'none',
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},
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},
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content: {
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gridArea: '1/1',
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},
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}));
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const
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const BreakpointSplitViewLevels = (0, mobx_react_1.observer)(function ({ model, }) {
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const { classes } = useStyles();
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const { views } = model;
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const { pluginManager } = (0, mobx_state_tree_1.getEnv)(model);
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return (react_1.default.createElement("div", { className: classes.content },
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react_1.default.createElement("div", { style: { position: 'relative' } }, views.map((view, idx) => {
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const { ReactComponent } = pluginManager.getViewType(view.type);
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const viewComponent = react_1.default.createElement(ReactComponent, { key: view.id, model: view });
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if (idx === views.length - 1) {
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return viewComponent;
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}
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return [
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viewComponent,
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react_1.default.createElement("div", { key: `${view.id}-divider`, className: classes.viewDivider }),
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];
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}))));
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});
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const BreakpointSplitView = (0, mobx_react_1.observer)(function ({ model, }) {
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const { classes } = useStyles();
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return (react_1.default.createElement("div", null,
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react_1.default.createElement("div", { className: classes.container },
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const { ReactComponent } = pluginManager.getViewType(view.type);
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const viewComponent = (react_1.default.createElement(ReactComponent, { key: view.id, model: view }));
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}
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];
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}))),
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react_1.default.createElement("div", { className: classes.overlay },
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react_1.default.createElement("svg", { ref: ref, style: {
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width: '100%',
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zIndex: 10,
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pointerEvents: model.interactToggled ? undefined : 'none',
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} }, model.matchedTracks.map(track => (
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// note: we must pass ref down, because the child component
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// and we cannot rely on using getBoundingClientRect in this
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// component to make sure this works because if it gets
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// shifted around by another element, this will not re-render
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// necessarily
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react_1.default.createElement(Overlay_1.default, { parentRef: ref, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId }))))))));
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react_1.default.createElement(BreakpointSplitViewLevels, { model: model }),
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react_1.default.createElement(BreakpointSplitViewOverlay_1.default, { model: model }))));
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});
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exports.default = BreakpointSplitView;
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"use strict";
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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}
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Object.defineProperty(o, k2, desc);
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}) : (function(o, m, k, k2) {
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o[k2] = m[k];
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}));
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var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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Object.defineProperty(o, "default", { enumerable: true, value: v });
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}) : function(o, v) {
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o["default"] = v;
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});
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var result = {};
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if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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__setModuleDefault(result, mod);
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return result;
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};
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const mui_1 = require("tss-react/mui");
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const Overlay_1 = __importDefault(require("./Overlay"));
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const mobx_react_1 = require("mobx-react");
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const useStyles = (0, mui_1.makeStyles)()({
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overlay: {
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display: 'flex',
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width: '100%',
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gridArea: '1/1',
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'& path': {
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cursor: 'crosshair',
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fill: 'none',
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},
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},
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});
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const BreakpointSplitViewOverlay = (0, mobx_react_1.observer)(function ({ model, }) {
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const { classes } = useStyles();
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const { matchedTracks, interactToggled } = model;
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const ref = (0, react_1.useRef)(null);
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return (react_1.default.createElement("div", { className: classes.overlay },
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react_1.default.createElement("svg", { ref: ref, style: {
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width: '100%',
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zIndex: 10,
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pointerEvents: interactToggled ? undefined : 'none',
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} }, matchedTracks.map(track => (
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// note: we must pass ref down, because the child component needs to
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// getBoundingClientRect on the this components SVG, and we cannot
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// rely on using getBoundingClientRect in this component to make
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// sure this works because if it gets shifted around by another
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// element, this will not re-render necessarily
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react_1.default.createElement(Overlay_1.default, { parentRef: ref, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId }))))));
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});
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exports.default = BreakpointSplitViewOverlay;
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const y2 = (0, util_3.yPos)(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
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yOffset;
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|
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*/
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}>;
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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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} | undefined;
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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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|
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|
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readonly allAliases: string[];
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|
+
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|
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|
+
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|
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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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|
+
readonly refNames: string[] | undefined;
|
|
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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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|
+
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|
|
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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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|
+
setRefNameAliases(aliases: {
|
|
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|
+
[x: string]: string | undefined;
|
|
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|
+
}, lcAliases: {
|
|
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|
+
[x: string]: string | undefined;
|
|
297
|
+
}): void;
|
|
298
|
+
setCytobands(cytobands: Feature[]): void; /**
|
|
299
|
+
* #property
|
|
300
|
+
*/
|
|
301
|
+
setLoadingP(p?: Promise<void> | undefined): void;
|
|
302
|
+
load(): Promise<void>;
|
|
303
|
+
loadPre(): Promise<void>;
|
|
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|
+
} & {
|
|
305
|
+
getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
306
|
+
getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
307
|
+
[x: string]: string | undefined;
|
|
308
|
+
}>;
|
|
309
|
+
getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
310
|
+
[x: string]: string | undefined;
|
|
311
|
+
}>;
|
|
312
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
313
|
+
}): Promise<void>;
|
|
192
314
|
navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
|
|
193
315
|
navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
|
|
194
316
|
navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
|
|
@@ -1,9 +1,10 @@
|
|
|
1
|
-
import { Feature } from '@jbrowse/core/util';
|
|
1
|
+
import { Feature, Region } from '@jbrowse/core/util';
|
|
2
2
|
import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
|
|
3
|
-
import {
|
|
4
|
-
type LGV = LinearGenomeViewModel;
|
|
3
|
+
import { IStateTreeNode } from 'mobx-state-tree';
|
|
5
4
|
export default class BreakpointSplitViewType extends ViewType {
|
|
6
|
-
snapshotFromBreakendFeature(feature: Feature, view:
|
|
5
|
+
snapshotFromBreakendFeature(feature: Feature, view: {
|
|
6
|
+
displayedRegions: Region[];
|
|
7
|
+
} & IStateTreeNode): {
|
|
7
8
|
type: string;
|
|
8
9
|
views: {
|
|
9
10
|
type: string;
|
|
@@ -18,6 +19,6 @@ export default class BreakpointSplitViewType extends ViewType {
|
|
|
18
19
|
offsetPx: number;
|
|
19
20
|
}[];
|
|
20
21
|
displayName: string;
|
|
22
|
+
featureData: unknown;
|
|
21
23
|
};
|
|
22
24
|
}
|
|
23
|
-
export {};
|
|
@@ -19,8 +19,7 @@ export default class BreakpointSplitViewType extends ViewType {
|
|
|
19
19
|
if (!assembly.regions) {
|
|
20
20
|
throw new Error(`assembly ${assemblyName} regions not loaded`);
|
|
21
21
|
}
|
|
22
|
-
const
|
|
23
|
-
const featureRefName = getCanonicalRefName(feature.get('refName'));
|
|
22
|
+
const featureRefName = assembly.getCanonicalRefName(feature.get('refName'));
|
|
24
23
|
const topRegion = assembly.regions.find(f => f.refName === featureRefName);
|
|
25
24
|
let mateRefName;
|
|
26
25
|
let startMod = 0;
|
|
@@ -29,12 +28,12 @@ export default class BreakpointSplitViewType extends ViewType {
|
|
|
29
28
|
if (alt === '<TRA>') {
|
|
30
29
|
const INFO = feature.get('INFO');
|
|
31
30
|
endPos = INFO.END[0] - 1;
|
|
32
|
-
mateRefName = getCanonicalRefName(INFO.CHR2[0]);
|
|
31
|
+
mateRefName = assembly.getCanonicalRefName(INFO.CHR2[0]);
|
|
33
32
|
}
|
|
34
33
|
else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
|
|
35
34
|
const matePosition = bnd.MatePosition.split(':');
|
|
36
35
|
endPos = +matePosition[1] - 1;
|
|
37
|
-
mateRefName = getCanonicalRefName(matePosition[0]);
|
|
36
|
+
mateRefName = assembly.getCanonicalRefName(matePosition[0]);
|
|
38
37
|
if (bnd.Join === 'left') {
|
|
39
38
|
startMod = -1;
|
|
40
39
|
}
|
|
@@ -45,7 +44,7 @@ export default class BreakpointSplitViewType extends ViewType {
|
|
|
45
44
|
else if (feature.get('mate')) {
|
|
46
45
|
// a generic 'mate' feature
|
|
47
46
|
const mate = feature.get('mate');
|
|
48
|
-
mateRefName = getCanonicalRefName(mate.refName);
|
|
47
|
+
mateRefName = assembly.getCanonicalRefName(mate.refName);
|
|
49
48
|
endPos = mate.start;
|
|
50
49
|
}
|
|
51
50
|
if (!mateRefName) {
|
|
@@ -80,6 +79,7 @@ export default class BreakpointSplitViewType extends ViewType {
|
|
|
80
79
|
},
|
|
81
80
|
],
|
|
82
81
|
displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
|
|
82
|
+
featureData: undefined,
|
|
83
83
|
};
|
|
84
84
|
}
|
|
85
85
|
}
|
|
@@ -57,26 +57,26 @@ const Breakends = observer(function ({ model, trackId, parentRef: ref, getTrackY
|
|
|
57
57
|
}
|
|
58
58
|
else {
|
|
59
59
|
const path = [
|
|
60
|
-
'M',
|
|
60
|
+
'M', // move to
|
|
61
61
|
x1 -
|
|
62
62
|
20 *
|
|
63
63
|
(relevantAlt.Join === 'left' ? -1 : 1) *
|
|
64
64
|
(reversed1 ? -1 : 1),
|
|
65
65
|
y1,
|
|
66
|
-
'L',
|
|
66
|
+
'L', // line to
|
|
67
67
|
x1,
|
|
68
68
|
y1,
|
|
69
|
-
'L',
|
|
69
|
+
'L', // line to
|
|
70
70
|
x2,
|
|
71
71
|
y2,
|
|
72
|
-
'L',
|
|
72
|
+
'L', // line to
|
|
73
73
|
x2 -
|
|
74
74
|
20 *
|
|
75
75
|
(relevantAlt.MateDirection === 'left' ? 1 : -1) *
|
|
76
76
|
(reversed2 ? -1 : 1),
|
|
77
77
|
y2,
|
|
78
78
|
].join(' ');
|
|
79
|
-
ret.push(React.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
|
|
79
|
+
ret.push(React.createElement("path", { d: path, "data-testid": "r2", key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
|
|
80
80
|
var _a, _b, _c;
|
|
81
81
|
const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
|
|
82
82
|
featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
|
|
@@ -1,8 +1,8 @@
|
|
|
1
|
-
import React
|
|
1
|
+
import React from 'react';
|
|
2
2
|
import { observer } from 'mobx-react';
|
|
3
3
|
import { getEnv } from 'mobx-state-tree';
|
|
4
4
|
import { makeStyles } from 'tss-react/mui';
|
|
5
|
-
import
|
|
5
|
+
import BreakpointSplitViewOverlay from './BreakpointSplitViewOverlay';
|
|
6
6
|
const useStyles = makeStyles()(theme => ({
|
|
7
7
|
viewDivider: {
|
|
8
8
|
background: theme.palette.secondary.main,
|
|
@@ -11,50 +11,32 @@ const useStyles = makeStyles()(theme => ({
|
|
|
11
11
|
container: {
|
|
12
12
|
display: 'grid',
|
|
13
13
|
},
|
|
14
|
-
overlay: {
|
|
15
|
-
display: 'flex',
|
|
16
|
-
width: '100%',
|
|
17
|
-
gridArea: '1/1',
|
|
18
|
-
'& path': {
|
|
19
|
-
cursor: 'crosshair',
|
|
20
|
-
fill: 'none',
|
|
21
|
-
},
|
|
22
|
-
},
|
|
23
14
|
content: {
|
|
24
15
|
gridArea: '1/1',
|
|
25
16
|
},
|
|
26
17
|
}));
|
|
27
|
-
const
|
|
18
|
+
const BreakpointSplitViewLevels = observer(function ({ model, }) {
|
|
28
19
|
const { classes } = useStyles();
|
|
29
20
|
const { views } = model;
|
|
30
21
|
const { pluginManager } = getEnv(model);
|
|
31
|
-
|
|
22
|
+
return (React.createElement("div", { className: classes.content },
|
|
23
|
+
React.createElement("div", { style: { position: 'relative' } }, views.map((view, idx) => {
|
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const { ReactComponent } = pluginManager.getViewType(view.type);
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const viewComponent = React.createElement(ReactComponent, { key: view.id, model: view });
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}
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return [
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viewComponent,
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React.createElement("div", { key: `${view.id}-divider`, className: classes.viewDivider }),
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];
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}))));
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});
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const BreakpointSplitView = observer(function ({ model, }) {
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const { classes } = useStyles();
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|
return (React.createElement("div", null,
|
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|
React.createElement("div", { className: classes.container },
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React.createElement(
|
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|
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const { ReactComponent } = pluginManager.getViewType(view.type);
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const viewComponent = (React.createElement(ReactComponent, { key: view.id, model: view }));
|
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|
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if (idx === views.length - 1) {
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|
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|
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return viewComponent;
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}
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return [
|
|
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|
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viewComponent,
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React.createElement("div", { key: `${view.id}-divider`, className: classes.viewDivider }),
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];
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}))),
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|
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|
-
React.createElement("div", { className: classes.overlay },
|
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|
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React.createElement("svg", { ref: ref, style: {
|
|
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width: '100%',
|
|
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|
-
zIndex: 10,
|
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|
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pointerEvents: model.interactToggled ? undefined : 'none',
|
|
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|
-
} }, model.matchedTracks.map(track => (
|
|
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|
-
// note: we must pass ref down, because the child component
|
|
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|
-
// needs to getBoundingClientRect on the this components SVG,
|
|
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// and we cannot rely on using getBoundingClientRect in this
|
|
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|
-
// component to make sure this works because if it gets
|
|
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|
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// shifted around by another element, this will not re-render
|
|
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|
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// necessarily
|
|
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|
-
React.createElement(Overlay, { parentRef: ref, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId }))))))));
|
|
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|
+
React.createElement(BreakpointSplitViewLevels, { model: model }),
|
|
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|
+
React.createElement(BreakpointSplitViewOverlay, { model: model }))));
|
|
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41
|
});
|
|
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42
|
export default BreakpointSplitView;
|
|
@@ -0,0 +1,33 @@
|
|
|
1
|
+
import React, { useRef } from 'react';
|
|
2
|
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import { makeStyles } from 'tss-react/mui';
|
|
3
|
+
import Overlay from './Overlay';
|
|
4
|
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import { observer } from 'mobx-react';
|
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|
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const useStyles = makeStyles()({
|
|
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|
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overlay: {
|
|
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|
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display: 'flex',
|
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|
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width: '100%',
|
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|
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gridArea: '1/1',
|
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|
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'& path': {
|
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|
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cursor: 'crosshair',
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|
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fill: 'none',
|
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|
+
},
|
|
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|
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},
|
|
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|
+
});
|
|
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|
+
const BreakpointSplitViewOverlay = observer(function ({ model, }) {
|
|
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|
+
const { classes } = useStyles();
|
|
18
|
+
const { matchedTracks, interactToggled } = model;
|
|
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|
+
const ref = useRef(null);
|
|
20
|
+
return (React.createElement("div", { className: classes.overlay },
|
|
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|
+
React.createElement("svg", { ref: ref, style: {
|
|
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|
+
width: '100%',
|
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|
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zIndex: 10,
|
|
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|
+
pointerEvents: interactToggled ? undefined : 'none',
|
|
25
|
+
} }, matchedTracks.map(track => (
|
|
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|
+
// note: we must pass ref down, because the child component needs to
|
|
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|
+
// getBoundingClientRect on the this components SVG, and we cannot
|
|
28
|
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// rely on using getBoundingClientRect in this component to make
|
|
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|
+
// sure this works because if it gets shifted around by another
|
|
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|
+
// element, this will not re-render necessarily
|
|
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|
+
React.createElement(Overlay, { parentRef: ref, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId }))))));
|
|
32
|
+
});
|
|
33
|
+
export default BreakpointSplitViewOverlay;
|
|
@@ -58,16 +58,16 @@ const Translocations = observer(function ({ model, trackId, parentRef: ref, getT
|
|
|
58
58
|
const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
|
|
59
59
|
yOffset;
|
|
60
60
|
const path = [
|
|
61
|
-
'M',
|
|
61
|
+
'M', // move to
|
|
62
62
|
x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
|
|
63
63
|
y1,
|
|
64
|
-
'L',
|
|
64
|
+
'L', // line to
|
|
65
65
|
x1,
|
|
66
66
|
y1,
|
|
67
|
-
'L',
|
|
67
|
+
'L', // line to
|
|
68
68
|
x2,
|
|
69
69
|
y2,
|
|
70
|
-
'L',
|
|
70
|
+
'L', // line to
|
|
71
71
|
x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
|
|
72
72
|
y2,
|
|
73
73
|
].join(' ');
|
|
@@ -84,7 +84,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
84
84
|
trackRefs: Record<string, HTMLDivElement>;
|
|
85
85
|
coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
|
|
86
86
|
coarseTotalBp: number;
|
|
87
|
-
leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
|
|
87
|
+
leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined; /**
|
|
88
|
+
* #action
|
|
89
|
+
*/
|
|
88
90
|
rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
|
|
89
91
|
} & {
|
|
90
92
|
readonly trackLabelsSetting: any;
|
|
@@ -139,7 +141,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
139
141
|
} & {
|
|
140
142
|
moveTrack(movingId: string, targetId: string): void;
|
|
141
143
|
closeView(): void;
|
|
142
|
-
toggleTrack(trackId: string):
|
|
144
|
+
toggleTrack(trackId: string): boolean;
|
|
143
145
|
setTrackLabels(setting: "hidden" | "offset" | "overlapping"): void;
|
|
144
146
|
toggleCenterLine(): void;
|
|
145
147
|
setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
@@ -189,6 +191,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
189
191
|
} & {
|
|
190
192
|
moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
|
|
191
193
|
navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
|
|
194
|
+
navToSearchString({ input, assembly, }: {
|
|
195
|
+
input: string;
|
|
196
|
+
assembly: {
|
|
197
|
+
configuration: any;
|
|
198
|
+
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
199
|
+
error: unknown;
|
|
200
|
+
loaded: boolean;
|
|
201
|
+
loadingP: Promise<void> | undefined;
|
|
202
|
+
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
203
|
+
refNameAliases: {
|
|
204
|
+
[x: string]: string | undefined;
|
|
205
|
+
} | undefined;
|
|
206
|
+
lowerCaseRefNameAliases: {
|
|
207
|
+
[x: string]: string | undefined;
|
|
208
|
+
} | undefined;
|
|
209
|
+
cytobands: Feature[] | undefined;
|
|
210
|
+
} & {
|
|
211
|
+
getConf(arg: string): any;
|
|
212
|
+
} & {
|
|
213
|
+
readonly initialized: boolean;
|
|
214
|
+
readonly name: string;
|
|
215
|
+
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
216
|
+
readonly aliases: string[];
|
|
217
|
+
readonly displayName: string | undefined;
|
|
218
|
+
hasName(name: string): boolean;
|
|
219
|
+
readonly allAliases: string[];
|
|
220
|
+
readonly allRefNames: string[] | undefined;
|
|
221
|
+
readonly lowerCaseRefNames: string[] | undefined;
|
|
222
|
+
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
223
|
+
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
224
|
+
readonly refNameColors: string[];
|
|
225
|
+
} & {
|
|
226
|
+
readonly refNames: string[] | undefined;
|
|
227
|
+
} & {
|
|
228
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
229
|
+
getRefNameColor(refName: string): string | undefined;
|
|
230
|
+
isValidRefName(refName: string): boolean;
|
|
231
|
+
} & {
|
|
232
|
+
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
233
|
+
setError(e: unknown): void;
|
|
234
|
+
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
235
|
+
setRefNameAliases(aliases: {
|
|
236
|
+
[x: string]: string | undefined;
|
|
237
|
+
}, lcAliases: {
|
|
238
|
+
[x: string]: string | undefined;
|
|
239
|
+
}): void;
|
|
240
|
+
setCytobands(cytobands: Feature[]): void; /**
|
|
241
|
+
* #property
|
|
242
|
+
*/
|
|
243
|
+
setLoadingP(p?: Promise<void> | undefined): void;
|
|
244
|
+
load(): Promise<void>;
|
|
245
|
+
loadPre(): Promise<void>;
|
|
246
|
+
} & {
|
|
247
|
+
getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
248
|
+
getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
249
|
+
[x: string]: string | undefined;
|
|
250
|
+
}>;
|
|
251
|
+
getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
252
|
+
[x: string]: string | undefined;
|
|
253
|
+
}>;
|
|
254
|
+
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
255
|
+
configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
256
|
+
}, {
|
|
257
|
+
error: unknown;
|
|
258
|
+
loaded: boolean;
|
|
259
|
+
loadingP: Promise<void> | undefined;
|
|
260
|
+
volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
261
|
+
refNameAliases: {
|
|
262
|
+
[x: string]: string | undefined;
|
|
263
|
+
} | undefined;
|
|
264
|
+
lowerCaseRefNameAliases: {
|
|
265
|
+
[x: string]: string | undefined;
|
|
266
|
+
} | undefined;
|
|
267
|
+
cytobands: Feature[] | undefined;
|
|
268
|
+
} & {
|
|
269
|
+
getConf(arg: string): any;
|
|
270
|
+
} & {
|
|
271
|
+
readonly initialized: boolean;
|
|
272
|
+
readonly name: string;
|
|
273
|
+
readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
|
|
274
|
+
readonly aliases: string[];
|
|
275
|
+
readonly displayName: string | undefined;
|
|
276
|
+
hasName(name: string): boolean;
|
|
277
|
+
readonly allAliases: string[];
|
|
278
|
+
readonly allRefNames: string[] | undefined;
|
|
279
|
+
readonly lowerCaseRefNames: string[] | undefined;
|
|
280
|
+
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
281
|
+
readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
|
|
282
|
+
readonly refNameColors: string[];
|
|
283
|
+
} & {
|
|
284
|
+
readonly refNames: string[] | undefined;
|
|
285
|
+
} & {
|
|
286
|
+
getCanonicalRefName(refName: string): string | undefined;
|
|
287
|
+
getRefNameColor(refName: string): string | undefined;
|
|
288
|
+
isValidRefName(refName: string): boolean;
|
|
289
|
+
} & {
|
|
290
|
+
setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
|
|
291
|
+
setError(e: unknown): void;
|
|
292
|
+
setRegions(regions: import("@jbrowse/core/util").Region[]): void;
|
|
293
|
+
setRefNameAliases(aliases: {
|
|
294
|
+
[x: string]: string | undefined;
|
|
295
|
+
}, lcAliases: {
|
|
296
|
+
[x: string]: string | undefined;
|
|
297
|
+
}): void;
|
|
298
|
+
setCytobands(cytobands: Feature[]): void; /**
|
|
299
|
+
* #property
|
|
300
|
+
*/
|
|
301
|
+
setLoadingP(p?: Promise<void> | undefined): void;
|
|
302
|
+
load(): Promise<void>;
|
|
303
|
+
loadPre(): Promise<void>;
|
|
304
|
+
} & {
|
|
305
|
+
getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
|
|
306
|
+
getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
307
|
+
[x: string]: string | undefined;
|
|
308
|
+
}>;
|
|
309
|
+
getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
310
|
+
[x: string]: string | undefined;
|
|
311
|
+
}>;
|
|
312
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
313
|
+
}): Promise<void>;
|
|
192
314
|
navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
|
|
193
315
|
navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
|
|
194
316
|
navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-breakpoint-split-view",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.9.0",
|
|
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": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
|
|
62
62
|
}
|