@jbrowse/plugin-linear-comparative-view 2.7.2 → 2.8.0
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/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts +7 -0
- package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js +68 -0
- package/dist/LGVSyntenyDisplay/components/util.d.ts +8 -0
- package/dist/LGVSyntenyDisplay/components/util.js +111 -0
- package/dist/LGVSyntenyDisplay/model.d.ts +15 -14
- package/dist/LGVSyntenyDisplay/model.js +35 -104
- package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts +7 -0
- package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js +42 -0
- package/esm/LGVSyntenyDisplay/components/util.d.ts +8 -0
- package/esm/LGVSyntenyDisplay/components/util.js +107 -0
- package/esm/LGVSyntenyDisplay/model.d.ts +15 -14
- package/esm/LGVSyntenyDisplay/model.js +14 -106
- package/package.json +2 -2
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"use strict";
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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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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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Object.defineProperty(exports, "__esModule", { value: true });
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const react_1 = __importStar(require("react"));
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const ui_1 = require("@jbrowse/core/ui");
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const util_1 = require("@jbrowse/core/util");
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const material_1 = require("@mui/material");
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const util_2 = require("./util");
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const mui_1 = require("tss-react/mui");
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const useStyles = (0, mui_1.makeStyles)()({
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padding: {
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margin: 10,
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border: '1px solid #ccc',
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},
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});
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function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
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const { classes } = useStyles();
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const inverted = feature.get('strand') === -1;
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const [horizontallyFlip, setHorizontallyFlip] = (0, react_1.useState)(inverted);
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const [windowSize, setWindowSize] = (0, react_1.useState)('1000');
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return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
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react_1.default.createElement(material_1.DialogContent, null,
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inverted ? (react_1.default.createElement(material_1.FormControlLabel, { className: classes.padding, control: react_1.default.createElement(material_1.Checkbox, { checked: horizontallyFlip, onChange: event => setHorizontallyFlip(event.target.checked) }), label: "Note: The feature is inverted in orientation on the target\n sequence. This will result in the lower panel having genomic\n coordinates decreasing left to right. Horizontally flip?" })) : null,
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react_1.default.createElement(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => setWindowSize(event.target.value) })),
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react_1.default.createElement(material_1.DialogActions, null,
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react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
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// eslint-disable-next-line @typescript-eslint/no-floating-promises
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;
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(async () => {
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try {
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await (0, util_2.navToSynteny)({
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feature,
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windowSize: +windowSize,
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horizontallyFlip,
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model,
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});
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}
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catch (e) {
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(0, util_1.getSession)(model).notify(`${e}`, 'error');
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}
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})();
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handleClose();
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} }, "Submit"),
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react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
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}
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exports.default = LaunchSyntenyViewDialog;
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import { Feature } from '@jbrowse/core/util';
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import { IAnyStateTreeNode } from 'mobx-state-tree';
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export declare function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }: {
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windowSize: number;
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horizontallyFlip: boolean;
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feature: Feature;
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model: IAnyStateTreeNode;
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}): Promise<void>;
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.navToSynteny = void 0;
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const util_1 = require("@jbrowse/core/util");
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const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
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const mobx_1 = require("mobx");
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const { parseCigar } = plugin_alignments_1.MismatchParser;
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function f(n) {
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return Math.floor(n);
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}
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function findPosInCigar(cigar, startX) {
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let featX = 0;
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let mateX = 0;
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for (let i = 0; i < cigar.length; i++) {
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const len = +cigar[i];
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const op = cigar[i + 1];
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const min = Math.min(len, startX - featX);
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if (featX >= startX) {
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break;
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}
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else if (op === 'I') {
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mateX += len;
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}
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else if (op === 'D') {
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featX += min;
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}
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else if (op === 'M') {
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mateX += min;
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featX += min;
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}
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}
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return [featX, mateX];
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}
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async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }) {
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const session = (0, util_1.getSession)(model);
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const track = (0, util_1.getContainingTrack)(model);
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const view = (0, util_1.getContainingView)(model);
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const reg = view.dynamicBlocks.contentBlocks[0];
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const cigar = feature.get('CIGAR');
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const strand = feature.get('strand');
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const regStart = reg.start;
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const regEnd = reg.end;
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const featStart = feature.get('start');
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const featEnd = feature.get('end');
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const mate = feature.get('mate');
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const mateStart = mate.start;
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const mateEnd = mate.end;
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const mateAsm = mate.assemblyName;
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const mateRef = mate.refName;
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const featAsm = reg.assemblyName;
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const featRef = reg.refName;
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let rMateStart;
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let rMateEnd;
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let rFeatStart;
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let rFeatEnd;
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if (cigar) {
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const p = parseCigar(cigar);
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const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
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const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
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// avoid multiply by 0 with strand undefined
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const flipper = strand === -1 ? -1 : 1;
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rFeatStart = featStart + fStartX;
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rFeatEnd = featStart + fEndX;
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rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
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rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
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}
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else {
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rFeatStart = featStart;
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rFeatEnd = featEnd;
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rMateStart = mateStart;
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rMateEnd = mateEnd;
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}
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const trackId = track.configuration.trackId;
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const view2 = session.addView('LinearSyntenyView', {
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type: 'LinearSyntenyView',
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views: [
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{
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id: `${Math.random()}`,
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type: 'LinearGenomeView',
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hideHeader: true,
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},
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{
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id: `${Math.random()}`,
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type: 'LinearGenomeView',
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hideHeader: true,
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},
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],
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tracks: [
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{
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configuration: trackId,
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type: 'SyntenyTrack',
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displays: [
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{
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type: 'LinearSyntenyDisplay',
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configuration: `${trackId}-LinearSyntenyDisplay`,
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},
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],
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},
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],
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});
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const l1 = `${featRef}:${f(rFeatStart - ws)}-${f(rFeatEnd + ws)}`;
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const m1 = Math.min(rMateStart, rMateEnd);
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const m2 = Math.max(rMateStart, rMateEnd);
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const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
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await (0, mobx_1.when)(() => view2.width !== undefined);
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await Promise.all([
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view2.views[0].navToLocString(l1, featAsm),
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view2.views[1].navToLocString(l2, mateAsm),
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]);
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}
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exports.navToSynteny = navToSynteny;
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/// <reference types="react" />
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import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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import { Feature } from '@jbrowse/core/util';
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/**
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* #stateModel LGVSyntenyDisplay
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* extends `LinearPileupDisplay`, displays location of "synteny" feature in a
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renderInProgress: AbortController | undefined;
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filled: boolean;
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reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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features: Map<string, Feature> | undefined;
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features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
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layout: any;
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status: string;
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error: unknown;
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setMessage(messageText: string): void;
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setRendered(props: {
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reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
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features: Map<string, Feature>;
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features: Map<string, import("@jbrowse/core/util").Feature>;
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layout: any;
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maxHeightReached: boolean;
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renderProps: any;
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};
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fetchSizeLimit: {
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type: string;
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defaultValue: number;
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defaultValue: number; /**
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* #property
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*/
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description: string;
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};
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height: {
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
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} & {
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featureIdUnderMouse: string | undefined;
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contextMenuFeature: Feature | undefined;
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contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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} & {
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readonly blockType: "dynamicBlocks" | "staticBlocks";
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readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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readonly selectedFeatureId: string | undefined;
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readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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} & {
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readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
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readonly featureUnderMouse: Feature | undefined;
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readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
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getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
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getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
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searchFeatureByID(id: string): [number, number, number, number] | undefined;
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} & {
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addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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deleteBlock(key: string): void;
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selectFeature(feature: Feature): void;
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selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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clearFeatureSelection(): void;
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setFeatureIdUnderMouse(feature?: string | undefined): void;
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setContextMenuFeature(feature?: Feature | undefined): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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} & {
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reload(): Promise<void>;
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} & {
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afterAttach(): void;
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} & {
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colorTagMap: import("mobx").ObservableMap<string, string>;
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featureUnderMouseVolatile: Feature | undefined;
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featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
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tagsReady: boolean;
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} & {
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readonly autorunReady: boolean;
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extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
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}): void;
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updateColorTagMap(uniqueTag: string[]): void;
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setFeatureUnderMouse(feat?: Feature | undefined): void;
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selectFeature(feature: Feature): void;
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copyFeatureToClipboard(feature: Feature): void;
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setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
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const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
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}
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const trackId = track.configuration.trackId;
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const view2 = session.addView('LinearSyntenyView', {
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|
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],
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tracks: [
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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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|
-
const f = (n) => Math.floor(n);
|
|
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|
-
const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`;
|
|
101
|
-
const m1 = Math.min(rMateStart, rMateEnd);
|
|
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|
-
const m2 = Math.max(rMateStart, rMateEnd);
|
|
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|
-
const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`;
|
|
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|
-
await (0, mobx_1.when)(() => view2.width !== undefined);
|
|
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|
-
await Promise.all([
|
|
106
|
-
view2.views[0].navToLocString(l1, featAsm),
|
|
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|
-
view2.views[1].navToLocString(l2, mateAsm),
|
|
108
|
-
]);
|
|
109
|
-
}
|
|
31
|
+
const LaunchSyntenyViewDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LaunchSyntenyViewDialog'))));
|
|
110
32
|
/**
|
|
111
33
|
* #stateModel LGVSyntenyDisplay
|
|
112
34
|
* extends `LinearPileupDisplay`, displays location of "synteny" feature in a
|
|
@@ -135,7 +57,16 @@ function stateModelFactory(schema) {
|
|
|
135
57
|
? [
|
|
136
58
|
{
|
|
137
59
|
label: 'Open synteny view for this position',
|
|
138
|
-
onClick: () =>
|
|
60
|
+
onClick: () => {
|
|
61
|
+
(0, util_1.getSession)(self).queueDialog(handleClose => [
|
|
62
|
+
LaunchSyntenyViewDialog,
|
|
63
|
+
{
|
|
64
|
+
model: self,
|
|
65
|
+
handleClose,
|
|
66
|
+
feature,
|
|
67
|
+
},
|
|
68
|
+
]);
|
|
69
|
+
},
|
|
139
70
|
},
|
|
140
71
|
]
|
|
141
72
|
: []),
|
|
@@ -0,0 +1,42 @@
|
|
|
1
|
+
import React, { useState } from 'react';
|
|
2
|
+
import { Dialog } from '@jbrowse/core/ui';
|
|
3
|
+
import { getSession } from '@jbrowse/core/util';
|
|
4
|
+
import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, } from '@mui/material';
|
|
5
|
+
import { navToSynteny } from './util';
|
|
6
|
+
import { makeStyles } from 'tss-react/mui';
|
|
7
|
+
const useStyles = makeStyles()({
|
|
8
|
+
padding: {
|
|
9
|
+
margin: 10,
|
|
10
|
+
border: '1px solid #ccc',
|
|
11
|
+
},
|
|
12
|
+
});
|
|
13
|
+
export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
|
|
14
|
+
const { classes } = useStyles();
|
|
15
|
+
const inverted = feature.get('strand') === -1;
|
|
16
|
+
const [horizontallyFlip, setHorizontallyFlip] = useState(inverted);
|
|
17
|
+
const [windowSize, setWindowSize] = useState('1000');
|
|
18
|
+
return (React.createElement(Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
|
|
19
|
+
React.createElement(DialogContent, null,
|
|
20
|
+
inverted ? (React.createElement(FormControlLabel, { className: classes.padding, control: React.createElement(Checkbox, { checked: horizontallyFlip, onChange: event => setHorizontallyFlip(event.target.checked) }), label: "Note: The feature is inverted in orientation on the target\n sequence. This will result in the lower panel having genomic\n coordinates decreasing left to right. Horizontally flip?" })) : null,
|
|
21
|
+
React.createElement(TextField, { label: "Add window size in bp", value: windowSize, onChange: event => setWindowSize(event.target.value) })),
|
|
22
|
+
React.createElement(DialogActions, null,
|
|
23
|
+
React.createElement(Button, { variant: "contained", onClick: () => {
|
|
24
|
+
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
25
|
+
;
|
|
26
|
+
(async () => {
|
|
27
|
+
try {
|
|
28
|
+
await navToSynteny({
|
|
29
|
+
feature,
|
|
30
|
+
windowSize: +windowSize,
|
|
31
|
+
horizontallyFlip,
|
|
32
|
+
model,
|
|
33
|
+
});
|
|
34
|
+
}
|
|
35
|
+
catch (e) {
|
|
36
|
+
getSession(model).notify(`${e}`, 'error');
|
|
37
|
+
}
|
|
38
|
+
})();
|
|
39
|
+
handleClose();
|
|
40
|
+
} }, "Submit"),
|
|
41
|
+
React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
|
|
42
|
+
}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
import { Feature } from '@jbrowse/core/util';
|
|
2
|
+
import { IAnyStateTreeNode } from 'mobx-state-tree';
|
|
3
|
+
export declare function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }: {
|
|
4
|
+
windowSize: number;
|
|
5
|
+
horizontallyFlip: boolean;
|
|
6
|
+
feature: Feature;
|
|
7
|
+
model: IAnyStateTreeNode;
|
|
8
|
+
}): Promise<void>;
|
|
@@ -0,0 +1,107 @@
|
|
|
1
|
+
import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
|
|
2
|
+
import { MismatchParser } from '@jbrowse/plugin-alignments';
|
|
3
|
+
import { when } from 'mobx';
|
|
4
|
+
const { parseCigar } = MismatchParser;
|
|
5
|
+
function f(n) {
|
|
6
|
+
return Math.floor(n);
|
|
7
|
+
}
|
|
8
|
+
function findPosInCigar(cigar, startX) {
|
|
9
|
+
let featX = 0;
|
|
10
|
+
let mateX = 0;
|
|
11
|
+
for (let i = 0; i < cigar.length; i++) {
|
|
12
|
+
const len = +cigar[i];
|
|
13
|
+
const op = cigar[i + 1];
|
|
14
|
+
const min = Math.min(len, startX - featX);
|
|
15
|
+
if (featX >= startX) {
|
|
16
|
+
break;
|
|
17
|
+
}
|
|
18
|
+
else if (op === 'I') {
|
|
19
|
+
mateX += len;
|
|
20
|
+
}
|
|
21
|
+
else if (op === 'D') {
|
|
22
|
+
featX += min;
|
|
23
|
+
}
|
|
24
|
+
else if (op === 'M') {
|
|
25
|
+
mateX += min;
|
|
26
|
+
featX += min;
|
|
27
|
+
}
|
|
28
|
+
}
|
|
29
|
+
return [featX, mateX];
|
|
30
|
+
}
|
|
31
|
+
export async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }) {
|
|
32
|
+
const session = getSession(model);
|
|
33
|
+
const track = getContainingTrack(model);
|
|
34
|
+
const view = getContainingView(model);
|
|
35
|
+
const reg = view.dynamicBlocks.contentBlocks[0];
|
|
36
|
+
const cigar = feature.get('CIGAR');
|
|
37
|
+
const strand = feature.get('strand');
|
|
38
|
+
const regStart = reg.start;
|
|
39
|
+
const regEnd = reg.end;
|
|
40
|
+
const featStart = feature.get('start');
|
|
41
|
+
const featEnd = feature.get('end');
|
|
42
|
+
const mate = feature.get('mate');
|
|
43
|
+
const mateStart = mate.start;
|
|
44
|
+
const mateEnd = mate.end;
|
|
45
|
+
const mateAsm = mate.assemblyName;
|
|
46
|
+
const mateRef = mate.refName;
|
|
47
|
+
const featAsm = reg.assemblyName;
|
|
48
|
+
const featRef = reg.refName;
|
|
49
|
+
let rMateStart;
|
|
50
|
+
let rMateEnd;
|
|
51
|
+
let rFeatStart;
|
|
52
|
+
let rFeatEnd;
|
|
53
|
+
if (cigar) {
|
|
54
|
+
const p = parseCigar(cigar);
|
|
55
|
+
const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
|
|
56
|
+
const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
|
|
57
|
+
// avoid multiply by 0 with strand undefined
|
|
58
|
+
const flipper = strand === -1 ? -1 : 1;
|
|
59
|
+
rFeatStart = featStart + fStartX;
|
|
60
|
+
rFeatEnd = featStart + fEndX;
|
|
61
|
+
rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
|
|
62
|
+
rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
|
|
63
|
+
}
|
|
64
|
+
else {
|
|
65
|
+
rFeatStart = featStart;
|
|
66
|
+
rFeatEnd = featEnd;
|
|
67
|
+
rMateStart = mateStart;
|
|
68
|
+
rMateEnd = mateEnd;
|
|
69
|
+
}
|
|
70
|
+
const trackId = track.configuration.trackId;
|
|
71
|
+
const view2 = session.addView('LinearSyntenyView', {
|
|
72
|
+
type: 'LinearSyntenyView',
|
|
73
|
+
views: [
|
|
74
|
+
{
|
|
75
|
+
id: `${Math.random()}`,
|
|
76
|
+
type: 'LinearGenomeView',
|
|
77
|
+
hideHeader: true,
|
|
78
|
+
},
|
|
79
|
+
{
|
|
80
|
+
id: `${Math.random()}`,
|
|
81
|
+
type: 'LinearGenomeView',
|
|
82
|
+
hideHeader: true,
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},
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],
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tracks: [
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{
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configuration: trackId,
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type: 'SyntenyTrack',
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displays: [
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{
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type: 'LinearSyntenyDisplay',
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configuration: `${trackId}-LinearSyntenyDisplay`,
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},
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const l1 = `${featRef}:${f(rFeatStart - ws)}-${f(rFeatEnd + ws)}`;
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const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
|
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await when(() => view2.width !== undefined);
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await Promise.all([
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view2.views[0].navToLocString(l1, featAsm),
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view2.views[1].navToLocString(l2, mateAsm),
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]);
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}
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|
@@ -1,6 +1,5 @@
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/// <reference types="react" />
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import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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3
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-
import { Feature } from '@jbrowse/core/util';
|
|
4
3
|
/**
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|
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* #stateModel LGVSyntenyDisplay
|
|
6
5
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* extends `LinearPileupDisplay`, displays location of "synteny" feature in a
|
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@@ -35,7 +34,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
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renderInProgress: AbortController | undefined;
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filled: boolean;
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reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
|
|
38
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-
features: Map<string, Feature> | undefined;
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features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
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layout: any;
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status: string;
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|
error: unknown;
|
|
@@ -53,7 +52,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
|
|
53
52
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setMessage(messageText: string): void;
|
|
54
53
|
setRendered(props: {
|
|
55
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reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
|
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features: Map<string, Feature>;
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+
features: Map<string, import("@jbrowse/core/util").Feature>;
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layout: any;
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maxHeightReached: boolean;
|
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renderProps: any;
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@@ -70,7 +69,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
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};
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fetchSizeLimit: {
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type: string;
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-
defaultValue: number;
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+
defaultValue: number; /**
|
|
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+
* #property
|
|
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+
*/
|
|
74
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|
description: string;
|
|
75
76
|
};
|
|
76
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height: {
|
|
@@ -208,7 +209,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
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|
regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
|
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} & {
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featureIdUnderMouse: string | undefined;
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contextMenuFeature: Feature | undefined;
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+
contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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} & {
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readonly blockType: "dynamicBlocks" | "staticBlocks";
|
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readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
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@@ -218,18 +219,18 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
|
|
218
219
|
readonly selectedFeatureId: string | undefined;
|
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220
|
readonly DisplayMessageComponent: import("react").FC<any> | undefined;
|
|
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|
} & {
|
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|
-
readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
|
|
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|
-
readonly featureUnderMouse: Feature | undefined;
|
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|
+
readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
|
|
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|
+
readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
|
|
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224
|
getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
|
|
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|
getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
|
|
225
226
|
searchFeatureByID(id: string): [number, number, number, number] | undefined;
|
|
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227
|
} & {
|
|
227
228
|
addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
|
|
228
229
|
deleteBlock(key: string): void;
|
|
229
|
-
selectFeature(feature: Feature): void;
|
|
230
|
+
selectFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
230
231
|
clearFeatureSelection(): void;
|
|
231
232
|
setFeatureIdUnderMouse(feature?: string | undefined): void;
|
|
232
|
-
setContextMenuFeature(feature?: Feature | undefined): void;
|
|
233
|
+
setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
|
|
233
234
|
} & {
|
|
234
235
|
reload(): Promise<void>;
|
|
235
236
|
} & {
|
|
@@ -241,7 +242,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
|
|
241
242
|
afterAttach(): void;
|
|
242
243
|
} & {
|
|
243
244
|
colorTagMap: import("mobx").ObservableMap<string, string>;
|
|
244
|
-
featureUnderMouseVolatile: Feature | undefined;
|
|
245
|
+
featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
|
|
245
246
|
tagsReady: boolean;
|
|
246
247
|
} & {
|
|
247
248
|
readonly autorunReady: boolean;
|
|
@@ -256,9 +257,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
|
|
256
257
|
extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
|
|
257
258
|
}): void;
|
|
258
259
|
updateColorTagMap(uniqueTag: string[]): void;
|
|
259
|
-
setFeatureUnderMouse(feat?: Feature | undefined): void;
|
|
260
|
-
selectFeature(feature: Feature): void;
|
|
261
|
-
copyFeatureToClipboard(feature: Feature): void;
|
|
260
|
+
setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
|
|
261
|
+
selectFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
262
|
+
copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
|
|
262
263
|
setConfig(conf: {
|
|
263
264
|
[x: string]: any;
|
|
264
265
|
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
@@ -275,7 +276,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
|
|
|
275
276
|
} & {
|
|
276
277
|
readonly maxHeight: any;
|
|
277
278
|
readonly featureHeightSetting: any;
|
|
278
|
-
readonly featureUnderMouse: Feature | undefined;
|
|
279
|
+
readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
|
|
279
280
|
renderReady(): boolean;
|
|
280
281
|
readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
|
|
281
282
|
} & {
|
|
@@ -1,110 +1,9 @@
|
|
|
1
|
+
import { lazy } from 'react';
|
|
1
2
|
import { ConfigurationReference, } from '@jbrowse/core/configuration';
|
|
2
|
-
import { getSession
|
|
3
|
-
import {
|
|
3
|
+
import { getSession } from '@jbrowse/core/util';
|
|
4
|
+
import { SharedLinearPileupDisplayMixin } from '@jbrowse/plugin-alignments';
|
|
4
5
|
import { types } from 'mobx-state-tree';
|
|
5
|
-
|
|
6
|
-
const { parseCigar } = MismatchParser;
|
|
7
|
-
function findPosInCigar(cigar, startX) {
|
|
8
|
-
let featX = 0;
|
|
9
|
-
let mateX = 0;
|
|
10
|
-
for (let i = 0; i < cigar.length; i++) {
|
|
11
|
-
const len = +cigar[i];
|
|
12
|
-
const op = cigar[i + 1];
|
|
13
|
-
const min = Math.min(len, startX - featX);
|
|
14
|
-
if (featX >= startX) {
|
|
15
|
-
break;
|
|
16
|
-
}
|
|
17
|
-
else if (op === 'I') {
|
|
18
|
-
mateX += len;
|
|
19
|
-
}
|
|
20
|
-
else if (op === 'D') {
|
|
21
|
-
featX += min;
|
|
22
|
-
}
|
|
23
|
-
else if (op === 'M') {
|
|
24
|
-
mateX += min;
|
|
25
|
-
featX += min;
|
|
26
|
-
}
|
|
27
|
-
}
|
|
28
|
-
return [featX, mateX];
|
|
29
|
-
}
|
|
30
|
-
async function navToSynteny(feature, self) {
|
|
31
|
-
const session = getSession(self);
|
|
32
|
-
const track = getContainingTrack(self);
|
|
33
|
-
const view = getContainingView(self);
|
|
34
|
-
const reg = view.dynamicBlocks.contentBlocks[0];
|
|
35
|
-
const cigar = feature.get('CIGAR');
|
|
36
|
-
const strand = feature.get('strand');
|
|
37
|
-
const regStart = reg.start;
|
|
38
|
-
const regEnd = reg.end;
|
|
39
|
-
const featStart = feature.get('start');
|
|
40
|
-
const featEnd = feature.get('end');
|
|
41
|
-
const mate = feature.get('mate');
|
|
42
|
-
const mateStart = mate.start;
|
|
43
|
-
const mateEnd = mate.end;
|
|
44
|
-
const mateAsm = mate.assemblyName;
|
|
45
|
-
const mateRef = mate.refName;
|
|
46
|
-
const featAsm = reg.assemblyName;
|
|
47
|
-
const featRef = reg.refName;
|
|
48
|
-
let rMateStart;
|
|
49
|
-
let rMateEnd;
|
|
50
|
-
let rFeatStart;
|
|
51
|
-
let rFeatEnd;
|
|
52
|
-
if (cigar) {
|
|
53
|
-
const p = parseCigar(cigar);
|
|
54
|
-
const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
|
|
55
|
-
const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
|
|
56
|
-
// avoid multiply by 0 with strand undefined
|
|
57
|
-
const flipper = strand === -1 ? -1 : 1;
|
|
58
|
-
rFeatStart = featStart + fStartX;
|
|
59
|
-
rFeatEnd = featStart + fEndX;
|
|
60
|
-
rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
|
|
61
|
-
rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
|
|
62
|
-
}
|
|
63
|
-
else {
|
|
64
|
-
rFeatStart = featStart;
|
|
65
|
-
rFeatEnd = featEnd;
|
|
66
|
-
rMateStart = mateStart;
|
|
67
|
-
rMateEnd = mateEnd;
|
|
68
|
-
}
|
|
69
|
-
const trackId = track.configuration.trackId;
|
|
70
|
-
const view2 = session.addView('LinearSyntenyView', {
|
|
71
|
-
type: 'LinearSyntenyView',
|
|
72
|
-
views: [
|
|
73
|
-
{
|
|
74
|
-
id: `${Math.random()}`,
|
|
75
|
-
type: 'LinearGenomeView',
|
|
76
|
-
hideHeader: true,
|
|
77
|
-
},
|
|
78
|
-
{
|
|
79
|
-
id: `${Math.random()}`,
|
|
80
|
-
type: 'LinearGenomeView',
|
|
81
|
-
hideHeader: true,
|
|
82
|
-
},
|
|
83
|
-
],
|
|
84
|
-
tracks: [
|
|
85
|
-
{
|
|
86
|
-
configuration: trackId,
|
|
87
|
-
type: 'SyntenyTrack',
|
|
88
|
-
displays: [
|
|
89
|
-
{
|
|
90
|
-
type: 'LinearSyntenyDisplay',
|
|
91
|
-
configuration: `${trackId}-LinearSyntenyDisplay`,
|
|
92
|
-
},
|
|
93
|
-
],
|
|
94
|
-
},
|
|
95
|
-
],
|
|
96
|
-
});
|
|
97
|
-
const f = (n) => Math.floor(n);
|
|
98
|
-
const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`;
|
|
99
|
-
const m1 = Math.min(rMateStart, rMateEnd);
|
|
100
|
-
const m2 = Math.max(rMateStart, rMateEnd);
|
|
101
|
-
const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`;
|
|
102
|
-
await when(() => view2.width !== undefined);
|
|
103
|
-
await Promise.all([
|
|
104
|
-
view2.views[0].navToLocString(l1, featAsm),
|
|
105
|
-
view2.views[1].navToLocString(l2, mateAsm),
|
|
106
|
-
]);
|
|
107
|
-
}
|
|
6
|
+
const LaunchSyntenyViewDialog = lazy(() => import('./components/LaunchSyntenyViewDialog'));
|
|
108
7
|
/**
|
|
109
8
|
* #stateModel LGVSyntenyDisplay
|
|
110
9
|
* extends `LinearPileupDisplay`, displays location of "synteny" feature in a
|
|
@@ -133,7 +32,16 @@ function stateModelFactory(schema) {
|
|
|
133
32
|
? [
|
|
134
33
|
{
|
|
135
34
|
label: 'Open synteny view for this position',
|
|
136
|
-
onClick: () =>
|
|
35
|
+
onClick: () => {
|
|
36
|
+
getSession(self).queueDialog(handleClose => [
|
|
37
|
+
LaunchSyntenyViewDialog,
|
|
38
|
+
{
|
|
39
|
+
model: self,
|
|
40
|
+
handleClose,
|
|
41
|
+
feature,
|
|
42
|
+
},
|
|
43
|
+
]);
|
|
44
|
+
},
|
|
137
45
|
},
|
|
138
46
|
]
|
|
139
47
|
: []),
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-linear-comparative-view",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.8.0",
|
|
4
4
|
"description": "JBrowse 2 linear comparative view",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -62,5 +62,5 @@
|
|
|
62
62
|
"publishConfig": {
|
|
63
63
|
"access": "public"
|
|
64
64
|
},
|
|
65
|
-
"gitHead": "
|
|
65
|
+
"gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
|
|
66
66
|
}
|