@jbrowse/plugin-breakpoint-split-view 2.6.1

package/dist/BreakpointSplitView/components/Breakends.js

@@ -0,0 +1,117 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+// locals
+const util_2 = require("./util");
+const util_3 = require("../util");
+const [LEFT] = [0, 1, 2, 3];
+const Breakends = (0, mobx_react_1.observer)(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
+    const { views } = model;
+    const session = (0, util_1.getSession)(model);
+    const { assemblyManager } = session;
+    const totalFeatures = model.getTrackFeatures(trackId);
+    const layoutMatches = (0, react_1.useMemo)(() => model.getMatchedFeaturesInLayout(trackId, (0, util_2.getMatchedBreakendFeatures)(totalFeatures)), [totalFeatures, trackId, model]);
+    const [mouseoverElt, setMouseoverElt] = (0, react_1.useState)();
+    const snap = (0, mobx_state_tree_1.getSnapshot)(model);
+    (0, util_3.useNextFrame)(snap);
+    const assembly = assemblyManager.get(views[0].assemblyNames[0]);
+    if (!assembly) {
+        return null;
+    }
+    let yoff = 0;
+    if (ref.current) {
+        const rect = ref.current.getBoundingClientRect();
+        yoff = rect.top;
+    }
+    return (react_1.default.createElement("g", { stroke: "green", strokeWidth: 5, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
+        const ret = [];
+        // we follow a path in the list of chunks, not from top to bottom, just
+        // in series following x1,y1 -> x2,y2
+        for (let i = 0; i < chunk.length - 1; i += 1) {
+            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+            const { layout: c2, feature: f2, level: level2 } = chunk[i + 1];
+            const id = f1.id();
+            const relevantAlt = (0, util_2.findMatchingAlt)(f1, f2);
+            if (!c1 || !c2) {
+                return null;
+            }
+            const f1origref = f1.get('refName');
+            const f2origref = f2.get('refName');
+            const f1ref = assembly.getCanonicalRefName(f1origref);
+            const f2ref = assembly.getCanonicalRefName(f2origref);
+            if (!f1ref || !f2ref) {
+                throw new Error(`unable to find ref for ${f1ref || f2ref}`);
+            }
+            const x1 = (0, util_3.getPxFromCoordinate)(views[level1], f1ref, c1[LEFT]);
+            const x2 = (0, util_3.getPxFromCoordinate)(views[level2], f2ref, c2[LEFT]);
+            const reversed1 = views[level1].pxToBp(x1).reversed;
+            const reversed2 = views[level2].pxToBp(x2).reversed;
+            const tracks = views.map(v => v.getTrack(trackId));
+            const y1 = (0, util_3.yPos)(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                yoff;
+            const y2 = (0, util_3.yPos)(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                yoff;
+            if (!relevantAlt) {
+                console.warn('the relevant ALT allele was not found, cannot render');
+            }
+            else {
+                const path = [
+                    'M',
+                    x1 -
+                        20 *
+                            (relevantAlt.Join === 'left' ? -1 : 1) *
+                            (reversed1 ? -1 : 1),
+                    y1,
+                    'L',
+                    x1,
+                    y1,
+                    'L',
+                    x2,
+                    y2,
+                    'L',
+                    x2 -
+                        20 *
+                            (relevantAlt.MateDirection === 'left' ? 1 : -1) *
+                            (reversed2 ? -1 : 1),
+                    y2,
+                ].join(' ');
+                ret.push(react_1.default.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
+                        var _a, _b, _c;
+                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
+                            featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
+                        });
+                        (_c = session.showWidget) === null || _c === void 0 ? void 0 : _c.call(session, featureWidget);
+                    }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+            }
+        }
+        return ret;
+    })));
+});
+exports.default = Breakends;
+//# sourceMappingURL=Breakends.js.map

package/dist/BreakpointSplitView/components/Breakends.js.map

@@ -0,0 +1 @@
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package/dist/BreakpointSplitView/components/BreakpointSplitView.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const BreakpointSplitView: ({ model, }: {
+    model: BreakpointViewModel;
+}) => React.JSX.Element;
+export default BreakpointSplitView;

package/dist/BreakpointSplitView/components/BreakpointSplitView.js

@@ -0,0 +1,89 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
+const Overlay_1 = __importDefault(require("./Overlay"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    viewDivider: {
+        background: theme.palette.secondary.main,
+        height: 3,
+    },
+    container: {
+        display: 'grid',
+    },
+    overlay: {
+        display: 'flex',
+        width: '100%',
+        gridArea: '1/1',
+        '& path': {
+            cursor: 'crosshair',
+            fill: 'none',
+        },
+    },
+    content: {
+        gridArea: '1/1',
+    },
+}));
+const BreakpointSplitView = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { classes } = useStyles();
+    const { views } = model;
+    const { pluginManager } = (0, mobx_state_tree_1.getEnv)(model);
+    const ref = (0, react_1.useRef)(null);
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement("div", { className: classes.container },
+            react_1.default.createElement("div", { className: classes.content },
+                react_1.default.createElement("div", { style: { position: 'relative' } }, views.map((view, idx) => {
+                    const { ReactComponent } = pluginManager.getViewType(view.type);
+                    const viewComponent = (react_1.default.createElement(ReactComponent, { key: view.id, model: view }));
+                    if (idx === views.length - 1) {
+                        return viewComponent;
+                    }
+                    return [
+                        viewComponent,
+                        react_1.default.createElement("div", { key: `${view.id}-divider`, className: classes.viewDivider }),
+                    ];
+                }))),
+            react_1.default.createElement("div", { className: classes.overlay },
+                react_1.default.createElement("svg", { ref: ref, style: {
+                        width: '100%',
+                        zIndex: 10,
+                        pointerEvents: model.interactToggled ? undefined : 'none',
+                    } }, model.matchedTracks.map(track => (
+                // note: we must pass ref down, because the child component
+                // needs to getBoundingClientRect on the this components SVG,
+                // and we cannot rely on using getBoundingClientRect in this
+                // component to make sure this works because if it gets
+                // shifted around by another element, this will not re-render
+                // necessarily
+                react_1.default.createElement(Overlay_1.default, { parentRef: ref, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId }))))))));
+});
+exports.default = BreakpointSplitView;
+//# sourceMappingURL=BreakpointSplitView.js.map

package/dist/BreakpointSplitView/components/BreakpointSplitView.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BreakpointSplitView.js","sourceRoot":"","sources":["../../../src/BreakpointSplitView/components/BreakpointSplitView.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAqC;AACrC,2CAAqC;AACrC,qDAAwC;AACxC,uCAA0C;AAI1C,wDAA+B;AAE/B,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,SAAS,CAAC,IAAI;QACxC,MAAM,EAAE,CAAC;KACV;IACD,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;KAChB;IACD,OAAO,EAAE;QACP,OAAO,EAAE,MAAM;QACf,KAAK,EAAE,MAAM;QACb,QAAQ,EAAE,KAAK;QACf,QAAQ,EAAE;YACR,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,MAAM;SACb;KACF;IACD,OAAO,EAAE;QACP,QAAQ,EAAE,KAAK;KAChB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,mBAAmB,GAAG,IAAA,qBAAQ,EAAC,UAAU,EAC7C,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,wBAAM,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,GAAG,GAAG,IAAA,cAAM,EAAC,IAAI,CAAC,CAAA;IAExB,OAAO,CACL;QACE,uCAAK,SAAS,EAAE,OAAO,CAAC,SAAS;YAC/B,uCAAK,SAAS,EAAE,OAAO,CAAC,OAAO;gBAC7B,uCAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE,IACjC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;oBACvB,MAAM,EAAE,cAAc,EAAE,GAAG,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;oBAC/D,MAAM,aAAa,GAAG,CACpB,8BAAC,cAAc,IAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,EAAE,IAAI,GAAI,CAC9C,CAAA;oBACD,IAAI,GAAG,KAAK,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE;wBAC5B,OAAO,aAAa,CAAA;qBACrB;oBACD,OAAO;wBACL,aAAa;wBACb,uCACE,GAAG,EAAE,GAAG,IAAI,CAAC,EAAE,UAAU,EACzB,SAAS,EAAE,OAAO,CAAC,WAAW,GAC9B;qBACH,CAAA;gBACH,CAAC,CAAC,CACE,CACF;YACN,uCAAK,SAAS,EAAE,OAAO,CAAC,OAAO;gBAC7B,uCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE;wBACL,KAAK,EAAE,MAAM;wBACb,MAAM,EAAE,EAAE;wBACV,aAAa,EAAE,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM;qBAC1D,IAEA,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;gBAChC,2DAA2D;gBAC3D,6DAA6D;gBAC7D,4DAA4D;gBAC5D,uDAAuD;gBACvD,6DAA6D;gBAC7D,cAAc;gBACd,8BAAC,iBAAO,IACN,SAAS,EAAE,GAAG,EACd,GAAG,EAAE,KAAK,CAAC,aAAa,CAAC,OAAO,EAChC,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,KAAK,CAAC,aAAa,CAAC,OAAO,GACpC,CACH,CAAC,CACE,CACF,CACF,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,mBAAmB,CAAA"}

package/dist/BreakpointSplitView/components/ExportSvgDialog.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { ExportSvgOptions } from '../model';
+export default function ExportSvgDlg({ model, handleClose, }: {
+    model: {
+        exportSvg(opts: ExportSvgOptions): Promise<void>;
+    };
+    handleClose: () => void;
+}): React.JSX.Element;

package/dist/BreakpointSplitView/components/ExportSvgDialog.js

@@ -0,0 +1,84 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+function LoadingMessage() {
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }),
+        react_1.default.createElement(material_1.Typography, { display: "inline" }, "Creating SVG")));
+}
+function useSvgLocal(key, val) {
+    return (0, util_1.useLocalStorage)('svg-' + key, val);
+}
+function ExportSvgDlg({ model, handleClose, }) {
+    const session = (0, util_1.getSession)(model);
+    const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
+    const [rasterizeLayers, setRasterizeLayers] = (0, react_1.useState)(offscreenCanvas);
+    const [loading, setLoading] = (0, react_1.useState)(false);
+    const [error, setError] = (0, react_1.useState)();
+    const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
+    const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
+    const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
+        react_1.default.createElement(material_1.DialogContent, null,
+            error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
+            react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            react_1.default.createElement("br", null),
+            react_1.default.createElement(material_1.TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+                react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
+                react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
+                react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
+                react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
+            react_1.default.createElement("br", null),
+            session.allThemes ? (react_1.default.createElement(material_1.TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            // @ts-expect-error
+            val.name || '(Unknown name)'))))) : null,
+            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
+                    setLoading(true);
+                    setError(undefined);
+                    try {
+                        await model.exportSvg({
+                            rasterizeLayers,
+                            filename,
+                            trackLabels,
+                            themeName,
+                        });
+                        handleClose();
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setError(e);
+                        setLoading(false);
+                    }
+                } }, "Submit"))));
+}
+exports.default = ExportSvgDlg;
+//# sourceMappingURL=ExportSvgDialog.js.map

package/dist/BreakpointSplitView/components/ExportSvgDialog.js.map

@@ -0,0 +1 @@
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package/dist/BreakpointSplitView/components/Overlay.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const _default: (props: {
+    parentRef: React.RefObject<SVGSVGElement>;
+    model: BreakpointViewModel;
+    trackId: string;
+    getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
+}) => React.JSX.Element | null;
+export default _default;

package/dist/BreakpointSplitView/components/Overlay.js

@@ -0,0 +1,23 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const AlignmentConnections_1 = __importDefault(require("./AlignmentConnections"));
+const Breakends_1 = __importDefault(require("./Breakends"));
+const Translocations_1 = __importDefault(require("./Translocations"));
+exports.default = (0, mobx_react_1.observer)(function (props) {
+    var _a, _b;
+    const { model, trackId } = props;
+    const tracks = model.getMatchedTracks(trackId);
+    if (((_a = tracks[0]) === null || _a === void 0 ? void 0 : _a.type) === 'AlignmentsTrack') {
+        return react_1.default.createElement(AlignmentConnections_1.default, { ...props });
+    }
+    if (((_b = tracks[0]) === null || _b === void 0 ? void 0 : _b.type) === 'VariantTrack') {
+        return model.hasTranslocations(trackId) ? (react_1.default.createElement(Translocations_1.default, { ...props })) : (react_1.default.createElement(Breakends_1.default, { ...props }));
+    }
+    return null;
+});
+//# sourceMappingURL=Overlay.js.map

package/dist/BreakpointSplitView/components/Overlay.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Overlay.js","sourceRoot":"","sources":["../../../src/BreakpointSplitView/components/Overlay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAIrC,kFAAyD;AACzD,4DAAmC;AACnC,sEAA6C;AAE7C,kBAAe,IAAA,qBAAQ,EAAC,UAAU,KAKjC;;IACC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,MAAM,GAAG,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;IAC9C,IAAI,CAAA,MAAA,MAAM,CAAC,CAAC,CAAC,0CAAE,IAAI,MAAK,iBAAiB,EAAE;QACzC,OAAO,8BAAC,8BAAoB,OAAK,KAAK,GAAI,CAAA;KAC3C;IACD,IAAI,CAAA,MAAA,MAAM,CAAC,CAAC,CAAC,0CAAE,IAAI,MAAK,cAAc,EAAE;QACtC,OAAO,KAAK,CAAC,iBAAiB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CACxC,8BAAC,wBAAc,OAAK,KAAK,GAAI,CAC9B,CAAC,CAAC,CAAC,CACF,8BAAC,mBAAS,OAAK,KAAK,GAAI,CACzB,CAAA;KACF;IACD,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA"}

package/dist/BreakpointSplitView/components/Translocations.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const Translocations: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
+    model: BreakpointViewModel;
+    trackId: string;
+    parentRef: React.RefObject<SVGSVGElement>;
+    getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
+}) => React.JSX.Element | null;
+export default Translocations;

package/dist/BreakpointSplitView/components/Translocations.js

@@ -0,0 +1,113 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+// locals
+const util_2 = require("./util");
+const util_3 = require("../util");
+const [LEFT] = [0, 1, 2, 3];
+const Translocations = (0, mobx_react_1.observer)(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
+    const { views } = model;
+    const session = (0, util_1.getSession)(model);
+    const { assemblyManager } = session;
+    const totalFeatures = model.getTrackFeatures(trackId);
+    const layoutMatches = (0, react_1.useMemo)(() => model.getMatchedFeaturesInLayout(trackId, (0, util_2.getMatchedTranslocationFeatures)(totalFeatures)), [totalFeatures, trackId, model]);
+    const [mouseoverElt, setMouseoverElt] = (0, react_1.useState)();
+    const snap = (0, mobx_state_tree_1.getSnapshot)(model);
+    (0, util_3.useNextFrame)(snap);
+    const assembly = assemblyManager.get(views[0].assemblyNames[0]);
+    if (!assembly) {
+        return null;
+    }
+    let yOffset = 0;
+    if (ref.current) {
+        const rect = ref.current.getBoundingClientRect();
+        yOffset = rect.top;
+    }
+    // we hardcode the TRA to go to the "other view" and if there is none, we
+    // just return null here note: would need to do processing of the INFO
+    // CHR2/END and see which view could contain those coordinates to really do
+    // it properly
+    if (views.length < 2) {
+        return null;
+    }
+    return (react_1.default.createElement("g", { fill: "none", stroke: "green", strokeWidth: 5, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
+        // we follow a path in the list of chunks, not from top to bottom,
+        // just in series following x1,y1 -> x2,y2
+        const ret = [];
+        for (let i = 0; i < chunk.length; i += 1) {
+            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+            const level2 = level1 === 0 ? 1 : 0;
+            const id = f1.id();
+            if (!c1) {
+                return null;
+            }
+            const info = f1.get('INFO');
+            const chr2 = info.CHR2[0];
+            const end2 = info.END[0];
+            const [myDirection, mateDirection] = info.STRANDS[0].split('');
+            const r = (0, util_3.getPxFromCoordinate)(views[level2], chr2, end2);
+            if (r) {
+                const c2 = [r, 0, r + 1, 0];
+                const x1 = (0, util_3.getPxFromCoordinate)(views[level1], f1.get('refName'), c1[LEFT]);
+                const x2 = r;
+                const reversed1 = views[level1].pxToBp(x1).reversed;
+                const reversed2 = views[level2].pxToBp(x2).reversed;
+                const tracks = views.map(v => v.getTrack(trackId));
+                const y1 = (0, util_3.yPos)(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                    yOffset;
+                const y2 = (0, util_3.yPos)(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                    yOffset;
+                const path = [
+                    'M',
+                    x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
+                    y1,
+                    'L',
+                    x1,
+                    y1,
+                    'L',
+                    x2,
+                    y2,
+                    'L',
+                    x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
+                    y2,
+                ].join(' ');
+                ret.push(react_1.default.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
+                        var _a, _b;
+                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
+                            featureData: (totalFeatures.get(id) || { toJSON: () => { } }).toJSON(),
+                        });
+                        (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
+                    }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+            }
+        }
+        return ret;
+    })));
+});
+exports.default = Translocations;
+//# sourceMappingURL=Translocations.js.map

package/dist/BreakpointSplitView/components/Translocations.js.map

@@ -0,0 +1 @@
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package/dist/BreakpointSplitView/components/util.d.ts

@@ -0,0 +1,7 @@
+import { Feature } from '@jbrowse/core/util';
+export declare function getBadlyPairedAlignments(features: Map<string, Feature>): Feature[][];
+export declare function getMatchedAlignmentFeatures(features: Map<string, Feature>): Feature[][];
+export declare function hasPairedReads(features: Map<string, Feature>): boolean;
+export declare function findMatchingAlt(feat1: Feature, feat2: Feature): import("@gmod/vcf").Breakend | undefined;
+export declare function getMatchedBreakendFeatures(feats: Map<string, Feature>): Feature[][];
+export declare function getMatchedTranslocationFeatures(feats: Map<string, Feature>): Feature[][];

package/dist/BreakpointSplitView/components/util.js

@@ -0,0 +1,116 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMatchedTranslocationFeatures = exports.getMatchedBreakendFeatures = exports.findMatchingAlt = exports.hasPairedReads = exports.getMatchedAlignmentFeatures = exports.getBadlyPairedAlignments = void 0;
+const util_1 = require("@jbrowse/core/util");
+const vcf_1 = require("@gmod/vcf");
+// this finds candidate alignment features, aimed at plotting split reads from
+// BAM/CRAM files
+function getBadlyPairedAlignments(features) {
+    const candidates = new Map();
+    const alreadySeen = new Set();
+    // this finds candidate features that share the same name
+    for (const feature of features.values()) {
+        const flags = feature.get('flags');
+        const id = feature.id();
+        const unmapped = flags & 4;
+        const correctlyPaired = flags & 2;
+        if (!alreadySeen.has(id) && !correctlyPaired && !unmapped) {
+            const n = feature.get('name');
+            let val = candidates.get(n);
+            if (!val) {
+                val = [];
+                candidates.set(n, val);
+            }
+            val.push(feature);
+        }
+        alreadySeen.add(feature.id());
+    }
+    return [...candidates.values()].filter(v => v.length > 1);
+}
+exports.getBadlyPairedAlignments = getBadlyPairedAlignments;
+function getTag(f, tag) {
+    const tags = f.get('tags');
+    return tags ? tags[tag] : f.get(tag);
+}
+// this finds candidate alignment features, aimed at plotting split reads from
+// BAM/CRAM files
+function getMatchedAlignmentFeatures(features) {
+    const candidates = new Map();
+    const alreadySeen = new Set();
+    // this finds candidate features that share the same name
+    for (const feature of features.values()) {
+        const id = feature.id();
+        const unmapped = feature.get('flags') & 4;
+        const hasSA = !!getTag(feature, 'SA');
+        if (!alreadySeen.has(id) && !unmapped && hasSA) {
+            const n = feature.get('name');
+            let val = candidates.get(n);
+            if (!val) {
+                val = [];
+                candidates.set(n, val);
+            }
+            val.push(feature);
+        }
+        alreadySeen.add(feature.id());
+    }
+    return [...candidates.values()].filter(v => v.length > 1);
+}
+exports.getMatchedAlignmentFeatures = getMatchedAlignmentFeatures;
+function hasPairedReads(features) {
+    for (const f of features.values()) {
+        if (f.get('flags') & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+exports.hasPairedReads = hasPairedReads;
+function findMatchingAlt(feat1, feat2) {
+    const alts = feat1.get('ALT');
+    if (alts) {
+        return new Map(alts === null || alts === void 0 ? void 0 : alts.map(alt => (0, vcf_1.parseBreakend)(alt)).filter(util_1.notEmpty).map(bnd => [bnd.MatePosition, bnd])).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`);
+    }
+    return undefined;
+}
+exports.findMatchingAlt = findMatchingAlt;
+// Returns paired BND features across multiple views by inspecting the ALT
+// field to get exact coordinate matches
+function getMatchedBreakendFeatures(feats) {
+    const candidates = new Map();
+    const alreadySeen = new Set();
+    for (const f of feats.values()) {
+        if (!alreadySeen.has(f.id()) && f.get('type') === 'breakend') {
+            const alts = f.get('ALT');
+            alts === null || alts === void 0 ? void 0 : alts.forEach(a => {
+                const cur = `${f.get('refName')}:${f.get('start') + 1}`;
+                const bnd = (0, vcf_1.parseBreakend)(a);
+                if (bnd) {
+                    const val = candidates.get(cur);
+                    if (!val) {
+                        candidates.set(bnd.MatePosition || 'none', [f]);
+                    }
+                    else {
+                        val.push(f);
+                    }
+                }
+            });
+        }
+        alreadySeen.add(f.id());
+    }
+    return [...candidates.values()].filter(v => v.length > 1);
+}
+exports.getMatchedBreakendFeatures = getMatchedBreakendFeatures;
+// Getting "matched" TRA means just return all TRA
+function getMatchedTranslocationFeatures(feats) {
+    const ret = [];
+    const alreadySeen = new Set();
+    for (const f of feats.values()) {
+        if (!alreadySeen.has(f.id()) && f.get('ALT')[0] === '<TRA>') {
+            ret.push([f]);
+        }
+        alreadySeen.add(f.id());
+    }
+    return ret;
+}
+exports.getMatchedTranslocationFeatures = getMatchedTranslocationFeatures;
+//# sourceMappingURL=util.js.map