@jbrowse/plugin-breakpoint-split-view 3.7.0 → 4.0.0

package/dist/BreakpointSplitView/BreakpointSplitView.js

@@ -1,84 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const vcf_1 = require("@gmod/vcf");
-const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
-const util_1 = require("@jbrowse/core/util");
-class BreakpointSplitViewType extends ViewType_1.default {
-    getBreakendCoveringRegions({ feature, assembly, }) {
-        var _a;
-        const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
-        const bnd = alt ? (0, vcf_1.parseBreakend)(alt) : undefined;
-        const startPos = feature.get('start');
-        const refName = feature.get('refName');
-        const f = (ref) => assembly.getCanonicalRefName(ref) || ref;
-        if (alt === '<TRA>') {
-            const INFO = feature.get('INFO');
-            return {
-                pos: startPos,
-                refName: f(refName),
-                mateRefName: f(INFO.CHR2[0]),
-                matePos: INFO.END[0] - 1,
-            };
-        }
-        else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
-            const matePosition = bnd.MatePosition.split(':');
-            return {
-                pos: startPos,
-                refName: f(refName),
-                mateRefName: f(matePosition[0]),
-                matePos: +matePosition[1] - 1,
-            };
-        }
-        else if (feature.get('mate')) {
-            const mate = feature.get('mate');
-            return {
-                pos: startPos,
-                refName: f(refName),
-                mateRefName: f(mate.refName),
-                matePos: mate.start,
-            };
-        }
-        else {
-            return {
-                pos: startPos,
-                refName: f(refName),
-                mateRefName: f(refName),
-                matePos: feature.get('end'),
-            };
-        }
-    }
-    singleLevelSnapshotFromBreakendFeature({ feature, session, assemblyName, }) {
-        const { assemblyManager } = session;
-        const assembly = assemblyManager.get(assemblyName);
-        if (!assembly) {
-            throw new Error(`assembly ${assemblyName} not found`);
-        }
-        if (!assembly.regions) {
-            throw new Error(`assembly ${assemblyName} regions not loaded`);
-        }
-        const coverage = this.getBreakendCoveringRegions({
-            feature,
-            assembly,
-        });
-        const { refName, mateRefName } = coverage;
-        const topRegion = assembly.regions.find(f => f.refName === refName);
-        const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
-        return {
-            coverage,
-            snap: {
-                type: 'BreakpointSplitView',
-                views: [
-                    {
-                        type: 'LinearGenomeView',
-                        displayedRegions: (0, util_1.gatherOverlaps)([topRegion, bottomRegion]),
-                    },
-                ],
-                displayName: `${feature.get('name') || feature.get('id') || 'breakend'} split detail`,
-            },
-        };
-    }
-}
-exports.default = BreakpointSplitViewType;

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

@@ -1,8 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const AlignmentConnections: ({ model, trackId, parentRef, getTrackYPosOverride, }: {
-    model: BreakpointViewModel;
-    trackId: string;
-    parentRef: React.RefObject<SVGSVGElement | null>;
-    getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default AlignmentConnections;

package/dist/BreakpointSplitView/components/AlignmentConnections.js

@@ -1,133 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_2 = require("./util");
-const util_3 = require("../util");
-const getOrientationColor_1 = require("./getOrientationColor");
-const [LEFT, , RIGHT] = [0, 1, 2, 3];
-const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, trackId, parentRef, getTrackYPosOverride, }) {
-    const { interactiveOverlay, views, showIntraviewLinks } = model;
-    const theme = (0, material_1.useTheme)();
-    const session = (0, util_1.getSession)(model);
-    const snap = (0, mobx_state_tree_1.getSnapshot)(model);
-    const { assemblyManager } = session;
-    const v0 = views[0];
-    const assembly = v0 ? assemblyManager.get(v0.assemblyNames[0]) : undefined;
-    (0, util_3.useNextFrame)(snap);
-    const allFeatures = model.getTrackFeatures(trackId);
-    const hasPaired = (0, react_1.useMemo)(() => (0, util_2.hasPairedReads)(allFeatures), [allFeatures]);
-    const layoutMatches = (0, react_1.useMemo)(() => {
-        const layoutMatches = model.getMatchedFeaturesInLayout(trackId, hasPaired
-            ? (0, util_2.getBadlyPairedAlignments)(allFeatures)
-            : (0, util_2.getMatchedAlignmentFeatures)(allFeatures));
-        if (!hasPaired) {
-            for (const m of layoutMatches) {
-                m.sort((a, b) => a.clipPos - b.clipPos);
-            }
-        }
-        return layoutMatches;
-    }, [allFeatures, trackId, hasPaired, model]);
-    const [mouseoverElt, setMouseoverElt] = (0, react_1.useState)();
-    let yOffset = 0;
-    if (parentRef.current) {
-        const rect = parentRef.current.getBoundingClientRect();
-        yOffset = rect.top;
-    }
-    return assembly ? ((0, jsx_runtime_1.jsx)("g", { fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId, children: layoutMatches.map(chunk => {
-            const ret = [];
-            for (let i = 0; i < chunk.length - 1; i++) {
-                const { layout: c1, feature: f1, level: level1 } = chunk[i];
-                const { layout: c2, feature: f2, level: level2 } = chunk[i + 1];
-                if (!c1 || !c2) {
-                    console.warn('received null layout for a overlay feature');
-                    return null;
-                }
-                if (!showIntraviewLinks && level1 === level2) {
-                    return null;
-                }
-                const f1ref = assembly.getCanonicalRefName(f1.get('refName'));
-                const f2ref = assembly.getCanonicalRefName(f2.get('refName'));
-                if (!f1ref || !f2ref) {
-                    throw new Error(`unable to find ref for ${f1ref || f2ref}`);
-                }
-                const r = {
-                    pair_orientation: f1.get('pair_orientation'),
-                };
-                const s1 = f1.get('strand');
-                const s2 = f2.get('strand');
-                const sameRef = f1ref === f2ref;
-                const checkOrientation = sameRef;
-                let orientationColor = '';
-                let isAbnormal = false;
-                if (checkOrientation) {
-                    if (hasPaired) {
-                        orientationColor = (0, getOrientationColor_1.getPairedOrientationColor)(r);
-                        isAbnormal = (0, getOrientationColor_1.isAbnormalOrientation)(r);
-                    }
-                    else {
-                        orientationColor = (0, getOrientationColor_1.getLongReadOrientationColorOrDefault)(s1, s2);
-                        isAbnormal = (0, getOrientationColor_1.getLongReadOrientationAbnormal)(s1, s2);
-                    }
-                }
-                const p1 = c1[s1 === -1 ? LEFT : RIGHT];
-                const sn1 = s2 === -1;
-                const p2 = hasPaired ? c2[sn1 ? LEFT : RIGHT] : c2[sn1 ? RIGHT : LEFT];
-                const x1 = (0, util_3.getPxFromCoordinate)(views[level1], f1ref, p1);
-                const x2 = (0, util_3.getPxFromCoordinate)(views[level2], f2ref, p2);
-                const reversed1 = views[level1].pxToBp(x1).reversed;
-                const reversed2 = views[level2].pxToBp(x2).reversed;
-                const rf1 = reversed1 ? -1 : 1;
-                const rf2 = reversed2 ? -1 : 1;
-                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 sameLevel = level1 === level2;
-                const abnormalSpecialRenderFlag = sameLevel && isAbnormal;
-                const trackHeight = abnormalSpecialRenderFlag
-                    ? tracks[level1].displays[0].height
-                    : 0;
-                const pf1 = hasPaired ? -1 : 1;
-                const y0 = (0, util_3.heightFromSpecificLevel)(views, trackId, level1, getTrackYPosOverride);
-                const path = [
-                    'M',
-                    x1,
-                    y1,
-                    'C',
-                    x1 + 200 * f1.get('strand') * rf1,
-                    abnormalSpecialRenderFlag
-                        ? Math.min(y0 - yOffset + trackHeight, y1 + trackHeight)
-                        : y1,
-                    x2 - 200 * f2.get('strand') * rf2 * pf1,
-                    abnormalSpecialRenderFlag
-                        ? Math.min(y0 - yOffset + trackHeight, y2 + trackHeight)
-                        : y2,
-                    x2,
-                    y2,
-                ].join(' ');
-                const id = `${f1.id()}-${f2.id()}`;
-                ret.push((0, jsx_runtime_1.jsx)("path", { d: path, "data-testid": "r1", pointerEvents: interactiveOverlay ? 'auto' : undefined, strokeWidth: mouseoverElt === id ? 5 : 1, ...(0, util_1.getStrokeProps)(orientationColor || theme.palette.text.disabled), onClick: () => {
-                        var _a, _b;
-                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'BreakpointAlignmentsWidget', 'breakpointAlignments', {
-                            featureData: {
-                                feature1: (allFeatures.get(f1.id()) || { toJSON: () => { } }).toJSON(),
-                                feature2: (allFeatures.get(f2.id()) || { toJSON: () => { } }).toJSON(),
-                            },
-                        });
-                        (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
-                    }, onMouseOver: () => {
-                        setMouseoverElt(id);
-                    }, onMouseOut: () => {
-                        setMouseoverElt(undefined);
-                    } }, id));
-            }
-            return ret;
-        }) })) : null;
-});
-exports.default = AlignmentConnections;

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

@@ -1,8 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const Breakends: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
-    model: BreakpointViewModel;
-    trackId: string;
-    parentRef: React.RefObject<SVGSVGElement | null>;
-    getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default Breakends;

package/dist/BreakpointSplitView/components/Breakends.js

@@ -1,95 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = 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");
-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 { interactiveOverlay, 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 ((0, jsx_runtime_1.jsx)("g", { stroke: "green", strokeWidth: 5, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId, children: layoutMatches.map(chunk => {
-            const ret = [];
-            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((0, jsx_runtime_1.jsx)("path", { d: path, "data-testid": "r2", pointerEvents: interactiveOverlay ? 'auto' : undefined, 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);
-                        } }, JSON.stringify(path)));
-                }
-            }
-            return ret;
-        }) }));
-});
-exports.default = Breakends;

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

@@ -1,5 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const BreakpointSplitView: ({ model, }: {
-    model: BreakpointViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default BreakpointSplitView;

package/dist/BreakpointSplitView/components/BreakpointSplitView.js

@@ -1,46 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const BreakpointSplitViewOverlay_1 = __importDefault(require("./BreakpointSplitViewOverlay"));
-const Header_1 = __importDefault(require("./Header"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    viewDivider: {
-        background: theme.palette.secondary.main,
-        height: 3,
-    },
-    container: {
-        display: 'grid',
-    },
-    content: {
-        gridArea: '1/1',
-    },
-    rel: {
-        position: 'relative',
-    },
-}));
-const BreakpointSplitViewLevels = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const { views } = model;
-    const { pluginManager } = (0, util_1.getEnv)(model);
-    return ((0, jsx_runtime_1.jsx)("div", { className: classes.content, children: (0, jsx_runtime_1.jsx)("div", { className: classes.rel, children: views.map((view, idx) => {
-                const { ReactComponent } = pluginManager.getViewType(view.type);
-                const viewComponent = (0, jsx_runtime_1.jsx)(ReactComponent, { model: view }, view.id);
-                return idx === views.length - 1
-                    ? viewComponent
-                    : [
-                        viewComponent,
-                        (0, jsx_runtime_1.jsx)("div", { className: classes.viewDivider }, `${view.id}-divider`),
-                    ];
-            }) }) }));
-});
-const BreakpointSplitView = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [model.showHeader ? (0, jsx_runtime_1.jsx)(Header_1.default, { model: model }) : null, (0, jsx_runtime_1.jsxs)("div", { className: classes.container, children: [(0, jsx_runtime_1.jsx)(BreakpointSplitViewLevels, { model: model }), (0, jsx_runtime_1.jsx)(BreakpointSplitViewOverlay_1.default, { model: model })] })] }));
-});
-exports.default = BreakpointSplitView;

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

@@ -1,5 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const BreakpointSplitViewOverlay: ({ model, }: {
-    model: BreakpointViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default BreakpointSplitViewOverlay;

package/dist/BreakpointSplitView/components/BreakpointSplitViewOverlay.js

@@ -1,33 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const Overlay_1 = __importDefault(require("./Overlay"));
-const useStyles = (0, mui_1.makeStyles)()({
-    overlay: {
-        display: 'flex',
-        width: '100%',
-        gridArea: '1/1',
-        '& path': {
-            cursor: 'crosshair',
-            fill: 'none',
-        },
-    },
-    base: {
-        pointerEvents: 'none',
-        width: '100%',
-        zIndex: 100,
-    },
-});
-const BreakpointSplitViewOverlay = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const { matchedTracks } = model;
-    const ref = (0, react_1.useRef)(null);
-    return ((0, jsx_runtime_1.jsx)("div", { className: classes.overlay, children: (0, jsx_runtime_1.jsx)("svg", { ref: ref, className: classes.base, children: matchedTracks.map(track => ((0, jsx_runtime_1.jsx)(Overlay_1.default, { parentRef: ref, model: model, trackId: track.configuration.trackId }, track.configuration.trackId))) }) }));
-});
-exports.default = BreakpointSplitViewOverlay;

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

@@ -1,7 +0,0 @@
-import type { ExportSvgOptions } from '../types';
-export default function ExportSvgDialog({ model, handleClose, }: {
-    model: {
-        exportSvg(opts: ExportSvgOptions): Promise<void>;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/BreakpointSplitView/components/ExportSvgDialog.js

@@ -1,57 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ExportSvgDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-function LoadingMessage() {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }), (0, jsx_runtime_1.jsx)(material_1.Typography, { display: "inline", children: "Creating SVG" })] }));
-}
-function TextField2({ children, ...rest }) {
-    return ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { ...rest, children: children }) }));
-}
-function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
-}
-function ExportSvgDialog({ 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 ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(LoadingMessage, {})) : null, (0, jsx_runtime_1.jsx)(TextField2, { helperText: "filename", value: filename, onChange: event => {
-                            setFilename(event.target.value);
-                        } }), (0, jsx_runtime_1.jsxs)(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => {
-                            setTrackLabels(event.target.value);
-                        }, children: [(0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "offset", children: "Offset" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "overlay", children: "Overlay" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "left", children: "Left" }), (0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: "none", children: "None" })] }), (0, jsx_runtime_1.jsx)("br", {}), session.allThemes ? ((0, jsx_runtime_1.jsx)(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => {
-                            setThemeName(event.target.value);
-                        }, children: Object.entries(session.allThemes()).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, offscreenCanvas ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
-                                setRasterizeLayers(val => !val);
-                            } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : ((0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Note: rasterizing layers not yet supported in this browser, so SVG size may be large" }))] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" }), (0, jsx_runtime_1.jsx)(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);
-                            }
-                            finally {
-                                setLoading(false);
-                            }
-                        }, children: "Submit" })] })] }));
-}

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

@@ -1,5 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const Header: ({ model }: {
-    model: BreakpointViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default Header;

package/dist/BreakpointSplitView/components/Header.js

@@ -1,52 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
-const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
-const Search_1 = __importDefault(require("@mui/icons-material/Search"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const HeaderSearchBoxes_1 = __importDefault(require("./HeaderSearchBoxes"));
-const useStyles = (0, mui_1.makeStyles)()({
-    inline: {
-        display: 'inline-flex',
-    },
-});
-const Header = (0, mobx_react_1.observer)(function ({ model }) {
-    const { classes } = useStyles();
-    const { views } = model;
-    const [showSearchBoxes, setShowSearchBoxes] = (0, react_1.useState)(views.length <= 3);
-    const [sideBySide, setSideBySide] = (0, react_1.useState)(views.length <= 3);
-    return ((0, jsx_runtime_1.jsxs)(material_1.FormGroup, { row: true, children: [(0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: model.menuItems(), children: (0, jsx_runtime_1.jsx)(MoreVert_1.default, {}) }), (0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
-                    {
-                        label: 'Show search boxes',
-                        type: 'checkbox',
-                        checked: showSearchBoxes,
-                        onClick: () => {
-                            setShowSearchBoxes(!showSearchBoxes);
-                        },
-                    },
-                    {
-                        label: 'Orientation - Side-by-side',
-                        type: 'radio',
-                        checked: sideBySide,
-                        onClick: () => {
-                            setSideBySide(!sideBySide);
-                        },
-                    },
-                    {
-                        label: 'Orientation - Vertical',
-                        type: 'radio',
-                        checked: !sideBySide,
-                        onClick: () => {
-                            setSideBySide(!sideBySide);
-                        },
-                    },
-                ], children: (0, jsx_runtime_1.jsx)(Search_1.default, {}) }), showSearchBoxes ? ((0, jsx_runtime_1.jsx)("span", { className: sideBySide ? classes.inline : undefined, children: views.map(view => ((0, jsx_runtime_1.jsx)(HeaderSearchBoxes_1.default, { view: view }, view.id))) })) : null] }));
-});
-exports.default = Header;

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

@@ -1,5 +0,0 @@
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-declare const HeaderSearchBoxes: ({ view, }: {
-    view: LinearGenomeViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default HeaderSearchBoxes;

package/dist/BreakpointSplitView/components/HeaderSearchBoxes.js

@@ -1,24 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
-    bp: {
-        display: 'flex',
-        alignItems: 'center',
-        marginLeft: 10,
-    },
-    searchBox: {
-        display: 'flex',
-    },
-}));
-const HeaderSearchBoxes = (0, mobx_react_1.observer)(function ({ view, }) {
-    const { classes } = useStyles();
-    const { assemblyDisplayNames, coarseTotalBp } = view;
-    return ((0, jsx_runtime_1.jsxs)("span", { className: classes.searchBox, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SearchBox, { model: view, showHelp: false }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyDisplayNames.join(','), " ", (0, util_1.getBpDisplayStr)(coarseTotalBp)] })] }));
-});
-exports.default = HeaderSearchBoxes;

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

@@ -1,8 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const Overlay: (props: {
-    parentRef: React.RefObject<SVGSVGElement | null>;
-    model: BreakpointViewModel;
-    trackId: string;
-    getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default Overlay;

package/dist/BreakpointSplitView/components/Overlay.js

@@ -1,27 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const mobx_react_1 = require("mobx-react");
-const AlignmentConnections_1 = __importDefault(require("./AlignmentConnections"));
-const Breakends_1 = __importDefault(require("./Breakends"));
-const PairedFeatures_1 = __importDefault(require("./PairedFeatures"));
-const Translocations_1 = __importDefault(require("./Translocations"));
-const Overlay = (0, mobx_react_1.observer)(function (props) {
-    var _a;
-    const { model, trackId } = props;
-    const tracks = model.getMatchedTracks(trackId);
-    const type = (_a = tracks[0]) === null || _a === void 0 ? void 0 : _a.type;
-    if (type === 'AlignmentsTrack') {
-        return (0, jsx_runtime_1.jsx)(AlignmentConnections_1.default, { ...props });
-    }
-    else if (type === 'VariantTrack') {
-        return model.hasTranslocations(trackId) ? ((0, jsx_runtime_1.jsx)(Translocations_1.default, { ...props })) : model.hasPairedFeatures(trackId) ? ((0, jsx_runtime_1.jsx)(PairedFeatures_1.default, { ...props })) : ((0, jsx_runtime_1.jsx)(Breakends_1.default, { ...props }));
-    }
-    else {
-        return null;
-    }
-});
-exports.default = Overlay;

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

@@ -1,8 +0,0 @@
-import type { BreakpointViewModel } from '../model';
-declare const PairedFeatures: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
-    model: BreakpointViewModel;
-    trackId: string;
-    parentRef: React.RefObject<SVGSVGElement | null>;
-    getTrackYPosOverride?: (trackId: string, level: number) => number;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default PairedFeatures;