@jbrowse/plugin-linear-genome-view 2.18.0 → 3.0.0

package/esm/LinearGenomeView/components/VerticalGuide.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { stringify } from '@jbrowse/core/util';
 import { Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -14,10 +14,9 @@ const useStyles = makeStyles()({
 });
 const VerticalGuide = observer(function VerticalGuide({ model, coordX, }) {
     const { classes } = useStyles();
-    return (React.createElement(Tooltip, { open: true, placement: "top", title: stringify(model.pxToBp(coordX)), arrow: true },
-        React.createElement("div", { className: classes.guide, style: {
+    return (_jsx(Tooltip, { open: true, placement: "top", title: stringify(model.pxToBp(coordX)), arrow: true, children: _jsx("div", { className: classes.guide, style: {
                 left: coordX,
                 background: 'red',
-            } })));
+            } }) }));
 });
 export default VerticalGuide;

package/esm/LinearGenomeView/components/useRangeSelect.d.ts

@@ -5,7 +5,7 @@ interface AnchorPosition {
     clientX: number;
     clientY: number;
 }
-export declare function useRangeSelect(ref: React.RefObject<HTMLDivElement>, model: LinearGenomeViewModel, shiftOnly?: boolean): {
+export declare function useRangeSelect(ref: React.RefObject<HTMLDivElement | null>, model: LinearGenomeViewModel, shiftOnly?: boolean): {
     open: boolean;
     guideX: number | undefined;
     mouseDown: (event: React.MouseEvent<HTMLDivElement>) => void;

package/esm/LinearGenomeView/components/useWheelScroll.d.ts

@@ -1,5 +1,5 @@
 import type React from 'react';
-export declare function useWheelScroll(ref: React.RefObject<HTMLDivElement>, model: {
+export declare function useWheelScroll(ref: React.RefObject<HTMLDivElement | null>, model: {
     bpPerPx: number;
     zoomTo: (arg: number, arg2?: number) => void;
     setScaleFactor: (arg: number) => void;

package/esm/LinearGenomeView/components/useWheelScroll.js

@@ -1,7 +1,7 @@
 import { useEffect, useRef } from 'react';
 export function useWheelScroll(ref, model) {
     const delta = useRef(0);
-    const timeout = useRef();
+    const timeout = useRef(null);
     const scheduled = useRef(false);
     useEffect(() => {
         const curr = ref.current;

package/esm/LinearGenomeView/model.d.ts

@@ -1,4 +1,5 @@
 import type React from 'react';
+import type { BpOffset, ExportSvgOptions, HighlightType, NavLocation } from './types';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
@@ -7,44 +8,6 @@ import type { ParsedLocString } from '@jbrowse/core/util';
 import type { BaseBlock, BlockSet } from '@jbrowse/core/util/blockTypes';
 import type { Region } from '@jbrowse/core/util/types';
 import type { Instance } from 'mobx-state-tree';
-export interface BpOffset {
-    refName?: string;
-    index: number;
-    offset: number;
-    start?: number;
-    end?: number;
-    coord?: number;
-    reversed?: boolean;
-    assemblyName?: string;
-    oob?: boolean;
-}
-export interface ExportSvgOptions {
-    rasterizeLayers?: boolean;
-    filename?: string;
-    Wrapper?: React.FC<{
-        children: React.ReactNode;
-    }>;
-    fontSize?: number;
-    rulerHeight?: number;
-    textHeight?: number;
-    paddingHeight?: number;
-    headerHeight?: number;
-    cytobandHeight?: number;
-    trackLabels?: string;
-    themeName?: string;
-}
-export interface HighlightType {
-    start: number;
-    end: number;
-    assemblyName: string;
-    refName: string;
-}
-export interface NavLocation {
-    refName: string;
-    start?: number;
-    end?: number;
-    assemblyName?: string;
-}
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -271,5 +234,4 @@ export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
 export { default as LinearGenomeView, default as ReactComponent, } from './components/LinearGenomeView';
 export { default as RefNameAutocomplete } from './components/RefNameAutocomplete';
 export { default as SearchBox } from './components/SearchBox';
-export { default as ZoomControls } from './components/ZoomControls';
 export { renderToSvg } from './svgcomponents/SVGLinearGenomeView';

package/esm/LinearGenomeView/model.js

@@ -2,7 +2,7 @@ import { lazy } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
-import { assembleLocString, clamp, findLast, getSession, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, localStorageSetItem, measureText, springAnimate, sum, } from '@jbrowse/core/util';
+import { assembleLocString, clamp, findLast, getSession, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetBoolean, localStorageGetItem, localStorageSetItem, measureText, springAnimate, sum, } from '@jbrowse/core/util';
 import { bpToPx, moveTo, pxToBp } from '@jbrowse/core/util/Base1DUtils';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
@@ -22,7 +22,7 @@ import { saveAs } from 'file-saver';
 import { autorun, transaction, when } from 'mobx';
 import { addDisposer, cast, getParent, getRoot, getSnapshot, resolveIdentifier, types, } from 'mobx-state-tree';
 import Header from './components/Header';
-import { generateLocations, parseLocStrings } from './util';
+import { calculateVisibleLocStrings, generateLocations, parseLocStrings, } from './util';
 import { handleSelectedRegion } from '../searchUtils';
 import MiniControls from './components/MiniControls';
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, INTER_REGION_PADDING_WIDTH, RESIZE_HANDLE_HEIGHT, SCALE_BAR_HEIGHT, } from './consts';
@@ -31,19 +31,6 @@ const SequenceSearchDialog = lazy(() => import('./components/SequenceSearchDialo
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
 const GetSequenceDialog = lazy(() => import('./components/GetSequenceDialog'));
 const SearchResultsDialog = lazy(() => import('./components/SearchResultsDialog'));
-function calculateVisibleLocStrings(contentBlocks) {
-    if (!contentBlocks.length) {
-        return '';
-    }
-    const isSingleAssemblyName = contentBlocks.every(b => b.assemblyName === contentBlocks[0].assemblyName);
-    const locs = contentBlocks.map(block => assembleLocString({
-        ...block,
-        start: Math.round(block.start),
-        end: Math.round(block.end),
-        assemblyName: isSingleAssemblyName ? undefined : block.assemblyName,
-    }));
-    return locs.join(' ');
-}
 export function stateModelFactory(pluginManager) {
     return types
         .compose('LinearGenomeView', BaseViewModel, types.model({
@@ -57,13 +44,13 @@ export function stateModelFactory(pluginManager) {
         hideHeaderOverview: false,
         hideNoTracksActive: false,
         trackSelectorType: types.optional(types.enumeration(['hierarchical']), 'hierarchical'),
-        showCenterLine: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false'))),
-        showCytobandsSetting: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true'))),
+        showCenterLine: types.optional(types.boolean, () => localStorageGetBoolean('lgv-showCenterLine', false)),
+        showCytobandsSetting: types.optional(types.boolean, () => localStorageGetBoolean('lgv-showCytobands', true)),
         trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') || ''),
         showGridlines: true,
         highlight: types.optional(types.array(types.frozen()), []),
-        colorByCDS: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-colorByCDS') || 'false'))),
-        showTrackOutlines: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showTrackOutlines') || 'true'))),
+        colorByCDS: types.optional(types.boolean, () => localStorageGetBoolean('lgv-colorByCDS', false)),
+        showTrackOutlines: types.optional(types.boolean, () => localStorageGetBoolean('lgv-showTrackOutlines', true)),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -145,10 +132,12 @@ export function stateModelFactory(pluginManager) {
             if (self.hideHeader) {
                 return 0;
             }
-            if (self.hideHeaderOverview) {
+            else if (self.hideHeaderOverview) {
                 return HEADER_BAR_HEIGHT;
             }
-            return HEADER_BAR_HEIGHT + HEADER_OVERVIEW_HEIGHT;
+            else {
+                return HEADER_BAR_HEIGHT + HEADER_OVERVIEW_HEIGHT;
+            }
         },
         get trackHeights() {
             return sum(self.tracks.map(t => t.displays[0].height));
@@ -965,5 +954,4 @@ export function stateModelFactory(pluginManager) {
 export { default as LinearGenomeView, default as ReactComponent, } from './components/LinearGenomeView';
 export { default as RefNameAutocomplete } from './components/RefNameAutocomplete';
 export { default as SearchBox } from './components/SearchBox';
-export { default as ZoomControls } from './components/ZoomControls';
 export { renderToSvg } from './svgcomponents/SVGLinearGenomeView';

package/esm/LinearGenomeView/svgcomponents/SVGBackground.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 export default function SVGBackground({ width, height, shift, }: {
     width: number;
     height: number;
     shift: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/LinearGenomeView/svgcomponents/SVGBackground.js

@@ -1,7 +1,7 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { stripAlpha } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
 export default function SVGBackground({ width, height, shift, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
+    return (_jsx("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearGenomeViewModel } from '..';
 export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }: {
     model: LinearGenomeViewModel;
     rulerHeight: number;
     fontSize: number;
     cytobandHeight: number;
-}): React.JSX.Element | null;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getSession, stripAlpha } from '@jbrowse/core/util';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { useTheme } from '@mui/material';
@@ -37,15 +37,5 @@ export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight
         coord: last.reversed ? last.start : last.end,
     }) || 0;
     const y = +showCytobands * cytobandHeight;
-    return (React.createElement("g", { id: "header" },
-        React.createElement("text", { x: 0, y: 0, dominantBaseline: "hanging", fontSize: fontSize, fill: c }, assemblyName),
-        showCytobands ? (React.createElement("g", { transform: `translate(0 ${rulerHeight})` },
-            React.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }),
-            React.createElement("rect", { stroke: "red", fill: "rgb(255,0,0)", fillOpacity: 0.1, width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
-            React.createElement("g", { transform: `translate(0,${HEADER_OVERVIEW_HEIGHT})` },
-                React.createElement(OverviewScalebarPolygon, { overview: overview, model: model, useOffset: false })))) : null,
-        React.createElement("g", { transform: `translate(0 ${fontSize + y})` },
-            React.createElement(SVGScalebar, { model: model, fontSize: fontSize })),
-        React.createElement("g", { transform: `translate(0 ${rulerHeight + y})` },
-            React.createElement(SVGRuler, { model: model, fontSize: fontSize }))));
+    return (_jsxs("g", { id: "header", children: [_jsx("text", { x: 0, y: 0, dominantBaseline: "hanging", fontSize: fontSize, fill: c, children: assemblyName }), showCytobands ? (_jsxs("g", { transform: `translate(0 ${rulerHeight})`, children: [_jsx(Cytobands, { overview: overview, assembly: assembly, block: block }), _jsx("rect", { stroke: "red", fill: "rgb(255,0,0)", fillOpacity: 0.1, width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }), _jsx("g", { transform: `translate(0,${HEADER_OVERVIEW_HEIGHT})`, children: _jsx(OverviewScalebarPolygon, { overview: overview, model: model, useOffset: false }) })] })) : null, _jsx("g", { transform: `translate(0 ${fontSize + y})`, children: _jsx(SVGScalebar, { model: model, fontSize: fontSize }) }), _jsx("g", { transform: `translate(0 ${rulerHeight + y})`, children: _jsx(SVGRuler, { model: model, fontSize: fontSize }) })] }));
 }

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.d.ts

@@ -1,4 +1,5 @@
-import type { ExportSvgOptions, LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '..';
+import type { ExportSvgOptions } from '../types';
 type LGV = LinearGenomeViewModel;
 export declare function renderToSvg(model: LGV, opts: ExportSvgOptions): Promise<string>;
 export { default as SVGRuler } from './SVGRuler';

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -1,10 +1,9 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { getSession, max, measureText, renderToStaticMarkup, } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import { ThemeProvider } from '@mui/material';
 import { when } from 'mobx';
-import { getRoot } from 'mobx-state-tree';
 import SVGBackground from './SVGBackground';
 import SVGHeader from './SVGHeader';
 import SVGTracks from './SVGTracks';
@@ -14,7 +13,6 @@ export async function renderToSvg(model, opts) {
     const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => children, } = opts;
     const session = getSession(model);
     const { allThemes } = session;
-    const { createRootFn } = getRoot(model);
     const theme = allThemes === null || allThemes === void 0 ? void 0 : allThemes()[themeName];
     const { width, tracks, showCytobands } = model;
     const shift = 50;
@@ -29,15 +27,7 @@ export async function renderToSvg(model, opts) {
     const trackLabelMaxLen = max(tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize)), 0) + 40;
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
     const w = width + trackLabelOffset;
-    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: createJBrowseTheme(theme) },
-        React.createElement(Wrapper, null,
-            React.createElement("svg", { width: w, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, height].toString() },
-                React.createElement(SVGBackground, { width: w, height: height, shift: shift }),
-                React.createElement("g", { transform: `translate(${shift} 0)` },
-                    React.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        React.createElement(SVGHeader, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight })),
-                    React.createElement("g", { transform: `translate(0 ${offset})` },
-                        React.createElement(SVGTracks, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset })))))), createRootFn);
+    return renderToStaticMarkup(_jsx(ThemeProvider, { theme: createJBrowseTheme(theme), children: _jsx(Wrapper, { children: _jsxs("svg", { width: w, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, height].toString(), children: [_jsx(SVGBackground, { width: w, height: height, shift: shift }), _jsxs("g", { transform: `translate(${shift} 0)`, children: [_jsx("g", { transform: `translate(${trackLabelOffset})`, children: _jsx(SVGHeader, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight }) }), _jsx("g", { transform: `translate(0 ${offset})`, children: _jsx(SVGTracks, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }) })] })] }) }) }));
 }
 export { default as SVGRuler } from './SVGRuler';
 export { default as SVGTracks } from './SVGTracks';

package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 export default function SVGRegionSeparators({ model, height, }: {
     height: number;
     model: LGV;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.js

@@ -1,5 +1,5 @@
-import React from 'react';
+import { jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
 export default function SVGRegionSeparators({ model, height, }) {
     const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
-    return (React.createElement(React.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(block => (React.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, fill: "grey" })))));
+    return (_jsx(_Fragment, { children: dynamicBlocks.contentBlocks.slice(1).map(block => (_jsx("rect", { x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, fill: "grey" }, block.key))) }));
 }

package/esm/LinearGenomeView/svgcomponents/SVGRuler.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 export default function SVGRuler({ model, fontSize, }: {
     model: LGV;
     fontSize: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { getTickDisplayStr, stripAlpha } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
 import { makeTicks } from '../util';
@@ -7,39 +7,27 @@ function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = tr
     const ticks = makeTicks(start, end, bpPerPx, major, minor);
     const theme = useTheme();
     const c = stripAlpha(theme.palette.text.secondary);
-    return (React.createElement(React.Fragment, null,
-        ticks.map(tick => {
-            const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (React.createElement("line", { key: `tick-${tick.base}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }));
-        }),
-        !hideText
-            ? ticks
-                .filter(tick => tick.type === 'major')
-                .map(tick => {
+    return (_jsxs(_Fragment, { children: [ticks.map(tick => {
                 const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-                return (React.createElement("text", { key: `label-${tick.base}`, x: x - 3, y: 7 + 11, fontSize: 11, fill: c }, getTickDisplayStr(tick.base + 1, bpPerPx)));
-            })
-            : null));
+                return (_jsx("line", { x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }, `tick-${tick.base}`));
+            }), !hideText
+                ? ticks
+                    .filter(tick => tick.type === 'major')
+                    .map(tick => {
+                    const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
+                    return (_jsx("text", { x: x - 3, y: 7 + 11, fontSize: 11, fill: c, children: getTickDisplayStr(tick.base + 1, bpPerPx) }, `label-${tick.base}`));
+                })
+                : null] }));
 }
 export default function SVGRuler({ model, fontSize, }) {
     const { dynamicBlocks: { contentBlocks }, offsetPx: viewOffsetPx, bpPerPx, } = model;
     const renderRuler = contentBlocks.length < 5;
     const theme = useTheme();
     const c = stripAlpha(theme.palette.text.primary);
-    return (React.createElement(React.Fragment, null,
-        React.createElement(SVGRegionSeparators, { model: model, height: 30 }),
-        contentBlocks.map(block => {
-            const { start, end, key, reversed, offsetPx, refName, widthPx } = block;
-            const offset = offsetPx - viewOffsetPx;
-            const clipid = `clip-${key}`;
-            return (React.createElement("g", { key: key },
-                React.createElement("defs", null,
-                    React.createElement("clipPath", { id: clipid },
-                        React.createElement("rect", { x: 0, y: 0, width: widthPx, height: 100 }))),
-                React.createElement("g", { transform: `translate(${offset} 0)` },
-                    React.createElement("g", { clipPath: `url(#${clipid})` },
-                        React.createElement("text", { x: 4, y: fontSize, fontSize: fontSize, fill: c }, refName),
-                        React.createElement("g", { transform: "translate(0 20)" },
-                            React.createElement(Ruler, { hideText: !renderRuler, start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }))))));
-        })));
+    return (_jsxs(_Fragment, { children: [_jsx(SVGRegionSeparators, { model: model, height: 30 }), contentBlocks.map(block => {
+                const { start, end, key, reversed, offsetPx, refName, widthPx } = block;
+                const offset = offsetPx - viewOffsetPx;
+                const clipid = `clip-${key}`;
+                return (_jsxs("g", { children: [_jsx("defs", { children: _jsx("clipPath", { id: clipid, children: _jsx("rect", { x: 0, y: 0, width: widthPx, height: 100 }) }) }), _jsx("g", { transform: `translate(${offset} 0)`, children: _jsxs("g", { clipPath: `url(#${clipid})`, children: [_jsx("text", { x: 4, y: fontSize, fontSize: fontSize, fill: c, children: refName }), _jsx("g", { transform: "translate(0 20)", children: _jsx(Ruler, { hideText: !renderRuler, start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }) })] }) })] }, key));
+            })] }));
 }

package/esm/LinearGenomeView/svgcomponents/SVGScalebar.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 export default function SVGScalebar({ model, fontSize, }: {
     model: LGV;
     fontSize: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGScalebar.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { getBpDisplayStr, stripAlpha } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
 export default function SVGScalebar({ model, fontSize, }) {
@@ -10,9 +10,5 @@ export default function SVGScalebar({ model, fontSize, }) {
     const c = stripAlpha(theme.palette.text.secondary);
     const x = x0 + (x1 - x0) / 2;
     const y = fontSize;
-    return (React.createElement(React.Fragment, null,
-        React.createElement("line", { x1: x0, x2: x1, y1: 10, y2: 10, stroke: c }),
-        React.createElement("line", { x1: x0, x2: x0, y1: 5, y2: 15, stroke: c }),
-        React.createElement("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: c }),
-        React.createElement("text", { x: x, y: y, textAnchor: "middle", dominantBaseline: "hanging", fontSize: fontSize, fill: c }, displayBp)));
+    return (_jsxs(_Fragment, { children: [_jsx("line", { x1: x0, x2: x1, y1: 10, y2: 10, stroke: c }), _jsx("line", { x1: x0, x2: x0, y1: 5, y2: 15, stroke: c }), _jsx("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: c }), _jsx("text", { x: x, y: y, textAnchor: "middle", dominantBaseline: "hanging", fontSize: fontSize, fill: c, children: displayBp })] }));
 }

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }: {
     trackName: string;
     trackLabels: string;
     fontSize: number;
     trackLabelOffset: number;
     x: number;
-}): React.JSX.Element | null;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { coarseStripHTML, stripAlpha } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
 export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
@@ -7,5 +7,5 @@ export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackL
     const xoff = trackLabels === 'overlay' ? 5 : 0;
     const yoff = trackLabels === 'offset' ? 5 : 0;
     const name = coarseStripHTML(trackName);
-    return trackLabels !== 'none' ? (React.createElement("g", null, trackLabels === 'left' ? (React.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, name)) : (React.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, name)))) : null;
+    return trackLabels !== 'none' ? (_jsx("g", { children: trackLabels === 'left' ? (_jsx("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end", children: name })) : (_jsx("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", children: name })) })) : null;
 }

package/esm/LinearGenomeView/svgcomponents/SVGTracks.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { LinearGenomeViewModel } from '..';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 type LGV = LinearGenomeViewModel;
@@ -18,5 +17,5 @@ export default function SVGTracks({ displayResults, model, textHeight, fontSize,
     fontSize: number;
     trackLabels?: string;
     trackLabelOffset?: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;
 export {};

package/esm/LinearGenomeView/svgcomponents/SVGTracks.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { getSession } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import SVGRegionSeparators from './SVGRegionSeparators';
@@ -6,18 +6,21 @@ import SVGTrackLabel from './SVGTrackLabel';
 export default function SVGTracks({ displayResults, model, textHeight, fontSize, trackLabels = 'offset', trackLabelOffset = 0, }) {
     const session = getSession(model);
     const textOffset = trackLabels === 'offset' ? textHeight : 0;
-    let offset = 0;
-    return (React.createElement(React.Fragment, null, displayResults.map(({ track, result }) => {
-        const current = offset;
-        const conf = track.configuration;
-        const trackName = getTrackName(conf, session);
-        const display = track.displays[0];
-        const x = Math.max(-model.offsetPx, 0);
-        offset += display.height + textOffset;
-        return (React.createElement("g", { key: conf.trackId, transform: `translate(0 ${current})` },
-            React.createElement("g", { transform: `translate(${trackLabelOffset} ${textOffset})` },
-                React.createElement(SVGRegionSeparators, { model: model, height: display.height }),
-                result),
-            React.createElement(SVGTrackLabel, { trackName: trackName, fontSize: fontSize, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset, x: x })));
-    })));
+    return (_jsx(_Fragment, { children: displayResults.reduce(({ prevOffset, reactElements }, { track, result }) => {
+            const conf = track.configuration;
+            const trackName = getTrackName(conf, session);
+            const display = track.displays[0];
+            const x = Math.max(-model.offsetPx, 0);
+            const currOffset = prevOffset + display.height + textOffset;
+            return {
+                prevOffset: currOffset,
+                reactElements: [
+                    ...reactElements,
+                    _jsxs("g", { transform: `translate(0 ${prevOffset})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset} ${textOffset})`, children: [_jsx(SVGRegionSeparators, { model: model, height: display.height }), result] }), _jsx(SVGTrackLabel, { trackName: trackName, fontSize: fontSize, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset, x: x })] }, conf.trackId),
+                ],
+            };
+        }, {
+            prevOffset: 0,
+            reactElements: [],
+        }).reactElements }));
 }

package/esm/LinearGenomeView/types.d.ts

@@ -0,0 +1,38 @@
+export interface BpOffset {
+    refName?: string;
+    index: number;
+    offset: number;
+    start?: number;
+    end?: number;
+    coord?: number;
+    reversed?: boolean;
+    assemblyName?: string;
+    oob?: boolean;
+}
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    filename?: string;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
+}
+export interface HighlightType {
+    start: number;
+    end: number;
+    assemblyName: string;
+    refName: string;
+}
+export interface NavLocation {
+    refName: string;
+    start?: number;
+    end?: number;
+    assemblyName?: string;
+}

package/esm/LinearGenomeView/types.js

@@ -0,0 +1 @@
+export {};

package/esm/LinearGenomeView/util.d.ts

@@ -1,4 +1,5 @@
 import type { AssemblyManager, ParsedLocString } from '@jbrowse/core/util';
+import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
 export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
     majorPitch: number;
     minorPitch: number;
@@ -12,8 +13,9 @@ export declare function generateLocations(regions: ParsedLocString[], assemblyMa
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;
-    reversed?: boolean | undefined;
     start?: number | undefined;
     refName: string;
+    reversed?: boolean | undefined;
 }[]>;
 export declare function parseLocStrings(input: string, assemblyName: string, isValidRefName: (str: string, assemblyName: string) => boolean): ParsedLocString[];
+export declare function calculateVisibleLocStrings(contentBlocks: BaseBlock[]): string;

package/esm/LinearGenomeView/util.js

@@ -1,4 +1,4 @@
-import { parseLocString } from '@jbrowse/core/util';
+import { assembleLocString, parseLocString } from '@jbrowse/core/util';
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
@@ -100,3 +100,18 @@ export function parseLocStrings(input, assemblyName, isValidRefName) {
         throw e;
     }
 }
+export function calculateVisibleLocStrings(contentBlocks) {
+    if (!contentBlocks.length) {
+        return '';
+    }
+    else {
+        const isSingleAssemblyName = contentBlocks.every(b => b.assemblyName === contentBlocks[0].assemblyName);
+        const locs = contentBlocks.map(block => assembleLocString({
+            ...block,
+            start: Math.round(block.start),
+            end: Math.round(block.end),
+            assemblyName: isSingleAssemblyName ? undefined : block.assemblyName,
+        }));
+        return locs.join(' ');
+    }
+}