@jbrowse/plugin-linear-genome-view 2.3.4 → 2.4.1

package/esm/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -0,0 +1,45 @@
+import React from 'react';
+import { getTickDisplayStr } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
+// locals
+import { makeTicks } from '../util';
+import SVGRegionSeparators from './SVGRegionSeparators';
+function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = true, hideText = false, }) {
+    const ticks = makeTicks(start, end, bpPerPx, major, minor);
+    const theme = useTheme();
+    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.base, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: theme.palette.text.secondary }));
+        }),
+        !hideText
+            ? ticks
+                .filter(tick => tick.type === 'major')
+                .map(tick => {
+                const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
+                return (React.createElement("text", { x: x - 3, y: 7 + 11, key: `label-${tick.base}`, fontSize: 11, fill: theme.palette.text.primary }, getTickDisplayStr(tick.base + 1, bpPerPx)));
+            })
+            : null));
+}
+export default function SVGRuler({ model, fontSize, }) {
+    const { dynamicBlocks: { contentBlocks }, offsetPx: viewOffsetPx, bpPerPx, } = model;
+    const renderRuler = contentBlocks.length < 5;
+    const theme = useTheme();
+    return (React.createElement(React.Fragment, null,
+        React.createElement(SVGRegionSeparators, { model: model, height: 30 }),
+        contentBlocks.map(block => {
+            const { start, end, key, reversed, offsetPx, refName, widthPx } = block;
+            const offset = offsetPx - viewOffsetPx;
+            const clipid = `clip-${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: theme.palette.text.primary }, refName),
+                        React.createElement("g", { transform: "translate(0 20)" },
+                            React.createElement(Ruler, { hideText: !renderRuler, start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }))))));
+        })));
+}
+//# sourceMappingURL=SVGRuler.js.map

package/esm/LinearGenomeView/svgcomponents/SVGRuler.js.map

@@ -0,0 +1 @@
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package/esm/LinearGenomeView/svgcomponents/SVGScalebar.d.ts

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGScalebar({ model, fontSize, }: {
+    model: LGV;
+    fontSize: number;
+}): JSX.Element;
+export {};

package/esm/LinearGenomeView/svgcomponents/SVGScalebar.js

@@ -0,0 +1,16 @@
+import React from 'react';
+import { getBpDisplayStr } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
+export default function SVGScalebar({ model, fontSize, }) {
+    const { offsetPx, dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp }, } = model;
+    const theme = useTheme();
+    const displayBp = getBpDisplayStr(totalBp);
+    const x0 = Math.max(-offsetPx, 0);
+    const x1 = x0 + totalWidthPx;
+    return (React.createElement(React.Fragment, null,
+        React.createElement("line", { x1: x0, x2: x1, y1: 10, y2: 10, stroke: theme.palette.text.secondary }),
+        React.createElement("line", { x1: x0, x2: x0, y1: 5, y2: 15, stroke: theme.palette.text.secondary }),
+        React.createElement("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: theme.palette.text.secondary }),
+        React.createElement("text", { x: x0 + (x1 - x0) / 2, y: fontSize * 2, textAnchor: "middle", fontSize: fontSize, fill: theme.palette.text.primary }, displayBp)));
+}
+//# sourceMappingURL=SVGScalebar.js.map

package/esm/LinearGenomeView/svgcomponents/SVGScalebar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGScalebar.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGScalebar.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAKxC,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAClC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EAAE,EAAE,0BAA0B,EAAE,YAAY,EAAE,OAAO,EAAE,GACrE,GAAG,KAAK,CAAA;IACT,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,SAAS,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;IAC1C,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAA;IACjC,MAAM,EAAE,GAAG,EAAE,GAAG,YAAY,CAAA;IAC5B,OAAO,CACL;QACE,8BACE,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,8BACE,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,EAAE,EACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,8BACE,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,EAAE,EACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,8BACE,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,GAAG,CAAC,EACrB,CAAC,EAAE,QAAQ,GAAG,CAAC,EACf,UAAU,EAAC,QAAQ,EACnB,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,SAAS,CACL,CACN,CACJ,CAAA;AACH,CAAC"}

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

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }: {
+    trackName: string;
+    trackLabels: string;
+    fontSize: number;
+    trackLabelOffset: number;
+    x: number;
+}): JSX.Element | null;

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -0,0 +1,10 @@
+import React from 'react';
+import { useTheme } from '@mui/material';
+export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
+    const theme = useTheme();
+    const fill = theme.palette.text.primary;
+    const xoff = trackLabels === 'overlay' ? 5 : 0;
+    const yoff = trackLabels === 'offset' ? 5 : 0;
+    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" }, trackName)) : (React.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, trackName)))) : null;
+}
+//# sourceMappingURL=SVGTrackLabel.js.map

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGTrackLabel.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGTrackLabel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,WAAW,EACX,SAAS,EACT,QAAQ,EACR,gBAAgB,EAChB,CAAC,GAOF;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAA;IACvC,MAAM,IAAI,GAAG,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,WAAW,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7C,OAAO,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CAC9B,+BACG,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CACxB,8BACE,CAAC,EAAE,gBAAgB,GAAG,EAAE,EACxB,CAAC,EAAE,EAAE,EACL,IAAI,EAAE,IAAI,EACV,QAAQ,EAAE,QAAQ,EAClB,gBAAgB,EAAC,SAAS,EAC1B,UAAU,EAAC,KAAK,IAEf,SAAS,CACL,CACR,CAAC,CAAC,CAAC,CACF,8BACE,CAAC,EAAE,CAAC,GAAG,IAAI,EACX,CAAC,EAAE,IAAI,EACP,IAAI,EAAE,IAAI,EACV,QAAQ,EAAE,QAAQ,EAClB,gBAAgB,EAAC,SAAS,IAEzB,SAAS,CACL,CACR,CACC,CACL,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC"}

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

@@ -0,0 +1,23 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+interface DisplayResult {
+    track: {
+        configuration: AnyConfigurationModel;
+        displays: {
+            height: number;
+        }[];
+    };
+    result: string;
+}
+export default function SVGTracks({ displayResults, model, offset, textHeight, fontSize, trackLabels, trackLabelOffset, }: {
+    displayResults: DisplayResult[];
+    model: LGV;
+    offset: number;
+    textHeight: number;
+    fontSize: number;
+    trackLabels?: string;
+    trackLabelOffset?: number;
+}): JSX.Element;
+export {};

package/esm/LinearGenomeView/svgcomponents/SVGTracks.js

@@ -0,0 +1,24 @@
+import React from 'react';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import { getSession } from '@jbrowse/core/util';
+import SVGRegionSeparators from './SVGRegionSeparators';
+import SVGTrackLabel from './SVGTrackLabel';
+// SVG component, tracks
+export default function SVGTracks({ displayResults, model, offset, textHeight, fontSize, trackLabels = 'offset', trackLabelOffset = 0, }) {
+    const session = getSession(model);
+    const textOffset = trackLabels === 'offset' ? textHeight : 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 })));
+    })));
+}
+//# sourceMappingURL=SVGTracks.js.map

package/esm/LinearGenomeView/svgcomponents/SVGTracks.js.map

@@ -0,0 +1 @@
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package/esm/LinearGenomeView/util.js

@@ -6,7 +6,7 @@
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;
@@ -47,7 +47,7 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
     const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
     let index = 0;
     const ticks = [];
-    for (let base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
+    for (let base = Math.floor(minBase / iterPitch) * iterPitch; base < Math.ceil(maxBase / iterPitch) * iterPitch + 1; base += iterPitch) {
         if (emitMinor && base % (gridPitch.majorPitch * 2)) {
             ticks.push({ type: 'minor', base: base - 1, index });
             index += 1;

package/esm/LinearGenomeView/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearGenomeView/util.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAC7B,KAAa,EACb,eAAuB,EACvB,eAAuB;IAEvB,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IACvB,MAAM,eAAe,GAAG,eAAe,GAAG,KAAK,CAAA;IAC/C,MAAM,cAAc,GAAG,MAAM,CAAC,QAAQ,CACpC,MAAM,CAAC,eAAe,CAAC,CAAC,aAAa,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EACtD,EAAE,CACH,CAAA;IAED,IAAI,UAAU,GAAG,EAAE,IAAI,cAAc,CAAA;IACrC,OAAO,UAAU,GAAG,eAAe,EAAE;QACnC,UAAU,IAAI,CAAC,CAAA;QACf,IAAI,UAAU,IAAI,eAAe,EAAE;YACjC,MAAK;SACN;QACD,UAAU,IAAI,GAAG,CAAA;KAClB;IAED,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;IAEpC,MAAM,YAAY,GAAG,UAAU,GAAG,KAAK,CAAA;IAEvC,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,IAAI,CAAC,CAAC,UAAU,GAAG,EAAE,CAAC,IAAI,YAAY,GAAG,EAAE,IAAI,eAAe,EAAE;QAC9D,UAAU,GAAG,UAAU,GAAG,EAAE,CAAA;KAC7B;SAAM,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,eAAe,EAAE;QACnE,UAAU,GAAG,UAAU,GAAG,CAAC,CAAA;KAC5B;SAAM,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,eAAe,EAAE;QACnE,UAAU,GAAG,UAAU,GAAG,CAAC,CAAA;KAC5B;IAED,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AACnC,CAAC;AAED,MAAM,UAAU,SAAS,CACvB,KAAa,EACb,GAAW,EACX,OAAe,EACf,SAAS,GAAG,IAAI,EAChB,SAAS,GAAG,IAAI;IAEhB,MAAM,SAAS,GAAG,eAAe,CAAC,OAAO,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;IAElD,IAAI,OAAO,GAAG,KAAK,CAAA;IACnB,IAAI,OAAO,GAAG,GAAG,CAAA;IACjB,IAAI,OAAO,KAAK,IAAI,IAAI,OAAO,KAAK,IAAI,EAAE;QACxC,OAAO,EAAE,CAAA;KACV;IAED,IAAI,OAAO,GAAG,CAAC,EAAE;QACf,CAAC;QAAA,CAAC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;KACzC;IAED,yEAAyE;IACzE,iDAAiD;IACjD,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;IACrC,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;IAErC,MAAM,SAAS,GAAG,SAAS,CAAC,UAAU,IAAI,SAAS,CAAC,UAAU,CAAA;IAC9D,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KACE,IAAI,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,EACtD,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,GAAG,CAAC,EACrD,IAAI,IAAI,SAAS,EACjB;QACA,IAAI,SAAS,IAAI,IAAI,GAAG,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,CAAC,EAAE;YAClD,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;YACpD,KAAK,IAAI,CAAC,CAAA;SACX;aAAM,IAAI,SAAS,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,EAAE;YAC5D,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;YACpD,KAAK,IAAI,CAAC,CAAA;SACX;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/index.d.ts

@@ -1,10 +1,6 @@
 /// <reference types="react" />
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { BaseLinearDisplay, BaseLinearDisplayComponent, BlockModel, BlockMsg, baseLinearDisplayConfigSchema } from './BaseLinearDisplay';
-import { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
-import { renderToSvg, LinearGenomeViewModel, LinearGenomeViewStateModel, RefNameAutocomplete, SearchBox } from './LinearGenomeView';
-import { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory } from './LinearBasicDisplay';
 export default class LinearGenomeViewPlugin extends Plugin {
     name: string;
     exports: {
@@ -13,7 +9,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 id: string;
                 type: string;
                 rpcDriverName: string | undefined;
-                height: number;
+                heightPreConfig: number | undefined;
                 blockState: import("mobx-state-tree").IMSTMap<import("mobx-state-tree").IModelType<{
                     key: import("mobx-state-tree").ISimpleType<string>;
                     region: import("mobx-state-tree").IModelType<{
@@ -168,6 +164,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
                 estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
             } & {
+                readonly height: number;
                 readonly blockType: "dynamicBlocks" | "staticBlocks";
                 readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
             } & {
@@ -230,13 +227,14 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
                     overrideHeight: number;
+                    theme: import("@mui/material").ThemeOptions;
                 }): Promise<JSX.Element>;
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 type: import("mobx-state-tree").ISimpleType<string>;
                 rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
             } & {
-                height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+                heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
                 blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
                     key: import("mobx-state-tree").ISimpleType<string>;
                     region: import("mobx-state-tree").IModelType<{
@@ -346,6 +344,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
                 estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
             } & {
+                readonly height: number;
                 readonly blockType: "dynamicBlocks" | "staticBlocks";
                 readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
             } & {
@@ -408,12 +407,67 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
                     overrideHeight: number;
+                    theme: import("@mui/material").ThemeOptions;
                 }): Promise<JSX.Element>;
-            }, import("mobx-state-tree")._NotCustomized, {
+            }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                type: import("mobx-state-tree").ISimpleType<string>;
+                rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            } & {
+                heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+                blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+                    key: import("mobx-state-tree").ISimpleType<string>;
+                    region: import("mobx-state-tree").IModelType<{
+                        refName: import("mobx-state-tree").ISimpleType<string>;
+                        start: import("mobx-state-tree").ISimpleType<number>;
+                        end: import("mobx-state-tree").ISimpleType<number>;
+                        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                    } & {
+                        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                    }, {
+                        setRefName(newRefName: string): void;
+                    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+                    reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+                    isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                    isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                }, {
+                    renderInProgress: AbortController | undefined;
+                    filled: boolean;
+                    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                    features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                    layout: any;
+                    status: string;
+                    error: unknown;
+                    message: string | undefined;
+                    maxHeightReached: boolean;
+                    ReactComponent: ({ model, }: {
+                        model: any;
+                    }) => any;
+                    renderProps: any;
+                } & {
+                    doReload(): void;
+                    afterAttach(): void;
+                    setStatus(message: string): void;
+                    setLoading(abortController: AbortController): void;
+                    setMessage(messageText: string): void;
+                    setRendered(props: {
+                        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+                        features: Map<string, import("@jbrowse/core/util").Feature>;
+                        layout: any;
+                        maxHeightReached: boolean;
+                        renderProps: any;
+                    } | undefined): void;
+                    setError(error: unknown): void;
+                    reload(): void;
+                    beforeDestroy(): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+                userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            }>>, {
                 type: string;
-                height: number;
                 id: string;
                 rpcDriverName: string | undefined;
+                heightPreConfig: number | undefined;
                 userBpPerPxLimit: number | undefined;
                 userByteSizeLimit: number | undefined;
             }>>;
@@ -424,7 +478,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         } & {
-            height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+            heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
             blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
                 key: import("mobx-state-tree").ISimpleType<string>;
                 region: import("mobx-state-tree").IModelType<{
@@ -534,6 +588,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
             estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
         } & {
+            readonly height: number;
             readonly blockType: "dynamicBlocks" | "staticBlocks";
             readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
         } & {
@@ -596,12 +651,67 @@ export default class LinearGenomeViewPlugin extends Plugin {
         } & {
             renderSvg(opts: import("./LinearGenomeView").ExportSvgOptions & {
                 overrideHeight: number;
+                theme: import("@mui/material").ThemeOptions;
             }): Promise<JSX.Element>;
-        }, import("mobx-state-tree")._NotCustomized, {
+        }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        } & {
+            heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+                key: import("mobx-state-tree").ISimpleType<string>;
+                region: import("mobx-state-tree").IModelType<{
+                    refName: import("mobx-state-tree").ISimpleType<string>;
+                    start: import("mobx-state-tree").ISimpleType<number>;
+                    end: import("mobx-state-tree").ISimpleType<number>;
+                    reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                } & {
+                    assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                }, {
+                    setRefName(newRefName: string): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+                reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+                isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            }, {
+                renderInProgress: AbortController | undefined;
+                filled: boolean;
+                reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                layout: any;
+                status: string;
+                error: unknown;
+                message: string | undefined;
+                maxHeightReached: boolean;
+                ReactComponent: ({ model, }: {
+                    model: any;
+                }) => any;
+                renderProps: any;
+            } & {
+                doReload(): void;
+                afterAttach(): void;
+                setStatus(message: string): void;
+                setLoading(abortController: AbortController): void;
+                setMessage(messageText: string): void;
+                setRendered(props: {
+                    reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+                    features: Map<string, import("@jbrowse/core/util").Feature>;
+                    layout: any;
+                    maxHeightReached: boolean;
+                    renderProps: any;
+                } | undefined): void;
+                setError(error: unknown): void;
+                reload(): void;
+                beforeDestroy(): void;
+            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+            userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+        }>>, {
             type: string;
-            height: number;
             id: string;
             rpcDriverName: string | undefined;
+            heightPreConfig: number | undefined;
             userBpPerPxLimit: number | undefined;
             userByteSizeLimit: number | undefined;
         }>;
@@ -682,9 +792,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
-                readonly trackHeights: any;
-                readonly trackHeightsWithResizeHandles: any;
-                readonly height: any;
+                readonly trackHeights: number;
+                readonly trackHeightsWithResizeHandles: number;
+                readonly height: number;
                 readonly totalBp: number;
                 readonly maxBpPerPx: number;
                 readonly minBpPerPx: number;
@@ -711,7 +821,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 toggleNoTracksActive(): void;
                 toggleShowGridlines(): void;
                 scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number): number;
+                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
                 setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
                 setGetSequenceDialogOpen(open: boolean): void;
@@ -723,7 +833,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -874,9 +984,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
-                readonly trackHeights: any;
-                readonly trackHeightsWithResizeHandles: any;
-                readonly height: any;
+                readonly trackHeights: number;
+                readonly trackHeightsWithResizeHandles: number;
+                readonly height: number;
                 readonly totalBp: number;
                 readonly maxBpPerPx: number;
                 readonly minBpPerPx: number;
@@ -903,7 +1013,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 toggleNoTracksActive(): void;
                 toggleShowGridlines(): void;
                 scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number): number;
+                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
                 setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
                 setGetSequenceDialogOpen(open: boolean): void;
@@ -915,7 +1025,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1076,9 +1186,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
-                readonly trackHeights: any;
-                readonly trackHeightsWithResizeHandles: any;
-                readonly height: any;
+                readonly trackHeights: number;
+                readonly trackHeightsWithResizeHandles: number;
+                readonly height: number;
                 readonly totalBp: number;
                 readonly maxBpPerPx: number;
                 readonly minBpPerPx: number;
@@ -1105,7 +1215,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 toggleNoTracksActive(): void;
                 toggleShowGridlines(): void;
                 scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number): number;
+                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
                 setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
                 setGetSequenceDialogOpen(open: boolean): void;
@@ -1117,7 +1227,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1268,9 +1378,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
-                readonly trackHeights: any;
-                readonly trackHeightsWithResizeHandles: any;
-                readonly height: any;
+                readonly trackHeights: number;
+                readonly trackHeightsWithResizeHandles: number;
+                readonly height: number;
                 readonly totalBp: number;
                 readonly maxBpPerPx: number;
                 readonly minBpPerPx: number;
@@ -1297,7 +1407,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 toggleNoTracksActive(): void;
                 toggleShowGridlines(): void;
                 scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number): number;
+                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
                 setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
                 setGetSequenceDialogOpen(open: boolean): void;
@@ -1309,7 +1419,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1470,9 +1580,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
-                readonly trackHeights: any;
-                readonly trackHeightsWithResizeHandles: any;
-                readonly height: any;
+                readonly trackHeights: number;
+                readonly trackHeightsWithResizeHandles: number;
+                readonly height: number;
                 readonly totalBp: number;
                 readonly maxBpPerPx: number;
                 readonly minBpPerPx: number;
@@ -1499,7 +1609,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 toggleNoTracksActive(): void;
                 toggleShowGridlines(): void;
                 scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number): number;
+                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
                 setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
                 setGetSequenceDialogOpen(open: boolean): void;
@@ -1511,7 +1621,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1662,9 +1772,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 readonly isSearchDialogDisplayed: boolean;
                 readonly scaleBarHeight: number;
                 readonly headerHeight: number;
-                readonly trackHeights: any;
-                readonly trackHeightsWithResizeHandles: any;
-                readonly height: any;
+                readonly trackHeights: number;
+                readonly trackHeightsWithResizeHandles: number;
+                readonly height: number;
                 readonly totalBp: number;
                 readonly maxBpPerPx: number;
                 readonly minBpPerPx: number;
@@ -1691,7 +1801,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 toggleNoTracksActive(): void;
                 toggleShowGridlines(): void;
                 scrollTo(offsetPx: number): number;
-                zoomTo(bpPerPx: number): number;
+                zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
                 setSearchResults(results?: import("@jbrowse/core/TextSearch/BaseResults").default[] | undefined, query?: string | undefined): void;
                 setGetSequenceDialogOpen(open: boolean): void;
@@ -1703,7 +1813,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): void;
-                setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+                setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
@@ -1793,6 +1903,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
 }
-export { baseLinearDisplayConfigSchema, linearBareDisplayConfigSchemaFactory, linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, renderToSvg, BaseLinearDisplayComponent, BaseLinearDisplay, RefNameAutocomplete, SearchBox, BlockMsg, };
-export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel };
-export type { BaseLinearDisplayModel } from './BaseLinearDisplay';
+export type { BaseLinearDisplayModel, BlockModel } from './BaseLinearDisplay';
+export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
+export { BlockMsg, baseLinearDisplayConfigSchema, BaseLinearDisplayComponent, BaseLinearDisplay, } from './BaseLinearDisplay';
+export { type LinearGenomeViewModel, RefNameAutocomplete, type LinearGenomeViewStateModel, SearchBox, } from './LinearGenomeView';
+export { renderToSvg, SVGTracks, totalHeight, SVGRuler, } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView';
+export { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory, } from './LinearBasicDisplay';