@jbrowse/plugin-linear-comparative-view 2.7.1 → 2.8.0

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { Feature } from '@jbrowse/core/util';
+export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }: {
+    model: unknown;
+    feature: Feature;
+    handleClose: () => void;
+}): React.JSX.Element;

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -0,0 +1,42 @@
+import React, { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, } from '@mui/material';
+import { navToSynteny } from './util';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    padding: {
+        margin: 10,
+        border: '1px solid #ccc',
+    },
+});
+export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
+    const { classes } = useStyles();
+    const inverted = feature.get('strand') === -1;
+    const [horizontallyFlip, setHorizontallyFlip] = useState(inverted);
+    const [windowSize, setWindowSize] = useState('1000');
+    return (React.createElement(Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
+        React.createElement(DialogContent, null,
+            inverted ? (React.createElement(FormControlLabel, { className: classes.padding, control: React.createElement(Checkbox, { checked: horizontallyFlip, onChange: event => setHorizontallyFlip(event.target.checked) }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null,
+            React.createElement(TextField, { label: "Add window size in bp", value: windowSize, onChange: event => setWindowSize(event.target.value) })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            await navToSynteny({
+                                feature,
+                                windowSize: +windowSize,
+                                horizontallyFlip,
+                                model,
+                            });
+                        }
+                        catch (e) {
+                            getSession(model).notify(`${e}`, 'error');
+                        }
+                    })();
+                    handleClose();
+                } }, "Submit"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
+}

package/esm/LGVSyntenyDisplay/components/util.d.ts

@@ -0,0 +1,8 @@
+import { Feature } from '@jbrowse/core/util';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }: {
+    windowSize: number;
+    horizontallyFlip: boolean;
+    feature: Feature;
+    model: IAnyStateTreeNode;
+}): Promise<void>;

package/esm/LGVSyntenyDisplay/components/util.js

@@ -0,0 +1,107 @@
+import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
+import { MismatchParser } from '@jbrowse/plugin-alignments';
+import { when } from 'mobx';
+const { parseCigar } = MismatchParser;
+function f(n) {
+    return Math.floor(n);
+}
+function findPosInCigar(cigar, startX) {
+    let featX = 0;
+    let mateX = 0;
+    for (let i = 0; i < cigar.length; i++) {
+        const len = +cigar[i];
+        const op = cigar[i + 1];
+        const min = Math.min(len, startX - featX);
+        if (featX >= startX) {
+            break;
+        }
+        else if (op === 'I') {
+            mateX += len;
+        }
+        else if (op === 'D') {
+            featX += min;
+        }
+        else if (op === 'M') {
+            mateX += min;
+            featX += min;
+        }
+    }
+    return [featX, mateX];
+}
+export async function navToSynteny({ feature, windowSize: ws, model, horizontallyFlip, }) {
+    const session = getSession(model);
+    const track = getContainingTrack(model);
+    const view = getContainingView(model);
+    const reg = view.dynamicBlocks.contentBlocks[0];
+    const cigar = feature.get('CIGAR');
+    const strand = feature.get('strand');
+    const regStart = reg.start;
+    const regEnd = reg.end;
+    const featStart = feature.get('start');
+    const featEnd = feature.get('end');
+    const mate = feature.get('mate');
+    const mateStart = mate.start;
+    const mateEnd = mate.end;
+    const mateAsm = mate.assemblyName;
+    const mateRef = mate.refName;
+    const featAsm = reg.assemblyName;
+    const featRef = reg.refName;
+    let rMateStart;
+    let rMateEnd;
+    let rFeatStart;
+    let rFeatEnd;
+    if (cigar) {
+        const p = parseCigar(cigar);
+        const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
+        const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
+        // avoid multiply by 0 with strand undefined
+        const flipper = strand === -1 ? -1 : 1;
+        rFeatStart = featStart + fStartX;
+        rFeatEnd = featStart + fEndX;
+        rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
+        rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
+    }
+    else {
+        rFeatStart = featStart;
+        rFeatEnd = featEnd;
+        rMateStart = mateStart;
+        rMateEnd = mateEnd;
+    }
+    const trackId = track.configuration.trackId;
+    const view2 = session.addView('LinearSyntenyView', {
+        type: 'LinearSyntenyView',
+        views: [
+            {
+                id: `${Math.random()}`,
+                type: 'LinearGenomeView',
+                hideHeader: true,
+            },
+            {
+                id: `${Math.random()}`,
+                type: 'LinearGenomeView',
+                hideHeader: true,
+            },
+        ],
+        tracks: [
+            {
+                configuration: trackId,
+                type: 'SyntenyTrack',
+                displays: [
+                    {
+                        type: 'LinearSyntenyDisplay',
+                        configuration: `${trackId}-LinearSyntenyDisplay`,
+                    },
+                ],
+            },
+        ],
+    });
+    const l1 = `${featRef}:${f(rFeatStart - ws)}-${f(rFeatEnd + ws)}`;
+    const m1 = Math.min(rMateStart, rMateEnd);
+    const m2 = Math.max(rMateStart, rMateEnd);
+    const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
+    await when(() => view2.width !== undefined);
+    await Promise.all([
+        view2.views[0].navToLocString(l1, featAsm),
+        view2.views[1].navToLocString(l2, mateAsm),
+    ]);
+}

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -1,6 +1,5 @@
 /// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
 /**
  * #stateModel LGVSyntenyDisplay
  * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
@@ -35,7 +34,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -53,7 +52,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            features: Map<string, Feature>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -70,7 +69,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number;
+            defaultValue: number; /**
+             * #property
+             */
             description: string;
         };
         height: {
@@ -208,7 +209,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
     featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -218,18 +219,18 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly selectedFeatureId: string | undefined;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
-    readonly featureUnderMouse: Feature | undefined;
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -241,7 +242,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: Feature | undefined;
+    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
@@ -256,9 +257,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
     }): void;
     updateColorTagMap(uniqueTag: string[]): void;
-    setFeatureUnderMouse(feat?: Feature | undefined): void;
-    selectFeature(feature: Feature): void;
-    copyFeatureToClipboard(feature: Feature): void;
+    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -275,7 +276,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly featureUnderMouse: Feature | undefined;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     renderReady(): boolean;
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {

package/esm/LGVSyntenyDisplay/model.js

@@ -1,110 +1,9 @@
+import { lazy } from 'react';
 import { ConfigurationReference, } from '@jbrowse/core/configuration';
-import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
-import { MismatchParser, SharedLinearPileupDisplayMixin, } from '@jbrowse/plugin-alignments';
+import { getSession } from '@jbrowse/core/util';
+import { SharedLinearPileupDisplayMixin } from '@jbrowse/plugin-alignments';
 import { types } from 'mobx-state-tree';
-import { when } from 'mobx';
-const { parseCigar } = MismatchParser;
-function findPosInCigar(cigar, startX) {
-    let featX = 0;
-    let mateX = 0;
-    for (let i = 0; i < cigar.length; i++) {
-        const len = +cigar[i];
-        const op = cigar[i + 1];
-        const min = Math.min(len, startX - featX);
-        if (featX >= startX) {
-            break;
-        }
-        else if (op === 'I') {
-            mateX += len;
-        }
-        else if (op === 'D') {
-            featX += min;
-        }
-        else if (op === 'M') {
-            mateX += min;
-            featX += min;
-        }
-    }
-    return [featX, mateX];
-}
-async function navToSynteny(feature, self) {
-    const session = getSession(self);
-    const track = getContainingTrack(self);
-    const view = getContainingView(self);
-    const reg = view.dynamicBlocks.contentBlocks[0];
-    const cigar = feature.get('CIGAR');
-    const strand = feature.get('strand');
-    const regStart = reg.start;
-    const regEnd = reg.end;
-    const featStart = feature.get('start');
-    const featEnd = feature.get('end');
-    const mate = feature.get('mate');
-    const mateStart = mate.start;
-    const mateEnd = mate.end;
-    const mateAsm = mate.assemblyName;
-    const mateRef = mate.refName;
-    const featAsm = reg.assemblyName;
-    const featRef = reg.refName;
-    let rMateStart;
-    let rMateEnd;
-    let rFeatStart;
-    let rFeatEnd;
-    if (cigar) {
-        const p = parseCigar(cigar);
-        const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
-        const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
-        // avoid multiply by 0 with strand undefined
-        const flipper = strand === -1 ? -1 : 1;
-        rFeatStart = featStart + fStartX;
-        rFeatEnd = featStart + fEndX;
-        rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
-        rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
-    }
-    else {
-        rFeatStart = featStart;
-        rFeatEnd = featEnd;
-        rMateStart = mateStart;
-        rMateEnd = mateEnd;
-    }
-    const trackId = track.configuration.trackId;
-    const view2 = session.addView('LinearSyntenyView', {
-        type: 'LinearSyntenyView',
-        views: [
-            {
-                id: `${Math.random()}`,
-                type: 'LinearGenomeView',
-                hideHeader: true,
-            },
-            {
-                id: `${Math.random()}`,
-                type: 'LinearGenomeView',
-                hideHeader: true,
-            },
-        ],
-        tracks: [
-            {
-                configuration: trackId,
-                type: 'SyntenyTrack',
-                displays: [
-                    {
-                        type: 'LinearSyntenyDisplay',
-                        configuration: `${trackId}-LinearSyntenyDisplay`,
-                    },
-                ],
-            },
-        ],
-    });
-    const f = (n) => Math.floor(n);
-    const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`;
-    const m1 = Math.min(rMateStart, rMateEnd);
-    const m2 = Math.max(rMateStart, rMateEnd);
-    const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`;
-    await when(() => view2.width !== undefined);
-    await Promise.all([
-        view2.views[0].navToLocString(l1, featAsm),
-        view2.views[1].navToLocString(l2, mateAsm),
-    ]);
-}
+const LaunchSyntenyViewDialog = lazy(() => import('./components/LaunchSyntenyViewDialog'));
 /**
  * #stateModel LGVSyntenyDisplay
  * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
@@ -133,7 +32,16 @@ function stateModelFactory(schema) {
                         ? [
                             {
                                 label: 'Open synteny view for this position',
-                                onClick: () => navToSynteny(feature, self),
+                                onClick: () => {
+                                    getSession(self).queueDialog(handleClose => [
+                                        LaunchSyntenyViewDialog,
+                                        {
+                                            model: self,
+                                            handleClose,
+                                            feature,
+                                        },
+                                    ]);
+                                },
                             },
                         ]
                         : []),

package/esm/LinearComparativeView/model.d.ts

@@ -46,9 +46,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         width: number;
@@ -71,6 +71,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
         rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
     } & {
+        readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];

package/esm/LinearSyntenyView/components/{ImportCustomTrack.js → ImportForm/ImportCustomTrack.js}

@@ -1,21 +1,8 @@
 import React, { useState, useEffect } from 'react';
-import path from 'path';
 import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
-function getName(sessionTrackData) {
-    return sessionTrackData
-        ? // @ts-expect-error
-            sessionTrackData.uri ||
-                // @ts-expect-error
-                sessionTrackData.localPath ||
-                // @ts-expect-error
-                sessionTrackData.name
-        : undefined;
-}
-function stripGz(fileName) {
-    return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
-}
+import { extName, getName, stripGz, basename } from './util';
 function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Location, bed2Location, }) {
     if (radioOption === '.paf') {
         return {
@@ -68,7 +55,7 @@ function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Locat
         };
     }
     else {
-        throw new Error('Unknown type');
+        throw new Error(`Unknown to detect type ${radioOption} from filename (select radio button to clarify)`);
     }
 }
 const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
@@ -78,11 +65,11 @@ const OpenTrack = observer(({ assembly1, assembly2, setSessionTrackData, }) => {
     const [value, setValue] = useState('');
     const [error, setError] = useState();
     const fileName = getName(fileLocation);
-    const radioOption = value || (fileName ? path.extname(stripGz(fileName)) : '');
+    const radioOption = value || (fileName ? extName(stripGz(fileName)) : '');
     useEffect(() => {
         try {
             if (fileLocation) {
-                const fn = fileName ? path.basename(fileName) : 'MyTrack';
+                const fn = fileName ? basename(fileName) : 'MyTrack';
                 const trackId = `${fn}-${Date.now()}`;
                 setError(undefined);
                 setSessionTrackData({

package/esm/LinearSyntenyView/components/{ImportSyntenyTrackSelector.d.ts → ImportForm/ImportSyntenyTrackSelector.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearSyntenyViewModel } from '../model';
+import { LinearSyntenyViewModel } from '../../model';
 declare const Selector: ({ model, assembly1, assembly2, setShowTrackId, }: {
     model: LinearSyntenyViewModel;
     assembly1: string;

package/{dist/LinearSyntenyView/components/ImportForm.d.ts → esm/LinearSyntenyView/components/ImportForm/index.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearSyntenyViewModel } from '../model';
+import { LinearSyntenyViewModel } from '../../model';
 declare const LinearSyntenyViewImportForm: ({ model, }: {
     model: LinearSyntenyViewModel;
 }) => React.JSX.Element;

package/esm/LinearSyntenyView/components/ImportForm/util.d.ts

@@ -0,0 +1,10 @@
+export declare function getName(sessionTrackData?: {
+    uri: string;
+} | {
+    localPath: string;
+} | {
+    name: string;
+}): any;
+export declare function stripGz(fileName: string): string;
+export declare function basename(str: string): string | undefined;
+export declare function extName(str: string): string;

package/esm/LinearSyntenyView/components/ImportForm/util.js

@@ -0,0 +1,20 @@
+export function getName(sessionTrackData) {
+    return sessionTrackData
+        ? // @ts-expect-error
+            sessionTrackData.uri ||
+                // @ts-expect-error
+                sessionTrackData.localPath ||
+                // @ts-expect-error
+                sessionTrackData.name
+        : undefined;
+}
+export function stripGz(fileName) {
+    return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
+}
+export function basename(str) {
+    return str.split('#')[0].split('?')[0].split('/').pop();
+}
+export function extName(str) {
+    const r = str.split('.').pop();
+    return r ? `.${r}` : '';
+}

package/esm/LinearSyntenyView/model.d.ts

@@ -57,9 +57,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         width: number;
@@ -82,6 +82,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
         rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
     } & {
+        readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
@@ -271,9 +272,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }>>[]): void;
     removeView(view: {
@@ -307,9 +308,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         hideHeaderOverview: boolean;
         hideNoTracksActive: boolean;
         trackSelectorType: string;
-        trackLabels: string;
         showCenterLine: boolean;
         showCytobandsSetting: boolean;
+        trackLabels: string;
         showGridlines: boolean;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         width: number;
@@ -332,6 +333,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
         rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
     } & {
+        readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
@@ -495,9 +497,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         width: number;
@@ -520,6 +522,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
         rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
     } & {
+        readonly trackLabelsSetting: any;
         readonly width: number;
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];

package/esm/LinearSyntenyView/model.js

@@ -19,7 +19,7 @@ const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
  */
 export default function stateModelFactory(pluginManager) {
     return types
-        .compose(baseModel(pluginManager), types.model('LinearSyntenyView', {
+        .compose('LinearSyntenyView', baseModel(pluginManager), types.model({
         /**
          * #property
          */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.7.1",
+  "version": "2.8.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -62,5 +62,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "2cda1611eebd12517f2a3cfc1b612face27005d4"
+  "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
 }