@jbrowse/plugin-linear-comparative-view 2.6.1

package/esm/LinearSyntenyView/model.js

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+import { lazy } from 'react';
+import { types } from 'mobx-state-tree';
+import { transaction } from 'mobx';
+import { getSession } from '@jbrowse/core/util';
+import { saveAs } from 'file-saver';
+// icons
+import CropFreeIcon from '@mui/icons-material/CropFree';
+import LinkIcon from '@mui/icons-material/Link';
+import VisibilityIcon from '@mui/icons-material/Visibility';
+import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
+import { Curves } from './components/Icons';
+// locals
+import baseModel from '../LinearComparativeView/model';
+// lazies
+const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
+/**
+ * #stateModel LinearSyntenyView
+ * extends the `LinearComparativeView` base model
+ */
+export default function stateModelFactory(pluginManager) {
+    return types
+        .compose(baseModel(pluginManager), types.model('LinearSyntenyView', {
+        /**
+         * #property
+         */
+        type: types.literal('LinearSyntenyView'),
+        /**
+         * #property/
+         */
+        drawCIGAR: true,
+        /**
+         * #property
+         */
+        drawCurves: false,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        toggleCurves() {
+            self.drawCurves = !self.drawCurves;
+        },
+        /**
+         * #action
+         */
+        toggleCIGAR() {
+            self.drawCIGAR = !self.drawCIGAR;
+        },
+        /**
+         * #action
+         */
+        showAllRegions() {
+            transaction(() => {
+                self.views.forEach(view => view.showAllRegionsInAssembly());
+            });
+        },
+    }))
+        .actions(self => ({
+        async exportSvg(opts) {
+            const { renderToSvg } = await import('./svgcomponents/SVGLinearSyntenyView');
+            const html = await renderToSvg(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            saveAs(blob, opts.filename || 'image.svg');
+        },
+    }))
+        .views(self => {
+        const superHeaderMenuItems = self.headerMenuItems;
+        const superMenuItems = self.menuItems;
+        return {
+            /**
+             * #method
+             * includes a subset of view menu options because the full list is a
+             * little overwhelming
+             */
+            headerMenuItems() {
+                return [
+                    ...superHeaderMenuItems(),
+                    {
+                        label: 'Square view',
+                        onClick: self.squareView,
+                        description: 'Makes both views use the same zoom level, adjusting to the average of each',
+                        icon: CropFreeIcon,
+                    },
+                    {
+                        label: 'Show all regions',
+                        onClick: self.showAllRegions,
+                        description: 'Show entire genome assemblies',
+                        icon: VisibilityIcon,
+                    },
+                    {
+                        label: 'Draw CIGAR',
+                        onClick: self.toggleCIGAR,
+                        checked: self.drawCIGAR,
+                        type: 'checkbox',
+                        description: 'Draws per-base CIGAR level alignments',
+                    },
+                    {
+                        label: 'Link views',
+                        type: 'checkbox',
+                        checked: self.linkViews,
+                        onClick: self.toggleLinkViews,
+                        icon: LinkIcon,
+                    },
+                    {
+                        label: 'Use curved lines',
+                        type: 'checkbox',
+                        checked: self.drawCurves,
+                        onClick: self.toggleCurves,
+                        icon: Curves,
+                    },
+                    {
+                        label: 'Export SVG',
+                        icon: PhotoCameraIcon,
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                ExportSvgDialog,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                ];
+            },
+            menuItems() {
+                return [
+                    ...superMenuItems(),
+                    {
+                        label: 'Export SVG',
+                        icon: PhotoCameraIcon,
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                ExportSvgDialog,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                ];
+            },
+        };
+    });
+}
+//# sourceMappingURL=model.js.map

package/esm/LinearSyntenyView/model.js.map

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

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+import React from 'react';
+export default function SVGBackground({ width, height, shift, }: {
+    width: number;
+    height: number;
+    shift: number;
+}): React.JSX.Element;

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -0,0 +1,7 @@
+import React from 'react';
+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: theme.palette.background.default }));
+}
+//# sourceMappingURL=SVGBackground.js.map

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js.map

@@ -0,0 +1 @@
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package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts

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+import { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
+type LSV = LinearSyntenyViewModel;
+export declare function renderToSvg(model: LSV, opts: ExportSvgOptions): Promise<string>;
+export {};

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

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+import React from 'react';
+import { ThemeProvider } from '@mui/material';
+import { renderToStaticMarkup } from 'react-dom/server';
+import { when } from 'mobx';
+import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, sum, } from '@jbrowse/core/util';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { SVGTracks, SVGRuler, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
+// locals
+import SVGBackground from './SVGBackground';
+import { drawRef } from '../../LinearSyntenyDisplay/drawSynteny';
+// render LGV to SVG
+export async function renderToSvg(model, opts) {
+    var _a;
+    await when(() => model.initialized);
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), themeName = 'default', } = opts;
+    const session = getSession(model);
+    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { width, views, middleComparativeHeight: synH, tracks } = model;
+    const shift = 50;
+    const offset = headerHeight + rulerHeight;
+    const heights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels) + offset);
+    const totalHeightSvg = sum(heights) + synH + 100;
+    const displayResults = await Promise.all(views.map(async (view) => ({
+        view,
+        data: await Promise.all(view.tracks.map(async (track) => {
+            const d = track.displays[0];
+            await when(() => (d.ready !== undefined ? d.ready : true));
+            return { track, result: await d.renderSvg({ ...opts, theme }) };
+        })),
+    })));
+    const renderings = await Promise.all(tracks.map(async (track) => {
+        const d = track.displays[0];
+        await when(() => (d.ready !== undefined ? d.ready : true));
+        const r = await renderToAbstractCanvas(width, synH, { exportSVG: opts }, ctx => drawRef(d, ctx));
+        if ('imageData' in r) {
+            throw new Error('found a canvas in svg export, probably a bug');
+        }
+        else if ('canvasRecordedData' in r) {
+            return {
+                html: await getSerializedSvg({
+                    ...r,
+                    width,
+                    height: synH,
+                }),
+            };
+        }
+        else {
+            return r;
+        }
+    }));
+    const trackLabelMaxLen = max(views.flatMap(view => view.tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize))), 0) + 40;
+    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
+    const w = width + trackLabelOffset;
+    const t = createJBrowseTheme(theme);
+    // the xlink namespace is used for rendering <image> tag
+    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: createJBrowseTheme(theme) },
+        React.createElement(Wrapper, null,
+            React.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
+                React.createElement(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }),
+                React.createElement("g", { transform: `translate(${shift} ${fontSize})` },
+                    React.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
+                        React.createElement(SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
+                    React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, offset: offset, trackLabelOffset: trackLabelOffset })),
+                React.createElement("defs", null,
+                    React.createElement("clipPath", { id: 'synclip' },
+                        React.createElement("rect", { x: 0, y: 0, width: width, height: synH }))),
+                React.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: `url(#synclip)` }, renderings.map((r, i) => (React.createElement(ReactRendering, { key: i, rendering: r })))),
+                React.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
+                    React.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
+                        React.createElement(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
+                    React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))));
+}
+//# sourceMappingURL=SVGLinearSyntenyView.js.map

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js.map

@@ -0,0 +1 @@
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package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
+    model: any;
+}) => React.JSX.Element;
+export default BreakpointAlignmentsFeatureDetail;

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -0,0 +1,38 @@
+import React, { useState } from 'react';
+import copy from 'copy-to-clipboard';
+import { Paper } from '@mui/material';
+import { observer } from 'mobx-react';
+import { BaseCoreDetails, BaseAttributes, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+function Formatter({ value }) {
+    const [show, setShow] = useState(false);
+    const [copied, setCopied] = useState(false);
+    const display = String(value);
+    if (display.length > 100) {
+        return (React.createElement(React.Fragment, null,
+            React.createElement("button", { type: "button", onClick: () => {
+                    copy(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                } }, copied ? 'Copied to clipboard' : 'Copy'),
+            React.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            React.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
+    }
+    return React.createElement("div", null, display);
+}
+function CustomFeatureDetails(props) {
+    return (React.createElement(BaseAttributes, { ...props, formatter: (value) => React.createElement(Formatter, { value: value }) }));
+}
+const BreakpointAlignmentsFeatureDetail = observer(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ model }) => {
+    const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
+    return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
+        React.createElement(BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
+        React.createElement(BaseCoreDetails, { title: "Feature 2", feature: feature2 }),
+        React.createElement(CustomFeatureDetails, { feature: feature1 }),
+        React.createElement(CustomFeatureDetails, { feature: feature2 })));
+});
+export default BreakpointAlignmentsFeatureDetail;
+//# sourceMappingURL=SyntenyFeatureDetail.js.map

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SyntenyFeatureDetail.js","sourceRoot":"","sources":["../../src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,IAAI,MAAM,mBAAmB,CAAA;AACpC,OAAO,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AACrC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,eAAe,EACf,cAAc,GACf,MAAM,mDAAmD,CAAA;AAG1D,SAAS,SAAS,CAAC,EAAE,KAAK,EAAsB;IAC9C,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,OAAO,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC7B,IAAI,OAAO,CAAC,MAAM,GAAG,GAAG,EAAE;QACxB,OAAO,CACL;YACE,gCACE,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC,OAAO,CAAC,CAAA;oBACb,SAAS,CAAC,IAAI,CAAC,CAAA;oBACf,UAAU,CAAC,GAAG,EAAE;wBACd,SAAS,CAAC,KAAK,CAAC,CAAA;oBAClB,CAAC,EAAE,GAAG,CAAC,CAAA;gBACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,MAAM,CACjC;YACT,gCAAQ,IAAI,EAAC,QAAQ,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IACtD,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAC1B;YACT,iCAAM,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAO,CAC1D,CACJ,CAAA;KACF;IACD,OAAO,iCAAM,OAAO,CAAO,CAAA;AAC7B,CAAC;AAED,SAAS,oBAAoB,CAAC,KAA2C;IACvE,OAAO,CACL,oBAAC,cAAc,OACT,KAAK,EACT,SAAS,EAAE,CAAC,KAAc,EAAE,EAAE,CAAC,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,GAC1D,CACH,CAAA;AACH,CAAC;AAED,MAAM,iCAAiC,GAAG,QAAQ;AAChD,8DAA8D;AAC9D,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC5B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAA;IAC5E,OAAO,CACL,oBAAC,KAAK,mBAAa,uBAAuB;QACxC,oBAAC,eAAe,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,QAAQ,GAAI;QACxD,oBAAC,eAAe,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,QAAQ,GAAI;QACxD,oBAAC,oBAAoB,IAAC,OAAO,EAAE,QAAQ,GAAI;QAC3C,oBAAC,oBAAoB,IAAC,OAAO,EAAE,QAAQ,GAAI,CACrC,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,iCAAiC,CAAA"}

package/esm/SyntenyFeatureDetail/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/SyntenyFeatureDetail/index.js

@@ -0,0 +1,30 @@
+import { lazy } from 'react';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from 'mobx-state-tree';
+const configSchema = ConfigurationSchema('SyntenyFeatureWidget', {});
+const stateModel = types
+    .model('SyntenyFeatureWidget', {
+    id: ElementId,
+    type: types.literal('SyntenyFeatureWidget'),
+    featureData: types.frozen(),
+})
+    .actions(self => ({
+    setFeatureData(data) {
+        self.featureData = data;
+    },
+    clearFeatureData() {
+        self.featureData = undefined;
+    },
+}));
+export default (pluginManager) => {
+    pluginManager.addWidgetType(() => new WidgetType({
+        name: 'SyntenyFeatureWidget',
+        heading: 'Synteny feature details',
+        configSchema,
+        stateModel,
+        ReactComponent: lazy(() => import('./SyntenyFeatureDetail')),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/SyntenyFeatureDetail/index.js.map

@@ -0,0 +1 @@
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package/esm/SyntenyTrack/configSchema.d.ts

@@ -0,0 +1,75 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+export default configSchema;

package/esm/SyntenyTrack/configSchema.js

@@ -0,0 +1,14 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes/models';
+/**
+ * #config SyntenyTrack
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (pluginManager) => ConfigurationSchema('SyntenyTrack', {}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: createBaseTrackConfig(pluginManager),
+});
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/SyntenyTrack/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/SyntenyTrack/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pm: PluginManager) => void;
+export default _default;

package/esm/SyntenyTrack/index.js

@@ -0,0 +1,14 @@
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import configSchemaF from './configSchema';
+export default (pm) => {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
+        return new TrackType({
+            name: 'SyntenyTrack',
+            configSchema,
+            stateModel: createBaseTrackModel(pm, 'SyntenyTrack', configSchema),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/SyntenyTrack/index.js.map

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package/esm/index.d.ts

@@ -0,0 +1,7 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+    configure(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,41 @@
+import Plugin from '@jbrowse/core/Plugin';
+import { isAbstractMenuManager } from '@jbrowse/core/util';
+import CalendarIcon from '@mui/icons-material/CalendarViewDay';
+import LinearComparativeDisplayF from './LinearComparativeDisplay';
+import LinearComparativeViewF from './LinearComparativeView';
+import LinearSyntenyDisplayF from './LinearSyntenyDisplay';
+import LGVSyntenyDisplayF from './LGVSyntenyDisplay';
+import LinearSyntenyViewF from './LinearSyntenyView';
+import LaunchLinearSyntenyViewF from './LaunchLinearSyntenyView';
+import SyntenyTrackF from './SyntenyTrack';
+import SyntenyFeatureWidgetF from './SyntenyFeatureDetail';
+import LinearReadVsRefMenuItem from './LinearReadVsRef';
+export default class extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'LinearComparativeViewPlugin';
+    }
+    install(pluginManager) {
+        LinearComparativeViewF(pluginManager);
+        LinearSyntenyViewF(pluginManager);
+        LinearComparativeDisplayF(pluginManager);
+        LinearSyntenyDisplayF(pluginManager);
+        LGVSyntenyDisplayF(pluginManager);
+        LaunchLinearSyntenyViewF(pluginManager);
+        SyntenyTrackF(pluginManager);
+        SyntenyFeatureWidgetF(pluginManager);
+        LinearReadVsRefMenuItem(pluginManager);
+    }
+    configure(pluginManager) {
+        if (isAbstractMenuManager(pluginManager.rootModel)) {
+            pluginManager.rootModel.appendToSubMenu(['Add'], {
+                label: 'Linear synteny view',
+                icon: CalendarIcon,
+                onClick: (session) => {
+                    session.addView('LinearSyntenyView', {});
+                },
+            });
+        }
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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package/esm/util.d.ts

@@ -0,0 +1,25 @@
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export type LayoutRecord = [number, number, number, number];
+export interface ReducedLinearGenomeView {
+    bpPerPx: number;
+    offsetPx: number;
+    staticBlocks: Region[];
+    dynamicBlocks: Region[];
+    displayedRegions: Region[];
+    headerHeight: number;
+    scaleBarHeight: number;
+    height: number;
+    features: Feature[];
+    tracks: {
+        scrollTop: number;
+        height: number;
+        configuration: string;
+        skip: number;
+    }[];
+}
+export declare function cheight(chunk: LayoutRecord): number;
+export declare function getTrackPos(view: ReducedLinearGenomeView, trackConfigId: string): number;
+export declare function getPxFromCoordinate(view: ReducedLinearGenomeView, refName: string, coord: number): number;
+export declare function overlayYPos(trackConfigId: string, level: number, views: ReducedLinearGenomeView[], c: LayoutRecord, cond: boolean): number;
+export declare function interstitialYPos(cond: boolean, height: number): number;

package/esm/util.js

@@ -0,0 +1,69 @@
+import { clamp } from '@jbrowse/core/util';
+const [, TOP, , BOTTOM] = [0, 1, 2, 3];
+export function cheight(chunk) {
+    return chunk[BOTTOM] - chunk[TOP];
+}
+function heightFromSpecificLevel(views, trackConfigId, level) {
+    const heightUpUntilThisPoint = views
+        .slice(0, level)
+        .map(v => v.height + 7)
+        .reduce((a, b) => a + b, 0);
+    return (heightUpUntilThisPoint +
+        views[level].headerHeight +
+        views[level].scaleBarHeight +
+        getTrackPos(views[level], trackConfigId) +
+        1);
+}
+export function getTrackPos(view, trackConfigId) {
+    const idx = view.tracks.findIndex(t => t.configuration === trackConfigId);
+    let accum = 0;
+    for (let i = 0; i < idx; i += 1) {
+        accum += view.tracks[i].height + 3; // +1px for trackresizehandle
+    }
+    return accum;
+}
+// Uses bpToPx to get the screen pixel coordinates but ignores some conditions
+// where bpToPx could return undefined
+export function getPxFromCoordinate(view, refName, coord) {
+    return (((bpToPx(view, { refName, coord }) || {}).offsetPx || 0) - view.offsetPx);
+}
+// Retrieves the y-position of a layout record in a track
+// If track not found returns 0
+export function overlayYPos(trackConfigId, level, views, c, cond) {
+    const track = views[level].tracks.find(t => t.configuration === trackConfigId);
+    const ypos = track
+        ? clamp(c[TOP] - (track.scrollTop || 0), 0, track.height) +
+            heightFromSpecificLevel(views, trackConfigId, level) +
+            track.skip
+        : 0;
+    return ypos + (cond ? cheight(c) : 0);
+}
+// Returns the pixel screen position of a refName:coord input, or undefined if
+// the input could not be located. Uses view.displayedRegions as a representation
+// of what is on the screen
+//
+// Note: does not consider that this refName:coord input could multi-match
+function bpToPx(view, { refName, coord }) {
+    let offsetBp = 0;
+    const index = view.displayedRegions.findIndex(r => {
+        if (refName === r.refName && coord >= r.start && coord <= r.end) {
+            offsetBp += coord - r.start;
+            return true;
+        }
+        offsetBp += r.end - r.start;
+        return false;
+    });
+    const foundRegion = view.displayedRegions[index];
+    if (foundRegion) {
+        return {
+            index,
+            offsetPx: Math.round(offsetBp / view.bpPerPx),
+        };
+    }
+    return undefined;
+}
+// Returns either 0 or height depending on condition
+export function interstitialYPos(cond, height) {
+    return cond ? 0 : height;
+}
+//# sourceMappingURL=util.js.map

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