@jbrowse/plugin-linear-comparative-view 2.10.3 → 2.11.1

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { ThemeProvider } from '@mui/material';
 import { getRoot } from 'mobx-state-tree';
 import { when } from 'mobx';
-import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, renderToStaticMarkup, sum, } from '@jbrowse/core/util';
+import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, renderToStaticMarkup, sum, getFillProps, } 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';
@@ -13,9 +13,9 @@ import { drawRef } from '../../LinearSyntenyDisplay/drawSynteny';
 export async function renderToSvg(model, opts) {
     var _a;
     await when(() => model.initialized);
-    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), themeName = 'default', } = opts;
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
     const session = getSession(model);
-    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const themeVar = (_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;
@@ -28,7 +28,10 @@ export async function renderToSvg(model, opts) {
         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 }) };
+            return {
+                track,
+                result: await d.renderSvg({ ...opts, theme: themeVar }),
+            };
         })),
     })));
     const renderings = await Promise.all(tracks.map(async (track) => {
@@ -54,15 +57,15 @@ export async function renderToSvg(model, opts) {
     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);
+    const theme = createJBrowseTheme(themeVar);
     // the xlink namespace is used for rendering <image> tag
-    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: createJBrowseTheme(theme) },
+    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: 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("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.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,
@@ -71,7 +74,7 @@ export async function renderToSvg(model, opts) {
                 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("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.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 }))))), createRootFn);
 }

package/esm/SyntenyFeatureDetail/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function SyntenyFeatureWidgetF(pluginManager: PluginManager): void;

package/esm/SyntenyFeatureDetail/index.js

@@ -18,7 +18,7 @@ const stateModel = types
         self.featureData = undefined;
     },
 }));
-export default (pluginManager) => {
+export default function SyntenyFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType({
         name: 'SyntenyFeatureWidget',
         heading: 'Synteny feature details',
@@ -26,4 +26,4 @@ export default (pluginManager) => {
         stateModel,
         ReactComponent: lazy(() => import('./SyntenyFeatureDetail')),
     }));
-};
+}

package/esm/index.d.ts

@@ -1,6 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-export default class extends Plugin {
+export default class LinearComparativeViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;

package/esm/index.js

@@ -9,8 +9,8 @@ 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 {
+import LinearReadVsRefMenuItemF from './LinearReadVsRef';
+export default class LinearComparativeViewPlugin extends Plugin {
     constructor() {
         super(...arguments);
         this.name = 'LinearComparativeViewPlugin';
@@ -24,7 +24,7 @@ export default class extends Plugin {
         LaunchLinearSyntenyViewF(pluginManager);
         SyntenyTrackF(pluginManager);
         SyntenyFeatureWidgetF(pluginManager);
-        LinearReadVsRefMenuItem(pluginManager);
+        LinearReadVsRefMenuItemF(pluginManager);
     }
     configure(pluginManager) {
         if (isAbstractMenuManager(pluginManager.rootModel)) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.10.3",
+  "version": "2.11.1",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -61,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }