@jbrowse/plugin-dotplot-view 2.17.0 → 2.18.0

package/dist/DotplotView/model.js

@@ -29,22 +29,19 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.Dotplot1DView = void 0;
 exports.default = stateModelFactory;
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const file_saver_1 = require("file-saver");
-const mobx_1 = require("mobx");
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const configuration_1 = require("@jbrowse/core/configuration");
 const BaseViewModel_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/models/BaseViewModel"));
+const Icons_1 = require("@jbrowse/core/ui/Icons");
 const util_1 = require("@jbrowse/core/util");
-const configuration_1 = require("@jbrowse/core/configuration");
+const tracks_1 = require("@jbrowse/core/util/tracks");
 const mst_1 = require("@jbrowse/core/util/types/mst");
-// icons
-const Icons_1 = require("@jbrowse/core/ui/Icons");
 const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
 const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
-// locals
+const file_saver_1 = require("file-saver");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const _1dview_1 = require("./1dview");
 const util_2 = require("./components/util");
-// lazies
 const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
 const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
 function stringLenPx(a) {
@@ -58,84 +55,28 @@ function pxWidthForBlocks(blocks, bpPerPx, hide) {
             .map(b => stringLenPx((0, util_1.getTickDisplayStr)(b.end, bpPerPx))),
     ]);
 }
-/**
- * #stateModel DotplotView
- * #category view
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
 function stateModelFactory(pm) {
     return mobx_state_tree_1.types
         .compose('DotplotView', BaseViewModel_1.default, mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('DotplotView'),
-        /**
-         * #property
-         */
         height: 600,
-        /**
-         * #property
-         */
         borderSize: 20,
-        /**
-         * #property
-         */
         tickSize: 5,
-        /**
-         * #property
-         */
         vtextRotation: 0,
-        /**
-         * #property
-         */
         htextRotation: -90,
-        /**
-         * #property
-         */
         fontSize: 15,
-        /**
-         * #property
-         */
         trackSelectorType: 'hierarchical',
-        /**
-         * #property
-         */
         assemblyNames: mobx_state_tree_1.types.array(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
         drawCigar: true,
-        /**
-         * #property
-         */
         hview: mobx_state_tree_1.types.optional(_1dview_1.DotplotHView, {}),
-        /**
-         * #property
-         */
         vview: mobx_state_tree_1.types.optional(_1dview_1.DotplotVView, {}),
-        /**
-         * #property
-         */
         tracks: mobx_state_tree_1.types.array(pm.pluggableMstType('track', 'stateModel')),
-        /**
-         * #property
-         * this represents tracks specific to this view specifically used
-         * for read vs ref dotplots where this track would not really apply
-         * elsewhere
-         */
         viewTrackConfigs: mobx_state_tree_1.types.array(pm.pluggableConfigSchemaType('track')),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
         volatileError: undefined,
-        // these are 'personal preferences', stored in volatile and
-        // loaded/written to localStorage
         cursorMode: (0, util_1.localStorageGetItem)('dotplot-cursorMode') || 'crosshair',
         showPanButtons: Boolean(JSON.parse((0, util_1.localStorageGetItem)('dotplot-showPanbuttons') || 'true')),
         wheelMode: (0, util_1.localStorageGetItem)('dotplot-wheelMode') || 'zoom',
@@ -143,9 +84,6 @@ function stateModelFactory(pm) {
         borderY: 100,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get width() {
             if (!self.volatileWidth) {
                 throw new Error('width not initialized');
@@ -154,9 +92,6 @@ function stateModelFactory(pm) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get assemblyErrors() {
             const { assemblyManager } = (0, util_1.getSession)(self);
             return self.assemblyNames
@@ -164,27 +99,18 @@ function stateModelFactory(pm) {
                 .filter(f => !!f)
                 .join(', ');
         },
-        /**
-         * #getter
-         */
         get assembliesInitialized() {
             const { assemblyManager } = (0, util_1.getSession)(self);
             return self.assemblyNames.every(n => { var _a, _b; return (_b = (_a = assemblyManager.get(n)) === null || _a === void 0 ? void 0 : _a.initialized) !== null && _b !== void 0 ? _b : true; });
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get initialized() {
             return (self.volatileWidth !== undefined &&
                 self.hview.displayedRegions.length > 0 &&
                 self.vview.displayedRegions.length > 0 &&
                 self.assembliesInitialized);
         },
-        /**
-         * #getter
-         */
         get hticks() {
             const { hview } = self;
             const { dynamicBlocks, staticBlocks, bpPerPx } = hview;
@@ -192,9 +118,6 @@ function stateModelFactory(pm) {
                 ? []
                 : (0, util_2.makeTicks)(staticBlocks.contentBlocks, bpPerPx);
         },
-        /**
-         * #getter
-         */
         get vticks() {
             const { vview } = self;
             const { dynamicBlocks, staticBlocks, bpPerPx } = vview;
@@ -202,33 +125,18 @@ function stateModelFactory(pm) {
                 ? []
                 : (0, util_2.makeTicks)(staticBlocks.contentBlocks, bpPerPx);
         },
-        /**
-         * #getter
-         */
         get loading() {
             return self.assemblyNames.length > 0 && !this.initialized;
         },
-        /**
-         * #getter
-         */
         get viewWidth() {
             return self.width - self.borderX;
         },
-        /**
-         * #getter
-         */
         get viewHeight() {
             return self.height - self.borderY;
         },
-        /**
-         * #getter
-         */
         get views() {
             return [self.hview, self.vview];
         },
-        /**
-         * #method
-         */
         renderProps() {
             const session = (0, util_1.getSession)(self);
             return {
@@ -239,89 +147,49 @@ function stateModelFactory(pm) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setShowPanButtons(flag) {
             self.showPanButtons = flag;
         },
-        /**
-         * #action
-         */
         setWheelMode(str) {
             self.wheelMode = str;
         },
-        /**
-         * #action
-         */
         setCursorMode(str) {
             self.cursorMode = str;
         },
-        /**
-         * #action
-         */
         setDrawCigar(flag) {
             self.drawCigar = flag;
         },
-        /**
-         * #action
-         * returns to the import form
-         */
         clearView() {
             self.hview.setDisplayedRegions([]);
             self.vview.setDisplayedRegions([]);
             self.assemblyNames = (0, mobx_state_tree_1.cast)([]);
             self.tracks.clear();
         },
-        /**
-         * #action
-         */
         setBorderX(n) {
             self.borderX = n;
         },
-        /**
-         * #action
-         */
         setBorderY(n) {
             self.borderY = n;
         },
-        /**
-         * #action
-         */
         setWidth(newWidth) {
             self.volatileWidth = newWidth;
             return self.volatileWidth;
         },
-        /**
-         * #action
-         */
         setHeight(newHeight) {
             self.height = newHeight;
             return self.height;
         },
-        /**
-         * #action
-         */
         setError(e) {
             self.volatileError = e;
         },
-        /**
-         * #action
-         */
         zoomOut() {
             self.hview.zoomOut();
             self.vview.zoomOut();
         },
-        /**
-         * #action
-         */
         zoomIn() {
             self.hview.zoomIn();
             self.vview.zoomIn();
         },
-        /**
-         * #action
-         */
         activateTrackSelector() {
             if (self.trackSelectorType === 'hierarchical') {
                 const session = (0, util_1.getSession)(self);
@@ -333,9 +201,6 @@ function stateModelFactory(pm) {
             }
             throw new Error(`invalid track selector type ${self.trackSelectorType}`);
         },
-        /**
-         * #action
-         */
         showTrack(trackId, initialSnapshot = {}) {
             const schema = pm.pluggableConfigSchemaType('track');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -356,9 +221,6 @@ function stateModelFactory(pm) {
             });
             self.tracks.push(track);
         },
-        /**
-         * #action
-         */
         hideTrack(trackId) {
             const schema = pm.pluggableConfigSchemaType('track');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -368,9 +230,6 @@ function stateModelFactory(pm) {
             });
             return t.length;
         },
-        /**
-         * #action
-         */
         toggleTrack(trackId) {
             const hiddenCount = this.hideTrack(trackId);
             if (!hiddenCount) {
@@ -379,22 +238,13 @@ function stateModelFactory(pm) {
             }
             return false;
         },
-        /**
-         * #action
-         */
         setAssemblyNames(target, query) {
             self.assemblyNames = (0, mobx_state_tree_1.cast)([target, query]);
         },
-        /**
-         * #action
-         */
         setViews(arr) {
             self.hview = (0, mobx_state_tree_1.cast)(arr[0]);
             self.vview = (0, mobx_state_tree_1.cast)(arr[1]);
         },
-        /**
-         * #action
-         */
         getCoords(mousedown, mouseup) {
             const [xmin, xmax] = (0, util_1.minmax)(mouseup[0], mousedown[0]);
             const [ymin, ymax] = (0, util_1.minmax)(mouseup[1], mousedown[1]);
@@ -407,10 +257,6 @@ function stateModelFactory(pm) {
                 ]
                 : undefined;
         },
-        /**
-         * #action
-         * zooms into clicked and dragged region
-         */
         zoomInToMouseCoords(mousedown, mouseup) {
             const result = this.getCoords(mousedown, mouseup);
             if (result) {
@@ -419,19 +265,12 @@ function stateModelFactory(pm) {
                 self.vview.moveTo(y2, y1);
             }
         },
-        /**
-         * #action
-         */
         showAllRegions() {
             self.hview.zoomTo(self.hview.maxBpPerPx);
             self.vview.zoomTo(self.vview.maxBpPerPx);
             self.vview.center();
             self.hview.center();
         },
-        /**
-         * #action
-         * creates a linear synteny view from the clicked and dragged region
-         */
         onDotplotView(mousedown, mouseup) {
             const result = this.getCoords(mousedown, mouseup);
             if (result) {
@@ -453,9 +292,6 @@ function stateModelFactory(pm) {
                 d2.moveTo(y2, y1);
                 d1.zoomTo(d1.bpPerPx / (self.width / self.hview.width), 0);
                 d2.zoomTo(d2.bpPerPx / (self.width / self.vview.width), 0);
-                // add the specific evidence tracks to the LGVs in the split view
-                // note: scales the bpPerPx by scaling proportional of the dotplot
-                // width to the eventual lgv width
                 const tracks = self.tracks
                     .map(track => track.configuration.displays.find((display) => display.type === 'LinearSyntenyDisplay'))
                     .filter(f => !!f)
@@ -494,17 +330,12 @@ function stateModelFactory(pm) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         * creates an svg export and save using FileSaver
-         */
         async exportSvg(opts = {}) {
             const { renderToSvg } = await Promise.resolve().then(() => __importStar(require('./svgcomponents/SVGDotplotView')));
             const html = await renderToSvg(self, opts);
             const blob = new Blob([html], { type: 'image/svg+xml' });
             (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
         },
-        // if any of our assemblies are temporary assemblies
         beforeDestroy() {
             var _a;
             const session = (0, util_1.getSession)(self);
@@ -524,13 +355,10 @@ function stateModelFactory(pm) {
             }));
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 const session = (0, util_1.getSession)(self);
-                // don't operate if width not set yet
                 if (self.volatileWidth === undefined ||
                     !self.assembliesInitialized) {
                     return;
                 }
-                // also don't operate if displayedRegions already set, this is a
-                // helper autorun to load regions from assembly
                 if (self.hview.displayedRegions.length > 0 &&
                     self.vview.displayedRegions.length > 0) {
                     return;
@@ -546,7 +374,6 @@ function stateModelFactory(pm) {
                 });
             }, { delay: 1000 }));
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(function borderSetter() {
-                // make sure we have a width on the view before trying to load
                 if (self.volatileWidth === undefined) {
                     return;
                 }
@@ -560,14 +387,10 @@ function stateModelFactory(pm) {
                 const hhide = (0, util_2.getBlockLabelKeysToHide)(hblocks, viewWidth, hoffset);
                 const by = pxWidthForBlocks(hblocks, vview.bpPerPx, hhide);
                 const bx = pxWidthForBlocks(vblocks, hview.bpPerPx, vhide);
-                // these are set via autorun to avoid dependency cycle
                 self.setBorderY(Math.max(by + padding, 50));
                 self.setBorderX(Math.max(bx + padding, 50));
             }));
         },
-        /**
-         * #action
-         */
         squareView() {
             const { hview, vview } = self;
             const avg = (hview.bpPerPx + vview.bpPerPx) / 2;
@@ -578,9 +401,6 @@ function stateModelFactory(pm) {
             vview.setBpPerPx(avg);
             vview.centerAt(vpx.coord, vpx.refName, vpx.index);
         },
-        /**
-         * #action
-         */
         squareViewProportional() {
             const { hview, vview } = self;
             const ratio = hview.width / vview.width;
@@ -594,9 +414,6 @@ function stateModelFactory(pm) {
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         menuItems() {
             const session = (0, util_1.getSession)(self);
             return [
@@ -649,9 +466,6 @@ function stateModelFactory(pm) {
                     : []),
             ];
         },
-        /**
-         * #getter
-         */
         get error() {
             return self.volatileError || self.assemblyErrors;
         },

package/dist/DotplotView/svgcomponents/SVGBackground.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SVGBackground;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 function SVGBackground({ width, height, }) {
     const theme = (0, material_1.useTheme)();
     return (react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));

package/dist/DotplotView/svgcomponents/SVGDotplotView.d.ts

@@ -1,2 +1,2 @@
-import { DotplotViewModel, ExportSvgOptions } from '../model';
+import type { DotplotViewModel, ExportSvgOptions } from '../model';
 export declare function renderToSvg(model: DotplotViewModel, opts: ExportSvgOptions): Promise<string>;

package/dist/DotplotView/svgcomponents/SVGDotplotView.js

@@ -5,15 +5,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderToSvg = renderToSvg;
 const react_1 = __importDefault(require("react"));
-const mobx_1 = require("mobx");
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
-const ui_1 = require("@jbrowse/core/ui");
+const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
-const Grid_1 = require("../components/Grid");
-const Axes_1 = require("../components/Axes");
 const SVGBackground_1 = __importDefault(require("./SVGBackground"));
-// render LGV to SVG
+const Axes_1 = require("../components/Axes");
+const Grid_1 = require("../components/Grid");
 async function renderToSvg(model, opts) {
     var _a;
     await (0, mobx_1.when)(() => model.initialized);
@@ -29,7 +28,6 @@ async function renderToSvg(model, opts) {
         return { track, result: await display.renderSvg({ ...opts, theme }) };
     }));
     const w = width + shift * 2;
-    // the xlink namespace is used for rendering <image> tag
     return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme) },
         react_1.default.createElement(Wrapper, null,
             react_1.default.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w, height].toString() },
@@ -40,9 +38,7 @@ async function renderToSvg(model, opts) {
                     react_1.default.createElement("defs", null,
                         react_1.default.createElement("clipPath", { id: "clip-ruler" },
                             react_1.default.createElement("rect", { x: 0, y: 0, width: viewWidth, height: viewHeight }))),
-                    react_1.default.createElement("g", { clipPath: "url(#clip-ruler)" }, displayResults.map(({ result }, i) => (
-                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
-                    react_1.default.createElement("g", { key: i }, result))))),
+                    react_1.default.createElement("g", { clipPath: "url(#clip-ruler)" }, displayResults.map(({ result }, i) => (react_1.default.createElement("g", { key: i }, result))))),
                 react_1.default.createElement("g", { transform: `translate(${borderX} ${viewHeight})` },
                     react_1.default.createElement(Axes_1.HorizontalAxisRaw, { model: model }))))), createRootFn);
 }

package/dist/LaunchDotplotView.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LaunchDotplotView(pluginManager: PluginManager): void;

package/dist/LaunchDotplotView.js

@@ -3,9 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LaunchDotplotView;
 const mobx_1 = require("mobx");
 function LaunchDotplotView(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-DotplotView', 
-    // @ts-expect-error
-    async ({ session, views, tracks = [], }) => {
+    pluginManager.addToExtensionPoint('LaunchView-DotplotView', async ({ session, views, tracks = [], }) => {
         try {
             const model = session.addView('DotplotView', {});
             const assemblyNames = views.map(view => view.assembly);
@@ -16,7 +14,6 @@ function LaunchDotplotView(pluginManager) {
                 ]);
                 model.setAssemblyNames(assemblyNames[0], assemblyNames[1]);
             });
-            // http://localhost:3000/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-{"views":[{"type":"DotplotView","views":[{"assembly":"volvox"},{"assembly":"volvox"}],"tracks":["volvox_fake_synteny"]}]}
             const idsNotFound = [];
             tracks.forEach(track => {
                 tryTrack(model, track, idsNotFound);

package/dist/ServerSideRenderedBlockContent.d.ts

@@ -1,4 +1,5 @@
-import React, { CSSProperties } from 'react';
+import type { CSSProperties } from 'react';
+import React from 'react';
 declare const ServerSideRenderedDotplotContent: ({ model, style, }: {
     model: {
         error?: unknown;

package/dist/ServerSideRenderedBlockContent.js

@@ -24,10 +24,10 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mui_1 = require("tss-react/mui");
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => {
     const bg = theme.palette.action.disabledBackground;
     return {
@@ -49,7 +49,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
     };
 });
 function LoadingMessage() {
-    // only show the loading message after 300ms to prevent excessive flickering
     const [shown, setShown] = (0, react_1.useState)(false);
     const { classes } = useStyles();
     (0, react_1.useEffect)(() => {

package/dist/ServerSideSyntenyRendering.d.ts

@@ -1,8 +1,4 @@
 import React from 'react';
-/**
- * A block whose content is rendered outside of the main thread and hydrated by
- * this component.
- */
 interface ModelType {
     imageData: string;
     style: Record<string, string>;

package/dist/ServerSideSyntenyRendering.js

@@ -24,8 +24,8 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
 const offscreenCanvasPonyfill_1 = require("@jbrowse/core/util/offscreenCanvasPonyfill");
+const mobx_react_1 = require("mobx-react");
 const ServerSideSyntenyRendering = (0, mobx_react_1.observer)(function ({ model, }) {
     const { imageData, style, renderProps } = model;
     const { width, height, highResolutionScaling = 1 } = renderProps;

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class DotplotPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -5,15 +5,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
-// icons
 const Timeline_1 = __importDefault(require("@mui/icons-material/Timeline"));
-// locals
-const DotplotView_1 = __importDefault(require("./DotplotView"));
+const ComparativeRenderer_1 = __importDefault(require("./ComparativeRenderer"));
 const DotplotDisplay_1 = __importDefault(require("./DotplotDisplay"));
+const DotplotReadVsRef_1 = __importDefault(require("./DotplotReadVsRef"));
 const DotplotRenderer_1 = __importDefault(require("./DotplotRenderer"));
+const DotplotView_1 = __importDefault(require("./DotplotView"));
 const LaunchDotplotView_1 = __importDefault(require("./LaunchDotplotView"));
-const ComparativeRenderer_1 = __importDefault(require("./ComparativeRenderer"));
-const DotplotReadVsRef_1 = __importDefault(require("./DotplotReadVsRef"));
 class DotplotPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -25,7 +23,6 @@ class DotplotPlugin extends Plugin_1.default {
         (0, DotplotRenderer_1.default)(pluginManager);
         (0, LaunchDotplotView_1.default)(pluginManager);
         (0, DotplotReadVsRef_1.default)(pluginManager);
-        // install our comparative rendering rpc callback
         pluginManager.addRpcMethod(() => new ComparativeRenderer_1.default(pluginManager));
     }
     configure(pluginManager) {

package/dist/util.d.ts

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 export interface ReducedFeature {
     refName: string;
     start: number;

package/esm/ComparativeRenderer/index.d.ts

@@ -1,6 +1,6 @@
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import ComparativeRenderer, { RenderArgs as ComparativeRenderArgs, RenderArgsSerialized as ComparativeRenderArgsSerialized, RenderResults, ResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import type { RenderArgs as ComparativeRenderArgs, RenderArgsSerialized as ComparativeRenderArgsSerialized, RenderResults, ResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
+import type ComparativeRenderer from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
 interface RenderArgs extends ComparativeRenderArgs {
     adapterConfig: Record<string, unknown>;
     rendererType: string;
@@ -9,18 +9,13 @@ interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
     adapterConfig: Record<string, unknown>;
     rendererType: string;
 }
-/**
- * call a synteny renderer with the given args
- * param views: a set of views that each contain a set of regions
- * used instead of passing regions directly as in render()
- */
 export default class ComparativeRender extends RpcMethodType {
     name: string;
     renameRegionsIfNeeded(args: RenderArgs, rend: ComparativeRenderer): Promise<ComparativeRenderArgs>;
     getRenderer(rendererType: string): ComparativeRenderer;
     serializeArguments(args: RenderArgs, rpcDriver: string): Promise<ComparativeRenderArgs | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized>;
     execute(args: RenderArgsSerialized & {
-        signal?: RemoteAbortSignal;
+        stopToken?: string;
     }, rpcDriver: string): Promise<RenderResults | import("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType").ResultsSerialized>;
     deserializeReturn(val: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
 }