@jbrowse/plugin-linear-comparative-view 2.13.1 → 2.14.0

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

@@ -27,7 +27,9 @@ function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData,
     return (React.createElement(React.Fragment, null,
         React.createElement(FormControl, null,
             React.createElement(FormLabel, { id: "group-label" }, "(Optional) Select or add a synteny track"),
-            React.createElement(RadioGroup, { row: true, value: choice, onChange: event => setChoice(event.target.value), "aria-labelledby": "group-label" },
+            React.createElement(RadioGroup, { row: true, value: choice, onChange: event => {
+                    setChoice(event.target.value);
+                }, "aria-labelledby": "group-label" },
                 React.createElement(FormControlLabel, { value: "none", control: React.createElement(Radio, null), label: "None" }),
                 React.createElement(FormControlLabel, { value: "tracklist", control: React.createElement(Radio, null), label: "Existing track" }),
                 React.createElement(FormControlLabel, { value: "custom", control: React.createElement(Radio, null), label: "New track" }))),
@@ -64,8 +66,12 @@ const LinearSyntenyViewImportForm = observer(function ({ model, }) {
                     displayedRegions: asm.regions,
                 };
             })));
-            model.views.forEach(view => view.setWidth(model.width));
-            model.views.forEach(view => view.showAllRegions());
+            model.views.forEach(view => {
+                view.setWidth(model.width);
+            });
+            model.views.forEach(view => {
+                view.showAllRegions();
+            });
             if (sessionTrackData) {
                 session.addTrackConf(sessionTrackData);
                 model.toggleTrack(sessionTrackData.trackId);
@@ -89,9 +95,13 @@ const LinearSyntenyViewImportForm = observer(function ({ model, }) {
                     React.createElement("p", { style: { textAlign: 'center' } }, "Select assemblies for linear synteny view"),
                     React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
                         React.createElement(Grid, { item: true },
-                            React.createElement(AssemblySelector, { selected: assembly1, onChange: val => setAssembly1(val), session: session })),
+                            React.createElement(AssemblySelector, { selected: assembly1, onChange: val => {
+                                    setAssembly1(val);
+                                }, session: session })),
                         React.createElement(Grid, { item: true },
-                            React.createElement(AssemblySelector, { selected: assembly2, onChange: val => setAssembly2(val), session: session })),
+                            React.createElement(AssemblySelector, { selected: assembly2, onChange: val => {
+                                    setAssembly2(val);
+                                }, session: session })),
                         React.createElement(Grid, { item: true },
                             React.createElement(FormControl, null,
                                 React.createElement(Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),

package/esm/LinearSyntenyView/model.d.ts

@@ -54,7 +54,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         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>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -70,7 +70,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         minimumBlockWidth: number;
         draggingTrackId: undefined | string;
         volatileError: unknown;
-        afterDisplayedRegionsSetCallbacks: Function[];
+        afterDisplayedRegionsSetCallbacks: (() => void)[];
         scaleFactor: number;
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
@@ -83,7 +83,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly interRegionPaddingWidth: number;
         readonly assemblyNames: string[];
     } & {
-        scaleBarDisplayPrefix(): string;
+        scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
         readonly assemblyErrors: string;
@@ -98,7 +98,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: {};
+        readonly error: unknown;
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -122,9 +122,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
-        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
@@ -139,7 +139,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         moveTrackToTop(id: string): void;
         moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
-        closeView(): void;
         toggleTrack(trackId: string): boolean;
         setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         setShowCenterLine(b: boolean): void;
@@ -159,7 +158,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             variant?: string;
             isLeftEndOfDisplayedRegion?: boolean;
         }[];
-        afterDisplayedRegionsSet(cb: Function): void;
+        afterDisplayedRegionsSet(cb: () => void): void;
         horizontalScroll(distance: number): number;
         center(): void;
         showAllRegions(): void;
@@ -252,7 +251,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         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>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;
@@ -282,7 +281,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setWidth(newWidth: number): void;
     setViews(views: import("mobx-state-tree").SnapshotIn<import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel>[]): void;
     removeView(view: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel): void;
-    closeView(): void;
     setMiddleComparativeHeight(n: number): number;
     activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
     toggleTrack(trackId: string): boolean;

package/esm/LinearSyntenyView/model.js

@@ -51,7 +51,9 @@ export default function stateModelFactory(pluginManager) {
          */
         showAllRegions() {
             transaction(() => {
-                self.views.forEach(view => view.showAllRegionsInAssembly());
+                self.views.forEach(view => {
+                    view.showAllRegionsInAssembly();
+                });
             });
         },
     }))

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -19,7 +19,6 @@ export async function renderToSvg(model, opts) {
     const { width, views, middleComparativeHeight: synH, tracks } = model;
     const shift = 50;
     const offset = headerHeight + rulerHeight;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = getRoot(model);
     const heights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels) + offset);
     const totalHeightSvg = sum(heights) + synH + 100;
@@ -37,11 +36,14 @@ export async function renderToSvg(model, opts) {
     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));
+        const r = await renderToAbstractCanvas(width, synH, { exportSVG: opts }, ctx => {
+            drawRef(d, ctx);
+            return undefined;
+        });
         if ('imageData' in r) {
             throw new Error('found a canvas in svg export, probably a bug');
         }
-        else if ('canvasRecordedData' in r) {
+        if ('canvasRecordedData' in r) {
             return {
                 html: await getSerializedSvg({
                     ...r,
@@ -50,9 +52,7 @@ export async function renderToSvg(model, opts) {
                 }),
             };
         }
-        else {
-            return r;
-        }
+        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;
@@ -71,7 +71,9 @@ export async function renderToSvg(model, opts) {
                 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 + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: 'url(#synclip)' }, renderings.map((r, i) => (
+                /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                React.createElement(ReactRendering, { key: i, rendering: r })))),
                 React.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
                     React.createElement("g", { transform: `translate(${trackLabelOffset})` },
                         React.createElement("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary) }, views[1].assemblyNames.join(', ')),

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -16,7 +16,9 @@ function Formatter({ value }) {
                         setCopied(false);
                     }, 700);
                 } }, copied ? 'Copied to clipboard' : 'Copy'),
-            React.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            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);

package/esm/util.js

@@ -8,10 +8,11 @@ function heightFromSpecificLevel(views, trackConfigId, level) {
         .slice(0, level)
         .map(v => v.height + 7)
         .reduce((a, b) => a + b, 0);
+    const v = views[level];
     return (heightUpUntilThisPoint +
-        views[level].headerHeight +
-        views[level].scaleBarHeight +
-        getTrackPos(views[level], trackConfigId) +
+        v.headerHeight +
+        v.scaleBarHeight +
+        getTrackPos(v, trackConfigId) +
         1);
 }
 export function getTrackPos(view, trackConfigId) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.13.1",
+  "version": "2.14.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/linear-comparative-view",
+    "test": "cd ../..; jest --passWithNoTests plugins/linear-comparative-view",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -61,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }