@jbrowse/plugin-dotplot-view 2.13.1 → 2.14.0

package/dist/ComparativeRenderer/index.d.ts

@@ -2,11 +2,11 @@ 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';
 interface RenderArgs extends ComparativeRenderArgs {
-    adapterConfig: {};
+    adapterConfig: Record<string, unknown>;
     rendererType: string;
 }
 interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
-    adapterConfig: {};
+    adapterConfig: Record<string, unknown>;
     rendererType: string;
 }
 /**

package/dist/DotplotDisplay/index.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = DotplotDisplayF;
 exports.configSchemaFactory = configSchemaFactory;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));

package/dist/DotplotDisplay/stateModelFactory.d.ts

@@ -43,7 +43,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
@@ -56,9 +56,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #method
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -107,7 +105,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #method
      */
     renderSvg(opts: ExportSvgOptions & {
-        theme: ThemeOptions;
+        theme?: ThemeOptions;
     }): Promise<React.JSX.Element | null>;
 } & {
     afterAttach(): void;

package/dist/DotplotDisplay/stateModelFactory.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = __importDefault(require("react"));
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");

package/dist/DotplotReadVsRef/index.js

@@ -25,7 +25,9 @@ function DotplotReadVsRefMenuItem(pluginManager) {
                                         {
                                             label: 'Dotplot of read vs ref',
                                             icon: Add_1.default,
-                                            onClick: () => (0, DotplotReadVsRef_1.onClick)(feature, self),
+                                            onClick: () => {
+                                                (0, DotplotReadVsRef_1.onClick)(feature, self);
+                                            },
                                         },
                                     ]
                                     : []),

package/dist/DotplotRenderer/ComparativeRenderRpc.d.ts

@@ -2,11 +2,11 @@ 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';
 interface RenderArgs extends ComparativeRenderArgs {
-    adapterConfig: {};
+    adapterConfig: Record<string, unknown>;
     rendererType: string;
 }
 interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
-    adapterConfig: {};
+    adapterConfig: Record<string, unknown>;
     rendererType: string;
 }
 /**

package/dist/DotplotRenderer/DotplotRenderer.d.ts

@@ -3,6 +3,7 @@ import { Region } from '@jbrowse/core/util';
 import ComparativeRenderer, { RenderArgsDeserialized, RenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
 import { Dotplot1DViewModel } from '../DotplotView/model';
 export interface DotplotRenderArgsDeserialized extends RenderArgsDeserialized {
+    adapterConfig: AnyConfigurationModel;
     height: number;
     width: number;
     highResolutionScaling: number;

package/dist/DotplotRenderer/DotplotRenderer.js

@@ -58,7 +58,8 @@ class DotplotRenderer extends ComparativeServerSideRendererType_1.default {
         const thresholds = (0, configuration_1.readConfObject)(config, 'thresholds');
         const palette = (0, configuration_1.readConfObject)(config, 'thresholdsPalette');
         const isCallback = config.color.isCallback;
-        const [hview, vview] = views;
+        const hview = views[0];
+        const vview = views[1];
         const db1 = (_a = hview.dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.offsetPx;
         const db2 = (_b = vview.dynamicBlocks.contentBlocks[0]) === null || _b === void 0 ? void 0 : _b.offsetPx;
         const warnings = [];
@@ -139,12 +140,12 @@ class DotplotRenderer extends ComparativeServerSideRendererType_1.default {
             const refName = feature.get('refName');
             const mate = feature.get('mate');
             const mateRef = mate.refName;
-            let r;
+            let r = 'black';
             if (colorBy === 'identity') {
                 const identity = feature.get('identity');
                 for (let i = 0; i < thresholds.length; i++) {
                     if (identity > +thresholds[i]) {
-                        r = palette[i];
+                        r = palette[i] || 'black';
                         break;
                     }
                 }

package/dist/DotplotView/1dview.js

@@ -77,7 +77,6 @@ exports.Dotplot1DView = Dotplot1DView;
 const DotplotHView = Dotplot1DView.extend(self => ({
     views: {
         get width() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return (0, mobx_state_tree_1.getParent)(self).viewWidth;
         },
     },
@@ -86,7 +85,6 @@ exports.DotplotHView = DotplotHView;
 const DotplotVView = Dotplot1DView.extend(self => ({
     views: {
         get width() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return (0, mobx_state_tree_1.getParent)(self).viewHeight;
         },
     },

package/dist/DotplotView/components/Axes.js

@@ -70,7 +70,7 @@ exports.HorizontalAxisRaw = (0, mobx_react_1.observer)(function ({ model, }) {
         ticks.map(([tick, x]) => x > 0 && x < width ? (react_1.default.createElement("line", { key: `line-${JSON.stringify(tick)}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, ...(0, util_1.getFillProps)(theme.palette.text.primary) })) : null),
         ticks
             .filter(t => t[0].type === 'major')
-            .map(([tick, x]) => x > 10 && x < width ? (react_1.default.createElement("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},${0})`, key: `text-${JSON.stringify(tick)}`, fontSize: 11, dominantBaseline: "middle", textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx))) : null),
+            .map(([tick, x]) => x > 10 && x < width ? (react_1.default.createElement("text", { x: x - 7, y: 0, transform: `rotate(${htextRotation},${x},0)`, key: `text-${JSON.stringify(tick)}`, fontSize: 11, dominantBaseline: "middle", textAnchor: "end", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx))) : null),
         react_1.default.createElement("text", { y: borderY - 12, x: (viewWidth - borderX) / 2, textAnchor: "middle", fontSize: 11, dominantBaseline: "hanging", ...(0, util_1.getFillProps)(theme.palette.text.primary) }, hview.assemblyNames.join(','))));
 });
 exports.VerticalAxis = (0, mobx_react_1.observer)(function ({ model, }) {

package/dist/DotplotView/components/DotplotControls.js

@@ -23,25 +23,35 @@ const DotplotControls = (0, mobx_react_1.observer)(function ({ model, }) {
             react_1.default.createElement(Icons_1.TrackSelector, null)),
         react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
                 {
-                    onClick: () => model.squareView(),
+                    onClick: () => {
+                        model.squareView();
+                    },
                     label: 'Square view - same base pairs per pixel',
                 },
                 {
-                    onClick: () => model.squareViewProportional(),
+                    onClick: () => {
+                        model.squareViewProportional();
+                    },
                     label: 'Rectanglularize view - same total bp',
                 },
                 {
-                    onClick: () => model.showAllRegions(),
+                    onClick: () => {
+                        model.showAllRegions();
+                    },
                     label: 'Show all regions',
                 },
                 {
-                    onClick: () => model.setDrawCigar(!model.drawCigar),
+                    onClick: () => {
+                        model.setDrawCigar(!model.drawCigar);
+                    },
                     type: 'checkbox',
                     label: 'Draw CIGAR',
                     checked: model.drawCigar,
                 },
                 {
-                    onClick: () => model.setShowPanButtons(!model.showPanButtons),
+                    onClick: () => {
+                        model.setShowPanButtons(!model.showPanButtons);
+                    },
                     label: 'Show pan buttons',
                     type: 'checkbox',
                     checked: model.showPanButtons,
@@ -50,14 +60,18 @@ const DotplotControls = (0, mobx_react_1.observer)(function ({ model, }) {
                     label: 'Click and drag mode',
                     subMenu: [
                         {
-                            onClick: () => model.setCursorMode('move'),
+                            onClick: () => {
+                                model.setCursorMode('move');
+                            },
                             label: 'Pan by default, select region when ctrl/cmd key is held',
                             icon: CursorIcon_1.CursorMove,
                             type: 'radio',
                             checked: model.cursorMode === 'move',
                         },
                         {
-                            onClick: () => model.setCursorMode('crosshair'),
+                            onClick: () => {
+                                model.setCursorMode('crosshair');
+                            },
                             label: 'Select region by default, pan when ctrl/cmd key is held',
                             icon: CursorIcon_1.CursorMouse,
                             type: 'radio',
@@ -69,19 +83,25 @@ const DotplotControls = (0, mobx_react_1.observer)(function ({ model, }) {
                     label: 'Wheel scroll mode',
                     subMenu: [
                         {
-                            onClick: () => model.setWheelMode('pan'),
+                            onClick: () => {
+                                model.setWheelMode('pan');
+                            },
                             label: 'Pans view',
                             type: 'radio',
                             checked: model.wheelMode === 'pan',
                         },
                         {
-                            onClick: () => model.setWheelMode('zoom'),
+                            onClick: () => {
+                                model.setWheelMode('zoom');
+                            },
                             label: 'Zooms view',
                             type: 'radio',
                             checked: model.wheelMode === 'zoom',
                         },
                         {
-                            onClick: () => model.setWheelMode('none'),
+                            onClick: () => {
+                                model.setWheelMode('none');
+                            },
                             label: 'Disable',
                             type: 'radio',
                             checked: model.wheelMode === 'none',

package/dist/DotplotView/components/DotplotTooltip.js

@@ -46,7 +46,7 @@ exports.TooltipWhereMouseovered = (0, mobx_react_1.observer)(function ({ model,
         }
         : undefined);
     const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);
-    const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
+    const popperTheme = (_a = theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
     return mouserect ? (react_1.default.createElement(material_1.Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
         react_1.default.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
                 ...floatingStyles,
@@ -70,7 +70,7 @@ exports.TooltipWhereClicked = (0, mobx_react_1.observer)(function ({ model, mous
     });
     const clientPoint = (0, react_2.useClientPoint)(context, { x, y });
     const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);
-    const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
+    const popperTheme = (_a = theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
     return mousedown && Math.abs(xdistance) > 3 && Math.abs(ydistance) > 3 ? (react_1.default.createElement(material_1.Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
         react_1.default.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
                 ...floatingStyles,

package/dist/DotplotView/components/DotplotView.js

@@ -150,7 +150,9 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
         if (ref.current) {
             const curr = ref.current;
             curr.addEventListener('wheel', onWheel);
-            return () => curr.removeEventListener('wheel', onWheel);
+            return () => {
+                curr.removeEventListener('wheel', onWheel);
+            };
         }
         return () => { };
     }, [hview, vview, wheelMode, mousecurr, rootRect.height]);
@@ -163,17 +165,10 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
             }
         }
         window.addEventListener('mousemove', globalMouseMove);
-        return () => window.removeEventListener('mousemove', globalMouseMove);
-    }, [
-        validPan,
-        mousecurrClient,
-        mousedownClient,
-        cursorMode,
-        ctrlKeyWasUsed,
-        mouseupClient,
-        hview,
-        vview,
-    ]);
+        return () => {
+            window.removeEventListener('mousemove', globalMouseMove);
+        };
+    }, [validPan, mousecurrClient, mousedownClient, mouseupClient, hview, vview]);
     (0, react_1.useEffect)(() => {
         function globalCtrlKeyDown(event) {
             if (event.metaKey || event.ctrlKey) {
@@ -209,19 +204,8 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
                 window.removeEventListener('mouseup', globalMouseUp, true);
             };
         }
-        else {
-            return () => { };
-        }
-    }, [
-        validSelect,
-        mousedown,
-        mousecurr,
-        mouseup,
-        xdistance,
-        ydistance,
-        ctrlKeyWasUsed,
-        cursorMode,
-    ]);
+        return () => { };
+    }, [validSelect, mousedown, mouseup, xdistance, ydistance]);
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(Header_1.default, { model: model, selection: !validSelect || !(mousedown && mouserect)
                 ? undefined
@@ -229,7 +213,11 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
                     width: Math.abs(xdistance),
                     height: Math.abs(ydistance),
                 } }),
-        react_1.default.createElement("div", { ref: root, className: classes.root, onMouseLeave: () => setMouseOvered(false), onMouseEnter: () => setMouseOvered(true) },
+        react_1.default.createElement("div", { ref: root, className: classes.root, onMouseLeave: () => {
+                setMouseOvered(false);
+            }, onMouseEnter: () => {
+                setMouseOvered(true);
+            } },
             react_1.default.createElement("div", { className: classes.container },
                 react_1.default.createElement(Axes_1.VerticalAxis, { model: model }),
                 react_1.default.createElement(Axes_1.HorizontalAxis, { model: model }),
@@ -283,7 +271,7 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
                     ] })),
             react_1.default.createElement(ui_1.ResizeHandle, { onDrag: n => model.setHeight(model.height + n), className: classes.resizeHandle }))));
 });
-const DotplotView = (0, mobx_react_1.observer)(({ model }) => {
+const DotplotView = (0, mobx_react_1.observer)(function ({ model }) {
     const { initialized, loading, error } = model;
     if ((!initialized && !loading) || error) {
         return react_1.default.createElement(ImportForm_1.default, { model: model });

package/dist/DotplotView/components/DotplotWarnings.js

@@ -35,8 +35,14 @@ const DotplotWarnings = (0, mobx_react_1.observer)(function ({ model, }) {
     return trackWarnings.length && !hide ? (react_1.default.createElement(material_1.Alert, { severity: "warning" },
         "Warnings during render",
         ' ',
-        react_1.default.createElement(material_1.Button, { onClick: () => setShown(true) }, "More info"),
-        shown ? (react_1.default.createElement(WarningDialog, { trackWarnings: trackWarnings, handleClose: () => setShown(false) })) : null,
-        react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setHide(true) }, "Dismiss"))) : null;
+        react_1.default.createElement(material_1.Button, { onClick: () => {
+                setShown(true);
+            } }, "More info"),
+        shown ? (react_1.default.createElement(WarningDialog, { trackWarnings: trackWarnings, handleClose: () => {
+                setShown(false);
+            } })) : null,
+        react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                setHide(true);
+            } }, "Dismiss"))) : null;
 });
 exports.default = DotplotWarnings;

package/dist/DotplotView/components/ExportSvgDialog.js

@@ -38,7 +38,7 @@ function TextField2({ children, ...rest }) {
         react_1.default.createElement(material_1.TextField, { ...rest }, children)));
 }
 function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)('svg-' + key, val);
+    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
 }
 function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
@@ -51,13 +51,21 @@ function ExportSvgDialog({ model, handleClose, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
-            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => {
+                    setFilename(event.target.value);
+                } }),
+            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => {
+                    setThemeName(event.target.value);
+                } }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
-            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
+                        setRasterizeLayers(val => !val);
+                    } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
                     setLoading(true);
                     setError(undefined);

package/dist/DotplotView/components/Grid.js

@@ -28,8 +28,8 @@ exports.GridRaw = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const ry = Math.max(viewHeight - vtop, 0);
     const w = Math.min(htop - hbottom, viewWidth);
     const h = Math.min(viewHeight - vbottom - ry, viewHeight);
-    let lastx = Infinity;
-    let lasty = Infinity;
+    let lastx = Number.POSITIVE_INFINITY;
+    let lasty = Number.POSITIVE_INFINITY;
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement("rect", { x: rx, y: ry, width: w, height: h, ...(0, util_1.getFillProps)(theme.palette.background.default) }),
         react_1.default.createElement("g", null,

package/dist/DotplotView/components/ImportForm/ImportCustomTrack.js

@@ -130,7 +130,9 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
     return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
         error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
         react_1.default.createElement(material_1.Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view in the dotplot. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
-        react_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => setValue(event.target.value) },
+        react_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => {
+                setValue(event.target.value);
+            } },
             react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
                 react_1.default.createElement(material_1.Grid, { item: true },
                     react_1.default.createElement(material_1.FormControlLabel, { value: ".paf", control: react_1.default.createElement(material_1.Radio, null), label: ".paf" })),
@@ -154,10 +156,18 @@ const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSession
                     react_1.default.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
                 react_1.default.createElement("div", { style: { display: 'flex' } },
                     react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) })),
+                        react_1.default.createElement(ui_1.FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => {
+                                setFileLocation(loc);
+                            } })),
                     react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => setBed1Location(loc) })),
+                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
+                                setBed1Location(loc);
+                            } })),
                     react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
+                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
+                                setBed2Location(loc);
+                            } }))))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
+                    setFileLocation(loc);
+                } }))))));
 });
 exports.default = OpenTrack;

package/dist/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.js

@@ -66,6 +66,8 @@ const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setS
             react_1.default.createElement("i", null, "inside"),
             " the DotplotView, which can turn on one or more SyntenyTracks (more than one can be displayed at once). Look for the track selector icon ",
             react_1.default.createElement(Icons_1.TrackSelector, null)),
-        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
+        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => {
+                setValue(event.target.value);
+            } }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
 });
 exports.default = Selector;

package/dist/DotplotView/components/ImportForm/index.js

@@ -56,7 +56,9 @@ function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData,
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.FormControl, null,
             react_1.default.createElement(material_1.FormLabel, { id: "group-label" }, "(Optional) Select or add a synteny track"),
-            react_1.default.createElement(material_1.RadioGroup, { row: true, value: choice, onChange: event => setChoice(event.target.value), "aria-labelledby": "group-label" },
+            react_1.default.createElement(material_1.RadioGroup, { row: true, value: choice, onChange: event => {
+                    setChoice(event.target.value);
+                }, "aria-labelledby": "group-label" },
                 react_1.default.createElement(material_1.FormControlLabel, { value: "none", control: react_1.default.createElement(material_1.Radio, null), label: "None" }),
                 react_1.default.createElement(material_1.FormControlLabel, { value: "tracklist", control: react_1.default.createElement(material_1.Radio, null), label: "Existing track" }),
                 react_1.default.createElement(material_1.FormControlLabel, { value: "custom", control: react_1.default.createElement(material_1.Radio, null), label: "New track" }))),
@@ -109,9 +111,13 @@ const DotplotImportForm = (0, mobx_react_1.observer)(({ model }) => {
                     react_1.default.createElement(material_1.Typography, { style: { textAlign: 'center' } }, "Select assemblies for dotplot view"),
                     react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
                         react_1.default.createElement(material_1.Grid, { item: true },
-                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly1, onChange: val => setAssembly1(val), session: session })),
+                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly1, onChange: val => {
+                                    setAssembly1(val);
+                                }, session: session })),
                         react_1.default.createElement(material_1.Grid, { item: true },
-                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly2, onChange: val => setAssembly2(val), session: session })),
+                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly2, onChange: val => {
+                                    setAssembly2(val);
+                                }, session: session })),
                         react_1.default.createElement(material_1.Grid, { item: true },
                             react_1.default.createElement(material_1.FormControl, null,
                                 react_1.default.createElement(material_1.Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),

package/dist/DotplotView/components/WarningDialog.js

@@ -22,9 +22,10 @@ const WarningDialog = (0, mobx_react_1.observer)(function WarningDialog({ trackW
     for (let i = 0; i < trackWarnings.length; i++) {
         const track = trackWarnings[i];
         const name = (0, configuration_1.getConf)(track, 'name');
-        for (let j = 0; j < track.displays[0].warnings.length; j++) {
-            const warning = track.displays[0].warnings[j];
-            rows.push({ name, ...warning, id: i + '_' + j });
+        const d = track.displays[0];
+        for (let j = 0; j < d.warnings.length; j++) {
+            const warning = d.warnings[j];
+            rows.push({ name, ...warning, id: `${i}_${j}` });
         }
     }
     const columns = [

package/dist/DotplotView/components/util.js

@@ -9,7 +9,7 @@ function locstr(px, view, includeAsm = true) {
     const coord = Math.floor(start + offset);
     return oob
         ? 'out of bounds'
-        : `${includeAsm ? '{' + assemblyName + '}' : ''}${refName}:${coord.toLocaleString('en-US')}`;
+        : `${includeAsm ? `{${assemblyName}}` : ''}${refName}:${coord.toLocaleString('en-US')}`;
 }
 function getBlockLabelKeysToHide(blocks, length, viewOffsetPx) {
     const blockLabelKeysToHide = new Set();
@@ -39,7 +39,9 @@ function getBlockLabelKeysToHide(blocks, length, viewOffsetPx) {
 function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = +Number(minMajorPitchBp)
+        .toExponential()
+        .split(/e/i)[1];
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;

package/dist/DotplotView/model.d.ts

@@ -448,12 +448,6 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
      * #action
      */
     setError(e: unknown): void;
-    /**
-     * #action
-     * removes the view itself from the state tree entirely by calling the
-     * parent removeView
-     */
-    closeView(): void;
     /**
      * #action
      */
@@ -552,7 +546,7 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
     /**
      * #getter
      */
-    readonly error: {};
+    readonly error: unknown;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type DotplotViewStateModel = ReturnType<typeof stateModelFactory>;
 export type DotplotViewModel = Instance<DotplotViewStateModel>;

package/dist/DotplotView/model.js

@@ -305,15 +305,6 @@ function stateModelFactory(pm) {
         setError(e) {
             self.volatileError = e;
         },
-        /**
-         * #action
-         * removes the view itself from the state tree entirely by calling the
-         * parent removeView
-         */
-        closeView() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
-        },
         /**
          * #action
          */
@@ -372,7 +363,9 @@ function stateModelFactory(pm) {
             const schema = pm.pluggableConfigSchemaType('track');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
             const t = self.tracks.filter(t => t.configuration === conf);
-            (0, mobx_1.transaction)(() => t.forEach(t => self.tracks.remove(t)));
+            (0, mobx_1.transaction)(() => {
+                t.forEach(t => self.tracks.remove(t));
+            });
             return t.length;
         },
         /**
@@ -619,15 +612,21 @@ function stateModelFactory(pm) {
                 },
                 {
                     label: 'Square view - same bp per pixel',
-                    onClick: () => self.squareView(),
+                    onClick: () => {
+                        self.squareView();
+                    },
                 },
                 {
                     label: 'Rectangular view - same total bp',
-                    onClick: () => self.squareView(),
+                    onClick: () => {
+                        self.squareView();
+                    },
                 },
                 {
                     label: 'Show all regions',
-                    onClick: () => self.showAllRegions(),
+                    onClick: () => {
+                        self.showAllRegions();
+                    },
                 },
                 {
                     label: 'Export SVG',

package/dist/DotplotView/svgcomponents/SVGDotplotView.js

@@ -18,7 +18,6 @@ async function renderToSvg(model, opts) {
     var _a;
     await (0, mobx_1.when)(() => model.initialized);
     const { themeName = 'default', Wrapper = ({ children }) => children } = opts;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = (0, mobx_state_tree_1.getRoot)(model);
     const session = (0, util_1.getSession)(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
@@ -41,7 +40,9 @@ 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) => (react_1.default.createElement("g", { key: i }, result))))),
+                    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", { transform: `translate(${borderX} ${viewHeight})` },
                     react_1.default.createElement(Axes_1.HorizontalAxisRaw, { model: model }))))), createRootFn);
 }