@jbrowse/plugin-dotplot-view 3.7.0 → 4.0.1

package/esm/DotplotView/components/MinLengthSlider.js

@@ -1,9 +1,10 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useEffect, useState } from 'react';
+import { toLocale } from '@jbrowse/core/util';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Slider, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import SliderTooltip from './SliderTooltip';
+import SliderTooltip from "./SliderTooltip.js";
 const useStyles = makeStyles()({
     container: {
         display: 'flex',
@@ -13,11 +14,10 @@ const useStyles = makeStyles()({
         minWidth: 150,
     },
 });
-const MinLengthSlider = observer(function ({ model, }) {
-    var _a, _b;
+const MinLengthSlider = observer(function MinLengthSlider({ model, }) {
     const { classes } = useStyles();
-    const firstDisplay = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
-    const minAlignmentLength = (_b = firstDisplay === null || firstDisplay === void 0 ? void 0 : firstDisplay.minAlignmentLength) !== null && _b !== void 0 ? _b : 0;
+    const firstDisplay = model.tracks[0]?.displays[0];
+    const minAlignmentLength = firstDisplay?.minAlignmentLength ?? 0;
     const [minLengthValue, setMinLengthValue] = useState(Math.log2(Math.max(1, minAlignmentLength)) * 100);
     useEffect(() => {
         setMinLengthValue(Math.log2(Math.max(1, minAlignmentLength)) * 100);
@@ -32,7 +32,7 @@ const MinLengthSlider = observer(function ({ model, }) {
                             display.setMinAlignmentLength(newMinLength);
                         }
                     }
-                }, min: 0, max: Math.log2(1000000) * 100, valueLabelDisplay: "auto", valueLabelFormat: newValue => Math.round(2 ** (newValue / 100)).toLocaleString(), size: "small", style: { minWidth: 100 }, slots: {
+                }, min: 0, max: Math.log2(1000000) * 100, valueLabelDisplay: "auto", valueLabelFormat: newValue => toLocale(Math.round(2 ** (newValue / 100))), size: "small", style: { minWidth: 100 }, slots: {
                     valueLabel: SliderTooltip,
                 } })] }));
 });

package/esm/DotplotView/components/MouseInteractionLayer.d.ts

@@ -1,4 +1,4 @@
-import type { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model.ts';
 type Coord = [number, number] | undefined;
 interface MouseInteractionLayerProps {
     model: DotplotViewModel;
@@ -13,5 +13,5 @@ interface MouseInteractionLayerProps {
     setMouseCurrClient: (coord: Coord) => void;
     setCtrlKeyWasUsed: (wasUsed: boolean) => void;
 }
-export default function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }: MouseInteractionLayerProps): import("react/jsx-runtime").JSX.Element;
-export {};
+declare const MouseInteractionLayer: ({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }: MouseInteractionLayerProps) => import("react/jsx-runtime").JSX.Element;
+export default MouseInteractionLayer;

package/esm/DotplotView/components/MouseInteractionLayer.js

@@ -1,6 +1,7 @@
 import { jsx as _jsx } from "react/jsx-runtime";
-import Grid from './Grid';
-export default function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }) {
+import { observer } from 'mobx-react';
+import DotplotGridWrapper from "./DotplotGridWrapper.js";
+const MouseInteractionLayer = observer(function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }) {
     return (_jsx("div", { style: { cursor: ctrlKeyDown ? 'pointer' : cursorMode }, onMouseDown: event => {
             if (event.button === 0) {
                 const { clientX, clientY } = event;
@@ -8,5 +9,6 @@ export default function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode,
                 setMouseCurrClient([clientX, clientY]);
                 setCtrlKeyWasUsed(ctrlKeyDown);
             }
-        }, children: _jsx(Grid, { model: model, children: validSelect && mousedown && mouserect ? (_jsx("rect", { fill: "rgba(255,0,0,0.3)", x: Math.min(mouserect[0], mousedown[0]), y: Math.min(mouserect[1], mousedown[1]), width: Math.abs(xdistance), height: Math.abs(ydistance) })) : null }) }));
-}
+        }, children: _jsx(DotplotGridWrapper, { model: model, children: validSelect && mousedown && mouserect ? (_jsx("rect", { fill: "rgba(255,0,0,0.3)", x: Math.min(mouserect[0], mousedown[0]), y: Math.min(mouserect[1], mousedown[1]), width: Math.abs(xdistance), height: Math.abs(ydistance) })) : null }) }));
+});
+export default MouseInteractionLayer;

package/esm/DotplotView/components/OpacitySlider.d.ts

@@ -1,4 +1,4 @@
-import type { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model.ts';
 declare const OpacitySlider: ({ model, }: {
     model: DotplotViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/DotplotView/components/OpacitySlider.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Slider, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import SliderTooltip from './SliderTooltip';
+import SliderTooltip from "./SliderTooltip.js";
 const useStyles = makeStyles()({
     container: {
         display: 'flex',
@@ -12,11 +12,10 @@ const useStyles = makeStyles()({
         minWidth: 150,
     },
 });
-const OpacitySlider = observer(function ({ model, }) {
-    var _a, _b;
+const OpacitySlider = observer(function OpacitySlider({ model, }) {
     const { classes } = useStyles();
-    const firstDisplay = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
-    const alpha = (_b = firstDisplay === null || firstDisplay === void 0 ? void 0 : firstDisplay.alpha) !== null && _b !== void 0 ? _b : 1;
+    const firstDisplay = model.tracks[0]?.displays[0];
+    const alpha = firstDisplay?.alpha ?? 1;
     const exponent = 3;
     const alphaToSlider = (a) => Math.pow(a, 1 / exponent);
     const sliderToAlpha = (s) => Math.pow(s, exponent);

package/esm/DotplotView/components/PanButtons.d.ts

@@ -1,4 +1,4 @@
-import type { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model.ts';
 declare const PanButtons: ({ model, }: {
     model: DotplotViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/DotplotView/components/PanButtons.js

@@ -1,4 +1,5 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import ArrowDropDown from '@mui/icons-material/ArrowDropDown';
 import ArrowDropUp from '@mui/icons-material/ArrowDropUp';
 import ArrowLeft from '@mui/icons-material/ArrowLeft';
@@ -7,7 +8,6 @@ import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
 import { IconButton, Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     dpad: {
         display: 'grid',

package/esm/DotplotView/components/SelectionContextMenu.d.ts

@@ -1,4 +1,4 @@
-import type { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model.ts';
 type Coord = [number, number] | undefined;
 interface SelectionContextMenuProps {
     model: DotplotViewModel;

package/esm/DotplotView/components/WarningDialog.js

@@ -2,10 +2,10 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getConf } from '@jbrowse/core/configuration';
 import { Dialog } from '@jbrowse/core/ui';
 import { measureGridWidth } from '@jbrowse/core/util';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { DialogContent, DialogContentText } from '@mui/material';
 import { DataGrid } from '@mui/x-data-grid';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     content: {
         minWidth: 600,

package/esm/DotplotView/components/util.d.ts

@@ -1,4 +1,4 @@
-import type { Dotplot1DViewModel } from '../model';
+import type { Dotplot1DViewModel } from '../model.ts';
 import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
 export declare function locstr(px: number, view: Dotplot1DViewModel, includeAsm?: boolean): string;
 export declare function getBlockLabelKeysToHide(blocks: BaseBlock[], length: number, viewOffsetPx: number): Set<string>;

package/esm/DotplotView/components/util.js

@@ -1,9 +1,10 @@
+import { toLocale } from '@jbrowse/core/util';
 export function locstr(px, view, includeAsm = true) {
     const { assemblyName, refName, start, offset, oob } = view.pxToBp(px);
     const coord = Math.floor(start + offset);
     return oob
         ? 'out of bounds'
-        : `${includeAsm ? `{${assemblyName}}` : ''}${refName}:${coord.toLocaleString('en-US')}`;
+        : `${includeAsm ? `{${assemblyName}}` : ''}${refName}:${toLocale(coord)}`;
 }
 export function getBlockLabelKeysToHide(blocks, length, viewOffsetPx) {
     const blockLabelKeysToHide = new Set();
@@ -12,15 +13,26 @@ export function getBlockLabelKeysToHide(blocks, length, viewOffsetPx) {
         const blen = b.end - b.start;
         return blen - alen;
     });
-    const positions = Array.from({ length: Math.round(length) });
+    const occupiedPositions = new Set();
     for (const { key, offsetPx } of sortedBlocks) {
         const y = Math.round(length - offsetPx + viewOffsetPx);
-        const labelBounds = [Math.max(y - 12, 0), y];
-        if (y === 0 || positions.slice(...labelBounds).some(Boolean)) {
+        const labelStart = Math.max(y - 12, 0);
+        let hasOverlap = y === 0;
+        if (!hasOverlap) {
+            for (let i = labelStart; i < y; i++) {
+                if (occupiedPositions.has(i)) {
+                    hasOverlap = true;
+                    break;
+                }
+            }
+        }
+        if (hasOverlap) {
             blockLabelKeysToHide.add(key);
         }
         else {
-            positions.fill(true, ...labelBounds);
+            for (let i = labelStart; i < y; i++) {
+                occupiedPositions.add(i);
+            }
         }
     }
     return blockLabelKeysToHide;

package/esm/DotplotView/index.js

@@ -1,13 +1,13 @@
 import { lazy } from 'react';
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import stateModelFactory from './model';
+import stateModelFactory from "./model.js";
 export default function DotplotViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType({
             name: 'DotplotView',
             displayName: 'Dotplot view',
             stateModel: stateModelFactory(pluginManager),
-            ReactComponent: lazy(() => import('./components/DotplotView')),
+            ReactComponent: lazy(() => import("./components/DotplotView.js")),
         });
     });
 }

package/esm/DotplotView/model.d.ts

@@ -1,9 +1,9 @@
 import type React from 'react';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
-import type { ImportFormSyntenyTrack } from './types';
+import type { DotplotViewInit, ImportFormSyntenyTrack } from './types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
-import type { Instance, SnapshotIn } from 'mobx-state-tree';
+import type { Instance, SnapshotIn } from '@jbrowse/mobx-state-tree';
 type Coord = [number, number];
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
@@ -13,29 +13,29 @@ export interface ExportSvgOptions {
     }>;
     themeName?: string;
 }
-export default function stateModelFactory(pm: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+export default function stateModelFactory(pm: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 } & {
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"DotplotView">;
-    height: import("mobx-state-tree").IType<number | undefined, number, number>;
-    borderSize: import("mobx-state-tree").IType<number | undefined, number, number>;
-    tickSize: import("mobx-state-tree").IType<number | undefined, number, number>;
-    vtextRotation: import("mobx-state-tree").IType<number | undefined, number, number>;
-    htextRotation: import("mobx-state-tree").IType<number | undefined, number, number>;
-    fontSize: import("mobx-state-tree").IType<number | undefined, number, number>;
-    trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
-    assemblyNames: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
-    drawCigar: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hview: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"DotplotView">;
+    height: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    borderSize: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    tickSize: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    vtextRotation: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    htextRotation: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    fontSize: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    trackSelectorType: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    assemblyNames: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    drawCigar: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+        bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         features: undefined | import("@jbrowse/core/util").Feature[];
         volatileWidth: number;
@@ -94,14 +94,14 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly minOffset: number;
     } & {
         readonly width: any;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    vview: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    vview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+        bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         features: undefined | import("@jbrowse/core/util").Feature[];
         volatileWidth: number;
@@ -160,48 +160,10 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly minOffset: number;
     } & {
         readonly width: any;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        type: import("mobx-state-tree").ISimpleType<string>;
-        configuration: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        pinned: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
-    }, {
-        readonly rpcSessionId: any;
-        readonly name: any;
-        readonly textSearchAdapter: any;
-        readonly adapterConfig: any;
-        readonly adapterType: import("@jbrowse/core/pluggableElementTypes").AdapterType;
-        readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-        readonly canConfigure: boolean | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
-    } & {
-        setPinned(flag: boolean): void;
-        setMinimized(flag: boolean): void;
-        showDisplay(displayId: string, initialSnapshot?: {}): void;
-        hideDisplay(displayId: string): number;
-        replaceDisplay(oldId: string, newId: string, initialSnapshot?: {}): void;
-    } & {
-        trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
-            type: string;
-            label: string;
-            priority: number;
-            subMenu: {
-                type: string;
-                label: string;
-                checked: boolean;
-                onClick: () => void;
-            }[];
-        })[];
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    init: import("@jbrowse/mobx-state-tree").IType<DotplotViewInit | undefined, DotplotViewInit | undefined, DotplotViewInit | undefined>;
 }, {
     width: number;
 } & {
@@ -242,17 +204,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         index: number;
         refName: string;
     }[];
-    readonly loading: boolean;
+    readonly hasSomethingToShow: boolean;
+    readonly showLoading: boolean;
+    readonly showImportForm: boolean;
+    readonly loadingMessage: "Loading" | undefined;
     readonly viewWidth: number;
     readonly viewHeight: number;
     readonly views: ({
         id: string;
-        displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
+        displayedRegions: import("@jbrowse/core/util").Region[] & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
         bpPerPx: number;
         offsetPx: number;
         interRegionPaddingWidth: number;
         minimumBlockWidth: number;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         features: undefined | import("@jbrowse/core/util").Feature[];
         volatileWidth: number;
     } & {
@@ -310,13 +275,13 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly minOffset: number;
     } & {
         readonly width: any;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
-        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+        bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         features: undefined | import("@jbrowse/core/util").Feature[];
         volatileWidth: number;
@@ -375,7 +340,7 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly minOffset: number;
     } & {
         readonly width: any;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>)[];
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>)[];
     renderProps(): any;
 } & {
     setShowPanButtons(flag: boolean): void;
@@ -388,13 +353,14 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
     setWidth(newWidth: number): number;
     setHeight(newHeight: number): number;
     setError(e: unknown): void;
+    setInit(init?: DotplotViewInit): void;
     zoomOut(): void;
     zoomIn(): void;
 } & {
     activateTrackSelector(): import("@jbrowse/core/util").Widget;
-    showTrack(trackId: string, initialSnapshot?: {}): void;
-    hideTrack(trackId: string): number;
-    toggleTrack(trackId: string): boolean;
+    showTrack(trackId: string, initialSnapshot?: {}): any;
+    hideTrack(trackId: string): 0 | 1;
+    toggleTrack(trackId: string): void;
     setAssemblyNames(target: string, query: string): void;
     setViews(arr: SnapshotIn<Base1DViewModel>[]): void;
     getCoords(mousedown: Coord, mouseup: Coord): {
@@ -414,6 +380,7 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         borderY: number;
     };
     showAllRegions(): void;
+    initializeDisplayedRegions(): void;
     onDotplotView(mousedown: Coord, mouseup: Coord): void;
 } & {
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
@@ -434,7 +401,158 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         icon: typeof TrackSelectorIcon;
     })[];
     readonly error: unknown;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"DotplotView">;
+    height: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    borderSize: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    tickSize: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    vtextRotation: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    htextRotation: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    fontSize: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    trackSelectorType: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    assemblyNames: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    drawCigar: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+        bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }, {
+        features: undefined | import("@jbrowse/core/util").Feature[];
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed?: boolean;
+        };
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number;
+        }): number | undefined;
+    } & {
+        setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: number): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
+    } & {
+        setScaleFactor(n: number): void;
+        center(): void;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly scaleFactor: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+    } & {
+        readonly width: any;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    vview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+        bpPerPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }, {
+        features: undefined | import("@jbrowse/core/util").Feature[];
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed?: boolean;
+        };
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number;
+        }): number | undefined;
+    } & {
+        setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: number): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
+    } & {
+        setScaleFactor(n: number): void;
+        center(): void;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly scaleFactor: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+    } & {
+        readonly width: any;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    viewTrackConfigs: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    init: import("@jbrowse/mobx-state-tree").IType<DotplotViewInit | undefined, DotplotViewInit | undefined, DotplotViewInit | undefined>;
+}>>;
 export type DotplotViewStateModel = ReturnType<typeof stateModelFactory>;
 export type DotplotViewModel = Instance<DotplotViewStateModel>;
-export { Dotplot1DView, type Dotplot1DViewModel } from './1dview';
+export { Dotplot1DView, type Dotplot1DViewModel } from './1dview.ts';