@jbrowse/plugin-dotplot-view 2.17.0 → 2.18.0

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

@@ -1,12 +1,11 @@
-import React, { useState, useEffect } from 'react';
-import { Select, MenuItem, Paper, Typography } from '@mui/material';
-import { getTrackName } from '@jbrowse/core/util/tracks';
-import { getSession } from '@jbrowse/core/util';
+import React, { useEffect, useState } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage } from '@jbrowse/core/ui';
-import { readConfObject, } from '@jbrowse/core/configuration';
-import { observer } from 'mobx-react';
-// icons
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+import { getSession } from '@jbrowse/core/util';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import { MenuItem, Paper, Select, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
 function f(track, assembly1, assembly2) {
     const assemblyNames = readConfObject(track, 'assemblyNames');
     return (assemblyNames.includes(assembly1) &&
@@ -25,13 +24,9 @@ const Selector = observer(({ model, assembly1, assembly2, setShowTrackId, }) =>
     const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
     const [value, setValue] = useState(resetTrack);
     useEffect(() => {
-        // if assembly1/assembly2 changes, then we will want to use this effect to change
-        // the state of the useState because it otherwise gets locked to a stale value
         setValue(resetTrack);
     }, [resetTrack]);
     useEffect(() => {
-        // sets track data in a useEffect because the initial load is needed as well as
-        // onChange's to the select box
         setShowTrackId(value);
     }, [value, setShowTrackId]);
     return (React.createElement(Paper, { style: { padding: 12 } },

package/esm/DotplotView/components/ImportForm/index.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { DotplotViewModel } from '../../model';
+import type { DotplotViewModel } from '../../model';
 declare const DotplotImportForm: ({ model }: {
     model: DotplotViewModel;
 }) => React.JSX.Element;

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

@@ -1,10 +1,10 @@
-import React, { useState, useEffect } from 'react';
-import { Button, Container, FormControl, FormLabel, FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { observer } from 'mobx-react';
-import { transaction } from 'mobx';
+import React, { useEffect, useState } from 'react';
+import { AssemblySelector, ErrorMessage } from '@jbrowse/core/ui';
 import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util';
-import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
+import { Button, Container, FormControl, FormControlLabel, FormLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
+import { transaction } from 'mobx';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 import ImportCustomTrack from './ImportCustomTrack';
 import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelector';
 const useStyles = makeStyles()(theme => ({
@@ -73,7 +73,6 @@ const DotplotImportForm = observer(({ model }) => {
             setError(e);
         }
     }
-    // this is a combination of any displayed error message we have
     const displayError = error || model.error;
     return (React.createElement(Container, { className: classes.importFormContainer },
         displayError ? React.createElement(ErrorMessage, { error: displayError }) : null,

package/esm/DotplotView/components/ImportForm/util.js

@@ -1,10 +1,8 @@
 export function getName(sessionTrackData) {
     return sessionTrackData
-        ? // @ts-expect-error
+        ?
             sessionTrackData.uri ||
-                // @ts-expect-error
                 sessionTrackData.localPath ||
-                // @ts-expect-error
                 sessionTrackData.name
         : undefined;
 }

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model';
 declare const PanButtons: ({ model, }: {
     model: DotplotViewModel;
 }) => React.JSX.Element;

package/esm/DotplotView/components/PanButtons.js

@@ -1,14 +1,13 @@
 import React from 'react';
-import { IconButton, Paper } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { observer } from 'mobx-react';
-// icons
 import ArrowDropDown from '@mui/icons-material/ArrowDropDown';
 import ArrowDropUp from '@mui/icons-material/ArrowDropUp';
 import ArrowLeft from '@mui/icons-material/ArrowLeft';
 import ArrowRight from '@mui/icons-material/ArrowRight';
 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/WarningDialog.d.ts

@@ -1,12 +1,13 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+interface Warning {
+    message: string;
+    effect: string;
+}
 interface TrackWarning {
     configuration: AnyConfigurationModel;
     displays: {
-        warnings: {
-            message: string;
-            effect: string;
-        }[];
+        warnings: Warning[];
     }[];
 }
 declare const WarningDialog: ({ trackWarnings, handleClose, }: {

package/esm/DotplotView/components/WarningDialog.js

@@ -1,18 +1,17 @@
 import React from 'react';
-import { DialogContent, DialogContentText } from '@mui/material';
+import { getConf } from '@jbrowse/core/configuration';
 import { Dialog } from '@jbrowse/core/ui';
+import { measureGridWidth } from '@jbrowse/core/util';
+import { DialogContent, DialogContentText } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { DataGrid } from '@mui/x-data-grid';
-import { getConf } from '@jbrowse/core/configuration';
-import { measureGridWidth } from '@jbrowse/core/util';
 const useStyles = makeStyles()({
     content: {
         minWidth: 600,
     },
 });
-const WarningDialog = observer(function WarningDialog({ trackWarnings, handleClose, }) {
-    const { classes } = useStyles();
+function getTrackWarnings({ trackWarnings, }) {
     const rows = [];
     for (let i = 0; i < trackWarnings.length; i++) {
         const track = trackWarnings[i];
@@ -23,6 +22,11 @@ const WarningDialog = observer(function WarningDialog({ trackWarnings, handleClo
             rows.push({ name, ...warning, id: `${i}_${j}` });
         }
     }
+    return rows;
+}
+const WarningDialog = observer(function WarningDialog({ trackWarnings, handleClose, }) {
+    const { classes } = useStyles();
+    const rows = getTrackWarnings({ trackWarnings });
     const columns = [
         { field: 'name' },
         { field: 'message', width: measureGridWidth(rows.map(r => r.message)) },

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

@@ -1,12 +1,7 @@
-import { BaseBlock } from '@jbrowse/core/util/blockTypes';
-import { Dotplot1DViewModel } from '../model';
+import type { Dotplot1DViewModel } from '../model';
+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>;
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
 export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
     majorPitch: number;
     minorPitch: number;

package/esm/DotplotView/components/util.js

@@ -25,11 +25,6 @@ export function getBlockLabelKeysToHide(blocks, length, viewOffsetPx) {
     }
     return blockLabelKeysToHide;
 }
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;

package/esm/DotplotView/index.d.ts

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

package/esm/DotplotView/index.js

@@ -1,6 +1,5 @@
 import { lazy } from 'react';
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-// locals
 import stateModelFactory from './model';
 export default function DotplotViewF(pluginManager) {
     pluginManager.addViewType(() => {

package/esm/DotplotView/model.d.ts

@@ -1,8 +1,8 @@
-import React from 'react';
-import { Instance, SnapshotIn } from 'mobx-state-tree';
-import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type React from 'react';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+import type { Instance, SnapshotIn } from 'mobx-state-tree';
 type Coord = [number, number];
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
@@ -12,12 +12,6 @@ export interface ExportSvgOptions {
     }>;
     themeName?: string;
 }
-/**
- * #stateModel DotplotView
- * #category view
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
 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>>;
@@ -221,57 +215,27 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
     borderX: number;
     borderY: number;
 } & {
-    /**
-     * #getter
-     */
     readonly width: number;
 } & {
-    /**
-     * #getter
-     */
     readonly assemblyErrors: string;
-    /**
-     * #getter
-     */
     readonly assembliesInitialized: boolean;
 } & {
-    /**
-     * #getter
-     */
     readonly initialized: boolean;
-    /**
-     * #getter
-     */
     readonly hticks: {
         type: string;
         base: number;
         index: number;
         refName: string;
     }[];
-    /**
-     * #getter
-     */
     readonly vticks: {
         type: string;
         base: number;
         index: number;
         refName: string;
     }[];
-    /**
-     * #getter
-     */
     readonly loading: boolean;
-    /**
-     * #getter
-     */
     readonly viewWidth: number;
-    /**
-     * #getter
-     */
     readonly viewHeight: number;
-    /**
-     * #getter
-     */
     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]>>;
@@ -403,87 +367,26 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
     } & {
         readonly width: any;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>)[];
-    /**
-     * #method
-     */
     renderProps(): any;
 } & {
-    /**
-     * #action
-     */
     setShowPanButtons(flag: boolean): void;
-    /**
-     * #action
-     */
     setWheelMode(str: string): void;
-    /**
-     * #action
-     */
     setCursorMode(str: string): void;
-    /**
-     * #action
-     */
     setDrawCigar(flag: boolean): void;
-    /**
-     * #action
-     * returns to the import form
-     */
     clearView(): void;
-    /**
-     * #action
-     */
     setBorderX(n: number): void;
-    /**
-     * #action
-     */
     setBorderY(n: number): void;
-    /**
-     * #action
-     */
     setWidth(newWidth: number): number;
-    /**
-     * #action
-     */
     setHeight(newHeight: number): number;
-    /**
-     * #action
-     */
     setError(e: unknown): void;
-    /**
-     * #action
-     */
     zoomOut(): void;
-    /**
-     * #action
-     */
     zoomIn(): void;
-    /**
-     * #action
-     */
     activateTrackSelector(): import("@jbrowse/core/util").Widget;
-    /**
-     * #action
-     */
     showTrack(trackId: string, initialSnapshot?: {}): void;
-    /**
-     * #action
-     */
     hideTrack(trackId: string): number;
-    /**
-     * #action
-     */
     toggleTrack(trackId: string): boolean;
-    /**
-     * #action
-     */
     setAssemblyNames(target: string, query: string): void;
-    /**
-     * #action
-     */
     setViews(arr: SnapshotIn<Base1DViewModel>[]): void;
-    /**
-     * #action
-     */
     getCoords(mousedown: Coord, mouseup: Coord): {
         coord: number;
         index: number;
@@ -495,40 +398,16 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         end: number;
         reversed?: boolean;
     }[] | undefined;
-    /**
-     * #action
-     * zooms into clicked and dragged region
-     */
     zoomInToMouseCoords(mousedown: Coord, mouseup: Coord): void;
-    /**
-     * #action
-     */
     showAllRegions(): void;
-    /**
-     * #action
-     * creates a linear synteny view from the clicked and dragged region
-     */
     onDotplotView(mousedown: Coord, mouseup: Coord): void;
 } & {
-    /**
-     * #action
-     * creates an svg export and save using FileSaver
-     */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
     beforeDestroy(): void;
     afterAttach(): void;
-    /**
-     * #action
-     */
     squareView(): void;
-    /**
-     * #action
-     */
     squareViewProportional(): void;
 } & {
-    /**
-     * #method
-     */
     menuItems(): ({
         label: string;
         onClick: () => void;
@@ -544,11 +423,8 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         onClick: () => import("@jbrowse/core/util").Widget;
         icon: typeof TrackSelectorIcon;
     })[];
-    /**
-     * #getter
-     */
     readonly error: unknown;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type DotplotViewStateModel = ReturnType<typeof stateModelFactory>;
 export type DotplotViewModel = Instance<DotplotViewStateModel>;
-export { type Dotplot1DViewModel, Dotplot1DView } from './1dview';
+export { Dotplot1DView, type Dotplot1DViewModel } from './1dview';