@jbrowse/plugin-dotplot-view 2.17.0 → 2.18.0

package/dist/DotplotView/components/Grid.js

@@ -6,9 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.GridRaw = void 0;
 exports.default = Grid;
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 exports.GridRaw = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { viewWidth, viewHeight, hview, vview } = model;
     const hblocks = hview.dynamicBlocks.contentBlocks;
@@ -22,8 +22,6 @@ exports.GridRaw = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const vbottom = vblocks[0].offsetPx - vview.offsetPx;
     const theme = (0, material_1.useTheme)();
     const stroke = theme.palette.divider;
-    // Uses math.max/min avoid making very large SVG rect offscreen element,
-    // which can sometimes fail to draw
     const rx = Math.max(hbottom, 0);
     const ry = Math.max(viewHeight - vtop, 0);
     const w = Math.min(htop - hbottom, viewWidth);

package/dist/DotplotView/components/Header.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model';
 declare const DotplotHeader: ({ model, selection, }: {
     model: DotplotViewModel;
     selection?: {

package/dist/DotplotView/components/Header.js

@@ -4,13 +4,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
+const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const util_1 = require("@jbrowse/core/util");
+const DotplotControls_1 = __importDefault(require("./DotplotControls"));
 const DotplotWarnings_1 = __importDefault(require("./DotplotWarnings"));
 const PanButtons_1 = __importDefault(require("./PanButtons"));
-const DotplotControls_1 = __importDefault(require("./DotplotControls"));
 const useStyles = (0, mui_1.makeStyles)()({
     bp: {
         display: 'flex',

package/dist/DotplotView/components/ImportForm/ImportCustomTrack.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SnapshotIn } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { SnapshotIn } from 'mobx-state-tree';
 type Conf = SnapshotIn<AnyConfigurationModel>;
 declare const ImportCustomTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
     sessionTrackData: Conf;

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

@@ -24,8 +24,8 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("./util");
 function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }) {

package/dist/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { DotplotViewModel } from '../../model';
+import type { DotplotViewModel } from '../../model';
 declare const Selector: ({ model, assembly1, assembly2, setShowTrackId, }: {
     model: DotplotViewModel;
     assembly1: string;

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

@@ -24,14 +24,13 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const util_1 = require("@jbrowse/core/util");
-const ui_1 = require("@jbrowse/core/ui");
 const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_react_1 = require("mobx-react");
-// icons
+const ui_1 = require("@jbrowse/core/ui");
 const Icons_1 = require("@jbrowse/core/ui/Icons");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 function f(track, assembly1, assembly2) {
     const assemblyNames = (0, configuration_1.readConfObject)(track, 'assemblyNames');
     return (assemblyNames.includes(assembly1) &&
@@ -50,13 +49,9 @@ const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setS
     const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
     const [value, setValue] = (0, react_1.useState)(resetTrack);
     (0, react_1.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]);
     (0, react_1.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_1.default.createElement(material_1.Paper, { style: { padding: 12 } },

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

@@ -27,12 +27,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const mobx_react_1 = require("mobx-react");
 const mobx_1 = require("mobx");
-const util_1 = require("@jbrowse/core/util");
-const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const ImportCustomTrack_1 = __importDefault(require("./ImportCustomTrack"));
 const ImportSyntenyTrackSelector_1 = __importDefault(require("./ImportSyntenyTrackSelector"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
@@ -101,7 +101,6 @@ const DotplotImportForm = (0, mobx_react_1.observer)(({ model }) => {
             setError(e);
         }
     }
-    // this is a combination of any displayed error message we have
     const displayError = error || model.error;
     return (react_1.default.createElement(material_1.Container, { className: classes.importFormContainer },
         displayError ? react_1.default.createElement(ui_1.ErrorMessage, { error: displayError }) : null,

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

@@ -6,11 +6,9 @@ exports.basename = basename;
 exports.extName = extName;
 function getName(sessionTrackData) {
     return sessionTrackData
-        ? // @ts-expect-error
+        ?
             sessionTrackData.uri ||
-                // @ts-expect-error
                 sessionTrackData.localPath ||
-                // @ts-expect-error
                 sessionTrackData.name
         : undefined;
 }

package/dist/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/dist/DotplotView/components/PanButtons.js

@@ -4,16 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const mobx_react_1 = require("mobx-react");
-// icons
 const ArrowDropDown_1 = __importDefault(require("@mui/icons-material/ArrowDropDown"));
 const ArrowDropUp_1 = __importDefault(require("@mui/icons-material/ArrowDropUp"));
 const ArrowLeft_1 = __importDefault(require("@mui/icons-material/ArrowLeft"));
 const ArrowRight_1 = __importDefault(require("@mui/icons-material/ArrowRight"));
 const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
 const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     dpad: {
         display: 'grid',

package/dist/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/dist/DotplotView/components/WarningDialog.js

@@ -4,20 +4,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
+const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const x_data_grid_1 = require("@mui/x-data-grid");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const x_data_grid_1 = require("@mui/x-data-grid");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
 const useStyles = (0, mui_1.makeStyles)()({
     content: {
         minWidth: 600,
     },
 });
-const WarningDialog = (0, mobx_react_1.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];
@@ -28,6 +27,11 @@ const WarningDialog = (0, mobx_react_1.observer)(function WarningDialog({ trackW
             rows.push({ name, ...warning, id: `${i}_${j}` });
         }
     }
+    return rows;
+}
+const WarningDialog = (0, mobx_react_1.observer)(function WarningDialog({ trackWarnings, handleClose, }) {
+    const { classes } = useStyles();
+    const rows = getTrackWarnings({ trackWarnings });
     const columns = [
         { field: 'name' },
         { field: 'message', width: (0, util_1.measureGridWidth)(rows.map(r => r.message)) },

package/dist/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/dist/DotplotView/components/util.js

@@ -31,11 +31,6 @@ 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.
- */
 function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;

package/dist/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/dist/DotplotView/index.js

@@ -29,7 +29,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = DotplotViewF;
 const react_1 = require("react");
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
-// locals
 const model_1 = __importDefault(require("./model"));
 function DotplotViewF(pluginManager) {
     pluginManager.addViewType(() => {

package/dist/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';