@jbrowse/plugin-dotplot-view 2.17.0 → 3.0.0

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 { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 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',
@@ -26,36 +25,18 @@ const useStyles = makeStyles()({
 });
 const PanButtons = observer(function PanButtons({ model, }) {
     const { classes } = useStyles();
-    return (React.createElement(Paper, { className: classes.dpad, elevation: 6 },
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.vview.scroll(100);
-            } },
-            React.createElement(ArrowDropUp, null)),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.hview.scroll(-100);
-            } },
-            React.createElement(ArrowLeft, null)),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.hview.scroll(100);
-            } },
-            React.createElement(ArrowRight, null)),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.vview.scroll(-100);
-            } },
-            React.createElement(ArrowDropDown, null)),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.zoomIn();
-            } },
-            React.createElement(ZoomIn, null)),
-        React.createElement("div", null),
-        React.createElement(IconButton, { className: classes.icon, onClick: () => {
-                model.zoomOut();
-            } },
-            React.createElement(ZoomOut, null))));
+    return (_jsxs(Paper, { className: classes.dpad, elevation: 6, children: [_jsx("div", {}), _jsx(IconButton, { className: classes.icon, onClick: () => {
+                    model.vview.scroll(100);
+                }, children: _jsx(ArrowDropUp, {}) }), _jsx("div", {}), _jsx(IconButton, { className: classes.icon, onClick: () => {
+                    model.hview.scroll(-100);
+                }, children: _jsx(ArrowLeft, {}) }), _jsx("div", {}), _jsx(IconButton, { className: classes.icon, onClick: () => {
+                    model.hview.scroll(100);
+                }, children: _jsx(ArrowRight, {}) }), _jsx("div", {}), _jsx(IconButton, { className: classes.icon, onClick: () => {
+                    model.vview.scroll(-100);
+                }, children: _jsx(ArrowDropDown, {}) }), _jsx("div", {}), _jsx(IconButton, { className: classes.icon, onClick: () => {
+                    model.zoomIn();
+                }, children: _jsx(ZoomIn, {}) }), _jsx("div", {}), _jsx(IconButton, { className: classes.icon, onClick: () => {
+                    model.zoomOut();
+                }, children: _jsx(ZoomOut, {}) })] }));
 });
 export default PanButtons;

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

@@ -1,16 +1,16 @@
-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, }: {
     handleClose: () => void;
     trackWarnings: TrackWarning[];
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default WarningDialog;

package/esm/DotplotView/components/WarningDialog.js

@@ -1,18 +1,17 @@
-import React from 'react';
-import { DialogContent, DialogContentText } from '@mui/material';
+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 { 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];
@@ -23,15 +22,16 @@ 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)) },
         { field: 'effect', width: measureGridWidth(rows.map(r => r.effect)) },
     ];
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings" },
-        React.createElement(DialogContent, { className: classes.content },
-            React.createElement(DialogContentText, null, "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared."),
-            React.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
-                React.createElement(DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true })))));
+    return (_jsx(Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: _jsxs(DialogContent, { className: classes.content, children: [_jsx(DialogContentText, { children: "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared." }), _jsx("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: _jsx(DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }) })] }) }));
 });
 export default WarningDialog;

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 +1,9 @@
-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 { ImportFormSyntenyTrack } from './types';
+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 +13,6 @@ 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>>;
@@ -220,58 +215,33 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
     wheelMode: string;
     borderX: number;
     borderY: number;
+    importFormSyntenyTrackSelections: import("mobx").IObservableArray<ImportFormSyntenyTrack>;
+} & {
+    importFormRemoveRow(idx: number): void;
+    clearImportFormSyntenyTracks(): void;
+    setImportFormSyntenyTrack(arg: number, val: ImportFormSyntenyTrack): void;
 } & {
-    /**
-     * #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 +373,26 @@ 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;
@@ -495,60 +404,29 @@ 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;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
-    } | {
-        label: string;
         onClick: () => void;
-        icon?: undefined;
     } | {
         label: string;
         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';