@jbrowse/plugin-dotplot-view 2.17.0 → 3.0.0

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

@@ -0,0 +1,23 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const ImportSyntenyOpenCustomTrack_1 = __importDefault(require("./ImportSyntenyOpenCustomTrack"));
+const ImportSyntenyTrackSelector_1 = __importDefault(require("./ImportSyntenyTrackSelector"));
+const TrackSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, model, }) {
+    const [choice, setChoice] = (0, react_1.useState)('tracklist');
+    (0, react_1.useEffect)(() => {
+        if (choice === 'none') {
+            model.setImportFormSyntenyTrack(0, { type: 'none' });
+        }
+    }, [model, choice]);
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.FormControl, { children: [(0, jsx_runtime_1.jsx)(material_1.FormLabel, { id: "group-label", children: "(Optional) Select or add a synteny track" }), (0, jsx_runtime_1.jsxs)(material_1.RadioGroup, { row: true, value: choice, onChange: event => {
+                            setChoice(event.target.value);
+                        }, "aria-labelledby": "group-label", children: [(0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "none", control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: "None" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "tracklist", control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: "Existing track" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "custom", control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: "New track" })] })] }), choice === 'custom' ? ((0, jsx_runtime_1.jsx)(ImportSyntenyOpenCustomTrack_1.default, { model: model, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? ((0, jsx_runtime_1.jsx)(ImportSyntenyTrackSelector_1.default, { model: model, assembly1: assembly1, assembly2: assembly2 })) : null] }));
+});
+exports.default = TrackSelector;

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

@@ -0,0 +1,117 @@
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }: {
+    radioOption: string;
+    assembly1: string;
+    assembly2: string;
+    fileLocation?: FileLocation;
+    indexFileLocation?: FileLocation;
+    bed1Location?: FileLocation;
+    bed2Location?: FileLocation;
+}): {
+    type: string;
+    pafLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    outLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    pafLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    deltaLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    pafLocation?: undefined;
+    outLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    chainLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    pafLocation?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    mcscanAnchorsLocation: FileLocation | undefined;
+    bed1Location: FileLocation | undefined;
+    bed2Location: FileLocation | undefined;
+    assemblyNames: string[];
+    pafLocation?: undefined;
+    queryAssembly?: undefined;
+    targetAssembly?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    mcscanSimpleAnchorsLocation: FileLocation | undefined;
+    bed1Location: FileLocation | undefined;
+    bed2Location: FileLocation | undefined;
+    assemblyNames: string[];
+    pafLocation?: undefined;
+    queryAssembly?: undefined;
+    targetAssembly?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    pifGzLocation: FileLocation | undefined;
+    index: {
+        location: FileLocation | undefined;
+    };
+    assemblyNames: string[];
+    pafLocation?: undefined;
+    queryAssembly?: undefined;
+    targetAssembly?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+};

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

@@ -0,0 +1,68 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getAdapter = getAdapter;
+function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }) {
+    if (radioOption === '.paf') {
+        return {
+            type: 'PAFAdapter',
+            pafLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.out') {
+        return {
+            type: 'MashMapAdapter',
+            outLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.delta') {
+        return {
+            type: 'DeltaAdapter',
+            deltaLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.chain') {
+        return {
+            type: 'ChainAdapter',
+            chainLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.anchors') {
+        return {
+            type: 'MCScanAnchorsAdapter',
+            mcscanAnchorsLocation: fileLocation,
+            bed1Location,
+            bed2Location,
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else if (radioOption === '.anchors.simple') {
+        return {
+            type: 'MCScanSimpleAnchorsAdapter',
+            mcscanSimpleAnchorsLocation: fileLocation,
+            bed1Location,
+            bed2Location,
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else if (radioOption === '.pif.gz') {
+        return {
+            type: 'PairwiseIndexedPAFAdapter',
+            pifGzLocation: fileLocation,
+            index: {
+                location: indexFileLocation,
+            },
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else {
+        throw new Error(`Unknown to detect type ${radioOption} from filename (select radio button to clarify)`);
+    }
+}

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

@@ -1,6 +1,5 @@
-import React from 'react';
-import { DotplotViewModel } from '../../model';
-declare const DotplotImportForm: ({ model }: {
+import type { DotplotViewModel } from '../../model';
+declare const DotplotImportForm: ({ model, }: {
     model: DotplotViewModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default DotplotImportForm;

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

@@ -1,40 +1,17 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = 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 ImportCustomTrack_1 = __importDefault(require("./ImportCustomTrack"));
-const ImportSyntenyTrackSelector_1 = __importDefault(require("./ImportSyntenyTrackSelector"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const TrackSelector_1 = __importDefault(require("./TrackSelector"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     importFormContainer: {
         padding: theme.spacing(4),
@@ -45,82 +22,55 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         margin: '0 auto',
     },
 }));
-function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
-    const [choice, setChoice] = (0, react_1.useState)('tracklist');
-    (0, react_1.useEffect)(() => {
-        if (choice === 'none') {
-            setSessionTrackData(undefined);
-            setShowTrackId(undefined);
+function doSubmit({ model, assembly1, assembly2, }) {
+    const session = (0, util_1.getSession)(model);
+    const { importFormSyntenyTrackSelections } = model;
+    model.setError(undefined);
+    (0, mobx_1.transaction)(() => {
+        if ((0, util_1.isSessionWithAddTracks)(session)) {
+            (0, mobx_1.toJS)(importFormSyntenyTrackSelections).map((f, idx) => {
+                var _a;
+                if (f.type === 'userOpened') {
+                    session.addTrackConf(f.value);
+                    model.toggleTrack((_a = f.value) === null || _a === void 0 ? void 0 : _a.trackId);
+                }
+                else if (f.type === 'preConfigured') {
+                    model.showTrack(f.value, idx);
+                }
+            });
         }
-    }, [choice, setSessionTrackData, setShowTrackId]);
-    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.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" }))),
-        choice === 'custom' ? (react_1.default.createElement(ImportCustomTrack_1.default, { setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, assembly2: assembly2, assembly1: assembly1 })) : null,
-        choice === 'tracklist' ? (react_1.default.createElement(ImportSyntenyTrackSelector_1.default, { model: model, assembly1: assembly1, assembly2: assembly2, setShowTrackId: setShowTrackId })) : null));
+        model.showAllRegions();
+        model.setAssemblyNames(assembly2, assembly1);
+    });
 }
-const DotplotImportForm = (0, mobx_react_1.observer)(({ model }) => {
+const DotplotImportForm = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { assemblyNames } = session;
     const [assembly2, setAssembly2] = (0, react_1.useState)(assemblyNames[0] || '');
     const [assembly1, setAssembly1] = (0, react_1.useState)(assemblyNames[0] || '');
     const [error, setError] = (0, react_1.useState)();
-    const [sessionTrackData, setSessionTrackData] = (0, react_1.useState)();
-    const [showTrackId, setShowTrackId] = (0, react_1.useState)();
-    function onOpenClick() {
-        try {
-            if (!(0, util_1.isSessionWithAddTracks)(session)) {
-                return;
-            }
-            setError(undefined);
-            model.setError(undefined);
-            (0, mobx_1.transaction)(() => {
-                if (sessionTrackData) {
-                    session.addTrackConf(sessionTrackData);
-                    model.toggleTrack(sessionTrackData.trackId);
-                }
-                else if (showTrackId) {
-                    model.showTrack(showTrackId);
-                }
-                model.setViews([
-                    { bpPerPx: 0.1, offsetPx: 0 },
-                    { bpPerPx: 0.1, offsetPx: 0 },
-                ]);
-                model.setAssemblyNames(assembly2, assembly1);
-            });
-        }
-        catch (e) {
-            console.error(e);
-            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,
-        react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", className: classes.assemblySelector },
-            react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
-                    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(material_1.Grid, { item: true },
-                            react_1.default.createElement(ui_1.AssemblySelector, { selected: assembly2, onChange: val => {
+    return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [displayError ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: displayError }) : null, (0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Select assemblies for dotplot view" }), (0, jsx_runtime_1.jsxs)(material_1.Grid2, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [(0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "x-axis assembly", selected: assembly2, session: session, 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"))))),
-                react_1.default.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
+                                } }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "y-axis assembly", selected: assembly1, session: session, onChange: val => {
+                                    setAssembly1(val);
+                                } }), (0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                                        ;
+                                        (async () => {
+                                            try {
+                                                setError(undefined);
+                                                doSubmit({
+                                                    assembly1,
+                                                    assembly2,
+                                                    model,
+                                                });
+                                            }
+                                            catch (e) {
+                                                console.error(e);
+                                                setError(e);
+                                            }
+                                        })();
+                                    }, variant: "contained", color: "primary", children: "Launch" }) })] }), (0, jsx_runtime_1.jsx)(TrackSelector_1.default, { assembly2: assembly2, assembly1: assembly1, model: model })] })] }));
 });
 exports.default = DotplotImportForm;

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

@@ -1,6 +1,5 @@
-import React from 'react';
-import { DotplotViewModel } from '../model';
+import type { DotplotViewModel } from '../model';
 declare const PanButtons: ({ model, }: {
     model: DotplotViewModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default PanButtons;

package/dist/DotplotView/components/PanButtons.js

@@ -3,17 +3,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": 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 jsx_runtime_1 = require("react/jsx-runtime");
 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',
@@ -31,36 +30,18 @@ const useStyles = (0, mui_1.makeStyles)()({
 });
 const PanButtons = (0, mobx_react_1.observer)(function PanButtons({ model, }) {
     const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Paper, { className: classes.dpad, elevation: 6 },
-        react_1.default.createElement("div", null),
-        react_1.default.createElement(material_1.IconButton, { className: classes.icon, onClick: () => {
-                model.vview.scroll(100);
-            } },
-            react_1.default.createElement(ArrowDropUp_1.default, null)),
-        react_1.default.createElement("div", null),
-        react_1.default.createElement(material_1.IconButton, { className: classes.icon, onClick: () => {
-                model.hview.scroll(-100);
-            } },
-            react_1.default.createElement(ArrowLeft_1.default, null)),
-        react_1.default.createElement("div", null),
-        react_1.default.createElement(material_1.IconButton, { className: classes.icon, onClick: () => {
-                model.hview.scroll(100);
-            } },
-            react_1.default.createElement(ArrowRight_1.default, null)),
-        react_1.default.createElement("div", null),
-        react_1.default.createElement(material_1.IconButton, { className: classes.icon, onClick: () => {
-                model.vview.scroll(-100);
-            } },
-            react_1.default.createElement(ArrowDropDown_1.default, null)),
-        react_1.default.createElement("div", null),
-        react_1.default.createElement(material_1.IconButton, { className: classes.icon, onClick: () => {
-                model.zoomIn();
-            } },
-            react_1.default.createElement(ZoomIn_1.default, null)),
-        react_1.default.createElement("div", null),
-        react_1.default.createElement(material_1.IconButton, { className: classes.icon, onClick: () => {
-                model.zoomOut();
-            } },
-            react_1.default.createElement(ZoomOut_1.default, null))));
+    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.dpad, elevation: 6, children: [(0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
+                    model.vview.scroll(100);
+                }, children: (0, jsx_runtime_1.jsx)(ArrowDropUp_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
+                    model.hview.scroll(-100);
+                }, children: (0, jsx_runtime_1.jsx)(ArrowLeft_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
+                    model.hview.scroll(100);
+                }, children: (0, jsx_runtime_1.jsx)(ArrowRight_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
+                    model.vview.scroll(-100);
+                }, children: (0, jsx_runtime_1.jsx)(ArrowDropDown_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
+                    model.zoomIn();
+                }, children: (0, jsx_runtime_1.jsx)(ZoomIn_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
+                    model.zoomOut();
+                }, children: (0, jsx_runtime_1.jsx)(ZoomOut_1.default, {}) })] }));
 });
 exports.default = PanButtons;

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

@@ -1,23 +1,19 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+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];
@@ -28,15 +24,16 @@ 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)) },
         { field: 'effect', width: (0, util_1.measureGridWidth)(rows.map(r => r.effect)) },
     ];
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings" },
-        react_1.default.createElement(material_1.DialogContent, { className: classes.content },
-            react_1.default.createElement(material_1.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_1.default.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
-                react_1.default.createElement(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true })))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.content, children: [(0, jsx_runtime_1.jsx)(material_1.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." }), (0, jsx_runtime_1.jsx)("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }) })] }) }));
 });
 exports.default = WarningDialog;

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

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -29,7 +39,6 @@ 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(() => {