@jbrowse/plugin-dotplot-view 2.6.1

package/dist/DotplotView/components/ImportForm.js

@@ -0,0 +1,121 @@
+"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 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 useStyles = (0, mui_1.makeStyles)()(theme => ({
+    importFormContainer: {
+        padding: theme.spacing(4),
+        margin: '0 auto',
+    },
+    assemblySelector: {
+        width: '75%',
+        margin: '0 auto',
+    },
+}));
+function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
+    const [choice, setChoice] = (0, react_1.useState)('none');
+    (0, react_1.useEffect)(() => {
+        if (choice === 'none') {
+            setSessionTrackData(undefined);
+            setShowTrackId(undefined);
+        }
+    }, [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));
+}
+const DotplotImportForm = (0, mobx_react_1.observer)(({ 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 => 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 })))));
+});
+exports.default = DotplotImportForm;
+//# sourceMappingURL=ImportForm.js.map

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

@@ -0,0 +1 @@
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package/dist/DotplotView/components/ImportSyntenyTrackSelector.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { DotplotViewModel } from '../model';
+declare const Selector: ({ model, assembly1, assembly2, setShowTrackId, }: {
+    model: DotplotViewModel;
+    assembly1: string;
+    assembly2: string;
+    setShowTrackId: (arg: string) => void;
+}) => React.JSX.Element;
+export default Selector;

package/dist/DotplotView/components/ImportSyntenyTrackSelector.js

@@ -0,0 +1,69 @@
+"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;
+};
+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 Icons_1 = require("@jbrowse/core/ui/Icons");
+function f(track, assembly1, assembly2) {
+    const assemblyNames = (0, configuration_1.readConfObject)(track, 'assemblyNames');
+    return (assemblyNames.includes(assembly1) &&
+        assemblyNames.includes(assembly2) &&
+        track.type.includes('Synteny'));
+}
+const Selector = (0, mobx_react_1.observer)(({ model, assembly1, assembly2, setShowTrackId, }) => {
+    var _a;
+    const session = (0, util_1.getSession)(model);
+    const { tracks, sessionTracks } = session;
+    const allTracks = [...tracks, ...sessionTracks];
+    const filteredTracks = allTracks.filter(t => f(t, assembly2, assembly1));
+    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 } },
+        react_1.default.createElement(material_1.Typography, { paragraph: true }, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
+        react_1.default.createElement(material_1.Typography, { paragraph: true },
+            "Note: there is a track selector ",
+            react_1.default.createElement("i", null, "inside"),
+            " the DotplotView, which can turn on one or more SyntenyTracks (more than one can be displayed at once). Look for the track selector icon ",
+            react_1.default.createElement(Icons_1.TrackSelector, null)),
+        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
+});
+exports.default = Selector;
+//# sourceMappingURL=ImportSyntenyTrackSelector.js.map

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

@@ -0,0 +1 @@
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package/dist/DotplotView/components/PanButtons.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { DotplotViewModel } from '../model';
+declare const _default: ({ model, }: {
+    model: DotplotViewModel;
+}) => React.JSX.Element;
+export default _default;

package/dist/DotplotView/components/PanButtons.js

@@ -0,0 +1,60 @@
+"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 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 useStyles = (0, mui_1.makeStyles)()({
+    dpad: {
+        display: 'grid',
+        gridTemplateColumns: 'repeat(3, 1fr)',
+        margin: 0,
+        position: 'absolute',
+        right: 50,
+        zIndex: 1000,
+        top: 50,
+    },
+    icon: {
+        padding: 0,
+        margin: 0,
+    },
+});
+exports.default = (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.hview.zoomIn();
+                model.vview.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.hview.zoomOut();
+                model.vview.zoomOut();
+            } },
+            react_1.default.createElement(ZoomOut_1.default, null))));
+});
+//# sourceMappingURL=PanButtons.js.map

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

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

@@ -0,0 +1,16 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+interface TrackWarning {
+    configuration: AnyConfigurationModel;
+    displays: {
+        warnings: {
+            message: string;
+            effect: string;
+        }[];
+    }[];
+}
+declare const _default: ({ trackWarnings, handleClose, }: {
+    handleClose: () => void;
+    trackWarnings: TrackWarning[];
+}) => React.JSX.Element;
+export default _default;

package/dist/DotplotView/components/WarningDialog.js

@@ -0,0 +1,41 @@
+"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 ui_1 = require("@jbrowse/core/ui");
+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,
+    },
+});
+exports.default = (0, mobx_react_1.observer)(function WarningDialog({ trackWarnings, handleClose, }) {
+    const { classes } = useStyles();
+    const rows = [];
+    for (let i = 0; i < trackWarnings.length; i++) {
+        const track = trackWarnings[i];
+        const name = (0, configuration_1.getConf)(track, 'name');
+        for (let j = 0; j < track.displays[0].warnings.length; j++) {
+            const warning = track.displays[0].warnings[j];
+            rows.push({ name, ...warning, id: i + '_' + j });
+        }
+    }
+    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 })))));
+});
+//# sourceMappingURL=WarningDialog.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"WarningDialog.js","sourceRoot":"","sources":["../../../src/DotplotView/components/WarningDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAgE;AAChE,yCAAyC;AACzC,2CAAqC;AACrC,uCAA0C;AAC1C,kDAA2C;AAC3C,+DAA4E;AAC5E,6CAAqD;AAErD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,OAAO,EAAE;QACP,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAOF,kBAAe,IAAA,qBAAQ,EAAC,SAAS,aAAa,CAAC,EAC7C,aAAa,EACb,WAAW,GAIZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,EAKV,CAAA;IACH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC7C,MAAM,KAAK,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,IAAI,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1D,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC7C,IAAI,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,OAAO,EAAE,EAAE,EAAE,CAAC,GAAG,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;SACjD;KACF;IACD,MAAM,OAAO,GAAG;QACd,EAAE,KAAK,EAAE,MAAM,EAAE;QACjB,EAAE,KAAK,EAAE,SAAS,EAAE,KAAK,EAAE,IAAA,uBAAgB,EAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,EAAE;QACvE,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,IAAA,uBAAgB,EAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE;KACtE,CAAA;IACD,OAAO,CACL,8BAAC,WAAM,IACL,IAAI,QACJ,OAAO,EAAE,WAAW,EACpB,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,gCAAgC;QAEtC,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,OAAO;YACvC,8BAAC,4BAAiB,oQAKE;YACpB,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE;gBAC1D,8BAAC,sBAAQ,IACP,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,OAAO,EAChB,0BAA0B,QAC1B,SAAS,EAAE,EAAE,EACb,iBAAiB,SACjB,CACE,CACQ,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA"}

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

@@ -0,0 +1,19 @@
+import { BaseBlock } from '@jbrowse/core/util/blockTypes';
+import { Dotplot1DViewModel } from '../model';
+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;
+};
+export declare function makeTicks(regions: BaseBlock[], bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
+    type: string;
+    base: number;
+    index: number;
+    refName: string;
+}[];

package/dist/DotplotView/components/util.js

@@ -0,0 +1,90 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeTicks = exports.chooseGridPitch = exports.getBlockLabelKeysToHide = exports.locstr = void 0;
+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')}`;
+}
+exports.locstr = locstr;
+function getBlockLabelKeysToHide(blocks, length, viewOffsetPx) {
+    const blockLabelKeysToHide = new Set();
+    const sortedBlocks = [...blocks].sort((a, b) => {
+        const alen = a.end - a.start;
+        const blen = b.end - b.start;
+        return blen - alen;
+    });
+    const positions = Array.from({ length: Math.round(length) });
+    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)) {
+            blockLabelKeysToHide.add(key);
+        }
+        else {
+            positions.fill(true, ...labelBounds);
+        }
+    }
+    return blockLabelKeysToHide;
+}
+exports.getBlockLabelKeysToHide = getBlockLabelKeysToHide;
+/**
+ * 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;
+    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    let majorPitch = 10 ** majorMagnitude;
+    while (majorPitch < minMajorPitchBp) {
+        majorPitch *= 2;
+        if (majorPitch >= minMajorPitchBp) {
+            break;
+        }
+        majorPitch *= 2.5;
+    }
+    majorPitch = Math.max(majorPitch, 5);
+    const majorPitchPx = majorPitch / scale;
+    let minorPitch = 0;
+    if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
+        minorPitch = majorPitch / 10;
+    }
+    else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
+        minorPitch = majorPitch / 5;
+    }
+    else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
+        minorPitch = majorPitch / 2;
+    }
+    return { majorPitch, minorPitch };
+}
+exports.chooseGridPitch = chooseGridPitch;
+function makeTicks(regions, bpPerPx, emitMajor = true, emitMinor = true) {
+    const ticks = [];
+    const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
+    const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
+    for (let i = 0; i < regions.length; i++) {
+        const region = regions[i];
+        const { start, end, refName } = region;
+        let index = 0;
+        const minBase = start;
+        const maxBase = end;
+        for (let base = Math.floor(minBase / iterPitch) * iterPitch; base < Math.ceil(maxBase / iterPitch) * iterPitch + 1; base += iterPitch) {
+            if (emitMinor && base % gridPitch.majorPitch) {
+                ticks.push({ type: 'minor', base: base - 1, index, refName });
+                index += 1;
+            }
+            else if (emitMajor &&
+                Math.abs(base - region.start) > gridPitch.minorPitch) {
+                ticks.push({ type: 'major', base: base - 1, index, refName });
+                index += 1;
+            }
+        }
+    }
+    return ticks;
+}
+exports.makeTicks = makeTicks;
+//# sourceMappingURL=util.js.map

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

@@ -0,0 +1 @@
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package/dist/DotplotView/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pluginManager: PluginManager): void;

package/dist/DotplotView/index.js

@@ -0,0 +1,44 @@
+"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 = require("react");
+const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
+// locals
+const model_1 = __importDefault(require("./model"));
+function default_1(pluginManager) {
+    pluginManager.addViewType(() => {
+        return new ViewType_1.default({
+            name: 'DotplotView',
+            displayName: 'Dotplot view',
+            stateModel: (0, model_1.default)(pluginManager),
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/DotplotView')))),
+        });
+    });
+}
+exports.default = default_1;
+//# sourceMappingURL=index.js.map

package/dist/DotplotView/index.js.map

@@ -0,0 +1 @@
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