@jbrowse/plugin-linear-genome-view 2.5.0 → 2.6.2

package/esm/index.js

@@ -44,8 +44,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
     }
 }
 export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
-export { BlockMsg, baseLinearDisplayConfigSchema, BaseLinearDisplayComponent, BaseLinearDisplay, } from './BaseLinearDisplay';
+export { baseLinearDisplayConfigSchema, BaseLinearDisplay, BlockMsg, BaseLinearDisplayComponent, TrackHeightMixin, FeatureDensityMixin, TooLargeMessage, } from './BaseLinearDisplay';
 export { RefNameAutocomplete, SearchBox, } from './LinearGenomeView';
 export { renderToSvg, SVGTracks, totalHeight, SVGRuler, } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView';
 export { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory, } from './LinearBasicDisplay';
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.5.0",
+  "version": "2.6.2",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -22,14 +22,13 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
     "prebuild": "npm run clean",
     "build": "npm-run-all build:*",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo",
     "test": "cd ../..; jest plugins/linear-genome-view",
     "prepublishOnly": "yarn test",
@@ -66,5 +65,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js.map

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package/dist/BaseLinearDisplay/components/Block.js.map

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package/dist/BaseLinearDisplay/components/BlockMsg.js.map

@@ -1 +0,0 @@
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package/dist/BaseLinearDisplay/components/LinearBlocks.js.map

@@ -1 +0,0 @@
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package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js.map

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package/dist/BaseLinearDisplay/components/TooLargeMessage.js.map

@@ -1 +0,0 @@
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package/dist/BaseLinearDisplay/components/Tooltip.js.map

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package/dist/BaseLinearDisplay/models/configSchema.js.map

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package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js.map

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package/dist/LinearGenomeView/components/Cytobands.js.map

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package/dist/LinearGenomeView/components/ExportSvgDialog.js.map

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package/dist/LinearGenomeView/components/GetSequenceDialog.js.map

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package/dist/LinearGenomeView/components/Gridlines.js.map

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package/dist/LinearGenomeView/components/Header.js.map

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package/dist/LinearGenomeView/components/HelpDialog.js.map

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

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package/dist/LinearGenomeView/components/LinearGenomeView.js.map

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package/dist/LinearGenomeView/components/MiniControls.js.map

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package/dist/LinearGenomeView/components/OverviewRubberband.js.map

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package/dist/LinearGenomeView/components/OverviewScalebar.js.map

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package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts

@@ -1,23 +0,0 @@
-import React from 'react';
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { TextFieldProps as TFP } from '@mui/material';
-import { LinearGenomeViewModel } from '..';
-export interface Option {
-    group?: string;
-    result: BaseResult;
-}
-declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
-    model: LinearGenomeViewModel;
-    onSelect?: (region: BaseResult) => void;
-    onChange?: (val: string) => void;
-    assemblyName?: string;
-    value?: string;
-    fetchResults: (query: string) => Promise<BaseResult[]>;
-    style?: React.CSSProperties;
-    minWidth?: number;
-    maxWidth?: number;
-    showHelp?: boolean;
-    TextFieldProps?: TFP;
-}): JSX.Element;
-declare const _default: typeof RefNameAutocomplete;
-export default _default;

package/dist/LinearGenomeView/components/RefNameAutocomplete.js

@@ -1,189 +0,0 @@
-"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 mobx_react_1 = require("mobx-react");
-const util_1 = require("@jbrowse/core/util");
-const BaseResults_1 = __importStar(require("@jbrowse/core/TextSearch/BaseResults"));
-const material_1 = require("@mui/material");
-// icons
-const Search_1 = __importDefault(require("@mui/icons-material/Search"));
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
-// lazy
-const HelpDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./HelpDialog'))));
-function aggregateResults(results) {
-    const m = {};
-    for (const result of results) {
-        const displayString = result.getDisplayString();
-        if (!m[displayString]) {
-            m[displayString] = [];
-        }
-        m[displayString].push(result);
-    }
-    return m;
-}
-function getDeduplicatedResult(results) {
-    return Object.entries(aggregateResults(results)).map(([displayString, results]) => results.length === 1
-        ? {
-            result: results[0],
-        }
-        : {
-            // deduplicate a "multi-result"
-            result: new BaseResults_1.default({
-                displayString,
-                results,
-                label: displayString,
-            }),
-        });
-}
-// the logic of this method is to only apply a filter to RefSequenceResults
-// because they do not have a matchedObject. the trix search results already
-// filter so don't need re-filtering
-function filterOptions(options, searchQuery) {
-    return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
-        result.matchedObject);
-}
-function getFiltered(opts, inputValue) {
-    const filtered = filterOptions(opts, inputValue.toLocaleLowerCase());
-    return [
-        ...filtered.slice(0, 100),
-        ...(filtered.length > 100
-            ? [
-                {
-                    group: 'limitOption',
-                    result: new BaseResults_1.default({
-                        label: 'keep typing for more results',
-                    }),
-                },
-            ]
-            : []),
-    ];
-}
-function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
-    const session = (0, util_1.getSession)(model);
-    const { assemblyManager } = session;
-    const [open, setOpen] = (0, react_1.useState)(false);
-    const [loaded, setLoaded] = (0, react_1.useState)(true);
-    const [currentSearch, setCurrentSearch] = (0, react_1.useState)('');
-    const [inputValue, setInputValue] = (0, react_1.useState)('');
-    const [searchOptions, setSearchOptions] = (0, react_1.useState)();
-    const debouncedSearch = (0, util_1.useDebounce)(currentSearch, 300);
-    const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
-    const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
-    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
-    const options = (0, react_1.useMemo)(() => (regions === null || regions === void 0 ? void 0 : regions.map(option => ({
-        result: new BaseResults_1.RefSequenceResult({
-            refName: option.refName,
-            label: option.refName,
-            matchedAttribute: 'refName',
-        }),
-    }))) || [], [regions]);
-    (0, react_1.useEffect)(() => {
-        let active = true;
-        (async () => {
-            try {
-                if (debouncedSearch === '' || !assemblyName) {
-                    return;
-                }
-                setLoaded(false);
-                const results = await fetchResults(debouncedSearch);
-                if (active) {
-                    setLoaded(true);
-                    setSearchOptions(getDeduplicatedResult(results));
-                }
-            }
-            catch (e) {
-                console.error(e);
-                if (active) {
-                    session.notify(`${e}`, 'error');
-                }
-            }
-        })();
-        return () => {
-            active = false;
-        };
-    }, [assemblyName, fetchResults, debouncedSearch, session, model]);
-    const inputBoxVal = coarseVisibleLocStrings || value || '';
-    // heuristic, text width + 60 accommodates help icon and search
-    // icon
-    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth);
-    // notes on implementation:
-    // The selectOnFocus setting helps highlight the field when clicked
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
-                setInputValue(newInputValue);
-                onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
-            }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
-                setOpen(false);
-                setLoaded(true);
-                if (hasDisplayedRegions) {
-                    setCurrentSearch('');
-                    setSearchOptions(undefined);
-                }
-            }, onChange: (_event, selectedOption) => {
-                if (!selectedOption || !assemblyName) {
-                    return;
-                }
-                if (typeof selectedOption === 'string') {
-                    // handles string inputs on keyPress enter
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
-                }
-                else {
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
-                }
-                setInputValue(inputBoxVal);
-            }, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? options : searchOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => getFiltered(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
-}
-function AutocompleteTextField({ TextFieldProps, inputBoxVal, params, showHelp, setInputValue, setCurrentSearch, }) {
-    const { helperText, InputProps = {} } = TextFieldProps;
-    return (react_1.default.createElement(material_1.TextField, { onBlur: () => 
-        // this is used to restore a refName or the non-user-typed input
-        // to the box on blurring
-        setInputValue(inputBoxVal), ...params, ...TextFieldProps, size: "small", helperText: helperText, InputProps: {
-            ...params.InputProps,
-            ...InputProps,
-            endAdornment: (react_1.default.createElement(EndAdornment, { showHelp: showHelp, endAdornment: params.InputProps.endAdornment })),
-        }, placeholder: "Search for location", onChange: e => setCurrentSearch(e.target.value) }));
-}
-function HelpAdornment() {
-    const [isHelpDialogDisplayed, setHelpDialogDisplayed] = (0, react_1.useState)(false);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpDialogDisplayed(true), size: "small" },
-            react_1.default.createElement(Help_1.default, { fontSize: "small" })),
-        isHelpDialogDisplayed ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-            react_1.default.createElement(HelpDialog, { handleClose: () => setHelpDialogDisplayed(false) }))) : null));
-}
-function EndAdornment({ showHelp, endAdornment, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.InputAdornment, { position: "end", style: { marginRight: 7 } },
-            react_1.default.createElement(Search_1.default, { fontSize: "small" }),
-            showHelp ? react_1.default.createElement(HelpAdornment, null) : null),
-        endAdornment));
-}
-exports.default = (0, mobx_react_1.observer)(RefNameAutocomplete);
-//# sourceMappingURL=RefNameAutocomplete.js.map

package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map

@@ -1 +0,0 @@
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