@jbrowse/plugin-linear-genome-view 2.4.2 → 2.6.1

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

@@ -0,0 +1,111 @@
+"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");
+const util_2 = require("./util");
+const AutocompleteTextField_1 = __importDefault(require("./AutocompleteTextField"));
+exports.default = (0, mobx_react_1.observer)(function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
+    var _a;
+    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;
+    (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((0, util_2.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)
+                ? ((_a = assembly === null || assembly === void 0 ? void 0 : assembly.regions) === null || _a === void 0 ? void 0 : _a.map(option => ({
+                    result: new BaseResults_1.RefSequenceResult({
+                        refName: option.refName,
+                        label: option.refName,
+                        matchedAttribute: 'refName',
+                    }),
+                }))) || []
+                : searchOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => (0, util_2.getFiltered)(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField_1.default, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
+});
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/RefNameAutocomplete/util.d.ts

@@ -0,0 +1,12 @@
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+export interface Option {
+    group?: string;
+    result: BaseResult;
+}
+export declare function getFiltered(opts: Option[], inputValue: string): Option[];
+export declare function aggregateResults(results: BaseResult[]): {
+    [key: string]: BaseResult[];
+};
+export declare function getDeduplicatedResult(results: BaseResult[]): {
+    result: BaseResult;
+}[];

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

@@ -0,0 +1,59 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getDeduplicatedResult = exports.aggregateResults = exports.getFiltered = void 0;
+const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+// filter so don't need re-filtering
+function filterOptions(options, searchQuery) {
+    return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
+        result.matchedObject);
+}
+// 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
+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',
+                    }),
+                },
+            ]
+            : []),
+    ];
+}
+exports.getFiltered = getFiltered;
+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;
+}
+exports.aggregateResults = aggregateResults;
+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,
+            }),
+        });
+}
+exports.getDeduplicatedResult = getDeduplicatedResult;
+//# sourceMappingURL=util.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/Rubberband.d.ts

@@ -4,6 +4,6 @@ type LGV = LinearGenomeViewModel;
 declare function Rubberband({ model, ControlComponent, }: {
     model: LGV;
     ControlComponent?: React.ReactElement;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof Rubberband;
 export default _default;

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

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 interface Offset {
     coord: number;
     refName?: string;
@@ -10,5 +10,5 @@ export default function RubberbandSpan({ leftBpOffset, rightBpOffset, numOfBpSel
     numOfBpSelected?: number;
     left: number;
     width: number;
-}): JSX.Element;
+}): React.JSX.Element;
 export {};

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

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '..';
 declare function SearchBox({ model, showHelp, }: {
     showHelp?: boolean;
     model: LinearGenomeViewModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SearchBox;
 export default _default;

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

@@ -1,7 +1,10 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearGenomeViewModel } from '../..';
-export default function SearchResultsDialog({ model, optAssemblyName, handleClose, }: {
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+export default function SearchResultsDialog({ model, assemblyName, searchQuery, searchResults, handleClose, }: {
     model: LinearGenomeViewModel;
-    optAssemblyName?: string;
+    assemblyName?: string;
+    searchQuery: string;
+    searchResults?: BaseResult[];
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;

package/dist/LinearGenomeView/components/SearchResultsDialog.js

@@ -4,94 +4,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
-function SearchResultsDialog({ model, optAssemblyName, handleClose, }) {
-    var _a, _b;
-    const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, util_1.getEnv)(session);
-    const { assemblyManager } = session;
-    let assemblyName = optAssemblyName;
-    if (model.displayedRegions.length > 0) {
-        assemblyName = (_a = model.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.assemblyName;
-    }
-    if (!assemblyName) {
-        throw new Error(`Assembly name not found`);
-    }
-    const assembly = assemblyManager.get(assemblyName);
-    if (!assembly) {
-        throw new Error(`assembly ${assemblyName} not found`);
-    }
-    if (!assembly.regions) {
-        throw new Error(`assembly ${assemblyName} regions not loaded`);
-    }
-    const assemblyRegions = assembly.regions;
-    async function handleClick(location) {
-        try {
-            const newRegion = assemblyRegions.find(region => location === region.refName);
-            if (newRegion) {
-                model.setDisplayedRegions([newRegion]);
-                // we use showAllRegions after setDisplayedRegions to make the entire
-                // region visible, xref #1703
-                model.showAllRegions();
-            }
-            else {
-                await model.navToLocString(location, assemblyName);
-            }
-        }
-        catch (e) {
-            console.warn(e);
-            session.notify(`${e}`, 'warning');
-        }
-    }
-    function getTrackName(trackId) {
-        var _a;
-        if (trackId) {
-            const schema = pluginManager.pluggableConfigSchemaType('track');
-            const configuration = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(model), trackId);
-            return ((_a = configuration === null || configuration === void 0 ? void 0 : configuration.name) === null || _a === void 0 ? void 0 : _a.value) || '';
-        }
-        return '';
-    }
+const SearchResultsTable_1 = __importDefault(require("./SearchResultsTable"));
+function SearchResultsDialog({ model, assemblyName, searchQuery, searchResults, handleClose, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, maxWidth: "xl", onClose: handleClose, title: "Search results" },
-        react_1.default.createElement(material_1.DialogContent, null, !((_b = model.searchResults) === null || _b === void 0 ? void 0 : _b.length) ? (react_1.default.createElement(material_1.Typography, null,
+        react_1.default.createElement(material_1.DialogContent, null, !(searchResults === null || searchResults === void 0 ? void 0 : searchResults.length) ? (react_1.default.createElement(material_1.Typography, null,
             "No results found for ",
-            react_1.default.createElement("b", null, model.searchQuery))) : (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement("b", null, searchQuery))) : (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement(material_1.Typography, null,
                 "Showing results for ",
-                react_1.default.createElement("b", null, model.searchQuery)),
-            react_1.default.createElement(material_1.TableContainer, { component: material_1.Paper },
-                react_1.default.createElement(material_1.Table, null,
-                    react_1.default.createElement(material_1.TableHead, null,
-                        react_1.default.createElement(material_1.TableRow, null,
-                            react_1.default.createElement(material_1.TableCell, null, "Name"),
-                            react_1.default.createElement(material_1.TableCell, { align: "right" }, "Location"),
-                            react_1.default.createElement(material_1.TableCell, { align: "right" }, "Track"),
-                            react_1.default.createElement(material_1.TableCell, { align: "right" }))),
-                    react_1.default.createElement(material_1.TableBody, null, model.searchResults.map(result => (react_1.default.createElement(material_1.TableRow, { key: `${result.getId()}` },
-                        react_1.default.createElement(material_1.TableCell, { component: "th", scope: "row" }, result.getLabel()),
-                        react_1.default.createElement(material_1.TableCell, { align: "right" }, result.getLocation()),
-                        react_1.default.createElement(material_1.TableCell, { align: "right" }, getTrackName(result.getTrackId()) || 'N/A'),
-                        react_1.default.createElement(material_1.TableCell, { align: "right" },
-                            react_1.default.createElement(material_1.Button, { onClick: async () => {
-                                    try {
-                                        const location = result.getLocation();
-                                        if (location) {
-                                            await handleClick(location);
-                                            const resultTrackId = result.getTrackId();
-                                            if (resultTrackId) {
-                                                model.showTrack(resultTrackId);
-                                            }
-                                        }
-                                    }
-                                    catch (e) {
-                                        console.error(e);
-                                        session.notify(`${e}`, 'error');
-                                    }
-                                    handleClose();
-                                }, color: "primary", variant: "contained" }, "Go"))))))))))),
+                react_1.default.createElement("b", null, searchQuery)),
+            react_1.default.createElement(SearchResultsTable_1.default, { model: model, handleClose: handleClose, assemblyName: assemblyName, searchResults: searchResults })))),
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), color: "primary" }, "Cancel"))));

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

@@ -1 +1 @@
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+{"version":3,"file":"SearchResultsDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/SearchResultsDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,yCAAyC;AACzC,4CAMsB;AAItB,8EAAqD;AAErD,SAAwB,mBAAmB,CAAC,EAC1C,KAAK,EACL,YAAY,EACZ,WAAW,EACX,aAAa,EACb,WAAW,GAOZ;IACC,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,QAAQ,EAAC,IAAI,EAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACrE,8BAAC,wBAAa,QACX,CAAC,CAAA,aAAa,aAAb,aAAa,uBAAb,aAAa,CAAE,MAAM,CAAA,CAAC,CAAC,CAAC,CACxB,8BAAC,qBAAU;;YACY,yCAAI,WAAW,CAAK,CAC9B,CACd,CAAC,CAAC,CAAC,CACF;YACE,8BAAC,qBAAU;;gBACW,yCAAI,WAAW,CAAK,CAC7B;YACb,8BAAC,4BAAkB,IACjB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,WAAW,EACxB,YAAY,EAAE,YAAY,EAC1B,aAAa,EAAE,aAAa,GAC5B,CACD,CACJ,CACa;QAChB,8BAAC,kBAAO,OAAG;QACX,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,aAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC;AA1CD,sCA0CC"}

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

@@ -0,0 +1,9 @@
+import React from 'react';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { LinearGenomeViewModel } from '../..';
+export default function SearchResultsTable({ searchResults, assemblyName: optAssemblyName, model, handleClose, }: {
+    searchResults: BaseResult[];
+    assemblyName?: string;
+    model: LinearGenomeViewModel;
+    handleClose: () => void;
+}): React.JSX.Element;

package/dist/LinearGenomeView/components/SearchResultsTable.js

@@ -0,0 +1,83 @@
+"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 mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+function SearchResultsTable({ searchResults, assemblyName: optAssemblyName, model, handleClose, }) {
+    var _a;
+    const session = (0, util_1.getSession)(model);
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    const { assemblyManager } = session;
+    const assemblyName = optAssemblyName || ((_a = model.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.assemblyName);
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    if (!assembly.regions) {
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
+    }
+    function getTrackName(trackId) {
+        var _a;
+        if (trackId) {
+            const schema = pluginManager.pluggableConfigSchemaType('track');
+            const configuration = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(model), trackId);
+            return ((_a = configuration === null || configuration === void 0 ? void 0 : configuration.name) === null || _a === void 0 ? void 0 : _a.value) || '';
+        }
+        return '';
+    }
+    async function handleClick(location) {
+        var _a;
+        try {
+            const newRegion = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.regions) === null || _a === void 0 ? void 0 : _a.find(region => location === region.refName);
+            if (newRegion) {
+                model.setDisplayedRegions([newRegion]);
+                // we use showAllRegions after setDisplayedRegions to make the entire
+                // region visible, xref #1703
+                model.showAllRegions();
+            }
+            else {
+                await model.navToLocString(location, assemblyName);
+            }
+        }
+        catch (e) {
+            console.warn(e);
+            session.notify(`${e}`, 'warning');
+        }
+    }
+    return (react_1.default.createElement(material_1.TableContainer, { component: material_1.Paper },
+        react_1.default.createElement(material_1.Table, null,
+            react_1.default.createElement(material_1.TableHead, null,
+                react_1.default.createElement(material_1.TableRow, null,
+                    react_1.default.createElement(material_1.TableCell, null, "Name"),
+                    react_1.default.createElement(material_1.TableCell, { align: "right" }, "Location"),
+                    react_1.default.createElement(material_1.TableCell, { align: "right" }, "Track"),
+                    react_1.default.createElement(material_1.TableCell, { align: "right" }))),
+            react_1.default.createElement(material_1.TableBody, null, searchResults.map(result => (react_1.default.createElement(material_1.TableRow, { key: `${result.getId()}` },
+                react_1.default.createElement(material_1.TableCell, { component: "th", scope: "row" }, result.getLabel()),
+                react_1.default.createElement(material_1.TableCell, { align: "right" }, result.getLocation()),
+                react_1.default.createElement(material_1.TableCell, { align: "right" }, getTrackName(result.getTrackId()) || 'N/A'),
+                react_1.default.createElement(material_1.TableCell, { align: "right" },
+                    react_1.default.createElement(material_1.Button, { onClick: async () => {
+                            try {
+                                const location = result.getLocation();
+                                if (location) {
+                                    await handleClick(location);
+                                    const resultTrackId = result.getTrackId();
+                                    if (resultTrackId) {
+                                        model.showTrack(resultTrackId);
+                                    }
+                                }
+                            }
+                            catch (e) {
+                                console.error(e);
+                                session.notify(`${e}`, 'error');
+                            }
+                            handleClose();
+                        }, color: "primary", variant: "contained" }, "Go")))))))));
+}
+exports.default = SearchResultsTable;
+//# sourceMappingURL=SearchResultsTable.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"SearchResultsTable.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/SearchResultsTable.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CASsB;AAEtB,qDAA4D;AAC5D,6CAAuD;AAKvD,SAAwB,kBAAkB,CAAC,EACzC,aAAa,EACb,YAAY,EAAE,eAAe,EAC7B,KAAK,EACL,WAAW,GAMZ;;IACC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,OAAO,CAAC,CAAA;IACzC,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IACnC,MAAM,YAAY,GAChB,eAAe,KAAI,MAAA,KAAK,CAAC,gBAAgB,CAAC,CAAC,CAAC,0CAAE,YAAY,CAAA,CAAA;IAE5D,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,YAAY,YAAY,YAAY,CAAC,CAAA;KACtD;IACD,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE;QACrB,MAAM,IAAI,KAAK,CAAC,YAAY,YAAY,qBAAqB,CAAC,CAAA;KAC/D;IAED,SAAS,YAAY,CAAC,OAA2B;;QAC/C,IAAI,OAAO,EAAE;YACX,MAAM,MAAM,GAAG,aAAa,CAAC,yBAAyB,CAAC,OAAO,CAAC,CAAA;YAC/D,MAAM,aAAa,GAAG,IAAA,mCAAiB,EAAC,MAAM,EAAE,IAAA,yBAAO,EAAC,KAAK,CAAC,EAAE,OAAO,CAAC,CAAA;YACxE,OAAO,CAAA,MAAA,aAAa,aAAb,aAAa,uBAAb,aAAa,CAAE,IAAI,0CAAE,KAAK,KAAI,EAAE,CAAA;SACxC;QACD,OAAO,EAAE,CAAA;IACX,CAAC;IACD,KAAK,UAAU,WAAW,CAAC,QAAgB;;QACzC,IAAI;YACF,MAAM,SAAS,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,OAAO,0CAAE,IAAI,CACvC,MAAM,CAAC,EAAE,CAAC,QAAQ,KAAK,MAAM,CAAC,OAAO,CACtC,CAAA;YACD,IAAI,SAAS,EAAE;gBACb,KAAK,CAAC,mBAAmB,CAAC,CAAC,SAAS,CAAC,CAAC,CAAA;gBACtC,qEAAqE;gBACrE,6BAA6B;gBAC7B,KAAK,CAAC,cAAc,EAAE,CAAA;aACvB;iBAAM;gBACL,MAAM,KAAK,CAAC,cAAc,CAAC,QAAQ,EAAE,YAAY,CAAC,CAAA;aACnD;SACF;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;SAClC;IACH,CAAC;IACD,OAAO,CACL,8BAAC,yBAAc,IAAC,SAAS,EAAE,gBAAK;QAC9B,8BAAC,gBAAK;YACJ,8BAAC,oBAAS;gBACR,8BAAC,mBAAQ;oBACP,8BAAC,oBAAS,eAAiB;oBAC3B,8BAAC,oBAAS,IAAC,KAAK,EAAC,OAAO,eAAqB;oBAC7C,8BAAC,oBAAS,IAAC,KAAK,EAAC,OAAO,YAAkB;oBAC1C,8BAAC,oBAAS,IAAC,KAAK,EAAC,OAAO,GAAG,CAClB,CACD;YACZ,8BAAC,oBAAS,QACP,aAAa,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAC3B,8BAAC,mBAAQ,IAAC,GAAG,EAAE,GAAG,MAAM,CAAC,KAAK,EAAE,EAAE;gBAChC,8BAAC,oBAAS,IAAC,SAAS,EAAC,IAAI,EAAC,KAAK,EAAC,KAAK,IAClC,MAAM,CAAC,QAAQ,EAAE,CACR;gBACZ,8BAAC,oBAAS,IAAC,KAAK,EAAC,OAAO,IAAE,MAAM,CAAC,WAAW,EAAE,CAAa;gBAC3D,8BAAC,oBAAS,IAAC,KAAK,EAAC,OAAO,IACrB,YAAY,CAAC,MAAM,CAAC,UAAU,EAAE,CAAC,IAAI,KAAK,CACjC;gBACZ,8BAAC,oBAAS,IAAC,KAAK,EAAC,OAAO;oBACtB,8BAAC,iBAAM,IACL,OAAO,EAAE,KAAK,IAAI,EAAE;4BAClB,IAAI;gCACF,MAAM,QAAQ,GAAG,MAAM,CAAC,WAAW,EAAE,CAAA;gCACrC,IAAI,QAAQ,EAAE;oCACZ,MAAM,WAAW,CAAC,QAAQ,CAAC,CAAA;oCAC3B,MAAM,aAAa,GAAG,MAAM,CAAC,UAAU,EAAE,CAAA;oCACzC,IAAI,aAAa,EAAE;wCACjB,KAAK,CAAC,SAAS,CAAC,aAAa,CAAC,CAAA;qCAC/B;iCACF;6BACF;4BAAC,OAAO,CAAC,EAAE;gCACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gCAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;6BAChC;4BACD,WAAW,EAAE,CAAA;wBACf,CAAC,EACD,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,SAGZ,CACC,CACH,CACZ,CAAC,CACQ,CACN,CACO,CAClB,CAAA;AACH,CAAC;AAtGD,qCAsGC"}

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

@@ -1,10 +1,10 @@
-/// <reference types="react" />
+import React from 'react';
 declare function SequenceDialog({ model, handleClose, }: {
     model: {
         assemblyNames: string[];
         toggleTrack(trackId: string): void;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SequenceDialog;
 export default _default;

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

@@ -1,10 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
-declare function TrackContainer({ model, track, }: {
+declare const _default: ({ model, track, }: {
     model: LGV;
     track: BaseTrackModel;
-}): JSX.Element;
-declare const _default: typeof TrackContainer;
+}) => React.JSX.Element;
 export default _default;

package/dist/LinearGenomeView/components/TrackContainer.js

@@ -32,10 +32,10 @@ const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const react_error_boundary_1 = require("react-error-boundary");
-const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-const TrackLabel_1 = __importDefault(require("./TrackLabel"));
+const TrackLabelContainer_1 = __importDefault(require("./TrackLabelContainer"));
+const TrackRenderingContainer_1 = __importDefault(require("./TrackRenderingContainer"));
 const useStyles = (0, mui_1.makeStyles)()({
     root: {
         marginTop: 2,
@@ -54,82 +54,32 @@ const useStyles = (0, mui_1.makeStyles)()({
         width: '100%',
         zIndex: 3,
     },
-    trackLabel: {
-        zIndex: 3,
-    },
-    // aligns with block boundaries. check for example the breakpoint split view
-    // demo to see if features align if wanting to change things
-    renderingComponentContainer: {
-        position: 'absolute',
-        // -1 offset because of the 1px border of the Paper
-        left: -1,
-        height: '100%',
-        width: '100%',
-    },
-    trackLabelOffset: {
-        position: 'relative',
-        display: 'inline-block',
-    },
-    trackLabelOverlap: {
-        position: 'absolute',
-    },
-    trackRenderingContainer: {
-        overflowY: 'auto',
-        overflowX: 'hidden',
-        whiteSpace: 'nowrap',
-        position: 'relative',
-        background: 'none',
-        zIndex: 2,
-    },
 });
-const TrackContainerLabel = (0, mobx_react_1.observer)(({ model, view }) => {
-    const { classes, cx } = useStyles();
-    const display = model.displays[0];
-    const { trackLabel, trackLabelOverlap, trackLabelOffset } = classes;
-    const labelStyle = view.trackLabels !== 'overlapping' || display.prefersOffset
-        ? trackLabelOffset
-        : trackLabelOverlap;
-    return view.trackLabels !== 'hidden' ? (react_1.default.createElement(TrackLabel_1.default, { track: model, className: cx(trackLabel, labelStyle) })) : null;
-});
-function TrackContainer({ model, track, }) {
+exports.default = (0, mobx_react_1.observer)(function TrackContainer({ model, track, }) {
     const { classes } = useStyles();
     const display = track.displays[0];
-    const { horizontalScroll, draggingTrackId, moveTrack } = model;
-    const { height, RenderingComponent, DisplayBlurb } = display;
-    const trackId = (0, configuration_1.getConf)(track, 'trackId');
-    const ref = (0, react_1.useRef)(null);
+    const { draggingTrackId } = model;
+    const ref2 = (0, react_1.useRef)(null);
     const dimmed = draggingTrackId !== undefined && draggingTrackId !== display.id;
-    const minimized = track.minimized;
     const debouncedOnDragEnter = (0, util_1.useDebouncedCallback)(() => {
         if ((0, mobx_state_tree_1.isAlive)(display) && dimmed) {
-            moveTrack(draggingTrackId, track.id);
+            model.moveTrack(draggingTrackId, track.id);
         }
     }, 100);
-    (0, react_1.useEffect)(() => {
-        if (ref.current) {
-            model.trackRefs[trackId] = ref.current;
-        }
-        return () => {
-            delete model.trackRefs[trackId];
-        };
-    }, [model.trackRefs, trackId]);
-    return (react_1.default.createElement(material_1.Paper, { className: classes.root, variant: "outlined" },
-        react_1.default.createElement(TrackContainerLabel, { model: track, view: model }),
-        react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { key: track.id, FallbackComponent: ({ error }) => react_1.default.createElement(ui_1.ErrorMessage, { error: error }) },
-            react_1.default.createElement("div", { className: classes.trackRenderingContainer, style: { height: minimized ? 20 : height }, onScroll: evt => display.setScrollTop(evt.currentTarget.scrollTop), onDragEnter: debouncedOnDragEnter, "data-testid": `trackRenderingContainer-${model.id}-${trackId}` }, !minimized ? (react_1.default.createElement(react_1.default.Fragment, null,
-                react_1.default.createElement("div", { ref: ref, className: classes.renderingComponentContainer, style: { transform: `scaleX(${model.scaleFactor})` } },
-                    react_1.default.createElement(RenderingComponent, { model: display, onHorizontalScroll: horizontalScroll })),
-                DisplayBlurb ? (react_1.default.createElement("div", { style: {
-                        position: 'absolute',
-                        left: 0,
-                        top: display.height - 20,
-                    } },
-                    react_1.default.createElement(DisplayBlurb, { model: display }))) : null)) : null)),
+    return (react_1.default.createElement(material_1.Paper, { ref: ref2, className: classes.root, variant: "outlined", onClick: event => {
+            var _a;
+            if (event.detail === 2 && !track.displays[0].featureIdUnderMouse) {
+                const left = ((_a = ref2.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
+                model.zoomTo(model.bpPerPx / 2, event.clientX - left, true);
+            }
+        } },
+        react_1.default.createElement(TrackLabelContainer_1.default, { track: track, view: model }),
+        react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: e => react_1.default.createElement(ui_1.ErrorMessage, { error: e.error }) },
+            react_1.default.createElement(TrackRenderingContainer_1.default, { model: model, track: track, onDragEnter: debouncedOnDragEnter })),
         react_1.default.createElement("div", { className: classes.overlay, style: {
                 height: display.height,
                 background: dimmed ? 'rgba(0, 0, 0, 0.4)' : undefined,
             }, onDragEnter: debouncedOnDragEnter }),
         react_1.default.createElement(ui_1.ResizeHandle, { onDrag: display.resizeHeight, className: classes.resizeHandle })));
-}
-exports.default = (0, mobx_react_1.observer)(TrackContainer);
+});
 //# sourceMappingURL=TrackContainer.js.map

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

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