npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.1.0 → 2.1.3 - Mend

@jbrowse/plugin-linear-genome-view 2.1.0 → 2.1.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (139) hide show

package/esm/LinearGenomeView/components/RubberBand.js.map CHANGED Viewed

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1	+ {"version":3,"file":"RubberBand.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/RubberBand.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAC9C,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AAKvC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE;IACrC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;IAC3C,MAAM,UAAU,GAAG,QAAQ;QACzB,CAAC,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,EAAE,GAAG,CAAC;QAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;IAC5B,OAAO;QACL,UAAU,EAAE;YACV,MAAM,EAAE,MAAM;YACd,UAAU;YACV,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,EAAE;YACV,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,QAAQ;SACnB;QACD,iBAAiB,EAAE;YACjB,MAAM,EAAE,WAAW;YACnB,KAAK,EAAE,MAAM;YACb,SAAS,EAAE,CAAC;SACb;QACD,cAAc,EAAE;YACd,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY;SAC/D;QACD,OAAO,EAAE;YACP,WAAW,EAAE,MAAM;YACnB,MAAM,EAAE,WAAW;SACpB;QACD,KAAK,EAAE;YACL,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;YAC7B,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC/B;QACD,KAAK,EAAE;YACL,aAAa,EAAE,MAAM;YACrB,MAAM,EAAE,MAAM;YACd,KAAK,EAAE,CAAC;YACR,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,EAAE;SACX;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,aAAa,GAAG,QAAQ,CAC5B,CAAC,EAAE,KAAK,EAAE,MAAM,EAAkC,EAAE,EAAE;IACpD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,OAAO,IACN,IAAI,QACJ,SAAS,EAAC,KAAK,EACf,KAAK,EAAE,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,EACtC,KAAK;QAEL,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,MAAM;gBACZ,UAAU,EAAE,KAAK;aAClB,GACD,CACM,CACX,CAAA;AACH,CAAC,CACF,CAAA;AAED,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,gBAAgB,GAAG,gCAAO,GAI3B;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAU,CAAA;IAElD,uDAAuD;IACvD,yDAAyD;IACzD,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,EAIhD,CAAA;IACJ,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,WAAW,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAChD,MAAM,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAClC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,aAAa,GAAG,MAAM,KAAK,SAAS,IAAI,cAAc,KAAK,SAAS,CAAA;IAE1E,MAAM,EAAE,UAAU,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAEpC,SAAS,CAAC,GAAG,EAAE;QACb,SAAS,cAAc,CAAC,OAAe;YACrC,IAAI,MAAM,KAAK,SAAS,EAAE;gBACxB,OAAM;aACP;YACD,IAAI,MAAM,GAAG,MAAM,CAAA;YACnB,IAAI,OAAO,GAAG,OAAO,CAAA;YACrB,IAAI,OAAO,GAAG,MAAM,EAAE;gBACpB,CAAC;gBAAA,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,EAAE,MAAM,CAAC,CAAA;aACvC;YACD,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAA;YACjC,MAAM,WAAW,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;YAEnC,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,CAAA;QACpC,CAAC;QAED,SAAS,eAAe,CAAC,KAAiB;YACxC,IAAI,WAAW,CAAC,OAAO,IAAI,aAAa,EAAE;gBACxC,MAAM,SAAS,GACb,KAAK,CAAC,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;gBAClE,WAAW,CAAC,SAAS,CAAC,CAAA;aACvB;QACH,CAAC;QAED,SAAS,aAAa,CAAC,KAAiB;YACtC,IAAI,MAAM,KAAK,SAAS,IAAI,WAAW,CAAC,OAAO,EAAE;gBAC/C,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;gBAClC,MAAM,GAAG,GAAG,WAAW,CAAC,OAAO,CAAA;gBAC/B,MAAM,OAAO,GAAG,OAAO,GAAG,GAAG,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;gBAC1D,kEAAkE;gBAClE,WAAW;gBACX,iBAAiB,CAAC;oBAChB,OAAO;oBACP,OAAO;oBACP,OAAO;iBACR,CAAC,CAAA;gBACF,MAAM,IAAI,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;gBACpC,IAAI,IAAI,EAAE;oBACR,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBACxC,UAAU,CAAC,UAAU,EAAE,WAAW,CAAC,CAAA;iBACpC;gBACD,SAAS,CAAC,SAAS,CAAC,CAAA;aACrB;QACH,CAAC;QACD,IAAI,aAAa,EAAE;YACjB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,CAAC,CAAA;YACrD,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,CAAC,CAAA;YACjD,OAAO,GAAG,EAAE;gBACV,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,CAAC,CAAA;gBACxD,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,CAAC,CAAA;YACtD,CAAC,CAAA;SACF;QACD,OAAO,GAAG,EAAE,GAAE,CAAC,CAAA;IACjB,CAAC,EAAE,CAAC,MAAM,EAAE,aAAa,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,CAAC,CAAC,CAAA;IAE/D,SAAS,CAAC,GAAG,EAAE;QACb,IACE,CAAC,aAAa;YACd,QAAQ,KAAK,SAAS;YACtB,MAAM,KAAK,SAAS;YACpB,IAAI,CAAC,GAAG,CAAC,QAAQ,GAAG,MAAM,CAAC,IAAI,CAAC,EAChC;YACA,WAAW,EAAE,CAAA;SACd;IACH,CAAC,EAAE,CAAC,aAAa,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAA;IAEpD,SAAS,SAAS,CAAC,KAAuC;QACxD,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,KAAK,CAAC,eAAe,EAAE,CAAA;QACvB,MAAM,SAAS,GACb,KAAK,CAAC,OAAO;YACZ,KAAK,CAAC,MAAyB,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;QAC/D,SAAS,CAAC,SAAS,CAAC,CAAA;QACpB,WAAW,CAAC,SAAS,CAAC,CAAA;IACxB,CAAC;IAED,SAAS,SAAS,CAAC,KAAuC;QACxD,MAAM,MAAM,GAAG,KAAK,CAAC,MAAwB,CAAA;QAC7C,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,MAAM,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAC,CAAA;IAChE,CAAC;IAED,SAAS,QAAQ;QACf,SAAS,CAAC,SAAS,CAAC,CAAA;QACpB,KAAK,CAAC,UAAU,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IACxC,CAAC;IAED,SAAS,WAAW;QAClB,iBAAiB,CAAC,SAAS,CAAC,CAAA;QAC5B,SAAS,CAAC,SAAS,CAAC,CAAA;QACpB,WAAW,CAAC,SAAS,CAAC,CAAA;IACxB,CAAC;IAED,MAAM,IAAI,GAAG,OAAO,CAAC,cAAc,CAAC,CAAA;IAEpC,SAAS,mBAAmB,CAAC,CAAU,EAAE,QAAkB;QACzD,QAAQ,EAAE,CAAA;QACV,WAAW,EAAE,CAAA;IACf,CAAC;IAED,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,OAAO,CACL;YACG,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CACtB,oBAAC,aAAa,IAA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package/esm/LinearGenomeView/components/SearchBox.js CHANGED Viewed

@@ -5,7 +5,7 @@ import { makeStyles } from 'tss-react/mui';
 import { getSession } from '@jbrowse/core/util';
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete';
-import { fetchResults } from './util';
+import { fetchResults, splitLast } from './util';
 import { SPACING, WIDGET_HEIGHT } from '..';
 const useStyles = makeStyles()(() => ({
     headerRefName: {
@@ -21,48 +21,52 @@ function SearchBox({ model, showHelp, }) {
     const assemblyName = assemblyNames[0];
     const assembly = assemblyManager.get(assemblyName);
     const searchScope = model.searchScope(assemblyName);
+    function navToOption(option) {
+        const location = option.getLocation();
+        const trackId = option.getTrackId();
+        if (location) {
+            model.navToLocString(location, assemblyName);
+            if (trackId) {
+                model.showTrack(trackId);
+            }
+        }
+    }
     // gets a string as input, or use stored option results from previous query,
     // then re-query and
     // 1) if it has multiple results: pop a dialog
     // 2) if it's a single result navigate to it
     // 3) else assume it's a locstring and navigate to it
     async function handleSelectedRegion(option) {
-        let trackId = option.getTrackId();
-        let location = option.getLocation();
-        const label = option.getLabel();
-        const [ref, rest] = location.split(':');
-        const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) || [];
         try {
-            // instead of querying text-index, first:
-            // - check if input matches a refName directly
-            // - or looks like locString
-            // then just navigate as if it were a locString
-            if (allRefs.includes(location) ||
-                (allRefs.includes(ref) &&
-                    rest !== undefined &&
-                    !Number.isNaN(parseInt(rest, 10)))) {
-                model.navToLocString(location, assemblyName);
+            if (option.hasLocation()) {
+                navToOption(option);
             }
             else {
-                const results = await fetchResults({
-                    queryString: label,
-                    searchType: 'exact',
-                    searchScope,
-                    rankSearchResults,
-                    textSearchManager,
-                    assembly,
-                });
-                if (results.length > 1) {
-                    model.setSearchResults(results, label.toLowerCase());
-                    return;
-                }
-                else if (results.length === 1) {
-                    location = results[0].getLocation();
-                    trackId = results[0].getTrackId();
+                const input = option.getLabel();
+                const [ref, rest] = splitLast(input, ':');
+                const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
+                if (allRefs.includes(input) ||
+                    (allRefs.includes(ref) && !Number.isNaN(parseInt(rest, 10)))) {
+                    model.navToLocString(input, assemblyName);
                 }
-                model.navToLocString(location, assemblyName);
-                if (trackId) {
-                    model.showTrack(trackId);
+                else {
+                    const results = await fetchResults({
+                        queryString: input,
+                        searchType: 'exact',
+                        searchScope,
+                        rankSearchResults,
+                        textSearchManager,
+                        assembly,
+                    });
+                    if (results.length > 1) {
+                        model.setSearchResults(results, input.toLowerCase());
+                    }
+                    else if (results.length === 1) {
+                        navToOption(results[0]);
+                    }
+                    else {
+                        model.navToLocString(input, assemblyName);
+                    }
                 }
             }
         }

package/esm/LinearGenomeView/components/SearchBox.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearGenomeView/components/SearchResultsDialog.js CHANGED Viewed

@@ -93,10 +93,13 @@ export default function SearchResultsDialog({ model, optAssemblyName, handleClos
                         React.createElement(TableCell, { align: "right" }, getTrackName(result.getTrackId()) || 'N/A'),
                         React.createElement(TableCell, { align: "right" },
                             React.createElement(Button, { onClick: () => {
-                                    handleClick(result.getLocation());
-                                    const resultTrackId = result.getTrackId();
-                                    if (resultTrackId) {
-                                        model.showTrack(resultTrackId);
+                                    const location = result.getLocation();
+                                    if (location) {
+                                        handleClick(location);
+                                        const resultTrackId = result.getTrackId();
+                                        if (resultTrackId) {
+                                            model.showTrack(resultTrackId);
+                                        }
                                     }
                                     handleClose();
                                 }, color: "primary", variant: "contained" }, "Go"))))))))))),

package/esm/LinearGenomeView/components/SearchResultsDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearGenomeView/components/{SequenceDialog.d.ts → SequenceSearchDialog.d.ts} RENAMED Viewed

File without changes

package/esm/LinearGenomeView/components/SequenceSearchDialog.js ADDED Viewed

@@ -0,0 +1,76 @@
+import React, { useState } from 'react';
+import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, Divider, FormGroup, FormControlLabel, IconButton, TextField, Typography, } from '@mui/material';
+import { getSnapshot } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+// icons
+import CloseIcon from '@mui/icons-material/Close';
+const useStyles = makeStyles()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    dialogContent: {
+        width: '40em',
+    },
+}));
+function SequenceDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const [value, setValue] = useState('');
+    const [searchForward, setSearchForward] = useState(true);
+    const [searchReverse, setSearchReverse] = useState(true);
+    const [caseInsensitive, setCaseInsensitive] = useState(true);
+    let error;
+    try {
+        new RegExp(value);
+    }
+    catch (e) {
+        error = e;
+    }
+    return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: handleClose },
+        React.createElement(DialogTitle, null,
+            "Sequence search",
+            handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose(), size: "large" },
+                React.createElement(CloseIcon, null))) : null),
+        React.createElement(Divider, null),
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            React.createElement(Typography, null, "Supply a sequence to search for. A track will be created with the resulting matches once submitted. You can also supply regex style expressions e.g. AACT(C|T)."),
+            React.createElement(TextField, { value: value, onChange: e => setValue(e.target.value), helperText: "Sequence search pattern" }),
+            React.createElement(FormGroup, null,
+                React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: searchForward, onChange: event => setSearchForward(event.target.checked) }), label: "Search forward strand" }),
+                React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: searchReverse, onChange: event => setSearchReverse(event.target.checked) }), label: "Search reverse strand" }),
+                React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: caseInsensitive, onChange: event => setCaseInsensitive(event.target.checked) }), label: "Case insensitive" })),
+            error ? React.createElement(Typography, { color: "error" }, `${error}`) : null),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => {
+                    var _a;
+                    if (value) {
+                        const trackId = `sequence_search_${+Date.now()}`;
+                        const session = getSession(model);
+                        const { assemblyManager } = session;
+                        const assemblyName = model.assemblyNames[0];
+                        session.addTrackConf({
+                            trackId,
+                            name: `Sequence search ${value}`,
+                            assemblyNames: [assemblyName],
+                            type: 'FeatureTrack',
+                            adapter: {
+                                type: 'SequenceSearchAdapter',
+                                search: value,
+                                searchForward,
+                                searchReverse,
+                                caseInsensitive,
+                                sequenceAdapter: getSnapshot((_a = assemblyManager.get(assemblyName)) === null || _a === void 0 ? void 0 : _a.configuration.sequence.adapter),
+                            },
+                        });
+                        model.toggleTrack(trackId);
+                    }
+                    handleClose();
+                }, variant: "contained", color: "primary" }, "Submit"),
+            React.createElement(Button, { onClick: () => handleClose(), variant: "contained", color: "secondary" }, "Close"))));
+}
+export default observer(SequenceDialog);
+//# sourceMappingURL=SequenceSearchDialog.js.map

package/esm/LinearGenomeView/components/SequenceSearchDialog.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"SequenceSearchDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/SequenceSearchDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,OAAO,EACP,SAAS,EACT,gBAAgB,EAChB,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,QAAQ;AACR,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAKjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;IACD,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,WAAW,GAIZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACtC,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IACxD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IACxD,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAE5D,IAAI,KAAK,CAAA;IAET,IAAI;QACF,IAAI,MAAM,CAAC,KAAK,CAAC,CAAA;KAClB;IAAC,OAAO,CAAC,EAAE;QACV,KAAK,GAAG,CAAC,CAAA;KACV;IAED,OAAO,CACL,oBAAC,MAAM,IAAC,QAAQ,EAAC,IAAI,EAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC7C,oBAAC,WAAW;;YAET,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,IAAI,EAAC,OAAO;gBAEZ,oBAAC,SAAS,OAAG,CACF,CACd,CAAC,CAAC,CAAC,IAAI,CACI;QACd,oBAAC,OAAO,OAAG;QAEX,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC7C,oBAAC,UAAU,0KAIE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EACvC,UAAU,EAAC,yBAAyB,GACpC;YACF,oBAAC,SAAS;gBACR,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACzD,EAEJ,KAAK,EAAC,uBAAuB,GAC7B;gBACF,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACzD,EAEJ,KAAK,EAAC,uBAAuB,GAC7B;gBACF,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,eAAe,EACxB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GAC3D,EAEJ,KAAK,EAAC,kBAAkB,GACxB,CACQ;YACX,KAAK,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CAAC,CAAC,CAAC,IAAI,CACrD;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;;oBACZ,IAAI,KAAK,EAAE;wBACT,MAAM,OAAO,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,EAAE,EAAE,CAAA;wBAChD,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;wBACjC,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;wBACnC,MAAM,YAAY,GAAG,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;wBAC3C,OAAO,CAAC,YAAY,CAAC;4BACnB,OAAO;4BACP,IAAI,EAAE,mBAAmB,KAAK,EAAE;4BAChC,aAAa,EAAE,CAAC,YAAY,CAAC;4BAC7B,IAAI,EAAE,cAAc;4BACpB,OAAO,EAAE;gCACP,IAAI,EAAE,uBAAuB;gCAC7B,MAAM,EAAE,KAAK;gCACb,aAAa;gCACb,aAAa;gCACb,eAAe;gCACf,eAAe,EAAE,WAAW,CAC1B,MAAA,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,0CAAE,aAAa,CAAC,QAAQ,CACtD,OAAO,CACX;6BACF;yBACF,CAAC,CAAA;wBACF,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;qBAC3B;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,aAGR;YAET,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,YAGV,CACK,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}

package/esm/LinearGenomeView/components/TrackLabel.js CHANGED Viewed

@@ -45,7 +45,7 @@ function getTrackName(track, session) {
         const asm = session.assemblies.find(a => a.sequence === track.configuration);
         return (trackName ||
             (asm
-                ? `Reference Sequence (${readConfObject(asm, 'name')})`
+                ? `Reference Sequence (${readConfObject(asm, 'displayName') || readConfObject(asm, 'name')})`
                 : 'Reference Sequence'));
     }
     return trackName;

package/esm/LinearGenomeView/components/TrackLabel.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"TrackLabel.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/TrackLabel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAEL,OAAO,EACP,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,aAAa,MAAM,gCAAgC,CAAA;AAC1D,OAAO,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAElE,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EACL,WAAW,EACX,WAAW,EACX,aAAa,GACd,MAAM,+BAA+B,CAAA;AAEtC,QAAQ;AACR,OAAO,YAAY,MAAM,8BAA8B,CAAA;AACvD,OAAO,QAAQ,MAAM,mCAAmC,CAAA;AACxD,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAIjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,EAAE,GAAG,CAAC;QACtD,SAAS,EAAE;YACT,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;SAC3C;QACD,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,EAAE;YACnD,QAAQ,EAAE,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,QAAQ;SAC9C,CAAC;KACH;IACD,SAAS,EAAE;QACT,MAAM,EAAE,QAAQ;QAChB,KAAK,EAAE,KAAK;QACZ,QAAQ,EAAE,QAAQ;QAClB,aAAa,EAAE,MAAM;KACtB;IACD,UAAU,EAAE;QACV,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,SAAS;KACjB;IACD,cAAc,EAAE;QACd,OAAO,EAAE,cAAc;QACvB,aAAa,EAAE,QAAQ;QACvB,aAAa,EAAE,MAAM;KACtB;IACD,UAAU,EAAE;QACV,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;CACF,CAAC,CAAC,CAAA;AASH,SAAS,YAAY,CACnB,KAAqB,EACrB,OAAgD;IAEhD,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACxC,IAAI,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,KAAK,wBAAwB,EAAE;QACvD,MAAM,GAAG,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,KAAK,CAAC,aAAa,CAAC,CAAA;QAC5E,OAAO,CACL,SAAS;YACT,CAAC,GAAG;gBACF,CAAC,CAAC,uBACE,cAAc,CAAC,GAAG,EAAE,aAAa,CAAC,IAAI,cAAc,CAAC,GAAG,EAAE,MAAM,CAClE,GAAG;gBACL,CAAC,CAAC,oBAAoB,CAAC,CAC1B,CAAA;KACF;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AACD,MAAM,UAAU,GAAG,KAAK,CAAC,UAAU,CACjC,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,EAAE,GAAG,EAAE,EAAE;;IAC5B,MAAM,EAAE,OAAO,EAAE,EAAE,EAAE,GAAG,SAAS,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAAQ,CAAA;IAC5C,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,SAAS,GAAG,KAAK,CAAC,aAAa,CAAA;IACrC,MAAM,OAAO,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;IACzC,MAAM,SAAS,GAAG,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAA;IAE9C,MAAM,UAAU,GAAG,aAAa,CAAC;QAC/B,OAAO,EAAE,gBAAgB;QACzB,OAAO,EAAE,SAAS;KACnB,CAAC,CAAA;IAEF,MAAM,WAAW,GAAG,CAAC,KAAuC,EAAE,EAAE;QAC9D,MAAM,MAAM,GAAG,KAAK,CAAC,aAAa,CAAA;QAClC,IAAI,MAAM,CAAC,UAAU,EAAE;YACrB,MAAM,MAAM,GAAG,MAAM,CAAC,UAAyB,CAAA;YAC/C,KAAK,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;YAC/C,IAAI,CAAC,kBAAkB,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;SAClC;IACH,CAAC,CAAA;IAED,MAAM,KAAK,GAAG;QACZ,GAAG,CAAC,CAAA,MAAA,OAAO,CAAC,uBAAuB,wDAAG,SAAS,CAAC,KAAI,EAAE,CAAC;QACvD,GAAG,KAAK,CAAC,cAAc,EAAE;KAC1B,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAA;IAEvD,OAAO,CACL,oBAAC,KAAK,IAAC,GAAG,EAAE,GAAG,EAAE,SAAS,EAAE,EAAE,CAAC,SAAS,EAAE,OAAO,CAAC,IAAI,CAAC;QACrD,8BACE,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,iBACtC,cAAc,IAAI,CAAC,EAAE,IAAI,OAAO,EAAE;YAE/C,oBAAC,QAAQ,IAAC,SAAS,EAAE,OAAO,CAAC,cAAc,EAAE,QAAQ,EAAC,OAAO,GAAG,CAC3D;QACP,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EACtC,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,KAAK,EAAC,kBAAkB,EACxB,KAAK,EAAC,WAAW;YAEjB,oBAAC,SAAS,IAAC,QAAQ,EAAC,OAAO,GAAG,CACnB;QACb,oBAAC,UAAU,IACT,OAAO,EAAC,OAAO,EACf,SAAS,EAAC,MAAM,EAChB,SAAS,EAAE,OAAO,CAAC,SAAS,IAE3B,SAAS,CACC;QACb,oBAAC,UAAU,OACL,WAAW,CAAC,UAAU,CAAC,EAC3B,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,KAAK,EAAC,WAAW,iBACL,iBAAiB,EAC7B,QAAQ,EAAE,CAAC,KAAK,CAAC,MAAM;YAEvB,oBAAC,YAAY,IAAC,QAAQ,EAAC,OAAO,GAAG,CACtB;QACb,oBAAC,aAAa,OACR,WAAW,CAAC,UAAU,CAAC,EAC3B,eAAe,EAAE,CAAC,CAAU,EAAE,QAAkB,EAAE,EAAE,CAAC,QAAQ,EAAE,EAC/D,SAAS,EAAE,KAAK,EAChB,UAAU,EAAE,UAAU,GACtB,CACI,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,QAAQ,CAAC,UAAU,CAAC,CAAA"}

package/esm/LinearGenomeView/components/util.d.ts CHANGED Viewed

@@ -12,3 +12,4 @@ export declare function fetchResults({ queryString, searchType, searchScope, ran
     textSearchManager?: TextSearchManager;
     assembly?: Assembly;
 }): Promise<BaseResult[]>;
+export declare function splitLast(str: string, split: string): [string, string];

package/esm/LinearGenomeView/components/util.js CHANGED Viewed

@@ -14,4 +14,16 @@ export async function fetchResults({ queryString, searchType, searchScope, rankS
     const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResult({ label: r }));
     return dedupe([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
 }
+// splits on the last instance of a character
+export function splitLast(str, split) {
+    const lastIndex = str.lastIndexOf(split);
+    if (lastIndex === -1) {
+        return [str, ''];
+    }
+    else {
+        const before = str.slice(0, lastIndex);
+        const after = str.slice(lastIndex + 1);
+        return [before, after];
+    }
+}
 //# sourceMappingURL=util.js.map

package/esm/LinearGenomeView/components/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearGenomeView/index.d.ts CHANGED Viewed

@@ -57,7 +57,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<"hierarchical">, [undefined]>;
+    trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -128,9 +128,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     toggleShowGridlines(): void;
     scrollTo(offsetPx: number): number;
     zoomTo(bpPerPx: number): number;
-    setOffsets(left: undefined | BpOffset, right: undefined | BpOffset): void;
-    setSearchResults(results: BaseResult[] | undefined, query: string | undefined): void;
-    setSequenceDialogOpen(open: boolean): void;
+    setOffsets(left?: BpOffset, right?: BpOffset): void;
+    setSearchResults(results?: BaseResult[], query?: string): void;
+    setGetSequenceDialogOpen(open: boolean): void;
     setNewView(bpPerPx: number, offsetPx: number): void;
     horizontallyFlip(): void;
     showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;

package/esm/LinearGenomeView/index.js CHANGED Viewed

@@ -1,3 +1,4 @@
+import { lazy } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { ElementId, Region as MUIRegion } from '@jbrowse/core/util/types/mst';
@@ -26,6 +27,7 @@ import { renderToSvg } from './components/LinearGenomeViewSvg';
 import RefNameAutocomplete from './components/RefNameAutocomplete';
 import SearchBox from './components/SearchBox';
 import ExportSvgDlg from './components/ExportSvgDialog';
+const SequenceSearchDialog = lazy(() => import('./components/SequenceSearchDialog'));
 function calculateVisibleLocStrings(contentBlocks) {
     if (!contentBlocks.length) {
         return '';
@@ -298,7 +300,7 @@ export function stateModelFactory(pluginManager) {
             self.searchResults = results;
             self.searchQuery = query;
         },
-        setSequenceDialogOpen(open) {
+        setGetSequenceDialogOpen(open) {
             self.seqDialogDisplayed = open;
         },
         setNewView(bpPerPx, offsetPx) {
@@ -424,7 +426,6 @@ export function stateModelFactory(pluginManager) {
         getSelectedRegions(leftOffset, rightOffset) {
             const snap = getSnapshot(self);
             const simView = Base1DView.create({
-                // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
                 ...snap,
                 interRegionPaddingWidth: self.interRegionPaddingWidth,
             });
@@ -550,6 +551,15 @@ export function stateModelFactory(pluginManager) {
                     },
                     icon: FolderOpenIcon,
                 },
+                {
+                    label: 'Sequence search',
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            SequenceSearchDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
                 {
                     label: 'Export SVG',
                     icon: PhotoCameraIcon,
@@ -606,12 +616,23 @@ export function stateModelFactory(pluginManager) {
                     onClick: self.toggleNoTracksActive,
                 },
                 {
-                    label: 'Show gridlines',
+                    label: 'Show guidelines',
                     icon: VisibilityIcon,
                     type: 'checkbox',
                     checked: self.showGridlines,
                     onClick: self.toggleShowGridlines,
                 },
+                ...(canShowCytobands
+                    ? [
+                        {
+                            label: 'Show ideogram',
+                            icon: VisibilityIcon,
+                            type: 'checkbox',
+                            checked: self.showCytobands,
+                            onClick: () => self.setShowCytobands(!showCytobands),
+                        },
+                    ]
+                    : []),
                 {
                     label: 'Track labels',
                     icon: LabelIcon,
@@ -639,24 +660,12 @@ export function stateModelFactory(pluginManager) {
                         },
                     ],
                 },
-                ...(canShowCytobands
-                    ? [
-                        {
-                            label: showCytobands ? 'Hide ideogram' : 'Show ideograms',
-                            onClick: () => {
-                                self.setShowCytobands(!showCytobands);
-                            },
-                        },
-                    ]
-                    : []),
             ];
             // add track's view level menu options
             for (const [key, value] of self.trackTypeActions.entries()) {
                 if (value.length) {
                     menuItems.push({ type: 'divider' }, { type: 'subHeader', label: key });
-                    value.forEach(action => {
-                        menuItems.push(action);
-                    });
+                    value.forEach(action => menuItems.push(action));
                 }
             }
             return menuItems;
@@ -937,9 +946,7 @@ export function stateModelFactory(pluginManager) {
                 {
                     label: 'Get sequence',
                     icon: MenuOpenIcon,
-                    onClick: () => {
-                        self.setSequenceDialogOpen(true);
-                    },
+                    onClick: () => self.setGetSequenceDialogOpen(true),
                 },
             ];
         },