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

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Files changed (139) hide show

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

@@ -0,0 +1 @@

+ {"version":3,"file":"GetSequenceDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/GetSequenceDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC3D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EACL,MAAM,EACN,gBAAgB,EAChB,SAAS,EACT,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,OAAO,EACP,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AACnC,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,IAAI,MAAM,mBAAmB,CAAA;AACpC,OAAO,EAAE,UAAU,EAAmB,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,cAAc,EAAE,MAAM,uCAAuC,CAAA;AAEtE,QAAQ;AACR,OAAO,EAAE,WAAW,IAAI,eAAe,EAAE,MAAM,wBAAwB,CAAA;AACvE,OAAO,SAAS,MAAM,2BAA2B,CAAA;AACjD,OAAO,UAAU,MAAM,4BAA4B,CAAA;AAKnD,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;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAC,CAAA;AAIH;;GAEG;AACH,KAAK,UAAU,aAAa,CAC1B,KAAU,EACV,OAAiB,EACjB,MAAoB;IAEpB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAEzC,IAAI,CAAC,UAAU,IAAI,CAAC,WAAW,EAAE;QAC/B,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;KACxD;IAED,IAAI,UAAU,CAAC,YAAY,KAAK,WAAW,CAAC,YAAY,EAAE;QACxD,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;KACxE;IACD,MAAM,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,YAAY,GAAG,UAAU,CAAC,YAAY,IAAI,WAAW,CAAC,YAAY,IAAI,EAAE,CAAA;IAC9E,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,MAAM,aAAa,GAAG,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC,CAAA;IAEhE,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,OAAO,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QACnD,aAAa;QACb,OAAO;QACP,SAAS;QACT,MAAM;KACP,CAAuB,CAAA;AAC1B,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,WAAW,GAIZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAU,CAAA;IAClD,MAAM,OAAO,GAAG,OAAO,CAAC,QAAQ,KAAK,SAAS,CAAC,CAAA;IAC/C,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAEzC,sCAAsC;IACtC,0EAA0E;IAC1E,yEAAyE;IACzE,MAAM,eAAe,GAAG,OAAO,CAC7B,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,UAAU,EAAE,WAAW,CAAC,EACvD,CAAC,KAAK,EAAE,UAAU,EAAE,WAAW,CAAC,CACjC,CAAA;IAED,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,MAAM,GAAG,IAAI,CAAA;QACjB,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAEvC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI;gBACF,IAAI,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC9B,MAAM,MAAM,GAAG,MAAM,aAAa,CAChC,KAAK,EACL,eAAe,EACf,UAAU,CAAC,MAAM,CAClB,CAAA;oBACD,IAAI,MAAM,EAAE;wBACV,WAAW,CACT,cAAc,CACZ,MAAM;6BACH,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;6BAChB,GAAG,CAAC,KAAK,CAAC,EAAE;4BACX,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;4BACjC,MAAM,YAAY,GAAG,KAAK,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;4BACzC,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;4BACzC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;4BACjC,MAAM,cAAc,GAAG,GAAG,YAAY,IAAI,UAAU,IAAI,QAAQ,EAAE,CAAA;4BAClE,IAAI,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,MAAM,MAAK,QAAQ,GAAG,UAAU,GAAG,CAAC,EAAE;gCAClD,MAAM,IAAI,KAAK,CACb,GAAG,cAAc,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CAChG,QAAQ,GAAG,UAAU,CACtB,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;6BACF;4BACD,OAAO,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAA;wBAClD,CAAC,CAAC,CACL,CACF,CAAA;qBACF;iBACF;qBAAM;oBACL,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAA;iBACpD;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,IAAI,MAAM,EAAE;oBACV,QAAQ,CAAC,CAAC,CAAC,CAAA;iBACZ;aACF;QACH,CAAC,CAAC,EAAE,CAAA;QAEJ,OAAO,GAAG,EAAE;YACV,UAAU,CAAC,KAAK,EAAE,CAAA;YAClB,MAAM,GAAG,KAAK,CAAA;QAChB,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,eAAe,EAAE,WAAW,CAAC,CAAC,CAAA;IAElD,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,OAAS,CAAC,CAAC,CAAC,KAAK,CAAA;IAEvE,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;oBACZ,WAAW,EAAE,CAAA;oBACb,KAAK,CAAC,UAAU,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;gBACxC,CAAC,EACD,IAAI,EAAC,OAAO;gBAEZ,oBAAC,SAAS,OAAG,CACF,CACd,CAAC,CAAC,CAAC,IAAI,CACI;QACd,oBAAC,OAAO,OAAG;QAEX,oBAAC,aAAa;YACX,KAAK,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CAAC,CAAC,CAAC,IAAI;YAClE,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CACnB,oBAAC,SAAS;;gBAER,oBAAC,gBAAgB,IACf,KAAK,EAAE;wBACL,UAAU,EAAE,EAAE;qBACf,EACD,IAAI,EAAE,EAAE,EACR,aAAa,SACb,CACQ,CACb,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,SAAS,mBACI,qBAAqB,EACjC,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,QAAQ,EAAE,gBAAgB,EAC1B,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,SAAS,QACT,KAAK,EACH,gBAAgB;oBACd,CAAC,CAAC,wEAAwE;oBAC1E,CAAC,CAAC,QAAQ,EAEd,UAAU,EAAE;oBACV,QAAQ,EAAE,IAAI;oBACd,OAAO,EAAE;wBACP,KAAK,EAAE,OAAO,CAAC,YAAY;qBAC5B;iBACF,GACD,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package/esm/LinearGenomeView/components/ImportForm.js CHANGED Viewed

@@ -4,11 +4,10 @@ import { observer } from 'mobx-react';
 import { getSession } from '@jbrowse/core/util';
 import { Button, CircularProgress, Container, Grid } from '@mui/material';
 import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import CloseIcon from '@mui/icons-material/Close';
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete';
-import { fetchResults } from './util';
+import { fetchResults, splitLast } from './util';
 import { WIDGET_HEIGHT } from '..';
 const SearchResultsDialog = lazy(() => import('./SearchResultsDialog'));
 const useStyles = makeStyles()(theme => ({
@@ -30,6 +29,7 @@ const ImportForm = observer(({ model }) => {
     const { rankSearchResults, isSearchDialogDisplayed, error } = model;
     const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0]);
     const [importError, setImportError] = useState(error);
+    const [option, setOption] = useState();
     const searchScope = model.searchScope(selectedAsm);
     const assembly = assemblyManager.get(selectedAsm);
     const assemblyError = assemblyNames.length
@@ -39,55 +39,51 @@ const ImportForm = observer(({ model }) => {
     const err = assemblyError || importError;
     const [myVal, setValue] = useState('');
     const value = myVal || ((_a = regions[0]) === null || _a === void 0 ? void 0 : _a.refName);
-    // use this instead of useState initializer because the useState initializer
-    // won't update in response to an observable
-    const option = new BaseResult({
-        label: value,
-    });
+    function navToOption(option) {
+        const location = option.getLocation();
+        const trackId = option.getTrackId();
+        if (location) {
+            model.navToLocString(location, selectedAsm);
+            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(input) {
-        if (!option) {
-            return;
-        }
-        let trackId = option.getTrackId();
-        let location = input || option.getLocation() || '';
-        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, selectedAsm);
+            if ((option === null || option === void 0 ? void 0 : option.getDisplayString()) === input && option.hasLocation()) {
+                navToOption(option);
             }
             else {
-                const results = await fetchResults({
-                    queryString: input,
-                    searchType: 'exact',
-                    searchScope,
-                    rankSearchResults,
-                    textSearchManager,
-                    assembly,
-                });
-                if (results.length > 1) {
-                    model.setSearchResults(results, input.toLowerCase());
-                    return;
+                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, selectedAsm);
                 }
-                else if (results.length === 1) {
-                    location = results[0].getLocation();
-                    trackId = results[0].getTrackId();
-                }
-                model.navToLocString(location, selectedAsm);
-                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, selectedAsm);
+                    }
                 }
             }
         }
@@ -114,6 +110,7 @@ const ImportForm = observer(({ model }) => {
                         React.createElement(AssemblySelector, { onChange: val => {
                                 setImportError('');
                                 setSelectedAsm(val);
+                                setValue('');
                             }, session: session, selected: selectedAsm, InputProps: { style: { height } } })),
                     React.createElement(Grid, { item: true }, selectedAsm ? (err ? (React.createElement(CloseIcon, { style: { color: 'red' } })) : value ? (React.createElement(RefNameAutocomplete, { fetchResults: queryString => fetchResults({
                             queryString,
@@ -123,7 +120,7 @@ const ImportForm = observer(({ model }) => {
                             searchScope,
                         }), model: model, assemblyName: assemblyError ? undefined : selectedAsm, value: value,
                         // note: minWidth 270 accomodates full width of helperText
-                        minWidth: 270, onChange: str => setValue(str), TextFieldProps: {
+                        minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
                             variant: 'outlined',
                             helperText: 'Enter sequence name, feature name, or location',
                             style: { minWidth: '175px' },

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

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

@@ -8,7 +8,7 @@ import TrackContainer from './TrackContainer';
 import TracksContainer from './TracksContainer';
 import ImportForm from './ImportForm';
 import MiniControls from './MiniControls';
-import SequenceDialog from './SequenceDialog';
+import GetSequenceDialog from './GetSequenceDialog';
 import SearchResultsDialog from './SearchResultsDialog';
 const useStyles = makeStyles()(theme => ({
     note: {
@@ -47,7 +47,7 @@ const LinearGenomeView = observer(({ model }) => {
         return React.createElement(ImportForm, { model: model });
     }
     return (React.createElement("div", { style: { position: 'relative' } },
-        model.seqDialogDisplayed ? (React.createElement(SequenceDialog, { model: model, handleClose: () => model.setSequenceDialogOpen(false) })) : null,
+        model.seqDialogDisplayed ? (React.createElement(GetSequenceDialog, { model: model, handleClose: () => model.setGetSequenceDialogOpen(false) })) : null,
         model.isSearchDialogDisplayed ? (React.createElement(SearchResultsDialog, { model: model, handleClose: () => model.setSearchResults(undefined, undefined) })) : null,
         !hideHeader ? (React.createElement(Header, { model: model })) : (React.createElement("div", { style: {
                 position: 'absolute',

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

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

@@ -96,7 +96,8 @@ function SVGTracks({ displayResults, model, offset, }) {
     return (React.createElement(React.Fragment, null, displayResults.map(({ track, result }) => {
         const current = offset;
         const trackName = getConf(track, 'name') ||
-            `Reference sequence (${readConfObject(getParent(track.configuration), 'name')})`;
+            `Reference sequence (${readConfObject(getParent(track.configuration), 'displayName') ||
+                readConfObject(getParent(track.configuration), 'name')})`;
         const display = track.displays[0];
         offset += display.height + paddingHeight + textHeight;
         return (React.createElement("g", { key: track.configuration.trackId, transform: `translate(0 ${current})` },

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

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

@@ -1,5 +1,4 @@
 import React from 'react';
-import ReactPropTypes from 'prop-types';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { LinearGenomeViewModel } from '..';
 declare type LGV = LinearGenomeViewModel;
@@ -8,15 +7,5 @@ declare function OverviewRubberBand({ model, overview, ControlComponent, }: {
     overview: Base1DViewModel;
     ControlComponent?: React.ReactElement;
 }): JSX.Element;
-declare namespace OverviewRubberBand {
-    var propTypes: {
-        model: ReactPropTypes.Validator<any>;
-        overview: ReactPropTypes.Validator<any>;
-        ControlComponent: ReactPropTypes.Requireable<ReactPropTypes.ReactNodeLike>;
-    };
-    var defaultProps: {
-        ControlComponent: JSX.Element;
-    };
-}
 declare const _default: typeof OverviewRubberBand;
 export default _default;

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

@@ -2,11 +2,9 @@ import React, { useRef, useEffect, useState } from 'react';
 import { Popover, Tooltip, Typography, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { getSession, stringify } from '@jbrowse/core/util';
-import { observer, PropTypes as MobxPropTypes } from 'mobx-react';
-import ReactPropTypes from 'prop-types';
+import { observer } from 'mobx-react';
 import { HEADER_OVERVIEW_HEIGHT } from '..';
 const useStyles = makeStyles()(theme => {
-    // @ts-ignore
     const { tertiary, primary } = theme.palette;
     const background = tertiary
         ? alpha(tertiary.main, 0.7)
@@ -81,7 +79,9 @@ function OverviewRubberBand({ model, overview, ControlComponent = React.createEl
             // click and drag
             if (startX !== undefined && currentX !== undefined) {
                 if (Math.abs(currentX - startX) > 3) {
-                    model.moveTo(overview.pxToBp(startX - cytobandOffset), overview.pxToBp(currentX - cytobandOffset));
+                    const left = Math.min(startX, currentX);
+                    const right = Math.max(startX, currentX);
+                    model.moveTo(overview.pxToBp(left - cytobandOffset), overview.pxToBp(right - cytobandOffset));
                 }
             }
             // just a click
@@ -185,13 +185,5 @@ function OverviewRubberBand({ model, overview, ControlComponent = React.createEl
             } }),
         React.createElement("div", { "data-testid": "rubberBand_controls", className: classes.rubberBandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
 }
-OverviewRubberBand.propTypes = {
-    model: MobxPropTypes.objectOrObservableObject.isRequired,
-    overview: MobxPropTypes.objectOrObservableObject.isRequired,
-    ControlComponent: ReactPropTypes.node,
-};
-OverviewRubberBand.defaultProps = {
-    ControlComponent: React.createElement("div", null),
-};
 export default observer(OverviewRubberBand);
 //# sourceMappingURL=OverviewRubberBand.js.map

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

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"OverviewRubberBand.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/OverviewRubberBand.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAyB,sBAAsB,EAAE,MAAM,IAAI,CAAA;AAIlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE;IACrC,MAAM,EAAE,QAAQ,EAAE,OAAO,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,YAAY,GAAG,QAAQ,CAC3B,CAAC,EACC,KAAK,EACL,IAAI,EACJ,MAAM,EACN,QAAQ,GAMT,EAAE,EAAE;;IACH,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAE7C,MAAM,EAAE,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,GAAG,cAAc,CAAC,CAAA;IACnD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,YAAY,CAAC,CAAA;IACrD,MAAM,QAAQ,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,IAAI,CACxC,CAAC,CAAC,EAAE,CACF,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;QACzB,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;QACvB,EAAE,CAAC,OAAO,KAAK,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAChE,CAAA;IAED,OAAO,CACL,oBAAC,OAAO,IACN,IAAI,EAAE,IAAI,EACV,SAAS,EAAC,KAAK,EACf,KAAK,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,EAAE,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EACvD,KAAK;QAEL,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,MAAM;aACb,GACD,CACM,CACX,CAAA;AACH,CAAC,CACF,CAAA;AAED,SAAS,kBAAkB,CAAC,EAC1B,KAAK,EACL,QAAQ,EACR,gBAAgB,GAAG,gCAAO,GAK3B;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAU,CAAA;IAClD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,WAAW,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAChD,MAAM,aAAa,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAClD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,aAAa,GAAG,MAAM,KAAK,SAAS,CAAA;IAE1C,SAAS,CAAC,GAAG,EAAE;QACb,SAAS,eAAe,CAAC,KAAiB;YACxC,MAAM,GAAG,GAAG,WAAW,CAAC,OAAO,CAAA;YAC/B,IAAI,GAAG,IAAI,aAAa,EAAE;gBACxB,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,GAAG,GAAG,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;gBAClE,WAAW,CAAC,SAAS,CAAC,CAAA;aACvB;QACH,CAAC;QAED,SAAS,aAAa;YACpB,iBAAiB;YACjB,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;gBAClD,IAAI,IAAI,CAAC,GAAG,CAAC,QAAQ,GAAG,MAAM,CAAC,GAAG,CAAC,EAAE;oBACnC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;oBACvC,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;oBACxC,KAAK,CAAC,MAAM,CACV,QAAQ,CAAC,MAAM,CAAC,IAAI,GAAG,cAAc,CAAC,EACtC,QAAQ,CAAC,MAAM,CAAC,KAAK,GAAG,cAAc,CAAC,CACxC,CAAA;iBACF;aACF;YAED,eAAe;YACf,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;gBAClD,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,GAAG,cAAc,CAAC,CAAA;gBACtD,IAAI,CAAC,KAAK,CAAC,OAAO,EAAE;oBAClB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAA;oBACpD,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,KAAK,CAAC,CAAA;iBACjD;qBAAM;oBACL,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,CAAA;iBACpE;aACF;YACD,SAAS,CAAC,SAAS,CAAC,CAAA;YACpB,WAAW,CAAC,SAAS,CAAC,CAAA;YAEtB,IAAI,MAAM,KAAK,SAAS,EAAE;gBACxB,SAAS,CAAC,SAAS,CAAC,CAAA;aACrB;QACH,CAAC;QAED,SAAS,aAAa,CAAC,KAAoB;YACzC,IAAI,KAAK,CAAC,GAAG,KAAK,QAAQ,EAAE;gBAC1B,SAAS,CAAC,SAAS,CAAC,CAAA;gBACpB,WAAW,CAAC,SAAS,CAAC,CAAA;aACvB;QACH,CAAC;QAED,IAAI,aAAa,EAAE;YACjB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,EAAE;gBACV,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;gBAC1D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;SACF;QACD,OAAO,GAAG,EAAE,GAAE,CAAC,CAAA;IACjB,CAAC,EAAE,CAAC,aAAa,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,cAAc,CAAC,CAAC,CAAA;IAEtE,SAAS,SAAS,CAAC,KAAuC;QACxD,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,KAAK,CAAC,eAAe,EAAE,CAAA;QACvB,IAAI,WAAW,CAAC,OAAO,EAAE;YACvB,SAAS,CACP,KAAK,CAAC,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAC,IAAI,CACjE,CAAA;SACF;IACH,CAAC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package/esm/LinearGenomeView/components/OverviewScaleBar.d.ts CHANGED Viewed

@@ -28,10 +28,13 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         readonly initialized: boolean;
         readonly name: string;
         readonly aliases: string[];
+        readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
+        readonly lowerCaseRefNames: string[] | undefined;
+        readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
     } & {
@@ -62,17 +65,17 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
             forwardMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
             reverseMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
         }>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
@@ -90,10 +93,13 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         readonly initialized: boolean;
         readonly name: string;
         readonly aliases: string[];
+        readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
+        readonly lowerCaseRefNames: string[] | undefined;
+        readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
     } & {
@@ -124,17 +130,17 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
             forwardMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
             reverseMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
         }>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;

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

@@ -65,7 +65,6 @@ const Polygon = observer(({ model, overview, useOffset = true, }) => {
     const multiplier = Number(useOffset);
     const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
     const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks;
-    // @ts-ignore
     const { tertiary, primary } = theme.palette;
     const polygonColor = tertiary ? tertiary.light : primary.light;
     if (!contentBlocks.length) {
@@ -229,7 +228,6 @@ const ScaleBar = observer(({ model, scale, overview, }) => {
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
-    // @ts-ignore
     const { tertiary, primary } = theme.palette;
     const scaleBarColor = tertiary ? tertiary.light : primary.light;
     if (!visibleRegions.length) {

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

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

@@ -6,7 +6,6 @@ import { Autocomplete, CircularProgress, IconButton, InputAdornment, TextField,
 // icons
 import SearchIcon from '@mui/icons-material/Search';
 import HelpIcon from '@mui/icons-material/Help';
-import { dedupe } from './util';
 // lazy
 const HelpDialog = lazy(() => import('./HelpDialog'));
 // the logic of this method is to only apply a filter to RefSequenceResults
@@ -29,8 +28,8 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
     const [inputValue, setInputValue] = useState('');
     const [searchOptions, setSearchOptions] = useState();
     const debouncedSearch = useDebounce(currentSearch, 300);
-    const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
+    const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     // eslint-disable-next-line react-hooks/exhaustive-deps
     const regions = (assembly === null || assembly === void 0 ? void 0 : assembly.regions) || [];
     const options = useMemo(() => regions.map(option => ({
@@ -50,9 +49,30 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
                 setLoaded(false);
                 const results = await fetchResults(debouncedSearch);
                 if (active) {
-                    setSearchOptions(dedupe(results, r => r.getDisplayString()).map(result => ({
-                        result,
-                    })));
+                    const m = {};
+                    for (let i = 0; i < results.length; i++) {
+                        const r = results[i];
+                        const d = r.getDisplayString();
+                        if (!m[d]) {
+                            m[d] = [];
+                        }
+                        m[d].push(r);
+                    }
+                    const display = Object.entries(m).map(([displayString, results]) => {
+                        if (results.length === 1) {
+                            return { result: results[0] };
+                        }
+                        else {
+                            return {
+                                result: new BaseResult({
+                                    displayString,
+                                    results,
+                                    label: displayString,
+                                }),
+                            };
+                        }
+                    });
+                    setSearchOptions(display);
                     setLoaded(true);
                 }
             }
@@ -74,7 +94,7 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
     return (React.createElement(React.Fragment, null,
-        React.createElement(Autocomplete, { id: `refNameAutocomplete-${model.id}`, "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (event, newInputValue) => {
+        React.createElement(Autocomplete, { id: `refNameAutocomplete-${model.id}`, "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: () => {

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

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

@@ -5,7 +5,6 @@ import { makeStyles } from 'tss-react/mui';
 import { stringify } from '@jbrowse/core/util';
 import { Menu } from '@jbrowse/core/ui';
 const useStyles = makeStyles()(theme => {
-    // @ts-ignore
     const { primary, tertiary } = theme.palette;
     const background = tertiary
         ? alpha(tertiary.main, 0.7)