@jbrowse/plugin-linear-genome-view 3.2.0 → 3.4.0

package/dist/searchUtils.js

@@ -14,7 +14,7 @@ async function navToOption({ option, model, assemblyName, }) {
     const location = option.getLocation();
     const trackId = option.getTrackId();
     if (location) {
-        await model.navToLocString(location, assemblyName);
+        await model.navToLocString(location, assemblyName, 0.2);
         if (trackId) {
             model.showTrack(trackId);
         }

package/esm/BaseLinearDisplay/components/LinearBlocks.js

@@ -20,7 +20,7 @@ const useStyles = makeStyles()({
         width: '100%',
         fontWeight: 'bold',
         textAlign: 'center',
-        zIndex: 2000,
+        zIndex: 999,
         boxSizing: 'border-box',
     },
 });

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -206,7 +206,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
 } & {
     addBlock(key: string, block: BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -1,9 +1,9 @@
 import { lazy } from 'react';
-import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
 import { getContainingTrack, getContainingView, getSession, isFeature, isSelectionContainer, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
-import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { getParentRenderProps, getRpcSessionId, } from '@jbrowse/core/util/tracks';
 import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import { autorun } from 'mobx';
@@ -99,15 +99,23 @@ function stateModelFactory() {
         deleteBlock(key) {
             self.blockState.delete(key);
         },
-        selectFeature(feature) {
+        async selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {
-                const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
-                    view: getContainingView(self),
-                    track: getContainingTrack(self),
-                    featureData: feature.toJSON(),
+                const { rpcManager } = session;
+                const sessionId = getRpcSessionId(self);
+                const track = getContainingTrack(self);
+                const view = getContainingView(self);
+                const adapterConfig = getConf(track, 'adapter');
+                const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                    adapterConfig,
                 });
-                session.showWidget(featureWidget);
+                session.showWidget(session.addWidget('BaseFeatureWidget', 'baseFeature', {
+                    featureData: feature.toJSON(),
+                    view,
+                    track,
+                    descriptions,
+                }));
             }
             if (isSelectionContainer(session)) {
                 session.setSelection(feature);
@@ -158,7 +166,11 @@ function stateModelFactory() {
                             icon: MenuOpenIcon,
                             onClick: () => {
                                 if (self.contextMenuFeature) {
-                                    self.selectFeature(self.contextMenuFeature);
+                                    self
+                                        .selectFeature(self.contextMenuFeature)
+                                        .catch((e) => {
+                                        getSession(e).notifyError(`${e}`, e);
+                                    });
                                 }
                             },
                         },
@@ -189,7 +201,9 @@ function stateModelFactory() {
                     else {
                         const feature = self.features.get(f);
                         if (feature) {
-                            self.selectFeature(feature);
+                            self.selectFeature(feature).catch((e) => {
+                                getSession(e).notifyError(`${e}`, e);
+                            });
                         }
                     }
                 },

package/esm/LinearBareDisplay/model.d.ts

@@ -190,7 +190,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/LinearBasicDisplay/components/AddFiltersDialog.js

@@ -41,7 +41,7 @@ const AddFiltersDialog = observer(function ({ model, handleClose, }) {
             setError(e);
         }
     }, [data]);
-    return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [_jsxs(DialogContent, { children: [_jsxs("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', _jsxs("ul", { children: [_jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] })] })] }), error ? _jsx("p", { className: classes.error, children: `${error}` }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
+    return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [_jsxs(DialogContent, { children: [_jsxs("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', _jsxs("ul", { children: [_jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'end') - get(feature,'start') < 1000000" }), ' ', "- show only features with length less than 1Mbp"] })] })] }), error ? _jsx("p", { className: classes.error, children: `${error}` }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
                             setData(event.target.value);
                         }, slotProps: {
                             input: {

package/esm/LinearBasicDisplay/model.d.ts

@@ -198,7 +198,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/LinearBasicDisplay/model.js

@@ -127,7 +127,10 @@ function stateModelFactory(configSchema) {
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 SetMaxHeightDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
@@ -136,7 +139,10 @@ function stateModelFactory(configSchema) {
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 AddFiltersDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/esm/LinearGenomeView/components/Cytobands.js

@@ -9,14 +9,14 @@ function rightRoundedRect(x, y, width, height, radius) {
 function leftRoundedRect(x, y, width, height, radius) {
     return `M${x + radius},${y}h${width - radius}v${height}h${radius - width}a${radius},${radius} 0 0 1 ${-radius},${-radius}v${2 * radius - height}a${radius},${radius} 0 0 1 ${radius},${-radius}z`;
 }
-function leftTriangle(x, y, width, height) {
+function leftTriangle(x, _y, width, height) {
     return [
         [x, 0],
         [x + width, height / 2],
         [x, height],
     ].toString();
 }
-function rightTriangle(x, y, width, height) {
+function rightTriangle(x, _y, width, height) {
     return [
         [x, height / 2],
         [x + width, 0],
@@ -40,14 +40,28 @@ const Cytobands = observer(function ({ overview, block, assembly, }) {
     const rcap = reversed ? 0 : cytobands.length - 1;
     const h = HEADER_OVERVIEW_HEIGHT;
     let centromereSeen = false;
+    let curr = '';
+    let idx = 0;
     return (_jsx("g", { transform: `translate(-${offsetPx})`, children: cytobands.map((args, index) => {
             const k = JSON.stringify(args);
-            const { refName, type, start, end } = args;
+            const { refName, name, type, start, end } = args;
             const s = overview.bpToPx({ refName, coord: start }) || 0;
             const e = overview.bpToPx({ refName, coord: end }) || 0;
             const l = Math.min(s, e);
             const w = Math.abs(e - s);
-            const c = colorMap[type] || 'black';
+            if (type === 'n/a') {
+                const match = name === null || name === void 0 ? void 0 : name.match(/^(\d+)([A-Za-z])/);
+                const ret = match[1] + match[2];
+                if (ret && ret !== curr) {
+                    curr = ret;
+                    idx++;
+                }
+            }
+            const c = type === 'n/a'
+                ? idx % 2
+                    ? 'black'
+                    : '#a77'
+                : colorMap[type] || 'black';
             if (type === 'acen' && !centromereSeen) {
                 centromereSeen = true;
                 return (_jsx("polygon", { points: reversed

package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -28,8 +28,9 @@ async function fetchSequence(model, regions) {
     if (!leftOffset || !rightOffset) {
         throw new Error('no offsets on model to use for range');
     }
-    if (leftOffset.assemblyName !== rightOffset.assemblyName) {
-        throw new Error('not able to fetch sequences from multiple assemblies');
+    const assemblyNames = new Set(regions.map(r => r.assemblyName));
+    if (assemblyNames.size > 1) {
+        throw new Error('not able to fetch sequences from multiple assemblies currently');
     }
     const { rpcManager, assemblyManager } = session;
     const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';

package/esm/LinearGenomeView/components/HeaderZoomControls.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { lazy, useEffect, useState } from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import { getSession } from '@jbrowse/core/util';
+import { getBpDisplayStr, getSession } from '@jbrowse/core/util';
 import MoreVert from '@mui/icons-material/MoreVert';
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
@@ -20,9 +20,13 @@ const useStyles = makeStyles()(theme => ({
         color: theme.palette.text.secondary,
     },
 }));
+function ValueLabelComponent(props) {
+    const { children, open, value } = props;
+    return (_jsx(Tooltip, { open: open, enterTouchDelay: 0, placement: "top", title: value, arrow: true, children: children }));
+}
 const HeaderZoomControls = observer(function ({ model, }) {
     const { classes } = useStyles();
-    const { maxBpPerPx, minBpPerPx, bpPerPx } = model;
+    const { width, maxBpPerPx, minBpPerPx, bpPerPx } = model;
     const [value, setValue] = useState(-Math.log2(bpPerPx) * 100);
     useEffect(() => {
         setValue(-Math.log2(bpPerPx) * 100);
@@ -31,7 +35,9 @@ const HeaderZoomControls = observer(function ({ model, }) {
     const zoomOutDisabled = bpPerPx >= maxBpPerPx - 0.0001;
     return (_jsxs("div", { className: classes.container, children: [_jsx(Tooltip, { title: "Zoom out 2x", children: _jsx("span", { children: _jsx(IconButton, { "data-testid": "zoom_out", disabled: zoomOutDisabled, onClick: () => {
                             model.zoom(bpPerPx * 2);
-                        }, children: _jsx(ZoomOut, {}) }) }) }), _jsx(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), onChange: (_, val) => {
+                        }, children: _jsx(ZoomOut, {}) }) }) }), _jsx(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), valueLabelDisplay: "auto", valueLabelFormat: newValue => `Window size: ${getBpDisplayStr(2 ** (-newValue / 100) * width)}`, slots: {
+                    valueLabel: ValueLabelComponent,
+                }, onChange: (_, val) => {
                     setValue(val);
                 } }), _jsx(Tooltip, { title: "Zoom in 2x", children: _jsx("span", { children: _jsx(IconButton, { "data-testid": "zoom_in", disabled: zoomInDisabled, onClick: () => {
                             model.zoom(model.bpPerPx / 2);

package/esm/LinearGenomeView/components/ImportForm.js

@@ -3,7 +3,7 @@ import { useEffect, useState } from 'react';
 import { AssemblySelector, ErrorMessage } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import CloseIcon from '@mui/icons-material/Close';
-import { Button, CircularProgress, Container, FormControl, Grid2 as Grid, } from '@mui/material';
+import { Button, CircularProgress, Container, FormControl, Grid as Grid, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import ImportFormRefNameAutocomplete from './ImportFormRefNameAutocomplete';

package/esm/LinearGenomeView/components/OverviewRubberband.js

@@ -12,12 +12,6 @@ const useStyles = makeStyles()({
         width: '100%',
         minHeight: 8,
     },
-    guide: {
-        pointerEvents: 'none',
-        height: '100%',
-        width: 1,
-        position: 'absolute',
-    },
     rel: {
         position: 'relative',
     },

package/esm/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js

@@ -4,20 +4,12 @@ import { Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
-    rubberbandControl: {
-        cursor: 'crosshair',
-        width: '100%',
-        minHeight: 8,
-    },
     guide: {
         pointerEvents: 'none',
         height: '100%',
         width: 1,
         position: 'absolute',
     },
-    rel: {
-        position: 'relative',
-    },
 });
 const OverviewRubberbandHoverTooltip = observer(function ({ model, open, guideX, overview, }) {
     var _a;
@@ -29,6 +21,6 @@ const OverviewRubberbandHoverTooltip = observer(function ({ model, open, guideX,
     const cytoband = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.find(f => px.coord > f.get('start') &&
         px.coord < f.get('end') &&
         px.refName === assembly.getCanonicalRefName(f.get('refName')));
-    return (_jsx(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true, children: _jsx("div", { className: classes.guide, style: { left: guideX } }) }));
+    return (_jsx(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name'), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('type')].join(' '), arrow: true, children: _jsx("div", { className: classes.guide, style: { left: guideX } }) }));
 });
 export default OverviewRubberbandHoverTooltip;

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

@@ -25,27 +25,31 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
                     return;
                 }
                 setLoaded(false);
-                const results = await fetchResults(debouncedSearch);
-                setLoaded(true);
-                setSearchOptions(getDeduplicatedResult(results));
+                setSearchOptions(getDeduplicatedResult(await fetchResults(debouncedSearch)));
             }
             catch (e) {
                 console.error(e);
                 session.notifyError(`${e}`, e);
             }
+            finally {
+                setLoaded(true);
+            }
         })();
     }, [assemblyName, fetchResults, debouncedSearch, session]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
-    const width = Math.min(Math.max(measureText(inputBoxVal, 14) + 100, minWidth), maxWidth);
-    const refNames = assembly === null || assembly === void 0 ? void 0 : assembly.refNames;
-    const regionOptions = (refNames === null || refNames === void 0 ? void 0 : refNames.map(refName => ({
+    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
+    const regionOptions = (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
         result: new RefSequenceResult({
-            refName,
-            label: refName,
+            refName: region.refName,
+            label: region.refName,
+            displayString: region.refName,
             matchedAttribute: 'refName',
         }),
     }))) || [];
-    return (_jsx(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) => {
+    return (_jsx(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: {
+            ...style,
+            width: Math.min(Math.max(measureText(inputBoxVal, 14) + 100, minWidth), maxWidth),
+        }, 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: () => {
@@ -62,7 +66,9 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
                 return;
             }
             if (typeof selectedOption === 'string') {
-                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({ label: selectedOption }));
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({
+                    label: selectedOption,
+                }));
             }
             else {
                 onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);

package/esm/LinearGenomeView/components/RubberbandSpan.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
-import { stringify, toLocale } from '@jbrowse/core/util';
+import { getBpDisplayStr, stringify } from '@jbrowse/core/util';
 import { Typography, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import RubberbandTooltip from './RubberbandTooltip';
@@ -28,10 +28,10 @@ const useStyles = makeStyles()(theme => {
 export default function RubberbandSpan({ leftBpOffset, rightBpOffset, numOfBpSelected, left, width, top = 0, sticky = false, }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = useState(null);
-    return (_jsxs(_Fragment, { children: [anchorEl ? (_jsxs(_Fragment, { children: [_jsx(RubberbandTooltip, { side: "left", anchorEl: anchorEl, text: stringify(leftBpOffset) }), _jsx(RubberbandTooltip, { side: "right", anchorEl: anchorEl, text: stringify(rightBpOffset) })] })) : null, _jsx("div", { className: classes.rubberband, style: { left, width }, children: numOfBpSelected ? (_jsxs(Typography, { ref: el => {
+    return (_jsxs(_Fragment, { children: [anchorEl ? (_jsxs(_Fragment, { children: [_jsx(RubberbandTooltip, { side: "left", anchorEl: anchorEl, text: stringify(leftBpOffset) }), _jsx(RubberbandTooltip, { side: "right", anchorEl: anchorEl, text: stringify(rightBpOffset) })] })) : null, _jsx("div", { className: classes.rubberband, style: { left, width }, children: numOfBpSelected ? (_jsx(Typography, { ref: el => {
                         setAnchorEl(el);
                     }, variant: "h6", className: classes.rubberbandText, style: {
                         top,
                         position: sticky ? 'sticky' : undefined,
-                    }, children: [toLocale(numOfBpSelected), " bp"] })) : null })] }));
+                    }, children: getBpDisplayStr(numOfBpSelected) })) : null })] }));
 }

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../model';
 declare const SearchBox: ({ model, showHelp, }: {
     showHelp?: boolean;
     model: LinearGenomeViewModel;

package/esm/LinearGenomeView/components/SearchBox.js

@@ -8,11 +8,33 @@ import EndAdornment from './RefNameAutocomplete/EndAdornment';
 import { fetchResults } from './util';
 import { handleSelectedRegion, navToOption } from '../../searchUtils';
 import { SPACING, WIDGET_HEIGHT } from '../consts';
-const useStyles = makeStyles()(() => ({
+const useStyles = makeStyles()({
     headerRefName: {
         minWidth: 100,
     },
-}));
+});
+async function onSelect({ option, model, assemblyName, }) {
+    var _a;
+    const { assemblyManager } = getSession(model);
+    const assembly = assemblyManager.get(assemblyName);
+    if (option.hasLocation()) {
+        await navToOption({
+            option,
+            model,
+            assemblyName,
+        });
+    }
+    else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
+        model.setSearchResults(option.results, option.getLabel());
+    }
+    else if (assembly) {
+        await handleSelectedRegion({
+            input: option.getLabel(),
+            assembly,
+            model,
+        });
+    }
+}
 const SearchBox = observer(function ({ model, showHelp = true, }) {
     const { classes } = useStyles();
     const theme = useTheme();
@@ -23,21 +45,12 @@ const SearchBox = observer(function ({ model, showHelp = true, }) {
     const assembly = assemblyManager.get(assemblyName);
     const searchScope = model.searchScope(assemblyName);
     return (_jsx(RefNameAutocomplete, { onSelect: async (option) => {
-            var _a;
             try {
-                if (option.hasLocation()) {
-                    await navToOption({ option, model, assemblyName });
-                }
-                else if ((_a = option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                    model.setSearchResults(option.results, option.getLabel());
-                }
-                else if (assembly) {
-                    await handleSelectedRegion({
-                        input: option.getLabel(),
-                        assembly,
-                        model,
-                    });
-                }
+                await onSelect({
+                    model,
+                    assemblyName,
+                    option,
+                });
             }
             catch (e) {
                 console.error(e);

package/esm/LinearGenomeView/components/useWheelScroll.js

@@ -1,14 +1,25 @@
 import { useEffect, useRef } from 'react';
+import { sum } from '@jbrowse/core/util';
 export function useWheelScroll(ref, model) {
     const delta = useRef(0);
     const timeout = useRef(null);
     const scheduled = useRef(false);
     useEffect(() => {
+        let samples = [];
         const curr = ref.current;
         function onWheel(event) {
             if (event.ctrlKey) {
                 event.preventDefault();
-                delta.current += event.deltaY / 500;
+                samples.push(event.deltaY);
+                const averageDeltaY = Math.abs(sum(samples)) / samples.length;
+                const normalizer = averageDeltaY < 6
+                    ? 25
+                    : averageDeltaY > 30
+                        ? averageDeltaY > 150
+                            ? 500
+                            : 150
+                        : 75;
+                delta.current += event.deltaY / normalizer;
                 model.setScaleFactor(delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current));
                 if (timeout.current) {
                     clearTimeout(timeout.current);
@@ -19,6 +30,7 @@ export function useWheelScroll(ref, model) {
                         ? model.bpPerPx * (1 + delta.current)
                         : model.bpPerPx / (1 - delta.current), event.clientX - ((curr === null || curr === void 0 ? void 0 : curr.getBoundingClientRect().left) || 0));
                     delta.current = 0;
+                    samples = [];
                 }, 300);
             }
             else {

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

@@ -21,4 +21,5 @@ export declare function getCytobands(assembly: Assembly | undefined, refName: st
     start: number;
     end: number;
     type: string;
+    name: any;
 }[];

package/esm/LinearGenomeView/components/util.js

@@ -5,12 +5,14 @@ export async function fetchResults({ queryString, searchType, searchScope, rankS
     if (!textSearchManager) {
         console.warn('No text search manager');
     }
-    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+    const textSearchResults = (await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
         queryString,
         searchType,
-    }, searchScope, rankSearchResults));
-    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());
+    }, searchScope, rankSearchResults))) || [];
+    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());
 }
 export function splitLast(str, split) {
     const lastIndex = str.lastIndexOf(split);
@@ -33,5 +35,6 @@ export function getCytobands(assembly, refName) {
         start: f.get('start'),
         end: f.get('end'),
         type: f.get('gieStain'),
+        name: f.get('name'),
     })).filter(f => f.refName === refName)) || []);
 }

package/esm/LinearGenomeView/model.d.ts

@@ -169,12 +169,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setCoarseDynamicBlocks(blocks: BlockSet): void;
 } & {
     moveTo(start?: BpOffset, end?: BpOffset): void;
-    navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+    navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
     navToSearchString({ input, assembly, }: {
         input: string;
         assembly: Assembly;
     }): Promise<void>;
-    navToLocations(parsedLocStrings: ParsedLocString[], assemblyName?: string): Promise<void>;
+    navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
+    navToLocations(regions: ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
     navTo(query: NavLocation): void;
     navToMultiple(locations: NavLocation[]): void;
 } & {
@@ -242,9 +243,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     displayName: string | undefined;
     tracks: any[];
     minimized: boolean;
-    displayedRegions: Region[];
     offsetPx: number;
     bpPerPx: number;
+    displayedRegions: Region[];
     hideHeader: boolean;
     hideHeaderOverview: boolean;
     hideNoTracksActive: boolean;

package/esm/LinearGenomeView/model.js

@@ -222,12 +222,6 @@ export function stateModelFactory(pluginManager) {
             return self.tracks.find(t => t.configuration.trackId === id);
         },
         rankSearchResults(results) {
-            const openTrackIds = new Set(self.tracks.map(track => track.configuration.trackId));
-            for (const result of results) {
-                if (openTrackIds.has(result.trackId)) {
-                    result.updateScore(result.getScore() + 1);
-                }
-            }
             return results;
         },
         rewriteOnClicks(trackType, viewMenuActions) {
@@ -800,14 +794,14 @@ export function stateModelFactory(pluginManager) {
         moveTo(start, end) {
             moveTo(self, start, end);
         },
-        async navToLocString(input, optAssemblyName) {
+        async navToLocString(input, optAssemblyName, grow) {
             const { assemblyNames } = self;
             const { assemblyManager } = getSession(self);
             const assemblyName = optAssemblyName || assemblyNames[0];
             if (assemblyName) {
                 await assemblyManager.waitForAssembly(assemblyName);
             }
-            return this.navToLocations(parseLocStrings(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName);
+            return this.navToLocations(parseLocStrings(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName, grow);
         },
         async navToSearchString({ input, assembly, }) {
             await handleSelectedRegion({
@@ -816,10 +810,18 @@ export function stateModelFactory(pluginManager) {
                 model: self,
             });
         },
-        async navToLocations(parsedLocStrings, assemblyName) {
+        async navToLocation(parsedLocString, assemblyName, grow) {
+            return this.navToLocations([parsedLocString], assemblyName, grow);
+        },
+        async navToLocations(regions, assemblyName, grow) {
             const { assemblyManager } = getSession(self);
             await when(() => self.volatileWidth !== undefined);
-            const locations = await generateLocations(parsedLocStrings, assemblyManager, assemblyName);
+            const locations = await generateLocations({
+                regions,
+                assemblyManager,
+                assemblyName,
+                grow,
+            });
             if (locations.length === 1) {
                 const loc = locations[0];
                 const { reversed, parentRegion, start, end } = loc;

package/esm/LinearGenomeView/util.d.ts

@@ -9,7 +9,12 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
     base: number;
     index: number;
 }[];
-export declare function generateLocations(regions: ParsedLocString[], assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
+export declare function generateLocations({ regions, assemblyManager, assemblyName, grow, }: {
+    regions: ParsedLocString[];
+    assemblyManager: AssemblyManager;
+    assemblyName?: string;
+    grow?: number;
+}): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;