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

package/dist/BaseLinearDisplay/components/LinearBlocks.js

@@ -23,7 +23,7 @@ const useStyles = (0, mui_1.makeStyles)()({
         width: '100%',
         fontWeight: 'bold',
         textAlign: 'center',
-        zIndex: 2000,
+        zIndex: 999,
         boxSizing: 'border-box',
     },
 });

package/dist/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/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -138,15 +138,23 @@ function stateModelFactory() {
         deleteBlock(key) {
             self.blockState.delete(key);
         },
-        selectFeature(feature) {
+        async selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('BaseFeatureWidget', 'baseFeature', {
-                    view: (0, util_1.getContainingView)(self),
-                    track: (0, util_1.getContainingTrack)(self),
-                    featureData: feature.toJSON(),
+                const { rpcManager } = session;
+                const sessionId = (0, tracks_1.getRpcSessionId)(self);
+                const track = (0, util_1.getContainingTrack)(self);
+                const view = (0, util_1.getContainingView)(self);
+                const adapterConfig = (0, configuration_1.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 ((0, util_1.isSelectionContainer)(session)) {
                 session.setSelection(feature);
@@ -197,7 +205,11 @@ function stateModelFactory() {
                             icon: MenuOpen_1.default,
                             onClick: () => {
                                 if (self.contextMenuFeature) {
-                                    self.selectFeature(self.contextMenuFeature);
+                                    self
+                                        .selectFeature(self.contextMenuFeature)
+                                        .catch((e) => {
+                                        (0, util_1.getSession)(e).notifyError(`${e}`, e);
+                                    });
                                 }
                             },
                         },
@@ -228,7 +240,9 @@ function stateModelFactory() {
                     else {
                         const feature = self.features.get(f);
                         if (feature) {
-                            self.selectFeature(feature);
+                            self.selectFeature(feature).catch((e) => {
+                                (0, util_1.getSession)(e).notifyError(`${e}`, e);
+                            });
                         }
                     }
                 },

package/dist/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/dist/LinearBasicDisplay/components/AddFiltersDialog.js

@@ -43,7 +43,7 @@ const AddFiltersDialog = (0, mobx_react_1.observer)(function ({ model, handleClo
             setError(e);
         }
     }, [data]);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] })] })] }), error ? (0, jsx_runtime_1.jsx)("p", { className: classes.error, children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] }), (0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("code", { children: "jexl:get(feature,'end') - get(feature,'start') < 1000000" }), ' ', "- show only features with length less than 1Mbp"] })] })] }), error ? (0, jsx_runtime_1.jsx)("p", { className: classes.error, children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(material_1.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/dist/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/dist/LinearBasicDisplay/model.js

@@ -165,7 +165,10 @@ function stateModelFactory(configSchema) {
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 SetMaxHeightDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
@@ -174,7 +177,10 @@ function stateModelFactory(configSchema) {
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 AddFiltersDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/dist/LinearGenomeView/components/Cytobands.js

@@ -11,14 +11,14 @@ 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],
@@ -42,14 +42,28 @@ const Cytobands = (0, mobx_react_1.observer)(function ({ overview, block, assemb
     const rcap = reversed ? 0 : cytobands.length - 1;
     const h = consts_1.HEADER_OVERVIEW_HEIGHT;
     let centromereSeen = false;
+    let curr = '';
+    let idx = 0;
     return ((0, jsx_runtime_1.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 ((0, jsx_runtime_1.jsx)("polygon", { points: reversed

package/dist/LinearGenomeView/components/GetSequenceDialog.js

@@ -33,8 +33,9 @@ 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/dist/LinearGenomeView/components/HeaderZoomControls.js

@@ -58,9 +58,13 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         color: theme.palette.text.secondary,
     },
 }));
+function ValueLabelComponent(props) {
+    const { children, open, value } = props;
+    return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: open, enterTouchDelay: 0, placement: "top", title: value, arrow: true, children: children }));
+}
 const HeaderZoomControls = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
-    const { maxBpPerPx, minBpPerPx, bpPerPx } = model;
+    const { width, maxBpPerPx, minBpPerPx, bpPerPx } = model;
     const [value, setValue] = (0, react_1.useState)(-Math.log2(bpPerPx) * 100);
     (0, react_1.useEffect)(() => {
         setValue(-Math.log2(bpPerPx) * 100);
@@ -69,7 +73,9 @@ const HeaderZoomControls = (0, mobx_react_1.observer)(function ({ model, }) {
     const zoomOutDisabled = bpPerPx >= maxBpPerPx - 0.0001;
     return ((0, jsx_runtime_1.jsxs)("div", { className: classes.container, children: [(0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Zoom out 2x", children: (0, jsx_runtime_1.jsx)("span", { children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "zoom_out", disabled: zoomOutDisabled, onClick: () => {
                             model.zoom(bpPerPx * 2);
-                        }, children: (0, jsx_runtime_1.jsx)(ZoomOut_1.default, {}) }) }) }), (0, jsx_runtime_1.jsx)(material_1.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: (0, jsx_runtime_1.jsx)(ZoomOut_1.default, {}) }) }) }), (0, jsx_runtime_1.jsx)(material_1.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: ${(0, util_1.getBpDisplayStr)(2 ** (-newValue / 100) * width)}`, slots: {
+                    valueLabel: ValueLabelComponent,
+                }, onChange: (_, val) => {
                     setValue(val);
                 } }), (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Zoom in 2x", children: (0, jsx_runtime_1.jsx)("span", { children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "zoom_in", disabled: zoomInDisabled, onClick: () => {
                             model.zoom(model.bpPerPx / 2);

package/dist/LinearGenomeView/components/ImportForm.js

@@ -70,7 +70,7 @@ const LinearGenomeViewImportForm = (0, mobx_react_1.observer)(function ({ model,
                                 session.notify(`${e}`, 'warning');
                             }
                         }
-                    }, children: (0, jsx_runtime_1.jsxs)(material_1.Grid2, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [(0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { onChange: val => {
+                    }, children: (0, jsx_runtime_1.jsxs)(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [(0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { onChange: val => {
                                         setSelectedAsm(val);
                                     }, localStorageKey: "lgv", session: session, selected: selectedAsm }) }), selectedAsm ? (assemblyError ? ((0, jsx_runtime_1.jsx)(Close_1.default, { style: { color: 'red' } })) : assemblyLoaded ? ((0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(ImportFormRefNameAutocomplete_1.default, { value: value, setValue: setValue, selectedAsm: selectedAsm, setOption: setOption, model: model }) })) : ((0, jsx_runtime_1.jsx)(material_1.CircularProgress, { size: 20, disableShrink: true }))) : null, (0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary", children: "Open" }) }), (0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !value, className: classes.button, onClick: () => {
                                         model.setError(undefined);

package/dist/LinearGenomeView/components/OverviewRubberband.js

@@ -17,12 +17,6 @@ const useStyles = (0, mui_1.makeStyles)()({
         width: '100%',
         minHeight: 8,
     },
-    guide: {
-        pointerEvents: 'none',
-        height: '100%',
-        width: 1,
-        position: 'absolute',
-    },
     rel: {
         position: 'relative',
     },

package/dist/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js

@@ -6,20 +6,12 @@ const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
-    rubberbandControl: {
-        cursor: 'crosshair',
-        width: '100%',
-        minHeight: 8,
-    },
     guide: {
         pointerEvents: 'none',
         height: '100%',
         width: 1,
         position: 'absolute',
     },
-    rel: {
-        position: 'relative',
-    },
 });
 const OverviewRubberbandHoverTooltip = (0, mobx_react_1.observer)(function ({ model, open, guideX, overview, }) {
     var _a;
@@ -31,6 +23,6 @@ const OverviewRubberbandHoverTooltip = (0, mobx_react_1.observer)(function ({ mo
     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 ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: open, placement: "top", title: [(0, util_1.stringify)(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true, children: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: { left: guideX } }) }));
+    return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { open: open, placement: "top", title: [(0, util_1.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: (0, jsx_runtime_1.jsx)("div", { className: classes.guide, style: { left: guideX } }) }));
 });
 exports.default = OverviewRubberbandHoverTooltip;

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

@@ -63,27 +63,31 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                     return;
                 }
                 setLoaded(false);
-                const results = await fetchResults(debouncedSearch);
-                setLoaded(true);
-                setSearchOptions((0, util_2.getDeduplicatedResult)(results));
+                setSearchOptions((0, util_2.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((0, util_1.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 BaseResults_1.RefSequenceResult({
-            refName,
-            label: refName,
+            refName: region.refName,
+            label: region.refName,
+            displayString: region.refName,
             matchedAttribute: 'refName',
         }),
     }))) || [];
-    return ((0, jsx_runtime_1.jsx)(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
+    return ((0, jsx_runtime_1.jsx)(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: {
+            ...style,
+            width: Math.min(Math.max((0, util_1.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: () => {
@@ -100,7 +104,9 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                 return;
             }
             if (typeof selectedOption === 'string') {
-                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({
+                    label: selectedOption,
+                }));
             }
             else {
                 onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);

package/dist/LinearGenomeView/components/RubberbandSpan.js

@@ -34,10 +34,10 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
 function RubberbandSpan({ leftBpOffset, rightBpOffset, numOfBpSelected, left, width, top = 0, sticky = false, }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [anchorEl ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(RubberbandTooltip_1.default, { side: "left", anchorEl: anchorEl, text: (0, util_1.stringify)(leftBpOffset) }), (0, jsx_runtime_1.jsx)(RubberbandTooltip_1.default, { side: "right", anchorEl: anchorEl, text: (0, util_1.stringify)(rightBpOffset) })] })) : null, (0, jsx_runtime_1.jsx)("div", { className: classes.rubberband, style: { left, width }, children: numOfBpSelected ? ((0, jsx_runtime_1.jsxs)(material_1.Typography, { ref: el => {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [anchorEl ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(RubberbandTooltip_1.default, { side: "left", anchorEl: anchorEl, text: (0, util_1.stringify)(leftBpOffset) }), (0, jsx_runtime_1.jsx)(RubberbandTooltip_1.default, { side: "right", anchorEl: anchorEl, text: (0, util_1.stringify)(rightBpOffset) })] })) : null, (0, jsx_runtime_1.jsx)("div", { className: classes.rubberband, style: { left, width }, children: numOfBpSelected ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { ref: el => {
                         setAnchorEl(el);
                     }, variant: "h6", className: classes.rubberbandText, style: {
                         top,
                         position: sticky ? 'sticky' : undefined,
-                    }, children: [(0, util_1.toLocale)(numOfBpSelected), " bp"] })) : null })] }));
+                    }, children: (0, util_1.getBpDisplayStr)(numOfBpSelected) })) : null })] }));
 }

package/dist/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/dist/LinearGenomeView/components/SearchBox.js

@@ -13,11 +13,33 @@ const EndAdornment_1 = __importDefault(require("./RefNameAutocomplete/EndAdornme
 const util_2 = require("./util");
 const searchUtils_1 = require("../../searchUtils");
 const consts_1 = require("../consts");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
+const useStyles = (0, mui_1.makeStyles)()({
     headerRefName: {
         minWidth: 100,
     },
-}));
+});
+async function onSelect({ option, model, assemblyName, }) {
+    var _a;
+    const { assemblyManager } = (0, util_1.getSession)(model);
+    const assembly = assemblyManager.get(assemblyName);
+    if (option.hasLocation()) {
+        await (0, searchUtils_1.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 (0, searchUtils_1.handleSelectedRegion)({
+            input: option.getLabel(),
+            assembly,
+            model,
+        });
+    }
+}
 const SearchBox = (0, mobx_react_1.observer)(function ({ model, showHelp = true, }) {
     const { classes } = useStyles();
     const theme = (0, material_1.useTheme)();
@@ -28,21 +50,12 @@ const SearchBox = (0, mobx_react_1.observer)(function ({ model, showHelp = true,
     const assembly = assemblyManager.get(assemblyName);
     const searchScope = model.searchScope(assemblyName);
     return ((0, jsx_runtime_1.jsx)(RefNameAutocomplete_1.default, { onSelect: async (option) => {
-            var _a;
             try {
-                if (option.hasLocation()) {
-                    await (0, searchUtils_1.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 (0, searchUtils_1.handleSelectedRegion)({
-                        input: option.getLabel(),
-                        assembly,
-                        model,
-                    });
-                }
+                await onSelect({
+                    model,
+                    assemblyName,
+                    option,
+                });
             }
             catch (e) {
                 console.error(e);

package/dist/LinearGenomeView/components/useWheelScroll.js

@@ -2,16 +2,27 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.useWheelScroll = useWheelScroll;
 const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
 function useWheelScroll(ref, model) {
     const delta = (0, react_1.useRef)(0);
     const timeout = (0, react_1.useRef)(null);
     const scheduled = (0, react_1.useRef)(false);
     (0, react_1.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((0, util_1.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);
@@ -22,6 +33,7 @@ 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/dist/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/dist/LinearGenomeView/components/util.js

@@ -14,12 +14,14 @@ async function fetchResults({ queryString, searchType, searchScope, rankSearchRe
     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 BaseResults_1.default({ label: r }));
-    return (0, util_1.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 BaseResults_1.default({
+        label: r,
+    }))) || [];
+    return (0, util_1.dedupe)([...refNameResults, ...textSearchResults], elt => elt.getId());
 }
 function splitLast(str, split) {
     const lastIndex = str.lastIndexOf(split);
@@ -42,5 +44,6 @@ 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/dist/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/dist/LinearGenomeView/model.js

@@ -262,12 +262,6 @@ 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) {
@@ -840,14 +834,14 @@ function stateModelFactory(pluginManager) {
         moveTo(start, end) {
             (0, Base1DUtils_1.moveTo)(self, start, end);
         },
-        async navToLocString(input, optAssemblyName) {
+        async navToLocString(input, optAssemblyName, grow) {
             const { assemblyNames } = self;
             const { assemblyManager } = (0, util_1.getSession)(self);
             const assemblyName = optAssemblyName || assemblyNames[0];
             if (assemblyName) {
                 await assemblyManager.waitForAssembly(assemblyName);
             }
-            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName);
+            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName, grow);
         },
         async navToSearchString({ input, assembly, }) {
             await (0, searchUtils_1.handleSelectedRegion)({
@@ -856,10 +850,18 @@ 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 } = (0, util_1.getSession)(self);
             await (0, mobx_1.when)(() => self.volatileWidth !== undefined);
-            const locations = await (0, util_2.generateLocations)(parsedLocStrings, assemblyManager, assemblyName);
+            const locations = await (0, util_2.generateLocations)({
+                regions,
+                assemblyManager,
+                assemblyName,
+                grow,
+            });
             if (locations.length === 1) {
                 const loc = locations[0];
                 const { reversed, parentRegion, start, end } = loc;

package/dist/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;

package/dist/LinearGenomeView/util.js

@@ -57,7 +57,7 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     }
     return ticks;
 }
-async function generateLocations(regions, assemblyManager, assemblyName) {
+async function generateLocations({ regions, assemblyManager, assemblyName, grow, }) {
     return Promise.all(regions.map(async (region) => {
         const asmName = region.assemblyName || assemblyName;
         if (!asmName) {
@@ -80,11 +80,25 @@ async function generateLocations(regions, assemblyManager, assemblyName) {
         if (!parentRegion) {
             throw new Error(`Could not find refName ${refName} in ${asmName}`);
         }
-        return {
-            ...region,
-            assemblyName: asmName,
-            parentRegion,
-        };
+        const { start, end } = region;
+        if (grow && start && end) {
+            const len = end - start;
+            const margin = len * grow;
+            return {
+                ...region,
+                start: Math.max(0, start - margin),
+                end: end + margin,
+                assemblyName: asmName,
+                parentRegion,
+            };
+        }
+        else {
+            return {
+                ...region,
+                assemblyName: asmName,
+                parentRegion,
+            };
+        }
     }));
 }
 function parseLocStrings(input, assemblyName, isValidRefName) {

package/dist/index.d.ts

@@ -195,7 +195,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
         } & {
             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;