@jbrowse/plugin-linear-genome-view 2.3.4 → 2.4.1

package/esm/LinearGenomeView/components/ImportForm.js

@@ -2,13 +2,14 @@ import React, { useState, useEffect, lazy } from 'react';
 import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 import { getSession } from '@jbrowse/core/util';
-import { Button, CircularProgress, FormControl, Container, Grid, } from '@mui/material';
+import { Button, FormControl, Container, Grid, CircularProgress, } from '@mui/material';
 import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
 // icons
 import CloseIcon from '@mui/icons-material/Close';
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete';
 import { fetchResults, splitLast } from './util';
+// lazies
 const SearchResultsDialog = lazy(() => import('./SearchResultsDialog'));
 const useStyles = makeStyles()(theme => ({
     importFormContainer: {
@@ -21,7 +22,7 @@ const useStyles = makeStyles()(theme => ({
         padding: theme.spacing(4),
     },
 }));
-const ImportForm = observer(({ model }) => {
+export default observer(function ({ model }) {
     var _a;
     const { classes } = useStyles();
     const session = getSession(model);
@@ -34,14 +35,16 @@ const ImportForm = observer(({ model }) => {
     const assemblyError = assemblyNames.length
         ? assembly === null || assembly === void 0 ? void 0 : assembly.error
         : 'No configured assemblies';
-    const regions = (assembly === null || assembly === void 0 ? void 0 : assembly.regions) || [];
     const displayError = assemblyError || error;
     const [value, setValue] = useState('');
-    const r0 = (_a = regions[0]) === null || _a === void 0 ? void 0 : _a.refName;
-    // useEffect resets to an "initial state" of displaying first region from assembly
-    // after assembly change. needs to react to selectedAsm as well as r0 because changing
-    // assembly will run setValue('') and then r0 may not change if assembly names are the
-    // same across assemblies, but it still needs to be reset
+    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
+    const assemblyLoaded = !!regions;
+    const r0 = regions ? (_a = regions[0]) === null || _a === void 0 ? void 0 : _a.refName : '';
+    // useEffect resets to an "initial state" of displaying first region from
+    // assembly after assembly change. needs to react to selectedAsm as well as
+    // r0 because changing assembly will run setValue('') and then r0 may not
+    // change if assembly names are the same across assemblies, but it still
+    // needs to be reset
     useEffect(() => {
         setValue(r0);
     }, [r0, selectedAsm]);
@@ -73,7 +76,7 @@ const ImportForm = observer(({ model }) => {
                 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)))) {
+                    (allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10)))) {
                     await model.navToLocString(input, selectedAsm);
                 }
                 else {
@@ -118,24 +121,18 @@ const ImportForm = observer(({ model }) => {
                 React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
                     React.createElement(Grid, { item: true },
                         React.createElement(FormControl, null,
-                            React.createElement(AssemblySelector, { onChange: val => {
-                                    setSelectedAsm(val);
-                                    setValue('');
-                                }, localStorageKey: "lgv", session: session, selected: selectedAsm }))),
-                    React.createElement(Grid, { item: true }, selectedAsm ? (assemblyError ? (React.createElement(CloseIcon, { style: { color: 'red' } })) : value ? (React.createElement(FormControl, null,
+                            React.createElement(AssemblySelector, { onChange: val => setSelectedAsm(val), localStorageKey: "lgv", session: session, selected: selectedAsm }))),
+                    React.createElement(Grid, { item: true }, selectedAsm ? (assemblyError ? (React.createElement(CloseIcon, { style: { color: 'red' } })) : assemblyLoaded ? (React.createElement(FormControl, null,
                         React.createElement(RefNameAutocomplete, { fetchResults: queryString => fetchResults({
                                 queryString,
                                 assembly,
                                 textSearchManager,
                                 rankSearchResults,
                                 searchScope,
-                            }), model: model, assemblyName: assemblyError ? undefined : selectedAsm, value: value, 
-                            // note: minWidth 270 accommodates full width of helperText
-                            minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
+                            }), model: model, assemblyName: selectedAsm, value: value, minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
                                 variant: 'outlined',
                                 helperText: 'Enter sequence name, feature name, or location',
-                                style: { minWidth: '175px' },
-                            } }))) : (React.createElement(CircularProgress, { role: "progressbar", size: 20, disableShrink: true }))) : null),
+                            } }))) : (React.createElement(CircularProgress, { size: 20, disableShrink: true }))) : null),
                     React.createElement(Grid, { item: true },
                         React.createElement(FormControl, null,
                             React.createElement(Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary" }, "Open")),
@@ -146,5 +143,4 @@ const ImportForm = observer(({ model }) => {
                                 }, variant: "contained", color: "secondary" }, "Show all regions in assembly")))))),
         isSearchDialogDisplayed ? (React.createElement(SearchResultsDialog, { model: model, optAssemblyName: selectedAsm, handleClose: () => model.setSearchResults(undefined, undefined) })) : null));
 });
-export default ImportForm;
 //# sourceMappingURL=ImportForm.js.map

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

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package/esm/LinearGenomeView/components/LinearGenomeView.js

@@ -20,7 +20,7 @@ const LinearGenomeView = observer(({ model }) => {
     const { tracks, error, initialized, hasDisplayedRegions } = model;
     const { classes } = useStyles();
     if (!initialized && !error) {
-        return React.createElement(LoadingEllipses, { variant: "h5" });
+        return React.createElement(LoadingEllipses, { variant: "h6" });
     }
     if (!hasDisplayedRegions || error) {
         return React.createElement(ImportForm, { model: model });

package/esm/LinearGenomeView/components/MiniControls.js

@@ -1,21 +1,22 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
 import { IconButton, Paper } from '@mui/material';
+import Menu from '@jbrowse/core/ui/Menu';
+// icons
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
 import ArrowDown from '@mui/icons-material/KeyboardArrowDown';
-import Menu from '@jbrowse/core/ui/Menu';
 const MiniControls = observer((props) => {
     const { model } = props;
     const { bpPerPx, maxBpPerPx, minBpPerPx, scaleFactor, hideHeader } = model;
     const [anchorEl, setAnchorEl] = useState();
     return hideHeader ? (React.createElement("div", { style: { position: 'absolute', right: '0px', zIndex: '1001' } },
         React.createElement(Paper, { style: { background: '#aaa7' } },
-            React.createElement(IconButton, { color: "secondary", onClick: event => setAnchorEl(event.currentTarget) },
+            React.createElement(IconButton, { onClick: event => setAnchorEl(event.currentTarget) },
                 React.createElement(ArrowDown, { fontSize: "small" })),
-            React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, color: "secondary" },
+            React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
                 React.createElement(ZoomOut, { fontSize: "small" })),
-            React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, color: "secondary" },
+            React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
                 React.createElement(ZoomIn, { fontSize: "small" })),
             React.createElement(Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onMenuItemClick: (_, callback) => {
                     callback();

package/esm/LinearGenomeView/components/MiniControls.js.map

@@ -1 +1 @@
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package/esm/LinearGenomeView/components/OverviewRubberband.d.ts

@@ -2,10 +2,9 @@ import React from 'react';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
-declare function OverviewRubberband({ model, overview, ControlComponent, }: {
+declare const _default: ({ model, overview, ControlComponent, }: {
     model: LGV;
     overview: Base1DViewModel;
-    ControlComponent?: React.ReactElement;
-}): JSX.Element;
-declare const _default: typeof OverviewRubberband;
+    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+}) => JSX.Element;
 export default _default;

package/esm/LinearGenomeView/components/OverviewRubberband.js

@@ -19,7 +19,7 @@ const useStyles = makeStyles()({
         zIndex: 10,
     },
 });
-const HoverTooltip = observer(({ model, open, guideX, overview, }) => {
+const HoverTooltip = observer(function ({ model, open, guideX, overview, }) {
     var _a;
     const { classes } = useStyles();
     const { cytobandOffset } = model;
@@ -30,11 +30,9 @@ const HoverTooltip = observer(({ model, open, guideX, overview, }) => {
         px.coord < f.get('end') &&
         px.refName === assembly.getCanonicalRefName(f.get('refName')));
     return (React.createElement(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true },
-        React.createElement("div", { className: classes.guide, style: {
-                left: guideX,
-            } })));
+        React.createElement("div", { className: classes.guide, style: { left: guideX } })));
 });
-function OverviewRubberband({ model, overview, ControlComponent = React.createElement("div", null), }) {
+export default observer(function OverviewRubberband({ model, overview, ControlComponent = React.createElement("div", null), }) {
     const { cytobandOffset } = model;
     const [startX, setStartX] = useState();
     const [currentX, setCurrentX] = useState();
@@ -107,7 +105,7 @@ function OverviewRubberband({ model, overview, ControlComponent = React.createEl
     if (startX === undefined) {
         return (React.createElement("div", { style: { position: 'relative' } },
             guideX !== undefined ? (React.createElement(HoverTooltip, { model: model, open: !mouseDragging, overview: overview, guideX: guideX })) : null,
-            React.createElement("div", { className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+            React.createElement("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
     }
     let left = startX || 0;
     let width = 0;
@@ -121,14 +119,13 @@ function OverviewRubberband({ model, overview, ControlComponent = React.createEl
     if (startX) {
         leftBpOffset = overview.pxToBp(startX - cytobandOffset);
         rightBpOffset = overview.pxToBp(startX + width - cytobandOffset);
-        if (currentX && currentX < startX) {
+        if (currentX !== undefined && currentX < startX) {
             ;
             [leftBpOffset, rightBpOffset] = [rightBpOffset, leftBpOffset];
         }
     }
     return (React.createElement("div", { style: { position: 'relative' } },
-        leftBpOffset && rightBpOffset ? (React.createElement(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, width: width, left: left })) : null,
-        React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
-}
-export default observer(OverviewRubberband);
+        leftBpOffset && rightBpOffset ? (React.createElement(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, width: Math.abs(width), left: left })) : null,
+        React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+});
 //# sourceMappingURL=OverviewRubberband.js.map

package/esm/LinearGenomeView/components/OverviewRubberband.js.map

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

@@ -1,7 +1,5 @@
 import React from 'react';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
-import { ContentBlock } from '@jbrowse/core/util/blockTypes';
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 import { LinearGenomeViewModel } from '..';
 declare const Polygon: ({ model, overview, useOffset, }: {
     model: LGV;
@@ -9,123 +7,10 @@ declare const Polygon: ({ model, overview, useOffset, }: {
     useOffset?: boolean | undefined;
 }) => JSX.Element | null;
 type LGV = LinearGenomeViewModel;
-declare const Cytobands: ({ overview, block, assembly, }: {
-    overview: Base1DViewModel;
-    assembly?: ({
-        configuration: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loaded: boolean;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string | undefined;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-    } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }, lcAliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setLoadingP(p?: Promise<void> | undefined): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: 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>>;
-    }, {
-        error: unknown;
-        loaded: boolean;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string | undefined;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-    } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }, lcAliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setLoadingP(p?: Promise<void> | undefined): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-    block: ContentBlock;
-}) => JSX.Element;
-declare function OverviewScalebar({ model, children, }: {
+declare const _default: ({ model, children, }: {
     model: LGV;
     children: React.ReactNode;
-}): JSX.Element;
-declare const _default: typeof OverviewScalebar;
+}) => JSX.Element;
 export default _default;
-export { Cytobands, Polygon };
+export { Polygon };
+export { default as Cytobands } from './Cytobands';

package/esm/LinearGenomeView/components/OverviewScalebar.js

@@ -10,6 +10,8 @@ import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, } from '..';
 import { chooseGridPitch } from '../util';
 import OverviewRubberband from './OverviewRubberband';
+import Cytobands from './Cytobands';
+import { getCytobands } from './util';
 const wholeSeqSpacer = 2;
 const useStyles = makeStyles()(theme => ({
     scalebar: {
@@ -23,13 +25,14 @@ const useStyles = makeStyles()(theme => ({
         position: 'absolute',
         top: 0,
         height: HEADER_OVERVIEW_HEIGHT,
+        overflow: 'hidden',
     },
     scalebarContigForward: {
-        backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E")`,
+        backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='${theme.palette.divider}'/%3E%3C/svg%3E")`,
         backgroundRepeat: 'repeat',
     },
     scalebarContigReverse: {
-        backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M6 0L0 4.5L6 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E")`,
+        backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M6 0L0 4.5L6 9' fill='none' stroke='${theme.palette.divider}'/%3E%3C/svg%3E")`,
         backgroundRepeat: 'repeat',
     },
     scalebarRefName: {
@@ -61,7 +64,7 @@ const useStyles = makeStyles()(theme => ({
         position: 'absolute',
     },
 }));
-const Polygon = observer(({ model, overview, useOffset = true, }) => {
+const Polygon = observer(function ({ model, overview, useOffset = true, }) {
     const theme = useTheme();
     const multiplier = Number(useOffset);
     const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
@@ -95,98 +98,9 @@ const Polygon = observer(({ model, overview, useOffset = true, }) => {
     ];
     return (React.createElement("polygon", { points: points.toString(), fill: alpha(polygonColor, 0.3), stroke: alpha(polygonColor, 0.8) }));
 });
-// rounded rect from https://stackoverflow.com/a/45889603/2129219
-// prettier-ignore
-function rightRoundedRect(x, y, width, height, radius) {
-    return "M" + x + "," + y
-        + "h" + (width - radius)
-        + "a" + radius + "," + radius + " 0 0 1 " + radius + "," + radius
-        + "v" + (height - 2 * radius)
-        + "a" + radius + "," + radius + " 0 0 1 " + -radius + "," + radius
-        + "h" + (radius - width)
-        + "z";
-}
-// prettier-ignore
-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";
-}
-const colorMap = {
-    gneg: 'rgb(227,227,227)',
-    gpos25: 'rgb(142,142,142)',
-    gpos50: 'rgb(85,85,85)',
-    gpos100: 'rgb(0,0,0)',
-    gpos75: 'rgb(57,57,57)',
-    gvar: 'rgb(0,0,0)',
-    stalk: 'rgb(127,127,127)',
-    acen: '#800',
-};
-function getCytobands(assembly, refName) {
-    var _a;
-    return (((_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.map(f => ({
-        refName: assembly.getCanonicalRefName(f.get('refName')),
-        start: f.get('start'),
-        end: f.get('end'),
-        type: f.get('type'),
-    })).filter(f => f.refName === refName)) || []);
-}
-const Cytobands = observer(({ overview, block, assembly, }) => {
-    const { offsetPx, reversed } = block;
-    const cytobands = getCytobands(assembly, block.refName);
-    const coords = cytobands.map(f => {
-        const { refName, start, end, type } = f;
-        return [
-            overview.bpToPx({
-                refName,
-                coord: start,
-            }),
-            overview.bpToPx({
-                refName,
-                coord: end,
-            }),
-            type,
-        ];
-    });
-    const arr = cytobands || [];
-    const lcap = reversed ? arr.length - 1 : 0;
-    const rcap = reversed ? 0 : arr.length - 1;
-    let firstCent = true;
-    return (React.createElement("g", { transform: `translate(-${offsetPx})` }, coords.map(([start, end, type], index) => {
-        const key = `${start}-${end}-${type}`;
-        if (type === 'acen' && firstCent) {
-            firstCent = false;
-            return (React.createElement("polygon", { key: key, points: [
-                    [start, 0],
-                    [end, HEADER_OVERVIEW_HEIGHT / 2],
-                    [start, HEADER_OVERVIEW_HEIGHT],
-                ].toString(), fill: colorMap[type] }));
-        }
-        if (type === 'acen' && !firstCent) {
-            return (React.createElement("polygon", { key: key, points: [
-                    [start, HEADER_OVERVIEW_HEIGHT / 2],
-                    [end, 0],
-                    [end, HEADER_OVERVIEW_HEIGHT],
-                ].toString(), fill: colorMap[type] }));
-        }
-        if (lcap === index) {
-            return (React.createElement("path", { key: key, d: leftRoundedRect(Math.min(start, end), 0, Math.abs(end - start), HEADER_OVERVIEW_HEIGHT, 8), fill: colorMap[type] }));
-        }
-        else if (rcap === index) {
-            return (React.createElement("path", { key: key, d: rightRoundedRect(Math.min(start, end), 0, Math.abs(end - start) - 2, HEADER_OVERVIEW_HEIGHT, 8), fill: colorMap[type] }));
-        }
-        else {
-            return (React.createElement("rect", { key: key, x: Math.min(start, end), y: 0, width: Math.abs(end - start), height: HEADER_OVERVIEW_HEIGHT, fill: colorMap[type] }));
-        }
-    })));
-});
-const OverviewBox = observer(({ scale, model, block, overview, }) => {
+const OverviewBox = observer(function ({ scale, model, block, overview, }) {
     const { classes, cx } = useStyles();
+    const theme = useTheme();
     const { cytobandOffset, showCytobands } = model;
     const { start, end, reversed, refName, assemblyName } = block;
     const { majorPitch } = chooseGridPitch(scale, 120, 15);
@@ -202,7 +116,9 @@ const OverviewBox = observer(({ scale, model, block, overview, }) => {
     return (React.createElement("div", null,
         React.createElement(Typography, { style: {
                 left: block.offsetPx + 3,
-                color: canDisplayCytobands ? 'black' : refNameColor,
+                color: canDisplayCytobands
+                    ? theme.palette.primary.contrastText
+                    : refNameColor,
             }, className: classes.scalebarRefName }, refName),
         React.createElement("div", { className: cx(classes.scalebarContig, canDisplayCytobands
                 ? undefined
@@ -223,7 +139,7 @@ const OverviewBox = observer(({ scale, model, block, overview, }) => {
             canDisplayCytobands ? (React.createElement("svg", { style: { width: '100%' } },
                 React.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }))) : null)));
 });
-const Scalebar = observer(({ model, scale, overview, }) => {
+const Scalebar = observer(function ({ model, scale, overview, }) {
     const { classes } = useStyles();
     const theme = useTheme();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
@@ -262,7 +178,7 @@ const Scalebar = observer(({ model, scale, overview, }) => {
                 } })) : (React.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: `${JSON.stringify(block)}-${idx}` }));
         })));
 });
-function OverviewScalebar({ model, children, }) {
+export default observer(function OverviewScalebar({ model, children, }) {
     const { classes } = useStyles();
     const { totalBp, width, cytobandOffset, displayedRegions } = model;
     const overview = Base1DView.create({
@@ -280,7 +196,7 @@ function OverviewScalebar({ model, children, }) {
             React.createElement("svg", { height: HEADER_BAR_HEIGHT, className: classes.overviewSvg },
                 React.createElement(Polygon, { model: model, overview: overview })),
             children)));
-}
-export default observer(OverviewScalebar);
-export { Cytobands, Polygon };
+});
+export { Polygon };
+export { default as Cytobands } from './Cytobands';
 //# sourceMappingURL=OverviewScalebar.js.map