@jbrowse/plugin-linear-genome-view 2.2.1 → 2.2.2

package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -1,30 +1,24 @@
 import React, { useEffect, useMemo, useState } from 'react';
 import { makeStyles } from 'tss-react/mui';
-import { Button, CircularProgress, Container, Dialog, DialogActions, DialogContent, DialogTitle, Divider, IconButton, TextField, Typography, } from '@mui/material';
+import { Button, CircularProgress, Container, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { saveAs } from 'file-saver';
 import { getConf } from '@jbrowse/core/configuration';
 import copy from 'copy-to-clipboard';
+import { Dialog } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { formatSeqFasta } from '@jbrowse/core/util/formatFastaStrings';
 // icons
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
-import CloseIcon from '@mui/icons-material/Close';
 import GetAppIcon from '@mui/icons-material/GetApp';
-const useStyles = makeStyles()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
+const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
     },
     textAreaFont: {
         fontFamily: 'Courier New',
     },
-}));
+});
 /**
  * Fetches and returns a list features for a given list of regions
  */
@@ -103,15 +97,10 @@ function SequenceDialog({ model, handleClose, }) {
         };
     }, [model, session, regionsSelected, setSequence]);
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
-    return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Reference sequence",
-            handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => {
-                    handleClose();
-                    model.setOffsets(undefined, undefined);
-                }, size: "large" },
-                React.createElement(CloseIcon, null))) : null),
-        React.createElement(Divider, null),
+    return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: () => {
+            handleClose();
+            model.setOffsets(undefined, undefined);
+        }, title: "Reference sequence" },
         React.createElement(DialogContent, null,
             error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
             loading && !error ? (React.createElement(Container, null,

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

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package/esm/LinearGenomeView/components/Header.js

@@ -9,7 +9,7 @@ import ArrowForwardIcon from '@mui/icons-material/ArrowForward';
 import ArrowBackIcon from '@mui/icons-material/ArrowBack';
 // locals
 import { WIDGET_HEIGHT, SPACING, HEADER_BAR_HEIGHT, } from '..';
-import OverviewScaleBar from './OverviewScaleBar';
+import OverviewScalebar from './OverviewScalebar';
 import ZoomControls from './ZoomControls';
 import SearchBox from './SearchBox';
 const useStyles = makeStyles()(theme => ({
@@ -74,7 +74,7 @@ const Controls = ({ model }) => {
         React.createElement("div", { className: classes.spacer })));
 };
 const LinearGenomeViewHeader = observer(({ model }) => {
-    return !model.hideHeader ? (model.hideHeaderOverview ? (React.createElement(Controls, { model: model })) : (React.createElement(OverviewScaleBar, { model: model },
+    return !model.hideHeader ? (model.hideHeaderOverview ? (React.createElement(Controls, { model: model })) : (React.createElement(OverviewScalebar, { model: model },
         React.createElement(Controls, { model: model })))) : null;
 });
 export default LinearGenomeViewHeader;

package/esm/LinearGenomeView/components/HelpDialog.js

@@ -1,23 +1,8 @@
 import React from 'react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, Divider, IconButton, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
-const useStyles = makeStyles()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+import { Button, DialogActions, DialogContent, Divider } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
 export default function HelpDialog({ handleClose, }) {
-    const { classes } = useStyles();
-    return (React.createElement(Dialog, { open: true, maxWidth: "xl", onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Using the search box",
-            handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
-                React.createElement(CloseIcon, null))) : null),
-        React.createElement(Divider, null),
+    return (React.createElement(Dialog, { open: true, maxWidth: "xl", onClose: handleClose, title: "Using the search box" },
         React.createElement(DialogContent, null,
             React.createElement("h3", null, "Searching"),
             React.createElement("ul", null,

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

@@ -1 +1 @@
-{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,OAAO,EACP,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,QAAQ,EAAC,IAAI,EAAC,OAAO,EAAE,WAAW;QAC7C,oBAAC,WAAW;;YAET,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE;gBAE5B,oBAAC,SAAS,OAAG,CACF,CACd,CAAC,CAAC,CAAC,IAAI,CACI;QACd,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,4CAAkB;YAClB;gBACE,qIAGK;gBACL;;oBAEM,mDAA2B;;oBAAI,kDAA0B;wKAI1D,CACF;YACL,mDAAyB;YACzB;gBACE;oBACE,yCAAiB;6DACd;gBACL;oBACE,yCAAiB;+CACd;gBACL;oBACE,gEAAwC;mFAErC;gBACL;oBACE,0DAAkC;0EAE/B;gBACL;oBACE,mDAA2B;8DACxB;gBACL;oBACE,+DAAuC;0FAEpC;gBACL;oBACE,iDAAyB;sEAEtB,CACF,CACS;QAChB,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC"}
+{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,WAAW,EACpB,KAAK,EAAC,sBAAsB;QAE5B,oBAAC,aAAa;YACZ,4CAAkB;YAClB;gBACE,qIAGK;gBACL;;oBAEM,mDAA2B;;oBAAI,kDAA0B;wKAI1D,CACF;YACL,mDAAyB;YACzB;gBACE;oBACE,yCAAiB;6DACd;gBACL;oBACE,yCAAiB;+CACd;gBACL;oBACE,gEAAwC;mFAErC;gBACL;oBACE,0DAAkC;0EAE/B;gBACL;oBACE,mDAA2B;8DACxB;gBACL;oBACE,+DAAuC;0FAEpC;gBACL;oBACE,iDAAyB;sEAEtB,CACF,CACS;QAChB,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC"}

package/esm/LinearGenomeView/components/ImportForm.js

@@ -45,11 +45,11 @@ const ImportForm = observer(({ model }) => {
     useEffect(() => {
         setValue(r0);
     }, [r0, selectedAsm]);
-    function navToOption(option) {
+    async function navToOption(option) {
         const location = option.getLocation();
         const trackId = option.getTrackId();
         if (location) {
-            model.navToLocString(location, selectedAsm);
+            await model.navToLocString(location, selectedAsm);
             if (trackId) {
                 model.showTrack(trackId);
             }
@@ -63,14 +63,14 @@ const ImportForm = observer(({ model }) => {
     async function handleSelectedRegion(input) {
         try {
             if ((option === null || option === void 0 ? void 0 : option.getDisplayString()) === input && option.hasLocation()) {
-                navToOption(option);
+                await navToOption(option);
             }
             else {
                 const [ref, rest] = splitLast(input, ':');
                 const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
                 if (allRefs.includes(input) ||
                     (allRefs.includes(ref) && !Number.isNaN(parseInt(rest, 10)))) {
-                    model.navToLocString(input, selectedAsm);
+                    await model.navToLocString(input, selectedAsm);
                 }
                 else {
                     const results = await fetchResults({
@@ -85,10 +85,10 @@ const ImportForm = observer(({ model }) => {
                         model.setSearchResults(results, input.toLowerCase());
                     }
                     else if (results.length === 1) {
-                        navToOption(results[0]);
+                        await navToOption(results[0]);
                     }
                     else {
-                        model.navToLocString(input, selectedAsm);
+                        await model.navToLocString(input, selectedAsm);
                     }
                 }
             }
@@ -103,11 +103,12 @@ const ImportForm = observer(({ model }) => {
     return (React.createElement("div", { className: classes.container },
         displayError ? React.createElement(ErrorMessage, { error: displayError }) : null,
         React.createElement(Container, { className: classes.importFormContainer },
-            React.createElement("form", { onSubmit: event => {
+            React.createElement("form", { onSubmit: async (event) => {
                     event.preventDefault();
                     model.setError(undefined);
                     if (value) {
-                        handleSelectedRegion(value);
+                        // has it's own error handling
+                        await handleSelectedRegion(value);
                     }
                 } },
                 React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
@@ -125,7 +126,7 @@ const ImportForm = observer(({ model }) => {
                                 rankSearchResults,
                                 searchScope,
                             }), model: model, assemblyName: assemblyError ? undefined : selectedAsm, value: value, 
-                            // note: minWidth 270 accomodates full width of helperText
+                            // note: minWidth 270 accommodates full width of helperText
                             minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
                                 variant: 'outlined',
                                 helperText: 'Enter sequence name, feature name, or location',

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

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

@@ -8,8 +8,8 @@ import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 // locals
 import Ruler from './Ruler';
 import { HEADER_OVERVIEW_HEIGHT, } from '..';
-import { Polygon, Cytobands } from './OverviewScaleBar';
-function ScaleBar({ model, fontSize }) {
+import { Polygon, Cytobands } from './OverviewScalebar';
+function Scalebar({ model, fontSize }) {
     const { offsetPx, dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp }, } = model;
     const displayBp = getBpDisplayStr(totalBp);
     const x0 = Math.max(-offsetPx, 0);
@@ -82,7 +82,7 @@ const SVGHeader = ({ model }) => {
             React.createElement("g", { transform: `translate(0,${HEADER_OVERVIEW_HEIGHT})` },
                 React.createElement(Polygon, { overview: overview, model: model, useOffset: false })))) : null,
         React.createElement("g", { transform: `translate(0 ${fontSize + cytobandHeight})` },
-            React.createElement(ScaleBar, { model: model, fontSize: fontSize })),
+            React.createElement(Scalebar, { model: model, fontSize: fontSize })),
         React.createElement("g", { transform: `translate(0 ${rulerHeight + cytobandHeight})` },
             React.createElement(SVGRuler, { model: model, fontSize: fontSize, width: width }))));
 };

package/esm/LinearGenomeView/components/{OverviewRubberBand.d.ts → OverviewRubberband.d.ts}

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

package/esm/LinearGenomeView/components/{OverviewRubberBand.js → OverviewRubberband.js}

@@ -1,47 +1,23 @@
 import React, { useRef, useEffect, useState } from 'react';
-import { Popover, Tooltip, Typography, alpha } from '@mui/material';
+import { Tooltip } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { getSession, stringify } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { HEADER_OVERVIEW_HEIGHT } from '..';
-const useStyles = makeStyles()(theme => {
-    const { tertiary, primary } = theme.palette;
-    const background = tertiary
-        ? alpha(tertiary.main, 0.7)
-        : alpha(primary.main, 0.7);
-    return {
-        rubberBand: {
-            height: '100%',
-            background,
-            position: 'absolute',
-            zIndex: 10,
-            textAlign: 'center',
-            overflow: 'hidden',
-        },
-        rubberBandControl: {
-            cursor: 'crosshair',
-            width: '100%',
-            minHeight: 8,
-        },
-        rubberBandText: {
-            color: tertiary ? tertiary.contrastText : primary.contrastText,
-        },
-        popover: {
-            mouseEvents: 'none',
-            cursor: 'crosshair',
-        },
-        paper: {
-            paddingLeft: theme.spacing(1),
-            paddingRight: theme.spacing(1),
-        },
-        guide: {
-            pointerEvents: 'none',
-            height: '100%',
-            width: 1,
-            position: 'absolute',
-            zIndex: 10,
-        },
-    };
+import RubberbandSpan from './RubberbandSpan';
+import { getRelativeX } from './util';
+const useStyles = makeStyles()({
+    rubberbandControl: {
+        cursor: 'crosshair',
+        width: '100%',
+        minHeight: 8,
+    },
+    guide: {
+        pointerEvents: 'none',
+        height: '100%',
+        width: 1,
+        position: 'absolute',
+        zIndex: 10,
+    },
 });
 const HoverTooltip = observer(({ model, open, guideX, overview, }) => {
     var _a;
@@ -58,21 +34,19 @@ const HoverTooltip = observer(({ model, open, guideX, overview, }) => {
                 left: guideX,
             } })));
 });
-function OverviewRubberBand({ model, overview, ControlComponent = React.createElement("div", null), }) {
+function OverviewRubberband({ model, overview, ControlComponent = React.createElement("div", null), }) {
     const { cytobandOffset } = model;
     const [startX, setStartX] = useState();
     const [currentX, setCurrentX] = useState();
     const [guideX, setGuideX] = useState();
     const controlsRef = useRef(null);
-    const rubberBandRef = useRef(null);
     const { classes } = useStyles();
     const mouseDragging = startX !== undefined;
     useEffect(() => {
         function globalMouseMove(event) {
             const ref = controlsRef.current;
             if (ref && mouseDragging) {
-                const relativeX = event.clientX - ref.getBoundingClientRect().left;
-                setCurrentX(relativeX);
+                setCurrentX(getRelativeX(event, ref));
             }
         }
         function globalMouseUp() {
@@ -122,14 +96,10 @@ function OverviewRubberBand({ model, overview, ControlComponent = React.createEl
     function mouseDown(event) {
         event.preventDefault();
         event.stopPropagation();
-        if (controlsRef.current) {
-            setStartX(event.clientX - controlsRef.current.getBoundingClientRect().left);
-        }
+        setStartX(getRelativeX(event, controlsRef.current));
     }
     function mouseMove(event) {
-        if (controlsRef.current) {
-            setGuideX(event.clientX - controlsRef.current.getBoundingClientRect().left);
-        }
+        setGuideX(getRelativeX(event, controlsRef.current));
     }
     function mouseOut() {
         setGuideX(undefined);
@@ -137,7 +107,7 @@ 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, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
     }
     let left = startX || 0;
     let width = 0;
@@ -157,33 +127,8 @@ function OverviewRubberBand({ model, overview, ControlComponent = React.createEl
         }
     }
     return (React.createElement("div", { style: { position: 'relative' } },
-        rubberBandRef.current ? (React.createElement(React.Fragment, null,
-            React.createElement(Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberBandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'left',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'right',
-                }, keepMounted: true, disableRestoreFocus: true },
-                React.createElement(Typography, null, leftBpOffset ? stringify(leftBpOffset) : '')),
-            React.createElement(Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberBandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'right',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'left',
-                }, keepMounted: true, disableRestoreFocus: true },
-                React.createElement(Typography, null, rightBpOffset ? stringify(rightBpOffset) : '')))) : null,
-        React.createElement("div", { ref: rubberBandRef, className: classes.rubberBand, style: {
-                left,
-                width: Math.abs(width),
-                height: HEADER_OVERVIEW_HEIGHT,
-            } }),
-        React.createElement("div", { "data-testid": "rubberBand_controls", className: classes.rubberBandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+        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);
-//# sourceMappingURL=OverviewRubberBand.js.map
+export default observer(OverviewRubberband);
+//# sourceMappingURL=OverviewRubberband.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"OverviewRubberband.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/OverviewRubberband.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AACvC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAIrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,iBAAiB,EAAE;QACjB,MAAM,EAAE,WAAW;QACnB,KAAK,EAAE,MAAM;QACb,SAAS,EAAE,CAAC;KACb;IACD,KAAK,EAAE;QACL,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,CAAC;QACR,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;KACX;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAC3B,CAAC,EACC,KAAK,EACL,IAAI,EACJ,MAAM,EACN,QAAQ,GAMT,EAAE,EAAE;;IACH,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAE7C,MAAM,EAAE,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,GAAG,cAAc,CAAC,CAAA;IACnD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,YAAY,CAAC,CAAA;IACrD,MAAM,QAAQ,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,IAAI,CACxC,CAAC,CAAC,EAAE,CACF,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;QACzB,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;QACvB,EAAE,CAAC,OAAO,KAAK,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAChE,CAAA;IAED,OAAO,CACL,oBAAC,OAAO,IACN,IAAI,EAAE,IAAI,EACV,SAAS,EAAC,KAAK,EACf,KAAK,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,EAAE,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EACvD,KAAK;QAEL,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,MAAM;aACb,GACD,CACM,CACX,CAAA;AACH,CAAC,CACF,CAAA;AAED,SAAS,kBAAkB,CAAC,EAC1B,KAAK,EACL,QAAQ,EACR,gBAAgB,GAAG,gCAAO,GAK3B;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAU,CAAA;IAClD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,WAAW,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAChD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,aAAa,GAAG,MAAM,KAAK,SAAS,CAAA;IAE1C,SAAS,CAAC,GAAG,EAAE;QACb,SAAS,eAAe,CAAC,KAAiB;YACxC,MAAM,GAAG,GAAG,WAAW,CAAC,OAAO,CAAA;YAC/B,IAAI,GAAG,IAAI,aAAa,EAAE;gBACxB,WAAW,CAAC,YAAY,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAA;aACtC;QACH,CAAC;QAED,SAAS,aAAa;YACpB,iBAAiB;YACjB,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;gBAClD,IAAI,IAAI,CAAC,GAAG,CAAC,QAAQ,GAAG,MAAM,CAAC,GAAG,CAAC,EAAE;oBACnC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;oBACvC,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;oBACxC,KAAK,CAAC,MAAM,CACV,QAAQ,CAAC,MAAM,CAAC,IAAI,GAAG,cAAc,CAAC,EACtC,QAAQ,CAAC,MAAM,CAAC,KAAK,GAAG,cAAc,CAAC,CACxC,CAAA;iBACF;aACF;YAED,eAAe;YACf,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;gBAClD,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,GAAG,cAAc,CAAC,CAAA;gBACtD,IAAI,CAAC,KAAK,CAAC,OAAO,EAAE;oBAClB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAA;oBACpD,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,KAAK,CAAC,CAAA;iBACjD;qBAAM;oBACL,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,CAAA;iBACpE;aACF;YACD,SAAS,CAAC,SAAS,CAAC,CAAA;YACpB,WAAW,CAAC,SAAS,CAAC,CAAA;YAEtB,IAAI,MAAM,KAAK,SAAS,EAAE;gBACxB,SAAS,CAAC,SAAS,CAAC,CAAA;aACrB;QACH,CAAC;QAED,SAAS,aAAa,CAAC,KAAoB;YACzC,IAAI,KAAK,CAAC,GAAG,KAAK,QAAQ,EAAE;gBAC1B,SAAS,CAAC,SAAS,CAAC,CAAA;gBACpB,WAAW,CAAC,SAAS,CAAC,CAAA;aACvB;QACH,CAAC;QAED,IAAI,aAAa,EAAE;YACjB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,EAAE;gBACV,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;gBAC1D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;SACF;QACD,OAAO,GAAG,EAAE,GAAE,CAAC,CAAA;IACjB,CAAC,EAAE,CAAC,aAAa,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,cAAc,CAAC,CAAC,CAAA;IAEtE,SAAS,SAAS,CAAC,KAAuC;QACxD,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,KAAK,CAAC,eAAe,EAAE,CAAA;QACvB,SAAS,CAAC,YAAY,CAAC,KAAK,EAAE,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,SAAS,SAAS,CAAC,KAAuC;QACxD,SAAS,CAAC,YAAY,CAAC,KAAK,EAAE,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,SAAS,QAAQ;QACf,SAAS,CAAC,SAAS,CAAC,CAAA;IACtB,CAAC;IAED,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;YACjC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,CACtB,oBAAC,YAAY,IACX,KAAK,EAAE,KAAK,EACZ,IAAI,EAAE,CAAC,aAAa,EACpB,QAAQ,EAAE,QAAQ,EAClB,MAAM,EAAE,MAAM,GACd,CACH,CAAC,CAAC,CAAC,IAAI;YACR,6BACE,SAAS,EAAE,OAAO,CAAC,iBAAiB,EACpC,IAAI,EAAC,cAAc,EACnB,GAAG,EAAE,WAAW,EAChB,WAAW,EAAE,SAAS,EACtB,UAAU,EAAE,QAAQ,EACpB,WAAW,EAAE,SAAS,IAErB,gBAAgB,CACb,CACF,CACP,CAAA;KACF;IAED,IAAI,IAAI,GAAG,MAAM,IAAI,CAAC,CAAA;IACtB,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;QAClD,IAAI,GAAG,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAA;QAC5C,KAAK,GAAG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package/{dist/LinearGenomeView/components/OverviewScaleBar.d.ts → esm/LinearGenomeView/components/OverviewScalebar.d.ts}

@@ -122,10 +122,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;
 }) => JSX.Element;
-declare function OverviewScaleBar({ model, children, }: {
+declare function OverviewScalebar({ model, children, }: {
     model: LGV;
     children: React.ReactNode;
 }): JSX.Element;
-declare const _default: typeof OverviewScaleBar;
+declare const _default: typeof OverviewScalebar;
 export default _default;
 export { Cytobands, Polygon };

package/esm/LinearGenomeView/components/{OverviewScaleBar.js → OverviewScalebar.js}

@@ -2,49 +2,50 @@ import React from 'react';
 import { Typography, useTheme, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
+// core
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { getSession, getTickDisplayStr } from '@jbrowse/core/util';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 // locals
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, } from '..';
 import { chooseGridPitch } from '../util';
-import OverviewRubberBand from './OverviewRubberBand';
+import OverviewRubberband from './OverviewRubberband';
 const wholeSeqSpacer = 2;
 const useStyles = makeStyles()(theme => ({
-    scaleBar: {
+    scalebar: {
         height: HEADER_OVERVIEW_HEIGHT,
     },
-    scaleBarBorder: {
+    scalebarBorder: {
         border: '1px solid',
     },
-    scaleBarContig: {
+    scalebarContig: {
         backgroundColor: theme.palette.background.default,
         position: 'absolute',
         top: 0,
         height: HEADER_OVERVIEW_HEIGHT,
     },
-    scaleBarContigForward: {
+    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")`,
         backgroundRepeat: 'repeat',
     },
-    scaleBarContigReverse: {
+    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")`,
         backgroundRepeat: 'repeat',
     },
-    scaleBarRefName: {
+    scalebarRefName: {
         position: 'absolute',
         fontWeight: 'bold',
         pointerEvents: 'none',
         zIndex: 100,
     },
-    scaleBarLabel: {
+    scalebarLabel: {
         height: HEADER_OVERVIEW_HEIGHT,
         position: 'absolute',
         display: 'flex',
         justifyContent: 'center',
         pointerEvents: 'none',
     },
-    scaleBarVisibleRegion: {
+    scalebarVisibleRegion: {
         position: 'absolute',
         height: HEADER_OVERVIEW_HEIGHT,
         pointerEvents: 'none',
@@ -202,18 +203,18 @@ const OverviewBox = observer(({ scale, model, block, overview, }) => {
         React.createElement(Typography, { style: {
                 left: block.offsetPx + 3,
                 color: canDisplayCytobands ? 'black' : refNameColor,
-            }, className: classes.scaleBarRefName }, refName),
-        React.createElement("div", { className: cx(classes.scaleBarContig, canDisplayCytobands
+            }, className: classes.scalebarRefName }, refName),
+        React.createElement("div", { className: cx(classes.scalebarContig, canDisplayCytobands
                 ? undefined
                 : reversed
-                    ? classes.scaleBarContigReverse
-                    : classes.scaleBarContigForward, !canDisplayCytobands ? classes.scaleBarBorder : undefined), style: {
+                    ? classes.scalebarContigReverse
+                    : classes.scalebarContigForward, !canDisplayCytobands ? classes.scalebarBorder : undefined), style: {
                 left: block.offsetPx + cytobandOffset,
                 width: block.widthPx,
                 borderColor: refNameColor,
             } },
             !canDisplayCytobands
-                ? tickLabels.map((tickLabel, labelIdx) => (React.createElement(Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scaleBarLabel, variant: "body2", style: {
+                ? tickLabels.map((tickLabel, labelIdx) => (React.createElement(Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scalebarLabel, variant: "body2", style: {
                         left: ((labelIdx + 1) * majorPitch) / scale,
                         pointerEvents: 'none',
                         color: refNameColor,
@@ -222,14 +223,14 @@ 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(({ model, scale, overview, }) => {
     const { classes } = useStyles();
     const theme = useTheme();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
     const { tertiary, primary } = theme.palette;
-    const scaleBarColor = tertiary ? tertiary.light : primary.light;
+    const scalebarColor = tertiary ? tertiary.light : primary.light;
     if (!visibleRegions.length) {
         return null;
     }
@@ -243,17 +244,17 @@ const ScaleBar = observer(({ model, scale, overview, }) => {
         ...last,
         coord: last.reversed ? last.start : last.end,
     }) || 0;
-    const color = showCytobands ? '#f00' : scaleBarColor;
+    const color = showCytobands ? '#f00' : scalebarColor;
     const transparency = showCytobands ? 0.1 : 0.3;
-    return (React.createElement("div", { className: classes.scaleBar },
-        React.createElement("div", { className: classes.scaleBarVisibleRegion, style: {
+    return (React.createElement("div", { className: classes.scalebar },
+        React.createElement("div", { className: classes.scalebarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
                 left: firstOverviewPx + cytobandOffset,
                 background: alpha(color, transparency),
                 borderColor: color,
             } }),
         overviewVisibleRegions.map((block, idx) => {
-            return !(block instanceof ContentBlock) ? (React.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scaleBarContig, style: {
+            return !(block instanceof ContentBlock) ? (React.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scalebarContig, style: {
                     width: block.widthPx,
                     left: block.offsetPx,
                     backgroundColor: '#999',
@@ -261,7 +262,7 @@ 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, }) {
+function OverviewScalebar({ model, children, }) {
     const { classes } = useStyles();
     const { totalBp, width, cytobandOffset, displayedRegions } = model;
     const overview = Base1DView.create({
@@ -274,12 +275,12 @@ function OverviewScaleBar({ model, children, }) {
     overview.showAllRegions();
     const scale = totalBp / (modWidth - (displayedRegions.length - 1) * wholeSeqSpacer);
     return (React.createElement("div", null,
-        React.createElement(OverviewRubberBand, { model: model, overview: overview, ControlComponent: React.createElement(ScaleBar, { model: model, overview: overview, scale: scale }) }),
+        React.createElement(OverviewRubberband, { model: model, overview: overview, ControlComponent: React.createElement(Scalebar, { model: model, overview: overview, scale: scale }) }),
         React.createElement("div", { className: classes.overview },
             React.createElement("svg", { height: HEADER_BAR_HEIGHT, className: classes.overviewSvg },
                 React.createElement(Polygon, { model: model, overview: overview })),
             children)));
 }
-export default observer(OverviewScaleBar);
+export default observer(OverviewScalebar);
 export { Cytobands, Polygon };
-//# sourceMappingURL=OverviewScaleBar.js.map
+//# sourceMappingURL=OverviewScalebar.js.map