npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.3.3 → 2.4.0 - Mend

@jbrowse/plugin-linear-genome-view 2.3.3 → 2.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (198) hide show

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

@@ -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;

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

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

@@ -5,8 +5,8 @@ import { stringify, toLocale } from '@jbrowse/core/util';
 const useStyles = makeStyles()(theme => {
     const { primary, tertiary } = theme.palette;
     const background = tertiary
-        ? alpha(tertiary.main, 0.7)
-        : alpha(primary.main, 0.7);
+        ? alpha(tertiary.light, 0.7)
+        : alpha(primary.light, 0.7);
     return {
         rubberband: {
             height: '100%',

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

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

@@ -3,9 +3,10 @@ import { IconButton, Paper, Typography, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 import { getConf } from '@jbrowse/core/configuration';
-import CascadingMenu from '@jbrowse/core/ui/CascadingMenu';
 import { getSession, getContainingView } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
+import { SanitizedHTML } from '@jbrowse/core/ui';
+import CascadingMenu from '@jbrowse/core/ui/CascadingMenu';
 import { bindTrigger, bindPopover, usePopupState, } from 'material-ui-popup-state/hooks';
 // icons
 import MoreVertIcon from '@mui/icons-material/MoreVert';
@@ -31,7 +32,6 @@ const useStyles = makeStyles()(theme => ({
     },
     dragHandle: {
         cursor: 'grab',
-        color: '#135560',
     },
     dragHandleIcon: {
         display: 'inline-block',
@@ -74,10 +74,11 @@ const TrackLabel = React.forwardRef(({ track, className }, ref) => {
                 }
             }, onDragEnd: () => view.setDraggingTrackId(undefined), "data-testid": `dragHandle-${view.id}-${trackId}` },
             React.createElement(DragIcon, { className: classes.dragHandleIcon, fontSize: "small" })),
-        React.createElement(IconButton, { onClick: () => view.hideTrack(trackId), className: classes.iconButton, title: "close this track", color: "secondary" },
+        React.createElement(IconButton, { onClick: () => view.hideTrack(trackId), className: classes.iconButton, title: "close this track" },
             React.createElement(CloseIcon, { fontSize: "small" })),
-        React.createElement(Typography, { variant: "body1", component: "span", className: classes.trackName }, trackName + (minimized ? ' (minimized)' : '')),
-        React.createElement(IconButton, { ...bindTrigger(popupState), className: classes.iconButton, color: "secondary", "data-testid": "track_menu_icon", disabled: !items.length },
+        React.createElement(Typography, { variant: "body1", component: "span", className: classes.trackName },
+            React.createElement(SanitizedHTML, { html: trackName + (minimized ? ' (minimized)' : '') })),
+        React.createElement(IconButton, { ...bindTrigger(popupState), className: classes.iconButton, "data-testid": "track_menu_icon", disabled: !items.length },
             React.createElement(MoreVertIcon, { fontSize: "small" })),
         React.createElement(CascadingMenu, { ...bindPopover(popupState), onMenuItemClick: (_, callback) => callback(), menuItems: items, popupState: popupState })));
 });

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"TrackLabel.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/TrackLabel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAA;AAExD,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,aAAa,MAAM,gCAAgC,CAAA;AAE1D,OAAO,EACL,WAAW,EACX,WAAW,EACX,aAAa,GACd,MAAM,+BAA+B,CAAA;AAEtC,QAAQ;AACR,OAAO,YAAY,MAAM,8BAA8B,CAAA;AACvD,OAAO,QAAQ,MAAM,mCAAmC,CAAA;AACxD,OAAO,SAAS,MAAM,2BAA2B,CAAA;AACjD,OAAO,YAAY,MAAM,8BAA8B,CAAA;AACvD,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAI7C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,EAAE,GAAG,CAAC;QACtD,SAAS,EAAE;YACT,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;SAC3C;QACD,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,EAAE;YACnD,QAAQ,EAAE,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,QAAQ;SAC9C,CAAC;KACH;IACD,SAAS,EAAE;QACT,MAAM,EAAE,QAAQ;QAChB,KAAK,EAAE,KAAK;QACZ,QAAQ,EAAE,QAAQ;QAClB,aAAa,EAAE,MAAM;KACtB;IACD,UAAU,EAAE;QACV,MAAM,EAAE,MAAM;KACf;IACD,cAAc,EAAE;QACd,OAAO,EAAE,cAAc;QACvB,aAAa,EAAE,QAAQ;QACvB,aAAa,EAAE,MAAM;KACtB;IACD,UAAU,EAAE;QACV,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;CACF,CAAC,CAAC,CAAA;AASH,MAAM,UAAU,GAAG,KAAK,CAAC,UAAU,CACjC,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,EAAE,GAAG,EAAE,EAAE;;IAC5B,MAAM,EAAE,OAAO,EAAE,EAAE,EAAE,GAAG,SAAS,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAAQ,CAAA;IAC5C,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,SAAS,GAAG,KAAK,CAAC,aAAa,CAAA;IACrC,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,CAAA;IACjC,MAAM,OAAO,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;IACzC,MAAM,SAAS,GAAG,YAAY,CAAC,SAAS,EAAE,OAAO,CAAC,CAAA;IAElD,MAAM,UAAU,GAAG,aAAa,CAAC;QAC/B,OAAO,EAAE,gBAAgB;QACzB,OAAO,EAAE,SAAS;KACnB,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ;YACE,KAAK,EAAE,SAAS,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,gBAAgB;YACrD,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,YAAY;YACxC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,SAAS,CAAC;SAC9C;QACD,GAAG,CAAC,CAAA,MAAA,OAAO,CAAC,uBAAuB,wDAAG,SAAS,CAAC,KAAI,EAAE,CAAC;QACvD,GAAG,KAAK,CAAC,cAAc,EAAE;KAC1B,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAA;IAEvD,OAAO,CACL,oBAAC,KAAK,IAAC,GAAG,EAAE,GAAG,EAAE,SAAS,EAAE,EAAE,CAAC,SAAS,EAAE,OAAO,CAAC,IAAI,CAAC;QACrD,8BACE,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,MAAM,MAAM,GAAG,KAAK,CAAC,aAAa,CAAA;gBAClC,IAAI,MAAM,CAAC,UAAU,EAAE;oBACrB,MAAM,MAAM,GAAG,MAAM,CAAC,UAAyB,CAAA;oBAC/C,KAAK,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;oBAC/C,IAAI,CAAC,kBAAkB,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;iBAClC;YACH,CAAC,EACD,SAAS,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,iBACtC,cAAc,IAAI,CAAC,EAAE,IAAI,OAAO,EAAE;YAE/C,oBAAC,QAAQ,IAAC,SAAS,EAAE,OAAO,CAAC,cAAc,EAAE,QAAQ,EAAC,OAAO,GAAG,CAC3D;QACP,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EACtC,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,KAAK,EAAC,kBAAkB;YAExB,oBAAC,SAAS,IAAC,QAAQ,EAAC,OAAO,GAAG,CACnB;QAEb,oBAAC,UAAU,IACT,OAAO,EAAC,OAAO,EACf,SAAS,EAAC,MAAM,EAChB,SAAS,EAAE,OAAO,CAAC,SAAS;YAE5B,oBAAC,aAAa,IAAC,IAAI,EAAE,SAAS,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,GAAI,CAC3D;QACb,oBAAC,UAAU,OACL,WAAW,CAAC,UAAU,CAAC,EAC3B,SAAS,EAAE,OAAO,CAAC,UAAU,iBACjB,iBAAiB,EAC7B,QAAQ,EAAE,CAAC,KAAK,CAAC,MAAM;YAEvB,oBAAC,YAAY,IAAC,QAAQ,EAAC,OAAO,GAAG,CACtB;QACb,oBAAC,aAAa,OACR,WAAW,CAAC,UAAU,CAAC,EAC3B,eAAe,EAAE,CAAC,CAAU,EAAE,QAAkB,EAAE,EAAE,CAAC,QAAQ,EAAE,EAC/D,SAAS,EAAE,KAAK,EAChB,UAAU,EAAE,UAAU,GACtB,CACI,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,QAAQ,CAAC,UAAU,CAAC,CAAA"}

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

@@ -4,7 +4,7 @@ import { Slider, IconButton } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
-const useStyles = makeStyles()({
+const useStyles = makeStyles()(theme => ({
     container: {
         display: 'flex',
         flexDirection: 'row',
@@ -12,8 +12,9 @@ const useStyles = makeStyles()({
     },
     slider: {
         width: 70,
+        color: theme.palette.text.secondary,
     },
-});
+}));
 function ZoomControls({ model }) {
     const { classes } = useStyles();
     const { maxBpPerPx, minBpPerPx, bpPerPx, scaleFactor } = model;
@@ -22,10 +23,10 @@ function ZoomControls({ model }) {
         setValue(-Math.log2(bpPerPx) * 100);
     }, [setValue, bpPerPx]);
     return (React.createElement("div", { className: classes.container },
-        React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+        React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, size: "large" },
             React.createElement(ZoomOut, null)),
         React.createElement(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), disabled: scaleFactor !== 1 }),
-        React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+        React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, size: "large" },
             React.createElement(ZoomIn, null))));
 }
 export default observer(ZoomControls);

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ZoomControls.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/ZoomControls.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,OAAO,MAAM,6BAA6B,CAAA;AAGjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,KAAK;QACpB,UAAU,EAAE,QAAQ;KACrB;IACD,MAAM,EAAE;QACN,KAAK,EAAE,EAAE;QACT,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS;KACpC;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,YAAY,CAAC,EAAE,KAAK,EAAoC;IAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC9D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAA;IAC7D,SAAS,CAAC,GAAG,EAAE;QACb,QAAQ,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAA;IACrC,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAA;IAEvB,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS;QAC/B,oBAAC,UAAU,mBACG,UAAU,EACtB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,CAAC,EACtC,QAAQ,EAAE,OAAO,IAAI,UAAU,GAAG,MAAM,IAAI,WAAW,KAAK,CAAC,EAC7D,IAAI,EAAC,OAAO;YAEZ,oBAAC,OAAO,OAAG,CACA;QAEb,oBAAC,MAAM,IACL,IAAI,EAAC,OAAO,EACZ,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,EACjC,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,EACjC,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAa,CAAC,EAC7C,iBAAiB,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,CAAC,EAC1D,QAAQ,EAAE,WAAW,KAAK,CAAC,GAC3B;QACF,oBAAC,UAAU,mBACG,SAAS,EACrB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC,EAC5C,QAAQ,EAAE,OAAO,IAAI,UAAU,GAAG,MAAM,IAAI,WAAW,KAAK,CAAC,EAC7D,IAAI,EAAC,OAAO;YAEZ,oBAAC,MAAM,OAAG,CACC,CACT,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,YAAY,CAAC,CAAA"}

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

@@ -16,3 +16,9 @@ export declare function getRelativeX<T extends {
     clientX: number;
     target: EventTarget | null;
 }>(event: T, element: HTMLElement | null): number;
+export declare function getCytobands(assembly: Assembly | undefined, refName: string): {
+    refName: string;
+    start: number;
+    end: number;
+    type: any;
+}[];

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

@@ -27,4 +27,13 @@ export function splitLast(str, split) {
 export function getRelativeX(event, element) {
     return event.clientX - ((element === null || element === void 0 ? void 0 : element.getBoundingClientRect().left) || 0);
 }
+export 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)) || []);
+}
 //# sourceMappingURL=util.js.map

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

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

@@ -5,7 +5,7 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { renderToSvg } from './components/LinearGenomeViewSvg';
+import { renderToSvg } from './svgcomponents/SVGLinearGenomeView';
 import RefNameAutocomplete from './components/RefNameAutocomplete';
 import SearchBox from './components/SearchBox';
 import ZoomControls from './components/ZoomControls';
@@ -25,6 +25,14 @@ export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
     Wrapper?: React.FC<any>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
 }
 export interface NavLocation {
     refName: string;
@@ -366,7 +374,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     clearView(): void;
     /**
-     * #action
+     * #method
      * creates an svg export and save using FileSaver
      */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;

package/esm/LinearGenomeView/model.js CHANGED Viewed

@@ -23,7 +23,7 @@ import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
 import ZoomInIcon from '@mui/icons-material/ZoomIn';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 // locals
-import { renderToSvg } from './components/LinearGenomeViewSvg';
+import { renderToSvg } from './svgcomponents/SVGLinearGenomeView';
 import RefNameAutocomplete from './components/RefNameAutocomplete';
 import SearchBox from './components/SearchBox';
 import ExportSvgDlg from './components/ExportSvgDialog';
@@ -119,12 +119,12 @@ export function stateModelFactory(pluginManager) {
          * #property
          * show the "center line"
          */
-        showCenterLine: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false')),
+        showCenterLine: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false'))),
         /**
          * #property
          * show the "cytobands" in the overview scale bar
          */
-        showCytobandsSetting: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true')),
+        showCytobandsSetting: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true'))),
         /**
          * #property
          * show the "gridlines" in the track area
@@ -730,7 +730,7 @@ export function stateModelFactory(pluginManager) {
             self.zoomTo(10);
         },
         /**
-         * #action
+         * #method
          * creates an svg export and save using FileSaver
          */
         async exportSvg(opts = {}) {

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

	@@ -1 +1 @@
1	- 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package/esm/LinearGenomeView/svgcomponents/SVGBackground.d.ts ADDED Viewed

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+export default function SVGBackground({ width, height, shift, }: {
+    width: number;
+    height: number;
+    shift: number;
+}): JSX.Element;

package/esm/LinearGenomeView/svgcomponents/SVGBackground.js ADDED Viewed

@@ -0,0 +1,7 @@
+import React from 'react';
+import { useTheme } from '@mui/material';
+export default function SVGBackground({ width, height, shift, }) {
+    const theme = useTheme();
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+}
+//# sourceMappingURL=SVGBackground.js.map

package/esm/LinearGenomeView/svgcomponents/SVGBackground.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,EACN,KAAK,GAKN;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,OAAO,CACL,8BACE,KAAK,EAAE,KAAK,GAAG,KAAK,GAAG,CAAC,EACxB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC,CACH,CAAA;AACH,CAAC"}