react-msaview 6.2.2 → 6.3.0

package/dist/components/MSAViewer.d.ts

@@ -1,4 +1,5 @@
 import React from 'react';
+import type { ColumnTrackSpec, Highlight } from '../types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 interface MSAViewerProps {
     msa?: string;
@@ -15,8 +16,16 @@ interface MSAViewerProps {
     rowHeight?: number;
     /** alignment columns (0-based) to highlight with a persistent overlay */
     highlightColumns?: number[];
+    /**
+     * labeled highlights in 1-based inclusive coordinates: `{start, end}` for
+     * alignment columns, `{row, start, end}` for residues of that row, `{rows}`
+     * for whole rows, each with an optional `label` and `color`
+     */
+    highlights?: Highlight[];
     /** row name to diff every other row against (matches render as ".") */
     relativeTo?: string;
+    /** tracks supplied as data: per-column bar values or a text row (see docs/layers.md) */
+    columnTracks?: ColumnTrackSpec[];
     /** draw the phylogenetic tree (default true); false leaves a labels-only gutter */
     drawTree?: boolean;
     /** fixed width (px) of the tree/label area */
@@ -24,5 +33,5 @@ interface MSAViewerProps {
     /** auto-size the tree/label area to the labels (used when drawTree is false) */
     autoTreeAreaWidth?: boolean;
 }
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, relativeTo, drawTree, treeAreaWidth, autoTreeAreaWidth, }: MSAViewerProps): React.JSX.Element;
+export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, highlights, relativeTo, columnTracks, drawTree, treeAreaWidth, autoTreeAreaWidth, }: MSAViewerProps): React.JSX.Element;
 export {};

package/dist/components/MSAViewer.js

@@ -5,7 +5,7 @@ import { ThemeProvider } from '@mui/material/styles';
 import MSAModelF from '../model.js';
 import Loading from './Loading.js';
 const theme = createJBrowseTheme();
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, relativeTo, drawTree, treeAreaWidth, autoTreeAreaWidth, }) {
+export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, highlights, relativeTo, columnTracks, drawTree, treeAreaWidth, autoTreeAreaWidth, }) {
     // lazy initializer: the model is created exactly once from the initial props
     // (a stable MST instance — not a value safe to recompute, so not useMemo)
     const [model] = useState(() => MSAModelF().create({
@@ -21,7 +21,9 @@ export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandl
         ...(colWidth ? { colWidth } : {}),
         ...(rowHeight ? { rowHeight } : {}),
         ...(highlightColumns ? { highlightColumns } : {}),
+        ...(highlights ? { highlights } : {}),
         ...(relativeTo ? { relativeTo } : {}),
+        ...(columnTracks ? { columnTracks } : {}),
         ...(drawTree !== undefined ? { drawTree } : {}),
         ...(treeAreaWidth ? { treeAreaWidth } : {}),
         ...(autoTreeAreaWidth ? { autoTreeAreaWidth } : {}),

package/dist/components/MSAViewer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAViewer.js","sourceRoot":"","sources":["../../src/components/MSAViewer.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,kBAAkB,EAAE,MAAM,wBAAwB,CAAA;AAC3D,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AAEpD,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,OAAO,MAAM,cAAe,CAAA;AAKnC,MAAM,KAAK,GAAG,kBAAkB,EAAE,CAAA;AAmClC,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,GAAG,EACH,IAAI,EACJ,GAAG,EACH,aAAa,EACb,cAAc,EACd,aAAa,EACb,WAAW,EACX,MAAM,EACN,QAAQ,EACR,SAAS,EACT,gBAAgB,EAChB,UAAU,EACV,UAAU,EACV,YAAY,EACZ,QAAQ,EACR,aAAa,EACb,iBAAiB,GACF;IACf,6EAA6E;IAC7E,0EAA0E;IAC1E,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,GAAG,EAAE,CAC5B,SAAS,EAAE,CAAC,MAAM,CAAC;QACjB,IAAI,EAAE,SAAS;QACf,GAAG,CAAC,GAAG,IAAI,IAAI,IAAI,GAAG;YACpB,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,GAAG,EAAE,GAAG,IAAI,EAAE,EAAE,IAAI,EAAE,IAAI,IAAI,EAAE,EAAE,GAAG,EAAE,EAAE;YACrD,CAAC,CAAC,EAAE,CAAC;QACP,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC3C,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC7C,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC3C,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,eAAe,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACxD,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC7B,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACjC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACnC,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACjD,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACrC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACrC,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACzC,GAAG,CAAC,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC/C,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC3C,GAAG,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,iBAAiB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KACpD,CAAC,CACH,CAAA;IAED,MAAM,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACrC,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;QACvB,CAAC;IACH,CAAC,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,CAAA;IAElB,OAAO,CACL,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK;QACzB,6BAAK,GAAG,EAAE,GAAG;YACX,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrB,CACQ,CACjB,CAAA;AACH,CAAC"}

package/dist/components/minimap/Minimap.js

@@ -45,7 +45,7 @@ const Minimap = observer(function ({ model }) {
                 width: msaCanvasWidth,
                 height: MINIMAP_BAR_HEIGHT,
                 boxSizing: 'border-box',
-                border: '1px solid #555',
+                border: `1px solid ${theme.palette.text.secondary}`,
             } }),
         React.createElement(DragHandle, { axis: "x", variant: "thumb", getStart: () => model.scrollX, onDrag: onDrag, style: {
                 top: 0,

package/dist/components/minimap/Minimap.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Minimap.js","sourceRoot":"","sources":["../../../src/components/minimap/Minimap.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,UAAU,EAAE,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AAClE,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAClD,OAAO,EAAE,kBAAkB,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAIzE,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,aAAa,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAE5E,4EAA4E;IAC5E,qEAAqE;IACrE,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAChE,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YACxC,MAAM,SAAS,GAAG,YAAY,CAAC;gBAC7B,KAAK;gBACL,KAAK;gBACL,MAAM,EAAE,kBAAkB;aAC3B,CAAC,CAAA;YACF,IAAI,SAAS,EAAE,CAAC;gBACd,GAAG,CAAC,qBAAqB,GAAG,IAAI,CAAA;gBAChC,GAAG,CAAC,SAAS,CACX,SAAS,EACT,CAAC,EACD,CAAC,EACD,SAAS,CAAC,KAAK,EACf,SAAS,CAAC,MAAM,EAChB,CAAC,EACD,CAAC,EACD,QAAQ,EACR,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,KAAK,EAAE,QAAQ;QACf,MAAM,EAAE,SAAS;QACjB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;KACrB,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CAAA;IAED,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,aAAa;YACrB,KAAK,EAAE,cAAc;YACrB,UAAU,EAAE,CAAC;SACd;QAED,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,QAAQ,EACf,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE;gBACL,OAAO,EAAE,OAAO;gBAChB,KAAK,EAAE,cAAc;gBACrB,MAAM,EAAE,kBAAkB;gBAC1B,SAAS,EAAE,YAAY;gBACvB,MAAM,EAAE,aAAa,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EAAE;aACpD,GACD;QACF,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,OAAO,EACf,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACpB,MAAM,EAAE,kBAAkB;gBAC1B,KAAK,EAAE,CAAC;aACT,GACD;QAEF,6BAAK,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc;YAC/C,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CACxD,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/minimap/MinimapSVG.js

@@ -13,8 +13,8 @@ export default function MinimapSVG({ model, theme, }) {
     const href = canvasHref(msaThumbnail({ model, theme, height: MINIMAP_BAR_HEIGHT }));
     return (React.createElement(React.Fragment, null,
         href ? (React.createElement("image", { href: href, x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, preserveAspectRatio: "none" })) : null,
-        React.createElement("rect", { x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, stroke: "#555", fill: "none" }),
-        React.createElement("rect", { x: Math.max(0, s), y: 0, width: w, height: MINIMAP_BAR_HEIGHT, fill: scrollbarThumbFill, stroke: "#555" }),
+        React.createElement("rect", { x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, stroke: theme.palette.text.secondary, fill: "none" }),
+        React.createElement("rect", { x: Math.max(0, s), y: 0, width: w, height: MINIMAP_BAR_HEIGHT, fill: scrollbarThumbFill, stroke: theme.palette.text.secondary }),
         React.createElement("g", { transform: `translate(0 ${MINIMAP_BAR_HEIGHT})` },
             React.createElement("polygon", { fill: scrollbarThumbFill, points: polygonPoints }))));
 }

package/dist/components/minimap/MinimapSVG.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MinimapSVG.js","sourceRoot":"","sources":["../../../src/components/minimap/MinimapSVG.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAC9D,OAAO,EAAE,kBAAkB,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAKzE,+EAA+E;AAC/E,gFAAgF;AAChF,0BAA0B;AAC1B,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACvD,0EAA0E;IAC1E,0EAA0E;IAC1E,MAAM,IAAI,GAAG,UAAU,CACrB,YAAY,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,CAAC,CAC3D,CAAA;IAED,OAAO,CACL;QACG,IAAI,CAAC,CAAC,CAAC,CACN,+BACE,IAAI,EAAE,IAAI,EACV,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,cAAc,EACrB,MAAM,EAAE,kBAAkB,EAC1B,mBAAmB,EAAC,MAAM,GAC1B,CACH,CAAC,CAAC,CAAC,IAAI;QACR,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,cAAc,EACrB,MAAM,EAAE,kBAAkB,EAC1B,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EACpC,IAAI,EAAC,MAAM,GACX;QACF,8BACE,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACjB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,kBAAkB,EAC1B,IAAI,EAAE,kBAAkB,EACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,2BAAG,SAAS,EAAE,eAAe,kBAAkB,GAAG;YAChD,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CAC1D,CACH,CACJ,CAAA;AACH,CAAC"}

package/dist/components/msa/MSAMouseoverCanvas.js

@@ -1,21 +1,23 @@
 import React from 'react';
 import { isAlive } from '@jbrowse/mobx-state-tree';
+import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { renderMouseover } from './renderMSAMouseover.js';
 const MSAMouseoverCanvas = observer(function ({ model, }) {
     const { height, msaCanvasWidth: width, highResScaleFactor } = model;
+    const theme = useTheme();
     const canvasWidth = width * highResScaleFactor;
     const canvasHeight = height * highResScaleFactor;
     const ref = useCanvasAutorun({
         draw: ctx => {
             if (isAlive(model)) {
-                renderMouseover({ ctx, model });
+                renderMouseover({ ctx, model, theme });
             }
         },
         width: canvasWidth,
         height: canvasHeight,
-        deps: [model],
+        deps: [model, theme],
     });
     return (React.createElement("canvas", { ref: ref, id: "mouseover", width: canvasWidth, height: canvasHeight, style: {
             position: 'absolute',

package/dist/components/msa/MSAMouseoverCanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAMouseoverCanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSAMouseoverCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAA;AAIzD,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,GAGN;IACC,MAAM,EAAE,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAChD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBACnB,eAAe,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;YACxC,CAAC;QACH,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;KACrB,CAAC,CAAA;IAEF,OAAO,CACL,gCACE,GAAG,EAAE,GAAG,EACR,EAAE,EAAC,WAAW,EACd,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,KAAK;YACL,MAAM;YACN,MAAM,EAAE,IAAI;YACZ,aAAa,EAAE,MAAM;SACtB,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/components/msa/msaRaster.d.ts

@@ -53,11 +53,12 @@ export declare function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }:
 /**
  * A raster canvas as a PNG data URI, for embedding in the SVG export.
  *
- * toDataURL is the synchronous read-back and only the DOM canvas has it, so an
+ * toDataURL is the synchronous read-back. The DOM canvas has it, and so does a
+ * node canvas standing in for OffscreenCanvas headlessly; a browser
  * OffscreenCanvas -- which is what the tile and thumbnail caches hold wherever
- * it exists -- gets copied onto one first. Returns undefined wherever the
- * read-back is unavailable (jsdom) rather than throwing, which is the signal to
- * fall back to drawing the thing in vector.
+ * it exists -- gets copied onto a DOM canvas first. Returns undefined wherever
+ * the read-back is unavailable (jsdom) rather than throwing, which is the
+ * signal to fall back to drawing the thing in vector.
  */
 export declare function canvasHref(canvas: RasterCanvas | undefined): string | undefined;
 /**

package/dist/components/msa/msaRaster.js

@@ -229,20 +229,24 @@ export function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }) {
 /**
  * A raster canvas as a PNG data URI, for embedding in the SVG export.
  *
- * toDataURL is the synchronous read-back and only the DOM canvas has it, so an
+ * toDataURL is the synchronous read-back. The DOM canvas has it, and so does a
+ * node canvas standing in for OffscreenCanvas headlessly; a browser
  * OffscreenCanvas -- which is what the tile and thumbnail caches hold wherever
- * it exists -- gets copied onto one first. Returns undefined wherever the
- * read-back is unavailable (jsdom) rather than throwing, which is the signal to
- * fall back to drawing the thing in vector.
+ * it exists -- gets copied onto a DOM canvas first. Returns undefined wherever
+ * the read-back is unavailable (jsdom) rather than throwing, which is the
+ * signal to fall back to drawing the thing in vector.
  */
 export function canvasHref(canvas) {
-    if (!canvas || typeof document === 'undefined') {
+    if (!canvas) {
         return undefined;
     }
     try {
-        if (canvas instanceof HTMLCanvasElement) {
+        if ('toDataURL' in canvas && typeof canvas.toDataURL === 'function') {
             return canvas.toDataURL('image/png');
         }
+        if (typeof document === 'undefined') {
+            return undefined;
+        }
         const out = document.createElement('canvas');
         out.width = canvas.width;
         out.height = canvas.height;

package/dist/components/msa/msaRaster.js.map

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package/dist/components/msa/renderHighlights.d.ts

@@ -0,0 +1,31 @@
+import type { MsaViewModel } from '../../model.ts';
+import type { RenderCtx } from '../renderCtx.ts';
+import type { Theme } from '@mui/material';
+export declare const highlightFill = "rgba(255,140,0,0.28)";
+export declare const highlightBorder = "rgba(210,90,0,0.95)";
+export declare const highlightRowFill = "rgba(255,140,0,0.18)";
+export declare const labelFontSize = 11;
+export declare function drawHighlightLabel({ ctx, theme, label, x, y, spanWidth, }: {
+    ctx: RenderCtx;
+    theme: Theme;
+    label: string;
+    x: number;
+    y: number;
+    spanWidth: number;
+}): void;
+/**
+ * The persistent `highlights` overlay on the alignment: row tints, bordered
+ * column bands, and a label above each band. `offsetX`/`offsetY` are the
+ * content coordinates at the canvas origin, the convention renderMSABlock
+ * uses, so the live overlay passes -scrollX/-scrollY and the export passes its
+ * layout offsets.
+ */
+export declare function renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }: {
+    ctx: RenderCtx;
+    model: MsaViewModel;
+    theme: Theme;
+    offsetX: number;
+    offsetY: number;
+    width: number;
+    height: number;
+}): void;

package/dist/components/msa/renderHighlights.js

@@ -0,0 +1,49 @@
+import { setFontSize } from '../../setFontSize.js';
+export const highlightFill = 'rgba(255,140,0,0.28)';
+export const highlightBorder = 'rgba(210,90,0,0.95)';
+export const highlightRowFill = 'rgba(255,140,0,0.18)';
+export const labelFontSize = 11;
+const labelPad = 3;
+export function drawHighlightLabel({ ctx, theme, label, x, y, spanWidth, }) {
+    setFontSize(ctx, labelFontSize);
+    ctx.textAlign = 'start';
+    const boxWidth = ctx.measureText(label).width + labelPad * 2;
+    const boxHeight = labelFontSize + labelPad * 2;
+    const left = boxWidth <= spanWidth ? x : x + spanWidth + 2;
+    ctx.fillStyle = theme.palette.background.paper;
+    ctx.fillRect(left, y, boxWidth, boxHeight);
+    ctx.fillStyle = theme.palette.text.primary;
+    ctx.fillText(label, left + labelPad, y + labelPad + labelFontSize - 2);
+}
+/**
+ * The persistent `highlights` overlay on the alignment: row tints, bordered
+ * column bands, and a label above each band. `offsetX`/`offsetY` are the
+ * content coordinates at the canvas origin, the convention renderMSABlock
+ * uses, so the live overlay passes -scrollX/-scrollY and the export passes its
+ * layout offsets.
+ */
+export function renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }) {
+    const { resolvedHighlights, colWidth, rowHeight } = model;
+    ctx.lineWidth = 2;
+    for (const { rowIndices, color } of resolvedHighlights) {
+        ctx.fillStyle = color ?? highlightRowFill;
+        for (const index of rowIndices) {
+            ctx.fillRect(0, index * rowHeight - offsetY, width, rowHeight);
+        }
+    }
+    for (const { startCol, endCol, label, color } of resolvedHighlights) {
+        if (startCol === undefined || endCol === undefined) {
+            continue;
+        }
+        const x = startCol * colWidth - offsetX;
+        const spanWidth = (endCol - startCol + 1) * colWidth;
+        ctx.fillStyle = color ?? highlightFill;
+        ctx.fillRect(x, 0, spanWidth, height);
+        ctx.strokeStyle = color ?? highlightBorder;
+        ctx.strokeRect(x, 0, spanWidth, height);
+        if (label) {
+            drawHighlightLabel({ ctx, theme, label, x, y: 0, spanWidth });
+        }
+    }
+}
+//# sourceMappingURL=renderHighlights.js.map

package/dist/components/msa/renderHighlights.js.map

@@ -0,0 +1 @@
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package/dist/components/msa/renderMSAMouseover.d.ts

@@ -1,5 +1,7 @@
 import type { MsaViewModel } from '../../model.ts';
-export declare function renderMouseover({ ctx, model, }: {
+import type { Theme } from '@mui/material';
+export declare function renderMouseover({ ctx, model, theme, }: {
     ctx: CanvasRenderingContext2D;
     model: MsaViewModel;
+    theme: Theme;
 }): void;

package/dist/components/msa/renderMSAMouseover.js

@@ -1,10 +1,11 @@
 import { clickColor, hoverColor, multiRowHoverColor, referenceColor, } from '../overlayColors.js';
+import { renderHighlights } from './renderHighlights.js';
 // the persistent highlightColumns overlay: a stronger fill plus a solid border
 // so a domain/motif band reads clearly over the colored alignment cells (the
 // faint hover-style wash alone is invisible against clustalx coloring)
 const highlightColumnsFill = 'rgba(255,140,0,0.28)';
 const highlightColumnsBorder = 'rgba(210,90,0,0.95)';
-export function renderMouseover({ ctx, model, }) {
+export function renderMouseover({ ctx, model, theme, }) {
     const { mouseCol, colWidth, msaCanvasWidth: width, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, highResScaleFactor, referenceRowIndex, hoveredRowIndices, highlightedColumnRuns, } = model;
     ctx.resetTransform();
     ctx.clearRect(0, 0, width * highResScaleFactor, height * highResScaleFactor);
@@ -38,6 +39,15 @@ export function renderMouseover({ ctx, model, }) {
         ctx.strokeStyle = highlightColumnsBorder;
         ctx.strokeRect(x, 0, w, height);
     }
+    renderHighlights({
+        ctx,
+        model,
+        theme,
+        offsetX: -scrollX,
+        offsetY: -scrollY,
+        width,
+        height,
+    });
     ctx.fillStyle = hoverColor;
     if (mouseCol !== undefined) {
         colBand(mouseCol);

package/dist/components/msa/renderMSAMouseover.js.map

@@ -1 +1 @@
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package/dist/components/tracks/drawTracks.js

@@ -18,6 +18,10 @@ export function drawConservationBars({ ctx, values, color, colWidth, trackHeight
 // the bar-track values live on model getters (kept off the plain track object so
 // the live canvas autorun stays reactive); select the right one by track id
 export function barTrackValues(model, trackId) {
+    const supplied = model.columnTrackContent.get(trackId)?.values;
+    if (supplied) {
+        return supplied;
+    }
     return trackId === 'property-conservation'
         ? model.propertyConservation
         : model.conservation;

package/dist/components/tracks/drawTracks.js.map

@@ -1 +1 @@
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package/dist/components/tree/renderTreeCanvas.js

@@ -1,6 +1,7 @@
 import { calcDepthToLeaf, forEachDescendant, forEachLink, } from '../../hierarchy.js';
 import { setFontSize } from '../../setFontSize.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
+import { drawHighlightLabel, highlightRowFill, } from '../msa/renderHighlights.js';
 export const padding = 600;
 const extendBounds = 5;
 const radius = 2.5;
@@ -217,6 +218,34 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
     }
     ctx.setLineDash([]);
 }
+// the row sets of `highlights`, tinted across the tree area under the labels
+// with the label in the gutter at the first row of each set
+function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }) {
+    const { resolvedHighlights, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
+    const by = blockSizeYOverride ?? blockSize;
+    for (const { rowIndices, label, color } of resolvedHighlights) {
+        ctx.fillStyle = color ?? highlightRowFill;
+        for (const index of rowIndices) {
+            const y = index * rowHeight;
+            if (inYBlock(y + rowHeight / 2, offsetY, by)) {
+                ctx.fillRect(-marginLeft, y, treeAreaWidth, rowHeight);
+            }
+        }
+        const first = Math.min(...rowIndices);
+        if (label &&
+            rowIndices.length &&
+            inYBlock(first * rowHeight, offsetY, by)) {
+            drawHighlightLabel({
+                ctx,
+                theme,
+                label,
+                x: -marginLeft + 2,
+                y: first * rowHeight,
+                spanWidth: treeAreaWidth,
+            });
+        }
+    }
+}
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
     // Defer the finish call until after all inserts are done
@@ -241,6 +270,8 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     // built once for all three passes: each of them asks about a different node on
     // every block of every redraw, and `collapsed` is a list
     const collapsedSet = new Set(model.collapsed);
+    renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride });
+    setFontSize(ctx, fontSize);
     if (!noTree && drawTree) {
         renderTree({
             ctx,

package/dist/components/tree/renderTreeCanvas.js.map

@@ -1 +1 @@
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package/dist/exportFileName.d.ts

@@ -0,0 +1,6 @@
+import type { FileLocation } from '@jbrowse/core/util/types';
+/**
+ * The name to save an export under: the loaded alignment's file name with the
+ * extension swapped, or a plain default when the alignment was pasted in.
+ */
+export declare function exportFileName(location: FileLocation | undefined, extension: string): string;

package/dist/exportFileName.js

@@ -0,0 +1,15 @@
+/**
+ * The name to save an export under: the loaded alignment's file name with the
+ * extension swapped, or a plain default when the alignment was pasted in.
+ */
+export function exportFileName(location, extension) {
+    const loc = location;
+    const path = loc?.uri ?? loc?.localPath ?? loc?.name;
+    const base = path
+        ?.split(/[?#]/)[0]
+        ?.split(/[/\\]/)
+        .pop()
+        ?.replace(/\.[^.]*$/, '');
+    return `${base || 'image'}.${extension}`;
+}
+//# sourceMappingURL=exportFileName.js.map

package/dist/exportFileName.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"exportFileName.js","sourceRoot":"","sources":["../src/exportFileName.ts"],"names":[],"mappings":"AAEA;;;GAGG;AACH,MAAM,UAAU,cAAc,CAC5B,QAAkC,EAClC,SAAiB;IAEjB,MAAM,GAAG,GAAG,QACqD,CAAA;IACjE,MAAM,IAAI,GAAG,GAAG,EAAE,GAAG,IAAI,GAAG,EAAE,SAAS,IAAI,GAAG,EAAE,IAAI,CAAA;IACpD,MAAM,IAAI,GAAG,IAAI;QACf,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QAClB,EAAE,KAAK,CAAC,OAAO,CAAC;SACf,GAAG,EAAE;QACN,EAAE,OAAO,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;IAC3B,OAAO,GAAG,IAAI,IAAI,OAAO,IAAI,SAAS,EAAE,CAAA;AAC1C,CAAC"}

package/dist/headlessRenderEnv.d.ts

@@ -39,7 +39,10 @@ export declare class HeadlessDOMPoint {
  * average for layout and, more usefully, exactly predictable: a caller can
  * compute the width a renderer will see rather than hardcoding a number
  * measured from one machine's fonts.
+ *
+ * `contextExtras` adds to the context a test hands out -- the raster test
+ * supplies the ImageData methods that make the export take its image path.
  */
-export declare function installHeadlessRenderEnv(win?: unknown): void;
+export declare function installHeadlessRenderEnv(win?: unknown, contextExtras?: Partial<CanvasRenderingContext2D>): void;
 /** the per-character width factor `measureText` above reports */
 export declare const CHAR_WIDTH_RATIO = 0.6;