react-msaview 7.0.0 → 8.0.0

package/dist/renderToStaticMarkup.d.ts

@@ -2,29 +2,20 @@ import type React from 'react';
 /**
  * Render a React element to a static markup string, for the SVG export.
  *
- * Inlined rather than imported from `@jbrowse/core/util` on purpose, and this
- * one is the removal direction of the rule in CLAUDE.md rather than the
- * addition direction. Core dropped `renderToStaticMarkup` from that barrel in
- * jbrowse-components 0d034e2bd8 -- deliberately, because it was the barrel's
- * only reach into react-dom and the barrel is loaded in the RPC worker, which
- * never renders. The export path is the only caller, so nothing here or in
- * jbrowse-plugin-msaview/-tview failed to build, lint, typecheck, or boot; the
- * published 3.4.0 and 2.2.1 bundles simply threw the first time a user asked
- * for an SVG on a v5 host.
- *
- * A rendering library asking its host for a renderer was the odd coupling. Both
- * `react-dom` and `react-dom/client` are long-established host externals, so
- * this costs a few hundred bytes in the plugin bundle and no duplicate react.
+ * Inlined because core removed `renderToStaticMarkup` from the
+ * `@jbrowse/core/util` barrel in jbrowse-components 0d034e2bd8; see the
+ * `@jbrowse/core` note in CLAUDE.md. `react-dom` and `react-dom/client` are
+ * host externals, so this adds a few hundred bytes to the plugin bundle and no
+ * duplicate react.
  */
 export declare function renderToStaticMarkup(node: React.ReactElement): string;
 /**
  * Rewrites every color an SVG 1.1 presentation attribute cannot hold.
  *
- * `fill`, `stroke` and `stop-color` take a <color>, which is a keyword, a hex
- * triplet or rgb() -- not rgba(), which MUI palette values are full of, and not
- * hsl(), which the percent-identity scheme colors with. Illustrator and older
- * Inkscape drop an element whose fill they cannot parse, so the minimap thumb
- * came out opaque and the identity coloring came out missing. Alpha moves to
- * the matching -opacity attribute, unless the element already carries one.
+ * `fill`, `stroke` and `stop-color` take a keyword, a hex triplet or rgb(). MUI
+ * palette values use rgba() and the percent-identity scheme uses hsl(), and
+ * Illustrator and older Inkscape drop an element whose fill they cannot parse.
+ * Alpha moves to the matching -opacity attribute unless the element already
+ * carries one.
  */
 export declare function svgSafeColors(html: string): string;

package/dist/renderToStaticMarkup.js

@@ -4,19 +4,11 @@ import { createRoot } from 'react-dom/client';
 /**
  * Render a React element to a static markup string, for the SVG export.
  *
- * Inlined rather than imported from `@jbrowse/core/util` on purpose, and this
- * one is the removal direction of the rule in CLAUDE.md rather than the
- * addition direction. Core dropped `renderToStaticMarkup` from that barrel in
- * jbrowse-components 0d034e2bd8 -- deliberately, because it was the barrel's
- * only reach into react-dom and the barrel is loaded in the RPC worker, which
- * never renders. The export path is the only caller, so nothing here or in
- * jbrowse-plugin-msaview/-tview failed to build, lint, typecheck, or boot; the
- * published 3.4.0 and 2.2.1 bundles simply threw the first time a user asked
- * for an SVG on a v5 host.
- *
- * A rendering library asking its host for a renderer was the odd coupling. Both
- * `react-dom` and `react-dom/client` are long-established host externals, so
- * this costs a few hundred bytes in the plugin bundle and no duplicate react.
+ * Inlined because core removed `renderToStaticMarkup` from the
+ * `@jbrowse/core/util` barrel in jbrowse-components 0d034e2bd8; see the
+ * `@jbrowse/core` note in CLAUDE.md. `react-dom` and `react-dom/client` are
+ * host externals, so this adds a few hundred bytes to the plugin bundle and no
+ * duplicate react.
  */
 export function renderToStaticMarkup(node) {
     const div = document.createElement('div');
@@ -29,11 +21,9 @@ export function renderToStaticMarkup(node) {
         html = div.innerHTML;
     }
     finally {
-        // A real client root, not a server render: effects run, so every `observer`
-        // in the tree gets a live MobX reaction. Left mounted, an export of a large
-        // alignment keeps tens of thousands of detached nodes subscribed to the
-        // model and re-rendering into a dead div on every pan and zoom, once per
-        // export ever taken. The markup is a string by here and needs no DOM.
+        // effects run in a client root, so every `observer` holds a MobX reaction;
+        // a mounted export of a large alignment would keep tens of thousands of
+        // detached nodes re-rendering on every pan and zoom
         root.unmount();
     }
     return html;
@@ -43,12 +33,11 @@ const colorAttr = /\b(fill|stroke|stop-color)="([^"]+)"/g;
 /**
  * Rewrites every color an SVG 1.1 presentation attribute cannot hold.
  *
- * `fill`, `stroke` and `stop-color` take a <color>, which is a keyword, a hex
- * triplet or rgb() -- not rgba(), which MUI palette values are full of, and not
- * hsl(), which the percent-identity scheme colors with. Illustrator and older
- * Inkscape drop an element whose fill they cannot parse, so the minimap thumb
- * came out opaque and the identity coloring came out missing. Alpha moves to
- * the matching -opacity attribute, unless the element already carries one.
+ * `fill`, `stroke` and `stop-color` take a keyword, a hex triplet or rgb(). MUI
+ * palette values use rgba() and the percent-identity scheme uses hsl(), and
+ * Illustrator and older Inkscape drop an element whose fill they cannot parse.
+ * Alpha moves to the matching -opacity attribute unless the element already
+ * carries one.
  */
 export function svgSafeColors(html) {
     return html.replaceAll(tag, el => el.replaceAll(colorAttr, (match, attr, value) => {

package/dist/renderToStaticMarkup.js.map

@@ -1 +1 @@
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package/dist/renderToSvg.js

@@ -3,33 +3,44 @@ import React from 'react';
 import { when } from 'mobx';
 import { visibleRowRange } from './components/getVisibleLeaves.js';
 import MinimapSVG from './components/minimap/MinimapSVG.js';
+import { legendRows } from './components/msa/legendRows.js';
 import { rasterImageHref, rasterSupported } from './components/msa/msaRaster.js';
 import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock.js';
 import { renderPersistentHighlights } from './components/msa/renderHighlights.js';
 import { renderMSABlock } from './components/msa/renderMSABlock.js';
 import { visibleColRange } from './components/msa/visibleColRange.js';
+import { headerRunsAcross } from './components/rowpanels/headerLayout.js';
+import { renderRowPanels } from './components/rowpanels/renderRowPanel.js';
 import { renderAllTracks } from './components/tracks/drawTracks.js';
+import { bracketGap, cladeHeight, cladeInGutter, cladeLabelHorizontal, cladeLabelOffset, } from './components/tree/cladeBrackets.js';
 import { renderTreeCanvas } from './components/tree/renderTreeCanvas.js';
+import { renderTreeOverview } from './components/tree/renderTreeOverview.js';
+import { treeScaleBarHeight } from './constants.js';
+import { measureTextCanvas } from './measureTextCanvas.js';
 import { renderToStaticMarkup, svgSafeColors } from './renderToStaticMarkup.js';
-// domain-legend geometry, shared by the width calculation and the renderer so
-// the reserved column on the right exactly fits the drawn legend
+import { outlineColor } from './util.js';
+// legend geometry, shared by the width calculation and the renderer so the
+// reserved column on the right exactly fits the drawn legends
 const LEGEND_PAD = 8;
 const LEGEND_ROW_H = 16;
 const LEGEND_SWATCH = 12;
 const LEGEND_FONT = 12;
 const LEGEND_CHAR_W = 7;
+// the width of a character as a fraction of the font size, close enough for a
+// sans-serif average
+const CHAR_WIDTH = 0.6;
 const LEGEND_MAX_W = 360;
 const LEGEND_TEXT_X = LEGEND_PAD + LEGEND_SWATCH + 6;
-function getLegendWidth(model) {
-    const maxLen = model.visibleDomainTypes.reduce((a, d) => Math.max(a, d.name.length), 0);
+function getLegendWidth(rows) {
+    const maxLen = rows.reduce((a, r) => Math.max(a, r.label.length), 0);
     const w = LEGEND_TEXT_X + LEGEND_PAD + maxLen * LEGEND_CHAR_W;
     return Math.min(LEGEND_MAX_W, Math.max(120, w));
 }
-function legendHeight(domainTypes) {
-    return LEGEND_PAD * 2 + domainTypes.length * LEGEND_ROW_H;
+function legendHeight(rows) {
+    return LEGEND_PAD * 2 + rows.length * LEGEND_ROW_H;
 }
 function getLayout(model, opts) {
-    const { scrollX, scrollY, totalWidth, totalHeight, treeAreaWidth, totalTrackAreaHeight, minimapHeight, msaAreaHeight, msaCanvasWidth, showHorizontalScrollbar, } = model;
+    const { scrollX, scrollY, totalWidth, totalHeight, treeAreaWidth, rowPanelsWidth, rowPanelsHeaderHeight, totalTrackAreaHeight, minimapHeight, msaAreaHeight, msaCanvasWidth, showHorizontalScrollbar, treeOverviewHeight, treeScaleBar, } = model;
     const trackHeight = opts.includeTracks ? totalTrackAreaHeight : 0;
     // the minimap reflects the live viewport scroll position, so it's only
     // meaningful for a viewport export, never for the entire alignment -- and
@@ -38,9 +49,10 @@ function getLayout(model, opts) {
     const includeMinimap = opts.exportType === 'viewport' &&
         !!opts.includeMinimap &&
         showHorizontalScrollbar;
-    const legendWidth = model.actuallyShowDomains && model.visibleDomainTypes.length > 0
-        ? getLegendWidth(model)
-        : 0;
+    const rows = legendRows(model.legends);
+    const legendWidth = rows.length > 0 ? getLegendWidth(rows) : 0;
+    const topHeight = Math.max(includeMinimap ? minimapHeight : 0, rowPanelsHeaderHeight, treeOverviewHeight + (treeScaleBar ? treeScaleBarHeight : 0));
+    const gutterWidth = treeAreaWidth + rowPanelsWidth;
     // width stays content-only; the legend occupies an extra column added at the
     // svg root in MsaSvg. The viewport export takes the alignment canvas's own
     // size rather than the widget's -- the widget box also covers the header, the
@@ -48,22 +60,24 @@ function getLayout(model, opts) {
     // columns the scrollbars hide on screen
     return opts.exportType === 'entire'
         ? {
-            width: totalWidth + treeAreaWidth,
+            width: totalWidth + gutterWidth,
             msaAreaWidth: totalWidth,
-            height: totalHeight + trackHeight,
+            height: totalHeight + trackHeight + topHeight,
             contentHeight: totalHeight,
             trackHeight,
+            topHeight,
             offsetX: 0,
             offsetY: 0,
             includeMinimap,
             legendWidth,
         }
         : {
-            width: msaCanvasWidth + treeAreaWidth,
+            width: msaCanvasWidth + gutterWidth,
             msaAreaWidth: msaCanvasWidth,
-            height: msaAreaHeight + (includeMinimap ? minimapHeight : 0) + trackHeight,
+            height: msaAreaHeight + topHeight + trackHeight,
             contentHeight: msaAreaHeight,
             trackHeight,
+            topHeight,
             offsetX: -scrollX,
             offsetY: -scrollY,
             includeMinimap,
@@ -86,18 +100,18 @@ export async function renderToSvg(model, opts) {
     const markup = renderToStaticMarkup(React.createElement(MsaSvg, { model: model, theme: opts.theme, Context: Context, layout: getLayout(model, opts), layers: layers }));
     return svgSafeColors(markup.replaceAll(/<g data-layer="([^"]+)"><\/g>/g, (match, id) => {
         const ctx = layers.get(id);
-        return ctx ? `<g>${ctx.getSvg().innerHTML}</g>` : match;
+        return ctx ? `<g id="${id}">${ctx.getSvg().innerHTML}</g>` : match;
     }));
 }
 function MsaSvg({ model, theme, Context, layout, layers, }) {
-    const { width, trackHeight, includeMinimap, legendWidth } = layout;
-    const { treeAreaWidth, minimapHeight, visibleDomainTypes } = model;
+    const { width, trackHeight, includeMinimap, legendWidth, topHeight } = layout;
+    const { treeAreaWidth, rowPanelsWidth } = model;
     const totalWidth = width + legendWidth;
-    const legendTop = includeMinimap ? minimapHeight : 0;
-    // a short alignment with many domain types has a key taller than its rows,
+    const legendTop = topHeight;
+    // a short alignment with many legend entries has a key taller than its rows,
     // and the page has to hold the whole key
     const height = legendWidth > 0
-        ? Math.max(layout.height, legendTop + legendHeight(visibleDomainTypes))
+        ? Math.max(layout.height, legendTop + legendHeight(legendRows(model.legends)))
         : layout.height;
     const props = { Context, model, theme, layout, layers };
     const body = (React.createElement(React.Fragment, null,
@@ -106,35 +120,124 @@ function MsaSvg({ model, theme, Context, layout, layers, }) {
             React.createElement(CoreRendering, { ...props }))));
     return (React.createElement("svg", { width: totalWidth, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: `0 0 ${totalWidth} ${height}` },
         React.createElement("rect", { width: "100%", height: "100%", fill: theme.palette.background.default }),
-        includeMinimap ? (React.createElement(React.Fragment, null,
-            React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
-                React.createElement(MinimapSVG, { model: model, theme: theme })),
-            React.createElement("g", { transform: `translate(0 ${minimapHeight})` }, body))) : (body),
-        legendWidth > 0 ? (React.createElement("g", { transform: `translate(${width} ${legendTop})` },
+        topHeight > 0 ? (React.createElement(React.Fragment, null,
+            includeMinimap ? (React.createElement("g", { id: "minimap-panel", transform: `translate(${treeAreaWidth + rowPanelsWidth} 0)` },
+                React.createElement(MinimapSVG, { model: model, theme: theme }))) : null,
+            React.createElement(RowPanelHeadersSVG, { model: model, theme: theme, bandHeight: topHeight }),
+            model.showTreeOverview ? (React.createElement(TreeOverviewSVG, { model: model, theme: theme, Context: Context, layers: layers })) : null,
+            React.createElement(TreeScaleBarSVG, { model: model, theme: theme }),
+            React.createElement("g", { transform: `translate(0 ${topHeight})` }, body))) : (body),
+        legendWidth > 0 ? (React.createElement("g", { id: "legend-panel", transform: `translate(${width} ${legendTop})` },
             React.createElement(LegendSVG, { model: model, theme: theme, width: legendWidth }))) : null));
 }
-// the domain color key drawn as a reserved column to the right of the
-// alignment, mirroring the on-screen AnnotationLegend overlay
+// The tree overview in the top band, over the tree column, where the live view
+// puts it. It is part of the figure rather than chrome: the inset is what says
+// where the focused clade sits in the whole tree.
+function TreeOverviewSVG({ model, theme, Context, layers, }) {
+    const { treeAreaWidth, overviewHeight, id } = model;
+    const ctx = new Context(treeAreaWidth, overviewHeight);
+    renderTreeOverview({
+        model,
+        ctx,
+        theme,
+        width: treeAreaWidth,
+        height: overviewHeight,
+    });
+    return (React.createElement(ClipGroup, { panelId: "tree-overview", clipId: `tree-overview-${id}`, width: treeAreaWidth, height: overviewHeight, ctx: ctx, layers: layers }));
+}
+// The branch-length scale bar under the tree overview, where the live view puts
+// it (see TreeRuler). A phylogram whose branch lengths are drawn to a scale
+// nothing states is a figure a reader cannot measure, so the export carries the
+// bar even though it is chrome on screen.
+function TreeScaleBarSVG({ model, theme, }) {
+    const { marginLeft, treeScaleBar: bar, treeOverviewHeight } = model;
+    if (!bar) {
+        return null;
+    }
+    const y = treeOverviewHeight + treeScaleBarHeight;
+    const color = theme.palette.text.primary;
+    return (React.createElement("g", { id: "tree-scalebar" },
+        React.createElement("text", { x: marginLeft, y: y - 9, fontSize: 10, fill: color }, bar.label),
+        React.createElement("path", { d: `M${marginLeft} ${y - 7} v6 h${bar.px} v-6`, fill: "none", stroke: color })));
+}
+// Each strip's header over the column it names, turned on its side, where the
+// live view puts it (see RowPanelHeaders). The baseline runs up the figure, so
+// the name sits to the left of it, the way TrackLabelsSVG offsets a horizontal
+// baseline by a third of the font size.
+function RowPanelHeadersSVG({ model, theme, bandHeight, }) {
+    const { resolvedRowPanels, treeAreaWidth, fontSize } = model;
+    const y = bandHeight - 4;
+    return resolvedRowPanels.length === 0 ? null : (React.createElement("g", { id: "rowpanel-headers" }, resolvedRowPanels.map(panel => {
+        const across = headerRunsAcross(panel.width);
+        const size = across ? fontSize : Math.min(fontSize, panel.width);
+        const center = treeAreaWidth + panel.offsetX + panel.width / 2;
+        const x = across ? center : center + size / 3;
+        const room = across ? panel.width : y - LEGEND_PAD;
+        const maxChars = Math.floor(room / (size * CHAR_WIDTH));
+        return size < 5 ? null : (React.createElement("text", { key: panel.id, x: x, y: y, ...(across
+                ? { textAnchor: 'middle' }
+                : { transform: `rotate(-90 ${x} ${y})` }), fontSize: size, fill: theme.palette.text.primary }, panel.header.length > maxChars
+            ? `${panel.header.slice(0, Math.max(1, maxChars - 1))}…`
+            : panel.header));
+    })));
+}
+// A label past the room it has, cut to what fits with an ellipsis. The measure
+// is the one cladeGutterWidth sizes the gutter with, so a label the gutter
+// holds keeps every character.
+function clipCladeLabel(label, room, fontSize) {
+    const width = measureTextCanvas(label, fontSize);
+    if (width <= room) {
+        return label;
+    }
+    const fits = Math.floor((label.length * room) / width);
+    return `${label.slice(0, Math.max(1, fits - 1))}…`;
+}
+// Each bracket's label in the gutter beside its bar, where the live view puts
+// it (see CladeLabels). The canvas layer draws the bar; a label longer than the
+// gutter or the clade is clipped, since text that overruns runs off the figure.
+function CladeLabelsSVG({ model, theme, offsetY, }) {
+    const { resolvedClades, cladeGutterWidth, rowHeight, treeAreaWidth, fontSize, } = model;
+    if (cladeGutterWidth === 0) {
+        return null;
+    }
+    const gutterLeft = treeAreaWidth - cladeGutterWidth;
+    return (React.createElement("g", { id: "clade-labels" }, resolvedClades.map((clade, index) => {
+        const { label, markColor, rows } = clade;
+        if (!label || !cladeInGutter(clade)) {
+            return null;
+        }
+        const left = gutterLeft + cladeLabelOffset(clade);
+        const top = rows[0] * rowHeight - offsetY;
+        const height = cladeHeight(clade, rowHeight);
+        const horizontal = cladeLabelHorizontal(clade, rowHeight, fontSize);
+        const room = horizontal ? treeAreaWidth - left - bracketGap : height;
+        const x = horizontal ? left : left + fontSize;
+        const y = horizontal ? top + height / 2 + fontSize / 3 : top + height;
+        return (React.createElement("text", { key: `${rows[0]}-${rows[1]}-${index}`, x: x, y: y, transform: horizontal ? undefined : `rotate(-90 ${x} ${y})`, fontSize: fontSize, fill: markColor ?? theme.palette.text.primary }, clipCladeLabel(label, room, fontSize)));
+    })));
+}
+// the color keys drawn as a reserved column to the right of the alignment,
+// mirroring the on-screen AnnotationLegend overlay
 function LegendSVG({ model, theme, width, }) {
-    const { visibleDomainTypes, fillPalette, strokePalette } = model;
-    const boxHeight = legendHeight(visibleDomainTypes);
+    const rows = legendRows(model.legends);
+    const boxHeight = legendHeight(rows);
     // the column is capped at LEGEND_MAX_W, so a name too long for it has to be
     // clipped here -- text that overruns the reserved width runs off the figure
     const maxChars = Math.floor((width - LEGEND_TEXT_X - LEGEND_PAD) / LEGEND_CHAR_W);
     return (React.createElement("g", null,
         React.createElement("rect", { x: 0, y: 0, width: width - 4, height: boxHeight, fill: theme.palette.background.paper, stroke: theme.palette.divider, rx: 2 }),
-        visibleDomainTypes.map((d, i) => {
+        rows.map((row, i) => {
             const y = LEGEND_PAD + i * LEGEND_ROW_H;
-            return (React.createElement("g", { key: d.accession },
-                React.createElement("rect", { x: LEGEND_PAD, y: y, width: LEGEND_SWATCH, height: LEGEND_SWATCH, fill: fillPalette[d.accession], stroke: strokePalette[d.accession] }),
-                React.createElement("text", { x: LEGEND_TEXT_X, y: y + LEGEND_SWATCH - 1, fontSize: LEGEND_FONT, fill: theme.palette.text.primary }, d.name.length > maxChars
-                    ? `${d.name.slice(0, Math.max(1, maxChars - 1))}…`
-                    : d.name)));
+            return (React.createElement("g", { key: row.key },
+                row.color ? (React.createElement("rect", { x: LEGEND_PAD, y: y, width: LEGEND_SWATCH, height: LEGEND_SWATCH, fill: row.color, stroke: outlineColor(row.color) })) : null,
+                React.createElement("text", { x: row.color ? LEGEND_TEXT_X : LEGEND_PAD, y: y + LEGEND_SWATCH - 1, fontSize: LEGEND_FONT, fontWeight: row.color ? undefined : 'bold', fill: theme.palette.text.primary }, row.label.length > maxChars
+                    ? `${row.label.slice(0, Math.max(1, maxChars - 1))}…`
+                    : row.label)));
         })));
 }
 function CoreRendering({ model, theme, layout, Context, layers }) {
     const { contentHeight, offsetX, offsetY, msaAreaWidth } = layout;
-    const { treeAreaWidth, id } = model;
+    const { treeAreaWidth, rowPanelsWidth, id } = model;
     const treeCtx = new Context(treeAreaWidth, contentHeight);
     renderTreeCanvas({
         model,
@@ -144,10 +247,24 @@ function CoreRendering({ model, theme, layout, Context, layers }) {
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
+    const rowPanelsCtx = rowPanelsWidth
+        ? new Context(rowPanelsWidth, contentHeight)
+        : undefined;
+    if (rowPanelsCtx) {
+        renderRowPanels({
+            model,
+            theme,
+            ctx: rowPanelsCtx,
+            offsetY,
+            blockSizeYOverride: contentHeight,
+            highResScaleFactorOverride: 1,
+        });
+    }
     const raster = rasterBackground({ model, theme, layout });
     const msaCtx = new Context(msaAreaWidth, contentHeight);
     renderBoxFeatureCanvasBlock({
         model,
+        theme,
         ctx: msaCtx,
         offsetX,
         offsetY,
@@ -179,19 +296,19 @@ function CoreRendering({ model, theme, layout, Context, layers }) {
         height: contentHeight,
     });
     return (React.createElement(React.Fragment, null,
-        React.createElement(ClipGroup, { clipId: `tree-${id}`, width: treeAreaWidth, height: contentHeight, ctx: treeCtx, layers: layers }),
-        React.createElement(ClipGroup, { clipId: `msa-${id}`, width: msaAreaWidth, height: contentHeight, transform: `translate(${treeAreaWidth} 0)`, ctx: msaCtx, layers: layers, underlay: raster })));
+        React.createElement(ClipGroup, { panelId: "tree-panel", clipId: `tree-${id}`, width: treeAreaWidth, height: contentHeight, ctx: treeCtx, layers: layers }),
+        React.createElement(CladeLabelsSVG, { model: model, theme: theme, offsetY: offsetY }),
+        rowPanelsCtx ? (React.createElement(ClipGroup, { panelId: "rowpanels-panel", clipId: `rowpanels-${id}`, width: rowPanelsWidth, height: contentHeight, transform: `translate(${treeAreaWidth} 0)`, ctx: rowPanelsCtx, layers: layers })) : null,
+        React.createElement(ClipGroup, { panelId: "msa-panel", clipId: `msa-${id}`, width: msaAreaWidth, height: contentHeight, transform: `translate(${treeAreaWidth + rowPanelsWidth} 0)`, ctx: msaCtx, layers: layers, underlay: raster })));
 }
 /**
- * The alignment background as a single <image>, on the same terms the live
- * canvas uses it: no domain overlay painting its own boxes, background coloring
- * on, and a canvas we can actually read back.
+ * The alignment background as a single <image>, under the live canvas's
+ * conditions: no domain overlay boxes, background coloring on, and a canvas
+ * that reads back.
  *
- * One node replaces the <rect>-per-cell the vector path emits, which is what
- * lets an export of a real alignment finish at all. The image is one pixel per
- * cell drawn across the cells' own rectangle, so it upscales by whole cells --
- * image-rendering keeps those edges hard rather than smearing them, making it
- * pixel-for-pixel what the rects drew.
+ * The vector path's <rect> per cell exhausts the heap on a real alignment. The
+ * image is one pixel per cell, and image-rendering keeps the upscaled cell
+ * edges hard, so it matches the rects pixel for pixel.
  */
 function rasterBackground({ model, theme, layout, }) {
     const { contentHeight, offsetX, offsetY, msaAreaWidth } = layout;
@@ -223,7 +340,7 @@ function rasterBackground({ model, theme, layout, }) {
 }
 function TrackRendering({ model, theme, layout, Context, layers }) {
     const { trackHeight, offsetX, msaAreaWidth } = layout;
-    const { treeAreaWidth, id } = model;
+    const { treeAreaWidth, rowPanelsWidth, id } = model;
     const ctx = new Context(msaAreaWidth, trackHeight);
     renderAllTracks({
         model,
@@ -235,8 +352,8 @@ function TrackRendering({ model, theme, layout, Context, layers }) {
     });
     return (React.createElement(React.Fragment, null,
         React.createElement(TrackLabelsSVG, { model: model, theme: theme }),
-        React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
-            React.createElement(ClipGroup, { clipId: `tracks-${id}`, width: msaAreaWidth, height: trackHeight, ctx: ctx, layers: layers }))));
+        React.createElement("g", { transform: `translate(${treeAreaWidth + rowPanelsWidth} 0)` },
+            React.createElement(ClipGroup, { panelId: "tracks-panel", clipId: `tracks-${id}`, width: msaAreaWidth, height: trackHeight, ctx: ctx, layers: layers }))));
 }
 // Each track's name in the tree-width column beside it, where the live view puts
 // it (see TrackLabel). Without these the figure has an unlabeled bar chart and
@@ -246,26 +363,33 @@ function TrackLabelsSVG({ model, theme, }) {
     if (!drawLabels) {
         return null;
     }
-    let y = 0;
-    return (React.createElement(React.Fragment, null, turnedOnTracks.map(track => {
+    const labels = turnedOnTracks.map((track, i) => {
         const { id, name, height } = track.model;
         const size = Math.min(height, fontSize);
-        const baseline = y + height / 2 + size / 3;
-        y += height;
+        const top = turnedOnTracks
+            .slice(0, i)
+            .reduce((acc, t) => acc + t.model.height, 0);
+        return { id, name, size, baseline: top + height / 2 + size / 3 };
+    });
+    return (React.createElement(React.Fragment, null, labels.map(({ id, name, size, baseline }) => {
         return size < 5 ? null : (React.createElement("text", { key: id, x: treeAreaWidth - 4, y: baseline, fontSize: size, textAnchor: "end", fill: theme.palette.text.primary }, name));
     })));
 }
 // Clips a svgcanvas Context to its box and leaves a placeholder for renderToSvg
 // to splice the layer's own markup into. `underlay` draws beneath that markup,
 // inside the same clip, for the parts of a layer React emits directly.
-function ClipGroup({ clipId, width, height, transform, ctx, layers, underlay, }) {
-    layers.set(clipId, ctx);
+//
+// `panelId` names the spliced group in the output, the same name in every
+// export, so a figure can be taken apart in Illustrator or svgutils. `clipId`
+// carries the model id, which keeps two viewers on one page from colliding.
+function ClipGroup({ panelId, clipId, width, height, transform, ctx, layers, underlay, }) {
+    layers.set(panelId, ctx);
     return (React.createElement(React.Fragment, null,
         React.createElement("defs", null,
             React.createElement("clipPath", { id: clipId },
                 React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
         React.createElement("g", { clipPath: `url(#${clipId})`, transform: transform },
             underlay,
-            React.createElement("g", { "data-layer": clipId }))));
+            React.createElement("g", { "data-layer": panelId }))));
 }
 //# sourceMappingURL=renderToSvg.js.map

package/dist/renderToSvg.js.map

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package/dist/rowCoordinateCalculations.d.ts

@@ -38,9 +38,8 @@ export declare function globalColToVisibleCol(blanks: number[], globalCol: numbe
  * that is its own visible index; for a hidden one it is the index of the next
  * visible column, i.e. where the hidden column collapses to.
  *
- * That total answer is what spans want: resolving both ends of a span through
- * globalColToVisibleCol instead loses the whole span whenever either end lands
- * in a hidden column.
+ * Spans use this, since globalColToVisibleCol drops a span whenever either end
+ * lands in a hidden column.
  *
  * @param blanks - Sorted array of global column indices that are hidden
  * @param globalCol - The global column index in the full MSA
@@ -50,9 +49,8 @@ export declare function visibleColsBefore(blanks: number[], globalCol: number):
  * The ungapped position a row holds at a global column, or undefined when that
  * column is a gap in the row or past its end.
  *
- * A binary search of the row's seqPos index (ascending), not a scan of the row:
- * this answers on every mouse move, and scanning a 30k-column row per event is
- * the whole frame.
+ * Binary-searches the row's ascending seqPos index; it runs on every mouse
+ * move, and scanning a 30k-column row per event takes the whole frame.
  *
  * @param index - The row's seqPos -> global column index (buildSeqPosIndex)
  * @param globalCol - The global column index in the full MSA

package/dist/rowCoordinateCalculations.js

@@ -70,9 +70,8 @@ function countBlanksBefore(blanks, globalCol) {
  * that is its own visible index; for a hidden one it is the index of the next
  * visible column, i.e. where the hidden column collapses to.
  *
- * That total answer is what spans want: resolving both ends of a span through
- * globalColToVisibleCol instead loses the whole span whenever either end lands
- * in a hidden column.
+ * Spans use this, since globalColToVisibleCol drops a span whenever either end
+ * lands in a hidden column.
  *
  * @param blanks - Sorted array of global column indices that are hidden
  * @param globalCol - The global column index in the full MSA
@@ -84,9 +83,8 @@ export function visibleColsBefore(blanks, globalCol) {
  * The ungapped position a row holds at a global column, or undefined when that
  * column is a gap in the row or past its end.
  *
- * A binary search of the row's seqPos index (ascending), not a scan of the row:
- * this answers on every mouse move, and scanning a 30k-column row per event is
- * the whole frame.
+ * Binary-searches the row's ascending seqPos index; it runs on every mouse
+ * move, and scanning a 30k-column row per event takes the whole frame.
  *
  * @param index - The row's seqPos -> global column index (buildSeqPosIndex)
  * @param globalCol - The global column index in the full MSA

package/dist/rowCoordinateCalculations.js.map

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