react-msaview 6.5.0 → 8.0.0

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -1,98 +1,62 @@
-import { subFeatureRowHeight } from '../../constants.js';
+import { domainUnderlineHeight, subFeatureRowHeight } from '../../constants.js';
+import { contrastTextFn } from '../../util.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
-export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { blockSize, rowHeight, highResScaleFactor, actuallyShowDomains } = model;
-    if (actuallyShowDomains) {
-        const k = highResScaleFactorOverride ?? highResScaleFactor;
-        const bx = blockSizeXOverride ?? blockSize;
-        const by = blockSizeYOverride ?? blockSize;
-        ctx.resetTransform();
-        ctx.scale(k, k);
-        ctx.translate(-offsetX, rowHeight / 2 - offsetY);
-        drawTiles({
-            model,
-            ctx,
-            visibleLeaves: getVisibleLeaves({ model, offsetY, blockSizeY: by }),
-            offsetX,
-            blockWidth: bx,
-        });
+import { drawFeatureSpans, spanRows } from './drawFeatureSpans.js';
+export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
+    const { blockSize, rowHeight, highResScaleFactor, actuallyShowDomains, subFeatureRows, colWidth, featureColors, featureLabels, segmentLabels, showMsaLetters, domainUnderline, domainBands, } = model;
+    if (!actuallyShowDomains) {
+        return;
     }
-}
-function drawTiles({ model, ctx, visibleLeaves, offsetX, blockWidth, }) {
-    const { subFeatureRows, colWidth, rowHeight, fillPalette, strokePalette, segmentLabels, showMsaLetters, domainBands, } = model;
-    const h = subFeatureRows ? subFeatureRowHeight : rowHeight;
+    const k = highResScaleFactorOverride ?? highResScaleFactor;
+    const bx = blockSizeXOverride ?? blockSize;
+    const by = blockSizeYOverride ?? blockSize;
+    ctx.resetTransform();
+    ctx.scale(k, k);
+    ctx.translate(-offsetX, rowHeight / 2 - offsetY);
+    // the plain and underline modes give every band the same height; a sub-row
+    // band is thinner, and how thin depends on how many lanes its row needs
+    const barHeight = domainUnderline
+        ? Math.min(domainUnderlineHeight, rowHeight)
+        : rowHeight;
     // exon numbers label the bands only when residue letters aren't drawn (zoomed
     // out); when letters show, the alternating shades alone mark the boundaries
-    // and a number would collide with the sequence
-    const drawSegmentLabels = !showMsaLetters && !subFeatureRows && h >= 9;
-    // gene arrow heads stick out one row-height past the band, so pad the cull
-    // window enough that a band just outside the block still draws its head
-    const cull = h + colWidth;
-    const xMin = offsetX - cull;
-    const xMax = offsetX + blockWidth + cull;
+    // and a number would collide with the sequence. A featureLabel encoding names
+    // what every span carries instead
+    const drawSegmentLabels = !featureLabels && !showMsaLetters && !subFeatureRows && barHeight >= 9;
     // a segment (exon) number labels its band once per block, on the topmost
     // visible row carrying that segment, so it reads as a column header for the
     // whole band. Keyed by accession rather than drawn on row 0, because the rows
     // carrying the gene model are often not the first ones in the alignment
     const labelled = drawSegmentLabels ? new Set() : undefined;
-    for (const node of visibleLeaves) {
-        const y = node.x;
-        const bands = domainBands.get(node.data.name);
-        if (bands) {
-            for (const { annotation, startCol, endCol, stackIndex } of bands) {
-                const { accession, strand } = annotation;
-                const x = startCol * colWidth;
-                const lw = colWidth * (endCol - startCol);
-                if (x + lw >= xMin && x <= xMax) {
-                    const t = y - rowHeight + (subFeatureRows ? stackIndex * h : 0);
-                    ctx.fillStyle = fillPalette[accession];
-                    ctx.strokeStyle = strokePalette[accession];
-                    if (strand === undefined) {
-                        ctx.fillRect(x, t, lw, h);
-                        ctx.strokeRect(x, t, lw, h);
-                        const label = labelled && !labelled.has(accession)
-                            ? segmentLabels.get(accession)
-                            : undefined;
-                        if (label !== undefined) {
-                            const fontSize = Math.min(h - 2, 11);
-                            ctx.font = `${fontSize}px sans-serif`;
-                            if (ctx.measureText(label).width + 2 <= lw) {
-                                labelled.add(accession);
-                                ctx.fillStyle = '#222';
-                                ctx.textAlign = 'center';
-                                ctx.textBaseline = 'middle';
-                                ctx.fillText(label, x + lw / 2, t + h / 2);
-                            }
-                        }
-                    }
-                    else {
-                        drawGeneArrow({ ctx, x, t, w: lw, h, strand });
-                    }
-                }
-            }
-        }
-    }
-}
-// A gene arrow: a full-width rectangular body spanning the feature's
-// start..end columns, plus a triangular head that points *beyond* that end in
-// the strand direction (right for +, left for -). Keeping the body aligned to
-// the exact start/end columns means + and - strand features read as having the
-// same boundaries; the arrow lives outside them purely to show transcription
-// direction, preserving the column-by-column homology down the rows.
-function drawGeneArrow({ ctx, x, t, w, h, strand, }) {
-    // body spans bodyStart..bodyEnd (the exact columns); the head extends one
-    // row-height past bodyEnd in the strand direction
-    const dir = strand > 0 ? 1 : -1;
-    const bodyStart = strand > 0 ? x : x + w;
-    const bodyEnd = strand > 0 ? x + w : x;
-    ctx.beginPath();
-    ctx.moveTo(bodyStart, t);
-    ctx.lineTo(bodyEnd, t);
-    ctx.lineTo(bodyEnd + dir * h, t + h / 2);
-    ctx.lineTo(bodyEnd, t + h);
-    ctx.lineTo(bodyStart, t + h);
-    ctx.closePath();
-    ctx.fill();
-    ctx.stroke();
+    // gene arrow heads stick out up to a row height past the band, so pad the
+    // cull window enough that a band just outside the block still draws its head
+    const cull = rowHeight + colWidth;
+    drawFeatureSpans({
+        ctx,
+        rows: spanRows(getVisibleLeaves({ model, offsetY, blockSizeY: by }), domainBands),
+        layout: {
+            // sub-rows are thin, but a row whose lanes would spill onto the row below
+            // shares out the row height between them instead
+            height: laneCount => subFeatureRows
+                ? Math.min(subFeatureRowHeight, rowHeight / laneCount)
+                : barHeight,
+            top: (y, lane, h) => y -
+                rowHeight +
+                (subFeatureRows ? lane * h : domainUnderline ? rowHeight - h : 0),
+            // the head keeps its full size on an underline bar, since a head as short
+            // as the bar reads as a nub rather than as a direction
+            headLength: h => (domainUnderline ? rowHeight / 2 : h),
+        },
+        xOf: band => [band.startCol * colWidth, band.endCol * colWidth],
+        colors: featureColors,
+        labelOf: band => featureLabels?.get(band.annotation) ??
+            (labelled && !labelled.has(band.annotation.accession)
+                ? segmentLabels.get(band.annotation.accession)
+                : undefined),
+        labelDrawn: band => labelled?.add(band.annotation.accession),
+        contrastText: contrastTextFn(theme),
+        xMin: offsetX - cull,
+        xMax: offsetX + bx + cull,
+    });
 }
 //# sourceMappingURL=renderBoxFeatureCanvasBlock.js.map

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

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

@@ -5,20 +5,45 @@ 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, }: {
+export declare const highlightLabelHeight: number;
+export interface LabelBox {
+    left: number;
+    right: number;
+    top: number;
+    bottom: number;
+}
+/**
+ * A highlight's label, over its band where it fits and beside it where it does
+ * not, kept inside `bounds` and out of the way of the labels already placed.
+ *
+ * `bounds` keeps the label of a band scrolled partly off the left edge visible.
+ * With `placed`, a label that would overlap an earlier one, as two
+ * single-residue highlights a column apart do, steps down a row.
+ */
+export declare function drawHighlightLabel({ ctx, theme, label, x, y, spanWidth, bounds, placed, }: {
     ctx: RenderCtx;
     theme: Theme;
     label: string;
     x: number;
     y: number;
     spanWidth: number;
+    bounds?: {
+        min: number;
+        max: number;
+    };
+    placed?: LabelBox[];
 }): 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
+ * The persistent overlay on the alignment: the band behind each clade of
+ * `clades`, the `rowTint` encoding's wash, the row tints and bordered column
+ * bands of `highlights`, 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.
+ *
+ * Rows are culled to the ones this block covers. A tint over every row of a
+ * large alignment would otherwise draw the whole column of rects in each block,
+ * and again on every pointer move through renderMouseover.
  */
 export declare function renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }: {
     ctx: RenderCtx;
@@ -29,3 +54,18 @@ export declare function renderHighlights({ ctx, model, theme, offsetX, offsetY,
     width: number;
     height: number;
 }): void;
+/**
+ * The overlay parts that come from the snapshot: the reference row's tint, a
+ * bordered band per run of highlighted columns, and the `highlights` layer. The
+ * live overlay draws these under its hover and click bands; the SVG export
+ * draws only these.
+ */
+export declare function renderPersistentHighlights({ 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

@@ -1,34 +1,90 @@
 import { setFontSize } from '../../setFontSize.js';
+import { referenceColor } from '../overlayColors.js';
+// a fill plus a solid border; the hover wash alone is invisible over clustalx
+// coloring
 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, }) {
+// the label box above a highlight band; tree blocks also check rows this far
+// outside themselves
+export const highlightLabelHeight = labelFontSize + labelPad * 2;
+/**
+ * A highlight's label, over its band where it fits and beside it where it does
+ * not, kept inside `bounds` and out of the way of the labels already placed.
+ *
+ * `bounds` keeps the label of a band scrolled partly off the left edge visible.
+ * With `placed`, a label that would overlap an earlier one, as two
+ * single-residue highlights a column apart do, steps down a row.
+ */
+export function drawHighlightLabel({ ctx, theme, label, x, y, spanWidth, bounds, placed, }) {
     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;
+    const boxHeight = highlightLabelHeight;
+    let left = boxWidth <= spanWidth ? x : x + spanWidth + 2;
+    if (bounds) {
+        left = Math.max(bounds.min, Math.min(left, bounds.max - boxWidth));
+    }
+    let top = y;
+    if (placed) {
+        const overlaps = (box) => box.left < left + boxWidth &&
+            box.right > left &&
+            box.top < top + boxHeight &&
+            box.bottom > top;
+        while (placed.some(overlaps)) {
+            top += boxHeight;
+        }
+        placed.push({ left, right: left + boxWidth, top, bottom: top + boxHeight });
+    }
     ctx.fillStyle = theme.palette.background.paper;
-    ctx.fillRect(left, y, boxWidth, boxHeight);
+    ctx.fillRect(left, top, boxWidth, boxHeight);
     ctx.fillStyle = theme.palette.text.primary;
-    ctx.fillText(label, left + labelPad, y + labelPad + labelFontSize - 2);
+    ctx.fillText(label, left + labelPad, top + 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
+ * The persistent overlay on the alignment: the band behind each clade of
+ * `clades`, the `rowTint` encoding's wash, the row tints and bordered column
+ * bands of `highlights`, 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.
+ *
+ * Rows are culled to the ones this block covers. A tint over every row of a
+ * large alignment would otherwise draw the whole column of rects in each block,
+ * and again on every pointer move through renderMouseover.
  */
 export function renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }) {
-    const { resolvedHighlights, colWidth, rowHeight } = model;
+    const { resolvedClades, resolvedHighlights, rowTints, colWidth, rowHeight } = model;
+    const placed = [];
     ctx.lineWidth = 2;
+    const firstRow = Math.max(0, Math.floor(offsetY / rowHeight));
+    const lastRow = Math.ceil((offsetY + height) / rowHeight);
+    const fillRow = (index) => {
+        ctx.fillRect(0, index * rowHeight - offsetY, width, rowHeight);
+    };
+    for (const { rows, color, mark } of resolvedClades) {
+        if (mark === 'highlight' && rows[1] >= firstRow && rows[0] <= lastRow) {
+            ctx.fillStyle = color;
+            ctx.fillRect(0, rows[0] * rowHeight - offsetY, width, (rows[1] - rows[0] + 1) * rowHeight);
+        }
+    }
+    if (rowTints) {
+        for (let index = firstRow; index <= Math.min(lastRow, rowTints.length - 1); index++) {
+            const color = rowTints[index];
+            if (color) {
+                ctx.fillStyle = color;
+                fillRow(index);
+            }
+        }
+    }
     for (const { rowIndices, color } of resolvedHighlights) {
         ctx.fillStyle = color ?? highlightRowFill;
         for (const index of rowIndices) {
-            ctx.fillRect(0, index * rowHeight - offsetY, width, rowHeight);
+            if (index >= firstRow && index <= lastRow) {
+                fillRow(index);
+            }
         }
     }
     for (const { startCol, endCol, label, color } of resolvedHighlights) {
@@ -42,8 +98,40 @@ export function renderHighlights({ ctx, model, theme, offsetX, offsetY, width, h
         ctx.strokeStyle = color ?? highlightBorder;
         ctx.strokeRect(x, 0, spanWidth, height);
         if (label) {
-            drawHighlightLabel({ ctx, theme, label, x, y: 0, spanWidth });
+            drawHighlightLabel({
+                ctx,
+                theme,
+                label,
+                x,
+                y: 0,
+                spanWidth,
+                bounds: { min: 0, max: width },
+                placed,
+            });
         }
     }
 }
+/**
+ * The overlay parts that come from the snapshot: the reference row's tint, a
+ * bordered band per run of highlighted columns, and the `highlights` layer. The
+ * live overlay draws these under its hover and click bands; the SVG export
+ * draws only these.
+ */
+export function renderPersistentHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }) {
+    const { colWidth, rowHeight, referenceRowIndex, highlightedColumnRuns } = model;
+    if (referenceRowIndex !== undefined) {
+        ctx.fillStyle = referenceColor;
+        ctx.fillRect(0, referenceRowIndex * rowHeight - offsetY, width, rowHeight);
+    }
+    ctx.lineWidth = 2;
+    for (const { start, end } of highlightedColumnRuns) {
+        const x = start * colWidth - offsetX;
+        const w = (end - start + 1) * colWidth;
+        ctx.fillStyle = highlightFill;
+        ctx.fillRect(x, 0, w, height);
+        ctx.strokeStyle = highlightBorder;
+        ctx.strokeRect(x, 0, w, height);
+    }
+    renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height });
+}
 //# sourceMappingURL=renderHighlights.js.map

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

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

@@ -1,12 +1,11 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
-export declare function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, }: {
+export declare function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, }: {
     offsetX: number;
     offsetY: number;
     theme: Theme;
     model: MsaViewModel;
-    contrastScheme: Record<string, string>;
     ctx: RenderCtx;
     highResScaleFactorOverride?: number;
     blockSizeXOverride?: number;

package/dist/components/msa/renderMSABlock.js

@@ -1,10 +1,10 @@
 import { setFontSize } from '../../setFontSize.js';
-import { adjustColorForContrast } from '../../util.js';
+import { adjustColorForContrast, contrastTextFn } from '../../util.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
 import { domainBandCursor } from './domainBandCursor.js';
 import { tileColorFn } from './tileColor.js';
 import { visibleColRange } from './visibleColRange.js';
-export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, }) {
+export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, }) {
     const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, bgColor, } = model;
     const k = highResScaleFactorOverride ?? highResScaleFactor;
     const bx = blockSizeXOverride ?? blockSize;
@@ -29,7 +29,6 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
         model,
         ctx,
         theme,
-        contrastScheme,
         xStart,
         xEnd,
         visibleLeaves,
@@ -50,35 +49,28 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     });
     ctx.resetTransform();
 }
-// Letter color to use over a domain box, keyed by accession. Domain fills come
-// from a categorical palette that has no fixed lightness, so ask the theme for a
-// readable text color per fill instead of assuming dark-on-light.
-function domainLetterColors(model, theme) {
-    return new Map(Object.entries(model.fillPalette).map(([accession, fill]) => [
-        accession,
-        theme.palette.getContrastText(fill),
-    ]));
-}
-function drawTilesAndText({ model, ctx, theme, contrastScheme, visibleLeaves, xStart, xEnd, referenceSeq, drawTiles, rasterTiles, }) {
-    const { bgColor, columns, colWidth, rowHeight, relativeTo, showMsaLetters, subFeatureRows, domainBandsByStart, } = model;
+function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, referenceSeq, drawTiles, rasterTiles, }) {
+    const { bgColor, columns, colWidth, rowHeight, relativeTo, showMsaLetters, subFeatureRows, domainUnderline, domainBandsByStart, } = model;
     const tiles = drawTiles && bgColor;
     const paintTiles = tiles && !rasterTiles;
     if (paintTiles || showMsaLetters) {
-        // over raster tiles the letters take their color from contrastScheme, so
-        // the scheme lookup per cell is pure waste
-        const needsColor = paintTiles || !tiles;
+        // a letter takes its color from the cell it lands on, so the scheme lookup
+        // is only waste when nothing draws letters
+        const needsColor = paintTiles || showMsaLetters;
         const tileColor = tileColorFn(model);
+        // Domain fills come from a categorical palette with no fixed lightness, and
+        // a dynamic scheme colors a cell from its column, so a readable letter color
+        // is a question about the cell's own color rather than about its letter.
+        const contrastText = contrastTextFn(theme);
         const offsetXAligned = xStart * colWidth;
         const halfColWidth = colWidth / 2;
         // note: -rowHeight/4 matches +rowHeight/4 in tree
         const quarterRowHeight = rowHeight / 4;
         // with the tiles coming from the domain overlay instead, letters sit either
         // on a domain box or on the plain background; sub-row layout stacks the boxes
-        // above the letters, so those rows are all plain background
-        const overDomains = !drawTiles && !subFeatureRows;
-        const domainColors = overDomains
-            ? domainLetterColors(model, theme)
-            : undefined;
+        // above the letters and letter-color mode shrinks them to a bar under the
+        // row, so neither leaves anything behind a letter
+        const overDomains = !drawTiles && !subFeatureRows && !domainUnderline;
         for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
             const node = visibleLeaves[i];
             const { name } = node.data;
@@ -104,15 +96,20 @@ function drawTilesAndText({ model, ctx, theme, contrastScheme, visibleLeaves, xS
                         const covering = bandAt(col);
                         ctx.fillStyle = covering
                             ? // on top of a domain box: contrast against the box fill
-                                domainColors.get(covering.annotation.accession)
-                            : tiles
-                                ? // on top of a colored tile
-                                    (contrastScheme[letter] ?? 'black')
-                                : !drawTiles || !color
-                                    ? // plain background, uncolored letters
-                                        theme.palette.text.primary
-                                    : // letter-color mode: darken/lighten to stay readable
-                                        adjustColorForContrast(color, theme.palette.background.default);
+                                contrastText(model.fillPalette[covering.annotation.accession])
+                            : isMatchingReference
+                                ? // the dot sits on the faint reference-match wash, which is
+                                    // the theme's background with a little of its text color in it
+                                    theme.palette.text.primary
+                                : tiles
+                                    ? // on top of a colored tile, or on the background where the
+                                        // scheme gives that cell no color
+                                        contrastText(color)
+                                    : bgColor || !color
+                                        ? // plain background, uncolored letters
+                                            theme.palette.text.primary
+                                        : // letter-color mode: darken/lighten to stay readable
+                                            adjustColorForContrast(color, theme.palette.background.default);
                         ctx.fillText(isMatchingReference ? '.' : letter, x + halfColWidth, textY);
                     }
                 }

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

@@ -1 +1 @@
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package/dist/components/msa/renderMSAMouseover.js

@@ -1,12 +1,7 @@
-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)';
+import { clickColor, hoverColor, multiRowHoverColor } from '../overlayColors.js';
+import { renderPersistentHighlights } from './renderHighlights.js';
 export function renderMouseover({ ctx, model, theme, }) {
-    const { mouseCol, colWidth, msaCanvasWidth: width, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, highResScaleFactor, referenceRowIndex, hoveredRowIndices, highlightedColumnRuns, } = model;
+    const { mouseCol, colWidth, msaCanvasWidth: width, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, highResScaleFactor, hoveredRowIndices, } = model;
     ctx.resetTransform();
     ctx.clearRect(0, 0, width * highResScaleFactor, height * highResScaleFactor);
     ctx.scale(highResScaleFactor, highResScaleFactor);
@@ -18,28 +13,7 @@ export function renderMouseover({ ctx, model, theme, }) {
     const colBand = (index) => {
         ctx.fillRect(index * colWidth + scrollX, 0, colWidth, height);
     };
-    // the reference row (relativeTo) stays lit, as does every tip under a hovered
-    // tree node
-    if (referenceRowIndex !== undefined) {
-        ctx.fillStyle = referenceColor;
-        rowBand(referenceRowIndex);
-    }
-    ctx.fillStyle = multiRowHoverColor;
-    for (const rowIndex of hoveredRowIndices) {
-        rowBand(rowIndex);
-    }
-    // each contiguous run of highlighted columns draws as one filled, bordered
-    // band, so a domain/motif highlight stays visible over the alignment
-    ctx.lineWidth = 2;
-    for (const { start, end } of highlightedColumnRuns) {
-        const x = start * colWidth + scrollX;
-        const w = (end - start + 1) * colWidth;
-        ctx.fillStyle = highlightColumnsFill;
-        ctx.fillRect(x, 0, w, height);
-        ctx.strokeStyle = highlightColumnsBorder;
-        ctx.strokeRect(x, 0, w, height);
-    }
-    renderHighlights({
+    renderPersistentHighlights({
         ctx,
         model,
         theme,
@@ -48,6 +22,11 @@ export function renderMouseover({ ctx, model, theme, }) {
         width,
         height,
     });
+    // every tip under a hovered tree node stays lit
+    ctx.fillStyle = multiRowHoverColor;
+    for (const rowIndex of hoveredRowIndices) {
+        rowBand(rowIndex);
+    }
     ctx.fillStyle = hoverColor;
     if (mouseCol !== undefined) {
         colBand(mouseCol);