react-msaview 6.5.0 → 8.0.0

package/dist/components/tree/renderTreeCanvas.js

@@ -1,15 +1,46 @@
-import { calcDepthToLeaf, forEachDescendant, forEachLink, } from '../../hierarchy.js';
+import { calcDepthToLeaf, nodeCoveringRows } 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;
+import { drawHighlightLabel, highlightLabelHeight, highlightRowFill, } from '../msa/renderHighlights.js';
+import { bracketBarWidth, bracketGap } from './cladeBrackets.js';
 const radius = 2.5;
 const d = radius * 2;
-// whether a node's row-center y falls within the block being drawn, padded by
-// extendBounds so bubbles/labels/triangles straddling the edge still render
-function inYBlock(y, offsetY, by) {
-    return y > offsetY - extendBounds && y < offsetY + by + extendBounds;
+// How far outside a block a node's row-center can sit and still draw into it: a
+// collapsed triangle reaches 0.42 rows each way, a tip label an em, and a
+// highlight label its whole box. Five pixels clipped all three at block edges.
+function blockPad(model) {
+    return Math.max(model.rowHeight, highlightLabelHeight);
+}
+// whether a node's row-center y falls within the block being drawn, padded so
+// bubbles/labels/triangles straddling the edge still render
+function inYBlock(y, offsetY, by, pad) {
+    return y > offsetY - pad && y < offsetY + by + pad;
+}
+/**
+ * Every node whose subtree reaches into the block, skipping the subtrees that
+ * do not. A subtree's leaves are one contiguous run of rows, recorded by
+ * clusterLayout as xMin/xMax, so a block of a 200k-tip tree visits a few dozen
+ * nodes.
+ *
+ * A link out of a visited node is drawn even when its child is pruned, so a
+ * branch crossing the block stays visible.
+ */
+function forEachNodeInBlock(root, offsetY, by, pad, cb) {
+    const top = offsetY - pad;
+    const bottom = offsetY + by + pad;
+    const stack = [root];
+    while (stack.length > 0) {
+        const node = stack.pop();
+        if (node.xMax < top || node.xMin > bottom) {
+            continue;
+        }
+        cb(node);
+        if (node.children) {
+            for (const child of node.children) {
+                stack.push(child);
+            }
+        }
+    }
 }
 // Calculate node x-coordinate for both phylogram (with branch lengths) and
 // cladogram (topology only) modes. tipX is the pixel x the tips sit at.
@@ -27,33 +58,44 @@ export function getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) {
     return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * tipX;
 }
 function renderTree({ offsetY, ctx, model, theme, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
-    const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
+    const { hierarchy, showBranchLenEffective: showBranchLen, blockSize, branchColors, } = model;
     const by = blockSizeYOverride ?? blockSize;
-    ctx.strokeStyle = theme.palette.text.primary;
-    forEachLink(hierarchy, (source, target) => {
+    const defaultStroke = theme.palette.text.primary;
+    ctx.strokeStyle = defaultStroke;
+    forEachNodeInBlock(hierarchy, offsetY, by, blockPad(model), source => {
         const sy = source.x;
-        const ty = target.x;
-        const tx = getNodeX(target, showBranchLen, tipX, maxDepthToLeaf);
         const sx = getNodeX(source, showBranchLen, tipX, maxDepthToLeaf);
-        if (tx === undefined || sx === undefined) {
+        if (sx === undefined || !source.children) {
             return;
         }
-        const y1 = Math.min(sy, ty);
-        const y2 = Math.max(sy, ty);
-        // 1d line intersection to check if line crosses block at all, this is an
-        // optimization that allows us to skip drawing most tree links outside the
-        // block
-        if (offsetY + by >= y1 && y2 >= offsetY) {
-            ctx.beginPath();
-            ctx.moveTo(sx, sy);
-            ctx.lineTo(sx, ty);
-            ctx.lineTo(tx, ty);
-            ctx.stroke();
+        for (const target of source.children) {
+            const ty = target.x;
+            const tx = getNodeX(target, showBranchLen, tipX, maxDepthToLeaf);
+            if (tx === undefined) {
+                continue;
+            }
+            const y1 = Math.min(sy, ty);
+            const y2 = Math.max(sy, ty);
+            // 1d line intersection to check if line crosses block at all, this is an
+            // optimization that allows us to skip drawing most tree links outside the
+            // block
+            if (offsetY + by >= y1 && y2 >= offsetY) {
+                // the edge belongs to the child, whose id the branch channel colors
+                if (branchColors) {
+                    ctx.strokeStyle = branchColors.get(target.data.id) ?? defaultStroke;
+                }
+                ctx.beginPath();
+                ctx.moveTo(sx, sy);
+                ctx.lineTo(sx, ty);
+                ctx.lineTo(tx, ty);
+                ctx.stroke();
+            }
         }
     });
+    ctx.strokeStyle = defaultStroke;
 }
 function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, }) {
-    const { hierarchy, showBranchLenEffective: showBranchLen, blockSize, rowHeight, fontSize, marginLeft: ml, } = model;
+    const { hierarchy, showBranchLenEffective: showBranchLen, blockSize, rowHeight, fontSize, marginLeft: ml, branchColors, } = model;
     // nothing collapsed is the common case, and the traversal below visits every
     // node in the tree on every block of every redraw
     if (collapsedSet.size === 0) {
@@ -61,12 +103,12 @@ function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX,
     }
     const by = blockSizeYOverride ?? blockSize;
     const halfHeight = Math.max(2, rowHeight * 0.42);
-    forEachDescendant(hierarchy, node => {
+    forEachNodeInBlock(hierarchy, offsetY, by, blockPad(model), node => {
         const { id, name } = node.data;
         if (collapsedSet.has(id)) {
             const apexX = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf);
             const y = node.x;
-            const inBlock = inYBlock(y, offsetY, by);
+            const inBlock = inYBlock(y, offsetY, by, blockPad(model));
             // in cladogram mode the hidden tips align at the right edge, otherwise use
             // the branch-length extent recorded in the model's hierarchy getter
             const baseX = showBranchLen ? (node.collapsedTipXFar ?? tipX) : tipX;
@@ -76,7 +118,7 @@ function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX,
                 ctx.lineTo(baseX, y - halfHeight);
                 ctx.lineTo(baseX, y + halfHeight);
                 ctx.closePath();
-                ctx.fillStyle = theme.palette.action.disabled;
+                ctx.fillStyle = branchColors?.get(id) ?? theme.palette.action.disabled;
                 ctx.fill();
                 ctx.strokeStyle = theme.palette.text.primary;
                 ctx.stroke();
@@ -106,10 +148,10 @@ function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX,
 }
 // the bubbles are click targets whether or not they are painted, so this pass
 // always runs and `draw` only decides whether it also strokes the circles
-function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, draw, }) {
+function renderNodeBubbles({ ctx, theme, clickMap, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, draw, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride ?? blockSize;
-    forEachDescendant(hierarchy, node => {
+    forEachNodeInBlock(hierarchy, offsetY, by, blockPad(model), node => {
         const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf);
         if (x === undefined) {
             return;
@@ -117,11 +159,13 @@ function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf
         const { data } = node;
         const y = node.x;
         const { id, name } = data;
-        if (node.height >= 1 && inYBlock(y, offsetY, by)) {
+        if (node.height >= 1 && inYBlock(y, offsetY, by, blockPad(model))) {
             const isCollapsed = collapsedSet.has(id);
             if (draw) {
-                ctx.strokeStyle = 'black';
-                ctx.fillStyle = isCollapsed ? 'black' : 'white';
+                ctx.strokeStyle = theme.palette.text.primary;
+                ctx.fillStyle = isCollapsed
+                    ? theme.palette.text.primary
+                    : theme.palette.background.default;
                 ctx.beginPath();
                 ctx.arc(x, y, radius, 0, 2 * Math.PI);
                 ctx.fill();
@@ -143,12 +187,38 @@ function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf
         }
     });
 }
+// The label a newick file puts on an internal node, which is where a bootstrap
+// or posterior support value lands: ((A,B)95,(C,D)80);. withId falls back to the
+// path-derived id for an unnamed node, so a node whose name is its id has no
+// label of its own and an ungated pass prints node-0-1-1 across the tree.
+function renderNodeLabels({ ctx, theme, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
+    const { hierarchy, showBranchLenEffective: showBranchLen, blockSize, fontSize, } = model;
+    const by = blockSizeYOverride ?? blockSize;
+    const pad = blockPad(model);
+    setFontSize(ctx, Math.max(6, fontSize - 3));
+    ctx.fillStyle = theme.palette.text.primary;
+    ctx.textAlign = 'right';
+    forEachNodeInBlock(hierarchy, offsetY, by, pad, node => {
+        const { id, name } = node.data;
+        if (node.height < 1 || name === id) {
+            return;
+        }
+        const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf);
+        const y = node.x;
+        if (x !== undefined && inYBlock(y, offsetY, by, pad)) {
+            ctx.fillText(name, x - radius - 1, y - radius - 1);
+        }
+    });
+    ctx.textAlign = 'start';
+    setFontSize(ctx, fontSize);
+}
 function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, labelWidthScale, } = model;
+    const { fontSize, showBranchLenEffective: showBranchLen, tipLabelColors, blockSize, labelsAlignRight, drawTree, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, labelWidthScale, } = model;
     const by = blockSizeYOverride ?? blockSize;
     // labels only exist for leaves, which are laid out top to bottom, so take the
     // same slice the MSA renderer uses instead of walking every tip per block
     const visibleLeaves = getVisibleLeaves({ model, offsetY, blockSizeY: by });
+    const pad = blockPad(model);
     const emHeight = ctx.measureText('M').width;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -161,11 +231,11 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
     for (const node of visibleLeaves) {
         const { data: { name, id }, } = node;
         const y = node.x;
-        const displayName = treeMetadata[name]?.genome || name;
+        const displayName = model.rowDataOf(name)?.genome || name;
         // a collapsed clade is drawn as a triangle + tip count; suppress its leaf
         // label when the "name" is just the auto-generated internal-node id
         const isAnonymousCollapsed = collapsedSet.has(id) && name === id;
-        if (!isAnonymousCollapsed && inYBlock(y, offsetY, by)) {
+        if (!isAnonymousCollapsed && inYBlock(y, offsetY, by, pad)) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + fontSize / 4;
             let xp = 0;
@@ -176,7 +246,7 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
             const width = measured === undefined
                 ? ctx.measureText(displayName).width
                 : measured * labelWidthScale;
-            ctx.fillStyle = theme.palette.text.primary;
+            ctx.fillStyle = tipLabelColors?.get(name) ?? theme.palette.text.primary;
             if (labelsAlignRight) {
                 const smallPadding = 2;
                 const offset = treeAreaWidthMinusMargin - smallPadding;
@@ -218,23 +288,104 @@ 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
+// the first row of a set, as a loop: spreading into Math.min passes one
+// argument per row, and the ~125k argument limit throws RangeError on a set
+// covering the 230k-tip COVID tree
+function firstRow(rowIndices) {
+    let min = Infinity;
+    for (const index of rowIndices) {
+        if (index < min) {
+            min = index;
+        }
+    }
+    return min;
+}
+// the highlight mark of the `clades` layer: a translucent rectangle from the
+// clade's common ancestor to the right edge of the tree area, under the
+// branches. A clade spanning hundreds of rows crosses several blocks, so each
+// block draws the whole rectangle and the canvas takes the part that is its.
+function renderCladeHighlights({ ctx, model, offsetY, tipX, maxDepthToLeaf, blockSizeYOverride, }) {
+    const { resolvedClades, hierarchy, showBranchLenEffective: showBranchLen, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
+    const by = blockSizeYOverride ?? blockSize;
+    const right = treeAreaWidth - marginLeft;
+    for (const { rows, color, mark } of resolvedClades) {
+        if (mark !== 'highlight') {
+            continue;
+        }
+        const top = rows[0] * rowHeight;
+        const bottom = (rows[1] + 1) * rowHeight;
+        if (bottom < offsetY || top > offsetY + by) {
+            continue;
+        }
+        const node = nodeCoveringRows(hierarchy, top + rowHeight / 2, bottom - rowHeight / 2);
+        const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0;
+        ctx.fillStyle = color;
+        ctx.fillRect(x, top, right - x, bottom - top);
+    }
+}
+// the bar of the bracket mark, in the gutter `cladeGutterWidth` reserves at the
+// right of the tree area. The label beside it is DOM text on screen and a
+// <text> in the export, since the canvas layer has no rotation.
+function renderCladeBrackets({ ctx, model, theme, offsetY, blockSizeYOverride, }) {
+    const { resolvedClades, cladeGutterWidth, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
+    if (cladeGutterWidth === 0) {
+        return;
+    }
+    const by = blockSizeYOverride ?? blockSize;
+    const x = treeAreaWidth -
+        marginLeft -
+        cladeGutterWidth +
+        bracketGap +
+        bracketBarWidth / 2;
+    ctx.lineWidth = bracketBarWidth;
+    for (const { rows, mark, markColor } of resolvedClades) {
+        const top = rows[0] * rowHeight + 1;
+        const bottom = (rows[1] + 1) * rowHeight - 1;
+        if (mark !== 'bracket' || bottom < offsetY || top > offsetY + by) {
+            continue;
+        }
+        ctx.strokeStyle = markColor ?? theme.palette.text.primary;
+        ctx.beginPath();
+        ctx.moveTo(x, top);
+        ctx.lineTo(x, bottom);
+        ctx.stroke();
+    }
+    ctx.lineWidth = 1;
+    ctx.strokeStyle = theme.palette.text.primary;
+}
+// the `rowTint` encoding and the row sets of `highlights`, washed across the
+// tree area under the labels, with each set's label in the gutter at its first
+// row
 function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }) {
-    const { resolvedHighlights, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
+    const { resolvedHighlights, rowTints, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
     const by = blockSizeYOverride ?? blockSize;
+    const pad = blockPad(model);
+    const placed = [];
+    const fillRow = (index) => {
+        ctx.fillRect(-marginLeft, index * rowHeight, treeAreaWidth, rowHeight);
+    };
+    if (rowTints) {
+        const top = Math.max(0, Math.floor((offsetY - pad) / rowHeight));
+        const bottom = Math.min(rowTints.length - 1, Math.ceil((offsetY + by + pad) / rowHeight));
+        for (let index = top; index <= bottom; index++) {
+            const color = rowTints[index];
+            if (color) {
+                ctx.fillStyle = color;
+                fillRow(index);
+            }
+        }
+    }
     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);
+            if (inYBlock(index * rowHeight + rowHeight / 2, offsetY, by, pad)) {
+                fillRow(index);
             }
         }
-        const first = Math.min(...rowIndices);
+        const first = firstRow(rowIndices);
         if (label &&
             rowIndices.length &&
-            inYBlock(first * rowHeight, offsetY, by)) {
+            inYBlock(first * rowHeight, offsetY, by, pad)) {
             drawHighlightLabel({
                 ctx,
                 theme,
@@ -242,6 +393,8 @@ function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }
                 x: -marginLeft + 2,
                 y: first * rowHeight,
                 spanWidth: treeAreaWidth,
+                bounds: { min: -marginLeft, max: treeAreaWidth - marginLeft },
+                placed,
             });
         }
     }
@@ -249,7 +402,7 @@ function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
     // Defer the finish call until after all inserts are done
-    const { noTree, drawTree, drawNodeBubbles, highResScaleFactor, fontSize, showTreeText, marginLeft, 
+    const { noTree, drawTree, drawNodeBubbles, drawNodeLabels, highResScaleFactor, fontSize, showTreeText, marginLeft, 
     // eslint-disable-next-line  @typescript-eslint/no-unused-vars
     rowHeight: _rowHeight, // read so the draw autorun re-fires after a zoom change
      } = model;
@@ -270,6 +423,14 @@ 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);
+    renderCladeHighlights({
+        ctx,
+        model,
+        offsetY,
+        tipX,
+        maxDepthToLeaf,
+        blockSizeYOverride,
+    });
     renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride });
     setFontSize(ctx, fontSize);
     if (!noTree && drawTree) {
@@ -295,6 +456,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
         });
         renderNodeBubbles({
             ctx,
+            theme,
             offsetY,
             clickMap,
             model,
@@ -304,6 +466,17 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             collapsedSet,
             draw: drawNodeBubbles,
         });
+        if (drawNodeLabels) {
+            renderNodeLabels({
+                ctx,
+                theme,
+                offsetY,
+                model,
+                tipX,
+                maxDepthToLeaf,
+                blockSizeYOverride,
+            });
+        }
     }
     if (showTreeText) {
         renderTreeLabels({
@@ -318,6 +491,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             collapsedSet,
         });
     }
+    renderCladeBrackets({ ctx, model, theme, offsetY, blockSizeYOverride });
     // Finish the index so it's ready for queries
     clickMap?.finish();
 }

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

@@ -1 +1 @@
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package/dist/components/tree/renderTreeOverview.d.ts

@@ -0,0 +1,52 @@
+import type { MsaViewModel } from '../../model.ts';
+import type { RasterCanvas } from '../msa/msaRaster.ts';
+import type { RenderCtx } from '../renderCtx.ts';
+import type { Theme } from '@mui/material';
+interface OverviewArgs {
+    model: MsaViewModel;
+    ctx: RenderCtx;
+    theme: Theme;
+    width: number;
+    height: number;
+}
+/**
+ * The whole tree at the size of the overview band, with the clade highlights
+ * under it.
+ *
+ * A branch that moves less than a pixel on both axes is dropped. The 230k-tip
+ * COVID tree has 460k of them over a 120px band, and the ones landing on the
+ * pixel their parent already covers cost a path segment each and change no
+ * pixel; the test in renderTreeOverview.test.ts measures a 200k-tip tree.
+ */
+export declare function drawTreeOverview({ model, ctx, theme, width, height, }: OverviewArgs): void;
+/**
+ * A box across the overview around a run of tip rows: the focused subtree's
+ * extent, or the one a hovered pixel would focus.
+ */
+export declare function drawTreeOverviewBox({ model, ctx, color, rows, width, height, }: Omit<OverviewArgs, 'theme'> & {
+    color: string;
+    rows: [number, number];
+}): void;
+/**
+ * The overview as the figure carries it: the tree, the clade highlights and
+ * the focus box. The SVG export draws it straight onto a svgcanvas Context,
+ * and the live canvas blits `treeOverviewImage` in place of the first two.
+ */
+export declare function renderTreeOverview(args: OverviewArgs): void;
+/**
+ * The tree and its clade highlights on an offscreen canvas, drawn once per
+ * change of anything they depend on and blitted every frame after that. A
+ * 230k-branch tree takes hundreds of milliseconds to walk and cannot be redrawn
+ * as the focus box follows the pointer.
+ *
+ * Returns undefined where a canvas has no 2d context (jsdom), and the caller
+ * then draws the tree itself.
+ */
+export declare function treeOverviewImage({ model, theme, width, height, scale, }: {
+    model: MsaViewModel;
+    theme: Theme;
+    width: number;
+    height: number;
+    scale: number;
+}): RasterCanvas | undefined;
+export {};