react-msaview 5.6.1 → 5.6.3

package/dist/components/tree/TreeCanvasBlock.js

@@ -1,11 +1,11 @@
-import React, { useEffect, useRef, useState } from 'react';
+import React, { useState } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import TreeBranchMenu from "./TreeBranchMenu.js";
 import TreeNodeMenu from "./TreeNodeMenu.js";
-import { ClickMapIndex } from "./clickMap.js";
 import { padding, renderTreeCanvas } from "./renderTreeCanvas.js";
+import { useTreeHover } from "./useTreeHover.js";
 import { useCanvasAutorun } from "../../useCanvasAutorun.js";
 const useStyles = makeStyles()(theme => ({
     tooltip: {
@@ -22,73 +22,33 @@ const useStyles = makeStyles()(theme => ({
         overflow: 'hidden',
         textOverflow: 'ellipsis',
     },
+    hover: {
+        position: 'absolute',
+        pointerEvents: 'none',
+        zIndex: 100,
+        background: 'rgba(0,0,0,0.1)',
+    },
 }));
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const { classes } = useStyles();
     const theme = useTheme();
-    const clickMap = useRef(new ClickMapIndex());
-    const mouseoverRef = useRef(null);
     const [branchMenu, setBranchMenu] = useState();
-    const [toggleNodeMenu, setToggleNodeMenu] = useState();
-    const [hoverElt, setHoverElt] = useState();
-    const [tooltipInfo, setTooltipInfo] = useState();
+    const [nodeMenu, setNodeMenu] = useState();
+    const { clickMap, hovered, hitTest, onMouseMove, onMouseLeave } = useTreeHover({ model, offsetY });
     const { scrollY, treeAreaWidth, blockSize, highResScaleFactor } = model;
     const width = treeAreaWidth + padding;
     const height = blockSize;
-    const w2 = width * highResScaleFactor;
-    const h2 = height * highResScaleFactor;
     const ref = useCanvasAutorun(ctx => {
         ctx.resetTransform();
-        ctx.clearRect(0, 0, w2, h2);
+        ctx.clearRect(0, 0, width * highResScaleFactor, height * highResScaleFactor);
         renderTreeCanvas({
             ctx,
             model,
             offsetY,
-            clickMap: clickMap.current,
+            clickMap,
             theme,
         });
-    }, [model, blockSize, highResScaleFactor, treeAreaWidth, offsetY, theme]);
-    useEffect(() => {
-        const ctx = mouseoverRef.current?.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.clearRect(0, 0, treeAreaWidth + padding, blockSize);
-        ctx.translate(0, -offsetY);
-        // Highlight tree element being directly hovered
-        if (hoverElt) {
-            const { minX, maxX, minY, maxY } = hoverElt;
-            ctx.fillStyle = 'rgba(0,0,0,0.1)';
-            ctx.fillRect(minX, minY, maxX - minX, maxY - minY);
-        }
-    }, [hoverElt, offsetY, blockSize, treeAreaWidth]);
-    function hoverBranchClickMap(event) {
-        const x = event.nativeEvent.offsetX;
-        const y = event.nativeEvent.offsetY;
-        const [entry] = clickMap.current.search({
-            minX: x,
-            maxX: x + 1,
-            minY: y + offsetY,
-            maxY: y + 1 + offsetY,
-        });
-        return entry?.branch
-            ? { ...entry, x: event.clientX, y: event.clientY }
-            : undefined;
-    }
-    function hoverNameClickMap(event) {
-        const x = event.nativeEvent.offsetX;
-        const y = event.nativeEvent.offsetY;
-        const [entry] = clickMap.current.search({
-            minX: x,
-            maxX: x + 1,
-            minY: y + offsetY,
-            maxY: y + 1 + offsetY,
-        });
-        return entry && !entry.branch
-            ? { ...entry, x: event.clientX, y: event.clientY }
-            : undefined;
-    }
+    }, [model, clickMap, offsetY, theme]);
     const style = {
         width,
         height,
@@ -97,71 +57,40 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
         position: 'absolute',
     };
     return (React.createElement(React.Fragment, null,
-        branchMenu?.id ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => {
+        branchMenu ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => {
                 setBranchMenu(undefined);
             } })) : null,
-        toggleNodeMenu?.id ? (React.createElement(TreeNodeMenu, { node: toggleNodeMenu, model: model, onClose: () => {
-                setToggleNodeMenu(undefined);
+        nodeMenu ? (React.createElement(TreeNodeMenu, { node: nodeMenu, model: model, onClose: () => {
+                setNodeMenu(undefined);
             } })) : null,
-        React.createElement("canvas", { width: w2, height: h2, style: style, onMouseMove: event => {
-                if (!ref.current) {
-                    return;
-                }
-                const hoveredLeaf = hoverNameClickMap(event);
-                const hoveredBranch = hoverBranchClickMap(event);
-                const hoveredAny = hoveredLeaf || hoveredBranch;
-                ref.current.style.cursor = hoveredAny ? 'pointer' : 'default';
-                setHoverElt(hoveredLeaf); // Only show direct hover highlight for leaf nodes
-                // Set tooltip info
-                if (hoveredAny) {
-                    setTooltipInfo({
-                        name: hoveredAny.name,
+        React.createElement("canvas", { ref: ref, width: width * highResScaleFactor, height: height * highResScaleFactor, style: { ...style, cursor: hovered ? 'pointer' : 'default' }, onMouseMove: event => {
+                onMouseMove(event);
+            }, onMouseLeave: () => {
+                onMouseLeave();
+            }, onClick: event => {
+                const entry = hitTest(event);
+                if (entry) {
+                    const menu = {
                         x: event.clientX,
                         y: event.clientY,
-                    });
-                }
-                else {
-                    setTooltipInfo(undefined);
-                }
-                // Handle tree node hover for multi-row highlighting
-                if (hoveredAny) {
-                    model.setHoveredTreeNode(hoveredAny.id);
-                    // For leaf nodes, also set single row highlight for backward compatibility
-                    if (hoveredLeaf?.name) {
-                        const rowIndex = model.rowNamesSet.get(hoveredLeaf.name);
-                        if (rowIndex !== undefined) {
-                            model.setMousePos(undefined, rowIndex);
-                        }
+                        id: entry.id,
+                        name: entry.name,
+                    };
+                    if (entry.branch) {
+                        setBranchMenu(menu);
+                    }
+                    else {
+                        setNodeMenu(menu);
                     }
                 }
-                else {
-                    // Clear all highlighting when not hovering over any tree node
-                    model.setHoveredTreeNode(undefined);
-                    model.setMousePos(undefined, undefined);
-                }
-            }, onClick: event => {
-                const { clientX: x, clientY: y } = event;
-                const data = hoverBranchClickMap(event);
-                if (data?.id) {
-                    setBranchMenu({ x, y, id: data.id, name: data.name });
-                }
-                const data2 = hoverNameClickMap(event);
-                if (data2?.id) {
-                    setToggleNodeMenu({ ...data2, x, y });
-                }
-            }, onMouseLeave: () => {
-                setHoverElt(undefined);
-                setTooltipInfo(undefined);
-                // Clear all highlighting when leaving tree area
-                model.setHoveredTreeNode(undefined);
-                model.setMousePos(undefined, undefined);
-            }, ref: ref }),
-        React.createElement("canvas", { style: {
-                ...style,
-                pointerEvents: 'none',
-                zIndex: 100,
-            }, width: width, height: height, ref: mouseoverRef }),
-        tooltipInfo ? (React.createElement("div", { className: classes.tooltip, style: { left: tooltipInfo.x + 12, top: tooltipInfo.y + 12 } }, tooltipInfo.name)) : null));
+            } }),
+        hovered && !hovered.branch ? (React.createElement("div", { className: classes.hover, style: {
+                left: hovered.minX,
+                top: hovered.minY + scrollY,
+                width: hovered.maxX - hovered.minX,
+                height: hovered.maxY - hovered.minY,
+            } })) : null,
+        hovered ? (React.createElement("div", { className: classes.tooltip, style: { left: hovered.clientX + 12, top: hovered.clientY + 12 } }, hovered.name)) : null));
 });
 export default TreeCanvasBlock;
 //# sourceMappingURL=TreeCanvasBlock.js.map

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

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package/dist/components/tree/renderTreeCanvas.d.ts

@@ -1,8 +1,10 @@
 import type { ClickMapIndex } from './clickMap.ts';
+import type { HierarchyNode } from '../../hierarchy.ts';
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
 export declare const padding = 600;
+export declare function getNodeX(node: HierarchyNode, showBranchLen: boolean, maxBranchLen: number, maxDepthToLeaf: number): number | undefined;
 export declare function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
     offsetY: number;
     ctx: RenderCtx;

package/dist/components/tree/renderTreeCanvas.js

@@ -1,5 +1,6 @@
 import { calcDepthToLeaf, forEachDescendant, forEachLink, } from "../../hierarchy.js";
 import { setFontSize } from "../../setFontSize.js";
+import { getVisibleLeaves } from "../getVisibleLeaves.js";
 export const padding = 600;
 const extendBounds = 5;
 const radius = 2.5;
@@ -13,7 +14,7 @@ function inYBlock(y, offsetY, by) {
 // For cladograms: x = (maxDepthToLeaf - nodeDepthToLeaf) / maxDepthToLeaf * maxWidth
 // This positions: leaves at maxWidth (rightmost), root at 0 (leftmost), internal nodes proportionally in between
 // Matches ape's: xx <- max(xx) - xx (where xx is depth from each node to tips)
-function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
+export function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
     if (showBranchLen) {
         return node.len;
     }
@@ -134,17 +135,25 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen,
     });
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, labelWidthMap, collapsed, } = model;
+    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, collapsed, } = model;
+    // 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: blockSizeYOverride ?? model.blockSize,
+    });
     const by = blockSizeYOverride ?? blockSize;
     const emHeight = ctx.measureText('M').width;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
         ctx.setLineDash([1, 3]);
+        ctx.strokeStyle = theme.palette.text.primary;
     }
     else {
         ctx.textAlign = 'start';
     }
-    for (const node of leaves) {
+    for (const node of visibleLeaves) {
         const { data: { name, id }, } = node;
         const y = node.x;
         const displayName = treeMetadata[name]?.genome || name;
@@ -164,6 +173,9 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBran
                 const smallPadding = 2;
                 const offset = treeAreaWidthMinusMargin - smallPadding;
                 if (drawTree && !noTree) {
+                    // beginPath is load-bearing: without it every leader line re-strokes
+                    // all the ones before it, which is quadratic in the label count
+                    ctx.beginPath();
                     ctx.moveTo(xp + radius + 2, y);
                     ctx.lineTo(offset - smallPadding - width, y);
                     ctx.stroke();

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

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

@@ -0,0 +1,24 @@
+import type React from 'react';
+import { ClickMapIndex } from './clickMap.ts';
+import type { ClickEntry } from './clickMap.ts';
+import type { MsaViewModel } from '../../model.ts';
+export interface TreeHoverTarget extends ClickEntry {
+    clientX: number;
+    clientY: number;
+}
+/**
+ * Owns hit-testing for one tree block: the spatial index the render pass fills
+ * in, the entry currently under the pointer, and the model hover state that the
+ * MSA panel mirrors. The index is a render artifact rather than display state, so
+ * it lives in a ref; everything the component draws comes back as plain state.
+ */
+export declare function useTreeHover({ model, offsetY, }: {
+    model: MsaViewModel;
+    offsetY: number;
+}): {
+    clickMap: ClickMapIndex;
+    hovered: TreeHoverTarget | undefined;
+    hitTest: (event: React.MouseEvent) => ClickEntry | undefined;
+    onMouseMove: (event: React.MouseEvent) => void;
+    onMouseLeave: () => void;
+};

package/dist/components/tree/useTreeHover.js

@@ -0,0 +1,44 @@
+import { useRef, useState } from 'react';
+import { ClickMapIndex } from "./clickMap.js";
+/**
+ * Owns hit-testing for one tree block: the spatial index the render pass fills
+ * in, the entry currently under the pointer, and the model hover state that the
+ * MSA panel mirrors. The index is a render artifact rather than display state, so
+ * it lives in a ref; everything the component draws comes back as plain state.
+ */
+export function useTreeHover({ model, offsetY, }) {
+    const clickMapRef = useRef(null);
+    clickMapRef.current ??= new ClickMapIndex();
+    const clickMap = clickMapRef.current;
+    const [hovered, setHovered] = useState();
+    // leaf labels win over the branch/bubble targets they overlap, so a click on a
+    // name opens the node menu rather than the branch menu
+    function hitTest(event) {
+        const x = event.nativeEvent.offsetX;
+        const y = event.nativeEvent.offsetY + offsetY;
+        const entries = clickMap.search({
+            minX: x,
+            maxX: x + 1,
+            minY: y,
+            maxY: y + 1,
+        });
+        return entries.find(entry => !entry.branch) ?? entries[0];
+    }
+    function onMouseMove(event) {
+        const entry = hitTest(event);
+        setHovered(entry
+            ? { ...entry, clientX: event.clientX, clientY: event.clientY }
+            : undefined);
+        // hovering an internal node highlights every tip below it; hovering a leaf
+        // label additionally drives the single-row highlight
+        model.setHoveredTreeNode(entry?.id);
+        model.setMousePos(undefined, entry && !entry.branch ? model.rowNamesSet.get(entry.name) : undefined);
+    }
+    function onMouseLeave() {
+        setHovered(undefined);
+        model.setHoveredTreeNode(undefined);
+        model.setMousePos(undefined, undefined);
+    }
+    return { clickMap, hovered, hitTest, onMouseMove, onMouseLeave };
+}
+//# sourceMappingURL=useTreeHover.js.map

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

@@ -0,0 +1 @@
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package/dist/hierarchy.js

@@ -225,17 +225,23 @@ export function collapsedSubtreeLengthExtent(node) {
 // x. Memoizes onto node.depthToLeaf since the layout walks the tree repeatedly.
 // See https://github.com/emmanuelparadis/ape/blob/master/R/plot.phylo.R
 export function calcDepthToLeaf(node) {
-    const nodes = descendants(node);
-    for (let i = nodes.length - 1; i >= 0; i--) {
-        const n = nodes[i];
-        if (n.depthToLeaf === undefined) {
-            let maxDepth = 0;
-            if (n.children) {
-                for (const child of n.children) {
-                    maxDepth = Math.max(maxDepth, 1 + child.depthToLeaf);
+    // the memo check has to guard the traversal, not just the arithmetic: the tree
+    // renderer asks for the depth of every node on every pass, and re-walking each
+    // subtree makes that quadratic (a 5000-tip caterpillar tree spent >1s per draw
+    // here). Once a node is memoized so are all of its descendants.
+    if (node.depthToLeaf === undefined) {
+        const nodes = descendants(node);
+        for (let i = nodes.length - 1; i >= 0; i--) {
+            const n = nodes[i];
+            if (n.depthToLeaf === undefined) {
+                let maxDepth = 0;
+                if (n.children) {
+                    for (const child of n.children) {
+                        maxDepth = Math.max(maxDepth, 1 + child.depthToLeaf);
+                    }
                 }
+                n.depthToLeaf = maxDepth;
             }
-            n.depthToLeaf = maxDepth;
         }
     }
     return node.depthToLeaf;

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package/dist/index.d.ts

@@ -5,4 +5,5 @@ export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export type { MSAFormat, MSAParserType } from 'msa-parsers';
 export type { HierarchyNode } from './hierarchy.ts';
 export type { InterProScanResults } from './launchInterProScan.ts';
-export type { Accession, BasicTrack, BasicTrackModel, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, } from './types.ts';
+export type { ColumnCounts } from './columnCounts.ts';
+export type { Accession, BasicTrack, BasicTrackModel, DomainBand, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, TidyDomainAnnotation, } from './types.ts';

package/dist/model/msaModel.js

@@ -1,5 +1,6 @@
 import { types } from '@jbrowse/mobx-state-tree';
 import { defaultBgColor, defaultColorSchemeName, defaultShowColumnStats, } from "../constants.js";
+import { stripDefault } from "../stripDefault.js";
 const msaFormats = ['stockholm', 'a3m', 'fasta', 'emf', 'clustal'];
 /**
  * #stateModel MSAModel
@@ -11,18 +12,18 @@ export function MSAModelF() {
          * #property
          * draw MSA tiles with a background color
          */
-        bgColor: types.stripDefault(types.boolean, defaultBgColor),
+        bgColor: stripDefault(types.boolean, defaultBgColor),
         /**
          * #property
          * default color scheme name
          */
-        colorSchemeName: types.stripDefault(types.string, defaultColorSchemeName),
+        colorSchemeName: stripDefault(types.string, defaultColorSchemeName),
         /**
          * #property
          * show a per-column statistics tooltip (consensus, conservation, gaps,
          * residue distribution) while hovering the alignment
          */
-        showColumnStats: types.stripDefault(types.boolean, defaultShowColumnStats),
+        showColumnStats: stripDefault(types.boolean, defaultShowColumnStats),
         /**
          * #property
          * force the MSA data to be parsed as a specific format instead of relying

package/dist/model/msaModel.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.js

@@ -1,5 +1,6 @@
 import { types } from '@jbrowse/mobx-state-tree';
 import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawTree, defaultLabelsAlignRight, defaultShowBranchLen, defaultTreeAreaWidth, defaultTreeWidth, } from "../constants.js";
+import { stripDefault } from "../stripDefault.js";
 /**
  * #stateModel Tree
  */
@@ -9,47 +10,47 @@ export function TreeModelF() {
         /**
          * #property
          */
-        drawLabels: types.stripDefault(types.boolean, defaultDrawLabels),
+        drawLabels: stripDefault(types.boolean, defaultDrawLabels),
         /**
          * #property
          * right-align the labels
          */
-        labelsAlignRight: types.stripDefault(types.boolean, defaultLabelsAlignRight),
+        labelsAlignRight: stripDefault(types.boolean, defaultLabelsAlignRight),
         /**
          * #property
          * width of the area the tree is drawn in, px
          */
-        treeAreaWidth: types.stripDefault(types.number, defaultTreeAreaWidth),
+        treeAreaWidth: stripDefault(types.number, defaultTreeAreaWidth),
         /**
          * #property
          * width of the tree within the treeArea, px. automatically synced to
          * fit within treeAreaWidth
          */
-        treeWidth: types.stripDefault(types.number, defaultTreeWidth),
+        treeWidth: stripDefault(types.number, defaultTreeWidth),
         /**
          * #property
          * use "branch length" e.g. evolutionary distance to draw tree branch
          * lengths. if false, the layout is a "cladogram" that does not take into
          * account evolutionary distances
          */
-        showBranchLen: types.stripDefault(types.boolean, defaultShowBranchLen),
+        showBranchLen: stripDefault(types.boolean, defaultShowBranchLen),
         /**
          * #property
          * draw tree, boolean
          */
-        drawTree: types.stripDefault(types.boolean, defaultDrawTree),
+        drawTree: stripDefault(types.boolean, defaultDrawTree),
         /**
          * #property
          * draw clickable node bubbles on the tree
          */
-        drawNodeBubbles: types.stripDefault(types.boolean, defaultDrawNodeBubbles),
+        drawNodeBubbles: stripDefault(types.boolean, defaultDrawNodeBubbles),
         /**
          * #property
          * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
          * instead of using a fixed width. useful when there is no tree, so the
          * label gutter isn't padded out to the default 400px
          */
-        autoTreeAreaWidth: types.stripDefault(types.boolean, false),
+        autoTreeAreaWidth: stripDefault(types.boolean, false),
     })
         .actions(self => ({
         /**

package/dist/model/treeModel.js.map

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