react-msaview 7.0.0 → 8.0.0

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 {};

package/dist/components/tree/renderTreeOverview.js

@@ -0,0 +1,138 @@
+import { descendants } from '../../hierarchy.js';
+import { getNodeX } from './renderTreeCanvas.js';
+// the tree draws this far inside the band, so a box around the first or the
+// last row keeps both of its edges
+const pad = 1;
+function rowScale(numTips, height) {
+    const inner = height - pad * 2;
+    return (row) => pad + (row / numTips) * inner;
+}
+/**
+ * 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 function drawTreeOverview({ model, ctx, theme, width, height, }) {
+    const layout = model.treeOverviewLayout;
+    if (!layout) {
+        return;
+    }
+    const { root, numTips, maxDepthToLeaf, showBranchLen } = layout;
+    const innerWidth = width - pad * 2;
+    const rowY = rowScale(numTips, height);
+    const nodeX = (node) => pad + (getNodeX(node, showBranchLen, 1, maxDepthToLeaf) ?? 0) * innerWidth;
+    for (const { rows, color } of model.treeOverviewClades) {
+        ctx.fillStyle = color;
+        ctx.fillRect(0, rowY(rows[0]), width, rowY(rows[1] + 1) - rowY(rows[0]));
+    }
+    ctx.strokeStyle = theme.palette.text.primary;
+    ctx.beginPath();
+    for (const source of descendants(root)) {
+        if (!source.children) {
+            continue;
+        }
+        const sx = nodeX(source);
+        const sy = rowY(source.x);
+        for (const target of source.children) {
+            const tx = nodeX(target);
+            const ty = rowY(target.x);
+            if (Math.abs(tx - sx) < 1 && Math.abs(ty - sy) < 1) {
+                continue;
+            }
+            ctx.moveTo(sx, sy);
+            ctx.lineTo(sx, ty);
+            ctx.lineTo(tx, ty);
+        }
+    }
+    ctx.stroke();
+}
+/**
+ * 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 function drawTreeOverviewBox({ model, ctx, color, rows, width, height, }) {
+    const layout = model.treeOverviewLayout;
+    if (!layout) {
+        return;
+    }
+    const rowY = rowScale(layout.numTips, height);
+    const top = rowY(rows[0]);
+    ctx.strokeStyle = color;
+    ctx.strokeRect(0.5, top, width - 1, Math.max(2, rowY(rows[1] + 1) - top));
+}
+/**
+ * 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 function renderTreeOverview(args) {
+    drawTreeOverview(args);
+    const rows = args.model.treeOverviewFocusRows;
+    if (rows) {
+        drawTreeOverviewBox({
+            ...args,
+            rows,
+            color: args.theme.palette.text.primary,
+        });
+    }
+}
+const caches = new WeakMap();
+/**
+ * Everything the drawn tree depends on. `treeOverviewLayout` and
+ * `treeOverviewClades` are computed views, which recompute on every read
+ * outside a reaction, so the key holds the values behind them instead.
+ */
+function overviewKeys({ model, theme, width, height, scale, }) {
+    return [
+        model.data.tree,
+        model.data.msa,
+        model.currentAlignment,
+        model.collapsed.join(','),
+        JSON.stringify(model.clades),
+        model.showBranchLen,
+        width,
+        height,
+        scale,
+        theme.palette.text.primary,
+    ];
+}
+function makeCanvas(width, height) {
+    const canvas = typeof OffscreenCanvas !== 'undefined'
+        ? new OffscreenCanvas(width, height)
+        : typeof document !== 'undefined'
+            ? Object.assign(document.createElement('canvas'), { width, height })
+            : undefined;
+    const ctx = canvas?.getContext('2d');
+    return ctx && typeof ctx.stroke === 'function'
+        ? { canvas: canvas, ctx: ctx }
+        : undefined;
+}
+/**
+ * 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 function treeOverviewImage({ model, theme, width, height, scale, }) {
+    const keys = overviewKeys({ model, theme, width, height, scale });
+    const prev = caches.get(model);
+    if (prev && keys.every((key, i) => key === prev.keys[i])) {
+        return prev.canvas;
+    }
+    const made = makeCanvas(Math.max(1, Math.round(width * scale)), Math.max(1, Math.round(height * scale)));
+    if (made) {
+        made.ctx.scale(scale, scale);
+        drawTreeOverview({ model, ctx: made.ctx, theme, width, height });
+    }
+    const next = { keys, canvas: made?.canvas };
+    caches.set(model, next);
+    return next.canvas;
+}
+//# sourceMappingURL=renderTreeOverview.js.map

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

@@ -0,0 +1 @@
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package/dist/components/tree/useTreeHover.js

@@ -1,4 +1,4 @@
-import { useRef, useState } from 'react';
+import { useState } from 'react';
 import { ClickMapIndex } from './clickMap.js';
 /**
  * Owns hit-testing for one tree block: the spatial index the render pass fills
@@ -7,9 +7,7 @@ import { ClickMapIndex } from './clickMap.js';
  * 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 [clickMap] = useState(() => new ClickMapIndex());
     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

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

@@ -1 +1 @@
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+{"version":3,"file":"useTreeHover.js","sourceRoot":"","sources":["../../../src/components/tree/useTreeHover.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEhC,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAW7C;;;;;GAKG;AACH,MAAM,UAAU,YAAY,CAAC,EAC3B,KAAK,EACL,OAAO,GAIR;IACC,MAAM,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAC,GAAG,EAAE,CAAC,IAAI,aAAa,EAAE,CAAC,CAAA;IACtD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,EAAmB,CAAA;IAEzD,+EAA+E;IAC/E,uDAAuD;IACvD,SAAS,OAAO,CAAC,KAAuB;QACtC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,GAAG,OAAO,CAAA;QAC7C,MAAM,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC;YAC9B,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;SACZ,CAAC,CAAA;QACF,OAAO,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,CAAA;IAC3D,CAAC;IAED,SAAS,WAAW,CAAC,KAAuB;QAC1C,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;QAC5B,UAAU,CACR,KAAK;YACH,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE;YAC9D,CAAC,CAAC,SAAS,CACd,CAAA;QACD,2EAA2E;QAC3E,qDAAqD;QACrD,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACnC,KAAK,CAAC,WAAW,CACf,SAAS,EACT,KAAK,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS,CACvE,CAAA;IACH,CAAC;IAED,SAAS,YAAY;QACnB,UAAU,CAAC,SAAS,CAAC,CAAA;QACrB,KAAK,CAAC,kBAAkB,CAAC,SAAS,CAAC,CAAA;QACnC,KAAK,CAAC,WAAW,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,CAAA;AAClE,CAAC"}

package/dist/constants.d.ts

@@ -10,10 +10,14 @@ export declare const defaultHideGaps = true;
 export declare const defaultAllowedGappyness = 100;
 export declare const defaultSubFeatureRows = false;
 export declare const subFeatureRowHeight = 4;
+export declare const domainUnderlineHeight = 3;
 export declare const segmentFeatureTypes: Set<string>;
 export declare const segmentShades: string[];
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultScrollZoom = false;
+export declare const scrollZoomAxes: readonly ['both', 'horizontal', 'vertical'];
+export type ScrollZoomAxis = (typeof scrollZoomAxes)[number];
+export declare const defaultScrollZoomAxis: ScrollZoomAxis;
 export declare const minLetterRowHeight = 8;
 export declare const minLetterColWidth = 5;
 export declare const labelReferenceFontSize = 16;
@@ -30,5 +34,16 @@ export declare const defaultTreeWidth = 300;
 export declare const defaultShowBranchLen = true;
 export declare const defaultDrawTree = true;
 export declare const defaultDrawNodeBubbles = true;
+export declare const defaultDrawNodeLabels = false;
+export declare const defaultShowTreeOverview = false;
+export declare const defaultOverviewHeight = 120;
 export declare const maxNeighborJoiningRows = 500;
+export declare const rowTintAlpha = 0.25;
+export declare const cladeHighlightColor = "#fff3c4";
+export declare const cladeHighlightAlpha = 0.6;
 export declare const maxInlineSnapshotBytes = 50000;
+export declare const rowPanelHeaderHeight = 56;
+export declare const treeScaleBarHeight = 22;
+export declare const defaultFeaturePanelWidth = 200;
+export declare const msaOverlayZIndex = 1000;
+export declare const legendZIndex: number;

package/dist/constants.js

@@ -5,21 +5,21 @@ export const defaultHeight = 550;
 export const defaultScrollX = 0;
 export const defaultScrollY = 0;
 export const defaultCurrentAlignment = 0;
-// Annotations are loaded on purpose -- a gff filehandle, a file picked in the
-// dialog -- so they are drawn unless the reader has said otherwise. Since only
-// the "no" is stored, a shared link with the overlay hidden reopens hidden, and
-// one that never mentions it opens showing whatever annotations it carries.
+// Only a hidden overlay is stored, so a link that never mentions it opens
+// showing its annotations.
 export const defaultShowDomains = true;
 export const defaultShowDomainLegend = true;
 export const defaultHideGaps = true;
 export const defaultAllowedGappyness = 100;
 export const defaultSubFeatureRows = false;
-// row height for each stacked feature when subFeatureRows is on
+// height of one sub-row when subFeatureRows is on, unless the row has more
+// lanes than fit at this height (see renderBoxFeatureCanvasBlock)
 export const subFeatureRowHeight = 4;
-// Feature types that are ordinal *segments* of a single transcript (exons and
-// the like) rather than categorical domains. Their identity is their position,
-// so the overlay alternates two shades to mark boundaries and labels them by
-// number, instead of assigning every one a distinct hue + legend row.
+// height of the bar the overlay draws under a row in letter-color mode
+export const domainUnderlineHeight = 3;
+// Feature types that are ordinal segments of one transcript. The overlay
+// alternates two shades across them and labels them by number, where a domain
+// type gets its own hue and legend row.
 export const segmentFeatureTypes = new Set([
     'exon',
     'CDS',
@@ -32,9 +32,14 @@ export const segmentFeatureTypes = new Set([
 export const segmentShades = ['#9fb6d4', '#d4dcea'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
+// Which cell dimensions a wheel zoom scales. 'horizontal' holds the row height,
+// which fixes the label and letter font size while the columns compress.
+// 'vertical' does the reverse.
+export const scrollZoomAxes = ['both', 'horizontal', 'vertical'];
+export const defaultScrollZoomAxis = 'both';
 // Cell size floors for drawing residue letters and tree labels. Below these a
-// 500px block holds thousands of glyphs, and fillText -- which no sprite atlas
-// beats, measured -- dominates every zoom frame.
+// 500px block holds thousands of glyphs, and fillText dominates every zoom
+// frame. A sprite atlas measured slower.
 export const minLetterRowHeight = 8;
 export const minLetterColWidth = 5;
 // Tree labels are measured once at this size and scaled to the current font
@@ -58,17 +63,38 @@ export const defaultTreeWidth = 300;
 export const defaultShowBranchLen = true;
 export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;
-// Neighbor joining refuses above this many rows. The distance matrix is O(n^2*L)
-// and the join loop O(n^3), both on the main thread with no progress and no
-// cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about seventy.
-// See agent-docs/ideas/neighbor-joining-scaling.md for why the RapidNJ fix is a
-// real algorithm change rather than a port, and why capping is the honest answer
-// -- NJ on thousands of sequences is the wrong tool however fast it runs.
+export const defaultDrawNodeLabels = false;
+export const defaultShowTreeOverview = false;
+export const defaultOverviewHeight = 120;
+// Neighbor joining does not run above this many rows. The distance matrix is
+// O(n^2*L) and the join loop O(n^3), both on the main thread with no progress
+// and no cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about
+// seventy. See agent-docs/ideas/neighbor-joining-scaling.md.
 export const maxNeighborJoiningRows = 500;
-// The largest inline document the snapshot carries. Past this a pasted or
-// locally-opened file stays in the live model and leaves the snapshot, since a
-// session or a shared URL holding megabytes of sequence is not a link anyone
-// can send. `unshareableData` reads the same number, so what the viewer warns
-// about and what the snapshot drops cannot drift apart.
+// The opacity a `rowTint` encoding draws its scale's color at, so the residues
+// under the wash stay readable. A color the producer already gave an alpha
+// keeps it.
+export const rowTintAlpha = 0.25;
+// The fill a `clades` record with the `highlight` mark draws behind its rows,
+// and the opacity a producer's own color takes when it carries none.
+export const cladeHighlightColor = '#fff3c4';
+export const cladeHighlightAlpha = 0.6;
+// The largest inline document the snapshot carries. A larger pasted or
+// locally-opened file stays in the live model and out of the snapshot, keeping
+// shared URLs sendable. `unshareableData` warns using the same number.
 export const maxInlineSnapshotBytes = 50_000;
+// Height of the band the `rowPanels` headers draw in, above the strips in the
+// top area beside the tree ruler and the minimap. A panel wider than the band
+// is tall writes its header across, where it has more room.
+export const rowPanelHeaderHeight = 56;
+// Height of the branch-length scale bar above the tree.
+export const treeScaleBarHeight = 22;
+// Width of a `features` row panel that names none, wide enough for a gene
+// neighborhood of a few arrows to read.
+export const defaultFeaturePanelWidth = 200;
+// The alignment's overlay canvas draws the mouseover, the persisted highlights
+// and the row tints over the residues, and the legend key floats above that,
+// so a tint reaching the top right corner leaves the key readable.
+export const msaOverlayZIndex = 1000;
+export const legendZIndex = msaOverlayZIndex + 1;
 //# sourceMappingURL=constants.js.map

package/dist/constants.js.map

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

@@ -1,10 +1,11 @@
 /**
- * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
- * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
- * overlay with one feature per exon — we generate evenly spaced HSL hues so
- * every key still gets a distinct, stable color instead of running off the end
- * of the palette.
+ * Creates a map from keys to colors. `palette` names the colors to take in
+ * order, such as the list a scale asked for by name; without it the keys take
+ * the ggplot palette of their own size. Beyond the colors available — a
+ * gene-structure overlay with one feature per exon, or nine keys on an
+ * eight-color palette — every key gets an evenly spaced HSL hue instead, so no
+ * two keys share a color.
  */
-export declare function createPaletteMap(keys: string[]): {
+export declare function createPaletteMap(keys: string[], palette?: readonly string[]): {
     [k: string]: string;
 };

package/dist/createPaletteMap.js

@@ -1,17 +1,18 @@
 import { colord } from 'colord';
 import palettes from './ggplotPalettes.js';
 /**
- * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
- * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
- * overlay with one feature per exon — we generate evenly spaced HSL hues so
- * every key still gets a distinct, stable color instead of running off the end
- * of the palette.
+ * Creates a map from keys to colors. `palette` names the colors to take in
+ * order, such as the list a scale asked for by name; without it the keys take
+ * the ggplot palette of their own size. Beyond the colors available — a
+ * gene-structure overlay with one feature per exon, or nine keys on an
+ * eight-color palette — every key gets an evenly spaced HSL hue instead, so no
+ * two keys share a color.
  */
-export function createPaletteMap(keys) {
+export function createPaletteMap(keys, palette) {
     const n = keys.length;
-    if (n <= palettes.length) {
-        const palette = palettes[n - 1];
-        return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+    const colors = palette ?? palettes[n - 1];
+    if (colors && n <= colors.length) {
+        return Object.fromEntries(keys.map((key, i) => [key, colors[i]]));
     }
     return Object.fromEntries(keys.map((key, i) => [
         key,

package/dist/createPaletteMap.js.map

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package/dist/element.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Registers a custom element that renders MSAViewer, for pages with no React.
+ * Attributes: msa-url, tree-url, gff-url, color-scheme, height, hide-header,
+ * theme, tree-area-width and reference-row. Properties: msa, tree and gff text, highlights,
+ * columnTracks and residueMappings. Events: cell-hover, cell-click and
+ * viewport-change, each with the MSAViewer callback's value as detail.
+ *
+ * Inside a <nightingale-manager>, the element registers with it and speaks its
+ * protocol: it follows the display-start, display-end and highlight attributes
+ * the manager writes, and reports its own range and hovered residue as change
+ * events. Positions are residues of reference-row, or columns without one.
+ */
+export declare function defineMsaElement(tagName?: string): CustomElementConstructor;