react-msaview 6.5.0 → 7.0.0

package/dist/components/tracks/drawTracks.js

@@ -1,5 +1,6 @@
 import { columnLogoStack } from '../../sequenceLogo.js';
 import { setFontSize } from '../../setFontSize.js';
+import { contrastTextFn } from '../../util.js';
 import { visibleColRange } from '../msa/visibleColRange.js';
 export function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
@@ -26,14 +27,48 @@ export function barTrackValues(model, trackId) {
         ? model.propertyConservation
         : model.conservation;
 }
-export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, bgColor, textColor, colWidth, rowHeight, offsetX, blockSize, }) {
+// An arc's apex scales with how far it reaches, so a short helix stays shallow
+// and a long-range pair sweeps the full track height. The scale is sqrt rather
+// than linear because a contact map's spans are heavily skewed towards short
+// ones, which linear scaling flattens into a smear along the baseline.
+export function drawArcs({ ctx, arcs, color, colWidth, trackHeight, offsetX, blockSize, }) {
+    if (!arcs?.length) {
+        return;
+    }
+    const { xStart, xEnd } = visibleColRange({
+        offsetX,
+        blockWidth: blockSize,
+        colWidth,
+    });
+    let maxSpan = 1;
+    for (const arc of arcs) {
+        maxSpan = Math.max(maxSpan, arc.end - arc.start);
+    }
+    // a full-height apex would put the stroke half outside the track
+    const apexRoom = trackHeight - 1;
+    ctx.lineWidth = 1;
+    for (const arc of arcs) {
+        // an arc that spans the block draws even though neither foot is inside it
+        if (arc.end < xStart || arc.start > xEnd) {
+            continue;
+        }
+        const x1 = (arc.start + 0.5) * colWidth;
+        const x2 = (arc.end + 0.5) * colWidth;
+        const apex = apexRoom * Math.sqrt((arc.end - arc.start) / maxSpan);
+        ctx.strokeStyle = arc.color ?? color;
+        ctx.beginPath();
+        ctx.moveTo(x1, trackHeight);
+        ctx.quadraticCurveTo((x1 + x2) / 2, trackHeight - 2 * apex, x2, trackHeight);
+        ctx.stroke();
+    }
+}
+export function drawTextTrackContent({ ctx, data, colorScheme, contrastText, bgColor, drawLetters, colWidth, rowHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,
         colWidth,
     });
     const str = data?.slice(xStart, xEnd);
-    const drawLetters = rowHeight >= 10 && colWidth >= rowHeight / 2;
     for (let i = 0; str && i < str.length; i++) {
         const letter = str[i];
         const upper = letter.toUpperCase();
@@ -44,13 +79,53 @@ export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, b
             ctx.fillRect(x, 0, colWidth, rowHeight);
         }
         if (drawLetters) {
-            // a letter on a colored tile needs the tile's contrast color; otherwise it
-            // sits on the plain background and takes the theme's text color
-            ctx.fillStyle = fill ? (contrastScheme[upper] ?? 'black') : textColor;
-            ctx.fillText(letter, x + colWidth / 2, rowHeight / 2 + 1);
+            // a letter on a colored tile needs that tile's contrast color; otherwise
+            // it sits on the plain background and takes the theme's text color
+            ctx.fillStyle = contrastText(fill);
+            ctx.fillText(letter, x + colWidth / 2, rowHeight / 2);
         }
     }
 }
+// Column numbers every `step` columns, with a tick under each. The step is the
+// smallest 1/2/5 x 10^n that leaves room for a label, so a zoom changes how many
+// numbers appear rather than crowding them.
+export function rulerStep(colWidth, minPixels = 55) {
+    let step = 1;
+    const mantissas = [1, 2, 5];
+    for (let i = 0; step * colWidth < minPixels; i++) {
+        step = mantissas[i % 3] * 10 ** Math.floor(i / 3);
+    }
+    return step;
+}
+const RULER_FONT_SIZE = 10;
+const TICK_HEIGHT = 4;
+export function drawColumnRuler({ ctx, numColumns, label, textColor, colWidth, trackHeight, offsetX, blockSize, }) {
+    const { xStart, xEnd } = visibleColRange({
+        offsetX,
+        blockWidth: blockSize,
+        colWidth,
+    });
+    const step = rulerStep(colWidth);
+    const end = Math.min(xEnd, numColumns);
+    setFontSize(ctx, RULER_FONT_SIZE);
+    ctx.textAlign = 'center';
+    ctx.textBaseline = 'alphabetic';
+    ctx.fillStyle = textColor;
+    ctx.strokeStyle = textColor;
+    ctx.lineWidth = 1;
+    for (let col = Math.ceil(xStart / step) * step; col < end; col += step) {
+        const text = label(col);
+        if (text === undefined) {
+            continue;
+        }
+        const x = (col + 0.5) * colWidth;
+        ctx.fillText(text, x, trackHeight - TICK_HEIGHT - 2);
+        ctx.beginPath();
+        ctx.moveTo(x, trackHeight - TICK_HEIGHT);
+        ctx.lineTo(x, trackHeight);
+        ctx.stroke();
+    }
+}
 // Cap height as a fraction of the font size. Every logo letter is scaled from
 // one reference font size to the height its frequency earns, and that scale is
 // only right if we know how tall the glyph actually draws. Measuring per letter
@@ -116,9 +191,9 @@ export function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColo
  * canvas blocks and the SVG export -- draw into the same coordinate space, and
  * adding a track kind means a `kind`, a draw function above, and a case here.
  */
-export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }) {
-    const { blockSize, bgColor, colWidth, colStats, colorScheme: modelColorScheme, fontSize, rowHeight, alphabetMaxBits, highResScaleFactor, } = model;
-    const { id, kind, height: trackHeight, barColor, customColorScheme, data, } = track.model;
+export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme, blockSizeXOverride, highResScaleFactorOverride, }) {
+    const { blockSize, bgColor, colWidth, colStats, colorScheme: modelColorScheme, fontSize, rowHeight, showMsaLetters, alphabetMaxBits, highResScaleFactor, } = model;
+    const { id, kind, height: trackHeight, barColor, arcColor, arcs, customColorScheme, data, } = track.model;
     const blockSizeX = blockSizeXOverride ?? blockSize;
     const k = highResScaleFactorOverride ?? highResScaleFactor;
     const textColor = theme.palette.text.primary;
@@ -138,6 +213,18 @@ export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme,
             });
             break;
         }
+        case 'arc': {
+            drawArcs({
+                ctx,
+                arcs,
+                color: arcColor ?? theme.palette.text.primary,
+                colWidth,
+                trackHeight,
+                offsetX,
+                blockSize: blockSizeX,
+            });
+            break;
+        }
         case 'logo': {
             drawSequenceLogo({
                 ctx,
@@ -152,16 +239,40 @@ export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme,
             });
             break;
         }
+        case 'ruler': {
+            const { relativeTo, numColumns } = model;
+            drawColumnRuler({
+                ctx,
+                numColumns,
+                // numbered by the reference row's own residues when the alignment is
+                // drawn relative to one, which is what the rest of the view counts in
+                label: relativeTo
+                    ? col => {
+                        const pos = model.visibleColToSeqPosOneBased(relativeTo, col);
+                        return pos === undefined ? undefined : `${pos}`;
+                    }
+                    : col => `${col + 1}`,
+                textColor,
+                colWidth,
+                trackHeight,
+                offsetX,
+                blockSize: blockSizeX,
+            });
+            break;
+        }
         case 'text': {
             ctx.textAlign = 'center';
+            ctx.textBaseline = 'middle';
             setFontSize(ctx, fontSize);
             drawTextTrackContent({
                 ctx,
                 data,
                 colorScheme: customColorScheme ?? modelColorScheme,
-                contrastScheme,
+                contrastText: contrastTextFn(theme),
                 bgColor,
-                textColor,
+                // a text track is one alignment row tall, so it shows letters exactly
+                // when the alignment does
+                drawLetters: showMsaLetters,
                 colWidth,
                 rowHeight,
                 offsetX,
@@ -176,7 +287,7 @@ export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme,
  * Every turned-on track stacked top to bottom, for the SVG export. The live
  * view draws the same content one canvas block at a time -- see TrackBlocks.
  */
-export function renderAllTracks({ model, ctx, offsetX, contrastScheme, theme, blockSizeXOverride, highResScaleFactorOverride, }) {
+export function renderAllTracks({ model, ctx, offsetX, theme, blockSizeXOverride, highResScaleFactorOverride, }) {
     let currentY = 0;
     for (const track of model.turnedOnTracks) {
         drawTrackBlock({
@@ -186,7 +297,6 @@ export function renderAllTracks({ model, ctx, offsetX, contrastScheme, theme, bl
             offsetX,
             offsetY: currentY,
             theme,
-            contrastScheme,
             blockSizeXOverride,
             highResScaleFactorOverride,
         });

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package/dist/components/tree/TreeCanvas.js

@@ -5,10 +5,9 @@ import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { useWheelScroll } from '../../useWheelScroll.js';
 import { referenceColor, treeHoverColor } from '../overlayColors.js';
 import TreeCanvasBlock from './TreeCanvasBlock.js';
-import { padding } from './renderTreeCanvas.js';
 const TreeCanvas = observer(function ({ model }) {
     const ref = useRef(null);
-    const { treeWidth, height, blocksY, treeAreaWidth, scrollY } = model;
+    const { height, blocksY, treeAreaWidth, scrollY } = model;
     const onScrollY = useCallback((d) => {
         model.doScrollY(d);
     }, [model]);
@@ -48,7 +47,7 @@ const TreeCanvas = observer(function ({ model }) {
         }, style: {
             height,
             position: 'relative',
-            width: treeWidth + padding,
+            width: treeAreaWidth,
         } },
         React.createElement("div", { style: {
                 position: 'absolute',

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvas.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpE,OAAO,eAAe,MAAM,sBAAuB,CAAA;AAInD,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzD,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAErE,MAAM,YAAY,GAAG,gBAAgB,CAAC;QACpC,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBACnB,MAAM,EACJ,SAAS,EACT,aAAa,EAAE,CAAC,EAChB,MAAM,EAAE,CAAC,EACT,OAAO,EAAE,EAAE,EACX,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,GAClB,GAAG,KAAK,CAAA;gBACT,GAAG,CAAC,cAAc,EAAE,CAAA;gBACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;gBAEzB,oEAAoE;gBACpE,6DAA6D;gBAC7D,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;oBAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,EAAE,EAAE,CAAC,EAAE,SAAS,CAAC,CAAA;gBACvD,CAAC,CAAA;gBAED,IAAI,iBAAiB,KAAK,SAAS,EAAE,CAAC;oBACpC,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;oBAC9B,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBAC5B,CAAC;gBAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;gBAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;oBACtC,OAAO,CAAC,KAAK,CAAC,CAAA;gBAChB,CAAC;gBACD,IACE,QAAQ,KAAK,SAAS;oBACtB,QAAQ,KAAK,iBAAiB;oBAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;oBACD,OAAO,CAAC,QAAQ,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;QACD,KAAK,EAAE,aAAa;QACpB,MAAM;QACN,IAAI,EAAE,CAAC,KAAK,CAAC;KACd,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,KAAK,CAAC,EAAE;YACpB,KAAK,CAAC,cAAc,EAAE,CAAA;QACxB,CAAC,EACD,KAAK,EAAE;YACL,MAAM;YACN,QAAQ,EAAE,UAAU;YACpB,KAAK,EAAE,aAAa;SACrB;QAID,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,SAAS,EAAE,cAAc,OAAO,KAAK;gBACrC,UAAU,EAAE,WAAW;aACxB,IAEA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACpB,oBAAC,eAAe,IAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,GAAI,CAC9D,CAAC,CACE;QACN,gCACE,GAAG,EAAE,YAAY,EACjB,KAAK,EAAE,aAAa,EACpB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,KAAK,EAAE,aAAa;gBACpB,MAAM;gBACN,MAAM,EAAE,IAAI;gBACZ,aAAa,EAAE,MAAM;aACtB,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/tree/TreeCanvasBlock.js

@@ -6,7 +6,7 @@ import { createPortal } from 'react-dom';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import TreeBranchMenu from './TreeBranchMenu.js';
 import TreeNodeMenu from './TreeNodeMenu.js';
-import { padding, renderTreeCanvas } from './renderTreeCanvas.js';
+import { renderTreeCanvas } from './renderTreeCanvas.js';
 import { useTreeHover } from './useTreeHover.js';
 const useStyles = makeStyles()(theme => ({
     tooltip: {
@@ -37,7 +37,9 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const [nodeMenu, setNodeMenu] = useState();
     const { clickMap, hovered, hitTest, onMouseMove, onMouseLeave } = useTreeHover({ model, offsetY });
     const { treeAreaWidth, blockSize, highResScaleFactor } = model;
-    const width = treeAreaWidth + padding;
+    // TreePanel clips to treeAreaWidth, so anything wider is backing store the
+    // viewer never sees -- it was 600px of it per block, at dpr squared
+    const width = treeAreaWidth;
     const height = blockSize;
     const canvasWidth = width * highResScaleFactor;
     const canvasHeight = height * highResScaleFactor;

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAA;AAExC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAA;AAIhD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,QAAQ,EAAE,OAAO;QACjB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,KAAK;QACb,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;QACxC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;QACjC,OAAO,EAAE,SAAS;QAClB,YAAY,EAAE,CAAC;QACf,QAAQ,EAAE,EAAE;QACZ,UAAU,EAAE,QAAQ;QACpB,QAAQ,EAAE,GAAG;QACb,QAAQ,EAAE,QAAQ;QAClB,YAAY,EAAE,UAAU;KACzB;IACD,KAAK,EAAE;QACL,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,GAAG;QACX,UAAU,EAAE,iBAAiB;KAC9B;CACF,CAAC,CAAC,CAAA;AASH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAY,CAAA;IACxD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAY,CAAA;IACpD,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,GAC7D,YAAY,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAA;IAElC,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC9D,2EAA2E;IAC3E,oEAAoE;IACpE,MAAM,KAAK,GAAG,aAAa,CAAA;IAC3B,MAAM,MAAM,GAAG,SAAS,CAAA;IAExB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAChD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAA;YAC9C,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,CAAC;KACxC,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO;QACZ,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IAEV,OAAO,CACL;QACG,UAAU,CAAC,CAAC,CAAC,CACZ,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,aAAa,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,YAAY,IACX,IAAI,EAAE,QAAQ,EACd,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,WAAW,CAAC,SAAS,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,EAC5D,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,WAAW,CAAC,KAAK,CAAC,CAAA;YACpB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;gBAC5B,IAAI,KAAK,EAAE,CAAC;oBACV,MAAM,IAAI,GAAG;wBACX,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,EAAE,EAAE,KAAK,CAAC,EAAE;wBACZ,IAAI,EAAE,KAAK,CAAC,IAAI;qBACjB,CAAA;oBACD,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;wBACjB,aAAa,CAAC,IAAI,CAAC,CAAA;oBACrB,CAAC;yBAAM,CAAC;wBACN,WAAW,CAAC,IAAI,CAAC,CAAA;oBACnB,CAAC;gBACH,CAAC;YACH,CAAC,GACD;QAGD,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAC5B,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,OAAO,CAAC,IAAI;gBAClB,GAAG,EAAE,OAAO,CAAC,IAAI;gBACjB,KAAK,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;gBAClC,MAAM,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;aACpC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAKP,OAAO;YACN,CAAC,CAAC,YAAY,CACV,6BACE,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,CAAC,OAAO,GAAG,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,OAAO,GAAG,EAAE,EAAE,IAE/D,OAAO,CAAC,IAAI,CACT,EACN,QAAQ,CAAC,IAAI,CACd;YACH,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/tree/TreeRuler.js

@@ -1,11 +1,21 @@
 import React from 'react';
+import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { scaleBarLength } from './scaleBar.js';
+const BAR_HEIGHT = 22;
 // The gutter above the tree panel. It spans the resize handle too, so whatever
 // follows it in the top row starts exactly where the alignment canvas does --
-// MainArea has TreePanel + VerticalResizeHandle before the alignment.
+// MainArea has TreePanel + VerticalResizeHandle before the alignment. A
+// phylogram fills it with a scale bar: without one the branch lengths are drawn
+// to a scale nothing states.
 const TreeRuler = observer(({ model }) => {
-    const { treeAreaWidth, resizeHandleWidth } = model;
-    return (React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth + resizeHandleWidth } }));
+    const { treeAreaWidth, resizeHandleWidth, marginLeft, pxPerBranchLength } = model;
+    const theme = useTheme();
+    const width = treeAreaWidth + resizeHandleWidth;
+    const bar = scaleBarLength(pxPerBranchLength, treeAreaWidth - marginLeft * 2);
+    return (React.createElement("div", { style: { flexShrink: 0, width } }, bar ? (React.createElement("svg", { width: width, height: BAR_HEIGHT, style: { display: 'block' }, color: theme.palette.text.primary },
+        React.createElement("text", { x: marginLeft, y: BAR_HEIGHT - 9, fontSize: 10, fill: "currentColor" }, bar.label),
+        React.createElement("path", { d: `M${marginLeft} ${BAR_HEIGHT - 7} v6 h${bar.px} v-6`, fill: "none", stroke: "currentColor" }))) : null));
 });
 export default TreeRuler;
 //# sourceMappingURL=TreeRuler.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeRuler.js","sourceRoot":"","sources":["../../../src/components/tree/TreeRuler.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,eAAe,CAAA;AAI9C,MAAM,UAAU,GAAG,EAAE,CAAA;AAErB,+EAA+E;AAC/E,8EAA8E;AAC9E,wEAAwE;AACxE,gFAAgF;AAChF,6BAA6B;AAC7B,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,aAAa,EAAE,iBAAiB,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACvE,KAAK,CAAA;IACP,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,KAAK,GAAG,aAAa,GAAG,iBAAiB,CAAA;IAC/C,MAAM,GAAG,GAAG,cAAc,CAAC,iBAAiB,EAAE,aAAa,GAAG,UAAU,GAAG,CAAC,CAAC,CAAA;IAE7E,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,IACjC,GAAG,CAAC,CAAC,CAAC,CACL,6BACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,UAAU,EAClB,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,EAC3B,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO;QAEjC,8BACE,CAAC,EAAE,UAAU,EACb,CAAC,EAAE,UAAU,GAAG,CAAC,EACjB,QAAQ,EAAE,EAAE,EACZ,IAAI,EAAC,cAAc,IAElB,GAAG,CAAC,KAAK,CACL;QACP,8BACE,CAAC,EAAE,IAAI,UAAU,IAAI,UAAU,GAAG,CAAC,QAAQ,GAAG,CAAC,EAAE,MAAM,EACvD,IAAI,EAAC,MAAM,EACX,MAAM,EAAC,cAAc,GACrB,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

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

@@ -3,7 +3,6 @@ import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { ClickMapIndex } from './clickMap.ts';
 import type { Theme } from '@mui/material';
-export declare const padding = 600;
 export declare function getNodeX(node: HierarchyNode, showBranchLen: boolean, tipX: number, maxDepthToLeaf: number): number | undefined;
 export declare function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }: {
     model: MsaViewModel;

package/dist/components/tree/renderTreeCanvas.js

@@ -1,15 +1,45 @@
-import { calcDepthToLeaf, forEachDescendant, forEachLink, } from '../../hierarchy.js';
+import { calcDepthToLeaf } 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';
 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 -- clusterLayout
+ * records the run as xMin/xMax -- so a block of a 200k-tip tree visits a few
+ * dozen nodes instead of every one of them, three times over.
+ *
+ * A link out of a visited node is still drawn even when the child it reaches is
+ * pruned, which is what keeps a branch that crosses the block from vanishing.
+ */
+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.
@@ -30,25 +60,30 @@ function renderTree({ offsetY, ctx, model, theme, tipX, maxDepthToLeaf, blockSiz
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
     const by = blockSizeYOverride ?? blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
-    forEachLink(hierarchy, (source, target) => {
+    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) {
+                ctx.beginPath();
+                ctx.moveTo(sx, sy);
+                ctx.lineTo(sx, ty);
+                ctx.lineTo(tx, ty);
+                ctx.stroke();
+            }
         }
     });
 }
@@ -61,12 +96,12 @@ 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;
@@ -109,7 +144,7 @@ function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX,
 function renderNodeBubbles({ ctx, 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;
@@ -117,7 +152,7 @@ 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';
@@ -149,6 +184,7 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
     // 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';
@@ -165,7 +201,7 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
         // 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;
@@ -223,18 +259,20 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
 function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }) {
     const { resolvedHighlights, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
     const by = blockSizeYOverride ?? blockSize;
+    const pad = blockPad(model);
+    const placed = [];
     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)) {
+            if (inYBlock(y + rowHeight / 2, offsetY, by, pad)) {
                 ctx.fillRect(-marginLeft, y, treeAreaWidth, rowHeight);
             }
         }
         const first = Math.min(...rowIndices);
         if (label &&
             rowIndices.length &&
-            inYBlock(first * rowHeight, offsetY, by)) {
+            inYBlock(first * rowHeight, offsetY, by, pad)) {
             drawHighlightLabel({
                 ctx,
                 theme,
@@ -242,6 +280,8 @@ function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }
                 x: -marginLeft + 2,
                 y: first * rowHeight,
                 spanWidth: treeAreaWidth,
+                bounds: { min: -marginLeft, max: treeAreaWidth - marginLeft },
+                placed,
             });
         }
     }

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

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

@@ -0,0 +1,10 @@
+/**
+ * A round branch-length step and its width in pixels: the largest 1/2/5 x 10^n
+ * substitutions-per-site that fits in `maxPx`, aiming at about half of it.
+ * Returns undefined in cladogram mode, where the x-positions carry no length.
+ */
+export declare function scaleBarLength(pxPerUnit: number, maxPx: number): {
+    step: number;
+    px: number;
+    label: string;
+} | undefined;