react-msaview 8.4.1 → 9.1.0

package/dist/components/tree/cladeBrackets.js

@@ -1,3 +1,4 @@
+import { labelFitFontSize } from '../../constants.js';
 import { measureTextCanvas } from '../../measureTextCanvas.js';
 // The bar of the bracket mark and the space around it, in px.
 export const bracketBarWidth = 3;
@@ -10,37 +11,37 @@ export function cladeInGutter(clade) {
     return (clade.mark === 'bracket' || (clade.mark === 'highlight' && !!clade.label));
 }
 /** the pixel height of the rows a clade covers */
-export function cladeHeight(clade, rowHeight) {
+function cladeHeight(clade, rowHeight) {
     return (clade.rows[1] - clade.rows[0] + 1) * rowHeight;
 }
 /**
  * Whether a label reads across the rows. It does where they are taller than the
  * font, and runs up the bar where they are not.
  */
-export function cladeLabelHorizontal(clade, rowHeight, fontSize) {
+function cladeLabelHorizontal(clade, rowHeight, fontSize) {
     return cladeHeight(clade, rowHeight) >= fontSize;
 }
 /** the px between the left edge of the gutter and the label's own column */
-export function cladeLabelOffset(clade) {
+function cladeLabelOffset(clade) {
     return clade.mark === 'bracket'
         ? bracketGap + bracketBarWidth + bracketGap
         : bracketGap;
 }
 /**
  * The gutter the bracket mark needs at the right of the tree area: the bar plus
- * the widest label at the tree font, zero where no clade draws there, and at
- * most maxCladeGutterWidth.
+ * the widest label read across at labelFitFontSize, zero where no clade draws
+ * there, and at most maxCladeGutterWidth. The records size it, so a zoom, a
+ * collapse or a focus leaves it as it is, and a renderer clips a label that
+ * outgrows it.
  */
-export function cladeGutterWidth({ clades, rowHeight, fontSize, }) {
+export function cladeGutterWidth(clades) {
     let widest = 0;
     for (const clade of clades) {
         if (!cladeInGutter(clade)) {
             continue;
         }
         const text = clade.label
-            ? cladeLabelHorizontal(clade, rowHeight, fontSize)
-                ? measureTextCanvas(clade.label, fontSize)
-                : fontSize
+            ? measureTextCanvas(clade.label, labelFitFontSize)
             : 0;
         widest = Math.max(widest, cladeLabelOffset(clade) + text + bracketGap);
     }
@@ -48,4 +49,34 @@ export function cladeGutterWidth({ clades, rowHeight, fontSize, }) {
     // the measurement here sized the gutter for
     return Math.min(maxCladeGutterWidth, Math.ceil(widest));
 }
+/**
+ * The box each gutter label takes, in unscrolled tree-area px: from the
+ * label's column to the right edge of the gutter, across the clade's rows. The
+ * live view sets DOM text in it, and the SVG export a `<text>`.
+ */
+export function cladeLabelBoxes(model) {
+    const { resolvedClades, cladeGutterWidth, rowHeight, effectiveTreeAreaWidth, fontSize, } = model;
+    const gutterLeft = effectiveTreeAreaWidth - cladeGutterWidth;
+    return cladeGutterWidth === 0
+        ? []
+        : resolvedClades.flatMap((clade, index) => {
+            const { label, markColor, rows } = clade;
+            if (!label || !cladeInGutter(clade)) {
+                return [];
+            }
+            const left = gutterLeft + cladeLabelOffset(clade);
+            return [
+                {
+                    key: `${rows[0]}-${rows[1]}-${index}`,
+                    label,
+                    color: markColor,
+                    left,
+                    top: rows[0] * rowHeight,
+                    width: effectiveTreeAreaWidth - left - bracketGap,
+                    height: cladeHeight(clade, rowHeight),
+                    horizontal: cladeLabelHorizontal(clade, rowHeight, fontSize),
+                },
+            ];
+        });
+}
 //# sourceMappingURL=cladeBrackets.js.map

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

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

@@ -1,5 +1,7 @@
 export interface ClickEntry {
     name: string;
+    /** the text a tip label draws, which may be cut short */
+    label?: string;
     id: string;
     branch?: boolean;
     minX: number;

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

@@ -1 +1 @@
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+{"version":3,"file":"clickMap.js","sourceRoot":"","sources":["../../../src/components/tree/clickMap.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,UAAU,CAAA;AAqB/B,uEAAuE;AACvE,+EAA+E;AAC/E,6DAA6D;AAC7D,MAAM,OAAO,aAAa;IAChB,QAAQ,GAAoB,IAAI,CAAA;IAChC,OAAO,GAAiB,EAAE,CAAA;IAElC,KAAK;QACH,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,MAAM,CAAC,KAAiB;QACtB,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAC1B,CAAC;IAED,MAAM;QACJ,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;QACtB,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,QAAQ,GAAG,IAAI,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACjD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;gBACjC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,CAAA;YACnE,CAAC;YACD,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAA;QACxB,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAQ;QACb,OAAO,CACL,IAAI,CAAC,QAAQ;YACX,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;aAC/C,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CACpC,CAAA;IACH,CAAC;CACF"}

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

@@ -0,0 +1,8 @@
+/**
+ * the longest prefix of `text`, plus an ellipsis, that measures at most
+ * `room` px
+ */
+export declare function ellipsize(measure: (text: string) => number, text: string, room: number): {
+    text: string;
+    width: number;
+};

package/dist/components/tree/ellipsize.js

@@ -0,0 +1,20 @@
+const ellipsis = '…';
+/**
+ * the longest prefix of `text`, plus an ellipsis, that measures at most
+ * `room` px
+ */
+export function ellipsize(measure, text, room) {
+    const width = measure(text);
+    if (width <= room) {
+        return { text, width };
+    }
+    for (let n = Math.floor((text.length * room) / width); n > 0; n--) {
+        const truncated = text.slice(0, n).trimEnd() + ellipsis;
+        const truncatedWidth = measure(truncated);
+        if (truncatedWidth <= room) {
+            return { text: truncated, width: truncatedWidth };
+        }
+    }
+    return { text: '', width: 0 };
+}
+//# sourceMappingURL=ellipsize.js.map

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

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

@@ -4,6 +4,7 @@ import { getVisibleLeaves } from '../getVisibleLeaves.js';
 import { drawHighlightLabel, highlightLabelHeight, highlightRowFill, } from '../msa/renderHighlights.js';
 import { referenceColor } from '../overlayColors.js';
 import { bracketBarWidth, bracketGap } from './cladeBrackets.js';
+import { ellipsize } from './ellipsize.js';
 const radius = 2.5;
 const d = radius * 2;
 // How far outside a block a node's row-center can sit and still draw into it: a
@@ -20,7 +21,7 @@ function inYBlock(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
+ * layoutTree 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
@@ -219,7 +220,8 @@ function renderNodeLabels({ ctx, theme, offsetY, model, tipX, maxDepthToLeaf, bl
     setFontSize(ctx, fontSize);
 }
 function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, tipLabelColors, blockSize, labelsAlignRight, drawTree, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, labelWidthScale, } = model;
+    const { fontSize, showBranchLenEffective: showBranchLen, tipLabelColors, blockSize, labelsAlignRight, drawTree, treeAreaWidthMinusMargin, marginLeft, noTree, } = model;
+    const treeDrawn = drawTree && !noTree;
     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
@@ -245,19 +247,18 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
             // fontSize/4 below the row center, the baseline the alignment letters
             // share
             const yp = y + fontSize / 4;
-            let xp = 0;
-            if (!noTree) {
-                xp = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0;
-            }
-            const measured = labelWidthMap.get(name);
-            const width = measured === undefined
-                ? ctx.measureText(displayName).width
-                : measured * labelWidthScale;
+            const xp = treeDrawn
+                ? (getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0)
+                : 0;
+            const fit = (room) => ellipsize(text => ctx.measureText(text).width, displayName, room);
+            // a label cut to nothing still gets a click box the font size wide
+            const boxWidth = (width) => Math.max(width, fontSize);
             ctx.fillStyle = tipLabelColors?.get(name) ?? theme.palette.text.primary;
             if (labelsAlignRight) {
                 const smallPadding = 2;
                 const offset = treeAreaWidthMinusMargin - smallPadding;
-                if (drawTree && !noTree) {
+                const { text, width } = fit(offset - (treeDrawn ? xp + radius + 2 + smallPadding : 0));
+                if (treeDrawn) {
                     // 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();
@@ -265,29 +266,32 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
                     ctx.lineTo(offset - smallPadding - width, y);
                     ctx.stroke();
                 }
-                ctx.fillText(displayName, offset, yp);
+                ctx.fillText(text, offset, yp);
                 // everything here is drawn under translate(marginLeft), so the click box
                 // has to be the text's own right edge in that same space -- taking
-                // treeAreaWidth instead put the target smallPadding off the label
+                // the tree area width instead put the target smallPadding off the label
                 const labelRight = offset + marginLeft;
                 clickMap?.insert({
-                    minX: labelRight - width,
+                    minX: labelRight - boxWidth(width),
                     maxX: labelRight,
                     minY: yp - emHeight,
                     maxY: yp,
                     name,
+                    label: displayName,
                     id,
                 });
             }
             else {
-                const labelX = noTree ? 2 : xp + d;
-                ctx.fillText(displayName, labelX, yp);
+                const labelX = treeDrawn ? xp + d : 2;
+                const { text, width } = fit(treeAreaWidthMinusMargin - labelX);
+                ctx.fillText(text, labelX, yp);
                 clickMap?.insert({
                     minX: labelX + marginLeft,
-                    maxX: labelX + width + marginLeft,
+                    maxX: labelX + boxWidth(width) + marginLeft,
                     minY: yp - emHeight,
                     maxY: yp,
                     name,
+                    label: displayName,
                     id,
                 });
             }
@@ -312,9 +316,9 @@ function firstRow(rowIndices) {
 // 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 { resolvedClades, hierarchy, showBranchLenEffective: showBranchLen, rowHeight, effectiveTreeAreaWidth, marginLeft, blockSize, } = model;
     const by = blockSizeYOverride ?? blockSize;
-    const right = treeAreaWidth - marginLeft;
+    const right = effectiveTreeAreaWidth - marginLeft;
     for (const { rows, color, mark } of resolvedClades) {
         if (mark !== 'highlight') {
             continue;
@@ -334,12 +338,12 @@ function renderCladeHighlights({ ctx, model, offsetY, tipX, maxDepthToLeaf, bloc
 // 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;
+    const { resolvedClades, cladeGutterWidth, rowHeight, effectiveTreeAreaWidth, marginLeft, blockSize, } = model;
     if (cladeGutterWidth === 0) {
         return;
     }
     const by = blockSizeYOverride ?? blockSize;
-    const x = treeAreaWidth -
+    const x = effectiveTreeAreaWidth -
         marginLeft -
         cladeGutterWidth +
         bracketGap +
@@ -364,12 +368,12 @@ function renderCladeBrackets({ ctx, model, theme, offsetY, blockSizeYOverride, }
 // 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, rowTints, referenceRowIndex, rowHeight, treeAreaWidth, marginLeft, blockSize, } = model;
+    const { resolvedHighlights, rowTints, referenceRowIndex, rowHeight, effectiveTreeAreaWidth, marginLeft, blockSize, } = model;
     const by = blockSizeYOverride ?? blockSize;
     const pad = blockPad(model);
     const placed = [];
     const fillRow = (index) => {
-        ctx.fillRect(-marginLeft, index * rowHeight, treeAreaWidth, rowHeight);
+        ctx.fillRect(-marginLeft, index * rowHeight, effectiveTreeAreaWidth, rowHeight);
     };
     if (rowTints) {
         const top = Math.max(0, Math.floor((offsetY - pad) / rowHeight));
@@ -403,8 +407,8 @@ function renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride, }
                 label,
                 x: -marginLeft + 2,
                 y: first * rowHeight,
-                spanWidth: treeAreaWidth,
-                bounds: { min: -marginLeft, max: treeAreaWidth - marginLeft },
+                spanWidth: effectiveTreeAreaWidth,
+                bounds: { min: -marginLeft, max: effectiveTreeAreaWidth - marginLeft },
                 placed,
             });
         }
@@ -424,13 +428,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     setFontSize(ctx, fontSize);
     // memoized on the model and shared across the tree/bubble/label passes (and
     // across all tree blocks) rather than re-traversing the hierarchy in each
-    const { maxBranchLength, maxDepthToLeaf, showBranchLenEffective, treeWidth } = model;
-    // pixel x of the tips. A phylogram scales branch lengths so the longest
-    // root-to-tip path lands at maxBranchLength; a cladogram ignores lengths and
-    // spreads topological depth across the whole tree area instead. Reusing
-    // maxBranchLength for the cladogram would pin every node to x=0 for a tree
-    // with no branch lengths -- which is exactly what forces cladogram mode.
-    const tipX = showBranchLenEffective ? maxBranchLength : treeWidth;
+    const { maxDepthToLeaf, effectiveTreeWidth: tipX } = model;
     // 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);

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

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package/dist/components/tree/renderTreeMouseover.js

@@ -1,6 +1,6 @@
 import { treeHoverColor } from '../overlayColors.js';
 export function renderTreeMouseover({ ctx, model, }) {
-    const { rowHeight, treeAreaWidth: width, height, scrollY, mouseRow, referenceRowIndex, hoveredRowIndices, highResScaleFactor, } = model;
+    const { rowHeight, effectiveTreeAreaWidth: width, height, scrollY, mouseRow, referenceRowIndex, hoveredRowIndices, highResScaleFactor, } = model;
     ctx.resetTransform();
     ctx.clearRect(0, 0, width * highResScaleFactor, height * highResScaleFactor);
     ctx.scale(highResScaleFactor, highResScaleFactor);

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

@@ -1 +1 @@
-{"version":3,"file":"renderTreeMouseover.js","sourceRoot":"","sources":["../../../src/components/tree/renderTreeMouseover.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAIpD,MAAM,UAAU,mBAAmB,CAAC,EAClC,GAAG,EACH,KAAK,GAIN;IACC,MAAM,EACJ,SAAS,EACT,aAAa,EAAE,KAAK,EACpB,MAAM,EACN,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,EACjB,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,GAAG,kBAAkB,EAAE,MAAM,GAAG,kBAAkB,CAAC,CAAA;IAC5E,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;IAEjD,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;QAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IAChE,CAAC,CAAA;IAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;IAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;QACtC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IACD,IACE,QAAQ,KAAK,SAAS;QACtB,QAAQ,KAAK,iBAAiB;QAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;QACD,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;AACH,CAAC"}
+{"version":3,"file":"renderTreeMouseover.js","sourceRoot":"","sources":["../../../src/components/tree/renderTreeMouseover.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAIpD,MAAM,UAAU,mBAAmB,CAAC,EAClC,GAAG,EACH,KAAK,GAIN;IACC,MAAM,EACJ,SAAS,EACT,sBAAsB,EAAE,KAAK,EAC7B,MAAM,EACN,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,EACjB,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,GAAG,kBAAkB,EAAE,MAAM,GAAG,kBAAkB,CAAC,CAAA;IAC5E,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;IAEjD,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;QAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IAChE,CAAC,CAAA;IAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;IAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;QACtC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IACD,IACE,QAAQ,KAAK,SAAS;QACtB,QAAQ,KAAK,iBAAiB;QAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;QACD,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;AACH,CAAC"}

package/dist/components/tree/renderTreeOverview.js

@@ -1,4 +1,5 @@
 import { descendants } from '../../hierarchy.js';
+import { makeOffscreenCanvas } from '../msa/msaRaster.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
@@ -100,16 +101,8 @@ function overviewKeys({ model, theme, 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;
+function canStroke(ctx) {
+    return typeof ctx?.stroke === 'function';
 }
 /**
  * The tree and its clade highlights on an offscreen canvas, drawn once per
@@ -126,7 +119,7 @@ export function treeOverviewImage({ model, theme, width, height, scale, }) {
     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)));
+    const made = makeOffscreenCanvas(Math.max(1, Math.round(width * scale)), Math.max(1, Math.round(height * scale)), canStroke);
     if (made) {
         made.ctx.scale(scale, scale);
         drawTreeOverview({ model, ctx: made.ctx, theme, width, height });

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

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

@@ -22,7 +22,8 @@ export declare const defaultScrollZoomAxis: ScrollZoomAxis;
 export declare const minLetterRowHeight = 8;
 export declare const minLetterColWidth = 5;
 export declare const minFeatureLabelHeight = 9;
-export declare const labelReferenceFontSize = 16;
+export declare function fontSizeFor(rowHeight: number): number;
+export declare const labelFitFontSize: number;
 export declare const minColWidth = 0.2;
 export declare const minRowHeight = 1;
 export declare const maxCellSize = 80;
@@ -31,8 +32,10 @@ export declare const defaultColorSchemeName = "maeditor";
 export declare const defaultShowColumnStats = true;
 export declare const defaultDrawLabels = true;
 export declare const defaultLabelsAlignRight = false;
-export declare const defaultTreeAreaWidth = 400;
-export declare const defaultTreeWidth = 300;
+export declare const minTreeWidth = 70;
+export declare const maxFitTreeWidth = 160;
+export declare const pxPerTreeDepth = 10;
+export declare const maxTreeAreaShare = 0.3;
 export declare const defaultShowBranchLen = true;
 export declare const treeOrders: readonly ["branchLength", "input", "ladderize", "ladderizeReverse"];
 export declare const defaultTreeOrder: TreeOrder;

package/dist/constants.js

@@ -46,9 +46,13 @@ export const minLetterColWidth = 5;
 // so a span shorter than this holds no readable text: an underline bar, a
 // sub-row band or a features panel over small rows
 export const minFeatureLabelHeight = 9;
-// Tree labels are measured once at this size and scaled to the current font
-// size, so a vertical zoom never re-measures the tree.
-export const labelReferenceFontSize = 16;
+export function fontSizeFor(rowHeight) {
+    return Math.min(Math.max(6, rowHeight - 3), 18);
+}
+// The fitted tree area measures the tip labels and the clade labels at the
+// font a default row draws, so a vertical zoom leaves the alignment in place.
+// A larger font ellipsizes the labels.
+export const labelFitFontSize = fontSizeFor(defaultRowHeight);
 // Zoom limits, px per cell. maxCellSize caps both smooth zoom and the stepwise
 // zoom-in buttons (which otherwise grow unbounded). minColWidth/minRowHeight are
 // the smooth-zoom floors.
@@ -62,8 +66,14 @@ export const defaultShowColumnStats = true;
 // Tree model defaults
 export const defaultDrawLabels = true;
 export const defaultLabelsAlignRight = false;
-export const defaultTreeAreaWidth = 400;
-export const defaultTreeWidth = 300;
+// The fitted tree area gives the tree pxPerTreeDepth per level of its depth,
+// between minTreeWidth and maxFitTreeWidth, beside the widest label, and takes
+// at most maxTreeAreaShare of a view with an alignment. Where the share binds,
+// the tree keeps minTreeWidth and the labels ellipsize.
+export const minTreeWidth = 70;
+export const maxFitTreeWidth = 160;
+export const pxPerTreeDepth = 10;
+export const maxTreeAreaShare = 0.3;
 export const defaultShowBranchLen = true;
 export const treeOrders = [
     'branchLength',
@@ -80,7 +90,7 @@ 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.
+// seventy. See agent-docs/reference/neighbor-joining-scaling.md.
 export const maxNeighborJoiningRows = 500;
 // 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

package/dist/constants.js.map

@@ -1 +1 @@
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package/dist/element.js

@@ -13,9 +13,6 @@ const ownAttributes = [
 ];
 // the attributes a <nightingale-manager> writes on the elements it holds
 const nightingaleAttributes = ['display-start', 'display-end', 'highlight'];
-function location(uri) {
-    return uri ? { uri, locationType: 'UriLocation' } : undefined;
-}
 function numberAttribute(value) {
     const n = value ? Number(value) : Number.NaN;
     return Number.isFinite(n) ? n : undefined;
@@ -141,9 +138,9 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
             const theme = this.getAttribute('theme');
             return {
                 ...this.#data,
-                msaFilehandle: location(this.getAttribute('msa-url')),
-                treeFilehandle: location(this.getAttribute('tree-url')),
-                gffFilehandle: location(this.getAttribute('gff-url')),
+                msaUrl: this.getAttribute('msa-url') ?? undefined,
+                treeUrl: this.getAttribute('tree-url') ?? undefined,
+                gffUrl: this.getAttribute('gff-url') ?? undefined,
                 colorScheme: this.#data.colorScheme ??
                     this.getAttribute('color-scheme') ??
                     undefined,