archaeopteryx 3.24.0 → 3.26.0

package/README.md

@@ -64,23 +64,32 @@ Archaeopteryx.js has the following dependencies:
  * d3.js (version 7): https://www.npmjs.com/package/d3
  * sax.js (1.6.1): https://www.npmjs.com/package/sax/v/1.6.1
  
-For **raster PNG export** (optional — the PNG entry appears in the Download
-menu only when `window.Canvg` is present):
- * canvg (4.x): https://www.npmjs.com/package/canvg — publishes ES modules
-   only (no classic-script global build), so bridge it yourself:
-   ```html
-   <script type="module">
-       import {Canvg} from 'http://path/to/canvg.js'; // a self-contained build; see below
-       window.Canvg = Canvg;
-   </script>
-   ```
-   A module script is deferred regardless of where it sits in the page, and
-   PNG export only runs later from a Download click, so this can go anywhere
-   before the click — it does not need to precede archaeopteryx.js's own
-   `<script>` tag. `docs/lib/canvg.js` in this repository is one such
-   self-contained build (npm's `canvg@4.0.3` bundled into one file, e.g. via
-   `esm.sh/canvg@4?bundle`, with its one unnecessary Node-environment shim
-   import removed — see the file's own header comment).
+For **raster PNG export** (optional — the PNG entry, the Copy PNG button and
+the PNG-scale row appear only when `window.Canvg` is present):
+ * canvg (4.x): https://www.npmjs.com/package/canvg. **Load it before
+   `launch()` is called:** the Download menu looks for it at click time, but
+   the Copy PNG button and the PNG-scale row are built with the control
+   panel at launch, so a page that provides it later gets a PNG entry and
+   nothing else. canvg publishes ES modules only (no classic-script global
+   build); this repository ships two ready-made files:
+   * `docs/lib/canvg.global.js` — a classic-script build for a plain
+     `<script src="canvg.global.js"></script>`, or for one more file in a
+     site's concatenated bundle; it defines `window.Canvg` itself. This is
+     what the demo pages use. (Generated from `canvg.js` by
+     `test/make_canvg_global.js`; a unit test keeps the two in step.)
+   * `docs/lib/canvg.js` — the self-contained ES module build (npm's
+     `canvg@4.0.3` bundled into one file via `esm.sh/canvg@4?bundle`, with
+     its one unnecessary Node-environment shim import removed — see the
+     file's own header), for a page that prefers a module bridge of its own:
+     ```html
+     <script type="module">
+         import {Canvg} from 'http://path/to/canvg.js';
+         window.Canvg = Canvg;
+     </script>
+     ```
+     A module script runs after the document is parsed, so a page that calls
+     `launch()` from an inline script during parsing must use the classic
+     build instead.
 
 For **vector PDF export** (optional — the PDF entry appears in the Download
 menu only when both are loaded before archaeopteryx.js):
@@ -246,10 +255,14 @@ program's.
 
 A phylogram carries a **scale bar** at the bottom left: a round number of
 branch-length units (1, 2 or 5 × 10ᵏ, whichever makes the bar about 100 px)
-with its length written above it. It is drawn with the tree, so it zooms and
-exports with it and its label always holds. A cladogram has nothing to
-measure and shows none, and a tree under a scale axis leaves the measuring to
-the axis.
+with its length written above it, followed by the unit the tree states
+(phyloXML's `branch_length_unit`, e.g. `0.05 subs/site`) and by nothing when
+it states none: a tree that does not say what its lengths measure gets no
+guess. It is drawn with the tree, so it zooms and exports with it and its
+label always holds. A cladogram has nothing to measure and shows none, and a
+tree under a scale axis leaves the measuring to the axis. **Scale** under
+Display Data > Options hides it (on by default; config `showScaleBar`, view
+key `scaleBar`; the desktop's switch has the same name and defaults to off).
 
 **Scale Axis** under Display Data (off by default, as on the desktop) draws a
 labelled ruler under a phylogram, from 0 at the root out to the deepest tip, in
@@ -1056,8 +1069,8 @@ Both entry points take **exactly** the arguments shown — a call with the old
 trailing arguments (the separate settings bag, `nodeVisualizations`,
 `nodeLabels`, `specialVisualizations`, or the positional Newick parse
 options) **throws** with a message saying where each one went: everything now
-lives in the **one config object** (`nodeLabels` and
-`internalNumericLabels` are config keys). `config` itself is optional — `archaeopteryx.launch('#phylogram1',
+lives in the **one config object** (`internalNumericLabels` is a config key;
+`nodeLabels` is retired, see the deprecated keys below). `config` itself is optional — `archaeopteryx.launch('#phylogram1',
 tree)` works.
 
 `container` is a **CSS selector or the DOM element itself** (frameworks hand
@@ -1543,6 +1556,7 @@ copy-pastable JSON.
 | `geneFamily` | `'auto'` | The annotation namespace that colours the genes and anchors the rows: `'auto'` (the one most genes carry) or a prefix such as `'pgfam'`. |
 | `geneLabels` | `'genes'` | Where gene symbols go: `'genes'` (on the arrows), `'legend'` (a card of the families), or `'none'`. |
 | `showScaleAxis` | tree-derived | Open with the scale axis shown: the time axis on a time tree whose branches show time, a distance axis on any other phylogram. Default: on when the tree carries `<date>` elements and opens shown in time, off otherwise (a dated tree that opens in divergence is a divergence tree on screen) — an explicit `true`/`false` overrides that. |
+| `showScaleBar` | `true` | Open with the scale bar at the bottom left of a phylogram (a round length in the tree's branch-length unit). It gives way while the scale axis is shown either way. |
 | `showScaleGrid` | `false` | Open with the Scale Grid lines on (only meaningful — and only offered as a checkbox — while the scale axis itself is shown). |
 | `showSupportDots` | `false` | Open with the Support Dots marks on (the checkbox appears whenever the tree has confidences). |
 | `supportDotMinimum` | `95` | Support Dots threshold, as a percentage. On a tree whose confidences top out at 1 (posterior probabilities) it is read on the 0–1 scale, so the default means ≥ 0.95 there and ≥ 95 on a bootstrap tree. |
@@ -1551,14 +1565,13 @@ copy-pastable JSON.
 | `onViewChange` | `null` | `function (state, encoded)`, called once per settled redraw when the view changed: `state` as `getViewState()` returns it, `encoded` its hash-ready string. The demo pages write it into the URL. |
 | `searchBinitialValue` | `null` | Prefill search box B. |
 | `enableVisualizations` | `true` | Offer the Color / Shape visualizations (which fields they cover is decided from the tree). |
-| `initialVisualization` | `null` | The visualization to open with, by its Color-menu name (e.g. `'Host'`; case-insensitive). A name the tree cannot honour logs a console warning and falls back to the automatic choice, so a site-wide value is safe on trees without that field. Default: Archaeopteryx.js picks the most informative field itself. |
+| `initialVisualization` | `null` | The visualization to open with, by its Color-menu name (e.g. `'Host'`; case-insensitive). A name the tree cannot honour logs a console warning and falls back to the automatic choice, so a site-wide value is safe on trees without that field. A name the tree *can* honour is always honoured, but when it is a field the automatic choice would not have opened with -- more than 20 values, or a value on fewer than two thirds of the tips -- a console warning says so and names the field the viewer would have chosen. Default: Archaeopteryx.js picks the most informative field itself. |
 | `visualizationsLegendXpos` | `254` | Legend position, x. |
 | `visualizationsLegendYpos` | `30` | Legend position, y. |
 | `enableDownloads` | `true` | Offer the download buttons. |
 | `pngExportScale` | `4` | The PNG resolution the Download section starts on: 2, 4 or 8 (any other value is snapped to the nearest, with a console warning). |
 | `nhExportWriteConfidences` | `true` | Write confidences into exported Newick. |
 | `internalNumericLabels` | `'auto'` | Newick / Nexus parsing: how a bare numeric internal label (`)100:0.05`) is read. `'auto'` reads them as confidence values only when *every* internal label looks like support; `'confidence'` reads every numeric label as one, whatever its value; `'label'` keeps them as names. Replaces `nhConfidenceValuesAsInternalNames` (still accepted, with a warning; its `true` maps to `'confidence'`). |
-| `nodeLabels` | `null` | Custom label-field checkboxes: `{key: {label, description, propertyRef, showButton, selected}}` — each adds a panel checkbox labelling nodes with the named property's value. (Was `launch()`'s sixth positional argument.) |
 | `enableSubtreeDeletion` | `true` | Offer node / subtree deletion in the node menu. |
 | `enableAccessToDatabases` | `true` | Offer the “Access DB” link in the node menu. |
 | `enableManualNodeSelection` | `false` | Add the Select/Deselect entries to the node menu. |
@@ -1581,7 +1594,7 @@ whatever it names.
 
 ### Accepted, with a warning
 
-Four keys are neither current nor removed: they are accepted so an existing
+Five keys are neither current nor removed: they are accepted so an existing
 embed keeps working, and warn on the console.
 
 | Key | What happens |
@@ -1590,6 +1603,7 @@ embed keeps working, and warn on the console.
 | `nhConfidenceValuesInBrackets` | Retired: ignored. It gated whether `[95]` is read as a confidence, but setting it `false` never reinterpreted the bracket — it *discarded* it, so the option's only effect was to throw support values away. A bracket that is not a number is a Newick comment and was ignored either way, and NHX / BEAST blobs go through a different path. Bracketed values are now always read as confidences. |
 | `showTimeAxis` | Translated to `showScaleAxis`, value unchanged: the switch now also draws a distance axis on a tree that is not in time. An explicit `showScaleAxis` always wins. |
 | `timeAxisGrid` | Translated to `showScaleGrid`, value unchanged. |
+| `nodeLabels` | Retired in 3.25.0: ignored, with a warning. The custom label checkboxes it declared predate the Metadata checkbox and its "Metadata fields…" chooser, which offer exactly the fields the tree carries; a fixed site-wide list put checkboxes for absent fields on every tree. `labelProperties` sets the starting fields where the automatic choice is not wanted. Removed in a later release. |
 
 ### What replaced the rest
 
@@ -1734,6 +1748,21 @@ All 118 of them, alphabetically:
 | `visualizationsLegendXposOrig` | Internal bookkeeping; set visualizationsLegendXpos. |
 | `visualizationsLegendYposOrig` | Internal bookkeeping; set visualizationsLegendYpos. |
 
+### Removed from `forester` — calling these throws `TypeError`
+
+3.0.0 also dropped twelve exports of `forester.js` that the viewer no longer
+used. They are gone, not stubbed, so a 2.x embedding that calls one fails with
+`TypeError: forester.<name> is not a function` — inside its own parse step, if
+that is where it called it.
+
+| Function | Why, and what to do instead |
+| --- | --- |
+| `collectPropertyRefs` | Nothing to call. The viewer derives the Color-by candidates (`forester.visualizationCandidates(tree)`, below) and the label-field chooser's list from the tree itself, and substitutes a readable name property (`genome_name`) for identifier-like tip names on its own. A 2.x embedding that built `nodeLabels` from this function's result should delete that block together with the `nodeLabels` key; `labelProperties` sets the starting label fields where the automatic choice is not wanted. |
+| `collapse`, `unCollapse` | The subtree-collapse feature was removed; they were its only writers. |
+| `getChildren` | Only meant something while collapse existed; read `node.children`. |
+| `findByTaxonomyCode`, `findByTaxonomyScientificName` | Superseded by the search (the panel's search fields). |
+| `calcAverageTreeHeight`, `calcMaxDepth`, `calcBranchLengthSimpleStatistics`, `removeMaxBranchLength`, `isHasNodeData`, `getOneDistinctTaxonomy` | Never used by the viewer; nothing replaces them. |
+
 ## The automatic visualization system (developer spec)
 
 This section, together with **Value grouping** below, is written to be
@@ -1895,17 +1924,29 @@ exists, and clears the per-legend chip states.
 Highest first, at each paint:
 
 * **Label colour**: search/selection highlight → active Color visualization
-  → `style:font_color` → phyloXML branch colour → theme ink.
+  (its colour; the theme ink for a node without a value) → `style:font_color`
+  → phyloXML branch colour → theme ink.
 * **Node fill**: highlight → duplication/speciation event colour → active
-  Color visualization → `style:node_color` (else `style:font_color`) →
-  background.
+  Color visualization (its colour; a node without a value draws no dot,
+  or a hollow one while Node events are shown) → `style:node_color` (else
+  `style:font_color`) → background.
 * **Node outline**: darkened highlight → event colour → visualization fill
-  → style colour → branch colour → branch default.
+  → style colour (not while a Color visualization is active) → branch colour
+  → branch default.
 * **Node shape path**: suppressed for highlighted/event nodes; chosen Shape
   visualization → `style:node_shape`. A node earns its default dot when a
   Color visualization is active (and no shape was drawn), or when it
   carries `style:node_color` — `font_color` alone paints only the label.
 
+While a Color visualization is active the style colours are **not consulted
+for any node**, valued or not: not for the label, the dot, its outline, the
+hover glow or the clock plot's points. The visualization owns the colours and
+its legend explains them; a node without a value takes the default label
+colour and draws no dot. That is the desktop's rule (its TreePanel.setColor).
+Clearing the Color menu brings the file's colours back. Branch colours,
+shapes, font sizes and styles are not colours of the visualization's kind
+and stay.
+
 ### Legend anatomy
 
 One draggable SVG card per active visualization (colour, then shape,
@@ -2102,8 +2143,9 @@ honoured: `style:font_color`, `style:node_color`, `style:node_shape`
 The **Visual Styles** checkbox — the desktop's "Visual Styles/Branch Colors",
 shown when the tree carries either, on by default — turns them off and on,
 and gates phyloXML `<color>` branch colours too, exactly as on the desktop.
-An active Color visualization outranks `style:font_color`, also as on the
-desktop: set the Color menu to default to see the tree as its file styled it.
+An active Color visualization outranks the style colours for every node,
+valued or not, on labels and node dots alike, as on the desktop: set the
+Color menu to default to see the tree as its file styled it.
 `style:` never appears in the Color / Shape menus — it is rendering, not data.
 
 ### Moving the legends

package/archaeopteryx.d.ts

@@ -29,9 +29,13 @@ export interface Phylogeny extends PhylogenyNode {
 
 export type Layout = 'rectangular' | 'circular' | 'unrooted';
 
-/** One custom label-field entry (the config's nodeLabels values).
+/** @deprecated Retired in 3.25.0 with `nodeLabels`: accepted with a console
+ * warning, no effect; removed in a later release. The Metadata checkbox and
+ * its "Metadata fields…" chooser offer the tree's own fields.
  *
- * Two modes:
+ * One custom label-field entry (the config's nodeLabels values).
+ *
+ * Two modes (3.0.0 to 3.24.0):
  *  - a PANEL CHECKBOX needs label, description AND propertyRef set, plus
  *    showButton: true -- omit showButton (or any of the three) and no
  *    checkbox appears;
@@ -85,6 +89,10 @@ export interface ArchaeopteryxConfig {
     nhConfidenceValuesAsInternalNames?: boolean;
     nhConfidenceValuesInBrackets?: boolean;
     nhExportWriteConfidences?: boolean;
+    /** @deprecated Retired in 3.25.0: accepted with a console warning, no
+     * effect; removed in a later release. The Metadata checkbox and its
+     * "Metadata fields…" chooser offer the tree's own fields; labelProperties
+     * sets the starting fields. */
     nodeLabels?: Record<string, NodeLabelSpec> | null;
     /** Called once per settled redraw when the view changed: the state as
      * getViewState() returns it, and its hash-ready string. */
@@ -130,6 +138,8 @@ export interface ArchaeopteryxConfig {
      * branches show time, a distance axis on any other. Default: on for a
      * time tree, off otherwise. */
     showScaleAxis?: boolean;
+    /** The scale bar at the bottom left of a phylogram; on unless false. */
+    showScaleBar?: boolean;
     /** Grid lines (rings, in circular) at the scale axis's ticks. */
     showScaleGrid?: boolean;
     showSupportDots?: boolean;
@@ -176,8 +186,8 @@ export interface ViewState {
     shapeBy?: string;
     /** The panel's checked boxes: name, taxonomy, sequence, confidence,
      * madValues, branchLength, external, internal, nodeEvents, branchEvents,
-     * supportDots, shortNames, autoHide, visualizations, visualStyles, and
-     * custom:<key> for a nodeLabels checkbox. */
+     * supportDots, shortNames, autoHide, visualizations, visualStyles. (A
+     * custom:<key> flag from a 3.24.0 hash is read and ignored.) */
     show?: string[];
     font?: number;
     node?: number;
@@ -205,6 +215,7 @@ export interface ViewState {
     geneLabels?: 'none' | 'genes' | 'legend';
     scaleAxis?: boolean;
     scaleGrid?: boolean;
+    scaleBar?: boolean;
     /** @deprecated the name of scaleAxis in older links; still read. */
     timeAxis?: boolean;
     /** @deprecated the name of scaleGrid in older links; still read. */

package/archaeopteryx.js

@@ -20,7 +20,7 @@
  *
  */
 
-// v 3.24.0
+// v 3.26.0
 // 2026-09-17
 //
 // Archaeopteryx.js is a software tool for the visualization and
@@ -103,7 +103,7 @@ function (root, d3, forester, phyloXml) {
     // IIFE's own function name -- a plain object says what it is.)
     let archaeopteryx = {};
 
-    const VERSION = '3.24.0';
+    const VERSION = '3.26.0';
     const WEBSITE = 'https://cmzmasek.github.io/archaeopteryx-js/';
     const DESKTOP_WEBSITE = 'https://cmzmasek.github.io/archaeopteryx/';
     const SOURCE_WEBSITE = 'https://github.com/cmzmasek/archaeopteryx-js';
@@ -390,6 +390,7 @@ function (root, d3, forester, phyloXml) {
     const GENE_LABELS_SELECT = 'gene_labels';
     const SCALE_AXIS_CB = 'scaleaxis_cb';
     const SCALE_GRID_CB = 'scalegrid_cb';
+    const SCALE_BAR_CB = 'scalebar_cb';
     const MSA_SCROLL_ID = 'aptxmsascroll';
     const FONT_SIZE_SLIDER = 'fs_sl';
     const EXTERNAL_LABEL_CB = 'extl_cb';
@@ -539,7 +540,6 @@ function (root, d3, forester, phyloXml) {
     let _container = null;            // the resolved container ELEMENT (never a selector string)
     let _intervalId = 0;
     let _maxLabelLength = 0;
-    let _nodeLabels = null;
     let _state = null;      // live display state: what the control panel writes to
     let _root = null;
     let _root_const = null;
@@ -606,6 +606,7 @@ function (root, d3, forester, phyloXml) {
     const DOMAIN_SCALE_HEADROOM = 0.9;    // drawn length over reserved length
     const DOMAIN_BOX_MIN_H = 6;
     const DOMAIN_BOX_MAX_H = 16;
+    const LEGEND_MAX_ROWS = 20;           // value rows a legend lists before "n more"; the rest fold
     const DOMAIN_BACKBONE_COLOR = 'rgb(100,100,100)';   // the same in both themes and in exports
     const DOMAIN_SHADOW_COLOR = 'rgb(8,18,21)';
     const DOMAIN_SHADOWS = [[0.4, 0.7, 40], [0.9, 1.5, 28], [1.6, 2.5, 17]];   // dx, dy, alpha of 255, in drawing order
@@ -1447,8 +1448,9 @@ function (root, d3, forester, phyloXml) {
     // a node coloured by Host Group glows in its host colour -- and the UI
     // accent otherwise. As on the desktop (TreePanel.hoverGlowColor). The
     // precedence is the one the node itself is painted by: the Color-by
-    // value, then a per-node visual style, then an event colour, then a
-    // colourised clade's branch colour. NEVER the found/search colour: a
+    // value, then a per-node visual style (not while a Color-by is active,
+    // see nodeStyleColor), then an event colour, then a colourised clade's
+    // branch colour. NEVER the found/search colour: a
     // focus ring must not read as a selection state.
     //
     // The glow is a 13-23% alpha wash, so a dark or a pale colour would
@@ -1462,10 +1464,7 @@ function (root, d3, forester, phyloXml) {
             c = vis;
         }
         if (!c) {
-            let style = nodeStyle(d);
-            if (style && (style.nodeColor || style.fontColor)) {
-                c = style.nodeColor || style.fontColor;
-            }
+            c = nodeStyleColor(d);
         }
         if (!c && _state.showNodeEvents && d.events && d.children) {
             c = makeNodeEventsDependentColor(d.events);
@@ -1948,7 +1947,32 @@ function (root, d3, forester, phyloXml) {
             // an explicit request is honoured even for a wide field (21+
             // values) the automatic path would only offer, never impose;
             // autoColorId too, so it survives subtree views like the
-            // automatic pick does
+            // automatic pick does.
+            //
+            // Honoured, but not in silence. A request for a field the
+            // automatic choice would not open with -- wide, or sparse (on
+            // fewer than 2/3 of the tips; it opens only when nothing denser
+            // exists) -- says so in the console and names the field the
+            // viewer would have chosen. BV-BRC's virus trees carried a
+            // site-wide 'Host' from the influenza days: family trees opened
+            // coloured by 39 to 168 hosts while Genus (4 to 15 values) sat
+            // in the file, and nothing anywhere said the viewer had been
+            // overruled (Christian, 2026-10-08: a console warning when a
+            // sub-optimal visualization is forced is needed). A request for
+            // a clean field that merely ranks below the automatic pick is a
+            // site's taste and warns nothing; nor does a sparse field that
+            // is the automatic pick itself.
+            let auto = forester.openingVisualization(_vis.candidates);
+            if ((requested.wide || requested.sparse) && !(auto && auto.id === requested.id)) {
+                let why = requested.wide
+                    ? requested.values.length + ' distinct values on this tree, more than the '
+                        + LEGEND_MAX_ROWS + ' the legend lists'
+                    : 'a value on ' + requested.coverage + ' of the tree\'s ' + requested.total + ' tips';
+                console.warn(WARNING + ': initialVisualization "' + _settings.initialVisualization
+                    + '" names a field with ' + why + '; left to itself the viewer would '
+                    + (auto ? 'open with "' + auto.label + '" (' + auto.values.length + ' values)'
+                        : 'open uncoloured'));
+            }
             _vis.autoColorId = requested.id;
             _vis.colorId = requested.id;
             _state.showVisualizations = true;
@@ -2144,6 +2168,7 @@ function (root, d3, forester, phyloXml) {
         }
         dialog.addEventListener('close', close);
 
+        let placed = false;   // set by place() once the picker has been put somewhere
         render(false);
         dialog.show();
         place();
@@ -2151,40 +2176,67 @@ function (root, d3, forester, phyloXml) {
         // Beside the legend it edits, never on top of it -- a picker that hides
         // the swatch it is changing defeats the live preview.
         //
-        // Re-measured rather than remembered, for two reasons: every redraw
-        // DESTROYS and rebuilds the legend group, so a held reference goes
-        // stale and measures zero; and the card grows when the [reset colors]
-        // chip appears on the first pick, which would leave a
-        // positioned-once picker sitting over the counts. It only MOVES when
-        // it would otherwise overlap, so the dialog does not chase the legend
-        // around while the user drags.
+        // Placed OUTRIGHT the first time, viewport-fixed. A non-modal <dialog>
+        // appended to the body sits at its static position, the end of the
+        // document: on the demo page that is the top of the window (the
+        // container is out of flow), on a page that flows, such as BV-BRC's,
+        // it is below everything on it. Until 2026-10-08 the picker moved
+        // only when that spot overlapped the card, so on BV-BRC it opened
+        // under the site's own bars, off the bottom of the window
+        // (Christian's screenshot). Fixed positioning also keeps a scrolling
+        // page from carrying it away.
+        //
+        // Re-measured rather than remembered afterwards, for two reasons:
+        // every redraw DESTROYS and rebuilds the legend group, so a held
+        // reference goes stale and measures zero; and the card grows when the
+        // [reset colors] chip appears on the first pick, which would leave a
+        // positioned-once picker sitting over the counts. Once placed it only
+        // MOVES when it would otherwise overlap, so the dialog does not chase
+        // the legend around while the user drags.
         function place() {
             let el = anchorClass ? document.querySelector('g.' + anchorClass) : null;
             let box = el ? el.getBoundingClientRect() : null;
-            if (!box || !box.width) {
-                return;
+            if (box && !box.width) {
+                box = null;
             }
-            let now = dialog.getBoundingClientRect();
-            let overlaps = now.width > 0
-                && !(now.left >= box.right || now.right <= box.left
-                    || now.top >= box.bottom || now.bottom <= box.top);
-            if (now.width > 0 && !overlaps) {
-                return;
+            if (placed) {
+                if (!box) {
+                    return;
+                }
+                let now = dialog.getBoundingClientRect();
+                let overlaps = now.width > 0
+                    && !(now.left >= box.right || now.right <= box.left
+                        || now.top >= box.bottom || now.bottom <= box.top);
+                if (!overlaps) {
+                    return;
+                }
             }
             let w = dialog.offsetWidth;
             let h = dialog.offsetHeight;
-            // to the right of the card, or to its left when that would leave
-            // the viewport
-            let left = box.right + 10;
-            if (left + w > window.innerWidth - 6) {
-                left = box.left - w - 10;
+            let left;
+            let top;
+            if (box) {
+                // to the right of the card, or to its left when that would
+                // leave the viewport
+                left = box.right + 10;
+                if (left + w > window.innerWidth - 6) {
+                    left = box.left - w - 10;
+                }
+                top = box.top;
+            } else {
+                // no card to sit beside (the view has no swatch for the value):
+                // the tree area's top left corner, inside the window
+                let area = _container ? _container.getBoundingClientRect() : null;
+                left = area ? area.left + 14 : 10;
+                top = area ? Math.max(area.top, 0) + 14 : 10;
             }
             setStyles(dialog, {
                 'position': 'fixed',
                 'margin': '0',
                 'left': Math.max(6, Math.min(window.innerWidth - w - 6, left)) + 'px',
-                'top': Math.max(6, Math.min(window.innerHeight - h - 6, box.top)) + 'px'
+                'top': Math.max(6, Math.min(window.innerHeight - h - 6, top)) + 'px'
             });
+            placed = true;
         }
         setTimeout(function () {
             document.addEventListener('pointerdown', onOutside, true);
@@ -2377,6 +2429,36 @@ function (root, d3, forester, phyloXml) {
         return ((_vis && _vis.colorId) ? _vis.byId[_vis.colorId] : null) || null;
     }
 
+    // A Color visualization is on screen: it owns every node's colour, and the
+    // file's style colours wait until the Color menu is cleared (the desktop's
+    // rule; see makeLabelColor and makeNodeFillColor).
+    function colorVisActive() {
+        return !!_state.showVisualizations && !!currentColorVis();
+    }
+
+    // The colour a node's style gives it, or null: style:node_color (else
+    // style:font_color) for the node's mark, style:font_color for its label.
+    // Null while a Color visualization is active -- the desktop's rule
+    // (TreePanel.setColor): the visualization owns every node's colour and
+    // its legend explains them; a node without a value takes the default ink
+    // and no dot rather than the file's colour. Until 2026-10-08 the valueless
+    // nodes fell through to the file's colour on their dots, so BV-BRC's
+    // trees -- style:font_color on every tip, following Genus -- showed two
+    // palettes under Color by Host (Christian: adopt the desktop's rule).
+    // EVERY reader of a style colour goes through here, so none can forget
+    // the rule: the label, the dot, its outline, the hover glow, the clock
+    // plot's points (which a first version of the rule missed).
+    function nodeStyleColor(node, forLabel) {
+        if (colorVisActive()) {
+            return null;
+        }
+        let style = nodeStyle(node);
+        if (!style) {
+            return null;
+        }
+        return (forLabel ? style.fontColor : (style.nodeColor || style.fontColor)) || null;
+    }
+
     function currentShapeVis() {
         return ((_vis && _vis.shapeId) ? _vis.byId[_vis.shapeId] : null) || null;
     }
@@ -2521,7 +2603,6 @@ function (root, d3, forester, phyloXml) {
         // is then just its "no value" row
         const isRange = kind === 'color' && colorModeOf(vis) === 'range' && vis.values.length > 0;
 
-        const LEGEND_MAX_ROWS = 20;
         let rows = [];
         let hidden = 0;
         if (!isRange) {
@@ -3624,11 +3705,9 @@ function (root, d3, forester, phyloXml) {
         if (visColor !== _state.backgroundColorDefault) {
             return visColor;
         }
-        let style = nodeStyle(phynode);
-        if (style && (style.nodeColor || style.fontColor)) {
-            return style.nodeColor || style.fontColor;
-        }
-        return visColor;
+        // the style colour, or the background -- which, under an active Color
+        // visualization, drawTreeGeometry turns into no dot at all
+        return nodeStyleColor(phynode) || visColor;
     };
 
     // A darker shade of a node's found/selected highlight color, used as a thin
@@ -3661,10 +3740,11 @@ function (root, d3, forester, phyloXml) {
                 return v;
             }
         }
-        let style = nodeStyle(phynode);
-        if (style && (style.nodeColor || style.fontColor)) {
-            return style.nodeColor || style.fontColor;
+        let styleColor = nodeStyleColor(phynode);
+        if (styleColor) {
+            return styleColor;
         }
+        // the branch colour, unlike a style colour, holds under a Color-by (desktop)
         if (_state.useVisualStyles && phynode.color) {
             let c = phynode.color;
             return "rgb(" + c.red + "," + c.green + "," + c.blue + ")";
@@ -3677,17 +3757,15 @@ function (root, d3, forester, phyloXml) {
         if (foundColor) {
             return foundColor;
         }
-        if (_state.showVisualizations && currentColorVis()) {
-            let color = makeVisLabelColor(phynode);
-            if (color) {
-                return color;
-            }
+        // an active Color visualization owns the colours: its colour where
+        // the node has a value, the default ink where it has none (and
+        // nodeStyleColor is null meanwhile, see there)
+        if (colorVisActive()) {
+            return makeVisLabelColor(phynode);
         }
-        // an active Color visualization outranks style:font_color, as on the
-        // desktop; clear the Color menu to see the tree as its file styled it
-        let style = nodeStyle(phynode);
-        if (style && style.fontColor) {
-            return style.fontColor;
+        let fontColor = nodeStyleColor(phynode, true);
+        if (fontColor) {
+            return fontColor;
         }
         if (_state.useVisualStyles && phynode.color) {
             let c = phynode.color;
@@ -4725,25 +4803,6 @@ function (root, d3, forester, phyloXml) {
             l = append(l, labelPropertiesOf(phynode));
         }
 
-        if (_nodeLabels && phynode.properties) {
-            const props_length = phynode.properties.length;
-            if (props_length > 0) {
-                for (const value of Object.values(_nodeLabels)) {
-                    if (value.selected === true && value.propertyRef) {
-                        let prop_text = '';
-                        for (let pm = 0; pm < props_length; ++pm) {
-                            if (phynode.properties[pm].ref === value.propertyRef && phynode.properties[pm].datatype === 'xsd:string' && forester.isNodeScopedProperty(phynode.properties[pm])) {
-                                if (prop_text.length > 0) {
-                                    prop_text += ', '
-                                }
-                                prop_text += phynode.properties[pm].value;
-                            }
-                        }
-                        l = append(l, prop_text);
-                    }
-                }
-            }
-        }
 
 
         if (_state.showDistributions && phynode.distributions && phynode.distributions.length > 0) {
@@ -5522,6 +5581,21 @@ function (root, d3, forester, phyloXml) {
                 return v;
             },
             note: 'the grid follows the scale axis, time or distance'
+        },
+        // Retired in 3.25.0 (Christian, 2026-10-08: "go with the deprecation").
+        // The custom label checkboxes it declared -- a site's fixed list of
+        // property refs, one panel checkbox each, labelling nodes with the
+        // property's value -- predate the Metadata checkbox and its
+        // "Metadata fields…" chooser, which offer exactly the fields the tree
+        // carries and replace identifier-like tip names with a name property
+        // on their own. On BV-BRC the list, written for influenza, put eight
+        // checkboxes on every virus tree, six of them for fields the tree
+        // did not have. The checkbox code went with the key (the label
+        // text, the panel rows, the view state's custom:<key> flags, which
+        // an old hash may still carry and the reader now ignores). Accepted
+        // with this warning for one release cycle, then REMOVED_CONFIG.
+        nodeLabels: {
+            note: 'the Metadata checkbox and its "Metadata fields…" chooser offer the tree\'s own fields; labelProperties sets the starting fields'
         }
     };
 
@@ -5699,6 +5773,7 @@ function (root, d3, forester, phyloXml) {
         'geneFamily',
         'geneLabels',
         'showScaleAxis',
+        'showScaleBar',
         'showScaleGrid',
         'showSupportDots',
         'searchAinitialValue',
@@ -5721,7 +5796,6 @@ function (root, d3, forester, phyloXml) {
         'internalNumericLabels',
         'ladderizeTree',
         'nhExportWriteConfidences',
-        'nodeLabels',
         'onViewChange',
         'panelDensity',
         'pngExportScale',
@@ -6066,6 +6140,8 @@ function (root, d3, forester, phyloXml) {
             _state.showScaleAxis = !!(_timeInfo && _timeInfo.type) && !branchesShowDivergence();
         }
         _state.showScaleGrid = _state.showScaleGrid === true; // desktop default: off
+        // the scale bar is on unless the caller says no; it gives way to the axis anyway
+        _state.showScaleBar = _state.showScaleBar !== false;
         _state.showSupportDots = _state.showSupportDots === true;
         _state.showNodeEvents = _basicTreeProperties.nodeEvents === true;
         _state.showBranchEvents = _basicTreeProperties.branchEvents === true;
@@ -6321,19 +6397,6 @@ function (root, d3, forester, phyloXml) {
         } else if (typeof _settings.onViewChange !== 'function') {
             throw new Error(ERROR + '"onViewChange" must be a function (state, encoded) or null');
         }
-        if (_settings.nodeLabels === undefined) {
-            _settings.nodeLabels = null;
-        } else if (_settings.nodeLabels !== null && typeof _settings.nodeLabels !== 'object') {
-            throw new Error('nodeLabels must be an object (see the README) or null');
-        }
-        if (_settings.nodeLabels) {
-            // a DEEP copy: the viewer writes runtime state into these specs
-            // (the checkbox element id, the live checked state), and the
-            // caller's config object must stay declarative -- an embedder
-            // reusing one nodeLabels constant across launches must not
-            // inherit the previous session's checkbox state
-            _settings.nodeLabels = JSON.parse(JSON.stringify(_settings.nodeLabels));
-        }
         if (_settings.pngExportScale === undefined) {
             _settings.pngExportScale = 4;
         } else if (typeof _settings.pngExportScale !== 'number'
@@ -6593,7 +6656,7 @@ function (root, d3, forester, phyloXml) {
                 + ' trailing arguments were removed. The separate settings bag merged into the one'
                 + ' config object; "nodeVisualizations" and "specialVisualizations" are gone for good'
                 + ' (visualizations are derived automatically from the tree itself); "nodeLabels"'
-                + ' moved into the config as its "nodeLabels" key.');
+                + ' is retired (the Metadata checkbox offers the tree\'s own fields).');
         }
         if (phylo === undefined || phylo === null) {
             throw new Error(ERROR + 'input tree is undefined or null');
@@ -6684,9 +6747,8 @@ function (root, d3, forester, phyloXml) {
             .on('zoom', zoom);
         _basicTreeProperties = forester.collectBasicTreeProperties(_treeData);
 
-        // Every launch starts from a clean slate: _vis is rebuilt below and
-        // _nodeLabels reassigned, never inherited from a previous launch in
-        // the same page.
+        // Every launch starts from a clean slate: _vis is rebuilt below, never
+        // inherited from a previous launch in the same page.
         _radialRotation = 0;
         _radialLabelsHorizontal = false;
         _msaColOffset = 0;
@@ -6704,7 +6766,6 @@ function (root, d3, forester, phyloXml) {
         // candidate ranking over 13k tips before the card could even paint.
         checkLayoutValue(cfg.state ? cfg.state.layout : undefined);
         initializeSettings(cfg.settings);
-        _nodeLabels = _settings.nodeLabels || null;
 
         // whatever a previous launch left in this container (or in the
         // container before it) goes now, so the old tree does not sit under
@@ -9896,20 +9957,6 @@ function (root, d3, forester, phyloXml) {
         return found;
     }
 
-    // The config's custom label checkboxes (nodeLabels) that are offered
-    function customLabelEntries() {
-        let out = [];
-        if (_nodeLabels) {
-            Object.keys(_nodeLabels).forEach(function (key) {
-                let v = _nodeLabels[key];
-                if (v && v.label && v.showButton === true && v.propertyRef && v.description) {
-                    out.push({key: key, entry: v});
-                }
-            });
-        }
-        return out;
-    }
-
     function searchStateOf(idx) {
         let spec = currentSearchSpec(idx);
         let value = (spec.value === null || spec.value === undefined) ? '' : String(spec.value);
@@ -9957,11 +10004,6 @@ function (root, d3, forester, phyloXml) {
         }).map(function (f) {
             return f[0];
         });
-        customLabelEntries().forEach(function (c) {
-            if (c.entry.selected === true) {
-                s.show.push('custom:' + c.key);
-            }
-        });
         s.font = _state.externalNodeFontSize;
         s.node = _state.nodeSizeDefault;
         s.branch = _state.branchWidthDefault;
@@ -10005,6 +10047,7 @@ function (root, d3, forester, phyloXml) {
         if (_basicTreeProperties.branchLengths === true) {
             s.scaleAxis = _state.showScaleAxis === true;
             s.scaleGrid = _state.showScaleGrid === true;
+            s.scaleBar = _state.showScaleBar === true;
         }
         if (_branchScaleAvailable) {
             s.scale = _state.branchScale;   // time or divergence: which layout the branches show
@@ -10107,9 +10150,6 @@ function (root, d3, forester, phyloXml) {
             VIEW_SHOW_FLAGS.forEach(function (f) {
                 _state[f[2]] = on.has(f[0]);
             });
-            customLabelEntries().forEach(function (c) {
-                c.entry.selected = on.has('custom:' + c.key);
-            });
         }
         if (isFinite(s.font)) {
             setFontSizes(Number(s.font));
@@ -10189,6 +10229,9 @@ function (root, d3, forester, phyloXml) {
         if (typeof grid === 'boolean') {
             _state.showScaleGrid = grid;
         }
+        if (typeof s.scaleBar === 'boolean') {
+            _state.showScaleBar = s.scaleBar;
+        }
         if (!radialDisplay()) {
             _radialLabelsHorizontal = false;
         } else if ((_state.showDomainArchitectures && _basicTreeProperties.domainArchitectures)
@@ -10259,17 +10302,13 @@ function (root, d3, forester, phyloXml) {
         VIEW_SHOW_FLAGS.forEach(function (f) {
             setCheckboxValue(f[1], _state[f[2]] === true);
         });
-        customLabelEntries().forEach(function (c) {
-            if (c.entry.cb_id) {
-                setCheckboxValue(c.entry.cb_id, c.entry.selected === true);
-            }
-        });
         setCheckboxValue(MSA_CB, _state.showMsa === true);
         setCheckboxValue(MSA_LOGO_CB, _state.showMsaLogo === true);
         setCheckboxValue(HEATMAP_CB, _state.showHeatmap === true);
         syncHeatmapControls();
         setCheckboxValue(SCALE_AXIS_CB, _state.showScaleAxis === true);
         setCheckboxValue(SCALE_GRID_CB, _state.showScaleGrid === true);
+        setCheckboxValue(SCALE_BAR_CB, _state.showScaleBar === true);
         setCheckboxValue(DOMAIN_GLOW_CB, _state.domainGlow === true);
         setValue(DOMAIN_LABELS_SELECT, _state.domainLabels);
         syncDomainControls();
@@ -10350,7 +10389,7 @@ function (root, d3, forester, phyloXml) {
     const VIEW_INT_KEYS = ['tree', 'subtree', 'rotation', 'domainEvalue'];
     const VIEW_NUMBER_KEYS = ['font', 'node', 'branch'];
     const VIEW_BOOL_KEYS = ['horizontalLabels', 'msa', 'msaLogo', 'heatmap', 'domains', 'domainGlow', 'genes',
-        'scaleAxis', 'scaleGrid', 'timeAxis', 'timeGrid', 'matchCase', 'inverse'];
+        'scaleAxis', 'scaleGrid', 'scaleBar', 'timeAxis', 'timeGrid', 'matchCase', 'inverse'];
     // Lists of strings, comma-joined. A property ref carries ':' but never a
     // comma, and encodeViewValue leaves both readable in a hash.
     const VIEW_LIST_KEYS = ['heatmapManual', 'labelFields'];
@@ -11345,9 +11384,9 @@ function (root, d3, forester, phyloXml) {
         if (vis) {
             return vis;
         }
-        let style = nodeStyle(node);
-        if (style && (style.nodeColor || style.fontColor)) {
-            return style.nodeColor || style.fontColor;
+        let styleColor = nodeStyleColor(node);   // null under an active Color-by, as in the tree
+        if (styleColor) {
+            return styleColor;
         }
         if (_state.useVisualStyles && node.color) {
             return 'rgb(' + node.color.red + ',' + node.color.green + ',' + node.color.blue + ')';
@@ -13496,7 +13535,8 @@ function (root, d3, forester, phyloXml) {
     const SCALE_BAR_RESERVE = 30;
 
     function scaleBarShown() {
-        return _state.phylogram === true && _basicTreeProperties.branchLengths === true && !scaleAxisShown();
+        return _state.phylogram === true && _basicTreeProperties.branchLengths === true && !scaleAxisShown()
+            && _state.showScaleBar !== false;
     }
 
     // pixels per branch-length unit in the current layout's own coordinates
@@ -13522,7 +13562,9 @@ function (root, d3, forester, phyloXml) {
         if (!scaleBarShown()) {
             return;
         }
-        let bar = forester.scaleBarLength(branchLengthPixelsPerUnit(), SCALE_BAR_TARGET_PX);
+        // the unit the file states, as the distance axis prints it; none when it states none
+        let unit = _treeData && typeof _treeData.branch_length_unit === 'string' ? _treeData.branch_length_unit.trim() : '';
+        let bar = forester.scaleBarLength(branchLengthPixelsPerUnit(), SCALE_BAR_TARGET_PX, unit);
         if (!bar) {
             return;
         }
@@ -14156,6 +14198,11 @@ function (root, d3, forester, phyloXml) {
         scheduleUpdate(null, 0);
     }
 
+    function scaleBarCbClicked() {
+        _state.showScaleBar = getCheckboxValue(SCALE_BAR_CB);
+        scheduleUpdate(null, 0);
+    }
+
     // Fit the circular tree into the viewport, centred. The root is at the
     // group origin (0,0), so we place that at the viewport centre and scale so
     // the outer label ring fits. Computed from the known radial extent rather
@@ -15314,6 +15361,12 @@ function (root, d3, forester, phyloXml) {
             gridCb.disabled = _state.unrootedDisplay === true || _state.phylogram !== true
                 || _state.showScaleAxis !== true;
         }
+        let barCb = byId(SCALE_BAR_CB);
+        if (barCb) {
+            // a cladogram has nothing to measure, and under the axis the bar
+            // has given way; every layout can carry it otherwise
+            barCb.disabled = _state.phylogram !== true || scaleAxisShown();
+        }
         let minus = byId(ZOOM_OUT_X);
         let plus = byId(ZOOM_IN_X);
         let expandV = byId(ZOOM_TO_EXPAND_Y);
@@ -15380,22 +15433,6 @@ function (root, d3, forester, phyloXml) {
     }
 
 
-    function customCbClicked(cb_id) {
-        if (_nodeLabels) {
-            const cb_value = getCheckboxValue(cb_id);
-            for (const value of Object.values(_nodeLabels)) {
-                if (value.label && value.showButton === true && value.propertyRef && value.description) {
-                    if (value.cb_id === cb_id) {
-                        value.selected = cb_value;
-                    }
-                }
-            }
-            search0();
-            search1();
-            update();
-        }
-    }
-
     function taxonomyCbClicked() {
         _state.showTaxonomy = getCheckboxValue(TAXONOMY_CB);
         if (_state.showTaxonomy) {
@@ -18418,6 +18455,7 @@ function (root, d3, forester, phyloXml) {
         on(GENE_ANCHOR_SELECT, 'change', geneAnchorChanged);
         on(GENE_FAMILY_SELECT, 'change', geneFamilyChanged);
         on(GENE_LABELS_SELECT, 'change', geneLabelsChanged);
+        on(SCALE_BAR_CB, 'click', scaleBarCbClicked);
         on(SCALE_AXIS_CB, 'click', scaleAxisCbClicked);
         on(SCALE_GRID_CB, 'click', scaleGridCbClicked);
 
@@ -18431,20 +18469,6 @@ function (root, d3, forester, phyloXml) {
 
         on(SHORTEN_NODE_NAME_CB, 'click', shortenCbClicked);
 
-        if (_nodeLabels) {
-            for (const [key, value] of Object.entries(_nodeLabels)) {
-                if (value.label && value.showButton === true && value.propertyRef && value.description) {
-                    const cb_id = makeIdForCustomCheckboxButton(key);
-                    on(cb_id, 'click', function () {
-                        customCbClicked(cb_id);
-                    });
-                    if (value.selected === true) {
-                        setCheckboxValue(cb_id, true);
-                    }
-                }
-            }
-        }
-
         on(LABEL_COLOR_SELECT_MENU, 'change', function () {
             let v = this.value;
             if (v && v !== DEFAULT && _vis && _vis.byId[v]) {
@@ -18885,10 +18909,6 @@ function (root, d3, forester, phyloXml) {
             return '<label class="aptx-seg" title="' + tooltip + '"><input type="radio" name="' + radioGroup + '" id="' + id + '">' + content + '</label>';
         }
 
-        function makeIdForCustomCheckboxButton(key) {
-            return key + '__cb';
-        }
-
         function makeDisplayControl() {
             let labels = [];
             let nodes = [];
@@ -18910,17 +18930,6 @@ function (root, d3, forester, phyloXml) {
                 labels.push(makeCheckboxItem('Metadata', PROPERTIES_CB, 'to show/hide the nodes\' metadata (phyloXML'
                     + ' properties: species, host, …) in their labels; Metadata fields… chooses which, and in what order'));
             }
-            if (_nodeLabels) {
-                for (const [key, value] of Object.entries(_nodeLabels)) {
-                    if (value.label && value.propertyRef && value.description) {
-                        const cb_id = makeIdForCustomCheckboxButton(key);
-                        if (value.showButton === true) {
-                            labels.push(makeCheckboxItem(value.label, cb_id, value.description));
-                        }
-                        value.cb_id = cb_id;
-                    }
-                }
-            }
             if (_basicTreeProperties.confidences) {
                 labels.push(makeCheckboxItem('Confidence', CONFIDENCE_VALUES_CB, 'to show/hide confidence values'));
             }
@@ -18984,6 +18993,9 @@ function (root, d3, forester, phyloXml) {
                 let timeAxis = _timeInfo && _timeInfo.type
                     ? (_timeInfo.type === 'geologic' ? 'the geologic (ICS) time axis' : 'the calendar time axis')
                     : null;
+                // "Scale", the desktop's label for the same switch (its Settings > Overlays > Scale & Grid)
+                opts.push(makeCheckboxItem('Scale', SCALE_BAR_CB, 'to show/hide the scale bar at the bottom left of a'
+                    + ' phylogram: a round length in the tree\'s branch-length unit (it gives way while the scale axis is on)'));
                 opts.push(makeCheckboxItem('Scale Axis', SCALE_AXIS_CB, 'to show/hide '
                     + (timeAxis ? timeAxis + ' and node-age bars (a distance axis while the branches show divergence)'
                         : 'a labeled distance axis from the root to the deepest tip')
@@ -19399,6 +19411,7 @@ function (root, d3, forester, phyloXml) {
         syncHeatmapControls();
         setCheckboxValue(SCALE_AXIS_CB, _state.showScaleAxis);
         setCheckboxValue(SCALE_GRID_CB, _state.showScaleGrid);
+        setCheckboxValue(SCALE_BAR_CB, _state.showScaleBar);
         setCheckboxValue(SHORTEN_NODE_NAME_CB, _state.shortenNodeNames);
         populateVisualizationMenus();
         initializeSearchOptions();

package/forester.js

@@ -20,7 +20,7 @@
  *
  */
 
-// v 3.24.0
+// v 3.26.0
 // 2026-09-17
 //
 // forester.js is a general suite for dealing with phylogenetic trees.
@@ -8784,7 +8784,11 @@
     // -- 1, 2 or 5 times a power of ten -- chosen so the bar comes out about
     // targetPx long at pxPerUnit pixels per unit. Returns {length, label,
     // px}, or null when the scale is unusable (zero, negative or infinite).
-    forester.scaleBarLength = function (pxPerUnit, targetPx) {
+    // The label carries the tree's stated unit after the number ("0.05
+    // subs/site"), as the distance axis does at its end, and nothing when
+    // the file states none: a tree that does not say what its lengths
+    // measure gets no guess (a BV-BRC user asked for units, 2026-10-08).
+    forester.scaleBarLength = function (pxPerUnit, targetPx, unit) {
         if (!(pxPerUnit > 0) || !isFinite(pxPerUnit)) {
             return null;
         }
@@ -8793,7 +8797,8 @@
         let base = raw / Math.pow(10, k);
         let nice = base < 1.5 ? 1 : (base < 3.5 ? 2 : (base < 7.5 ? 5 : 10));
         let length = Number((nice * Math.pow(10, k)).toPrecision(2));
-        return {length: length, label: String(length), px: length * pxPerUnit};
+        let u = typeof unit === 'string' ? unit.trim() : '';
+        return {length: length, label: String(length) + (u ? ' ' + u : ''), px: length * pxPerUnit};
     };
 
     // --------------------------------------------------------------

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "archaeopteryx",
-  "version": "3.24.0",
+  "version": "3.26.0",
   "description": "Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.",
   "main": "archaeopteryx.js",
   "types": "archaeopteryx.d.ts",
@@ -20,7 +20,7 @@
     "LICENSE"
   ],
   "scripts": {
-    "test": "node test/forester_test.js && node test/search_test.js && node test/visualization_test.js && node test/domain_test.js && node test/gene_test.js && node test/clock_test.js && node test/metadata_test.js && node test/heatmap_test.js && node test/clustering_test.js",
+    "test": "node test/forester_test.js && node test/search_test.js && node test/visualization_test.js && node test/domain_test.js && node test/gene_test.js && node test/clock_test.js && node test/metadata_test.js && node test/heatmap_test.js && node test/clustering_test.js && node test/canvg_global_test.js",
     "lint": "eslint .",
     "lint:fix": "eslint . --fix",
     "format": "prettier --write .",