archaeopteryx 3.25.0 → 3.27.0

package/README.md

@@ -255,10 +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
@@ -293,7 +297,8 @@ The card button in the panel header opens **Control panel**: one row for every
 control the panel is currently showing, in the order it shows them, each with
 the control's own glyph or name and the sentence that explains it — the layout
 and display-type buttons included, drawn with the very glyph they carry in the
-panel. The About box has a row for it too.
+panel. The About box has a row for it too, and one for
+[Diagnostics](#diagnostics).
 
 The display types say what they do and when they are greyed, whether or not
 they are greyed in the view you are looking at: *"phylogram: branch lengths
@@ -1144,103 +1149,69 @@ names exactly what is missing (including "the loaded d3 is not usable as d3
 version 7"). The optional export libraries stay page-level globals in every
 loading style: `window.Canvg` (PNG), `window.jspdf` + svg2pdf.js (PDF).
 
-The parser is picked from the data and the `location`: content starting with
-`#NEXUS` (or a name ending in `.nex`/`.nexus`) is read as Nexus, JSON content
-(or a name ending in `.json`) as an **Auspice/Nextstrain v2** `dataset.json`,
-a name ending in `xml` as phyloXML, anything else as New Hampshire (Newick).
-A file holding **several trees** — a Nexus TREES block, a Newick file with one
-tree per `;`, a phyloXML with several phylogenies — opens on the first, and a
-picker with previous / next buttons at the top of the control panel moves
-between them (also ⌘⇧< / ⌘⇧>). **Each tree is its own workspace:** you leave
-a tree as you had it — layout, display type, labels, colours, sizes, tracks,
-both searches, the clade you switched to and the ones you collapsed — and it
-comes back that way. A tree you have not opened yet starts on its own
-presets, read from its own content, in the layout and sizes you are already
-using: stepping through ten trees of one file keeps them all circular, while
-each still labels and colours itself its own way. Zoom and pan are not kept
-(a tree opens fitted), and the views last as long as the page.
-A protein/DNA/RNA characters matrix in a Nexus file
-(sequential or interleaved) lands on the tips as an aligned `mol_seq`, so the
-alignment track appears just as it does for phyloXML.
-
-An Auspice dataset has no branch lengths of its own, so it opens in the
-metric it states completely: the **time view** when every node states a
-`num_date` (branch lengths are the `num_date` differences, sign kept), else
-the divergence view when every node states a `div`, else time if any node is
-dated. In the time view the calendar time axis and node-age bars come from
-`num_date` and its confidence interval, and every trait (country, host,
-clade, ...) becomes a
-`nextstrain:<trait>` node property — so Color-by, search and the node dialog
-pick them up. Both metrics are retained, and
-`forester.applyTimeBranchLengths(phy)` /
-`forester.applyDivergenceBranchLengths(phy)` /
-`forester.hasTimeAndDivergence(phy)` are the plumbing behind the
-**Time | Div** switch (and `forester.clockPlotKind(phy)` /
-`forester.clockPlotData(phy, view)` / `forester.clockRegression(xs, ys)`
-behind the **Clock plot**: which trees have one, its points and its
-least-squares line). The two `apply` functions answer `true` when they
-laid the tree out, and `false` — leaving every branch length as it was —
-when their layout cannot state every branch.
-
-**BEAST-style and NHX annotations** in Newick/Nexus input are always parsed
-(they used to be discarded): in a `[&key=value,...]` blob — as written by
-BEAST, BEAST 2, TreeAnnotator, FigTree and MrBayes — `posterior`, `prob`
-(+`prob_stddev`) and `bootstrap` become confidences, node `height`
-(median/mean) with its `95%_HPD` (or range) becomes the node date the age
-bars draw, FigTree's `!color` becomes the branch colour, and every other
-field (`rate`, traits, ...) becomes a `beast:<key>` node property for
-Color-by and search (`mutations`, `mcc` and FigTree's `!`-prefixed display
-directives are always text, never a gradient). **TreeTime**'s trees open as
-what they are: its `timetree.nexus` carries dates only as `date=` annotations,
-and those become node dates — calendar axis and all — where the date
-differences reproduce the branch lengths, which is true of the time tree and
-not of `divergence_tree.nexus`, though both carry the same annotations. Its
-annotations land as `treetime:<key>` rather than `beast:<key>`, and its
-`auspice_tree.json` opens as the Auspice dataset it is. FigTree's colour on a **taxon** — `'name'[&!color=...]` in the
-TAXLABELS block — is that tip's **label** colour, carried as the desktop's
-`style:font_color` property and drawn by Visual Styles. A number is a plain
-decimal with an optional exponent: `0x1A` and `3f` are text.
-**Auspice's "download Nexus"** annotations land where the
-Auspice JSON reader puts the same dataset, so one Nextstrain build opens the
-same way in either format: `num_date` is the node's date in years (and a
-`nextstrain:num_date` property), `num_date_CI={lo,hi}` its interval — on a tip
-too, where it is the sampling-date uncertainty — and `div` a
-`nextstrain:div` property — but only on a tree that is actually time-scaled,
-since Auspice writes the same annotations on its divergence tree: where the
-year differences do not reproduce the branch lengths the dates stay properties
-and no calendar axis is drawn. Inside an annotation a quote opens a string
-only where a value starts, so a bare `country=Côte d'Ivoire` is one field with
-an apostrophe in it. Classic `[&&NHX:...]` tags map to their phyloXML
-equivalents (`S=` taxonomy, `T=` taxonomy id, `B=` support, `D=`
-duplication/speciation event, `GN=`/`AC=` sequence name/accession), read as
-the desktop reads them: unquoted whitespace is formatting noise (`S=Homo
-sapiens` is `Homosapiens`), a quoted value keeps its content
-(`S="Homo sapiens"` is `Homo sapiens`), and the quotes themselves are never
-part of the value. Plain
-`[number]` brackets keep their old meaning (confidence values).
-
-Both entry points **throw** on bad input — an undefined or empty tree, an
-unparseable file, or a config key that no longer exists. Nothing is reported by
-a popup any more, and nothing fails silently.
-
-## Supported file formats
-
-| Format | I/O | What Archaeopteryx.js does with it | Ref. |
-|---|---|---|---|
-| **Newick** / New Hampshire (`.nwk`, `.nh`, `.tre`) | in / out | The base tree: topology, names, branch lengths, and bracketed confidence values. | [1] |
-| **NHX** — New Hampshire eXtended | in | `[&&NHX:...]` tags riding on Newick: taxonomy (`S=`, `T=`), sequence (`GN=`, `AC=`), support (`B=`), duplication/speciation events (`D=`). | [2] |
-| **Nexus** (`.nex`, `.nexus`) | in / out | One file for the tree(s) and, in a `CHARACTERS`/`DATA` block, an aligned protein/DNA/RNA matrix (sequential or interleaved) — the tree and its alignment together. | [3] |
-| **phyloXML** (`.xml`) | in / out | The richest native format: taxonomy, sequences and alignments, dates, confidences, branch colours and arbitrary metadata (custom properties). | [4] |
-| **Auspice / Nextstrain** `dataset.json` (v2) | in | Phylodynamic builds: sampling dates and their confidence, cumulative divergence, and discrete traits (country, clade, host, ...) with their posterior distributions. | [5] |
-| **BEAST** / BEAST 2 / TreeAnnotator annotations | in (embedded in Newick/Nexus) | `[&posterior=...,height_95%_HPD={lo,hi},rate=...]`-style blobs: posterior clade support, node-age confidence intervals, per-branch rates and other traits. FigTree's `!color` is read the same way. | [6, 7] |
-| **MrBayes** annotations | in (embedded in Newick/Nexus) | `prob=`/`prob.stddev=` blobs: posterior-probability clade support. | [8] |
-| **Metadata table** (`.tsv`, `.csv`) | in (beside a tree) | A header row and one row per tip, the first column naming the tip: every other column is joined onto the tips as a property, so it is offered for Color-by and Shape, searched, shown in the node data and written into phyloXML exports. See [Metadata tables](#metadata-tables). | — |
-| **FASTA** | out | The molecular sequence(s) of the selected tip(s), or every sequence the tree carries. Offered in the Download menu only when the tree actually carries molecular sequences (aligned or not). | [9] |
-| SVG · PNG · vector PDF | out | The drawn tree for publication or further editing — vector (SVG, PDF) or raster (PNG), either as shown on screen or the whole tree at full size (see [Downloads](#downloads)). General-purpose graphics formats, not phylogenetic data, so no literature reference applies. | — |
-
-The parser for a given input is auto-detected (see **The entry points**
-above); the Download menu offers whichever output formats the current tree
-can carry.
+### Diagnostics
+
+Checking at use rather than at load makes the viewer hard to break — and lets
+it run half-equipped without a word: no PDF in the Download menu, a retired
+config key ignored, a forced visualization overruled, each mentioned only in a
+console nobody has open. **`archaeopteryx.doctor()`** says what state the
+program is in on this page:
+
+```javascript
+var report = archaeopteryx.doctor();
+report.ok;          // false when something is wrong that nobody chooses
+report.summary;     // "nothing to report", or "2 things to check"
+report.problems;    // ['jspdf: loaded without svg2pdf.js: PDF export needs both, so it is off', ...]
+report.notes;       // stated, not flagged
+report.libraries;   // [{name, role, loaded, version, status, detail}, ...]
+report.functions;   // [{name: 'PDF export', available: false, detail: 'jspdf and svg2pdf.js are not loaded'}, ...]
+report.launch;      // {config, tips, tree, trees, container}, or null when no tree is on view
+report.text;        // all of it as plain text, to paste into an issue
+console.log(archaeopteryx.doctor().text);
+```
+
+It works before a launch, after a launch that threw, and in Node, and it never
+throws. The same report is in the viewer: the **About** box (a click on the
+program name) has a **Diagnostics** row that opens it, with a **Copy report**
+button — the copied text adds the keys passed to `launch()` (a string or a
+number as given, anything else as its kind: a tree or a callback is never
+copied) and the browser.
+
+What is a **problem** and what is only stated:
+
+| | |
+|---|---|
+| An optional library that is not loaded (canvg, jspdf, svg2pdf.js) | **stated**: "PNG export: off". Leaving one out is a site's choice. |
+| Half of a pair: jspdf without svg2pdf.js, or the other way round; svg2pdf.js loaded before jspdf | **problem** |
+| A library under its 2.x-era global (`window.canvg`, `window.jsPDF`) and not under the one this version reads; a `window.Canvg` without `fromString` | **problem** |
+| A d3 that is not version 7 (d3 4 to 6 have `d3.zoom` and `d3.cluster` too, so the launch check lets them through) | **problem**; a d3 7 older than 7.9 is a note |
+| `forester.js` and `archaeopteryx.js` from different releases (`forester.VERSION`) | **problem** |
+| A phyloxml older than 1.1.7: one that drops something when saving, or writes a node's style as the earlier releases did | **problem** — and "Read and save phyloXML" stays **on**, since it still reads and saves |
+| A phyloxml that only lays the file out differently from 1.1.7 (a newer release) | **note** |
+| phyloxml or sax not loaded, or a phyloxml that cannot read or write at all | **problem** |
+| What the last launch printed about its **config**: a deprecated key, an `initialVisualization` the tree cannot honour or that was overruled, a bad `pngExportScale`, a thrown `onViewChange`, and why a launch threw (`launchArchaeopteryx` included) | **problem** |
+| An export that failed (a clipboard the browser refused, a canvas too large), what the viewer left out of a tree (a domain or a gene it could not place), a size setting ignored | **note**: nothing a site's configuration decides |
+
+Only forester, jsPDF and d3's script build state a version; the others are
+judged by what they do. The d3 the viewer was handed at load is the one
+reported, as `launch()` uses it — a d3 with no `version` (the ES-module build
+a bundler imports) is recognised by what only d3 7 has. phyloxml is given a
+small tree to write, and the result is read for what the older releases are
+known to do.
+
+**While the report has a problem, a small dot follows the program name** in
+the panel header, and the name's tooltip says how many. It is neutral, not a
+warning colour: most of the people who see it are a site's visitors, who can
+do nothing about it. Nothing appears when an optional library is merely
+absent. The dot is brought up to date when a problem is recorded, when the
+page finishes loading, when the pointer enters the panel, when the About box
+opens and when `doctor()` is called — so a library that arrives after the
+launch puts it out without a relaunch.
+
+The warnings belong to **the tree on view**: `showTree()` starts them afresh
+for the tree it moves to, and so does a new launch. A launch that is rejected
+while an earlier viewer is still on the page leaves that viewer's report as
+it was and adds one line saying what failed.
 
 ### Downloads
 
@@ -1552,6 +1523,7 @@ 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. |
@@ -1919,17 +1891,29 @@ 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,
@@ -2126,8 +2110,9 @@ 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

@@ -138,6 +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;
@@ -213,6 +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. */
@@ -256,6 +259,57 @@ export interface ViewerHandle {
  * value, 'label' keeps them as names. */
 export type InternalNumericLabels = 'auto' | 'confidence' | 'label';
 
+/** One library's row in the diagnostics report. `status`: 'ok'; 'absent'
+ * (not loaded, and that is no fault: an optional library, or d3 outside a
+ * page); 'note' (stated, not flagged); 'problem' (lights the dot). */
+export interface DoctorLibrary {
+    name: 'forester.js' | 'd3' | 'phyloxml' | 'sax' | 'canvg' | 'jspdf' | 'svg2pdf.js' | string;
+    role: 'required' | 'optional';
+    loaded: boolean;
+    /** Only d3 (its script build), jsPDF and forester state one. */
+    version: string | null;
+    status: 'ok' | 'absent' | 'note' | 'problem';
+    detail: string;
+}
+
+/** What the user gets or does not get, with the reason when it is off. */
+export interface DoctorFunction {
+    name: 'Read and save phyloXML' | 'PNG export' | 'Copy PNG' | 'PDF export' | string;
+    available: boolean;
+    detail: string;
+}
+
+/** The tree on view. A config value is given as passed when it is a
+ * string, a number, a boolean or null, and otherwise as its kind:
+ * '(function)', '(list of 3)', '(object)'. */
+export interface DoctorLaunch {
+    config: Record<string, string | number | boolean | null>;
+    tips: number | null;
+    /** 1-based, of `trees`. */
+    tree: number;
+    trees: number;
+    container: { width: number; height: number } | null;
+}
+
+/** archaeopteryx.doctor(): the state of the program on this page. */
+export interface DoctorReport {
+    program: string;
+    version: string;
+    /** false when something is wrong that nobody chooses. */
+    ok: boolean;
+    /** 'nothing to report', or '2 things to check'. */
+    summary: string;
+    problems: string[];
+    notes: string[];
+    libraries: DoctorLibrary[];
+    functions: DoctorFunction[];
+    /** null while no tree is on view. */
+    launch: DoctorLaunch | null;
+    environment: { userAgent: string | null; secureContext: boolean | null };
+    /** The whole report as plain text, for pasting into an issue. */
+    text: string;
+}
+
 export interface Archaeopteryx {
     /** Launch the viewer into a container (a CSS selector or the element
      * itself; an unresolvable container throws). Exactly three arguments.
@@ -294,6 +348,11 @@ export interface Archaeopteryx {
     /** Module-level twin of the handle's getSelectedNodes. */
     getSelectedNodes(): PhylogenyNode[];
 
+    /** The state of the program on this page: the libraries, the functions
+     * they switch off, what the launch on view warned about. Works before a
+     * launch, after one that threw, and in Node; never throws. */
+    doctor(): DoctorReport;
+
     /** A view as a "key=value&..." string for a URL hash, and back. decode
      * accepts a leading '#', ignores what it does not know, and returns
      * null for nothing. */