archaeopteryx 3.12.0 → 3.14.0

package/README.md

@@ -316,6 +316,25 @@ describe the MAD rooting only. A shared view remembers a MAD root. A phyloXML
 download keeps them as `<confidence type="MAD">`, as the desktop writes them;
 a Newick or Nexus download never puts one where a support value goes.
 
+A tip is written under its **name**; where it has none, under its taxonomy
+(code, then scientific, then common name), then its sequence's name, symbol or
+gene name, then its sequence **accession**, and only if it has none of those
+under a `node<N>` placeholder numbering it by position among the tips. Each
+step is tried in turn, so a taxonomy element that is present but empty does
+not stop the search. An unlabeled *internal* node stays unlabeled — a
+placeholder there would invent a name for an ancestor. Newick and Nexus use
+the one chain, so a tree saved in both formats names its tips identically, and
+it is the desktop Archaeopteryx's chain, compared byte for byte.
+
+Newick and Nexus have **one** support slot per branch and no place to name
+what kind of support it is, so a branch carrying several confidences is
+written with the first that is not a MAD value, exactly as the desktop writes
+it, and a `bootstrap` read back from such a file is typed `unknown`. phyloXML
+keeps every one of them, typed. Everything else survives a trip through
+either format unchanged — names, branch lengths (including zero-length and
+negative branches) and aligned sequences — in both directions, which the test
+suite pins as two standing round trips.
+
 1. Tria, F.D.K., Landan, G., Dagan, T. (2017). Phylogenetic rooting using
    minimal ancestor deviation. *Nature Ecology & Evolution*, 1, 0193.
    <https://www.nature.com/articles/s41559-017-0193>
@@ -555,7 +574,19 @@ column blank. Read `n` and judge.
 Alignments arrive with the tree: as phyloXML `<mol_seq is_aligned="true">`
 elements, or in a **Nexus** file whose characters matrix accompanies its tree.
 The **Nexus** entry in the Download menu writes the current tree *and* its
-alignment back into one Nexus file (Taxa, Characters and Trees blocks).
+alignment back into one Nexus file (Taxa, Characters and Trees blocks), in the
+same bytes the desktop Archaeopteryx writes: a row per taxon rather than per
+sequence, so a tip carrying no sequence gets a row of the missing symbol `?`
+and the matrix still covers every taxon the file declares. Reading it back,
+such a row is absence of data and not a sequence of question marks. Residues
+from a Nexus matrix are normalised as the desktop normalises them — raised to
+upper case, `.` read as a gap, and anything outside the declared alphabet read
+as the unspecified residue, `X` for protein and `N` for nucleotides, so the
+missing symbol `?` arrives as `X` or `N`. A phyloXML `<mol_seq>` is kept
+exactly as written, by both programs. Sequences
+of *unequal* length are not an alignment and cannot form a character matrix,
+so they are not written at all — the file says so in a bracketed comment
+rather than padding them into an alignment that does not exist.
 
 ## Heat maps
 
@@ -1021,11 +1052,45 @@ plus Search, and folds the ones that are adjustments to make later: Zoom,
 Sizes and the domain controls. Whatever you open or close is then remembered, for the
 page and across reloads, so a panel you have arranged stays arranged, even
 when you switch to another tree. In a short window it also keeps itself to one
-screen: opening a section folds the one you opened longest ago, but only while
-the panel would not otherwise fit — on a tall screen nothing is ever folded for
-you. Anything that puts something into a folded section opens it, so jumping to
-the search box (⌘F / Ctrl+F), revealing Search B, or a tool reporting its
-result as search hits all unfold Search. A host with little room to give can
+screen: opening a section folds the one you opened longest ago, and dragging
+the window (or the element it sits in) shorter does the same — but only while
+the panel would not otherwise fit, never past the last section left open, and
+never at all on a tall screen. Growing the window back leaves the folds where
+they are: what is open is your choice, and only running out of room overrules
+it. Anything that puts something into a folded section opens it, so jumping to
+the search box (⌘F / Ctrl+F) or a tool reporting its result as search hits
+unfolds Search. The **ⓘ** button in the panel header (or ⌘I / Ctrl+I) opens **Tree
+properties**, modelled on the desktop Archaeopteryx's *View › Tree
+Properties* and read-only:
+
+* **Tree** — name, description, identifier, type, branch-length unit,
+  rootedness and rerootability (each shown only where the file actually says
+  so), and "tree 2 of 3" when the file held several.
+* **Structure** — tips, internal nodes, total nodes, branches, whether the
+  tree is fully binary or how many polytomies it has and the widest of them,
+  depth from root to deepest tip, the longest tip label, and how many internal
+  nodes are named.
+* **Branch lengths** — how many branches carry one, then **minimum, median,
+  maximum and mean**, the sum as total tree length, the height from root to
+  farthest tip, any zero-length or negative branches, and whether the tree is
+  ultrametric.
+* **Support** — the same n / minimum / median / maximum / mean, **one section
+  per kind**. A bootstrap and a posterior on the same branch are not on one
+  scale, so they are never pooled; MAD values are not support and are counted
+  with the annotations instead.
+* **The tree carries** — taxonomies (and how many are distinct), taxonomy
+  identifiers, sequences, molecular sequences with the alignment width, domain
+  architectures, dates, distributions, events, branch colours, and **every
+  phyloXML property `ref` with the number of nodes carrying it** — each as
+  "n of m tips" or "n of m nodes".
+* **Time** — geologic ages or calendar years, dated nodes, the oldest node or
+  most recent tip, and whether there are confidence intervals.
+
+It describes what is on screen, so inside a subtree it describes the subtree
+and says so, and it is recomputed each time it opens rather than cached (24 ms
+on the 13,246-tip demo). There is no histogram.
+
+A host with little room to give can
 also start the whole panel tighter and narrower with
 [`panelDensity: 'compact'`](#configuration), or collapsed to its header bar
 with `collapseControlPanel`.
@@ -1733,7 +1798,7 @@ readout (`forester.msaResidueInfo`, `msaUngappedPosition`) names the residue
 
 Navigation: a lazily-created bar fixed at the viewport bottom — first / page
 back / slider / page forward / last, a jump-to-column box (1-based, matching
-the hover readout) and a live "column N – M of total" — plus wheel-over-track
+the hover readout) and a live "column N M of total" — plus wheel-over-track
 at a tenth of a screen per notch. Every route lands in one `msaScrollTo()`,
 which clamps and redraws; the tree never moves. A faint dashed guide runs
 from each tip's label (or its node, when labels are hidden) across to that