Talk to the engine in plain language. It routes across the Design → Build → Edit → Learn loop and runs the right tools — no menus to hunt through.
" + '" + para.join("
") + "
$1")
.replace(/\*\*([^*]+)\*\*/g, "$1")
.replace(/\*([^*\n]+)\*/g, "$1");
}
lines.forEach(function (line) {
var h = line.match(/^(#{1,4})\s+(.*)$/);
var b = line.match(/^[*-]\s+(.*)$/);
if (h) { flushPara(); flushList(); html += '' + inline(h[2]) + "
"; } else if (b) { flushPara(); list.push(" with no wrap rule — forcing
// the message wide and requiring horizontal scroll (reported
// 2026-07-11, screenshot showed both symptoms together). Fences are
// parsed out first; a long sequence inside one collapses exactly like a
// pasted sequence, anything shorter renders as a normal wrapped block.
var FENCE_RE = /```[a-zA-Z0-9_-]*\n?([\s\S]*?)```/g;
var _seqStore = {}; // seq element id -> full sequence text, for the toggle handler
var _seqIdCounter = 0;
function formatMessageText(s) {
s = String(s == null ? "" : s);
FENCE_RE.lastIndex = 0;
if (!FENCE_RE.test(s)) return formatProse(s); // common case — no fence, skip the split work
FENCE_RE.lastIndex = 0;
var html = "", last = 0, m;
while ((m = FENCE_RE.exec(s))) {
if (m.index > last) html += formatProse(s.slice(last, m.index));
html += fencedBlock(m[1]);
last = m.index + m[0].length;
}
if (last < s.length) html += formatProse(s.slice(last));
return html;
}
function fencedBlock(raw) {
var trimmed = raw.replace(/\n$/, "");
var collapsed = trimmed.replace(/\s+/g, "");
if (collapsed.length >= 60 && /^[A-Za-z*]+$/.test(collapsed)) return seqBlock(collapsed);
return '' + esc(trimmed) + "
";
}
// A paste where every line is itself sequence-looking is conventional
// FASTA-style line wrapping (typically 60-80 chars/line) — ONE sequence
// that happens to be pre-wrapped, not N separate ones. SEQ_RE alone
// can't see this: a character class never matches across the newline
// between lines, so each wrapped line tripped its own seqBlock — a
// routine multi-line paste rendered as a tall stack of near-identical
// "Show full" rows (reported 2026-07-12). Joining same-paragraph
// sequence lines back together BEFORE the scan below fixes it at the
// source: the merged text has one long unbroken run, so it becomes one
// block. The wrap was a paste-time artifact, not part of the sequence,
// so dropping it also makes the "Show full" text a clean, continuous,
// actually-copyable sequence instead of one with embedded line breaks.
var SEQ_LINE_RE = /^[A-Za-z*]{20,}$/;
function mergeWrappedSequenceParagraphs(s) {
// Scans every line (not per-paragraph — a paragraph containing one
// leading prose line + the wrapped sequence would otherwise fail an
// "every line qualifies" check and never merge at all). Consecutive
// sequence-looking lines accumulate into one run and get joined with
// no separator when the run ends (a non-sequence line, a blank
// line, or the end of input); everything else passes through
// untouched, so surrounding prose and genuine paragraph breaks
// between two SEPARATE pastes are both preserved.
var lines = s.split("\n");
var out = [];
var run = [];
function flushRun() {
if (run.length >= 2) out.push(run.join(""));
else if (run.length === 1) out.push(run[0]);
run = [];
}
lines.forEach(function (line) {
if (SEQ_LINE_RE.test(line.trim())) {
run.push(line.trim());
} else {
flushRun();
out.push(line);
}
});
flushRun();
return out.join("\n");
}
function formatProse(s) {
s = mergeWrappedSequenceParagraphs(s);
SEQ_RE.lastIndex = 0;
if (!SEQ_RE.test(s)) return fmt(s); // common case — no bare sequence, skip the split work
SEQ_RE.lastIndex = 0;
var html = "", last = 0, m;
while ((m = SEQ_RE.exec(s))) {
if (m.index > last) html += fmt(s.slice(last, m.index));
html += seqBlock(m[0]);
last = m.index + m[0].length;
}
if (last < s.length) html += fmt(s.slice(last));
return html;
}
function seqPreview(full) {
return full.length > 60 ? full.slice(0, 36) + "…" + full.slice(-10) : full;
}
// Renders `seq` as escaped HTML with `ranges` ([start,end) pairs, 0-
// indexed, half-open) wrapped in a highlight span. Ranges are the
// MUTATED CODON positions (see mutated_positions in agent_tools.py) —
// never a naive diff against a WT string, which would also catch
// unrelated silent codon differences from independent restriction-site
// scrubbing and mislabel them as "the mutation."
function seqHtmlWithHighlights(seq, ranges) {
if (!ranges || !ranges.length) return esc(seq);
var sorted = ranges.slice().sort(function (a, b) { return a[0] - b[0]; });
var html = "", last = 0;
sorted.forEach(function (r) {
var start = Math.max(last, r[0]), end = Math.min(seq.length, r[1]);
if (start >= end) return;
if (start > last) html += esc(seq.slice(last, start));
html += '' + esc(seq.slice(start, end)) + "";
last = end;
});
if (last < seq.length) html += esc(seq.slice(last));
return html;
}
// Client-side only — the sequence text is already in the browser, no
// server round-trip needed. Mirrors the Blob-download pattern already
// used elsewhere in the engine (app.js's export/save flows).
function downloadFasta(label, seq) {
var header = String(label || "sequence").replace(/\s+/g, "_").slice(0, 80);
var body = ">" + header + "\n" + seq.replace(/(.{70})/g, "$1\n").replace(/\n$/, "") + "\n";
var blob = new Blob([body], { type: "text/x-fasta" });
var url = URL.createObjectURL(blob);
var a = document.createElement("a");
a.href = url; a.download = header.replace(/[^A-Za-z0-9_.-]/g, "_") + ".fasta";
document.body.appendChild(a); a.click(); a.remove();
setTimeout(function () { URL.revokeObjectURL(url); }, 1000);
}
// opts.label becomes the FASTA header + suggested filename for the
// download button — e.g. a DE variant passes its mutation list so the
// downloaded file is self-describing, not "sequence.fasta" x N when a
// reply has several variants.
// opts.highlightRanges marks changed codons red (see
// seqHtmlWithHighlights). A block with highlights starts EXPANDED —
// showing red text inside a collapsed, truncated preview would usually
// just hide the very thing being pointed out, since the mutated codon
// is rarely within the first-36/last-10-char snippet.
function seqBlock(seq, opts) {
opts = opts || {};
var id = "seq" + (_seqIdCounter++);
var ranges = opts.highlightRanges || null;
_seqStore[id] = { seq: seq, label: opts.label || "sequence", ranges: ranges };
var startExpanded = !!(ranges && ranges.length);
var previewHtml = startExpanded ? seqHtmlWithHighlights(seq, ranges) : esc(seqPreview(seq));
return '' +
'' + previewHtml + "" +
'" +
'' +
'' +
'" +
"";
}
// ── Wire events ---------------------------------------------------------
els.newBtn.addEventListener("click", newChat);
els.send.addEventListener("click", send);
els.input.addEventListener("input", autoGrow);
els.input.addEventListener("keydown", function (e) {
if (e.key === "Enter" && !e.shiftKey) { e.preventDefault(); send(); }
});
els.list.addEventListener("click", function (e) {
var del = e.target.closest("[data-del]");
if (del) { e.stopPropagation(); deleteChat(del.getAttribute("data-del")); return; }
var row = e.target.closest("[data-id]");
if (row) selectChat(row.getAttribute("data-id"));
});
// .asst-chat rows are role="button" tabindex="0" but plain s — a
// real