DNA → Protein Translator

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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>DNA → Protein Translator</title>
<link rel="icon" href="data:,">
<style>
/* sloprun design tokens — inline this block into every demo (self-contained rule).
   Identity: instrument-panel. Machine facts in mono; human words in sans.
   Green is EARNED: only for "it ran / it worked" states, never decoration. */
:root {
  --bg: #F6F6F3;          /* neutral paper, not cream */
  --surface: #FFFFFF;
  --ink: #1A1D21;
  --muted: #5A6068;
  --line: #E3E2DC;
  --accent: #C05600;      /* phosphor amber, darkened for light bg */
  --accent-soft: #FFF3E6;
  --run: #1A7F37;         /* earned green */
  --run-soft: #E7F4EA;
  --danger: #C93C37;
  --radius: 10px;
  --font-sans: system-ui, -apple-system, "Segoe UI", sans-serif;
  --font-mono: ui-monospace, "SF Mono", "Cascadia Code", Menlo, Consolas, monospace;
}
@media (prefers-color-scheme: dark) {
  :root:not([data-theme="light"]) {
    --bg: #14161A; --surface: #1C1F26; --ink: #E8E6E1; --muted: #9AA0A8;
    --line: #2A2E36; --accent: #FFB454; --accent-soft: #2A2118;
    --run: #3FB950; --run-soft: #16281B; --danger: #F47067;
  }
}
:root[data-theme="dark"] {
  --bg: #14161A; --surface: #1C1F26; --ink: #E8E6E1; --muted: #9AA0A8;
  --line: #2A2E36; --accent: #FFB454; --accent-soft: #2A2118;
  --run: #3FB950; --run-soft: #16281B; --danger: #F47067;
}
body { background: var(--bg); color: var(--ink); font-family: var(--font-sans); }

/* ---------- amino-acid class palette (light) ---------- */
:root {
  --hydro: #96590B; --hydro-s: #FAF0E1;
  --arom:  #6C28D5; --arom-s:  #F2ECFD;
  --polar: #0C6B82; --polar-s: #E5F4F8;
  --basic: #3A38C0; --basic-s: #ECEBFD;
  --acid:  #A61D62; --acid-s:  #FCE9F2;
  --spec:  #59554E; --spec-s:  #EFEDE8;
  --unk:   #6B7178; --unk-s:   #EFEFEC;
}
@media (prefers-color-scheme: dark) {
  :root:not([data-theme="light"]) {
    --hydro: #E4A45C; --hydro-s: #2F2519;
    --arom:  #B99EFA; --arom-s:  #241E39;
    --polar: #4FC9E9; --polar-s: #10262E;
    --basic: #909CFF; --basic-s: #1B1E3B;
    --acid:  #F17FB7; --acid-s:  #341525;
    --spec:  #B7AEA2; --spec-s:  #272520;
    --unk:   #9AA0A8; --unk-s:   #23262C;
  }
}
:root[data-theme="dark"] {
  --hydro: #E4A45C; --hydro-s: #2F2519;
  --arom:  #B99EFA; --arom-s:  #241E39;
  --polar: #4FC9E9; --polar-s: #10262E;
  --basic: #909CFF; --basic-s: #1B1E3B;
  --acid:  #F17FB7; --acid-s:  #341525;
  --spec:  #B7AEA2; --spec-s:  #272520;
  --unk:   #9AA0A8; --unk-s:   #23262C;
}
.c-hydro { --c: var(--hydro); --cs: var(--hydro-s); }
.c-arom  { --c: var(--arom);  --cs: var(--arom-s);  }
.c-polar { --c: var(--polar); --cs: var(--polar-s); }
.c-basic { --c: var(--basic); --cs: var(--basic-s); }
.c-acid  { --c: var(--acid);  --cs: var(--acid-s);  }
.c-spec  { --c: var(--spec);  --cs: var(--spec-s);  }
.c-unk   { --c: var(--unk);   --cs: var(--unk-s);   }
.c-stop  { --c: var(--ink);   --cs: var(--ink);     }

/* ---------- base ---------- */
* { box-sizing: border-box; }
[hidden] { display: none !important; }
html, body { margin: 0; padding: 0; }
body { -webkit-text-size-adjust: 100%; line-height: 1.5; overflow-x: hidden; }
.wrap { max-width: 1180px; margin: 0 auto; padding: 22px 16px 28px; }
h1, h2, h3 { margin: 0; font-weight: 650; letter-spacing: -0.01em; }
p { margin: 0; }
:where(button, input, select, textarea, summary, [tabindex]):focus-visible {
  outline: 2px solid var(--accent); outline-offset: 2px; border-radius: 6px;
}
.sr { position: absolute; width: 1px; height: 1px; padding: 0; margin: -1px;
      overflow: hidden; clip: rect(0 0 0 0); white-space: nowrap; border: 0; }

/* ---------- header ---------- */
header { margin-bottom: 16px; }
.eyebrow { font-family: var(--font-mono); font-size: 11px; letter-spacing: .12em;
  text-transform: uppercase; color: var(--muted); display: flex; align-items: center;
  gap: 8px; flex-wrap: wrap; }
.eyebrow .dot { width: 5px; height: 5px; border-radius: 50%; background: var(--accent); flex: none; }
h1 { font-size: clamp(22px, 4.6vw, 30px); margin: 6px 0 6px; }
.lede { color: var(--muted); font-size: 15px; max-width: 70ch; text-wrap: pretty; }
.warnbar { margin-top: 12px; display: flex; gap: 9px; align-items: baseline; flex-wrap: wrap;
  border: 1px solid var(--line); border-left: 3px solid var(--accent);
  background: var(--accent-soft); border-radius: 4px; padding: 8px 11px; }
.warnbar b { font-family: var(--font-mono); font-size: 11px; letter-spacing: .1em;
  text-transform: uppercase; color: var(--accent); flex: none; }
.warnbar span { font-size: 13px; color: var(--ink); max-width: 78ch; }

/* ---------- layout ---------- */
.grid { display: grid; grid-template-columns: minmax(0, 1.55fr) minmax(0, 1fr);
  gap: 14px; align-items: start; }
@media (max-width: 940px) {
  .grid { grid-template-columns: minmax(0, 1fr); }
  .grid > .col { display: contents; }
  #cInput { order: 1; } #cStrip { order: 2; } #cProtein { order: 3; }
  #cRead { order: 4; } #cDetail { order: 5; }
  #cTable { order: 6; } #cMethod { order: 7; }
}
.col { display: grid; gap: 14px; min-width: 0; align-content: start; }
.card { background: var(--surface); border: 1px solid var(--line);
  border-radius: var(--radius); padding: 13px; min-width: 0; }
.card > h2, details.card > summary {
  font-family: var(--font-mono); font-size: 11px; letter-spacing: .12em;
  text-transform: uppercase; color: var(--muted); font-weight: 600;
  display: flex; justify-content: space-between; align-items: center; gap: 8px 10px;
  flex-wrap: wrap; }
.card > h2 { margin-bottom: 10px; }
.card > h2 .meta { font-size: 11px; letter-spacing: .04em; text-transform: none;
  color: var(--muted); font-weight: 500; white-space: nowrap; }

/* ---------- controls ---------- */
.seg { display: inline-flex; border: 1px solid var(--line); border-radius: 7px;
  overflow: hidden; background: var(--bg); flex: none; }
.seg button { appearance: none; border: 0; background: none; cursor: pointer;
  font-family: var(--font-mono); font-size: 11.5px; letter-spacing: .06em;
  color: var(--muted); padding: 4px 10px; border-right: 1px solid var(--line);
  transition: background .12s, color .12s; }
.seg button:last-child { border-right: 0; }
.seg button:hover { color: var(--ink); }
.seg button[aria-checked="true"] { background: var(--accent-soft); color: var(--accent); font-weight: 600; }
.seg button:focus-visible { outline-offset: -2px; border-radius: 0; }

.btn { appearance: none; cursor: pointer; font-family: var(--font-mono); font-size: 11.5px;
  padding: 5px 10px; border-radius: 7px; border: 1px solid var(--line);
  background: var(--surface); color: var(--ink); transition: border-color .12s, background .12s; }
.btn:hover { border-color: var(--accent); color: var(--accent); }
.btn.ok { border-color: var(--run); color: var(--run); background: var(--run-soft); }
.btn.fail { border-color: var(--danger); color: var(--danger); }
.btnrow { display: flex; flex-wrap: wrap; gap: 6px; margin-top: 9px; }
.btnrow .lab { font-family: var(--font-mono); font-size: 10.5px; letter-spacing: .1em;
  text-transform: uppercase; color: var(--muted); align-self: center; margin-right: 2px; }

textarea {
  width: 100%; min-height: 108px; resize: vertical; display: block;
  font-family: var(--font-mono); font-size: 12.5px; line-height: 1.7; letter-spacing: .04em;
  color: var(--ink); background: var(--bg); border: 1px solid var(--line);
  border-radius: 8px; padding: 9px 10px; }
textarea::placeholder { color: var(--muted); }
.hint { font-size: 12px; color: var(--muted); margin-top: 8px; text-wrap: pretty; }
.hint code { font-family: var(--font-mono); font-size: 11.5px; color: var(--ink); }
.notice { margin-top: 9px; font-family: var(--font-mono); font-size: 11.5px;
  color: var(--muted); border: 1px solid var(--line); border-left: 3px solid var(--danger);
  border-radius: 4px; padding: 7px 9px; display: flex; flex-wrap: wrap; gap: 4px 12px; }
.notice b { color: var(--danger); font-weight: 600; }
.notice.calm { border-left-color: var(--line); }

/* ---------- codon strip ---------- */
.strip { display: flex; flex-wrap: wrap; gap: 4px 3px; font-family: var(--font-mono);
  font-size: 12.5px; line-height: 1.25; }
.cod { display: flex; flex-direction: column; align-items: center; width: 3ch;
  padding: 1px 0 3px; border-radius: 4px; border: 1px solid transparent;
  cursor: pointer; background: none; transition: background .1s, border-color .1s; }
.cod .ix { font-size: 8.5px; letter-spacing: 0; color: var(--muted); height: 11px;
  line-height: 11px; opacity: .8; }
.cod .d { color: var(--muted); }
.cod .r { color: var(--ink); }
.cod .u { color: var(--accent); font-weight: 600; }
.cod .bad { color: var(--danger); font-weight: 700; }
.cod .amb { color: var(--muted); text-decoration: underline dotted; }
.cod:hover { background: var(--bg); }
.cod.sel { border-color: var(--accent); background: var(--accent-soft); }
.cod.orf { border-bottom-color: var(--c); }
.cod.start .d, .cod.start .r { font-weight: 700; }
.cod.start { background: var(--accent-soft); }
.cod.stopc .r { color: var(--danger); font-weight: 700; }
.cod.off { width: auto; padding: 1px 3px 3px; opacity: .8; cursor: default; }
.cod.off:hover { background: none; }
.stripnote { font-family: var(--font-mono); font-size: 10.5px; color: var(--muted);
  display: flex; gap: 14px; flex-wrap: wrap; margin-bottom: 9px; }
.stripnote i { font-style: normal; color: var(--ink); }

/* ---------- beads ---------- */
.beads { display: flex; flex-wrap: wrap; gap: 4px; }
.bead { appearance: none; cursor: pointer; font-family: var(--font-mono);
  font-size: 12.5px; font-weight: 600; line-height: 1;
  width: 28px; height: 28px; padding: 0; border-radius: 8px;
  display: inline-flex; align-items: center; justify-content: center;
  border: 1px solid var(--c); background: var(--cs); color: var(--c);
  transition: transform .1s, box-shadow .1s; }
.beads.three .bead { width: auto; min-width: 40px; padding: 0 7px; font-size: 11.5px; }
.bead:hover { transform: translateY(-1px); }
/* Outside the reading frame: drop the fill, keep the letter at full strength.
   (Dimming with opacity here made the residue unreadable — ~1.7:1.) */
.bead.out { background: none; border-color: var(--line); border-style: dashed; }
.bead.c-stop { background: var(--ink); color: var(--surface); }
.bead.c-unk { border-style: dashed; }
.bead.start { box-shadow: inset 0 0 0 2px var(--c); }
.bead[aria-current="true"] { outline: 2px solid var(--accent); outline-offset: 2px; opacity: 1; }
.chainnote { font-size: 12px; color: var(--muted); margin-top: 10px; }

/* ---------- readout ---------- */
.tiles { display: grid; grid-template-columns: repeat(3, minmax(0, 1fr)); gap: 1px;
  background: var(--line); border: 1px solid var(--line); border-radius: 8px; overflow: hidden; }
.tile { background: var(--surface); padding: 8px 9px; min-width: 0; }
.tile .k { font-family: var(--font-mono); font-size: 9.5px; letter-spacing: .1em;
  text-transform: uppercase; color: var(--muted); }
.tile .v { font-family: var(--font-mono); font-size: 15px; font-weight: 600; color: var(--ink);
  margin-top: 2px; overflow: hidden; text-overflow: ellipsis; }
.status { margin-top: 10px; border-radius: 7px; padding: 8px 10px; font-size: 13px;
  border: 1px solid var(--line); background: var(--bg); color: var(--muted); text-wrap: pretty; }
.status b { font-family: var(--font-mono); font-size: 11px; letter-spacing: .1em;
  text-transform: uppercase; display: block; margin-bottom: 3px; }
.status.good { background: var(--run-soft); border-color: var(--run); color: var(--ink); }
.status.good b { color: var(--run); }
.status.warn { background: var(--accent-soft); border-color: var(--accent); color: var(--ink); }
.status.warn b { color: var(--accent); }
.status.none b { color: var(--muted); }

/* ---------- detail ---------- */
.kv { display: grid; grid-template-columns: 84px minmax(0, 1fr); gap: 4px 10px;
  font-family: var(--font-mono); font-size: 12.5px; }
.kv .k { color: var(--muted); font-size: 10.5px; letter-spacing: .08em;
  text-transform: uppercase; padding-top: 2px; }
.kv .v { color: var(--ink); overflow-wrap: anywhere; }
.kv .v .u { color: var(--accent); }
.kv .v .sw { display: inline-block; width: 9px; height: 9px; border-radius: 3px;
  background: var(--c); margin-right: 6px; vertical-align: baseline; }
.detnote { margin-top: 10px; font-size: 12.5px; color: var(--muted); text-wrap: pretty; }
.detnote.hot { color: var(--accent); }

/* ---------- key ---------- */
.key { display: flex; flex-wrap: wrap; gap: 6px 14px; margin-top: 11px;
  padding-top: 10px; border-top: 1px solid var(--line); }
.key .row { display: flex; align-items: center; gap: 6px; font-size: 12px;
  color: var(--muted); white-space: nowrap; }
.key .chip { width: 13px; height: 13px; border-radius: 4px; flex: none;
  border: 1px solid var(--c); background: var(--cs); }
.key .chip.c-stop { background: var(--ink); }
.key .chip.c-unk { border-style: dashed; }
.key .row span.n { font-family: var(--font-mono); font-size: 10.5px; color: var(--muted); }

/* ---------- codon table ---------- */
details.card { padding: 13px; }
details.card > summary { cursor: pointer; list-style: none; }
details.card > summary::-webkit-details-marker { display: none; }
details.card > summary::after { content: "+"; font-size: 14px; color: var(--accent); }
details.card[open] > summary::after { content: "−"; }
details.card[open] > summary { margin-bottom: 11px; }
.ctwrap { display: grid; gap: 11px 12px; grid-template-columns: repeat(auto-fit, minmax(186px, 1fr)); }
.ctlab { font-family: var(--font-mono); font-size: 9.5px; letter-spacing: .1em;
  text-transform: uppercase; color: var(--muted); margin-bottom: 4px; }
.ctgrid { display: grid; grid-template-columns: repeat(4, minmax(0, 1fr)); gap: 3px; }
.ct { border: 1px solid var(--line); border-radius: 5px; padding: 4px 2px; text-align: center;
  background: var(--cs); }
.ct .c { font-family: var(--font-mono); font-size: 11.5px; font-weight: 600; color: var(--c); }
.ct .a { font-family: var(--font-mono); font-size: 9.5px; color: var(--muted); letter-spacing: .02em; }
.ct.sel { border-color: var(--accent); outline: 1px solid var(--accent); }
.ct.c-stop { background: var(--bg); }
.ct.c-stop .c { color: var(--danger); }
.body { font-size: 13px; color: var(--muted); display: grid; gap: 9px; text-wrap: pretty; }
.body b { color: var(--ink); font-weight: 600; }
.body code { font-family: var(--font-mono); font-size: 11.5px; color: var(--ink); }

.empty { font-family: var(--font-mono); font-size: 12px; color: var(--muted);
  border: 1px dashed var(--line); border-radius: 7px; padding: 14px; text-align: center; }

footer { margin-top: 22px; padding-top: 12px; border-top: 1px solid var(--line);
  font-family: var(--font-mono); font-size: 11px; color: var(--muted);
  display: flex; justify-content: space-between; gap: 10px; flex-wrap: wrap; }

@media (max-width: 420px) {
  .kv { grid-template-columns: 74px minmax(0, 1fr); }
  .bead { width: 26px; height: 26px; }
}
@media (prefers-reduced-motion: reduce) {
  * { transition-duration: .01ms !important; animation-duration: .01ms !important; }
  .bead:hover { transform: none; }
}
</style>
</head>
<body>
<div class="wrap">

<header>
  <div class="eyebrow"><span class="dot" aria-hidden="true"></span>pharma · pure js · no libraries</div>
  <h1>DNA → Protein Translator</h1>
  <p class="lede">Paste DNA. It is transcribed to mRNA, cut into triplets, and each triplet is looked up
  in the genetic code — the same 64-entry table every cell reads. Shift the reading frame by one base and
  watch a clean protein turn into nonsense.</p>
  <div class="warnbar">
    <b>teaching tool</b>
    <span>Standard genetic code only — no introns, no alternative codes, nothing that happens to a protein
    after it is made. Good for learning how the lookup works; not for lab or clinical work.</span>
  </div>
</header>

<div class="grid">

  <div class="col">

    <section class="card" id="cInput">
      <h2>DNA input <span class="meta" id="mInput">—</span></h2>
      <label class="sr" for="seq">DNA sequence</label>
      <textarea id="seq" spellcheck="false" autocapitalize="off" autocorrect="off"
        placeholder="paste a DNA sequence — A, C, G, T (U is read as T)"></textarea>
      <div class="btnrow">
        <span class="lab">load</span>
        <button class="btn" type="button" data-ex="ins">insulin precursor</button>
        <button class="btn" type="button" data-ex="hbb">hemoglobin β</button>
        <button class="btn" type="button" data-ex="messy">messy paste</button>
        <button class="btn" type="button" id="revcomp">reverse complement ⇄</button>
      </div>
      <p class="hint">Line numbers, spaces and <code>&gt;</code> header lines are ignored. Lowercase is fine.
      <code>N</code> and the other ambiguity letters are resolved whenever every possibility gives the same
      amino acid. Anything else is flagged and read as unknown.</p>
      <div class="notice" id="notice" hidden></div>
    </section>

    <section class="card" id="cStrip">
      <h2>Transcript
        <span class="seg" role="radiogroup" aria-label="Reading frame" id="frames">
          <button type="button" role="radio" aria-checked="true" data-v="0" tabindex="0">frame 1</button>
          <button type="button" role="radio" aria-checked="false" data-v="1" tabindex="-1">frame 2</button>
          <button type="button" role="radio" aria-checked="false" data-v="2" tabindex="-1">frame 3</button>
        </span>
      </h2>
      <div class="stripnote">
        <span><i>top</i> DNA</span>
        <span><i>bottom</i> mRNA, T→<i style="color:var(--accent)">U</i></span>
        <span><i>dimmed</i> bases outside the frame</span>
      </div>
      <div class="strip" id="strip" role="group" aria-label="DNA cut into codons with its mRNA transcript"></div>
    </section>

    <section class="card" id="cProtein">
      <h2>Protein chain
        <span class="seg" role="radiogroup" aria-label="Amino acid notation" id="notation">
          <button type="button" role="radio" aria-checked="true" data-v="1" tabindex="0">1-letter</button>
          <button type="button" role="radio" aria-checked="false" data-v="3" tabindex="-1">3-letter</button>
        </span>
      </h2>
      <div class="beads" id="beads" role="group" aria-label="Amino acid chain"></div>
      <div class="key">
        <div class="row c-hydro"><span class="chip c-hydro"></span>hydrophobic <span class="n">A V L I M</span></div>
        <div class="row c-arom"><span class="chip c-arom"></span>aromatic <span class="n">F W Y</span></div>
        <div class="row c-polar"><span class="chip c-polar"></span>polar <span class="n">S T N Q</span></div>
        <div class="row c-basic"><span class="chip c-basic"></span>basic + <span class="n">K R H</span></div>
        <div class="row c-acid"><span class="chip c-acid"></span>acidic − <span class="n">D E</span></div>
        <div class="row c-spec"><span class="chip c-spec"></span>special <span class="n">G P C</span></div>
        <div class="row c-stop"><span class="chip c-stop"></span>stop</div>
        <div class="row c-unk"><span class="chip c-unk"></span>unreadable</div>
      </div>
      <p class="chainnote">Click a bead to inspect its codon — or focus the chain and walk it with
      <b>←</b> / <b>→</b>. Residues outside the start-to-stop stretch are drawn hollow.</p>
    </section>

  </div>

  <div class="col">

    <section class="card" id="cRead">
      <h2>Readout</h2>
      <div class="tiles">
        <div class="tile"><div class="k">bases</div><div class="v" id="tBases">—</div></div>
        <div class="tile"><div class="k">gc</div><div class="v" id="tGC">—</div></div>
        <div class="tile"><div class="k">codons</div><div class="v" id="tCodons">—</div></div>
        <div class="tile"><div class="k">residues</div><div class="v" id="tRes">—</div></div>
        <div class="tile"><div class="k">stops</div><div class="v" id="tStops">—</div></div>
        <div class="tile"><div class="k">start→stop</div><div class="v" id="tOrf">—</div></div>
      </div>
      <div class="status none" id="status" role="status"><b>—</b><span id="statusText">waiting for a sequence</span></div>
      <div class="btnrow">
        <button class="btn" type="button" id="copyAA">copy protein</button>
        <button class="btn" type="button" id="copyRNA">copy mRNA</button>
      </div>
    </section>

    <section class="card" id="cDetail">
      <h2>Selected codon</h2>
      <div class="kv" id="detail"></div>
      <p class="detnote" id="detnote"></p>
    </section>

    <details class="card" id="cTable" open>
      <summary>the codon table · 64 entries</summary>
      <div class="ctwrap" id="ctwrap"></div>
      <p class="hint">Shown in mRNA letters, grouped by first base; rows are the second base, columns the
      third. The selected codon is ringed. Notice how often a whole row of four says the same thing —
      that redundancy is why many single-base typos change nothing.</p>
    </details>

    <details class="card" id="cMethod">
      <summary>how this works</summary>
      <div class="body">
        <p>The whole translator is one string: <code>FFLLSSSSYY**CC*W…</code> — 64 amino-acid letters in
        codon order, unpacked into a lookup map at load. Every triplet is one map read.</p>
        <p><b>Transcription</b> here is just T→U. Real cells copy the template strand, so the mRNA matches
        the coding strand you pasted — which is why the letters look unchanged apart from the U.</p>
        <p><b>Reading frame.</b> Nothing in the sequence says where to start counting. Frames 2 and 3 shift
        the cut by one and two bases, and almost always shatter into stop codons — that is the point.</p>
        <p><b>Ambiguity.</b> A codon containing <code>N</code> (or R, Y, S, W, K, M, B, D, H, V) is expanded
        into every base it could be. If all of them land on the same amino acid — <code>TCN</code> is always
        serine — the residue is called. If not, it is <code>X</code>.</p>
        <p><b>Stop codon nicknames</b> are the old lab ones: TAA ochre, TAG amber, TGA opal.</p>
        <p>What this does not do: introns and splicing, alternative codon tables, signal-peptide cleavage,
        folding, or anything else that happens after the ribosome lets go. The insulin precursor loaded
        here becomes actual insulin only after a lot of cutting this page knows nothing about.</p>
      </div>
    </details>

  </div>
</div>

<footer>
  <span>demo · sloprun.dev</span>
  <span>standard genetic code · 64 codons</span>
</footer>

</div>

<script>
(function () {
  'use strict';
  function $(id) { return document.getElementById(id); }

  /* ---------------- the embedded genetic code ----------------
     64 amino-acid letters, bases ordered T,C,A,G at each of the three positions. */
  var CODE = 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG';
  var ORD = 'TCAG';
  var TABLE = {};
  for (var i1 = 0; i1 < 4; i1++)
    for (var i2 = 0; i2 < 4; i2++)
      for (var i3 = 0; i3 < 4; i3++)
        TABLE[ORD.charAt(i1) + ORD.charAt(i2) + ORD.charAt(i3)] = CODE.charAt(i1 * 16 + i2 * 4 + i3);

  var AA = {
    A: ['Ala', 'alanine', 'hydro'],       R: ['Arg', 'arginine', 'basic'],
    N: ['Asn', 'asparagine', 'polar'],    D: ['Asp', 'aspartic acid', 'acid'],
    C: ['Cys', 'cysteine', 'spec'],       E: ['Glu', 'glutamic acid', 'acid'],
    Q: ['Gln', 'glutamine', 'polar'],     G: ['Gly', 'glycine', 'spec'],
    H: ['His', 'histidine', 'basic'],     I: ['Ile', 'isoleucine', 'hydro'],
    L: ['Leu', 'leucine', 'hydro'],       K: ['Lys', 'lysine', 'basic'],
    M: ['Met', 'methionine', 'hydro'],    F: ['Phe', 'phenylalanine', 'arom'],
    P: ['Pro', 'proline', 'spec'],        S: ['Ser', 'serine', 'polar'],
    T: ['Thr', 'threonine', 'polar'],     W: ['Trp', 'tryptophan', 'arom'],
    Y: ['Tyr', 'tyrosine', 'arom'],       V: ['Val', 'valine', 'hydro'],
    '*': ['Stop', 'stop', 'stop'],        X: ['Xaa', 'unknown', 'unk']
  };
  var CLASSNAME = { hydro: 'hydrophobic', arom: 'aromatic', polar: 'polar',
    basic: 'basic (+)', acid: 'acidic (−)', spec: 'special', stop: 'stop', unk: 'unreadable' };
  var STOPNICK = { TAA: 'ochre', TAG: 'amber', TGA: 'opal' };
  var IUPAC = { A: 'A', C: 'C', G: 'G', T: 'T', R: 'AG', Y: 'CT', S: 'CG', W: 'AT',
    K: 'GT', M: 'AC', B: 'CGT', D: 'AGT', H: 'ACT', V: 'ACG', N: 'ACGT' };
  var COMPL = { A: 'T', T: 'A', G: 'C', C: 'G', R: 'Y', Y: 'R', S: 'S', W: 'W',
    K: 'M', M: 'K', B: 'V', V: 'B', D: 'H', H: 'D', N: 'N' };
  var AMBIG = 'RYSWKMBDHVN';
  var MAX_BASES = 60000;
  var MAX_DRAW = 1500;

  function translate(codon) {
    var sets = [];
    for (var i = 0; i < 3; i++) {
      var s = IUPAC[codon.charAt(i)];
      if (!s) return 'X';
      sets.push(s);
    }
    var found = null;
    for (var a = 0; a < sets[0].length; a++)
      for (var b = 0; b < sets[1].length; b++)
        for (var c = 0; c < sets[2].length; c++) {
          var aa = TABLE[sets[0].charAt(a) + sets[1].charAt(b) + sets[2].charAt(c)];
          if (found === null) found = aa;
          else if (found !== aa) return 'X';
        }
    return found === null ? 'X' : found;
  }

  /* ---------------- examples ---------------- */
  var EX = {
    ins:
      'GATCACTGTCCTTCTGCC\n' +
      'ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCC\n' +
      'TTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTC\n' +
      'TTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCT\n' +
      'GGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGT\n' +
      'ACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG',
    hbb:
      'ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTT\n' +
      'GGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACC',
    messy:
      '>notebook paste — two flagged bases, one stray letter\n' +
      '  1 atggccctgt ggatgcgcct cctgcccctg ctggcgctgc\n' +
      ' 41 tggccctctg gggacctgac ccagccgcag cctttgtgaa\n' +
      ' 81 ccaacacctg tgcggctcnc acctggtgga agctctctnc\n' +
      '121 ctagtgtgcg gggaacgagg cttcttctac acacccaaga\n' +
      '161 cccgccggga ggcagaggac ctgcaggtgz ggcaggtgga\n' +
      '201 gctgggcggg ggccctggtg caggcagcct gcagcccttg\n' +
      '241 gccctggagg ggtccctgca gaagcgtggc attgtggaac\n' +
      '281 aatgctgtac cagcatctgc tccctctacc agctggagaa\n' +
      '321 ctactgcaac tag'
  };

  /* ---------------- parsing ---------------- */
  function parse(raw) {
    var bases = [], bad = {}, badN = 0, ambN = 0, ignored = 0, headers = 0, gc = 0, truncated = false;
    var lines = raw.split(/\r?\n/);
    for (var li = 0; li < lines.length; li++) {
      var line = lines[li];
      if (/^\s*>/.test(line)) { headers++; continue; }
      for (var i = 0; i < line.length; i++) {
        if (bases.length >= MAX_BASES) { truncated = true; break; }
        var ch = line.charAt(i).toUpperCase();
        if (ch === ' ' || ch === '\t' || ch === '\r' || ch === '\f' || ch === '\v'
            || (ch >= '0' && ch <= '9') || ch === '-' || ch === '.') {
          ignored++; continue;
        }
        if (ch === 'U') ch = 'T';
        if (ch === 'A' || ch === 'C' || ch === 'G' || ch === 'T') {
          if (ch === 'G' || ch === 'C') gc++;
          bases.push({ c: ch, ok: true, amb: false });
        } else if (AMBIG.indexOf(ch) >= 0) {
          ambN++;
          bases.push({ c: ch, ok: true, amb: true });
        } else {
          badN++; bad[ch] = (bad[ch] || 0) + 1;
          bases.push({ c: ch, ok: false, amb: false });
        }
      }
      if (truncated) break;
    }
    return { bases: bases, bad: bad, badN: badN, ambN: ambN, ignored: ignored,
      headers: headers, gc: gc, truncated: truncated };
  }

  function frameModel(bases, frame) {
    var codons = [], stops = 0, orfStart = -1, orfStop = -1;
    for (var i = frame; i + 3 <= bases.length; i += 3) {
      var t0 = bases[i], t1 = bases[i + 1], t2 = bases[i + 2];
      var dna = t0.c + t1.c + t2.c;
      var aa = translate(dna);
      var c = {
        i: codons.length, at: i, dna: dna, rna: dna.replace(/T/g, 'U'), aa: aa,
        bases: [t0, t1, t2],
        ok: t0.ok && t1.ok && t2.ok,
        amb: !!(t0.amb || t1.amb || t2.amb),
        isStart: dna === 'ATG',
        isStop: aa === '*'
      };
      if (c.isStop) stops++;
      if (orfStart < 0 && c.isStart) orfStart = c.i;
      if (orfStart >= 0 && orfStop < 0 && c.isStop && c.i > orfStart) orfStop = c.i;
      codons.push(c);
    }
    return { codons: codons, stops: stops, orfStart: orfStart, orfStop: orfStop,
      lead: Math.min(frame, bases.length),
      tail: bases.length - frame - codons.length * 3 };
  }

  /* ---------------- state ---------------- */
  var S = { frame: 0, three: false, sel: -1, p: null, m: null, moved: false };

  function el(tag, cls, text) {
    var n = document.createElement(tag);
    if (cls) n.className = cls;
    if (text !== undefined) n.textContent = text;
    return n;
  }
  function cls(aa) { return 'c-' + (AA[aa] ? AA[aa][2] : 'unk'); }
  function inOrf(m, i) {
    return m.orfStart >= 0 && i >= m.orfStart && (m.orfStop < 0 ? true : i <= m.orfStop);
  }

  /* ---------------- render: codon strip ---------------- */
  function baseChars(parent, trio, rna) {
    for (var i = 0; i < trio.length; i++) {
      var b = trio[i];
      var ch = (rna && b.c === 'T') ? 'U' : b.c;
      var k = !b.ok ? 'bad' : (b.amb ? 'amb' : (rna && b.c === 'T' ? 'u' : ''));
      if (k) { var s = el('span', k, ch); parent.appendChild(s); }
      else parent.appendChild(document.createTextNode(ch));
    }
  }
  function offTile(bases, from, count, label) {
    if (count <= 0) return null;
    var t = el('span', 'cod off');
    t.appendChild(el('span', 'ix', label));
    var d = el('span', 'd'), r = el('span', 'r');
    var trio = bases.slice(from, from + count);
    baseChars(d, trio, false);
    baseChars(r, trio, true);
    t.appendChild(d); t.appendChild(r);
    t.title = count + (count === 1 ? ' base' : ' bases') + ' outside this reading frame';
    return t;
  }
  function renderStrip() {
    var host = $('strip');
    host.textContent = '';
    var m = S.m, bases = S.p.bases;
    if (!m.codons.length) {
      host.appendChild(el('div', 'empty', bases.length
        ? 'fewer than three readable bases in this frame'
        : 'no bases yet — paste a sequence, or load an example above'));
      return;
    }
    var frag = document.createDocumentFragment();
    var t = offTile(bases, 0, m.lead, "5′");
    if (t) frag.appendChild(t);
    var n = Math.min(m.codons.length, MAX_DRAW);
    for (var i = 0; i < n; i++) {
      var c = m.codons[i];
      var tile = el('span', 'cod ' + cls(c.aa));
      if (inOrf(m, i)) tile.className += ' orf';
      if (c.isStart) tile.className += ' start';
      if (c.isStop) tile.className += ' stopc';
      if (i === S.sel) tile.className += ' sel';
      tile.setAttribute('data-i', i);
      tile.appendChild(el('span', 'ix', (i + 1) % 10 === 0 ? String(i + 1) : ''));
      var d = el('span', 'd'), r = el('span', 'r');
      baseChars(d, c.bases, false);
      baseChars(r, c.bases, true);
      tile.appendChild(d); tile.appendChild(r);
      tile.title = 'codon ' + (i + 1) + ' · ' + c.dna + ' → ' + c.rna + ' · ' + AA[c.aa][0];
      frag.appendChild(tile);
    }
    if (m.codons.length > MAX_DRAW) {
      frag.appendChild(el('span', 'cod off', '…'));
    }
    var tt = offTile(bases, bases.length - m.tail, m.tail, "3′");
    if (tt) frag.appendChild(tt);
    host.appendChild(frag);
  }

  /* ---------------- render: beads ---------------- */
  function renderBeads() {
    var host = $('beads');
    host.textContent = '';
    host.className = 'beads' + (S.three ? ' three' : '');
    var m = S.m;
    if (!m.codons.length) {
      host.appendChild(el('div', 'empty', 'nothing to translate yet'));
      return;
    }
    var frag = document.createDocumentFragment();
    var n = Math.min(m.codons.length, MAX_DRAW);
    for (var i = 0; i < n; i++) {
      var c = m.codons[i];
      var meta = AA[c.aa];
      var b = el('button', 'bead ' + cls(c.aa), S.three ? meta[0] : c.aa);
      b.type = 'button';
      b.setAttribute('data-i', i);
      b.tabIndex = (i === S.sel) ? 0 : -1;
      b.setAttribute('aria-current', i === S.sel ? 'true' : 'false');
      /* Only mark residues as "outside" when there IS a reading frame to be
         outside of — otherwise every bead in frames 2/3 renders as a ghost. */
      if (m.orfStart >= 0 && !inOrf(m, i)) b.className += ' out';
      if (c.isStart) b.className += ' start';
      b.setAttribute('aria-label', 'codon ' + (i + 1) + ', ' + c.rna + ', ' + meta[1]
        + (c.isStart ? ', start codon' : '') + (c.isStop ? ', stop codon' : ''));
      frag.appendChild(b);
    }
    host.appendChild(frag);
    if (m.codons.length > MAX_DRAW) {
      var note = el('div', 'empty', 'long sequence — showing the first ' + MAX_DRAW + ' codons');
      note.style.width = '100%';
      host.appendChild(note);
    }
  }

  /* ---------------- render: readout ---------------- */
  function renderReadout() {
    var p = S.p, m = S.m;
    var n = p.bases.length;
    $('tBases').textContent = n ? String(n) : '—';
    $('tGC').textContent = n ? (p.gc / n * 100).toFixed(1) + '%' : '—';
    $('tCodons').textContent = m.codons.length ? String(m.codons.length) : '—';
    $('tRes').textContent = m.codons.length ? String(m.codons.length - m.stops) : '—';
    $('tStops').textContent = m.codons.length ? String(m.stops) : '—';

    var st = $('status'), txt = $('statusText'), lab = st.firstElementChild;
    var orfCell = $('tOrf');
    if (!m.codons.length) {
      orfCell.textContent = '—';
      st.className = 'status none'; lab.textContent = '—';
      txt.textContent = n ? 'not enough bases to make a codon in this frame.'
                          : 'waiting for a sequence.';
    } else if (m.orfStart >= 0 && m.orfStop >= 0) {
      var len = m.orfStop - m.orfStart;
      orfCell.textContent = len + ' aa';
      st.className = 'status good'; lab.textContent = 'complete reading frame';
      txt.textContent = 'ATG at codon ' + (m.orfStart + 1) + ' runs to '
        + m.codons[m.orfStop].dna + ' (' + (STOPNICK[m.codons[m.orfStop].dna] || 'stop')
        + ') at codon ' + (m.orfStop + 1) + ' — ' + len + ' amino acids, start to stop.';
    } else if (m.orfStart >= 0) {
      orfCell.textContent = 'open';
      st.className = 'status warn'; lab.textContent = 'runs off the end';
      txt.textContent = 'ATG at codon ' + (m.orfStart + 1)
        + ', but no stop codon after it — the sequence ends mid-protein.';
    } else {
      orfCell.textContent = 'none';
      st.className = 'status warn'; lab.textContent = 'no start codon';
      txt.textContent = 'no ATG in this frame'
        + (m.stops ? ', and ' + m.stops + ' stop codon' + (m.stops === 1 ? '' : 's') + ' chop it up' : '')
        + '. Try another frame.';
    }

    var meta = [];
    if (n) meta.push(n + ' bases');
    if (n) meta.push('GC ' + (p.gc / n * 100).toFixed(1) + '%');
    $('mInput').textContent = meta.length ? meta.join(' · ') : '—';

    var nt = $('notice');
    nt.textContent = '';
    nt.className = 'notice' + (p.badN ? '' : ' calm');
    var first = true;
    if (p.badN) {
      var keys = Object.keys(p.bad).sort();
      var lead = el('span');
      lead.appendChild(el('b', null, p.badN + ' unreadable character'
        + (p.badN === 1 ? '' : 's') + ' (' + keys.join(' ') + ')'));
      lead.appendChild(document.createTextNode(' kept in place, read as unknown'));
      nt.appendChild(lead);
      first = false;
    }
    var parts = [];
    if (p.ambN) parts.push(p.ambN + ' ambiguity code' + (p.ambN === 1 ? '' : 's') + ' resolved where possible');
    if (p.ignored) parts.push(p.ignored + ' spacing/number character' + (p.ignored === 1 ? '' : 's') + ' ignored');
    if (p.headers) parts.push(p.headers + ' header line' + (p.headers === 1 ? '' : 's') + ' skipped');
    if (p.truncated) parts.push('input trimmed to ' + MAX_BASES + ' bases');
    for (var i = 0; i < parts.length; i++) {
      nt.appendChild(el('span', null, (first && i === 0 ? '' : '· ') + parts[i]));
    }
    nt.hidden = !(p.badN || parts.length);
  }

  /* ---------------- render: detail ---------------- */
  function renderDetail() {
    var host = $('detail'), note = $('detnote');
    host.textContent = ''; note.textContent = ''; note.className = 'detnote';
    var m = S.m;
    if (!m.codons.length || S.sel < 0 || S.sel >= m.codons.length) {
      host.appendChild(el('div', 'k', 'codon'));
      host.appendChild(el('div', 'v', '—'));
      note.textContent = 'Nothing selected.';
      highlightTable(null);
      return;
    }
    var c = m.codons[S.sel], meta = AA[c.aa];
    function row(k, node) {
      host.appendChild(el('div', 'k', k));
      var v = el('div', 'v');
      if (typeof node === 'string') v.textContent = node; else v.appendChild(node);
      host.appendChild(v);
    }
    row('codon', (S.sel + 1) + ' of ' + m.codons.length);
    row('bases', (c.at + 1) + '–' + (c.at + 3));
    var conv = el('span');
    conv.appendChild(document.createTextNode(c.dna + '  →  '));
    for (var i = 0; i < 3; i++) {
      var ch = c.rna.charAt(i);
      if (ch === 'U') conv.appendChild(el('span', 'u', 'U'));
      else conv.appendChild(document.createTextNode(ch));
    }
    row('dna → mrna', conv);
    var resid = el('span');
    var sw = el('span', 'sw ' + cls(c.aa));
    resid.appendChild(sw);
    resid.appendChild(document.createTextNode(
      c.aa === '*' ? 'Stop' : meta[0] + ' · ' + c.aa));
    resid.className = cls(c.aa);
    row('residue', resid);
    row('name', meta[1]);
    row('class', CLASSNAME[meta[2]]);

    if (c.isStop) {
      note.className = 'detnote hot';
      note.textContent = 'Stop codon (' + (STOPNICK[c.dna] || 'stop')
        + ') — no amino acid, the chain is released here.';
    } else if (!c.ok) {
      note.className = 'detnote hot';
      note.textContent = 'This triplet contains a character that is not a base, so it cannot be read.';
    } else if (c.amb && c.aa === 'X') {
      note.className = 'detnote hot';
      note.textContent = 'Ambiguous: the possible bases lead to different amino acids, so the residue is unknown.';
    } else if (c.amb) {
      note.textContent = 'Ambiguous, but every possibility gives ' + meta[1] + ' — so the residue is certain anyway.';
    } else if (S.sel === m.orfStart) {
      note.className = 'detnote hot';
      note.textContent = 'Start codon — the first ATG in this frame. Translation begins here.';
    } else if (c.isStart) {
      note.textContent = 'Another ATG, downstream of the first. Methionine doubles as the start signal.';
    } else if (inOrf(m, S.sel)) {
      note.textContent = 'Residue ' + (S.sel - m.orfStart + 1) + ' of the reading frame.';
    } else if (m.orfStart < 0) {
      note.textContent = 'No ATG anywhere in this frame, so nothing here would ever be '
        + 'translated — this triplet is only what the letters happen to spell.';
    } else {
      note.textContent = 'Outside the reading frame — read, but never translated in a cell.';
    }
    highlightTable(c.rna);
  }

  /* ---------------- codon table ---------------- */
  var ctCells = {};
  function buildTable() {
    var host = $('ctwrap'), frag = document.createDocumentFragment();
    for (var a = 0; a < 4; a++) {
      var first = ORD.charAt(a) === 'T' ? 'U' : ORD.charAt(a);
      var block = el('div', 'ctblock');
      block.appendChild(el('div', 'ctlab', 'first base ' + first));
      var grid = el('div', 'ctgrid');
      for (var b = 0; b < 4; b++)
        for (var c = 0; c < 4; c++) {
          var dna = ORD.charAt(a) + ORD.charAt(b) + ORD.charAt(c);
          var aa = TABLE[dna], rna = dna.replace(/T/g, 'U');
          var cell = el('div', 'ct ' + cls(aa));
          cell.appendChild(el('div', 'c', rna));
          cell.appendChild(el('div', 'a', AA[aa][0]));
          ctCells[rna] = cell;
          grid.appendChild(cell);
        }
      block.appendChild(grid);
      frag.appendChild(block);
    }
    host.appendChild(frag);
  }
  var ctSel = null;
  function highlightTable(rna) {
    if (ctSel) ctSel.classList.remove('sel');
    ctSel = ctCells[rna] || null;
    if (ctSel) ctSel.classList.add('sel');
  }

  /* ---------------- selection ---------------- */
  function markSelection(scroll) {
    var beads = $('beads').children, strip = $('strip').children, i;
    for (i = 0; i < beads.length; i++) {
      var b = beads[i];
      if (!b.getAttribute) continue;
      var bi = b.getAttribute('data-i');
      if (bi === null) continue;
      var on = (+bi === S.sel);
      b.setAttribute('aria-current', on ? 'true' : 'false');
      b.tabIndex = on ? 0 : -1;
      if (on && scroll) { try { b.scrollIntoView({ block: 'nearest', inline: 'nearest' }); } catch (e) { } }
    }
    for (i = 0; i < strip.length; i++) {
      var t = strip[i];
      if (!t.getAttribute) continue;
      var ti = t.getAttribute('data-i');
      if (ti === null) continue;
      t.classList.toggle('sel', +ti === S.sel);
    }
    renderDetail();
  }
  function select(i, scroll, focus) {
    var m = S.m;
    if (!m.codons.length) return;
    if (i < 0) i = 0;
    if (i > Math.min(m.codons.length, MAX_DRAW) - 1) i = Math.min(m.codons.length, MAX_DRAW) - 1;
    S.sel = i;
    markSelection(scroll);
    if (focus) {
      var b = $('beads').querySelector('[data-i="' + i + '"]');
      if (b) b.focus();
    }
  }

  /* ---------------- build ---------------- */
  function build(resetSel) {
    S.p = parse($('seq').value);
    S.m = frameModel(S.p.bases, S.frame);
    var n = Math.min(S.m.codons.length, MAX_DRAW);
    if (resetSel || S.sel < 0 || S.sel >= n) {
      S.sel = (S.m.orfStart >= 0 && S.m.orfStart < n) ? S.m.orfStart : (n ? 0 : -1);
    }
    renderStrip();
    renderBeads();
    renderReadout();
    renderDetail();
  }

  /* ---------------- segmented controls ---------------- */
  function seg(id, onpick) {
    var host = $(id);
    var btns = [].slice.call(host.querySelectorAll('button'));
    function pick(idx, focus) {
      btns.forEach(function (b, i) {
        var on = i === idx;
        b.setAttribute('aria-checked', on ? 'true' : 'false');
        b.tabIndex = on ? 0 : -1;
      });
      if (focus) btns[idx].focus();
      onpick(btns[idx].getAttribute('data-v'));
    }
    btns.forEach(function (b, i) {
      b.addEventListener('click', function () { pick(i, false); });
    });
    host.addEventListener('keydown', function (e) {
      var cur = btns.indexOf(document.activeElement);
      if (cur < 0) return;
      var next = null;
      if (e.key === 'ArrowRight' || e.key === 'ArrowDown') next = (cur + 1) % btns.length;
      else if (e.key === 'ArrowLeft' || e.key === 'ArrowUp') next = (cur - 1 + btns.length) % btns.length;
      else if (e.key === 'Home') next = 0;
      else if (e.key === 'End') next = btns.length - 1;
      if (next !== null) { e.preventDefault(); pick(next, true); }
    });
  }

  /* ---------------- copy ---------------- */
  function fallbackCopy(text) {
    try {
      var ta = document.createElement('textarea');
      ta.value = text;
      ta.setAttribute('readonly', '');
      ta.style.position = 'fixed';
      ta.style.top = '-2000px';
      document.body.appendChild(ta);
      ta.select();
      var ok = document.execCommand('copy');
      document.body.removeChild(ta);
      return ok;
    } catch (e) { return false; }
  }
  function copy(btn, label, text) {
    if (!text) { flash(btn, label, false, 'nothing to copy'); return; }
    var done = function (ok) { flash(btn, label, ok, ok ? 'copied ✓' : 'copy blocked'); };
    if (navigator.clipboard && navigator.clipboard.writeText) {
      navigator.clipboard.writeText(text).then(function () { done(true); },
        function () { done(fallbackCopy(text)); });
    } else {
      done(fallbackCopy(text));
    }
  }
  var flashTimers = {};
  function flash(btn, label, ok, msg) {
    btn.textContent = msg;
    btn.classList.toggle('ok', ok);
    btn.classList.toggle('fail', !ok);
    clearTimeout(flashTimers[label]);
    flashTimers[label] = setTimeout(function () {
      btn.textContent = label;
      btn.classList.remove('ok', 'fail');
    }, 1500);
  }
  function proteinText() {
    var out = [];
    for (var i = 0; i < S.m.codons.length; i++) {
      var c = S.m.codons[i];
      out.push(S.three ? AA[c.aa][0] : c.aa);
    }
    return S.three ? out.join('-') : out.join('');
  }
  function rnaText() {
    var out = [];
    for (var i = 0; i < S.m.codons.length; i++) out.push(S.m.codons[i].rna);
    return out.join(' ');
  }

  /* ---------------- wiring ---------------- */
  var debounce = null;
  $('seq').addEventListener('input', function () {
    clearTimeout(debounce);
    debounce = setTimeout(function () { debounce = null; build(false); }, 110);
  });
  /* Any control that reads S.p / S.m must first settle a pending keystroke,
     or it acts on the sequence as it was up to 110ms ago. */
  function flush() {
    if (debounce !== null) { clearTimeout(debounce); debounce = null; build(false); }
  }

  seg('frames', function (v) {
    var f = +v;
    if (f === S.frame) return;
    S.frame = f;
    build(true);
  });
  seg('notation', function (v) {
    var three = v === '3';
    if (three === S.three) return;
    S.three = three;
    renderBeads();
    markSelection(false);
  });

  [].slice.call(document.querySelectorAll('[data-ex]')).forEach(function (b) {
    b.addEventListener('click', function () {
      $('seq').value = EX[b.getAttribute('data-ex')];
      build(true);
    });
  });

  $('revcomp').addEventListener('click', function () {
    flush();
    var b = S.p.bases, out = [];
    if (!b.length) { flash(this, 'reverse complement ⇄', false, 'no sequence'); return; }
    for (var i = b.length - 1; i >= 0; i--) out.push(COMPL[b[i].c] || b[i].c);
    var s = out.join(''), lines = [];
    for (var j = 0; j < s.length; j += 72) lines.push(s.slice(j, j + 72));
    $('seq').value = lines.join('\n');
    build(true);
  });

  $('copyAA').addEventListener('click', function () { flush(); copy(this, 'copy protein', proteinText()); });
  $('copyRNA').addEventListener('click', function () { flush(); copy(this, 'copy mRNA', rnaText()); });

  $('beads').addEventListener('click', function (e) {
    var t = e.target.closest ? e.target.closest('.bead') : null;
    if (!t) return;
    select(+t.getAttribute('data-i'), false, false);
  });
  $('beads').addEventListener('focusin', function (e) {
    var t = e.target.closest ? e.target.closest('.bead') : null;
    if (!t) return;
    var i = +t.getAttribute('data-i');
    if (i !== S.sel) select(i, false, false);
  });
  $('beads').addEventListener('keydown', function (e) {
    var next = null;
    if (e.key === 'ArrowRight') next = S.sel + 1;
    else if (e.key === 'ArrowLeft') next = S.sel - 1;
    else if (e.key === 'Home') next = 0;
    else if (e.key === 'End') next = Math.min(S.m.codons.length, MAX_DRAW) - 1;
    if (next === null) return;
    e.preventDefault();
    select(next, true, true);
  });
  $('strip').addEventListener('click', function (e) {
    var t = e.target.closest ? e.target.closest('.cod') : null;
    if (!t) return;
    var i = t.getAttribute('data-i');
    if (i === null) return;
    select(+i, false, false);
  });

  /* ---------------- theme ---------------- */
  window.addEventListener('message', function (e) {
    var d = e.data;
    if (d && d.type === 'sloprun:theme' && (d.theme === 'light' || d.theme === 'dark')) {
      document.documentElement.setAttribute('data-theme', d.theme);
    }
  });

  /* ---------------- boot ---------------- */
  buildTable();
  $('seq').value = EX.ins;
  build(true);
})();
</script>
</body>
</html>