/* Dark by default, light when the visitor asks for it. */

:root {
  --bg: #0b1220;
  --panel: #111a2e;
  --panel-2: #16223c;
  --line: #24324f;
  --ink: #e6edf7;
  --ink-dim: #93a4c0;
  --accent: #38bdf8;
  --accent-2: #fbbf24;
  --good: #4ade80;
  --bad: #f87171;
  --radius: 10px;
  /* A scale, because every gap and pad used to be a bare px literal. */
  --space-1: 4px;
  --space-2: 8px;
  --space-3: 12px;
  --space-4: 16px;
  --space-5: 24px;
  --text-sm: 12px;
  --text-md: 13px;
  --text-lg: 15px;
  --mono: ui-monospace, "SF Mono", "Cascadia Mono", Menlo, Consolas, monospace;
}

@media (prefers-color-scheme: light) {
  :root {
    --bg: #f6f8fc;
    --panel: #ffffff;
    --panel-2: #eef2f9;
    --line: #d7dfec;
    --ink: #0f172a;
    --ink-dim: #566178;
    --accent: #0284c7;
    --accent-2: #b45309;
  }
}

* { box-sizing: border-box; }

/* Several layout rules set `display`, which would otherwise beat the
   `hidden` attribute's default `display: none`. */
[hidden] { display: none !important; }

body {
  margin: 0;
  background: var(--bg);
  color: var(--ink);
  font: var(--text-lg)/1.55 system-ui, -apple-system, "Segoe UI", Roboto, sans-serif;
  -webkit-font-smoothing: antialiased;
  /* The shell: header measures itself, main takes the rest. */
  display: flex;
  flex-direction: column;
  height: 100dvh;
  margin: 0;
}

header {
  display: flex;
  flex-wrap: wrap;
  align-items: flex-end;
  justify-content: space-between;
  gap: var(--space-4);
  padding: var(--space-3) var(--space-5);
  border-bottom: 1px solid var(--line);
}

/* One status line and one progress bar, for a worker that runs one job. */
.statusbar {
  flex: 1 1 22rem;
  min-width: 0;
  display: flex;
  flex-direction: column;
  gap: var(--space-1);
  align-items: flex-end;
}

.statusbar .status,
.statusbar .hint { margin: 0; text-align: right; }
.statusbar .progress { width: min(100%, 22rem); }

h1 {
  margin: 0;
  font-size: 21px;
  letter-spacing: -0.02em;
  font-weight: 650;
}

h1 .dot { color: var(--accent); }

.tagline {
  margin: 2px 0 0;
  color: var(--ink-dim);
  font-size: var(--text-sm);
}

.credits { font-size: var(--text-sm); color: var(--ink-dim); }
.credits p { margin: var(--space-2) 0 0; }

h2 {
  margin: 0 0 12px;
  font-size: 13px;
  font-weight: 650;
  letter-spacing: 0.08em;
  text-transform: uppercase;
  color: var(--ink-dim);
}

/*
 * The app shell.
 *
 * A grid that fills the viewport rather than a document that scrolls: the
 * structure is the subject and should not be something you scroll away from.
 * Panes scroll internally; below the breakpoint they stack and the page scrolls
 * again, which is the only sensible thing on a phone.
 */
main {
  display: grid;
  gap: var(--space-3);
  padding: var(--space-3) var(--space-5) var(--space-5);
  /* The structure is the subject, so it gets the room: a bit under half the
     height and nearly two thirds of the width. The sequence track scrolls
     internally, so it needs only enough to show a few chains. */
  /*
   * The structure is the subject, so it gets the height -- and height is all
   * that matters: `drawTraces` fits the model into `min(width, height)`, so
   * canvas width beyond its height is just background. Hence a column split
   * nearer square than wide, and as much of the height as the other two rows
   * can spare. Both of those scroll internally, so they cope.
   */
  grid-template-columns: minmax(0, 1.45fr) minmax(0, 1fr);
  grid-template-rows: minmax(0, 3fr) minmax(112px, 0.5fr) minmax(0, 1.15fr);
  grid-template-areas:
    "structure inspector"
    "sequence  sequence"
    "results   analysis";
  flex: 1 1 auto;
  min-height: 0;
  box-sizing: border-box;
}

#viewer-panel   { grid-area: structure; }
#inspector      { grid-area: inspector; }
#sequence-panel { grid-area: sequence; }
#results-panel  { grid-area: results; display: flex; flex-direction: column; padding: var(--space-3); }
#results-panel .results { flex: 1 1 auto; overflow: auto; }
#analysis-panel { grid-area: analysis; }

/* Structure only, for as long as it is asked for. */
body.focus-structure main {
  grid-template-rows: minmax(0, 1fr) 0 0;
  grid-template-columns: minmax(0, 1fr) minmax(0, 22rem);
}
body.focus-structure #sequence-panel,
body.focus-structure #results-panel,
body.focus-structure #analysis-panel { display: none; }

/* Every pane owns its own scrollbar. */
main > .panel { overflow: auto; }

#viewer-panel {
  display: flex;
  flex-direction: column;
  overflow: hidden;
  padding: var(--space-2);
}

#viewer-panel .viewer-head { margin-bottom: var(--space-2); }

.panel {
  background: var(--panel);
  border: 1px solid var(--line);
  border-radius: var(--radius);
  padding: 18px;
  min-width: 0;
}

@media (max-width: 900px) {
  body { height: auto; }
  main {
    grid-template-columns: minmax(0, 1fr);
    grid-template-rows: none;
    grid-template-areas: "structure" "inspector" "sequence" "results" "analysis";
  }
  main > .panel { overflow: visible; }
  #viewer-panel { min-height: 60vh; }
}

/* --- controls ----------------------------------------------------------- */

.row {
  display: flex;
  gap: 8px;
  align-items: center;
  flex-wrap: wrap;
  margin-bottom: 10px;
}

input[type="text"], input[type="number"], select {
  background: var(--panel-2);
  border: 1px solid var(--line);
  color: var(--ink);
  border-radius: 8px;
  padding: 8px 10px;
  font: inherit;
  flex: 1 1 160px;
  min-width: 0;
}

input[type="number"] { flex: 0 0 100px; }

button {
  background: var(--panel-2);
  border: 1px solid var(--line);
  color: var(--ink);
  border-radius: 8px;
  padding: 8px 14px;
  font: inherit;
  cursor: pointer;
  transition: border-color 0.12s, background 0.12s;
}

button:hover:not(:disabled) { border-color: var(--accent); }
button:disabled { opacity: 0.45; cursor: not-allowed; }

button.primary {
  background: var(--accent);
  border-color: var(--accent);
  color: #04121e;
  font-weight: 600;
}

button.link {
  background: none;
  border: none;
  color: var(--accent);
  padding: 2px 4px;
  text-decoration: underline;
  text-underline-offset: 2px;
}

.check {
  display: inline-flex;
  gap: 6px;
  align-items: center;
  flex: 0 0 auto;
  color: var(--ink-dim);
  cursor: pointer;
}

.control { margin-bottom: 14px; }

.control > label {
  display: flex;
  justify-content: space-between;
  font-size: 13px;
  color: var(--ink-dim);
  margin-bottom: 4px;
}

.control output { font-family: var(--mono); color: var(--ink); }

input[type="range"] { width: 100%; accent-color: var(--accent); }

details > summary {
  cursor: pointer;
  font-size: 13px;
  color: var(--ink-dim);
  margin-bottom: 8px;
  user-select: none;
}

.hint, .status {
  font-size: 12.5px;
  color: var(--ink-dim);
  margin: 6px 0 0;
}

.status.error { color: var(--bad); }
.status.busy { color: var(--accent); }

.file-drop {
  flex: 1;
  border: 1px dashed var(--line);
  border-radius: 8px;
  padding: 18px;
  text-align: center;
  color: var(--ink-dim);
  cursor: pointer;
  font-size: 13px;
}

.file-drop.over { border-color: var(--accent); color: var(--accent); }

.examples { font-size: 13px; color: var(--ink-dim); }

.progress {
  height: 4px;
  background: var(--panel-2);
  border-radius: 2px;
  overflow: hidden;
  margin-top: 10px;
}

#progress-bar {
  height: 100%;
  width: 0%;
  background: var(--accent);
  transition: width 0.15s linear;
}

/* --- viewer ------------------------------------------------------------- */

.viewer-head {
  display: flex;
  justify-content: space-between;
  align-items: flex-start;
  gap: 12px;
  flex-wrap: wrap;
}

.viewer-tools { display: flex; gap: 6px; flex-wrap: wrap; margin-bottom: 12px; }
.viewer-tools select, .viewer-tools button { font-size: 13px; padding: 6px 10px; flex: 0 0 auto; }

.viewer-wrap {
  position: relative;
  flex: 1 1 auto;
  min-height: 0;
  background: var(--bg);
  border: 1px solid var(--line);
  border-radius: 8px;
  overflow: hidden;
}

#viewer {
  display: block;
  width: 100%;
  height: 100%;
  touch-action: none;
  cursor: grab;
}

#viewer:active { cursor: grabbing; }

.viewer-hint {
  position: absolute;
  left: 10px;
  bottom: 8px;
  font-size: 11px;
  color: var(--ink-dim);
  pointer-events: none;
}

.tooltip {
  position: absolute;
  background: var(--panel);
  border: 1px solid var(--line);
  border-radius: 6px;
  padding: 6px 9px;
  font-size: 12px;
  font-family: var(--mono);
  pointer-events: none;
  white-space: pre;
  z-index: 5;
}

/* --- sequence track ----------------------------------------------------- */

.sequence-wrap {
  margin-top: 12px;
  /* No max-height and no overflow here on purpose: the vendored viewer caps its
     own canvas and scrolls virtually inside it, and a second scroller wrapped
     around that eats the wheel events it wants. */
}

/* The vendored viewer builds its own canvas in here and sizes it to the box. */
#sequenceView {
  /* A drag across residues must not start a text selection on the page. */
  user-select: none;
}

.seq-hint { margin-top: 8px; }

.tie-list { display: flex; flex-direction: column; gap: 4px; margin-top: 8px; }

.tie-row {
  display: grid;
  grid-template-columns: 3em 1fr auto auto;
  align-items: center;
  gap: 8px;
  padding: 4px 6px;
  background: var(--panel-2);
  border: 1px solid var(--line);
  border-radius: 6px;
  font-size: 12px;
}

.tie-row .tie-label { font-family: var(--mono); color: var(--accent); }
.tie-row .tie-what { color: var(--ink-dim); }
.tie-row select { flex: 0 0 auto; font-size: 11px; padding: 2px 4px; }
.tie-row button { padding: 2px 7px; line-height: 1; }

/* Divides the pointing verbs from the ones that change the design mask. */
.viewer-tools .sep {
  width: 1px;
  align-self: stretch;
  margin: 2px 4px;
  background: var(--line);
}

/* --- results ------------------------------------------------------------ */

.results { min-height: 0; }

.results .empty { color: var(--ink-dim); font-size: 13px; }

.results-table {
  width: 100%;
  border-collapse: collapse;
  font-family: var(--mono);
  font-size: 12px;
}

.results-table th {
  position: sticky;
  top: 0;
  z-index: 1;
  background: var(--panel);
  border-bottom: 1px solid var(--line);
  padding: 5px 8px;
  text-align: right;
  font-weight: 500;
  color: var(--ink-dim);
  cursor: pointer;
  white-space: nowrap;
}

.results-table th:first-child,
.results-table td:first-child { text-align: left; }
.results-table th:hover { color: var(--ink); }
.results-table th[data-sorted]::after {
  content: " \2191";
  color: var(--accent);
}
.results-table th[data-sorted="desc"]::after { content: " \2193"; }

.results-table td {
  padding: 4px 8px;
  text-align: right;
  border-bottom: 1px solid var(--line);
  white-space: nowrap;
}

.results-table tbody tr { cursor: pointer; }
.results-table tbody tr:hover { background: var(--panel-2); }
.results-table tbody tr.active { background: var(--panel-2); }
.results-table tbody tr.active td:first-child {
  box-shadow: inset 2px 0 0 var(--accent);
}

/* --- sequence track ----------------------------------------------------- */

.sequence-wrap {
  margin-top: 12px;
  /* No max-height and no overflow here on purpose: the vendored viewer caps its
     own canvas and scrolls virtually inside it, and a second scroller wrapped
     around that eats the wheel events it wants. */
}

/* The vendored viewer builds its own canvas in here and sizes it to the box. */
#sequenceView {
  /* A drag across residues must not start a text selection on the page. */
  user-select: none;
}

.seq-hint { margin-top: 8px; }

.tie-list { display: flex; flex-direction: column; gap: 4px; margin-top: 8px; }

.tie-row {
  display: grid;
  grid-template-columns: 3em 1fr auto auto;
  align-items: center;
  gap: 8px;
  padding: 4px 6px;
  background: var(--panel-2);
  border: 1px solid var(--line);
  border-radius: 6px;
  font-size: 12px;
}

.tie-row .tie-label { font-family: var(--mono); color: var(--accent); }
.tie-row .tie-what { color: var(--ink-dim); }
.tie-row select { flex: 0 0 auto; font-size: 11px; padding: 2px 4px; }
.tie-row button { padding: 2px 7px; line-height: 1; }

/* Divides the pointing verbs from the ones that change the design mask. */
.viewer-tools .sep {
  width: 1px;
  align-self: stretch;
  margin: 2px 4px;
  background: var(--line);
}

/* --- results ------------------------------------------------------------ */

.results { min-height: 0; }

.results .empty { color: var(--ink-dim); font-size: 13px; }

.results-table {
  width: 100%;
  border-collapse: collapse;
  font-family: var(--mono);
  font-size: 12px;
}

.results-table th {
  position: sticky;
  top: 0;
  z-index: 1;
  background: var(--panel);
  border-bottom: 1px solid var(--line);
  padding: 5px 8px;
  text-align: right;
  font-weight: 500;
  color: var(--ink-dim);
  cursor: pointer;
  white-space: nowrap;
}

.results-table th:first-child,
.results-table td:first-child { text-align: left; }
.results-table th:hover { color: var(--ink); }
.results-table th[data-sorted]::after {
  content: " \2191";
  color: var(--accent);
}
.results-table th[data-sorted="desc"]::after { content: " \2193"; }

.results-table td {
  padding: 4px 8px;
  text-align: right;
  border-bottom: 1px solid var(--line);
  white-space: nowrap;
}

.results-table tbody tr { cursor: pointer; }
.results-table tbody tr:hover { background: var(--panel-2); }
.results-table tbody tr.active { background: var(--panel-2); }
.results-table tbody tr.active td:first-child {
  box-shadow: inset 2px 0 0 var(--accent);
}

.design {
  display: grid;
  grid-template-columns: auto 1fr;
  gap: 10px;
  padding: 8px 10px;
  border: 1px solid transparent;
  border-radius: 8px;
  cursor: pointer;
  align-items: baseline;
}

.design:hover { background: var(--panel-2); }
.design.active { border-color: var(--accent); background: var(--panel-2); }

.design .meta {
  font-family: var(--mono);
  font-size: 11.5px;
  color: var(--ink-dim);
  white-space: nowrap;
}

.design .seq {
  font-family: var(--mono);
  font-size: 12px;
  overflow-x: auto;
  white-space: nowrap;
}

.design .seq .same { color: var(--ink-dim); }
.design .seq .diff { color: var(--accent-2); }

/* --- sequence logo ------------------------------------------------------ */

.logo-wrap {
  position: relative;
  overflow-x: auto;
  overflow-y: hidden;
  border: 1px solid var(--line);
  border-radius: 8px;
  background: var(--panel);
  padding: 8px 0 4px 0;
}

#logo { display: block; cursor: pointer; }

/* --- amino-acid bias grid ---------------------------------------------- */

/* --- constraints pane ---------------------------------------------------- */

.constraints { display: flex; flex-direction: column; gap: var(--space-2); }

.ctable-head {
  display: flex;
  align-items: center;
  justify-content: space-between;
  gap: var(--space-2);
  flex-wrap: wrap;
}

/* Says what the editor will change, instead of a dropdown asking you to pick. */
.ctable-target {
  margin: 0;
  font-size: var(--text-sm);
  color: var(--ink-dim);
}

.seg { display: flex; }

.seg button {
  border-radius: 0;
  font-size: 11px;
  padding: 3px 8px;
}
.seg button:first-child { border-radius: 6px 0 0 6px; }
.seg button:last-child { border-radius: 0 6px 6px 0; }
.seg button + button { border-left: 0; }
.seg button[aria-pressed="true"] {
  background: var(--accent);
  border-color: var(--accent);
  color: #04121e;
}

.aa-editor {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(74px, 1fr));
  gap: var(--space-1);
}

.aa-editor .cell {
  display: flex;
  align-items: center;
  gap: var(--space-1);
  background: var(--panel-2);
  border: 1px solid var(--line);
  border-radius: 6px;
  padding: 2px 4px;
  font-family: var(--mono);
  font-size: var(--text-sm);
}

.aa-editor .cell.omitted { opacity: 0.4; }
.aa-editor .cell.omit-mixed { border-style: dashed; }
/* Overridden reads as accent, inherited as muted -- otherwise the sparse
   model is invisible and there was no point to it. */
.aa-editor .cell.override { border-color: var(--accent-2); }
.aa-editor .cell input { width: 100%; flex: 1; min-width: 0; padding: 2px 4px; }
.aa-editor .cell .letter { cursor: pointer; user-select: none; width: 1.2em; }

.ctable-scroll {
  max-height: 210px;
  overflow: auto;
  border: 1px solid var(--line);
  border-radius: 6px;
}

.ctable {
  width: 100%;
  border-collapse: collapse;
  font-family: var(--mono);
  font-size: 11px;
}

.ctable th {
  position: sticky;
  top: 0;
  background: var(--panel);
  border-bottom: 1px solid var(--line);
  padding: 3px 6px;
  text-align: left;
  font-weight: 500;
  color: var(--ink-dim);
  white-space: nowrap;
}

.ctable td { padding: 2px 6px; white-space: nowrap; }
.ctable tbody tr { cursor: default; }
.ctable tbody tr.selected { background: var(--panel-2); }
.ctable tbody tr.pad { background: none; }
.ctable td.pos { color: var(--ink-dim); }
.ctable td.bias.override { color: var(--accent-2); }
.ctable td.tie { color: var(--accent); }
.ctable input[type="checkbox"] { margin: 0; }

footer {
  max-width: 1400px;
  margin: 0 auto;
  padding: 8px 24px 48px;
  color: var(--ink-dim);
  font-size: 12.5px;
}

footer a { color: var(--accent); }

textarea {
  width: 100%;
  background: var(--panel-2);
  border: 1px solid var(--line);
  color: var(--ink);
  border-radius: 8px;
  padding: 8px 10px;
  font-family: var(--mono);
  font-size: 12px;
  resize: vertical;
}

#score-orders { flex: 0 0 60px; }

/* --- inspector ----------------------------------------------------------- */

/* One scrolling column of labelled groups, rather than four separate panels. */
.stack { display: flex; flex-direction: column; gap: var(--space-5); }

.group > h2 { margin-bottom: var(--space-2); }

/* A collapsible group: the heading is the summary, with the marker inline. */
details.group > summary {
  cursor: pointer;
  list-style: none;
  display: flex;
  align-items: baseline;
  gap: var(--space-2);
}
details.group > summary::-webkit-details-marker { display: none; }
details.group > summary h2 { margin: 0; }
details.group > summary::after {
  content: "\2212";
  color: var(--ink-dim);
  font-family: var(--mono);
  font-size: 13px;
}
details.group:not([open]) > summary::after { content: "\002B"; }

.group + .group { border-top: 1px solid var(--line); padding-top: var(--space-4); }

/* --- tabs ---------------------------------------------------------------- */

.tabs { display: flex; gap: var(--space-1); }

.tab {
  background: none;
  border: 0;
  border-bottom: 2px solid transparent;
  border-radius: 0;
  padding: 4px 8px;
  font-size: var(--text-md);
  font-weight: 650;
  letter-spacing: 0.06em;
  text-transform: uppercase;
  color: var(--ink-dim);
}

.tab:hover:not(:disabled) { color: var(--ink); border-color: var(--line); }
.tab[aria-selected="true"] { color: var(--ink); border-bottom-color: var(--accent); }

#sequence-panel { display: flex; flex-direction: column; padding: var(--space-2) var(--space-3); }

/* The track scrolls internally past its budget, which `seqview.js` measures
   from this wrap -- so a 9-chain complex cannot starve the structure pane. */
/* A floor, or the hint below it is squeezed over the top of the track. */
.sequence-wrap { flex: 1 1 auto; min-height: 26px; }
#analysis-panel { display: flex; flex-direction: column; padding: var(--space-3); }
#analysis-panel > div[id^="pane-"] { flex: 1 1 auto; min-height: 0; overflow: auto; }