:root {
  --bg: #ffffff;
  --fg: #1a1a1a;
  --muted: #6b7280;
  --border: #e5e7eb;
  --accent: #2563eb;
  --row-hover: #f3f4f6;
  --row-active: #dbeafe;
  --aa-hydrophobic: #f0f9ff;
  --aa-polar: #f0fdf4;
  --aa-acidic: #fef2f2;
  --aa-basic: #eff6ff;
  --aa-special: #fefce8;
  --mono: ui-monospace, SFMono-Regular, "SF Mono", Menlo, Consolas, "Liberation Mono", "Courier New", monospace;
}

* { box-sizing: border-box; }

[hidden] { display: none !important; }

html, body {
  margin: 0;
  height: 100%;
  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
  color: var(--fg);
  background: var(--bg);
  font-size: 14px;
}

.topbar {
  display: flex;
  align-items: center;
  gap: 16px;
  padding: 10px 16px;
  border-bottom: 1px solid var(--border);
  position: sticky;
  top: 0;
  background: var(--bg);
  z-index: 10;
}
.topbar h1 { margin: 0; font-size: 16px; font-weight: 600; }
.status { color: var(--muted); font-size: 13px; flex: 1; }

.file-btn {
  display: inline-block;
  padding: 6px 12px;
  background: var(--accent);
  color: white;
  border-radius: 6px;
  cursor: pointer;
  font-size: 13px;
}
.file-btn input { display: none; }
.file-btn:hover { filter: brightness(1.05); }

.dropzone {
  margin: 40px auto;
  max-width: 900px;
  padding: 40px 20px;
  border: 2px dashed var(--border);
  border-radius: 12px;
  text-align: center;
  color: var(--muted);
}
.dropzone.dragover { border-color: var(--accent); background: #eff6ff; }
.dropzone code { background: #f3f4f6; padding: 2px 6px; border-radius: 4px; }
.dropzone-or { margin-top: 22px; font-size: 13px; color: var(--muted); }

.sample-list {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(240px, 1fr));
  gap: 8px;
  margin: 8px auto 0;
  max-width: 900px;
  text-align: left;
}
.sample-btn {
  display: block;
  width: 100%;
  text-align: left;
  border: 1px solid var(--border);
  background: white;
  padding: 8px 12px;
  border-radius: 6px;
  cursor: pointer;
  font-family: inherit;
  font-size: 13px;
}
.sample-btn:hover { border-color: var(--accent); background: #f9fafb; }
.sample-name { display: block; font-weight: 600; color: var(--fg); }
.sample-desc { display: block; font-size: 12px; color: var(--muted); margin-top: 2px; }

main#app {
  display: grid;
  grid-template-columns: 340px 1fr;
  height: calc(100vh - 49px);
}

.sidebar {
  border-right: 1px solid var(--border);
  padding: 12px;
  overflow-y: auto;
  display: flex;
  flex-direction: column;
  gap: 8px;
  min-height: 0;
}
.sidebar input[type="search"] {
  width: 100%;
  padding: 6px 10px;
  border: 1px solid var(--border);
  border-radius: 6px;
  font-size: 13px;
}
.filters { display: flex; flex-direction: column; gap: 4px; font-size: 13px; }
.filters label { display: flex; align-items: center; gap: 6px; cursor: pointer; }
.select-row { display: flex; flex-direction: column; gap: 4px; font-size: 12px; color: var(--muted); }
.select-row label { display: flex; align-items: center; gap: 6px; }
.select-row select {
  flex: 1;
  padding: 3px 6px;
  border: 1px solid var(--border);
  border-radius: 4px;
  font-size: 12px;
  background: white;
}
.match-count { color: var(--muted); font-size: 12px; }

.file-info {
  border: 1px solid var(--border);
  border-radius: 6px;
  background: #f9fafb;
  font-size: 12px;
}
.file-info summary {
  padding: 6px 10px;
  cursor: pointer;
  font-weight: 500;
  color: var(--fg);
  list-style: revert;
}
.file-info[open] summary { border-bottom: 1px solid var(--border); }
#file-info-content {
  padding: 8px 10px;
  display: flex;
  flex-direction: column;
  gap: 6px;
  max-height: 240px;
  overflow-y: auto;
}
.stat-row { display: flex; justify-content: space-between; gap: 8px; }
.stat-row .k { color: var(--muted); }
.stat-row .v { font-weight: 600; font-variant-numeric: tabular-nums; }

.protein-list { list-style: none; margin: 0; padding: 0; overflow-y: auto; flex: 1; min-height: 0; }
.protein-list li {
  padding: 6px 8px;
  border-radius: 4px;
  cursor: pointer;
  font-size: 13px;
  border: 1px solid transparent;
}
.protein-list li:hover { background: var(--row-hover); }
.protein-list li.active { background: var(--row-active); border-color: #93c5fd; }
.protein-list .acc { font-weight: 600; font-family: var(--mono); font-size: 12px; }
.protein-list .meta { color: var(--muted); font-size: 12px; margin-top: 2px; }
.protein-list .len {
  float: right;
  color: var(--muted);
  font-size: 11px;
  font-variant-numeric: tabular-nums;
}

.detail { padding: 16px 20px; overflow-y: auto; min-height: 0; }

.header-card { margin-bottom: 12px; }
.header-card h2 { margin: 0 0 4px; font-size: 18px; font-family: var(--mono); }
.header-card .pname { font-weight: 500; }
.header-card .gname { color: var(--muted); font-size: 13px; }
.header-card .desc { color: var(--muted); font-size: 12px; font-style: italic; margin-top: 4px; word-break: break-word; }
.header-card .raw-header {
  margin-top: 6px;
  font-family: var(--mono);
  font-size: 11px;
  color: var(--muted);
  background: #f9fafb;
  padding: 4px 8px;
  border-radius: 4px;
  border: 1px solid var(--border);
  word-break: break-all;
}
.header-card .metrics { display: flex; flex-wrap: wrap; gap: 8px; margin-top: 10px; }
.metric { border: 1px solid var(--border); border-radius: 6px; padding: 4px 10px; font-size: 12px; }
.metric .label { color: var(--muted); display: block; }
.metric .value { font-weight: 600; font-size: 14px; word-break: break-word; }

.tabs { display: flex; gap: 4px; margin: 8px 0 0; border-bottom: 1px solid var(--border); }
.tab {
  border: none; background: none; padding: 8px 14px; cursor: pointer;
  font-size: 13px; color: var(--muted); border-bottom: 2px solid transparent;
}
.tab:hover { color: var(--fg); }
.tab.active { color: var(--accent); border-bottom-color: var(--accent); }

.sequence-toolbar {
  margin: 12px 0 6px;
  display: flex;
  gap: 12px;
  align-items: center;
  flex-wrap: wrap;
  font-size: 12px;
}
.sequence-toolbar label { display: inline-flex; align-items: center; gap: 4px; }
.sequence-toolbar .btn {
  border: 1px solid var(--border);
  background: white;
  padding: 4px 10px;
  border-radius: 4px;
  font-size: 12px;
  cursor: pointer;
  font-family: inherit;
}
.sequence-toolbar .btn:hover { border-color: var(--accent); color: var(--accent); }

.sequence-area {
  margin-top: 4px;
  padding: 8px 0;
  overflow-x: auto;
}
.seq-group {
  font-family: var(--mono);
  font-size: 14px;
  margin-bottom: 14px;
}
.seq-line {
  display: grid;
  grid-template-columns: 5ch repeat(60, 1ch) 6ch;
  line-height: 1.7em;
  align-items: center;
}
.seq-pos {
  text-align: right;
  padding-right: 0.5ch;
  color: var(--muted);
  font-size: 12px;
  font-variant-numeric: tabular-nums;
  user-select: none;
}
.seq-pos.end {
  text-align: left;
  padding-left: 0.5ch;
  padding-right: 0;
}
.aa { text-align: center; }
.aa.tick { border-right: 1px dotted #d1d5db; }
.aa.colored.hydrophobic { background: var(--aa-hydrophobic); }
.aa.colored.polar { background: var(--aa-polar); }
.aa.colored.acidic { background: var(--aa-acidic); color: #991b1b; }
.aa.colored.basic { background: var(--aa-basic); color: #1e40af; }
.aa.colored.special { background: var(--aa-special); }
.aa.match {
  background: #fde68a;
  color: #78350f;
  font-weight: 600;
  border-radius: 2px;
}
.aa.flash {
  animation: flashpulse 1.6s ease-out;
  border-radius: 3px;
}
@keyframes flashpulse {
  0%   { background: var(--accent); color: white; }
  60%  { background: var(--accent); color: white; }
  100% { background: transparent; color: inherit; }
}

.composition-grid {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(240px, 1fr));
  gap: 12px;
  margin-top: 12px;
}
.comp-card {
  border: 1px solid var(--border);
  border-radius: 6px;
  padding: 10px 12px;
}
.comp-card h4 {
  margin: 0 0 8px;
  font-size: 12px;
  color: var(--muted);
  text-transform: uppercase;
  letter-spacing: 0.5px;
  font-weight: 500;
}
.comp-bar-row {
  display: grid;
  grid-template-columns: 2.5ch 4ch 1fr 3ch;
  align-items: center;
  gap: 6px;
  font-size: 12px;
  margin-bottom: 3px;
  font-family: var(--mono);
}
.comp-bar-row .aa-label { font-weight: 600; }
.comp-bar-row .pct { color: var(--muted); text-align: right; font-variant-numeric: tabular-nums; }
.comp-bar-row .count { color: var(--muted); text-align: right; font-variant-numeric: tabular-nums; }
.comp-bar {
  height: 10px;
  background: #e5e7eb;
  border-radius: 2px;
  overflow: hidden;
}
.comp-bar > div {
  height: 100%;
  background: var(--accent);
}
.comp-bar.hydrophobic > div { background: #60a5fa; }
.comp-bar.polar > div { background: #34d399; }
.comp-bar.acidic > div { background: #f87171; }
.comp-bar.basic > div { background: #818cf8; }
.comp-bar.special > div { background: #fbbf24; }

/* Mass tab */
.mass-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
  gap: 12px;
  margin: 12px 0;
}
.mass-card {
  border: 1px solid var(--border);
  border-radius: 6px;
  padding: 10px 12px;
}
.mass-card .label {
  color: var(--muted);
  font-size: 11px;
  text-transform: uppercase;
  letter-spacing: 0.5px;
  display: block;
  margin-bottom: 4px;
}
.mass-card .value {
  font-size: 18px;
  font-weight: 600;
  font-variant-numeric: tabular-nums;
}
.mass-card .unit { color: var(--muted); font-size: 12px; font-weight: 400; }
.mass-card .formula { font-family: var(--mono); font-size: 14px; word-break: break-all; }

.mass-section { margin-top: 18px; }
.mass-section h3 {
  margin: 0 0 8px;
  font-size: 13px;
  color: var(--muted);
  font-weight: 500;
  text-transform: uppercase;
  letter-spacing: 0.5px;
}

.mz-table {
  width: 100%;
  border-collapse: collapse;
  font-size: 13px;
  font-variant-numeric: tabular-nums;
}
.mz-table th, .mz-table td {
  text-align: right;
  padding: 4px 10px;
  border-bottom: 1px solid var(--border);
}
.mz-table th:first-child, .mz-table td:first-child { text-align: left; }
.mz-table th { color: var(--muted); font-weight: 500; font-size: 12px; }
.mz-table tbody tr:hover td { background: var(--row-hover); }

.iso-chart {
  display: grid;
  grid-template-columns: 1fr;
  gap: 4px;
  margin-top: 6px;
}
.iso-row {
  display: grid;
  grid-template-columns: 10ch 6ch 1fr 7ch;
  align-items: center;
  gap: 8px;
  font-size: 12px;
  font-family: var(--mono);
  font-variant-numeric: tabular-nums;
}
.iso-row .mass { color: var(--fg); }
.iso-row .label { color: var(--muted); font-size: 11px; }
.iso-row .bar { height: 12px; background: #e5e7eb; border-radius: 2px; overflow: hidden; }
.iso-row .bar > div { height: 100%; background: var(--accent); }
.iso-row .ab { color: var(--muted); text-align: right; }

/* Digest tab */
.digest-controls {
  display: flex;
  flex-wrap: wrap;
  gap: 10px;
  align-items: end;
  padding: 10px 12px;
  margin: 10px 0;
  background: #f9fafb;
  border: 1px solid var(--border);
  border-radius: 6px;
}
.digest-controls label {
  display: flex;
  flex-direction: column;
  font-size: 11px;
  color: var(--muted);
  text-transform: uppercase;
  letter-spacing: 0.4px;
  gap: 3px;
}
.digest-controls select,
.digest-controls input {
  padding: 4px 8px;
  border: 1px solid var(--border);
  border-radius: 4px;
  font-size: 13px;
  background: white;
  font-family: inherit;
  text-transform: none;
  color: var(--fg);
  letter-spacing: normal;
}
.digest-controls input[type=number] { width: 6ch; }
.digest-summary {
  color: var(--muted);
  font-size: 12px;
  margin-bottom: 6px;
}
.digest-table {
  width: 100%;
  border-collapse: collapse;
  font-size: 13px;
}
.digest-table th, .digest-table td {
  text-align: left;
  padding: 4px 8px;
  border-bottom: 1px solid var(--border);
  font-variant-numeric: tabular-nums;
}
.digest-table th { color: var(--muted); font-weight: 500; font-size: 12px; cursor: pointer; user-select: none; }
.digest-table th:hover { color: var(--fg); }
.digest-table td.seq { font-family: var(--mono); font-size: 12px; word-break: break-all; max-width: 50ch; }
.digest-table td.num { text-align: right; }
.digest-table tr { cursor: pointer; }
.digest-table tr:hover td { background: var(--row-active); }

.spinner {
  display: inline-block;
  width: 12px;
  height: 12px;
  border: 2px solid var(--border);
  border-top-color: var(--accent);
  border-radius: 50%;
  animation: spin 0.8s linear infinite;
  vertical-align: middle;
  margin-left: 6px;
}
@keyframes spin { to { transform: rotate(360deg); } }
.computing { color: var(--muted); font-style: italic; padding: 8px 0; }

/* Cleavage marks on the sequence line */
.aa.cleave-after {
  border-right: 2px solid var(--accent);
}
.aa.match.cleave-after { border-right-color: #b45309; }

.header-card .mass-line {
  margin-top: 4px;
  font-size: 12px;
  color: var(--muted);
  font-family: var(--mono);
}
.header-card .mass-line .v { color: var(--fg); }

.empty { color: var(--muted); font-style: italic; padding: 8px 0; }
.raw-json {
  background: #f9fafb; border: 1px solid var(--border); border-radius: 6px;
  padding: 10px; font-family: var(--mono); font-size: 12px;
  white-space: pre-wrap; word-break: break-word;
  max-height: 70vh; overflow: auto;
}

.legend {
  display: flex; flex-wrap: wrap; gap: 6px 14px;
  font-size: 12px; color: var(--muted);
  padding: 6px 0 12px;
  border-bottom: 1px solid var(--border);
  margin-bottom: 12px;
}
.legend-item { display: inline-flex; align-items: center; gap: 5px; }
.legend-square {
  display: inline-block;
  width: 14px; height: 14px;
  border-radius: 2px;
  font-family: var(--mono);
  font-size: 11px;
  text-align: center;
  line-height: 14px;
  border: 1px solid var(--border);
}
.legend-square.hydrophobic { background: var(--aa-hydrophobic); }
.legend-square.polar { background: var(--aa-polar); }
.legend-square.acidic { background: var(--aa-acidic); color: #991b1b; }
.legend-square.basic { background: var(--aa-basic); color: #1e40af; }
.legend-square.special { background: var(--aa-special); }