/* static/style.css - Pure GitHub / Academic Minimalist Design System */

:root {
  --bg: #ffffff;
  --bg-subtle: #f6f8fa;
  --bg-alt: #f1f3f5;
  --border: #d0d7de;
  --border-muted: #e1e4e8;
  --text: #24292f;
  --text-muted: #57606a;
  --primary: #1f2328;
  --primary-hover: #0969da;
  --primary-fg: #ffffff;
  --accent: #0969da;
  --font-sans: -apple-system, BlinkMacSystemFont, "Segoe UI", "Noto Sans", Helvetica, Arial, sans-serif;
  --font-mono: ui-monospace, SFMono-Regular, "SF Mono", Menlo, Consolas, "Liberation Mono", monospace;
  --radius-sm: 4px;
  --radius-md: 6px;
  --radius-lg: 8px;
  
  --badge-pass-bg: #dafbe1;
  --badge-pass-fg: #1a7f37;
  --badge-pass-border: #4ac26b;
  
  --badge-warn-bg: #fff8c5;
  --badge-warn-fg: #9a6700;
  --badge-warn-border: #d4a72c;
  
  --badge-fail-bg: #ffebe9;
  --badge-fail-fg: #cf222e;
  --badge-fail-border: #ff8182;
  
  --badge-info-bg: #ddf4ff;
  --badge-info-fg: #0969da;
  --badge-info-border: #54aeff;
}

.theme-dark {
  --bg: #0d1117;
  --bg-subtle: #161b22;
  --bg-alt: #21262d;
  --border: #30363d;
  --border-muted: #21262d;
  --text: #c9d1d9;
  --text-muted: #8b949e;
  --primary: #f0f6fc;
  --primary-hover: #58a6ff;
  --primary-fg: #0d1117;
  --accent: #58a6ff;
  
  --badge-pass-bg: #122b1c;
  --badge-pass-fg: #3fb950;
  --badge-pass-border: #238636;
  
  --badge-warn-bg: #2d2200;
  --badge-warn-fg: #d29922;
  --badge-warn-border: #9e6a03;
  
  --badge-fail-bg: #3c1214;
  --badge-fail-fg: #f85149;
  --badge-fail-border: #da3633;
  
  --badge-info-bg: #0c2d6b;
  --badge-info-fg: #58a6ff;
  --badge-info-border: #1f6feb;
}

/* Matrix Webfonts */
@font-face {
  font-family: 'MatrixSansPrint';
  src: url('/static/fonts/MatrixSansPrint-Regular.woff2') format('woff2');
  font-weight: normal;
  font-style: normal;
  font-display: swap;
}

@font-face {
  font-family: 'MatrixSans';
  src: url('/static/fonts/MatrixSans-Regular.woff2') format('woff2');
  font-weight: normal;
  font-style: normal;
  font-display: swap;
}

.theme-matrix, [data-theme="matrix-terminal"], html.theme-matrix {
  --bg: #030706;
  --bg-subtle: #08100c;
  --bg-alt: #0d1a14;
  --border: #0f2e1e;
  --border-muted: #143d28;
  --text: #d1fae5;
  --text-muted: #6ee7b7;
  --primary: #00ff66;
  --primary-hover: #4ade80;
  --primary-fg: #030706;
  --accent: #00ff66;
  --font-mono: 'MatrixSansPrint', 'MatrixSans', ui-monospace, SFMono-Regular, monospace;
  
  --badge-pass-bg: #081a10;
  --badge-pass-fg: #00ff66;
  --badge-pass-border: #10b981;
  
  --badge-warn-bg: #1f1a05;
  --badge-warn-fg: #fbbf24;
  --badge-warn-border: #f59e0b;
  
  --badge-fail-bg: #2b0b0e;
  --badge-fail-fg: #ff4d6d;
  --badge-fail-border: #ef4444;
  
  --badge-info-bg: #061c14;
  --badge-info-fg: #34d399;
  --badge-info-border: #059669;

  --rain-color: #00ff66;
  --rain-head: #ffffff;
  --accent-warning: #fbbf24;
}

.matrix-canvas-container {
  position: fixed;
  top: 0;
  left: 0;
  width: 100vw;
  height: 100vh;
  pointer-events: none;
  z-index: 0;
  opacity: 0.42;
  overflow: hidden;
}

.matrix-canvas {
  width: 100%;
  height: 100%;
  display: block;
}

.theme-matrix .main-container,
.theme-matrix .app-header,
.theme-matrix .app-footer,
[data-theme="matrix-terminal"] .main-container,
[data-theme="matrix-terminal"] .app-header,
[data-theme="matrix-terminal"] .app-footer {
  position: relative;
  z-index: 1;
}

.theme-matrix .panel,
.theme-matrix .hero-section,
.theme-matrix .input-text,
.theme-matrix .input-textarea,
.theme-matrix .select-input,
[data-theme="matrix-terminal"] .panel,
[data-theme="matrix-terminal"] .hero-section,
[data-theme="matrix-terminal"] .input-text,
[data-theme="matrix-terminal"] .input-textarea,
[data-theme="matrix-terminal"] .select-input {
  backdrop-filter: blur(8px);
  background-color: rgba(8, 16, 12, 0.88);
  border-color: #0f2e1e;
  box-shadow: 0 0 15px rgba(0, 255, 102, 0.04);
}

.matrix-toast {
  position: fixed;
  bottom: 24px;
  right: 24px;
  background: rgba(8, 16, 12, 0.95);
  border: 1px solid #00ff66;
  color: #00ff66;
  padding: 12px 20px;
  border-radius: 6px;
  font-family: 'MatrixSansPrint', 'MatrixSans', monospace;
  font-size: 13px;
  box-shadow: 0 0 25px rgba(0, 255, 102, 0.45);
  z-index: 9999;
  animation: fadeInToast 0.35s cubic-bezier(0.16, 1, 0.3, 1);
  display: flex;
  align-items: center;
  gap: 10px;
}

@keyframes fadeInToast {
  from { opacity: 0; transform: translateY(12px); }
  to { opacity: 1; transform: translateY(0); }
}

/* Base Global Reset */
*, *::before, *::after {
  box-sizing: border-box;
  margin: 0;
  padding: 0;
}

html {
  height: 100%;
}

body {
  min-height: 100%;
  display: flex;
  flex-direction: column;
  background-color: var(--bg);
  color: var(--text);
  font-family: var(--font-sans);
  font-size: 14px;
  line-height: 1.5;
  -webkit-font-smoothing: antialiased;
}

.app-main {
  flex: 1 0 auto;
}

/* Header & Navigation */
.app-header {
  background-color: var(--bg-subtle);
  border-bottom: 1px solid var(--border);
  padding: 12px 24px;
}
.header-inner {
  max-width: 1060px;
  margin: 0 auto;
  display: flex;
  justify-content: space-between;
  align-items: center;
}
.brand-group {
  display: flex;
  align-items: center;
  gap: 8px;
}
.brand-title {
  font-size: 15px;
  font-weight: 600;
  color: var(--text);
  text-decoration: none;
  letter-spacing: -0.01em;
}
.brand-badge {
  font-size: 11px;
  font-weight: 600;
  color: var(--text-muted);
  background: var(--bg);
  border: 1px solid var(--border);
  padding: 1px 6px;
  border-radius: var(--radius-sm);
}
.header-nav {
  display: flex;
  align-items: center;
  gap: 8px;
}
.nav-chip {
  font-size: 12px;
  font-weight: 500;
  color: var(--badge-pass-fg);
  background: var(--badge-pass-bg);
  border: 1px solid var(--badge-pass-border);
  padding: 2px 8px;
  border-radius: var(--radius-sm);
}

/* Main Container */
.main-container {
  max-width: 1060px;
  margin: 24px auto;
  padding: 0 24px;
}

/* Hero Section */
.hero-section {
  margin-bottom: 20px;
  padding-bottom: 16px;
  border-bottom: 1px solid var(--border-muted);
}
.page-title {
  font-size: 20px;
  font-weight: 600;
  color: var(--text);
  letter-spacing: -0.02em;
}
.page-subtitle {
  font-size: 13px;
  color: var(--text-muted);
  margin-top: 4px;
}

/* Forms & Inputs */
.primary-inputs {
  display: grid;
  grid-template-columns: 1fr 1.6fr;
  gap: 16px;
}
@media (max-width: 768px) {
  .primary-inputs { grid-template-columns: 1fr; }
}

.field-col {
  display: flex;
  flex-direction: column;
  gap: 4px;
}
.field-label {
  font-size: 12px;
  font-weight: 600;
  color: var(--text);
  display: inline-block;
  width: fit-content;
}
.input-text, .input-textarea {
  width: 100%;
  padding: 6px 10px;
  font-size: 13px;
  font-family: var(--font-sans);
  color: var(--text);
  background-color: var(--bg);
  border: 1px solid var(--border);
  border-radius: var(--radius-md);
  outline: none;
  transition: border-color 0.15s, box-shadow 0.15s;
}
.input-text:focus, .input-textarea:focus {
  border-color: var(--accent);
  box-shadow: 0 0 0 3px rgba(9, 105, 218, 0.15);
}
.seq-input {
  font-family: var(--font-mono);
  font-size: 12.5px;
}

/* Native Floating Tooltip Engine */
[data-help] {
  position: relative;
  cursor: help;
}
[data-help]::after {
  content: attr(data-help);
  position: absolute;
  bottom: calc(100% + 6px);
  left: 0;
  max-width: 260px;
  min-width: 140px;
  background: #1f2328;
  color: #ffffff;
  border: 1px solid rgba(255, 255, 255, 0.12);
  padding: 5px 8px;
  font-size: 11px;
  font-weight: 400;
  font-family: var(--font-sans);
  line-height: 1.35;
  border-radius: 4px;
  white-space: normal;
  pointer-events: none;
  opacity: 0;
  visibility: hidden;
  transform: translateY(3px);
  transition: opacity 0.15s ease, transform 0.15s ease, visibility 0.15s;
  z-index: 1000;
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.2);
}
.theme-dark [data-help]::after {
  background: #030712;
  color: #e5e7eb;
  border: 1px solid #374151;
}
[data-help]:hover::after {
  opacity: 1;
  visibility: visible;
  transform: translateY(0);
}

/* Accordion Panel */
.accordion-panel {
  border: 1px solid var(--border);
  border-radius: var(--radius-md);
  background: var(--bg);
  overflow: visible;
}
.accordion-summary {
  display: flex;
  justify-content: space-between;
  align-items: center;
  padding: 10px 14px;
  background: var(--bg-subtle);
  font-weight: 600;
  font-size: 13px;
  cursor: pointer;
  user-select: none;
  border-bottom: 1px solid transparent;
  list-style: none;
}
.accordion-summary::-webkit-details-marker { display: none; }
.accordion-panel[open] .accordion-summary {
  border-bottom-color: var(--border);
}
.accordion-panel[open] .summary-toggle {
  transform: rotate(90deg);
}
.summary-toggle {
  display: inline-block;
  font-size: 11px;
  margin-right: 6px;
  color: var(--text-muted);
  transition: transform 0.15s ease;
}
.summary-left {
  display: flex;
  align-items: center;
}
.summary-presets {
  display: flex;
  gap: 6px;
}

.accordion-content {
  padding: 16px;
  display: flex;
  flex-direction: column;
  gap: 16px;
}
.settings-group {
  padding-bottom: 14px;
  border-bottom: 1px solid var(--border-muted);
}
.settings-group:last-child {
  padding-bottom: 0;
  border-bottom: none;
}
.group-header {
  margin-bottom: 10px;
}
.group-title {
  font-size: 12px;
  font-weight: 700;
  text-transform: uppercase;
  letter-spacing: 0.04em;
  color: var(--text-muted);
  display: inline-block;
}

.grid-fields {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(130px, 1fr));
  gap: 12px;
}

/* Controls (Radio & Checkbox) */
.control-row {
  display: flex;
  justify-content: space-between;
  align-items: center;
  flex-wrap: wrap;
  gap: 12px;
}
.radio-group {
  display: flex;
  align-items: center;
  gap: 12px;
  flex-wrap: wrap;
}
.control-label {
  font-size: 12px;
  font-weight: 600;
  color: var(--text);
}
.radio-label, .checkbox-label {
  display: inline-flex;
  align-items: center;
  gap: 5px;
  font-size: 12.5px;
  color: var(--text);
  cursor: pointer;
}
.checkbox-row {
  display: flex;
  flex-wrap: wrap;
  gap: 16px;
}

/* Seed wrap */
.seed-input-wrap {
  display: flex;
  gap: 4px;
}

/* Buttons */
.btn {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  padding: 5px 12px;
  font-size: 12.5px;
  font-weight: 500;
  line-height: 20px;
  border-radius: var(--radius-md);
  border: 1px solid var(--border);
  background-color: var(--bg-subtle);
  color: var(--text);
  cursor: pointer;
  text-decoration: none;
  transition: all 0.12s ease;
  white-space: nowrap;
}
.btn:hover {
  background-color: var(--border-muted);
  border-color: var(--border);
}
.btn-primary {
  background-color: var(--primary);
  color: var(--primary-fg);
  border-color: var(--primary);
  font-weight: 600;
}
.btn-primary:hover {
  background-color: #32383f;
}
.theme-dark .btn-primary:hover {
  background-color: #ffffff;
}
.btn-sm {
  padding: 3px 10px;
  font-size: 12px;
}
.btn-xs {
  padding: 2px 6px;
  font-size: 11px;
}
.btn-block {
  width: 100%;
  padding: 9px 16px;
  font-size: 13.5px;
}

/* Chips Flex */
.chips-flex-wrap {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
}
.btn-chip {
  display: inline-flex;
  align-items: center;
  gap: 4px;
  padding: 3px 8px;
  font-size: 11.5px;
  font-family: var(--font-mono);
  background: var(--bg-subtle);
  border: 1px solid var(--border);
  border-radius: var(--radius-sm);
  color: var(--text);
  cursor: pointer;
  transition: all 0.1s ease;
}
.btn-chip:hover {
  border-color: var(--accent);
  background: var(--bg);
}

.isomir-library-box {
  background: var(--bg-subtle);
  border: 1px solid var(--border);
  border-radius: var(--radius-md);
  padding: 10px;
}
.box-header {
  display: flex;
  justify-content: space-between;
  margin-bottom: 6px;
}
.box-title {
  font-size: 11.5px;
  font-weight: 600;
  color: var(--text-muted);
}
.box-meta {
  font-size: 11.5px;
  color: var(--text-muted);
}

/* Badges */
.badge {
  display: inline-flex;
  align-items: center;
  padding: 1px 6px;
  font-size: 11px;
  font-weight: 600;
  border-radius: var(--radius-sm);
  line-height: 16px;
}
.badge-pass {
  background: var(--badge-pass-bg);
  color: var(--badge-pass-fg);
  border: 1px solid var(--badge-pass-border);
}
.badge-warn {
  background: var(--badge-warn-bg);
  color: var(--badge-warn-fg);
  border: 1px solid var(--badge-warn-border);
}
.badge-fail {
  background: var(--badge-fail-bg);
  color: var(--badge-fail-fg);
  border: 1px solid var(--badge-fail-border);
}
.badge-info {
  background: var(--badge-info-bg);
  color: var(--badge-info-fg);
  border: 1px solid var(--badge-info-border);
}
.badge-neutral {
  background: var(--bg-subtle);
  color: var(--text-muted);
  border: 1px solid var(--border);
}

/* Results & Candidates */
.results-container {
  margin-top: 24px;
}
.results-header {
  display: flex;
  justify-content: space-between;
  align-items: flex-end;
  flex-wrap: wrap;
  gap: 12px;
  padding-bottom: 12px;
  border-bottom: 1px solid var(--border);
}
.results-title {
  font-size: 16px;
  font-weight: 600;
}
.results-subtitle {
  font-size: 12.5px;
  color: var(--text-muted);
  margin-top: 2px;
}
.results-actions {
  display: flex;
  gap: 6px;
  align-items: center;
  flex-wrap: wrap;
}

.candidate-card {
  margin-top: 14px;
  border: 1px solid var(--border);
  border-radius: var(--radius-md);
  background: var(--bg);
  overflow: hidden;
}
.candidate-summary {
  display: flex;
  justify-content: space-between;
  align-items: center;
  padding: 10px 14px;
  background: var(--bg-subtle);
  cursor: pointer;
  user-select: none;
  font-size: 13px;
  font-weight: 600;
  list-style: none;
}
.candidate-summary::-webkit-details-marker { display: none; }
.candidate-card[open] .candidate-summary {
  border-bottom: 1px solid var(--border);
}
.candidate-card[open] .summary-toggle {
  transform: rotate(90deg);
}

.candidate-body {
  padding: 16px;
  display: flex;
  flex-direction: column;
  gap: 16px;
}

.candidate-section-title {
  font-size: 12px;
  font-weight: 700;
  text-transform: uppercase;
  letter-spacing: 0.04em;
  color: var(--text-muted);
  margin-bottom: 8px;
  display: flex;
  justify-content: space-between;
  align-items: center;
}

/* Monospace Box & Copy */
.seq-box {
  display: flex;
  align-items: center;
  justify-content: space-between;
  gap: 8px;
  background: var(--bg-subtle);
  border: 1px solid var(--border);
  border-radius: var(--radius-md);
  padding: 6px 10px;
}
.seq-text {
  font-family: var(--font-mono);
  font-size: 12px;
  word-break: break-all;
  color: var(--text);
  line-height: 1.6;
}

/* Color-Coded RT Primer Segments */
.primer-segment-legend {
  display: flex;
  flex-wrap: wrap;
  gap: 12px;
  margin-bottom: 6px;
  font-size: 11px;
}
.legend-item {
  display: inline-flex;
  align-items: center;
  gap: 4px;
  color: var(--text-muted);
}
.legend-dot {
  width: 8px;
  height: 8px;
  border-radius: 50%;
  display: inline-block;
}

.rt-colored-seq span {
  padding: 1px 2px;
  border-radius: 3px;
  font-weight: 600;
  transition: opacity 0.15s ease;
}
.rt-colored-seq:hover span {
  opacity: 0.6;
}
.rt-colored-seq span:hover {
  opacity: 1 !important;
}

.seg-rt5 {
  color: #8250df;
  background: rgba(130, 80, 223, 0.12);
  border-bottom: 2px solid #8250df;
}
.seg-rand5 {
  color: #9a6700;
  background: rgba(217, 119, 6, 0.12);
  border-bottom: 2px solid #d97706;
}
.seg-hairpin {
  color: #0969da;
  background: rgba(9, 105, 218, 0.12);
  border-bottom: 2px solid #0969da;
}
.seg-rand3 {
  color: #1a7f37;
  background: rgba(26, 127, 55, 0.12);
  border-bottom: 2px solid #1a7f37;
}
.seg-rt3 {
  color: #cf222e;
  background: rgba(207, 34, 46, 0.12);
  border-bottom: 2px solid #cf222e;
}

:root.theme-dark .seg-rt5 { color: #a371f7; background: rgba(163, 113, 247, 0.15); border-bottom-color: #a371f7; }
:root.theme-dark .seg-rand5 { color: #d29922; background: rgba(210, 153, 34, 0.15); border-bottom-color: #d29922; }
:root.theme-dark .seg-hairpin { color: #58a6ff; background: rgba(88, 166, 255, 0.15); border-bottom-color: #58a6ff; }
:root.theme-dark .seg-rand3 { color: #3fb950; background: rgba(63, 185, 80, 0.15); border-bottom-color: #3fb950; }
:root.theme-dark .seg-rt3 { color: #f85149; background: rgba(248, 81, 73, 0.15); border-bottom-color: #f85149; }

.stats-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(110px, 1fr));
  gap: 8px;
  margin-top: 8px;
}
.stat-item {
  background: var(--bg-subtle);
  border: 1px solid var(--border-muted);
  border-radius: var(--radius-sm);
  padding: 6px 8px;
}
.stat-label {
  font-size: 10.5px;
  color: var(--text-muted);
  font-weight: 600;
  text-transform: uppercase;
}
.stat-val {
  font-size: 12px;
  font-weight: 600;
  color: var(--text);
  margin-top: 2px;
}

/* Tables */
.data-table {
  width: 100%;
  border-collapse: collapse;
  font-size: 12px;
}
.data-table th, .data-table td {
  padding: 6px 8px;
  border-bottom: 1px solid var(--border-muted);
  text-align: left;
}
.data-table th {
  font-size: 11px;
  font-weight: 600;
  text-transform: uppercase;
  color: var(--text-muted);
  background: var(--bg-subtle);
}

/* Error Box */
.error-box {
  padding: 10px 14px;
  background: var(--badge-fail-bg);
  border: 1px solid var(--badge-fail-border);
  border-radius: var(--radius-md);
  color: var(--badge-fail-fg);
  font-size: 12.5px;
  margin-bottom: 16px;
}

/* Visualization Box */
.forna-box {
  width: 100%;
  height: 400px;
  border: 1px solid var(--border);
  border-radius: var(--radius-md);
  background: var(--bg-subtle);
  position: relative;
  overflow: hidden;
}

/* Footer */
.app-footer {
  margin-top: auto;
  border-top: 1px solid var(--border);
  padding: 20px 24px;
  background: var(--bg-subtle);
  width: 100%;
}
.footer-inner {
  max-width: 1060px;
  margin: 0 auto;
  font-size: 13px;
  color: var(--text-muted);
  display: flex;
  justify-content: center;
  align-items: center;
  text-align: center;
  gap: 8px;
}
.footer-inner a {
  color: var(--text);
  font-weight: 500;
  text-decoration: none;
  border-bottom: 1px dotted var(--border);
  transition: color 0.15s ease, border-color 0.15s ease;
}
.footer-inner a:hover {
  color: var(--accent);
  border-bottom-style: solid;
}
.footer-meta {
  font-size: 11px;
}