@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600&family=Source+Serif+4:ital,wght@0,400;0,600;0,700;1,400&display=swap');

*,
*::before,
*::after {
  margin: 0;
  padding: 0;
  box-sizing: border-box;
}

:root {
  --bg: #FAFAF8;
  --text: #1a1a1a;
  --text-muted: #6b6b6b;
  --accent: #1E6B6B;
  --border: #e0e0dc;
  --serif: 'Source Serif 4', Georgia, serif;
  --sans: 'Inter', -apple-system, sans-serif;
}

html {
  font-size: 19px;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
}

body {
  font-family: var(--serif);
  color: var(--text);
  background: var(--bg);
  line-height: 1.75;
}

/* Top bar */
.top-bar {
  position: sticky;
  top: 0;
  z-index: 10;
  background: var(--bg);
  border-bottom: 1px solid var(--border);
  padding: 0.75rem 1.5rem;
  display: flex;
  justify-content: space-between;
  align-items: center;
  font-family: var(--sans);
  font-size: 0.74rem;
  letter-spacing: 0.02em;
}

.top-bar a {
  color: var(--text-muted);
  text-decoration: none;
  transition: color 0.2s;
  min-width: 0;
  overflow: hidden;
  text-overflow: ellipsis;
  white-space: nowrap;
}

.top-bar a:hover {
  color: var(--text);
}

.top-bar .chapter-label {
  color: var(--text-muted);
  flex-shrink: 0;
  white-space: nowrap;
  padding-left: 1rem;
}

/* Content container */
.container {
  max-width: 660px;
  margin: 0 auto;
  padding: 0 1.5rem;
}

/* Chapter header */
.chapter-header {
  padding-top: 5rem;
  padding-bottom: 3rem;
}

.chapter-number {
  font-family: var(--sans);
  font-size: 0.7rem;
  font-weight: 600;
  letter-spacing: 0.15em;
  text-transform: uppercase;
  color: var(--accent);
  margin-bottom: 1rem;
  display: block;
}

.chapter-title {
  font-family: var(--serif);
  font-size: 2.4rem;
  font-weight: 700;
  line-height: 1.2;
  color: var(--text);
}

/* Body content */
.content {
  overflow-wrap: break-word;
  hyphens: auto;
}

.content h2 {
  font-family: var(--sans);
  font-size: 1.1rem;
  font-weight: 600;
  margin-top: 3rem;
  margin-bottom: 1rem;
  color: var(--text);
}

.content p {
  margin-bottom: 1.25rem;
}

.content strong {
  font-weight: 600;
}

.content ul,
.content ol {
  margin-bottom: 1.25rem;
  padding-left: 1.5rem;
}

.content li {
  margin-bottom: 0.5rem;
}

.content a {
  color: var(--accent);
  text-decoration: underline;
  text-underline-offset: 2px;
  transition: opacity 0.2s;
}

.content a:hover {
  opacity: 0.7;
}

/* Bottom navigation */
.bottom-nav {
  display: flex;
  justify-content: space-between;
  align-items: center;
  padding: 3rem 0;
  margin-top: 3rem;
  border-top: 1px solid var(--border);
  font-family: var(--sans);
  font-size: 0.84rem;
}

.bottom-nav a {
  color: var(--text-muted);
  text-decoration: none;
  transition: color 0.2s;
  min-width: 0;
  max-width: 48%;
  word-break: break-word;
  padding: 0.5rem 0.25rem;
  display: inline-block;
}

.bottom-nav a:hover {
  color: var(--accent);
}

.bottom-nav .prev::before {
  content: '\2190\00a0';
}

.bottom-nav .next::after {
  content: '\00a0\2192';
}

/* Footer / Disclaimer */
.disclaimer {
  padding: 2rem 0 3rem;
  font-family: var(--sans);
  font-size: 0.68rem;
  color: var(--text-muted);
  line-height: 1.6;
  text-align: center;
}

/* ---- Landing page ---- */
.hero {
  min-height: 85vh;
  display: flex;
  flex-direction: column;
  justify-content: center;
  align-items: center;
  text-align: center;
  padding: 4rem 1.5rem;
}

.hero-title {
  font-family: var(--serif);
  font-size: 2.8rem;
  font-weight: 700;
  line-height: 1.15;
  max-width: 640px;
  color: var(--text);
}

.hero-subtitle {
  font-family: var(--sans);
  font-size: 1rem;
  color: var(--text-muted);
  margin-top: 1.5rem;
  max-width: 480px;
  line-height: 1.6;
}

.hero-cta {
  margin-top: 2.5rem;
  font-family: var(--sans);
  font-size: 0.9rem;
  font-weight: 500;
  color: var(--accent);
  text-decoration: none;
  letter-spacing: 0.03em;
  transition: opacity 0.2s;
  display: inline-block;
  padding: 0.75rem 1.25rem;
}

.hero-cta:hover {
  opacity: 0.7;
}

/* Table of contents */
.toc {
  padding: 4rem 0 6rem;
}

.toc h2 {
  font-family: var(--sans);
  font-size: 0.7rem;
  font-weight: 600;
  letter-spacing: 0.15em;
  text-transform: uppercase;
  color: var(--text-muted);
  margin-bottom: 2rem;
}

.toc-list {
  list-style: none;
  padding: 0;
}

.toc-list li {
  border-top: 1px solid var(--border);
}

.toc-list li:last-child {
  border-bottom: 1px solid var(--border);
}

.toc-list a {
  display: flex;
  align-items: baseline;
  gap: 1rem;
  padding: 0.85rem 0;
  text-decoration: none;
  color: var(--text);
  transition: color 0.2s;
  font-size: 1rem;
}

.toc-list a:hover {
  color: var(--accent);
}

.toc-list .toc-num {
  font-family: var(--sans);
  font-size: 0.74rem;
  font-weight: 500;
  color: var(--accent);
  min-width: 1.5rem;
}

/* Appendix specifics */
.content h3 {
  font-family: var(--sans);
  font-size: 0.95rem;
  font-weight: 600;
  margin-top: 2rem;
  margin-bottom: 0.75rem;
  color: var(--text);
}

/* Focus styles */
:focus-visible {
  outline: 2px solid var(--accent);
  outline-offset: 3px;
  border-radius: 2px;
}

/* Skip link */
.skip-link {
  position: absolute;
  top: -100%;
  left: 0;
  padding: 0.5rem 1rem;
  background: var(--text);
  color: var(--bg);
  font-family: var(--sans);
  font-size: 0.84rem;
  z-index: 100;
  text-decoration: none;
}

.skip-link:focus {
  top: 0;
}

/* Reduced motion */
@media (prefers-reduced-motion: reduce) {
  *,
  *::before,
  *::after {
    transition-duration: 0.01ms !important;
    animation-duration: 0.01ms !important;
    animation-iteration-count: 1 !important;
  }
}

/* Diagrams */
.figure {
  margin: 2.5rem 0;
  border: 1px solid #e0e0dc;
  border-radius: 3px;
  padding: 1.5rem 1.25rem;
  overflow-x: auto;
  background: #fff;
}

.figure svg {
  display: block;
  max-width: 100%;
  height: auto;
}

.figure figcaption {
  font-family: 'Inter', -apple-system, sans-serif;
  font-size: 0.74rem;
  color: #6b6b6b;
  text-align: center;
  margin-top: 0.85rem;
  line-height: 1.5;
}

/* Dark mode */
@media (prefers-color-scheme: dark) {
  :root {
    --bg: #18181a;
    --text: #e4e4e0;
    --text-muted: #9b9b96;
    --accent: #4ab8a8;
    --border: #2a2a2e;
  }

  .figure {
    border-color: #333336;
  }

  .figure figcaption {
    color: #9b9b96;
  }
}

/* ============================================================
   Interactive enhancements
   ============================================================ */

/* Reading progress bar */
#reading-progress {
  position: fixed;
  top: 0;
  left: 0;
  height: 3px;
  background: var(--accent);
  z-index: 20;
  width: 0;
  transition: width 0.1s linear;
}

/* Glossary tooltips */
.term {
  border-bottom: 1px dashed var(--accent);
  cursor: help;
}

#tooltip {
  position: fixed;
  background: #1a1a1a;
  color: #fff;
  font-size: 0.78rem;
  font-family: var(--sans);
  padding: 0.5rem 0.75rem;
  border-radius: 4px;
  max-width: 280px;
  pointer-events: none;
  z-index: 50;
  opacity: 0;
  transition: opacity 0.15s;
  line-height: 1.5;
}

#tooltip.visible {
  opacity: 1;
}

@media (prefers-color-scheme: dark) {
  #tooltip {
    background: #e4e4e0;
    color: #18181a;
  }
}

/* Step-through diagrams */
.stepper .step {
  display: none;
}

.stepper .step.active {
  display: block;
}

.stepper-controls {
  display: flex;
  align-items: center;
  gap: 1rem;
  margin-top: 1rem;
  font-family: var(--sans);
  font-size: 0.84rem;
  flex-wrap: wrap;
}

.stepper-controls button {
  padding: 0.4rem 0.9rem;
  border: 1px solid var(--accent);
  color: var(--accent);
  background: transparent;
  border-radius: 3px;
  cursor: pointer;
  font-family: var(--sans);
  font-size: 0.84rem;
}

.stepper-controls button:hover {
  background: var(--accent);
  color: #fff;
}

.stepper-controls button:disabled {
  opacity: 0.35;
  cursor: default;
}

.step-counter {
  color: var(--text-muted);
  font-size: 0.78rem;
  margin-left: auto;
}

.step-caption {
  font-family: var(--sans);
  font-size: 0.86rem;
  color: var(--text-muted);
  margin-top: 0.75rem;
  line-height: 1.55;
}

/* Key takeaways */
.key-takeaways {
  background: color-mix(in srgb, var(--accent) 8%, var(--bg));
  border-left: 3px solid var(--accent);
  padding: 1.25rem 1.5rem;
  margin: 2.5rem 0;
  border-radius: 0 4px 4px 0;
}

.key-takeaways h3 {
  font-family: var(--sans);
  font-size: 0.72rem;
  font-weight: 600;
  text-transform: uppercase;
  letter-spacing: 0.1em;
  color: var(--accent);
  margin-bottom: 0.75rem;
}

.key-takeaways ul {
  padding-left: 1.25rem;
  margin-bottom: 0;
}

.key-takeaways li {
  font-size: 0.92rem;
  margin-bottom: 0.35rem;
}

/* Interactive tool box */
.tool-box {
  border: 1px solid var(--border);
  border-radius: 4px;
  padding: 1.5rem;
  margin: 2.5rem 0;
  font-family: var(--sans);
}

.tool-box h3 {
  font-size: 0.9rem;
  font-weight: 600;
  margin-bottom: 0.5rem;
}

.tool-hint {
  font-size: 0.82rem;
  color: var(--text-muted);
  margin-bottom: 0.75rem;
}

.tool-box textarea {
  width: 100%;
  font-family: monospace;
  font-size: 0.9rem;
  border: 1px solid var(--border);
  padding: 0.5rem;
  border-radius: 3px;
  background: var(--bg);
  color: var(--text);
  resize: vertical;
}

.tool-box button {
  margin-top: 0.75rem;
  padding: 0.45rem 1rem;
  background: var(--accent);
  color: #fff;
  border: none;
  border-radius: 3px;
  cursor: pointer;
  font-family: var(--sans);
  font-size: 0.84rem;
}

.tool-box button:hover {
  opacity: 0.85;
}

.tool-output {
  margin-top: 1rem;
  font-family: monospace;
  font-size: 0.88rem;
  min-height: 2rem;
  line-height: 1.8;
}

.codon-tile {
  display: inline-block;
  padding: 0.1rem 0.35rem;
  border-radius: 3px;
  margin: 0.1rem;
  font-size: 0.82rem;
  cursor: help;
}

.codon-tile.start {
  background: #d4edda;
  color: #155724;
}

.codon-tile.stop {
  background: #f8d7da;
  color: #721c24;
}

.codon-tile.other {
  background: #d4ebeb;
  color: #1E6B6B;
}

@media (prefers-color-scheme: dark) {
  .codon-tile.start { background: #1a3a22; color: #7dcea0; }
  .codon-tile.stop  { background: #3a1a1a; color: #e8a5a5; }
  .codon-tile.other { background: #1a2e2e; color: #4ab8a8; }
}

/* Pipeline expandable steps */
.pipeline-step {
  border: 1px solid var(--border);
  border-radius: 4px;
  margin-bottom: 0.5rem;
}

.pipeline-step .step-toggle {
  cursor: pointer;
  padding: 0.85rem 1rem;
  font-family: var(--sans);
  font-size: 0.9rem;
  font-weight: 500;
  display: flex;
  justify-content: space-between;
  align-items: center;
  user-select: none;
}

.pipeline-step .step-toggle::after {
  content: '▸';
  font-size: 0.7rem;
  color: var(--accent);
  flex-shrink: 0;
  margin-left: 0.5rem;
}

.pipeline-step.open .step-toggle::after {
  content: '▾';
}

.pipeline-step-detail {
  display: none;
  background: color-mix(in srgb, var(--accent) 6%, var(--bg));
  border-top: 1px solid var(--border);
  padding: 1rem 1.25rem;
  font-family: var(--sans);
  font-size: 0.84rem;
  line-height: 1.6;
}

.pipeline-step.open .pipeline-step-detail {
  display: block;
}

/* MHC interactive diagram */
#mhc-interactive #cancer-panel {
  cursor: pointer;
}

#mhc-interactive #cancer-panel:hover #cancer-cell-body {
  filter: brightness(1.1);
}

#mhc-interactive .tcell-killer {
  transition: transform 0.5s ease;
}

#mhc-interactive.mhc-activated .tcell-killer {
  transform: translateY(30px);
}

#mhc-interactive .kill-arrow {
  transition: opacity 0.4s, stroke 0.4s;
}

#mhc-interactive.mhc-activated .kill-arrow {
  stroke: #e53935 !important;
  opacity: 1 !important;
}

#mhc-interactive .kill-bolt {
  transition: transform 0.4s, opacity 0.4s;
  transform-origin: center;
}

#mhc-interactive.mhc-activated .kill-bolt {
  transform: scale(1.4);
  opacity: 1;
}

@keyframes pulse-red {
  0%, 100% { opacity: 1; }
  50% { opacity: 0.4; }
}

#mhc-interactive.mhc-activated .kill-arrow {
  animation: pulse-red 1s ease-in-out infinite;
}

/* TOC completion checkmarks */
.toc-check {
  color: var(--accent);
  font-family: var(--sans);
  font-size: 0.8rem;
  margin-left: 0.5rem;
}

/* Interactive cost curve data points */
.cost-point {
  cursor: pointer;
  transition: r 0.15s, opacity 0.15s;
}

.cost-point:hover {
  r: 7;
}

/* Responsive */
@media (max-width: 720px) {
  html {
    font-size: 17px;
  }

  .hero-title {
    font-size: 2rem;
  }

  .chapter-title {
    font-size: 1.8rem;
  }

  .chapter-header {
    padding-top: 3rem;
    padding-bottom: 2rem;
  }
}

@media (max-width: 480px) {
  html {
    font-size: 16px;
  }

  .hero {
    min-height: 70vh;
    padding: 3rem 1rem;
  }

  .hero-title {
    font-size: 1.7rem;
  }

  .chapter-title {
    font-size: 1.5rem;
  }

  .top-bar {
    padding: 0.6rem 1rem;
  }

  .container {
    padding: 0 1rem;
  }
}

/* Print */
@media print {
  .top-bar,
  .skip-link,
  .bottom-nav {
    display: none;
  }

  .container {
    max-width: 100%;
    padding: 0;
  }

  .chapter-header {
    padding-top: 1.5cm;
    padding-bottom: 1cm;
  }

  .figure {
    break-inside: avoid;
    page-break-inside: avoid;
    border: 1px solid #ccc;
  }

  body {
    font-size: 11pt;
    line-height: 1.6;
    background: #fff;
    color: #000;
  }
}