/* ==========================================================================
   Myco_tissue_RNAseq — Modern Scientific Story & Results Portal
   Design: Clean, high-impact scientific journal & interactive dashboard
   ========================================================================== */

:root {
  --font-sans: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
  --font-mono: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;

  /* Dark Theme (Default) */
  --bg-base: #0b0f19;
  --bg-surface: #111827;
  --bg-surface-elevated: #1f293d;
  --bg-surface-hover: #28354f;
  --border-subtle: #1e293b;
  --border-strong: #334155;
  
  --text-primary: #f8fafc;
  --text-secondary: #94a3b8;
  --text-muted: #64748b;
  
  --accent-cyan: #38bdf8;
  --accent-cyan-bg: rgba(56, 189, 248, 0.12);
  --accent-emerald: #10b981;
  --accent-emerald-bg: rgba(16, 185, 129, 0.12);
  --accent-amber: #f59e0b;
  --accent-amber-bg: rgba(245, 158, 11, 0.12);
  --accent-rose: #f43f5e;
  --accent-rose-bg: rgba(244, 63, 94, 0.12);
  --accent-purple: #a855f7;
  --accent-purple-bg: rgba(168, 85, 247, 0.12);

  --shadow-sm: 0 1px 2px 0 rgba(0, 0, 0, 0.3);
  --shadow-md: 0 4px 6px -1px rgba(0, 0, 0, 0.4), 0 2px 4px -2px rgba(0, 0, 0, 0.3);
  --shadow-lg: 0 10px 15px -3px rgba(0, 0, 0, 0.5), 0 4px 6px -4px rgba(0, 0, 0, 0.4);
  --radius-sm: 6px;
  --radius-md: 10px;
  --radius-lg: 16px;
  --radius-full: 9999px;
  
  --header-height: 64px;
}

[data-theme="light"] {
  --bg-base: #f8fafc;
  --bg-surface: #ffffff;
  --bg-surface-elevated: #f1f5f9;
  --bg-surface-hover: #e2e8f0;
  --border-subtle: #e2e8f0;
  --border-strong: #cbd5e1;

  --text-primary: #0f172a;
  --text-secondary: #475569;
  --text-muted: #94a3b8;

  --accent-cyan: #0284c7;
  --accent-cyan-bg: rgba(2, 132, 199, 0.1);
  --accent-emerald: #059669;
  --accent-emerald-bg: rgba(5, 150, 105, 0.1);
  --accent-amber: #d97706;
  --accent-amber-bg: rgba(217, 119, 6, 0.1);
  --accent-rose: #e11d48;
  --accent-rose-bg: rgba(225, 29, 72, 0.1);
  --accent-purple: #9333ea;
  --accent-purple-bg: rgba(147, 51, 234, 0.1);

  --shadow-sm: 0 1px 3px 0 rgba(0, 0, 0, 0.08);
  --shadow-md: 0 4px 6px -1px rgba(0, 0, 0, 0.08);
  --shadow-lg: 0 10px 15px -3px rgba(0, 0, 0, 0.1);
}

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

html {
  scroll-behavior: smooth;
  font-family: var(--font-sans);
  background-color: var(--bg-base);
  color: var(--text-primary);
  line-height: 1.6;
  -webkit-font-smoothing: antialiased;
}

body {
  min-height: 100vh;
  display: flex;
  flex-direction: column;
}

a {
  color: var(--accent-cyan);
  text-decoration: none;
  transition: color 0.2s ease;
}

a:hover {
  text-decoration: underline;
}

code, pre {
  font-family: var(--font-mono);
  font-size: 0.9em;
}

code {
  background: var(--bg-surface-elevated);
  padding: 0.15em 0.4em;
  border-radius: var(--radius-sm);
  color: var(--accent-cyan);
  border: 1px solid var(--border-subtle);
}

/* Container */
.container {
  width: 100%;
  max-width: 1200px;
  margin: 0 auto;
  padding: 0 1.5rem;
}

/* Header & Nav */
.header {
  position: sticky;
  top: 0;
  z-index: 100;
  height: var(--header-height);
  background: rgba(11, 15, 25, 0.85);
  backdrop-filter: blur(12px);
  -webkit-backdrop-filter: blur(12px);
  border-bottom: 1px solid var(--border-subtle);
  display: flex;
  align-items: center;
}

[data-theme="light"] .header {
  background: rgba(255, 255, 255, 0.88);
}

.nav-container {
  display: flex;
  justify-content: space-between;
  align-items: center;
  width: 100%;
}

.brand {
  display: flex;
  align-items: center;
  gap: 0.75rem;
  font-weight: 700;
  font-size: 1.15rem;
  color: var(--text-primary);
}

.brand-icon {
  font-size: 1.5rem;
  line-height: 1;
}

.brand span.tag {
  font-size: 0.7rem;
  text-transform: uppercase;
  padding: 0.2rem 0.5rem;
  background: var(--accent-cyan-bg);
  color: var(--accent-cyan);
  border-radius: var(--radius-full);
  letter-spacing: 0.05em;
  font-weight: 600;
}

.nav-links {
  display: flex;
  align-items: center;
  gap: 1.5rem;
  list-style: none;
}

.nav-links a {
  color: var(--text-secondary);
  font-size: 0.9rem;
  font-weight: 500;
  transition: color 0.15s;
}

.nav-links a:hover {
  color: var(--text-primary);
  text-decoration: none;
}

.nav-actions {
  display: flex;
  align-items: center;
  gap: 0.75rem;
}

.btn {
  display: inline-flex;
  align-items: center;
  gap: 0.5rem;
  padding: 0.5rem 1rem;
  font-size: 0.875rem;
  font-weight: 600;
  border-radius: var(--radius-sm);
  cursor: pointer;
  border: 1px solid transparent;
  transition: all 0.2s ease;
  text-decoration: none;
}

.btn-primary {
  background: var(--accent-cyan);
  color: #0b0f19;
}

.btn-primary:hover {
  background: #7dd3fc;
  text-decoration: none;
  transform: translateY(-1px);
}

.btn-outline {
  background: var(--bg-surface);
  border-color: var(--border-strong);
  color: var(--text-primary);
}

.btn-outline:hover {
  background: var(--bg-surface-elevated);
  text-decoration: none;
}

.btn-icon {
  padding: 0.5rem;
  border-radius: var(--radius-sm);
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  color: var(--text-secondary);
  cursor: pointer;
  display: flex;
  align-items: center;
  justify-content: center;
}

.btn-icon:hover {
  color: var(--text-primary);
  background: var(--bg-surface-elevated);
}

/* Hero Section */
.hero {
  padding: 5rem 0 3.5rem;
  background: radial-gradient(circle at 50% 0%, rgba(56, 189, 248, 0.08), transparent 70%);
  border-bottom: 1px solid var(--border-subtle);
  text-align: center;
}

.hero-badge {
  display: inline-flex;
  align-items: center;
  gap: 0.5rem;
  padding: 0.35rem 0.85rem;
  background: var(--accent-cyan-bg);
  color: var(--accent-cyan);
  border: 1px solid rgba(56, 189, 248, 0.3);
  border-radius: var(--radius-full);
  font-size: 0.8rem;
  font-weight: 600;
  margin-bottom: 1.5rem;
}

.hero h1 {
  font-size: clamp(2rem, 4.5vw, 3.25rem);
  font-weight: 800;
  line-height: 1.2;
  margin-bottom: 1.25rem;
  letter-spacing: -0.02em;
}

.hero h1 span.highlight {
  background: linear-gradient(135deg, var(--accent-cyan), #38bdf8 40%, #818cf8 100%);
  -webkit-background-clip: text;
  -webkit-text-fill-color: transparent;
}

.hero-subtitle {
  font-size: clamp(1rem, 2vw, 1.25rem);
  color: var(--text-secondary);
  max-width: 840px;
  margin: 0 auto 2.5rem;
  line-height: 1.6;
}

/* Stats Ribbon */
.stats-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(160px, 1fr));
  gap: 1rem;
  margin-top: 2.5rem;
}

.stat-card {
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  padding: 1.25rem 1rem;
  text-align: center;
  box-shadow: var(--shadow-sm);
  transition: transform 0.2s, border-color 0.2s;
}

.stat-card:hover {
  transform: translateY(-2px);
  border-color: var(--border-strong);
}

.stat-number {
  font-size: 1.85rem;
  font-weight: 800;
  color: var(--accent-cyan);
  line-height: 1.1;
  margin-bottom: 0.35rem;
  font-family: var(--font-mono);
}

.stat-label {
  font-size: 0.8rem;
  color: var(--text-secondary);
  font-weight: 500;
  text-transform: uppercase;
  letter-spacing: 0.03em;
}

/* Chapter Sections */
.chapter {
  padding: 5rem 0;
  border-bottom: 1px solid var(--border-subtle);
}

.chapter:nth-child(even) {
  background: rgba(17, 24, 39, 0.4);
}

[data-theme="light"] .chapter:nth-child(even) {
  background: rgba(241, 245, 249, 0.5);
}

.chapter-header {
  margin-bottom: 2.5rem;
}

.chapter-tag {
  display: inline-block;
  font-size: 0.75rem;
  font-weight: 700;
  text-transform: uppercase;
  letter-spacing: 0.08em;
  color: var(--accent-cyan);
  margin-bottom: 0.5rem;
}

.chapter-title {
  font-size: clamp(1.6rem, 3vw, 2.2rem);
  font-weight: 700;
  color: var(--text-primary);
  margin-bottom: 0.75rem;
}

.chapter-desc {
  font-size: 1.05rem;
  color: var(--text-secondary);
  max-width: 850px;
  line-height: 1.65;
}

/* Grid & Cards */
.card-grid-2 {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(360px, 1fr));
  gap: 1.5rem;
  margin-top: 2rem;
}

.card-grid-3 {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
  gap: 1.5rem;
  margin-top: 2rem;
}

.card {
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  padding: 1.75rem;
  box-shadow: var(--shadow-sm);
}

.card-header {
  display: flex;
  align-items: center;
  justify-content: space-between;
  margin-bottom: 1rem;
}

.card-title {
  font-size: 1.15rem;
  font-weight: 700;
  color: var(--text-primary);
}

/* Forensic Catastrophe Callout */
.callout-danger {
  background: rgba(244, 63, 94, 0.08);
  border: 1px solid rgba(244, 63, 94, 0.3);
  border-radius: var(--radius-md);
  padding: 1.5rem;
  margin-bottom: 2rem;
}

.callout-success {
  background: rgba(16, 185, 129, 0.08);
  border: 1px solid rgba(16, 185, 129, 0.3);
  border-radius: var(--radius-md);
  padding: 1.5rem;
  margin-bottom: 2rem;
}

.callout-title {
  font-weight: 700;
  font-size: 1.05rem;
  margin-bottom: 0.5rem;
  display: flex;
  align-items: center;
  gap: 0.5rem;
}

.callout-danger .callout-title {
  color: var(--accent-rose);
}

.callout-success .callout-title {
  color: var(--accent-emerald);
}

/* Comparison Tables */
.table-responsive {
  width: 100%;
  overflow-x: auto;
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  background: var(--bg-surface);
  margin-top: 1.5rem;
  box-shadow: var(--shadow-sm);
}

table {
  width: 100%;
  border-collapse: collapse;
  text-align: left;
  font-size: 0.9rem;
}

th, td {
  padding: 0.85rem 1.15rem;
  border-bottom: 1px solid var(--border-subtle);
}

th {
  background: var(--bg-surface-elevated);
  font-weight: 600;
  color: var(--text-secondary);
  font-size: 0.8rem;
  text-transform: uppercase;
  letter-spacing: 0.05em;
  white-space: nowrap;
}

tr:last-child td {
  border-bottom: none;
}

tr:hover td {
  background: var(--bg-surface-hover);
}

.badge {
  display: inline-flex;
  align-items: center;
  gap: 0.35rem;
  padding: 0.2rem 0.55rem;
  border-radius: var(--radius-full);
  font-size: 0.75rem;
  font-weight: 600;
  line-height: 1;
}

.badge-nodule { background: rgba(245, 158, 11, 0.15); color: #f59e0b; border: 1px solid rgba(245, 158, 11, 0.3); }
.badge-exudophore { background: rgba(56, 189, 248, 0.15); color: #38bdf8; border: 1px solid rgba(56, 189, 248, 0.3); }
.badge-fuzzy { background: rgba(168, 85, 247, 0.15); color: #c084fc; border: 1px solid rgba(168, 85, 247, 0.3); }
.badge-exuding { background: rgba(16, 185, 129, 0.15); color: #34d399; border: 1px solid rgba(16, 185, 129, 0.3); }

.badge-success { background: var(--accent-emerald-bg); color: var(--accent-emerald); }
.badge-danger { background: var(--accent-rose-bg); color: var(--accent-rose); }
.badge-warning { background: var(--accent-amber-bg); color: var(--accent-amber); }
.badge-info { background: var(--accent-cyan-bg); color: var(--accent-cyan); }

/* Interactive PCA Section */
.pca-container {
  display: grid;
  grid-template-columns: 1fr 340px;
  gap: 2rem;
  margin-top: 2rem;
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-lg);
  padding: 1.75rem;
  box-shadow: var(--shadow-md);
}

@media (max-width: 900px) {
  .pca-container {
    grid-template-columns: 1fr;
  }
}

.pca-canvas-box {
  position: relative;
  width: 100%;
  aspect-ratio: 16 / 11;
  background: var(--bg-base);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  overflow: hidden;
}

canvas#pca-canvas {
  width: 100%;
  height: 100%;
  display: block;
}

.pca-controls {
  display: flex;
  flex-direction: column;
  gap: 1.25rem;
}

.control-group {
  display: flex;
  flex-direction: column;
  gap: 0.5rem;
}

.control-label {
  font-size: 0.85rem;
  font-weight: 600;
  color: var(--text-secondary);
  text-transform: uppercase;
  letter-spacing: 0.04em;
}

.toggle-group {
  display: flex;
  background: var(--bg-surface-elevated);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-sm);
  padding: 0.25rem;
  gap: 0.25rem;
}

.toggle-btn {
  flex: 1;
  padding: 0.5rem 0.75rem;
  background: transparent;
  border: none;
  color: var(--text-secondary);
  font-size: 0.825rem;
  font-weight: 600;
  border-radius: var(--radius-sm);
  cursor: pointer;
  transition: all 0.15s;
}

.toggle-btn.active {
  background: var(--accent-cyan);
  color: #0b0f19;
  box-shadow: var(--shadow-sm);
}

.pca-stats-card {
  background: var(--bg-surface-elevated);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  padding: 1rem;
}

.pca-stats-val {
  font-size: 1.4rem;
  font-weight: 800;
  font-family: var(--font-mono);
}

/* Tissue Legend */
.tissue-legend {
  display: flex;
  flex-direction: column;
  gap: 0.65rem;
  font-size: 0.85rem;
}

.legend-item {
  display: flex;
  align-items: center;
  gap: 0.65rem;
}

.legend-dot {
  width: 12px;
  height: 12px;
  border-radius: 50%;
  flex-shrink: 0;
}

/* Searchable Table Tool */
.search-bar-row {
  display: flex;
  flex-wrap: wrap;
  gap: 1rem;
  align-items: center;
  margin-top: 1.5rem;
  margin-bottom: 1rem;
}

.search-input {
  flex: 1;
  min-width: 240px;
  padding: 0.65rem 1rem;
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-sm);
  color: var(--text-primary);
  font-size: 0.9rem;
  font-family: inherit;
}

.search-input:focus {
  outline: none;
  border-color: var(--accent-cyan);
  box-shadow: 0 0 0 2px var(--accent-cyan-bg);
}

.filter-select {
  padding: 0.65rem 1rem;
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-sm);
  color: var(--text-primary);
  font-size: 0.9rem;
  font-family: inherit;
  cursor: pointer;
}

.filter-select:focus {
  outline: none;
  border-color: var(--accent-cyan);
}

/* Publication Figure Gallery */
.gallery-filters {
  display: flex;
  flex-wrap: wrap;
  gap: 0.5rem;
  margin-top: 1.5rem;
  margin-bottom: 2rem;
}

.filter-pill {
  padding: 0.4rem 0.85rem;
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-full);
  color: var(--text-secondary);
  font-size: 0.825rem;
  font-weight: 600;
  cursor: pointer;
  transition: all 0.15s;
}

.filter-pill:hover {
  background: var(--bg-surface-elevated);
  color: var(--text-primary);
}

.filter-pill.active {
  background: var(--accent-cyan);
  color: #0b0f19;
  border-color: var(--accent-cyan);
}

.gallery-grid {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(280px, 1fr));
  gap: 1.5rem;
}

.fig-card {
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  overflow: hidden;
  cursor: pointer;
  transition: transform 0.2s, box-shadow 0.2s, border-color 0.2s;
  display: flex;
  flex-direction: column;
}

.fig-card:hover {
  transform: translateY(-4px);
  border-color: var(--accent-cyan);
  box-shadow: var(--shadow-lg);
}

.fig-thumb-wrap {
  width: 100%;
  aspect-ratio: 16 / 10;
  background: #ffffff;
  display: flex;
  align-items: center;
  justify-content: center;
  overflow: hidden;
  border-bottom: 1px solid var(--border-subtle);
  padding: 0.75rem;
}

.fig-thumb-wrap img {
  max-width: 100%;
  max-height: 100%;
  object-fit: contain;
  transition: transform 0.3s ease;
}

.fig-card:hover .fig-thumb-wrap img {
  transform: scale(1.03);
}

.fig-info {
  padding: 1.25rem;
  display: flex;
  flex-direction: column;
  flex: 1;
}

.fig-meta-badge {
  font-size: 0.7rem;
  font-weight: 700;
  text-transform: uppercase;
  color: var(--accent-cyan);
  margin-bottom: 0.25rem;
}

.fig-card-title {
  font-size: 0.95rem;
  font-weight: 700;
  color: var(--text-primary);
  line-height: 1.35;
  margin-bottom: 0.5rem;
}

.fig-card-desc {
  font-size: 0.8rem;
  color: var(--text-secondary);
  line-height: 1.45;
  display: -webkit-box;
  -webkit-line-clamp: 2;
  -webkit-box-orient: vertical;
  overflow: hidden;
}

/* Lightbox Modal */
.modal-backdrop {
  position: fixed;
  inset: 0;
  background: rgba(0, 0, 0, 0.88);
  backdrop-filter: blur(8px);
  z-index: 1000;
  display: none;
  align-items: center;
  justify-content: center;
  padding: 1.5rem;
}

.modal-backdrop.open {
  display: flex;
  animation: fadeIn 0.2s ease-out;
}

.modal-content {
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-lg);
  max-width: 1100px;
  width: 100%;
  max-height: 92vh;
  display: flex;
  flex-direction: column;
  box-shadow: var(--shadow-lg);
  overflow: hidden;
}

.modal-header {
  display: flex;
  align-items: center;
  justify-content: space-between;
  padding: 1rem 1.5rem;
  border-bottom: 1px solid var(--border-subtle);
  background: var(--bg-surface-elevated);
}

.modal-title {
  font-size: 1.1rem;
  font-weight: 700;
}

.modal-body {
  padding: 1.5rem;
  overflow-y: auto;
  display: flex;
  flex-direction: column;
  align-items: center;
  gap: 1.5rem;
}

.modal-img-container {
  width: 100%;
  background: #ffffff;
  border-radius: var(--radius-md);
  padding: 1rem;
  display: flex;
  align-items: center;
  justify-content: center;
}

.modal-img-container img {
  max-width: 100%;
  max-height: 58vh;
  object-fit: contain;
}

.modal-caption {
  font-size: 0.9rem;
  color: var(--text-secondary);
  line-height: 1.6;
  width: 100%;
}

.modal-footer {
  display: flex;
  align-items: center;
  justify-content: space-between;
  padding: 0.75rem 1.5rem;
  border-top: 1px solid var(--border-subtle);
  background: var(--bg-surface-elevated);
}

/* Paper Cards */
.paper-card {
  background: var(--bg-surface);
  border: 1px solid var(--border-subtle);
  border-radius: var(--radius-md);
  padding: 1.75rem;
  display: flex;
  flex-direction: column;
  justify-content: space-between;
  box-shadow: var(--shadow-sm);
  transition: transform 0.2s, border-color 0.2s;
}

.paper-card:hover {
  transform: translateY(-2px);
  border-color: var(--accent-cyan);
}

.paper-num {
  font-size: 0.75rem;
  font-weight: 700;
  text-transform: uppercase;
  color: var(--accent-cyan);
  margin-bottom: 0.5rem;
}

.paper-title {
  font-size: 1.1rem;
  font-weight: 700;
  color: var(--text-primary);
  margin-bottom: 0.75rem;
  line-height: 1.4;
}

.paper-abstract {
  font-size: 0.85rem;
  color: var(--text-secondary);
  line-height: 1.55;
  margin-bottom: 1.25rem;
  flex: 1;
}

.paper-meta {
  display: flex;
  align-items: center;
  justify-content: space-between;
  padding-top: 1rem;
  border-top: 1px solid var(--border-subtle);
}

/* Footer */
.footer {
  margin-top: auto;
  background: var(--bg-surface);
  border-top: 1px solid var(--border-subtle);
  padding: 3.5rem 0 2rem;
  font-size: 0.9rem;
  color: var(--text-secondary);
}

.footer-grid {
  display: grid;
  grid-template-columns: 2fr 1fr 1fr;
  gap: 3rem;
  margin-bottom: 2.5rem;
}

@media (max-width: 768px) {
  .footer-grid {
    grid-template-columns: 1fr;
    gap: 2rem;
  }
}

.footer-col h4 {
  color: var(--text-primary);
  font-size: 1rem;
  margin-bottom: 1rem;
}

.footer-links {
  list-style: none;
  display: flex;
  flex-direction: column;
  gap: 0.5rem;
}

.footer-bottom {
  text-align: center;
  padding-top: 2rem;
  border-top: 1px solid var(--border-subtle);
  font-size: 0.8rem;
  color: var(--text-muted);
}

/* Animations */
@keyframes fadeIn {
  from { opacity: 0; }
  to { opacity: 1; }
}