/**
 * Plant Microsynteny Plotter - CSS Design System
 * Modern, premium design with dark mode support
 */

/* ============================================================================
   CSS Variables / Design Tokens
   ============================================================================ */
:root {
  /* Color Palette - Light Mode */
  --color-bg-primary: #f8fafc;
  --color-bg-secondary: #ffffff;
  --color-bg-tertiary: #f1f5f9;
  --color-bg-sidebar: linear-gradient(180deg, #1e293b 0%, #0f172a 100%);

  --color-text-primary: #1e293b;
  --color-text-secondary: #475569;
  --color-text-muted: #94a3b8;
  --color-text-inverse: #ffffff;

  --color-accent-primary: #6366f1;
  --color-accent-secondary: #8b5cf6;
  --color-accent-success: #10b981;
  --color-accent-warning: #f59e0b;
  --color-accent-danger: #ef4444;
  --color-accent-info: #06b6d4;

  --color-border: #e2e8f0;
  --color-border-light: #f1f5f9;

  /* Shadows */
  --shadow-sm: 0 1px 2px 0 rgba(0, 0, 0, 0.05);
  --shadow-md:
    0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -2px rgba(0, 0, 0, 0.1);
  --shadow-lg:
    0 10px 15px -3px rgba(0, 0, 0, 0.1), 0 4px 6px -4px rgba(0, 0, 0, 0.1);
  --shadow-xl:
    0 20px 25px -5px rgba(0, 0, 0, 0.1), 0 8px 10px -6px rgba(0, 0, 0, 0.1);
  --shadow-glow: 0 0 20px rgba(99, 102, 241, 0.3);

  /* Glassmorphism */
  --glass-bg: rgba(255, 255, 255, 0.7);
  --glass-border: rgba(255, 255, 255, 0.2);
  --glass-blur: blur(12px);

  /* Spacing */
  --space-xs: 0.25rem;
  --space-sm: 0.5rem;
  --space-md: 1rem;
  --space-lg: 1.5rem;
  --space-xl: 2rem;
  --space-2xl: 3rem;

  /* Border Radius */
  --radius-sm: 0.375rem;
  --radius-md: 0.5rem;
  --radius-lg: 0.75rem;
  --radius-xl: 1rem;
  --radius-full: 9999px;

  /* Transitions */
  --transition-fast: 150ms ease;
  --transition-normal: 250ms ease;
  --transition-slow: 350ms ease;

  /* Sidebar */
  --sidebar-width: 260px;
  --sidebar-collapsed: 70px;
}

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

html {
  font-size: 16px;
  scroll-behavior: smooth;
}

body {
  font-family:
    "Inter",
    -apple-system,
    BlinkMacSystemFont,
    "Segoe UI",
    Roboto,
    sans-serif;
  background: var(--color-bg-primary);
  color: var(--color-text-primary);
  line-height: 1.6;
  min-height: 100vh;
  overflow-x: hidden;
}

/* ============================================================================
   App Layout
   ============================================================================ */
.app-container {
  display: flex;
  min-height: 100vh;
}

/* ============================================================================
   Sidebar
   ============================================================================ */
.sidebar {
  width: var(--sidebar-width);
  background: var(--color-bg-sidebar);
  color: var(--color-text-inverse);
  display: flex;
  flex-direction: column;
  position: fixed;
  height: 100vh;
  z-index: 100;
  transition: width var(--transition-normal);
}

.sidebar-header {
  padding: var(--space-xl);
  border-bottom: 1px solid rgba(255, 255, 255, 0.1);
}

.logo {
  display: flex;
  align-items: center;
  gap: var(--space-md);
}

.logo-icon {
  font-size: 2rem;
  filter: drop-shadow(0 0 8px rgba(99, 102, 241, 0.5));
}

.nav-icon-img {
  width: 48px;
  height: 48px;
  object-fit: contain;
  border-radius: 4px;
  flex-shrink: 0;
}

/* Custom-Microsynteny icon slightly larger */
.nav-icon-img[alt="Custom-Microsynteny"] {
  width: 50px;
  height: 50px;
}

.logo-text {
  font-size: 1.2rem;
  font-weight: 700;
  background: linear-gradient(135deg, #6366f1, #a78bfa);
  -webkit-background-clip: text;
  -webkit-text-fill-color: transparent;
  background-clip: text;
}

.sidebar-nav {
  flex: 1;
  padding: var(--space-lg);
  display: flex;
  flex-direction: column;
  gap: var(--space-sm);
}

.nav-item {
  display: flex;
  align-items: center;
  gap: var(--space-sm);
  padding: var(--space-md) var(--space-md) var(--space-md) var(--space-sm);
  color: var(--color-text-muted);
  text-decoration: none;
  border-radius: var(--radius-lg);
  transition: all var(--transition-fast);
  position: relative;
  overflow: hidden;
}

.nav-item::before {
  content: "";
  position: absolute;
  left: 0;
  top: 0;
  width: 100%;
  height: 100%;
  background: linear-gradient(90deg, rgba(99, 102, 241, 0.2), transparent);
  opacity: 0;
  transition: opacity var(--transition-fast);
}

.nav-item:hover {
  color: var(--color-text-inverse);
  transform: translateX(4px);
}

.nav-item:hover::before {
  opacity: 1;
}

.nav-item.active {
  background: linear-gradient(
    90deg,
    rgba(99, 102, 241, 0.3),
    rgba(139, 92, 246, 0.1)
  );
  color: var(--color-text-inverse);
  border-left: 3px solid var(--color-accent-primary);
}

.nav-icon {
  font-size: 1.8rem;
}

.nav-text {
  font-weight: 500;
  font-size: 0.99rem;
}

/* ============================================================================
   Main Content
   ============================================================================ */
.main-content {
  flex: 1;
  margin-left: var(--sidebar-width);
  padding: var(--space-2xl);
  min-height: 100vh;
  overflow-x: hidden;
  max-width: calc(100vw - var(--sidebar-width));
}

.content-header {
  margin-bottom: var(--space-2xl);
}

.content-header h1 {
  font-size: 2rem;
  font-weight: 700;
  color: var(--color-text-primary);
  margin-bottom: var(--space-sm);
  text-align: center;
}

.subtitle {
  color: var(--color-text-secondary);
  font-size: 1.125rem;
}

/* ============================================================================
   Tab Content
   ============================================================================ */
.tab-content {
  display: none;
  animation: fadeIn 0.3s ease;
  max-width: 100%;
  overflow-x: hidden;
}

.tab-content.active {
  display: block;
}

@keyframes fadeIn {
  from {
    opacity: 0;
    transform: translateY(10px);
  }

  to {
    opacity: 1;
    transform: translateY(0);
  }
}

/* ============================================================================
   Cards
   ============================================================================ */
.card {
  background: var(--color-bg-secondary);
  border-radius: var(--radius-xl);
  border: 1px solid var(--color-border);
  box-shadow: var(--shadow-md);
  margin-bottom: var(--space-xl);
  overflow: hidden;
  transition: all var(--transition-normal);
}

/* Allow overflow for cards containing plot results - but NOT discovery-results */
.card:has(.plot-display) {
  overflow: visible;
}

/* Allow layout cards to grow with their content */
.card:has(.layout-preview-section) {
  overflow: visible;
}

/* Discovery results card must be contained */
#discovery-results.card {
  overflow: hidden !important;
}

.card:hover {
  box-shadow: var(--shadow-lg);
}

.card.highlight {
  border-color: var(--color-accent-primary);
  box-shadow: var(--shadow-glow);
}

.card-header {
  padding: var(--space-lg) var(--space-xl);
  background: var(--color-bg-tertiary);
  border-bottom: 1px solid var(--color-border);
  display: flex;
  align-items: center;
  gap: var(--space-md);
}

.step-badge {
  width: 32px;
  height: 32px;
  background: linear-gradient(
    135deg,
    var(--color-accent-primary),
    var(--color-accent-secondary)
  );
  color: white;
  border-radius: var(--radius-full);
  display: flex;
  align-items: center;
  justify-content: center;
  font-weight: 700;
  font-size: 0.875rem;
  flex-shrink: 0;
}

.card-header h2 {
  font-size: 1.125rem;
  font-weight: 600;
  flex: 1;
}

.cluster-category {
  background: linear-gradient(
    135deg,
    var(--color-accent-info),
    var(--color-accent-primary)
  );
  color: white;
  padding: var(--space-xs) var(--space-md);
  border-radius: var(--radius-full);
  font-size: 0.75rem;
  font-weight: 600;
  text-transform: uppercase;
}

.collapse-btn {
  background: none;
  border: none;
  color: var(--color-text-muted);
  cursor: pointer;
  padding: var(--space-sm);
  border-radius: var(--radius-sm);
  transition: all var(--transition-fast);
}

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

.card-body {
  padding: var(--space-xl);
}

/* ============================================================================
   Forms
   ============================================================================ */
.form-row {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
  gap: var(--space-lg);
}

.form-group {
  display: flex;
  flex-direction: column;
  gap: var(--space-sm);
}

.form-group label {
  font-weight: 500;
  font-size: 0.875rem;
  color: var(--color-text-secondary);
}

.form-select,
.form-input {
  padding: var(--space-md) var(--space-lg);
  border: 2px solid var(--color-border);
  border-radius: var(--radius-md);
  background: var(--color-bg-primary);
  color: var(--color-text-primary);
  font-size: 1rem;
  font-family: inherit;
  transition: all var(--transition-fast);
  cursor: pointer;
}

.form-select:focus,
.form-input:focus {
  outline: none;
  border-color: var(--color-accent-primary);
  box-shadow: 0 0 0 3px rgba(99, 102, 241, 0.2);
}

.form-select:hover,
.form-input:hover {
  border-color: var(--color-text-muted);
}

.help-text {
  color: var(--color-text-muted);
  font-size: 0.875rem;
  margin-bottom: var(--space-md);
}

/* ============================================================================
   Genome Grid & Selection
   ============================================================================ */
.genome-grid {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(150px, 1fr));
  gap: var(--space-md);
  margin-bottom: var(--space-lg);
}

.genome-checkbox {
  display: flex;
  flex-direction: column;
  align-items: center;
  justify-content: center;
  gap: var(--space-xs);
  padding: var(--space-md);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  cursor: pointer;
  transition: all var(--transition-fast);
  border: 2px solid transparent;
  min-height: 85px;
}

.genome-checkbox:hover {
  background: var(--color-bg-primary);
  border-color: var(--color-accent-primary);
}

.genome-checkbox input[type="checkbox"] {
  width: 18px;
  height: 18px;
  accent-color: var(--color-accent-primary);
  cursor: pointer;
}

.genome-checkbox.checked {
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.1),
    rgba(139, 92, 246, 0.1)
  );
  border-color: var(--color-accent-primary);
}

/* Genome label with display name and scientific name */
.genome-checkbox .genome-label {
  display: flex;
  flex-direction: column;
  align-items: center;
  gap: 2px;
  text-align: center;
}

.genome-checkbox .genome-display-name {
  font-weight: 500;
  color: var(--color-text-primary);
  text-align: center;
}

.genome-checkbox .genome-scientific-name {
  font-size: 0.7rem;
  color: var(--color-text-muted);
  font-style: italic;
  text-align: center;
  line-height: 1.3;
  min-height: 2.6em;
  display: flex;
  align-items: center;
}

.genome-order-section {
  margin-top: var(--space-lg);
  padding-top: var(--space-lg);
  border-top: 1px solid var(--color-border);
}

.genome-order-section h4 {
  font-size: 0.875rem;
  font-weight: 600;
  color: var(--color-text-secondary);
  margin-bottom: var(--space-md);
}

.sortable-list {
  list-style: none;
  display: flex;
  flex-direction: column;
  gap: var(--space-sm);
}

.sortable-list li {
  padding: var(--space-md) var(--space-lg);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  cursor: grab;
  display: flex;
  align-items: center;
  gap: var(--space-md);
  transition: all var(--transition-fast);
  border: 1px solid var(--color-border);
}

.sortable-list li:hover {
  background: var(--color-bg-primary);
  box-shadow: var(--shadow-md);
}

.sortable-list li:active {
  cursor: grabbing;
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.1),
    rgba(139, 92, 246, 0.1)
  );
}

.sortable-list .drag-handle {
  color: var(--color-text-muted);
  font-size: 1.25rem;
}

/* ============================================================================
   Gene Input
   ============================================================================ */
.gene-controls {
  display: flex;
  gap: var(--space-sm);
  margin-top: var(--space-lg);
  margin-bottom: 0;
}

.btn-sm {
  padding: var(--space-xs) var(--space-md);
  font-size: 0.75rem;
}

.genes-container {
  display: flex;
  flex-direction: column;
  gap: var(--space-md);
}

.gene-row {
  display: flex;
  flex-wrap: wrap;
  gap: var(--space-sm);
  align-items: center;
  padding: var(--space-md);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
}

.gene-row-main {
  display: flex;
  gap: var(--space-sm);
  align-items: center;
  flex: 1;
  min-width: 0;
}

.gene-row-annotation {
  width: 100%;
  display: flex;
  align-items: center;
  gap: var(--space-sm);
  margin-top: var(--space-xs);
  padding-left: 42px;
}

.genome-annotation-preview {
  display: inline-flex;
  align-items: center;
  padding: var(--space-xs) var(--space-sm);
  background: linear-gradient(135deg, #e0e7ff, #c7d2fe);
  border-radius: var(--radius-sm);
  font-size: 0.75rem;
  color: #4338ca;
  max-width: 100%;
  overflow: hidden;
  text-overflow: ellipsis;
  white-space: nowrap;
}

.genome-annotation-preview::before {
  content: "📄";
  margin-right: var(--space-xs);
}

@keyframes slideIn {
  from {
    opacity: 0;
    transform: translateX(-10px);
  }

  to {
    opacity: 1;
    transform: translateX(0);
  }
}

.gene-row .gene-number {
  width: 28px;
  height: 28px;
  background: var(--color-accent-primary);
  color: white;
  border-radius: var(--radius-full);
  display: flex;
  align-items: center;
  justify-content: center;
  font-weight: 600;
  font-size: 0.8rem;
  flex-shrink: 0;
}

.gene-row .gene-name-input {
  flex: 1;
  min-width: 180px;
}

.gene-row .form-input {
  width: auto;
}

.gene-row .gene-color-select {
  min-width: 80px;
}

.gene-row .gene-annotation-type-select {
  min-width: 140px;
}

.gene-row .gene-custom-annotation {
  flex: 1;
  min-width: 150px;
}

/* ============================================================================
   Buttons
   ============================================================================ */
.btn {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  gap: var(--space-sm);
  padding: var(--space-md) var(--space-xl);
  border: none;
  border-radius: var(--radius-md);
  font-size: 0.875rem;
  font-weight: 600;
  font-family: inherit;
  cursor: pointer;
  transition: all var(--transition-fast);
  text-decoration: none;
}

.btn:active {
  transform: scale(0.98);
}

.btn-primary {
  background: linear-gradient(
    135deg,
    var(--color-accent-primary),
    var(--color-accent-secondary)
  );
  color: white;
  box-shadow: 0 4px 14px rgba(99, 102, 241, 0.35);
}

.btn-primary:hover {
  box-shadow: 0 6px 20px rgba(99, 102, 241, 0.45);
  transform: translateY(-2px);
}

.btn-success {
  background: linear-gradient(135deg, var(--color-accent-success), #059669);
  color: white;
}

.btn-success:hover {
  box-shadow: 0 4px 14px rgba(16, 185, 129, 0.35);
}

.btn-warning {
  background: linear-gradient(135deg, var(--color-accent-warning), #d97706);
  color: white;
}

.btn-info {
  background: linear-gradient(135deg, var(--color-accent-info), #0891b2);
  color: white;
}

.btn-add {
  background: linear-gradient(135deg, #dcfce7, #bbf7d0);
  color: #166534;
  border: 1px solid #86efac;
}

.btn-add:hover {
  background: linear-gradient(135deg, #bbf7d0, #86efac);
}

.btn-remove {
  background: linear-gradient(135deg, #fee2e2, #fecaca);
  color: #991b1b;
  border: 1px solid #fca5a5;
}

.btn-remove:hover {
  background: linear-gradient(135deg, #fecaca, #fca5a5);
}

.btn-large {
  padding: var(--space-lg) var(--space-2xl);
  font-size: 1rem;
}

.btn-icon {
  font-size: 1.25rem;
}

/* ============================================================================
   Command Preview & Status
   ============================================================================ */
.command-preview {
  margin-top: var(--space-lg);
  padding: var(--space-lg);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
}

.command-preview h4 {
  font-size: 0.75rem;
  text-transform: uppercase;
  letter-spacing: 0.05em;
  color: var(--color-text-muted);
  margin-bottom: var(--space-sm);
}

.command-preview code {
  display: block;
  padding: var(--space-md);
  background: var(--color-bg-primary);
  border-radius: var(--radius-sm);
  font-family: "SF Mono", "Fira Code", "Consolas", monospace;
  font-size: 0.8125rem;
  color: var(--color-accent-primary);
  word-break: break-all;
  white-space: pre-wrap;
}

.status-display {
  margin-top: var(--space-lg);
  padding: var(--space-md) var(--space-lg);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  display: flex;
  align-items: center;
  gap: var(--space-md);
}

.status-display.success {
  background: linear-gradient(
    135deg,
    rgba(16, 185, 129, 0.1),
    rgba(5, 150, 105, 0.1)
  );
  border: 1px solid var(--color-accent-success);
}

.status-display.error {
  background: linear-gradient(
    135deg,
    rgba(239, 68, 68, 0.1),
    rgba(220, 38, 38, 0.1)
  );
  border: 1px solid var(--color-accent-danger);
}

.status-display.running {
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.1),
    rgba(139, 92, 246, 0.1)
  );
  border: 1px solid var(--color-accent-primary);
}

.status-icon {
  font-size: 1.25rem;
}

.status-text {
  font-weight: 500;
  color: var(--color-text-secondary);
}

/* ============================================================================
   Results & Plot Display
   ============================================================================ */
.results-card {
  animation: scaleIn 0.3s ease;
}

@keyframes scaleIn {
  from {
    opacity: 0;
    transform: scale(0.95);
  }

  to {
    opacity: 1;
    transform: scale(1);
  }
}

.plot-display {
  background: white;
  border-radius: var(--radius-lg);
  padding: var(--space-md);
  margin-bottom: var(--space-xl);
  border: 1px solid var(--color-border);
  text-align: center;
  width: 100%;
  box-sizing: border-box;
  overflow-x: auto;
}

.plot-display img {
  max-width: 100%;
  height: auto;
  border-radius: var(--radius-md);
  display: block;
  margin: 0 auto;
}

.download-buttons {
  display: flex;
  flex-wrap: wrap;
  gap: var(--space-md);
}

/* ============================================================================
   Advanced Options
   ============================================================================ */
.advanced-options-form {
  display: flex;
  flex-direction: column;
  gap: var(--space-lg);
}

.advanced-options-form .form-row {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: var(--space-lg);
}

@media (max-width: 768px) {
  .advanced-options-form .form-row {
    grid-template-columns: 1fr;
  }
}

.advanced-options-form .form-help {
  display: block;
  font-size: 0.75rem;
  color: var(--color-text-muted);
  margin-top: var(--space-xs);
}

#search-results-container {
  margin-top: var(--space-xl);
  padding-top: var(--space-xl);
  border-top: 1px solid var(--color-border);
}

#search-results-container h4 {
  margin-bottom: var(--space-md);
}

.search-summary {
  padding: var(--space-md);
  background: linear-gradient(135deg, #e0f2fe, #bae6fd);
  border-radius: var(--radius-md);
  margin-bottom: var(--space-lg);
  font-size: 0.875rem;
  color: #0369a1;
}

.search-summary strong {
  color: #0c4a6e;
}

.table-wrapper {
  overflow-x: auto;
  margin-bottom: var(--space-lg);
}

.search-download {
  display: flex;
  gap: var(--space-sm);
}

/* Collapsible card improvements */
.card.collapsible .card-header {
  cursor: pointer;
}

.card.collapsible .collapse-btn {
  margin-left: auto;
  background: none;
  border: none;
  font-size: 1rem;
  cursor: pointer;
  color: var(--color-text-muted);
  padding: var(--space-xs);
  transition: transform var(--transition-fast);
}

.card.collapsible .collapse-btn:hover {
  color: var(--color-text-primary);
}

/* ============================================================================
   Data Tables
   ============================================================================ */
.table-container {
  overflow-x: auto;
}

.data-table {
  width: 100%;
  border-collapse: collapse;
  table-layout: fixed;
}

.data-table th,
.data-table td {
  padding: var(--space-md);
  text-align: left;
  border-bottom: 1px solid var(--color-border);
  white-space: nowrap;
  overflow: hidden;
  text-overflow: ellipsis;
}

/* Specific column widths for search results table */
#search-results-table {
  table-layout: fixed;
  width: 100%;
}

#search-results-table th:nth-child(1),
#search-results-table td:nth-child(1) {
  width: 18%;
}

/* Query Gene */
#search-results-table th:nth-child(2),
#search-results-table td:nth-child(2) {
  width: 16%;
}

/* Comparison Genome */
#search-results-table th:nth-child(3),
#search-results-table td:nth-child(3) {
  width: 18%;
}

/* Ortholog Gene */
#search-results-table th:nth-child(4),
#search-results-table td:nth-child(4) {
  width: 12%;
}

/* Chromosome */
#search-results-table th:nth-child(5),
#search-results-table td:nth-child(5) {
  width: 12%;
}

/* Start */
#search-results-table th:nth-child(6),
#search-results-table td:nth-child(6) {
  width: 12%;
}

/* End */
#search-results-table th:nth-child(7),
#search-results-table td:nth-child(7) {
  width: 12%;
}

/* Identity % */

.data-table th {
  background: var(--color-bg-tertiary);
  font-weight: 600;
  font-size: 0.75rem;
  text-transform: uppercase;
  letter-spacing: 0.05em;
  color: var(--color-text-muted);
}

.data-table tbody tr:hover {
  background: var(--color-bg-tertiary);
}

.empty-message {
  text-align: center;
  color: var(--color-text-muted);
  font-style: italic;
  padding: var(--space-md) !important;
  white-space: nowrap;
}

/* Ensure empty-message spans full width in grid containers */
.layout-options .empty-message {
  grid-column: 1 / -1;
}

/* DataTables customization */
.dataTables_wrapper {
  font-size: 0.875rem;
  width: 100%;
}

/* Fix DataTables header/filter alignment */
.dataTables_wrapper .dataTables_filter,
.dataTables_wrapper .dataTables_length {
  margin-bottom: var(--space-md);
}

.dataTables_wrapper .dataTables_filter {
  float: right;
  text-align: right;
}

.dataTables_wrapper .dataTables_length {
  float: left;
}

/* Clear floats before table */
.dataTables_wrapper .dataTables_scroll,
.dataTables_wrapper table.dataTable {
  clear: both;
}

.dataTables_filter input {
  padding: var(--space-sm) var(--space-md);
  border: 1px solid var(--color-border);
  border-radius: var(--radius-sm);
  margin-left: var(--space-sm);
  width: 200px;
}

.dataTables_length select {
  padding: var(--space-sm);
  border: 1px solid var(--color-border);
  border-radius: var(--radius-sm);
}

/* Fix table alignment with DataTables */
.dataTables_wrapper table.dataTable {
  width: 100% !important;
  table-layout: fixed !important;
  margin: 0 !important;
}

.dataTables_wrapper table.dataTable thead th,
.dataTables_wrapper table.dataTable tbody td {
  box-sizing: border-box;
}

/* Ensure info and pagination align properly */
.dataTables_wrapper .dataTables_info {
  float: left;
  padding-top: var(--space-md);
}

.dataTables_wrapper .dataTables_paginate {
  float: right;
  padding-top: var(--space-sm);
}

.dataTables_paginate .paginate_button {
  padding: var(--space-sm) var(--space-md) !important;
  border-radius: var(--radius-sm) !important;
  margin: 0 var(--space-xs) !important;
}

.dataTables_paginate .paginate_button.current {
  background: var(--color-accent-primary) !important;
  color: white !important;
  border: none !important;
}

/* Clear floats after DataTables elements */
.dataTables_wrapper::after {
  content: "";
  display: table;
  clear: both;
}

/* ============================================================================
   About Page
   ============================================================================ */
.about-container h3 {
  font-size: 1.125rem;
  font-weight: 600;
  margin-top: var(--space-xl);
  margin-bottom: var(--space-md);
  display: flex;
  align-items: center;
  gap: var(--space-sm);
}

.about-container h3:first-child {
  margin-top: 0;
}

/* About page module icons */
.about-module-icon {
  width: 44px;
  height: 44px;
  object-fit: contain;
  vertical-align: middle;
  margin-right: 8px;
}

.feature-list,
.workflow-list {
  padding-left: var(--space-xl);
  color: var(--color-text-secondary);
}

.feature-list li,
.workflow-list li {
  margin-bottom: var(--space-sm);
}

.genome-list {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(200px, 1fr));
  gap: var(--space-md);
}

.genome-item {
  padding: var(--space-md);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
}

.genome-item strong {
  display: block;
  color: var(--color-accent-primary);
}

.genome-item em {
  font-size: 0.875rem;
  color: var(--color-text-muted);
}

/* ============================================================================
   Loading Spinner
   ============================================================================ */
.spinner {
  width: 20px;
  height: 20px;
  border: 2px solid var(--color-border);
  border-top-color: var(--color-accent-primary);
  border-radius: 50%;
  animation: spin 0.8s linear infinite;
}

@keyframes spin {
  to {
    transform: rotate(360deg);
  }
}

/* ============================================================================
   Layout Selection
   ============================================================================ */
.layout-options {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(80px, 1fr));
  gap: var(--space-md);
  margin-bottom: var(--space-sm);
}

.layout-option {
  aspect-ratio: 1;
  background: var(--color-bg-tertiary);
  border: 2px solid var(--color-border);
  border-radius: var(--radius-md);
  cursor: pointer;
  padding: var(--space-sm);
  transition: all var(--transition-fast);
  display: flex;
  flex-direction: column;
  justify-content: center;
  align-items: center;
  gap: 2px;
}

.layout-option:hover {
  border-color: var(--color-accent-primary);
  transform: scale(1.05);
}

.layout-option.selected {
  border-color: var(--color-accent-primary);
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.1),
    rgba(139, 92, 246, 0.1)
  );
  box-shadow: var(--shadow-glow);
}

.layout-option-row {
  display: flex;
  gap: 2px;
  justify-content: center;
}

.layout-option-slot {
  width: 12px;
  height: 12px;
  background: var(--color-accent-primary);
  border-radius: 2px;
  opacity: 0.7;
}

.layout-option-name {
  font-size: 0.625rem;
  color: var(--color-text-muted);
  margin-top: var(--space-xs);
}

/* Single-column layout notice (shown when > 8 genomes) */
.single-column-notice {
  grid-column: 1 / -1;
  background: var(--color-bg-tertiary);
  border: 1px solid var(--color-border);
  border-radius: var(--radius-md);
  padding: var(--space-md) var(--space-lg);
}

.single-column-notice p {
  margin: 0;
  font-size: 0.85rem;
  color: var(--color-text-secondary);
  line-height: 1.5;
}

/* Layout Grid Preview */
.layout-preview-section {
  margin-top: var(--space-lg);
  padding: var(--space-lg);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-lg);
  border: 1px solid var(--color-border);
  height: auto;
  overflow: visible;
}

.layout-preview-section h4 {
  font-size: 0.875rem;
  font-weight: 600;
  color: var(--color-text-secondary);
  margin-bottom: var(--space-md);
}

.layout-grid {
  display: flex;
  flex-direction: column;
  gap: var(--space-md);
  margin-bottom: var(--space-lg);
}

.layout-row {
  display: flex;
  gap: var(--space-md);
  justify-content: center;
  align-items: center;
  padding: var(--space-sm);
  background: var(--color-bg-secondary);
  border-radius: var(--radius-md);
  min-height: 60px;
}

.layout-row.query-row {
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.15),
    rgba(139, 92, 246, 0.1)
  );
  border: 2px solid var(--color-accent-primary);
}

.layout-row-label {
  font-size: 0.75rem;
  color: var(--color-text-muted);
  font-weight: 600;
  min-width: 50px;
}

.layout-slots {
  display: flex;
  gap: var(--space-sm);
  flex: 1;
  justify-content: center;
}

.layout-slot {
  min-width: 100px;
  min-height: 40px;
  background: var(--color-bg-primary);
  border: 2px dashed var(--color-border);
  border-radius: var(--radius-md);
  display: flex;
  align-items: center;
  justify-content: center;
  transition: all var(--transition-fast);
  padding: var(--space-sm);
}

.layout-slot.empty {
  color: var(--color-text-muted);
  font-size: 0.75rem;
}

.layout-slot.drag-over {
  border-color: var(--color-accent-primary);
  background: rgba(99, 102, 241, 0.1);
  transform: scale(1.05);
}

.layout-slot.has-genome {
  border-style: solid;
  border-color: var(--color-accent-success);
  background: linear-gradient(
    135deg,
    rgba(16, 185, 129, 0.1),
    rgba(5, 150, 105, 0.05)
  );
}

/* Genome Chips */
.genome-chip {
  display: inline-flex;
  align-items: center;
  gap: var(--space-xs);
  padding: var(--space-sm) var(--space-md);
  background: linear-gradient(
    135deg,
    var(--color-accent-primary),
    var(--color-accent-secondary)
  );
  color: white;
  border-radius: var(--radius-full);
  font-size: 0.75rem;
  font-weight: 600;
  cursor: grab;
  transition: all var(--transition-fast);
  user-select: none;
}

.genome-chip:hover {
  transform: scale(1.05);
  box-shadow: var(--shadow-md);
}

.genome-chip:active {
  cursor: grabbing;
}

.genome-chip.dragging {
  opacity: 0.5;
}

.genome-chip.query-genome {
  background: linear-gradient(135deg, #f59e0b, #d97706);
  cursor: default;
}

/* Available Genomes Section */
.available-genomes-section {
  margin-top: var(--space-lg);
  padding-top: var(--space-lg);
  border-top: 1px solid var(--color-border);
}

.available-genomes-section h5 {
  font-size: 0.75rem;
  font-weight: 600;
  color: var(--color-text-muted);
  margin-bottom: var(--space-md);
  text-transform: uppercase;
  letter-spacing: 0.05em;
}

.available-genomes {
  display: flex;
  flex-wrap: wrap;
  gap: var(--space-sm);
  min-height: 40px;
  max-height: none !important;
  height: auto !important;
  overflow: visible !important;
  overflow-y: visible !important;
  padding: var(--space-md);
  background: var(--color-bg-secondary);
  border-radius: var(--radius-md);
  border: 1px solid var(--color-border);
}

.available-genomes.empty-message {
  color: var(--color-text-muted);
  font-size: 0.875rem;
  font-style: italic;
}

/* ============================================================================
   Required Genes Checkboxes (Advanced Search)
   ============================================================================ */
.required-genes-checkboxes {
  display: flex;
  flex-wrap: wrap;
  gap: var(--space-sm);
  margin-top: var(--space-xs);
}

.required-gene-item {
  display: flex;
  align-items: center;
  gap: var(--space-xs);
  padding: var(--space-sm) var(--space-md);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  cursor: pointer;
  transition: all var(--transition-fast);
  border: 2px solid transparent;
  font-size: 0.875rem;
}

.required-gene-item:hover {
  background: var(--color-bg-primary);
  border-color: var(--color-accent-primary);
}

.required-gene-item input[type="checkbox"] {
  width: 16px;
  height: 16px;
  accent-color: var(--color-accent-primary);
  cursor: pointer;
}

.required-gene-item.checked {
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.1),
    rgba(139, 92, 246, 0.1)
  );
  border-color: var(--color-accent-primary);
}

/* Additional Genomes Section */
.additional-genomes-section {
  margin-top: var(--space-md);
  padding-top: var(--space-md);
  border-top: 1px dashed var(--color-border);
}

.additional-genome-item {
  display: flex;
  align-items: center;
  gap: var(--space-sm);
  padding: var(--space-md);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  border: 2px solid var(--color-accent-secondary);
}

.additional-genome-item .remove-btn {
  background: none;
  border: none;
  color: var(--color-accent-danger);
  cursor: pointer;
  font-size: 1rem;
  padding: 0;
  margin-left: auto;
  transition: transform var(--transition-fast);
}

.additional-genome-item .remove-btn:hover {
  transform: scale(1.2);
}

/* Search All Genomes Checkbox */
.checkbox-label {
  display: flex;
  align-items: center;
  gap: var(--space-sm);
  cursor: pointer;
  font-weight: 500;
}

.checkbox-label input[type="checkbox"] {
  width: 18px;
  height: 18px;
  accent-color: var(--color-accent-primary);
  cursor: pointer;
}

/* ============================================================================
   Custom Genome Components
   ============================================================================ */

/* Progress Bar */
.progress-bar {
  width: 100%;
  height: 8px;
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-full);
  overflow: hidden;
  margin-top: var(--space-sm);
}

.progress-fill {
  height: 100%;
  background: linear-gradient(
    90deg,
    var(--color-accent-primary),
    var(--color-accent-success)
  );
  border-radius: var(--radius-full);
  transition: width 0.5s ease;
}

/* Alerts */
.alert {
  padding: var(--space-md) var(--space-lg);
  border-radius: var(--radius-md);
  margin-bottom: var(--space-md);
}

.alert-info {
  background: linear-gradient(
    135deg,
    rgba(6, 182, 212, 0.1),
    rgba(8, 145, 178, 0.1)
  );
  border: 1px solid var(--color-accent-info);
  color: #0e7490;
}

.alert-warning {
  background: linear-gradient(
    135deg,
    rgba(245, 158, 11, 0.1),
    rgba(217, 119, 6, 0.1)
  );
  border: 1px solid var(--color-accent-warning);
  color: #92400e;
}

/* Custom Genome Items */
.custom-genome-item {
  display: flex;
  align-items: center;
  justify-content: space-between;
  padding: var(--space-md) var(--space-lg);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  margin-bottom: var(--space-sm);
  border: 1px solid var(--color-border);
}

.custom-genome-info {
  display: flex;
  flex-wrap: wrap;
  align-items: center;
  gap: var(--space-sm);
}

.custom-genome-key {
  font-family: "SF Mono", "Fira Code", monospace;
  font-size: 0.75rem;
  color: var(--color-text-muted);
  background: var(--color-bg-primary);
  padding: var(--space-xs) var(--space-sm);
  border-radius: var(--radius-sm);
}

.status-badge {
  font-size: 0.75rem;
  font-weight: 600;
  padding: var(--space-xs) var(--space-sm);
  border-radius: var(--radius-full);
  text-transform: uppercase;
}

.status-badge.success {
  background: linear-gradient(135deg, #d1fae5, #a7f3d0);
  color: #065f46;
}

.status-badge.error {
  background: linear-gradient(135deg, #fee2e2, #fecaca);
  color: #991b1b;
}

.status-badge.pending {
  background: linear-gradient(135deg, #e0e7ff, #c7d2fe);
  color: #3730a3;
}

/* Lookup Result Card */
.lookup-result-card {
  padding: var(--space-lg);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  border: 1px solid var(--color-border);
}

.lookup-result-card p {
  margin-bottom: var(--space-sm);
}

.success-message {
  color: var(--color-accent-success);
  font-weight: 500;
}

.error-message {
  color: var(--color-accent-danger);
  font-weight: 500;
}

/* Button Danger Variant */
.btn-danger {
  background: linear-gradient(135deg, var(--color-accent-danger), #dc2626);
  color: white;
}

.btn-danger:hover {
  box-shadow: 0 4px 14px rgba(239, 68, 68, 0.35);
}

/* Button Secondary Variant */
.btn-secondary {
  background: var(--color-bg-tertiary);
  color: var(--color-text-primary);
  border: 1px solid var(--color-border);
}

.btn-secondary:hover {
  background: var(--color-bg-primary);
  border-color: var(--color-accent-primary);
}

/* Format instructions */
.format-instructions h4 {
  margin-top: var(--space-md);
  margin-bottom: var(--space-sm);
  color: var(--color-text-primary);
}

.format-instructions ul {
  margin-left: var(--space-lg);
  margin-bottom: var(--space-md);
}

.format-instructions code {
  background: var(--color-bg-primary);
  padding: 2px 6px;
  border-radius: 3px;
  font-size: 0.875rem;
}

/* Form help text */
.form-help {
  font-size: 0.8rem;
  color: var(--color-text-muted);
  margin-top: var(--space-xs);
}

/* ============================================================================
   Responsive Design
   ============================================================================ */
@media (max-width: 1024px) {
  .sidebar {
    width: var(--sidebar-collapsed);
  }

  .sidebar .nav-text,
  .sidebar .logo-text {
    display: none;
  }

  .main-content {
    margin-left: var(--sidebar-collapsed);
  }
}

@media (max-width: 768px) {
  .sidebar {
    width: 100%;
    height: auto;
    position: relative;
    flex-direction: row;
  }

  .sidebar-nav {
    flex-direction: row;
    overflow-x: auto;
    padding: var(--space-sm);
  }

  .main-content {
    margin-left: 0;
    padding: var(--space-lg);
  }

  .form-row {
    grid-template-columns: 1fr;
  }

  .gene-row {
    grid-template-columns: auto 1fr;
  }

  .gene-row .form-input:last-child {
    grid-column: 1 / -1;
  }
}

/* ============================================================================
   Custom Genome Section Blocks
   ============================================================================ */
.section-block {
  border: 2px solid var(--color-border);
  transition: border-color var(--transition-normal);
}

.section-block:hover {
  border-color: var(--color-accent-primary);
}

.section-header {
  cursor: pointer;
  user-select: none;
}

.section-header:hover {
  background: linear-gradient(
    90deg,
    var(--color-bg-tertiary),
    var(--color-bg-secondary)
  );
}

.section-collapse-btn {
  font-size: 1.25rem;
  padding: var(--space-sm) var(--space-md);
}

.section-body {
  transition: all var(--transition-normal);
}

/* Active Run Banner */
.active-run-banner {
  border-left: 4px solid var(--color-accent-primary);
}

/* Search Stats for Advanced Search */
.search-stats {
  display: flex;
  gap: var(--space-xl);
  margin-bottom: var(--space-md);
}

.search-stats .stat {
  display: flex;
  flex-direction: column;
  align-items: center;
  padding: var(--space-md);
  background: var(--color-bg-tertiary);
  border-radius: var(--radius-md);
  min-width: 120px;
}

.search-stats .stat-value {
  font-size: 1.5rem;
  font-weight: 700;
  color: var(--color-accent-primary);
}

.search-stats .stat-label {
  font-size: 0.75rem;
  color: var(--color-text-muted);
  text-transform: uppercase;
}

.matching-genomes {
  padding: var(--space-md);
  background: linear-gradient(
    135deg,
    rgba(16, 185, 129, 0.1),
    rgba(5, 150, 105, 0.1)
  );
  border-radius: var(--radius-md);
  border-left: 4px solid var(--color-accent-success);
}

.no-matches {
  padding: var(--space-md);
  background: linear-gradient(
    135deg,
    rgba(239, 68, 68, 0.1),
    rgba(220, 38, 38, 0.1)
  );
  border-radius: var(--radius-md);
  border-left: 4px solid var(--color-accent-danger);
  color: var(--color-accent-danger);
}

/* Card Inner for Plotting Steps */
.card-inner {
  margin-bottom: var(--space-lg);
  width: 100%;
  box-sizing: border-box;
}

/* ============================================================================
   Discovery Table Horizontal Scrollbar - ONLY the table scrolls
   ============================================================================ */

/* Lock down the discovery results card completely */
#discovery-results {
  overflow: hidden !important;
  max-width: 100% !important;
  width: 100% !important;
}

#discovery-results > .card-body {
  overflow: hidden !important;
  max-width: 100% !important;
  width: 100% !important;
}

/* Container for table + sticky scrollbar */
#discovery-scroll-container {
  position: relative;
  max-width: 100%;
  width: 100%;
  margin-bottom: 16px;
}

/* The table wrapper - hide its scrollbar, we use sticky one instead */
#discovery-table-wrapper {
  display: block;
  overflow-x: scroll;
  overflow-y: visible;
  max-width: 100%;
  width: 100%;
  border: 2px solid #cbd5e1;
  border-radius: 8px 8px 0 0;
  background: #fff;
  box-sizing: border-box;
  /* Hide the native scrollbar */
  scrollbar-width: none; /* Firefox */
  -ms-overflow-style: none; /* IE/Edge */
}

#discovery-table-wrapper::-webkit-scrollbar {
  display: none; /* Chrome/Safari */
}

/* The table itself */
#discovery-results-table {
  border-collapse: collapse;
  table-layout: auto;
}

/* Sticky scrollbar - stays at bottom of viewport */
#discovery-sticky-scrollbar {
  position: sticky;
  bottom: 0;
  left: 0;
  right: 0;
  width: 100%;
  height: 18px;
  overflow-x: scroll;
  overflow-y: hidden;
  background: linear-gradient(to bottom, #f1f5f9, #e2e8f0);
  border: 2px solid #cbd5e1;
  border-top: 1px solid #cbd5e1;
  border-radius: 0 0 8px 8px;
  z-index: 100;
}

/* Inner div that creates the scrollable width */
#discovery-sticky-scrollbar-inner {
  height: 1px;
}

/* Firefox scrollbar styling for sticky bar */
#discovery-sticky-scrollbar {
  scrollbar-width: auto;
  scrollbar-color: #6366f1 #e2e8f0;
}

/* Chrome/Safari scrollbar styling for sticky bar */
#discovery-sticky-scrollbar::-webkit-scrollbar {
  height: 14px;
}

#discovery-sticky-scrollbar::-webkit-scrollbar-track {
  background: #e2e8f0;
  border-radius: 7px;
}

#discovery-sticky-scrollbar::-webkit-scrollbar-thumb {
  background: linear-gradient(135deg, #6366f1, #8b5cf6);
  border-radius: 7px;
  border: 2px solid #e2e8f0;
}

#discovery-sticky-scrollbar::-webkit-scrollbar-thumb:hover {
  background: linear-gradient(135deg, #4f46e5, #7c3aed);
}

/* Override any results-card overflow rules for discovery specifically */
#discovery-results.card.results-card {
  overflow: hidden !important;
}

/* Results cards (other than discovery) can have overflow */
.card-inner.results-card,
.card.results-card:not(#discovery-results) {
  overflow-x: auto;
}

.card-inner.collapsible .card-header-inner {
  cursor: pointer;
}

.card-inner.collapsible .card-header-inner:hover {
  opacity: 0.85;
}

/* ============================================================================
   Homepage Module Cards
   ============================================================================ */
.home-modules-grid {
  display: grid;
  grid-template-columns: repeat(2, 1fr);
  gap: var(--space-xl);
}

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

.home-module-card {
  display: flex;
  align-items: center;
  gap: var(--space-lg);
  padding: var(--space-xl);
  background: linear-gradient(
    135deg,
    #f5f3ff 0%,
    #ede9fe 100%
  );
  border: 2px solid #ddd6fe;
  border-radius: var(--radius-xl);
  text-decoration: none;
  color: inherit;
  transition: all var(--transition-normal);
  position: relative;
  overflow: hidden;
}

.home-module-card::before {
  content: "";
  position: absolute;
  top: 0;
  left: 0;
  right: 0;
  bottom: 0;
  background: linear-gradient(
    135deg,
    rgba(99, 102, 241, 0.05) 0%,
    rgba(139, 92, 246, 0.05) 100%
  );
  opacity: 0;
  transition: opacity var(--transition-normal);
}

.home-module-card:hover {
  border-color: var(--color-accent-primary);
  box-shadow:
    var(--shadow-lg),
    0 0 20px rgba(99, 102, 241, 0.15);
  transform: translateY(-4px);
}

.home-module-card:hover::before {
  opacity: 1;
}

.home-module-icon {
  width: 64px;
  height: 64px;
  flex-shrink: 0;
  display: flex;
  align-items: center;
  justify-content: center;
  background: transparent;
  border-radius: var(--radius-lg);
  padding: var(--space-sm);
}

.home-module-icon img {
  width: 100%;
  height: 100%;
  object-fit: contain;
}

.home-module-content {
  flex: 1;
  min-width: 0;
}

.home-module-content h3 {
  font-size: 1.05rem;
  font-weight: 600;
  color: var(--color-text-primary);
  margin-bottom: var(--space-xs);
}

.home-module-content p {
  font-size: 0.875rem;
  color: var(--color-text-secondary);
  line-height: 1.5;
  margin: 0;
}

.home-module-arrow {
  font-size: 1.5rem;
  color: var(--color-text-muted);
  transition: all var(--transition-fast);
  flex-shrink: 0;
}

.home-module-card:hover .home-module-arrow {
  color: var(--color-accent-primary);
  transform: translateX(4px);
}

/* Homepage Citation Section */
.home-citation-section {
  text-align: left;
  margin-top: var(--space-xl);
  padding: var(--space-xl) 0;
}

.home-citation-intro {
  font-size: 1rem;
  color: var(--color-text-secondary);
  margin-bottom: var(--space-md);
}

.home-citation-list {
  list-style: none;
  padding: 0;
  margin: 0;
  max-width: 800px;
  display: flex;
  flex-direction: column;
  gap: var(--space-sm);
  text-align: left;
}

.home-citation-list li {
  font-size: 0.9rem;
  color: var(--color-text-secondary);
  line-height: 1.5;
}

.home-citation-list li strong {
  color: var(--color-text-primary);
}

.home-citation-list li em {
  color: var(--color-accent-primary);
}