:root {
  /* Colors */
  --primary-dark: #2c3e50;
  --primary-blue: #2c5aa0;
  --primary-blue-light: #4a89dc;
  --accent-green-1: #66c2a5;
  --accent-green-2: #27ae60;
  --accent-red: #e74c3c;
  --neutral-bg: #f4f8fb;
  --neutral-bg-alt: #f8f9fa;
  --panel-bg: #ffffff;
  --text-dark: #333;
  --text-light: #ffffff;
  --border-color: #e1ecf4;
  --gray-medium: #95a5a6;
  --gray-dark: #7f8c8d;
  --gray-light: #d3d3d3;

  /* Spacing & Borders */
  --border-radius-sm: 5px;
  --border-radius-md: 10px;
  --border-radius-lg: 15px;
}

body {
    margin: 0;
    font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Open Sans', 'Helvetica Neue', sans-serif;
    background: var(--neutral-bg);
    color: var(--text-dark);
    line-height: 1.6;
}

.navbar {
    background: linear-gradient(90deg, var(--primary-blue), var(--primary-blue-light));
    color: var(--text-light);
    padding: 1.5rem 0;
    position: sticky;
    top: 0;
    z-index: 1000;
    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.2);
    border-bottom: 2px solid var(--accent-green-1);
}

.nav-container {
    max-width: 1400px;
    margin: 0 auto;
    display: flex;
    justify-content: space-between;
    align-items: center;
    padding: 0 2.5rem;
}

.logo {
    font-size: 2.2rem;
    font-weight: 800;
    text-decoration: none;
    color: var(--text-light);
    letter-spacing: 1px;
    transition: transform 0.3s ease;
}

.logo:hover {
    transform: scale(1.05);
    text-shadow: 0 0 10px rgba(255, 255, 255, 0.8);
}

.nav-links {
    list-style: none;
    display: flex;
    gap: 2rem;
    margin: 0;
    padding: 0;
}

.nav-links li a {
    color: var(--text-light);
    text-decoration: none;
    font-size: 1.2rem;
    font-weight: 500;
    padding: 0.5rem 1rem;
    border-radius: var(--border-radius-sm);
    transition: all 0.3s ease;
}

.nav-links li a:hover, .nav-links li a:focus-visible, .nav-links li a.active {
    background: rgba(255, 255, 255, 0.2);
    color: var(--accent-green-1);
    transform: translateY(-2px);
    box-shadow: 0 2px 8px rgba(0, 0, 0, 0.3);
    outline: none;
}

.main-container {
    display: flex;
    max-width: 1400px;
    margin: 0 auto;
    padding: 2rem;
    gap: 2rem;
}

/* Interactive cilium parts - Blue Theme */
.cilia-part {
    transition: fill 0.3s, stroke 0.3s, filter 0.3s;
}

/* Highlight for selected genes - a vibrant cyan for visibility */
.cilia-part.highlighted {
    stroke: #0dcaf0; /* Bright Cyan Highlight */
    stroke-width: 3px;
}

/* Hover effect */
.cilia-part:hover {
    filter: brightness(1.2);
    cursor: pointer;
}

/* Focus outline for accessibility - a standard interactive blue */
.cilia-part:focus {
    outline: 2px solid #0d6efd;
    outline-offset: 2px;
}

/* Fill for default ciliary parts - a light, soft blue */
.cilia-part.cilia {
    fill: #a8d8ff; /* Light Blue Fill */
}

/* Fill for user-searched genes - a deeper blue for clear contrast */
.cilia-part.search-gene {
    fill: #4191d5; /* Deeper Blue for Contrast */
}

/* Ensure the main cell and nucleus keep their SVG gradients */
#cell-body, #nucleus {
    /* Do not override fill; let SVG gradient show */
}

/* --- Gene Button Styles --- */
#geneButtons {
    display: flex;
    flex-direction: column;
    gap: 0.5rem;
}

.gene-btn {
    padding: 0.5rem;
    border: none;
    border-radius: var(--border-radius-sm);
    cursor: pointer;
    font-size: 0.9rem;
    transition: background 0.3s, color 0.3s;
}

/* Default buttons use the site's main primary blue */
.gene-btn.default {
    background: var(--primary-blue);
    color: var(--text-light);
}

/* Hover and searched genes use the site's lighter blue for feedback */
.gene-btn:hover,
.gene-btn:focus-visible,
.gene-btn.search-gene {
    background: var(--primary-blue-light);
    color: var(--text-light);
    outline: none;
}

/* Reset button uses a neutral gray for distinction */
.gene-btn.reset-btn {
    background: var(--gray-medium);
    color: var(--text-light);
}

.content-area {
    flex: 1;
    background: var(--panel-bg);
    padding: 2rem;
    border-radius: var(--border-radius-lg);
    box-shadow: 0 8px 32px rgba(44, 90, 160, 0.1);
}

.content-area-full {
    max-width: 100%;
}

.page-section h1, .page-section h2 {
    color: var(--primary-dark);
    margin-bottom: 1rem;
}

.page-section h1 {
    font-size: 2rem;
}

.page-section h2 {
    font-size: 1.5rem;
}

.search-container {
    display: flex;
    gap: 1rem;
    margin-bottom: 2rem;
    position: relative;
}

.search-container.sticky {
    position: fixed;
    top: 80px;
    left: 50%;
    transform: translateX(-50%);
    width: 90%;
    max-width: 1000px;
    background: var(--panel-bg);
    padding: 1.2rem;
    border-radius: var(--border-radius-md);
    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1);
    z-index: 999;
}

.search-wrapper {
    position: relative;
    flex: 1;
}

.search-wrapper input {
    width: 100%;
    padding: 1rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-md);
    font-size: 1.2rem;
}

.search-btn {
    padding: 0.8rem 1.5rem;
    background: var(--primary-blue);
    color: var(--text-light);
    border: none;
    border-radius: var(--border-radius-md);
    cursor: pointer;
    font-size: 1rem;
    transition: background 0.3s;
}

.search-btn:hover, .search-btn:focus-visible {
    background: var(--primary-blue-light);
    outline: none;
}

#search-suggestions, #compare-search-suggestions, #suggestions {
    position: absolute;
    top: 100%;
    left: 0;
    right: 0;
    background: var(--panel-bg);
    border: 1px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1);
    z-index: 1000;
    max-height: 200px;
    overflow-y: auto;
    display: none;
}

#search-suggestions ul, #compare-search-suggestions div, #suggestions div {
    margin: 0;
    padding: 0;
    list-style: none;
}

#search-suggestions li, #compare-search-suggestions div, #suggestions div {
    padding: 0.8rem;
    cursor: pointer;
    transition: background 0.2s;
}

#search-suggestions li:hover, #search-suggestions li.active, #compare-search-suggestions div:hover, #suggestions div:hover {
    background: var(--border-color);
    color: var(--primary-blue);
}

.filters {
    display: flex;
    gap: 1rem;
    margin-bottom: 1rem;
}

.filters label {
    font-weight: 600;
}

.filters input, .filters select {
    padding: 0.5rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    font-size: 0.9rem;
}

#batch-genes-input, #feedback-text {
    width: 100%;
    min-height: 100px;
    padding: 0.8rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-md);
    font-size: 1rem;
    resize: vertical;
}

#csv-upload {
    margin: 1rem 0;
}

/* ✨ This rule now styles the tables on all three pages ✨ */
#batch-results table, 
#comparison-table, 
#ciliahub-results-container table {
    width: 100%;
    border-collapse: collapse;
    margin-top: 1rem;
    position: relative;
}

/* ✨ This rule now styles the cells on all three pages ✨ */
#batch-results th, 
#batch-results td, 
#comparison-table th, 
#comparison-table td,
#ciliahub-results-container th,
#ciliahub-results-container td {
    padding: 0.8rem;
    border-bottom: 1px solid var(--border-color);
    text-align: left;
}

/* ✨ Add stripes for columns in ciliarhub-results-container table ✨ */
#ciliahub-results-container th:nth-child(odd),
#ciliahub-results-container td:nth-child(odd) {
    background-color: var(--neutral-bg-alt);
}

#ciliahub-results-container th:nth-child(even),
#ciliahub-results-container td:nth-child(even) {
    background-color: var(--panel-bg);
}

/* ✨ This rule now styles the headers on all three pages, with navbar blue for ciliarhub-results-container ✨ */
#batch-results th, 
#comparison-table th {
    background: var(--primary-blue);
    color: var(--text-light);
}

#ciliahub-results-container th {
    background: linear-gradient(90deg, var(--primary-blue), var(--primary-blue-light));
    color: var(--text-light);
    position: sticky;
    top: 160px;
    z-index: 998;
}

/* ✨ These rules now style the links on all three pages ✨ */
#batch-results a, 
#comparison-table a,
#ciliahub-results-container a {
    color: var(--primary-blue);
    text-decoration: none;
}

#batch-results a:hover, 
#batch-results a:focus-visible, 
#comparison-table a:hover, 
#comparison-table a:focus-visible,
#ciliahub-results-container a:hover,
#ciliahub-results-container a:focus-visible {
    text-decoration: underline;
    outline: none;
}

.comparison-tool {
    background: var(--neutral-bg-alt);
    padding: 1.5rem;
    border-radius: var(--border-radius-md);
}

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

.tabs {
    display: flex;
    gap: 0.5rem;
}

.tab-link {
    padding: 0.5rem 1rem;
    background: var(--border-color);
    border: none;
    border-radius: var(--border-radius-sm);
    cursor: pointer;
    font-size: 0.9rem;
    transition: background 0.3s;
}

.tab-link.active, .tab-link:hover, .tab-link:focus-visible {
    background: var(--primary-blue);
    color: var(--text-light);
    outline: none;
}

.tab-content {
    display: none;
}

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

.chart-container {
    position: relative;
    margin: auto;
}

.functional-comparison-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
    gap: 1rem;
}

.function-card {
    background: var(--neutral-bg-alt);
    padding: 1rem;
    border-radius: var(--border-radius-md);
    box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1);
}

.function-card h4 {
    margin: 0 0 0.5rem;
    color: var(--primary-dark);
}

.gene-tags-container {
    display: flex;
    flex-wrap: wrap;
    gap: 0.5rem;
    margin-top: 1rem;
}

.gene-tag {
    background: var(--mpb-border); /* Uses the #c2d9e6 color */
    padding: 0.5rem 1rem;
    border-radius: 15px;
    font-size: 0.9rem;
    display: flex;
    align-items: center;
    gap: 0.5rem;
}

.remove-tag {
    cursor: pointer;
    font-weight: bold;
}

.remove-tag:hover, .remove-tag:focus-visible {
    color: var(--accent-red);
    outline: none;
}

.error-message {
    color: var(--accent-red);
    font-size: 0.9rem;
}

.status-message {
    text-align: center;
    padding: 2rem;
    color: #666;
}

.success-message {
    color: var(--accent-green-2);
}

.gene-cards {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
    gap: 1rem;
    margin-top: 2rem;
}

.gene-card {
    background: var(--neutral-bg-alt);
    padding: 1.5rem;
    border-radius: var(--border-radius-md);
    box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1);
    cursor: pointer;
    transition: transform 0.3s, box-shadow 0.3s;
}

.gene-card:hover, .gene-card:focus-visible {
    transform: translateY(-5px);
    box-shadow: 0 5px 15px rgba(0, 0, 0, 0.2);
    outline: 2px solid var(--primary-blue);
    outline-offset: 2px;
}

.gene-card.search-result {
    background: #d5f4e6;
}

.gene-card.default {
    background: #e8f4fd;
}

.gene-name {
    font-size: 1.2rem;
    font-weight: 600;
    color: var(--primary-dark);
    margin-bottom: 0.5rem;
}

.gene-description {
    font-size: 0.9rem;
    color: #555;
    margin-bottom: 0.5rem;
}

.gene-info {
    font-size: 0.9rem;
    margin-bottom: 0.3rem;
}

.pagination {
    display: flex;
    justify-content: center;
    align-items: center;
    gap: 1rem;
    margin-top: 2rem;
}

.pagination button {
    padding: 0.5rem 1rem;
    background: var(--primary-blue);
    color: var(--text-light);
    border: none;
    border-radius: var(--border-radius-sm);
    cursor: pointer;
}

.pagination button:disabled {
    background: var(--gray-medium);
    cursor: not-allowed;
}

.download-options {
    display: flex;
    gap: 1rem;
    margin-top: 1rem;
}

.download-options a, .download-options button {
    padding: 0.8rem 1.5rem;
    background: var(--primary-blue);
    color: var(--text-light);
    text-decoration: none;
    border-radius: var(--border-radius-md);
    font-size: 1rem;
}

.download-options a:hover, .download-options a:focus-visible, .download-options button:hover, .download-options button:focus-visible {
    background: var(--primary-blue-light);
    outline: none;
}

.contact-info, .cite-list, .feedback-form {
    margin-bottom: 2rem;
}

.contact-info ul, .cite-list ul {
    list-style: none;
    padding: 0;
}

.contact-info li, .cite-list li {
    margin-bottom: 0.5rem;
}

.contact-info a, .cite-list a {
    color: var(--primary-blue);
    text-decoration: none;
}

.contact-info a:hover, .contact-info a:focus-visible, .cite-list a:hover, .cite-list a:focus-visible {
    text-decoration: underline;
    outline: none;
}

.btn {
    cursor: pointer;
    transition: background 0.3s;
}

.btn-primary {
    background: var(--primary-blue);
    color: var(--text-light);
    border: none;
    padding: 0.8rem 1.5rem;
    border-radius: var(--border-radius-md);
}

.btn-primary:hover, .btn-primary:focus-visible {
    background: var(--primary-blue-light);
    outline: none;
}

.btn-secondary {
    background: var(--gray-medium);
    color: var(--text-light);
    border: none;
    padding: 0.5rem 1rem;
    border-radius: var(--border-radius-sm);
}

.btn-secondary:hover, .btn-secondary:focus-visible {
    background: var(--gray-dark);
    outline: none;
}

.tooltip {
    position: relative;
    display: inline-block;
}

.tooltip-icon {
    background: var(--primary-blue);
    color: var(--text-light);
    border-radius: 50%;
    width: 16px;
    height: 16px;
    display: inline-flex;
    align-items: center;
    justify-content: center;
    font-size: 0.8rem;
    cursor: help;
}

.tooltip-text {
    visibility: hidden;
    width: 200px;
    background: var(--primary-dark);
    color: var(--text-light);
    text-align: center;
    padding: 0.5rem;
    border-radius: var(--border-radius-sm);
    position: absolute;
    z-index: 1;
    bottom: 125%;
    left: 50%;
    transform: translateX(-50%);
    font-size: 0.8rem;
}

.tooltip:hover .tooltip-text {
    visibility: visible;
}

@media (max-width: 768px) {
    .navbar {
        padding: 1rem 0;
    }

    .nav-container {
        flex-direction: column;
        gap: 1.5rem;
        padding: 0 1.5rem;
    }

    .logo {
        font-size: 1.8rem;
    }

    .nav-links {
        flex-direction: column;
        align-items: center;
        gap: 1rem;
    }

    .nav-links li a {
        font-size: 1rem;
        padding: 0.4rem 0.8rem;
    }

    .main-container {
        flex-direction: column;
        padding: 1rem;
    }

    .cilia-panel {
        position: static;
    }

    .search-container.sticky {
        position: static;
        transform: none;
        width: 100%;
    }

    .gene-cards, .functional-comparison-grid {
        grid-template-columns: 1fr;
    }
}

/* Suggested CSS for the gene summary table */
.gene-summary-table {
    width: 100%;
    border-collapse: collapse;
    margin-top: 10px;
    font-family: Arial, sans-serif;
    box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1);
}

.gene-summary-table th,
.gene-summary-table td {
    border: 1px solid #ddd;
    padding: 10px 12px;
    text-align: left;
}

.gene-summary-table th {
    background-color: var(--neutral-bg-alt);
    font-weight: bold;
    color: var(--text-dark);
}

.gene-summary-table tbody tr:nth-child(even) {
    background-color: #fdfdfd;
}

.gene-summary-table .status-found {
    color: var(--accent-green-2);
    font-weight: bold;
}

.gene-summary-table .status-not-found {
    color: var(--accent-red);
    font-weight: bold;
}

/* ---------- CiliaHub: Gene detail page tweaks (Medium Persian Blue) ---------- */
/* Paste at the end of styles.css */

/* Central color tokens */
:root {
  --mpb: #0067A5;
  --mpb-light: #e6f0f7;
  --mpb-border: #c2d9e6;
}

/* Scope everything to the gene detail page to avoid site-wide side effects */
.gene-detail-page,
.gene-detail-page * {
  box-sizing: border-box;
}

/* Breadcrumb & header background */
.gene-detail-page .breadcrumb,
.gene-detail-page .gene-header {
  background: var(--mpb-light) !important;
  border-color: var(--mpb-border) !important;
}

/* Gene name and description */
.gene-detail-page .gene-name {
  color: var(--mpb) !important;
  font-weight: 700;
  font-size: 2rem;
  margin: 0 0 0.25rem 0;
}
.gene-detail-page .gene-description {
  color: var(--mpb) !important;
  opacity: 0.95;
  margin: 0;
}

/* Cards (visual treatment) */
.gene-detail-page .detail-card {
  background: #fff !important;
  border: 1px solid var(--mpb-border) !important;
  border-radius: 0.6rem !important;
  padding: 1rem !important;
  box-shadow: 0 2px 8px rgba(0,0,0,0.04) !important;
}

/* Card title styling (applies to Identifiers, Subcellular Localization, Complex Info,
   Functional Information, References, etc.) */
.gene-detail-page .card-title {
  color: var(--mpb) !important;
  font-size: 1.05rem !important;
  font-weight: 600 !important;
  display: flex !important;
  align-items: center !important;
  gap: 0.5rem !important;
  margin: 0 0 0.75rem 0 !important;
  padding-bottom: 0.45rem !important;
  border-bottom: 1px solid var(--mpb-border) !important;
}

/* Ensure SVG/icons also follow the blue */
.gene-detail-page .card-title svg,
.gene-detail-page .detail-card svg {
  stroke: var(--mpb) !important;
  fill: none !important;
}

/* Strong/labels in info items */
.gene-detail-page .info-item strong,
.gene-detail-page .info-item .label {
  color: var(--mpb) !important;
  font-weight: 600 !important;
}

/* Generic paragraph and small text inside gene page */
.gene-detail-page .info-item p,
.gene-detail-page .info-item span,
.gene-detail-page .info-item div {
  color: var(--mpb) !important;
  line-height: 1.35 !important;
}

/* Tag pills (localization, functional category, etc.) */
.gene-detail-page .tag,
.gene-detail-page .tags-container .tag {
  display: inline-block !important;
  padding: 0.22rem 0.6rem !important;
  margin: 0.12rem 0.28rem !important;
  border-radius: 999px !important;
  background: var(--mpb-light) !important;
  color: var(--mpb) !important;
  font-weight: 500 !important;
  font-size: 0.85rem !important;
  vertical-align: middle !important;
  box-shadow: 0 1px 2px rgba(0,0,0,0.03) !important;
}

/* References list */
.gene-detail-page .reference-list {
  color: var(--mpb) !important;
}
.gene-detail-page .reference-list li {
  margin-bottom: 0.4rem;
  color: var(--mpb) !important;
}
.gene-detail-page .reference-list a {
  color: var(--mpb) !important;
  text-decoration: none !important;
}
.gene-detail-page .reference-list a:hover {
  text-decoration: underline !important;
}

/* Links inside the gene page — keep them consistent */
.gene-detail-page a {
  color: var(--mpb) !important;
}

/* Force card borders and accent where something else tries to override */
.gene-detail-page .detail-card,
.gene-detail-page .card-title,
.gene-detail-page .info-item strong {
  outline: none !important;
}

/* ---------- Layout: ensure left column = Functional Info + References,
   right column = Identifiers + Localization + Complex Info ---------- */

/* Standard two-column grid (desktop) */
.gene-details-grid {
  display: grid !important;
  grid-template-columns: 1fr 1fr !important;
  gap: 1.5rem !important;
  align-items: start !important;
}

/* Rely on the order the page injects the columns — usually the first .details-column is left.
   If your JS prints the columns in different order, prefer adding classes (see note below). */
.gene-details-grid > .details-column:first-child {
  grid-column: 1 / 2 !important;    /* left */
}
.gene-details-grid > .details-column:last-child {
  grid-column: 2 / 3 !important;    /* right */
}

/* Mobile: stack single column */
@media (max-width: 899px) {
  .gene-details-grid {
    grid-template-columns: 1fr !important;
  }
}

/* ---------- Utility overrides for Tailwind-style arbitrary classes that may not exist
   (these selectors escape the bracket syntax so they match when Tailwind classes are in HTML) */
.text-\\[\\#0067A5\\],
.text-\\[\\#0067A5\\] {
  color: var(--mpb) !important;
}
.bg-\\[\\#e6f0f7\\],
.bg-\\[\\#e6f0f7\\] {
  background: var(--mpb-light) !important;
}

/* ---------- Helpful debugging outline (comment out if not needed) ----------
.gene-detail-page .detail-card { outline: 1px dashed rgba(0,103,165,0.15) !important; }
---------------------------------------------------------------------------- */

/* Plot Customization Styling */
details {
    border: 1px solid #e1ecf4;
    border-radius: 4px;
    margin-bottom: 15px;
}

summary {
    padding: 8px;
    background-color: #e1ecf4;
    cursor: pointer;
    font-weight: bold;
    border-radius: 4px;
}

details[open] summary {
    border-bottom: 1px solid #d1dbe4;
}

label {
    display: block;
    font-size: 0.9rem;
    margin-bottom: 5px;
    color: #333;
}

input[type="text"],
input[type="number"],
select,
input[type="color"] {
    width: 100%;
    padding: 6px;
    border: 1px solid #ccc;
    border-radius: 4px;
    font-size: 0.9rem;
}

input[type="color"] {
    padding: 2px;
    height: 30px;
}

.plot-wrapper {
    position: relative;
    width: 100%;
}

/* =================================================== */
/* Styles for Compact CiliaHub Page Layout             */
/* =================================================== */

.ciliahub-page {
    display: flex;
    flex-direction: column;
    /* ✨ FIX: The fixed height properties have been removed to allow the page to grow. */
}

.ciliahub-header {
    flex-shrink: 0; /* Prevents header from shrinking */
}

.ciliahub-layout {
    display: grid;
    grid-template-columns: 380px 1fr; /* Gives more space to the plot */
    gap: 2rem;
    flex-grow: 1;
    overflow: hidden;
}

.ciliahub-controls-panel {
    display: flex;
    flex-direction: column;
    gap: 1.5rem;
    overflow-y: auto; /* Add scroll only to controls if they overflow */
    padding-right: 10px;
}



/* =================================================== */
/* CiliaHub: Redesigned Single Gene Page               */
/* =================================================== */

.gene-detail-page {
  display: flex;
  flex-direction: column;
  gap: 2rem;
}

/* Page Header */
.gene-header {
  background-color: var(--mpb-light);
  padding: 2rem;
  border-radius: var(--border-radius-lg);
  border: 1px solid var(--mpb-border);
}

.gene-header h1 {
  font-size: 2.5rem;
  font-weight: 800;
  color: var(--mpb);
  margin: 0 0 0.5rem 0;
  line-height: 1.2;
}

.gene-header .synonym-tags .tag {
  background-color: var(--mpb-border);
  font-size: 0.8rem;
}

.gene-header p {
  font-size: 1.1rem;
  color: var(--primary-dark);
  margin-top: 1rem;
  max-width: 80ch; /* Improves readability */
}

/* Two-Column Layout */
.gene-details-grid {
  display: grid;
  grid-template-columns: repeat(2, 1fr);
  gap: 2rem;
  align-items: start;
}

/* Card Styling */
.detail-card {
  background: var(--panel-bg);
  border: 1px solid var(--mpb-border);
  border-radius: 0.75rem; /* Slightly softer corners */
  padding: 1.5rem;
  box-shadow: 0 4px 12px rgba(0, 103, 165, 0.05);
  height: 100%; /* Make cards in the same row equal height */
}

.card-title {
  display: flex;
  align-items: center;
  gap: 0.75rem;
  font-size: 1.2rem;
  font-weight: 700;
  color: var(--mpb);
  margin: 0 0 1rem 0;
  padding-bottom: 0.75rem;
  border-bottom: 2px solid var(--mpb-border);
}

.card-title svg {
  width: 24px;
  height: 24px;
  stroke: var(--mpb);
  stroke-width: 2;
}

/* Key-Value Info Items */
.info-list {
  list-style: none;
  padding: 0;
  margin: 0;
  display: flex;
  flex-direction: column;
  gap: 0.75rem;
}

.info-item strong {
  display: block;
  color: var(--primary-dark);
  font-weight: 600;
  margin-bottom: 0.25rem;
  font-size: 0.9rem;
}

.info-item a {
  word-break: break-all;
}

/* Tag/Pill Styling */
.tags-container {
    display: flex;
    flex-wrap: wrap;
    gap: 0.5rem;
}

.tag {
  display: inline-block;
  padding: 0.25rem 0.75rem;
  border-radius: 999px;
  background-color: var(--mpb-light);
  color: var(--mpb);
  font-weight: 500;
  font-size: 0.85rem;
  line-height: 1.4;
}

.tag-ciliopathy {
    background-color: #fceded;
    color: var(--accent-red);
}

/* References List */
.reference-list {
    list-style-type: disc;
    padding-left: 1.5rem;
    margin: 0;
}

.reference-list li::marker {
    color: var(--mpb);
}

/* Responsive Breakpoint */
@media (max-width: 900px) {
  .gene-details-grid {
    grid-template-columns: 1fr; /* Stack columns on smaller screens */
  }
}

// CSS to ensure proper layout
const additionalCSS = `
<style>
.heatmap-container {
    margin-bottom: 30px;
    min-height: 400px;
}

.table-wrapper {
    clear: both;
    margin-top: 20px;
    padding: 15px;
    background: white;
    border-radius: 5px;
    box-shadow: 0 2px 4px rgba(0,0,0,0.1);
}

.gene-status-table {
    width: 100%;
    margin-bottom: 15px;
}

.download-csv-btn:hover {
    transform: translateY(-1px);
    box-shadow: 0 2px 8px rgba(0,123,255,0.3);
}

/* Ensure container is visible */
#table-container {
    display: block !important;
    visibility: visible !important;
    min-height: 50px;
    background: #f8f9fa;
    padding: 10px;
    margin-top: 20px;
    border-radius: 5px;
}

/* Debug helper */
.debug-visible {
    border: 2px dashed red !important;
    background: yellow !important;
    opacity: 0.8 !important;
}
</style>
`;

// Add debugging helper
function debugTableContainer() {
    const containers = document.querySelectorAll('[id*="table"], [class*="table"], [id*="container"]');
    console.log('Found potential containers:', containers);
    
    containers.forEach((el, i) => {
        console.log(`Container ${i}:`, {
            element: el,
            id: el.id,
            class: el.className,
            visible: el.offsetHeight > 0,
            styles: window.getComputedStyle(el)
        });
    });
}

// Call this in browser console to debug
// debugTableContainer();

/* Add this to styles.css for the download button layout */
.table-header-controls {
    display: flex;
    justify-content: space-between;
    align-items: center;
    flex-wrap: wrap;
    gap: 1rem;
}


/* =================================================== */
/* CiliaPlot Page Styles                              */
/* =================================================== */

.ciliaplot-page {
    background: var(--panel-bg);
    border-radius: var(--border-radius-lg);
    box-shadow: 0 8px 32px rgba(44, 90, 160, 0.1);
    padding: 1.5rem;
    max-width: 1000px;
    margin: 0 auto;
}

.ciliaplot-header {
    margin-bottom: 1.5rem;
    text-align: center;
}

.ciliaplot-header h1 {
    color: var(--primary-dark);
    font-size: 1.8rem;
    font-weight: 700;
    margin: 0 0 0.5rem;
}

.ciliaplot-header .info {
    color: var(--gray-medium);
    font-size: 0.95rem;
    display: flex;
    justify-content: center;
    align-items: center;
    gap: 0.5rem;
}

.ciliaplot-container-pro {
    display: flex;
    flex-direction: column;
    gap: 1rem;
}

.ciliaplot-input-section,
.ciliaplot-settings-section,
.ciliaplot-visualization-section,
.ciliaplot-results-section {
    display: flex;
    flex-direction: column;
    gap: 1rem;
}

.ciliaplot-settings-section h2 {
    color: var(--primary-dark);
    font-size: 1.3rem;
    font-weight: 600;
    margin: 0 0 0.5rem;
}

.control-card {
    background: var(--panel-bg);
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-md);
    padding: 1rem;
    box-shadow: 0 4px 12px rgba(44, 90, 160, 0.05);
}

.control-card label {
    font-weight: 600;
    color: var(--primary-dark);
    font-size: 0.9rem;
    margin-bottom: 0.5rem;
}

#ciliaplot-genes-input {
    width: 100%;
    min-height: 100px;
    padding: 0.75rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    font-size: 0.95rem;
    resize: vertical;
    transition: border-color 0.3s ease, box-shadow 0.3s ease;
}

#ciliaplot-genes-input:focus {
    border-color: var(--primary-blue);
    box-shadow: 0 0 0 3px rgba(44, 90, 160, 0.1);
    outline: none;
}

#plot-type-select,
.settings-grid select {
    width: 100%;
    padding: 0.5rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    font-size: 0.9rem;
    background: var(--panel-bg);
}

#plot-type-select:focus,
.settings-grid select:focus {
    border-color: var(--primary-blue);
    outline: none;
}

.settings-grid input[type="color"] {
    padding: 2px;
    height: 30px;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-sm);
}

.settings-grid input[type="number"] {
    padding: 0.5rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    font-size: 0.9rem;
}

.settings-grid input:focus {
    border-color: var(--primary-blue);
    outline: none;
}

.help-text {
    font-size: 0.85rem;
    color: var(--gray-medium);
    margin-top: 0.25rem;
}

.settings-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(150px, 1fr));
    gap: 0.75rem;
    padding: 0.5rem 0;
}

.settings-grid div {
    display: flex;
    flex-direction: column;
}

.btn-large {
    width: 100%;
    padding: 0.8rem;
    font-size: 1rem;
    font-weight: 600;
    border-radius: var(--border-radius-md);
    margin-top: 0.5rem;
}

.plot-card {
    background: var(--panel-bg);
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-md);
    box-shadow: 0 4px 12px rgba(44, 90, 160, 0.05);
}

.plot-card-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    padding: 0.75rem 1rem;
    background: var(--neutral-bg-alt);
    border-bottom: 2px solid var(--border-color);
}

.plot-card-header h3 {
    margin: 0;
    font-size: 1.1rem;
    font-weight: 600;
    color: var(--primary-dark);
}

.download-controls {
    display: flex;
    gap: 0.5rem;
    align-items: center;
}

.download-controls select {
    padding: 0.5rem;
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    font-size: 0.9rem;
}

.plot-container-pro {
    min-height: 500px;
    background: var(--panel-bg);
    border: 1px solid var(--border-color);
    border-radius: var(--border-radius-sm);
    padding: 0.5rem;
    position: relative;
}

.legend {
    display: flex;
    flex-wrap: wrap;
    gap: 0.5rem;
    padding: 0.5rem 1rem;
}

.tab-container {
    background: var(--panel-bg);
    border: 2px solid var(--border-color);
    border-radius: var(--border-radius-md);
    margin-top: 1rem;
}

.tab-buttons {
    display: flex;
    background: var(--neutral-bg-alt);
    border-bottom: 2px solid var(--border-color);
}

.tab-button {
    flex: 1;
    padding: 0.5rem 1rem;
    border: none;
    background: none;
    font-size: 0.95rem;
    font-weight: 500;
    color: var(--gray-dark);
    cursor: pointer;
    transition: all 0.3s ease;
}

.tab-button.active {
    color: var(--primary-blue);
    border-bottom: 2px solid var(--primary-blue);
    font-weight: 600;
}

.tab-button:hover,
.tab-button:focus {
    background: var(--accent-green-1);
    color: var(--text-light);
    outline: none;
}

.tab-pane {
    display: none;
    padding: 1rem;
}

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

.table-wrapper {
    overflow-x: auto;
    padding: 0.5rem;
    background: var(--panel-bg);
    border-radius: var(--border-radius-sm);
}

.stats-container {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(120px, 1fr));
    gap: 0.5rem;
    margin-top: 0.5rem;
}

@media (max-width: 768px) {
    .ciliaplot-page {
        padding: 1rem;
    }

    .plot-container-pro {
        min-height: 300px;
    }

    .settings-grid {
        grid-template-columns: 1fr;
    }

    .tab-buttons {
        flex-direction: column;
    }

    .tab-button {
        flex: none;
        width: 100%;
        text-align: left;
    }

    .ciliaplot-header h1 {
        font-size: 1.5rem;
    }
}

.version-box {
    flex: 1;
    min-width: 140px;
    background-color: #007bff;
    color: #fff;
    padding: 1rem;
    border-radius: 12px;
    box-shadow: 0 4px 10px rgba(0, 0, 0, 0.15);
    text-align: center;
    display: flex;
    flex-direction: column;
    align-items: center;
    justify-content: center;
}

.version-title {
    font-size: 1.2rem;
    font-weight: 700;
}

.gene-count-display {
    display: flex;
    align-items: baseline;
    gap: 0.5rem;
    margin-top: 0.25rem;
}

.gene-count-display #gene-count {
    font-size: 1.5rem;
    font-weight: 700;
}

.gene-count-display div {
    font-size: 1rem;
}