/* ============================================
   Lake Trout Genome Browser - Stylesheet
   A modern, scientific visualization interface
   ============================================ */

/* CSS Variables */
:root {
    /* Color Palette - Deep ocean inspired */
    --color-bg: #0a0e14;
    --color-bg-elevated: #111921;
    --color-bg-card: #151d28;
    --color-bg-subtle: #1a2332;
    
    /* Accent Colors */
    --color-lean: #3B82F6;
    --color-lean-light: #60A5FA;
    --color-lean-dark: #1D4ED8;
    
    --color-siscowet: #EF4444;
    --color-siscowet-light: #F87171;
    --color-siscowet-dark: #B91C1C;
    
    --color-accent: #06B6D4;
    --color-accent-light: #22D3EE;
    --color-accent-dim: #0891B2;
    
    --color-success: #10B981;
    --color-warning: #F59E0B;
    
    /* Text Colors */
    --color-text: #E2E8F0;
    --color-text-dim: #94A3B8;
    --color-text-muted: #64748B;
    
    /* Borders */
    --color-border: #1E293B;
    --color-border-subtle: #334155;
    
    /* Shadows */
    --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 -1px rgba(0, 0, 0, 0.3);
    --shadow-lg: 0 10px 15px -3px rgba(0, 0, 0, 0.5), 0 4px 6px -2px rgba(0, 0, 0, 0.3);
    --shadow-glow: 0 0 40px rgba(6, 182, 212, 0.15);
    
    /* Typography */
    --font-sans: 'Instrument Sans', system-ui, -apple-system, sans-serif;
    --font-mono: 'JetBrains Mono', 'Fira Code', monospace;
    
    /* Spacing */
    --spacing-xs: 0.25rem;
    --spacing-sm: 0.5rem;
    --spacing-md: 1rem;
    --spacing-lg: 1.5rem;
    --spacing-xl: 2rem;
    --spacing-2xl: 3rem;
    --spacing-3xl: 4rem;
    
    /* Border Radius */
    --radius-sm: 4px;
    --radius-md: 8px;
    --radius-lg: 12px;
    --radius-xl: 16px;
    --radius-full: 9999px;
    
    /* Transitions */
    --transition-fast: 150ms ease;
    --transition-base: 250ms ease;
    --transition-slow: 400ms ease;
}

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

html {
    scroll-behavior: smooth;
}

body {
    font-family: var(--font-sans);
    background-color: var(--color-bg);
    color: var(--color-text);
    line-height: 1.6;
    min-height: 100vh;
    -webkit-font-smoothing: antialiased;
    -moz-osx-font-smoothing: grayscale;
}

/* Scrollbar Styling */
::-webkit-scrollbar {
    width: 8px;
    height: 8px;
}

::-webkit-scrollbar-track {
    background: var(--color-bg-elevated);
}

::-webkit-scrollbar-thumb {
    background: var(--color-border-subtle);
    border-radius: var(--radius-full);
}

::-webkit-scrollbar-thumb:hover {
    background: var(--color-text-muted);
}

/* ============================================
   Header
   ============================================ */
.header {
    position: sticky;
    top: 0;
    z-index: 100;
    background: rgba(10, 14, 20, 0.9);
    backdrop-filter: blur(12px);
    border-bottom: 1px solid var(--color-border);
}

.header-content {
    max-width: 1400px;
    margin: 0 auto;
    padding: var(--spacing-md) var(--spacing-xl);
    display: flex;
    align-items: center;
    justify-content: space-between;
}

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

.logo-icon {
    width: 36px;
    height: 36px;
    color: var(--color-accent);
}

.logo-text {
    display: flex;
    flex-direction: column;
}

.logo-title {
    font-size: 1.125rem;
    font-weight: 600;
    color: var(--color-text);
    letter-spacing: -0.02em;
}

.logo-subtitle {
    font-size: 0.75rem;
    font-style: italic;
    color: var(--color-text-muted);
}

.nav {
    display: flex;
    align-items: center;
    gap: var(--spacing-lg);
}

.nav-link {
    font-size: 0.875rem;
    font-weight: 500;
    color: var(--color-text-dim);
    text-decoration: none;
    transition: color var(--transition-fast);
    display: flex;
    align-items: center;
    gap: var(--spacing-xs);
}

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

.external-icon {
    width: 14px;
    height: 14px;
}

/* ============================================
   Hero Section
   ============================================ */
.hero {
    position: relative;
    padding: var(--spacing-3xl) var(--spacing-xl);
    background: linear-gradient(135deg, var(--color-bg) 0%, var(--color-bg-elevated) 50%, var(--color-bg) 100%);
    overflow: hidden;
}

.hero-content {
    max-width: 800px;
    margin: 0 auto;
    text-align: center;
    position: relative;
    z-index: 2;
}

.hero-title {
    font-size: clamp(2rem, 5vw, 3.5rem);
    font-weight: 700;
    line-height: 1.2;
    margin-bottom: var(--spacing-lg);
    color: var(--color-text);
    letter-spacing: -0.03em;
}

.title-accent {
    background: linear-gradient(135deg, var(--color-accent) 0%, var(--color-accent-light) 100%);
    -webkit-background-clip: text;
    -webkit-text-fill-color: transparent;
    background-clip: text;
}

.hero-description {
    font-size: 1.125rem;
    color: var(--color-text-dim);
    margin-bottom: var(--spacing-xl);
    max-width: 600px;
    margin-left: auto;
    margin-right: auto;
}

.hero-badges {
    display: flex;
    justify-content: center;
    gap: var(--spacing-md);
    flex-wrap: wrap;
}

.badge {
    display: inline-flex;
    align-items: center;
    gap: var(--spacing-sm);
    padding: var(--spacing-sm) var(--spacing-md);
    border-radius: var(--radius-full);
    font-size: 0.875rem;
    font-weight: 500;
}

.badge-lean {
    background: rgba(59, 130, 246, 0.15);
    color: var(--color-lean-light);
    border: 1px solid rgba(59, 130, 246, 0.3);
}

.badge-siscowet {
    background: rgba(239, 68, 68, 0.15);
    color: var(--color-siscowet-light);
    border: 1px solid rgba(239, 68, 68, 0.3);
}

.badge-dot {
    width: 8px;
    height: 8px;
    border-radius: 50%;
}

.badge-lean .badge-dot {
    background: var(--color-lean);
    box-shadow: 0 0 8px var(--color-lean);
}

.badge-siscowet .badge-dot {
    background: var(--color-siscowet);
    box-shadow: 0 0 8px var(--color-siscowet);
}

/* Hero Decorations */
.hero-decoration {
    position: absolute;
    inset: 0;
    pointer-events: none;
    overflow: hidden;
}

.decoration-circle {
    position: absolute;
    border-radius: 50%;
    opacity: 0.1;
}

.circle-1 {
    width: 400px;
    height: 400px;
    background: var(--color-accent);
    top: -100px;
    left: -100px;
    filter: blur(80px);
}

.circle-2 {
    width: 300px;
    height: 300px;
    background: var(--color-lean);
    bottom: -50px;
    right: 10%;
    filter: blur(60px);
}

.circle-3 {
    width: 250px;
    height: 250px;
    background: var(--color-siscowet);
    top: 20%;
    right: -50px;
    filter: blur(60px);
}

/* ============================================
   Quick Navigation
   ============================================ */
.quick-nav {
    background: var(--color-bg-elevated);
    border-bottom: 1px solid var(--color-border);
    padding: var(--spacing-md) var(--spacing-xl);
}

.quick-nav-content {
    max-width: 1400px;
    margin: 0 auto;
    display: flex;
    gap: var(--spacing-md);
    flex-wrap: wrap;
    align-items: center;
}

.quick-nav-item {
    display: flex;
    flex-direction: column;
    gap: 2px;
    padding: var(--spacing-sm) var(--spacing-md);
    background: var(--color-bg-card);
    border: 1px solid var(--color-border);
    border-radius: var(--radius-md);
    cursor: pointer;
    transition: all var(--transition-fast);
}

.quick-nav-item:hover {
    border-color: var(--color-accent-dim);
    background: var(--color-bg-subtle);
}

.quick-nav-label {
    font-size: 0.7rem;
    text-transform: uppercase;
    letter-spacing: 0.05em;
    color: var(--color-text-muted);
}

.quick-nav-value {
    font-family: var(--font-mono);
    font-size: 0.8rem;
    color: var(--color-accent);
}

#search-box {
    flex: 1;
    min-width: 280px;
    cursor: default;
}

.region-input {
    width: 100%;
    padding: var(--spacing-sm);
    background: var(--color-bg);
    border: 1px solid var(--color-border);
    border-radius: var(--radius-sm);
    color: var(--color-text);
    font-family: var(--font-mono);
    font-size: 0.875rem;
    outline: none;
    transition: border-color var(--transition-fast);
}

.region-input:focus {
    border-color: var(--color-accent);
}

.region-input::placeholder {
    color: var(--color-text-muted);
}

/* ============================================
   Browser Section
   ============================================ */
.browser-section {
    padding: var(--spacing-xl);
    background: var(--color-bg);
}

.igv-container {
    max-width: 1400px;
    margin: 0 auto;
    background: var(--color-bg-card);
    border: 1px solid var(--color-border);
    border-radius: var(--radius-lg);
    overflow: hidden;
    box-shadow: var(--shadow-lg), var(--shadow-glow);
    min-height: 500px;
}

/* IGV.js Custom Styling */
.igv-container .igv-track-label {
    font-family: var(--font-sans) !important;
    font-size: 0.75rem !important;
}

.igv-container .igv-navbar {
    background: var(--color-bg-elevated) !important;
}

/* ============================================
   Legend Section
   ============================================ */
.legend-section {
    padding: var(--spacing-3xl) var(--spacing-xl);
    background: var(--color-bg);
}

.section-title {
    font-size: 1.5rem;
    font-weight: 600;
    color: var(--color-text);
    text-align: center;
    margin-bottom: var(--spacing-2xl);
    letter-spacing: -0.02em;
}

.legend-grid {
    max-width: 1200px;
    margin: 0 auto;
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(260px, 1fr));
    gap: var(--spacing-lg);
}

.legend-card {
    background: var(--color-bg-card);
    border: 1px solid var(--color-border);
    border-radius: var(--radius-lg);
    padding: var(--spacing-lg);
    transition: all var(--transition-base);
}

.legend-card:hover {
    border-color: var(--color-border-subtle);
    transform: translateY(-2px);
    box-shadow: var(--shadow-md);
}

.legend-header {
    display: flex;
    align-items: center;
    gap: var(--spacing-md);
    margin-bottom: var(--spacing-md);
}

.legend-color {
    width: 16px;
    height: 16px;
    border-radius: var(--radius-sm);
    flex-shrink: 0;
}

.legend-title {
    font-size: 1rem;
    font-weight: 600;
    color: var(--color-text);
}

.legend-desc {
    font-size: 0.875rem;
    color: var(--color-text-dim);
    line-height: 1.5;
}

/* ============================================
   About Section
   ============================================ */
.about-section {
    padding: var(--spacing-3xl) var(--spacing-xl);
    background: var(--color-bg-elevated);
}

.about-content {
    max-width: 1200px;
    margin: 0 auto;
}

.about-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
    gap: var(--spacing-xl);
}

.about-card {
    background: var(--color-bg-card);
    border: 1px solid var(--color-border);
    border-radius: var(--radius-lg);
    padding: var(--spacing-xl);
    transition: all var(--transition-base);
}

.about-card:hover {
    border-color: var(--color-accent-dim);
}

.about-icon {
    width: 48px;
    height: 48px;
    margin-bottom: var(--spacing-md);
    color: var(--color-accent);
}

.about-icon svg {
    width: 100%;
    height: 100%;
}

.about-card h3 {
    font-size: 1.125rem;
    font-weight: 600;
    color: var(--color-text);
    margin-bottom: var(--spacing-sm);
}

.about-card p {
    font-size: 0.9rem;
    color: var(--color-text-dim);
    line-height: 1.6;
}

/* ============================================
   Samples Table Section
   ============================================ */
.samples-section {
    padding: var(--spacing-3xl) var(--spacing-xl);
    background: var(--color-bg);
}

.table-container {
    max-width: 1000px;
    margin: 0 auto;
    overflow-x: auto;
}

.samples-table {
    width: 100%;
    border-collapse: collapse;
    font-size: 0.9rem;
}

.samples-table th,
.samples-table td {
    padding: var(--spacing-md);
    text-align: left;
    border-bottom: 1px solid var(--color-border);
}

.samples-table th {
    background: var(--color-bg-elevated);
    color: var(--color-text-muted);
    font-weight: 500;
    text-transform: uppercase;
    font-size: 0.75rem;
    letter-spacing: 0.05em;
}

.samples-table tbody tr {
    transition: background var(--transition-fast);
}

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

.samples-table code {
    font-family: var(--font-mono);
    background: var(--color-bg-elevated);
    padding: 2px 6px;
    border-radius: var(--radius-sm);
    font-size: 0.85em;
}

.ecotype-badge {
    display: inline-block;
    padding: 4px 10px;
    border-radius: var(--radius-full);
    font-size: 0.75rem;
    font-weight: 600;
    text-transform: uppercase;
    letter-spacing: 0.03em;
}

.ecotype-badge.lean {
    background: rgba(59, 130, 246, 0.2);
    color: var(--color-lean-light);
}

.ecotype-badge.siscowet {
    background: rgba(239, 68, 68, 0.2);
    color: var(--color-siscowet-light);
}

.lean-row:hover {
    background: rgba(59, 130, 246, 0.05);
}

.siscowet-row:hover {
    background: rgba(239, 68, 68, 0.05);
}

/* ============================================
   Footer
   ============================================ */
.footer {
    background: var(--color-bg-elevated);
    border-top: 1px solid var(--color-border);
    padding: var(--spacing-xl);
}

.footer-content {
    max-width: 1400px;
    margin: 0 auto;
    display: flex;
    justify-content: space-between;
    align-items: center;
    flex-wrap: wrap;
    gap: var(--spacing-md);
}

.footer-info p {
    color: var(--color-text-dim);
    font-size: 0.875rem;
}

.footer-sub {
    font-size: 0.75rem !important;
    color: var(--color-text-muted) !important;
    font-family: var(--font-mono);
}

.footer-links {
    display: flex;
    align-items: center;
    gap: var(--spacing-md);
}

.footer-links a {
    color: var(--color-text-muted);
    text-decoration: none;
    font-size: 0.875rem;
    transition: color var(--transition-fast);
}

.footer-links a:hover {
    color: var(--color-accent);
}

.footer-divider {
    color: var(--color-border);
}

/* ============================================
   Loading State
   ============================================ */
.loading-overlay {
    position: absolute;
    inset: 0;
    display: flex;
    align-items: center;
    justify-content: center;
    background: var(--color-bg-card);
}

.loading-spinner {
    width: 40px;
    height: 40px;
    border: 3px solid var(--color-border);
    border-top-color: var(--color-accent);
    border-radius: 50%;
    animation: spin 1s linear infinite;
}

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

/* ============================================
   Responsive Design
   ============================================ */
@media (max-width: 768px) {
    .header-content {
        flex-direction: column;
        gap: var(--spacing-md);
        padding: var(--spacing-md);
    }
    
    .nav {
        gap: var(--spacing-md);
    }
    
    .hero {
        padding: var(--spacing-2xl) var(--spacing-md);
    }
    
    .hero-title {
        font-size: 1.75rem;
    }
    
    .quick-nav-content {
        flex-direction: column;
        align-items: stretch;
    }
    
    .quick-nav-item {
        width: 100%;
    }
    
    .browser-section {
        padding: var(--spacing-md);
    }
    
    .igv-container {
        border-radius: var(--radius-md);
    }
    
    .legend-section,
    .about-section,
    .samples-section {
        padding: var(--spacing-2xl) var(--spacing-md);
    }
    
    .footer-content {
        flex-direction: column;
        text-align: center;
    }
}

/* ============================================
   Print Styles
   ============================================ */
@media print {
    .header,
    .quick-nav,
    .footer {
        display: none;
    }
    
    body {
        background: white;
        color: black;
    }
    
    .igv-container {
        box-shadow: none;
        border: 1px solid #ccc;
    }
}