:root {
    /* --- COLORS (Light Mode) --- */
    --bg-primary: #ffffff;
    --bg-secondary: #f8f9fa;
    --text-primary: #000000;
    --text-secondary: #4a5568;
    --accent-color: #2563eb;
    /* Blue */
    --accent-hover: #1d4ed8;
    --grid-color: rgba(0, 0, 0, 0.04);
    --border-color: #e2e8f0;
    --card-bg: #ffffff;

    /* --- 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);

    /* --- FONTS --- */
    --font-heading: 'Doto', monospace;
    --font-body: 'Poppins', sans-serif;
}

[data-theme='dark'] {
    /* --- COLORS (Dark Mode) --- */
    --bg-primary: #0f172a;
    --bg-secondary: #1e293b;
    --text-primary: #ffffff;
    --text-secondary: #dae5f5;
    --accent-color: #3b82f6;
    /* Lighter Blue */
    --accent-hover: #60a5fa;
    --grid-color: rgba(255, 255, 255, 0.05);
    --border-color: #334155;
    --card-bg: #1e293b;

    --shadow-sm: 0 1px 2px 0 rgba(0, 0, 0, 0.3);
    --shadow-md: 0 4px 6px -1px rgba(0, 0, 0, 0.5);
}

/* --- RESET & BASE --- */
* {
    box-sizing: border-box;
    margin: 0;
    padding: 0;
}

body {
    font-family: var(--font-body);
    background-color: var(--bg-primary);
    color: var(--text-primary);

    /* Grid Background Pattern */
    background-image:
        linear-gradient(to right, var(--grid-color) 1px, transparent 1px),
        linear-gradient(to bottom, var(--grid-color) 1px, transparent 1px);
    background-size: 40px 40px;

    min-height: 100vh;
    transition: background-color 0.3s ease, color 0.3s ease;
}

h1,
h2,
h3,
h4,
h5,
h6,
button,
.nav-logo,
.animated-title {
    font-family: var(--font-heading);
    letter-spacing: -0.02em;
}

button {
    cursor: pointer;
    border: none;
    border-radius: 8px;
    padding: 0.75rem 1.5rem;
    font-weight: 600;
    transition: all 0.2s ease;
}

/* --- UTILITIES --- */
.app-container {
    min-height: 100vh;
    display: flex;
    flex-direction: column;
}

.main-content {
    flex: 1;
    padding: 2rem;
    max-width: 1200px;
    margin: 0 auto;
    width: 100%;
}

.btn-primary {
    background-color: var(--accent-color);
    color: white;
}

.btn-primary:hover {
    background-color: var(--accent-hover);
    transform: translateY(-2px);
}

.btn-secondary {
    background-color: var(--bg-secondary);
    color: var(--text-primary);
    border: 1px solid var(--border-color);
}

.card {
    background-color: var(--card-bg);
    border: 1px solid var(--border-color);
    border-radius: 12px;
    padding: 2rem;
    box-shadow: var(--shadow-sm);
    transition: border-color 0.3s ease, background-color 0.3s ease;
}

.card:hover {
    box-shadow: var(--shadow-md);
    border-color: var(--accent-color);
}

.error {
    color: #ef4444;
    margin-top: 1rem;
}

/* --- PAGE VISIBILITY (SPA) --- */
.page-section {
    display: none;
    animation: fadeIn 0.3s ease-in-out;
}

.page-section.active {
    display: block;
}

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

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

/* --- NAVBAR --- */
.navbar {
    background-color: var(--bg-primary);
    /* Use explicit rgba if possible or fallback */
    background-color: rgba(var(--bg-primary), 0.8);
    /* Note: CSS vars inside rgba are not spec-compliant unless raw values. 
     For simple fix without raw vars, we just rely on base background. */
    border-bottom: 1px solid var(--border-color);
    position: sticky;
    top: 0;
    z-index: 100;
    backdrop-filter: blur(8px);
}

.nav-container {
    max-width: 1200px;
    margin: 0 auto;
    padding: 1rem 2rem;
    display: flex;
    justify-content: space-between;
    align-items: center;
}

.nav-logo {
    font-size: 1.5rem;
    font-weight: 700;
    color: var(--text-primary);
    text-decoration: none;
}

.dot {
    color: var(--accent-color);
}

.nav-menu.desktop {
    display: flex;
    align-items: center;
    gap: 2rem;
}

.nav-link {
    color: var(--text-secondary);
    text-decoration: none;
    font-weight: 500;
    font-family: var(--font-body);
    transition: color 0.2s;
    cursor: pointer;
}

.nav-link:hover,
.nav-link.active {
    color: var(--text-primary);
}

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

.theme-toggle {
    background: none;
    padding: 0.5rem;
    color: var(--text-primary);
}

.theme-toggle:hover {
    background-color: var(--bg-secondary);
}

.mobile-toggle {
    display: none;
    background: none;
    color: var(--text-primary);
}

/* Mobile Menu */
.mobile-menu {
    display: none;
    position: absolute;
    top: 100%;
    left: 0;
    right: 0;
    background-color: var(--bg-primary);
    border-bottom: 1px solid var(--border-color);
    padding: 1rem;
    flex-direction: column;
    gap: 1rem;
    z-index: 99;
}

.mobile-menu.open {
    display: flex;
}

.mobile-link {
    text-decoration: none;
    color: var(--text-secondary);
    padding: 0.5rem;
    font-size: 1.1rem;
}

.mobile-link.active {
    color: var(--accent-color);
}

@media (max-width: 768px) {
    .nav-menu.desktop {
        display: none;
    }

    .mobile-toggle {
        display: block;
    }
}

/* --- FOOTER --- */
.footer {
    background-color: var(--card-bg);
    border-top: 1px solid var(--border-color);
    padding: 1.5rem 0;
    margin-top: auto;
    width: 100%;
}

.footer-content {
    max-width: 1200px;
    margin: 0 auto;
    padding: 0 2rem;
    display: flex;
    justify-content: space-between;
    align-items: center;
}

.footer-content p {
    color: var(--text-secondary);
    font-size: 0.9rem;
}

.contact-btn {
    background-color: var(--accent-color);
    color: white;
    padding: 0.6rem 1.5rem;
    border-radius: 10px !important;
    text-decoration: none;
    font-weight: 500;
    font-family: var(--font-body);
    transition: all 0.2s ease;
    display: inline-block;
}

.contact-btn:hover {
    background-color: var(--accent-hover);
    transform: translateY(-2px);
    box-shadow: var(--shadow-sm);
}

@media (max-width: 768px) {
    .footer-content {
        flex-direction: column;
        gap: 1rem;
        text-align: center;
    }
}

/* --- HOME PAGE --- */
.home-container {
    display: flex;
    flex-direction: column;
    gap: 4rem;
}

.hero {
    padding: 4rem 0;
    text-align: center;
}

.hero h1 {
    font-size: 3.5rem;
    margin-bottom: 1.5rem;
    color: var(--accent-color);
}

.animated-title {
    min-height: 1.1em;
}

.hero p {
    font-size: 1.25rem;
    color: var(--text-secondary);
    max-width: 600px;
    margin: 0 auto 2rem;
    line-height: 1.6;
}

.hero-buttons {
    display: flex;
    gap: 1.5rem;
    justify-content: center;
    flex-wrap: wrap;
}

.btn {
    display: inline-flex;
    align-items: center;
    gap: 0.5rem;
    text-decoration: none;
}

.btn:hover {
    transform: translateY(-2px);
}

.hero-buttons .btn {
    padding: 1rem 3rem;
    border-radius: 35px;
    font-weight: 600;
    backdrop-filter: blur(10px);
    -webkit-backdrop-filter: blur(10px);
    transition: all 0.3s ease;
    min-width: 200px;
    justify-content: center;
    box-shadow: 0 8px 32px 0 rgba(31, 38, 135, 0.15);
}

.hero-buttons .btn-primary {
    background: rgba(37, 99, 235, 0.75);
    border: 1px solid rgba(255, 255, 255, 0.18);
    color: white;
}

.hero-buttons .btn-primary:hover {
    background: rgba(37, 99, 235, 0.85);
    box-shadow: 0 8px 32px 0 rgba(37, 99, 235, 0.3);
    transform: translateY(-3px);
}

.hero-buttons .btn-secondary {
    background: rgba(var(--bg-secondary), 0.6);
    border: 1px solid rgba(255, 255, 255, 0.18);
    color: var(--text-primary);
}

.hero-buttons .btn-secondary:hover {
    background: rgba(var(--bg-secondary), 0.8);
    box-shadow: 0 8px 32px 0 rgba(0, 0, 0, 0.1);
    transform: translateY(-3px);
}

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


.icon-box {
    width: 60px;
    height: 60px;
    background: var(--bg-secondary);
    border-radius: 12px;
    display: flex;
    align-items: center;
    justify-content: center;
    margin-bottom: 1.5rem;
    color: var(--accent-color);
}

.feature-card h3 {
    margin-bottom: 1rem;
    font-size: 1.5rem;
}

.feature-card p {
    color: var(--text-secondary);
    line-height: 1.6;
}

/* --- CALCULATORS PAGE --- */
.calculators-page {
    display: flex;
    flex-direction: column;
    gap: 2rem;
}

.tabs {
    display: flex;
    gap: 1rem;
    border-bottom: 2px solid var(--border-color);
    padding-bottom: 1rem;
}

.tab-btn {
    background: none;
    color: var(--text-secondary);
    font-size: 1.1rem;
    padding: 0.5rem 1rem;
    border-radius: 6px;
}

.tab-btn.active {
    color: white;
    background-color: var(--accent-color);
}

.calculator-content-tab {
    display: none;
}

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

/* Phred Upload */
.upload-section {
    display: flex;
    flex-direction: column;
    align-items: center;
    margin: 2rem 0;
}

.file-upload-btn {
    display: inline-flex;
    align-items: center;
    justify-content: center;
    gap: 0.5rem;
    background-color: var(--accent-color);
    color: white;
    padding: 1rem 3rem;
    border-radius: 30px;
    font-family: 'Doto', sans-serif;
    font-weight: 700;
    font-size: 1.1rem;
    cursor: pointer;
    width: 100%;
    max-width: 400px;
    box-shadow: 0 0 15px rgba(37, 99, 235, 0.5);
    transition: all 0.3s ease;
}

.file-upload-btn:hover {
    transform: translateY(-2px);
    box-shadow: 0 0 25px rgba(37, 99, 235, 0.7);
}

/* Results Grid */
.results-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(150px, 1fr));
    gap: 1rem;
    margin-bottom: 2rem;
}

.stat-box {
    background: var(--bg-secondary);
    padding: 1rem;
    border-radius: 8px;
    text-align: center;
}

.stat-box h4 {
    color: var(--text-secondary);
    font-size: 0.9rem;
    margin-bottom: 0.5rem;
}

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

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

.download-chart-btn {
    display: inline-flex;
    align-items: center;
    gap: 0.5rem;
    background-color: var(--accent-color);
    color: white;
    border: none;
    padding: 0.5rem 1.5rem;
    border-radius: 20px;
    font-family: 'Doto', sans-serif;
    font-weight: 600;
    cursor: pointer;
    box-shadow: 0 0 10px rgba(37, 99, 235, 0.4);
    transition: all 0.3s ease;
}

.download-chart-btn:hover {
    background-color: #1d4ed8;
    box-shadow: 0 0 20px rgba(37, 99, 235, 0.7);
    transform: translateY(-2px);
}

/* Alignment Form */
.algo-selector {
    display: flex;
    flex-wrap: wrap;
    gap: 1.5rem;
    margin-bottom: 2rem;
    justify-content: center;
}

.algo-btn {
    padding: 0.75rem 2rem;
    border-radius: 50px;
    border: 2px solid var(--accent-color);
    background: transparent;
    color: var(--accent-color);
    font-family: 'Doto', sans-serif;
    font-weight: 700;
    font-size: 1rem;
    cursor: pointer;
    transition: all 0.3s ease;
    min-width: 250px;
    flex: 1;
    max-width: 300px;
}

@media (max-width: 600px) {
    .algo-selector {
        gap: 0.75rem;
        flex-direction: column;
        align-items: center;
    }

    .algo-btn {
        width: 100%;
        max-width: 100%;
        min-width: auto;
    }
}

.algo-btn:hover {
    background: rgba(var(--accent-color), 0.1);
    transform: translateY(-2px);
}

.algo-btn.active {
    background: var(--accent-color);
    color: white;
    box-shadow: 0 4px 12px rgba(37, 99, 235, 0.3);
}

.params-section {
    display: grid;
    grid-template-columns: repeat(3, 1fr);
    gap: 1rem;
    margin-bottom: 2rem;
    padding: 1rem;
    background: var(--bg-secondary);
    border-radius: 8px;
}

.param-group label {
    display: block;
    font-size: 0.9rem;
    margin-bottom: 0.5rem;
    color: var(--text-secondary);
}

.param-group input {
    width: 100%;
    padding: 0.5rem;
    border: 1px solid var(--border-color);
    border-radius: 4px;
    background: var(--bg-primary);
    color: var(--text-primary);
}

.input-group {
    margin-bottom: 1.5rem;
}

.input-group label {
    display: block;
    margin-bottom: 0.5rem;
    font-weight: 500;
    color: var(--text-secondary);
}

textarea {
    width: 100%;
    padding: 1rem;
    border: 1px solid var(--border-color);
    border-radius: 8px;
    background: var(--bg-primary);
    color: var(--text-primary);
    font-family: monospace;
    min-height: 100px;
    text-transform: uppercase;
    /* Auto Capslock Visual */
}

/* Alignment Results */
.alignment-result {
    margin-top: 2rem;
}

.result-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    margin-bottom: 1.5rem;
}

.score-badge {
    background: var(--accent-color);
    color: white;
    padding: 0.5rem 1rem;
    border-radius: 20px;
    font-weight: bold;
}

.variations-section {
    margin-bottom: 2rem;
}

.subtitle {
    font-size: 0.9rem;
    color: var(--text-secondary);
    margin-bottom: 1rem;
}

.variations-list {
    display: flex;
    flex-direction: column;
    gap: 1rem;
}

.variation-item {
    background: var(--bg-secondary);
    padding: 1rem;
    border-radius: 8px;
    border: 2px solid transparent;
    cursor: pointer;
    transition: all 0.2s;
}

.variation-item:hover {
    border-color: rgba(var(--accent-color), 0.5);
}

.variation-item.selected {
    border-color: var(--accent-color);
    background-color: rgba(var(--accent-color), 0.05);
}

.var-header {
    display: flex;
    justify-content: space-between;
    margin-bottom: 0.5rem;
}

.var-label {
    font-size: 0.8rem;
    color: var(--text-secondary);
    text-transform: uppercase;
    letter-spacing: 0.05em;
}

.alignment-display {
    font-family: monospace;
    font-size: 1.2rem;
    letter-spacing: 0.2rem;
    white-space: pre;
    overflow-x: auto;
}

/* Matrix Table */
.matrix-section {
    background: var(--bg-secondary);
    padding: 1.5rem;
    border-radius: 12px;
    overflow: hidden;
}

.matrix-wrapper {
    overflow-x: auto;
    margin-top: 1rem;
}

.matrix-table {
    border-collapse: collapse;
    font-family: monospace;
    width: 100%;
}

.matrix-table th,
.matrix-table td {
    border: 1px solid var(--border-color);
    padding: 0.5rem;
    text-align: center;
    min-width: 40px;
}

.matrix-table th {
    background-color: rgba(0, 0, 0, 0.05);
    font-weight: bold;
}

.matrix-table td.highlight-path {
    background-color: #86efac !important;
    color: #064e3b;
    font-weight: bold;
}

[data-theme='dark'] .matrix-table td.highlight-path {
    background-color: #22c55e !important;
    color: #ffffff;
}

/* --- DOWNLOADS PAGE --- */
.downloads-page .header {
    text-align: center;
    margin-bottom: 3rem;
}

.software-grid {
    display: grid;
    grid-template-columns: repeat(auto-fill, minmax(280px, 1fr));
    gap: 2rem;
}

.software-card {
    /* Inherits .card */
    display: flex;
    flex-direction: column;
    align-items: flex-start;
    height: 100%;
}

.software-card h3 {
    font-size: 1.5rem;
    margin-bottom: 0.5rem;
}

.software-card p {
    color: var(--text-secondary);
    margin-bottom: 1.5rem;
    flex-grow: 1;
}

.download-link-btn {
    width: 100%;
    justify-content: center;
    border-radius: 20px;
    padding: 1rem;
    font-family: 'Doto', sans-serif;
    font-weight: 700;
    letter-spacing: 0.5px;
    display: flex;
    align-items: center;
    gap: 0.5rem;
    margin-top: auto;
    box-shadow: 0 4px 15px rgba(37, 99, 235, 0.3);
    transition: transform 0.2s, box-shadow 0.2s;
    background-color: var(--accent-color);
    color: white;
    text-decoration: none;
}

.download-link-btn:hover {
    box-shadow: 0 6px 20px rgba(37, 99, 235, 0.5);
    transform: translateY(-2px);
}

/* --- TUTORIAL PAGE --- */
.tutorial-page {
    max-width: 800px;
    margin: 0 auto;
}

.tutorial-content {
    padding: 3rem;
}

.tutorial-content h1 {
    color: var(--accent-color);
    margin-bottom: 2rem;
    text-align: center;
}

.tutorial-content h2 {
    margin-top: 2rem;
    margin-bottom: 1rem;
    border-bottom: 1px solid var(--border-color);
    padding-bottom: 0.5rem;
}

.tutorial-content h3 {
    margin-top: 1.5rem;
    font-size: 1.1rem;
    color: var(--text-secondary);
}

.tutorial-content ol {
    margin-left: 1.5rem;
    line-height: 1.8;
    color: var(--text-secondary);
}

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

.tutorial-content a {
    color: var(--accent-color);
    text-decoration: none;
}

.tutorial-content a:hover {
    text-decoration: underline;
}

.code-block {
    background: #1e1e1e;
    color: #d4d4d4;
    padding: 1rem;
    border-radius: 8px;
    position: relative;
    margin: 1rem 0;
    overflow-x: auto;
    font-family: monospace;
}

.copy-btn {
    position: absolute;
    top: 0.5rem;
    right: 0.5rem;
    background: rgba(255, 255, 255, 0.1);
    color: white;
    padding: 0.25rem;
    border-radius: 4px;
}

/* --- BIOINFORMATICS PAGE --- */
.bioinformatics-page .header {
    text-align: center;
    margin-bottom: 3rem;
}

.bioinformatics-page .header h1 {
    font-size: 2.5rem;
    margin-bottom: 1rem;
    background: linear-gradient(135deg, var(--accent-color) 0%, #8b5cf6 50%, #06b6d4 100%);
    -webkit-background-clip: text;
    background-clip: text;
    -webkit-text-fill-color: transparent;
}

.bioinformatics-page .header p {
    font-size: 1.15rem;
    color: var(--text-secondary);
    max-width: 700px;
    margin: 0 auto;
    line-height: 1.7;
}

/* Tutorial Steps */
.tutorial-steps {
    display: flex;
    flex-direction: column;
    gap: 2rem;
    max-width: 860px;
    margin: 0 auto;
}

.step-card {
    display: flex;
    gap: 1.5rem;
    padding: 2rem;
    position: relative;
    overflow: hidden;
    transition: all 0.3s ease;
}

.step-card::before {
    content: '';
    position: absolute;
    top: 0;
    left: 0;
    right: 0;
    height: 4px;
    background: linear-gradient(90deg, var(--accent-color), #8b5cf6, #06b6d4);
    opacity: 0;
    transition: opacity 0.3s ease;
}

.step-card:hover::before {
    opacity: 1;
}

.step-card:hover {
    transform: translateY(-3px);
    box-shadow: 0 12px 40px rgba(37, 99, 235, 0.12);
}

.step-number {
    flex-shrink: 0;
    width: 48px;
    height: 48px;
    background: linear-gradient(135deg, var(--accent-color), #8b5cf6);
    border-radius: 14px;
    display: flex;
    align-items: center;
    justify-content: center;
    font-family: var(--font-heading);
    font-size: 1.3rem;
    font-weight: 800;
    color: white;
}

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

.step-content h2 {
    font-size: 1.4rem;
    margin-bottom: 0.75rem;
    display: flex;
    align-items: center;
    gap: 0.6rem;
    color: var(--text-primary);
}

.step-content h3 {
    font-family: var(--font-body);
    font-size: 1.05rem;
    font-weight: 600;
    margin-top: 1.25rem;
    margin-bottom: 0.6rem;
    color: var(--text-primary);
    letter-spacing: normal;
}

.step-content h4 {
    font-size: 1.5rem;
    margin-top: 1.25rem;
    margin-bottom: 0.5rem;
    color: var(--accent-color);
}

.step-content p {
    color: var(--text-secondary);
    line-height: 1.7;
    margin-bottom: 0.5rem;
}

.step-content ol {
    margin-left: 1.5rem;
    line-height: 1.9;
    color: var(--text-secondary);
    margin-bottom: 0.75rem;
}

.step-content li {
    margin-bottom: 0.35rem;
}

.step-content a {
    color: var(--accent-color);
    text-decoration: none;
}

.step-content a:hover {
    text-decoration: underline;
}

.step-content code {
    background: var(--bg-secondary);
    padding: 0.15rem 0.45rem;
    border-radius: 4px;
    font-size: 0.9em;
    color: var(--accent-color);
    border: 1px solid var(--border-color);
}

.step-content kbd {
    background: var(--bg-secondary);
    padding: 0.15rem 0.5rem;
    border-radius: 4px;
    font-size: 0.85em;
    border: 1px solid var(--border-color);
    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);
    font-family: var(--font-body);
}

/* Action Buttons */
.step-actions {
    margin-top: 1.25rem;
    display: flex;
    flex-wrap: wrap;
    gap: 0.75rem;
}

.action-btn {
    display: inline-flex;
    align-items: center;
    gap: 0.6rem;
    padding: 0.85rem 2rem;
    border-radius: 30px;
    font-family: var(--font-heading);
    font-weight: 700;
    font-size: 1rem;
    letter-spacing: 0.03em;
    text-decoration: none;
    transition: all 0.3s ease;
    cursor: pointer;
}

.primary-action {
    background: transparent;
    color: #000000;
    border: 2px solid var(--accent-color);
    box-shadow: 0 4px 18px rgba(37, 99, 235, 0.15);
}

.primary-action:hover {
    background: var(--accent-color);
    color: #ffffff;
    transform: translateY(-3px);
    box-shadow: 0 8px 28px rgba(37, 99, 235, 0.35);
    text-decoration: none !important;
}

.success-action {
    background: transparent;
    color: #000000;
    border: 2px solid #10b981;
    box-shadow: 0 4px 18px rgba(16, 185, 129, 0.15);
}

.success-action:hover {
    background: #10b981;
    color: #ffffff;
    transform: translateY(-3px);
    box-shadow: 0 8px 28px rgba(16, 185, 129, 0.35);
    text-decoration: none !important;
}

.secondary-action {
    background: transparent;
    color: #000000;
    border: 2px solid var(--border-color);
    box-shadow: var(--shadow-sm);
}

.secondary-action:hover {
    border-color: var(--accent-color);
    color: var(--accent-color);
    transform: translateY(-3px);
    box-shadow: 0 6px 20px rgba(37, 99, 235, 0.15);
    text-decoration: none !important;
}

/* Dark mode overrides for action buttons */
[data-theme='dark'] .primary-action {
    color: #ffffff;
}

[data-theme='dark'] .success-action {
    color: #ffffff;
}

[data-theme='dark'] .secondary-action {
    color: #ffffff;
}

[data-theme='dark'] .primary-action:hover {
    color: #ffffff;
}

[data-theme='dark'] .success-action:hover {
    color: #ffffff;
}

[data-theme='dark'] .secondary-action:hover {
    color: #ffffff;
}

/* Method Chooser */
.method-chooser {
    display: flex;
    gap: 1rem;
    margin: 1.25rem 0;
}

.method-btn {
    flex: 1;
    display: flex;
    flex-direction: column;
    align-items: center;
    gap: 0.3rem;
    padding: 1.25rem 1rem;
    border-radius: 12px;
    border: 2px solid var(--border-color);
    background: var(--bg-secondary);
    color: var(--text-primary);
    cursor: pointer;
    transition: all 0.3s ease;
    font-family: var(--font-heading);
}

.method-btn span {
    font-weight: 700;
    font-size: 1rem;
}

.method-btn small {
    font-size: 0.8rem;
    color: var(--text-secondary);
    font-family: var(--font-body);
}

.method-btn:hover {
    border-color: var(--accent-color);
    transform: translateY(-2px);
}

.method-btn.active {
    border-color: var(--accent-color);
    background: linear-gradient(135deg, rgba(37, 99, 235, 0.08), rgba(139, 92, 246, 0.08));
    box-shadow: 0 4px 15px rgba(37, 99, 235, 0.15);
}

.method-btn.active small {
    color: var(--accent-color);
}

/* Method Content Toggle */
.method-content {
    display: none;
    margin-top: 1.5rem;
    padding-top: 1.5rem;
    border-top: 1px solid var(--border-color);
    animation: fadeIn 0.3s ease-in-out;
}

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

/* IDE Grid */
.ide-grid {
    display: grid;
    grid-template-columns: repeat(3, 1fr);
    gap: 0.75rem;
    margin: 1rem 0 1.5rem;
}

.ide-card {
    display: flex;
    flex-direction: column;
    align-items: center;
    gap: 0.5rem;
    padding: 1.25rem 0.75rem;
    border-radius: 10px;
    border: 1px solid var(--border-color);
    background: var(--bg-secondary);
    text-decoration: none;
    transition: all 0.3s ease;
}

.ide-card:hover {
    border-color: var(--accent-color);
    transform: translateY(-2px);
    box-shadow: var(--shadow-md);
    text-decoration: none !important;
}

.ide-name {
    font-family: var(--font-heading);
    font-weight: 700;
    font-size: 1rem;
    color: var(--text-primary);
}

.ide-dl {
    display: inline-flex;
    align-items: center;
    gap: 0.3rem;
    font-size: 0.8rem;
    color: var(--accent-color);
    font-weight: 500;
}

/* OS Sections */
.os-section {
    padding: 1rem 0;
    border-bottom: 1px solid var(--border-color);
}

.os-section:last-child {
    border-bottom: none;
}

/* Alert Boxes */
.alert-box {
    display: flex;
    align-items: flex-start;
    gap: 0.75rem;
    padding: 1rem 1.25rem;
    border-radius: 10px;
    margin: 1rem 0;
    line-height: 1.6;
}

.alert-box p {
    margin: 0;
    font-size: 0.92rem;
}

.alert-box.warning {
    background: rgba(245, 158, 11, 0.1);
    border: 1px solid rgba(245, 158, 11, 0.25);
    color: #b45309;
}

.alert-box.warning i {
    color: #f59e0b;
    flex-shrink: 0;
    margin-top: 2px;
}

.alert-box.info {
    background: rgba(37, 99, 235, 0.08);
    border: 1px solid rgba(37, 99, 235, 0.2);
    color: var(--accent-color);
}

.alert-box.info i {
    color: var(--accent-color);
    flex-shrink: 0;
    margin-top: 2px;
}

[data-theme='dark'] .alert-box.warning {
    background: rgba(245, 158, 11, 0.08);
    border-color: rgba(245, 158, 11, 0.2);
    color: #fbbf24;
}

[data-theme='dark'] .alert-box.info {
    background: rgba(59, 130, 246, 0.1);
    border-color: rgba(59, 130, 246, 0.2);
    color: #93c5fd;
}

/* Tutorial Footer Note */
.tutorial-footer-note {
    text-align: center;
    margin-top: 3rem;
    padding: 1.5rem;
    border-top: 1px solid var(--border-color);
    color: var(--text-secondary);
    font-size: 0.95rem;
}

[data-theme='dark'] .step-card:hover {
    box-shadow: 0 12px 40px rgba(59, 130, 246, 0.1);
}

@media (max-width: 768px) {
    .bioinformatics-page .header h1 {
        font-size: 1.75rem;
    }

    .step-card {
        flex-direction: column;
        gap: 1rem;
    }

    .step-number {
        width: 40px;
        height: 40px;
        font-size: 1.1rem;
    }

    .method-chooser {
        flex-direction: column;
    }

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