/* ========== CSS Variables ========== */
:root {
    --primary: #2d6a4f;
    --primary-light: #40916c;
    --primary-dark: #1b4332;
    --secondary: #6b8e6b;
    --success: #38a169;
    --warning: #d69e2e;
    --danger: #e53e3e;
    --bg-body: #f1f8e9;
    --bg-card: #ffffff;
    --bg-sidebar: #1b4332;
    --bg-sidebar-hover: #2d6a4f;
    --text-main: #2d3748;
    --text-muted: #5a6c5a;
    --text-light: #8faa8f;
    --border-color: #d9e8d0;
    --shadow: 0 1px 3px rgba(0,0,0,0.08), 0 1px 2px rgba(0,0,0,0.05);
    --shadow-lg: 0 10px 15px -3px rgba(0,0,0,0.08), 0 4px 6px -2px rgba(0,0,0,0.04);
    --radius: 8px;
    --radius-sm: 4px;
    --sidebar-width: 260px;
    --sidebar-collapsed: 60px;
    --transition: all 0.3s ease;

    /* Alignment colors */
    --match-bg: #38a169;
    --match-text: #fff;
    --mismatch-bg: #e53e3e;
    --mismatch-text: #fff;
    --gap-bg: #a0aec0;
    --gap-text: #fff;
    --base-a: #48bb78;
    --base-t: #f56565;
    --base-c: #4299e1;
    --base-g: #ed8936;
}

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

html {
    font-size: 16px;
    -webkit-font-smoothing: antialiased;
    -moz-osx-font-smoothing: grayscale;
}

body {
    font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, "Noto Sans SC", "PingFang SC", "Microsoft YaHei", sans-serif;
    background: var(--bg-body);
    color: var(--text-main);
    line-height: 1.6;
    min-height: 100vh;
}

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

/* ========== Sidebar ========== */
.sidebar {
    width: var(--sidebar-width);
    background: var(--bg-sidebar);
    color: #fff;
    display: flex;
    flex-direction: column;
    position: fixed;
    left: 0;
    top: 0;
    bottom: 0;
    z-index: 100;
    transition: var(--transition);
    overflow-y: auto;
    overflow-x: hidden;
}

.sidebar.collapsed {
    width: var(--sidebar-collapsed);
}

.sidebar-header {
    padding: 24px 20px 16px;
    border-bottom: 1px solid rgba(255,255,255,0.1);
}

.sidebar-header h1 {
    font-size: 1.15rem;
    font-weight: 700;
    letter-spacing: 0.5px;
    white-space: nowrap;
}

.sidebar-header .subtitle {
    font-size: 0.75rem;
    color: var(--text-light);
    margin-top: 4px;
    white-space: nowrap;
}

.sidebar.collapsed .sidebar-header h1,
.sidebar.collapsed .sidebar-header .subtitle,
.sidebar.collapsed .nav-text,
.sidebar.collapsed .sidebar-footer p {
    opacity: 0;
    pointer-events: none;
}

.sidebar-nav {
    flex: 1;
    padding: 12px 0;
}

.nav-item {
    display: flex;
    align-items: center;
    width: 100%;
    padding: 12px 20px;
    background: none;
    border: none;
    color: rgba(255,255,255,0.8);
    font-size: 0.9rem;
    cursor: pointer;
    transition: var(--transition);
    text-align: left;
    position: relative;
}

.nav-item:hover {
    background: var(--bg-sidebar-hover);
    color: #fff;
}

.nav-item.active {
    background: var(--primary-light);
    color: #fff;
    border-left: 3px solid #fff;
}

.nav-icon {
    font-size: 1.1rem;
    width: 24px;
    text-align: center;
    flex-shrink: 0;
}

.nav-text {
    margin-left: 12px;
    white-space: nowrap;
    transition: opacity 0.2s;
}

.sidebar-footer {
    padding: 16px 20px;
    border-top: 1px solid rgba(255,255,255,0.1);
    font-size: 0.75rem;
    color: var(--text-light);
}

.sidebar-toggle {
    position: absolute;
    top: 12px;
    right: -14px;
    width: 28px;
    height: 28px;
    background: var(--primary-light);
    border: 2px solid #fff;
    border-radius: 50%;
    color: #fff;
    font-size: 0.85rem;
    cursor: pointer;
    display: flex;
    align-items: center;
    justify-content: center;
    z-index: 101;
    transition: var(--transition);
}

.sidebar-toggle:hover {
    background: var(--primary);
    transform: scale(1.1);
}

.sidebar.collapsed .sidebar-toggle {
    transform: rotate(180deg);
}

/* ========== Main Content ========== */
.main-content {
    flex: 1;
    margin-left: var(--sidebar-width);
    padding: 24px 32px 48px;
    max-width: calc(100% - var(--sidebar-width));
    transition: var(--transition);
    min-height: 100vh;
}

.sidebar.collapsed + .main-content {
    margin-left: var(--sidebar-collapsed);
    max-width: calc(100% - var(--sidebar-collapsed));
}

/* ========== Module ========== */
.module {
    display: none;
    animation: fadeIn 0.3s ease;
}

.module.active {
    display: block;
}

@keyframes fadeIn {
    from { opacity: 0; transform: translateY(8px); }
    to { opacity: 1; transform: translateY(0); }
}

.module-header {
    margin-bottom: 24px;
}

.module-header h2 {
    font-size: 1.5rem;
    font-weight: 700;
    color: var(--primary-dark);
    margin-bottom: 6px;
}

.module-desc {
    color: var(--text-muted);
    font-size: 0.95rem;
}

/* ========== Card ========== */
.card {
    background: var(--bg-card);
    border-radius: var(--radius);
    box-shadow: var(--shadow);
    padding: 24px;
    margin-bottom: 20px;
}

.card h3 {
    font-size: 1.1rem;
    font-weight: 600;
    color: var(--primary-dark);
    margin-bottom: 16px;
}

.card-header-flex {
    display: flex;
    justify-content: space-between;
    align-items: center;
    margin-bottom: 16px;
}

.card-header-flex h3 {
    margin-bottom: 0;
}

/* ========== Tags ========== */
.tag {
    display: inline-block;
    padding: 2px 10px;
    border-radius: 12px;
    font-size: 0.75rem;
    font-weight: 600;
    background: var(--bg-body);
    color: var(--text-muted);
    border: 1px solid var(--border-color);
}

.tag-primary {
    background: var(--primary);
    color: #fff;
    border-color: var(--primary);
}

/* ========== Form ========== */
.form-group {
    margin-bottom: 16px;
}

.form-group label {
    display: block;
    font-size: 0.85rem;
    font-weight: 600;
    color: var(--text-main);
    margin-bottom: 6px;
}

.form-row {
    display: flex;
    gap: 16px;
    flex-wrap: wrap;
}

.form-row .form-group {
    flex: 1;
    min-width: 140px;
}

input[type="text"],
input[type="number"],
select,
textarea {
    width: 100%;
    padding: 10px 12px;
    border: 1px solid var(--border-color);
    border-radius: var(--radius-sm);
    font-size: 0.9rem;
    font-family: inherit;
    color: var(--text-main);
    background: var(--bg-card);
    transition: var(--transition);
}

input:focus,
select:focus,
textarea:focus {
    outline: none;
    border-color: var(--primary-light);
    box-shadow: 0 0 0 3px rgba(45, 106, 79, 0.15);
}

textarea {
    resize: vertical;
    font-family: "SF Mono", Monaco, "Cascadia Code", "Roboto Mono", Consolas, "Courier New", monospace;
    font-size: 0.85rem;
    line-height: 1.5;
}

select {
    cursor: pointer;
    appearance: none;
    background-image: url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' width='12' height='12' viewBox='0 0 12 12'%3E%3Cpath fill='%23718096' d='M6 8L1 3h10z'/%3E%3C/svg%3E");
    background-repeat: no-repeat;
    background-position: right 12px center;
    padding-right: 32px;
}

/* ========== Buttons ========== */
.btn-group {
    display: flex;
    gap: 10px;
    flex-wrap: wrap;
    margin-top: 8px;
}

.btn {
    display: inline-flex;
    align-items: center;
    justify-content: center;
    gap: 6px;
    padding: 10px 20px;
    border: none;
    border-radius: var(--radius-sm);
    font-size: 0.9rem;
    font-weight: 600;
    font-family: inherit;
    cursor: pointer;
    text-decoration: none;
    transition: var(--transition);
    white-space: nowrap;
}

.btn-primary {
    background: var(--primary);
    color: #fff;
}

.btn-primary:hover {
    background: var(--primary-dark);
}

.btn-accent {
    background: linear-gradient(135deg, #e53e3e 0%, #c53030 100%);
    color: #fff;
    box-shadow: 0 4px 6px rgba(229, 62, 62, 0.25);
}

.btn-accent:hover {
    background: linear-gradient(135deg, #c53030 0%, #9b2c2c 100%);
    transform: translateY(-1px);
    box-shadow: 0 6px 12px rgba(229, 62, 62, 0.3);
}

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

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

.btn-danger {
    background: #fff;
    color: var(--danger);
    border: 1px solid var(--danger);
}

.btn-danger:hover {
    background: var(--danger);
    color: #fff;
}

.btn-sm {
    padding: 6px 14px;
    font-size: 0.8rem;
}

.btn-large {
    width: 100%;
    padding: 14px;
    font-size: 1rem;
}

/* ========== Sequence Stats ========== */
.sequence-stats {
    display: flex;
    gap: 20px;
    margin-top: 8px;
    font-size: 0.85rem;
    color: var(--text-muted);
}

.sequence-stats strong {
    color: var(--primary);
}

.sequence-warning {
    margin-top: 8px;
    padding: 8px 12px;
    background: #fff5f5;
    border-left: 3px solid var(--danger);
    border-radius: var(--radius-sm);
    font-size: 0.8rem;
    color: var(--danger);
}

/* ========== Query Sequence List ========== */
.query-item {
    background: var(--bg-body);
    border-radius: var(--radius-sm);
    padding: 16px;
    margin-bottom: 12px;
    border: 1px solid var(--border-color);
}

.query-item-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    margin-bottom: 10px;
}

.query-item-header label {
    font-weight: 600;
    font-size: 0.9rem;
    color: var(--primary-dark);
}

.query-name {
    width: 100%;
    padding: 8px 10px;
    border: 1px solid var(--border-color);
    border-radius: var(--radius-sm);
    font-size: 0.9rem;
    font-family: inherit;
}

.query-seq {
    width: 100%;
    padding: 8px 10px;
    border: 1px solid var(--border-color);
    border-radius: var(--radius-sm);
    font-size: 0.85rem;
    font-family: "SF Mono", Monaco, "Cascadia Code", "Roboto Mono", Consolas, "Courier New", monospace;
    resize: vertical;
}

.query-item .btn-sm {
    padding: 4px 10px;
    font-size: 0.75rem;
}

/* ========== Parameter Description ========== */
.param-desc {
    font-size: 0.8rem;
    color: var(--text-muted);
    margin-top: 6px;
    line-height: 1.5;
}

/* ========== Alignment Visualization ========== */
.alignment-container {
    overflow-x: auto;
    padding: 16px;
    background: var(--bg-body);
    border-radius: var(--radius-sm);
    font-family: "SF Mono", Monaco, "Cascadia Code", "Roboto Mono", Consolas, "Courier New", monospace;
    font-size: 14px;
    line-height: 1.8;
    max-height: 600px;
    overflow-y: auto;
}

.alignment-block {
    margin-bottom: 20px;
    min-width: fit-content;
}

.alignment-header {
    font-weight: 700;
    color: var(--primary-dark);
    margin-bottom: 4px;
    font-size: 0.85rem;
}

.alignment-row {
    display: flex;
    align-items: center;
    white-space: nowrap;
    margin-bottom: 2px;
}

.alignment-label {
    width: 160px;
    flex-shrink: 0;
    text-align: right;
    padding-right: 12px;
    font-size: 0.8rem;
    color: var(--text-muted);
    overflow: hidden;
    text-overflow: ellipsis;
}

.alignment-pos {
    width: 60px;
    flex-shrink: 0;
    text-align: right;
    padding-right: 8px;
    font-size: 0.75rem;
    color: var(--text-light);
}

.alignment-seq {
    display: flex;
    gap: 1px;
}

.alignment-seq .base {
    width: 18px;
    height: 24px;
    display: flex;
    align-items: center;
    justify-content: center;
    border-radius: 2px;
    font-size: 13px;
    font-weight: 600;
}

.alignment-seq .base.match {
    background: var(--match-bg);
    color: var(--match-text);
}

.alignment-seq .base.mismatch {
    background: var(--mismatch-bg);
    color: var(--mismatch-text);
}

.alignment-seq .base.gap {
    background: var(--gap-bg);
    color: var(--gap-text);
}

.alignment-seq .base.base-a {
    color: var(--base-a);
}
.alignment-seq .base.base-t {
    color: var(--base-t);
}
.alignment-seq .base.base-c {
    color: var(--base-c);
}
.alignment-seq .base.base-g {
    color: var(--base-g);
}

.alignment-seq .base.match.base-a,
.alignment-seq .base.match.base-t,
.alignment-seq .base.match.base-c,
.alignment-seq .base.match.base-g {
    color: var(--match-text);
}

.alignment-consensus {
    display: flex;
    gap: 1px;
    margin-left: 160px;
    padding-left: 68px;
}

.alignment-consensus .cons-char {
    width: 18px;
    height: 20px;
    display: flex;
    align-items: center;
    justify-content: center;
    font-size: 12px;
    color: var(--text-muted);
}

/* ========== Legend ========== */
.legend-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
    gap: 12px;
    margin-top: 12px;
}

.legend-item {
    display: flex;
    align-items: center;
    gap: 10px;
    font-size: 0.85rem;
}

.legend-box {
    width: 28px;
    height: 28px;
    display: flex;
    align-items: center;
    justify-content: center;
    border-radius: 4px;
    font-weight: 700;
    font-size: 14px;
    font-family: monospace;
}

.legend-box.match {
    background: var(--match-bg);
    color: var(--match-text);
}

.legend-box.mismatch {
    background: var(--mismatch-bg);
    color: var(--mismatch-text);
}

.legend-box.gap {
    background: var(--gap-bg);
    color: var(--gap-text);
}

.legend-box.base-a {
    background: #e6fffa;
    color: var(--base-a);
    border: 1px solid var(--base-a);
}

.legend-box.base-t {
    background: #fff5f5;
    color: var(--base-t);
    border: 1px solid var(--base-t);
}

.legend-box.base-c {
    background: #ebf8ff;
    color: var(--base-c);
    border: 1px solid var(--base-c);
}

.legend-box.base-g {
    background: #fffaf0;
    color: var(--base-g);
    border: 1px solid var(--base-g);
}

/* ========== View Toggle ========== */
.view-toggle-group {
    display: flex;
    gap: 4px;
    background: var(--bg-body);
    padding: 4px;
    border-radius: var(--radius-sm);
}

.view-toggle-group .btn {
    padding: 6px 16px;
    font-size: 0.8rem;
    background: transparent;
    border: none;
    color: var(--text-muted);
}

.view-toggle-group .btn.active {
    background: var(--bg-card);
    color: var(--primary-dark);
    box-shadow: var(--shadow);
    font-weight: 600;
}

/* ========== Export Cards ========== */
.export-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(220px, 1fr));
    gap: 16px;
    margin-top: 16px;
}

.export-grid.compact {
    grid-template-columns: repeat(auto-fit, minmax(280px, 1fr));
    max-width: 600px;
}

.export-card {
    background: var(--bg-body);
    border-radius: var(--radius-sm);
    padding: 20px;
    text-align: center;
    border: 1px solid var(--border-color);
    transition: var(--transition);
}

.export-card:hover {
    border-color: var(--primary-light);
    box-shadow: var(--shadow);
}

.export-icon {
    font-size: 2rem;
    margin-bottom: 10px;
}

.export-card h4 {
    font-size: 0.95rem;
    font-weight: 600;
    margin-bottom: 6px;
}

.export-card p {
    font-size: 0.8rem;
    color: var(--text-muted);
    margin-bottom: 12px;
}

/* ========== Result Grid ========== */
.result-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(180px, 1fr));
    gap: 12px;
}

.result-item {
    background: var(--bg-body);
    padding: 14px;
    border-radius: var(--radius-sm);
    border-left: 3px solid var(--primary-light);
}

.result-item.good {
    border-left-color: var(--success);
}

.result-item.warn {
    border-left-color: var(--warning);
}

.result-item.bad {
    border-left-color: var(--danger);
}

.result-label {
    font-size: 0.75rem;
    color: var(--text-muted);
    text-transform: uppercase;
    letter-spacing: 0.5px;
    margin-bottom: 4px;
}

.result-value {
    font-size: 1.1rem;
    font-weight: 700;
    color: var(--text-main);
}

.result-detail {
    font-size: 0.75rem;
    color: var(--text-muted);
    margin-top: 4px;
}

/* ========== Feature Grid ========== */
.feature-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(220px, 1fr));
    gap: 16px;
    margin-top: 12px;
}

.feature-card {
    background: var(--bg-body);
    border-radius: var(--radius-sm);
    padding: 20px;
    text-align: center;
}

.feature-icon {
    font-size: 2rem;
    margin-bottom: 10px;
}

.feature-card h4 {
    font-size: 0.95rem;
    font-weight: 600;
    margin-bottom: 6px;
}

.feature-card p {
    font-size: 0.8rem;
    color: var(--text-muted);
}

/* ========== Steps ========== */
.steps {
    display: flex;
    flex-direction: column;
    gap: 16px;
}

.step {
    display: flex;
    gap: 14px;
    align-items: flex-start;
}

.step-num {
    width: 28px;
    height: 28px;
    background: var(--primary);
    color: #fff;
    border-radius: 50%;
    display: flex;
    align-items: center;
    justify-content: center;
    font-size: 0.85rem;
    font-weight: 700;
    flex-shrink: 0;
}

.step-content {
    flex: 1;
}

.step-content strong {
    display: block;
    margin-bottom: 4px;
    font-size: 0.9rem;
}

.step-content p {
    font-size: 0.85rem;
    color: var(--text-muted);
}

/* ========== Tips ========== */
.tip-box {
    background: #e8f5e9;
    border-left: 4px solid var(--primary-light);
    padding: 12px 16px;
    border-radius: var(--radius-sm);
    font-size: 0.85rem;
    color: var(--primary-dark);
    margin-top: 12px;
}

/* ========== Status ========== */
.status-good { color: var(--success); }
.status-warn { color: var(--warning); }
.status-bad { color: var(--danger); }

/* ========== Empty State ========== */
.empty-state {
    text-align: center;
    color: var(--text-muted);
    padding: 32px;
}

/* ========== Tables ========== */
.table-wrapper {
    overflow-x: auto;
    border-radius: var(--radius-sm);
    border: 1px solid var(--border-color);
}

.data-table {
    width: 100%;
    border-collapse: collapse;
    font-size: 0.85rem;
    min-width: 600px;
}

.data-table th,
.data-table td {
    padding: 10px 12px;
    text-align: left;
    border-bottom: 1px solid var(--border-color);
}

.data-table th {
    background: var(--bg-body);
    font-weight: 600;
    color: var(--text-main);
    white-space: nowrap;
}

.data-table tbody tr:hover {
    background: #f7fafc;
}

/* ========== Code ========== */
code {
    background: var(--bg-body);
    padding: 2px 6px;
    border-radius: 3px;
    font-family: "SF Mono", Monaco, "Cascadia Code", "Roboto Mono", Consolas, "Courier New", monospace;
    font-size: 0.85em;
    color: var(--primary-dark);
}

/* ========== Overview Chart ========== */
.overview-container {
    margin-top: 12px;
}

.overview-row {
    display: flex;
    align-items: center;
    margin-bottom: 8px;
    height: 20px;
}

.overview-label {
    width: 120px;
    flex-shrink: 0;
    font-size: 0.8rem;
    color: var(--text-muted);
    text-align: right;
    padding-right: 12px;
    white-space: nowrap;
    overflow: hidden;
    text-overflow: ellipsis;
}

.overview-track {
    flex: 1;
    position: relative;
    height: 16px;
    background: #f0f0f0;
    border-radius: 2px;
}

.overview-target-bar {
    position: absolute;
    left: 0;
    right: 0;
    top: 50%;
    transform: translateY(-50%);
    height: 4px;
    background: #333;
    border-radius: 2px;
}

.overview-match-bar {
    position: absolute;
    top: 2px;
    height: 12px;
    border-radius: 2px;
    opacity: 0.85;
    cursor: pointer;
    transition: opacity 0.2s;
}

.overview-match-bar:hover {
    opacity: 1;
    box-shadow: 0 0 0 2px rgba(0,0,0,0.1);
}

.overview-mismatch {
    position: absolute;
    top: 0;
    width: 2px;
    height: 16px;
    background: var(--danger);
    border-radius: 1px;
    cursor: pointer;
}

.overview-legend {
    display: flex;
    gap: 20px;
    margin-top: 12px;
    font-size: 0.8rem;
    color: var(--text-muted);
    flex-wrap: wrap;
}

.overview-legend > span {
    display: flex;
    align-items: center;
    gap: 6px;
}

.legend-dot {
    width: 12px;
    height: 12px;
    border-radius: 2px;
    display: inline-block;
    flex-shrink: 0;
}

/* ========== Responsive ========== */
@media (max-width: 768px) {
    .sidebar {
        width: var(--sidebar-collapsed);
    }

    .sidebar-header h1,
    .sidebar-header .subtitle,
    .nav-text,
    .sidebar-footer p {
        opacity: 0;
        pointer-events: none;
    }

    .main-content {
        margin-left: var(--sidebar-collapsed);
        max-width: calc(100% - var(--sidebar-collapsed));
        padding: 16px;
    }

    .sidebar-toggle {
        display: none;
    }

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

    .form-row {
        flex-direction: column;
        gap: 0;
    }

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

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

    .alignment-label {
        width: 80px;
        font-size: 0.7rem;
    }

    .alignment-pos {
        width: 40px;
        font-size: 0.7rem;
    }

    .alignment-consensus {
        margin-left: 80px;
        padding-left: 48px;
    }
}

@media (max-width: 480px) {
    .btn-group {
        flex-direction: column;
    }

    .btn {
        width: 100%;
    }

    .card {
        padding: 16px;
    }

    .main-content {
        padding: 12px;
    }
}