:root {
    --bg-main: #F8FAFC;
    --bg-card: #FFFFFF;
    --bg-card-hover: #F1F5F9;
    --border-color: #E2E8F0;
    --text-main: #0F172A;
    --text-muted: #64748B;
    --accent-blue: #2563EB;
    --accent-green: #059669;
    --accent-purple: #7C3AED;
    --accent-amber: #D97706;
    --accent-rose: #E11D48;
    --shadow-sm: 0 1px 3px rgba(0, 0, 0, 0.05), 0 1px 2px rgba(0, 0, 0, 0.1);
    --shadow-md: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -1px rgba(0, 0, 0, 0.06);
}

* { box-sizing: border-box; margin: 0; padding: 0; }
body {
    font-family: 'Inter', sans-serif;
    background-color: var(--bg-main);
    color: var(--text-main);
    line-height: 1.5;
    padding: 20px;
    min-height: 100vh;
}

.container {
    max-width: 1500px;
    margin: 0 auto;
    display: flex;
    flex-direction: column;
    gap: 20px;
}

/* --- Header --- */
header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    padding: 16px 24px;
    background: var(--bg-card);
    border: 1px solid var(--border-color);
    border-radius: 12px;
    box-shadow: var(--shadow-sm);
}

.header-title {
    display: flex;
    align-items: center;
    gap: 12px;
}

.header-title .logo {
    font-size: 26px;
    color: var(--text-main);
    font-weight: 800;
}

.header-title p {
    font-size: 13px;
    color: var(--text-muted);
    margin-top: 2px;
}

/* --- Input Cards --- */
.card {
    background: var(--bg-card);
    border: 1px solid var(--border-color);
    border-radius: 12px;
    padding: 20px;
    box-shadow: var(--shadow-sm);
}

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

.card-title {
    font-size: 16px;
    font-weight: 700;
    color: var(--text-main);
    display: flex;
    align-items: center;
    gap: 8px;
}

.input-grid {
    display: grid;
    grid-template-columns: 2fr 1fr;
    gap: 16px;
}

label {
    font-size: 12px;
    font-weight: 600;
    color: var(--text-muted);
    display: block;
    margin-bottom: 6px;
}

textarea {
    width: 100%;
    height: 96px;
    background-color: #F8FAFC;
    border: 1px solid var(--border-color);
    border-radius: 8px;
    color: var(--text-main);
    font-family: 'JetBrains Mono', monospace;
    font-size: 12px;
    padding: 12px;
    resize: vertical;
    transition: border-color 0.2s, box-shadow 0.2s;
}

textarea:focus {
    outline: none;
    border-color: var(--accent-blue);
    box-shadow: 0 0 0 3px rgba(37, 99, 235, 0.15);
    background-color: #FFFFFF;
}

/* --- Buttons & Inputs --- */
.btn {
    background: linear-gradient(135deg, #2563EB, #1D4ED8);
    color: white;
    border: none;
    border-radius: 8px;
    padding: 9px 18px;
    font-weight: 600;
    font-size: 13px;
    cursor: pointer;
    display: inline-flex;
    align-items: center;
    gap: 8px;
    transition: all 0.2s;
    box-shadow: 0 2px 4px rgba(37, 99, 235, 0.2);
}

.btn:hover {
    transform: translateY(-1px);
    box-shadow: 0 4px 8px rgba(37, 99, 235, 0.3);
}

.btn:disabled {
    opacity: 0.45;
    cursor: not-allowed;
}

.btn:disabled:hover {
    transform: none;
    box-shadow: 0 2px 4px rgba(37, 99, 235, 0.2);
}

.btn-secondary {
    background: #F1F5F9;
    color: #334155;
    border: 1px solid var(--border-color);
    box-shadow: none;
}

.btn-secondary:hover {
    background: #E2E8F0;
    color: var(--text-main);
    transform: none;
}

.btn-outline {
    background: transparent;
    color: var(--accent-blue);
    border: 1px solid var(--accent-blue);
    box-shadow: none;
}

.btn-outline:hover {
    background: #EFF6FF;
}

.action-bar {
    display: flex;
    align-items: center;
    gap: 16px;
    margin-top: 16px;
}

#status {
    font-size: 13px;
    color: var(--accent-green);
    font-weight: 500;
}

/* --- Controls Toolbar --- */
.controls-toolbar {
    display: flex;
    flex-wrap: wrap;
    gap: 16px;
    align-items: center;
    background: #F8FAFC;
    padding: 14px 18px;
    border-radius: 8px;
    border: 1px solid var(--border-color);
    margin-bottom: 16px;
}

.control-group {
    display: flex;
    flex-direction: column;
    gap: 4px;
}

.control-group label {
    font-size: 11px;
    text-transform: uppercase;
    letter-spacing: 0.5px;
    color: var(--text-muted);
    margin-bottom: 0;
}

select, input[type="number"], input[type="range"] {
    background: #FFFFFF;
    border: 1px solid var(--border-color);
    color: var(--text-main);
    padding: 6px 10px;
    border-radius: 6px;
    font-size: 13px;
    font-family: inherit;
}

select:focus, input:focus {
    outline: none;
    border-color: var(--accent-blue);
}

/* --- Genome Plot Container --- */
#plot-wrapper {
    background: #FFFFFF;
    border: 1px solid var(--border-color);
    border-radius: 12px;
    padding: 16px;
    position: relative;
    min-height: 400px;
    /* wide plots scroll horizontally in here; tall plots just make the
       page longer (normal window scroll). */
    overflow-x: auto;
    box-shadow: var(--shadow-sm);
}

#plot {
    min-height: 360px;
}

/* --- Footer --- */
.site-footer {
    text-align: center;
    font-size: 12px;
    color: var(--text-muted);
    padding: 4px 0 12px;
}

#plot svg.genomeViewer {
    display: block;
}

/* --- Annotation loading banner --- */
.annot-loading {
    display: flex;
    align-items: center;
    gap: 10px;
    margin-bottom: 12px;
    padding: 10px 14px;
    font-size: 13px;
    font-weight: 500;
    color: var(--accent-blue);
    background: #EFF6FF;
    border: 1px solid #BFDBFE;
    border-radius: 8px;
}

.spinner {
    flex: none;
    width: 15px;
    height: 15px;
    border: 2px solid #BFDBFE;
    border-top-color: var(--accent-blue);
    border-radius: 50%;
    animation: spin 0.7s linear infinite;
}

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

/* --- Threshold precise input, alongside the slider --- */
.threshold-row {
    display: flex;
    align-items: center;
    gap: 8px;
}

.threshold-row input[type="range"] {
    flex: 1 1 auto;
}

.threshold-row input[type="number"] {
    width: 80px;
    flex: none;
}

/* --- Colour legend --- */
.legend {
    display: flex;
    flex-wrap: wrap;
    gap: 6px 14px;
    padding: 12px 18px;
    margin-bottom: 16px;
    background: #F8FAFC;
    border: 1px solid var(--border-color);
    border-radius: 8px;
}

.legend-empty {
    font-size: 12px;
    color: var(--text-muted);
}

.legend-item {
    display: flex;
    align-items: center;
    gap: 6px;
    font-size: 12px;
    color: var(--text-main);
    max-width: 260px;
}

.legend-swatch {
    flex: none;
    width: 11px;
    height: 11px;
    border-radius: 3px;
}

.legend-label {
    overflow: hidden;
    text-overflow: ellipsis;
    white-space: nowrap;
}

/* --- Custom Genome Viewer --- */
#plot svg.genomeViewer { display: block; }
.gv-gene:hover { filter: brightness(1.1); }
.gv-link { transition: fill-opacity 0.1s; }
.gv-link:hover { fill-opacity: 0.9 !important; }
.gv-controls text, .gv-controls { user-select: none; -webkit-user-select: none; }
.gv-btn:hover rect { filter: brightness(0.96); }