/* ============================================================================
   EpiFlow D3 — Stylesheet
   Serrano Lab | Boston University
   ============================================================================ */

:root {
  --primary: #0084b8;
  --primary-dark: #006a94;
  --accent: #bd5e00;
  --accent-light: #d4853d;
  --green: #7a923d;
  --plum: #694657;
  --teal: #5dae9d;
  --bg: #f5f7fa;
  --surface: #ffffff;
  --surface-alt: #f8f9fa;
  --border: #e2e8f0;
  --text: #1a202c;
  --text-secondary: #64748b;
  --text-muted: #94a3b8;
  --danger: #dc2626;
  --sidebar-width: 280px;
  --topbar-height: 48px;
  --radius: 6px;
  --shadow: 0 1px 3px rgba(0,0,0,0.08);
  --shadow-md: 0 4px 12px rgba(0,0,0,0.1);
}

* { margin: 0; padding: 0; box-sizing: border-box; }

body {
  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
  background: var(--bg);
  color: var(--text);
  font-size: 14px;
  line-height: 1.5;
  overflow: hidden;
  height: 100vh;
}

/* ---- Top bar ---- */
.top-bar {
  height: var(--topbar-height);
  background: linear-gradient(135deg, #1e3a5f 0%, #2d5a3f 100%);
  color: white;
  display: flex;
  align-items: center;
  justify-content: space-between;
  padding: 0 20px;
  z-index: 100;
}
.top-bar-left { display: flex; align-items: center; gap: 10px; }
.logo-text { font-size: 18px; font-weight: 700; letter-spacing: -0.5px; }
.version-badge {
  font-size: 10px;
  background: rgba(255,255,255,0.2);
  padding: 2px 8px;
  border-radius: 10px;
}
.top-bar-center { display: flex; align-items: center; gap: 8px; font-size: 13px; opacity: 0.9; }
.status-dot {
  width: 8px; height: 8px; border-radius: 50%;
  background: #4ade80;
}
.status-dot.inactive { background: #94a3b8; }
.top-bar-right { font-size: 12px; opacity: 0.7; }
.lab-name { font-style: italic; }

/* ---- Layout ---- */
.app-layout {
  display: flex;
  height: calc(100vh - var(--topbar-height));
}

/* ---- Sidebar ---- */
.sidebar {
  width: var(--sidebar-width);
  min-width: var(--sidebar-width);
  background: var(--surface);
  border-right: 1px solid var(--border);
  overflow-y: auto;
  padding: 16px;
}
.sidebar-section { margin-bottom: 20px; }
.sidebar-section h3 {
  font-size: 13px;
  font-weight: 600;
  text-transform: uppercase;
  letter-spacing: 0.5px;
  color: var(--text-secondary);
  margin-bottom: 12px;
  display: flex;
  align-items: center;
  gap: 8px;
}
.sidebar-section h3 i { color: var(--primary); }

/* ---- Upload ---- */
.upload-area {
  border: 2px dashed var(--border);
  border-radius: var(--radius);
  padding: 16px;
  text-align: center;
  transition: border-color 0.2s;
}
.upload-area:hover, .upload-area.dragover {
  border-color: var(--primary);
  background: rgba(0, 132, 184, 0.04);
}
.upload-hint { font-size: 11px; color: var(--text-muted); margin-top: 8px; }
.data-summary {
  padding: 12px;
  background: var(--surface-alt);
  border-radius: var(--radius);
  font-size: 12px;
  margin-top: 12px;
}
.data-summary .stat-label { color: var(--text-secondary); }
.data-summary .stat-value { font-weight: 600; color: var(--text); }

/* ---- Filter controls ---- */
.filter-group { margin-bottom: 14px; }
.filter-group label {
  display: block;
  font-size: 12px;
  font-weight: 600;
  color: var(--text-secondary);
  margin-bottom: 6px;
}
.checkbox-group {
  max-height: 120px;
  overflow-y: auto;
  border: 1px solid var(--border);
  border-radius: var(--radius);
  padding: 6px;
}
.checkbox-group label {
  display: flex;
  align-items: center;
  gap: 6px;
  padding: 3px 4px;
  border-radius: 3px;
  cursor: pointer;
  font-weight: 400;
  font-size: 12px;
}
.checkbox-group label:hover { background: var(--surface-alt); }
.checkbox-group input[type="checkbox"] { accent-color: var(--primary); }
.filter-summary {
  font-size: 11px;
  padding: 8px;
  background: rgba(0, 132, 184, 0.06);
  border-radius: var(--radius);
  border-left: 3px solid var(--primary);
}

/* ---- Buttons ---- */
.btn {
  display: inline-flex;
  align-items: center;
  gap: 6px;
  padding: 8px 16px;
  border: none;
  border-radius: var(--radius);
  font-size: 13px;
  font-weight: 500;
  cursor: pointer;
  transition: all 0.15s;
}
.btn:hover { transform: translateY(-1px); box-shadow: var(--shadow); }
.btn:active { transform: translateY(0); }
.btn-primary { background: var(--primary); color: white; }
.btn-primary:hover { background: var(--primary-dark); }
.btn-accent { background: var(--accent); color: white; }
.btn-accent:hover { background: #a35200; }
.btn-outline { background: transparent; border: 1px solid var(--border); color: var(--text-secondary); }
.btn-outline:hover { border-color: var(--primary); color: var(--primary); }
.btn-sm { padding: 5px 10px; font-size: 12px; }
.btn-block { width: 100%; justify-content: center; margin-top: 8px; }
.btn-danger { background: var(--danger); color: white; }

/* ---- Form inputs ---- */
.select-input {
  padding: 6px 10px;
  border: 1px solid var(--border);
  border-radius: var(--radius);
  font-size: 13px;
  background: white;
  color: var(--text);
  min-width: 140px;
}
.select-input:focus { outline: none; border-color: var(--primary); }
.checkbox-inline {
  display: inline-flex;
  align-items: center;
  gap: 4px;
  font-size: 12px;
  color: var(--text-secondary);
}

/* ---- Main content ---- */
.main-content {
  flex: 1;
  display: flex;
  flex-direction: column;
  overflow: hidden;
  position: relative;
}

/* ---- Tab navigation ---- */
.tab-nav {
  display: flex;
  gap: 2px;
  padding: 8px 16px 0;
  background: var(--surface);
  border-bottom: 1px solid var(--border);
  overflow-x: auto;
}
.tab-btn {
  padding: 8px 14px;
  border: none;
  background: transparent;
  color: var(--text-secondary);
  font-size: 13px;
  font-weight: 500;
  cursor: pointer;
  border-bottom: 2px solid transparent;
  white-space: nowrap;
  display: flex;
  align-items: center;
  gap: 6px;
  transition: all 0.15s;
}
.tab-btn:hover { color: var(--primary); }
.tab-btn.active {
  color: var(--primary);
  border-bottom-color: var(--primary);
}
.tab-btn i { font-size: 12px; }

/* ---- Tab panels ---- */
.tab-panels {
  flex: 1;
  overflow-y: auto;
  padding: 16px;
}
.tab-panel { display: none; }
.tab-panel.active { display: block; }

.panel-header {
  display: flex;
  align-items: center;
  justify-content: space-between;
  margin-bottom: 16px;
  flex-wrap: wrap;
  gap: 10px;
}
.panel-header h2 { font-size: 18px; font-weight: 600; }
.panel-controls { display: flex; align-items: center; gap: 8px; flex-wrap: wrap; }
.help-text { font-size: 12px; color: var(--text-muted); font-style: italic; }

/* ---- Chart containers ---- */
.chart-container {
  background: var(--surface);
  border: 1px solid var(--border);
  border-radius: var(--radius);
  padding: 16px;
  min-height: 400px;
  position: relative;
  margin-bottom: 16px;
}
.chart-container.half { min-height: 250px; }
.chart-container svg {
  width: 100%;
  display: block;
}

/* ---- Statistics results table ---- */
.stats-results {
  margin-bottom: 16px;
}
.stats-table {
  width: 100%;
  border-collapse: collapse;
  font-size: 12px;
}
.stats-table th {
  background: var(--surface-alt);
  padding: 8px 12px;
  text-align: left;
  font-weight: 600;
  color: var(--text-secondary);
  border-bottom: 2px solid var(--border);
  position: sticky;
  top: 0;
}
.stats-table td {
  padding: 6px 12px;
  border-bottom: 1px solid var(--border);
}
.stats-table tr:hover { background: var(--surface-alt); }
.sig { color: var(--danger); font-weight: 600; }
.ns { color: var(--text-muted); }

/* ---- Loading overlay ---- */
.loading-overlay {
  position: absolute;
  inset: 0;
  background: rgba(255,255,255,0.92);
  display: flex;
  flex-direction: column;
  align-items: center;
  justify-content: center;
  z-index: 50;
  backdrop-filter: blur(2px);
}
.spinner {
  width: 48px; height: 48px;
  border: 4px solid var(--border);
  border-top-color: var(--primary);
  border-radius: 50%;
  animation: spin 0.7s linear infinite;
}
@keyframes spin { to { transform: rotate(360deg); } }
.loading-overlay p { margin-top: 14px; color: var(--text-secondary); font-size: 14px; font-weight: 500; }

/* ---- Welcome card ---- */
.welcome-card {
  max-width: 600px;
  margin: 80px auto;
  text-align: center;
}
.welcome-card h1 { font-size: 36px; font-weight: 700; margin-bottom: 8px; }
.welcome-card .accent { color: var(--primary); }
.welcome-card p { color: var(--text-secondary); margin-bottom: 4px; }
.welcome-card .subtitle { font-size: 15px; margin-bottom: 32px; }
.feature-grid {
  display: grid;
  grid-template-columns: repeat(3, 1fr);
  gap: 12px;
}
.feature {
  padding: 16px 12px;
  background: var(--surface);
  border: 1px solid var(--border);
  border-radius: var(--radius);
  font-size: 13px;
  color: var(--text-secondary);
  display: flex;
  align-items: center;
  gap: 8px;
}
.feature i { color: var(--primary); font-size: 16px; }

/* ---- Tooltip ---- */
.d3-tooltip {
  position: absolute;
  pointer-events: none;
  background: rgba(15, 23, 42, 0.92);
  color: white;
  padding: 8px 12px;
  border-radius: 6px;
  font-size: 12px;
  line-height: 1.4;
  max-width: 250px;
  z-index: 200;
  box-shadow: 0 4px 12px rgba(0,0,0,0.3);
}

/* ---- Utilities ---- */
.hidden { display: none !important; }
.text-center { text-align: center; }
.mt-8 { margin-top: 8px; }
.mb-8 { margin-bottom: 8px; }

/* ---- D3 chart styling ---- */
.axis text { font-size: 11px; fill: var(--text-secondary); }
.axis line, .axis path { stroke: var(--border); }
.grid line { stroke: var(--border); stroke-opacity: 0.5; stroke-dasharray: 2,2; }
.chart-title { font-size: 14px; font-weight: 600; fill: var(--text); }
.chart-subtitle { font-size: 12px; fill: var(--text-secondary); }

/* ---- Responsive ---- */
@media (max-width: 768px) {
  .sidebar { width: 100%; min-width: unset; border-right: none; border-bottom: 1px solid var(--border); }
  .app-layout { flex-direction: column; }
  .feature-grid { grid-template-columns: repeat(2, 1fr); }
}

/* ============================================================================
   Phase 1 additions
   ============================================================================ */

/* ---- Help panels ---- */
.help-panel {
  background: rgba(0, 132, 184, 0.05);
  border-left: 3px solid var(--primary);
  border-radius: 0 var(--radius) var(--radius) 0;
  padding: 10px 14px;
  margin-bottom: 16px;
  font-size: 12px;
  color: var(--text-secondary);
  line-height: 1.5;
}
.help-panel i { color: var(--primary); margin-right: 4px; }
.help-panel strong { color: var(--text); }

/* ---- Phase 2 placeholder messages ---- */
.placeholder-message {
  text-align: center;
  padding: 60px 40px;
  color: var(--text-muted);
}
.placeholder-message i {
  font-size: 40px;
  display: block;
  margin-bottom: 16px;
  color: var(--border);
}
.placeholder-message h3 {
  color: var(--text-secondary);
  margin-bottom: 8px;
  font-size: 16px;
}
.placeholder-message p {
  max-width: 400px;
  margin: 0 auto;
  font-size: 13px;
}

/* ---- Coming soon badge ---- */
.badge-coming {
  font-size: 10px;
  background: var(--accent);
  color: white;
  padding: 2px 8px;
  border-radius: 10px;
  font-weight: 600;
  text-transform: uppercase;
  letter-spacing: 0.5px;
}

/* ---- Option warning text ---- */
.option-warning {
  font-size: 11px;
  color: var(--accent);
  margin-top: 4px;
  padding: 6px 8px;
  background: rgba(189, 94, 0, 0.06);
  border-radius: var(--radius);
  line-height: 1.4;
}

/* ---- Improved tab nav scrolling for many tabs ---- */
.tab-nav {
  flex-wrap: nowrap;
  -webkit-overflow-scrolling: touch;
  scrollbar-width: thin;
}
.tab-nav::-webkit-scrollbar {
  height: 3px;
}
.tab-nav::-webkit-scrollbar-thumb {
  background: var(--border);
  border-radius: 2px;
}

/* ---- Notification toast (for error recovery) ---- */
.toast-notification {
  position: fixed;
  bottom: 20px;
  right: 20px;
  background: rgba(15, 23, 42, 0.92);
  color: white;
  padding: 12px 20px;
  border-radius: var(--radius);
  font-size: 13px;
  z-index: 300;
  max-width: 400px;
  box-shadow: var(--shadow-md);
  animation: slideIn 0.3s ease;
}
.toast-notification.error {
  border-left: 3px solid var(--danger);
}
.toast-notification.success {
  border-left: 3px solid #4ade80;
}
@keyframes slideIn {
  from { transform: translateX(100%); opacity: 0; }
  to { transform: translateX(0); opacity: 1; }
}

/* ---- Feature selection bar ---- */
.feature-select-bar {
  display: flex;
  flex-wrap: wrap;
  align-items: center;
  gap: 4px;
  padding: 8px 12px;
  background: #f8fafc;
  border: 1px solid #e2e8f0;
  border-radius: 6px;
  margin-bottom: 10px;
}
.inline-checkbox-group {
  display: flex;
  flex-wrap: wrap;
  gap: 6px;
}
.inline-checkbox-group label {
  display: flex;
  align-items: center;
  gap: 3px;
  font-size: 11px;
  padding: 2px 8px;
  background: #fff;
  border: 1px solid #e2e8f0;
  border-radius: 4px;
  cursor: pointer;
  white-space: nowrap;
  transition: all 0.15s;
}
.inline-checkbox-group label:hover {
  border-color: #0084b8;
}
.inline-checkbox-group label:has(input:checked) {
  background: #e0f2fe;
  border-color: #0084b8;
  font-weight: 500;
}
.inline-checkbox-group input[type="checkbox"] {
  width: 12px;
  height: 12px;
  margin: 0;
}

/* ---- Inline message banner ---- */
.inline-message {
  padding: 10px 16px;
  border-radius: 6px;
  font-size: 13px;
  margin-bottom: 10px;
  display: flex;
  align-items: center;
  gap: 8px;
}
.inline-message.error {
  background: #fef2f2;
  border: 1px solid #fecaca;
  color: #991b1b;
}
.inline-message.warning {
  background: #fffbeb;
  border: 1px solid #fde68a;
  color: #92400e;
}
.inline-message.info {
  background: #eff6ff;
  border: 1px solid #bfdbfe;
  color: #1e40af;
}

/* ---- Overview cards ---- */
.overview-cards {
  display: grid;
  grid-template-columns: repeat(auto-fill, minmax(140px, 1fr));
  gap: 12px;
  margin-bottom: 16px;
}
.ov-card {
  background: #fff;
  border: 1px solid #e2e8f0;
  border-radius: 8px;
  padding: 16px 12px;
  text-align: center;
  transition: box-shadow 0.15s;
}
.ov-card:hover { box-shadow: 0 2px 8px rgba(0,0,0,0.08); }
.ov-card-value {
  font-size: 24px;
  font-weight: 700;
  color: #0084b8;
  line-height: 1.2;
}
.ov-card-label {
  font-size: 11px;
  color: #64748b;
  margin-top: 4px;
  text-transform: uppercase;
  letter-spacing: 0.03em;
}
.overview-section {
  background: #fff;
  border: 1px solid #e2e8f0;
  border-radius: 8px;
  padding: 16px;
}
.overview-section h3 {
  font-size: 13px;
  font-weight: 600;
  color: #334155;
  margin: 0 0 10px 0;
}

/* ---- ML comparison grid ---- */
.ml-comparison-grid {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 16px;
  margin-top: 12px;
}
.ml-panel {
  background: #fff;
  border: 1px solid #e2e8f0;
  border-radius: 8px;
  padding: 14px;
}
.ml-panel-title {
  font-size: 13px;
  font-weight: 600;
  color: #334155;
  margin: 0 0 10px 0;
  padding-bottom: 8px;
  border-bottom: 1px solid #f1f5f9;
}
.ml-panel-title i {
  color: #0084b8;
  margin-right: 4px;
}
.ml-placeholder {
  color: #94a3b8;
  text-align: center;
  padding: 20px;
  font-size: 12px;
  font-style: italic;
}