/* Sequencing Lab — module-specific styles */

/* Mode bar (reused from mutations) */
.mode-bar {
  display: flex;
  justify-content: space-between;
  align-items: center;
  padding: 0.4rem 0.8rem;
  border-bottom: 1px solid var(--border);
  gap: 0.5rem;
}
.mode-tabs { display: flex; gap: 2px; }
.mode-tab {
  background: none;
  border: 1px solid var(--border);
  color: var(--text-dim);
  padding: 0.25rem 0.6rem;
  border-radius: 5px;
  cursor: pointer;
  font-size: 0.75rem;
  font-family: inherit;
  transition: all 0.12s;
}
.mode-tab:hover { color: var(--text-muted); border-color: var(--accent-dim); }
.mode-tab.active { background: var(--accent-dim); border-color: var(--accent); color: #fff; }

.mode-panel { display: none; }
.mode-panel.active { display: block; }

/* ─── LEARN MODE ─── */

.step-indicator {
  display: flex;
  padding: 0.4rem 0.6rem;
  gap: 2px;
  border-bottom: 1px solid var(--border);
  overflow-x: auto;
  scrollbar-width: thin;
}
.step {
  flex: 0 0 auto;
  display: flex;
  align-items: center;
  gap: 0.2rem;
  padding: 0.2rem 0.35rem;
  border-radius: 4px;
  border: 1px solid var(--border);
  background: var(--bg);
  font-size: 0.62rem;
  color: var(--text-dim);
  cursor: pointer;
  transition: all 0.12s;
  white-space: nowrap;
}
.step:hover { color: var(--text-muted); border-color: var(--accent-dim); }
.step.active { background: var(--accent-dim); border-color: var(--accent); color: #fff; }
.step.completed { color: var(--success); border-color: var(--success); }
.step-num {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  width: 14px; height: 14px;
  border-radius: 50%;
  background: var(--border);
  font-size: 0.55rem;
  font-weight: 700;
}
.step.active .step-num { background: var(--accent); color: #000; }

.learn-step { display: none; padding: 0.6rem 0.8rem; }
.learn-step.active { display: block; }

.step-intro {
  font-size: 0.78rem;
  line-height: 1.45;
  color: var(--text-muted);
  margin-bottom: 0.6rem;
}
.step-intro strong { color: var(--accent); }

.step-nav {
  display: flex;
  justify-content: space-between;
  margin-top: 0.8rem;
  padding-top: 0.6rem;
  border-top: 1px solid var(--border);
}
.next-step-btn, .prev-step-btn {
  background: none;
  border: 1px solid var(--accent-dim);
  color: var(--accent);
  padding: 0.3rem 0.7rem;
  border-radius: 5px;
  cursor: pointer;
  font-size: 0.75rem;
  font-family: inherit;
  text-decoration: none;
  transition: all 0.12s;
}
.next-step-btn:hover, .prev-step-btn:hover { background: var(--accent-dim); color: #fff; }

.ghost-btn {
  background: none;
  border: 1px solid var(--border);
  color: var(--text-muted);
  padding: 0.3rem 0.6rem;
  border-radius: 5px;
  cursor: pointer;
  font-size: 0.75rem;
  font-family: inherit;
  transition: all 0.12s;
}
.ghost-btn:hover { border-color: var(--accent-dim); color: var(--accent); }

.case-select {
  background: var(--bg);
  border: 1px solid var(--border);
  color: var(--text);
  padding: 0.25rem 0.5rem;
  border-radius: 5px;
  font-size: 0.72rem;
  font-family: inherit;
  outline: none;
}

/* ─── BAM VIEWER ─── */

.bam-viewer-container {
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 8px;
  overflow: hidden;
}

.bam-toolbar {
  display: flex;
  align-items: center;
  gap: 0.4rem;
  padding: 0.4rem 0.6rem;
  border-bottom: 1px solid var(--border);
  flex-wrap: wrap;
}

.tech-toggle {
  background: var(--bg-card);
  border: 1px solid var(--border);
  color: var(--text-dim);
  padding: 0.2rem 0.5rem;
  border-radius: 4px;
  font-size: 0.68rem;
  cursor: pointer;
  font-family: inherit;
  transition: all 0.12s;
}
.tech-toggle:hover { border-color: var(--accent-dim); color: var(--accent); }
.tech-toggle.active { background: var(--accent-dim); border-color: var(--accent); color: #fff; }

.bam-option {
  display: flex;
  align-items: center;
  gap: 0.2rem;
  font-size: 0.68rem;
  color: var(--text-dim);
  cursor: pointer;
}
.bam-option input { accent-color: var(--accent); width: 12px; height: 12px; }

.bam-reference {
  padding: 0.2rem 0.6rem;
  font-family: 'Courier New', monospace;
  font-size: 0.65rem;
  letter-spacing: 0.5px;
  color: var(--text-dim);
  background: var(--bg-card);
  border-bottom: 1px solid var(--border);
  overflow-x: auto;
  white-space: nowrap;
}

.bam-coverage-bar {
  height: 24px;
  padding: 0 0.6rem;
  border-top: 1px solid var(--border);
  display: flex;
  align-items: center;
}

.bam-variant-info {
  padding: 0.4rem 0.6rem;
  font-size: 0.72rem;
  color: var(--text-muted);
  border-top: 1px solid var(--border);
  line-height: 1.4;
}
.bam-variant-info strong { color: var(--accent); }
.bam-variant-info .var-tag {
  display: inline-block;
  background: var(--accent-dim);
  color: #fff;
  padding: 0.05rem 0.3rem;
  border-radius: 3px;
  font-size: 0.62rem;
  font-weight: 600;
  margin-right: 0.3rem;
}

/* ─── COVERAGE PROFILE (CNV) ─── */

.coverage-profile {
  position: relative;
  border-top: 1px solid var(--border);
}

.cnv-marker {
  position: absolute;
  top: 0;
  height: 100%;
  background: rgba(239, 68, 68, 0.15);
  border-left: 2px dashed var(--danger);
  border-right: 2px dashed var(--danger);
  pointer-events: none;
}

/* ─── STRATEGY COMPARISON ─── */

.strategy-cards {
  display: grid;
  grid-template-columns: repeat(3, 1fr);
  gap: 0.4rem;
  margin-bottom: 0.6rem;
}
.strategy-card {
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 6px;
  padding: 0.5rem;
  text-align: center;
  cursor: pointer;
  transition: all 0.12s;
}
.strategy-card:hover { border-color: var(--accent-dim); }
.strategy-card.active { border-color: var(--accent); background: var(--accent-dim); }
.sc-icon { font-size: 1.2rem; margin-bottom: 0.2rem; }
.sc-title { font-size: 0.8rem; font-weight: 600; margin-bottom: 0.3rem; }
.sc-stats {
  display: flex;
  flex-direction: column;
  gap: 0.1rem;
  font-size: 0.65rem;
  color: var(--text-dim);
}
.sc-stats small { font-size: 0.55rem; }
.sc-cov { color: var(--accent); font-family: monospace; font-weight: 600; }
.sc-cost { color: var(--warning); }

.strategy-finding {
  padding: 0.5rem;
  font-size: 0.72rem;
  color: var(--text-muted);
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 6px;
  margin-top: 0.4rem;
  line-height: 1.4;
}
.strategy-finding strong { color: var(--accent); }

/* ─── FILTER FUNNEL ─── */

.filter-funnel {
  display: flex;
  flex-direction: column;
  gap: 2px;
  margin-bottom: 0.5rem;
}
.funnel-step {
  display: flex;
  align-items: center;
  gap: 0.4rem;
  padding: 0.3rem 0.6rem;
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 4px;
  font-size: 0.72rem;
  transition: all 0.15s;
}
.funnel-step.active { border-color: var(--accent-dim); }
.funnel-step.result { border-color: var(--success); background: rgba(16, 185, 129, 0.08); }

.funnel-label {
  flex: 1;
  color: var(--text-muted);
}

.funnel-count {
  font-family: monospace;
  font-weight: 700;
  font-size: 0.78rem;
  color: var(--accent);
  min-width: 80px;
  text-align: right;
}
.funnel-step.result .funnel-count { color: var(--success); }

.filt-check { accent-color: var(--accent); width: 14px; height: 14px; }
.filt-slider { width: 60px; accent-color: var(--accent); }

.filter-warning {
  padding: 0.4rem 0.6rem;
  font-size: 0.7rem;
  color: var(--warning);
  background: rgba(245, 158, 11, 0.08);
  border: 1px solid var(--warning);
  border-radius: 5px;
  display: none;
  line-height: 1.35;
}
.filter-warning.visible { display: block; margin-bottom: 0.4rem; }

.filter-case-select {
  margin-top: 0.4rem;
}

/* ─── ACMG WORKSPACE ─── */

.acmg-workspace {
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 8px;
  overflow: hidden;
}

.acmg-variant-card {
  padding: 0.5rem 0.6rem;
  border-bottom: 1px solid var(--border);
  font-size: 0.75rem;
  line-height: 1.4;
}
.acmg-variant-card .av-gene { font-weight: 700; color: var(--accent); }
.acmg-variant-card .av-hgvs { font-family: monospace; font-size: 0.72rem; }
.acmg-variant-card .av-info { color: var(--text-dim); font-size: 0.68rem; margin-top: 0.15rem; }

.acmg-criteria-grid {
  padding: 0.5rem 0.6rem;
  display: flex;
  gap: 0.6rem;
}

.acmg-group {
  flex: 1;
  display: flex;
  flex-direction: column;
  gap: 3px;
}
.acmg-group-label {
  font-size: 0.62rem;
  font-weight: 700;
  text-transform: uppercase;
  letter-spacing: 0.5px;
  color: var(--text-dim);
  margin-bottom: 0.2rem;
}
.acmg-group.pathogenic .acmg-group-label { color: var(--danger); }
.acmg-group.benign .acmg-group-label { color: var(--success); }

.acmg-crit {
  display: flex;
  align-items: center;
  gap: 0.3rem;
  background: var(--bg-card);
  border: 1px solid var(--border);
  color: var(--text-muted);
  padding: 0.2rem 0.4rem;
  border-radius: 4px;
  font-size: 0.68rem;
  font-family: inherit;
  font-weight: 600;
  cursor: pointer;
  transition: all 0.12s;
}
.acmg-crit:hover { border-color: var(--accent-dim); }
.acmg-crit.selected { border-color: var(--accent); background: var(--accent-dim); color: #fff; }
.acmg-group.pathogenic .acmg-crit.selected { border-color: var(--danger); background: rgba(239, 68, 68, 0.2); color: var(--danger); }
.acmg-group.benign .acmg-crit.selected { border-color: var(--success); background: rgba(16, 185, 129, 0.2); color: var(--success); }

.crit-desc {
  font-weight: 400;
  font-size: 0.6rem;
  color: var(--text-dim);
  margin-left: auto;
}
.acmg-crit.selected .crit-desc { color: inherit; opacity: 0.7; }

.acmg-explain-box {
  padding: 0.5rem 0.6rem;
  border-top: 1px solid var(--border);
  background: var(--bg-card);
  font-size: 0.72rem;
  line-height: 1.4;
}
.acmg-explain-title {
  font-weight: 700;
  color: var(--accent);
  margin-bottom: 0.2rem;
}
.acmg-explain-text {
  color: var(--text-muted);
}
.acmg-explain-text strong { color: var(--text); }

/* Filter causal variant tracker */
.funnel-causal {
  font-size: 0.6rem;
  margin-left: 0.3rem;
}
.funnel-causal.survived { color: var(--success); }
.funnel-causal.filtered { color: var(--danger); }

.funnel-removed {
  font-size: 0.58rem;
  color: var(--text-dim);
  margin-left: 0.2rem;
}

.acmg-result {
  padding: 0.5rem 0.6rem;
  border-top: 1px solid var(--border);
  text-align: center;
}

.acmg-points-bar {
  position: relative;
  height: 8px;
  background: linear-gradient(90deg, var(--success) 0%, var(--success) 25%, var(--text-dim) 40%, var(--text-dim) 60%, var(--danger) 75%, var(--danger) 100%);
  border-radius: 4px;
  margin-bottom: 0.4rem;
}
.acmg-bar-fill {
  position: absolute;
  height: 100%;
  border-radius: 4px;
  transition: width 0.3s;
}
.acmg-bar-marker {
  position: absolute;
  top: -3px;
  width: 4px;
  height: 14px;
  background: #fff;
  border-radius: 2px;
  transition: left 0.3s;
  left: 50%;
}

.acmg-classification {
  font-size: 0.9rem;
  font-weight: 700;
  margin-bottom: 0.1rem;
}
.acmg-classification.pathogenic { color: var(--danger); }
.acmg-classification.likely-pathogenic { color: #f97316; }
.acmg-classification.vus { color: var(--text-dim); }
.acmg-classification.likely-benign { color: #22d3ee; }
.acmg-classification.benign { color: var(--success); }

.acmg-points-text {
  font-size: 0.68rem;
  color: var(--text-dim);
  font-family: monospace;
}

/* ─── SPLIT VIEWER (Short vs Long Read) ─── */

.split-viewer {
  display: flex;
  gap: 0;
  border: 1px solid var(--border);
  border-radius: 8px;
  overflow: hidden;
}
.split-pane {
  flex: 1;
  background: var(--bg);
}
.split-label {
  padding: 0.3rem 0.5rem;
  font-size: 0.65rem;
  font-weight: 600;
  color: var(--text-dim);
  border-bottom: 1px solid var(--border);
  text-align: center;
}
.split-divider {
  width: 2px;
  background: var(--border);
}

.split-info {
  margin-top: 0.5rem;
  padding: 0.4rem 0.6rem;
  font-size: 0.72rem;
  color: var(--text-muted);
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 6px;
  line-height: 1.4;
}

/* ─── PATHWAY VIEWER ─── */

.pathway-viewer {
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 8px;
  overflow: hidden;
}
.pathway-viewer svg {
  width: 100%;
  display: block;
}
.pathway-controls {
  display: flex;
  gap: 0.4rem;
  padding: 0.4rem 0.6rem;
  border-top: 1px solid var(--border);
  align-items: center;
}
.pathway-explain {
  padding: 0.4rem 0.6rem;
  font-size: 0.72rem;
  color: var(--text-muted);
  border-top: 1px solid var(--border);
  line-height: 1.4;
}

/* ─── EXPLORE MODE ─── */

.explore-tabs {
  display: flex;
  gap: 2px;
  padding: 0.4rem 0.6rem;
  border-bottom: 1px solid var(--border);
  overflow-x: auto;
  scrollbar-width: thin;
}
.explore-tab {
  background: none;
  border: 1px solid var(--border);
  color: var(--text-dim);
  padding: 0.2rem 0.5rem;
  border-radius: 4px;
  cursor: pointer;
  font-size: 0.68rem;
  font-family: inherit;
  white-space: nowrap;
  transition: all 0.12s;
}
.explore-tab:hover { color: var(--text-muted); border-color: var(--accent-dim); }
.explore-tab.active { background: var(--accent-dim); border-color: var(--accent); color: #fff; }

.explore-panel { display: none; padding: 0.6rem 0.8rem; }
.explore-panel.active { display: block; }

/* Filter Workbench */
.filter-wb-toolbar {
  display: flex;
  align-items: center;
  gap: 0.5rem;
  margin-bottom: 0.5rem;
}
.filter-count {
  font-family: monospace;
  font-size: 0.75rem;
  color: var(--accent);
  font-weight: 600;
}
.filter-controls {
  display: flex;
  flex-direction: column;
  gap: 0.3rem;
  margin-bottom: 0.5rem;
}
.fc-row {
  display: flex;
  align-items: center;
  gap: 0.5rem;
  font-size: 0.72rem;
  color: var(--text-muted);
}
.fc-row label { min-width: 90px; }
.fc-row input[type="range"] { width: 100px; }
.fc-row select {
  background: var(--bg);
  border: 1px solid var(--border);
  color: var(--text);
  padding: 0.2rem 0.4rem;
  border-radius: 4px;
  font-size: 0.7rem;
  font-family: inherit;
}

.filter-results-table {
  max-height: 280px;
  overflow-y: auto;
  scrollbar-width: thin;
}
.frt-row {
  display: grid;
  grid-template-columns: 70px 1fr 60px 50px 60px;
  gap: 0.3rem;
  padding: 0.25rem 0.4rem;
  font-size: 0.68rem;
  border-bottom: 1px solid var(--border);
  align-items: center;
}
.frt-row:hover { background: var(--bg-hover); }
.frt-header {
  color: var(--text-dim);
  font-weight: 600;
  font-size: 0.62rem;
  text-transform: uppercase;
  letter-spacing: 0.3px;
}
.frt-gene { font-weight: 600; color: var(--accent); }
.frt-hgvs { font-family: monospace; font-size: 0.65rem; color: var(--text-muted); overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
.frt-maf { font-family: monospace; font-size: 0.65rem; }
.frt-effect { font-size: 0.62rem; }
.frt-acmg {
  font-size: 0.6rem;
  font-weight: 600;
  padding: 0.05rem 0.25rem;
  border-radius: 3px;
  text-align: center;
}
.frt-acmg.p { background: rgba(239, 68, 68, 0.2); color: var(--danger); }
.frt-acmg.lp { background: rgba(249, 115, 22, 0.2); color: #f97316; }
.frt-acmg.vus { background: rgba(71, 85, 105, 0.2); color: var(--text-dim); }
.frt-acmg.lb { background: rgba(34, 211, 238, 0.2); color: #22d3ee; }
.frt-acmg.b { background: rgba(16, 185, 129, 0.2); color: var(--success); }

/* Coverage Compare */
.cov-toolbar {
  display: flex;
  align-items: center;
  gap: 0.5rem;
  margin-bottom: 0.5rem;
  flex-wrap: wrap;
}
.cov-legend {
  display: flex;
  gap: 0.8rem;
  font-size: 0.65rem;
  color: var(--text-dim);
  margin-top: 0.3rem;
}
.cov-legend-item {
  display: flex;
  align-items: center;
  gap: 0.2rem;
}
.cov-legend-dot {
  width: 8px;
  height: 8px;
  border-radius: 50%;
}
.cov-info {
  margin-top: 0.4rem;
  font-size: 0.72rem;
  color: var(--text-muted);
  line-height: 1.4;
}

/* ─── QUIZ MODE ─── */

.quiz-start { padding: 0.8rem; }
.quiz-intro { margin-bottom: 0.8rem; }
.quiz-intro h2 { font-size: 0.95rem; color: var(--accent); margin-bottom: 0.2rem; }
.quiz-intro p { font-size: 0.75rem; color: var(--text-muted); }

.quiz-levels { display: flex; flex-direction: column; gap: 0.4rem; }
.quiz-level {
  display: flex;
  align-items: center;
  gap: 0.6rem;
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 8px;
  padding: 0.6rem 0.8rem;
  cursor: pointer;
  transition: all 0.12s;
  text-align: left;
  font-family: inherit;
  color: var(--text);
}
.quiz-level:hover { border-color: var(--accent-dim); background: var(--bg-hover); }
.ql-num {
  width: 28px; height: 28px;
  display: flex;
  align-items: center;
  justify-content: center;
  border-radius: 50%;
  background: var(--accent-dim);
  color: #fff;
  font-weight: 700;
  font-size: 0.85rem;
  flex-shrink: 0;
}
.ql-title { font-size: 0.82rem; font-weight: 600; }
.ql-desc { font-size: 0.68rem; color: var(--text-dim); margin-top: 0.1rem; }

.quiz-game { padding: 0.6rem 0.8rem; }
.quiz-progress {
  display: flex;
  align-items: center;
  gap: 0.5rem;
  margin-bottom: 0.5rem;
  font-size: 0.72rem;
  color: var(--text-dim);
}
.quiz-progress-bar {
  flex: 1;
  height: 4px;
  background: var(--border);
  border-radius: 2px;
  overflow: hidden;
}
.quiz-progress-fill {
  height: 100%;
  background: var(--accent);
  border-radius: 2px;
  transition: width 0.3s;
}

.quiz-question {
  font-size: 0.8rem;
  line-height: 1.45;
  margin-bottom: 0.5rem;
}
.quiz-question strong { color: var(--accent); }

.quiz-visual {
  margin-bottom: 0.5rem;
}
.quiz-visual canvas {
  width: 100%;
  border: 1px solid var(--border);
  border-radius: 6px;
}

.quiz-options {
  display: flex;
  flex-direction: column;
  gap: 4px;
  margin-bottom: 0.5rem;
}
.quiz-option {
  background: var(--bg);
  border: 1px solid var(--border);
  color: var(--text);
  padding: 0.4rem 0.6rem;
  border-radius: 5px;
  cursor: pointer;
  font-size: 0.75rem;
  font-family: inherit;
  text-align: left;
  transition: all 0.12s;
}
.quiz-option:hover { border-color: var(--accent-dim); }
.quiz-option.correct { border-color: var(--success); background: rgba(16, 185, 129, 0.1); color: var(--success); }
.quiz-option.wrong { border-color: var(--danger); background: rgba(239, 68, 68, 0.1); color: var(--danger); }

.quiz-feedback {
  font-size: 0.72rem;
  line-height: 1.4;
  color: var(--text-muted);
  padding: 0.4rem 0.5rem;
  background: var(--bg);
  border-radius: 5px;
  display: none;
}
.quiz-feedback.visible { display: block; margin-bottom: 0.4rem; }

.quiz-nav {
  display: flex;
  gap: 0.4rem;
}

.quiz-result {
  padding: 0.8rem;
  text-align: center;
}
.quiz-result h2 { color: var(--accent); margin-bottom: 0.5rem; }
.quiz-final-score {
  font-size: 1.5rem;
  font-weight: 700;
  font-family: monospace;
  margin-bottom: 0.3rem;
}
.quiz-final-feedback {
  font-size: 0.75rem;
  color: var(--text-muted);
  margin-bottom: 0.6rem;
}

/* ─── SEQUENCE DEMO (Step 1) ─── */

.seq-demo {
  background: var(--bg);
  border: 1px solid var(--border);
  border-radius: 8px;
  overflow: hidden;
}
.seq-ref-track {
  padding: 0.3rem 0.6rem;
  font-family: 'Courier New', monospace;
  font-size: 0.65rem;
  color: var(--text-dim);
  border-bottom: 1px solid var(--border);
  overflow-x: auto;
  white-space: nowrap;
}
.seq-controls {
  padding: 0.4rem 0.6rem;
  border-top: 1px solid var(--border);
}
.seq-controls .slider-group { margin-bottom: 0.3rem; }
.seq-controls .slider-group:last-child { margin-bottom: 0; }

.step-explain {
  margin-top: 0.5rem;
  font-size: 0.72rem;
  color: var(--text-muted);
  line-height: 1.4;
  padding: 0.4rem 0.5rem;
  background: var(--bg);
  border-radius: 5px;
}

/* Pathway Explorer (Explore mode) */
.pathway-toolbar {
  margin-bottom: 0.5rem;
}
.pathway-metabolites {
  display: flex;
  gap: 0.4rem;
  padding: 0.4rem 0.6rem;
  flex-wrap: wrap;
}
.metabolite-bar {
  display: flex;
  flex-direction: column;
  align-items: center;
  gap: 0.1rem;
  font-size: 0.6rem;
  color: var(--text-dim);
}
.metabolite-level {
  width: 24px;
  background: var(--border);
  border-radius: 2px;
  position: relative;
  overflow: hidden;
}
.metabolite-fill {
  position: absolute;
  bottom: 0;
  width: 100%;
  background: var(--accent);
  border-radius: 2px;
  transition: height 0.5s;
}
.metabolite-fill.elevated { background: var(--danger); }
.metabolite-fill.depleted { background: var(--warning); }

/* ─── RESPONSIVE ─── */

@media (max-width: 500px) {
  .step-indicator { gap: 1px; padding: 0.3rem 0.4rem; }
  .step { padding: 0.15rem 0.25rem; font-size: 0.58rem; }
  .strategy-cards { grid-template-columns: 1fr; }
  .acmg-criteria-grid { flex-direction: column; }
  .split-viewer { flex-direction: column; }
  .split-divider { width: 100%; height: 2px; }
}