/*
 * GENT3 Custom Theme
 * Salt & Pepper Color Palette
 * Clean grayscale design with scientific professionalism
 */

/* ============================================
   Color Palette (Salt & Pepper)
   ============================================ */
:root {
    /* Primary Colors */
    --color-white: #FFFFFF;
    --color-light-gray: #D4D4D4;
    --color-medium-gray: #B3B3B3;
    --color-dark-gray: #2B2B2B;

    /* Semantic Colors */
    --color-background: #FFFFFF;
    --color-surface: #F8F9FA;
    --color-border: #D4D4D4;
    --color-text-primary: #2B2B2B;
    --color-text-secondary: #6C757D;
    --color-text-muted: #9CA3AF;

    /* Interactive States */
    --color-hover: #E9ECEF;
    --color-active: #DEE2E6;
    --color-focus: #B3B3B3;

    /* Accents */
    --color-accent-primary: #2B2B2B;
    --color-accent-secondary: #6C757D;

    /* Status Colors (Grayscale) */
    --color-success: #495057;
    --color-warning: #6C757D;
    --color-danger: #343A40;
    --color-info: #ADB5BD;

    /* 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), 0 2px 4px -1px rgba(0, 0, 0, 0.06);
    --shadow-lg: 0 10px 15px -3px rgba(0, 0, 0, 0.1), 0 4px 6px -2px rgba(0, 0, 0, 0.05);
    --shadow-xl: 0 20px 25px -5px rgba(0, 0, 0, 0.1), 0 10px 10px -5px rgba(0, 0, 0, 0.04);

    /* Transitions */
    --transition-fast: 150ms ease-in-out;
    --transition-base: 300ms ease-in-out;
    --transition-slow: 500ms ease-in-out;
}

/* ============================================
   Global Styles
   ============================================ */
body {
    background-color: var(--color-background);
    color: var(--color-text-primary);
    font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
    line-height: 1.6;
}

/* ============================================
   Navigation Bar
   ============================================ */
.navbar {
    background-color: var(--color-dark-gray) !important;
    border-bottom: 1px solid var(--color-border);
    box-shadow: var(--shadow-sm);
    padding: 0.75rem 1rem;
}

.navbar-brand {
    color: var(--color-white) !important;
    font-weight: 600;
    font-size: 1.25rem;
    display: flex;
    align-items: center;
    gap: 0.75rem;
}

.navbar-brand img {
    height: 36px;
    width: auto;
}

.navbar-brand:hover {
    color: var(--color-light-gray) !important;
}

.nav-link {
    color: rgba(255, 255, 255, 0.85) !important;
    font-weight: 500;
    padding: 0.5rem 1rem !important;
    transition: color var(--transition-fast);
}

.nav-link:hover {
    color: var(--color-white) !important;
}

.nav-link.active {
    color: var(--color-white) !important;
    background-color: rgba(255, 255, 255, 0.1);
    border-radius: 0.25rem;
}

/* ============================================
   Cards
   ============================================ */
.card {
    border: 1px solid var(--color-border);
    border-radius: 0.5rem;
    box-shadow: var(--shadow-sm);
    transition: box-shadow var(--transition-base), transform var(--transition-base);
    background-color: var(--color-white);
}

.card:hover {
    box-shadow: var(--shadow-md);
    transform: translateY(-2px);
}

.card-header {
    background-color: var(--color-surface);
    border-bottom: 1px solid var(--color-border);
    font-weight: 600;
    color: var(--color-text-primary);
}

.card-body {
    padding: 1.5rem;
}

.card-title {
    color: var(--color-text-primary);
    font-weight: 600;
    margin-bottom: 0.75rem;
}

.card-text {
    color: var(--color-text-secondary);
}

/* ============================================
   Buttons
   ============================================ */
.btn {
    border-radius: 0.375rem;
    font-weight: 500;
    padding: 0.5rem 1rem;
    transition: all var(--transition-fast);
    border: 1px solid transparent;
}

.btn-primary {
    background-color: var(--color-dark-gray);
    border-color: var(--color-dark-gray);
    color: var(--color-white);
}

.btn-primary:hover {
    background-color: var(--color-text-primary);
    border-color: var(--color-text-primary);
    transform: translateY(-1px);
    box-shadow: var(--shadow-md);
}

.btn-primary:active {
    transform: translateY(0);
}

.btn-outline-primary {
    color: var(--color-dark-gray);
    border-color: var(--color-dark-gray);
    background-color: transparent;
}

.btn-outline-primary:hover {
    color: var(--color-white);
    background-color: var(--color-dark-gray);
    border-color: var(--color-dark-gray);
}

.btn-secondary {
    background-color: var(--color-medium-gray);
    border-color: var(--color-medium-gray);
    color: var(--color-white);
}

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

.btn-light {
    background-color: var(--color-surface);
    border-color: var(--color-border);
    color: var(--color-text-primary);
}

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

/* ============================================
   Forms
   ============================================ */
.form-control {
    border: 1px solid var(--color-border);
    border-radius: 0.375rem;
    padding: 0.5rem 0.75rem;
    transition: border-color var(--transition-fast), box-shadow var(--transition-fast);
    color: var(--color-text-primary);
    background-color: var(--color-white);
}

.form-control:focus {
    border-color: var(--color-focus);
    box-shadow: 0 0 0 0.2rem rgba(43, 43, 43, 0.15);
    outline: none;
}

.form-control::placeholder {
    color: var(--color-text-muted);
}

.input-group-text {
    background-color: var(--color-surface);
    border-color: var(--color-border);
    color: var(--color-text-secondary);
}

/* ============================================
   Chat Interface
   ============================================ */
.chat-container {
    background-color: var(--color-white);
    border: 1px solid var(--color-border);
    border-radius: 0.5rem;
    box-shadow: var(--shadow-md);
}

.chat-messages {
    background-color: var(--color-surface);
    border-top: 1px solid var(--color-border);
    border-bottom: 1px solid var(--color-border);
}

.message {
    padding: 1rem;
    margin-bottom: 0.5rem;
    border-radius: 0.5rem;
    max-width: 80%;
}

.message.user {
    background-color: var(--color-dark-gray);
    color: var(--color-white);
    margin-left: auto;
}

.message.assistant {
    background-color: var(--color-white);
    border: 1px solid var(--color-border);
    color: var(--color-text-primary);
}

.message-header {
    font-weight: 600;
    margin-bottom: 0.25rem;
    font-size: 0.875rem;
    opacity: 0.8;
}

.message.user .message-header {
    color: rgba(255, 255, 255, 0.9);
}

.message.assistant .message-header {
    color: var(--color-text-secondary);
}

.message-content {
    line-height: 1.5;
}

.message-content code {
    background-color: rgba(43, 43, 43, 0.08);
    padding: 0.125rem 0.375rem;
    border-radius: 0.25rem;
    font-family: 'Courier New', monospace;
    font-size: 0.9em;
}

.message.user .message-content code {
    background-color: rgba(255, 255, 255, 0.2);
}

/* Markdown headers/lists inside a chat bubble — kept compact so a ### heading
   doesn't dominate a message the way a real page h3 would. */
.message-content h3, .message-content h4, .message-content h5, .message-content h6 {
    margin: 0.6rem 0 0.3rem;
    font-size: 1rem;
    font-weight: 700;
}
.message-content h3:first-child, .message-content h4:first-child,
.message-content h5:first-child, .message-content h6:first-child { margin-top: 0; }
.message-content ul, .message-content ol {
    margin: 0.25rem 0 0.5rem;
    padding-left: 1.4rem;
}
.message-content li { margin-bottom: 0.15rem; }

/* ============================================
   Autocomplete
   ============================================ */
.autocomplete-dropdown {
    background-color: var(--color-white);
    border: 1px solid var(--color-border);
    border-radius: 0.375rem;
    box-shadow: var(--shadow-lg);
}

.autocomplete-item {
    padding: 0.75rem 1rem;
    cursor: pointer;
    transition: background-color var(--transition-fast);
    border-bottom: 1px solid var(--color-border);
}

.autocomplete-item:last-child {
    border-bottom: none;
}

.autocomplete-item:hover,
.autocomplete-item.active {
    background-color: var(--color-hover);
}

.autocomplete-item-command {
    font-weight: 600;
    color: var(--color-text-primary);
    font-family: 'Courier New', monospace;
}

.autocomplete-item-description {
    font-size: 0.875rem;
    color: var(--color-text-secondary);
    margin-top: 0.25rem;
}

/* ============================================
   Charts & Visualizations
   ============================================ */
.chart-container {
    background-color: var(--color-white);
    border: 1px solid var(--color-border);
    border-radius: 0.5rem;
    padding: 1.5rem;
    margin-bottom: 1rem;
    box-shadow: var(--shadow-sm);
}

.chart-container h6 {
    color: var(--color-text-primary);
    font-weight: 600;
    margin-bottom: 1rem;
}

/* ============================================
   Tables
   ============================================ */
.table {
    color: var(--color-text-primary);
}

.table thead th {
    background-color: var(--color-surface);
    color: var(--color-text-primary);
    font-weight: 600;
    border-bottom: 2px solid var(--color-border);
}

.table-striped tbody tr:nth-of-type(odd) {
    background-color: rgba(0, 0, 0, 0.02);
}

.table-hover tbody tr:hover {
    background-color: var(--color-hover);
}

.stats-table-header {
    background-color: var(--color-surface);
    padding: 1rem;
    border-radius: 0.375rem;
    margin-bottom: 0.5rem;
}

.stats-table-header h6 {
    margin: 0;
    color: var(--color-text-primary);
}

/* ============================================
   Badges & Tags
   ============================================ */
.badge {
    padding: 0.375rem 0.75rem;
    font-weight: 500;
    border-radius: 0.25rem;
}

.badge-primary {
    background-color: var(--color-dark-gray);
    color: var(--color-white);
}

.badge-secondary {
    background-color: var(--color-medium-gray);
    color: var(--color-white);
}

.badge-light {
    background-color: var(--color-surface);
    color: var(--color-text-primary);
    border: 1px solid var(--color-border);
}

/* ============================================
   Alerts
   ============================================ */
.alert {
    border-radius: 0.375rem;
    border: 1px solid var(--color-border);
}

.alert-info {
    background-color: var(--color-surface);
    color: var(--color-text-primary);
    border-color: var(--color-border);
}

.alert-success {
    background-color: #F8F9FA;
    color: var(--color-success);
    border-color: var(--color-border);
}

.alert-warning {
    background-color: #F8F9FA;
    color: var(--color-warning);
    border-color: var(--color-border);
}

.alert-danger {
    background-color: #F8F9FA;
    color: var(--color-danger);
    border-color: var(--color-border);
}

/* ============================================
   Loading Spinner
   ============================================ */
.spinner-border {
    border-color: var(--color-light-gray);
    border-right-color: var(--color-dark-gray);
}

/* ============================================
   Feature Cards (Index Page)
   ============================================ */
.feature-card {
    text-align: center;
    padding: 2rem;
    border: 1px solid var(--color-border);
    border-radius: 0.5rem;
    transition: all var(--transition-base);
    background-color: var(--color-white);
    height: 100%;
}

.feature-card:hover {
    box-shadow: var(--shadow-lg);
    transform: translateY(-4px);
    border-color: var(--color-medium-gray);
}

.feature-icon {
    font-size: 3rem;
    color: var(--color-dark-gray);
    margin-bottom: 1rem;
}

.feature-card h3 {
    color: var(--color-text-primary);
    font-weight: 600;
    margin-bottom: 1rem;
}

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

/* ============================================
   Hero Section
   ============================================ */
.hero-section {
    background: linear-gradient(135deg, var(--color-surface) 0%, var(--color-white) 100%);
    border-bottom: 1px solid var(--color-border);
}

.hero-title {
    color: var(--color-text-primary);
    font-weight: 700;
}

.hero-subtitle {
    color: var(--color-text-secondary);
}

.hero-logo {
    max-width: 120px;
    height: auto;
    margin-bottom: 1.5rem;
}

/* ============================================
   Code Blocks
   ============================================ */
pre {
    background-color: var(--color-surface);
    border: 1px solid var(--color-border);
    border-radius: 0.375rem;
    padding: 1rem;
    overflow-x: auto;
}

code {
    color: var(--color-text-primary);
    font-family: 'Courier New', monospace;
}

/* ============================================
   Footer
   ============================================ */
.footer {
    background-color: var(--color-surface);
    border-top: 1px solid var(--color-border);
    color: var(--color-text-secondary);
    padding: 2rem 0;
    margin-top: 4rem;
}

.footer a {
    color: var(--color-text-primary);
    text-decoration: none;
    transition: color var(--transition-fast);
}

.footer a:hover {
    color: var(--color-text-secondary);
}

/* ============================================
   Utilities
   ============================================ */
.text-muted {
    color: var(--color-text-muted) !important;
}

.text-secondary {
    color: var(--color-text-secondary) !important;
}

.bg-light {
    background-color: var(--color-surface) !important;
}

.border {
    border-color: var(--color-border) !important;
}

/* ============================================
   Responsive Design
   ============================================ */
@media (max-width: 768px) {
    .navbar-brand img {
        height: 28px;
    }

    .feature-card {
        padding: 1.5rem;
    }

    .feature-icon {
        font-size: 2.5rem;
    }

    .message {
        max-width: 90%;
    }
}

/* ============================================
   Deep-dive panel (COPAL druggability / biomarker)
   ============================================
   Deliberately breaks out of the grayscale theme with a dark navy identity so a
   deep-dive reads as a distinct, "heavier" analysis. GENT3's own box style — not
   copied from COPAL's UI. */
.deepdive-panel {
    border: 2px solid #1a2b4c;              /* dark navy — stands out from grayscale */
    border-left-width: 6px;
    border-radius: 10px;
    background: linear-gradient(180deg, #f7f9fc 0%, #eef2f8 100%);
    padding: 1rem 1.25rem;
    margin: 0.75rem 0;
    box-shadow: var(--shadow-md);
}

.deepdive-panel .deepdive-header {
    display: flex;
    align-items: center;
    gap: 0.5rem;
    font-weight: 700;
    color: #1a2b4c;
    border-bottom: 1px solid #d7deea;
    padding-bottom: 0.5rem;
    margin-bottom: 0.75rem;
}

.deepdive-panel .deepdive-header .deepdive-badge {
    font-size: 0.7rem;
    font-weight: 700;
    letter-spacing: 0.04em;
    text-transform: uppercase;
    color: #fff;
    background: #1a2b4c;
    border-radius: 999px;
    padding: 0.1rem 0.55rem;
}

/* Multi-agent execution flow chart — the pipeline is pre-drawn as connected
   agent nodes; each node lights up (pending -> running -> done) as its real
   SSE step lands, so the user watches the multi-agent flow progress rather
   than reading a plain checklist. Navy identity, not COPAL's UI. */
.deepdive-flow {
    display: flex;
    align-items: stretch;
    flex-wrap: wrap;
    gap: 0.35rem;
    margin: 0.25rem 0 0.25rem;
    padding-bottom: 0.25rem;
}

.flow-node {
    flex: 1 1 8.5rem;
    min-width: 8rem;
    max-width: 12rem;
    display: flex;
    flex-direction: column;
    gap: 0.15rem;
    padding: 0.5rem 0.6rem;
    border: 1.5px dashed #b9c3d6;              /* pending: faint dashed */
    border-radius: 8px;
    background: #fff;
    opacity: 0.5;
    transition: opacity 0.4s ease-out, border-color 0.4s ease-out,
                background 0.4s ease-out, box-shadow 0.4s ease-out;
}
.flow-node .flow-node-top {
    display: flex;
    align-items: center;
    gap: 0.4rem;
    font-weight: 700;
    font-size: 0.82rem;
    color: #1a2b4c;
}
.flow-node .flow-node-icon { width: 1rem; text-align: center; flex: 0 0 auto; }
.flow-node .flow-node-src { font-size: 0.68rem; font-weight: 600; color: var(--color-text-muted); text-transform: uppercase; letter-spacing: 0.03em; }
.flow-node .flow-node-detail { font-size: 0.74rem; color: var(--color-text-secondary); line-height: 1.3; min-height: 0.9rem; }

.flow-node.status-running {
    opacity: 1;
    border-style: solid;
    border-color: #1a2b4c;
    box-shadow: 0 0 0 3px rgba(26, 43, 76, 0.12);
}
.flow-node.status-done {
    opacity: 1;
    border-style: solid;
    border-color: #1a2b4c;
    background: linear-gradient(180deg, #fff 0%, #eef2f8 100%);
}
.flow-node.status-skipped {
    opacity: 0.85;
    border-style: dashed;
    border-color: #b9c3d6;
}
.flow-node.status-skipped .flow-node-top { color: var(--color-text-muted); }
.flow-node.status-error {
    opacity: 1;
    border-style: solid;
    border-color: var(--color-danger);
}
.flow-node.status-error .flow-node-top { color: var(--color-danger); }

/* Connector arrow between agent nodes */
.flow-arrow {
    display: flex;
    align-items: center;
    color: #b9c3d6;
    font-size: 0.8rem;
    flex: 0 0 auto;
    transition: color 0.4s ease-out;
}
.flow-arrow.passed { color: #1a2b4c; }
@media (max-width: 640px) {
    /* Stack vertically on narrow screens; rotate the arrows to point down. */
    .deepdive-flow { flex-direction: column; align-items: stretch; }
    .flow-node { max-width: none; }
    .flow-arrow { transform: rotate(90deg); align-self: center; }
}

/* Score card (druggability) */
.deepdive-scorecard {
    display: flex;
    align-items: center;
    gap: 1rem;
    margin: 0.75rem 0;
    padding: 0.75rem 1rem;
    background: #fff;
    border: 1px solid #d7deea;
    border-radius: 8px;
}
.deepdive-scorecard .score-value { font-size: 2rem; font-weight: 800; color: #1a2b4c; line-height: 1; }
.deepdive-scorecard .score-meta { font-size: 0.8rem; color: var(--color-text-secondary); }

.deepdive-body { margin-top: 0.75rem; line-height: 1.55; }
.deepdive-body h6 { color: #1a2b4c; margin-top: 0.75rem; }

.deepdive-lit { list-style: none; margin: 0.25rem 0 0; padding: 0; font-size: 0.82rem; }
.deepdive-lit li { padding: 0.15rem 0; color: var(--color-text-secondary); }
.deepdive-lit a { color: #1a2b4c; text-decoration: none; }
.deepdive-lit a:hover { text-decoration: underline; }

.deepdive-suggestion {
    display: flex;
    align-items: center;
    flex-wrap: wrap;
    gap: 0.5rem;
    margin: 0.5rem 0 0.75rem;
    padding: 0.5rem 0.75rem;
    border: 1px dashed #1a2b4c;
    border-radius: 8px;
    background: #f7f9fc;
}
.deepdive-suggestion .suggestion-text { color: #1a2b4c; font-size: 0.88rem; }
.deepdive-suggestion .btn { border-color: #1a2b4c; color: #1a2b4c; }
.deepdive-suggestion .btn:hover { background: #1a2b4c; color: #fff; }

/* ============================================
   Print Styles
   ============================================ */
@media print {
    .navbar,
    .footer,
    .btn,
    .chat-input-container {
        display: none;
    }

    .card,
    .chart-container {
        box-shadow: none;
        page-break-inside: avoid;
    }
}