/* --- START OF FILE style.css --- */

/* --- 1. THEME & COLOR PALETTE DEFINITION --- */
:root {
    /* Light Mode Palette */
    --primary-color: #3b82f6;  /* Teal */
    --primary-dark: #0f766e;
    --primary-light: #ccfbf1;
    --secondary-color: #52525b; /* Dark Gray */
    --accent-color: #f59e0b;    /* Amber/Orange for highlights */

    --mirna-color: var(--primary-color);
    --gene-color: #22c55e;   /* Green */
    --protein-color: #ef4444; /* Red */
    
    --body-bg: #f8fafc;        /* Light Gray background for the main content area */
    --panel-bg: #ffffff;
    --text-color: #3f3f46;
    --text-muted: #71717a;
    --border-color: #e2e8f0;
    --sidebar-text: #52525b;
    --sidebar-text-hover: #ffffff;

    --border-radius: 0.5rem;
    --shadow-sm: 0 1px 2px 0 rgb(0 0 0 / 0.05);
    --shadow-md: 0 4px 6px -1px rgb(0 0 0 / 0.1), 0 2px 4px -2px rgb(0 0 0 / 0.1);
    --sidebar-width: 260px;
}

/* Dark Mode Palette */
body.dark-mode {
    --body-bg: #111827;         /* Very Dark Blue/Gray */
    --panel-bg: #1f2937;        /* Dark Blue/Gray */
    --text-color: #d1d5db;      /* Light Gray */
    --text-muted: #9ca3af;      /* Medium Gray */
    --border-color: #374151;    /* Gray */
    --sidebar-text: #d1d5db;
    --secondary-color: #d1d5db;
}

/* --- 2. GENERAL BODY & LAYOUT --- */
body {
    background-color: var(--body-bg);
    font-family: 'Inter', -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
    color: var(--text-color);
    transition: background-color 0.3s, color 0.3s;
}

/* --- 3. NEW SIDEBAR STYLES --- */
#sidebar {
    position: fixed;
    top: 0;
    left: 0;
    width: var(--sidebar-width);
    height: 100vh;
    background-color: var(--panel-bg);
    border-right: 1px solid var(--border-color);
    display: flex;
    flex-direction: column;
    padding: 1rem;
    transition: background-color 0.3s, border-color 0.3s;
    z-index: 1030; /* High z-index to stay on top */
}

.sidebar-header {
    padding: 0.5rem 0.5rem 1.5rem 0.5rem;
}

#app-logo-sidebar {
    font-weight: 600;
    color: var(--secondary-color);
    display: flex;
    align-items: center;
    gap: 0.75rem;
    font-size: 1.3rem;
}
#app-logo-sidebar .fa-atom {
    color: var(--primary-color);
}

.bar-label-inner {
    fill: white;
    font-weight: 500;
}

.bar-label-outer {
    fill: var(--text-muted);
}

/* --- START: Add this entire block to the end of style.css --- */

/* 11. LOADING OVERLAY STYLES */
#loading-overlay {
    position: fixed;
    top: 0;
    left: 0;
    width: 100%;
    height: 100%;
    background-color: rgba(0, 0, 0, 0.5); /* Semi-transparent black */
    display: flex;
    justify-content: center;
    align-items: center;
    z-index: 9999; /* Ensure it's on top of everything */
    opacity: 1;
    transition: opacity 0.3s ease-in-out;
}

/* Blur effect for dark mode background */
body.dark-mode #loading-overlay {
    background-color: rgba(17, 24, 39, 0.7); /* Darker, more opaque background */
    backdrop-filter: blur(4px);
}

#loading-overlay.d-none {
    opacity: 0;
    pointer-events: none; /* Make it non-interactive when hidden */
}

/* Spinner SVG Animation */
/* ...and replace it with this simplified version */
.spinner-svg {
    animation: rotate 2s linear infinite;
    width: 80px;  /* Adjust size as needed */
    height: 80px; /* Adjust size as needed */
}

@keyframes rotate {
    100% {
        transform: rotate(360deg);
    }
}
/* --- END: New style block --- */
/* Add this to the end of static/css/style.css */

/* Add/Replace this in your static/css/style.css file */

/* --- Enhanced Legend Styles --- */
#cy-legend {
    padding: 12px;
    background-color: var(--sidebar-bg);
    border-radius: 8px;
    border: 1px solid var(--border-color);
}

#cy-legend .legend-title {
    font-weight: 600;
    margin-bottom: 10px;
    font-size: 1rem;
    color: var(--text-primary);
    border-bottom: 1px solid var(--border-color);
    padding-bottom: 5px;
}

#cy-legend .legend-section {
    margin-bottom: 12px;
}
#cy-legend .legend-section:last-child {
    margin-bottom: 0;
}

#cy-legend .legend-subtitle {
    font-weight: 500;
    font-size: 0.8rem;
    color: var(--text-muted);
    text-transform: uppercase;
    margin-bottom: 8px;
}

#landing-logo {
    max-width: 750px; /* Adjust this value to make the logo bigger or smaller */
    width: 100%;
    height: auto;
    margin-bottom: 1rem;
}

#cy-legend .legend-item {
    display: flex;
    align-items: center;
    margin-bottom: 8px;
    font-size: 0.85rem;
}

#cy-legend .legend-text {
    margin-left: 10px;
    color: var(--text-secondary);
}

#cy-legend .fa-circle-info {
    cursor: help;
}

/* --- Node and Modifier Icons --- */
.legend-icon {
    width: 24px;
    height: 24px;
    flex-shrink: 0;
    position: relative; /* For centering content */
    display: flex;
    align-items: center;
    justify-content: center;
}

.legend-icon.miRNA { background-color: #0d9488; transform: rotate(45deg); }
.legend-icon.gene { background-color: #22c55e; }
.legend-icon.protein { background-color: #ef4444; border-radius: 50%; }

/* Modifier styles applied to icons */
.legend-icon.ev { border: 4px solid #f59e0b; }
.legend-icon.shared {
    background: linear-gradient(135deg, #7dd3fc 0%, #a855f7 100%);
    border-radius: 4px; /* Optional: adds nice rounded corners */
}

/* CHANGED: Inferred style now uses opacity */
.legend-icon.inferred {
    opacity: 0.65;
}


/* --- Edge Icons --- */
.legend-edge {
    width: 32px;
    height: 12px;
    position: relative;
    flex-shrink: 0;
}

.legend-edge::after {
    content: '';
    position: absolute;
    left: 0;
    top: 50%;
    width: 100%;
    transform: translateY(-50%);
}

.legend-edge.confidence::after {
    height: 3px;
    background-color: #94a3b8;
}

/* CHANGED: Coding edge icon is now dotted */
.legend-edge.coding::after {
    height: 0; /* We don't need height for a border-based line */
    border-top: 3px dotted #cbd5e1;
}

.sidebar-nav {
    list-style: none;
    padding-left: 0;
    flex-grow: 1; /* Pushes footer to the bottom */
}

.sidebar-nav .nav-link {
    display: flex;
    align-items: center;
    gap: 1rem;
    padding: 0.8rem 1rem;
    margin-bottom: 0.5rem;
    border-radius: var(--border-radius);
    color: var(--sidebar-text);
    font-weight: 500;
    text-decoration: none;
    transition: background-color 0.2s, color 0.2s;
}

#selected-cells-pill {
    font-size: 0.8rem;
    padding: 0.4em 0.8em;
}

.sticky-header {
    position: sticky;
    top: 0;
    z-index: 10;
}

.sidebar-nav .nav-link:hover {
    background-color: var(--primary-dark);
    color: var(--sidebar-text-hover);
}

.sidebar-nav .nav-link.active {
    background-color: var(--primary-color);
    color: var(--sidebar-text-hover);
}

#cell-comm-heatmap-legend-container .axis text {
    fill: var(--text-muted);
}

.sidebar-nav .nav-link i {
    width: 20px; /* Aligns text */
    text-align: center;
}

.sidebar-footer {
    padding-top: 1rem;
    border-top: 1px solid var(--border-color);
    display: flex;
    flex-direction: column;
    gap: 1rem;
}

.feedback-btn {
    display: flex;
    align-items: center;
    gap: 1rem;
    color: var(--sidebar-text);
    text-decoration: none;
    padding: 0.5rem;
    border-radius: var(--border-radius);
    font-weight: 500;
}
.feedback-btn:hover {
    background-color: var(--border-color);
    color: var(--text-color);
}
.feedback-btn i {
    width: 20px;
    text-align: center;
}

.legend-list .border-inferred {
    width: 14px; height: 14px;
    border: 3px dashed #a855f7;
    background-color: #ccc;
    opacity: 0.8;
}

/* --- 4. NEW, CORRECTED THEME SWITCHER STYLES --- */
.theme-switch-wrapper {
    display: flex;
    align-items: center;
    gap: 1rem;
    padding: 0.5rem;
}

.theme-label {
    font-weight: 500;
    color: var(--sidebar-text);
}

.theme-switch {
    position: relative;
    display: inline-block;
    width: 60px;
    height: 30px;
}

.theme-switch input { 
    opacity: 0;
    width: 0;
    height: 0;
}

.slider {
    position: absolute;
    cursor: pointer;
    top: 0;
    left: 0;
    right: 0;
    bottom: 0;
    background-color: #73C0D5; /* Day blue */
    transition: .4s;
    border-radius: 34px;
    display: flex;
    align-items: center;
}

.slider:before {
    position: absolute;
    content: "";
    height: 22px;
    width: 22px;
    left: 4px;
    bottom: 4px;
    background-color: white;
    transition: .4s;
    border-radius: 50%;
    z-index: 2;
}

.slider .sun-icon, .slider .moon-icon {
    position: absolute;
    top: 50%;
    transform: translateY(-50%);
    color: white;
    font-size: 0.8rem;
    transition: opacity 0.3s;
    z-index: 1;
}

.slider .sun-icon { right: 7px; opacity: 1; }
.slider .moon-icon { left: 7px; opacity: 0; }

/* Checked State (Dark Mode) */
input:checked + .slider { background-color: #2c3e50; } /* Night blue */
input:checked + .slider:before { transform: translateX(30px); }
input:checked + .slider .sun-icon { opacity: 0; }
input:checked + .slider .moon-icon { opacity: 1; }

/* --- 5. NEW MAIN CONTENT WRAPPER & HEADER --- */
#main-content-wrapper {
    margin-left: var(--sidebar-width);
    padding: 0;
}

.app-header {
    background-color: var(--panel-bg);
    border-bottom: 1px solid var(--border-color);
    padding: 0.75rem 2rem;
    transition: background-color 0.3s, border-color 0.3s;
}

#header-title {
    color: var(--text-color);
    font-weight: 600;
    margin-bottom: 0;
}

/* --- 5. EDITABLE HEADER TITLE STYLES --- */
#header-title.editable-header {
    background-color: transparent;
    border: none;
    outline: none;
    font-size: 1.5rem; /* Matches original h4 size */
    font-weight: 600;
    width: 100%;
    padding: 0.25rem;
    color: var(--text-color);
    border-radius: var(--border-radius);
    transition: background-color 0.2s, box-shadow 0.2s;
}
#header-title.editable-header:focus {
    background-color: var(--body-bg);
    box-shadow: 0 0 0 2px var(--primary-color);
}

main.container-fluid {
    padding-top: 2rem;
    padding-bottom: 2rem;
}

/* --- 6. SIDEBAR SEARCH HISTORY STYLES --- */
#history-container {
    padding-left: 1rem;
    padding-right: 1rem;
    overflow-y: auto;
}
.history-header {
    display: flex;
    align-items: center;
    gap: 1rem;
    padding: 0.8rem 0;
    color: var(--text-muted);
    font-weight: 600;
    font-size: 0.9rem;
    text-transform: uppercase;
    letter-spacing: 0.05em;
}
#history-list .list-group-item {
    cursor: pointer;
    background-color: transparent;
    color: var(--sidebar-text);
    border: none;
    border-radius: var(--border-radius);
    padding: 0.6rem 1rem;
    margin-bottom: 0.25rem;
    transition: background-color 0.2s, color 0.2s;
}
#history-list .list-group-item:hover {
    background-color: var(--primary-dark);
    color: var(--sidebar-text-hover);
}

/* --- 7. LANDING PAGE & APP VIEW STYLES (ADJUSTED FOR THEME) --- */
#landing-view {
    text-align: center;
}

.landing-content {
    max-width: 700px;
    margin: 2rem auto;
}

.landing-content h1 {
    font-weight: 700;
    color: var(--secondary-color);
    margin-bottom: 0.5rem;
}

.card {
    background-color: var(--panel-bg);
    border-color: var(--border-color);
    border-radius: var(--border-radius);
    transition: background-color 0.3s, border-color 0.3s;
}

#restore-system-view-btn {
    position: absolute;
    bottom: 15px;
    left: 15px;
    z-index: 500; /* Ensures it's on top of the graph canvas */
}
.card-header {
    background-color: var(--body-bg);
    border-bottom: 1px solid var(--border-color);
    color: var(--text-color);
}
.card-body {
    color: var(--text-color);
}
.search-container {
    margin-top: 2.5rem;
    text-align: left;
}
.search-container .nav-pills .nav-link {
    font-weight: 500;
    color: var(--text-muted);
}
.search-container .nav-pills .nav-link.active {
    background-color: var(--primary-color);
    color: #fff;
}
.search-container .form-label {
    font-size: 0.9rem;
    color: var(--text-muted);
    font-weight: 500;
}
.search-container .btn-primary {
    background-color: var(--primary-color);
    border-color: var(--primary-color);
}
.search-container .btn-primary:hover {
    background-color: var(--primary-dark);
    border-color: var(--primary-dark);
}

/* Theme-aware form controls */
.form-control, .form-range, .form-select {
    background-color: var(--body-bg);
    color: var(--text-color);
    border-color: var(--border-color);
}
.form-control:focus {
    background-color: var(--body-bg);
    color: var(--text-color);
    border-color: var(--primary-color);
    box-shadow: 0 0 0 0.25rem rgba(13, 148, 136, 0.25);
}
.form-control::placeholder {
    color: var(--text-muted);
    opacity: 0.7;
}

/* --- 8. CYTOSCAPE & RESULTS PANEL (ADJUSTED FOR THEME) --- */
#cy {
    width: 100%;
    height: 85vh;
    border: 1px solid var(--border-color);
    border-radius: var(--border-radius);
    background-color: var(--panel-bg);
    transition: background-color 0.3s, border-color 0.3s;
}

/* --- 9. ORIGINAL COMPONENT STYLES (FROM YOUR FILE) --- */
.text-muted {
    color: var(--text-muted) !important;
}

.ev-status-localization {
    color: #92400e; background-color: #fef3c7; border-color: #fde68a;
}

/* --- 10. NEW LAYOUT, CONTROLS, AND LEGEND STYLES --- */

/* Resizable Panel Layout */
.main-view-container {
    display: flex;
    height: calc(100vh - 60px); 
}

#left-panel-col {
    width: 33%; /* Initial width */
    min-width: 350px;
    max-width: 700px;
    display: flex; /* Make card fill height */
}

#resizer {
    width: 8px;
    cursor: col-resize;
    background-color: var(--body-bg);
    border-left: 1px solid var(--border-color);
    border-right: 1px solid var(--border-color);
    transition: background-color 0.3s;
}
#resizer:hover {
    background-color: var(--primary-light);
}

#right-panel-col {
    flex-grow: 1; /* Take remaining space */
    min-width: 400px;
    display: flex;
}

/* Fixed Height and Scrolling for Left Panel */
#results-panel {
    width: 100%;
    display: flex;
    flex-direction: column;
    height: 100%; /* Fill the parent column */
}
#results-panel .card-body {
    flex-grow: 1; /* Allow body to fill space */
    overflow-y: auto; /* Add scrollbar only when needed */
}

/* Graph Wrapper and Controls */
.graph-wrapper {
    position: relative; /* Anchor for absolute children */
    width: 100%;
    height: 100%;
}
#cy {
    height: 100%; /* Ensure graph fills wrapper */
}

#cy-controls {
    position: absolute;
    top: 1rem;
    right: 1rem;
    z-index: 10;
    display: flex;
    flex-direction: column;
    gap: 0.5rem;
}
#cy-controls .btn {
    background-color: var(--panel-bg);
    color: var(--text-color);
    border: 1px solid var(--border-color);
    box-shadow: var(--shadow-sm);
}

/* Graph Legend */
#cy-legend {
    position: absolute;
    bottom: 1rem;
    right: 1rem;
    z-index: 10;
    background-color: var(--panel-bg);
    border: 1px solid var(--border-color);
    border-radius: var(--border-radius);
    padding: 0.75rem 1rem;
    box-shadow: var(--shadow-md);
    font-size: 0.8rem;
    color: var(--text-color);
}
.legend-title {
    font-weight: 600;
    margin-bottom: 0.5rem;
    border-bottom: 1px solid var(--border-color);
    padding-bottom: 0.25rem;
}
.legend-list {
    list-style: none;
    padding: 0;
    margin: 0;
    display: grid;
    grid-template-columns: 1fr;
    gap: 0.4rem;
}
.legend-list li {
    display: flex;
    align-items: center;
    gap: 0.5rem;
}
.legend-list span {
    display: inline-block;
}
.legend-list .shape-miRNA {
    width: 14px; height: 14px;
    background-color: #0d9488;
    transform: rotate(45deg);
}
.legend-list .shape-gene {
    width: 16px; height: 12px;
    background-color: #22c55e;
}
.legend-list .shape-protein {
    width: 14px; height: 14px;
    background-color: #ef4444;
    border-radius: 50%;
}
.legend-list .border-ev {
    width: 14px; height: 14px;
    border: 3px solid #f59e0b;
    background-color: #ccc;
}
.legend-list .edge-thick, .legend-list .edge-thin {
    width: 20px;
    background-color: #94a3b8;
}
.legend-list .edge-thick { height: 4px; }
.legend-list .edge-thin { height: 1.5px; }

#cell-comm-heatmap-container .axis text { font-size: 11px; fill: var(--text-muted); }
#cell-comm-heatmap-container .axis .domain { stroke: none; }
#cell-comm-heatmap-container .heatmap-cell:hover { stroke: #000; stroke-width: 1.5px; cursor: pointer; }
.ev-corroborated-icon { color: var(--gene-color); font-weight: bold; font-size: 1.1rem; }
.effect-icon { font-weight: bold; font-size: 1.2rem; line-height: 1; }
.effect-stim { color: #22c55e; }
.effect-inhib { color: #ef4444; }
.effect-other { color: #a1a1aa; }

#chord-diagram-container text { fill: var(--text-color); font-size: 11px; }

.compartments-header {
    padding-bottom: 0.5rem; margin-bottom: 0.5rem; border-bottom: 1px solid var(--border-color);
}

.level-high, .level-medium, .level-low, .level-na {
    font-size: 0.75em; font-weight: 600; padding: 0.25em 0.5em;
    border: 1px solid; border-radius: 4px; min-width: 55px; text-align: center;
}
.level-high { color: #065f46; background-color: #d1fae5; border-color: #a7f3d0; }
.level-medium { color: #92400e; background-color: #fef9c3; border-color: #fef08a; }
.level-low { color: #991b1b; background-color: #fee2e2; border-color: #fecaca; }
.level-na { color: #4b5563; background-color: #f3f4f6; border-color: #e5e7eb; }

.source-badge {
    font-size: 0.75em; font-weight: 600; padding: 0.25em 0.5em;
    border: 1px solid; border-radius: 4px;
    color: #1e40af; background-color: #dbeafe; border-color: #bfdbfe;
}

.pubmed-badge, .ev-track-badge {
    font-weight: 500; text-decoration: none; padding: 0.25em 0.5em;
    border-radius: 4px; font-size: 0.8rem; display: inline-block;
}
.pubmed-badge { background-color: #e0e7ff; color: #3730a3; }
.pubmed-badge:hover { background-color: #c7d2fe; color: #312e81; }
.ev-track-badge { background-color: #cffafe; color: #0e7490; }
.ev-track-badge:hover { background-color: #a5f3fc; color: #155e75; }

.evidence-experimental, .evidence-predicted {
    font-size: 0.75em; font-weight: 600; padding: 0.25em 0.5em;
    border: 1px solid; border-radius: 4px;
}
.evidence-experimental { color: #059669; background-color: #d1fae5; border-color: #a7f3d0; }
.evidence-predicted { color: #4b5563; background-color: #f3f4f6; border-color: #e5e7eb; }

.ev-status-badge {
    font-size: 0.8rem; font-weight: 600; padding: 0.35em 0.65em;
    border: 1px solid; display: inline-block; margin-top: 0.5rem;
}
.ev-status-confirmed { color: #065f46; background-color: #d1fae5; border-color: #a7f3d0; }
.ev-status-reported { color: #4b5563; background-color: #f3f4f6; border-color: #e5e7eb; }

.progress-bar.bg-mirna { background-color: var(--mirna-color); color: #fff; }
.progress-bar.bg-gene { background-color: var(--gene-color); color: #fff; }

.localization-summary-view { display: flex; flex-direction: column; gap: 0.25rem; }
.system-summary-item { border: 1px solid var(--border-color); border-radius: var(--border-radius); overflow: hidden; }
.system-summary-header {
    display: grid; grid-template-columns: 1fr 1fr 35px;
    gap: 1rem; align-items: center; padding: 0.5rem 0.75rem;
    cursor: pointer; background-color: var(--panel-bg);
    transition: background-color 0.2s ease-in-out;
}
.system-summary-header:hover { background-color: var(--body-bg); }
.system-summary-header .system-name {
    font-size: 0.85rem; font-weight: 500; white-space: nowrap;
    overflow: hidden; text-overflow: ellipsis;
}
.system-summary-header .progress { background-color: #e9ecef; border-radius: 4px; }
.system-summary-header .progress-bar small { font-weight: 600; }
.system-detail-body {
    padding: 0.25rem 0.5rem 0.5rem; background-color: var(--body-bg);
    border-top: 1px solid var(--border-color);
}

.evidence-table { font-size: 0.85rem; }
.expression-summary .progress { height: 14px; background-color: #e9ecef; }
.expression-summary .bg-success { background-color: var(--gene-color) !important; }
#collective-view-tab .bg-primary { background-color: var(--mirna-color) !important; }

/* ================================================= */
/* ===== NEW STYLES FOR CELL COMM ENHANCEMENTS ===== */
/* ================================================= */
.cell-group-badge {
    font-size: 0.9em;
    font-weight: 500;
    padding: 0.2em 0.4em;
    border-radius: 4px;
    background-color: var(--body-bg);
    color: var(--text-muted);
    border: 1px solid var(--border-color);
    white-space: nowrap;
}

.gene-link {
    cursor: pointer;
}
.gene-link:not(.badge):hover {
    text-decoration: underline !important;
}

.ev-corroborated-row {
    background-color: #dcfce7 !important; /* A light green color */
}
body.dark-mode .ev-corroborated-row {
    background-color: #166534 !important; /* A dark green color */
}

.ev-corroborated-row-legend {
    display: inline-block;
    width: 1em;
    height: 1em;
    background-color: #dcfce7;
    border: 1px solid #166534;
}
body.dark-mode .ev-corroborated-row-legend {
    background-color: #166534;
    border: 1px solid #dcfce7;
}


/* ================================================= */
/* ===== NEW: DARK MODE OVERRIDES (FIX) ========== */
/* ================================================= */

/* Main Tabs Container */
body.dark-mode .card-header.bg-light {
    background-color: var(--panel-bg) !important;
}

body.dark-mode .nav-tabs {
    border-bottom-color: var(--border-color);
}
body.dark-mode .nav-tabs .nav-link {
    color: var(--text-muted);
    border-color: transparent;
}
body.dark-mode .nav-tabs .nav-link:hover {
    border-color: var(--border-color);
}
body.dark-mode .nav-tabs .nav-link.active {
    color: var(--text-color);
    background-color: var(--body-bg);
    border-color: var(--border-color);
    border-bottom-color: var(--body-bg);
}

/* Inner Pills (Summary, Localization, etc.) */
body.dark-mode .nav-pills .nav-link {
    color: var(--text-muted);
}
body.dark-mode .nav-pills .nav-link:hover {
    background-color: #374151; 
}
body.dark-mode .nav-pills .nav-link.active {
    background-color: var(--primary-color);
    color: #fff;
}

/* Lists (Pathways) */
body.dark-mode .list-group-item {
    background-color: var(--panel-bg);
    border-color: var(--border-color);
    color: var(--text-color);
}

/* Source Badges */
body.dark-mode .source-badge {
    color: #93c5fd;
    background-color: #374151;
    border-color: #4b5563;
}

/* Table Styles (EV Evidence & Cell Comm) */
body.dark-mode .table {
    color: var(--text-color);
    --bs-table-border-color: var(--border-color);
    --bs-table-color: var(--text-color);
    --bs-table-striped-bg: rgba(255, 255, 255, 0.03);
}
body.dark-mode .table-hover > tbody > tr:hover {
    --bs-table-hover-bg: rgba(255, 255, 255, 0.05);
}
body.dark-mode .table-light {
    --bs-table-bg: var(--body-bg);
    --bs-table-border-color: var(--border-color);
    color: var(--text-color);
}

/* Custom Scrollbar */
body.dark-mode ::-webkit-scrollbar {
  width: 10px;
  height: 10px;
}
body.dark-mode ::-webkit-scrollbar-track {
  background: var(--body-bg);
}
body.dark-mode ::-webkit-scrollbar-thumb {
  background-color: #4b5563;
  border-radius: 6px;
  border: 2px solid var(--body-bg);
}
body.dark-mode ::-webkit-scrollbar-thumb:hover {
  background-color: #6b7280;
}

#cy .hidden {
    display: none;
}

/* Basic styling for the logo images */
#app-logo-sidebar img {
    width: 200px; /* Adjust this value as needed */
    height: auto;
}

/* 2. By default, hide the dark mode logo */
.logo-dark {
    display: none;
}

/* 3. When dark mode is active... */
body.dark-mode .logo-light {
    display: none; /* ...hide the light logo */
}

body.dark-mode .logo-dark {
    display: block; /* ...and show the dark logo */
}

/* Original Font Awesome icon styling (if you want to adjust the color of other icons) */
#app-logo-sidebar .fa-atom {
    color: var(--primary-color);
}

/* --- Styles for PPI Modal --- */
#ppi-modal .modal-content {
    background-color: var(--panel-bg);
    border-color: var(--border-color);
}
#ppi-modal .modal-header {
    background-color: var(--body-bg);
    color: var(--text-color);
    border-bottom-color: var(--border-color);
}
#ppi-modal .modal-body {
    padding: 0;
}
#ppi-modal .btn-close {
    filter: var(--bs-btn-close-white-filter);
}
body.dark-mode #ppi-modal .btn-close {
    filter: invert(1) grayscale(100%) brightness(200%);
}

/* Make Bootstrap popovers theme-aware */
.popover {
    background-color: var(--panel-bg);
    border-color: var(--border-color);
}
.popover-header {
    background-color: var(--body-bg);
    color: var(--text-color);
    border-bottom-color: var(--border-color);
}
.popover-body {
    color: var(--text-color);
}
.popover .popover-arrow::before {
    border-top-color: var(--border-color) !important;
}
.popover .popover-arrow::after {
     border-top-color: var(--panel-bg) !important;
}
body.dark-mode .popover .popover-arrow::after {
     border-top-color: var(--body-bg) !important;
}

/* --- START: Styles for On-Graph PPI Expansion --- */

/* The floating action button on a node */
#node-action-button {
    position: absolute;
    z-index: 1001; /* Above Cytoscape canvas */
    border-radius: 50%;
    width: 30px;
    height: 30px;
    padding: 0;
    line-height: 1;
    font-size: 0.9rem;
    box-shadow: var(--shadow-md);
    transform: translate(-50%, -50%); /* Center on cursor */
}

/* Style for newly added PPI-expanded nodes */
#cy node.ppi-expanded {
    opacity: 0.7;
    border-color: #a855f7;
    border-style: dotted;
    border-width: 3px;
}

/* Style for Protein-Protein Interaction Edges from STRING */
#cy edge[source_db="STRING-PPI"] {
    line-color: #a855f7; /* Purple */
    target-arrow-color: #a855f7;
    target-arrow-shape: none; /* PPIs are usually undirected */
    line-style: solid;
    width: mapData(combined_score, 700, 1000, 1, 6); /* Map width to score */
    opacity: 0.6;
}

/* Feedback toast for when no new interactors are found */
.ppi-feedback-toast {
    position: absolute;
    top: 20px;
    left: 50%;
    transform: translateX(-50%);
    background-color: rgba(31, 41, 55, 0.9); /* From dark mode panel bg */
    color: white;
    padding: 0.75rem 1.25rem;
    border-radius: var(--border-radius);
    font-weight: 500;
    z-index: 1002;
    box-shadow: var(--shadow-md);
}
/* --- END: Styles for On-Graph PPI Expansion --- */

/* --- START: Beta Banner Styles --- */
#beta-banner {
    position: fixed;
    bottom: 0;
    left: var(--sidebar-width); /* Aligns with the main content, skipping sidebar */
    right: 0;
    background-color: #ffc107; /* Warning Yellow */
    color: #212529;
    padding: 0.5rem 1.5rem;
    z-index: 2000;
    box-shadow: 0 -2px 10px rgba(0,0,0,0.1);
    font-size: 0.9rem;
}

/* Make sure it doesn't overlap nicely on mobile if sidebar collapses (responsive safety) */
@media (max-width: 768px) {
    #beta-banner {
        left: 0;
    }
}
/* --- END: Beta Banner Styles --- */