/* assets/css/styles.css */

:root {
  /* Light Mode (Default) */
  --bg-primary: #ffffff;
  --bg-secondary: #f8f9fa;
  --bg-tertiary: #f0f0f0;
  --text-primary: #212529;
  --text-secondary: #6c757d;
  --text-tertiary: #495057;
  --border-color: #dee2e6;
  --primary-color: #0d6efd;
  --primary-color-rgb: 13, 110, 253;
  --secondary-color: #6c757d;
  --secondary-color-rgb: 108, 117, 125;
  --success-color: #198754;
  --success-color-rgb: 25, 135, 84;
  --danger-color: #dc3545;
  --danger-color-rgb: 220, 53, 69;
  --warning-color: #ffc107;
  --warning-color-rgb: 255, 193, 7;
  --info-color: #0dcaf0;
  --info-color-rgb: 13, 202, 240;
  --shadow-color: rgba(0, 0, 0, 0.1);
  --table-header-bg: #f8f9fa;
  --table-row-hover: rgba(0, 0, 0, 0.05);
  --card-bg: #ffffff;
  --navbar-bg: #ffffff;
  --input-bg: #ffffff;
  --input-border: #ced4da;
  --scrollbar-track: #f1f1f1;
  --scrollbar-thumb: #c1c1c1;
  --toast-bg: rgba(255, 255, 255, 0.9);
  --modal-bg: #ffffff;
  --dropdown-bg: #ffffff;
  --dropdown-hover: #f8f9fa;

  /* Transitions */
  --tran-02: all 0.2s ease;
  --tran-03: all 0.3s ease;
  --tran-04: all 0.4s ease;
  --tran-05: all 0.5s ease;
}

body.dark {
  /* Dark Mode */
  --bg-primary: #121212;
  --bg-secondary: #1e1e1e;
  --bg-tertiary: #252525;
  --text-primary: #e4e6eb;
  --text-secondary: #b0b3b8;
  --text-tertiary: #9fa4a9;
  --border-color: #3a3b3c;
  --primary-color: #3b82f6;
  --primary-color-rgb: 59, 130, 246;
  --secondary-color: #8899ac;
  --secondary-color-rgb: 136, 153, 172;
  --success-color: #22c55e;
  --success-color-rgb: 34, 197, 94;
  --danger-color: #ef4444;
  --danger-color-rgb: 239, 68, 68;
  --warning-color: #f59e0b;
  --warning-color-rgb: 245, 158, 11;
  --info-color: #38bdf8;
  --info-color-rgb: 56, 189, 248;
  --shadow-color: rgba(0, 0, 0, 0.3);
  --table-header-bg: #252525;
  --table-row-hover: rgba(255, 255, 255, 0.05);
  --card-bg: #1e1e1e;
  --navbar-bg: #1a1a1a;
  --input-bg: #2c2c2c;
  --input-border: #3a3b3c;
  --scrollbar-track: #252525;
  --scrollbar-thumb: #505050;
  --toast-bg: rgba(30, 30, 30, 0.9);
  --modal-bg: #1e1e1e;
  --dropdown-bg: #1e1e1e;
  --dropdown-hover: #2c2c2c;
}

/* General element styling */
body {
  background-color: var(--bg-primary);
  color: var(--text-primary);
  transition: var(--tran-03);
}

.card {
  background-color: var(--card-bg);
  border-color: var(--border-color);
  box-shadow: 0 0.125rem 0.25rem var(--shadow-color);
  transition: var(--tran-03);
}

.card-header, .card-footer {
  background-color: var(--bg-secondary);
  border-color: var(--border-color);
}

.navbar-brand {
    font-weight: 700;
}

.btn {
    border-radius: 0.375rem;
}

.table {
    margin-bottom: 0;
    color: var(--text-primary);
    border-color: var(--border-color);
}

.table thead th {
    background-color: var(--table-header-bg);
    color: var(--text-primary);
    border-color: var(--border-color);
}

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

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

.table-striped tbody tr:nth-of-type(odd) {
    background-color: var(--bg-secondary);
}

.analysis-container {
    min-height: 600px;
}

.sample-analysis-card {
    border-left: 4px solid #007bff;
}

.exon-checkbox {
    margin-right: 10px;
}

.mutation-modal .dropdown-menu {
    max-height: 250px;
    overflow-y: auto;
}

.filter-section {
    background-color: #fff;
    padding: 20px;
    border-radius: 0.375rem;
    box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);
    margin-bottom: 20px;
}

.sample-card {
    transition: transform 0.2s;
}

.sample-card:hover {
    transform: translateY(-2px);
}

.exon-section {
    border: 1px solid #dee2e6;
    border-radius: 0.375rem;
    padding: 15px;
    margin-bottom: 15px;
    background-color: #fff;
}

.exon-header {
    font-weight: 600;
    color: #495057;
    margin-bottom: 10px;
}

.mutation-tag {
    background-color: #e3f2fd;
    border: 1px solid #2196f3;
    padding: 5px 10px;
    border-radius: 15px;
    margin: 2px;
    display: inline-block;
    font-size: 0.875rem;
}

.note-tag {
    background-color: #fff3e0;
    border: 1px solid #ff9800;
    padding: 5px 10px;
    border-radius: 15px;
    margin: 2px;
    display: inline-block;
    font-size: 0.875rem;
}

.loading-spinner {
    text-align: center;
    padding: 50px;
}

.empty-state {
    text-align: center;
    padding: 50px;
    color: #6c757d;
}

.form-floating {
    margin-bottom: 15px;
}

.pool-assignment {
    border: 1px solid #dee2e6;
    border-radius: 0.375rem;
    padding: 15px;
    margin-bottom: 15px;
    background-color: #fff;
}

.pool-assignment.assigned {
    border-color: #28a745;
    background-color: #f8fff9;
}

.admin-section {
    background-color: #fff;
    border-radius: 0.375rem;
    padding: 20px;
    margin-bottom: 20px;
    box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);
}

.status-badge {
    font-size: 0.75rem;
    padding: 0.375rem 0.75rem;
}

.export-section {
    background-color: #fff;
    border-radius: 0.375rem;
    padding: 20px;
    margin-top: 20px;
    box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);
}

/* Responsive adjustments */
@media (max-width: 768px) {
    .card-header h5 {
        font-size: 1.1rem;
    }
    
    .btn-sm {
        font-size: 0.8rem;
        padding: 0.25rem 0.5rem;
    }
    
    .table-responsive {
        font-size: 0.875rem;
    }
    
    .analysis-container {
        padding: 10px;
    }
}

/* Print styles */
@media print {
    .no-print {
        display: none !important;
    }
    
    body {
        background-color: white;
    }
    
    .card {
        box-shadow: none;
        border: 1px solid #dee2e6;
    }
}

/* Custom scrollbar */
.custom-scrollbar {
    scrollbar-width: thin;
    scrollbar-color: #6c757d #f8f9fa;
}

.custom-scrollbar::-webkit-scrollbar {
    width: 8px;
}

.custom-scrollbar::-webkit-scrollbar-track {
    background: #f8f9fa;
}

.custom-scrollbar::-webkit-scrollbar-thumb {
    background-color: #6c757d;
    border-radius: 4px;
}

.custom-scrollbar::-webkit-scrollbar-thumb:hover {
    background-color: #495057;
}
/* Profile page styles */
.profile-wrapper { max-width: 900px; }
.profile-card {
    border: none;
    border-radius: 0.5rem;
    box-shadow: 0 2px 6px rgba(0,0,0,0.05);
}
.profile-card .card-header {
    background: linear-gradient(135deg, var(--bs-primary), var(--bs-info));
    color: #fff;
    border-bottom: none;
    border-radius: 0.5rem 0.5rem 0 0;
    text-align: center;
}
.profile-avatar {
    width: 100px;
    height: 100px;
    border-radius: 50%;
    background: var(--bs-primary);
    color: #fff;
    display: flex;
    align-items: center;
    justify-content: center;
    font-size: 2rem;
    margin: -55px auto 15px;
    box-shadow: 0 0 0 4px #fff;
}
/* Google Font Import - Poppins */
@import url('https://fonts.googleapis.com/css2?family=Poppins:wght@300;400;500;600;700&display=swap');
*{
    margin: 0;
    padding: 0;
    box-sizing: border-box;
    font-family: 'Poppins', sans-serif;
}
:root{
    /* ===== Colors ===== */
    --body-color: #E4E9F7;
    --sidebar-color: #FFF;
    --primary-color: #695CFE;
    --primary-color-light: #F6F5FF;
    --toggle-color: #DDD;
    --text-color: #707070;
    /* ====== Transition ====== */
    --tran-03: all 0.2s ease;
    --tran-03: all 0.3s ease;
    --tran-04: all 0.3s ease;
    --tran-05: all 0.3s ease;
}
body{
    min-height: 100vh;
    background-color: var(--body-color);
    transition: var(--tran-05);
    font-size: 0.9rem;
}
::selection{
    background-color: var(--primary-color);
    color: #fff;
}
body.dark{
    --body-color: #18191a;
    --sidebar-color: #242526;
    --primary-color: #3a3b3c;
    --primary-color-light: #3a3b3c;
    --toggle-color: #fff;
    --text-color: #ccc;
}
/* Dark mode styles */
body.dark {
  background-color: #121212;
  color: #f8f9fa;
}

body.dark .card,
body.dark .admin-section,
body.dark .filter-section,
body.dark .pool-assignment,
body.dark .exon-section,
body.dark .export-section {
  background-color: #1e1e1e;
  color: #f8f9fa;
}
body.dark .card-header,
body.dark .profile-card .card-header {
  background-color: #2c2c2c;
  border-color: #444;
  color: #fff;
}
body.dark #sidebar {
  background: linear-gradient(180deg, #1d1f2c, #101116);
}

body.dark #sidebar a:hover,
body.dark #sidebar a.active {

  background-color: rgba(255, 255, 255, 0.1);
}

/* Enhanced dark mode readability */
body.dark a {
  color: #9ecbff;
}

body.dark a:hover {
  color: #c6e2ff;
}

body.dark .form-control {
  background-color: #333;
  color: #f8f9fa;
  border-color: #555;
}

body.dark .form-control::placeholder {
  color: #bbb;
}

body.dark .table,
body.dark .table th,
body.dark .table td {
  color: #f8f9fa;
}

body.dark .table-striped > tbody > tr:nth-of-type(odd) {
  background-color: #2a2a2a;
}

body.dark .dropdown-menu {
  background-color: #2c2c2c;
  color: #f8f9fa;
}

body.dark .dropdown-item:hover {
  background-color: #3d3d3d;
}

body.dark .profile-card .card-header {
  background: linear-gradient(135deg, #333, #444);
}

/* Generic dark mode overrides */
body.dark .bg-light,
body.dark .bg-white {
  background-color: #2c2c2c !important;
  color: #f8f9fa;
}

body.dark footer.bg-light {
  background-color: #1e1e1e !important;
}

body.dark .text-dark {
  color: #f8f9fa !important;
}

body.dark .border-secondary {
  border-color: #555 !important;
}

/* Dark mode overrides for analysis components */
body.dark .exon-box,
body.dark .sample-analysis-section,
body.dark .result-summary,
body.dark .filter-card,
body.dark .phase-info,
body.dark .amino-acid-display,
body.dark .amino-preview {
  background: #1e1e1e;
  color: #f8f9fa;
  border-color: #555;
}

body.dark .exon-box.is-normal,
body.dark .exon-box.has-mutations {
  background: #2c2c2c;
}

body.dark .search-section,
body.dark .table-responsive .table-warning,
body.dark .table-warning,
body.dark .table-success {
  background-color: #1e1e1e !important;
  color: #f8f9fa;
}
/* Password toggle button */
.password-toggle {
  cursor: pointer;
  border-left: 0;
}

/* Redesigned sidebar */
#sidebar {
    position: fixed;
    top: 0;
    left: 0;
    width: 260px;
    height: 100vh;
    background-color: var(--card-bg);
    color: var(--text-primary);
    transition: var(--tran-03);
    z-index: 999;
    box-shadow: 0 0 10px var(--shadow-color);
    border-right: 1px solid var(--border-color);
    display: flex;
    flex-direction: column;
}

/* Sidebar Header */
.sidebar-header {
    padding: 20px;
    display: flex;
    align-items: center;
    justify-content: space-between;
    border-bottom: 1px solid var(--border-color);
}

.sidebar-header .logo {
    display: flex;
    align-items: center;
    font-weight: 600;
    font-size: 1.25rem;
}

.sidebar-header .logo i {
    font-size: 1.5rem;
    margin-right: 12px;
    color: var(--text-primary);
}

.sidebar-close {
    cursor: pointer;
    font-size: 1.25rem;
    color: var(--text-primary);
}

.sidebar-close:hover {
    color: var(--primary-color);
}

/* Sidebar Search */
.sidebar-search {
    padding: 15px;
    border-bottom: 1px solid var(--border-color);
}

.sidebar-search .input-group-text,
.sidebar-search .form-control {
    background-color: var(--bg-tertiary);
    border-color: var(--border-color);
    color: var(--text-primary);
}

.sidebar-search .form-control::placeholder {
    color: var(--text-secondary);
}

.sidebar-search .form-control:focus {
    box-shadow: none;
    border-color: var(--primary-color);
}

/* Sidebar Menu */
.sidebar-menu {
    list-style: none;
    padding: 0;
    margin: 0;
    overflow-y: auto;
    flex-grow: 1;
}

.sidebar-item a {
  display: flex;
  align-items: center;
    padding: 12px 20px;
    color: var(--text-primary);
    text-decoration: none;
    position: relative;
    border-left: 3px solid transparent;
    transition: all 0.2s ease;
}

.sidebar-item a:hover {
    background-color: var(--bg-tertiary);
    color: var(--primary-color);
    border-left-color: var(--primary-color);
}

.sidebar-item a.active {
    color: var(--primary-color);
    background-color: var(--bg-tertiary);
    border-left-color: var(--primary-color);
}

.sidebar-icon {
    width: 25px;
    margin-right: 10px;
    text-align: center;
    font-size: 1.1rem;
    color: var(--text-primary);
}

.sidebar-badge {
    margin-left: auto;
    font-size: 0.7rem;
    font-weight: 400;
}

.sidebar-divider {
    padding: 10px 20px;
    color: var(--text-secondary);
    font-size: 0.8rem;
    text-transform: uppercase;
    letter-spacing: 1px;
    margin-top: 10px;
    border-bottom: 1px solid var(--border-color);
}

.sidebar-divider span {
    position: relative;
    padding-right: 15px;
}

.sidebar-divider span:after {
    content: "";
    position: absolute;
    left: 100%;
  top: 50%;
    width: 40px;
    height: 1px;
    background-color: var(--border-color);
}

/* Sidebar Footer */
.sidebar-footer {
    padding: 15px;
    border-top: 1px solid var(--border-color);
    overflow: hidden;
}

.sidebar-footer .theme-switch {
    width: 100%;
    display: flex;
    align-items: center;
}

/* Toggler Button */
#sidebar-toggle {
    position: fixed;
    top: 15px;
    left: 220px;
    width: 40px;
    height: 40px;
    background: #fff;
    border-radius: 50%;
    box-shadow: 0 3px 10px rgba(0, 0, 0, 0.2);
    display: flex;
    align-items: center;
    justify-content: center;
    z-index: 1000;
    cursor: pointer;
    transition: all 0.3s;
    color: var(--text-primary);
}

#sidebar-toggle:hover {
    background-color: var(--bg-tertiary);
}

body.sidebar-collapsed #sidebar-toggle {
    left: 60px;
}

/* Body adjustments for sidebar */
body.with-sidebar { 
    margin-left: 260px; 
    transition: margin-left 0.3s ease; 
}

body.sidebar-collapsed.with-sidebar { 
    margin-left: 75px; 
}

/* Collapsed sidebar */
body.sidebar-collapsed #sidebar { 
    width: 70px; 
}

body.sidebar-collapsed #sidebar .menu-text,
body.sidebar-collapsed #sidebar .sidebar-search,
body.sidebar-collapsed #sidebar .sidebar-badge,
body.sidebar-collapsed #sidebar .theme-switch .menu-text {
    display: none;
}

body.sidebar-collapsed #sidebar .sidebar-divider {
    text-align: center;
}

body.sidebar-collapsed #sidebar .sidebar-divider span {
    display: none;
}

body.sidebar-collapsed #sidebar .sidebar-item a {
    justify-content: center;
}

body.sidebar-collapsed #sidebar .sidebar-icon {
    margin-right: 0;
}

body.sidebar-collapsed #sidebar .theme-switch {
    justify-content: center;
}

body.sidebar-collapsed .sidebar-footer {
    padding: 15px 7px;
    text-align: center;
}

body.sidebar-collapsed .dark-mode-toggle {
    width: 45px;
    height: 24px;
    margin: 0 auto;
}

body.sidebar-collapsed .dark-mode-ball {
    width: 20px;
    height: 20px;
}

body.sidebar-collapsed .dark-mode-input:checked + .dark-mode-label .dark-mode-ball {
    left: calc(100% - 22px);
}

body.sidebar-collapsed .dark-mode-sun,
body.sidebar-collapsed .dark-mode-moon {
    font-size: 12px;
    top: 4px;
}

/* Mobile adjustments */
@media (max-width: 768px) {
    body.with-sidebar { margin-left: 0; }
    #sidebar { transform: translateX(-100%); width: 260px; }
    body.sidebar-open #sidebar { transform: translateX(0); }
    #sidebar-toggle { left: 15px; }
    body.sidebar-collapsed #sidebar-toggle { left: 15px; }
    body.sidebar-collapsed.with-sidebar { margin-left: 0; }
}

/* Dark mode adjustments */
body.dark #sidebar {
    background: linear-gradient(180deg, #1a1d2d, #1d232d);
    color: var(--text-primary);
}

body.dark #sidebar-toggle {
    background: #2d3748;
    color: var(--text-primary);
}

body.dark #sidebar-toggle:hover {
    background: #374151;
}

body.dark .sidebar-search .input-group-text,
body.dark .sidebar-search .form-control {
    background-color: rgba(0, 0, 0, 0.2) !important;
    border-color: rgba(255, 255, 255, 0.05);
}

/* Modern Dark Mode Toggle */
.dark-mode-toggle {
  position: relative;
  width: 55px;
  height: 28px;
  margin: 0;
  flex-shrink: 0;
}

.dark-mode-input {
  opacity: 0;
  width: 0;
  height: 0;
}

.dark-mode-label {
  position: relative;
  display: block;
  width: 100%;
  height: 100%;
  background: linear-gradient(to right, #f6d365 0%, #fda085 100%);
  border-radius: 50px;
  cursor: pointer;
  box-shadow: 0 2px 4px rgba(0, 0, 0, 0.2);
  transition: all 0.4s ease;
}

body.dark .dark-mode-label {
  background: linear-gradient(to right, #4a4a6a 0%, #232336 100%);
}

.dark-mode-ball {
  position: absolute;
  width: 24px;
  height: 24px;
  top: 2px;
  left: 2px;
  background: #fff;
  border-radius: 50%;
  transition: all 0.3s cubic-bezier(0.68, -0.55, 0.27, 1.55);
  box-shadow: 0 2px 4px rgba(0, 0, 0, 0.2);
}

.dark-mode-input:checked + .dark-mode-label .dark-mode-ball {
  left: calc(100% - 26px);
}

.dark-mode-sun {
  position: absolute;
  left: 6px;
  top: 6px;
  font-size: 14px;
  color: #ffb300;
  z-index: 1;
  transition: all 0.3s ease;
}

.dark-mode-moon {
  position: absolute;
  right: 6px;
  top: 6px;
  font-size: 14px;
  color: #bbe1fa;
  z-index: 1;
  opacity: 0;
  transition: all 0.3s ease;
}

.dark-mode-input:checked + .dark-mode-label .dark-mode-sun {
  opacity: 0;
}

.dark-mode-input:checked + .dark-mode-label .dark-mode-moon {
  opacity: 1;
}

/* Mobile adjustments */
@media (max-width: 768px) {
    body.with-sidebar { margin-left: 0; }
    #sidebar { transform: translateX(-100%); }
    body.sidebar-open #sidebar { transform: translateX(0); }
    #sidebar-toggle { left: 15px; }
}

/* Utility classes moved from inline styles */
.icon-muted-lg { font-size: 2rem; color: #6c757d; }
.icon-muted-xl { font-size: 3rem; color: #6c757d; }
.icon-muted-xxl { font-size: 4rem; color: #6c757d; }
.min-w-130 { min-width: 130px; }
.progress-xs { height: 6px; }
.scroll-100 { max-height: 100px; overflow-y: auto; }
.max-h-400 { max-height: 400px; overflow-y: auto; }
.w-200 { width: 200px; }
.h-80 { height: 80px; }
.h-60 { height: 60px; }
.max-w-1200 { max-width: 1200px; }
.notification-fixed { position: fixed; top: 20px; right: 20px; z-index: 9999; min-width: 300px; }
.spinner-lg { width: 3rem; height: 3rem; }
/* Styles from dashboard.php */
.card { transition: transform 0.2s ease, box-shadow 0.2s ease; }
.card:hover { transform: translateY(-2px); box-shadow: 0 4px 8px rgba(0,0,0,0.1); }
.badge { font-size: 0.75em; }
.progress { height: 8px; }
.list-group-item { border-left: none; border-right: none; }
.list-group-item:first-child { border-top: none; }
.list-group-item:last-child { border-bottom: none; }
/* Styles from analysis.php */
.card-header[data-bs-toggle="collapse"] { transition: all 0.3s ease; }
.card-header[data-bs-toggle="collapse"]:hover { background-color: var(--bg-tertiary); }
.collapse-icon { transition: transform 0.3s ease; }
.card-header[aria-expanded="false"] .collapse-icon { transform: rotate(0deg); }
.card-header[aria-expanded="true"] .collapse-icon { transform: rotate(180deg); }
.analysis-active #samplesCollapse.collapse:not(.show) { border-top: 2px dashed var(--border-color); margin-top: 10px; }
#toggleSamplesBtn { font-size: 0.875rem; padding: 0.25rem 0.5rem; }
.table-dark .form-check-label { font-size: 0.875rem; color: white !important; }
.table-dark .form-check-input { margin-top: 0.125rem; }
/* Styles from test_simple.php */
body { font-family: Arial; margin: 20px; }
h2, h3 { color: #333; }
.success { color: green; font-weight: bold; }
.error { color: red; font-weight: bold; }
/* Styles from test-analysis.php */
.exon-box { border: 2px solid var(--border-color); border-radius: 12px; padding: 15px; margin: 10px; min-height: 200px; position: relative; background: var(--card-bg); transition: all 0.3s ease; }
.exon-box.is-normal { border-color: var(--success-color); background: linear-gradient(135deg, #fff 0%, #f8fff9 100%); }
.exon-box.has-mutations { border-color: var(--danger-color); background: linear-gradient(135deg, #fff 0%, #fff5f5 100%); }
.exon-box.compact { width: 90px; min-height: 120px; padding: 10px; }
.exon-grid {
    display: flex;
    flex-wrap: wrap;
    gap: 5px;
}
.exon-grid .exon-box { margin: 0; }
.exon-buttons { position: absolute; bottom: 10px; right: 10px; }
.mutation-tag { display: inline-block; padding: 4px 10px; margin: 3px 2px; border-radius: 15px; font-size: 0.8em; background: var(--bg-tertiary); border: 1px solid var(--border-color); }
/* Styles from admin/mutation_management.php */
.search-section { background: linear-gradient(135deg, var(--bg-tertiary) 0%, #e9ecef 100%); padding: 2rem; border-radius: 0.5rem; position: relative; }
.search-section .form-floating { position: relative; }
.autocomplete-results { position: absolute; top: 100%; left: 0; right: 0; z-index: 1050; background: var(--card-bg); border: 1px solid var(--border-color); border-top: none; border-radius: 0 0 0.375rem 0.375rem; box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15); max-height: 300px; overflow-y: auto; }
.autocomplete-results .list-group-item { border-radius: 0; border-left: none; border-right: none; }
.autocomplete-results .list-group-item:hover { background-color: var(--bg-tertiary); }
#geneStats .card { transition: transform 0.2s ease; }
#geneStats .card:hover { transform: translateY(-2px); }
#mutationFilter { border-radius: 0.375rem 0 0 0.375rem; }
.table thead th { position: sticky; top: 0; z-index: 10; background-color: var(--table-header-bg); }
.table-responsive { border-radius: 0.375rem; box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075); max-height: 70vh; overflow-y: auto; }
.table th, .table td {
    vertical-align: middle;
    font-size: 0.9rem;
    white-space: nowrap;
    padding: 0.25rem;
}

.table code {
    font-size: inherit;
}
#geneMutationsTable { min-width: 1800px; }
#geneMutationsTable th:first-child, #geneMutationsTable td:first-child { min-width: 80px; }
#geneMutationsTable th:nth-child(12), #geneMutationsTable td:nth-child(12) { min-width: 120px; }
#geneMutationsTable th:nth-child(13), #geneMutationsTable td:nth-child(13) { max-width: 150px; white-space: normal; word-wrap: break-word; }
#geneMutationsTable th:last-child, #geneMutationsTable td:last-child { min-width: 100px; }
@media (max-width: 1200px) { #geneMutationsTable th:nth-child(2), #geneMutationsTable td:nth-child(2), #geneMutationsTable th:nth-child(3), #geneMutationsTable td:nth-child(3) { display: none; } }
@media (max-width: 992px) { #geneMutationsTable th:nth-child(7), #geneMutationsTable td:nth-child(7), #geneMutationsTable th:nth-child(16), #geneMutationsTable td:nth-child(16), #geneMutationsTable th:nth-child(17), #geneMutationsTable td:nth-child(17) { display: none; } }
.badge { font-size: 0.75em; }
.btn-group-sm > .btn, .btn-sm { font-size: 0.875rem; }
.card { transition: transform 0.2s; }
.card:hover { transform: translateY(-2px); box-shadow: 0 4px 8px rgba(0,0,0,0.1); }
.spinner-border-sm { width: 1rem; height: 1rem; }
.modal-xl { max-width: 1200px; }
@keyframes spin { 0% { transform: rotate(0deg); } 100% { transform: rotate(360deg); } }
.animate-spin { animation: spin 1s linear infinite; }
/* Styles from admin/mutation_check.php */
.table-warning { --bs-table-bg: #fff3cd; }
.table-success { --bs-table-bg: #d1e7dd; }
.comparison-checkbox:checked { background-color: var(--success-color); border-color: var(--success-color); }
.card { box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075); border: 1px solid rgba(0, 0, 0, 0.125); }
.badge a { color: inherit; text-decoration: none; }
.badge:hover { transform: scale(1.05); transition: transform 0.2s; }
.btn-group-sm > .btn, .btn-sm { font-size: 0.875rem; }
#selectAllComparisons:indeterminate { background-color: var(--success-color); border-color: var(--success-color); }
.modal-xl { max-width: 1200px; }
.container-fluid { max-width: 1400px; }
/* Styles from admin/analysis_control.php */
.table-success { --bs-table-bg: #d1e7dd; }
.sample-checkbox:checked { background-color: var(--success-color); border-color: var(--success-color); }
#selectAll:indeterminate { background-color: var(--success-color); border-color: var(--success-color); }
.card { box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075); border: 1px solid rgba(0, 0, 0, 0.125); }
textarea.form-control-sm { min-height: 80px; resize: vertical; }
.container-fluid { max-width: 1600px; }
.text-wrap { white-space: normal !important; word-wrap: break-word; }
.badge.text-wrap { display: inline-block; max-width: 100%; text-align: left; }
.bg-gradient { background: linear-gradient(135deg, #007bff 0%, #0056b3 100%); color: white; }
.card-header.bg-gradient h5 { color: white; }
.h-100 { height: 100% !important; }
.border-secondary { border-color: var(--border-color) !important; }
.bg-light .card-header { background-color: var(--bg-tertiary) !important; }
/* Styles from admin/user_management.php */
.user-avatar { width: 40px; height: 40px; border-radius: 50%; background: linear-gradient(135deg, #007bff, #6610f2); color: white; display: flex; align-items: center; justify-content: center; font-weight: bold; font-size: 0.875rem; }
.permission-badge { font-size: 0.7rem; margin: 1px; }
.stats-card { background: linear-gradient(135deg, var(--bs-primary), var(--bs-info)); color: white; border: none; }
.search-box { background: var(--bg-tertiary); border-radius: 1rem; padding: 1.5rem; margin-bottom: 1.5rem; }
.table-wrapper { background: var(--card-bg); border-radius: 0.5rem; box-shadow: 0 2px 10px rgba(0,0,0,0.1); }
.modal-header { border-bottom: 2px solid var(--border-color); }
.form-floating { margin-bottom: 1rem; }
.btn-group-actions { gap: 0.25rem; }

.h-100px { height: 100px; }
.icon-success-xl { font-size: 3rem; color: var(--success-color); }
.note-cell {
    max-width: 120px;
    overflow: hidden;
    text-overflow: ellipsis;
    white-space: nowrap;
}

/* Geliştirilmiş sekmeler */
.nav-custom .nav-link {
    font-weight: 500;
    display: flex;
    align-items: center;
    gap: 0.25rem;
    font-size: 1.25rem;
    padding: 0.75rem 1.5rem;
}

.nav-custom .nav-link.active {
    background-color: var(--bs-primary);
    color: #fff;
}

.nav-custom .nav-link i {
    font-size: 1.5rem;
}

/* Forms */
.form-control, .form-select {
  background-color: var(--input-bg);
  border-color: var(--input-border);
  color: var(--text-primary);
}

.form-control:focus, .form-select:focus {
  background-color: var(--input-bg);
  color: var(--text-primary);
  border-color: var(--primary-color);
  box-shadow: 0 0 0 0.25rem rgba(var(--primary-color-rgb), 0.25);
}

.input-group-text {
  background-color: var(--bg-tertiary);
  border-color: var(--input-border);
  color: var(--text-primary);
}

.form-check-input {
  background-color: var(--input-bg);
  border-color: var(--input-border);
}

/* Labels and text */
.text-muted {
  color: var(--text-secondary) !important;
}

.form-label, .col-form-label {
  color: var(--text-primary);
}

/* Buttons */
.btn-light {
  background-color: var(--bg-tertiary);
  border-color: var(--border-color);
  color: var(--text-primary);
}

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

.btn-outline-secondary {
  color: var(--secondary-color);
  border-color: var(--secondary-color);
}

/* Modals */
.modal-content {
  background-color: var(--modal-bg);
  border-color: var(--border-color);
}

.modal-header, .modal-footer {
  border-color: var(--border-color);
}

/* Dropdowns */
.dropdown-menu {
  background-color: var(--dropdown-bg);
  border-color: var(--border-color);
}

.dropdown-item {
  color: var(--text-primary);
}

.dropdown-item:hover, .dropdown-item:focus {
  background-color: var(--dropdown-hover);
  color: var(--text-primary);
}

/* Navs */
.nav-tabs {
  border-bottom-color: var(--border-color);
}

.nav-tabs .nav-link.active {
  background-color: var(--bg-primary);
  color: var(--text-primary);
  border-color: var(--border-color);
}

.nav-tabs .nav-link:not(.active) {
  color: var(--text-secondary);
}

/* Alerts */
.alert {
  border-color: transparent;
}

/* Progress */
.progress {
  background-color: var(--bg-tertiary);
}

/* Pagination */
.pagination .page-item .page-link {
  background-color: var(--bg-tertiary);
  border-color: var(--border-color);
  color: var(--text-primary);
}

.pagination .page-item.active .page-link {
  background-color: var(--primary-color);
  border-color: var(--primary-color);
  color: #fff;
}

/* List groups */
.list-group-item {
  background-color: var(--card-bg);
  border-color: var(--border-color);
  color: var(--text-primary);
}

/* Code */
pre, code {
  background-color: var(--bg-tertiary);
  color: var(--text-primary);
}

/* Accordion */
.accordion-item {
  background-color: var(--card-bg);
  border-color: var(--border-color);
}

.accordion-button {
  background-color: var(--bg-tertiary);
  color: var(--text-primary);
}

.accordion-button:not(.collapsed) {
  background-color: var(--bg-secondary);
  color: var(--text-primary);
}

/* Links */
a {
  color: var(--primary-color);
}

a:hover {
  color: rgba(var(--primary-color-rgb), 0.8);
}

/* Scrollbar styling */
::-webkit-scrollbar {
  width: 8px;
  height: 8px;
}

::-webkit-scrollbar-track {
  background: var(--scrollbar-track);
}

::-webkit-scrollbar-thumb {
  background: var(--scrollbar-thumb);
  border-radius: 4px;
}

::-webkit-scrollbar-thumb:hover {
  background: var(--text-secondary);
}

/* Toast Notifications */
.toast {
    background-color: var(--toast-bg);
    border-color: var(--border-color);
    color: var(--text-primary);
}

.toast-header {
    background-color: var(--bg-secondary);
    color: var(--text-primary);
    border-bottom-color: var(--border-color);
}

.toast-body {
    color: var(--text-primary);
}

/* Gene chips and chip selections */
.gene-chip {
    background-color: var(--bg-tertiary);
    border: 1px solid var(--border-color);
    color: var(--text-primary);
}

.gene-chip.selected, .gene-chip:hover {
    background-color: var(--primary-color);
    color: #ffffff;
    border-color: var(--primary-color);
}

/* Search highlight */
.highlight-match {
    background-color: rgba(var(--warning-color-rgb), 0.3);
    padding: 0 2px;
    border-radius: 2px;
}

/* Mutation management specific styles */
.mutation-management .table th, .mutation-management .table td {
    color: var(--text-primary);
    border-color: var(--border-color);
}

.mutation-management .table thead th {
    background-color: var(--table-header-bg);
}

/* Export buttons and tools */
.export-buttons .btn {
    color: var(--text-primary);
    background-color: var(--bg-tertiary);
    border-color: var(--border-color);
}

.export-buttons .btn:hover {
    background-color: var(--bg-secondary);
}

/* Analysis page */
.analysis-section {
    background-color: var(--card-bg);
    border-color: var(--border-color);
}

.analysis-results {
    background-color: var(--bg-secondary);
}

.analysis-step {
    border-bottom: 1px solid var(--border-color);
}

.analysis-step.active {
    background-color: var(--bg-tertiary);
}

/* Dashboard widgets */
.stat-card {
    background-color: var(--card-bg);
    border-color: var(--border-color);
}

.stat-card .stat-icon {
    color: var(--primary-color);
}

/* Bootstrap dark mode overrides */
body.dark .btn-outline-primary {
  color: var(--primary-color);
  border-color: var(--primary-color);
}

body.dark .btn-outline-primary:hover {
  color: #fff;
  background-color: var(--primary-color);
}

body.dark .btn-outline-secondary {
  color: var(--secondary-color);
  border-color: var(--secondary-color);
}

body.dark .btn-outline-secondary:hover {
  color: #fff;
  background-color: var(--secondary-color);
}

body.dark .btn-outline-success {
  color: var(--success-color);
  border-color: var(--success-color);
}

body.dark .btn-outline-success:hover {
  color: #fff;
  background-color: var(--success-color);
}

body.dark .btn-outline-danger {
  color: var(--danger-color);
  border-color: var(--danger-color);
}

body.dark .btn-outline-danger:hover {
  color: #fff;
  background-color: var(--danger-color);
}

/* Bootstrap badges dark mode */
body.dark .badge.bg-primary {
  background-color: var(--primary-color) !important;
}

body.dark .badge.bg-secondary {
  background-color: var(--secondary-color) !important;
}

body.dark .badge.bg-success {
  background-color: var(--success-color) !important;
}

body.dark .badge.bg-danger {
  background-color: var(--danger-color) !important;
}

body.dark .badge.bg-warning {
  background-color: var(--warning-color) !important;
}

body.dark .badge.bg-info {
  background-color: var(--info-color) !important;
}

/* Special case: gradient backgrounds for dark mode */
body.dark .bg-gradient {
  background-image: linear-gradient(180deg, rgba(255, 255, 255, 0.05), rgba(255, 255, 255, 0)) !important;
}

/* Charts and graphs in dark mode */
body.dark .chart-container canvas {
  filter: brightness(0.9) contrast(1.1);
}

/* Fix for bootstrap table striped in dark mode */
body.dark .table-striped > tbody > tr:nth-of-type(odd) > * {
  color: var(--text-primary);
  background-color: rgba(255, 255, 255, 0.05);
}

/* Fix for default bootstrap table borders in dark mode */
body.dark .table {
  --bs-table-color: var(--text-primary);
  --bs-table-bg: transparent;
  --bs-table-border-color: var(--border-color);
}

/* Custom shadows for dark mode */
body.dark .shadow-sm {
  box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.3) !important;
}

body.dark .shadow {
  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.4) !important;
}

body.dark .shadow-lg {
  box-shadow: 0 1rem 3rem rgba(0, 0, 0, 0.5) !important;
}

/* Theme-specific gradients for dark mode */
body.dark .gradient-dark {
  background: linear-gradient(135deg, #13151a 0%, #1e2029 100%);
}

body.dark .gradient-primary {
  background: linear-gradient(135deg, #1a365d 0%, #2563eb 100%);
}

body.dark .gradient-success {
  background: linear-gradient(135deg, #064e3b 0%, #059669 100%);
}

body.dark .gradient-danger {
  background: linear-gradient(135deg, #7f1d1d 0%, #dc2626 100%);
}

/* Sidebar additional dark mode styling */
body.dark #sidebar {
  background: linear-gradient(180deg, #1a1d2d, #1d232d);
  color: var(--text-primary);
}

body.dark .sidebar-header {
  border-bottom-color: rgba(255, 255, 255, 0.1);
}

body.dark .sidebar-item a {
  color: var(--text-secondary);
}

body.dark .sidebar-item a:hover, 
body.dark .sidebar-item a.active {
  background-color: rgba(255, 255, 255, 0.1);
  color: #fff;
}

body.dark .sidebar-search .form-control:focus {
  border-color: rgba(255, 255, 255, 0.3);
}

body.dark .sidebar-divider:after {
  background-color: rgba(255, 255, 255, 0.1);
}

body.dark .sidebar-footer {
  border-top: 1px solid rgba(255, 255, 255, 0.1);
}

body.dark #sidebar-collapse-btn {
  background-color: rgba(255, 255, 255, 0.1);
  color: var(--text-secondary);
  border-color: rgba(255, 255, 255, 0.1);
}

body.dark #sidebar-collapse-btn:hover {
  background-color: rgba(255, 255, 255, 0.2);
  color: #fff;
}

/* Fixes for hard-coded colors in exon displays */
body.dark .exon-box {
  background: var(--card-bg);
  border-color: var(--border-color);
}

body.dark .exon-box.is-normal {
  border-color: var(--success-color);
  background: linear-gradient(135deg, var(--bg-secondary) 0%, rgba(var(--success-color-rgb), 0.1) 100%);
}

body.dark .exon-box.has-mutations {
  border-color: var(--danger-color);
  background: linear-gradient(135deg, var(--bg-secondary) 0%, rgba(var(--danger-color-rgb), 0.1) 100%);
}

/* Fix for color codes in gene chips */
body.dark .gene-chip {
  background-color: rgba(255, 255, 255, 0.1);
  border: 1px solid var(--border-color);
}

/* Fix for search section gradients */
body.dark .search-section {
  background: linear-gradient(135deg, var(--bg-secondary) 0%, var(--bg-tertiary) 100%);
}

/* Fix for stats cards */
body.dark .stats-card {
  background: linear-gradient(135deg, rgba(var(--primary-color-rgb), 0.8), rgba(var(--info-color-rgb), 0.8));
}

/* Make alerts in dark mode slightly transparent */
body.dark .alert-success {
  background-color: rgba(var(--success-color-rgb), 0.2);
  color: var(--success-color);
  border-color: rgba(var(--success-color-rgb), 0.3);
}

body.dark .alert-danger {
  background-color: rgba(var(--danger-color-rgb), 0.2);
  color: var(--danger-color);
  border-color: rgba(var(--danger-color-rgb), 0.3);
}

body.dark .alert-warning {
  background-color: rgba(var(--warning-color-rgb), 0.2);
  color: var(--warning-color);
  border-color: rgba(var(--warning-color-rgb), 0.3);
}

body.dark .alert-info {
  background-color: rgba(var(--info-color-rgb), 0.2);
  color: var(--info-color);
  border-color: rgba(var(--info-color-rgb), 0.3);
}

/* Fix for table variants in dark mode */
body.dark .table-success, 
body.dark .table-success > th, 
body.dark .table-success > td {
  background-color: rgba(var(--success-color-rgb), 0.2) !important;
}

body.dark .table-danger, 
body.dark .table-danger > th, 
body.dark .table-danger > td {
  background-color: rgba(var(--danger-color-rgb), 0.2) !important;
}

body.dark .table-warning, 
body.dark .table-warning > th, 
body.dark .table-warning > td {
  background-color: rgba(var(--warning-color-rgb), 0.2) !important;
}

body.dark .table-info, 
body.dark .table-info > th, 
body.dark .table-info > td {
  background-color: rgba(var(--info-color-rgb), 0.2) !important;
}

/* Custom purple color for rare polymorphisms */
.bg-purple {
  background-color: #6f42c1 !important;
  color: #fff !important;
}

.text-purple {
  color: #6f42c1 !important;
}

.border-purple {
  border-color: #6f42c1 !important;
}

/* Dark mode renkler için düzenleme */
body.dark .bg-purple {
  background-color: #8540e6 !important;
}

body.dark .text-purple {
  color: #a87ff3 !important;
}

body.dark .border-purple {
  border-color: #8540e6 !important;
}

/* Mobil Başlık Stili */
.mobile-header {
  background-color: var(--navbar-bg);
  box-shadow: 0 2px 4px var(--shadow-color);
  height: 60px;
  position: fixed;
  top: 0;
  left: 0;
  right: 0;
  z-index: 1040;
  padding: 0 15px;
}

.mobile-logo {
  display: flex;
  align-items: center;
  font-weight: 600;
  font-size: 1.25rem;
  color: var(--text-primary);
}

.mobile-logo i {
  margin-right: 8px;
  color: var(--primary-color);
  font-size: 1.5rem;
}

#mobile-toggle {
  border: none;
  background: transparent;
  color: var(--text-primary);
  font-size: 1.5rem;
  padding: 0;
  display: flex;
  align-items: center;
  justify-content: center;
  width: 40px;
  height: 40px;
  border-radius: 8px;
}

#mobile-toggle:hover {
  background-color: var(--bg-tertiary);
}

/* Dark mode mobile header */
body.dark .mobile-header {
  background-color: var(--navbar-bg);
  border-bottom: 1px solid var(--border-color);
}

body.dark .mobile-logo {
  color: var(--text-primary);
}

body.dark #mobile-toggle:hover {
  background-color: var(--bg-tertiary);
}

/* Mobil görünüm için sidebar ve içerik ayarı */
@media (max-width: 768px) {
  body.with-sidebar {
    margin-left: 0;
    padding-top: 60px; /* Mobil header'ın yüksekliği */
  }
  
  #sidebar {
    transform: translateX(-100%);
    width: 260px;
    top: 60px; /* Mobil header'ın yüksekliği */
  }
  
  body.sidebar-open #sidebar {
    transform: translateX(0);
  }
  
  /* Sidebar toggle butonu pozisyonu */
  #sidebar-toggle {
    left: 15px;
    top: 70px; /* Mobil header'ın altında */
    display: none; /* Mobil versiyon için gizliyoruz */
  }
}

.content-wrapper {
  padding: 2rem;
  width: 100%;
  min-height: 100vh; 
  transition: var(--tran-03);
}

@media (max-width: 768px) {
  .content-wrapper {
    padding: 1rem;
    padding-top: 70px; /* Mobil header'dan dolayı ek padding */
  }
}

/* Sistem ayarları sayfası stil düzeltmeleri */
.bg-gradient-primary {
  background: linear-gradient(135deg, var(--primary-color) 0%, #4d92ff 100%);
}

.bg-gradient-success {
  background: linear-gradient(135deg, var(--success-color) 0%, #2fd86d 100%);
}

.bg-gradient-info {
  background: linear-gradient(135deg, var(--info-color) 0%, #40d9ff 100%);
}

.bg-gradient-secondary {
  background: linear-gradient(135deg, #6c757d 0%, #495057 100%);
}

.bg-gradient-warning {
  background: linear-gradient(135deg, var(--warning-color) 0%, #ffcc2d 100%);
}

.bg-gradient-purple {
  background: linear-gradient(135deg, #6f42c1 0%, #8540e6 100%);
}

.stat-icon-container {
  width: 54px;
  height: 54px;
  border-radius: 12px;
  display: flex;
  align-items: center;
  justify-content: center;
}