:root {
    /* Base non-changing vars */
    --primary: #6C2A6A;
    --primary-rgb: 108, 42, 106;
    --primary-hover: #4a1c49;
    --primary-text: #6C2A6A;
    --transition: 0.3s cubic-bezier(0.4, 0, 0.2, 1);
}

:root, .theme-dark {
    --bg-color: #1B1B1B;
    --text-main: #f5f5f5;
    --text-muted: #b5b5b5;
    --link-color: #d79bd5;
    --link-hover: #ebb1e9;
    --primary-text: #d79bd5;
    --glass-bg: rgba(40, 40, 40, 0.85);
    --glass-border: rgba(255, 255, 255, 0.1);
    
    --glass-header-bg: var(--glass-panel-bg);
    --glass-panel-bg: rgba(0, 0, 0, 0.2);
    --glass-panel-bg-light: rgba(0, 0, 0, 0.1);
    --glass-hover-bg: rgba(255, 255, 255, 0.1);
    --glass-overlay-bg: rgba(27, 27, 27, 0.85);
    --glass-border-faint: rgba(255, 255, 255, 0.05);
    
    --table-header-bg: rgba(0, 0, 0, 0.3);
    
    --db-k-color: rgba(108, 42, 106, 0.25); /* Purple tint for K-locus */
    --db-o-color: rgba(141, 203, 137, 0.25); /* Green tint for O-locus */
}

.theme-light {
    --bg-color: #f8fafc;
    --text-main: #0f172a;
    --text-muted: #475569;
    --link-color: #6C2A6A;
    --link-hover: #4a1c49;
    --primary-text: #6C2A6A;
    --glass-bg: rgba(255, 255, 255, 0.85);
    --glass-border: rgba(0, 0, 0, 0.1);
    
    --glass-header-bg: var(--glass-panel-bg);
    --glass-panel-bg: rgba(0, 0, 0, 0.04);
    --glass-panel-bg-light: rgba(0, 0, 0, 0.02);
    --glass-hover-bg: rgba(0, 0, 0, 0.05);
    --glass-overlay-bg: rgba(255, 255, 255, 0.85);
    --glass-border-faint: rgba(0, 0, 0, 0.05);
    
    --table-header-bg: rgba(0, 0, 0, 0.04);
    
    --db-k-color: rgba(108, 42, 106, 0.15);
    --db-o-color: rgba(141, 203, 137, 0.15);
}

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

body {
    font-family: 'Varela Round', sans-serif;
    background-color: var(--bg-color);
    color: var(--text-main);
    overflow: hidden;
    height: 100vh;
}

/* Custom Scrollbars */
::-webkit-scrollbar {
    width: 10px;
    height: 10px;
}

::-webkit-scrollbar-track {
    background: transparent;
}

::-webkit-scrollbar-thumb {
    background: rgba(128, 128, 128, 0.4);
    border-radius: 5px;
    border: 2px solid transparent;
    background-clip: padding-box;
}

::-webkit-scrollbar-thumb:hover {
    background: rgba(128, 128, 128, 0.6);
    border: 2px solid transparent;
    background-clip: padding-box;
}

::-webkit-scrollbar-corner {
    background: transparent;
}

a {
    color: var(--link-color);
    text-decoration: none;
    transition: color var(--transition);
}

a:hover {
    color: var(--link-hover);
    text-decoration: underline;
}

/* Background Shapes for Glassmorphism Context */
.bg-shape {
    position: absolute;
    border-radius: 50%;
    filter: blur(100px);
    z-index: -1;
    opacity: 0.5;
}

.shape-1 {
    top: 10%;
    left: -10%;
    width: 50vw;
    height: 50vw;
    background: radial-gradient(circle, rgba(108,42,106,0.4) 0%, rgba(0,0,0,0) 70%);
}

.shape-2 {
    bottom: -10%;
    right: -10%;
    width: 40vw;
    height: 40vw;
    background: radial-gradient(circle, rgba(141,203,137,0.3) 0%, rgba(0,0,0,0) 70%);
}

/* Buttons */
.btn {
    display: inline-flex;
    align-items: center;
    justify-content: center;
    gap: 0.5rem;
    padding: 0.5rem 1rem;
    border-radius: 6px;
    font-family: inherit;
    font-weight: 500;
    font-size: 0.9rem;
    cursor: pointer;
    border: none;
    transition: background-color var(--transition), transform 0.1s;
    text-decoration: none;
}

.btn:active { transform: scale(0.97); }

.btn-primary {
    background-color: var(--primary);
    color: white;
}
.btn-primary:hover { background-color: var(--primary-hover); }

.btn-secondary {
    background-color: var(--glass-hover-bg);
    color: var(--text-main);
    border: 1px solid var(--glass-border);
}
.btn-secondary:hover { background-color: var(--glass-panel-bg); }

.btn-ghost {
    background: transparent;
    color: var(--text-muted);
}
.btn-ghost:hover {
    color: var(--text-main);
    background: var(--glass-border-faint);
}

.btn-icon { padding: 0.4rem; border-radius: 4px; }

/* View Management */
.view-container {
    display: none;
    height: 100vh;
    width: 100vw;
}
.view-container.active { display: flex; flex-direction: column; }

/* ---------------- Auth View ---------------- */
#auth-view {
    align-items: center;
    justify-content: center;
}

.glass-card {
    background: var(--glass-bg);
    backdrop-filter: blur(16px);
    -webkit-backdrop-filter: blur(16px);
    border: 1px solid var(--glass-border);
    border-radius: 16px;
    padding: 3rem;
    text-align: center;
    box-shadow: 0 25px 50px -12px rgba(0, 0, 0, 0.5);
}

.brand-title { font-size: 3rem; margin-bottom: 0.5rem; font-weight: 700; }
.brand-subtitle { color: var(--text-muted); margin-bottom: 2rem; }
.highlight { color: var(--primary-text); font-weight: 700; }

.login-inputs {
    display: flex;
    flex-direction: column;
    gap: 1rem;
    margin-bottom: 1.5rem;
}

.form-input {
    background: var(--glass-panel-bg);
    border: 1px solid var(--glass-border);
    color: var(--text-main);
    padding: 0.75rem 1rem;
    border-radius: 6px;
    font-family: inherit;
    font-size: 1rem;
    outline: none;
    transition: border-color var(--transition);
    box-sizing: border-box;
}
.form-input:focus { border-color: var(--primary); }

.divider {
    display: flex;
    align-items: center;
    color: var(--text-muted);
    font-size: 0.85rem;
    margin-bottom: 1.5rem;
}
.divider::before, .divider::after {
    content: "";
    flex: 1;
    border-bottom: 1px solid var(--glass-border);
}
.divider span { padding: 0 1rem; }

/* ---------------- Dashboard View ---------------- */
.glass-header {
    background: var(--glass-header-bg);
    backdrop-filter: blur(24px);
    -webkit-backdrop-filter: blur(24px);
    border-bottom: 1px solid var(--glass-border);
    padding: 0 2rem;
    display: flex;
    justify-content: space-between;
    align-items: center;
    height: 70px;
}

.logo-container {
    display: flex;
    align-items: center;
    gap: 0.75rem;
}

.header-logo {
    height: 36px;
    width: auto;
}

.logo { font-size: 1.5rem; font-weight: 700; }

.header-tabs {
    display: flex;
    height: 100%;
    gap: 2rem;
}

.tab-btn {
    background: none;
    border: none;
    color: var(--text-muted);
    font-family: inherit;
    font-size: 1rem;
    font-weight: 500;
    cursor: pointer;
    padding: 0 0.5rem;
    height: 100%;
    position: relative;
    transition: color 0.2s;
}

.tab-btn:hover { color: var(--text-main); }

.tab-btn.active { color: var(--primary-text); }
.tab-btn.active::after {
    content: '';
    position: absolute;
    bottom: 0;
    left: 0;
    right: 0;
    height: 3px;
    background: var(--primary-text);
    border-top-left-radius: 3px;
    border-top-right-radius: 3px;
}

.header-actions {
    display: flex;
    gap: 1.5rem;
    align-items: center;
}

.user-profile {
    display: flex;
    align-items: center;
    gap: 1rem;
    border-left: 1px solid var(--glass-border);
    padding-left: 1.5rem;
}

/* Tab Layout */
.tab-content-container {
    flex: 1;
    overflow: hidden;
    position: relative;
}

.tab-pane {
    position: absolute;
    inset: 0;
    display: none;
    padding: 1rem;
}
.tab-pane.active {
    display: flex; /* or block depending on pane */
}
.tab-pane.block-tab.active {
    display: block;
}

/* Home Grid */
.home-grid {
    display: grid;
    grid-template-columns: 1fr 1fr;
    gap: 1.5rem;
    width: 100%;
    max-width: 1280px;
    margin: 0 auto;
    height: 100%;
}
.home-grid .glass-panel {
    padding: 1.5rem;
}
.home-grid h2 { margin-bottom: 0.25rem; }
.home-grid .subtitle {
    color: var(--text-muted);
    margin-bottom: 1.5rem;
    font-size: 0.9rem;
}

/* Dropdown Menu */
.dropdown {
    position: relative;
    display: inline-block;
}

.dropdown-content {
    display: none;
    position: absolute;
    right: 0;
    top: calc(100% + 4px);
    background-color: var(--glass-bg);
    min-width: 200px;
    box-shadow: 0 8px 32px 0 rgba(0, 0, 0, 0.3);
    z-index: 100;
    border: 1px solid var(--glass-border);
    border-radius: 12px;
    backdrop-filter: blur(12px);
    -webkit-backdrop-filter: blur(12px);
    padding: 4px;
}

.dropdown-content.show {
    display: flex;
    flex-direction: column;
    gap: 2px;
}

.dropdown-item {
    padding: 8px 12px;
    text-decoration: none;
    display: flex;
    align-items: center;
    gap: 8px;
    color: var(--text-color);
    cursor: pointer;
    background: transparent;
    border: none;
    border-radius: 4px;
    width: 100%;
    text-align: left;
    font-size: 0.9rem;
    font-family: inherit;
    white-space: nowrap;
}

.dropdown-item:hover {
    background-color: rgba(255, 255, 255, 0.1);
}

.dropdown-item:disabled {
    opacity: 0.5;
    cursor: not-allowed;
}

.dropdown-item.danger {
    color: #fca5a5;
}

.dropdown-item.danger:hover {
    background-color: rgba(220, 38, 38, 0.2);
}

.db-list {
    display: flex;
    flex-direction: column;
    gap: 1rem;
    overflow-y: auto;
    padding-right: 0.5rem;
}

/* Align select dropdown to match the db-list cards width */
.species-select-container {
    padding-right: 0.5rem;
    margin-bottom: 1.5rem;
}

.db-card {
    background: var(--glass-panel-bg);
    border: 1px solid var(--glass-border);
    border-radius: 8px;
    padding: 1rem;
}
.db-card h4 { color: var(--primary-text); margin-bottom: 0.25rem; }
.db-card p { font-size: 0.85rem; color: var(--text-muted); margin-bottom: 0.5rem; }
.db-card .doi { font-size: 0.75rem; background: var(--glass-hover-bg); padding: 2px 6px; border-radius: 4px;}

/* Upload Panel */
.relative { position: relative; }
.dropzone {
    border: 2px dashed var(--glass-border);
    border-radius: 12px;
    padding: 3rem 2rem;
    text-align: center;
    background: var(--glass-panel-bg-light);
    transition: all 0.2s;
    margin-bottom: 1rem;
}
.dropzone.dragover {
    border-color: var(--primary);
    background: rgba(108, 42, 106, 0.1);
}
.drop-icon { font-size: 2.5rem; display: block; margin-bottom: 1rem; }

.upload-actions {
    display: flex;
    justify-content: space-between;
    align-items: center;
}

.lock-overlay {
    position: absolute;
    inset: 0;
    background: var(--glass-overlay-bg);
    backdrop-filter: blur(8px);
    display: flex;
    flex-direction: column;
    align-items: center;
    justify-content: center;
    text-align: center;
    border-radius: 12px;
    z-index: 10;
}
.lock-icon { font-size: 3rem; margin-bottom: 1rem; }

/* Floating Progress Bar */
#floating-progress {
    position: fixed;
    bottom: 24px;
    right: 24px;
    width: 300px;
    padding: 1.5rem;
    z-index: 9999;
    box-shadow: var(--shadow-hover, 0 12px 32px rgba(108, 42, 106, 0.25));
}

#floating-progress.hidden { display: none; }

.progress-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    margin-bottom: 1rem;
}

.progress-track {
    height: 6px;
    background: var(--glass-header-bg);
    border-radius: 3px;
    overflow: hidden;
    margin-bottom: 0.5rem;
}

.progress-fill {
    height: 100%;
    width: 50%;
    background: var(--primary);
    animation: indeterminate 1.5s infinite linear;
}

@keyframes indeterminate {
    0% { transform: translateX(-100%); width: 50%; }
    100% { transform: translateX(200%); width: 50%; }
}

.spinner-small {
    width: 16px;
    height: 16px;
    border: 2px solid rgba(255,255,255,0.1);
    border-radius: 50%;
    border-top-color: var(--primary);
    animation: spin 1s ease-in-out infinite;
}

.text-xs { font-size: 0.75rem; }
.hidden { display: none !important; }

/* Master/Detail Split Layout */
.split-layout {
    gap: 1rem;
}

.glass-panel {
    background: var(--glass-bg);
    backdrop-filter: blur(12px);
    border: 1px solid var(--glass-border);
    border-radius: 12px;
    display: flex;
    flex-direction: column;
    overflow: hidden;
    transition: flex var(--transition), min-width var(--transition);
}

.master-pane {
    flex: 1; /* Takes remaining space */
    position: relative;
}

.detail-pane {
    position: fixed;
    bottom: 20px;
    right: 20px;
    width: 800px;
    height: 500px;
    min-width: 400px;
    min-height: 200px;
    z-index: 1000;
    box-shadow: 0 10px 30px rgba(0, 0, 0, 0.3);
    resize: both;
    overflow: hidden;
    transition: opacity var(--transition);
    display: flex;
    flex-direction: column;
}

.detail-pane.minimized {
    opacity: 0;
    pointer-events: none;
    display: none;
}

.detail-pane.maximized {
    top: 0 !important;
    left: 0 !important;
    width: 100vw !important;
    height: 100vh !important;
    resize: none;
    border-radius: 0;
}
.master-pane.minimized {
    flex: 0 0 0%;
    min-width: 0;
    opacity: 0;
    border: none;
}

/* Table Toolbar */
.table-toolbar {
    display: flex;
    justify-content: space-between;
    padding: 1rem;
    border-bottom: 1px solid var(--glass-border);
}

#search-input {
    background: var(--glass-panel-bg);
    border: 1px solid var(--glass-border);
    color: var(--text-main);
    padding: 0.5rem 1rem;
    border-radius: 6px;
    width: 300px;
    font-family: inherit;
    outline: none;
    transition: border-color var(--transition);
}
#search-input:focus { border-color: var(--primary); }

.toolbar-actions { display: flex; gap: 0.5rem; }

/* Table Setup */
.table-scroll-container {
    flex: 1;
    overflow: auto;
}

table {
    width: 100%;
    border-collapse: collapse;
    text-align: left;
    white-space: nowrap;
}

th {
    background: var(--table-header-bg);
    padding: 0.75rem 1rem;
    font-weight: 500;
    color: var(--text-muted);
    font-size: 0.85rem;
    text-transform: uppercase;
    letter-spacing: 0.05em;
    position: sticky;
    top: 0;
    z-index: 10;
}
th.db-header { text-align: center; border-bottom: 1px solid var(--glass-border); }
th.db-k { background: var(--db-k-color); color: #d493d2; }
th.db-o { background: var(--db-o-color); color: #8DCB89; }

tr.sub-headers th { top: 40px; } /* Sticky offset for 2nd row headers */

th.filterable {
    cursor: pointer;
    user-select: none;
    transition: background-color 0.2s;
}
th.filterable:hover {
    background: var(--glass-border-faint);
}
.th-content {
    display: flex;
    justify-content: space-between;
    align-items: center;
    gap: 0.5rem;
}
.filter-icon {
    opacity: 0.3;
    font-size: 0.8rem;
    transition: opacity 0.2s, color 0.2s;
}
th.filterable:hover .filter-icon {
    opacity: 0.8;
}
th.filterable.filtered .filter-icon {
    opacity: 1;
    color: var(--primary-text);
}
.filter-checkbox-item {
    display: flex;
    align-items: center;
    gap: 0.5rem;
    padding: 0.3rem;
    border-radius: 4px;
    cursor: pointer;
}
.filter-checkbox-item:hover {
    background: var(--glass-hover-bg);
}
.filter-checkbox-item input[type="checkbox"] {
    cursor: pointer;
}

td {
    padding: 0.75rem 1rem;
    border-bottom: 1px solid var(--glass-border-faint);
    font-size: 0.9rem;
}

tbody tr { transition: background-color 0.15s; }
tbody tr:hover { background-color: var(--glass-border-faint); }

/* Detail Pane */
.viewport-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    padding: 1rem;
    border-bottom: 1px solid var(--glass-border);
    background: var(--glass-panel-bg);
    cursor: grab;
}
.viewport-header:active {
    cursor: grabbing;
}
.viewport-header h3 { 
    font-size: 1.1rem; 
    font-weight: 500; 
    min-width: 0; 
    flex: 1;
}
#viewport-genome-id {
    overflow: hidden;
    text-overflow: ellipsis;
    white-space: nowrap;
    min-width: 0;
    flex: 1;
}
.viewport-controls {
    flex-shrink: 0;
}

#plotly-wrapper {
    flex: 1;
    position: relative;
    background: transparent;
    display: flex;
    align-items: stretch;
}

#plotly-container {
    width: 100%;
    height: 100%;
}

.empty-state {
    position: absolute;
    inset: 0;
    display: flex;
    align-items: center;
    justify-content: center;
    color: #64748b;
    font-style: italic;
    background: transparent;
}

/* Loading States */
.loading-overlay {
    position: absolute;
    inset: 0;
    background: var(--glass-header-bg);
    backdrop-filter: blur(4px);
    display: flex;
    flex-direction: column;
    align-items: center;
    justify-content: center;
    gap: 1rem;
    z-index: 50;
}
.loading-overlay.hidden { display: none; }

.spinner {
    width: 40px;
    height: 40px;
    border: 3px solid rgba(255,255,255,0.1);
    border-radius: 50%;
    border-top-color: var(--primary);
    animation: spin 1s ease-in-out infinite;
}

@keyframes spin {
    to { transform: rotate(360deg); }
}

/* Row Selection */
#results-tbody tr.selected {
    background-color: rgba(var(--primary-rgb), 0.1);
    box-shadow: inset 3px 0 0 var(--primary);
}
#results-tbody tr:hover {
    background-color: var(--bg-hover);
}
#results-tbody tr.selected:hover {
    background-color: rgba(var(--primary-rgb), 0.15);
}

/* Modals */
.modal-overlay {
    position: fixed;
    top: 0;
    left: 0;
    width: 100vw;
    height: 100vh;
    background: var(--glass-overlay-bg);
    backdrop-filter: blur(4px);
    display: flex;
    align-items: center;
    justify-content: center;
    z-index: 1000;
}
.modal-overlay.hidden {
    display: none !important;
}

.modal-content {
    background: var(--bg-color);
    border: 1px solid var(--glass-border);
    border-radius: var(--radius-lg);
    box-shadow: 0 25px 50px -12px rgba(0, 0, 0, 0.5);
    padding: 1.5rem;
    position: relative;
    max-width: 90vw;
    max-height: 90vh;
    display: flex;
    flex-direction: column;
}

.modal-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    margin-bottom: 1rem;
    border-bottom: 1px solid var(--glass-border);
    padding-bottom: 0.5rem;
}

.modal-close {
    background: none;
    border: none;
    color: var(--text-muted);
    font-size: 1.5rem;
    cursor: pointer;
    padding: 0;
    line-height: 1;
}
.modal-close:hover {
    color: var(--text-main);
}