/* ============================================================
   CSS Custom Properties
   ============================================================ */
:root {
    --color-primary:       #1a3a5c;
    --color-primary-light: #2d5f8a;
    --color-accent:        #2d7dd2;
    --color-accent-hover:  #1f5fa3;
    --color-bg:            #f4f7fb;
    --color-surface:       #ffffff;
    --color-text:          #1e293b;
    --color-muted:         #64748b;
    --color-border:        #d1d9e6;
    --color-success:       #198754;
    --header-height:       64px;
    --banner-height:       34px;
    --total-header:        98px; /* navbar + version banner */
    --radius:              0.4rem;
    --shadow-sm:           0 1px 3px rgba(0,0,0,0.08);
    --shadow-md:           0 2px 8px rgba(0,0,0,0.10);
    --transition:          0.18s ease;
}

/* ============================================================
   Reset & Base
   ============================================================ */
*, *:before, *:after {
    box-sizing: border-box;
}

html, body {
    font-family: Arial, Helvetica, sans-serif;
    font-size: 15px;
    color: var(--color-text);
    background-color: var(--color-bg);
    margin: 0;
}

/* Sticky-footer layout */
body {
    display: flex;
    flex-direction: column;
    min-height: 100vh;
}

#page-body {
    flex: 1;
}

a {
    text-decoration: none;
    color: var(--color-accent);
}
a:hover {
    color: var(--color-accent-hover);
    text-decoration: underline;
}

hr {
    width: 100%;
    height: 3px;
    margin: 1rem 0;
    background-color: var(--color-primary);
    border: 0;
    opacity: 0.2;
}

/* ============================================================
   Site Header — Sticky, unified logo + nav
   ============================================================ */
.site-header {
    position: sticky;
    top: 0;
    z-index: 1050;
    background: var(--color-primary);
    box-shadow: 0 2px 6px rgba(0,0,0,0.25);
}

/* Version banner inside header */
.site-header .version-banner {
    background: rgba(0,0,0,0.18);
    font-size: 0.8rem;
    padding: 4px 1rem;
    color: #c8dff5;
    border-bottom: 1px solid rgba(255,255,255,0.08);
}
.site-header .version-banner a {
    color: #ffd966;
}
.site-header .version-banner .close {
    color: #c8dff5;
    opacity: 0.7;
    font-size: 1rem;
    padding: 0 0.5rem;
}
.site-header .version-banner .close:hover {
    opacity: 1;
}

/* Navbar inside the header */
.site-header .navbar {
    background: transparent !important;
    padding: 0 1rem;
    min-height: var(--header-height);
}
.site-header .navbar-brand img {
    max-height: 44px;
    width: auto;
    background: white;
    padding: 3px 10px;
    border-radius: 6px;
}
.site-header .navbar-toggler {
    border-color: rgba(255,255,255,0.4);
}
.site-header .navbar-toggler-icon {
    background-image: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.85%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");
}
.site-header .nav-link {
    color: rgba(255,255,255,0.82) !important;
    padding: 0.6rem 0.9rem !important;
    font-size: 0.9rem;
    font-weight: 500;
    letter-spacing: 0.01em;
    border-bottom: 2px solid transparent;
    transition: color var(--transition), border-color var(--transition);
}
.site-header .nav-link:hover {
    color: #ffffff !important;
    text-decoration: none;
    border-bottom-color: rgba(255,255,255,0.5);
}
.site-header .nav-item.active .nav-link {
    color: #ffffff !important;
    border-bottom-color: #ffd966;
}
.site-header .navbar-text {
    color: rgba(255,255,255,0.6) !important;
    font-size: 0.8rem;
}

/* ============================================================
   Site Footer
   ============================================================ */
.site-footer {
    background: var(--color-primary);
    color: rgba(255,255,255,0.85);
    padding: 1rem 1.5rem;
    font-size: 0.82rem;
    border-top: 2px solid rgba(0,0,0,0.2);
    display: flex;
    flex-wrap: wrap;
    align-items: center;
    justify-content: space-between;
    gap: 0.5rem;
}
.site-footer .footer-copy {
    margin: 0;
}
.site-footer .footer-privacy {
    color: rgba(255,255,255,0.7);
}
.site-footer .footer-privacy a {
    color: #ffd966;
    text-decoration: underline;
}
.site-footer .footer-privacy a:hover {
    color: #ffe999;
}
@media (max-width: 576px) {
    .site-footer {
        flex-direction: column;
        text-align: center;
    }
}

/* ============================================================
   Main Content
   ============================================================ */
#main-content {
    padding-top: 1.5rem;
    padding-bottom: 2rem;
}

/* ============================================================
   Buttons
   ============================================================ */
.btn-primary {
    background-color: var(--color-accent) !important;
    border-color: var(--color-accent) !important;
    transition: background-color var(--transition), border-color var(--transition), box-shadow var(--transition);
}
.btn-primary:hover, .btn-primary:focus {
    background-color: var(--color-accent-hover) !important;
    border-color: var(--color-accent-hover) !important;
    box-shadow: 0 0 0 3px rgba(45,125,210,0.3) !important;
}

.btn-submit {
    background-color: var(--color-accent);
    color: white;
    padding: 12px 20px;
    margin: 8px 0;
    border: none;
    border-radius: var(--radius);
    cursor: pointer;
    width: 100%;
    font-size: 1rem;
    font-weight: 600;
    letter-spacing: 0.02em;
    transition: background-color var(--transition), box-shadow var(--transition);
}
.btn-submit:hover {
    background-color: var(--color-accent-hover);
    box-shadow: 0 3px 10px rgba(45,125,210,0.35);
}

/* ============================================================
   Forms
   ============================================================ */
input[type=text], input[type=password] {
    width: 50%;
    padding: 7px 10px;
    display: inline-block;
    border: 1px solid var(--color-border);
    border-radius: var(--radius);
    background: #f8fafc;
    transition: border-color var(--transition), box-shadow var(--transition);
}
input[type=text]:focus, input[type=password]:focus {
    border-color: var(--color-accent);
    box-shadow: 0 0 0 3px rgba(45,125,210,0.2);
    outline: none;
    background: var(--color-surface);
}

.form-control:focus {
    border-color: var(--color-accent) !important;
    box-shadow: 0 0 0 3px rgba(45,125,210,0.2) !important;
}

/* Form section fieldsets on initialiser */
.form-section {
    background: var(--color-surface);
    border: 1px solid var(--color-border) !important;
    border-left: 4px solid var(--color-accent) !important;
    border-radius: var(--radius) !important;
    padding: 1.25rem 1.5rem !important;
    margin-bottom: 1.5rem !important;
    box-shadow: var(--shadow-sm);
}
.form-section legend {
    font-size: 1rem;
    font-weight: 600;
    color: var(--color-primary);
    padding: 0 0.4rem;
    width: auto;
    margin-bottom: 0.75rem;
}
.form-section label {
    font-weight: 500;
    margin-bottom: 4px;
    color: var(--color-text);
}

/* ============================================================
   Analytics — Report section fieldsets
   ============================================================ */
.report-section {
    background: var(--color-surface);
    border: 1px solid var(--color-border);
    border-radius: var(--radius);
    padding: 1.25rem 1.5rem;
    margin-bottom: 1.5rem;
    box-shadow: var(--shadow-sm);
    scroll-margin-top: calc(var(--total-header) + 0.75rem);
}
.report-section h3 {
    font-size: 1.1rem;
    font-weight: 600;
    color: var(--color-primary);
    margin-bottom: 0.75rem;
    padding-bottom: 0.5rem;
    border-bottom: 1px solid var(--color-border);
}
.report-section .section-info {
    background: #e8f0fe;
    border-left: 3px solid var(--color-accent);
    padding: 0.6rem 0.9rem;
    border-radius: 0 var(--radius) var(--radius) 0;
    font-size: 0.88rem;
    margin-bottom: 1rem;
    color: var(--color-text);
}

/* ============================================================
   Table of Contents Sidebar
   ============================================================ */
.toc-sidebar {
    position: sticky;
    top: calc(var(--total-header) + 0.5rem);
    max-height: calc(100vh - var(--total-header) - 1rem);
    overflow-y: auto;
    align-self: flex-start;
    width: 190px;
    flex-shrink: 0;
    padding: 0.75rem 0;
    margin-right: 1.25rem;
    background: var(--color-surface);
    border: 1px solid var(--color-border);
    border-radius: var(--radius);
    box-shadow: var(--shadow-sm);
}
.toc-sidebar .toc-title {
    font-size: 0.7rem;
    font-weight: 700;
    text-transform: uppercase;
    letter-spacing: 0.08em;
    color: var(--color-muted);
    padding: 0 0.9rem 0.5rem;
    margin: 0;
    border-bottom: 1px solid var(--color-border);
    margin-bottom: 0.4rem;
}
.toc-sidebar .toc-link {
    display: block;
    padding: 0.3rem 0.9rem;
    font-size: 0.82rem;
    color: var(--color-muted);
    border-left: 3px solid transparent;
    line-height: 1.4;
    transition: color var(--transition), border-color var(--transition), background var(--transition);
    white-space: nowrap;
    overflow: hidden;
    text-overflow: ellipsis;
}
.toc-sidebar .toc-link:hover {
    color: var(--color-accent);
    background: #f0f6ff;
    text-decoration: none;
}
.toc-sidebar .toc-link.active {
    color: var(--color-accent);
    font-weight: 600;
    border-left-color: var(--color-accent);
    background: #e8f0fe;
}

.report-layout {
    display: flex;
    align-items: flex-start;
}
.report-main {
    flex: 1;
    min-width: 0;
}

/* ============================================================
   Scrollable filter/view panel pairs (overlap, gibbs, allele-upset)
   ============================================================ */
.scroll-panel {
    max-height: 1000px;
    overflow-y: auto;
    overflow-x: hidden;
    word-break: break-word;
}
.view-panel {
    max-height: 1000px;
    overflow-y: auto;
}
.view-panel--padded {
    padding-left: 30px;
    padding-right: 30px;
}
.scroll-panel .form-check-label {
    display: block;
    word-break: break-word;
    overflow-wrap: anywhere;
}

/* ============================================================
   Gibbs Cluster Row — flat flex-wrap layout (replaces Slick carousel)
   ============================================================ */
.gibbs-cluster-row {
    display: flex;
    flex-wrap: wrap;
    align-items: flex-start;
    gap: 12px;
    margin-bottom: 12px;
}
.gibbs-cluster-row > img {
    max-height: 210px;
    width: auto;
    flex-shrink: 0;
}
.gibbs-cluster-row .image-container {
    display: flex;
    flex-direction: column;
    align-items: center;
    justify-content: flex-start;
    padding: 4px;
    text-align: center;
    min-width: 180px;
    max-width: 260px;
    flex: 1 1 200px;
}
.gibbs-cluster-row .image-container img {
    width: 100%;
    height: auto;
}

/* ============================================================
   Cards & Misc
   ============================================================ */
.card {
    box-shadow: var(--shadow-sm);
    border-radius: var(--radius);
    border-color: var(--color-border);
}

.error-message {
    color: #dc3545;
    font-size: 0.875rem;
}

.seqlogo {
    margin: 0 auto;
}

.upset {
    width: 100%;
    height: 100%;
    margin: 0;
    display: flex;
    align-items: center;
    justify-content: center;
}

.tooltip {
    font-size: 15px;
}
.tooltip-inner {
    text-align: left;
}

/* ============================================================
   Loading Spinner
   ============================================================ */
.lds-hourglass {
    display: inline-block;
    position: fixed;
    top: 50%;
    left: 50%;
    transform: translate(-50%, -50%);
    z-index: 9000;
}
.lds-hourglass:after {
    content: " ";
    display: block;
    border-radius: 50%;
    width: 0;
    height: 0;
    margin: 8px;
    box-sizing: border-box;
    border: 32px solid #fff;
    border-color: var(--color-primary) transparent var(--color-primary) transparent;
    animation: lds-hourglass 1.2s infinite;
}
@keyframes lds-hourglass {
    0%   { transform: rotate(0);      animation-timing-function: cubic-bezier(0.55, 0.055, 0.675, 0.19); }
    50%  { transform: rotate(900deg); animation-timing-function: cubic-bezier(0.215, 0.61, 0.355, 1); }
    100% { transform: rotate(1800deg); }
}

/* ============================================================
   Motif Tooltip
   ============================================================ */
.tooltip-motif-image {
    position: fixed;
    background-color: white;
    border: 1px solid var(--color-border);
    padding: 4px;
    box-shadow: var(--shadow-md);
    display: none;
    z-index: 9999;
    pointer-events: none;
    border-radius: var(--radius);
}
.tooltip-motif-image img {
    max-width: 200px;
    height: auto;
}
.motif-ref {
    color: var(--color-accent);
    text-decoration: underline;
    cursor: pointer;
    position: relative;
}
.mhctp-predictions { font-size: 0.78em; margin-top: 4px; }
.mhctp-row { display: flex; align-items: center; gap: 4px; margin-bottom: 2px; }
.mhctp-row.top-match { font-weight: 600; }
.mhctp-rank { color: #888; min-width: 18px; }
.mhctp-allele { min-width: 54px; font-family: monospace; white-space: nowrap; }
.mhctp-bar-wrap { flex: 1; background: #eee; border-radius: 3px; height: 6px; }
.mhctp-bar-fill { background: #4a90d9; height: 6px; border-radius: 3px; }
.mhctp-score { min-width: 32px; color: #555; }
.mhctp-na { color: #bbb; font-size: 0.78em; }

/* ============================================================
   Top Proteins Table
   ============================================================ */
#topprotiens td,
#topprotiens th {
    word-wrap: break-word;
    white-space: normal;
    vertical-align: top;
    padding: 6px 8px;
    font-size: 0.875rem;
    text-align: left;
}
#topprotiens th {
    white-space: nowrap;
    font-weight: 600;
    background-color: #f4f7fb;
    color: var(--color-primary);
}
.table-container {
    max-height: 300px;
    overflow-y: auto;
}
#topprotiens a {
    color: var(--color-accent);
    text-decoration: none;
}
#topprotiens a:hover {
    text-decoration: underline;
}
#topprotiens tr:nth-child(even) {
    background-color: #f9fafb;
}

/* ============================================================
   Pepscanner form fields
   ============================================================ */
.pepscan-field {
    padding-left: 18px;
}

#pepscannerimage {
    max-width: 100%;
    height: auto;
    border: 1px solid var(--color-border);
    border-radius: var(--radius);
}

/* ============================================================
   Badges
   ============================================================ */
.badge {
    padding: 0.4em 0.7em;
    font-size: 0.82em;
}

/* ============================================================
   Chip links (Gibbs/seq2logo "download" links)
   ============================================================ */
.chip-link {
    font-size: 0.7rem;
    padding: 1px 5px;
    color: var(--color-muted);
    background-color: transparent;
    border: 1px solid var(--color-border);
    border-radius: 4px;
    text-decoration: none;
}

/* ============================================================
   Reference table (binding prediction tool/threshold summary)
   ============================================================ */
.ref-table {
    border-collapse: collapse;
    margin-bottom: 10px;
}
.ref-table th,
.ref-table td {
    border: 1px solid var(--color-border);
    padding: 4px;
}
.ref-table th {
    background-color: var(--color-bg);
}