/* ===== Alignment viewer ===== */

.aln-wrap {
    overflow-x: auto;
    font-family: 'Courier New', Courier, monospace;
    font-size: 12px;
    line-height: 1.4;
    background: #fafafa;
    border: 1px solid #dee2e6;
    border-radius: 6px;
}

.aln-table {
    border-collapse: collapse;
    white-space: nowrap;
}

.aln-table td, .aln-table th {
    padding: 0;
    text-align: center;
    min-width: 14px;
    max-width: 14px;
    height: 20px;
    line-height: 20px;
}

.aln-table tr {
    height: 20px;
}

/* Tree+alignment: strict 20px row height so SVG and table line up */
.tree-aln-table tr,
.tree-aln-table td,
.tree-aln-table th {
    height: 20px !important;
    max-height: 20px !important;
    line-height: 20px !important;
    vertical-align: middle !important;
}
.tree-aln-table .tree-aln-label {
    padding: 0 !important;
    font-size: 10px !important;
    line-height: 20px !important;
    height: 20px !important;
    overflow: visible;
    background: #fff;
    z-index: 2;
    box-shadow: 2px 0 6px rgba(0, 0, 0, 0.04);
}

.tree-aln-table .tree-aln-label .aln-label-inner {
    padding: 0 4px 0 2px;
    min-height: 20px;
    height: 20px;
    font-size: 10px !important;
    line-height: 20px !important;
    overflow: hidden;
}

.tree-inner .tree-flex-row {
    display: flex;
    align-items: flex-start;
    width: 100%;
}

.tree-inner .tree-svg-col {
    flex-shrink: 0;
}

.tree-inner .tree-aln-scroll {
    overflow-x: auto;
    flex: 1;
    min-width: 0;
    border-left: 2px solid #dee2e6;
    border-radius: 0;
}

.tree-aln-table .tree-aln-ref {
    background: #fff3cd !important;
    font-weight: bold;
    color: #856404;
}

/* Conservation strip */
.conservation-strip {
    display: flex;
    flex-wrap: nowrap;
    height: 28px;
    border: 1px solid #dee2e6;
    border-radius: 6px;
    overflow: hidden;
    background: #f8f9fa;
}

/* Bar aligned to sequence width (50 chars), same grayscale scale, thin black outline */
.conservation-strip-bar {
    width: 50em;
    max-width: 100%;
    margin-left: auto;
    margin-right: auto;
    border: 1px solid #000;
    font-family: 'Courier New', Courier, monospace;
    font-size: 14px;
    letter-spacing: 1px;
    box-sizing: content-box;
}

.conservation-cell {
    flex: 1;
    min-width: 2px;
    transition: background 0.1s;
}

.conservation-cell:hover {
    filter: brightness(0.95);
}

/* Tree panel: height fits plot (no scroll; .tree-inner has no max-height) */

/* Conservation: reference sequence (grayscale, no gaps) */
.conservation-seq-wrap {
    font-family: 'Courier New', Courier, monospace;
    font-size: 14px;
    line-height: 1.6;
    letter-spacing: 1px;
    margin-top: 1rem;
    margin-left: auto;
    margin-right: auto;
    text-align: left;
    width: fit-content;
    max-width: 100%;
}
.conservation-seq-line {
    white-space: pre;
    word-break: break-all;
    text-align: left;
}
.conservation-pos {
    display: inline-block;
    min-width: 3em;
    text-align: right;
    margin-right: 0.5em;
    color: #6c757d;
    font-size: 0.9em;
}
.conservation-seq-line .conservation-pos:last-of-type {
    text-align: left;
    margin-left: 0.5em;
    margin-right: 0;
}
.conservation-aa {
    display: inline-block;
    min-width: 1em;
    text-align: center;
}

.aln-label {
    text-align: left !important;
    padding: 0 !important;
    min-width: auto !important;
    max-width: none !important;
    position: sticky;
    left: 0;
    background: #fafafa;
    z-index: 2;
    border-right: 2px solid #dee2e6;
    white-space: nowrap;
    font-weight: 500;
    vertical-align: middle;
    box-shadow: 2px 0 6px rgba(0, 0, 0, 0.04);
}

.aln-ruler .aln-label {
    z-index: 3;
    background: #fafafa;
}

.aln-label-inner {
    display: flex;
    align-items: center;
    justify-content: space-between;
    gap: 0.35rem;
    white-space: nowrap;
    padding: 1px 10px 1px 6px;
    min-height: 20px;
}

.aln-label-with-exc .aln-label-text {
    min-width: 0;
    overflow: hidden;
    text-overflow: ellipsis;
}

.aln-exc-btn {
    flex-shrink: 0;
    line-height: 1;
}

/* Panel “remove from views”: bordered dash-square icon, muted until hover */
.gene-exc-btn {
    opacity: 0.72;
    transition: opacity 0.12s ease, color 0.12s ease;
}

.gene-exc-btn .gene-exc-bi {
    font-size: 1.05rem;
    vertical-align: -0.15em;
}

.gene-exc-btn:hover,
.gene-exc-btn:focus-visible {
    opacity: 1;
    color: var(--bs-secondary) !important;
}

.aln-gid {
    font-size: 10px;
    color: #888;
    font-weight: normal;
    margin-left: 6px;
}

.aln-label-ref {
    font-weight: bold;
    color: #2d6a4f;
    background: #e9f5ef !important;
}

.aln-label-inner.aln-label-highlight {
    background: #fff3cd !important;
    font-weight: bold;
}

.aln-ref-row {
    border-bottom: 2px solid #dee2e6;
}

.aln-ref-row td.ref-aa {
    color: #6c757d;
    font-weight: bold;
}

.aln-ref-row td.aln-label-ref {
    background: #e9f5ef;
}

.aln-ruler td {
    color: #adb5bd;
    font-size: 10px;
    border-bottom: 1px solid #dee2e6;
}

/* Residue hover tooltip (Alignment + Tree tabs) */
#aln-residue-tooltip {
    position: fixed;
    z-index: 4000;
    pointer-events: none;
    display: none;
    max-width: min(320px, 90vw);
    background: rgba(33, 37, 41, 0.94);
    color: #fff;
    padding: 5px 9px;
    border-radius: 5px;
    font-size: 11px;
    font-family: system-ui, -apple-system, "Segoe UI", Roboto, sans-serif;
    line-height: 1.35;
    box-shadow: 0 4px 14px rgba(0, 0, 0, 0.2);
    white-space: normal;
}

.aa-match { color: #d0d4d8; }
.aa-match-full { color: #6c757d; }
.aa-gap { color: #dee2e6; }

.aa-diff {
    font-weight: bold;
    border-radius: 2px;
}

.aa-diff-plain {
    font-weight: bold;
    color: #d63384;
}

/* Amino acid coloring (Taylor-inspired) */
.aa-A { background: #d4f0d4; color: #1a5c1a; }
.aa-R { background: #d4d4f0; color: #1a1a8c; }
.aa-N { background: #d4e8f0; color: #1a5c7a; }
.aa-D { background: #f0d4d4; color: #8c1a1a; }
.aa-C { background: #f0f0d4; color: #7a7a1a; }
.aa-E { background: #f0d4d4; color: #8c1a1a; }
.aa-Q { background: #d4e8f0; color: #1a5c7a; }
.aa-G { background: #f0e8d4; color: #7a5c1a; }
.aa-H { background: #d4d4f0; color: #1a1a8c; }
.aa-I { background: #d4f0d4; color: #1a5c1a; }
.aa-L { background: #d4f0d4; color: #1a5c1a; }
.aa-K { background: #d4d4f0; color: #1a1a8c; }
.aa-M { background: #d4f0d4; color: #1a5c1a; }
.aa-F { background: #d4d4f0; color: #1a1a8c; }
.aa-P { background: #f0e8d4; color: #7a5c1a; }
.aa-S { background: #f0e8d4; color: #7a5c1a; }
.aa-T { background: #f0e8d4; color: #7a5c1a; }
.aa-W { background: #d4d4f0; color: #1a1a8c; }
.aa-Y { background: #d4e8f0; color: #1a5c7a; }
.aa-V { background: #d4f0d4; color: #1a5c1a; }
.aa-X { background: #e0e0e0; color: #666; }

/* ===== Variants (transposed matrix) ===== */

.variant-matrix-wrap {
    max-height: 70vh;
    overflow: auto;
}

.variant-matrix-table {
    font-size: 0.78rem;
    white-space: nowrap;
}

.variant-matrix-table th,
.variant-matrix-table td {
    vertical-align: middle;
}

.variant-matrix-table .var-cell-ref {
    background: #dee2e6;
    color: #212529;
    font-weight: 600;
}

.variant-matrix-table .var-cell-ref-match {
    background: #e7f1ff;
    color: #0d47a1;
}

/* Conservation: SS strip + letters + secstructartist share one width for alignment */
.pb-ss-align-block {
    width: 50em;
    max-width: 100%;
    margin-left: auto;
    margin-right: auto;
    box-sizing: border-box;
}

.pb-ss-align-block .conservation-strip-bar {
    width: 100%;
    max-width: 100%;
}

.pb-ss-align-block .conservation-seq-wrap {
    width: 100%;
    max-width: 100%;
}

.pb-ss-align-block .conservation-seq-line {
    width: 100%;
}

.pb-ss-plot-inner .pb-ss-svg,
.pb-ss-plot-inner .pb-ss-svg svg {
    width: 100%;
    max-width: 100%;
    height: auto;
    display: block;
}

/* ===== Variant cards (legacy; matrix is primary) ===== */

.variant-list {
    max-height: 650px;
    overflow-y: auto;
}

.vp-card {
    border: 1px solid #e9ecef;
    border-radius: 6px;
    margin-bottom: 6px;
    background: #fff;
}

.vp-header {
    display: flex;
    align-items: center;
    gap: 10px;
    padding: 8px 12px;
    cursor: pointer;
    transition: background 0.15s;
}

.vp-header:hover {
    background: #f8f9fa;
}

.vp-pos {
    font-weight: 700;
    font-variant-numeric: tabular-nums;
    min-width: 70px;
    color: #495057;
}

.vp-bar {
    flex: 1;
    height: 6px;
    background: #e9ecef;
    border-radius: 3px;
    min-width: 60px;
    max-width: 150px;
}

.vp-bar-fill {
    height: 100%;
    border-radius: 3px;
    background: linear-gradient(90deg, #ffc107, #e67700);
}

.vp-chev {
    color: #adb5bd;
    transition: transform 0.15s;
}

.vp-detail {
    padding: 4px 12px 10px 12px;
    border-top: 1px solid #f1f3f5;
}

.vg {
    margin-bottom: 4px;
}

.vg-header {
    display: flex;
    align-items: center;
    padding: 5px 8px;
    cursor: pointer;
    border-radius: 4px;
    transition: background 0.15s;
}

.vg-header:hover {
    background: #f8f9fa;
}

.vg-chev {
    color: #adb5bd;
}

.al {
    padding: 4px 8px 6px 32px;
    display: flex;
    flex-wrap: wrap;
    gap: 4px;
}

.acc-chip {
    display: inline-block;
    padding: 2px 8px;
    background: #e9ecef;
    border-radius: 12px;
    font-size: 0.78rem;
    color: #495057;
    cursor: default;
}

.acc-chip:hover {
    background: #dee2e6;
}

/* secstructartist SVG (Conservation tab, embedded from /api/ss_plot) */
.pb-ss-svg {
    overflow-x: auto;
    max-width: 100%;
}
.pb-ss-svg svg {
    max-width: 100%;
    height: auto;
    display: block;
    margin: 0 auto;
}

/* Alignment / Tree: short SS legend under controls */
.pb-ss-tab-hint {
    font-size: 0.72rem;
    line-height: 1.4;
}

/* ─── CSS-driven alignment toggle modes (no JS re-render needed) ─── */

/* Same-ref cells: pre-render both residue letter and dot spans;
   CSS picks which is visible based on showAll/colorMode state. */
.aln-res-full { display: inline; }
.aln-res-dot  { display: none;   }

/* Show All Residues = OFF → show dot, suppress background */
.aln-table[data-show-all="false"] .aln-same-ref .aln-res-full,
.tree-aln-table[data-show-all="false"] .aln-same-ref .aln-res-full { display: none; }
.aln-table[data-show-all="false"] .aln-same-ref .aln-res-dot,
.tree-aln-table[data-show-all="false"] .aln-same-ref .aln-res-dot  { display: inline; }
.aln-table[data-show-all="false"] .aln-same-ref,
.tree-aln-table[data-show-all="false"] .aln-same-ref { background: transparent !important; color: #d0d4d8; }

/* Color mode: none — no residue background, bold pink for variants */
.aln-table[data-color-mode="none"] td.aln-same-ref,
.aln-table[data-color-mode="none"] td.aa-diff,
.tree-aln-table[data-color-mode="none"] td.aln-same-ref,
.tree-aln-table[data-color-mode="none"] td.aa-diff { background: transparent !important; }
.aln-table[data-color-mode="none"] td.aa-diff,
.tree-aln-table[data-color-mode="none"] td.aa-diff { color: #d63384; }

/* Color mode: variants — only variant cells keep residue color */
.aln-table[data-color-mode="variants"] td.aln-same-ref,
.tree-aln-table[data-color-mode="variants"] td.aln-same-ref { background: transparent !important; color: #6c757d; }

/* Show Ref Gaps = OFF — hide cells in reference-gap columns */
.aln-table[data-show-gaps="false"] .aln-ref-gap,
.tree-aln-table[data-show-gaps="false"] .aln-ref-gap { display: none; }