/* Author: Flavio Ballante, Chemical Biology Consortium Sweden (CBCS-KI), Karolinska Institutet - 2026 */
/* Acknowledgments: thanks to Dr. Francesco Massai, Chemical Biology Consortium Sweden (CBCS-KI), Karolinska Institutet, */
/* for valuable scientific input and feedback during the development of CHASE. */
/* CHASE - Shiny edition. It looks the same as the HTML version (light theme). */
/* The basic colours, fonts and corner radius. The --bs-* values recolour Bootstrap (which Shiny uses) */
/* so it matches. */
:root {
  --bg: #f3f5f4; --surface: #ffffff; --surface-2: #eaeeec; --ink: #131715; --ink-2: #48514d; --ink-3: #737d78;
  --line: #d9dfdc; --accent: #0e6a5e; --accent-soft: #d7ebe7; --tile: #ffffff;
  --good: #1f7a3c; --warn: #9a6a00; --bad: #b8322a; --good-bg: #dff0e3; --warn-bg: #f7ecd0; --bad-bg: #f8dedb;
  --f-body: "Public Sans", "Segoe UI", system-ui, -apple-system, Helvetica, Arial, sans-serif;
  --f-mono: "JetBrains Mono", ui-monospace, "SFMono-Regular", Menlo, Consolas, monospace;
  --r: 10px;
  --bs-body-font-family: var(--f-body); --bs-body-bg: var(--bg); --bs-body-color: var(--ink);
  --bs-primary: #0e6a5e; --bs-primary-rgb: 14,106,94; --bs-link-color: #0e6a5e; --bs-link-color-rgb: 14,106,94;
}
/* ---- the page, the top bar and the sidebar steps */
body { background: var(--bg); color: var(--ink); font-size: 14px; }
.mono { font-family: var(--f-mono); font-variant-numeric: tabular-nums; }
.navbar { background: var(--surface) !important; border-bottom: 1px solid var(--line); }
.navbar-brand .brand { font-weight: 700; letter-spacing: -0.01em; font-size: 21px; color: var(--ink); }
.navbar-brand .acro { font-size: 13px; color: var(--ink-3); margin-left: 10px; font-weight: 400; }
.navbar-brand .acro b { color: var(--ink); font-weight: 700; }
.btn-primary { --bs-btn-bg: #0e6a5e; --bs-btn-border-color: #0e6a5e; --bs-btn-hover-bg: #0c5d53; --bs-btn-hover-border-color: #0c5d53; --bs-btn-active-bg: #0a5047; }
.bslib-sidebar-layout > .sidebar { background: var(--bg); }
.step { background: var(--surface); border: 1px solid var(--line); border-radius: var(--r); padding: 12px 14px; margin-bottom: 12px; }
.step h2 { display: flex; align-items: center; gap: 8px; margin: 0 0 8px; font-size: 15px; font-weight: 600; }
.step h2 .n { display: inline-grid; place-items: center; width: 22px; height: 22px; border-radius: 50%; background: var(--accent-soft); color: var(--accent); font-family: var(--f-mono); font-size: 12px; }
.step .form-group, .step .shiny-input-container { margin-bottom: 8px; width: 100% !important; }
.step label, .step .control-label { font-size: 11px; text-transform: uppercase; letter-spacing: .06em; color: var(--ink-2); font-weight: 600; }
.step .input-group label, .step .input-group .btn, .step .form-control { text-transform: none; letter-spacing: 0; font-size: 13px; font-weight: 500; }
.step .input-group .btn { padding: 6px 10px; }
.step .shiny-input-radiogroup label.radio-inline, .step .form-check-label { text-transform: none; letter-spacing: 0; font-weight: 500; font-size: 13px; color: var(--ink); }
.hint { color: var(--ink-3); font-size: 12px; margin: 0; }
.filehint { color: var(--ink-2); font-size: 12px; margin: -4px 0 8px; overflow-wrap: anywhere; }
.row2 { display: grid; grid-template-columns: 1fr 1fr; gap: 8px; }
.sessrow { display: flex; gap: 8px; flex-wrap: wrap; align-items: flex-start; }
.sessrow > * { flex: 1; }
/* ---- the main area: messages, summary tiles and cards */
.bench { display: flex; flex-direction: column; gap: 16px; min-width: 0; }
.banner { background: var(--warn-bg); border-radius: var(--r); padding: 10px 14px; font-size: 13px; }
.banner b { color: var(--warn); }
.alert-chase { background: var(--bad-bg); border-radius: var(--r); padding: 10px 14px; font-size: 13px; }
.stats { display: grid; grid-template-columns: repeat(auto-fit, minmax(130px, 1fr)); gap: 1px; background: var(--line); border: 1px solid var(--line); border-radius: var(--r); overflow: hidden; }
.stat { background: var(--surface); padding: 10px 14px; display: flex; flex-direction: column; gap: 2px; min-width: 0; }
.stat .k { font-size: 11px; text-transform: uppercase; letter-spacing: .06em; color: var(--ink-3); font-weight: 600; }
.stat .v { font-family: var(--f-mono); font-size: 20px; font-variant-numeric: tabular-nums; }
.stat .s { font-size: 12px; color: var(--ink-3); }
.ccard { background: var(--surface); border: 1px solid var(--line); border-radius: var(--r); min-width: 0; }
.ccard-h { display: flex; align-items: center; gap: 10px; flex-wrap: wrap; padding: 10px 14px; border-bottom: 1px solid var(--line); }
.ccard-h h3 { margin: 0; font-size: 16px; font-weight: 600; }
.ccard-h .meta { color: var(--ink-3); font-size: 12px; }
.ccard-h .spacer, .sp { flex: 1; }
.ccard-h .shiny-input-container { margin: 0; width: auto !important; }
.ccard-h .form-check { margin: 0; }
.ctools { display: flex; gap: 14px; align-items: center; flex-wrap: wrap; padding: 8px 14px; border-bottom: 1px solid var(--line); font-size: 12px; color: var(--ink-2); }
.ctools .shiny-input-container { margin: 0; width: auto !important; }
.ctools .form-label, .ctools label { font-size: 12px; margin: 0 6px 0 0; text-transform: none; letter-spacing: 0; font-weight: 500; }
.ctools .form-group { display: flex; align-items: center; gap: 6px; }
.ctools input[type=number] { width: 76px; }
.ctools .irs { min-width: 160px; }
/* ---- the % response plot (fixed height, plotly fills the width) */
#plot { width: 100%; height: 470px; }
.plot-foot { padding: 8px 14px 12px; color: var(--ink-3); font-size: 12px; }
/* Chemotypes and the detail panel side by side. On narrow screens they are stacked. */
.split { display: grid; grid-template-columns: minmax(0, 1.65fr) minmax(0, 1fr); gap: 16px; align-items: start; }
@media (max-width: 1280px) { .split { grid-template-columns: minmax(0, 1fr); } }
/* ---- chemotype cards and structure tiles */
.cgrid { display: grid; grid-template-columns: repeat(auto-fill, minmax(196px, 1fr)); gap: 10px; padding: 14px; }
.chemo { border: 1px solid var(--line); border-radius: 9px; padding: 8px; display: flex; flex-direction: column; gap: 6px; cursor: pointer; background: var(--surface); text-align: left; }
.chemo:hover { border-color: var(--ink-3); }
.chemo[aria-pressed="true"] { border-color: var(--accent); box-shadow: 0 0 0 2px var(--accent-soft); }
.tilebox { background: var(--tile); border-radius: 6px; aspect-ratio: 4 / 3; width: 100%; display: grid; place-items: center; overflow: hidden; }
.tilebox svg { width: 100%; height: 100%; display: block; }
.tilebox .na { color: #7a827e; font-size: 12px; }
.chemo .l1 { display: flex; justify-content: space-between; align-items: baseline; gap: 6px; }
.chemo .id { font-family: var(--f-mono); font-size: 12px; }
.chemo .n { font-size: 12px; color: var(--ink-3); }
.chemo .l2 { display: flex; gap: 8px; flex-wrap: wrap; font-size: 12px; color: var(--ink-2); }
.chemo .l2 b { font-family: var(--f-mono); font-weight: 500; color: var(--ink); }
.chemo .enr { color: var(--ink-3); }
.strip { width: 100%; height: 18px; display: block; }
.empty { padding: 28px 18px; color: var(--ink-3); text-align: center; font-size: 13px; }
/* ---- chips: small coloured labels (good, warn, bad, accent). The covalent chip (.cov) is further down. */
.chip { display: inline-flex; align-items: center; gap: 5px; font-size: 11px; font-weight: 600; padding: 2px 7px; border-radius: 10px; background: var(--surface-2); color: var(--ink-2); white-space: nowrap; }
.chip i { width: 8px; height: 8px; border-radius: 50%; display: inline-block; }
.chip.good { background: var(--good-bg); color: var(--good); }
.chip.warn { background: var(--warn-bg); color: var(--warn); }
.chip.bad { background: var(--bad-bg); color: var(--bad); }
.chip.acc { background: var(--accent-soft); color: var(--accent); }
/* ---- the detail panel: pinned compound, chemotype members and triage buttons */
.dsec { padding: 14px; display: flex; flex-direction: column; gap: 10px; border-bottom: 1px solid var(--line); }
.dsec:last-child { border-bottom: 0; }
.dsec h4 { margin: 0; font-size: 15px; font-weight: 600; display: flex; gap: 8px; align-items: center; flex-wrap: wrap; }
.kv { display: grid; grid-template-columns: auto 1fr; gap: 3px 12px; font-size: 13px; margin: 0; }
.kv dt { color: var(--ink-3); font-weight: 400; }
.kv dd { margin: 0; font-family: var(--f-mono); font-size: 12.5px; overflow-wrap: anywhere; }
.big .tilebox { aspect-ratio: 16 / 10; }
.mlist { display: flex; flex-direction: column; gap: 6px; max-height: 640px; overflow: auto; }
.mrow { display: grid; grid-template-columns: 92px minmax(0, 1fr) auto; gap: 10px; align-items: center; padding: 6px; border-radius: 8px; border: 1px solid transparent; cursor: pointer; background: transparent; text-align: left; }
.mrow:hover { background: var(--surface-2); }
.mrow[aria-pressed="true"] { border-color: var(--accent); }
.mrow .who { display: flex; flex-direction: column; min-width: 0; font-size: 12px; align-items: flex-start; }
.mrow .who b { font-family: var(--f-mono); font-weight: 500; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; max-width: 100%; }
.mrow .who span { color: var(--ink-3); }
.mrow .pct { font-family: var(--f-mono); font-size: 13px; display: flex; flex-direction: column; align-items: flex-end; gap: 3px; }
.mrow .pct .sm { font-size: 11px; color: var(--ink-3); }
/* Triage buttons: a pressed button takes the colour of its decision. */
.seg.tri { display: grid; grid-template-columns: repeat(2, minmax(0, 1fr)); gap: 2px; border: 1px solid var(--line); border-radius: 8px; padding: 2px; background: var(--surface-2); }
.seg.tri button { border: 0; background: transparent; padding: 5px 6px; border-radius: 6px; font-size: 12px; font-weight: 600; color: var(--ink-2); cursor: pointer; }
.seg.tri button:hover { background: var(--surface); }
.seg.tri button[aria-pressed="true"][data-status="confirm"] { background: var(--good-bg); color: var(--good); }
.seg.tri button[aria-pressed="true"][data-status="resynth"] { background: var(--warn-bg); color: var(--warn); }
.seg.tri button[aria-pressed="true"][data-status="analogues"] { background: var(--accent-soft); color: var(--accent); }
.seg.tri button[aria-pressed="true"][data-status="discard"] { background: var(--bad-bg); color: var(--bad); }
.trictl { display: flex; flex-direction: column; gap: 6px; }
.trictl .lbl { font-size: 11px; text-transform: uppercase; letter-spacing: .06em; color: var(--ink-2); font-weight: 600; }
.trictl textarea { width: 100%; border: 1px solid var(--line); border-radius: 7px; padding: 6px 8px; font: inherit; font-size: 13px; resize: vertical; }
.trirow { display: flex; justify-content: space-between; align-items: center; gap: 8px; flex-wrap: wrap; }
.tmeta { font-size: 11px; color: var(--ink-3); }
/* ---- the triage board: four columns (two on narrow screens) */
.board { display: grid; grid-template-columns: repeat(4, minmax(0, 1fr)); gap: 10px; padding: 14px; }
@media (max-width: 1100px) { .board { grid-template-columns: repeat(2, minmax(0, 1fr)); } }
.bcol { background: var(--surface-2); border-radius: 9px; padding: 8px; display: flex; flex-direction: column; gap: 8px; min-width: 0; max-height: 560px; overflow: auto; }
.bcol h5 { margin: 0; display: flex; justify-content: space-between; align-items: center; font-size: 12px; }
.bcol h5 .c { font-family: var(--f-mono); color: var(--ink-3); }
.titem { border: 1px solid var(--line); background: var(--surface); border-radius: 8px; padding: 6px; display: flex; flex-direction: column; gap: 4px; text-align: left; cursor: pointer; min-width: 0; }
.titem:hover { border-color: var(--ink-3); }
.titem.gone { opacity: .7; }
.titem .tilebox { aspect-ratio: 2 / 1; }
.titem .tl { display: flex; justify-content: space-between; gap: 6px; font-size: 12px; }
.titem .tl b { font-family: var(--f-mono); font-weight: 500; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
.titem .tn { font-size: 11.5px; color: var(--ink-3); }
.titem .tnote { font-size: 12px; overflow-wrap: anywhere; }
.trinotice { padding: 8px 14px; font-size: 13px; color: var(--ink-2); border-bottom: 1px solid var(--line); }
/* ---- the activity-cliff list and the cliff pair in the detail panel */
.cliffs { display: flex; flex-direction: column; gap: 8px; padding: 14px; }
.cliff { display: grid; grid-template-columns: minmax(0, 1fr) auto minmax(0, 1fr); gap: 10px; align-items: center; border: 1px solid var(--line); border-radius: 9px; padding: 8px; background: var(--surface); cursor: pointer; text-align: left; }
.cliff:hover { border-color: var(--ink-3); }
.cliff[aria-pressed="true"] { border-color: var(--accent); box-shadow: 0 0 0 2px var(--accent-soft); }
.cside { display: grid; grid-template-columns: 110px minmax(0, 1fr); column-gap: 10px; align-items: center; min-width: 0; }
.cside .tilebox { grid-row: 1 / span 3; }
.cside .who { display: flex; flex-direction: column; min-width: 0; font-size: 12px; }
.cside .who b { font-family: var(--f-mono); font-weight: 500; }
.cside .who span { color: var(--ink-3); }
.cside .pct { font-size: 15px; }
.cside .chip { justify-self: start; }
.cmid { display: flex; flex-direction: column; align-items: center; gap: 2px; font-size: 12px; color: var(--ink-2); padding: 0 4px; }
.cmid .big { font-size: 16px; color: var(--ink); }
.cmid .sm { font-size: 11px; color: var(--ink-3); }
.pair { display: grid; grid-template-columns: 1fr 1fr; gap: 8px; }
.pairside { display: flex; flex-direction: column; gap: 4px; border: 1px solid var(--line); border-radius: 8px; padding: 6px; background: var(--surface); text-align: left; cursor: pointer; font-size: 12px; align-items: flex-start; }
.pairside .who { display: flex; flex-direction: column; }
.pairside .who b { font-family: var(--f-mono); font-weight: 500; }
.pairside .who span { color: var(--ink-3); }
/* ---- plates: heatmap legend, small plate maps, large map, replicates and QC table */
.hmlegend { gap: 8px; }
.hmbar { width: 160px; height: 10px; border-radius: 3px; background: linear-gradient(90deg, #6250d6 0%, #eef1ef 29.4%, #eb6834 88.2%, #eb6834 100%); border: 1px solid var(--line); display: inline-block; }
.minigrid { display: grid; grid-template-columns: repeat(auto-fill, minmax(150px, 1fr)); gap: 10px; padding: 14px; }
.mini { border: 1px solid var(--line); border-radius: 8px; padding: 6px; background: var(--surface); cursor: pointer; display: flex; flex-direction: column; gap: 4px; }
.mini:hover { border-color: var(--ink-3); }
.mini[aria-pressed="true"] { border-color: var(--accent); box-shadow: 0 0 0 2px var(--accent-soft); }
.mini svg { width: 100%; height: auto; display: block; border-radius: 3px; background: #fff; }
.mini .ml { display: flex; justify-content: space-between; align-items: center; font-size: 12px; }
.bighead { display: flex; align-items: center; gap: 14px; flex-wrap: wrap; padding: 4px 14px 0; font-size: 12.5px; color: var(--ink-2); }
.bighead b { color: var(--ink); }
#bigmap { width: 100%; height: 420px; }
#repplot { width: 100%; height: 460px; }
.repstats { margin: 12px 14px; }
.replist { padding: 0 14px 14px; }
.replist h4 { font-size: 14px; font-weight: 600; margin: 4px 0 8px; }
.rlist { display: grid; grid-template-columns: repeat(auto-fill, minmax(280px, 1fr)); gap: 6px; }
.tablewrap { overflow-x: auto; }
table.qc { border-collapse: collapse; width: 100%; font-size: 12.5px; }
table.qc th, table.qc td { padding: 6px 12px; text-align: right; border-bottom: 1px solid var(--line); white-space: nowrap; }
table.qc th { font-size: 11px; text-transform: uppercase; letter-spacing: .05em; color: var(--ink-3); background: var(--surface-2); }
table.qc th:first-child, table.qc td:first-child { text-align: left; }
table.qc td { font-family: var(--f-mono); }
/* ---- data checks */
.notes { padding: 12px 14px; font-size: 13px; color: var(--ink-2); display: flex; flex-direction: column; gap: 6px; }
.notes code, .help code { font-family: var(--f-mono); font-size: 12px; background: var(--surface-2); padding: 1px 5px; border-radius: 4px; }
/* ---- the structure tooltip that follows the mouse (chase.js creates it) */
.chase-tip { position: fixed; z-index: 2000; width: 250px; background: var(--surface); border: 1px solid var(--line); border-radius: 10px; box-shadow: 0 8px 28px rgba(0,0,0,.18); padding: 8px; pointer-events: none; display: flex; flex-direction: column; gap: 6px; }
.chase-tip[hidden] { display: none; }
.chase-tip .tt { display: flex; justify-content: space-between; gap: 8px; align-items: baseline; }
.chase-tip .tt b { font-family: var(--f-mono); font-size: 12.5px; font-weight: 500; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
.chase-tip .pv { font-family: var(--f-mono); font-size: 15px; }
.chase-tip .sm { font-size: 11.5px; color: var(--ink-3); display: flex; gap: 8px; flex-wrap: wrap; }
.nav-underline .nav-link, .ccard .nav-link { font-size: 13px; }
.ccard .card { border: 0; }
/* ---- the How to use page */
.help { max-width: 880px; margin: 0 auto; padding: 24px 16px 48px; display: flex; flex-direction: column; gap: 26px; }
.help h2 { font-size: 22px; font-weight: 700; margin: 0; }
.help section { display: flex; flex-direction: column; gap: 10px; }
.help h3 { margin: 0; font-size: 18px; font-weight: 600; }
.help h4 { margin: 6px 0 0; font-size: 14px; font-weight: 700; }
.help p, .help li { color: var(--ink-2); margin: 0; }
.help sup { font-size: 0.72em; line-height: 0; }   /* reference numbers: keep the line spacing even */
.help ul, .help ol { margin: 0; padding-left: 20px; display: flex; flex-direction: column; gap: 6px; }
.help b { color: var(--ink); }
.help .formula { font-family: var(--f-mono); font-size: 13px; background: var(--surface); border: 1px solid var(--line); border-radius: 8px; padding: 10px 12px; white-space: pre; overflow-x: auto; }
.help table { border-collapse: collapse; width: 100%; font-size: 13px; background: var(--surface); }
.help th, .help td { padding: 6px 10px; border-bottom: 1px solid var(--line); text-align: left; vertical-align: top; }
.help th { font-size: 11px; text-transform: uppercase; letter-spacing: .05em; color: var(--ink-3); background: var(--surface-2); }
.help .acro b { color: var(--ink); }
.help .foot { border-top: 1px solid var(--line); padding-top: 16px; font-size: 13px; color: var(--ink-3); }

/* ---- colour pickers */
.colorrow { gap: 16px; background: var(--surface-2); }
.cpick { display: inline-flex; align-items: center; gap: 6px; font-size: 12px; color: var(--ink-2); cursor: pointer; }
.cpick input[type=color] { width: 28px; height: 22px; padding: 0; border: 1px solid var(--line); border-radius: 5px; background: none; cursor: pointer; }
.ccard-h .shiny-download-link { white-space: nowrap; }

/* ---- PAINS and covalent chips, and the list of alerts */
.chip.cov { background: #e6e2fb; color: #4b3cb0; }
.chips { display: inline-flex; gap: 4px; flex-wrap: wrap; }
.alerts { display: flex; flex-direction: column; gap: 4px; }
.alerts .lbl { font-size: 11px; text-transform: uppercase; letter-spacing: .06em; color: var(--ink-2); font-weight: 600; }
.alerts ul { margin: 0; padding: 0; list-style: none; display: flex; flex-direction: column; gap: 3px; font-size: 12.5px; }

/* ---- 'Import triage (.csv)': make Shiny's file input look like a normal button in the card header */
.trimport .shiny-input-container { margin: 0; width: auto !important; }
.trimport .form-group { margin: 0; }
.trimport .input-group { flex-wrap: nowrap; }
.trimport .input-group > input.form-control { display: none; }
.trimport .btn-file, .trimport .input-group-btn .btn, .trimport label.input-group-btn { font-size: 12px; border-radius: 6px !important; }
.trimport .progress { display: none; }