832428cffce91e64b62eb16c0ca2edff8de29501 max Tue Aug 4 07:58:47 2026 -0700 hgBlat table view: give the header the house-style tan/wheat title band The results header was steel-blue, which left the whole page a single blue family (navy nav, blue-grey table, navy buttons/links) - it read as a generic blue dashboard. Per the UCSC UI style guide the results bar is a title band (page title + right-aligned primary action), so make it the signature wheat #e9cf9a band with navy bold title, matching hgGateway/hgCollection. Steel-blue stays for the section headers on the alignment page. refs #37893 diff --git src/hg/js/hgBlat.js src/hg/js/hgBlat.js index 8e069edbe07..9333e2e06ab 100644 --- src/hg/js/hgBlat.js +++ src/hg/js/hgBlat.js @@ -1,474 +1,475 @@ // hgBlat.js - client-side rendering of the hgBlat "Table" output mode. // // hgBlat.c emits an inline object var hgBlatData = { config, hits } and an empty //
. This script builds the whole results UI from that data: // - a card with a summary strip (query / length / assembly / hit count + actions) // - a sortable, filterable DataTable whose cells are rendered here (identity bar, // query-coverage bar, linked loci, action links, comma-formatted position) // - a docked "selected hit" detail panel updated on row click // Header tooltips reuse the Genome Browser's own mechanism (title + convertTitleTagsToMouseovers). /* jshint esnext: true */ /* global $, hgBlatData, convertTitleTagsToMouseovers */ var blatSelectedRank = null; // rank of the row shown in the detail panel function blatFmt(n) { // 12345 -> "12,345" return Number(n).toLocaleString('en-US'); } function blatEsc(s) { // HTML-escape a value for safe insertion as text return $('
').text(s === null || s === undefined ? '' : String(s)).html(); } function blatIdColor(id) { // UCSC identity semantic colors if (id >= 98) { return '#1f7a34'; } if (id >= 95) { return '#4d7c0f'; } if (id >= 90) { return '#b45309'; } return '#b1301f'; } function blatInjectStyle() { if (document.getElementById('blatStyle')) { return; } // UCSC house style (per the project's UCSC UI Style Guide): steel-blue section header, tan/white // content, navy links with maroon hover, #dbe4ee table header, zebra rows, navy selection bar. var css = ` table.hgInside { background:#eef1f4; } #blatResults { --accent:#0a3a7a; --accentHover:#8b1a1a; --navy:#0a2b6b; --ink:#1e2833; --muted:#5b6572; --faint:#93a0ad; --line:#c4cdd6; --lineSoft:#e4e9ef; --card:#ffffff; --panel:#f4f7fb; --section:#4c7093; --headrow:#dbe4ee; --headrowLine:#a9bcd1; --sel:#cfe0f5; --hover:#eef3fb; --stripe:#f4f7fb; + --title:#e9cf9a; --titleLine:#d9bd82; --titleSub:#5a4a24; --btn:#ffffff; --btnLine:#999999; --btnText:#0a2b6b; --btnHover:#eef2f7; --btnDark:#0a2b6b; --btnDarkHover:#0a2350; font-family:'Helvetica Neue',Helvetica,Arial,sans-serif; color:var(--ink); font-size:14px; } .blatCard { background:var(--card); border:1px solid var(--line); border-radius:3px; overflow:hidden; box-shadow:0 1px 2px rgba(20,40,70,.10); margin:12px 0 24px; } .blatHead { display:flex; align-items:center; justify-content:space-between; gap:12px; flex-wrap:wrap; - padding:9px 18px; background:var(--section); } - .blatHead .t { font-weight:700; font-size:16px; color:#ffffff; } - .blatHead .t .sub { color:#d7e2ee; font-weight:400; } + padding:9px 18px; background:var(--title); border-bottom:1px solid var(--titleLine); } + .blatHead .t { font-weight:700; font-size:16px; color:var(--navy); } + .blatHead .t .sub { color:var(--titleSub); font-weight:400; } .blatHeadActions { display:flex; gap:8px; align-items:center; flex-wrap:wrap; } .blatStrip { display:flex; align-items:center; gap:24px; flex-wrap:wrap; padding:11px 18px; border-bottom:1px solid var(--line); background:var(--panel); } .blatStat { display:flex; flex-direction:column; gap:1px; } .blatStat .k { font-size:12px; color:var(--muted); font-weight:700; } .blatStat .v { font-size:14px; font-weight:700; color:var(--ink); } .blatDiv { width:1px; height:28px; background:var(--line); } .blatStripActions { margin-left:auto; display:flex; gap:8px; align-items:center; flex-wrap:wrap; } #blatResults .blatPill, #blatResults .blatStripActions input[type=submit], #blatResults .blatStripActions input[type=button] { font-family:inherit; font-size:13px; font-weight:700; color:var(--btnText); background:var(--btn); border:1px solid var(--btnLine); border-radius:3px; padding:5px 12px; cursor:pointer; text-decoration:none; display:inline-block; line-height:1.5; } #blatResults .blatPill:hover, #blatResults .blatStripActions input[type=submit]:hover, #blatResults .blatStripActions input[type=button]:hover { background:var(--btnHover); text-decoration:none; } #blatResults .blatPill.primary { background:var(--btnDark); color:#fff; border-color:var(--btnDark); } #blatResults .blatPill.primary:hover { background:var(--btnDarkHover); } .blatShareBox { display:flex; align-items:center; gap:10px; flex-wrap:wrap; padding:11px 18px; border-bottom:1px solid var(--line); background:var(--panel); } .blatShareMsg { font-size:14px; color:var(--muted); } .blatShareInput { flex:1; min-width:260px; font-size:13px; padding:5px 8px; border:1px solid var(--btnLine); border-radius:3px; background:#fff; } #blatTable { font-size:13px; width:100%; border-collapse:collapse; } #blatTable thead th { background:var(--headrow); border-bottom:1px solid var(--headrowLine); font-size:12px; color:var(--navy); font-weight:700; padding:8px 12px; white-space:nowrap; } #blatTable tbody td { padding:8px 12px; border-bottom:1px solid var(--lineSoft); white-space:nowrap; vertical-align:middle; } #blatTable tbody tr { cursor:pointer; } #blatTable tbody tr:nth-child(even) { background:var(--stripe); } #blatTable tbody tr:hover { background:var(--hover); } #blatTable tbody tr.blatSel { background:var(--sel); box-shadow:inset 3px 0 0 var(--navy); } #blatTable td.num, #blatTable th.num { text-align:right; font-variant-numeric:tabular-nums; } #blatTable td.rankCol { color:var(--faint); } #blatTable td.strandCol { text-align:center; color:var(--muted); } #blatTable td.actionsCol a { color:var(--accent); font-weight:700; } #blatTable td.actionsCol .blatActSep { color:var(--line); margin:0 10px; } #blatTable a { color:var(--accent); text-decoration:none; } #blatTable a:hover { color:var(--accentHover); text-decoration:underline; } .blatRowHint { padding:11px 18px 2px; font-size:13px; color:var(--muted); } .blatLocus { max-width:230px; overflow:hidden; text-overflow:ellipsis; white-space:nowrap; } .chrNote { color:var(--faint); cursor:help; margin-left:4px; } .blatIdWrap { display:flex; align-items:center; gap:9px; justify-content:flex-end; } .blatIdBar { flex:0 0 54px; height:8px; background:var(--headrow); border:1px solid var(--headrowLine); overflow:hidden; } .blatIdBar > i { display:block; height:100%; } .blatIdPct { font-size:13px; font-weight:700; width:48px; text-align:right; font-variant-numeric:tabular-nums; } .blatCov { position:relative; display:block; width:150px; height:10px; background:var(--headrow); border:1px solid var(--headrowLine); } .blatCov > i { position:absolute; top:0; bottom:0; background:var(--accent); } #blatTable_filter { float:left; margin:0 0 10px; } #blatTable_filter input { width:300px; max-width:55vw; border:1px solid var(--btnLine); border-radius:3px; padding:5px 9px; font-size:14px; } #blatTable_wrapper { padding:6px 18px 4px; } .blatDetail { border-bottom:1px solid var(--line); background:var(--panel); padding:14px 18px 16px; } .blatDetail .dhead { display:flex; align-items:baseline; gap:10px; margin-bottom:12px; flex-wrap:wrap; } .blatDetail .dhead .lab { font-size:13px; color:var(--muted); } .blatDetail .dhead .loc { font-size:14px; font-weight:700; color:var(--ink); } .blatDetailCard { display:flex; gap:26px; flex-wrap:wrap; padding:14px 16px; background:var(--card); border:1px solid var(--line); border-radius:3px; } .blatTiles { display:grid; grid-template-columns:repeat(4,auto); gap:14px 26px; } .blatTile .k { font-size:13px; color:var(--muted); cursor:help; } .blatTile .v { font-size:14px; font-weight:700; color:var(--ink); } .blatDetailActions { display:flex; gap:8px; margin-top:14px; flex-wrap:wrap; } `; var st = document.createElement('style'); st.id = 'blatStyle'; st.textContent = css; document.head.appendChild(st); } // ---- cell renderers ------------------------------------------------------ function blatPositionCell(hit) { var note = hit.chromNote ? ` ` : ''; return `${blatEsc(hit.chrom)}:` + `${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}${note}`; } function blatActionsCell(hit) { // detailsUrl is the base-by-base alignment page (htcUserAli on a fresh search, htcBlatAlign on a // shared-link reopen); it is always present now, but guard in case a future caller omits it. var parts = [`Browser`, `New tab`]; if (hit.detailsUrl) { parts.push(`Alignment`); } // a thin divider between the links makes the grouping clearer return parts.join('|'); } function blatLocusCell(hit, cfg) { if (!hit.locusText) { return ''; } var inner; if (hit.locusType && hit.locusGenes && hit.locusGenes.length) { var links = hit.locusGenes.map(function(g) { return `${blatEsc(g)}`; }).join('-'); inner = `${blatEsc(hit.locusType)} ${links}`; } else { inner = blatEsc(hit.locusText); } return `
${inner}
`; } function blatIdentityCell(hit) { var c = blatIdColor(hit.identity); return `` + `` + `${hit.identity.toFixed(1)}%`; } function blatCoverageCell(hit) { var left = (hit.qStart - 1) / hit.qSize * 100; var width = (hit.qEnd - hit.qStart + 1) / hit.qSize * 100; var tip = `query ${blatFmt(hit.qStart)}–${blatFmt(hit.qEnd)} of ${blatFmt(hit.qSize)} bp`; return ``; } // ---- summary strip + detail panel --------------------------------------- function blatSummaryStrip(cfg, queryCount) { var stat = (k, v) => `
${k}` + `${v}
`; var div = ''; var assembly = stat('Assembly', blatEsc(cfg.organism) + ' / ' + blatEsc(cfg.db)) + div + stat('Hits', blatFmt(cfg.hitCount)); var stats; if (cfg.multiQuery) { // With more than one query sequence a single query name/length would be wrong, so show the // number of distinct queries; each hit's own query is in the table's Query column. stats = stat('Queries', blatFmt(queryCount)) + div + assembly; } else { stats = stat('Query', blatEsc(cfg.queryName)) + div + stat('Length', blatFmt(cfg.querySize) + ' bp') + div + assembly; } var actions = ''; // "Share a link" saves a durable anonymous session that reopens these results; it only works // when a stable custom track was made from them (cfg.canShare, i.e. autoBigPsl is on). if (cfg.canShare) { actions += ''; } if (cfg.viewAllUrl) { actions += `View all in browser`; } // custom-track Rename/Delete buttons (emitted by hgBlat.c) get relocated here after render return `
${stats}${actions}
`; } var BLAT_TILE_TIPS = { 'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.', 'Identity': 'Percent identity of the aligned bases.', 'Matches': 'Query bases that match the genome.', 'Mismatch': 'Bases that differ between query and genome.', 'Gaps': 'Number of gaps (insertions or deletions) in the alignment.', 'Blocks': 'Number of ungapped aligned blocks.', 'Strand': 'Genome strand the query matched (+ or -).', 'Q span': 'Range of the query sequence that aligned (1-based).' }; function blatTileSkeleton(label, id, color) { var style = color ? ` style="color:${color}"` : ''; var tip = BLAT_TILE_TIPS[label] || ''; return `
${label}
` + `
`; } function blatDetailSkeleton() { // Built once; blatRenderDetail() only updates values, so the tile-label tooltips // are wired a single time by convertTitleTagsToMouseovers. var tiles = blatTileSkeleton('Score', 'dvScore') + blatTileSkeleton('Identity', 'dvIdentity') + blatTileSkeleton('Matches', 'dvMatches') + blatTileSkeleton('Mismatch', 'dvMismatch') + blatTileSkeleton('Gaps', 'dvGaps') + blatTileSkeleton('Blocks', 'dvBlocks') + blatTileSkeleton('Strand', 'dvStrand') + blatTileSkeleton('Q span', 'dvQspan'); document.getElementById('blatDetail').innerHTML = `
Selected hit` + `
` + `
` + `
${tiles}
` + `
` + `
` + `
Alignment
` + `
` + `` + `View alignment
`; if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); } } function blatSet(id, prop, val) { var e = document.getElementById(id); if (!e) { return; } if (prop === 'text') { e.textContent = val; } else if (prop === 'html') { e.innerHTML = val; } else if (prop === 'href') { e.setAttribute('href', val); } else if (prop === 'color') { e.style.color = val; } } function blatRenderDetail(hit) { if (!hit || !document.getElementById('blatDetail')) { return; } if (!document.getElementById('dvScore')) { blatDetailSkeleton(); } var idc = blatIdColor(hit.identity); var locus = hit.locusText ? blatEsc(hit.locusText) + ' · ' : ''; var q = hgBlatData.config.multiQuery ? blatEsc(hit.qName) + ' · ' : ''; blatSet('dvLoc', 'html', `#${hit.rank} · ${q}${locus}${blatEsc(hit.chrom)}:${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}`); blatSet('dvScore', 'text', blatFmt(hit.score)); blatSet('dvIdentity', 'text', hit.identity.toFixed(1) + '%'); blatSet('dvIdentity', 'color', idc); blatSet('dvMatches', 'text', blatFmt(hit.matches)); blatSet('dvMismatch', 'text', blatFmt(hit.misMatch)); blatSet('dvGaps', 'text', blatFmt(hit.gaps)); blatSet('dvBlocks', 'text', blatFmt(hit.blocks)); blatSet('dvStrand', 'text', hit.strand); blatSet('dvQspan', 'text', blatFmt(hit.qStart) + '–' + blatFmt(hit.qEnd)); blatSet('dvBrowser', 'href', hit.browserUrl); blatSet('dvNewTab', 'href', hit.newTabUrl); // Show the Alignment box whenever a base-by-base alignment page is available (htcUserAli on a // fresh search, htcBlatAlign on a shared-link reopen); hide it only if detailsUrl is missing. var alignBox = document.getElementById('dvAlignBox'); if (alignBox) { alignBox.style.display = hit.detailsUrl ? '' : 'none'; } if (hit.detailsUrl) { blatSet('dvViewAlign', 'href', hit.detailsUrl); blatSet('dvAlign', 'text', 'See the base-by-base alignment of your query against ' + hit.chrom + ': matches, mismatches and gaps across the whole span.'); } } function blatSelect(dt, rank) { blatSelectedRank = rank; $('#blatTable tbody tr').each(function() { var d = dt.row(this).data(); $(this).toggleClass('blatSel', !!d && d.rank === rank); }); var hit = hgBlatData.hits.find(h => h.rank === rank); blatRenderDetail(hit); } // ---- header tooltips (reuse the browser's title -> mouseover system) ----- var BLAT_HEADER_TIPS = { '#': 'Rank by the chosen sort order', 'Query': 'The query sequence this hit came from', 'Position': 'Genomic location of the match (1-based). Click to open the Genome Browser.', 'Actions': 'Open the match in the browser, see the alignment details, or open in a new tab', 'Locus': 'Nearest gene(s), and whether the hit falls in an exon, intron, or intergenic region', 'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.', 'Identity': 'Percent identity of the aligned bases', 'Strand': 'Genome strand the query matched (+ or -)', 'Query coverage': 'Which part of the query aligned (blue) across its full length', 'Span': 'Length of the match on the genome (bp). Larger than the query length means ' + 'the alignment crosses introns or deletions.' }; function blatApplyTooltips() { $('#blatTable thead th').each(function() { var tip = BLAT_HEADER_TIPS[$(this).text().trim()]; if (tip) { $(this).attr('title', tip); } }); if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); } } // ---- share a link -------------------------------------------------------- function blatShareLink() { // Save the current cart as an anonymous shared session (hgSession API), then build a link back // to this page that restores it. The restored cart carries the durable bigPsl custom track // made from these results, which hgBlat rebuilds this table from (no BLAT re-run) on open. var cfg = hgBlatData.config; var box = document.getElementById('blatShareBox'); box.style.display = 'flex'; box.innerHTML = 'Creating shareable link…'; // Save the cart as an anonymous shared session; same endpoint/params as topLinks.js "Share a link". $.ajax({ type: 'POST', url: '../cgi-bin/hgSession', data: { hgsid: cfg.hgsid, 'hgS_doSaveSessionJson': 1, 'hgS_shareAnon': 1 }, dataType: 'json', success: function(data) { if (!data || !data.name) { box.innerHTML = 'Could not create link: ' + blatEsc(data && data.error ? data.error : 'unknown error') + ''; return; } // anonymous sessions are saved under the reserved user "l"; hgBlat maps the short // u=/s= params to the session load and rebuilds this table from the durable bigPsl // custom track (no BLAT re-run) var link = window.location.origin + window.location.pathname + '?u=l&s=' + encodeURIComponent(data.name); box.innerHTML = 'Shareable link (opens these results for anyone):' + '' + ''; var inp = document.getElementById('blatShareInput'); inp.value = link; inp.focus(); inp.select(); $('#blatShareCopy').on('click', function() { inp.select(); if (navigator.clipboard) { navigator.clipboard.writeText(link); } else { document.execCommand('copy'); } document.getElementById('blatShareCopy').textContent = 'Copied'; }); }, error: function() { box.innerHTML = 'Could not reach the server. Please try again.'; } }); } // ---- build --------------------------------------------------------------- function blatBuild() { var cfg = hgBlatData.config; var hits = hgBlatData.hits; blatInjectStyle(); var back = cfg.backUrl ? `Back to browser` : ''; // "Old BLAT result page" re-renders the classic list from this session's fresh trash files and // clears the blatNewPage preference (blatNewPage=0), so future searches use the classic page // until the user opts back in. Only offered on a fresh search (cfg.canOldPage), not a reopen. var oldPage = cfg.canOldPage ? `Old BLAT result page` : ''; var headHtml = `
BLAT results` + `${oldPage}${back}` + `New BLAT search
`; var queryCount = new Set(hits.map(h => h.qName)).size; var th = []; th.push('#'); if (cfg.multiQuery) { th.push('Query'); } th.push('Position'); th.push('Actions'); if (cfg.hasLocus) { th.push('Locus'); } th.push('Score'); th.push('Identity'); th.push('Strand'); th.push('Query coverage'); th.push('Span'); // detail dock sits above the table: with long hit lists a bottom dock scrolls out of view document.getElementById('blatResults').innerHTML = `
${headHtml}${blatSummaryStrip(cfg, queryCount)}` + `` + `
` + `
Click any row to inspect it in the panel above.
` + `${th.join('')}
`; // relocate the C-emitted custom-track buttons into the summary strip var actionBar = document.querySelector('.blatStripActions'); ['renameFormItem', 'deleteCtForm'].forEach(function(id) { var el = document.getElementById(id); if (el && actionBar) { actionBar.appendChild(el); } }); $('#blatShareBtn').on('click', blatShareLink); var columns = []; columns.push({ data: 'rank', className: 'num rankCol' }); if (cfg.multiQuery) { columns.push({ data: 'qName', className: 'queryCol' }); } columns.push({ data: null, orderable: false, className: 'blatPos', render: (d, type, row) => (type === 'display' ? blatPositionCell(row) : row.chrom + ':' + row.tStart) }); columns.push({ data: null, orderable: false, className: 'actionsCol', render: (d, type, row) => (type === 'display' ? blatActionsCell(row) : '') }); if (cfg.hasLocus) { columns.push({ data: 'locusText', render: (d, type, row) => (type === 'display' ? blatLocusCell(row, cfg) : (d || '')) }); } columns.push({ data: 'score', className: 'num' }); columns.push({ data: 'identity', className: 'num', render: (d, type, row) => (type === 'display' ? blatIdentityCell(row) : d) }); columns.push({ data: 'strand', className: 'strandCol' }); columns.push({ data: null, className: 'covCol', orderable: false, render: (d, type, row) => (type === 'display' ? blatCoverageCell(row) : (row.qEnd - row.qStart + 1)) }); columns.push({ data: 'span', className: 'num' }); var dt = $('#blatTable').DataTable({ data: hits, columns: columns, paging: false, info: false, order: [], language: { search: '', searchPlaceholder: 'Filter hits by locus, chrom, position…' } }); $('#blatTable tbody').on('click', 'tr', function(ev) { if ($(ev.target).closest('a').length) { return; } // let links work normally var d = dt.row(this).data(); if (d) { blatSelect(dt, d.rank); } }); // Keep the selected-row highlight after sort/filter. Header tooltips are wired once below (the // persists across draws); we deliberately do NOT re-run convertTitleTagsToMouseovers on // every draw, as it re-scans the whole document and adds global listeners on each call. dt.on('draw', function() { if (blatSelectedRank !== null) { blatSelect(dt, blatSelectedRank); } }); // No hit is pre-selected: several hits are often tied on score/identity, so picking one for the // user is misleading. The detail panel shows a prompt until a row is clicked. document.getElementById('blatDetail').innerHTML = `
Select a hit below to see its alignment details.
`; blatApplyTooltips(); } $(document).ready(function() { if (typeof hgBlatData !== 'undefined' && document.getElementById('blatResults')) { blatBuild(); } });