cee097b75fe4d1b29f0debd8af938ba6bf729d53 max Tue Aug 11 08:18:42 2026 -0700 hgBlat: new client-rendered BLAT search form and sortable results page, refs #37893 An opt-in modern alternative to the classic hyperlink output, gated by the blatNewForm / blatNewPage hg.conf flags. hgBlat.c emits the hit data and form config as inline JSON (hgBlatData / hgBlatFormData) into empty containers, and hgBlat.js builds the UI: the search form, a sortable/filterable DataTable with identity and query-coverage bars, a docked per-hit detail panel, a FASTA query viewer, and share-link and rename-track modals. - hgBlat.css: all styling for both pages, loaded via webIncludeResourceFile (not injected from JS); layout uses CSS classes rather than inline styles. - utils.js: setupGenomeSelector, the combobox genome picker the form uses. - hgc.c: blatOldTracks / blatKeepResults - the "Keep results" checkbox lets a user accumulate BLAT result tracks instead of each search replacing the last. - hgConfCatalog: register the blatNewForm / blatNewFormBanner gates. - blatExample.fa: the example query the form loads on demand. Markup is built in JS (escaped values via htmlEncode, everything else set through DOM properties); no HTML strings in the C or a template engine. diff --git src/hg/js/hgBlat.js src/hg/js/hgBlat.js index 45e3b2c0126..d3f66718551 100644 --- src/hg/js/hgBlat.js +++ src/hg/js/hgBlat.js @@ -1,693 +1,899 @@ // hgBlat.js - client-side rendering of the hgBlat "Table" output mode. // // hgBlat.c emits an inline object var hgBlatData = { config, hits } and an empty // <div id="blatResults">. 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, htmlEncode */ 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 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 = ` - /* Plain white page background, matching the track-settings model (gb.css). The framework body - * is cream (#FFF9D2) and the hgInside content table carries a BGCOLOR=#FFFEE8 attribute; override - * both to white so the results sit on one uniform white background. */ - body.cgi { background:#fff; } - table.hgInside { background:#fff; } - /* Main page header, styled like gb.css .gbTrackTitleBanner (hgGtexTrackSettings model): black - * title on the house gold. The framework's #sectTtl already holds "<assembly> BLAT Results". */ - .subheadingBar { background:#eaca92; padding:9px 16px; margin:0; border:0; box-sizing:border-box; } - .subheadingBar #sectTtl { color:#000; font-weight:700; font-size:18px; - display:flex; align-items:center; justify-content:space-between; flex-wrap:wrap; gap:12px; } - #blatResults { --accent:#003a72; --accentHover:#8b1a1a; --navy:#0a2b6b; --ink:#1e2833; - --muted:#5b6572; --faint:#93a0ad; --line:#d0d0d0; --lineSoft:#ececec; --card:#ffffff; - --panel:#ffffff; --section:#4c759c; --headrow:#ededed; --headrowLine:#cccccc; - --sel:#cfe0f5; --hover:#f0f0f0; --stripe:#f7f7f7; - --title:#eaca92; --titleLine:#d9bd82; --titleSub:#5a4a24; - --btn:#ffffff; --btnLine:#999999; --btnText:#003a72; --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:0; overflow:hidden; - box-shadow:0 1px 2px rgba(20,40,70,.10); margin:12px 0 24px; } - /* Page actions sit in the gold main header (#sectTtl); no separate toolbar. */ - .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; } - /* Buttons live both inside the card (#blatResults) and in the gold header (#sectTtl); scope to - * both ids so the framework's link styles (which would add an underline) can't beat them. */ - #blatResults .blatPill, #sectTtl .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:0; padding:5px 12px; cursor:pointer; - text-decoration:none; display:inline-block; line-height:1.5; } - #blatResults .blatPill:hover, #sectTtl .blatPill:hover, - #blatResults .blatStripActions input[type=submit]:hover, - #blatResults .blatStripActions input[type=button]:hover { background:var(--btnHover); text-decoration:none; } - #blatResults .blatPill.primary, #sectTtl .blatPill.primary { background:var(--btnDark); color:#fff; border-color:var(--btnDark); } - #blatResults .blatPill.primary:hover, #sectTtl .blatPill.primary:hover { background:var(--btnDarkHover); } - /* In the gold header (#sectTtl) the framework's link styles would otherwise beat .blatPill, so - * re-assert the button look with id-level specificity. */ - #sectTtl .blatPill { color:#003a72; background:#fff; border:1px solid #999; text-decoration:none; } - #sectTtl .blatPill:hover { background:#eef2f7; text-decoration:none; } - #sectTtl .blatPill.primary { background:#0a2b6b; color:#fff; border-color:#0a2b6b; } - #sectTtl .blatPill.primary:hover { background:#0a2350; } - .blatShareIcon { vertical-align:-2px; margin-right:6px; } - .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:0; background:#fff; } - .blatBanner { background:#fbf3e2; border:1px solid var(--titleLine); padding:10px 14px; - margin:12px 0 0; font-size:14px; color:var(--ink); } - .blatBanner a { color:var(--accent); } - .blatBanner a:hover { color:var(--accentHover); } - .blatSeqBar { flex:1 1 100%; display:flex; gap:8px; align-items:center; flex-wrap:wrap; } - .blatSeqText { flex:1 1 100%; min-height:150px; margin-top:10px; padding:8px; white-space:pre; - font-family:'Roboto Mono','Courier New',monospace; font-size:13px; color:var(--ink); - border:1px solid var(--btnLine); background:#fff; overflow:auto; } - #blatTable { font-size:13px; width:100%; border-collapse:collapse; } - /* Let the long text columns wrap so the table shrinks to fit smaller screens, while the fixed - * bar columns keep a min-width so they never compress into an overlap; when even that won't fit, - * #blatTable_wrapper scrolls horizontally. */ - #blatTable td.blatPos, #blatTable td.queryCol { white-space:normal; word-break:break-word; } - #blatTable td.scoreCol { min-width:118px; } - #blatTable td.covCol { min-width:120px; } - #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; } - /* "New tab" shown as the usual box-with-arrow icon (via a CSS background so it isn't repeated in - * every row's markup), sitting right after the position link with just a space between them. */ - #blatTable a.blatNewTab { display:inline-block; width:11px; height:11px; - margin-left:4px; vertical-align:-1px; background-repeat:no-repeat; background-position:center; - background-size:contain; background-image:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 512 512'%3E%3Cpath fill='%23003a72' d='M320 0c-17.7 0-32 14.3-32 32s14.3 32 32 32h82.7L201.4 265.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L448 109.3V192c0 17.7 14.3 32 32 32s32-14.3 32-32V32c0-17.7-14.3-32-32-32H320zM80 32C35.8 32 0 67.8 0 112V432c0 44.2 35.8 80 80 80H400c44.2 0 80-35.8 80-80V320c0-17.7-14.3-32-32-32s-32 14.3-32 32V432c0 8.8-7.2 16-16 16H80c-8.8 0-16-7.2-16-16V112c0-8.8 7.2-16 16-16H192c17.7 0 32-14.3 32-32s-14.3-32-32-32H80z'/%3E%3C/svg%3E"); } - #blatTable a.blatNewTab:hover { opacity:.65; } - #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:280px; white-space:nowrap; overflow:hidden; text-overflow:ellipsis; } - .chrNote { color:var(--faint); text-decoration:none; margin-left:4px; } - .chrNote:hover { color:var(--accent); } - .blatScoreWrap { display:flex; align-items:center; gap:9px; justify-content:flex-end; } - .blatScoreVal { font-size:13px; font-weight:700; text-align:right; font-variant-numeric:tabular-nums; } - .blatScoreBar { flex:0 0 54px; height:8px; background:var(--headrow); border:1px solid var(--headrowLine); overflow:hidden; } - .blatScoreBar > i { display:block; height:100%; background:var(--accent); } - .blatIdPct { font-size:13px; font-weight:700; font-variant-numeric:tabular-nums; } - .blatCov { position:relative; display:block; width:150px; max-width:100%; 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:0; padding:5px 9px; font-size:14px; } - #blatTable_wrapper { padding:6px 0 4px; overflow-x:auto; } - .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); } - .blatSelectHint { font-size:14px; color:var(--ink); } - .blatSelectHint a { color:var(--accent); } - .blatSelectHint a:hover { color:var(--accentHover); } - .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:0; } - .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; } - /* Rename modal. On this page the old C-emitted inline rename form (#renameFormItem / #renameForm) - * is replaced by the JS button + modal below, so keep the C markup hidden even though hgBlat.c - * flips its display to block after buildBigPsl (our !important beats that inline style). */ - #renameFormItem, #renameForm { display:none !important; } - .blatModalBg { position:fixed; top:0; right:0; bottom:0; left:0; z-index:1000; - background:rgba(0,0,0,.4); display:flex; align-items:center; justify-content:center; } - .blatModal { background:#fff; border:1px solid var(--line); border-radius:0; - box-shadow:0 4px 18px rgba(0,0,0,.28); padding:18px 20px; min-width:340px; max-width:92vw; } - .blatModalTitle { font-size:16px; font-weight:700; color:var(--ink); margin-bottom:12px; } - .blatModalText { font-size:13px; color:var(--ink); line-height:1.5; max-width:430px; margin-bottom:14px; } - .blatModalText a { color:var(--accent); } - .blatModalText a:hover { color:var(--accentHover); } - .blatModalLabel { display:block; font-size:12px; font-weight:700; color:var(--muted); - margin:10px 0 3px; } - .blatModalInput { width:100%; box-sizing:border-box; border:1px solid var(--btnLine); - border-radius:0; padding:6px 8px; font-size:14px; font-family:inherit; background:#fff; } - .blatModalBtns { display:flex; gap:8px; justify-content:flex-end; margin-top:18px; } - `; - var st = document.createElement('style'); - st.id = 'blatStyle'; - st.textContent = css; - document.head.appendChild(st); -} - // ---- cell renderers ------------------------------------------------------ function blatPositionCell(hit) { // For alt/fix/random/chrUn sequences show an info icon linking to the FAQ ("What is chr_alt & // chr_fix?"), with the short explanation as its tooltip. (Sits after the position link, not // nested inside it.) var note = hit.chromNote ? ` <a class="chrNote" target="_blank" href="../FAQ/FAQblat.html#blat1c" ` + `title="${htmlEncode(hit.chromNote)} Click to learn more in the BLAT FAQ.">ⓘ</a>` : ''; // The position links to the Genome Browser at this match; the new-tab icon right after it opens // the same in a new tab (whitespace between them, no divider). // URLs are htmlEncode'd before going into href="": they can carry the user's query name, so an // unescaped double-quote would otherwise break out of the attribute (XSS). return `<a class="blatPos" title="Open the Genome Browser at this location" ` + `href="${htmlEncode(hit.browserUrl)}">${htmlEncode(hit.chrom)}:` + `${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}</a>` + ` <a class="blatNewTab" target="_blank" href="${htmlEncode(hit.newTabUrl)}" ` + `title="Open match in a new tab" aria-label="Open match in a new tab"></a>${note}`; } function blatActionsCell(hit) { // The "Open" column now holds just the base-by-base alignment link (Browser moved to the Position // column). detailsUrl is htcUserAli on a fresh search, htcBlatAlign on a shared-link reopen; guard // in case a future caller omits it. if (!hit.detailsUrl) { return ''; } // htmlEncode the URL: detailsUrl embeds the user's query name, so an unescaped quote could break // out of the href attribute (XSS). return `<a title="Show the base-by-base alignment of your sequence to the genome" ` + `href="${htmlEncode(hit.detailsUrl)}">Alignment</a>`; } function blatLocusCell(hit) { // Locus is plain text (not a link): the gene names are shown for context only. The cell grows with // its content up to a max-width, then a very long locus (many overlapping genes) is clipped with a // CSS ellipsis; the full string is always available on mouseover (title). if (!hit.locusText) { return ''; } return `<div class="blatLocus" title="${htmlEncode(hit.locusText)}">${htmlEncode(hit.locusText)}</div>`; } function blatScoreCell(hit, maxScore) { // Score with a little bar chart after it, scaled to the highest score in this result set. var pct = maxScore > 0 ? (hit.score / maxScore * 100) : 0; return `<span class="blatScoreWrap"><span class="blatScoreVal">${blatFmt(hit.score)}</span>` + `<span class="blatScoreBar"><i style="width:${pct.toFixed(1)}%"></i></span></span>`; } function blatIdentityCell(hit) { // Just the percentage now (the bar chart moved to the Score column), kept in its semantic color. var c = blatIdColor(hit.identity); return `<span class="blatIdPct" style="color:${c}">${hit.identity.toFixed(1)}%</span>`; } function blatCoverageCell(hit) { var left = (hit.qStart - 1) / hit.qSize * 100; var width = (hit.qEnd - hit.qStart + 1) / hit.qSize * 100; var tip = `Query matches the genome at ${blatFmt(hit.qStart)}-${blatFmt(hit.qEnd)}bp out of ${blatFmt(hit.qSize)}bp`; return `<span class="blatCov" title="${tip}"><i style="left:${left.toFixed(1)}%;` + `width:${width.toFixed(1)}%"></i></span>`; } // ---- summary strip + detail panel --------------------------------------- function blatSummaryStrip(cfg, queryCount) { var stat = (k, v) => `<div class="blatStat"><span class="k">${k}</span>` + `<span class="v">${v}</span></div>`; var div = '<span class="blatDiv"></span>'; var assembly = stat('Assembly', htmlEncode(cfg.organism) + ' / ' + htmlEncode(cfg.db)) + div + stat('Matches', 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', htmlEncode(cfg.queryName)) + div + stat('Length', blatFmt(cfg.querySize) + ' bp') + div + assembly; } var actions = ''; // "View all in browser" is the primary action, so it comes first. if (cfg.viewAllUrl) { actions += `<a class="blatPill" title="Open the Genome Browser with all these BLAT hits shown together as one custom track" href="${htmlEncode(cfg.viewAllUrl)}">View all in browser</a>`; } // "Show Query Sequence" opens the query FASTA in a panel (with Download / Copy). Only on a fresh // search, where the uploaded sequence is available (cfg.querySeqs emitted by hgBlat.c). if (cfg.querySeqs && cfg.querySeqs.length) { actions += '<button type="button" class="blatPill" id="blatSeqBtn" ' + 'title="Show the sequence you searched with, in FASTA format">Show Query Sequence</button>'; } // "Share a link" just reveals the page's stable URL (cfg.shareUrl, a trash-backed reopen link). // cfg.canShare covers old session-based links (?u=&s=), where the current URL is already shareable. if (cfg.shareUrl || cfg.canShare) { // A small share-nodes icon precedes the label so users learn to associate it with sharing. var shareIcon = '<svg class="blatShareIcon" viewBox="0 0 24 24" width="13" height="13" ' + 'fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" ' + 'stroke-linejoin="round" aria-hidden="true"><circle cx="18" cy="5" r="3"></circle>' + '<circle cx="6" cy="12" r="3"></circle><circle cx="18" cy="19" r="3"></circle>' + '<line x1="8.6" y1="10.5" x2="15.4" y2="6.5"></line>' + '<line x1="8.6" y1="13.5" x2="15.4" y2="17.5"></line></svg>'; actions += '<button type="button" class="blatPill" id="blatShareBtn" ' + 'title="Show a link that reopens these results (works for a limited time)">' + shareIcon + 'Share a link</button>'; } // "Rename BLAT Track" opens a modal to rename the results custom track. This is a JS-native // button (renders immediately with the strip) that replaces the old C-emitted inline form, which // only appeared after the buildBigPsl AJAX finished and reflowed the page when clicked. if (cfg.canRename) { actions += '<button type="button" class="blatPill" id="blatRenameBtn" ' + 'title="Rename this BLAT results custom track and its description">Rename BLAT Track</button>'; } return `<div class="blatStrip">${stats}<span class="blatStripActions">${actions}</span></div>`; } var BLAT_TILE_TIPS = { 'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.', 'Identity': 'Percent identity of the aligned bases.', 'Matches': 'Query bases that match the genome.', 'Mismatch': 'Bases that differ between query and genome.', 'Gaps': 'Number of gaps (insertions or deletions) in the alignment.', 'Blocks': 'Number of ungapped aligned blocks.', 'Strand': 'Genome strand the query matched (+ or -).', 'Q span': 'Range of the query sequence that aligned (1-based).' }; function blatTileSkeleton(label, id, color) { var style = color ? ` style="color:${color}"` : ''; var tip = BLAT_TILE_TIPS[label] || ''; return `<div class="blatTile"><div class="k" title="${htmlEncode(tip)}">${label}</div>` + `<div class="v" id="${id}"${style}></div></div>`; } 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 = `<div class="dhead"><span class="lab">Selected hit</span>` + `<span class="loc" id="dvLoc"></span></div>` + - `<div class="blatDetailCard"><div style="display:flex;flex-direction:column;gap:16px;min-width:250px">` + + `<div class="blatDetailCard"><div class="blatDetailCol">` + `<div class="blatTiles">${tiles}</div>` + `<div class="blatDetailActions">` + `<a class="blatPill" id="dvBrowser" title="Open this hit in the Genome Browser" href="#">Open in browser</a>` + `<a class="blatPill" id="dvNewTab" target="_blank" title="Open this hit in the Genome Browser in a new tab" href="#">Open in new tab</a></div></div>` + - `<div id="dvAlignBox" style="flex:1;min-width:320px;border-left:1px solid var(--line);padding-left:24px;` + - `display:flex;flex-direction:column;justify-content:center">` + + `<div id="dvAlignBox" class="blatAlignBox">` + `<div class="blatTile"><div class="k">Alignment</div></div>` + - `<div id="dvAlign" style="font-size:14px;color:var(--muted);line-height:1.55;` + - `margin:8px 0 14px;max-width:360px"></div>` + - `<a class="blatPill" id="dvViewAlign" style="align-self:flex-start" ` + + `<div id="dvAlign" class="blatAlignText"></div>` + + `<a class="blatPill" id="dvViewAlign" ` + `title="See the base-by-base alignment of your query against this hit" href="#">` + `View alignment</a></div></div>`; if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); } } function blatSet(id, prop, val) { var e = document.getElementById(id); if (!e) { return; } if (prop === 'text') { e.textContent = val; } - else if (prop === 'html') { e.innerHTML = val; } else if (prop === 'href') { e.setAttribute('href', val); } else if (prop === 'color') { e.style.color = val; } } function blatRenderDetail(hit) { if (!hit || !document.getElementById('blatDetail')) { return; } if (!document.getElementById('dvScore')) { blatDetailSkeleton(); } var idc = blatIdColor(hit.identity); - var locus = hit.locusText ? htmlEncode(hit.locusText) + ' · ' : ''; - var q = hgBlatData.config.multiQuery ? htmlEncode(hit.qName) + ' · ' : ''; - blatSet('dvLoc', 'html', - `#${hit.rank} · ${q}${locus}${htmlEncode(hit.chrom)}:${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}`); + // Location line is plain text, so set it via textContent (blatSet 'text') - no HTML, nothing to + // escape. q and locus stay raw here for that reason. + var locus = hit.locusText ? hit.locusText + ' · ' : ''; + var q = hgBlatData.config.multiQuery ? hit.qName + ' · ' : ''; + blatSet('dvLoc', 'text', + `#${hit.rank} · ${q}${locus}${hit.chrom}:${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', 'Open in Genome Browser': 'Genomic location of the match (1-based). Click the position to ' + 'open the Genome Browser there, or the icon to open it in a new tab.', 'Show': 'Show the base-by-base alignment of your sequence to the genome', '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() { // No session, no AJAX: the results page already has a stable, shareable URL (hgBlat.c emits it as // cfg.shareUrl and blatBuild() pins it into the address bar with history.replaceState), so this // just shows/copies window.location. The link reopens straight from the trash .pslx/.fa, so it // works until those trash files are cleaned - hence the retention note. var box = document.getElementById('blatShareBox'); if (!box) { return; } if (box.style.display === 'flex') { box.style.display = 'none'; return; } // toggle off var url = window.location.href; box.style.display = 'flex'; box.innerHTML = - '<span class="blatShareMsg" style="flex:1 1 100%">Shareable link — anyone with it can reopen ' + + '<span class="blatShareMsg blatShareFull">Shareable link — anyone with it can reopen ' + 'these results. The results are stored temporarily, so the link works for at least 48 hours ' + 'after they were last viewed.</span>' + '<input id="blatShareInput" class="blatShareInput" type="text" readonly>' + '<button type="button" class="blatPill" id="blatShareCopy" title="Copy the link to the clipboard">Copy</button>'; var inp = document.getElementById('blatShareInput'); inp.value = url; inp.focus(); inp.select(); $('#blatShareCopy').on('click', function() { inp.select(); if (navigator.clipboard) { navigator.clipboard.writeText(url); } else { document.execCommand('copy'); } this.textContent = 'Copied'; }); } // ---- Rename BLAT track (modal) ------------------------------------------- // The results custom track is built (and renamed) by hgBlat.c's inline code, which exposes a small // window.blatRenameCt(name, description) helper (it POSTs to hgc's buildBigPsl and rebuilds the // track). We reuse that helper (no new endpoint), just swapping its old inline toggle-form UI for a // proper modal dialog. The current name/description come from cfg (hgBlat.c), not a global, so this // does not depend on any generic page-global. function blatRenameModalHtml(cfg) { // hgSession link is relative (same /cgi-bin/), carrying db + hgsid so the session page opens in // this assembly and cart. var sessionUrl = `hgSession?db=${encodeURIComponent(cfg.db)}&hgsid=${encodeURIComponent(cfg.hgsid)}`; return '<div id="blatModalBg" class="blatModalBg" style="display:none">' + '<div class="blatModal" role="dialog" aria-modal="true" aria-labelledby="blatModalTitle">' + '<div class="blatModalTitle" id="blatModalTitle">Rename BLAT Track</div>' + '<div class="blatModalText">Every BLAT result is stored in its own track in the Genome ' + 'Browser. You can rename the track here. Results will disappear after 2–3 days, unless ' + `they are saved into a <a href="${sessionUrl}">Session link</a>.</div>` + '<label class="blatModalLabel" for="blatRenameName">Track name</label>' + '<input id="blatRenameName" class="blatModalInput" type="text" maxlength="80">' + '<label class="blatModalLabel" for="blatRenameDesc">Description</label>' + '<input id="blatRenameDesc" class="blatModalInput" type="text" maxlength="120">' + '<div class="blatModalBtns">' + '<button type="button" class="blatPill" id="blatRenameCancel">Cancel</button>' + '<button type="button" class="blatPill primary" id="blatRenameOk">OK</button>' + '</div></div></div>'; } function blatCloseRename() { var bg = document.getElementById('blatModalBg'); if (bg) { bg.style.display = 'none'; } } function blatOpenRename() { var bg = document.getElementById('blatModalBg'); if (!bg) { return; } // Pre-fill with the track's current name/description (emitted by hgBlat.c in cfg). var cfg = hgBlatData.config; document.getElementById('blatRenameName').value = cfg.trackName || ''; document.getElementById('blatRenameDesc').value = cfg.trackDescription || ''; bg.style.display = 'flex'; document.getElementById('blatRenameName').focus(); document.getElementById('blatRenameName').select(); } function blatWireRename() { $('#blatRenameBtn').on('click', blatOpenRename); $('#blatRenameCancel').on('click', blatCloseRename); // Click on the dark backdrop (but not the dialog itself) closes. $('#blatModalBg').on('click', function(ev) { if (ev.target === this) { blatCloseRename(); } }); $(document).on('keydown.blatRename', function(ev) { var bg = document.getElementById('blatModalBg'); if (bg && bg.style.display !== 'none' && ev.key === 'Escape') { blatCloseRename(); } }); $('#blatRenameOk').on('click', function() { var name = document.getElementById('blatRenameName').value.trim(); var desc = document.getElementById('blatRenameDesc').value.trim(); if (!name) { document.getElementById('blatRenameName').focus(); return; } // Reuse hgBlat.c's window.blatRenameCt(name, description): rebuilds the custom track under the // new name via the existing hgc buildBigPsl call. Keep cfg in sync so a re-open of the modal // shows the new values. if (typeof window.blatRenameCt === 'function') { hgBlatData.config.trackName = name; hgBlatData.config.trackDescription = desc; window.blatRenameCt(name, desc); } blatCloseRename(); }); } // ---- FASTA viewer (generic) ---------------------------------------------- function blatToFasta(seqs) { // seqs: [{name, seq}, ...] -> FASTA text, sequence wrapped at 60 chars per line. return seqs.map(function(s) { var body = String(s.seq || '').toUpperCase().replace(/(.{60})/g, '$1\n').replace(/\n$/, ''); return '>' + s.name + '\n' + body; }).join('\n'); } function blatShowFasta(box, seqs, fileName) { // Render seqs as FASTA inside `box`, with Copy-to-clipboard and Download buttons. Generic — takes // any [{name, seq}] list so it can be reused for other sequences later. var fasta = blatToFasta(seqs); box.style.display = 'flex'; box.innerHTML = '<div class="blatSeqBar">' + '<span class="blatShareMsg">Query sequence (FASTA):</span>' + '<button type="button" class="blatPill" id="blatSeqCopy" title="Copy the FASTA to the clipboard">Copy to Clipboard</button>' + '<button type="button" class="blatPill" id="blatSeqDownload" title="Download the FASTA as a .fa file">Download</button>' + '<button type="button" class="blatPill" id="blatSeqClose" title="Hide the query sequence">Close</button>' + '</div><textarea id="blatSeqText" class="blatSeqText" readonly></textarea>'; var ta = document.getElementById('blatSeqText'); ta.value = fasta; document.getElementById('blatSeqCopy').addEventListener('click', function() { ta.select(); if (navigator.clipboard) { navigator.clipboard.writeText(fasta); } else { document.execCommand('copy'); } this.textContent = 'Copied'; }); document.getElementById('blatSeqDownload').addEventListener('click', function() { var a = document.createElement('a'); a.href = URL.createObjectURL(new Blob([fasta], { type: 'text/plain' })); a.download = fileName || 'query.fa'; document.body.appendChild(a); a.click(); document.body.removeChild(a); setTimeout(function() { URL.revokeObjectURL(a.href); }, 0); }); document.getElementById('blatSeqClose').addEventListener('click', function() { box.style.display = 'none'; }); } function blatShowQuerySeq() { var box = document.getElementById('blatSeqBox'); if (box.style.display === 'flex') { box.style.display = 'none'; return; } // toggle off blatShowFasta(box, hgBlatData.config.querySeqs, 'blatQuery.fa'); } // ---- build --------------------------------------------------------------- function blatBuild() { var cfg = hgBlatData.config; var hits = hgBlatData.hits; - blatInjectStyle(); // Pin a stable, shareable URL into the address bar (no server redirect) so refresh, bookmark and // "Share a link" all use the trash-backed reopen link instead of the transient POST/search URL. if (cfg.shareUrl) { try { history.replaceState(null, '', cfg.shareUrl); } catch (e) { /* older browsers: ignore */ } } var back = cfg.backUrl ? `<a class="blatPill" title="Return to the Genome Browser at your previous location (${htmlEncode(cfg.backPos)})" ` + `href="${htmlEncode(cfg.backUrl)}">Back to Genome Browser</a>` : ''; // The page actions live in the gold main-header bar (framework #sectTtl), next to the title - // so there is no separate toolbar (.blatHead is gone). Injected into #sectTtl below. var headActions = `${back}<a class="blatPill primary" title="Start a new BLAT search" href="${htmlEncode(cfg.newSearchUrl)}">New BLAT search</a>`; // Top banner: note this is the new page, link back to the classic page (fresh searches only, // where the trash files still exist), and invite feedback. The old page also clears the // blatNewPage preference so later searches use the classic page until the user opts back in. var origPage = cfg.canOldPage ? ` You can go back to <a title="Show these results on the classic BLAT results page" ` + `href="hgBlat?blatNewPage=0&blatReopen=1&hgsid=${encodeURIComponent(cfg.hgsid)}">the original page</a> anytime.` : ''; var bannerHtml = `<div class="blatBanner">We are testing a new BLAT output page.${origPage} ` + `If you have feedback on this new page, do not hesitate to let us know via ` + `<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</div>`; var queryCount = new Set(hits.map(h => h.qName)).size; var th = []; th.push('<th class="num">#</th>'); if (cfg.multiQuery) { th.push('<th>Query</th>'); } th.push('<th>Open in Genome Browser</th>'); th.push('<th>Show</th>'); th.push('<th>Query coverage</th>'); if (cfg.hasLocus) { th.push('<th>Locus</th>'); } th.push('<th class="num">Score</th>'); th.push('<th class="num">Identity</th>'); th.push('<th>Strand</th>'); th.push('<th class="num">Span</th>'); // detail dock sits above the table: with long hit lists a bottom dock scrolls out of view document.getElementById('blatResults').innerHTML = bannerHtml + `<div class="blatCard">${blatSummaryStrip(cfg, queryCount)}` + `<div id="blatShareBox" class="blatShareBox" style="display:none"></div>` + `<div id="blatSeqBox" class="blatShareBox" style="display:none"></div>` + `<div id="blatDetail" class="blatDetail"></div>` + - `<table id="blatTable" class="display" style="width:100%"><thead><tr>${th.join('')}</tr></thead></table></div>` + + `<table id="blatTable" class="display"><thead><tr>${th.join('')}</tr></thead></table></div>` + (cfg.canRename ? blatRenameModalHtml(cfg) : ''); // Put the page actions in the gold main-header bar, to the right of the title (framework #sectTtl). var sectTtl = document.getElementById('sectTtl'); if (sectTtl) { var acts = document.createElement('span'); acts.className = 'blatHeadActions'; acts.innerHTML = headActions; sectTtl.appendChild(acts); } $('#blatShareBtn').on('click', blatShareLink); $('#blatSeqBtn').on('click', blatShowQuerySeq); blatWireRename(); 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) : '') }); columns.push({ data: null, className: 'covCol', orderable: false, render: (d, type, row) => (type === 'display' ? blatCoverageCell(row) : (row.qEnd - row.qStart + 1)) }); if (cfg.hasLocus) { columns.push({ data: 'locusText', render: (d, type, row) => (type === 'display' ? blatLocusCell(row) : (d || '')) }); } // Score carries a bar scaled to the highest score in this result set (raw score kept for sorting). var maxScore = hits.reduce((m, h) => Math.max(m, h.score || 0), 0); columns.push({ data: 'score', className: 'num scoreCol', render: (d, type, row) => (type === 'display' ? blatScoreCell(row, maxScore) : d) }); columns.push({ data: 'identity', className: 'num identCol', render: (d, type, row) => (type === 'display' ? blatIdentityCell(row) : d) }); columns.push({ data: 'strand', className: 'strandCol' }); columns.push({ data: 'span', className: 'num', render: (d, type, row) => (type === 'display' ? blatFmt(d) : d) }); 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 // <thead> 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 = `<div class="blatSelectHint">Click a hit below to see its alignment details. ` + `If you are missing matches that you think should be there, ` + `<a target="_blank" href="../FAQ/FAQblat.html#blat1b">read our BLAT FAQ</a> or ` + `<a href="mailto:genome@soe.ucsc.edu">contact us</a>.</div>`; blatApplyTooltips(); } +// ==== search form (the input page) ======================================== +// hgBlat.c emits var hgBlatFormData = {...} together with a real <form name="mainForm"> that +// contains an empty <div id="blatFormBox"> and the C-generated genome search bar. We build the +// controls as real form fields *inside that form*, so the browser serializes them natively - +// including the file input - and Submit / I'm feeling lucky / Clear stay plain submit buttons +// handled by the existing C code. There is no shadow form and no copying of values on submit. +// Styling comes from hgBlat.css (loaded by webIncludeResourceFile in hgBlat.c), shared with the results page. + +// The Genome Browser's standard info icon, copied from printInfoIconSvg() in hg/lib/hui.c so the +// form's icons are pixel-identical to the C-rendered ones elsewhere in the browser. +var BLAT_INFO_SVG = + "<svg style='height:1.1em; vertical-align:top' viewBox='0 0 24 24' fill='none' " + + "xmlns='http://www.w3.org/2000/svg'>" + + "<circle cx='12' cy='12' r='10' stroke='#1C274C' stroke-width='1.5'/>" + + "<path d='M12 17V11' stroke='#1C274C' stroke-width='1.5' stroke-linecap='round'/>" + + "<circle cx='1' cy='1' r='1' transform='matrix(1 0 0 -1 11 9)' fill='#1C274C'/></svg>"; + +// The assembly-search syntax help. setupGenomeSelector hides the info icon that +// printGenomeSearchBar (hg/lib/web.c) normally puts next to the box, so the new form loses that +// explanation of +word/-word/word*/"phrase"; we re-attach it to an icon after the label instead. +// Kept word-for-word in sync with searchHelpText in web.c so both pickers explain the box the same +// way. This is HTML (a bullet list), rendered as such by the mouseover, so it is NOT htmlEncode'd - +// like the C printInfoIcon, it relies on the string containing no double quotes to sit in a title=. +var BLAT_GENOME_SEARCH_HELP = + "All genome searches are case-insensitive. Single-word searches default to prefix " + + "matching if an exact match is not found. " + + "<ul id='searchTipList' class='noBullets'>" + + "<li> Force inclusion: Use a + sign before <b>+word</b> to ensure it appears in result.</li>" + + "<li> Exclude words: Use a - sign before <b>-word</b> to exclude it from the search result.</li>" + + "<li> Wildcard search: Add an * (asterisk) at end of <b>word*</b> to search for all terms starting with that prefix.</li>" + + "<li> Phrase search: Enclose 'words in quotes' to search for the exact phrase.</li>" + + "</ul>"; + +// Cross-session memory of the "Keep results" checkbox. A plain '1'/'0' string under one key; +// wrapped in try/catch because localStorage throws in private-mode / disabled-storage browsers, in +// which case we simply fall back to the cart-supplied default and skip persistence. +var BLAT_KEEP_RESULTS_KEY = 'blatKeepResults'; + +function blatGetKeepResultsPref() { + // Returns true/false for a stored preference, or null if the user has never set one here. + try { + var v = localStorage.getItem(BLAT_KEEP_RESULTS_KEY); + return v === null ? null : (v === '1'); + } catch (e) { return null; } +} + +function blatSetKeepResultsPref(on) { + try { localStorage.setItem(BLAT_KEEP_RESULTS_KEY, on ? '1' : '0'); } catch (e) { /* ignore */ } +} + +function blatOpts(list, cur) { + return list.map(function(v) { + return `<option value="${htmlEncode(v)}"${v === cur ? ' selected' : ''}>${htmlEncode(v)}</option>`; + }).join(''); +} + +function blatFormCount() { + // Live character count under the textarea. Only these two nodes are touched on input - the + // textarea itself is never re-rendered, so the caret stays where the user put it. + var ta = document.getElementById('blatUserSeq'); + var out = document.getElementById('blatCountText'); + if (!ta || !out) { return; } + var n = ta.value.replace(/[^A-Za-z*]/g, '').length; + out.textContent = blatFmt(n) + ' of 25,000 characters'; + $('#blatLimitLink').toggleClass('over', n > 25000); +} + +function blatFormTab(showUpload) { + $('#blatTabPaste').toggleClass('on', !showUpload); + $('#blatTabUpload').toggleClass('on', showUpload); + $('#blatPanePaste').toggle(!showUpload); + $('#blatPaneUpload').toggle(showUpload); +} + +function blatFormLimitsModal() { + var row = (k, v) => `<div class="blatLimitRow"><span>${k}</span><strong>${v}</strong></div>`; + return '<div id="blatLimitsBg" class="blatModalBg" style="display:none">' + + '<div class="blatModal" role="dialog" aria-modal="true" aria-labelledby="blatLimitsTitle">' + + '<div class="blatModalTitle" id="blatLimitsTitle">Input limits</div>' + + row('DNA per sequence', '25,000 bases') + + row('Protein / translated', '10,000 letters') + + row('Sequences per run', '25') + + row('Total per submission', '50,000 bases') + + '<div class="blatModalText blatModalNote">Queries above these limits are rejected ' + + 'before alignment. For larger jobs, run BLAT from the ' + + '<a target="_blank" href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">' + + 'command line</a> on your own server.</div>' + + '<div class="blatModalBtns"><button type="button" class="blatPill" id="blatLimitsClose">Close</button></div>' + + '</div></div>'; +} + +function blatFormSetDb(db) { + // Called by hgBlat.c's setupGenomeSearchBar onSelect. Picking a genome does not reload the + // page, so everything on it that depends on db is updated here instead: the hidden field that + // the search is submitted with, and the sidebar links that carry a db= parameter. The current + // assembly label is updated by setupGenomeSearchBar itself. + document.mainForm.db.value = db; + $('#blatFormBox a[data-urltpl]').each(function() { + this.href = this.getAttribute('data-urltpl').replace('$DB$', encodeURIComponent(db)); + }); +} + +function blatFormSidebar(cfg) { + // Same links the classic page offered. hgBlat.c supplies them as templates holding $DB$ (see + // blatFormSetDb); the template is kept in data-urltpl so the link can be retargeted later. + var tools = ''; + var tplLink = (tpl, label) => { + var href = tpl.replace('$DB$', encodeURIComponent(hgBlatFormData.db)); + return `<a data-urltpl="${htmlEncode(tpl)}" href="${htmlEncode(href)}">${label}</a>`; + }; + if (cfg.pcrUrlTpl) { + tools += `<div>${tplLink(cfg.pcrUrlTpl, 'In-Silico PCR')} — better than BLAT for ` + + 'locating PCR primers.</div>'; + } + if (cfg.oligoMatchUrlTpl) { + tools += `<div>${tplLink(cfg.oligoMatchUrlTpl, 'Short Sequence Match')} — for ` + + 'sequences under 20 bp, within the region shown in the Genome Browser.</div>'; + } + tools += '<div><a target="_blank" href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">' + + 'findMotifs</a> — command-line search across a whole genome.</div>'; + return '<div>' + + (tools ? `<div class="blatCard"><h3>Similar tools</h3>${tools}</div>` : '') + + '<div class="blatCard"><h3>Help</h3>' + + '<div><a href="../FAQ/FAQblat.html">BLAT FAQ</a></div>' + + '<div><a href="../goldenPath/help/hgTracksHelp.html#BLATAlign">BLAT documentation</a></div>' + + // No "Search all genomes FAQ" here: that link now lives in the "Search many genomes" + // tooltip, next to the checkbox it actually explains. + '<div><a href="../FAQ/FAQblat.html#blat14">Programmatic / batch BLAT</a></div>' + + '</div>' + + '<div class="blatCard"><h3>About BLAT</h3>' + + '<div>DNA BLAT quickly finds sequences of 95% and greater similarity that are at least 25 bases ' + + 'long; it finds perfect matches down to 20 bases, and may miss shorter or more divergent ' + + 'alignments. Protein BLAT finds sequences of 80% and greater similarity at least 20 amino acids ' + + 'long.</div>' + + '<div>Kent WJ. <a target="_blank" href="https://genome.cshlp.org/content/12/4/656.abstract">' + + 'BLAT — the BLAST-like alignment tool</a>. Genome Res. 2002 Apr;12(4):656-64.</div>' + + '</div></div>'; +} + +function blatFormBuild() { + var cfg = hgBlatFormData; + + var banner = ''; + if (cfg.classicUrl) { + banner = '<div class="blatBanner">We are testing a new BLAT search page. You can go back to ' + + `<a href="${htmlEncode(cfg.classicUrl)}">the original page</a> anytime. If you have feedback ` + + 'on this new page, do not hesitate to let us know via ' + + '<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</div>'; + } + + // Checkbox plus the browser's standard info icon. Same SVG and same title + + // convertTitleTagsToMouseovers mechanism as printInfoIcon()/printInfoIconSvg() in hg/lib/hui.c, + // so these read identically to the info icons on every other Genome Browser page. + var check = (name, on, label, tip) => + `<span class="blatCheck"><label><input type="checkbox" name="${name}" ` + + `id="blat_${name}"${on ? ' checked' : ''}>${label}</label>` + + `<span class="blatInfo" title="${htmlEncode(tip)}">${BLAT_INFO_SVG}</span></span>`; + + // "Keep results" starting state. The cart (cfg.keepResults) only remembers the choice within a + // session; localStorage carries it across sessions so a user who wants their BLAT results to + // accumulate does not have to re-tick the box on every visit. localStorage wins when set (it is + // the more durable record of the user's own preference); the cart is the fallback for a browser + // that has never stored one. Only consulted where the box is actually shown (blatOldTracks= + // delete); elsewhere the choice has no effect, so there is nothing worth persisting. + var keepResultsInit = cfg.keepResults; + if (cfg.showKeepResults) { + var storedKeep = blatGetKeepResultsPref(); + if (storedKeep !== null) { keepResultsInit = storedKeep; } + } + + document.getElementById('blatFormBox').innerHTML = + banner + + '<div class="blatFormGrid"><div>' + + + '<div class="blatSection">Search – type keywords to find the target assembly</div>' + + '<div class="blatRow">' + + '<div class="blatField blatGenomeSlot"><span>Genome or assembly ' + + `<span class="blatInfo" title="${BLAT_GENOME_SEARCH_HELP}">${BLAT_INFO_SVG}</span>` + + '</span>' + + '<div id="blatGenomeSlot"></div></div>' + + `<label class="blatField"><span>Query type</span><select name="type">${blatOpts(cfg.types, cfg.type)}</select></label>` + + // Sort and output are submitted but not offered: sorting by anything other than score + // is rarely useful, and this page always wants the hyperlink (results table) output. + // Kept as hidden fields so the request hgBlat receives is unchanged. + `<input type="hidden" name="sort" value="${htmlEncode(cfg.sort)}">` + + `<input type="hidden" name="output" value="${htmlEncode(cfg.output)}">` + + '</div>' + + + '<div class="blatChecks">' + + // The mouseover popup keeps itself open while the pointer is inside it (see the + // mouseoverContainer mouseenter handler in utils.js), and renders its text as HTML, so + // a link in the tip is genuinely clickable. htmlEncode keeps the title attribute + // well-formed; the browser decodes it back to markup before it is injected. + check('allGenomes', cfg.allGenomes, 'Search many genomes', + 'Runs the same query against every default assembly and attached hub that has a ' + + 'dedicated BLAT server. Dynamic BLAT servers are skipped and listed as such in the ' + + "output. See our <a target='_blank' href='../FAQ/FAQblat.html#blat9'>BLAT All FAQ</a> " + + 'for more information.') + + check('allResults', cfg.allResults, 'No min. score', + 'Turns off minimum-match filtering so every alignment is returned. A human DNA search ' + + 'normally requires 20 matching bases, based on the genome size, to filter out ' + + 'lower-quality results; useful for short queries and the tiny genomes of ' + + 'microorganisms.') + + check('autoRearr', cfg.autoRearr, 'Show rearrangements', + 'Shows duplications of the query sequence using multiple lines with connecting lines ' + + 'between fragments, and displays inversions better (the "snakes" display). Can also ' + + 'be switched on or off from the BLAT track configuration page.') + + // Only offered where hg.conf blatOldTracks=delete, i.e. where there is something to opt + // out of. Unlike the three above (which keep the classic form's plain-checkbox + // behaviour), this one is submitted through an explicit hidden field: a checkbox sends + // nothing when unticked, so cartUsualBoolean would never see it go back to false and + // "Keep results" could not be switched off again once used. + (cfg.showKeepResults ? + '<span class="blatCheck">' + + `<input type="hidden" name="blatKeepResults" id="blatKeepResultsVal" value="${keepResultsInit ? 1 : 0}">` + + `<label><input type="checkbox" id="blat_keepResults"${keepResultsInit ? ' checked' : ''}>` + + 'Keep results</label>' + + `<span class="blatInfo" title="${htmlEncode( + 'A new BLAT search always overrides your previous BLAT results: each search ' + + 'replaces the result track of the one before it in the Genome Browser. Check ' + + 'this box to keep earlier results instead, so every search adds its own track ' + + 'and results accumulate. Your choice is remembered for next time.')}">` + + `${BLAT_INFO_SVG}</span></span>` : '') + + '</div>' + + + '<div class="blatSection">Query sequence</div>' + + '<div class="blatTabs">' + + '<button type="button" class="blatTab on" id="blatTabPaste">Paste sequence</button>' + + '<button type="button" class="blatTab" id="blatTabUpload">Upload file</button>' + + '</div>' + + + '<div id="blatPanePaste">' + + '<div class="blatPaneHint"><span>Separate multiple sequences with a >name line. ' + + 'Up to 25 sequences.</span>' + + `<a href="#" id="blatExample">${htmlEncode(cfg.exampleLabel)}</a></div>` + + '<textarea class="blatSeq" name="userSeq" id="blatUserSeq" spellcheck="false" ' + + 'aria-label="Paste in a query sequence"></textarea>' + + '<div class="blatCount"><span id="blatCountText"></span>' + + '<a href="#" id="blatLimitLink">Show input limits</a></div>' + + '</div>' + + + '<div id="blatPaneUpload" style="display:none">' + + '<div class="blatDrop" id="blatDrop">' + + '<div class="blatDropTitle">Drop a sequence file here</div>' + + '<div class="blatDropSub">Plain text or FASTA, up to 50,000 bases total</div>' + + '<input type="file" name="seqFile" id="blatSeqFile">' + + '<div class="blatFileName" id="blatFileName"></div>' + + '</div>' + + '</div>' + + + '<div class="blatActions">' + + '<input type="submit" class="blatPill primary" name="Submit" value="Submit" ' + + `title="${htmlEncode('Align the sequence and show all matches')}">` + + '<input type="submit" class="blatPill" name="Lucky" value="I'm feeling lucky" ' + + `title="${htmlEncode('Skip the list of matches and open the best-scoring one straight ' + + 'away in the Genome Browser. Ignored when "Search many genomes" is ticked.')}">` + + '<input type="submit" class="blatPill" name="Clear" value="Clear" ' + + `title="${htmlEncode('Empty the query sequence box')}">` + + '</div>' + + + '</div>' + blatFormSidebar(cfg) + '</div>' + + blatFormLimitsModal(); + + // Move the C-generated genome search bar (real autocomplete over every assembly, already wired + // by setupGenomeSearchBar) into its slot, rather than reimplementing it with a hardcoded list. + var holder = document.getElementById('blatGenomeHolder'); + if (holder) { document.getElementById('blatGenomeSlot').appendChild(holder); } + + + // Show the current assembly in the search bar itself instead of in a separate "Current genome:" + // line - the bar is wide enough for the whole description. setupGenomeSearchBar writes the new + // one in on each pick, and focusing the bar selects all of it, so it reads as a filled-in search + // box rather than as a value the user has to clear by hand. + var genomeInput = document.getElementById('genomeSearch'); + if (genomeInput && cfg.dbLabel) { genomeInput.value = cfg.dbLabel; } + + // Restore the sequence from the cart without going through innerHTML (avoids re-escaping). + document.getElementById('blatUserSeq').value = cfg.userSeq || ''; + blatFormCount(); + + $('#blatUserSeq').on('input', blatFormCount); + // Mirror the "Keep results" checkbox into its hidden field so an unticked box submits an + // explicit 0 rather than nothing at all, and remember the choice in localStorage so it comes + // back pre-set on the user's next visit (see keepResultsInit above). + $('#blat_keepResults').on('change', function() { + document.getElementById('blatKeepResultsVal').value = this.checked ? '1' : '0'; + blatSetKeepResultsPref(this.checked); + }); + $('#blatTabPaste').on('click', function() { blatFormTab(false); }); + $('#blatTabUpload').on('click', function() { blatFormTab(true); }); + // The example sequence is a real ~14 kb query, fetched on demand so it is not carried in every + // page load. The link doubles as its own status indicator while the request is in flight. + $('#blatExample').on('click', function(ev) { + ev.preventDefault(); + var link = this; + var label = cfg.exampleLabel; + link.textContent = 'Loading example…'; + fetch(cfg.exampleUrl) + .then(function(resp) { + if (!resp.ok) { throw new Error('HTTP ' + resp.status); } + return resp.text(); + }) + .then(function(fa) { + var ta = document.getElementById('blatUserSeq'); + ta.value = fa.trim(); + blatFormCount(); + ta.focus(); + ta.setSelectionRange(0, 0); + ta.scrollTop = 0; + link.textContent = label; + blatFormTab(false); // in case the user was on the upload tab + }) + .catch(function(err) { + link.textContent = 'Could not load example'; + // Leave the message up briefly, then let the user try again. + setTimeout(function() { link.textContent = label; }, 4000); + console.error('hgBlat: example fetch failed:', err); + }); + }); + $('#blatLimitLink').on('click', function(ev) { + ev.preventDefault(); + $('#blatLimitsBg').css('display', 'flex'); + }); + $('#blatLimitsClose').on('click', function() { $('#blatLimitsBg').hide(); }); + $('#blatLimitsBg').on('click', function(ev) { if (ev.target === this) { $(this).hide(); } }); + $(document).on('keydown.blatLimits', function(ev) { + if (ev.key === 'Escape') { $('#blatLimitsBg').hide(); } + }); + + var fileInput = document.getElementById('blatSeqFile'); + var drop = document.getElementById('blatDrop'); + $(fileInput).on('change', function() { + document.getElementById('blatFileName').textContent = + this.files && this.files.length ? this.files[0].name : ''; + }); + ['dragenter', 'dragover'].forEach(function(e) { + drop.addEventListener(e, function(ev) { ev.preventDefault(); drop.classList.add('hot'); }); + }); + ['dragleave', 'drop'].forEach(function(e) { + drop.addEventListener(e, function(ev) { ev.preventDefault(); drop.classList.remove('hot'); }); + }); + drop.addEventListener('drop', function(ev) { + if (ev.dataTransfer.files.length) { + fileInput.files = ev.dataTransfer.files; + $(fileInput).trigger('change'); + } + }); + + if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); } +} + $(document).ready(function() { if (typeof hgBlatData !== 'undefined' && document.getElementById('blatResults')) { blatBuild(); } + if (typeof hgBlatFormData !== 'undefined' && document.getElementById('blatFormBox')) { + blatFormBuild(); + } });