@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/chunk-NPBN3PPZ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/block.ds.itemtable.js", "../src/block.ds.vcf.js", "../src/block.ds.sun1.js", "../src/block.sunburst.js", "../src/block.ds.numericmode.js", "../src/block.ds.js", "../src/block.legend.js"],
-  "sourcesContent": ["import * as client from './client'\nimport * as common from '#shared/common.js'\nimport * as vcf from '#shared/vcf.js'\nimport { stratify } from 'd3-hierarchy'\n\n/*\n\n********************** EXPORTED\n\nitemtable()\nruntimeattr_snvindel()\nruntimeattr_sv()\nruntimeattr_itd()\nruntimeattr_del()\nruntimeattr_trunc()\n\nquery_vcfcohorttrack()\n\n\n********************** INTERNAL\n\ntable_snvindel\ntable_sv\ntable_itd\ntable_truncation\ntable_del\ntable_sort\n\nvcfmdetail\nmayshowcovmafplot\nmayshowgermline2dvaf\nmayshowgenotype2boxplot\n\nvcfvepbutton\nvcfannbutton\n\nmay_info2singletable\nmay_info2table\ninfo2table_value\n*/\n\nconst separatorvp = '__'\n\nexport function itemtable(arg) {\n\t/*\n\t.mlst\n\t.block\n\t.tk\n\t.pane\n\t.holder\n\t*/\n\n\tconst { mlst, tk, block } = arg\n\tif (!mlst || mlst.length == 0) return\n\tlet holder\n\tif (arg.pane) {\n\t\tconst pane = client.newpane({ x: arg.x, y: arg.y })\n\t\tpane.header.html(mlst2headerhtml(mlst))\n\t\tholder = pane.body\n\t} else {\n\t\tholder = arg.holder\n\t}\n\tif (!holder) {\n\t\tconsole.error('no holder provided for showing table')\n\t\treturn\n\t}\n\n\t/*\n\tmlst can be a mixture of dt\n\tshow separate table for each datatype\n\tfollowing incrementally adds components to the mlst panel\n\t*/\n\tconst dt2mlst = new Map()\n\tfor (const m of mlst) {\n\t\tif (!dt2mlst.has(m.dt)) {\n\t\t\tdt2mlst.set(m.dt, [])\n\t\t}\n\t\tdt2mlst.get(m.dt).push(m)\n\t}\n\n\t/**** a very quick fix!\n\tin any type of variant, only set this when mlst is just one variant with occurrence=1\n\tso that variant2samples can append rows to it (not in use)\n\t*/\n\tdelete tk.__singlevariant_table\n\n\tfor (const [dt, lst] of dt2mlst) {\n\t\tconst div = holder.append('div').style('margin', '10px')\n\t\tif (dt2mlst.size > 1) {\n\t\t\tdiv.append('p').text(common.dt2label[dt]).style('color', '#858585')\n\t\t}\n\t\tswitch (dt) {\n\t\t\tcase common.dtsnvindel:\n\t\t\t\ttable_snvindel(lst, div, tk, block)\n\t\t\t\tbreak\n\t\t\tcase common.dtsv:\n\t\t\tcase common.dtfusionrna:\n\t\t\t\ttable_sv(lst, div, tk, block)\n\t\t\t\tbreak\n\t\t\tcase common.dtitd:\n\t\t\t\ttable_itd(lst, div, tk, block.genome)\n\t\t\t\tbreak\n\t\t\tcase common.dtnloss:\n\t\t\tcase common.dtcloss:\n\t\t\t\ttable_truncation(lst, div, tk, block.genome)\n\t\t\t\tbreak\n\t\t\tcase common.dtdel:\n\t\t\t\ttable_del(lst, div, tk, block.genome)\n\t\t\t\tbreak\n\t\t\tcase common.dtcnv:\n\t\t\t\tdiv.append('p').text('cnv not supported yet')\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tdiv.append('p').text('unknown dt: ' + dt)\n\t\t}\n\t}\n\n\thandle_samplecart(mlst, holder, tk, block)\n}\n\nfunction mlst2headerhtml(mlst) {\n\tif (mlst.length == 1) {\n\t\tconst m = mlst[0]\n\t\tconst c = common.mclass[m.class]\n\t\tif (m.dt == common.dtsnvindel) {\n\t\t\treturn (\n\t\t\t\t'<span style=\"font-weight:bold;color:' +\n\t\t\t\tc.color +\n\t\t\t\t'\">' +\n\t\t\t\t(m.mname ? m.mname : m.pos ? m.chr + ':' + (m.pos + 1) : '') +\n\t\t\t\t'</span> <span style=\"font-size:80%\">' +\n\t\t\t\tc.label +\n\t\t\t\t'</span>'\n\t\t\t)\n\t\t}\n\t\tif (m.dt == common.dtsv || m.dt == common.dtfusionrna) {\n\t\t\tconst names = []\n\t\t\tfor (let i = 0; i < m.pairlst.length; i++) {\n\t\t\t\tif (i == 0) names.push(m.pairlst[i].a.name ? m.pairlst[i].a.name : m.pairlst[i].a.chr)\n\t\t\t\tnames.push(m.pairlst[i].b.name ? m.pairlst[i].b.name : m.pairlst[i].b.chr)\n\t\t\t}\n\t\t\treturn names.join(' - ') + '&nbsp;&nbsp;<span style=\"font-size:80%\">' + c.label + '</span>'\n\t\t}\n\t\tif (\n\t\t\tm.dt == common.dtnloss ||\n\t\t\tm.dt == common.dtcloss ||\n\t\t\tm.dt == common.dtitd ||\n\t\t\tm.dt == common.dtdel ||\n\t\t\tm.dt == common.dtcnv\n\t\t) {\n\t\t\treturn '<span style=\"font-size:80%\">' + c.label + '</span>'\n\t\t}\n\t\treturn 'unknown dt ' + m.dt\n\t}\n\tconst set = new Set()\n\tfor (const m of mlst) {\n\t\tset.add(m.dt)\n\t}\n\tif (set.size == 1) {\n\t\tconst dt = [...set][0]\n\t\treturn mlst.length + ' ' + common.dt2label[dt]\n\t}\n\treturn mlst.length + ' mutations'\n}\n\nfunction table_snvindel(mlst, holder, tk, block) {\n\tif (tk.ds && tk.ds.id2vcf) {\n\t\tif (mlst.length == 1) {\n\t\t\tconst vcfobj = tk.ds.id2vcf[mlst[0].vcfid]\n\t\t\tif (!vcfobj) {\n\t\t\t\tholder.append('p').text('No vcf config file (id: ' + mlst[0].vcfid + ')')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tvcfmdetail(mlst[0], vcfobj, holder, tk, block)\n\t\t\treturn\n\t\t}\n\t\t// vcf item is only shown one at a time, but not in a table\n\t\tfor (const m of mlst) {\n\t\t\tconst vcfobj = tk.ds.id2vcf[m.vcfid]\n\t\t\tif (!vcfobj) {\n\t\t\t\tholder.append('p').text('No vcf config file (id: ' + m.vcfid + ')')\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst d = holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tconst pane = client.newpane({ x: event.clientX + 100, y: Math.max(100, event.clientY - 100) })\n\t\t\t\t\tvcfmdetail(m, vcfobj, pane.body, tk, block)\n\t\t\t\t})\n\t\t\tif (m.mname) {\n\t\t\t\td.append('span').html(\n\t\t\t\t\tm.mname + '\\t<span style=\"font-size:80%;color:#858585\">' + common.mclass[m.class].label + '</span>'\n\t\t\t\t)\n\t\t\t} else if (m.csq) {\n\t\t\t\td.append('span').html(\n\t\t\t\t\tm.csq[0]._mname + '\\t<span style=\"font-size:80%;color:#858585\">' + m.csq[0].Consequence + '</span>'\n\t\t\t\t)\n\t\t\t}\n\t\t\td.append('span').html(\n\t\t\t\t'&nbsp;&nbsp;' +\n\t\t\t\t\tm.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\t(m.pos + 1) +\n\t\t\t\t\t' <span style=\"font-size:70%\">REF</span> ' +\n\t\t\t\t\tm.ref +\n\t\t\t\t\t' <span style=\"font-size:70%\">ALT</span> ' +\n\t\t\t\t\tm.alt\n\t\t\t)\n\t\t}\n\t\treturn\n\t}\n\tconst hasSNP = block.genome.hasSNP\n\tconst snpfind = {\n\t\tchr: null,\n\t\tbprange: [], // {start/stop}\n\t\tholder: null,\n\t\tsays: null\n\t}\n\tconst variantpage = {\n\t\tset: new Map(),\n\t\t// k: chr SEP pos SEP ref SEP mut\n\t\t// v: {mname, class}\n\t\tbutholder: null\n\t}\n\tfor (const m of mlst) {\n\t\tif (hasSNP && m.chr && m.pos) {\n\t\t\tsnpfind.chr = m.chr\n\t\t\tlet nf = true\n\t\t\tfor (const r of snpfind.bprange) {\n\t\t\t\tif (r.start <= m.pos && r.stop >= m.pos) {\n\t\t\t\t\tnf = false\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (nf) {\n\t\t\t\tsnpfind.bprange.push({ start: m.pos, stop: m.pos + 1 })\n\t\t\t}\n\t\t}\n\t}\n\tif (!tk.snvindelattr) {\n\t\truntimeattr_snvindel(tk, mlst)\n\t}\n\n\tif (block.variantPageCall_snv) {\n\t\t// variant page button moved to panel top, per jinghui 1/25/2023\n\t\tvariantpage.butholder = holder.append('div').style('margin', '10px')\n\t}\n\n\tif (mlst.length == 1) {\n\t\tconst m = mlst[0]\n\t\tsnpfind.alleleLst = [m.ref, m.alt]\n\t\tif (block.variantPageCall_snv) {\n\t\t\tif (m.chr != undefined && m.pos != undefined && m.ref != undefined && m.alt != undefined) {\n\t\t\t\tvariantpage.set.set(m.chr + separatorvp + m.pos + separatorvp + m.ref + separatorvp + m.alt, {\n\t\t\t\t\tmname: m.mname,\n\t\t\t\t\tclass: m.class\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tconst data = []\n\t\tfor (const atr of tk.snvindelattr) {\n\t\t\tif (atr.lst) {\n\t\t\t\tconst kvlst = []\n\t\t\t\tfor (const at of atr.lst) {\n\t\t\t\t\tif (at.ismaf) {\n\t\t\t\t\t\tconst v = at.get(m)\n\t\t\t\t\t\tkvlst.push({\n\t\t\t\t\t\t\tk: at.label,\n\t\t\t\t\t\t\tv: v\n\t\t\t\t\t\t\t\t? Number.isFinite(v.f)\n\t\t\t\t\t\t\t\t\t? '<span style=\"color:' +\n\t\t\t\t\t\t\t\t\t  at.fill +\n\t\t\t\t\t\t\t\t\t  '\">' +\n\t\t\t\t\t\t\t\t\t  (v.f * 100).toFixed(0) +\n\t\t\t\t\t\t\t\t\t  '% (' +\n\t\t\t\t\t\t\t\t\t  v.v1 +\n\t\t\t\t\t\t\t\t\t  '/' +\n\t\t\t\t\t\t\t\t\t  v.v2 +\n\t\t\t\t\t\t\t\t\t  ')</span>'\n\t\t\t\t\t\t\t\t\t: 'n/a'\n\t\t\t\t\t\t\t\t: ''\n\t\t\t\t\t\t})\n\t\t\t\t\t} else {\n\t\t\t\t\t\tkvlst.push({ k: at.label, v: at.get(m) })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (kvlst.length) {\n\t\t\t\t\tdata.push({ k: atr.label, kvlst: kvlst })\n\t\t\t\t}\n\t\t\t} else if (atr.ismaf) {\n\t\t\t\tconst v = atr.get(m)\n\t\t\t\tdata.push({\n\t\t\t\t\tk: atr.label,\n\t\t\t\t\tv: v\n\t\t\t\t\t\t? Number.isFinite(v.f)\n\t\t\t\t\t\t\t? '<span style=\"color:' +\n\t\t\t\t\t\t\t  atr.fill +\n\t\t\t\t\t\t\t  '\">' +\n\t\t\t\t\t\t\t  (v.f * 100).toFixed(0) +\n\t\t\t\t\t\t\t  '% (' +\n\t\t\t\t\t\t\t  v.v1 +\n\t\t\t\t\t\t\t  '/' +\n\t\t\t\t\t\t\t  v.v2 +\n\t\t\t\t\t\t\t  ')</span>'\n\t\t\t\t\t\t\t: 'n/a'\n\t\t\t\t\t\t: ''\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\tlet v = atr.get(m)\n\t\t\t\tif (atr.hover) {\n\t\t\t\t\tconst hs = atr.hover(m)\n\t\t\t\t\tif (hs) {\n\t\t\t\t\t\tv += ' <span style=\"color:#aaa;font-size:80%\">' + hs + '</span>'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tdata.push({ k: atr.label, v: v })\n\t\t\t}\n\t\t}\n\t\tconst table = client.make_table_2col(holder, data)\n\t\tif (hasSNP) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').attr('colspan', 2).style('color', '#9e9e9e').text('dbSNP')\n\t\t\tsnpfind.says = tr.append('td').text('loading...')\n\t\t}\n\t\t// a row of possible buttons\n\t\t// - highlight samples in epaint\n\t\t// - legend\n\t\tconst buttonrow = holder.append('div').style('margin-top', '10px')\n\t\tif (tk.eplst) {\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tmayephl_butt(ep, buttonrow, mlst)\n\t\t\t}\n\t\t}\n\t\tif (tk.ds && tk.ds.snvindel_legend) {\n\t\t\tbuttonrow\n\t\t\t\t.append('button')\n\t\t\t\t.text('Legend')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (legenddiv.style('display') == 'none') {\n\t\t\t\t\t\tclient.appear(legenddiv)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tclient.disappear(legenddiv)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\tconst legenddiv = buttonrow\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('width', '400px')\n\t\t\t\t.html(tk.ds.snvindel_legend)\n\t\t}\n\t} else {\n\t\t// many m\n\t\tif (block.variantPageCall_snv) {\n\t\t\tfor (const m of mlst) {\n\t\t\t\tif (m.chr != undefined && m.pos != undefined && m.ref != undefined && m.alt != undefined) {\n\t\t\t\t\tvariantpage.set.set(m.chr + separatorvp + m.pos + separatorvp + m.ref + separatorvp + m.alt, {\n\t\t\t\t\t\tmname: m.mname,\n\t\t\t\t\t\tclass: m.class\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst table = holder\n\t\t\t.append('table')\n\t\t\t.style('border-spacing', '3px')\n\t\t\t.style('border-collapse', 'separate')\n\t\t\t.style('margin', '0px 7px 7px 0px')\n\t\t\t.style('font-size', '90%')\n\t\t\t.style('color', 'black')\n\t\t\t.style('background-color', 'white')\n\t\ttable_sort(mlst, table, tk.snvindelattr, tk)\n\t\t// button rows, bottom\n\t\tconst buttrow = holder.append('div').style('margin', '10px 5px')\n\t\t/*\n\t\tif (block.variantPageCall_snv) {\n\t\t\tvariantpage.butholder = buttrow.append('span')\n\t\t}\n\t\t*/\n\t\tlet h_col, h_snp, h_exp, h_leg\n\t\tbuttrow\n\t\t\t.append('button')\n\t\t\t.text('Table columns')\n\t\t\t.on('click', function () {\n\t\t\t\tif (h_col.style('display') == 'block') {\n\t\t\t\t\tthis.style.color = 'black'\n\t\t\t\t\tclient.disappear(h_col)\n\t\t\t\t} else {\n\t\t\t\t\tthis.style.color = 'red'\n\t\t\t\t\tclient.appear(h_col)\n\t\t\t\t}\n\t\t\t})\n\t\tif (hasSNP && snpfind.bprange.length) {\n\t\t\tsnpfind.button = buttrow\n\t\t\t\t.append('button')\n\t\t\t\t.text('loading...')\n\t\t\t\t.on('click', function () {\n\t\t\t\t\tif (h_snp.style('display') == 'block') {\n\t\t\t\t\t\tthis.style.color = 'black'\n\t\t\t\t\t\tclient.disappear(h_snp)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.style.color = 'red'\n\t\t\t\t\t\tclient.appear(h_snp)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t}\n\t\tif (tk.eplst) {\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tmayephl_butt(ep, buttrow, mlst)\n\t\t\t}\n\t\t}\n\t\tif (tk.ds && tk.ds.snvindel_legend) {\n\t\t\tbuttrow\n\t\t\t\t.append('button')\n\t\t\t\t.text('Legend')\n\t\t\t\t.on('click', function () {\n\t\t\t\t\tif (h_leg.style('display') == 'block') {\n\t\t\t\t\t\tthis.style.color = 'black'\n\t\t\t\t\t\tclient.disappear(h_leg)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.style.color = 'red'\n\t\t\t\t\t\tclient.appear(h_leg)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t}\n\t\th_col = holder.append('div').style('margin', '10px').style('display', 'none')\n\t\tfor (const at of tk.snvindelattr) {\n\t\t\tconst id = Math.random()\n\t\t\tconst check = h_col.append('input').attr('type', 'checkbox').attr('id', id)\n\t\t\tif (!at.hide) check.attr('checked', true)\n\t\t\tcheck.on('change', () => {\n\t\t\t\tat.hide = !check.node().checked\n\t\t\t\ttable_sort(mlst, table, tk.snvindelattr, tk)\n\t\t\t})\n\t\t\th_col.append('label').attr('for', id).text(at.label)\n\t\t\th_col.append('br')\n\t\t}\n\t\tif (hasSNP) {\n\t\t\th_snp = holder.append('div').style('margin', '10px').style('display', 'none')\n\t\t\tsnpfind.holder = h_snp\n\t\t\tsnpfind.says = h_snp\n\t\t}\n\t\tif (tk.ds && tk.ds.snvindel_legend) {\n\t\t\th_leg = holder.append('div').style('display', 'none').style('width', '300px').html(tk.ds.snvindel_legend)\n\t\t}\n\t}\n\n\tif (hasSNP && snpfind.bprange.length) {\n\t\tclient\n\t\t\t.may_findmatchingsnp(snpfind.chr, snpfind.bprange, block.genome, snpfind.alleleLst)\n\t\t\t.then(hits => {\n\t\t\t\tif (!hits || hits.length == 0) throw { message: 'no SNP' }\n\t\t\t\tsnpfind.says.text('')\n\t\t\t\tif (snpfind.button) {\n\t\t\t\t\tsnpfind.button.text(hits.length + ' SNP' + (hits.length > 1 ? 's' : ''))\n\t\t\t\t}\n\t\t\t\tfor (const item of hits) {\n\t\t\t\t\tconst d = snpfind.says.append('div')\n\t\t\t\t\tclient.snp_printhtml(item, d)\n\t\t\t\t}\n\t\t\t})\n\t\t\t.catch(err => {\n\t\t\t\tsnpfind.says.text(err.message)\n\t\t\t\tif (snpfind.button) {\n\t\t\t\t\tsnpfind.button.attr('disabled', true)\n\t\t\t\t}\n\t\t\t\tif (err.stack) console.log(err.stack)\n\t\t\t})\n\t}\n\tif (block.variantPageCall_snv) {\n\t\t// call variant page button generator\n\t\tconst vlst = []\n\t\tfor (const [what, m] of variantpage.set) {\n\t\t\tconst l = what.split(separatorvp)\n\t\t\tvlst.push({\n\t\t\t\tchr: l[0],\n\t\t\t\tposition: Number.parseInt(l[1]) + 1,\n\t\t\t\trefallele: l[2],\n\t\t\t\taltallele: l[3],\n\t\t\t\tclass: m.class,\n\t\t\t\taachange: m.mname\n\t\t\t})\n\t\t}\n\t\tif (vlst.length == 1) {\n\t\t\t// only one variant, call to generate button\n\t\t\tconst variant = vlst[0]\n\t\t\tvariant.container = variantpage.butholder\n\t\t\tblock.variantPageCall_snv(variant)\n\t\t} else if (vlst.length > 1) {\n\t\t\t// 2 or more variants\n\t\t\tvariantpage.butholder\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sja_variantpagesnv', true)\n\t\t\t\t.text('Variant Page')\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tconst table = tk.tktip.clear().showunder(event.target).d.append('table')\n\t\t\t\t\tfor (const variant of vlst) {\n\t\t\t\t\t\tconst tr = table.append('tr')\n\t\t\t\t\t\t// aa change\n\t\t\t\t\t\ttr.append('td').text(variant.aachange)\n\t\t\t\t\t\t// class\n\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t.text(common.mclass[variant.class].label)\n\t\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t\t.style('color', common.mclass[variant.class].color)\n\t\t\t\t\t\t// genomic change\n\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t.text(variant.chr + ':' + variant.position + ' ' + variant.refallele + '>' + variant.altallele)\n\t\t\t\t\t\t\t.attr('font-size', '.7em')\n\t\t\t\t\t\t// vp button\n\t\t\t\t\t\tvariant.container = tr.append('td')\n\t\t\t\t\t\tblock.variantPageCall_snv(variant)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t}\n\t}\n}\n\nfunction table_sort(mlst, table, attrlst, tk, trclick) {\n\ttable.selectAll('*').remove()\n\tlet sortkey = null\n\tfor (const a1 of attrlst) {\n\t\tif (a1.lst) {\n\t\t\tfor (const a2 of a1.lst) {\n\t\t\t\tif (a2.sort) sortkey = a2\n\t\t\t}\n\t\t} else if (a1.sort) sortkey = a1\n\t}\n\tif (sortkey) {\n\t\tmlst.sort((x, y) => {\n\t\t\tconst a = sortkey.get(x)\n\t\t\tconst b = sortkey.get(y)\n\t\t\tif (sortkey.ismaf) {\n\t\t\t\tif (a == undefined) {\n\t\t\t\t\tif (b == undefined) return 0\n\t\t\t\t\treturn 1\n\t\t\t\t} else {\n\t\t\t\t\tif (b == undefined) return -1\n\t\t\t\t\treturn sortkey.descend ? b.f - a.f : a.f - b.f\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (a == undefined || a === '') {\n\t\t\t\tif (b == undefined || b === '') return 0\n\t\t\t\treturn 1\n\t\t\t}\n\t\t\tif (b == undefined || b === '') return -1\n\t\t\tif (typeof a == 'string') {\n\t\t\t\tif (a < b) return sortkey.descend ? 1 : -1\n\t\t\t\tif (a > b) return sortkey.descend ? -1 : 1\n\t\t\t}\n\t\t\tif (typeof a == 'number') return sortkey.descend ? b - a : a - b\n\t\t\treturn 0\n\t\t})\n\t}\n\t// header row 1\n\tconst headtr = table.append('tr')\n\t// header row 2\n\tconst headtr2 = table.append('tr')\n\t// column 1, numerator\n\theadtr.append('td').attr('rowspan', 2)\n\tfor (const atr of attrlst) {\n\t\tif (atr.hide) continue\n\t\tif (atr.lst) {\n\t\t\theadtr\n\t\t\t\t.append('td')\n\t\t\t\t.attr('colspan', atr.lst.length)\n\t\t\t\t.style('color', '#aaa')\n\t\t\t\t.style('border-bottom', 'solid 1px #ccc')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.html(atr.label)\n\t\t\tfor (const at of atr.lst) {\n\t\t\t\theadtr2\n\t\t\t\t\t.append('td')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.html(at.label + (at.sort ? (at.descend ? ' &#9660;' : ' &#9650;') : ''))\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (at.sort) {\n\t\t\t\t\t\t\t// already sorting on this one\n\t\t\t\t\t\t\tat.descend = !at.descend\n\t\t\t\t\t\t}\n\t\t\t\t\t\tfor (const a1 of attrlst) {\n\t\t\t\t\t\t\tif (a1.lst) {\n\t\t\t\t\t\t\t\tfor (const a2 of a1.lst) a2.sort = false\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\ta1.sort = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tat.sort = true\n\t\t\t\t\t\ttable_sort(mlst, table, attrlst, tk, trclick)\n\t\t\t\t\t})\n\t\t\t}\n\t\t} else {\n\t\t\theadtr\n\t\t\t\t.append('td')\n\t\t\t\t.attr('rowspan', 2)\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t.html(atr.label + (atr.sort ? (atr.descend ? ' &#9660;' : ' &#9650;') : ''))\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (atr.sort) {\n\t\t\t\t\t\t// already sorting on this one\n\t\t\t\t\t\tatr.descend = !atr.descend\n\t\t\t\t\t}\n\t\t\t\t\tfor (const a1 of attrlst) {\n\t\t\t\t\t\tif (a1.lst) {\n\t\t\t\t\t\t\tfor (const a2 of a1.lst) a2.sort = false\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\ta1.sort = false\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tatr.sort = true\n\t\t\t\t\ttable_sort(mlst, table, attrlst, tk, trclick)\n\t\t\t\t})\n\t\t}\n\t}\n\tconst showcount = mlst.length > 1000 ? 900 : mlst.length\n\tfor (let i = 0; i < showcount; i++) {\n\t\tconst s = mlst[i]\n\t\tconst tr = table.append('tr').attr('class', 'sja_tr')\n\t\tif (trclick) {\n\t\t\ttr.on('click', () => trclick(s))\n\t\t}\n\t\tif (tk.eplst) {\n\t\t\ttr.on('mouseover', (event, m) => {\n\t\t\t\tfor (const ep of tk.eplst) ep.may_hl([s], true)\n\t\t\t}).on('mouseout', (event, m) => {\n\t\t\t\tfor (const ep of tk.eplst) ep.may_hl([s], false)\n\t\t\t})\n\t\t}\n\t\ttr.append('td')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text(i + 1)\n\t\tfor (const atr of attrlst) {\n\t\t\tif (atr.hide) continue\n\t\t\tif (atr.lst) {\n\t\t\t\tfor (const at of atr.lst) {\n\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\tif (at.ismaf) {\n\t\t\t\t\t\t// scattered maf fields\n\t\t\t\t\t\tconst v = at.get(s)\n\t\t\t\t\t\tif (v && typeof v == 'object') {\n\t\t\t\t\t\t\t// FIXME ep.p.maf returns data for both snv and fusion, but !!!\n\t\t\t\t\t\t\tif (v.v2 == 0) {\n\t\t\t\t\t\t\t\ttd.text('0/0')\n\t\t\t\t\t\t\t\ttd.attr('aria-label', 'No coverage')\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tclient.fillbar(td, v, at)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttd.html(at.get(s))\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconst td = tr.append('td')\n\t\t\t\tif (atr.hover) {\n\t\t\t\t\tconst hs = atr.hover(s)\n\t\t\t\t\tif (hs != undefined) {\n\t\t\t\t\t\ttd.attr('aria-label', hs)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (atr.tablecellwidth) {\n\t\t\t\t\ttd.style('width', atr.tablecellwidth).style('word-break', 'break-all')\n\t\t\t\t}\n\t\t\t\tif (atr.ismaf) {\n\t\t\t\t\t// scattered maf fields\n\t\t\t\t\tconst v = atr.get(s)\n\t\t\t\t\tif (v) {\n\t\t\t\t\t\tif (v.v2 == 0) {\n\t\t\t\t\t\t\ttd.text('0/0')\n\t\t\t\t\t\t\ttd.attr('aria-label', 'No coverage')\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tclient.fillbar(td, v, atr)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\ttd.html(atr.get(s))\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction tinylab(t) {\n\treturn '<span style=\"font-size:70%;color:#858585\">' + t + '</span>'\n}\n\nfunction vcfmdetail(m, vcfobj, holder, tk, block) {\n\t/*\n\tfor a single variant from vcf\n\tcan be from a single vcf, or multiple vcf\n\tthe variant can have .sampledata[]\n\tif \n\t*/\n\n\tif (!vcfobj) {\n\t\tholder.append('p').text('vcfobj config object missing')\n\t\treturn\n\t}\n\n\t// first row of buttons\n\n\tconst row1 = holder.append('div').style('margin-top', '10px')\n\trow1.append('span').text(m.type).style('padding-right', '10px')\n\trow1\n\t\t.append('span')\n\t\t.text(m.chr + ':' + (m.pos + 1))\n\t\t.style('padding-right', '10px')\n\n\tif (m.dt == common.dtsnvindel) {\n\t\t// alleles\n\t\trow1\n\t\t\t.append('span')\n\t\t\t.style('padding-right', '10px')\n\t\t\t.html(tinylab('REF') + ' ' + m.ref + ' ' + tinylab('ALT') + ' ' + m.alt)\n\t\tif (block.variantPageCall_snv) {\n\t\t\tconst variant = {\n\t\t\t\tchr: m.chr,\n\t\t\t\tposition: m.pos + 1,\n\t\t\t\trefallele: m.ref,\n\t\t\t\taltallele: m.alt,\n\t\t\t\tcontainer: row1.append('span').style('padding-left', '20px')\n\t\t\t}\n\t\t\tblock.variantPageCall_snv(variant)\n\t\t}\n\n\t\tif (tk.button4variant) {\n\t\t\tmake_button4variant(row1, m, tk.button4variant)\n\t\t}\n\t\tif (tk.url4variant) {\n\t\t\tmake_url4variant(row1, m, tk.url4variant)\n\t\t}\n\t}\n\n\tif (vcfobj.info && vcfobj.info.CSQ && vcfobj.info.CSQ.csqheader && m.csq) {\n\t\t// has VEP\n\t\tvcfvepbutton(m.csq, row1, tk, vcfobj.info.CSQ.csqheader)\n\t}\n\n\tif (vcfobj.info && vcfobj.info.ANN && vcfobj.info.ANN.annheader && m.ann) {\n\t\t// has ANN\n\t\tvcfannbutton(m.ann, row1, tk, vcfobj.info.ANN.annheader)\n\t}\n\n\tif (tk.variant2img) {\n\t\tvariant2imgbutton(m, row1, holder.append('div'), tk, block)\n\t}\n\n\t// if the variant has sample-level data\n\t// condition testingdoesn't make sense that .sampledata[] is there for all\n\n\tconst div = holder.append('div')\n\tif (mayshowgenotype2boxplot(m, tk, div)) {\n\t\t// boxplot shown\n\t\tdiv.style('margin-top', '10px')\n\t} else if (m.sampledata) {\n\t\tconst wait = div.append('div')\n\n\t\tPromise.resolve()\n\t\t\t.then(() => {\n\t\t\t\tif (m.sampledata.length == 0 && tk.ds.vcfcohorttrack) {\n\t\t\t\t\t// query cohort vcfobj file for sample info about this variant\n\t\t\t\t\twait.text('Loading ...')\n\n\t\t\t\t\treturn query_vcfcohorttrack(m, tk, block).then(m2 => {\n\t\t\t\t\t\tif (!m2) {\n\t\t\t\t\t\t\t// no hit\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tm.sampledata = m2.sampledata\n\t\t\t\t\t\treturn\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\treturn\n\t\t\t})\n\t\t\t.then(() => {\n\t\t\t\twait.remove()\n\t\t\t\tif (m.sampledata.length == 0) {\n\t\t\t\t\t// no sample\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\tif (m.sampledata.length == 1) {\n\t\t\t\t\t// single sample\n\t\t\t\t\tsingleSample2table(m, tk, div)\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\t/*\n\t\t\tmultiple samples\n\t\t\tmay show some kind of plots\n\t\t\t*/\n\n\t\t\t\tif (mayshowgermline2dvaf(m, tk, div)) {\n\t\t\t\t\tdiv.style('margin-top', '10px')\n\t\t\t\t} else if (mayshowcovmafplot(m, tk, div)) {\n\t\t\t\t\tdiv.style('margin-top', '10px')\n\t\t\t\t} else if (mayshowgenotype2boxplot(m, tk, div)) {\n\t\t\t\t\tdiv.style('margin-top', '10px')\n\t\t\t\t} else {\n\t\t\t\t\tvcfsamplelistbutton(m, row1, tk)\n\t\t\t\t}\n\t\t\t})\n\t\t\t.catch(err => {\n\t\t\t\twait.text(err)\n\t\t\t})\n\t}\n\n\tif (vcfobj.infopipejoin) {\n\t\t// for allele info only!\n\t\t// designed for old clinvar vcf, no longer used\n\t\tconst lst0 = []\n\t\tif (m.altinfo) {\n\t\t\tfor (const k of vcfobj.infopipejoin) {\n\t\t\t\tconst tmp = m.altinfo[k.key]\n\t\t\t\tif (tmp) {\n\t\t\t\t\tif (Array.isArray(tmp)) {\n\t\t\t\t\t\tlst0.push(tmp)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlst0.push(tmp.split(/[,|]/))\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tlst0.push([])\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (lst0.length) {\n\t\t\tconst row2 = holder.append('div')\n\t\t\tfor (let i = 0; i < lst0[0].length; i++) {\n\t\t\t\tconst lst = []\n\t\t\t\tfor (let j = 0; j < vcfobj.infopipejoin.length; j++) {\n\t\t\t\t\tconst k = vcfobj.infopipejoin[j]\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tk: k.label,\n\t\t\t\t\t\tv: k.values ? k.values[lst0[j][i]] : lst0[j][i]\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tclient\n\t\t\t\t\t.make_table_2col(row2, lst)\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('border', 'solid 1px black')\n\t\t\t\t\t.style('margin', '20px')\n\t\t\t}\n\t\t}\n\t}\n\n\tmay_info2singletable(m, holder, tk)\n\tmay_info2table(m, holder, tk)\n\n\tconst altkey2category = {} // alt allele\n\tconst lockey2category = {} // locus\n\tif (tk.vcfinfofilter) {\n\t\tfor (const mcset of tk.vcfinfofilter.lst) {\n\t\t\tif (mcset.categories) {\n\t\t\t\tif (mcset.altalleleinfo) {\n\t\t\t\t\taltkey2category[mcset.altalleleinfo.key] = mcset.categories\n\t\t\t\t} else if (mcset.locusinfo) {\n\t\t\t\t\tlockey2category[mcset.locusinfo.key] = mcset.categories\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t{\n\t\t// alt allele info\n\t\tconst lst = []\n\t\tfor (const k in m.altinfo) {\n\t\t\t// value from altinfo maybe array\n\t\t\tconst infovalue = Array.isArray(m.altinfo[k]) ? m.altinfo[k] : [m.altinfo[k]]\n\t\t\tlet showvalue\n\t\t\tif (altkey2category[k]) {\n\t\t\t\tshowvalue = infovalue.map(i => {\n\t\t\t\t\tconst cat = altkey2category[k][i]\n\t\t\t\t\tif (cat) {\n\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t'<span style=\"padding:1px 3px;background:' +\n\t\t\t\t\t\t\tcat.color +\n\t\t\t\t\t\t\t';color:' +\n\t\t\t\t\t\t\t(cat.textcolor || 'black') +\n\t\t\t\t\t\t\t';\">' +\n\t\t\t\t\t\t\ti +\n\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t}\n\t\t\t\t\treturn i\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\tshowvalue = infovalue\n\t\t\t}\n\t\t\tlst.push({\n\t\t\t\tk: k,\n\t\t\t\tv:\n\t\t\t\t\tshowvalue.join(', ') +\n\t\t\t\t\t(vcfobj.info && vcfobj.info[k]\n\t\t\t\t\t\t? ' <span style=\"font-size:70%;color:#858585\">' + vcfobj.info[k].Description + '</span>'\n\t\t\t\t\t\t: '')\n\t\t\t})\n\t\t}\n\t\tif (lst.length) {\n\t\t\tholder.append('h3').text('Alternative allele:')\n\t\t\tclient.make_table_2col(holder, lst)\n\t\t}\n\t}\n\n\t{\n\t\t// locus info\n\t\tconst lst = []\n\t\tfor (const k in m.info) {\n\t\t\tif (tk.info2table && tk.info2table[k]) {\n\t\t\t\t// already shown in previous section\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst infovalue = Array.isArray(m.info[k]) ? m.info[k] : [m.info[k]]\n\t\t\tlet showvalue\n\t\t\tif (lockey2category[k]) {\n\t\t\t\tshowvalue = infovalue.map(i => {\n\t\t\t\t\tconst cat = lockey2category[k][i]\n\t\t\t\t\tif (cat) {\n\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t'<span style=\"padding:1px 3px;background:' +\n\t\t\t\t\t\t\tcat.color +\n\t\t\t\t\t\t\t';color:' +\n\t\t\t\t\t\t\t(cat.textcolor || 'black') +\n\t\t\t\t\t\t\t';\">' +\n\t\t\t\t\t\t\ti +\n\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t}\n\t\t\t\t\treturn i\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\tshowvalue = infovalue\n\t\t\t}\n\t\t\tlst.push({\n\t\t\t\tk: k,\n\t\t\t\tv:\n\t\t\t\t\tshowvalue.join(', ') +\n\t\t\t\t\t(vcfobj.info && vcfobj.info[k]\n\t\t\t\t\t\t? ' <span style=\"font-size:70%;color:#858585\">' + vcfobj.info[k].Description + '</span>'\n\t\t\t\t\t\t: '')\n\t\t\t})\n\t\t}\n\t\tif (lst.length) {\n\t\t\tholder.append('h3').text('This locus:')\n\t\t\tclient.make_table_2col(holder, lst)\n\t\t}\n\t}\n}\n\nfunction may_info2singletable(m, holder, tk) {\n\t// from a csq-like field, only show first item as a vertical table with each row as a field of icfg.fields[]\n\tif (!tk.info2singletable) return\n\tfor (const infokey in tk.info2singletable) {\n\t\tconst icfg = tk.info2singletable[infokey]\n\t\tconst rawvaluelst = m.info[infokey]\n\t\tif (!rawvaluelst || !rawvaluelst[0]) continue\n\t\tconst table = []\n\t\tconst lst = rawvaluelst[0].split(icfg.col_separator)\n\t\tfor (let i = 0; i < icfg.fields.length; i++) {\n\t\t\tif (icfg.fields[i].hide) continue\n\t\t\ttable.push({\n\t\t\t\tk: icfg.fields[i].name,\n\t\t\t\tv: info2table_value(icfg, lst, i)\n\t\t\t})\n\t\t}\n\t\tclient.make_table_2col(holder, table)\n\t}\n}\n\nfunction may_info2table(m, holder, tk) {\n\tif (!tk.info2table) return\n\tfor (const infokey in tk.info2table) {\n\t\tconst icfg = tk.info2table[infokey]\n\t\tconst rawvaluelst = m.info[infokey]\n\t\tif (!rawvaluelst) continue\n\n\t\tif (icfg.separate_tables) {\n\t\t\tconst tables = JSON.parse(JSON.stringify(icfg.separate_tables))\n\t\t\ttables.forEach(i => (i.rows = []))\n\t\t\tfor (const row of rawvaluelst) {\n\t\t\t\tconst lst = row.split(icfg.col_separator)\n\t\t\t\tconst field2value = new Map()\n\t\t\t\tfor (let i = 0; i < icfg.fields.length; i++) {\n\t\t\t\t\tfield2value.set(icfg.fields[i].name, lst[i])\n\t\t\t\t}\n\t\t\t\tfor (const t of tables) {\n\t\t\t\t\tif (t.groupers.reduce((i, j) => (field2value.get(j.field) == j.value ? i : false), true)) {\n\t\t\t\t\t\tt.rows.push(field2value)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tfor (const t of tables) {\n\t\t\t\tif (t.rows.length == 0) continue\n\t\t\t\tholder.append('h3').html(t.headhtml)\n\t\t\t\tconst table = holder\n\t\t\t\t\t.append('table')\n\t\t\t\t\t.style('border-spacing', '2px')\n\t\t\t\t\t.style('border-collapse', 'separate')\n\t\t\t\t\t.style('font-size', '90%')\n\t\t\t\tconst tr = table.append('tr')\n\t\t\t\tfor (const field of icfg.fields) {\n\t\t\t\t\tif (field.hide) continue\n\t\t\t\t\ttr.append('td').text(field.name)\n\t\t\t\t}\n\t\t\t\tfor (const row of t.rows) {\n\t\t\t\t\tconst tr = table.append('tr').attr('class', 'sja_tr')\n\t\t\t\t\tconst lst = icfg.fields.map(i => row.get(i.name))\n\t\t\t\t\tfor (let i = 0; i < icfg.fields.length; i++) {\n\t\t\t\t\t\tif (icfg.fields[i].hide) continue\n\t\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\t\ttd.html(info2table_value(icfg, lst, i))\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\tconst table = holder\n\t\t\t.append('table')\n\t\t\t.style('border-spacing', '2px')\n\t\t\t.style('border-collapse', 'separate')\n\t\t\t.style('font-size', '90%')\n\t\tconst tr = table.append('tr')\n\t\tfor (const field of icfg.fields) {\n\t\t\tif (field.hide) continue\n\t\t\ttr.append('td').text(field.name)\n\t\t}\n\t\tfor (const row of rawvaluelst) {\n\t\t\tconst tr = table.append('tr').attr('class', 'sja_tr')\n\t\t\tconst lst = row.split(icfg.col_separator)\n\t\t\tfor (let i = 0; i < icfg.fields.length; i++) {\n\t\t\t\tif (icfg.fields[i].hide) continue\n\t\t\t\tconst td = tr.append('td')\n\t\t\t\ttd.html(info2table_value(icfg, lst, i))\n\t\t\t}\n\t\t}\n\t}\n}\n\n/*\nat index i, to match field config \"icfg.fields[i]\" with raw value \"lst[i]\" to produce a display value\n\nicfg: dataset.info2table\nlst: array of fields of a variant\ni: array index of both icfg.fields[] and lst[]\n*/\nfunction info2table_value(icfg, lst, i) {\n\tconst field = icfg.fields[i]\n\tif (field.hide) return\n\tlet value = lst[i]\n\tif (value == undefined) return\n\t// field config attributes are processed based on order of precedence\n\tif (field.eval) {\n\t\t// somehow decodeURIComponent() won't work here!!\n\t\t// TODO: use a more specific string-to-code conversion\n\t\t// per https://esbuild.github.io/content-types/#direct-eval\n\t\tvalue = (0, eval)('\"' + value + '\"')\n\t}\n\tif (field.isurl) return '<a href=' + value + ' target=_blank>' + value + '</a>'\n\tif (field.appendUrl) {\n\t\tif (field.separator) {\n\t\t\treturn value\n\t\t\t\t.split(field.separator)\n\t\t\t\t.map(v => '<a href=' + field.appendUrl + v + ' target=_blank>' + v + '</a>')\n\t\t\t\t.join(', ')\n\t\t}\n\t\treturn '<a href=' + field.appendUrl + value + ' target=_blank>' + value + '</a>'\n\t}\n\tif (field.insert2url) {\n\t\treturn '<a href=' + field.insert2url.left + value + field.insert2url.right + ' target=_blank>' + value + '</a>'\n\t}\n\tif (field.ampersand2br) return value.replace(/&/g, '<br>')\n\tif (field.urlMatchLst) {\n\t\t// 31566309_(PubMed), or 168986_(ASCO)\n\t\tconst lowervalue = value.toLowerCase()\n\t\tconst id = lowervalue.split(field.urlMatchLst.separator)[field.urlMatchLst.idIndex]\n\t\tif (id) {\n\t\t\tfor (const type of field.urlMatchLst.types) {\n\t\t\t\tif (lowervalue.indexOf(type.type) != -1) {\n\t\t\t\t\tif (type.appendUrl) {\n\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t'<span style=\"font-size:.7em\">' +\n\t\t\t\t\t\t\ttype.type.toUpperCase() +\n\t\t\t\t\t\t\t'</span> <a href=' +\n\t\t\t\t\t\t\ttype.appendUrl +\n\t\t\t\t\t\t\tid +\n\t\t\t\t\t\t\t' target=_blank>' +\n\t\t\t\t\t\t\tid +\n\t\t\t\t\t\t\t'</a>'\n\t\t\t\t\t\t)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\treturn value\n}\n\nfunction mayephl_butt(ep, holder, mlst) {\n\tlet notfound = true\n\tfor (const m of mlst) {\n\t\tif (m[ep.p.sampletype] in ep.sampletype2value) {\n\t\t\tnotfound = false\n\t\t\tbreak\n\t\t}\n\t}\n\tif (notfound) {\n\t\treturn\n\t\t/*\n\t\tholder\n\t\t\t.append('button')\n\t\t\t.text(ep.p.sampletype + ' not in ' + ep.p.name)\n\t\t\t.attr('disabled', 1)\n\t\t\t*/\n\t}\n\tlet hl = false\n\tholder\n\t\t.append('button')\n\t\t.text('Highlight in ' + ep.p.name)\n\t\t.on('click', () => {\n\t\t\thl = !hl\n\t\t\tep.may_hl(mlst, hl)\n\t\t})\n}\n\nfunction table_sv(mlst, holder, tk, block) {\n\tconst graphholder = holder.append('div').style('margin-bottom', '10px')\n\ttosvgraph(mlst[0].pairlst, block, graphholder)\n\tif (!tk.svattr) {\n\t\truntimeattr_sv(tk, mlst)\n\t}\n\tif (mlst.length == 1) {\n\t\tconst m = mlst[0]\n\t\tconst data = []\n\t\tfor (const at of tk.svattr) {\n\t\t\tdata.push({ k: at.label, v: at.get(m) })\n\t\t}\n\t\tconst table = client.make_table_2col(holder, data)\n\t\tif (tk.eplst) {\n\t\t\tconst butrow = holder.append('div').style('margin-top', '10px')\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t\t}\n\t\t}\n\t\treturn\n\t}\n\tconst table = holder\n\t\t.append('table')\n\t\t.style('font-size', '90%')\n\t\t.style('border-spacing', '2px')\n\t\t.style('border-collapse', 'separate')\n\tconst tr = table.append('tr')\n\tfor (const at of tk.svattr) {\n\t\ttr.append('td').text(at.label)\n\t}\n\ttable_sort(mlst, table, tk.svattr, tk, m => {\n\t\tgraphholder.selectAll('*').remove()\n\t\ttosvgraph(m.pairlst, block, graphholder)\n\t})\n\tif (tk.eplst) {\n\t\tconst butrow = holder.append('div').style('margin-top', '5px')\n\t\tfor (const ep of tk.eplst) {\n\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t}\n\t}\n}\n\nfunction tosvgraph(pairlst, block, holder) {\n\tfor (const p of pairlst) {\n\t\tif (p.a.isoform) {\n\t\t\tp.a.gm = { isoform: p.a.isoform }\n\t\t}\n\t\tif (p.b.isoform) {\n\t\t\tp.b.gm = { isoform: p.b.isoform }\n\t\t}\n\t}\n\tconst svarg = {\n\t\tjwt: block.jwt,\n\t\thostURL: block.hostURL,\n\t\tpairlst: pairlst,\n\t\tgenome: block.genome,\n\t\tholder: holder\n\t}\n\timport('./svgraph').then(p => {\n\t\tp.default(svarg)\n\t})\n}\n\nfunction table_itd(mlst, holder, tk, genome) {\n\tif (!tk.itdattr) {\n\t\truntimeattr_itd(tk, mlst)\n\t}\n\tif (mlst.length == 1) {\n\t\tconst m = mlst[0]\n\t\tconst data = []\n\t\tfor (const at of tk.itdattr) {\n\t\t\tdata.push({ k: at.label, v: at.get(m) })\n\t\t}\n\t\tconst table = client.make_table_2col(holder, data)\n\t\tif (tk.eplst) {\n\t\t\tconst butrow = holder.append('div').style('margin-top', '10px')\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t\t}\n\t\t}\n\t\treturn\n\t}\n\tconst table = holder\n\t\t.append('table')\n\t\t.style('font-size', '90%')\n\t\t.style('border-spacing', '2px')\n\t\t.style('border-collapse', 'separate')\n\tconst tr = table.append('tr')\n\tfor (const at of tk.itdattr) {\n\t\ttr.append('td').text(at.label)\n\t}\n\ttable_sort(mlst, table, tk.itdattr, tk)\n\tif (tk.eplst) {\n\t\tconst butrow = holder.append('div').style('margin-top', '5px')\n\t\tfor (const ep of tk.eplst) {\n\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t}\n\t}\n}\n\nfunction table_del(mlst, holder, tk, genome) {\n\tif (!tk.delattr) {\n\t\truntimeattr_del(tk, mlst)\n\t}\n\tif (mlst.length == 1) {\n\t\tconst m = mlst[0]\n\t\tconst data = []\n\t\tfor (const at of tk.delattr) {\n\t\t\tdata.push({ k: at.label, v: at.get(m) })\n\t\t}\n\t\tconst table = client.make_table_2col(holder, data)\n\t\tif (tk.eplst) {\n\t\t\tconst butrow = holder.append('div').style('margin-top', '10px')\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t\t}\n\t\t}\n\t\treturn\n\t}\n\tconst table = holder\n\t\t.append('table')\n\t\t.style('font-size', '90%')\n\t\t.style('border-spacing', '2px')\n\t\t.style('border-collapse', 'separate')\n\tconst tr = table.append('tr')\n\tfor (const at of tk.delattr) {\n\t\ttr.append('td').text(at.label)\n\t}\n\ttable_sort(mlst, table, tk.delattr, tk)\n\tif (tk.eplst) {\n\t\tconst butrow = holder.append('div').style('margin-top', '5px')\n\t\tfor (const ep of tk.eplst) {\n\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t}\n\t}\n}\n\nfunction table_truncation(mlst, holder, tk, genome) {\n\tif (!tk.truncattr) {\n\t\truntimeattr_trunc(tk, mlst)\n\t}\n\tif (mlst.length == 1) {\n\t\tconst m = mlst[0]\n\t\tconst data = []\n\t\tfor (const at of tk.truncattr) {\n\t\t\tdata.push({ k: at.label, v: at.get(m) })\n\t\t}\n\t\tconst table = client.make_table_2col(holder, data)\n\t\tif (tk.eplst) {\n\t\t\tconst butrow = holder.append('div').style('margin-top', '10px')\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t\t}\n\t\t}\n\t\treturn\n\t}\n\tconst table = holder\n\t\t.append('table')\n\t\t.style('font-size', '90%')\n\t\t.style('border-spacing', '2px')\n\t\t.style('border-collapse', 'separate')\n\tconst tr = table.append('tr')\n\tfor (const at of tk.truncattr) {\n\t\ttr.append('td').text(at.label)\n\t}\n\ttable_sort(mlst, table, tk.truncattr, tk)\n\tif (tk.eplst) {\n\t\tconst butrow = holder.append('div').style('margin-top', '5px')\n\t\tfor (const ep of tk.eplst) {\n\t\t\tmayephl_butt(ep, butrow, mlst)\n\t\t}\n\t}\n}\n\nexport function runtimeattr_snvindel(tk, mlst) {\n\ttk.snvindelattr = []\n\tif (tk.ds && tk.ds.snvindel_attributes) {\n\t\t// use predefined\n\t\tfor (const a of tk.ds.snvindel_attributes) {\n\t\t\ttk.snvindelattr.push(a)\n\t\t}\n\t} else {\n\t\t// ds-free or nothing available from ds, figure out from data\n\t\tconst nouse = new Set(['pos', 'aapos', 'rnapos', 'dt', 'vcfid', 'isrim1', 'isrim2', 'alt', '__x'])\n\t\tif (tk.ds.cohort && tk.ds.cohort.levels) {\n\t\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\t\tnouse.add(l.k)\n\t\t\t}\n\t\t}\n\t\tconst lst = []\n\t\tfor (const k in mlst[0]) {\n\t\t\tif (nouse.has(k)) continue\n\t\t\tswitch (k) {\n\t\t\t\tcase 'chr':\n\t\t\t\t\tlst.push({ label: 'Genome pos.', get: m => m.chr + ':' + (m.pos + 1) })\n\t\t\t\t\tbreak\n\t\t\t\tcase 'class':\n\t\t\t\t\tlst.push({ label: 'Class', get: m => common.mclass[m.class].label })\n\t\t\t\t\tbreak\n\t\t\t\tcase 'mname':\n\t\t\t\t\tlst.push({ label: 'Mutation', get: m => m.mname })\n\t\t\t\t\tbreak\n\t\t\t\tcase 'ref':\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tlabel: 'Allele',\n\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t{ label: 'Ref', get: m => m.ref },\n\t\t\t\t\t\t\t{ label: 'Alt', get: m => m.alt }\n\t\t\t\t\t\t]\n\t\t\t\t\t})\n\t\t\t\t\tbreak\n\t\t\t\tcase 'pmid':\n\t\t\t\t\tlst.push(caller_pmid())\n\t\t\t\t\tbreak\n\t\t\t\tcase 'maf_tumor':\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tget: m => m.maf_tumor,\n\t\t\t\t\t\tismaf: true,\n\t\t\t\t\t\twidth: 40,\n\t\t\t\t\t\theight: 12,\n\t\t\t\t\t\tlabel: 'Tumor MAF',\n\t\t\t\t\t\tfill: '#ff4d4d',\n\t\t\t\t\t\tfillbg: '#ffcccc'\n\t\t\t\t\t})\n\t\t\t\t\tbreak\n\t\t\t\tcase 'maf_normal':\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tget: m => m.maf_normal,\n\t\t\t\t\t\tismaf: true,\n\t\t\t\t\t\twidth: 40,\n\t\t\t\t\t\theight: 12,\n\t\t\t\t\t\tlabel: 'Germline MAF',\n\t\t\t\t\t\tfill: '#4d4dff',\n\t\t\t\t\t\tfillbg: '#ccccff'\n\t\t\t\t\t})\n\t\t\t\t\tbreak\n\t\t\t\tdefault:\n\t\t\t\t\tlst.push({ label: k, get: m => m[k] })\n\t\t\t}\n\t\t}\n\t\ttk.snvindelattr = lst\n\t}\n\tif (tk.ds.cohort && tk.ds.cohort.levels) {\n\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\ttk.snvindelattr.push({\n\t\t\t\tlabel: l.label || l.k,\n\t\t\t\thide: l.hide,\n\t\t\t\tget: m => {\n\t\t\t\t\tif (m[l.k])\n\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\tm[l.k] +\n\t\t\t\t\t\t\t(l.full ? (m[l.full] ? ' <span style=\"font-size:.8em;color:#858585\">' + m[l.full] + '</span>' : '') : '')\n\t\t\t\t\t\t)\n\t\t\t\t\treturn ''\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\tif (tk.eplst) {\n\t\tfor (const ep of tk.eplst) {\n\t\t\tif (!ep.p) {\n\t\t\t\tconsole.error('no config object for epaint')\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (ep.p.maf) {\n\t\t\t\t// both maf and expression value\n\t\t\t\ttk.snvindelattr.push({\n\t\t\t\t\tlabel: ep.p.name,\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: ep.p.datatype,\n\t\t\t\t\t\t\tget: m => {\n\t\t\t\t\t\t\t\tconst s = m[ep.p.sampletype]\n\t\t\t\t\t\t\t\tif (!s) return ''\n\t\t\t\t\t\t\t\treturn ep.sampletype2value[s]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: ep.p.maf.label,\n\t\t\t\t\t\t\twidth: 40,\n\t\t\t\t\t\t\theight: 12,\n\t\t\t\t\t\t\tfill: ep.p.hlcolor,\n\t\t\t\t\t\t\tfillbg: ep.p.hlcolor2,\n\t\t\t\t\t\t\tget: ep.p.maf.get,\n\t\t\t\t\t\t\treadcountcredible: ep.p.maf.readcountcredible,\n\t\t\t\t\t\t\tismaf: true\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\t// only expression value\n\t\t\t\ttk.snvindelattr.push({\n\t\t\t\t\tlabel: ep.p.name + ' ' + ep.p.datatype,\n\t\t\t\t\tget: m => {\n\t\t\t\t\t\tconst s = m[ep.p.sampletype]\n\t\t\t\t\t\tif (!s) return ''\n\t\t\t\t\t\treturn ep.sampletype2value[s]\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function runtimeattr_trunc(tk, mlst) {\n\tconst skipset = new Set([\n\t\t'__x',\n\t\t'mname',\n\t\t'gene',\n\t\t'strand',\n\t\t'isoform',\n\t\t'aapos',\n\t\t'rnapos',\n\t\t'chr',\n\t\t'pos',\n\t\t'class',\n\t\t'dt',\n\t\t'rnaposition',\n\t\t'partner'\n\t])\n\ttk.truncattr = []\n\tfor (const m of mlst) {\n\t\tif (m.sample) {\n\t\t\ttk.truncattr.push({ label: 'Sample', get: m => m.sample })\n\t\t\tskipset.add('sample')\n\t\t\tbreak\n\t\t}\n\t}\n\ttk.truncattr.push({\n\t\tlabel: 'Position',\n\t\tget: m => m.chr + ':' + m.pos\n\t})\n\tconst dtset = new Set()\n\tfor (const m of mlst) {\n\t\tdtset.add(m.dt)\n\t}\n\tif (dtset.size > 1) {\n\t\ttk.truncattr.push({\n\t\t\tlabel: 'Truncated',\n\t\t\tget: m => (m.dt == common.dtnloss ? 'N-term' : 'C-term')\n\t\t})\n\t}\n\tfor (const m of mlst) {\n\t\tif (m.pmid) {\n\t\t\ttk.truncattr.push(caller_pmid())\n\t\t\tskipset.add('pmid')\n\t\t\tbreak\n\t\t}\n\t}\n\tfor (const m of mlst) {\n\t\tif (m.partner) {\n\t\t\t// cicero exports\n\t\t\ttk.truncattr.push({\n\t\t\t\tget: m => {\n\t\t\t\t\tconst lst = []\n\t\t\t\t\tfor (const k in m.partner) {\n\t\t\t\t\t\tlst.push(k + ': ' + m.partner[k])\n\t\t\t\t\t}\n\t\t\t\t\treturn lst.join('&nbsp;&nbsp;')\n\t\t\t\t},\n\t\t\t\tlabel: 'Translocation'\n\t\t\t})\n\t\t\tbreak\n\t\t}\n\t}\n\tif (tk.ds && tk.ds.cohort && tk.ds.cohort.levels) {\n\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\tskipset.add(l.k)\n\t\t\tskipset.add(l.full)\n\t\t\ttk.truncattr.push({\n\t\t\t\tlabel: l.label || l.k,\n\t\t\t\t//hide:l.hide,\n\t\t\t\tget: m =>\n\t\t\t\t\tm[l.k] ? m[l.k] + (l.full ? ' <span style=\"color:#858585;font-size:.8em\">' + m[l.full] + '</span>' : '') : ''\n\t\t\t})\n\t\t}\n\t}\n\tfor (const k in mlst[0]) {\n\t\tif (skipset.has(k)) continue\n\t\ttk.truncattr.push({ label: k, get: m => m[k] })\n\t}\n}\n\nexport function runtimeattr_del(tk, mlst) {\n\tconst skipset = new Set([\n\t\t'__x',\n\t\t'mname',\n\t\t'isoform',\n\t\t'aapos',\n\t\t'rnapos',\n\t\t'chr',\n\t\t'pos',\n\t\t'class',\n\t\t'dt',\n\t\t'rnaposition',\n\t\t'rnadellength',\n\t\t'a',\n\t\t'b'\n\t])\n\ttk.delattr = []\n\tfor (const m of mlst) {\n\t\tif (m.sample) {\n\t\t\ttk.delattr.push({ label: 'Sample', get: m => m.sample })\n\t\t\tskipset.add('sample')\n\t\t\tbreak\n\t\t}\n\t}\n\ttk.delattr.push({\n\t\tlabel: 'Position',\n\t\tget: m => m.chr + ':' + m.pos\n\t})\n\ttk.delattr.push({\n\t\tlabel: 'Del. length',\n\t\tget: m => m.rnadellength + ' bp'\n\t})\n\tfor (const m of mlst) {\n\t\tif (m.pmid) {\n\t\t\ttk.delattr.push(caller_pmid())\n\t\t\tskipset.add('pmid')\n\t\t\tbreak\n\t\t}\n\t}\n\tif (tk.ds && tk.ds.cohort && tk.ds.cohort.levels) {\n\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\tskipset.add(l.k)\n\t\t\tskipset.add(l.full)\n\t\t\ttk.delattr.push({\n\t\t\t\tlabel: l.label || l.k,\n\t\t\t\t//hide:l.hide,\n\t\t\t\tget: m =>\n\t\t\t\t\tm[l.k] ? m[l.k] + (l.full ? ' <span style=\"color:#858585;font-size:.8em\">' + m[l.full] + '</span>' : '') : ''\n\t\t\t})\n\t\t}\n\t}\n\tfor (const k in mlst[0]) {\n\t\tif (skipset.has(k)) continue\n\t\ttk.delattr.push({ label: k, get: m => m[k] })\n\t}\n}\n\nexport function runtimeattr_itd(tk, mlst) {\n\tconst skipset = new Set([\n\t\t'__x',\n\t\t'mname',\n\t\t'isoform',\n\t\t'aapos',\n\t\t'rnapos',\n\t\t'chr',\n\t\t'pos',\n\t\t'class',\n\t\t'dt',\n\t\t'rnaposition',\n\t\t'rnaduplength',\n\t\t'a',\n\t\t'b'\n\t])\n\ttk.itdattr = []\n\tfor (const m of mlst) {\n\t\tif (m.sample) {\n\t\t\ttk.itdattr.push({ label: 'Sample', get: m => m.sample })\n\t\t\tskipset.add('sample')\n\t\t\tbreak\n\t\t}\n\t}\n\ttk.itdattr.push({\n\t\tlabel: 'Position',\n\t\tget: m => m.chr + ':' + m.pos\n\t})\n\ttk.itdattr.push({\n\t\tlabel: 'Dup. length',\n\t\tget: m => m.rnaduplength + ' bp'\n\t})\n\tfor (const m of mlst) {\n\t\tif (m.pmid) {\n\t\t\ttk.itdattr.push(caller_pmid())\n\t\t\tskipset.add('pmid')\n\t\t\tbreak\n\t\t}\n\t}\n\tif (tk.ds && tk.ds.cohort && tk.ds.cohort.levels) {\n\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\tskipset.add(l.k)\n\t\t\tskipset.add(l.full)\n\t\t\ttk.itdattr.push({\n\t\t\t\tlabel: l.label || l.k,\n\t\t\t\t//hide:l.hide,\n\t\t\t\tget: m =>\n\t\t\t\t\tm[l.k] ? m[l.k] + (l.full ? ' <span style=\"color:#858585;font-size:.8em\">' + m[l.full] + '</span>' : '') : ''\n\t\t\t})\n\t\t}\n\t}\n\tfor (const k in mlst[0]) {\n\t\tif (skipset.has(k)) continue\n\t\ttk.itdattr.push({ label: k, get: m => m[k] })\n\t}\n}\n\nexport function runtimeattr_sv(tk, mlst) {\n\tconst skipset = new Set([\n\t\t'__x',\n\t\t'mname',\n\t\t'aapos',\n\t\t'chr',\n\t\t'class',\n\t\t'dt',\n\t\t'inframe',\n\t\t'origin',\n\t\t'pos',\n\t\t'rnapos',\n\t\t'strand',\n\t\t'useNterm',\n\t\t'pairlst'\n\t])\n\ttk.svattr = []\n\tfor (const m of mlst) {\n\t\tif (m.sample) {\n\t\t\ttk.svattr.push({ label: 'Sample', get: m => m.sample })\n\t\t\tskipset.add('sample')\n\t\t\tbreak\n\t\t}\n\t}\n\ttk.svattr.push({\n\t\tlabel: 'Genomic breakpoint',\n\t\tget: m => {\n\t\t\tif (!m.pairlst) return 'no pairlst'\n\t\t\tconst lst = m.pairlst.map(\n\t\t\t\tp =>\n\t\t\t\t\t(p.a.name ? '<strong>' + p.a.name + '</strong> ' : '') +\n\t\t\t\t\t(p.a.chr\n\t\t\t\t\t\t? '<span style=\"color:#858585\">' +\n\t\t\t\t\t\t  p.a.chr +\n\t\t\t\t\t\t  ':' +\n\t\t\t\t\t\t  (p.a.position + 1) +\n\t\t\t\t\t\t  ' ' +\n\t\t\t\t\t\t  (p.a.strand == '+' ? 'forward' : 'reverse') +\n\t\t\t\t\t\t  '</span> &#10140; '\n\t\t\t\t\t\t: '') +\n\t\t\t\t\t(p.b.name ? '<strong>' + p.b.name + '</strong> ' : '') +\n\t\t\t\t\t(p.b.chr\n\t\t\t\t\t\t? '<span style=\"color:#858585\">' +\n\t\t\t\t\t\t  p.b.chr +\n\t\t\t\t\t\t  ':' +\n\t\t\t\t\t\t  (p.b.position + 1) +\n\t\t\t\t\t\t  ' ' +\n\t\t\t\t\t\t  (p.b.strand == '+' ? 'forward' : 'reverse') +\n\t\t\t\t\t\t  '</span>'\n\t\t\t\t\t\t: '')\n\t\t\t)\n\t\t\treturn lst.join('<br>')\n\t\t}\n\t})\n\tfor (const m of mlst) {\n\t\tif (m.pairlst[0].a.rnaposition != undefined) {\n\t\t\ttk.svattr.push({\n\t\t\t\tlabel: 'RNA breakpoint',\n\t\t\t\tget: m => {\n\t\t\t\t\tif (!m.pairlst) return 'no pairlst'\n\t\t\t\t\tconst lst = m.pairlst.map(\n\t\t\t\t\t\tp =>\n\t\t\t\t\t\t\t(p.a.name ? '<strong>' + p.a.name + '</strong> ' : '') +\n\t\t\t\t\t\t\t'<span style=\"color:#858585\">r.' +\n\t\t\t\t\t\t\t(p.a.rnaposition + 1) +\n\t\t\t\t\t\t\t'</span> &#10140; ' +\n\t\t\t\t\t\t\t(p.b.name ? '<strong>' + p.b.name + '</strong> ' : '') +\n\t\t\t\t\t\t\t'<span style=\"color:#858585\">r.' +\n\t\t\t\t\t\t\t(p.b.rnaposition + 1) +\n\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t)\n\t\t\t\t\treturn lst.join('<br>')\n\t\t\t\t}\n\t\t\t})\n\t\t\tbreak\n\t\t}\n\t}\n\tfor (const m of mlst) {\n\t\tif (m.pmid) {\n\t\t\ttk.svattr.push(caller_pmid())\n\t\t\tskipset.add('pmid')\n\t\t\tbreak\n\t\t}\n\t}\n\t// cosmic attr\n\tlet hastn = false\n\tfor (const m of mlst) {\n\t\tif (hastn) break\n\t\tfor (const p of m.pairlst) {\n\t\t\tif (p.translocationname) {\n\t\t\t\ttk.svattr.push({\n\t\t\t\t\tget: m => m.pairlst.map(i => (i.translocationname ? i.translocationname : '')).join('_'),\n\t\t\t\t\tlabel: 'Translocation name'\n\t\t\t\t})\n\t\t\t\thastn = true\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\tif (mlst[0].pairlst[0].a.ratio != undefined) {\n\t\ttk.svattr.push({\n\t\t\tlabel: 'Chimeric reads ratio',\n\t\t\tget: m => {\n\t\t\t\tconst lst = []\n\t\t\t\tconst w = 40,\n\t\t\t\t\th = 12,\n\t\t\t\t\tfill = '#FF850A',\n\t\t\t\t\tfillbg = '#FFCF9E'\n\t\t\t\tfor (const i of m.pairlst) {\n\t\t\t\t\tlst.push(\n\t\t\t\t\t\t(i.a.name ? i.a.name : i.a.chr) +\n\t\t\t\t\t\t\t' <svg width=' +\n\t\t\t\t\t\t\tw +\n\t\t\t\t\t\t\t' height=' +\n\t\t\t\t\t\t\th +\n\t\t\t\t\t\t\t'><g><title>' +\n\t\t\t\t\t\t\ti.a.ratio +\n\t\t\t\t\t\t\t'</title><rect width=' +\n\t\t\t\t\t\t\tw +\n\t\t\t\t\t\t\t' height=' +\n\t\t\t\t\t\t\th +\n\t\t\t\t\t\t\t' fill=\"' +\n\t\t\t\t\t\t\tfillbg +\n\t\t\t\t\t\t\t'\"></rect>' +\n\t\t\t\t\t\t\t'<rect width=' +\n\t\t\t\t\t\t\tw * i.a.ratio +\n\t\t\t\t\t\t\t' height=' +\n\t\t\t\t\t\t\th +\n\t\t\t\t\t\t\t' fill=\"' +\n\t\t\t\t\t\t\tfill +\n\t\t\t\t\t\t\t'\"></rect>' +\n\t\t\t\t\t\t\t'</g></svg>' +\n\t\t\t\t\t\t\t'&nbsp;&nbsp;' +\n\t\t\t\t\t\t\t(i.b.name ? i.b.name : i.b.chr) +\n\t\t\t\t\t\t\t' <svg width=' +\n\t\t\t\t\t\t\tw +\n\t\t\t\t\t\t\t' height=' +\n\t\t\t\t\t\t\th +\n\t\t\t\t\t\t\t'><g><title>' +\n\t\t\t\t\t\t\ti.b.ratio +\n\t\t\t\t\t\t\t'</title><rect width=' +\n\t\t\t\t\t\t\tw +\n\t\t\t\t\t\t\t' height=' +\n\t\t\t\t\t\t\th +\n\t\t\t\t\t\t\t' fill=\"' +\n\t\t\t\t\t\t\tfillbg +\n\t\t\t\t\t\t\t'\"></rect>' +\n\t\t\t\t\t\t\t'<rect width=' +\n\t\t\t\t\t\t\tw * i.b.ratio +\n\t\t\t\t\t\t\t' height=' +\n\t\t\t\t\t\t\th +\n\t\t\t\t\t\t\t' fill=\"' +\n\t\t\t\t\t\t\tfill +\n\t\t\t\t\t\t\t'\"></rect>' +\n\t\t\t\t\t\t\t'</g></svg>'\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\treturn lst.join('<br>')\n\t\t\t}\n\t\t})\n\t}\n\ttk.svattr.push({\n\t\tlabel: 'Frame',\n\t\tget: m => {\n\t\t\tfunction label(f) {\n\t\t\t\tif (f == 0)\n\t\t\t\t\treturn (\n\t\t\t\t\t\t'<span style=\"white-space:nowrap;background-color:' +\n\t\t\t\t\t\tclient.coloroutframe +\n\t\t\t\t\t\t';font-size:80%;color:white;padding:1px 3px\">OUT of frame</span>'\n\t\t\t\t\t)\n\t\t\t\tif (f == 1)\n\t\t\t\t\treturn (\n\t\t\t\t\t\t'<span style=\"white-space:nowrap;background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';font-size:80%;color:white;padding:1px 3px\">IN frame</span>'\n\t\t\t\t\t)\n\t\t\t\tif (f == 2)\n\t\t\t\t\treturn (\n\t\t\t\t\t\t'<span style=\"white-space:nowrap;background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';font-size:80%;color:white;padding:1px 3px\">IN frame</span> <span style=\"font-size:80%;color:#858585\">promoter fusion</span>'\n\t\t\t\t\t)\n\t\t\t\tif (f == 3)\n\t\t\t\t\treturn (\n\t\t\t\t\t\t'<span style=\"white-space:nowrap;background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';font-size:80%;color:white;padding:1px 3px\">IN frame</span> <span style=\"font-size:80%;color:#858585\">alternative promoter</span>'\n\t\t\t\t\t)\n\t\t\t\treturn 'err (' + f + ')'\n\t\t\t}\n\t\t\tconst lst = []\n\t\t\tfor (const p of m.pairlst) {\n\t\t\t\tif (p.frame != undefined) {\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tframe: p.frame,\n\t\t\t\t\t\ta: p.a.name ? p.a.name : p.a.chr,\n\t\t\t\t\t\tb: p.b.name ? p.b.name : p.b.chr\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (lst.length == 1) return label(lst[0].frame)\n\t\t\treturn lst.map(l => l.a + '-' + l.b + ': ' + label(l.frame)).join('<br>')\n\t\t}\n\t})\n\tif (tk.ds && tk.ds.cohort && tk.ds.cohort.levels) {\n\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\tskipset.add(l.k)\n\t\t\tskipset.add(l.full)\n\t\t\ttk.svattr.push({\n\t\t\t\tlabel: l.label || l.k,\n\t\t\t\thide: l.hide,\n\t\t\t\tget: m =>\n\t\t\t\t\tm[l.k] ? m[l.k] + (l.full ? ' <span style=\"color:#858585;font-size:.8em\">' + m[l.full] + '</span>' : '') : ''\n\t\t\t})\n\t\t}\n\t}\n\tfor (const k in mlst[0]) {\n\t\tif (skipset.has(k)) continue\n\t\ttk.svattr.push({ label: k, get: m => m[k] })\n\t}\n}\n\nfunction caller_pmid(m) {\n\treturn {\n\t\tget: m => {\n\t\t\tif (!m.pmid) {\n\t\t\t\treturn ''\n\t\t\t}\n\t\t\tif (typeof m.pmid == 'number') {\n\t\t\t\treturn '<a target=_blank href=https://pubmed.ncbi.nlm.nih.gov/' + m.pmid + '>' + m.pmid + '</a>'\n\t\t\t}\n\t\t\tconst lst = m.pmid.split(',')\n\t\t\tconst out = []\n\t\t\tfor (const i of lst) {\n\t\t\t\tif (i == '') continue\n\t\t\t\tconst j = Number.parseInt(i)\n\t\t\t\tif (Number.isNaN(j)) {\n\t\t\t\t\tout.push(i)\n\t\t\t\t} else {\n\t\t\t\t\tout.push('<a target=_blank href=https://pubmed.ncbi.nlm.nih.gov/' + i + '>' + i + '</a>')\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn out.join(' ')\n\t\t},\n\t\tlabel: 'PubMed'\n\t}\n}\n\nfunction vcfsamplelistbutton(m, holder, tk) {\n\t/*\n\tfor sample objects about this variant loaded from cohort vcf\n\tat header of itemtable\n\tmake a sample button\n\tclick to list samples\n\n\tthe variant is present is because at least 1 of the sample passed sample annotation filter\n\tso don't show samples that are filtered!\n\t*/\n\n\tlet samplelst = m.sampledata\n\t// check against annotation filter\n\n\tif (\n\t\ttk.ds &&\n\t\ttk.ds.cohort &&\n\t\ttk.ds.cohort.annotation &&\n\t\ttk.ds.cohort.key4annotation &&\n\t\ttk.ds.cohort.sampleattribute &&\n\t\ttk.ds.cohort.sampleattribute.runtimelst\n\t) {\n\t\tsamplelst = []\n\t\tfor (const s0 of m.sampledata) {\n\t\t\tconst s0name = s0.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\tif (!s0name) continue\n\n\t\t\tconst av = tk.ds.cohort.annotation[s0name]\n\t\t\tif (av) {\n\t\t\t\tlet hidden = false\n\t\t\t\tfor (const attr of tk.ds.cohort.sampleattribute.runtimelst) {\n\t\t\t\t\tif (attr.key && attr.key.k && attr.key.hiddenvalues && attr.key.hiddenvalues.size) {\n\t\t\t\t\t\tconst v = av[attr.key.k]\n\t\t\t\t\t\tif (attr.key.hiddenvalues.has(v)) {\n\t\t\t\t\t\t\thidden = true\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (hidden) continue\n\t\t\t}\n\t\t\tsamplelst.push(s0)\n\t\t}\n\t}\n\n\tholder\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-right', '10px')\n\t\t.text(samplelst.length + ' sample' + (samplelst.length > 1 ? 's' : ''))\n\t\t.on('click', event => {\n\t\t\ttk.tktip.showunder(event.target).clear()\n\t\t\tconst table = tk.tktip.d.append('table')\n\t\t\tconst tr = table.append('tr').style('font-size', '.8em').style('color', '#858585')\n\t\t\ttr.append('td').text('Name')\n\t\t\ttr.append('td').text('Genotype')\n\n\t\t\tlet hasgt = false\n\t\t\tif (samplelst[0].DP != undefined) {\n\t\t\t\ttr.append('td').text('Read depth')\n\t\t\t\thasgt = true\n\t\t\t}\n\t\t\tlet hascount = false\n\t\t\tif (samplelst[0].allele2readcount) {\n\t\t\t\ttr.append('td').text('Allele read count')\n\t\t\t\thascount = true\n\t\t\t}\n\t\t\tfor (const s of samplelst) {\n\t\t\t\tconst tr = table.append('tr')\n\t\t\t\ttr.append('td').text(s.sampleobj.name)\n\t\t\t\ttr.append('td').style('padding-left', '10px').text(s.genotype)\n\t\t\t\tif (hasgt) {\n\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t.style('padding-left', '10px')\n\t\t\t\t\t\t.text(s.DP || '')\n\t\t\t\t}\n\t\t\t\tif (hascount) {\n\t\t\t\t\tconst lst = []\n\t\t\t\t\tfor (const a in s.allele2readcount) {\n\t\t\t\t\t\tlst.push(a + ':' + s.allele2readcount[a])\n\t\t\t\t\t}\n\t\t\t\t\ttr.append('td').style('padding-left', '10px').text(lst.join(', '))\n\t\t\t\t}\n\t\t\t}\n\t\t})\n}\n\nfunction vcfvepbutton(csqlst, holder, tk, headers) {\n\tholder\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-right', '10px')\n\t\t.text('VEP annotation')\n\t\t.on('click', event => {\n\t\t\ttk.tktip.clear()\n\t\t\ttk.tktip.showunder(event.target)\n\t\t\tfor (const item of csqlst) {\n\t\t\t\tlet blown = false\n\t\t\t\tlet thislabel\n\t\t\t\t{\n\t\t\t\t\tconst lst = []\n\t\t\t\t\tif (item.HGVSp) {\n\t\t\t\t\t\tlst.push('<span style=\"font-size:.7em;color:#858585\">HGVSp</span> ' + item.HGVSp)\n\t\t\t\t\t} else if (item.HGVSc) {\n\t\t\t\t\t\tlst.push('<span style=\"font-size:.7em;color:#858585\">HGVSc</span> ' + item.HGVSc)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlst.push('no_HGVS')\n\t\t\t\t\t}\n\t\t\t\t\tif (item.Consequence) {\n\t\t\t\t\t\tlst.push('<span style=\"font-size:.7em;color:#858585\">CONSEQUENCE</span> ' + item.Consequence)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlst.push('no_consequence')\n\t\t\t\t\t}\n\t\t\t\t\tthislabel = lst.join(' ')\n\t\t\t\t}\n\t\t\t\tconst box = tk.tktip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.style('margin', '5px')\n\t\t\t\t\t.html(thislabel)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (blown) {\n\t\t\t\t\t\t\tblown = false\n\t\t\t\t\t\t\tbox.html(thislabel)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tblown = true\n\t\t\t\t\t\t\tbox.text('')\n\t\t\t\t\t\t\tconst lst = []\n\t\t\t\t\t\t\tfor (const h of headers) {\n\t\t\t\t\t\t\t\tconst v = item[h.name]\n\t\t\t\t\t\t\t\tif (v) {\n\t\t\t\t\t\t\t\t\tlst.push({ k: h.name, v: v })\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tclient.make_table_2col(box, lst)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t}\n\t\t\t/*\n\t\t// show controls\n\t\tconst div=tk.tktip.d.append('div').style('margin-top','10px')\n\t\tfor(const h of headers) {\n\t\t\tconst row=div.append('div')\n\t\t\tconst id=Math.random()\n\t\t\tconst input=row.append('input')\n\t\t\t\t.attr('type','checkbox')\n\t\t\t\t.style('margin-right','5px')\n\t\t\t\t.attr('id',id)\n\t\t\t\t.on('change',(event)=>{\n\t\t\t\t\th.hidden = !event.target.checked\n\t\t\t\t\tshowtable()\n\t\t\t\t})\n\t\t\tif(!h.hidden) {\n\t\t\t\tinput.attr('checked',1)\n\t\t\t}\n\t\t\trow.append('label')\n\t\t\t\t.text(h.name)\n\t\t\t\t.attr('for',id)\n\t\t}\n\t\t*/\n\t\t})\n}\n\nfunction vcfannbutton(annolst, holder, tk, headers) {\n\tholder\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-right', '10px')\n\t\t.text('Annotation')\n\t\t.on('click', event => {\n\t\t\ttk.tktip.clear()\n\t\t\ttk.tktip.showunder(event.target)\n\t\t\tfor (const item of annolst) {\n\t\t\t\tlet blown = false\n\t\t\t\tlet thislabel\n\t\t\t\t{\n\t\t\t\t\tconst lst = []\n\t\t\t\t\tif (item['HGVS.p']) {\n\t\t\t\t\t\tlst.push('<span style=\"font-size:.7em;color:#858585\">HGVS.p</span> ' + item['HGVS.p'])\n\t\t\t\t\t} else if (item['HGVS.c']) {\n\t\t\t\t\t\tlst.push('<span style=\"font-size:.7em;color:#858585\">HGVS.c</span> ' + item['HGVS.c'])\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlst.push('no_HGVS')\n\t\t\t\t\t}\n\t\t\t\t\tif (item.Annotation) {\n\t\t\t\t\t\tlst.push('<span style=\"font-size:.7em;color:#858585\">Annotation</span> ' + item.Annotation)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlst.push('no_annotation')\n\t\t\t\t\t}\n\t\t\t\t\tthislabel = lst.join(' ')\n\t\t\t\t}\n\t\t\t\tconst box = tk.tktip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.style('margin', '5px')\n\t\t\t\t\t.html(thislabel)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (blown) {\n\t\t\t\t\t\t\tblown = false\n\t\t\t\t\t\t\tbox.html(thislabel)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tblown = true\n\t\t\t\t\t\t\tbox.text('')\n\t\t\t\t\t\t\tconst lst = []\n\t\t\t\t\t\t\tfor (const h of headers) {\n\t\t\t\t\t\t\t\tconst v = item[h.name]\n\t\t\t\t\t\t\t\tif (v) {\n\t\t\t\t\t\t\t\t\tlst.push({ k: h.name, v: v })\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tclient.make_table_2col(box, lst)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t}\n\t\t})\n}\n\nfunction variant2imgbutton(m, buttonrow, imgholder, tk, block) {\n\tlet loaded = false\n\n\tbuttonrow\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-right', '10px')\n\t\t.text('Image')\n\t\t.on('click', async () => {\n\t\t\tif (loaded) return\n\t\t\tloaded = true\n\t\t\tconst wait = imgholder.append('div').style('margin', '20px').text('Loading...')\n\t\t\ttry {\n\t\t\t\tconst data = await client.dofetch('img', {\n\t\t\t\t\tfile: [\n\t\t\t\t\t\ttk.variant2img.path,\n\t\t\t\t\t\tm.chr + '.' + (m.pos + 1) + '.' + m.ref + '.' + m.alt + '.' + tk.variant2img.ext\n\t\t\t\t\t].join('/')\n\t\t\t\t})\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\twait.remove()\n\t\t\t\timgholder\n\t\t\t\t\t.append('img')\n\t\t\t\t\t.attr('src', data.src)\n\t\t\t\t\t.style('width', data.size.width + 'px')\n\t\t\t\t\t.style('height', data.size.height + 'px')\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Error loading image')\n\t\t\t}\n\t\t})\n}\n\nfunction mayshowcovmafplot(m, tk, holder) {\n\tif (!tk.ds.vaf2coverageplot) {\n\t\treturn false\n\t}\n\tif (!m.sampledata) {\n\t\treturn false\n\t}\n\n\t/*\n\tmay show cov-maf plot for samples from a vcf variant\n\tplottable samples should have .DP and valid read count for this allele\n\n\tm.sampledata[ {} ]\n\t\t.sampleobj\n\t\t\t.<k4a>\n\t\t.DP\n\t\t.allele2readcount\n\n\tdivide samples to groups by sampletype, make separate plot for each group\n\t*/\n\n\tconst nostlst = []\n\t/*\n\tsamples without sampletype, or vaf2coverageplot.samplegroupkey is not set\n\t*/\n\n\tconst st2lst = {}\n\t/*\n\tk: sampletype\n\tv: list of samples\n\twill not use if no vaf2coverageplot.samplegroupkey\n\t*/\n\n\tconst categorycount = new Map() // use then vaf2coverageplot.categories is set\n\n\tlet err = 0\n\tfor (const s of m.sampledata) {\n\t\tif (!s.allele2readcount) {\n\t\t\t// this is required\n\t\t\terr++\n\t\t\tcontinue\n\t\t}\n\n\t\tif (s.DP == undefined) {\n\t\t\ts.DP = 0\n\t\t\tfor (const k in s.allele2readcount) {\n\t\t\t\ts.DP += s.allele2readcount[k]\n\t\t\t}\n\t\t}\n\n\t\t/*\n\t\tif alt allele is missing from the hash\n\t\ttreat the coverage of it as zero\n\t\t*/\n\t\tconst altv = s.allele2readcount[m.alt] || 0\n\n\t\tif (altv > s.DP) {\n\t\t\tconsole.log('alt coverage > DP: ' + altv + ' ' + s.DP)\n\t\t\tcontinue\n\t\t}\n\n\t\t// is a plottable sample\n\t\t// ss is object to go to plotter\n\t\tconst ss = {\n\t\t\tsampleobj: {},\n\t\t\tmut: altv,\n\t\t\ttotal: s.DP,\n\t\t\tmaf: s.DP == 0 ? 0 : altv / s.DP,\n\t\t\tgenotype: s.genotype\n\t\t}\n\n\t\t// transfer metadata\n\t\tif (s.sampleobj) {\n\t\t\tif (tk.ds.cohort && tk.ds.cohort.annotation && tk.ds.cohort.key4annotation) {\n\t\t\t\tconst k4a = s.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\t\tif (k4a) {\n\t\t\t\t\tconst n = tk.ds.cohort.annotation[k4a]\n\t\t\t\t\tif (n) {\n\t\t\t\t\t\tif (tk.ds.cohort.levels) {\n\t\t\t\t\t\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\t\t\t\t\t\tif (!n[l.k]) continue\n\t\t\t\t\t\t\t\tss.sampleobj[l.label || l.k] =\n\t\t\t\t\t\t\t\t\tn[l.k] +\n\t\t\t\t\t\t\t\t\t(l.full && n[l.full] ? ' <span style=\"font-size:.8em;color:#858585\">' + n[l.full] + '</span>' : '')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t// also add k4a\n\t\t\t\t\t\t\tss.sampleobj[tk.ds.cohort.key4annotation] = k4a\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tfor (const k in n) {\n\t\t\t\t\t\t\t\tss.sampleobj[k] = n[k]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tfor (const k in s.sampleobj) {\n\t\t\t\t\tss.sampleobj[k] = s.sampleobj[k]\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (tk.ds.vaf2coverageplot.categorykey && tk.ds.vaf2coverageplot.categories) {\n\t\t\t/*\n\t\t\ttry to assign color to this sample by category\n\t\t\thardcoded: .categorykey only found in .sampleobj but not ds.cohort.annotation\n\t\t\t*/\n\t\t\tconst k = ss.sampleobj[tk.ds.vaf2coverageplot.categorykey]\n\t\t\tif (k && tk.ds.vaf2coverageplot.categories[k]) {\n\t\t\t\t// is valid category, assign color\n\t\t\t\tss.color = tk.ds.vaf2coverageplot.categories[k].color\n\t\t\t\t// count 4 legend\n\t\t\t\tif (!categorycount.has(k)) {\n\t\t\t\t\tcategorycount.set(k, 0)\n\t\t\t\t}\n\t\t\t\tcategorycount.set(k, categorycount.get(k) + 1)\n\n\t\t\t\t// will swap the attribute\n\t\t\t\tdelete ss.sampleobj[tk.ds.vaf2coverageplot.categorykey]\n\t\t\t\tss.sampleobj[tk.ds.vaf2coverageplot.categorylabel] = k\n\t\t\t}\n\t\t}\n\n\t\tif (tk.ds.vaf2coverageplot.samplegroupkey) {\n\t\t\t// will try to group samples\n\t\t\t/*\n\t\t\thardcoded\n\t\t\tsamplegroupkey will only be taken from ss.sampleobj\n\t\t\tbut not ds.cohort.annotation\n\t\t\t*/\n\t\t\tif (ss.sampleobj && ss.sampleobj[tk.ds.vaf2coverageplot.samplegroupkey]) {\n\t\t\t\tconst k = ss.sampleobj[tk.ds.vaf2coverageplot.samplegroupkey]\n\t\t\t\tif (!st2lst[k]) {\n\t\t\t\t\tst2lst[k] = []\n\t\t\t\t}\n\t\t\t\tst2lst[k].push(ss)\n\t\t\t} else {\n\t\t\t\t// no sampletype\n\t\t\t\tnostlst.push(ss)\n\t\t\t}\n\t\t} else {\n\t\t\t// not to group samples\n\t\t\tnostlst.push(ss)\n\t\t}\n\t}\n\n\tif (err) {\n\t\tconsole.log('skipped ' + err + ' items')\n\t}\n\n\t// group to be plotted\n\tconst plotgroups = []\n\n\tif (nostlst.length) {\n\t\tplotgroups.push({\n\t\t\tname: 'no ' + (tk.ds.vaf2coverageplot.samplegroupkey || 'sampletype'),\n\t\t\tlst: nostlst\n\t\t})\n\t}\n\tfor (const k in st2lst) {\n\t\tplotgroups.push({\n\t\t\tname: k,\n\t\t\tlst: st2lst[k]\n\t\t})\n\t}\n\n\tif (plotgroups.length == 0) {\n\t\treturn false\n\t}\n\n\tif (categorycount.size > 0) {\n\t\t// will show legend for counts per category\n\t\tconst div = holder.append('div').style('margin', '20px 20px 0px 20px')\n\t\tfor (const [k, count] of categorycount) {\n\t\t\tconst c = tk.ds.vaf2coverageplot.categories[k]\n\t\t\tconst row = div.append('div').style('margin-bottom', '3px')\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.style('background-color', c.color)\n\t\t\t\t.html('&nbsp;&nbsp;')\n\t\t\t// stop showing #sample as people may confuse with #patient\n\t\t\t//.text(count)\n\t\t\trow\n\t\t\t\t.append('span')\n\t\t\t\t.style('color', c.color)\n\t\t\t\t.text(c.label || k)\n\t\t}\n\t}\n\n\tconst row = holder.append('div').style('margin-bottom', '10px')\n\n\timport('./old/plot.vaf2cov').then(plotter => {\n\t\t/*\n\t\timport plotter, then plot all groups\n\t\teach plot will return data point -> svg cross,\n\t\tso to enable mouse over a sample in one plot, and highlight samples from other plots of the same patient\n\t\t*/\n\n\t\tconst name2sgp = {}\n\n\t\tfor (const g of plotgroups) {\n\t\t\tlet div = row.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\n\t\t\tif (plotgroups.length > 1) {\n\t\t\t\t// more than 1 group, emphasis\n\t\t\t\tdiv\n\t\t\t\t\t.style('margin-right', '30px')\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('margin-top', '10px')\n\t\t\t\t\t.style('padding', '3px 10px')\n\t\t\t\t\t.style('background-color', '#aaa')\n\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t\t.text(g.name.toUpperCase())\n\t\t\t\tdiv = div.append('div').style('border', 'solid 1px #aaa')\n\t\t\t}\n\n\t\t\tconst arg = {\n\t\t\t\tholder: div,\n\t\t\t\tdata: g.lst,\n\t\t\t\tname: g.name,\n\t\t\t\ttip: tk.tktip,\n\t\t\t\tautomax: true,\n\t\t\t\tmouseover: d => {\n\t\t\t\t\tif (!d.sampleobj) return\n\t\t\t\t\tfor (const groupname in name2sgp) {\n\t\t\t\t\t\tif (groupname == g.name) continue\n\t\t\t\t\t\tname2sgp[groupname]\n\t\t\t\t\t\t\t.filter(d2 => {\n\t\t\t\t\t\t\t\treturn d2.sampleobj.patient == d.sampleobj.patient\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.each(d2 => {\n\t\t\t\t\t\t\t\td2.crosshair1.attr('transform', 'scale(2.5)')\n\t\t\t\t\t\t\t\td2.crosshair2.attr('transform', 'scale(2.5)')\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tmouseout: d => {\n\t\t\t\t\tif (!d.sampleobj) return\n\t\t\t\t\tfor (const groupname in name2sgp) {\n\t\t\t\t\t\tif (groupname == g.name) continue\n\t\t\t\t\t\tname2sgp[groupname]\n\t\t\t\t\t\t\t.filter(d2 => {\n\t\t\t\t\t\t\t\treturn d2.sampleobj.patient == d.sampleobj.patient\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.each(d2 => {\n\t\t\t\t\t\t\t\td2.crosshair1.attr('transform', 'scale(1)')\n\t\t\t\t\t\t\t\td2.crosshair2.attr('transform', 'scale(1)')\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tname2sgp[g.name] = plotter.default(arg)\n\t\t}\n\t})\n\treturn true\n}\n\nexport function query_vcfcohorttrack(m, tk, block) {\n\t/*\n\tquery shadow track to get sample data for cov-vaf plot\n\t*/\n\n\tconst vobj = tk.ds.vcfcohorttrack\n\n\treturn Promise.resolve()\n\t\t.then(() => {\n\t\t\tif (vobj.info) {\n\t\t\t\t// info already loaded for cohort vcf file, next\n\t\t\t\treturn null\n\t\t\t}\n\n\t\t\tconst par = {\n\t\t\t\tjwt: block.jwt,\n\t\t\t\tfile: vobj.file,\n\t\t\t\turl: vobj.url,\n\t\t\t\tindexURL: vobj.indexURL,\n\t\t\t\theader: 1\n\t\t\t}\n\n\t\t\t// info not loaded for cohort vcf\n\t\t\treturn fetch(\n\t\t\t\tnew Request(block.hostURL + '/vcf', {\n\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\tbody: JSON.stringify(par)\n\t\t\t\t})\n\t\t\t).then(data => {\n\t\t\t\treturn data.json()\n\t\t\t})\n\t\t})\n\t\t.then(data => {\n\t\t\tif (data == null) return\n\t\t\t// parse meta lines\n\t\t\tif (!data.metastr) throw { message: 'no meta lines for the cohort vcf file ' }\n\t\t\tif (!data.chrstr) throw { message: 'no chromosome names found for the cohort vcf file' }\n\t\t\tconst [info, format, samples, errs] = vcf.vcfparsemeta(data.metastr.split('\\n'))\n\t\t\tif (errs) throw { message: 'vcf meta error for the cohort vcf file: ' + errs.join('; ') }\n\t\t\tvobj.info = info\n\t\t\tvobj.format = format\n\n\t\t\tif (vobj.samplenamemap) {\n\t\t\t\tvobj.samples = samples.map(vobj.samplenamemap)\n\t\t\t} else {\n\t\t\t\tvobj.samples = samples\n\t\t\t}\n\n\t\t\tvobj.nochr = common.contigNameNoChr(block.genome, data.chrstr.split('\\n'))\n\n\t\t\treturn\n\t\t})\n\t\t.then(() => {\n\t\t\t// fetch sample data from cohort vcf\n\t\t\tconst par = {\n\t\t\t\tjwt: block.jwt,\n\t\t\t\tfile: vobj.file,\n\t\t\t\turl: vobj.url,\n\t\t\t\tindexURL: vobj.indexURL,\n\t\t\t\trglst: [\n\t\t\t\t\t{\n\t\t\t\t\t\tchr: vobj.nochr ? m.chr.replace('chr', '') : m.chr,\n\t\t\t\t\t\tstart: m.pos + 1,\n\t\t\t\t\t\tstop: m.pos + 1\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t\treturn fetch(\n\t\t\t\tnew Request(block.hostURL + '/vcf', {\n\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\tbody: JSON.stringify(par)\n\t\t\t\t})\n\t\t\t)\n\t\t\t\t.then(data => {\n\t\t\t\t\treturn data.json()\n\t\t\t\t})\n\t\t\t\t.then(data => {\n\t\t\t\t\tif (data.error) throw { message: 'Error querying vcf file: ' + data.error }\n\t\t\t\t\tconst lines = data.linestr ? data.linestr.trim().split('\\n') : []\n\t\t\t\t\tfor (const line of lines) {\n\t\t\t\t\t\tconst [err, mlst, altinvalid] = vcf.vcfparseline(line, vobj)\n\t\t\t\t\t\tfor (const m2 of mlst) {\n\t\t\t\t\t\t\tif (m2.pos == m.pos && m2.ref == m.ref && m2.alt == m.alt) {\n\t\t\t\t\t\t\t\treturn m2\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\treturn null\n\t\t\t\t})\n\t\t})\n}\n\nfunction make_url4variant(holder, m, items) {\n\tfor (const item of items) {\n\t\tif (!item.makeurl) continue\n\t\tconst url = item.makeurl(m)\n\t\tif (!url) {\n\t\t\t// somehow this variant cannot yield a url, ignore\n\t\t\tcontinue\n\t\t}\n\t\tholder\n\t\t\t.append('a')\n\t\t\t.attr('href', url)\n\t\t\t.attr('target', '_blank')\n\t\t\t.text(item.makelabel ? item.makelabel(m) : item.label || 'link')\n\t\t\t.style('margin-right', '10px')\n\t}\n}\n\nfunction make_button4variant(holder, m, lst) {\n\tlst.forEach(item => {\n\t\tif (!item.makebutton) return\n\t\tconst div = holder.append('div').style('display', 'inline-block').style('margin', '0px 10px 2px 3px')\n\t\titem.makebutton(m, div.node())\n\t})\n}\n\nfunction mayshowgermline2dvaf(m, tk, holder) {\n\tconst cfg = tk.ds.germline2dvafplot\n\tif (!cfg) return false\n\n\tconst ik = cfg.individualkey\n\n\tconst individualset = new Map()\n\n\tlet err = 0\n\tfor (const s of m.sampledata) {\n\t\tif (s.DP == undefined || !s.allele2readcount) {\n\t\t\terr++\n\t\t\tcontinue\n\t\t}\n\t\t/*\n\t\tif alt allele is missing from the hash\n\t\ttreat the coverage of it as zero\n\t\t*/\n\t\tconst altv = s.allele2readcount[m.alt] || 0\n\t\tif (altv > s.DP) {\n\t\t\tconsole.log('alt coverage > DP: ' + altv + ' ' + s.DP)\n\t\t\tcontinue\n\t\t}\n\n\t\tconst individual = s.sampleobj[ik]\n\t\tif (!individual) {\n\t\t\tcontinue\n\t\t}\n\t\tconst sampletype = s.sampleobj[cfg.sampletypekey]\n\t\tif (!sampletype) {\n\t\t\tcontinue\n\t\t}\n\t\tif (!individualset.has(individual)) {\n\t\t\tconst obj = {\n\t\t\t\tsampletypes: {}\n\t\t\t}\n\t\t\tfor (const k in s.sampleobj) {\n\t\t\t\tobj[k] = s.sampleobj[k]\n\t\t\t}\n\n\t\t\tindividualset.set(individual, obj)\n\t\t}\n\t\tindividualset.get(individual).sampletypes[sampletype] = {\n\t\t\ttotal: s.DP,\n\t\t\tvaf: s.DP == 0 ? 0 : altv / s.DP\n\t\t}\n\t}\n\n\tif (err) {\n\t\tconsole.log(err + ' samples has no valid DP/allele2readcount')\n\t}\n\n\t// for yleftsampletype and yrightsampletype, each add a new datapoint\n\tconst data = []\n\tfor (const [k, obj] of individualset) {\n\t\tif (!obj.sampletypes[cfg.xsampletype]) {\n\t\t\tcontinue\n\t\t}\n\n\t\tif (obj.sampletypes[cfg.yleftsampletype]) {\n\t\t\tconst n = {}\n\t\t\tfor (const k in obj) {\n\t\t\t\tn[k] = obj[k]\n\t\t\t}\n\t\t\tn.sampletypes = {}\n\t\t\tn.sampletypes[cfg.xsampletype] = obj.sampletypes[cfg.xsampletype]\n\t\t\tn.sampletypes[cfg.yleftsampletype] = obj.sampletypes[cfg.yleftsampletype]\n\t\t\tdata.push(n)\n\t\t}\n\n\t\tif (cfg.yrightsampletype && obj.sampletypes[cfg.yrightsampletype]) {\n\t\t\tconst n = {}\n\t\t\tfor (const k in obj) {\n\t\t\t\tn[k] = obj[k]\n\t\t\t}\n\t\t\tn.sampletypes = {}\n\t\t\tn.sampletypes[cfg.xsampletype] = obj.sampletypes[cfg.xsampletype]\n\t\t\tn.sampletypes[cfg.yrightsampletype] = obj.sampletypes[cfg.yrightsampletype]\n\t\t\tdata.push(n)\n\t\t}\n\t}\n\tif (data.length) {\n\t\tconst div = holder.append('div').style('display', 'inline-block')\n\t\timport('./old/plot.2dvaf').then(p => {\n\t\t\tp.default(data, cfg, div)\n\t\t})\n\t\treturn true\n\t}\n\treturn false\n}\n\nfunction mayshowgenotype2boxplot(m, tk, holder) {\n\tconst cfg = tk.ds.genotype2boxplot\n\tif (!cfg) return false\n\n\tif (cfg.boxplotvaluekey) {\n\t\tconst v = m.info[cfg.boxplotvaluekey]\n\t\tif (!v) return false\n\t\tconst tmp = v.split('|')\n\t\tconst plots = []\n\t\tfor (const s of tmp) {\n\t\t\tconst x = s.split('/')\n\n\t\t\tconst p1 = Number.parseFloat(x[1])\n\t\t\tconst p2 = Number.parseFloat(x[2])\n\t\t\tconst p3 = Number.parseFloat(x[3])\n\t\t\tconst p4 = Number.parseFloat(x[4])\n\t\t\tconst p5 = Number.parseFloat(x[5])\n\t\t\tif (Number.isNaN(p1) || Number.isNaN(p2) || Number.isNaN(p3) || Number.isNaN(p4) || Number.isNaN(p5)) {\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tplots.push({\n\t\t\t\tlabel: x[0],\n\t\t\t\tcolor: '#4F8F38',\n\t\t\t\tminvalue: p1,\n\t\t\t\tmaxvalue: p5,\n\t\t\t\tpercentile: {\n\t\t\t\t\tp05: p1,\n\t\t\t\t\tp25: p2,\n\t\t\t\t\tp50: p3,\n\t\t\t\t\tp75: p4,\n\t\t\t\t\tp95: p5\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\tconst div = holder.append('div').style('display', 'inline-block')\n\t\timport('./old/plot.boxplot').then(p => {\n\t\t\tconst err = p.default({\n\t\t\t\tholder: div,\n\t\t\t\taxislabel: cfg.axislabel,\n\t\t\t\tlist: plots\n\t\t\t})\n\t\t\tif (err) {\n\t\t\t\tclient.sayerror(div, 'Boxplot: ' + err)\n\t\t\t}\n\t\t})\n\t\treturn true\n\t}\n\n\tif (!tk.ds.cohort || !tk.ds.cohort.annotation || !tk.ds.cohort.key4annotation) {\n\t\tconsole.log('genotype2boxplot but ds.cohort is incomplete')\n\t\treturn false\n\t}\n\n\tconst gt2samples = new Map()\n\tm.sampledata.forEach(s => {\n\t\tif (!s.genotype) return\n\t\tconst k4a = s.sampleobj[tk.ds.cohort.key4annotation]\n\t\tif (!k4a) return\n\t\tconst n = tk.ds.cohort.annotation[k4a]\n\t\tif (!n) return\n\t\tconst value = n[cfg.sampleannotationkey]\n\t\tif (!Number.isFinite(value)) return\n\t\tif (!gt2samples.has(s.genotype)) {\n\t\t\tgt2samples.set(s.genotype, [])\n\t\t}\n\t\tgt2samples.get(s.genotype).push({\n\t\t\tvalue: value,\n\t\t\tkey: k4a\n\t\t})\n\t})\n\n\tif (gt2samples.size == 0) {\n\t\treturn false\n\t}\n\n\tconst groups = []\n\tfor (const [genotype, samples] of gt2samples) {\n\t\tgroups.push({\n\t\t\tlabel: genotype,\n\t\t\tcolor: '#4F8F38',\n\t\t\tsamples: samples\n\t\t})\n\t}\n\tconst div = holder.append('div').style('display', 'inline-block')\n\timport('./old/plot.boxplot').then(p => {\n\t\tconst err = p.default({\n\t\t\tholder: div,\n\t\t\taxislabel: cfg.axislabel,\n\t\t\tlist: groups\n\t\t})\n\t\tif (err) {\n\t\t\tclient.sayerror(div, 'Boxplot: ' + err)\n\t\t}\n\t})\n\treturn true\n}\n\nfunction singleSample2table(m, tk, holder) {\n\t// only 1 sample\n\tconst s = m.sampledata[0]\n\tconst lst = []\n\tif (s.genotype) {\n\t\tlst.push({ k: 'genotype', v: s.genotype })\n\t}\n\tif (s.DP != undefined) {\n\t\tlst.push({ k: 'total reads', v: s.DP })\n\t}\n\tif (s.allele2readcount && s.allele2readcount[m.alt] != undefined) {\n\t\tlst.push({ k: 'alt reads', v: s.allele2readcount[m.alt] })\n\t} else {\n\t\tmay_addformat_singlesample(lst, m, tk)\n\t}\n\tif (s.sampleobj) {\n\t\tif (tk.ds.cohort && tk.ds.cohort.annotation && tk.ds.cohort.key4annotation) {\n\t\t\tconst k4a = s.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\tif (k4a) {\n\t\t\t\t// has valid key\n\n\t\t\t\tlst.push({ k: tk.ds.cohort.key4annotation, v: k4a })\n\n\t\t\t\tconst na = tk.ds.cohort.annotation[k4a]\n\n\t\t\t\tif (na) {\n\t\t\t\t\t// can find annotation\n\n\t\t\t\t\tif (tk.ds.cohort.levels) {\n\t\t\t\t\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\t\t\t\t\tif (!na[l.k]) continue\n\n\t\t\t\t\t\t\tlst.push({\n\t\t\t\t\t\t\t\tk: l.label || l.k,\n\t\t\t\t\t\t\t\tv:\n\t\t\t\t\t\t\t\t\tna[l.k] +\n\t\t\t\t\t\t\t\t\t(l.full && na[l.full] ? ' <span style=\"font-size:.8em;color:#858585\">' + na[l.full] + '</span>' : '')\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// no levels, show all from annotation\n\t\t\t\t\t\tfor (const k in na) {\n\t\t\t\t\t\t\tif (k == 'color') continue\n\t\t\t\t\t\t\tlst.push({ k: k, v: na[k] })\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (s.sampleobj.name) {\n\t\t\tlst.push({ k: 'name', v: s.sampleobj.name })\n\t\t}\n\t}\n\tclient.make_table_2col(holder, lst)\n}\n\nfunction may_addformat_singlesample(lst, m, tk) {\n\t// quick fix: may add format\n\tlet vcfobj\n\tif (m.vcfid && tk.ds && tk.ds.id2vcf) vcfobj = tk.ds.id2vcf[m.vcfid]\n\tif (!vcfobj) return\n\tif (!vcfobj.format) return\n\tconst s = m.sampledata[0]\n\tfor (const formatfield in vcfobj.format) {\n\t\tconst formatdesc = vcfobj.format[formatfield]\n\t\tif (!(formatfield in s)) continue\n\t\t/* following are duplicated from block.mds.svcnv.clickitem.js, lines 1629\n\t\t */\n\t\t// if the FORMAT has per-allele value, like AD in vcf 4.2+\n\t\tlet isperallelevalue = formatdesc.Number == 'R' || formatdesc.Number == 'A'\n\t\tif (!isperallelevalue) {\n\t\t\tif (formatfield == 'AD') {\n\t\t\t\t// vcf 4.1 has AD as '.'\n\t\t\t\tisperallelevalue = true\n\t\t\t}\n\t\t}\n\n\t\tif (isperallelevalue) {\n\t\t\t// per allele value\n\n\t\t\tconst alleles = []\n\t\t\tconst values = []\n\t\t\tlet altvalue\n\n\t\t\t// add alt first\n\t\t\tfor (const ale in s[formatfield]) {\n\t\t\t\tif (ale == m.ref) continue\n\t\t\t\talleles.push(ale)\n\t\t\t\taltvalue = s[formatfield][ale]\n\t\t\t\tvalues.push(altvalue)\n\t\t\t}\n\n\t\t\t// add ref after alt\n\t\t\tconst refvalue = s[formatfield][m.ref]\n\t\t\tif (refvalue != undefined) {\n\t\t\t\talleles.push(m.ref)\n\t\t\t\tvalues.push(refvalue)\n\t\t\t}\n\n\t\t\tlet barsvg\n\t\t\tif (refvalue + altvalue > 0) {\n\t\t\t\tbarsvg = client.fillbar(null, { f: altvalue / (altvalue + refvalue) })\n\t\t\t}\n\n\t\t\tlst.push({\n\t\t\t\tk: formatfield,\n\t\t\t\tv:\n\t\t\t\t\t(barsvg ? barsvg + ' ' : '') +\n\t\t\t\t\t'<span style=\"font-size:.8em;opacity:.5\">' +\n\t\t\t\t\talleles.join(' / ') +\n\t\t\t\t\t'</span> ' +\n\t\t\t\t\tvalues.join(' / ') +\n\t\t\t\t\t(formatdesc.Description\n\t\t\t\t\t\t? ' <span style=\"font-size:.7em;opacity:.5\">' + formatdesc.Description + '</span>'\n\t\t\t\t\t\t: '')\n\t\t\t})\n\t\t} else {\n\t\t\tlst.push({\n\t\t\t\tk: formatfield,\n\t\t\t\tv: s[formatfield]\n\t\t\t})\n\t\t}\n\t}\n}\n\nfunction handle_samplecart(mlst, holder, tk, block) {\n\tif (!block.samplecart || !tk.ds || !tk.ds.sampleselectable) return\n\t/* select sample API applicable to this track\n\twill make one single button for selecting sample, independent of how many datatypes\n\t*/\n\tconst sampleset = new Set()\n\tfor (const m of mlst) {\n\t\tif (m.sample) {\n\t\t\t// FIXME hardcoded attribute\n\t\t\tsampleset.add(m.sample)\n\t\t}\n\t}\n\tif (sampleset.size == 0) {\n\t\t// no samples\n\t\treturn\n\t}\n\t// note for selection, try to use mname\n\tconst nameset = new Set()\n\tfor (const m of mlst) {\n\t\tconst classlab = common.mclass[m.class].label\n\t\tlet thisnote\n\t\tif (m.dt == common.dtfusionrna || m.dt == common.dtsv) {\n\t\t\tif (m.mname) {\n\t\t\t\tif (m.useNterm) {\n\t\t\t\t\tthisnote = (block.usegm ? block.usegm.name + '-' : '') + m.mname + ' ' + classlab\n\t\t\t\t} else {\n\t\t\t\t\tthisnote = m.mname + (block.usegm ? '-' + block.usegm.name : '') + ' ' + classlab\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthisnote = (block.usegm ? block.usegm.name : '') + ' ' + classlab\n\t\t\t}\n\t\t} else {\n\t\t\tthisnote = (m.mname ? m.mname + ' ' : '') + classlab + (block.usegm ? ' in ' + block.usegm.name : '')\n\t\t}\n\t\tnameset.add(thisnote)\n\t}\n\tlet note\n\tif (nameset.size == 1) {\n\t\tnote = 'having ' + [...nameset][0]\n\t} else {\n\t\tnote = 'having mutations' + (block.usegm ? ' in ' + block.usegm.name : '')\n\t}\n\n\tblock.samplecart.setBtns({\n\t\tsamplelst: [...sampleset],\n\t\tid: nameset.size ? [...nameset][0] : block.usegm ? block.usegm.name : '',\n\t\tbasket: 'Gene Mutation',\n\t\tcontainer: holder.append('div').style('margin-left', '10px').append('div')\n\t})\n}\n", "import * as client from './client'\nimport * as vcf from '#shared/vcf.js'\nimport * as coord from './coord'\nimport * as common from '#shared/common.js'\nimport { load2tk } from './block.ds'\n\n/*\n\nload vcf for vcf track, should be custom track from embedding api\n\nif has vcfcohorttrack, server will not preload the header, must be loaded here along with first data request\n\n\n********************** EXPORTED\n\nloadvcftk\ndata2tk\n\n\n*/\n\nexport function loadvcftk(block, tk) {\n\t// single file\n\n\tlet vcfconfig = null\n\tfor (const id in tk.ds.id2vcf) {\n\t\tvcfconfig = tk.ds.id2vcf[id]\n\t}\n\tif (!vcfconfig) {\n\t\tblock.tkcloakoff(tk, { error: 'no vcf config found' })\n\t\treturn\n\t}\n\n\tPromise.resolve()\n\t\t.then(() => {\n\t\t\tif (!vcfconfig.headernotloaded) return\n\t\t\tdelete vcfconfig.headernotloaded\n\t\t\tconst arg = ['genome=' + block.genome.name]\n\t\t\tif (vcfconfig.file) {\n\t\t\t\targ.push('file=' + vcfconfig.file)\n\t\t\t} else {\n\t\t\t\targ.push('url=' + vcfconfig.url)\n\t\t\t\tif (vcfconfig.indexURL) arg.push('indexURL=' + vcfconfig.indexURL)\n\t\t\t}\n\t\t\treturn client.dofetch2('vcfheader?' + arg.join('&')).then(data => {\n\t\t\t\tif (data.error) throw { message: data.error }\n\t\t\t\tif (!data.metastr) throw { message: 'no meta lines for vcf file ' + tk.name }\n\t\t\t\tconst [info, format, samples, errs] = vcf.vcfparsemeta(data.metastr.split('\\n'))\n\t\t\t\tif (errs) throw { error: 'vcf meta error for file ' + tk.name + ': ' + errs.join('; ') }\n\t\t\t\tvcfconfig.info = info\n\t\t\t\tvcfconfig.format = format\n\t\t\t\tif (vcfconfig.samplenamemap) {\n\t\t\t\t\tvcfconfig.samples = samples.map(vcfconfig.samplenamemap)\n\t\t\t\t} else {\n\t\t\t\t\tvcfconfig.samples = samples\n\t\t\t\t}\n\t\t\t\tvcfconfig.nochr = data.nochr\n\t\t\t})\n\t\t})\n\t\t.then(() => {\n\t\t\t// load m data for vcf\n\t\t\tconst arg = {\n\t\t\t\tfile: vcfconfig.file,\n\t\t\t\turl: vcfconfig.url,\n\t\t\t\tindexURL: vcfconfig.indexURL,\n\t\t\t\trglst: block.tkarg_maygm(tk)\n\t\t\t}\n\t\t\tif (vcfconfig.nochr) {\n\t\t\t\tfor (const r of arg.rglst) {\n\t\t\t\t\tr.chr = r.chr.replace('chr', '')\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn client.dofetch2('vcf', { method: 'POST', body: JSON.stringify(arg) }).then(data => {\n\t\t\t\tif (data.error) throw { message: data.error }\n\t\t\t\tconst lines = data.linestr ? data.linestr.trim().split('\\n') : []\n\t\t\t\tload2tk([{ vcfid: vcfconfig.vcfid, lines: lines }], block, tk)\n\t\t\t\treturn\n\t\t\t})\n\t\t})\n\t\t.catch(err => {\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t\treturn err.message\n\t\t})\n\t\t.then(errmsg => {\n\t\t\tblock.tkcloakoff(tk, { error: errmsg })\n\t\t})\n}\n\nexport function data2tk(data, tk, block) {\n\tconst vcfconfig = tk.ds.id2vcf[data.vcfid]\n\tif (!vcfconfig) {\n\t\tblock.error('vcf not found by id: ' + data.vcfid)\n\t\treturn\n\t}\n\tif (!data.lines) {\n\t\tblock.error('no vcf lines from vcf file ' + data.vcfid)\n\t\treturn\n\t}\n\n\tconst errors = []\n\n\tfor (const line of data.lines) {\n\t\tconst [errmsg, mlst, altinvalid] = vcf.vcfparseline(line, vcfconfig)\n\t\tif (errmsg) {\n\t\t\terrors.push(errmsg)\n\t\t}\n\t\tif (!mlst) {\n\t\t\t// error\n\t\t\tcontinue\n\t\t}\n\n\t\tfor (const m of mlst) {\n\t\t\tif (m.alt == 'NON_REF') {\n\t\t\t\t// discard such from gVCF\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (tk.ds.discardsymbolicallele && m.issymbolicallele) {\n\t\t\t\t// user setting\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (block.usegm) {\n\t\t\t\tconst t = coord.genomic2gm(m.pos, block.usegm)\n\t\t\t\tm.rnapos = t.rnapos\n\t\t\t\tm.aapos = t.aapos\n\t\t\t}\n\t\t\tm.vcfid = data.vcfid\n\n\t\t\t/* what problem is this?\n\t\t\tif(m2.ref.length>m2.alt.length) {\n\t\t\t\tconst nt1=m2.ref[0]\n\t\t\t\tconst nt2=m2.alt[0]\n\t\t\t\tif(common.basecolor[nt1] && common.basecolor[nt2] && nt1==nt2) {\n\t\t\t\t\tis small deletion, both alleles are valid nucleotides\n\t\t\t\t\tfirst nt of both alleles are the same and it's the padding base\n\t\t\t\t\ttrim the padding base, shift the m.pos\n\t\t\t\t\tm2.ref=m2.ref.substr(1)\n\t\t\t\t\tif(m2.alt.length==1) {\n\t\t\t\t\t\tm2.alt='-'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tm2.alt=m2.alt.substr(1)\n\t\t\t\t\t}\n\t\t\t\t\tm2.pos++\n\t\t\t\t\tif(block.usegm) {\n\t\t\t\t\t\tconst t=coord.genomic2gm(m2.pos,block.usegm)\n\t\t\t\t\t\tm2.rnapos=t.rnapos\n\t\t\t\t\t\tm2.aapos=t.aapos\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\t*/\n\n\t\t\tcommon.vcfcopymclass(m, block)\n\n\t\t\ttk.mlst.push(m)\n\t\t}\n\t}\n\tif (!tk.dstk_novcferror && errors.length) {\n\t\tblock.error(\n\t\t\terrors[0] + (errors.length == 1 ? '' : ' and ' + (errors.length - 1) + ' more errors with the VCF track')\n\t\t)\n\t}\n}\n", "import { select as d3select } from 'd3-selection'\nimport { stratify, partition } from 'd3-hierarchy'\nimport { arc as d3arc } from 'd3-shape'\nimport { rgb as d3rgb } from 'd3-color'\nimport { itemtable } from './block.ds.itemtable'\nimport { stratinput } from '#shared/tree.js'\nimport { scaleOrdinal } from 'd3-scale'\nimport { schemeCategory10 } from 'd3-scale-chromatic'\nimport * as client from './client'\n\nexport default function (tk, block, arg) {\n\t/*\narg:\n\t.cx\n\t.cy\n\t\tcircle center x/y\n\t\toffset in tk.glider\n\t.mlst\n\t\tfrom tk.mlst[]\n\t.label\n\t.cohort\n\t\t.root\n\t\t\tif available, the cohort has all its samples stratified by levels[], and ready to present percentage in given sub set\n\t\t.levels[]\n\t\t.key2color - hardcoded colors\n\t\t.suncolor\n\n\t.noclickring\n\t.m2detail\n*/\n\n\tif (!arg.cohort) {\n\t\tconsole.error('arg.cohort missing')\n\t\treturn\n\t}\n\tif (!arg.cohort.levels) {\n\t\tconsole.error('arg.cohort.levels missing')\n\t\treturn\n\t}\n\n\tif (!arg.cohort.key2color && !arg.cohort.suncolor) {\n\t\t// auto color maker\n\t\targ.cohort.suncolor = scaleOrdinal(schemeCategory10)\n\t}\n\n\tlet itemlst\n\n\tif (!arg.cohort.annotation) {\n\t\titemlst = arg.mlst\n\t\t// itemlst must not be empty\n\t} else {\n\t\tif (!arg.cohort.key4annotation) {\n\t\t\tconsole.error('arg.cohort.key4annotation missing')\n\t\t\treturn\n\t\t}\n\t\t/*\n\tmlst:\n\t\tfor official ds with maf-db:\n\t\t\tone m is a variant in a sample\n\t\tfor multi-sample vcf:\n\t\t\tm.sampledata has per-sample info\n\twill normalize such and put to itemlst, each contains necessary annotation that match .cohort.levels and can be used to make sunburst\n\t*/\n\n\t\titemlst = []\n\n\t\tif (arg.mlst[0].sampledata) {\n\t\t\t// multi-sample vcf\n\t\t\tfor (const m of arg.mlst) {\n\t\t\t\tif (!m.sampledata) {\n\t\t\t\t\t// error\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\tconst k4a = s.sampleobj[arg.cohort.key4annotation]\n\t\t\t\t\tif (!k4a) {\n\t\t\t\t\t\t// this sample dont map to a proper key for cohort.annotation\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tconst sanno = arg.cohort.annotation[k4a]\n\t\t\t\t\tif (!sanno) {\n\t\t\t\t\t\t// not annotated\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tconst s2 = {\n\t\t\t\t\t\tk4a: k4a\n\t\t\t\t\t}\n\t\t\t\t\tfor (const l of arg.cohort.levels) {\n\t\t\t\t\t\ts2[l.k] = sanno[l.k]\n\t\t\t\t\t\tif (l.full) {\n\t\t\t\t\t\t\ts2[l.full] = sanno[l.full]\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\titemlst.push(s2)\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t// each m is one variant per sample\n\t\t\tfor (const m of arg.mlst) {\n\t\t\t\tconst k4a = m[arg.cohort.key4annotation]\n\t\t\t\tif (!k4a) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst sanno = arg.cohort.annotation[k4a]\n\t\t\t\tif (!sanno) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst s2 = {\n\t\t\t\t\tk4a: k4a\n\t\t\t\t}\n\t\t\t\tfor (const l of arg.cohort.levels) {\n\t\t\t\t\ts2[l.k] = sanno[l.k]\n\t\t\t\t\tif (l.full) {\n\t\t\t\t\t\ts2[l.full] = sanno[l.full]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\titemlst.push(s2)\n\t\t\t}\n\t\t}\n\n\t\tif (itemlst.length == 0) {\n\t\t\t/*\n\t\tsince itemlst is recalculated, it maybe empty\n\t\tterminate\n\t\t*/\n\t\t\tif (arg.m2detail) {\n\t\t\t\titemtable({\n\t\t\t\t\tmlst: [arg.m2detail],\n\t\t\t\t\tpane: true,\n\t\t\t\t\tx: arg.cx,\n\t\t\t\t\ty: arg.cy,\n\t\t\t\t\ttk: tk,\n\t\t\t\t\tblock: block\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\titemtable({\n\t\t\t\t\tmlst: arg.mlst,\n\t\t\t\t\tpane: true,\n\t\t\t\t\tx: arg.cx,\n\t\t\t\t\ty: arg.cy,\n\t\t\t\t\ttk: tk,\n\t\t\t\t\tblock: block\n\t\t\t\t})\n\t\t\t}\n\t\t\treturn\n\t\t}\n\t}\n\n\tlet cx = arg.cx,\n\t\tcy = arg.cy,\n\t\tdur1 = 500,\n\t\tdur2 = 250\n\tconst g = tk.glider.append('g').attr('transform', 'translate(' + cx + ',' + cy + ')')\n\tconst pica = tk.pica\n\tconst eye = g.append('g')\n\tconst ring = g.append('g')\n\tconst sun = {\n\t\tg: g,\n\t\teye: eye,\n\t\tring: ring,\n\t\tpica: pica,\n\t\tbusy: false\n\t}\n\n\tlet radius = Math.log(itemlst.length) * 24\n\tif (radius > tk.height * 0.42) {\n\t\tradius = tk.height * 0.42\n\t} else if (radius < tk.height * 0.2) {\n\t\tradius = tk.height * 0.2\n\t}\n\t// radius is set, shift g if it get outside\n\tlet newcx = cx,\n\t\tnewcy = cy\n\tif (cx - radius < 0) {\n\t\tnewcx = radius\n\t} else if (cx + radius > block.width) {\n\t\tnewcx = block.width - radius\n\t}\n\tif (cy - radius < 0) {\n\t\tnewcy = radius\n\t} else if (cy + radius > tk.height) {\n\t\tnewcy = tk.height - radius\n\t}\n\tif (newcx != cx || newcy != cy) {\n\t\tg.transition()\n\t\t\t.delay(dur1 + dur2)\n\t\t\t.attr('transform', 'translate(' + newcx + ',' + newcy + ')')\n\t\tcx = newcx\n\t\tcy = newcy\n\t}\n\t// hierarchy\n\tconst dat = stratinput(itemlst, arg.cohort.levels)\n\tconst root = stratify()(dat)\n\troot.sum(i => i.value)\n\troot.sort((a, b) => b.value - a.value)\n\tpartition().size([1, Math.pow(radius, 2)])(root)\n\t// blocker\n\teye.append('circle').attr('r', radius).attr('fill', 'white').attr('fill-opacity', 0)\n\n\tlet emptyspace\n\tconst arcfunc = d3arc()\n\t\t.startAngle(d => Math.PI * 2 * d.x0)\n\t\t.endAngle(d => Math.PI * 2 * d.x1)\n\t\t.innerRadius(d => {\n\t\t\tif (!d.parent) {\n\t\t\t\temptyspace = Math.sqrt(d.y1) - radius / 15\n\t\t\t\treturn emptyspace\n\t\t\t}\n\t\t\treturn Math.sqrt(d.y0)\n\t\t})\n\t\t.outerRadius(d => {\n\t\t\td.outradius = Math.sqrt(d.y1)\n\t\t\treturn d.outradius\n\t\t})\n\n\tring\n\t\t.selectAll()\n\t\t.data(root.descendants())\n\t\t.enter()\n\t\t.append('path')\n\t\t.attr('d', arcfunc)\n\t\t.attr('stroke', 'white')\n\t\t.attr('fill', d => {\n\t\t\tif (!d.parent) {\n\t\t\t\t// is root\n\t\t\t\treturn 'white'\n\t\t\t}\n\t\t\tlet key\n\t\t\tif (d.children) {\n\t\t\t\tkey = d.id\n\t\t\t} else {\n\t\t\t\tif (!d.parent.parent) {\n\t\t\t\t\t// parent is root, still use self\n\t\t\t\t\tkey = d.id\n\t\t\t\t} else {\n\t\t\t\t\tkey = d.parent.id\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// what color\n\t\t\tlet c\n\t\t\tif (arg.cohort.key2color) {\n\t\t\t\tc = arg.cohort.key2color[key]\n\t\t\t\tif (!c) {\n\t\t\t\t\tconsole.log(key)\n\t\t\t\t\tc = '#858585'\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tc = arg.cohort.suncolor(key)\n\t\t\t}\n\t\t\td._color = c\n\n\t\t\treturn c\n\t\t})\n\t\t.on('mouseover', (event, d) => {\n\t\t\tif (!d.parent) return\n\t\t\tif (sun.busy) return\n\n\t\t\tevent.target.setAttribute('fill', d3rgb(d._color).darker(0.5).toString())\n\t\t\tslicemouseover(d, pica, arg, cx, cy, tk, block)\n\t\t})\n\t\t.on('mouseout', (event, d) => {\n\t\t\tpica.g.selectAll('*').remove()\n\t\t\tif (!d.parent) return\n\t\t\tevent.target.setAttribute('fill', d._color)\n\t\t})\n\n\t\t.on('click', (event, d) => {\n\t\t\t// clicking on slice\n\t\t\tif (arg.noclickring) {\n\t\t\t\t// no clicking rings\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!d.parent) {\n\t\t\t\t// root not clickable\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (arg.cohort.annotation) {\n\t\t\t\t// external annotation\n\t\t\t\tif (d.data.lst.length == 1) {\n\t\t\t\t\t// single sample\n\t\t\t\t\tshowsinglesample(d.data.lst[0].k4a, arg.cohort.annotation[d.data.lst[0].k4a], event.clientX, event.clientY)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tshowmanysample(d.data.lst, arg.cohort, event.clientX, event.clientY)\n\t\t\t\treturn\n\t\t\t}\n\t\t\t// old style official ds\n\t\t\titemtable({\n\t\t\t\tmlst: d.data.lst,\n\t\t\t\tx: event.clientX,\n\t\t\t\ty: event.clientY,\n\t\t\t\ttk: tk,\n\t\t\t\tblock: block,\n\t\t\t\tpane: true\n\t\t\t})\n\t\t})\n\n\tconst eyeheight = emptyspace * 2\n\tring\n\t\t.attr('transform', 'scale(.3,.3)')\n\t\t.attr('fill-opacity', 0)\n\t\t.transition()\n\t\t.duration(dur1)\n\t\t.attr('transform', 'scale(1,1)')\n\t\t.attr('fill-opacity', 1)\n\t\t.on('end', () => {\n\t\t\teye.shutter = eye\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', -emptyspace)\n\t\t\t\t.attr('y', -emptyspace)\n\t\t\t\t.attr('width', emptyspace * 2)\n\t\t\t\t.attr('height', 0)\n\t\t\t\t.attr('fill', '#ededed')\n\t\t\t\t.on('click', () => remove(sun))\n\t\t\teye.shutter\n\t\t\t\t.transition()\n\t\t\t\t.duration(dur2)\n\t\t\t\t.attr('height', emptyspace * 2)\n\t\t\t\t.on('end', () => {\n\t\t\t\t\t// shutter done, add things\n\t\t\t\t\teye.fore = eye.append('g')\n\t\t\t\t\tconst fontsize1 = Math.min(eyeheight / (arg.label.length * client.textlensf), emptyspace * 0.6)\n\t\t\t\t\teye.fore\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(arg.label)\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t\t\t\t.attr('font-weight', 'bold')\n\t\t\t\t\t\t.attr('font-family', 'Arial')\n\t\t\t\t\t\t.attr('font-size', fontsize1)\n\t\t\t\t\tconst fontsize = Math.min(\n\t\t\t\t\t\t18,\n\t\t\t\t\t\tMath.min(\n\t\t\t\t\t\t\t(emptyspace * 0.7) / (itemlst.length.toString().length * client.textlensf),\n\t\t\t\t\t\t\t(emptyspace - fontsize1 / 2) * 0.7\n\t\t\t\t\t\t)\n\t\t\t\t\t)\n\t\t\t\t\teye.fore\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(itemlst.length)\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t\t\t\t.attr('y', -fontsize1 / 2 - 2)\n\t\t\t\t\t\t.attr('font-family', 'Arial')\n\t\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\teye\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('x', -emptyspace)\n\t\t\t\t\t\t.attr('y', -emptyspace)\n\t\t\t\t\t\t.attr('width', emptyspace * 2)\n\t\t\t\t\t\t.attr('height', emptyspace * 2)\n\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tif (sun.busy) return\n\t\t\t\t\t\t\tremove(sun)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mousedown', event => {\n\t\t\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\t\t\tevent.stopPropagation()\n\t\t\t\t\t\t\tlet cx0 = cx,\n\t\t\t\t\t\t\t\tcy0 = cy,\n\t\t\t\t\t\t\t\tmx = event.clientX,\n\t\t\t\t\t\t\t\tmy = event.clientY,\n\t\t\t\t\t\t\t\tbody = d3select(document.body)\n\t\t\t\t\t\t\tbody\n\t\t\t\t\t\t\t\t.on('mousemove', event => {\n\t\t\t\t\t\t\t\t\tsun.busy = true // must set here but not mousedown\n\t\t\t\t\t\t\t\t\tcx = cx0 + event.clientX - mx\n\t\t\t\t\t\t\t\t\tcy = cy0 + event.clientY - my\n\t\t\t\t\t\t\t\t\tg.attr('transform', 'translate(' + cx + ',' + cy + ')')\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t.on('mouseup', () => {\n\t\t\t\t\t\t\t\t\tsetTimeout(() => (sun.busy = false), 10)\n\t\t\t\t\t\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\n\t\t\t\t\t// button at bottom\n\t\t\t\t\tsun.listbutt = eye.append('g').attr('transform', 'translate(0,' + fontsize1 / 2 + ')')\n\t\t\t\t\tconst listbutt_bg = sun.listbutt\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('x', -eyeheight / 2)\n\t\t\t\t\t\t.attr('width', eyeheight)\n\t\t\t\t\t\t.attr('height', emptyspace - fontsize1 / 2)\n\t\t\t\t\t\t.attr('fill', '#d9d9d9')\n\t\t\t\t\tconst listbutt_text = sun.listbutt\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(arg.m2detail ? 'Show' : 'List')\n\t\t\t\t\t\t.attr('y', (emptyspace - fontsize1 / 2) / 2)\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('font-family', 'Arial')\n\t\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t\t\t\t.attr('font-size', Math.min(18, fontsize))\n\t\t\t\t\tsun.listbutt\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('x', -eyeheight / 2)\n\t\t\t\t\t\t.attr('width', eyeheight)\n\t\t\t\t\t\t.attr('height', emptyspace - fontsize1 / 2)\n\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\t\tlistbutt_bg.attr('fill', '#bababa')\n\t\t\t\t\t\t\tlistbutt_text.attr('fill', 'white')\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\tlistbutt_bg.attr('fill', '#d9d9d9')\n\t\t\t\t\t\t\tlistbutt_text.attr('fill', '#858585')\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\t\tif (arg.m2detail) {\n\t\t\t\t\t\t\t\tremove(sun)\n\t\t\t\t\t\t\t\titemtable({\n\t\t\t\t\t\t\t\t\tmlst: [arg.m2detail],\n\t\t\t\t\t\t\t\t\tpane: true,\n\t\t\t\t\t\t\t\t\tx: event.clientX - radius,\n\t\t\t\t\t\t\t\t\ty: event.clientY - radius * 2,\n\t\t\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\t\tremove(sun)\n\t\t\t\t\t\t\tsetTimeout(\n\t\t\t\t\t\t\t\t() =>\n\t\t\t\t\t\t\t\t\titemtable({\n\t\t\t\t\t\t\t\t\t\tmlst: arg.mlst,\n\t\t\t\t\t\t\t\t\t\tx: p.left,\n\t\t\t\t\t\t\t\t\t\ty: p.top,\n\t\t\t\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\t\t\t\tblock: block,\n\t\t\t\t\t\t\t\t\t\tpane: true\n\t\t\t\t\t\t\t\t\t}),\n\t\t\t\t\t\t\t\t500\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\t})\n\t\t\t\t})\n\t\t})\n}\n\nfunction remove(sun) {\n\tsun.busy = true\n\tif (sun.eye.fore) {\n\t\tsun.eye.fore.remove()\n\t}\n\tif (sun.listbutt) {\n\t\tsun.listbutt.remove()\n\t}\n\tif (sun.eye.shutter) {\n\t\tsun.eye.shutter\n\t\t\t.transition()\n\t\t\t.attr('height', 0)\n\t\t\t.on('end', () => {\n\t\t\t\tsun.ring\n\t\t\t\t\t.transition()\n\t\t\t\t\t.attr('transform', 'scale(.5,.5)')\n\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t.on('end', () => {\n\t\t\t\t\t\tsun.g.remove()\n\t\t\t\t\t\tsun.pica.g.selectAll('*').remove()\n\t\t\t\t\t})\n\t\t\t})\n\t} else {\n\t\tsun.ring\n\t\t\t.transition()\n\t\t\t.attr('transform', 'scale(.5,.5)')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.on('end', () => {\n\t\t\t\tsun.g.remove()\n\t\t\t\tsun.pica.g.selectAll('*').remove()\n\t\t\t})\n\t}\n\tsun.pica.g.selectAll('*').remove()\n}\n\nfunction slicemouseover(d, pica, arg, cx, cy, tk, block) {\n\tconst cht = arg.cohort\n\n\tconst fontsize = 13\n\tconst barheight = 10\n\tconst ypad = 1\n\n\tlet toangle = (d.x0 + d.x1) / 2\n\t/*\n\tmid angle determines pica placement, \n\t*/\n\tif (toangle >= 0.375 && toangle <= 0.625) {\n\t\t// around PI, see if need to shift to >PI or <PI\n\t\t// get low point yoff given angle PI and d.outradius and placement in tk\n\t\tconst yoff = tk.yoff + cy + d.outradius\n\t\tconst alltkh = Number.parseFloat(block.svg.attr('height'))\n\n\t\t// need to get pica height by # of rows\n\t\tconst picaheight = fontsize + ypad + fontsize + (cht && cht.root ? ypad + barheight + 5 : 0)\n\n\t\tif (yoff >= alltkh - 30) {\n\t\t\t// not enough space in block at angle PI, shift\n\t\t\tif (toangle <= 0.5) {\n\t\t\t\ttoangle = Math.max(0.25, d.x0)\n\t\t\t} else {\n\t\t\t\ttoangle = Math.min(0.75, d.x1)\n\t\t\t}\n\t\t}\n\t}\n\n\tpica.g.selectAll('*').remove()\n\tconst x = cx + (d.outradius + 5) * Math.sin(Math.PI * 2 * toangle)\n\tconst y = cy - (d.outradius + 5) * Math.cos(Math.PI * 2 * toangle)\n\tpica.g.attr('transform', 'translate(' + x + ',' + y + ')')\n\n\tconst barwidth = 60\n\n\tlet bar = null,\n\t\tcohortsize = 0\n\n\tif (cht && cht.root) {\n\t\tbar = pica.g.append('g')\n\t\tbar\n\t\t\t.append('rect')\n\t\t\t.attr('width', barwidth + 4)\n\t\t\t.attr('height', barheight + 4)\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\tbar\n\t\t\t.append('rect')\n\t\t\t.attr('x', 2)\n\t\t\t.attr('y', 2)\n\t\t\t.attr('width', barwidth)\n\t\t\t.attr('height', barheight)\n\t\t\t.attr('fill', cht.fbarbg || '#ededed')\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\tcht.root.each(i => {\n\t\t\tif (i.id == d.id) {\n\t\t\t\tcohortsize = i.value\n\t\t\t}\n\t\t})\n\t\tif (cohortsize > 0) {\n\t\t\tbar\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', 2)\n\t\t\t\t.attr('y', 2)\n\t\t\t\t.attr('width', (barwidth * d.value) / cohortsize)\n\t\t\t\t.attr('height', barheight)\n\t\t\t\t.attr('fill', cht.fbarfg || '#858585')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t}\n\t}\n\tconst text0 = pica.g\n\t\t.append('text')\n\t\t.attr('stroke', 'white')\n\t\t.attr('stroke-width', 3)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('font-family', 'Arial')\n\tconst text = pica.g\n\t\t.append('text')\n\t\t.attr('fill', 'black')\n\t\t.attr('fill-opacity', 1)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('font-family', 'Arial')\n\t// FIXME \"sample\" hardcoded\n\tconst textt = d.data.name + ', ' + d.value + ' sample' + (d.value > 1 ? 's' : '')\n\ttext0.text(d.data.name)\n\ttext.text(d.data.name)\n\tconst text20 = pica.g\n\t\t.append('text')\n\t\t.attr('stroke', 'white')\n\t\t.attr('stroke-width', 3)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('font-family', 'Arial')\n\tconst text2 = pica.g\n\t\t.append('text')\n\t\t.attr('fill', 'black')\n\t\t.attr('fill-opacity', 1)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('font-family', 'Arial')\n\tconst tt = d.value + ' sample' + (d.value > 1 ? 's' : '') + (bar ? ' (' + cohortsize + ' total)' : '')\n\ttext20.text(tt)\n\ttext2.text(tt)\n\tconst textwidth = Math.max(text.node().getBBox().width, text2.node().getBBox().width)\n\n\tif (toangle < 0.25) {\n\t\ttext20.attr('y', bar ? -3 - barheight - ypad : 0)\n\t\ttext2.attr('y', bar ? -3 - barheight - ypad : 0)\n\t\ttext0.attr('y', (bar ? -3 - barheight - ypad : 0) - fontsize - ypad)\n\t\ttext.attr('y', (bar ? -3 - barheight - ypad : 0) - fontsize - ypad)\n\t\tif (bar) {\n\t\t\tbar.attr('transform', 'translate(0,-' + barheight + ')')\n\t\t}\n\t} else if (toangle < 0.5) {\n\t\ttext0.attr('dominant-baseline', 'hanging').attr('y', 0)\n\t\ttext.attr('dominant-baseline', 'hanging').attr('y', 0)\n\t\ttext20.attr('dominant-baseline', 'hanging').attr('y', ypad + fontsize)\n\t\ttext2.attr('dominant-baseline', 'hanging').attr('y', ypad + fontsize)\n\t\tif (bar) {\n\t\t\tbar.attr('transform', 'translate(0,' + (fontsize + ypad) * 2 + ')')\n\t\t}\n\t} else if (toangle < 0.75) {\n\t\ttext0.attr('dominant-baseline', 'hanging').attr('text-anchor', 'end').attr('y', 0)\n\t\ttext.attr('dominant-baseline', 'hanging').attr('text-anchor', 'end').attr('y', 0)\n\t\ttext20\n\t\t\t.attr('dominant-baseline', 'hanging')\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('y', ypad + fontsize)\n\t\ttext2\n\t\t\t.attr('dominant-baseline', 'hanging')\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('y', ypad + fontsize)\n\t\tif (bar) {\n\t\t\tbar.attr('transform', 'translate(-' + barwidth + ',' + (fontsize + ypad) * 2 + ')')\n\t\t}\n\t} else {\n\t\ttext20.attr('text-anchor', 'end').attr('y', bar ? -3 - barheight - ypad : 0)\n\t\ttext2.attr('text-anchor', 'end').attr('y', bar ? -3 - barheight - ypad : 0)\n\t\ttext0.attr('text-anchor', 'end').attr('y', (bar ? -3 - barheight - ypad : 0) - fontsize - ypad)\n\t\ttext.attr('text-anchor', 'end').attr('y', (bar ? -3 - barheight - ypad : 0) - fontsize - ypad)\n\t\tif (bar) {\n\t\t\tbar.attr('transform', 'translate(-' + barwidth + ',-' + barheight + ')')\n\t\t}\n\t}\n}\n\nfunction showsinglesample(samplename, anno, x, y) {\n\tconst lst = []\n\tfor (const k in anno) {\n\t\tlst.push({ k: k, v: anno[k] })\n\t}\n\tconst pane = client.newpane({ x: x, y: y })\n\tpane.header.text(samplename)\n\tclient.make_table_2col(pane.body, lst)\n}\n\nfunction showmanysample(samples, cohort, x, y) {\n\t// each sample has k4a\n\tconst attrset = new Set()\n\tfor (const s of samples) {\n\t\tconst a = cohort.annotation[s.k4a]\n\t\tfor (const k in a) {\n\t\t\tattrset.add(k)\n\t\t}\n\t}\n\tconst pane = client.newpane({ x: x, y: y })\n\tpane.header.text(samples.length + ' ' + cohort.key4annotation + 's')\n\tconst table = pane.body.append('table')\n\n\tconst headers = [...attrset]\n\t{\n\t\t// header\n\t\tconst tr = table.append('tr')\n\t\tfor (const h of headers) {\n\t\t\ttr.append('td').text(h).style('color', '#858585').style('font-size', '.7em')\n\t\t}\n\t}\n\n\tfor (const s of samples) {\n\t\tconst tr = table.append('tr').attr('class', 'sja_tr')\n\t\tconst anno = cohort.annotation[s.k4a]\n\t\tfor (const h of headers) {\n\t\t\ttr.append('td').text(anno[h] == undefined ? '' : anno[h])\n\t\t}\n\t}\n}\n", "import sun1 from './block.ds.sun1'\nimport { itemtable } from './block.ds.itemtable'\n\n/*\nmay show sunburst chart using several possible data sources\neither server-side computed summary, or client-side computed\n\ntodo: as the central place for making sunburst\nsunburst.js to replace sun1\n*/\n\nexport default async function(occurrence, mlst, cx, cy, tk, block) {\n\tif (tk.ds) {\n\t\t// legacy ds\n\t\tif (tk.ds.cohort) {\n\t\t\t// legacy cohort config on legacy ds\n\t\t\tlet showsunburst = false\n\t\t\tif (tk.ds.cohort.annotation) {\n\t\t\t\tif (tk.ds.cohort.variantsunburst) {\n\t\t\t\t\tshowsunburst = true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// no annotation, should be old-style official ds\n\t\t\t\t// FIXME update to new ds\n\t\t\t\t// or all update to mds altogether\n\t\t\t\tshowsunburst = true\n\t\t\t}\n\t\t\tif (showsunburst) {\n\t\t\t\tsun1(tk, block, {\n\t\t\t\t\tcx,\n\t\t\t\t\tcy,\n\t\t\t\t\tmlst: mlst,\n\t\t\t\t\tlabel: mlst[0].mname,\n\t\t\t\t\tcohort: tk.ds.cohort\n\t\t\t\t})\n\t\t\t\treturn true\n\t\t\t}\n\t\t}\n\t}\n\treturn false\n}\n", "import { scaleLinear } from 'd3-scale'\nimport { axisLeft } from 'd3-axis'\nimport { format as d3format } from 'd3-format'\nimport { arc as d3arc } from 'd3-shape'\nimport { rgb as d3rgb } from 'd3-color'\nimport { select as d3select } from 'd3-selection'\nimport { itemtable, query_vcfcohorttrack } from './block.ds.itemtable'\nimport * as client from './client'\nimport * as coord from './coord'\nimport * as common from '#shared/common.js'\nimport may_sunburst from './block.sunburst'\nimport {\n\tmlst_pretreat,\n\ttkdata_update_x,\n\tminbpwidth,\n\tdisclabelspacing,\n\tgetter_mcset_key,\n\tmiddlealignshift,\n\tepaint_may_hl,\n\tdone_tknodata\n} from './block.ds'\n\n/*\n\nnew:\n\tsamplebynumericvalue\n\n\nFIXME ITD stack bars not working\n\n\n********************** EXPORTED\n\nrendernumerictk()\n\n********************** INTERNAL\n\nnumeric_make()\n\n*/\n\nconst clustercrowdlimit = 7 // at least 8 px per disc, otherwise won't show mname label\n\nconst mnamegetter = s => {\n\tif (!s) return ''\n\t// trim too long names\n\tif (s.length > 25) {\n\t\treturn s.substr(0, 20) + '...'\n\t}\n\treturn s\n}\n\nexport function rendernumerictk(tk, block, originhidden) {\n\t/*\n\tmakes:\n\n\ttk.data\n\ttk.skewer2\n\n\t*/\n\n\tconst nm = tk.numericmode\n\n\tif (!nm.axisheight) {\n\t\tnm.axisheight = 100\n\t}\n\n\t// do not skip grouping!?\n\n\t// create group and plot anew\n\ttk.glider.selectAll('*').remove()\n\tdelete tk.skewer\n\n\tconst usemlst = mlst_pretreat(tk, block, originhidden)\n\n\tconst x2mlst = new Map()\n\tfor (const m of usemlst) {\n\t\tif (m.__x == undefined) {\n\t\t\t// dropped by filter\n\t\t\tcontinue\n\t\t}\n\t\tif (!x2mlst.has(m.__x)) {\n\t\t\tx2mlst.set(m.__x, [])\n\t\t}\n\t\tx2mlst.get(m.__x).push(m)\n\t}\n\tconst datagroup = []\n\tconst topxbins = []\n\t// by resolution\n\tif (block.exonsf >= minbpwidth) {\n\t\t// # pixel per nt is big enough\n\t\t// group by each nt\n\t\tfor (const [x, mlst] of x2mlst) {\n\t\t\tdatagroup.push({\n\t\t\t\tchr: mlst[0].chr,\n\t\t\t\tpos: mlst[0].pos,\n\t\t\t\tmlst: mlst,\n\t\t\t\tx: x\n\t\t\t})\n\t\t}\n\t} else {\n\t\t// # pixel per nt is too small\n\t\tif (block.usegm && block.usegm.coding && block.gmmode != client.gmmode.genomic) {\n\t\t\t// by aa\n\t\t\t// in gmsum, rglst may include introns, need to distinguish symbolic and rglst introns, use __x difference by a exonsf*3 limit\n\t\t\tconst aa2mlst = new Map()\n\t\t\tfor (const [x, mlst] of x2mlst) {\n\t\t\t\tif (mlst[0].chr != block.usegm.chr) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\t// TODO how to identify if mlst belongs to regulatory region rather than gm\n\t\t\t\tlet aapos = undefined\n\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\tif (Number.isFinite(m.aapos)) aapos = m.aapos\n\t\t\t\t}\n\t\t\t\tif (aapos == undefined) {\n\t\t\t\t\taapos = coord.genomic2gm(mlst[0].pos, block.usegm).aapos\n\t\t\t\t}\n\t\t\t\tif (aapos == undefined) {\n\t\t\t\t\tconsole.error('data item cannot map to aaposition')\n\t\t\t\t\tconsole.log(mlst[0])\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\t// this group can be anchored to a aa\n\t\t\t\tx2mlst.delete(x)\n\n\t\t\t\tif (!aa2mlst.has(aapos)) {\n\t\t\t\t\taa2mlst.set(aapos, [])\n\t\t\t\t}\n\t\t\t\tlet notmet = true\n\t\t\t\tfor (const lst of aa2mlst.get(aapos)) {\n\t\t\t\t\tif (Math.abs(lst[0].__x - mlst[0].__x) <= block.exonsf * 3) {\n\t\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\t\tlst.push(m)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tnotmet = false\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (notmet) {\n\t\t\t\t\taa2mlst.get(aapos).push(mlst)\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst utr5len = block.usegm.utr5 ? block.usegm.utr5.reduce((i, j) => i + j[1] - j[0], 0) : 0\n\t\t\tfor (const llst of aa2mlst.values()) {\n\t\t\t\tfor (const mlst of llst) {\n\t\t\t\t\tlet m = null\n\t\t\t\t\tfor (const m2 of mlst) {\n\t\t\t\t\t\tif (Number.isFinite(m2.rnapos)) m = m2\n\t\t\t\t\t}\n\t\t\t\t\tif (m == null) {\n\t\t\t\t\t\tconsole.log('trying to map mlst to codon, but no rnapos found')\n\t\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\t\tconsole.log(m)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tdatagroup.push({\n\t\t\t\t\t\tchr: mlst[0].chr,\n\t\t\t\t\t\tpos: m.pos,\n\t\t\t\t\t\tmlst: mlst,\n\t\t\t\t\t\tx: mlst[0].__x\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t// leftover by px bin\n\t\tconst pxbin = []\n\t\tconst binpx = 2\n\t\tfor (const [x, mlst] of x2mlst) {\n\t\t\tconst i = Math.floor(x / binpx)\n\t\t\tif (!pxbin[i]) {\n\t\t\t\tpxbin[i] = []\n\t\t\t}\n\t\t\tpxbin[i] = [...pxbin[i], ...mlst]\n\t\t}\n\t\tfor (const mlst of pxbin) {\n\t\t\tif (!mlst) continue\n\t\t\tconst xsum = mlst.reduce((i, j) => i + j.__x, 0)\n\t\t\tdatagroup.push({\n\t\t\t\tisbin: true,\n\t\t\t\tchr: mlst[0].chr,\n\t\t\t\tpos: mlst[0].pos,\n\t\t\t\tmlst: mlst,\n\t\t\t\tx: xsum / mlst.length\n\t\t\t})\n\t\t}\n\t}\n\n\tdatagroup.sort((a, b) => a.x - b.x)\n\n\tif (tk.data && block.pannedpx != undefined && (!block.usegm || block.gmmode == client.gmmode.genomic)) {\n\t\t// inherit genomic mode and panned\n\t\tconst pastmode = {}\n\t\tfor (const g of tk.data) {\n\t\t\tpastmode[g.chr + '.' + g.pos] = {\n\t\t\t\txoffset: g.xoffset\n\t\t\t}\n\t\t}\n\t\tfor (const g of datagroup) {\n\t\t\tconst k = g.chr + '.' + g.pos\n\t\t\tif (pastmode[k]) {\n\t\t\t\tg.xoffset = pastmode[k].xoffset\n\t\t\t}\n\t\t}\n\t}\n\ttk.data = datagroup\n\n\tnumeric_make(tk, block)\n\n\ttk.height_main =\n\t\ttk.toppad +\n\t\tnm.toplabelheight +\n\t\t//+disclabelspacing\n\t\tnm.maxradius +\n\t\tnm.axisheight +\n\t\tnm.maxradius +\n\t\ttk.stem1 +\n\t\ttk.stem2 +\n\t\ttk.stem3 +\n\t\tnm.bottomlabelheight +\n\t\ttk.bottompad\n\n\tif (!tk.data || tk.data.length == 0) {\n\t\tdone_tknodata(tk, block)\n\t\treturn\n\t}\n\n\t/*\n\tvariants loaded for this track\n\t*/\n}\n\nfunction color4disc(m, tk) {\n\tif (tk.vcfinfofilter && tk.vcfinfofilter.setidx4mclass != undefined) {\n\t\tconst mcset = tk.vcfinfofilter.lst[tk.vcfinfofilter.setidx4mclass]\n\n\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\n\t\tif (err || vlst == undefined) return 'black'\n\n\t\tfor (const v of vlst) {\n\t\t\tif (mcset.categories[v]) {\n\t\t\t\treturn mcset.categories[v].color\n\t\t\t} else {\n\t\t\t\treturn 'black'\n\t\t\t}\n\t\t}\n\t}\n\n\t// mclass\n\tif (common.mclass[m.class]) {\n\t\treturn common.mclass[m.class].color\n\t}\n\treturn 'black'\n}\n\nfunction numeric_make(tk, block) {\n\t/*\n\t */\n\n\tconst nm = tk.numericmode\n\n\t// ITD/DEL stacked bars XXX won't do\n\tconst stackbars = []\n\tfor (const d of tk.data) {\n\t\td.x0 = d.x\n\t\tif (d.xoffset != undefined) {\n\t\t\td.x = d.x0 + d.xoffset\n\t\t}\n\n\t\tcontinue\n\t\t// TODO\n\t\t// updates x\n\t\t// create stack bars\n\t\tfor (const g of d.groups) {\n\t\t\tg.aa = d // disc reference group\n\t\t\tlet rnaspan = null\n\t\t\tif (g.dt == common.dtitd) {\n\t\t\t\trnaspan = g.mlst[0].rnaduplength\n\t\t\t\tfor (const m of g.mlst) {\n\t\t\t\t\trnaspan = Math.max(rnaspan, m.rnaduplength)\n\t\t\t\t}\n\t\t\t} else if (g.dt == common.dtdel) {\n\t\t\t\trnaspan = g.mlst[0].rnadellength\n\t\t\t\tfor (const m of g.mlst) {\n\t\t\t\t\trnaspan = Math.max(rnaspan, m.rnadellength)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// no business\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// no isInteger, rna position can have .5\n\t\t\tif (!Number.isFinite(rnaspan) || rnaspan < 0) {\n\t\t\t\t// support if genomic pos is available\n\t\t\t\tconsole.log('no rnaspan for stack bar from itd/del')\n\t\t\t\tconsole.log(g.mlst)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tlet pxspan = null\n\t\t\tif (block.usegm) {\n\t\t\t\tconst rnapos = g.mlst[0].rnapos // rnapos should always be available!\n\t\t\t\tconst genomicpos = coord.rna2gmcoord(rnapos + rnaspan, block.usegm)\n\t\t\t\tconst hits = block.seekcoord(block.usegm.chr, genomicpos)\n\t\t\t\tif (hits.length > 0) {\n\t\t\t\t\tpxspan = hits[0].x - d.x\n\t\t\t\t} else {\n\t\t\t\t\tconsole.log(genomicpos + ' no hit on rglst')\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!Number.isFinite(pxspan)) {\n\t\t\t\tconsole.log('no pxspan for stack bar from itd/del')\n\t\t\t\tconsole.log(g.mlst)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tg.stackbar = {\n\t\t\t\taa: d.mlst[0].aapos,\n\t\t\t\tpxspan: pxspan,\n\t\t\t\theight: 4, // fixed bar height\n\t\t\t\tgrp: g\n\t\t\t}\n\t\t\td.hasstackbar = true\n\t\t\tstackbars.push(g.stackbar)\n\t\t}\n\t}\n\t// todo: done stack bars\n\n\tlet stackbarmaxheight = 0 // for setting stem3\n\tif (stackbars.length > 0) {\n\t\t// XXX\n\t\tlet ypad = 1\n\t\tfor (let i = 0; i < stackbars.length; i++) {\n\t\t\tconst si = stackbars[i]\n\t\t\tconst overlap = []\n\t\t\tfor (let j = 0; j < i; j++) {\n\t\t\t\tconst sj = stackbars[j]\n\t\t\t\tif (Math.max(si.aa, sj.aa) < Math.min(si.pxspan + si.aa, sj.pxspan + sj.aa)) {\n\t\t\t\t\toverlap.push(sj)\n\t\t\t\t}\n\t\t\t}\n\t\t\tsi.y = 2\n\t\t\tfor (const sj of overlap) {\n\t\t\t\tif (Math.max(si.y, sj.y) < Math.min(si.y + si.height, sj.y + sj.height)) {\n\t\t\t\t\tsi.y = sj.y + sj.height + ypad\n\t\t\t\t}\n\t\t\t}\n\t\t\tstackbarmaxheight = Math.max(stackbarmaxheight, si.y + si.height)\n\t\t}\n\t}\n\n\t// diameter, also m label font size\n\tconst dotwidth = Math.max(14, block.width / 110)\n\n\tnm.dotwidth = dotwidth\n\tnm.maxradius = 0\n\n\tfor (const d of tk.data) {\n\t\tfor (const m of d.mlst) {\n\t\t\t// radius may be variable\n\t\t\tm.radius = dotwidth / 2\n\t\t\tnm.maxradius = Math.max(m.radius, nm.maxradius)\n\n\t\t\t// determine if has rim\n\t\t\tm.rimwidth = 0\n\n\t\t\tm.aa = d // m references data point\n\t\t}\n\t}\n\n\t/*\nset:\n- stack bar\n- stem size\n- dot radius\n\n*/\n\n\tconst showstem = adjustview(tk, block)\n\n\tnm.showsamplebar = showstem && tk.ds && tk.ds.samplebynumericvalue\n\n\tif (!nm.showsamplebar) {\n\t\t// do not show both at same time\n\t\tnm.showgenotypebyvalue = showstem && tk.ds && tk.ds.genotypebynumericvalue\n\t}\n\n\ttk.genotype2color.legend.style('display', nm.showsamplebar || nm.showgenotypebyvalue ? 'block' : 'none')\n\n\t// v is for variant-level values\n\tlet mcset\n\tlet vmin = null\n\tlet vmax = null\n\n\t// in case of plotting genotype circles, circle radius is set by relative # of samples\n\tlet genotypebyvaluesamplemax = 0\n\tlet genotypebyvaluecircleradiusscale = null\n\n\tif (nm.showsamplebar) {\n\t\tmcset = { name: tk.ds.samplebynumericvalue.axislabel }\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tif (!m.sampledata) continue\n\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\tconst sn = s.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\t\t\tif (!sn) continue\n\t\t\t\t\tconst a = tk.ds.cohort.annotation[sn]\n\t\t\t\t\tif (!a) continue\n\t\t\t\t\tconst v = a[tk.ds.samplebynumericvalue.attrkey]\n\t\t\t\t\tif (!Number.isFinite(v)) continue\n\t\t\t\t\tif (vmin == null) {\n\t\t\t\t\t\tvmin = v\n\t\t\t\t\t\tvmax = v\n\t\t\t\t\t} else {\n\t\t\t\t\t\tvmin = Math.min(vmin, v)\n\t\t\t\t\t\tvmax = Math.max(vmax, v)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} else if (nm.showgenotypebyvalue) {\n\t\tmcset = { name: tk.ds.genotypebynumericvalue.axislabel }\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tlet v = m.info[tk.ds.genotypebynumericvalue.refref.infokey]\n\t\t\t\tif (v != undefined) {\n\t\t\t\t\tif (vmin == null) {\n\t\t\t\t\t\tvmin = v\n\t\t\t\t\t\tvmax = v\n\t\t\t\t\t} else {\n\t\t\t\t\t\tvmin = Math.min(vmin, v)\n\t\t\t\t\t\tvmax = Math.max(vmax, v)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tv = m.info[tk.ds.genotypebynumericvalue.refalt.infokey]\n\t\t\t\tif (v != undefined) {\n\t\t\t\t\tif (vmin == null) {\n\t\t\t\t\t\tvmin = v\n\t\t\t\t\t\tvmax = v\n\t\t\t\t\t} else {\n\t\t\t\t\t\tvmin = Math.min(vmin, v)\n\t\t\t\t\t\tvmax = Math.max(vmax, v)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tv = m.info[tk.ds.genotypebynumericvalue.altalt.infokey]\n\t\t\t\tif (v != undefined) {\n\t\t\t\t\tif (vmin == null) {\n\t\t\t\t\t\tvmin = v\n\t\t\t\t\t\tvmax = v\n\t\t\t\t\t} else {\n\t\t\t\t\t\tvmin = Math.min(vmin, v)\n\t\t\t\t\t\tvmax = Math.max(vmax, v)\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\t// to get number of samples carrying each genotype\n\t\t\t\tlet num_refref = 0,\n\t\t\t\t\tnum_altalt = 0,\n\t\t\t\t\tnum_refalt = 0\n\n\t\t\t\tif (tk.ds.genotypebynumericvalue.refref.genotypeCountInfokey) {\n\t\t\t\t\t// get sample count from info field but not individuals\n\n\t\t\t\t\tlet v = m.info[tk.ds.genotypebynumericvalue.refref.genotypeCountInfokey]\n\t\t\t\t\tif (Number.isFinite(v)) {\n\t\t\t\t\t\tnum_refref = v\n\t\t\t\t\t}\n\t\t\t\t\tv = m.info[tk.ds.genotypebynumericvalue.refalt.genotypeCountInfokey]\n\t\t\t\t\tif (Number.isFinite(v)) {\n\t\t\t\t\t\tnum_refalt = v\n\t\t\t\t\t}\n\t\t\t\t\tv = m.info[tk.ds.genotypebynumericvalue.altalt.genotypeCountInfokey]\n\t\t\t\t\tif (Number.isFinite(v)) {\n\t\t\t\t\t\tnum_altalt = v\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tif (!m.sampledata) continue\n\t\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\t\tif (!s.allele2readcount) continue\n\t\t\t\t\t\tif (s.allele2readcount[m.alt]) {\n\t\t\t\t\t\t\tif (s.allele2readcount[m.ref]) {\n\t\t\t\t\t\t\t\tnum_refalt++\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tnum_altalt++\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tnum_refref++\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tgenotypebyvaluesamplemax = Math.max(genotypebyvaluesamplemax, num_refref, num_refalt, num_altalt)\n\t\t\t}\n\t\t}\n\n\t\t//genotypebyvaluecircleradiusscale = scaleLinear().domain([0, genotypebyvaluesamplemax]).range([4, 10])\n\t\t/*\n\tgenotypebyvaluecircleradiusscale = (x)=>{\n\t\treturn 2+ 8* (1 - Math.pow( (1- x/genotypebyvaluesamplemax), 4))\n\t}\n\t*/\n\t\tconst w = Math.pow(12 / 2, 2) * Math.PI // unit area\n\t\t/*\n\tlet mrd=0 // max disc radius\n\tif(genotypebyvaluesamplemax<=10) mrd=w*genotypebyvaluesamplemax*.9\n\telse if(genotypebyvaluesamplemax<=100) mrd=w*10\n\telse if(genotypebyvaluesamplemax<=1000) mrd=w*14\n\telse mrd=w*20\n\t*/\n\t\tconst mrd = w * 10\n\t\t// scale for disc radius\n\t\tgenotypebyvaluecircleradiusscale = scaleLinear()\n\t\t\t.domain([\n\t\t\t\t1,\n\t\t\t\tgenotypebyvaluesamplemax * 0.1,\n\t\t\t\tgenotypebyvaluesamplemax * 0.3,\n\t\t\t\tgenotypebyvaluesamplemax * 0.6,\n\t\t\t\tgenotypebyvaluesamplemax * 0.8,\n\t\t\t\tgenotypebyvaluesamplemax\n\t\t\t])\n\t\t\t.range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd])\n\t} else {\n\t\tmcset = tk.vcfinfofilter.lst[tk.vcfinfofilter.setidx4numeric]\n\n\t\t// get value for each m\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\t// default a valid number\n\t\t\t\tm._v = 0\n\n\t\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\t\t\t\tif (err) {\n\t\t\t\t\tconsole.log(err)\n\t\t\t\t} else if (vlst == undefined || vlst.length == 0) {\n\t\t\t\t} else {\n\t\t\t\t\tif (!Number.isFinite(vlst[0])) {\n\t\t\t\t\t\tconsole.log('invalid numerical value for variant: ' + vlst[0])\n\t\t\t\t\t} else {\n\t\t\t\t\t\tm._v = vlst[0]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (vmin == null) {\n\t\t\t\t\tvmin = m._v\n\t\t\t\t\tvmax = m._v\n\t\t\t\t} else {\n\t\t\t\t\tvmin = Math.min(m._v, vmin)\n\t\t\t\t\tvmax = Math.max(m._v, vmax)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst numscale = scaleLinear().domain([vmin, vmax]).range([0, nm.axisheight])\n\n\t// set m._y\n\tfor (const d of tk.data) {\n\t\tfor (const m of d.mlst) {\n\t\t\tm._y = numscale(m._v)\n\t\t}\n\t}\n\n\t/*\nset:\n.data[].width\n.data[].stemw\n.data[].xoffset\n.data[].x\n.data[].mlst[].xoff\n.data[].mlst[].rotate\n\n*/\n\n\tif (showstem) {\n\t\ttk.stem1 = 5\n\t\ttk.stem2 = 20\n\t\ttk.stem3 = 10 // should be determined by stackbars\n\t} else {\n\t\ttk.stem1 = 0\n\t\ttk.stem2 = 0\n\t\ttk.stem3 = 0\n\t}\n\n\t// get mname label width\n\tfor (const d of tk.data) {\n\t\tfor (const m of d.mlst) {\n\t\t\ttk.glider\n\t\t\t\t.append('text')\n\t\t\t\t.text(mnamegetter(m.mname))\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('font-size', m.radius * 2 - 2)\n\t\t\t\t.each(function () {\n\t\t\t\t\tm.labwidth = this.getBBox().width\n\t\t\t\t})\n\t\t\t\t.remove()\n\t\t}\n\t}\n\n\t// rotated labels, size protruding beyond y axis\n\tfor (const d of tk.data) {\n\t\t// reset all\n\t\tfor (const m of d.mlst) {\n\t\t\tdelete m.labattop\n\t\t\tdelete m.labatbottom\n\t\t}\n\t}\n\tif (showstem) {\n\t\t// show label for each disc, all rotated up\n\t\tfor (const d of tk.data) {\n\t\t\tif (d.mlst.length == 1) {\n\t\t\t\tconst m = d.mlst[0]\n\t\t\t\tm.labattop = true\n\t\t\t} else {\n\t\t\t\t// cluster\n\t\t\t\tif ((d.width - d.fixedgew) / (d.mlst.length - 1) < clustercrowdlimit) {\n\t\t\t\t\t// too crowded, no label\n\t\t\t\t} else {\n\t\t\t\t\t// show label for all m\n\t\t\t\t\tfor (const m of d.mlst) {\n\t\t\t\t\t\tm.labattop = true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} else {\n\t\t// no stem\n\t\t// sort items by v\n\t\tverticallabplace(tk)\n\t}\n\tnm.toplabelheight = 0\n\tnm.bottomlabelheight = 0\n\n\tif (nm.showsamplebar || nm.showgenotypebyvalue) {\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tnm.toplabelheight = Math.max(nm.toplabelheight, m.labwidth)\n\t\t\t}\n\t\t}\n\t} else {\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tif (m.labattop) {\n\t\t\t\t\tnm.toplabelheight = Math.max(nm.toplabelheight, m._y + m.labwidth - nm.axisheight)\n\t\t\t\t} else if (m.labatbottom) {\n\t\t\t\t\tnm.bottomlabelheight = Math.max(nm.bottomlabelheight, m.labwidth - m._y)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// adjust toplabelheight by tk labels\n\t{\n\t\tlet h = block.labelfontsize + tk.labyspace + block.labelfontsize // tk label and label_mcount\n\t\tif (tk.label_stratify) {\n\t\t\th += tk.label_stratify.length * (tk.labyspace + block.labelfontsize)\n\t\t}\n\t\tnm.toplabelheight = Math.max(nm.toplabelheight, h)\n\t}\n\n\t// 1: axis\n\ttk.leftaxis\n\t\t.attr('transform', 'translate(-' + dotwidth / 2 + ',' + (nm.toplabelheight + nm.maxradius) + ')')\n\t\t.selectAll('*')\n\t\t.remove()\n\t{\n\t\t// axis is inverse of numscale\n\t\tconst thisscale = scaleLinear().domain([vmin, vmax]).range([nm.axisheight, 0])\n\t\tconst thisaxis = axisLeft().scale(thisscale).ticks(4)\n\t\tif (mcset.numberIsInteger) {\n\t\t\tthisaxis.tickFormat(d3format('d'))\n\t\t\tif (vmax - vmin < 3) {\n\t\t\t\t/*\n\t\t\tmust do this to avoid axis showing redundant labels that doesn't make sense\n\t\t\te.g. -1 -2 -2\n\t\t\t*/\n\t\t\t\tthisaxis.ticks(vmax - vmin)\n\t\t\t}\n\t\t}\n\t\tclient.axisstyle({\n\t\t\taxis: tk.leftaxis.call(thisaxis),\n\t\t\tshowline: true,\n\t\t\tfontsize: dotwidth\n\t\t})\n\n\t\tif (vmin == vmax) {\n\t\t\ttk.leftaxis\n\t\t\t\t.append('text')\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('font-size', dotwidth)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('x', block.tkleftlabel_xshift)\n\t\t\t\t.attr('y', nm.axisheight)\n\t\t\t\t.text(vmin)\n\t\t\t\t.attr('fill', 'black')\n\t\t}\n\t\t// axis label, text must wrap\n\t\t{\n\t\t\t// read the max tick label width first\n\t\t\tlet maxw = 0\n\t\t\ttk.leftaxis.selectAll('text').each(function () {\n\t\t\t\tmaxw = Math.max(maxw, this.getBBox().width)\n\t\t\t})\n\t\t\tconst lst = mcset.name.split(' ')\n\t\t\tconst y = (nm.axisheight - lst.length * (dotwidth + 1)) / 2\n\t\t\tlet maxlabelw = 0\n\t\t\tlst.forEach((text, i) => {\n\t\t\t\ttk.leftaxis\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t.attr('font-size', dotwidth)\n\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t.attr('y', y + (dotwidth + 1) * i)\n\t\t\t\t\t.attr('x', -(maxw + 15))\n\t\t\t\t\t.text(text)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tmaxlabelw = Math.max(maxlabelw, this.getBBox().width + 15 + maxw)\n\t\t\t\t\t})\n\t\t\t})\n\n\t\t\ttk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, maxlabelw)\n\t\t}\n\t}\n\n\tconst _g = tk.glider.append('g').attr('transform', 'translate(0,0)')\n\n\t_g.append('line')\n\t\t.attr('y1', nm.toplabelheight + nm.maxradius)\n\t\t.attr('y2', nm.toplabelheight + nm.maxradius)\n\t\t.attr('x2', block.width)\n\t\t.attr('stroke', '#ededed')\n\t\t.attr('shape-rendering', 'crispEdges')\n\t_g.append('line')\n\t\t.attr('y1', nm.toplabelheight + nm.maxradius + nm.axisheight)\n\t\t.attr('y2', nm.toplabelheight + nm.maxradius + nm.axisheight)\n\t\t.attr('x2', block.width)\n\t\t.attr('stroke', '#ededed')\n\t\t.attr('shape-rendering', 'crispEdges')\n\n\ttk.skewer2 = _g\n\t\t.selectAll()\n\t\t.data(tk.data)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('class', 'sja_skg2')\n\t\t.each(function (d) {\n\t\t\t// compute radius for each group\n\t\t\td.g = this\n\t\t})\n\n\ttk.skewer2.attr(\n\t\t'transform',\n\t\td =>\n\t\t\t'translate(' +\n\t\t\td.x +\n\t\t\t',' +\n\t\t\t(nm.toplabelheight + disclabelspacing + nm.maxradius + nm.axisheight + nm.maxradius) +\n\t\t\t')'\n\t)\n\n\t// 2: stem\n\tif (showstem) {\n\t\ttk.skewer2\n\t\t\t.append('path')\n\t\t\t.attr('class', 'sja_aa_stem')\n\t\t\t.attr('d', d => skewer2_setstem(d, tk))\n\t\t\t.attr('stroke', d => color4disc(d.mlst[0], tk))\n\t\t\t.attr('fill', d => (d.mlst.length == 1 ? 'none' : '#ededed'))\n\t}\n\n\t// 3: discs\n\n\tconst discg = tk.skewer2\n\t\t.selectAll()\n\t\t.data(d => d.mlst)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('class', 'sja_aa_discg')\n\t\t.each(function (m) {\n\t\t\tm.g = this\n\t\t})\n\n\tif (nm.showsamplebar) {\n\t\tdiscg.attr('transform', m => 'translate(' + m.xoff + ',0)')\n\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tif (!m.sampledata) continue\n\t\t\t\tconst g = d3select(m.g)\n\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\tconst sn = s.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\t\t\tif (!sn) continue\n\t\t\t\t\tconst a = tk.ds.cohort.annotation[sn]\n\t\t\t\t\tif (!a) continue\n\t\t\t\t\tconst v = a[tk.ds.samplebynumericvalue.attrkey]\n\t\t\t\t\tif (!Number.isFinite(v)) continue\n\t\t\t\t\tconst y = -numscale(v) - nm.maxradius\n\t\t\t\t\tconst hasref = s.allele2readcount[m.ref]\n\t\t\t\t\tconst hasalt = s.allele2readcount[m.alt]\n\t\t\t\t\tif (hasalt) continue\n\t\t\t\t\tg.append('line')\n\t\t\t\t\t\t.attr('x1', -m.radius)\n\t\t\t\t\t\t.attr('x2', m.radius)\n\t\t\t\t\t\t.attr('y1', y)\n\t\t\t\t\t\t.attr('y2', y)\n\t\t\t\t\t\t.attr('stroke', hasref ? (hasalt ? tk.genotype2color.ra : tk.genotype2color.rr) : tk.genotype2color.aa)\n\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\tconst lst = [{ k: tk.ds.cohort.key4annotation, v: sn }]\n\t\t\t\t\t\t\tfor (const k in a) {\n\t\t\t\t\t\t\t\tlst.push({ k: k, v: a[k] })\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tlst.push({ k: 'genotype', v: s.genotype })\n\t\t\t\t\t\t\ttk.tktip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\t\t\tclient.make_table_2col(tk.tktip.d, lst)\n\t\t\t\t\t\t\tevent.target.setAttribute('stroke-width', 3)\n\t\t\t\t\t\t\tevent.target.setAttribute('x1', -m.radius - 3)\n\t\t\t\t\t\t\tevent.target.setAttribute('x2', m.radius + 3)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', event => {\n\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\tevent.target.setAttribute('stroke-width', 1)\n\t\t\t\t\t\t\tevent.target.setAttribute('x1', -m.radius)\n\t\t\t\t\t\t\tevent.target.setAttribute('x2', m.radius)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\tconst sn = s.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\t\t\tif (!sn) continue\n\t\t\t\t\tconst a = tk.ds.cohort.annotation[sn]\n\t\t\t\t\tif (!a) continue\n\t\t\t\t\tconst v = a[tk.ds.samplebynumericvalue.attrkey]\n\t\t\t\t\tif (!Number.isFinite(v)) continue\n\t\t\t\t\tconst y = -numscale(v) - nm.maxradius\n\t\t\t\t\tconst hasref = s.allele2readcount[m.ref]\n\t\t\t\t\tconst hasalt = s.allele2readcount[m.alt]\n\t\t\t\t\tif (!hasalt) continue\n\t\t\t\t\tg.append('line')\n\t\t\t\t\t\t.attr('x1', -m.radius)\n\t\t\t\t\t\t.attr('x2', m.radius)\n\t\t\t\t\t\t.attr('y1', y)\n\t\t\t\t\t\t.attr('y2', y)\n\t\t\t\t\t\t.attr('stroke', hasref ? (hasalt ? tk.genotype2color.ra : tk.genotype2color.rr) : tk.genotype2color.aa)\n\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\tconst lst = [{ k: tk.ds.cohort.key4annotation, v: sn }]\n\t\t\t\t\t\t\tfor (const k in a) {\n\t\t\t\t\t\t\t\tlst.push({ k: k, v: a[k] })\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tlst.push({ k: 'genotype', v: s.genotype })\n\t\t\t\t\t\t\ttk.tktip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\t\t\tclient.make_table_2col(tk.tktip.d, lst)\n\t\t\t\t\t\t\tevent.target.setAttribute('stroke-width', 3)\n\t\t\t\t\t\t\tevent.target.setAttribute('x1', -m.radius - 3)\n\t\t\t\t\t\t\tevent.target.setAttribute('x2', m.radius + 3)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', event => {\n\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\tevent.target.setAttribute('stroke-width', 1)\n\t\t\t\t\t\t\tevent.target.setAttribute('x1', -m.radius)\n\t\t\t\t\t\t\tevent.target.setAttribute('x2', m.radius)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} else if (nm.showgenotypebyvalue) {\n\t\tdiscg.attr('transform', m => 'translate(' + m.xoff + ',0)')\n\n\t\tfor (const d of tk.data) {\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tlet num_refref = 0,\n\t\t\t\t\tnum_altalt = 0,\n\t\t\t\t\tnum_refalt = 0\n\n\t\t\t\t// genotype count can either be encoded in INFO or figured from sampledata[]\n\t\t\t\tif (tk.ds.genotypebynumericvalue.refref.genotypeCountInfokey) {\n\t\t\t\t\t// from INFO\n\t\t\t\t\tnum_refref = m.info[tk.ds.genotypebynumericvalue.refref.genotypeCountInfokey]\n\t\t\t\t\tnum_altalt = m.info[tk.ds.genotypebynumericvalue.altalt.genotypeCountInfokey]\n\t\t\t\t\tnum_refalt = m.info[tk.ds.genotypebynumericvalue.refalt.genotypeCountInfokey]\n\t\t\t\t} else {\n\t\t\t\t\t// from samples, require matrix\n\t\t\t\t\tif (!m.sampledata) continue\n\t\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\t\tif (!s.allele2readcount) continue\n\t\t\t\t\t\tif (s.allele2readcount[m.alt]) {\n\t\t\t\t\t\t\tif (s.allele2readcount[m.ref]) {\n\t\t\t\t\t\t\t\tnum_refalt++\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tnum_altalt++\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tnum_refref++\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tconst g = d3select(m.g)\n\n\t\t\t\tif (num_refref) {\n\t\t\t\t\tconst v = m.info[tk.ds.genotypebynumericvalue.refref.infokey]\n\t\t\t\t\tif (v != undefined) {\n\t\t\t\t\t\tconst y = -numscale(v) - nm.maxradius\n\t\t\t\t\t\tg.append('circle')\n\t\t\t\t\t\t\t.attr('cy', y)\n\t\t\t\t\t\t\t//.attr('r', genotypebyvaluecircleradiusscale( num_refref) )\n\t\t\t\t\t\t\t.attr('r', Math.sqrt(genotypebyvaluecircleradiusscale(num_refref)) / Math.PI)\n\t\t\t\t\t\t\t.attr('stroke', tk.ds.genotypebynumericvalue.refref.color)\n\t\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\t\ttk.tktip.show(event.clientX, event.clientY).clear()\n\t\t\t\t\t\t\t\tconst lst = [\n\t\t\t\t\t\t\t\t\t{ k: 'Variant', v: m.chr + ':' + (m.pos + 1) + ' ' + m.ref + '>' + m.alt },\n\t\t\t\t\t\t\t\t\t{ k: 'Genotype', v: 'Ref/Ref' },\n\t\t\t\t\t\t\t\t\t{ k: '#sample', v: num_refref },\n\t\t\t\t\t\t\t\t\t{ k: tk.ds.genotypebynumericvalue.axislabel, v: v }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\tclient.make_table_2col(tk.tktip.d, lst)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (num_refalt) {\n\t\t\t\t\tconst v = m.info[tk.ds.genotypebynumericvalue.refalt.infokey]\n\t\t\t\t\tif (v != undefined) {\n\t\t\t\t\t\tconst y = -numscale(v) - nm.maxradius\n\t\t\t\t\t\tg.append('circle')\n\t\t\t\t\t\t\t.attr('cy', y)\n\t\t\t\t\t\t\t//.attr('r', genotypebyvaluecircleradiusscale( num_refalt) )\n\t\t\t\t\t\t\t.attr('r', Math.sqrt(genotypebyvaluecircleradiusscale(num_refalt)) / Math.PI)\n\t\t\t\t\t\t\t.attr('stroke', tk.ds.genotypebynumericvalue.refalt.color)\n\t\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\t\ttk.tktip.show(event.clientX, event.clientY).clear()\n\t\t\t\t\t\t\t\tconst lst = [\n\t\t\t\t\t\t\t\t\t{ k: 'Variant', v: m.chr + ':' + (m.pos + 1) + ' ' + m.ref + '>' + m.alt },\n\t\t\t\t\t\t\t\t\t{ k: 'Genotype', v: 'Ref/Alt' },\n\t\t\t\t\t\t\t\t\t{ k: '#sample', v: num_refalt },\n\t\t\t\t\t\t\t\t\t{ k: tk.ds.genotypebynumericvalue.axislabel, v: v }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\tclient.make_table_2col(tk.tktip.d, lst)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (num_altalt) {\n\t\t\t\t\tconst v = m.info[tk.ds.genotypebynumericvalue.altalt.infokey]\n\t\t\t\t\tif (v != undefined) {\n\t\t\t\t\t\tconst y = -numscale(v) - nm.maxradius\n\t\t\t\t\t\tg.append('circle')\n\t\t\t\t\t\t\t.attr('cy', y)\n\t\t\t\t\t\t\t//.attr('r', genotypebyvaluecircleradiusscale( num_altalt) )\n\t\t\t\t\t\t\t.attr('r', Math.sqrt(genotypebyvaluecircleradiusscale(num_altalt)) / Math.PI)\n\t\t\t\t\t\t\t.attr('stroke', tk.ds.genotypebynumericvalue.altalt.color)\n\t\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\t\ttk.tktip.show(event.clientX, event.clientY).clear()\n\t\t\t\t\t\t\t\tconst lst = [\n\t\t\t\t\t\t\t\t\t{ k: 'Variant', v: m.chr + ':' + (m.pos + 1) + ' ' + m.ref + '>' + m.alt },\n\t\t\t\t\t\t\t\t\t{ k: 'Genotype', v: 'Alt/Alt' },\n\t\t\t\t\t\t\t\t\t{ k: '#sample', v: num_altalt },\n\t\t\t\t\t\t\t\t\t{ k: tk.ds.genotypebynumericvalue.axislabel, v: v }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\tclient.make_table_2col(tk.tktip.d, lst)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} else {\n\t\tdiscg.attr('transform', m => {\n\t\t\treturn 'translate(' + m.xoff + ',' + (m._y + nm.maxradius) * -1 + ')'\n\t\t})\n\n\t\t// actual disc\n\t\tconst discdot = discg.append('circle')\n\t\t// hollow disc\n\t\tdiscdot\n\t\t\t.filter(m => m.dt == common.dtitd || m.dt == common.dtdel || m.dt == common.dtnloss || m.dt == common.dtcloss)\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('stroke-width', 2)\n\t\t\t.attr('stroke', m => color4disc(m, tk))\n\t\t\t.attr('r', m => m.radius - 2)\n\t\t// full filled\n\t\tdiscdot\n\t\t\t.filter(m => m.dt == common.dtsnvindel || m.dt == common.dtsv || m.dt == common.dtfusionrna)\n\t\t\t.attr('fill', m => color4disc(m, tk))\n\t\t\t.attr('stroke', 'white')\n\t\t\t.attr('r', m => m.radius - 0.5)\n\t\t// masking half\n\t\tdiscg\n\t\t\t.filter(m => m.dt == common.dtfusionrna || m.dt == common.dtsv)\n\t\t\t.append('path')\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('stroke', 'none')\n\t\t\t.attr('d', m =>\n\t\t\t\td3arc()({\n\t\t\t\t\tinnerRadius: 0,\n\t\t\t\t\touterRadius: m.radius - 2,\n\t\t\t\t\tstartAngle: m.useNterm ? 0 : Math.PI,\n\t\t\t\t\tendAngle: m.useNterm ? Math.PI : Math.PI * 2\n\t\t\t\t})\n\t\t\t)\n\n\t\t// no text in disc\n\n\t\t// disc kick\n\t\tdiscg\n\t\t\t.append('circle')\n\t\t\t.attr('r', m => m.radius - 0.5)\n\t\t\t.attr('stroke', m => color4disc(m, tk))\n\t\t\t.attr('class', 'sja_aa_disckick')\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('stroke-opacity', 0)\n\n\t\t\t.on('mousedown', event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t})\n\n\t\t\t.on('mouseover', (event, m) => {\n\t\t\t\tm_mouseover(m, tk)\n\t\t\t\tif (tk.disc_mouseover) {\n\t\t\t\t\ttk.disc_mouseover(m, event.target)\n\t\t\t\t} else {\n\t\t\t\t\tepaint_may_hl(tk, [m], true)\n\t\t\t\t}\n\t\t\t})\n\n\t\t\t.on('mouseout', (event, m) => {\n\t\t\t\tm_mouseout(m, tk)\n\t\t\t\tif (tk.disc_mouseout) {\n\t\t\t\t\ttk.disc_mouseout(m)\n\t\t\t\t} else {\n\t\t\t\t\tepaint_may_hl(tk, [m], false)\n\t\t\t\t}\n\t\t\t})\n\n\t\t\t.on('click', (event, m) => {\n\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\tm_click(m, p, tk, block)\n\t\t\t})\n\t}\n\n\t// m label\n\t// only make for those whose to appear on top or bottom\n\tconst textlabels = discg\n\t\t.filter(m => m.labattop || m.labatbottom)\n\t\t.append('text')\n\t\t.each(function (m) {\n\t\t\tm.textlabel = this\n\t\t})\n\t\t.text(m => mnamegetter(m.mname))\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', m => {\n\t\t\tm._labfontsize = Math.max(12, m.radius * 1.2)\n\t\t\treturn m._labfontsize\n\t\t})\n\t\t.attr('fill', m => color4disc(m, tk))\n\t\t.attr('x', m =>\n\t\t\tnm.showsamplebar || nm.showgenotypebyvalue\n\t\t\t\t? nm.axisheight + nm.maxradius + 4\n\t\t\t\t: m.radius + m.rimwidth + disclabelspacing\n\t\t)\n\t\t.attr('y', m => m._labfontsize * middlealignshift)\n\t\t.attr('class', 'sja_aa_disclabel')\n\t\t.attr('transform', m => 'rotate(' + (m.labattop ? '-' : '') + '90)')\n\t\t.on('mousedown', event => {\n\t\t\tevent.stopPropagation()\n\t\t})\n\t\t.on('mouseover', (event, m) => m_mouseover(m, tk))\n\t\t.on('mouseout', (event, m) => m_mouseout(m, tk))\n\t\t.on('click', (event, m) => {\n\t\t\tm_click(m, { left: event.clientX, top: event.clientY }, tk, block)\n\t\t})\n\n\tif (tk.hlaachange) {\n\t\t// special effect for highlighted variants\n\t\ttextlabels.filter(m => tk.hlaachange.has(m.mname)).classed('sja_pulse', true)\n\t}\n\n\t// disc rims\n\t/*\nconst rimfunc=d3arc()\n\t.innerRadius(d => d.radius )\n\t.outerRadius(d => d.radius+d.rimwidth )\n\t.startAngle(0)\n\t.endAngle(d=>{\n\t\td.rim1_startangle= Math.PI*2*d.rim1count/d.mlst.length\n\t\treturn d.rim1_startangle\n\t\t})\ndiscg.append('path')\n\t.attr('d',rimfunc)\n\t.attr('fill',d=> color4disc(d.mlst[0]) )\n\t.attr('class','sja_aa_discrim')\n\t.attr('fill-opacity',0)\nconst rimfunc2=d3arc()\n\t.innerRadius(d=>d.radius+.5)\n\t.outerRadius(d=>d.radius+.5+d.rimwidth)\n\t.startAngle(d=>d.rim1_startangle)\n\t.endAngle(d=>d.rim1_startangle+Math.PI*2*d.rim2count/d.mlst.length)\ndiscg\n\t.filter(d=>d.rim2count>0)\n\t.append('path')\n\t.attr('d',rimfunc2)\n\t.attr('stroke',d=>color4disc(d.mlst[0]))\n\t.attr('fill','none')\n\t.attr('class','sja_aa_discrim')\n\t.attr('stroke-opacity',0)\n\t*/\n}\n\nfunction m_mouseover(m, tk) {\n\tif (m.textlabel) {\n\t\td3select(m.textlabel).attr('font-size', m._labfontsize * 1.1)\n\t}\n\tconst nm = tk.numericmode\n\tif (nm.showsamplebar) return\n\tif (nm.showgenotypebyvalue) return\n\n\t// pica moves to center of m disc\n\ttk.pica.g.attr(\n\t\t'transform',\n\t\t'translate(' + (m.aa.x + m.xoff) + ',' + (nm.toplabelheight + nm.maxradius + nm.axisheight - m._y) + ')'\n\t)\n\n\tconst linelen = 10\n\tconst boxpad = 4\n\tconst fontsize = m._labfontsize || 13 // _labfontsize is undefined if this m has no lab\n\tconst color = color4disc(m, tk)\n\n\tlet textw = 0,\n\t\tshowlab = false\n\t// measure text w for value\n\ttk.pica.g\n\t\t.append('text')\n\t\t.attr('font-size', fontsize)\n\t\t.attr('font-family', client.font)\n\t\t.text(m._v)\n\t\t.each(function () {\n\t\t\ttextw = this.getBBox().width\n\t\t})\n\t\t.remove()\n\tif (!m.labattop && !m.labatbottom) {\n\t\t// pica also show label\n\t\tshowlab = true\n\t\ttk.pica.g\n\t\t\t.append('text')\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.text(m.mname)\n\t\t\t.each(function () {\n\t\t\t\ttextw = Math.max(textw, this.getBBox().width)\n\t\t\t})\n\t\t\t.remove()\n\t}\n\tconst boxw = boxpad * 2 + textw\n\tlet boxx,\n\t\tlinex1,\n\t\tonleft = true\n\tif (boxw + linelen > m.aa.x + m.xoff) {\n\t\t// pica on right\n\t\tonleft = false\n\t\tlinex1 = m.radius + m.rimwidth\n\t\tboxx = linex1 + linelen\n\t} else {\n\t\t// on left\n\t\tlinex1 = -m.radius - m.rimwidth - linelen\n\t\tboxx = linex1 - boxw\n\t}\n\n\t// bg box for white rim\n\ttk.pica.g\n\t\t.append('rect')\n\t\t.attr('x', boxx - 2)\n\t\t.attr('y', -2 - boxpad - (showlab ? fontsize : fontsize / 2))\n\t\t.attr('width', 4 + boxw)\n\t\t.attr('height', 4 + boxpad * 2 + fontsize * (showlab ? 2 : 1))\n\t\t.attr('fill', 'white')\n\ttk.pica.g\n\t\t.append('line')\n\t\t.attr('x1', linex1)\n\t\t.attr('x2', linex1 + linelen)\n\t\t.attr('stroke', 'white')\n\t\t.attr('stroke-width', 3)\n\t\t.attr('shape-rendering', 'crispEdges')\n\ttk.pica.g\n\t\t.append('line')\n\t\t.attr('x1', linex1)\n\t\t.attr('x2', linex1 + linelen)\n\t\t.attr('stroke', color)\n\t\t.attr('shape-rendering', 'crispEdges')\n\ttk.pica.g\n\t\t.append('rect')\n\t\t.attr('x', boxx)\n\t\t.attr('y', -boxpad - (showlab ? fontsize : fontsize / 2))\n\t\t.attr('width', boxw)\n\t\t.attr('height', boxpad * 2 + fontsize * (showlab ? 2 : 1))\n\t\t.attr('fill', 'none')\n\t\t.attr('stroke', color)\n\t\t.attr('shape-rendering', 'crispEdges')\n\ttk.pica.g\n\t\t.append('text')\n\t\t.text(m._v)\n\t\t.attr('text-anchor', onleft ? 'end' : 'start')\n\t\t.attr('font-size', fontsize)\n\t\t.attr('font-family', client.font)\n\t\t.attr('x', onleft ? linex1 - boxpad : boxx + boxpad)\n\t\t.attr('y', showlab ? -fontsize / 2 : 0)\n\t\t.attr('fill', color)\n\t\t.attr('dominant-baseline', 'central')\n\tif (showlab) {\n\t\ttk.pica.g\n\t\t\t.append('text')\n\t\t\t.text(m.mname)\n\t\t\t.attr('text-anchor', onleft ? 'end' : 'start')\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('x', onleft ? linex1 - boxpad : boxx + boxpad)\n\t\t\t.attr('y', showlab ? fontsize / 2 : 0)\n\t\t\t.attr('fill', color)\n\t\t\t.attr('dominant-baseline', 'central')\n\t}\n}\n\nfunction m_mouseout(m, tk) {\n\tif (m.textlabel) {\n\t\td3select(m.textlabel).attr('font-size', m._labfontsize)\n\t}\n\ttk.pica.g.selectAll('*').remove()\n}\n\nasync function m_click(m, p, tk, block) {\n\tif (m.dt == common.dtfusionrna || m.dt == common.dtsv) {\n\t\t// should not happen\n\t\titemtable({\n\t\t\tmlst: [m],\n\t\t\tpane: true,\n\t\t\tx: p.left - 10,\n\t\t\ty: p.top - 10,\n\t\t\ttk: tk,\n\t\t\tblock: block,\n\t\t\tsvgraph: true\n\t\t})\n\t\treturn\n\t}\n\n\tif (m.occurrence > 1) {\n\t\tif (\n\t\t\tawait may_sunburst(\n\t\t\t\tm.occurrence,\n\t\t\t\t[m],\n\t\t\t\tm.aa.x + m.xoff,\n\t\t\t\ttk.numericmode.toplabelheight + tk.numericmode.axisheight - m._y,\n\t\t\t\ttk,\n\t\t\t\tblock\n\t\t\t)\n\t\t)\n\t\t\treturn\n\t}\n\n\titemtable({\n\t\tmlst: [m],\n\t\tpane: true,\n\t\tx: p.left - 10,\n\t\ty: p.top - 10,\n\t\ttk: tk,\n\t\tblock: block\n\t})\n}\n\nfunction verticallabplace(tk) {\n\tconst mlst = []\n\tfor (const d of tk.data) {\n\t\tfor (const m of d.mlst) {\n\t\t\tmlst.push({\n\t\t\t\tm: m,\n\t\t\t\tw: 2 * (m.radius + m.rimwidth),\n\t\t\t\tx: d.x0,\n\t\t\t\ty: m._y\n\t\t\t})\n\t\t}\n\t}\n\n\tmlst.sort((i, j) => j.y - i.y) // descending\n\n\t// 1. labels pointing up, none has label yet\n\n\tfor (let i = 0; i < mlst.length; i++) {\n\t\tconst big = mlst[i]\n\t\tlet overlapwithdisc = false\n\t\tfor (let j = 0; j < i; j++) {\n\t\t\tconst small = mlst[j]\n\t\t\tif (Math.abs(big.x - small.x) < (big.w + small.w) / 2 - 2) {\n\t\t\t\toverlapwithdisc = true\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!overlapwithdisc) {\n\t\t\tbig.m.labattop = true\n\t\t}\n\t}\n\n\t// 2. labels pointing down\n\n\tfor (let i = mlst.length - 1; i >= 0; i--) {\n\t\tconst big = mlst[i]\n\t\tif (big.m.labattop) continue\n\t\tlet overlapwithlabeleddisc = false\n\t\tfor (let j = mlst.length - 1; j > i; j--) {\n\t\t\tconst small = mlst[j]\n\t\t\tif (small.m.labatbottom && Math.abs(small.x - big.x) < (small.w + big.w) / 2 - 2) {\n\t\t\t\toverlapwithlabeleddisc = true\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!overlapwithlabeleddisc) {\n\t\t\tbig.m.labatbottom = true\n\t\t}\n\t}\n}\n\nfunction skewer2_setstem(d, tk) {\n\tif (d.mlst.length == 1) {\n\t\treturn 'M0,0v' + tk.stem1 + 'l' + -d.xoffset + ',' + tk.stem2 + 'v' + tk.stem3\n\t}\n\t// funnel\n\treturn (\n\t\t'M0,0' +\n\t\t'v' +\n\t\ttk.stem1 + // vertical down\n\t\t'l' +\n\t\t-d.xoffset +\n\t\t',' +\n\t\ttk.stem2 + // slope 1\n\t\t'v' +\n\t\ttk.stem3 + // vertical down\n\t\t//+'h1' // to right 1\n\t\t'v-' +\n\t\ttk.stem3 + // veritical up\n\t\t'l' +\n\t\t(d.stemw + d.xoffset - 1) +\n\t\t',-' +\n\t\ttk.stem2 + // slope 2\n\t\t'v-' +\n\t\ttk.stem1\n\t)\n\t//+'Z'\n}\n\nfunction adjustview(tk, block) {\n\t/*\n\tself adjusting\n\tfor .data[], add:\n\t\t.x0\n\t\t.width\n\tfor .data[0].mlst[], add:\n\t\t.xoff\n\t\n\ttoggle between two views:\n\t1. cozy view, showing stem, x-shift, labels showing for all discs and point up\n\t2. crowded view, no stem, no x-shift, only show label for top/bottom items\n\n\t*/\n\n\tconst nm = tk.numericmode\n\n\tconst maxclusterwidth = 100\n\n\tlet sumwidth = 0\n\n\t// set initial width\n\n\tfor (const d of tk.data) {\n\t\tlet w = 0\n\t\tfor (const m of d.mlst) {\n\t\t\tw += 2 * (m.radius + m.rimwidth)\n\t\t}\n\n\t\tif (d.mlst.length == 1) {\n\t\t\td.width = w\n\t\t} else {\n\t\t\t// cluster, apply maximum allowed span\n\t\t\td.width = Math.min(maxclusterwidth, w)\n\n\t\t\tconst m0 = d.mlst[0]\n\t\t\tconst m1 = d.mlst[d.mlst.length - 1]\n\t\t\td.fixedgew = m0.radius + m0.rimwidth + m1.radius + m1.rimwidth\n\t\t}\n\n\t\tsumwidth += d.width\n\t}\n\n\tlet showstem = true\n\n\tif (sumwidth <= block.width) {\n\t\t// fits all\n\t\t// move all to left\n\t\tlet cum = 0\n\t\tfor (const d of tk.data) {\n\t\t\td.x = cum + d.mlst[0].radius + d.mlst[0].rimwidth\n\t\t\tcum += d.width\n\n\t\t\t// stemw required for placing\n\t\t\tif (d.mlst.length == 1) {\n\t\t\t\td.stemw = 0\n\t\t\t} else {\n\t\t\t\td.stemw = d.width - d.fixedgew\n\t\t\t}\n\t\t}\n\n\t\thoriplace1(tk.data, block.width)\n\n\t\tfor (const d of tk.data) {\n\t\t\td.xoffset = d.x - d.x0\n\n\t\t\tif (d.mlst.length == 1) {\n\t\t\t\td.mlst[0].xoff = 0\n\t\t\t\td.stemw = 0\n\t\t\t} else {\n\t\t\t\td.stemw = d.width - d.fixedgew\n\n\t\t\t\tconst span = d.stemw / (d.mlst.length - 1)\n\t\t\t\tfor (let i = 0; i < d.mlst.length; i++) {\n\t\t\t\t\td.mlst[i].xoff = span * i\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn true\n\t} else {\n\t\t/*\n\t\tover crowded\n\n\t\tlet singwidthsum = 0\n\t\tlet clustermcount = 0\n\t\tfor(const d of tk.data) {\n\t\t\tif(d.mlst.length==1) {\n\t\t\t\tsingwidthsum += d.width\n\t\t\t} else {\n\t\t\t\tclustermcount += d.mlst.length\n\t\t\t}\n\t\t}\n\n\t\tlet shrinkfactor=.99\n\t\twhile(1) {\n\t\t\tlet w=0\n\t\t\tfor(const d of tk.data) {\n\t\t\t\tif(d.mlst.length==1) {\n\t\t\t\t\tw+=d.width * shrinkfactor\n\t\t\t\t} else {\n\t\t\t\t\tif(d.shrinkfactor <= shrinkfactor) {\n\t\t\t\t\t\tw+=d.width\n\t\t\t\t\t} else {\n\t\t\t\t\t\tw+= d.originalwidth * shrinkfactor\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif(w<=block.width) {\n\t\t\t\t// accept\n\t\t\t\tfor(const d of tk.data) {\n\t\t\t\t\td.width *= shrinkfactor\n\t\t\t\t\tif(d.mlst.length>1) {\n\t\t\t\t\t\td.shrinkfactor = shrinkfactor\n\t\t\t\t\t\tif(d.stemw<=0) {\n\t\t\t\t\t\t\tconsole.log('.stemw < 0')\n\t\t\t\t\t\t}\n\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t\tshrinkfactor-=.02\n\t\t}\n\t\t*/\n\n\t\t// do not shrink and horiplace\n\t\tfor (const d of tk.data) {\n\t\t\td.x = d.x0\n\t\t\td.xoffset = 0\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tm.xoff = 0\n\t\t\t}\n\t\t}\n\n\t\t// do not show stem\n\t\treturn false\n\t}\n}\n\nfunction horiplace1(items, allwidth) {\n\t/*\n\tonly for numeric\n\t*/\n\tfor (let i = 0; i < items.length; i++) {\n\t\tif (items[i].x0 < 0) continue\n\t\tif (items[i].x0 > allwidth) break\n\n\t\twhile (1) {\n\t\t\tlet currsum = 0,\n\t\t\t\tnewsum = 0\n\t\t\tfor (let j = i; j < items.length; j++) {\n\t\t\t\tconst t = items[j]\n\t\t\t\tif (t.x0 > allwidth) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tcurrsum += Math.abs(t.x - t.x0 - t.stemw / 2)\n\t\t\t\tt.x++\n\t\t\t\tnewsum += Math.abs(t.x - t.x0 - t.stemw / 2)\n\t\t\t}\n\t\t\tif (items[i].x > items[i].x0 - items[i].stemw / 2) {\n\t\t\t\t// wind back to make sure stem [i] stem is straight\n\t\t\t\tfor (let j = i; j < items.length; j++) {\n\t\t\t\t\titems[j].x--\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t\tconst z = items[items.length - 1]\n\t\t\tif (z.x + z.width / 2 >= allwidth) {\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (newsum <= currsum) {\n\t\t\t\t// accept move\n\t\t\t} else {\n\t\t\t\t// reject move, procceed to next item\n\t\t\t\tfor (let j = i; j < items.length; j++) {\n\t\t\t\t\tif (items[j].x0 > allwidth) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\t// wind back\n\t\t\t\t\titems[j].x--\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n}\n", "import { scaleLinear, scaleOrdinal } from 'd3-scale'\nimport { arc as d3arc } from 'd3-shape'\nimport { select as d3select } from 'd3-selection'\nimport { itemtable } from './block.ds.itemtable'\nimport * as client from './client'\nimport * as coord from './coord'\nimport * as common from '#shared/common.js'\nimport { duplicate as svduplicate } from '#shared/bulk.sv.js'\nimport * as vcftk from './block.ds.vcf'\nimport { rendernumerictk } from './block.ds.numericmode'\nimport may_sunburst from './block.sunburst'\nimport { schemeCategory20 } from '#common/legacy-d3-polyfill'\n\n/*\na dstk can be vcf, server-hosted ds (sqlite and/or 1 or more vcf)\nhere do following things for dstk:\n- load data by querying server\n- parse and add data to the track\n- render the skewer track\n********************** EXPORTED \ndstkload(tk,block)\n\t- server query and load data from sqlite/vcf\nload2tk(datalst,block,tk)\n\t- add data to dstk\ndstkrender(tk, block)\ngetter_mcset_key\nepaint_may_hl\nmlst_pretreat\ndone_tknodata\n********************** INTERNAL\nrenderskewertk\nskewer_make()\nshowlegend_populationfrequencyfilter\nshowlegend_vcfinfofilter\nshowlegend_sampleattribute\nlegendmenu_vcfinfo\nlegendmenu_sampleattribute\ndsqueryresult_geneexpression()\ndsqueryresult_snvindelfusionitd()\n*/\n\n// vcfinfofilter in which a variant is not annotated by a given key\nconst vcfnotannotated_label = 'Not annotated'\n\n// for skewer track\nexport const middlealignshift = 0.3\nexport const disclabelspacing = 1 // px spacing between disc and label\n\n/*\ncutoff value of # pixel per bp\ncompared to exonsf\nwhen exonsf>:\n\tbasepairs are visible enough, and group mutation grps by basepair position\nelse exon<:\n\tbasepairs are too tiny and will group mutations by AA position\n*/\nexport const minbpwidth = 4\n\nconst modefold = 0\nconst modeshow = 1\n\nexport async function dstkload(tk, block) {\n\t/*\n\tthree sources of data\n\t1. vcf file, server query\n\t2. client in-memory data\n\t3. server ds.queries[]\n\t*/\n\n\ttry {\n\t\tif (!tk) throw 'no tk'\n\t\tif (!tk.ds) throw 'no ds'\n\n\t\tif (!block.gmmode || block.gmmode == client.gmmode.genomic) {\n\t\t\t// for dstk, only apply limit in genomic mode\n\t\t\tif (block.viewrangeabovelimit(tk.viewrangeupperlimit)) {\n\t\t\t\ttk.mlst = []\n\t\t\t\ttk.viewrangeupperlimit_above = true\n\t\t\t\tdstkrender(tk, block)\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\t\tdelete tk.viewrangeupperlimit_above\n\n\t\tif (tk.isvcf) {\n\t\t\t/* is one or a set of vcf tracks\n\t\t\tin this case won't require tk.ds (should be undefined)\n\t\t\tvcf-only, no mixture with db tk\n\t\t\t*/\n\t\t\tblock.tkcloakon(tk)\n\t\t\tvcftk.loadvcftk(block, tk)\n\t\t\treturn\n\t\t}\n\n\t\tif (block.ds2handle[tk.ds.label]) {\n\t\t\ttk.__handlesays = block.ds2handle[tk.ds.label].handlesays // quick fix\n\t\t}\n\n\t\tif (tk.ds.bulkdata || tk.ds.mlst) {\n\t\t\treturn await dstkload_fromclientdata(tk, block)\n\t\t}\n\n\t\t// will query the server-side ds.queries[]\n\t\tawait dstkload_fromdsquery(tk, block)\n\n\t\tmayAddSubtk_legacyDsFilter(tk, block)\n\n\t\ttk.ds.busy = false\n\t\tblock.tkcloakoff(tk, {})\n\t} catch (e) {\n\t\tif (e.stack) console.log(e.stack)\n\t\ttk.ds.busy = false\n\t\tblock.tkcloakoff(tk, { error: e.message || e })\n\t\tblock.setllabel(tk)\n\t\tblock.block_setheight()\n\t}\n}\n\nfunction mayAddSubtk_legacyDsFilter(tk, block) {\n\tif (!tk.legacyDsFilter) return\n\n\tif (!tk.legacyDsFilter.key || !tk.legacyDsFilter.value) throw 'legacyDsFilter is not {key,value}'\n\n\tconst mlst = tk.mlst.filter(m => m[tk.legacyDsFilter.key] == tk.legacyDsFilter.value)\n\tconst _ds = {\n\t\tlabel: tk.ds.label + ' - ' + tk.legacyDsFilter.value,\n\t\tbulkdata: {},\n\t\tparentname: tk.ds.label,\n\t\tiscustom: true,\n\t\tsampleselectable: tk.ds.sampleselectable\n\t}\n\t_ds.bulkdata[block.usegm.name.toUpperCase()] = mlst\n\tblock.addchilddsnoload(_ds)\n\tconst childtk = block.block_addtk_template({ type: client.tkt.ds, ds: _ds })\n\tdstkload(childtk, block)\n}\n\nasync function dstkload_fromclientdata(tk, block) {\n\t// custom ds with data stored on client\n\tif (block.usegm) {\n\t\tif (tk.__handlesays) {\n\t\t\ttk.__handlesays.style('background-color', '#ddd').style('color', 'black')\n\t\t}\n\t\tlet mlst = []\n\t\tif (tk.ds.bulkdata) {\n\t\t\tconst lst2 = tk.ds.bulkdata[block.usegm.name.toUpperCase()]\n\t\t\tif (lst2) {\n\t\t\t\tmlst = [...lst2]\n\t\t\t}\n\t\t}\n\t\tif (tk.ds.mlst) {\n\t\t\tfor (const m of tk.ds.mlst) {\n\t\t\t\tif (m.gene.toUpperCase() == block.usegm.name.toUpperCase()) {\n\t\t\t\t\tmlst.push(m)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (mlst.length) {\n\t\t\tconst isoformmatch = []\n\t\t\tfor (const m of mlst) {\n\t\t\t\tif (m.isoform && m.isoform == block.usegm.isoform) {\n\t\t\t\t\tisoformmatch.push(m)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (isoformmatch.length) {\n\t\t\t\tload2tk([{ lst: isoformmatch }], block, tk)\n\t\t\t} else {\n\t\t\t\tthrow 'No data from ' + tk.ds.label + ' for ' + block.usegm.isoform\n\t\t\t}\n\t\t} else {\n\t\t\tthrow 'No data from ' + tk.ds.label + ' for ' + block.usegm.name\n\t\t}\n\t\tif (tk.ds.dbexpression && (!tk.eplst || tk.eplst.length == 0)) {\n\t\t\t// custom expression set\n\t\t\tconst par = {\n\t\t\t\tjwt: block.jwt,\n\t\t\t\tdb: tk.ds.dbexpression.dbfile,\n\t\t\t\ttablename: tk.ds.dbexpression.tablename,\n\t\t\t\tkeyname: tk.ds.dbexpression.keyname,\n\t\t\t\tkey: block.usegm.name\n\t\t\t}\n\t\t\tconst data = await client.dofetch2('dbdata', { method: 'POST', body: JSON.stringify(par) })\n\t\t\tif (data.error) throw data.error\n\t\t\tif (!tk.eplst) tk.eplst = []\n\t\t\tif (tk.ds.dbexpression.tidy) tk.ds.dbexpression.tidy(data.rows)\n\t\t\tconst eparg = {\n\t\t\t\tdata: data.rows,\n\t\t\t\texpp: tk.ds.dbexpression.config,\n\t\t\t\tblock,\n\t\t\t\tgenome: block.genome,\n\t\t\t\tgenename: block.usegm.name,\n\t\t\t\tdsname: tk.ds.label\n\t\t\t}\n\t\t\tconst p = await import('./ep')\n\t\t\ttk.eplst.push(new p.default(eparg))\n\t\t}\n\t} else {\n\t\t// genomic view\n\t\tconst mlst = []\n\t\tconst chrset = new Map()\n\t\tfor (const r of block.rglst) {\n\t\t\tif (!chrset.has(r.chr)) {\n\t\t\t\tchrset.set(r.chr, [])\n\t\t\t}\n\t\t\tchrset.get(r.chr).push(r)\n\t\t}\n\t\tconst allmlst = []\n\t\tif (tk.ds.bulkdata) {\n\t\t\tfor (const k in tk.ds.bulkdata) {\n\t\t\t\tallmlst.push(...tk.ds.bulkdata[k])\n\t\t\t}\n\t\t}\n\t\tif (tk.ds.mlst) {\n\t\t\tallmlst.push(...tk.ds.mlst)\n\t\t}\n\t\tfor (const m of allmlst) {\n\t\t\tswitch (m.dt) {\n\t\t\t\tcase common.dtsnvindel:\n\t\t\t\tcase common.dtitd:\n\t\t\t\tcase common.dtdel:\n\t\t\t\tcase common.dtnloss:\n\t\t\t\tcase common.dtcloss:\n\t\t\t\t\tif (!m.pos) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\tif (!m.chr && !chrset.has(m.chr)) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\tfor (const r of chrset.get(m.chr)) {\n\t\t\t\t\t\tif (m.pos >= r.start && m.pos < r.stop) {\n\t\t\t\t\t\t\tmlst.push(m)\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tbreak\n\t\t\t\tcase common.dtsv:\n\t\t\t\tcase common.dtfusionrna:\n\t\t\t\t\tif (!m.pairlst) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\tlet hit = false\n\t\t\t\t\tfor (const pair of m.pairlst) {\n\t\t\t\t\t\t// a\n\t\t\t\t\t\tif (pair.a.chr && chrset.has(pair.a.chr)) {\n\t\t\t\t\t\t\tconst pos = pair.a.position || pair.a.pos\n\t\t\t\t\t\t\tif (pos) {\n\t\t\t\t\t\t\t\tfor (const r of chrset.get(pair.a.chr)) {\n\t\t\t\t\t\t\t\t\tif (pos >= r.start && pos < r.stop) {\n\t\t\t\t\t\t\t\t\t\thit = true\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\t// b\n\t\t\t\t\t\tif (pair.b.chr && chrset.has(pair.b.chr)) {\n\t\t\t\t\t\t\tconst pos = pair.b.position || pair.b.pos\n\t\t\t\t\t\t\tif (pos) {\n\t\t\t\t\t\t\t\tfor (const r of chrset.get(pair.b.chr)) {\n\t\t\t\t\t\t\t\t\tif (pos >= r.start && pos < r.stop) {\n\t\t\t\t\t\t\t\t\t\thit = true\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (hit) {\n\t\t\t\t\t\tmlst.push(m)\n\t\t\t\t\t}\n\t\t\t\t\tbreak\n\t\t\t\t// end of switch\n\t\t\t}\n\t\t}\n\t\tif (mlst.length) {\n\t\t\tload2tk([{ lst: mlst }], block, tk)\n\t\t}\n\t}\n}\n\nasync function dstkload_fromdsquery(tk, block) {\n\tif (tk.__handlesays) tk.__handlesays.text('Loading...')\n\ttk.ds.busy = true\n\tblock.tkcloakon(tk)\n\n\tconst par = {\n\t\tgenome: block.genome.name,\n\t\tdsname: tk.ds.label,\n\t\trange: block.tkarg_maygm(tk)[0] // FIXME no support for rglst!\n\t}\n\tif (block.usegm) {\n\t\tpar.genename = block.usegm.name\n\t\tpar.isoform = block.usegm.isoform\n\t}\n\tif (tk.eplst) {\n\t\t// hard-coded\n\t\t// means this track has already been loaded\n\t\tpar.noexpression = 1\n\t}\n\tif (block.hidedatasetexpression) {\n\t\t// embed customization\n\t\tpar.noexpression = 1\n\t}\n\t// ?? how to define regulatory regions associated with a gene (retrieve and show it by default)\n\t// ?? how to retrieve data over regulatory region from a db\n\n\tconst data = await client.dofetch2('dsdata', { method: 'POST', body: JSON.stringify(par) })\n\tif (tk.__handlesays) {\n\t\ttk.__handlesays.text(tk.ds.label).style('background-color', '#ddd').style('color', 'black')\n\t}\n\tif (data.error) throw data.error\n\tload2tk(data.data, block, tk)\n}\n\nexport function load2tk(datalst, block, tk) {\n\tif (tk.dsuninitiated) {\n\t\t// pull from tklst\n\t\tfor (let i = 0; i < block.tklst.length; i++) {\n\t\t\tif (block.tklst[i].tkid == tk.tkid) {\n\t\t\t\tblock.tklst.splice(i, 1)\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tdelete tk.dsuninitiated\n\t\t// above or below pbar\n\t\tlet gmtkidx = -1\n\t\tfor (let i = 0; i < block.tklst.length; i++) {\n\t\t\tconst t = block.tklst[i]\n\t\t\tif (t.type == client.tkt.usegm && !t.hidden) {\n\t\t\t\tgmtkidx = i\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\n\t\tlet aboveprotein = true\n\n\t\tif (gmtkidx == -1) {\n\t\t\t// no gmtk shown, just add\n\t\t\taboveprotein = true\n\t\t\tblock.tklst.push(tk)\n\t\t} else {\n\t\t\t// has gmtk\n\t\t\tlet dsabove = false\n\t\t\tfor (let i = 0; i < gmtkidx; i++) {\n\t\t\t\tconst t = block.tklst[i]\n\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\tdsabove = true\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (dsabove) {\n\t\t\t\t// this dstk to below gmtk\n\t\t\t\taboveprotein = false\n\t\t\t\tblock.tklst.splice(gmtkidx + 1, 0, tk)\n\t\t\t} else {\n\t\t\t\t// to above\n\t\t\t\taboveprotein = true\n\t\t\t\tif (gmtkidx == 0) {\n\t\t\t\t\tblock.tklst.unshift(tk)\n\t\t\t\t} else {\n\t\t\t\t\tblock.tklst.splice(gmtkidx - 1, 0, tk)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (tk.aboveprotein == undefined) {\n\t\t\t// do not override pointdown\n\t\t\ttk.aboveprotein = aboveprotein\n\t\t}\n\n\t\ttk.eplst = [] // only do it here!!!\n\t} else {\n\t\t// already in block.tklst, don't insert\n\t}\n\t// parse data\n\ttk.mlst = []\n\n\t/*\n\tpediatric has 2 ep\n\twill need to shift 2nd panel position\n\t*/\n\tconst eploaders = []\n\n\tfor (const dat of datalst) {\n\t\t// individual queries in this dataset\n\t\tif (dat.isgeneexpression) {\n\t\t\teploaders.push(dsqueryresult_geneexpression(dat, tk, block))\n\t\t\tcontinue\n\t\t}\n\t\tif (dat.vcfid) {\n\t\t\t// single vcf\n\t\t\tvcftk.data2tk(dat, tk, block)\n\t\t\tcontinue\n\t\t}\n\t\tif (dat.lst) {\n\t\t\t// variant dataset\n\t\t\tdsqueryresult_snvindelfusionitd(dat.lst, tk, block)\n\t\t\tmay_print_stratifycountfromserver(dat, tk)\n\t\t\tcontinue\n\t\t}\n\t\tblock.error('unknown data/query type from ' + tk.ds.label)\n\t\treturn\n\t}\n\n\tPromise.all(eploaders).then(() => {\n\t\tif (tk.eplst.length > 1) {\n\t\t\tfor (let i = 1; i < tk.eplst.length; i++) {\n\t\t\t\tconst ep = tk.eplst[i]\n\t\t\t\tep.pane.pane.style('left', Number.parseInt(tk.eplst[0].pane.pane.style('left')) + 50 * i + 'px')\n\t\t\t\tep.pane.pane.style('top', Number.parseInt(tk.eplst[0].pane.pane.style('top')) + 50 * i + 'px')\n\t\t\t}\n\t\t}\n\t})\n\n\tdstkrender(tk, block)\n}\n\nexport function dstkrender(tk, block) {\n\t/*\ntk.mlst[] is set\n*/\n\n\tblock.tkcloakoff(tk, {})\n\n\tmlst_set_occurrence(tk)\n\n\tif (tk.vcfinfofilter && tk.vcfinfofilter.setidx4numeric != undefined) {\n\t\tif (!tk.numericmode) {\n\t\t\t// entering numeric mode\n\t\t\ttk.numericmode = { axisheight: tk.axisheight }\n\t\t}\n\t} else {\n\t\tdelete tk.numericmode\n\t}\n\n\t/*\n\tjinghui asked to hide all nonpathogenic germline variants by default\n\tset common.morigin.GNP.hidden=true\n\tupon first rendering ds track, block.legend.morigins is not made yet, so no way of knowing who to hide by default\n\t*/\n\tconst originhidden = new Set()\n\tfor (const k in common.morigin) {\n\t\tif (common.morigin[k].hidden) {\n\t\t\toriginhidden.add(k)\n\t\t}\n\t}\n\n\tvcfinfofilter_mayupdateautocategory(tk, block)\n\n\tif (tk.numericmode) {\n\t\trendernumerictk(tk, block, originhidden)\n\t} else {\n\t\trenderskewertk(tk, block, originhidden)\n\t}\n\n\tblock.setllabel(tk)\n\n\tblock.block_setheight()\n\n\tblock.tkchangeaffectlegend(tk)\n\n\t/*\n\tcustom class, vcf info fields, sample annotation\n\tstuff to show on legend\n\t*/\n\tshowlegend_vcfinfofilter(tk, block)\n\tshowlegend_populationfrequencyfilter(tk, block)\n\t{\n\t\tconst err = showlegend_sampleattribute(tk, block)\n\t\tif (err) console.log('showlegend_sampleattribute: ' + err)\n\t}\n}\n\nfunction mlst_set_occurrence(tk) {\n\t/*\nhandle multiple ways of assigning occurrence\n.occurrence now applies to all legacy ds track, applications:\n- skewer graph to decide dot size\n- sunburst\n*/\n\tif (tk.vcfinfofilter && tk.vcfinfofilter.setidx4occurrence != undefined) {\n\t\tconst mcset = tk.vcfinfofilter.lst[tk.vcfinfofilter.setidx4occurrence]\n\t\tif (!mcset) throw 'mcset not found by setidx4occurrence'\n\t\tfor (const m of tk.mlst) {\n\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\t\t\tif (err || vlst == undefined) {\n\t\t\t\tm.occurrence = 1\n\t\t\t} else {\n\t\t\t\tm.occurrence = vlst[0]\n\t\t\t}\n\t\t}\n\t} else {\n\t\t// occurrence may not apply to the data at all, but still assigning it\n\t\tfor (const m of tk.mlst) {\n\t\t\tm.occurrence = 1\n\t\t}\n\t}\n}\n\nfunction renderskewertk(tk, block, originhidden) {\n\t/*\n\tmakes:\n\ttk.data\n\ttk.skewer\n\ttk.maxskewerheight\n\t*/\n\n\ttk.leftaxis.selectAll('*').remove() // in case turned from numericmode\n\n\t// when to skip grouping\n\tif (block.usegm && block.gmmode != client.gmmode.genomic && block.pannedpx != undefined && tk.skewer) {\n\t\t// in gmmode, browser panned, no re-requesting data\n\t\t// no need to re-group\n\t\t// set x\n\n\t\ttkdata_update_x(tk, block)\n\n\t\ttk.skewer.attr('transform', d => 'translate(' + d.x + ',' + d.y + ')')\n\t\tsettle_glyph(tk, block)\n\t} else {\n\t\t// create group and skewer anew\n\t\ttk.glider.selectAll('*').remove()\n\n\t\tconst usemlst = mlst_pretreat(tk, block, originhidden)\n\n\t\tconst x2mlst = new Map()\n\t\tfor (const m of tk.mlst) {\n\t\t\tif (m.__x == undefined) {\n\t\t\t\t// dropped by filter\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (!x2mlst.has(m.__x)) {\n\t\t\t\tx2mlst.set(m.__x, [])\n\t\t\t}\n\t\t\tx2mlst.get(m.__x).push(m)\n\t\t}\n\t\tconst datagroup = []\n\t\tconst topxbins = []\n\t\t// by resolution\n\t\tif (block.exonsf >= minbpwidth) {\n\t\t\t// # pixel per nt is big enough\n\t\t\t// group by each nt\n\t\t\tfor (const [x, mlst] of x2mlst) {\n\t\t\t\tdatagroup.push({\n\t\t\t\t\tchr: mlst[0].chr,\n\t\t\t\t\tpos: mlst[0].pos,\n\t\t\t\t\tmlst: mlst,\n\t\t\t\t\tx: x,\n\t\t\t\t\tgroups: mlst2disc(mlst, tk)\n\t\t\t\t})\n\t\t\t}\n\t\t} else {\n\t\t\t// # pixel per nt is too small\n\t\t\tif (block.usegm && block.usegm.coding && block.gmmode != client.gmmode.genomic) {\n\t\t\t\t// by aa\n\t\t\t\t// in gmsum, rglst may include introns, need to distinguish symbolic and rglst introns, use __x difference by a exonsf*3 limit\n\t\t\t\tconst aa2mlst = new Map()\n\t\t\t\tfor (const [x, mlst] of x2mlst) {\n\t\t\t\t\tif (mlst[0].chr != block.usegm.chr) {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\t// TODO how to identify if mlst belongs to regulatory region rather than gm\n\t\t\t\t\tlet aapos = undefined\n\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\tif (Number.isFinite(m.aapos)) aapos = m.aapos\n\t\t\t\t\t}\n\t\t\t\t\tif (aapos == undefined) {\n\t\t\t\t\t\taapos = coord.genomic2gm(mlst[0].pos, block.usegm).aapos\n\t\t\t\t\t}\n\t\t\t\t\tif (aapos == undefined) {\n\t\t\t\t\t\tconsole.error('data item cannot map to aaposition')\n\t\t\t\t\t\tconsole.log(mlst[0])\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tx2mlst.delete(x)\n\t\t\t\t\tif (!aa2mlst.has(aapos)) {\n\t\t\t\t\t\taa2mlst.set(aapos, [])\n\t\t\t\t\t}\n\t\t\t\t\tlet notmet = true\n\t\t\t\t\tfor (const lst of aa2mlst.get(aapos)) {\n\t\t\t\t\t\tif (Math.abs(lst[0].__x - mlst[0].__x) <= block.exonsf * 3) {\n\t\t\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\t\t\tlst.push(m)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tnotmet = false\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (notmet) {\n\t\t\t\t\t\taa2mlst.get(aapos).push(mlst)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tconst utr5len = block.usegm.utr5 ? block.usegm.utr5.reduce((i, j) => i + j[1] - j[0], 0) : 0\n\t\t\t\tfor (const llst of aa2mlst.values()) {\n\t\t\t\t\tfor (const mlst of llst) {\n\t\t\t\t\t\tlet m = null\n\t\t\t\t\t\tfor (const m2 of mlst) {\n\t\t\t\t\t\t\tif (Number.isFinite(m2.rnapos)) m = m2\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (m == null) {\n\t\t\t\t\t\t\tconsole.log('trying to map mlst to codon, but no rnapos found')\n\t\t\t\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t\t\t\tconsole.log(m)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t}\n\t\t\t\t\t\tdatagroup.push({\n\t\t\t\t\t\t\tchr: mlst[0].chr,\n\t\t\t\t\t\t\tpos: m.pos,\n\t\t\t\t\t\t\tmlst: mlst,\n\t\t\t\t\t\t\tx: mlst[0].__x,\n\t\t\t\t\t\t\tgroups: mlst2disc(mlst, tk)\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\t// leftover by px bin\n\t\t\tconst pxbin = []\n\t\t\tconst binpx = 2\n\t\t\tfor (const [x, mlst] of x2mlst) {\n\t\t\t\tconst i = Math.floor(x / binpx)\n\t\t\t\tif (!pxbin[i]) {\n\t\t\t\t\tpxbin[i] = []\n\t\t\t\t}\n\t\t\t\tpxbin[i] = [...pxbin[i], ...mlst]\n\t\t\t}\n\t\t\tfor (const mlst of pxbin) {\n\t\t\t\tif (!mlst) continue\n\t\t\t\tconst xsum = mlst.reduce((i, j) => i + j.__x, 0)\n\t\t\t\tdatagroup.push({\n\t\t\t\t\tisbin: true,\n\t\t\t\t\tchr: mlst[0].chr,\n\t\t\t\t\tpos: mlst[0].pos,\n\t\t\t\t\tmlst: mlst,\n\t\t\t\t\tx: xsum / mlst.length,\n\t\t\t\t\tgroups: mlst2disc(mlst, tk)\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tdatagroup.sort((a, b) => a.x - b.x)\n\t\tif (tk.data && block.pannedpx != undefined && (!block.usegm || block.gmmode == client.gmmode.genomic)) {\n\t\t\t// inherit genomic mode and panned\n\t\t\tconst pastmode = {}\n\t\t\tfor (const g of tk.data) {\n\t\t\t\tpastmode[g.chr + '.' + g.pos] = {\n\t\t\t\t\tmode: g.showmode,\n\t\t\t\t\txoffset: g.xoffset,\n\t\t\t\t\tslabelrotate: g.slabelrotate // no effect\n\t\t\t\t}\n\t\t\t}\n\t\t\tfor (const g of datagroup) {\n\t\t\t\tconst k = g.chr + '.' + g.pos\n\t\t\t\tif (pastmode[k]) {\n\t\t\t\t\tg.showmode = pastmode[k].mode\n\t\t\t\t\tg.xoffset = pastmode[k].xoffset\n\t\t\t\t\tg.slabelrotate = pastmode[k].slabelrotate\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\ttk.data = datagroup\n\t\tfor (const d of tk.data) {\n\t\t\td.occurrence = d.groups.reduce((i, j) => i + j.occurrence, 0)\n\t\t}\n\t\tskewer_make(tk, block)\n\t\ttk.height_main = tk.toppad + tk.maxskewerheight + tk.stem1 + tk.stem2 + tk.stem3 + tk.bottompad\n\t}\n\n\tif (!tk.data || tk.data.length == 0) {\n\t\tdone_tknodata(tk, block)\n\t\treturn\n\t}\n\n\t/*\n\tvariants loaded for this track\n\t*/\n\n\tif (tk.hlaachange || tk.hlvariants) {\n\t\t/*\n\t\tfor any variants to be highlighted, expanded and fold all the others\n\t\t*/\n\t\tconst fold = []\n\t\tconst unfold = []\n\n\t\tif (tk.hlaachange) {\n\t\t\t// is map\n\t\t\tfor (const d of tk.data) {\n\t\t\t\tlet has = false\n\t\t\t\tfor (const g of d.groups) {\n\t\t\t\t\tif (tk.hlaachange.has(g.mlst[0].mname)) {\n\t\t\t\t\t\thas = true\n\t\t\t\t\t\ttk.hlaachange.delete(g.mlst[0].mname)\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (has) {\n\t\t\t\t\tunfold.push(d)\n\t\t\t\t} else {\n\t\t\t\t\tfold.push(d)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (tk.hlaachange.size) {\n\t\t\t\tif (!block.usegm) {\n\t\t\t\t\tblock.error('cannot add items from hlaachange: not in gene-mode')\n\t\t\t\t} else {\n\t\t\t\t\thlaachange_addnewtrack(tk, block)\n\t\t\t\t}\n\t\t\t}\n\t\t\tdelete tk.hlaachange\n\t\t}\n\n\t\tif (tk.hlvariants) {\n\t\t\t// is array\n\t\t\tconst hlkeys = {}\n\t\t\tfor (const m of tk.hlvariants) {\n\t\t\t\thlkeys[m.chr + '.' + m.pos + '.' + m.ref + '.' + m.alt] = 1\n\t\t\t}\n\n\t\t\tfor (const d of tk.data) {\n\t\t\t\tlet has = false\n\t\t\t\tfor (const g of d.groups) {\n\t\t\t\t\tif (has) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\tfor (const m of g.mlst) {\n\t\t\t\t\t\tif (hlkeys[m.chr + '.' + m.pos + '.' + m.ref + '.' + m.alt]) {\n\t\t\t\t\t\t\thas = true\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (has) {\n\t\t\t\t\tunfold.push(d)\n\t\t\t\t} else {\n\t\t\t\t\tfold.push(d)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tfold_glyph(fold, tk)\n\t\tunfold_glyph(unfold, tk, block)\n\t} else {\n\t\t// natural expand\n\t\tsettle_glyph(tk, block)\n\t}\n}\n\nfunction group2occurrence(g, tk) {\n\tif (tk.vcfinfofilter && tk.vcfinfofilter.setidx4occurrence != undefined) {\n\t\tconst mcset = tk.vcfinfofilter.lst[tk.vcfinfofilter.setidx4occurrence]\n\t\tconst [err, vlst] = getter_mcset_key(mcset, g.mlst[0])\n\t\tif (err || vlst == undefined) return 1\n\t\treturn vlst[0]\n\t}\n\treturn g.mlst.length\n}\n\nfunction mlst2disc(mlst, tk) {\n\tconst k2g = new Map()\n\tfor (const m of mlst) {\n\t\tswitch (m.dt) {\n\t\t\tcase common.dtsnvindel:\n\t\t\t\tif (!k2g.has(m.dt)) {\n\t\t\t\t\tk2g.set(m.dt, new Map())\n\t\t\t\t}\n\t\t\t\tif (!k2g.get(m.dt).has(m.class)) {\n\t\t\t\t\tk2g.get(m.dt).set(m.class, new Map())\n\t\t\t\t}\n\t\t\t\tconst n = m.mname || ''\n\t\t\t\tif (!k2g.get(m.dt).get(m.class).has(n)) {\n\t\t\t\t\tk2g.get(m.dt).get(m.class).set(n, [])\n\t\t\t\t}\n\t\t\t\tk2g.get(m.dt).get(m.class).get(n).push(m)\n\t\t\t\tbreak\n\t\t\tcase common.dtsv:\n\t\t\tcase common.dtfusionrna:\n\t\t\t\tif (!k2g.has(m.dt)) {\n\t\t\t\t\tk2g.set(m.dt, new Map())\n\t\t\t\t}\n\t\t\t\tif (!k2g.get(m.dt).has(m.class)) {\n\t\t\t\t\tk2g.get(m.dt).set(m.class, {\n\t\t\t\t\t\tuse5: new Map(),\n\t\t\t\t\t\tuse3: new Map()\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tif (m.useNterm) {\n\t\t\t\t\tif (!k2g.get(m.dt).get(m.class).use5.has(m.mname)) {\n\t\t\t\t\t\tk2g.get(m.dt).get(m.class).use5.set(m.mname, [])\n\t\t\t\t\t}\n\t\t\t\t\tk2g.get(m.dt).get(m.class).use5.get(m.mname).push(m)\n\t\t\t\t} else {\n\t\t\t\t\tif (!k2g.get(m.dt).get(m.class).use3.has(m.mname)) {\n\t\t\t\t\t\tk2g.get(m.dt).get(m.class).use3.set(m.mname, [])\n\t\t\t\t\t}\n\t\t\t\t\tk2g.get(m.dt).get(m.class).use3.get(m.mname).push(m)\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase common.dtitd:\n\t\t\tcase common.dtdel:\n\t\t\tcase common.dtnloss:\n\t\t\tcase common.dtcloss:\n\t\t\t\tif (!k2g.has(m.dt)) {\n\t\t\t\t\tk2g.set(m.dt, [])\n\t\t\t\t}\n\t\t\t\tk2g.get(m.dt).push(m)\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tconsole.log('unknown datatype: ' + m.dt)\n\t\t\t\tconsole.log(m)\n\t\t\t\treturn\n\t\t}\n\t}\n\tconst groups = []\n\tfor (const [dt, tmp] of k2g) {\n\t\tswitch (dt) {\n\t\t\tcase common.dtsnvindel:\n\t\t\t\tfor (const t2 of tmp.values()) {\n\t\t\t\t\tfor (const mlst of t2.values()) {\n\t\t\t\t\t\tgroups.push({\n\t\t\t\t\t\t\tdt: dt,\n\t\t\t\t\t\t\tmlst: mlst\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase common.dtsv:\n\t\t\tcase common.dtfusionrna:\n\t\t\t\tfor (const classset of tmp.values()) {\n\t\t\t\t\tfor (const mlst of classset.use5.values()) {\n\t\t\t\t\t\tgroups.push({\n\t\t\t\t\t\t\tdt: dt,\n\t\t\t\t\t\t\tuseNterm: true,\n\t\t\t\t\t\t\tmlst: mlst\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tfor (const mlst of classset.use3.values()) {\n\t\t\t\t\t\tgroups.push({\n\t\t\t\t\t\t\tdt: dt,\n\t\t\t\t\t\t\tuseNterm: false,\n\t\t\t\t\t\t\tmlst: mlst\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase common.dtitd:\n\t\t\tcase common.dtdel:\n\t\t\tcase common.dtnloss:\n\t\t\tcase common.dtcloss:\n\t\t\t\tgroups.push({\n\t\t\t\t\tdt: dt,\n\t\t\t\t\tmlst: tmp\n\t\t\t\t})\n\t\t}\n\t}\n\tfor (const g of groups) {\n\t\tlet rim1count = 0,\n\t\t\trim2count = 0\n\t\tfor (const m of g.mlst) {\n\t\t\tif (m.isrim1) rim1count++\n\t\t\telse if (m.isrim2) rim2count++\n\t\t}\n\t\tg.rim1count = rim1count\n\t\tg.rim2count = rim2count\n\t\tg.occurrence = g.mlst.reduce((i, j) => i + j.occurrence, 0) //group2occurrence(g, tk)\n\t}\n\tgroups.sort((a, b) => {\n\t\treturn b.occurrence - a.occurrence\n\t})\n\treturn groups\n}\n\nfunction skewer_make(tk, block) {\n\t/*\nnew things:\nitd/del stacked bars\ncustom mclass from vcfinfofilter\n*/\n\n\tdelete tk.skewer2\n\n\tconst color4disc = m => {\n\t\tif (tk.vcfinfofilter && tk.vcfinfofilter.setidx4mclass != undefined) {\n\t\t\tconst mcset = tk.vcfinfofilter.lst[tk.vcfinfofilter.setidx4mclass]\n\n\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\n\t\t\tif (err || vlst == undefined) return 'black'\n\n\t\t\tfor (const v of vlst) {\n\t\t\t\t// no choice but simply use first value to ever have a valid color\n\t\t\t\tif (mcset.categories[v]) {\n\t\t\t\t\treturn mcset.categories[v].color\n\t\t\t\t} else {\n\t\t\t\t\treturn 'black'\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// mclass\n\t\tif (common.mclass[m.class]) {\n\t\t\treturn common.mclass[m.class].color\n\t\t}\n\t\treturn 'black'\n\t}\n\n\t// ITD/DEL stacked bars\n\tconst stackbars = []\n\tfor (const d of tk.data) {\n\t\td.x0 = d.x\n\t\tif (d.xoffset != undefined) {\n\t\t\td.x = d.x0 + d.xoffset\n\t\t}\n\t\t// updates x\n\t\t// create stack bars\n\t\tfor (const g of d.groups) {\n\t\t\tg.aa = d // disc reference group\n\t\t\tlet rnaspan = null\n\t\t\tif (g.dt == common.dtitd) {\n\t\t\t\trnaspan = g.mlst[0].rnaduplength\n\t\t\t\tfor (const m of g.mlst) {\n\t\t\t\t\trnaspan = Math.max(rnaspan, m.rnaduplength)\n\t\t\t\t}\n\t\t\t} else if (g.dt == common.dtdel) {\n\t\t\t\trnaspan = g.mlst[0].rnadellength\n\t\t\t\tfor (const m of g.mlst) {\n\t\t\t\t\trnaspan = Math.max(rnaspan, m.rnadellength)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// no business\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// no isInteger, rna position can have .5\n\t\t\tif (!Number.isFinite(rnaspan) || rnaspan < 0) {\n\t\t\t\t// support if genomic pos is available\n\t\t\t\tconsole.log('no rnaspan for stack bar from itd/del')\n\t\t\t\tconsole.log(g.mlst)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tlet pxspan = null\n\t\t\tif (block.usegm) {\n\t\t\t\tconst rnapos = g.mlst[0].rnapos // rnapos should always be available!\n\t\t\t\tconst genomicpos = coord.rna2gmcoord(rnapos + rnaspan, block.usegm)\n\t\t\t\tconst hits = block.seekcoord(block.usegm.chr, genomicpos)\n\t\t\t\tif (hits.length > 0) {\n\t\t\t\t\tpxspan = hits[0].x - d.x\n\t\t\t\t} else {\n\t\t\t\t\tconsole.log(genomicpos + ' no hit on rglst')\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!Number.isFinite(pxspan)) {\n\t\t\t\tconsole.log('no pxspan for stack bar from itd/del')\n\t\t\t\tconsole.log(g.mlst)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tg.stackbar = {\n\t\t\t\taa: d.mlst[0].aapos,\n\t\t\t\tpxspan: pxspan,\n\t\t\t\theight: 4, // fixed bar height\n\t\t\t\tgrp: g\n\t\t\t}\n\t\t\td.hasstackbar = true\n\t\t\tstackbars.push(g.stackbar)\n\t\t}\n\t}\n\tlet stackbarmaxheight = 0 // for setting stem3\n\t// TODO stairs may replace stackbars\n\tif (stackbars.length > 0) {\n\t\tlet ypad = 1\n\t\tfor (let i = 0; i < stackbars.length; i++) {\n\t\t\tconst si = stackbars[i]\n\t\t\tconst overlap = []\n\t\t\tfor (let j = 0; j < i; j++) {\n\t\t\t\tconst sj = stackbars[j]\n\t\t\t\tif (Math.max(si.aa, sj.aa) < Math.min(si.pxspan + si.aa, sj.pxspan + sj.aa)) {\n\t\t\t\t\toverlap.push(sj)\n\t\t\t\t}\n\t\t\t}\n\t\t\tsi.y = 2\n\t\t\tfor (const sj of overlap) {\n\t\t\t\tif (Math.max(si.y, sj.y) < Math.min(si.y + si.height, sj.y + sj.height)) {\n\t\t\t\t\tsi.y = sj.y + sj.height + ypad\n\t\t\t\t}\n\t\t\t}\n\t\t\tstackbarmaxheight = Math.max(stackbarmaxheight, si.y + si.height)\n\t\t}\n\t}\n\n\tconst dotwidth = Math.max(14, block.width / 110)\n\t// create skewers for all data (single or multiple) and compute width\n\n\t// get max m count for discs, for scaling disc radius\n\tlet mdc = 0\n\tfor (const d of tk.data) {\n\t\tfor (const g of d.groups) {\n\t\t\tmdc = Math.max(mdc, g.occurrence)\n\t\t}\n\t}\n\tlet mrd = 0 // max disc radius\n\tconst w = Math.pow(dotwidth / 2, 2) * Math.PI // unit area\n\tif (mdc <= 10) mrd = w * mdc * 0.9\n\telse if (mdc <= 100) mrd = w * 10\n\telse if (mdc <= 1000) mrd = w * 14\n\telse mrd = w * 20\n\t// scale for disc radius\n\tconst sf_discradius = scaleLinear()\n\t\t.domain([1, mdc * 0.5, mdc * 0.6, mdc * 0.7, mdc * 0.8, mdc])\n\t\t.range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd])\n\tlet globalmaxradius = dotwidth / 2\n\ttk.maxskewerheight = 0\n\ttk.skewer = tk.glider\n\t\t.selectAll()\n\t\t.data(tk.data)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('class', 'sja_skg')\n\t\t.each(function (d) {\n\t\t\t// determine dimension for this skewer, do not position or render yet\n\t\t\t// compute radius for each group\n\t\t\td.skewer = this\n\t\t\tif (d.showmode == undefined) {\n\t\t\t\td.showmode = modefold\n\t\t\t} else {\n\t\t\t\t// has already been set by past data from genomic panning\n\t\t\t}\n\t\t\td.maxradius = 0\n\t\t\td.maxrimwidth = 0\n\t\t\td.width = 0\n\t\t\td.slabelrotate = false\n\t\t\td.slabelwidth = 0\n\t\t\tfor (const r of d.groups) {\n\t\t\t\tif (r.occurrence == 1) {\n\t\t\t\t\tr.radius = dotwidth / 2\n\t\t\t\t} else {\n\t\t\t\t\tconst digc = r.occurrence.toString().length\n\t\t\t\t\tr.radius = Math.max(Math.sqrt(sf_discradius(r.occurrence) / Math.PI), digc * 5)\n\t\t\t\t}\n\t\t\t\td.maxradius = Math.max(d.maxradius, r.radius)\n\t\t\t\tglobalmaxradius = Math.max(globalmaxradius, r.radius)\n\n\t\t\t\tr.rimwidth = r.rim1count + r.rim2count == 0 ? 0 : Math.max(2, r.radius / 6)\n\t\t\t\td.maxrimwidth = Math.max(d.maxrimwidth, r.rimwidth)\n\t\t\t}\n\t\t\tlet totalheight = 0\n\t\t\tfor (const r of d.groups) {\n\t\t\t\tr.yoffset = totalheight + r.radius + r.rimwidth // immutable, y shift at expand mode\n\t\t\t\ttotalheight += (r.radius + r.rimwidth) * 2\n\t\t\t}\n\t\t\ttk.maxskewerheight = Math.max(tk.maxskewerheight, totalheight)\n\t\t})\n\t// disc containers\n\tconst discg = tk.skewer\n\t\t.selectAll()\n\t\t.data(d => d.groups)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr(\n\t\t\t'transform',\n\t\t\td => 'translate(0,' + (d.aa.showmode == modefold ? 0 : d.yoffset * (tk.aboveprotein ? -1 : 1)) + ')'\n\t\t)\n\t\t.attr('class', 'sja_aa_discg')\n\t\t.each(function (d) {\n\t\t\td.g = this\n\t\t})\n\t// actual disc\n\tconst discdot = discg.append('circle')\n\t// hollow disc\n\tdiscdot\n\t\t.filter(d => d.dt == common.dtitd || d.dt == common.dtdel || d.dt == common.dtnloss || d.dt == common.dtcloss)\n\t\t.attr('fill', 'white')\n\t\t.attr('stroke-width', 2)\n\t\t.attr('stroke', d => color4disc(d.mlst[0]))\n\t\t.attr('r', d => d.radius - 2)\n\t// full filled\n\tdiscdot\n\t\t.filter(d => d.dt == common.dtsnvindel || d.dt == common.dtsv || d.dt == common.dtfusionrna)\n\t\t.attr('fill', d => color4disc(d.mlst[0]))\n\t\t.attr('stroke', 'white')\n\t\t.attr('r', d => d.radius - 0.5)\n\t// masking half\n\tdiscg\n\t\t.filter(d => d.dt == common.dtfusionrna || d.dt == common.dtsv)\n\t\t.append('path')\n\t\t.attr('fill', 'white')\n\t\t.attr('stroke', 'none')\n\t\t.attr('d', d =>\n\t\t\td3arc()({\n\t\t\t\tinnerRadius: 0,\n\t\t\t\touterRadius: d.radius - 2,\n\t\t\t\tstartAngle: d.useNterm ? 0 : Math.PI,\n\t\t\t\tendAngle: d.useNterm ? Math.PI : Math.PI * 2\n\t\t\t})\n\t\t)\n\t// number in disc\n\tconst textslc = discg\n\t\t.filter(d => d.occurrence > 1)\n\t\t.append('text')\n\t\t.text(d => d.occurrence)\n\t\t.attr('font-family', client.font)\n\t\t.attr('class', 'sja_aa_discnum')\n\t\t.attr('fill-opacity', d => (d.aa.showmode == modefold ? 0 : 1))\n\t\t.attr('stroke-opacity', d => (d.aa.showmode == modefold ? 0 : 1))\n\t\t.attr('text-anchor', 'middle')\n\t\t.each(d => {\n\t\t\tconst s = d.radius * 1.5\n\t\t\td.discnumfontsize = Math.min(s / (d.occurrence.toString().length * client.textlensf), s)\n\t\t})\n\t\t.attr('font-size', d => d.discnumfontsize)\n\t\t.attr('y', d => d.discnumfontsize * middlealignshift)\n\ttextslc.filter(d => d.dt == common.dtsnvindel).attr('fill', 'white')\n\ttextslc\n\t\t.filter(d => d.dt == common.dtsv || d.dt == common.dtfusionrna)\n\t\t.attr('stroke', d => color4disc(d.mlst[0]))\n\t\t.attr('stroke-width', 0.8)\n\t\t.attr('font-weight', 'bold')\n\t\t.attr('fill', 'white')\n\ttextslc\n\t\t.filter(d => d.dt == common.dtitd || d.dt == common.dtdel || d.dt == common.dtcloss || d.dt == common.dtnloss)\n\t\t.attr('fill', d => color4disc(d.mlst[0]))\n\t// right-side label\n\tconst textlab = discg\n\t\t.append('text')\n\t\t.text(d => d.mlst[0].mname)\n\t\t.attr('font-size', d => {\n\t\t\td._labfontsize = Math.max(12, d.radius * 1.2)\n\t\t\treturn d._labfontsize\n\t\t})\n\t\t.each(function (d) {\n\t\t\t// after setting font size, set skewer width by label width\n\t\t\tconst lw = this.getBBox().width\n\t\t\td._label_width = lw\n\t\t\tif (d.aa.groups.length == 1) {\n\t\t\t\td.aa.slabelrotate = true\n\t\t\t\td.aa.slabelwidth = lw\n\t\t\t\t// skewer has single disc, label may rotate up, thus should be considerred in maxskewerheight\n\t\t\t\ttk.maxskewerheight = Math.max(tk.maxskewerheight, (d.radius + d.rimwidth) * 2 + 2 + lw)\n\t\t\t}\n\t\t})\n\t\t.attr('fill', d => color4disc(d.mlst[0]))\n\t\t.attr('x', d => d.radius + d.rimwidth + 1)\n\t\t.attr('y', d => d._labfontsize * middlealignshift)\n\t\t.attr('font-family', client.font)\n\t\t.classed('sja_aa_disclabel', true)\n\t\t.attr('fill-opacity', d => (d.aa.showmode == modefold ? 0 : 1))\n\t\t.attr('transform', 'scale(1) rotate(0)')\n\t\t.on('mousedown', event => {\n\t\t\tevent.stopPropagation()\n\t\t})\n\t\t.on('click', (event, d) => {\n\t\t\tfold_glyph([d.aa], tk)\n\t\t\tunfold_update(tk, block)\n\t\t\tif (block.debugmode) {\n\t\t\t\tconsole.log(d.aa)\n\t\t\t}\n\t\t})\n\n\tif (tk.hlaachange) {\n\t\t// special effect for highlighted variants\n\t\t//const big=1.3\n\t\ttextlab.filter(d => tk.hlaachange.has(d.mlst[0].mname)).classed('sja_pulse', true)\n\t\t/*\n\t.attr('font-weight',(d)=>{\n\t\treturn tk.hlaachange.has(d.mlst[0].mname) ? 'bold' : 'normal'\n\t})\n\t.attr('font-size',(d)=>{\n\t\treturn d._labfontsize*big\n\t})\n\t.attr('y',d=> d._labfontsize*big*middlealignshift)\n\t*/\n\t}\n\n\t// skewer width\n\tfor (const d of tk.data) {\n\t\tlet leftw = 0,\n\t\t\trightw = 0\n\t\tfor (const g of d.groups) {\n\t\t\tleftw = Math.max(leftw, g.radius + g.rimwidth)\n\t\t\trightw = Math.max(rightw, g.radius + g.rimwidth + disclabelspacing + g._label_width)\n\t\t}\n\t\td.width = leftw + rightw\n\t}\n\n\t// invisible kicking disc cover\n\tdiscg\n\t\t.append('circle')\n\t\t.attr('r', d => d.radius - 0.5)\n\t\t.attr('stroke', d => color4disc(d.mlst[0]))\n\t\t.attr('class', 'sja_aa_disckick')\n\t\t.attr('fill', 'white')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('stroke-opacity', 0)\n\t\t.on('mousedown', event => {\n\t\t\tevent.stopPropagation()\n\t\t})\n\t\t.on('mouseover', (event, d) => {\n\t\t\tif (tk.disc_mouseover) {\n\t\t\t\ttk.disc_mouseover(d, event.target)\n\t\t\t} else {\n\t\t\t\tepaint_may_hl(tk, d.mlst, true)\n\t\t\t}\n\t\t})\n\t\t.on('mouseout', (event, d) => {\n\t\t\tif (tk.disc_mouseout) {\n\t\t\t\ttk.disc_mouseout(d)\n\t\t\t} else {\n\t\t\t\tepaint_may_hl(tk, d.mlst, false)\n\t\t\t}\n\t\t})\n\t\t.on('click', async (event, d) => {\n\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\tif (d.dt == common.dtfusionrna || d.dt == common.dtsv) {\n\t\t\t\t// svgraph\n\t\t\t\titemtable({\n\t\t\t\t\tmlst: d.mlst,\n\t\t\t\t\tpane: true,\n\t\t\t\t\tx: p.left - 10,\n\t\t\t\t\ty: p.top - 10,\n\t\t\t\t\ttk,\n\t\t\t\t\tblock,\n\t\t\t\t\tsvgraph: true\n\t\t\t\t})\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (d.occurrence == 1) {\n\t\t\t\t// table for single\n\t\t\t\titemtable({ mlst: d.mlst, pane: true, x: p.left - 10, y: p.top - 10, tk: tk, block: block })\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (\n\t\t\t\tawait may_sunburst(\n\t\t\t\t\td.occurrence,\n\t\t\t\t\td.mlst,\n\t\t\t\t\td.aa.x,\n\t\t\t\t\tskewer_sety(d, tk) + d.yoffset * (tk.aboveprotein ? -1 : 1),\n\t\t\t\t\ttk,\n\t\t\t\t\tblock\n\t\t\t\t)\n\t\t\t) {\n\t\t\t\treturn\n\t\t\t}\n\t\t\t// many items to table\n\t\t\titemtable({\n\t\t\t\tmlst: d.mlst,\n\t\t\t\tpane: true,\n\t\t\t\tx: p.left - 10,\n\t\t\t\ty: p.top - 10,\n\t\t\t\ttk,\n\t\t\t\tblock\n\t\t\t})\n\t\t})\n\n\t// disc rims\n\tconst rimfunc = d3arc()\n\t\t.innerRadius(d => d.radius)\n\t\t.outerRadius(d => d.radius + d.rimwidth)\n\t\t.startAngle(0)\n\t\t.endAngle(d => {\n\t\t\td.rim1_startangle = (Math.PI * 2 * d.rim1count) / d.occurrence\n\t\t\treturn d.rim1_startangle\n\t\t})\n\tdiscg\n\t\t.append('path')\n\t\t.attr('d', rimfunc)\n\t\t.attr('fill', d => color4disc(d.mlst[0]))\n\t\t.attr('class', 'sja_aa_discrim')\n\t\t.attr('fill-opacity', 0)\n\tconst rimfunc2 = d3arc()\n\t\t.innerRadius(d => d.radius + 0.5)\n\t\t.outerRadius(d => d.radius + 0.5 + d.rimwidth)\n\t\t.startAngle(d => d.rim1_startangle)\n\t\t.endAngle(d => d.rim1_startangle + (Math.PI * 2 * d.rim2count) / d.occurrence)\n\tdiscg\n\t\t.filter(d => d.rim2count > 0)\n\t\t.append('path')\n\t\t.attr('d', rimfunc2)\n\t\t.attr('stroke', d => color4disc(d.mlst[0]))\n\t\t.attr('fill', 'none')\n\t\t.attr('class', 'sja_aa_discrim')\n\t\t.attr('stroke-opacity', 0)\n\t// set stem lengths\n\t{\n\t\t// stem 1,2\n\t\tlet lapcount = 0\n\t\tlet lastx = 0\n\t\tfor (const d of tk.data) {\n\t\t\tif (d.x - d.maxradius - d.maxrimwidth < lastx) {\n\t\t\t\tlapcount++\n\t\t\t}\n\t\t\tlastx = Math.max(lastx, d.x + d.width - d.maxradius - d.maxrimwidth)\n\t\t}\n\t\t// stem1\n\t\ttk.stem1 = lapcount == 0 ? 0 : dotwidth\n\t\t// stem2\n\t\ttk.stem2 = scaleLinear()\n\t\t\t.domain([0, 1, tk.data.length])\n\t\t\t.range([0, dotwidth, dotwidth * 3])(lapcount)\n\t}\n\t// stem3\n\tconst hbaseline = dotwidth * 0.7\n\t// to set stem3, get max group size\n\tlet maxm = 0\n\tfor (const d of tk.data) {\n\t\tfor (const g of d.groups) {\n\t\t\tmaxm = Math.max(maxm, g.occurrence)\n\t\t}\n\t}\n\ttk.stem3 = Math.max(stackbarmaxheight + 2, hbaseline + dotwidth * Math.min(5, maxm))\n\t// invisible kicking skewer cover when folded\n\ttk.skewer\n\t\t.append('circle')\n\t\t.attr('class', 'sja_aa_skkick')\n\t\t.attr('fill', 'white')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('stroke', 'none')\n\t\t.attr('r', d => d.maxradius + 1)\n\t\t.attr('cy', d => (tk.aboveprotein ? -1 : 1) * d.maxradius)\n\t\t.attr('transform', d => 'scale(' + (d.showmode == modefold ? 1 : 0) + ')')\n\t\t.on('mouseover', (event, d) => {\n\t\t\tepaint_may_hl(tk, d.mlst, true)\n\t\t\tconst abp = tk.aboveprotein\n\t\t\tlet cumh = 0\n\t\t\tlet boxw = 0\n\t\t\tconst hpad = 5\n\t\t\tconst tiph = abp ? 7 : 14\n\t\t\tfor (const g of d.groups) {\n\t\t\t\tg.pica_fontsize = Math.max(11, g.radius)\n\t\t\t\tcumh += g.pica_fontsize + 1\n\t\t\t\ttk.pica.g\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(g.mlst[0].mname + (g.occurrence > 1 ? ' x' + g.occurrence : ''))\n\t\t\t\t\t.attr('font-size', g.pica_fontsize)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tboxw = Math.max(boxw, this.getBBox().width)\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t}\n\t\t\tboxw += hpad * 2\n\t\t\tconst boxh = cumh + 5\n\t\t\ttk.pica.g\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('y', abp ? -boxh : 0)\n\t\t\t\t.attr('width', boxw)\n\t\t\t\t.attr('height', boxh)\n\t\t\t\t.attr('fill', 'white')\n\t\t\t\t.attr('fill-opacity', 0.8)\n\t\t\t\t.attr('stroke', '#ccc')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\tcumh = 0\n\t\t\tconst _g = tk.pica.g\n\t\t\t\t.selectAll()\n\t\t\t\t.data(d.groups)\n\t\t\t\t.enter()\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', (g, i) => {\n\t\t\t\t\tcumh += g.pica_fontsize + 1\n\t\t\t\t\treturn 'translate(' + hpad + ',' + cumh * (abp ? -1 : 1) + ')'\n\t\t\t\t})\n\t\t\t_g.append('text')\n\t\t\t\t.text(g => g.mlst[0].mname)\n\t\t\t\t.attr('font-size', g => g.pica_fontsize)\n\t\t\t\t.each(function (g) {\n\t\t\t\t\tg.pica_mlabelwidth = this.getBBox().width\n\t\t\t\t})\n\t\t\t\t.attr('fill', d => color4disc(d.mlst[0]))\n\t\t\t\t.attr('dominant-baseline', abp ? 'hanging' : 'auto')\n\t\t\tconst firstlabw = d.groups[0].pica_mlabelwidth\n\t\t\ttk.pica.x = d.x - hpad - firstlabw / 2\n\t\t\ttk.pica.y = d.y + (abp ? -1 : 1) * (d.maxradius * 2 + tiph + 2)\n\t\t\ttk.pica.g.attr('transform', 'translate(' + tk.pica.x + ',' + tk.pica.y + ')')\n\t\t\t_g.filter(g => g.occurrence > 1)\n\t\t\t\t.append('text')\n\t\t\t\t.text(g => 'x' + g.occurrence)\n\t\t\t\t.attr('x', g => g.pica_mlabelwidth + 5)\n\t\t\t\t.attr('font-size', g => g.pica_fontsize)\n\t\t\t\t.attr('dominant-baseline', abp ? 'hanging' : 'auto')\n\t\t\t\t.attr('fill', '#9e9e9e')\n\t\t\tconst handle = tk.pica.g\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', 'translate(' + (hpad + firstlabw / 2) + ',' + (abp ? 1 : -1) + ')')\n\t\t\thandle\n\t\t\t\t.append('line')\n\t\t\t\t.attr('y2', (abp ? 1 : -1) * tiph)\n\t\t\t\t.attr('stroke', '#858585')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\thandle\n\t\t\t\t.append('line')\n\t\t\t\t.attr('x1', -1)\n\t\t\t\t.attr('x2', -1)\n\t\t\t\t.attr('y2', (abp ? 1 : -1) * tiph)\n\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\thandle\n\t\t\t\t.append('line')\n\t\t\t\t.attr('x1', 1)\n\t\t\t\t.attr('x2', 1)\n\t\t\t\t.attr('y2', (abp ? 1 : -1) * tiph)\n\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t})\n\t\t.on('mouseout', (event, d) => {\n\t\t\ttk.pica.g.selectAll('*').remove()\n\t\t\tepaint_may_hl(tk, d.mlst, false)\n\t\t})\n\t\t.on('click', (event, d) => {\n\t\t\ttk.pica.g.selectAll('*').remove()\n\t\t\tunfold_glyph([d], tk, block)\n\t\t})\n\t// set fold y offset\n\t// get max mcount for skewers\n\tlet mm = 0\n\tfor (const d of tk.data) {\n\t\tmm = Math.max(mm, d.occurrence)\n\t}\n\tconst sf_foldyoff = scaleLinear()\n\t\t.domain([1, mm])\n\t\t.range([hbaseline, tk.stem3 - globalmaxradius])\n\ttk.skewer.attr('transform', d => {\n\t\td.foldyoffset = sf_foldyoff(d.occurrence)\n\t\td.y = skewer_sety(d, tk)\n\t\treturn 'translate(' + d.x + ',' + d.y + ')'\n\t})\n\tif (stackbars.length > 0) {\n\t\t// stack bars, make this before stem\n\t\ttk.skewer\n\t\t\t.filter(d => d.hasstackbar)\n\t\t\t.selectAll()\n\t\t\t.data(d => {\n\t\t\t\tconst bars = []\n\t\t\t\tfor (const g of d.groups) {\n\t\t\t\t\tif (g.stackbar) {\n\t\t\t\t\t\tbars.push(g.stackbar)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn bars\n\t\t\t})\n\t\t\t.enter()\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sja_aa_stackbar_g')\n\t\t\t.attr('transform', d => {\n\t\t\t\t// initially all skewers are folded so only use stem1\n\t\t\t\treturn 'translate(0,' + (tk.aboveprotein ? 1 : -1) * (tk.stem1 - d.y) + ')'\n\t\t\t})\n\t\t\t.append('rect')\n\t\t\t.attr('y', d => (tk.aboveprotein ? -d.height : 0))\n\t\t\t.attr('class', 'sja_aa_stackbar_rect')\n\t\t\t.attr('width', 0)\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t.attr('fill-opacity', 0.5)\n\t\t\t.attr('stroke', 'none')\n\t\t\t.attr('stroke-width', 1)\n\t\t\t.attr('height', d => d.height)\n\t\t\t.attr('fill', d => color4disc(d.grp.mlst[0]))\n\t\t\t.on('mouseover', (event, d) => {\n\t\t\t\tconst color = color4disc(d.grp.mlst[0])\n\t\t\t\td3select(event.target).attr('stroke', color)\n\t\t\t\tconst pica = tk.pica\n\t\t\t\tlet label1 = 'wrong label'\n\t\t\t\tlet label2 = 'wrong label, '\n\t\t\t\tswitch (d.grp.mlst[0].dt) {\n\t\t\t\t\tcase common.dtitd:\n\t\t\t\t\t\tlabel1 = common.mclass[d.grp.mlst[0].class].desc\n\t\t\t\t\t\tlabel2 = Math.ceil(d.grp.mlst[0].rnaduplength / 3) + ' aa, '\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase common.dtdel:\n\t\t\t\t\t\tlabel1 = common.mclass[d.grp.mlst[0].class].label\n\t\t\t\t\t\tlabel2 = Math.ceil(d.grp.mlst[0].rnadellength / 3) + ' aa, '\n\t\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tif (d.grp.occurrence == 1) {\n\t\t\t\t\tconst m = d.grp.mlst[0]\n\t\t\t\t\tif (m.sample) {\n\t\t\t\t\t\tlabel2 += m.sample\n\t\t\t\t\t} else if (m.patient) {\n\t\t\t\t\t\tlabel2 += m.patient\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlabel2 += '1 sample'\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tlabel2 += d.grp.occurrence + ' samples'\n\t\t\t\t}\n\t\t\t\tconst fontsize1 = 14,\n\t\t\t\t\tfontsize2 = 10,\n\t\t\t\t\tvpad = 2,\n\t\t\t\t\thpad = 4\n\t\t\t\tlet width = 0\n\t\t\t\tpica.g\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(label1)\n\t\t\t\t\t.attr('font-size', fontsize1)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\twidth = this.getBBox().width\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tpica.g\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(label2)\n\t\t\t\t\t.attr('font-size', fontsize2)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\twidth = Math.max(width, this.getBBox().width)\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tconst boxheight = vpad * 3 + fontsize1 + fontsize2\n\t\t\t\tpica.x = d.grp.aa.x0 + 3\n\t\t\t\tpica.y = tk.aboveprotein\n\t\t\t\t\t? tk.height_main - tk.toppad - tk.bottompad - d.y - d.height - 3 - boxheight\n\t\t\t\t\t: d.y + d.height + 3\n\t\t\t\tpica.g.attr('transform', 'translate(' + pica.x + ',' + pica.y + ')')\n\t\t\t\tpica.g\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('width', width + hpad * 2)\n\t\t\t\t\t.attr('height', boxheight)\n\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t.attr('stroke-width', 1)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t.attr('fill-opacity', 0.8)\n\t\t\t\tpica.g\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(label1)\n\t\t\t\t\t.attr('x', hpad)\n\t\t\t\t\t.attr('y', vpad + fontsize1 / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t.attr('font-size', fontsize1)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', color)\n\t\t\t\tpica.g\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(label2)\n\t\t\t\t\t.attr('x', hpad)\n\t\t\t\t\t.attr('y', vpad * 2 + fontsize1 + fontsize2 / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t.attr('font-size', fontsize2)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t})\n\t\t\t.on('mouseout', (event, d) => {\n\t\t\t\td3select(event.target).attr('stroke', 'none')\n\t\t\t\ttk.pica.g.selectAll('*').remove()\n\t\t\t})\n\t\t\t.on('click', (event, d) => {\n\t\t\t\titemtable({\n\t\t\t\t\tmlst: d.grp.mlst,\n\t\t\t\t\tpane: true,\n\t\t\t\t\tx: event.clientX,\n\t\t\t\t\ty: event.clientY,\n\t\t\t\t\ttk: tk,\n\t\t\t\t\tblock: block\n\t\t\t\t})\n\t\t\t})\n\t}\n\t// stem\n\ttk.skewer\n\t\t.append('path')\n\t\t.attr('class', 'sja_aa_stem')\n\t\t.attr('d', d => skewer_setstem(d, tk))\n\t\t.attr('stroke', d => color4disc(d.groups[0].mlst[0]))\n\t\t.attr('fill', 'none')\n\t// ssk: only for skewers with >1 groups\n\tconst mgsk = tk.skewer.filter(d => d.groups.length > 1)\n\tmgsk\n\t\t.append('rect')\n\t\t.attr('class', 'sja_aa_ssk_bg')\n\t\t.attr('shape-rendering', 'crispEdges')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('height', tk.stem1)\n\t\t.attr('fill', d => color4disc(d.groups[0].mlst[0]))\n\t\t.attr('width', d => {\n\t\t\td.ssk_width = Math.max(d.occurrence.toString().length * 8 + 6, 2 * (d.maxradius + d.maxrimwidth))\n\t\t\treturn d.ssk_width\n\t\t})\n\t\t.attr('x', d => -d.ssk_width / 2)\n\tmgsk\n\t\t.append('text')\n\t\t.attr('class', 'sja_aa_ssk_text')\n\t\t.attr('fill', 'white')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('font-weight', 'bold')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('dominant-baseline', 'central')\n\t\t.text(d => d.occurrence)\n\t\t.each(d => {\n\t\t\td.ssk_fontsize = Math.min(tk.stem1, d.ssk_width / (d.occurrence.toString().length * client.textlensf))\n\t\t})\n\t\t.attr('font-size', d => d.ssk_fontsize)\n\t// ssk - kick\n\tmgsk\n\t\t.append('rect')\n\t\t.attr('class', 'sja_aa_ssk_kick')\n\t\t.attr('fill', 'white')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('stroke', 'none')\n\t\t.attr('height', tk.stem1)\n\t\t.attr('x', d => -d.ssk_width / 2)\n\t\t.attr('width', d => d.ssk_width)\n\t\t.on('mouseover', (event, d) => {\n\t\t\tconst p = d3select(event.target.parentNode)\n\t\t\tp.selectAll('.sja_aa_disckick').transition().attr('stroke-opacity', 1)\n\t\t\tp.select('.sja_aa_ssk_bg').transition().attr('fill-opacity', 1).attr('stroke-opacity', 1)\n\t\t\tp.select('.sja_aa_ssk_text').transition().attr('fill-opacity', 1)\n\t\t\tepaint_may_hl(tk, d.mlst, true)\n\t\t})\n\t\t.on('mouseout', function (event, d) {\n\t\t\tconst p = d3select(event.target.parentNode)\n\t\t\tp.selectAll('.sja_aa_disckick').transition().attr('stroke-opacity', 0)\n\t\t\tp.select('.sja_aa_ssk_bg').transition().attr('fill-opacity', 0).attr('stroke-opacity', 0)\n\t\t\tp.select('.sja_aa_ssk_text').transition().attr('fill-opacity', 0)\n\t\t\tepaint_may_hl(tk, d.mlst, false)\n\t\t})\n\t\t.on('click', async (event, d) => {\n\t\t\t// must not check event after await as it will be voided\n\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\tif (d.occurrence > 1) {\n\t\t\t\tif (await may_sunburst(d.occurrence, d.mlst, d.x, d.y + ((tk.aboveprotein ? 1 : -1) * tk.stem1) / 2, tk, block))\n\t\t\t\t\treturn\n\t\t\t}\n\t\t\titemtable({\n\t\t\t\tmlst: d.mlst,\n\t\t\t\tpane: true,\n\t\t\t\tx: p.left - 10,\n\t\t\t\ty: p.top - 10,\n\t\t\t\ttk: tk,\n\t\t\t\tblock: block\n\t\t\t})\n\t\t})\n}\n\nexport function skewer_flip(tk) {\n\ttk.aboveprotein = !tk.aboveprotein\n\n\tif (tk.numericmode) {\n\t\t// won't do\n\t\treturn\n\t}\n\n\tconst abp = tk.aboveprotein\n\tconst dur = 1000\n\n\tconst skbars = tk.skewer.filter(d => d.hasstackbar)\n\tskbars\n\t\t.selectAll('.sja_aa_stackbar_g')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => {\n\t\t\tconst k = d.grp.aa\n\t\t\treturn (\n\t\t\t\t'translate(' +\n\t\t\t\t(k.showmode == modefold ? 0 : k.x0 - k.x) +\n\t\t\t\t',' +\n\t\t\t\t(abp ? 1 : -1) * (k.showmode == modefold ? tk.stem1 - d.y : tk.stem1 + tk.stem2 + tk.stem3 - d.y) +\n\t\t\t\t')'\n\t\t\t)\n\t\t})\n\tskbars\n\t\t.filter(d => d.showmode == modeshow)\n\t\t.selectAll('.sja_aa_stackbar_rect')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('y', d => (abp ? -d.height : 0))\n\ttk.skewer\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => {\n\t\t\td.y = skewer_sety(d, tk)\n\t\t\treturn 'translate(' + d.x + ',' + d.y + ')'\n\t\t})\n\ttk.skewer\n\t\t.selectAll('.sja_aa_stem')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('d', d => skewer_setstem(d, tk))\n\ttk.skewer\n\t\t.selectAll('.sja_aa_discg')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => {\n\t\t\td.y = (abp ? -1 : 1) * (d.aa.showmode == modefold ? d.aa.maxradius : d.yoffset)\n\t\t\treturn 'translate(0,' + d.y + ')'\n\t\t})\n\ttk.skewer.selectAll('.sja_aa_ssk_kick').attr('y', abp ? 0 : -tk.stem1)\n\ttk.skewer.selectAll('.sja_aa_ssk_bg').attr('y', abp ? 0 : -tk.stem1)\n\ttk.skewer.selectAll('.sja_aa_ssk_text').attr('y', ((abp ? 1 : -1) * tk.stem1) / 2)\n\ttk.skewer.selectAll('.sja_aa_skkick').attr('cy', d => (abp ? -1 : 1) * d.maxradius)\n\ttk.skewer\n\t\t.filter(d => d.showmode == modeshow && d.groups.length == 1)\n\t\t.selectAll('.sja_aa_disclabel')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => 'scale(1) rotate(' + (d.aa.slabelrotate ? (abp ? '-' : '') + '90' : '0') + ')')\n}\n\nfunction skewer_sety(d, tk) {\n\tif (tk.aboveprotein) {\n\t\tif (d.showmode == modefold) {\n\t\t\treturn tk.maxskewerheight + tk.stem1 + tk.stem2 + tk.stem3 - d.foldyoffset\n\t\t}\n\t\treturn tk.maxskewerheight\n\t}\n\tif (d.showmode == modefold) return d.foldyoffset\n\treturn tk.stem1 + tk.stem2 + tk.stem3\n}\n\nfunction skewer_setstem(d, tk) {\n\tif (tk.aboveprotein) {\n\t\tif (d.showmode == modefold) {\n\t\t\treturn 'M0,0v0l0,0v' + d.foldyoffset\n\t\t}\n\t\treturn 'M0,0v' + tk.stem1 + 'l' + (d.x0 - d.x) + ',' + tk.stem2 + 'v' + tk.stem3\n\t}\n\tif (d.showmode == modefold) {\n\t\treturn 'M0,0v0l0,0v-' + d.foldyoffset\n\t}\n\treturn 'M0,0v-' + tk.stem1 + 'l' + (d.x0 - d.x) + ',-' + tk.stem2 + 'v-' + tk.stem3\n}\n\nexport function settle_glyph(tk, block) {\n\tif (tk.data.length == 0) {\n\t\treturn\n\t}\n\tconst x1 = 0\n\tconst x2 = block.width\n\t// only settle those in view range\n\t// sum of skewer width, determines whether full or pack\n\tlet sumwidth = 0\n\tconst allinview = []\n\tconst beyondviewitems = []\n\tfor (const d of tk.data) {\n\t\tif (d.x0 < x1 || d.x0 > x2) {\n\t\t\tdelete d.xoffset\n\t\t\tbeyondviewitems.push(d)\n\t\t} else {\n\t\t\t// important: singleton label is rotated by default, must not include label width\n\t\t\tsumwidth += d.slabelrotate ? (d.groups[0].radius + d.groups[0].rimwidth) * 2 : d.width\n\t\t\tallinview.push(d)\n\t\t}\n\t}\n\n\t// reset those beyond view range\n\tfold_glyph(beyondviewitems, tk)\n\t// TODO may move d.x to +/-1000 out of sight\n\n\tlet expandlst = []\n\tconst foldlst = []\n\n\tif (sumwidth < x2 - x1) {\n\t\t// skewers can show in full\n\t\texpandlst = allinview\n\t} else {\n\t\t// rank skewers by ...\n\t\tallinview.sort((a, b) => {\n\t\t\tif (b.occurrence == a.occurrence) {\n\t\t\t\tif (b.groups.length == a.groups.length) {\n\t\t\t\t\t//return Math.abs(a.aapos*2-aarangestart-aarangestop)-Math.abs(b.aaposition*2-aarangestart-aarangestop);\n\t\t\t\t\treturn Math.abs(a.x0 * 2 - x1 - x2) - Math.abs(b.x0 * 2 - x1 - x2)\n\t\t\t\t} else {\n\t\t\t\t\treturn b.groups.length - a.groups.length\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn b.occurrence - a.occurrence\n\t\t})\n\t\t// collect top items to expand\n\t\tlet width = 0\n\t\tlet allowpx = (x2 - x1) * 0.8\n\t\tlet stop = false\n\t\tfor (const d of allinview) {\n\t\t\tif (stop) {\n\t\t\t\tdelete d.xoffset\n\t\t\t\tfoldlst.push(d)\n\t\t\t\td.showmode = modefold\n\t\t\t} else {\n\t\t\t\tif (width + d.width < allowpx) {\n\t\t\t\t\texpandlst.push(d)\n\t\t\t\t\twidth += d.width\n\t\t\t\t} else {\n\t\t\t\t\tstop = true\n\t\t\t\t\tdelete d.xoffset\n\t\t\t\t\tfoldlst.push(d)\n\t\t\t\t\td.showmode = modefold\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tfold_glyph(foldlst, tk)\n\tunfold_glyph(expandlst, tk, block)\n}\n\nfunction unfold_glyph(newlst, tk, block) {\n\tconst dur = 1000\n\tconst abp = tk.aboveprotein\n\t// set up new items\n\tconst expanded = new Set() // d.x as key\n\tconst folded = new Set()\n\tlet hasfolded = false\n\tfor (const d of newlst) {\n\t\tif (d.showmode == modeshow) {\n\t\t\texpanded.add(d.x0)\n\t\t} else {\n\t\t\td.showmode = modeshow\n\t\t\tfolded.add(d.x0)\n\t\t\thasfolded = true\n\t\t\td.y = skewer_sety(d, tk)\n\t\t}\n\t}\n\t/*\n\ttk.skewer\n\t\t.filter(d=>expanded.has(d.x0))\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform',d=> 'translate('+(d.x0+(d.xoffset==undefined ? 0 : d.xoffset))+','+d.y+')')\n\t\t*/\n\tif (hasfolded) {\n\t\t// vertical extending\n\t\tconst set = tk.skewer.filter(d => folded.has(d.x0))\n\t\tset\n\t\t\t.transition()\n\t\t\t.duration(dur)\n\t\t\t.attr('transform', d => 'translate(' + d.x + ',' + d.y + ')')\n\t\tset\n\t\t\t.selectAll('.sja_aa_discg')\n\t\t\t.transition()\n\t\t\t.duration(dur)\n\t\t\t.attr('transform', d => {\n\t\t\t\td.y = d.yoffset * (abp ? -1 : 1)\n\t\t\t\treturn 'translate(0,' + d.y + ')'\n\t\t\t})\n\t\tsetTimeout(function () {\n\t\t\tset.selectAll('.sja_aa_disckick').attr('transform', 'scale(1)')\n\t\t}, dur)\n\t\t/*\n\t\tset.selectAll('.sja_aa_qmg')\n\t\t\t.transition().duration(dur)\n\t\t\t.attr('transform','translate(0,'+(sk.maxskewerheight*(abp?-1:1))+') scale(1)')\n\t\t\t*/\n\t\tset.selectAll('.sja_aa_discnum').transition().duration(dur).attr('fill-opacity', 1).attr('stroke-opacity', 1)\n\t\tset\n\t\t\t.filter(d => d.groups.length > 1)\n\t\t\t.selectAll('.sja_aa_disclabel')\n\t\t\t.transition()\n\t\t\t.duration(dur)\n\t\t\t.attr('fill-opacity', 1)\n\t\t\t.attr('transform', 'scale(1)')\n\t\tset.selectAll('.sja_aa_discrim').transition().duration(dur).attr('fill-opacity', 1).attr('stroke-opacity', 1)\n\t\tset\n\t\t\t.selectAll('.sja_aa_ssk_kick')\n\t\t\t.attr('transform', 'scale(1)')\n\t\t\t.attr('y', abp ? 0 : -tk.stem1)\n\t\tset\n\t\t\t.selectAll('.sja_aa_ssk_bg')\n\t\t\t.attr('transform', 'scale(1)')\n\t\t\t.attr('y', abp ? 0 : -tk.stem1)\n\t\tset\n\t\t\t.selectAll('.sja_aa_ssk_text')\n\t\t\t.attr('transform', 'scale(1)')\n\t\t\t.attr('y', ((abp ? 1 : -1) * tk.stem1) / 2)\n\t\tset.selectAll('.sja_aa_skkick').attr('transform', 'scale(0)')\n\t\tset\n\t\t\t.filter(d => d.hasstackbar)\n\t\t\t.selectAll('.sja_aa_stackbar_g')\n\t\t\t// no transition, since the bar width is still 0\n\t\t\t.attr('transform', d => 'translate(0,' + (abp ? 1 : -1) * (tk.stem1 + tk.stem2 + tk.stem3 - d.y) + ')')\n\t\tlet counter = 0\n\t\tset\n\t\t\t.selectAll('.sja_aa_stem')\n\t\t\t.transition()\n\t\t\t.duration(dur)\n\t\t\t.attr('d', d => skewer_setstem(d, tk))\n\t\t\t.each(() => ++counter)\n\t\t\t.on('end', () => {\n\t\t\t\tif (!--counter) {\n\t\t\t\t\tunfold_update(tk, block)\n\t\t\t\t}\n\t\t\t})\n\t} else {\n\t\tunfold_update(tk, block)\n\t}\n}\n\nfunction unfold_update(tk, block) {\n\tconst dur = 1000\n\tconst abp = tk.aboveprotein\n\tconst alllst = [] // already expanded\n\tconst hash = new Set() // d.x0 as key\n\tconst x1 = 0\n\tconst x2 = block.width\n\tfor (const d of tk.data) {\n\t\tif (d.x0 < x1 || d.x0 > x2) continue\n\t\tif (d.showmode == modeshow) {\n\t\t\td.x = d.x0\n\t\t\talllst.push(d)\n\t\t\thash.add(d.x0)\n\t\t}\n\t}\n\tif (alllst.length == 0) {\n\t\treturn\n\t}\n\thoriplace(alllst, tk, block)\n\tfor (const d of alllst) {\n\t\td.xoffset = d.x - d.x0\n\t}\n\tfor (let i = 0; i < alllst.length; i++) {\n\t\tconst d = alllst[i]\n\t\tif (d.groups.length > 1) continue\n\t\t// single\n\t\tconst disc = d.groups[0]\n\t\tif (tk.slabel_forcerotate) {\n\t\t\td.slabelrotate = true\n\t\t} else {\n\t\t\tconst next = alllst[i + 1]\n\t\t\tconst rightx = next ? next.x - next.maxradius - next.maxrimwidth : x2\n\t\t\td.slabelrotate = rightx - d.x - disc.radius - disc.rimwidth - 1 < d.slabelwidth\n\t\t}\n\t\td.width = (disc.radius + disc.rimwidth) * 2 + (d.slabelrotate ? 0 : 2 + d.slabelwidth)\n\t}\n\t// horizontal shifting\n\tconst set = tk.skewer.filter(d => hash.has(d.x0))\n\tset\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => 'translate(' + d.x + ',' + d.y + ')')\n\tset\n\t\t.selectAll('.sja_aa_stem')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('d', d => skewer_setstem(d, tk))\n\tset\n\t\t.filter(d => d.groups.length == 1)\n\t\t.selectAll('.sja_aa_disclabel')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('fill-opacity', 1)\n\t\t.attr('transform', d => 'scale(1) rotate(' + (d.aa.slabelrotate ? (abp ? '-' : '') + '90' : '0') + ')')\n\ttk.slabel_forcerotate = false\n\tconst skbars = set.filter(d => d.hasstackbar)\n\tskbars\n\t\t.selectAll('.sja_aa_stackbar_g')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr(\n\t\t\t'transform',\n\t\t\td =>\n\t\t\t\t'translate(' + (d.grp.aa.x0 - d.grp.aa.x) + ',' + (abp ? 1 : -1) * (tk.stem1 + tk.stem2 + tk.stem3 - d.y) + ')'\n\t\t)\n\tskbars\n\t\t.selectAll('.sja_aa_stackbar_rect')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('width', d => {\n\t\t\treturn d.pxspan\n\t\t})\n\t\t.attr('y', d => {\n\t\t\treturn abp ? -d.height : 0\n\t\t})\n}\n\nfunction horiplace(items, tk, block) {\n\t// only arrange those in aa view range\n\tconst xoffset0 = 0\n\tconst x2 = block.width\n\tlet xoffset = xoffset0\n\t// those out of range are not touched\n\t// detect if any overlap\n\tlet overlap = false\n\tfor (const i of items) {\n\t\tif (i.x0 < xoffset0 || i.x0 > x2) continue\n\t\tif (i.groups.length == 1) {\n\t\t\ti.slabelrotate = true\n\t\t\tconst disc = i.groups[0]\n\t\t\ti.width = (disc.radius + disc.rimwidth) * 2\n\t\t}\n\t\tconst x = i.x - i.maxradius - i.maxrimwidth\n\t\tif (x < xoffset) {\n\t\t\toverlap = true\n\t\t}\n\t\tif (x + i.width > x2) {\n\t\t\toverlap = true\n\t\t}\n\t\txoffset = Math.max(xoffset, x + i.width)\n\t}\n\tif (!overlap) {\n\t\t// nothing to do\n\t\treturn false\n\t}\n\t// push and pack all to the left\n\txoffset = xoffset0\n\tfor (const i of items) {\n\t\tif (i.x0 < xoffset0 || i.x0 > x2) continue\n\t\ti.x = xoffset + i.maxradius + i.maxrimwidth\n\t\txoffset += i.width\n\t}\n\n\thoriplace0(items, block.width)\n}\n\nfunction horiplace0(items, allwidth) {\n\t/*\n\titems[]\n\t.width\n\t.x0\n\t.x\n\t\talready set by pushing to left\n\t*/\n\tfor (let i = 0; i < items.length; i++) {\n\t\tif (items[i].x0 < 0) continue\n\t\tif (items[i].x0 > allwidth) break\n\n\t\twhile (1) {\n\t\t\tlet currsum = 0,\n\t\t\t\tnewsum = 0\n\t\t\tfor (let j = i; j < items.length; j++) {\n\t\t\t\tconst t = items[j]\n\t\t\t\tif (t.x0 > allwidth) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tcurrsum += Math.abs(t.x - t.x0)\n\t\t\t\tt.x++\n\t\t\t\tnewsum += Math.abs(t.x - t.x0)\n\t\t\t}\n\t\t\tif (items[i].x >= items[i].x0) {\n\t\t\t\t// wind back to make sure stem [i] stem is straight\n\t\t\t\tfor (let j = i; j < items.length; j++) {\n\t\t\t\t\titems[j].x--\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t\tconst z = items[items.length - 1]\n\t\t\tif (z.x + z.width / 2 >= allwidth) {\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (newsum <= currsum) {\n\t\t\t\t// accept move\n\t\t\t} else {\n\t\t\t\t// reject move, procceed to next item\n\t\t\t\tfor (let j = i; j < items.length; j++) {\n\t\t\t\t\tif (items[j].x0 > allwidth) {\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\t// wind back\n\t\t\t\t\titems[j].x--\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function fold_glyph(lst, tk) {\n\tif (lst.length == 0) return\n\tconst dur = 1000\n\tconst abp = tk.aboveprotein\n\t// total number of discs, determines if disc details are visible prior to folding\n\tconst hash = new Set()\n\tfor (const d of lst) {\n\t\td.x = d.x0\n\t\thash.add(d.x0)\n\t\td.showmode = modefold\n\t\td.y = skewer_sety(d, tk)\n\t}\n\tconst set = tk.skewer.filter(d => hash.has(d.x0))\n\tset\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => 'translate(' + d.x + ',' + d.y + ')')\n\tset\n\t\t.selectAll('.sja_aa_stem')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('d', d => skewer_setstem(d, tk))\n\tset\n\t\t.selectAll('.sja_aa_discg')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => 'translate(0,' + (abp ? '-' : '') + d.aa.maxradius + ')')\n\tset.selectAll('.sja_aa_disckick').attr('transform', 'scale(0)')\n\t/*\n\tset.selectAll('.sja_aa_qmg')\n\t\t.transition().duration(dur)\n\t\t.attr('transform','translate(0,0) scale(0)')\n\t\t*/\n\tset.selectAll('.sja_aa_discnum').transition().duration(dur).attr('fill-opacity', 0).attr('stroke-opacity', 0)\n\tset.selectAll('.sja_aa_disclabel').transition().duration(dur).attr('fill-opacity', 0).attr('transform', 'scale(0)') // hide this label so it won't be tred\n\tset.selectAll('.sja_aa_discrim').transition().duration(dur).attr('fill-opacity', 0).attr('stroke-opacity', 0)\n\tset.selectAll('.sja_aa_ssk_kick').attr('transform', 'scale(0)')\n\tset.selectAll('.sja_aa_ssk_bg').attr('transform', 'scale(0)')\n\tset.selectAll('.sja_aa_ssk_text').attr('transform', 'scale(0)')\n\tset\n\t\t.selectAll('.sja_aa_skkick')\n\t\t.transition()\n\t\t.duration(dur) // to prevent showing pica over busy skewer\n\t\t.attr('transform', 'scale(1)')\n\tconst skbars = set.filter(d => d.hasstackbar)\n\tskbars\n\t\t.selectAll('.sja_aa_stackbar_g')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => 'translate(0,' + (abp ? 1 : -1) * (tk.stem1 - d.y) + ')')\n\tskbars.selectAll('.sja_aa_stackbar_rect').transition().duration(dur).attr('width', 0)\n}\n\nexport function epaint_may_hl(tk, mlst, hl) {\n\tif (!tk.eplst) return\n\tfor (const ep of tk.eplst) {\n\t\tep.may_hl(mlst, hl)\n\t}\n}\n\nfunction dsqueryresult_geneexpression(data, tk, block) {\n\tif (!data.config) {\n\t\tblock.error('config missing for expression data in ' + tk.ds.label)\n\t\treturn\n\t}\n\tif (data.config.maf) {\n\t\ttry {\n\t\t\tdata.config.maf.get = new Function(...data.config.maf.get)\n\t\t} catch (e) {\n\t\t\tblock.error('invalid javascript for config.maf.get of ' + tk.ds.label)\n\t\t\treturn\n\t\t}\n\t}\n\tconst config = data.config\n\tif (config.usecohort) {\n\t\tconfig.cohort = tk.ds.cohort\n\t}\n\tconst eparg = {\n\t\tdata: data.lst,\n\t\texpp: config,\n\t\tblock: block,\n\t\tgenome: block.genome,\n\t\tgenename: block.usegm.name,\n\t\tdsname: tk.ds.label\n\t}\n\tif (block.samplecart) {\n\t\t/* this api has been enabled in block\n\t\tsee if to pass it to ep\n\t\tonly if the ds also has matching attribute\n\t\tthis is to only activate sample selection in pediatric, but not in cosmic!\n\t\t*/\n\t\tif (tk.ds.sampleselectable) {\n\t\t\t// this ds has been configured to use it\n\t\t\teparg.samplecart = block.samplecart\n\t\t}\n\t}\n\treturn import('./ep').then(p => {\n\t\ttk.eplst.push(new p.default(eparg))\n\t})\n}\n\nfunction dsqueryresult_snvindelfusionitd(lst, tk, block) {\n\tfor (const m of lst) {\n\t\tswitch (m.dt) {\n\t\t\tcase common.dtsnvindel:\n\t\t\t\tif (block.usegm) {\n\t\t\t\t\tconst t = coord.genomic2gm(m.pos, block.usegm)\n\t\t\t\t\tm.rnapos = t.rnapos\n\t\t\t\t\tm.aapos = t.aapos\n\t\t\t\t}\n\t\t\t\ttk.mlst.push(m)\n\t\t\t\tbreak\n\t\t\tcase common.dtsv:\n\t\t\tcase common.dtfusionrna:\n\t\t\t\tif (!m.pairlst) {\n\t\t\t\t\tconsole.error('pairlst missing from sv/fusion')\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tif (block.usegm && m.dt == common.dtsv) {\n\t\t\t\t\t/*\n\t\t\t\tSV data correction to suit gene strand\n\t\t\t\tdo not look at strands\n\t\t\t\t*/\n\t\t\t\t\tif (m.pairlst.length == 1) {\n\t\t\t\t\t\t// only works for single pair\n\t\t\t\t\t\tconst a = m.pairlst[0].a\n\t\t\t\t\t\tconst b = m.pairlst[0].b\n\t\t\t\t\t\tif (a.chr != null && b.chr != null && a.chr == b.chr && a.position != null && b.position != null) {\n\t\t\t\t\t\t\t// good to check\n\t\t\t\t\t\t\tif (a.position < b.position) {\n\t\t\t\t\t\t\t\tif (block.usegm.strand == '+') {\n\t\t\t\t\t\t\t\t\t// no change\n\t\t\t\t\t\t\t\t\ta.strand = '+'\n\t\t\t\t\t\t\t\t\tb.strand = '+'\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\ta.strand = '-'\n\t\t\t\t\t\t\t\t\tb.strand = '-'\n\t\t\t\t\t\t\t\t\tm.pairlst[0].a = b\n\t\t\t\t\t\t\t\t\tm.pairlst[0].b = a\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// XXX current data format doesnt work for genomic range query!!!\n\t\t\t\tif (block.usegm && block.gmmode != client.gmmode.genomic) {\n\t\t\t\t\tm.isoform = block.usegm.isoform\n\t\t\t\t\t// gmmode, single datum over current gene\n\t\t\t\t\tlet nohit = true\n\t\t\t\t\tfor (let i = 0; i < m.pairlst.length; i++) {\n\t\t\t\t\t\tconst pair = m.pairlst[i]\n\t\t\t\t\t\t// try to match with both isoform and name, for IGH, without isoform, but the querying \"gene\" can be IGH\n\t\t\t\t\t\tif (block.usegm.isoform == (pair.a.isoform || pair.a.name)) {\n\t\t\t\t\t\t\tm.useNterm = i == 0\n\t\t\t\t\t\t\tm.chr = block.usegm.chr\n\t\t\t\t\t\t\tm.strand = pair.a.strand\n\t\t\t\t\t\t\tif (pair.a.position == undefined) {\n\t\t\t\t\t\t\t\tif (pair.a.rnaposition == undefined) {\n\t\t\t\t\t\t\t\t\tif (pair.a.codon == undefined) {\n\t\t\t\t\t\t\t\t\t\tconsole.error('no position/rnaposition/codon available for ' + block.usegm.isoform)\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\tm.pos = coord.aa2gmcoord(pair.a.codon, block.usegm)\n\t\t\t\t\t\t\t\t\t\tpair.a.position = m.pos\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\tm.pos = coord.rna2gmcoord(pair.a.rnaposition - 1, block.usegm)\n\t\t\t\t\t\t\t\t\tif (m.pos == null) {\n\t\t\t\t\t\t\t\t\t\tconsole.error('failed to convert rnaposition to genomic position: ' + pair.a.rnaposition)\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tpair.a.position = m.pos\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tm.pos = pair.a.position\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tconst t = coord.genomic2gm(m.pos, block.usegm)\n\t\t\t\t\t\t\tm.rnapos = t.rnapos\n\t\t\t\t\t\t\tm.aapos = t.aapos\n\t\t\t\t\t\t\tif (pair.a.codon) {\n\t\t\t\t\t\t\t\tm.aapos = pair.a.codon\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tm.mname = pair.b.name\n\t\t\t\t\t\t\tnohit = false\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (block.usegm.isoform == (pair.b.isoform || pair.b.name)) {\n\t\t\t\t\t\t\tm.useNterm = false // always\n\t\t\t\t\t\t\tm.chr = block.usegm.chr\n\t\t\t\t\t\t\tm.strand = pair.b.strand\n\t\t\t\t\t\t\tif (pair.b.position == undefined) {\n\t\t\t\t\t\t\t\tif (pair.b.rnaposition == undefined) {\n\t\t\t\t\t\t\t\t\tif (pair.b.codon == undefined) {\n\t\t\t\t\t\t\t\t\t\tconsole.error('no position/rnaposition/codon available for ' + block.usegm.isoform)\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\tm.pos = coord.aa2gmcoord(pair.b.codon, block.usegm)\n\t\t\t\t\t\t\t\t\t\tpair.b.position = m.pos\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\tm.pos = coord.rna2gmcoord(pair.b.rnaposition - 1, block.usegm)\n\t\t\t\t\t\t\t\t\tif (m.pos == null) {\n\t\t\t\t\t\t\t\t\t\tconsole.error('failed to convert rnaposition to genomic')\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tpair.b.position = m.pos\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tm.pos = pair.b.position\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tconst t = coord.genomic2gm(m.pos, block.usegm)\n\t\t\t\t\t\t\tm.rnapos = t.rnapos\n\t\t\t\t\t\t\tm.aapos = t.aapos\n\t\t\t\t\t\t\tif (pair.b.codon) {\n\t\t\t\t\t\t\t\tm.aapos = pair.b.codon\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tm.mname = pair.a.name\n\t\t\t\t\t\t\tnohit = false\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (nohit) {\n\t\t\t\t\t\tconsole.error('sv/fusion isoform no match to gm isoform: ' + block.usegm.isoform)\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttk.mlst.push(m)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// genomic mode, one m for each breakend\n\t\t\t\t\tfor (const pair of m.pairlst) {\n\t\t\t\t\t\tlet ain = false,\n\t\t\t\t\t\t\tbin = false\n\t\t\t\t\t\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\t\t\t\t\t\tconst r = block.rglst[i]\n\t\t\t\t\t\t\tif (pair.a.chr == r.chr && pair.a.position >= r.start && pair.a.position <= r.stop) {\n\t\t\t\t\t\t\t\tain = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tif (pair.b.chr == r.chr && pair.b.position >= r.start && pair.b.position <= r.stop) {\n\t\t\t\t\t\t\t\tbin = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (ain) {\n\t\t\t\t\t\t\tconst m2 = svduplicate(m)\n\t\t\t\t\t\t\tconst ma = pair.a\n\t\t\t\t\t\t\tm2.chr = ma.chr\n\t\t\t\t\t\t\tm2.strand = ma.strand\n\t\t\t\t\t\t\tm2.useNterm = ma.strand == '+'\n\t\t\t\t\t\t\tm2.pos = ma.pos || ma.position\n\t\t\t\t\t\t\tm2.mname = pair.b.name || pair.b.chr\n\t\t\t\t\t\t\tif (!Number.isFinite(m2.pos)) {\n\t\t\t\t\t\t\t\tconsole.error('no genomic pos for breakend a')\n\t\t\t\t\t\t\t} else if (!m2.chr) {\n\t\t\t\t\t\t\t\tconsole.error('no chromosome for breakend a')\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\ttk.mlst.push(m2)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (bin) {\n\t\t\t\t\t\t\tconst m2 = svduplicate(m)\n\t\t\t\t\t\t\tconst mb = pair.b\n\t\t\t\t\t\t\tm2.chr = mb.chr\n\t\t\t\t\t\t\tm2.strand = mb.strand\n\t\t\t\t\t\t\tm2.useNterm = mb.strand == '+'\n\t\t\t\t\t\t\tm2.pos = mb.pos || mb.position\n\t\t\t\t\t\t\tm2.mname = pair.a.name || pair.a.chr\n\t\t\t\t\t\t\tif (!Number.isFinite(m2.pos)) {\n\t\t\t\t\t\t\t\tconsole.error('no genomic pos for breakend b')\n\t\t\t\t\t\t\t} else if (!m2.chr) {\n\t\t\t\t\t\t\t\tconsole.error('no chromosome for breakend b')\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\ttk.mlst.push(m2)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase common.dtitd:\n\t\t\tcase common.dtdel:\n\t\t\t\tif (m.chrpos1 && m.chrpos2) {\n\t\t\t\t\t// translate genomic pos1/pos2 to rna span\n\t\t\t\t\tlet t = coord.genomic2gm(m.chrpos1, block.usegm)\n\t\t\t\t\tconst rnapos1 = t.rnapos\n\t\t\t\t\tt = coord.genomic2gm(m.chrpos2, block.usegm)\n\t\t\t\t\tconst rnapos2 = t.rnapos\n\t\t\t\t\tif (rnapos1 < rnapos2) {\n\t\t\t\t\t\tm.pos = m.chrpos1\n\t\t\t\t\t} else {\n\t\t\t\t\t\tm.pos = m.chrpos2\n\t\t\t\t\t}\n\t\t\t\t\tdelete m.chrpos1\n\t\t\t\t\tdelete m.chrpos2\n\t\t\t\t\tconst rnaspan = Math.abs(rnapos1 - rnapos2)\n\t\t\t\t\tif (m.dt == common.dtitd) {\n\t\t\t\t\t\tm.rnaduplength = rnaspan\n\t\t\t\t\t} else if (m.dt == common.dtdel) {\n\t\t\t\t\t\tm.rnadellength = rnaspan\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (m.position) {\n\t\t\t\t\tm.pos = m.position\n\t\t\t\t\tdelete m.position\n\t\t\t\t}\n\t\t\t\tif (!m.pos) {\n\t\t\t\t\tif (m.dt == common.dtitd) {\n\t\t\t\t\t\t// itd exported from cicero will have a{} b{}, where b is upstream of a\n\t\t\t\t\t\tif (m.b) {\n\t\t\t\t\t\t\tif (m.b.position) {\n\t\t\t\t\t\t\t\tm.pos = m.b.position\n\t\t\t\t\t\t\t\tm.chr = m.b.chr\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!m.pos) {\n\t\t\t\t\tif (m.rnaposition) {\n\t\t\t\t\t\tif (block.usegm) {\n\t\t\t\t\t\t\tm.pos = coord.rna2gmcoord(m.rnaposition - 1, block.usegm)\n\t\t\t\t\t\t\tm.chr = block.usegm.chr\n\t\t\t\t\t\t\tif (m.pos == null) {\n\t\t\t\t\t\t\t\tconsole.error('failed to convert rnaposition to genomic position: ' + m.rnaposition)\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (m.aapos) {\n\t\t\t\t\t\t// TODO\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!m.pos) {\n\t\t\t\t\tconsole.error('no genomic pos for itd')\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tif (block.usegm) {\n\t\t\t\t\tconst t = coord.genomic2gm(m.pos, block.usegm)\n\t\t\t\t\tif (m.rnaposition) {\n\t\t\t\t\t\tm.rnapos = m.rnaposition\n\t\t\t\t\t} else {\n\t\t\t\t\t\tm.rnapos = t.rnapos\n\t\t\t\t\t}\n\t\t\t\t\tm.aapos = t.aapos\n\t\t\t\t}\n\t\t\t\tif (m.dt == common.dtitd) {\n\t\t\t\t\tif (!m.rnaduplength) {\n\t\t\t\t\t\tconsole.error('itd has no rnaduplength')\n\t\t\t\t\t\tm.rnaduplength = 1\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tif (!m.rnadellength) {\n\t\t\t\t\t\tconsole.error('deletion has no rnadellength')\n\t\t\t\t\t\tm.rnadellength = 1\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\ttk.mlst.push(m)\n\t\t\t\tbreak\n\t\t\tcase common.dtnloss:\n\t\t\tcase common.dtcloss:\n\t\t\t\tif (m.position) {\n\t\t\t\t\tm.pos = m.position\n\t\t\t\t\tdelete m.position\n\t\t\t\t}\n\t\t\t\tif (!m.pos) {\n\t\t\t\t\tif (m.rnaposition) {\n\t\t\t\t\t\tif (block.usegm) {\n\t\t\t\t\t\t\tm.pos = coord.rna2gmcoord(m.rnaposition - 1, block.usegm)\n\t\t\t\t\t\t\tm.chr = block.usegm.chr\n\t\t\t\t\t\t\tif (m.pos == null) {\n\t\t\t\t\t\t\t\tconsole.error('failed to convert rnaposition to genomic position: ' + m.rnaposition)\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (m.aapos) {\n\t\t\t\t\t\t// TODO\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!m.pos) {\n\t\t\t\t\tconsole.error('no genomic pos for truncation')\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tif (block.usegm) {\n\t\t\t\t\tconst t = coord.genomic2gm(m.pos, block.usegm)\n\t\t\t\t\tif (m.rnaposition) {\n\t\t\t\t\t\tm.rnapos = m.rnaposition\n\t\t\t\t\t} else {\n\t\t\t\t\t\tm.rnapos = t.rnapos\n\t\t\t\t\t}\n\t\t\t\t\tm.aapos = t.aapos\n\t\t\t\t}\n\t\t\t\ttk.mlst.push(m)\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tconsole.error('unknown dt: ' + m.dt)\n\t\t}\n\t}\n}\n\nfunction hlaachange_addnewtrack(tk, block) {\n\t/*\n\tvariants to be highlighted were not found in track\n\tadd a new ds track and show them\n\t*/\n\tconst l2c = new Map()\n\tfor (const c in common.mclass) {\n\t\tl2c.set(common.mclass[c].label.toUpperCase(), c)\n\t}\n\tconst toadd = []\n\tfor (const [n, m] of tk.hlaachange) {\n\t\tif (m == false) {\n\t\t\t// came from urlparam, cannot add\n\t\t\tcontinue\n\t\t}\n\t\tif (!m.name) {\n\t\t\tblock.error('hlaachange item .name missing')\n\t\t\tcontinue\n\t\t}\n\t\tif (m.codon == undefined || !Number.isFinite(m.codon)) {\n\t\t\tblock.error('hlaachange invalid codon for ' + m.name)\n\t\t\tcontinue\n\t\t}\n\t\tif (!m.class) {\n\t\t\tblock.error('hlaachange .class missing')\n\t\t\tcontinue\n\t\t}\n\t\tconst c = common.mclass[m.class] ? m.class : l2c.get(m.class.toUpperCase())\n\t\tif (!c) {\n\t\t\tblock.error('hlaachange invalid class: ' + m.class)\n\t\t\tcontinue\n\t\t}\n\t\tm.class = c\n\t\tm.mname = m.name\n\t\tdelete m.name\n\t\tm.chr = block.usegm.chr\n\t\tm.pos = coord.aa2gmcoord(m.codon, block.usegm)\n\t\tdelete m.codon\n\t\tm.dt = common.dtsnvindel\n\t\tm.isoform = block.usegm.isoform\n\t\ttoadd.push(m)\n\t}\n\tif (toadd.length) {\n\t\tconst ds = {\n\t\t\tlabel: 'Highlight',\n\t\t\ttype: client.tkt.ds,\n\t\t\tiscustom: true,\n\t\t\tbulkdata: {}\n\t\t}\n\t\tds.bulkdata[block.usegm.name.toUpperCase()] = toadd\n\t\tblock.ownds[ds.label] = ds\n\t\tconst tk2 = block.block_addtk_template({ type: client.tkt.ds, ds: ds })\n\t\tdstkload(tk2, block)\n\t}\n}\n\nfunction showlegend_vcfinfofilter(tk, block) {\n\t/*\n\tcustom mclass from vcf info\n\tupdate legend for all sets\n\t*/\n\tif (!tk.vcfinfofilter) return\n\n\tfor (const mcset of tk.vcfinfofilter.lst) {\n\t\tmcset.holder.selectAll('*').remove()\n\n\t\tif (mcset.numericfilter) {\n\t\t\t// numeric\n\t\t\t// duplicative\n\t\t\tfor (const o of mcset.numericfilter) {\n\t\t\t\to.count = 0\n\t\t\t}\n\n\t\t\tfor (const m of tk.mlst) {\n\t\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\t\t\t\tif (err) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tif (!vlst) continue\n\t\t\t\tconst v = vlst[0]\n\t\t\t\tif (!Number.isFinite(v)) continue\n\n\t\t\t\tfor (const o of mcset.numericfilter) {\n\t\t\t\t\tif (o.side == '<') {\n\t\t\t\t\t\tif (v < o.value) {\n\t\t\t\t\t\t\to.count++\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (v > o.value) {\n\t\t\t\t\t\t\to.count++\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tfor (const o of mcset.numericfilter) {\n\t\t\t\t// lower-than or greater-than cutoff\n\n\t\t\t\tconst cell = mcset.holder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('padding', '10px')\n\t\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t// apply or cancel filter\n\t\t\t\t\t\tif (mcset.numericCutoff == o.value && mcset.numericCutoffSide == o.side) {\n\t\t\t\t\t\t\t// has been using this cutoff, to turn off filtering\n\t\t\t\t\t\t\tdelete mcset.numericCutoff\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// was not using this cutoff, apply this\n\t\t\t\t\t\t\tmcset.numericCutoff = o.value\n\t\t\t\t\t\t\tmcset.numericCutoffSide = o.side\n\t\t\t\t\t\t}\n\t\t\t\t\t\tdstkrender(tk, block)\n\t\t\t\t\t})\n\n\t\t\t\tif (mcset.numericCutoff == o.value && mcset.numericCutoffSide == o.side) {\n\t\t\t\t\tcell.style('border-bottom', 'solid 2px #ccc').style('background-color', '#f1f1f1')\n\t\t\t\t}\n\t\t\t\tif (o.count > 0) {\n\t\t\t\t\t// dot\n\t\t\t\t\tcell\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t\t\t.style('background-color', '#ccc')\n\t\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t\t.html(o.count > 1 ? o.count : '&nbsp;')\n\t\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t}\n\t\t\t\t// label\n\t\t\t\tcell.append('span').text(o.side + o.value)\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\tif (!mcset.categories) {\n\t\t\t/*\n\t\t\tquick fix, a numeric filter can lack both .numerifilter[] and .categories\n\t\t\t*/\n\t\t\tcontinue\n\t\t}\n\n\t\t// categorical attribute\n\n\t\tconst key2count = new Map()\n\n\t\tlet novaluemcount = 0\n\n\t\tfor (const m of tk.mlst) {\n\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\n\t\t\tif (err) {\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (vlst == undefined) {\n\t\t\t\tnovaluemcount++\n\t\t\t} else {\n\t\t\t\tfor (const v of vlst) {\n\t\t\t\t\tif (!key2count.has(v)) {\n\t\t\t\t\t\tkey2count.set(v, 0)\n\t\t\t\t\t}\n\t\t\t\t\tkey2count.set(v, key2count.get(v) + 1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst lst = [...key2count]\n\t\tif (novaluemcount) {\n\t\t\tlst.push([vcfnotannotated_label, novaluemcount])\n\t\t}\n\t\tlst.sort((i, j) => j[1] - i[1])\n\n\t\tfor (const [k, count] of lst) {\n\t\t\tconst v = mcset.categories[k] || { color: 'black', label: k }\n\n\t\t\tconst cell = mcset.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttk.vcfinfofilter.tip.showunder(cell.node())\n\t\t\t\t\tlegendmenu_vcfinfo(mcset, k, tk, block)\n\t\t\t\t})\n\t\t\t// dot\n\t\t\tcell\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.style('background-color', v.color)\n\t\t\t\t.style('color', 'white')\n\t\t\t\t.html(count > 1 ? count : '&nbsp;')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t// label\n\t\t\tconst lab = cell.append('span').text(v.label).style('color', v.color)\n\t\t\tif (mcset.categoryhidden[k]) {\n\t\t\t\tlab.style('text-decoration', 'line-through')\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction vcfinfofilter_mayupdateautocategory(tk, block) {\n\t/*\n\tcategorical info filter may use auto color\n\tcall this after updating mlst[] -- will update the color for all categories\n\t*/\n\tif (!tk.vcfinfofilter) return\n\n\tfor (const mcset of tk.vcfinfofilter.lst) {\n\t\tif (mcset.numericfilter) {\n\t\t\tcontinue\n\t\t}\n\n\t\tif (!mcset.autocategory) {\n\t\t\tcontinue\n\t\t}\n\n\t\t/* categorical attribute\n\t\tonly need to record categories used in mlst[]\n\t\tthen assign dynamic color\n\t\t*/\n\n\t\tconst key2count = new Map()\n\n\t\tfor (const m of tk.mlst) {\n\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\n\t\t\tif (err) {\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (vlst != undefined) {\n\t\t\t\tfor (const v of vlst) {\n\t\t\t\t\tif (!key2count.has(v)) {\n\t\t\t\t\t\tkey2count.set(v, 0)\n\t\t\t\t\t}\n\t\t\t\t\tkey2count.set(v, key2count.get(v) + 1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst lst = [...key2count]\n\t\tlst.sort((i, j) => j[1] - i[1])\n\n\t\tconst colorfunc = scaleOrdinal(schemeCategory20)\n\n\t\tmcset.categories = {}\n\n\t\tfor (const [k, count] of lst) {\n\t\t\tmcset.categories[k] = {\n\t\t\t\tlabel: k,\n\t\t\t\tcolor: colorfunc(k)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function getter_mcset_key(mcset, m) {\n\t/*\n\tget the key from an item (m) given a mcset\n\treturns list!!!\n\t*/\n\tif (mcset.altalleleinfo) {\n\t\tif (!m.altinfo) return ['no .altinfo']\n\n\t\tconst value = m.altinfo[mcset.altalleleinfo.key]\n\t\tif (value == undefined) {\n\t\t\t// no value\n\n\t\t\tif (mcset.numericfilter) {\n\t\t\t\t// for alleles without AF_ExAC e.g. not seem in that population, treat value as 0\n\t\t\t\t// FIXME: only work for population frequency, assumption won't hold for negative values\n\t\t\t\treturn [null, [0]]\n\t\t\t}\n\n\t\t\treturn [null, undefined]\n\t\t}\n\n\t\tlet vlst = Array.isArray(value) ? value : [value]\n\n\t\tif (mcset.altalleleinfo.separator) {\n\t\t\t// hardcoded separator for string\n\t\t\tvlst = vlst[0].split(mcset.altalleleinfo.separator)\n\t\t}\n\t\treturn [null, vlst]\n\t}\n\n\tif (mcset.locusinfo) {\n\t\tif (!m.info) return ['no .info']\n\n\t\tconst value = m.info[mcset.locusinfo.key]\n\t\tif (value == undefined) {\n\t\t\t// no value\n\t\t\tif (mcset.numericfilter) {\n\t\t\t\t// hard fix: for alleles without AF_ExAC e.g. not seem in that population, treat value as 0\n\t\t\t\treturn [null, [0]]\n\t\t\t}\n\t\t\treturn [null, undefined]\n\t\t}\n\n\t\tlet vlst = Array.isArray(value) ? value : [value]\n\n\t\tif (mcset.locusinfo.separator) {\n\t\t\tvlst = vlst[0].split(mcset.locusinfo.separator)\n\t\t}\n\t\treturn [null, vlst]\n\t}\n\n\treturn ['no trigger']\n}\n\nfunction legendmenu_vcfinfo(mcset, key, tk, block) {\n\t/*\n\ttk legend shows the values from certain vcf info fields\n\tvalues are clickable to make filtering on variants of the track\n\tshow tooltip menu for the annotation items\n\tkey is:\n\t- a key of mcset.categories\n\t- vcfnotannotated_label\n\t*/\n\tconst tip = tk.vcfinfofilter.tip\n\ttip.clear()\n\n\tconst thiskeyhidden = mcset.categoryhidden[key]\n\n\ttip.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show alone')\n\t\t.on('click', () => {\n\t\t\ttip.hide()\n\t\t\tmcset.categoryhidden = {}\n\t\t\tfor (const k in mcset.categories) {\n\t\t\t\tif (k != key) {\n\t\t\t\t\tmcset.categoryhidden[k] = 1\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (key != vcfnotannotated_label) {\n\t\t\t\tmcset.categoryhidden[vcfnotannotated_label] = 1\n\t\t\t}\n\t\t\tdstkrender(tk, block)\n\t\t})\n\tif (thiskeyhidden) {\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show')\n\t\t\t.on('click', () => {\n\t\t\t\ttip.hide()\n\t\t\t\tdelete mcset.categoryhidden[key]\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\t} else {\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.html('<div style=\"display:inline-block;width:25px\">&times;</div> hide')\n\t\t\t.on('click', () => {\n\t\t\t\ttip.hide()\n\t\t\t\tmcset.categoryhidden[key] = 1\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\t}\n\n\tlet hidenum = 0\n\tfor (const k in mcset.categoryhidden) {\n\t\thidenum++\n\t}\n\tif (hidenum > 1) {\n\t\t// more than 1 class is hidden, make \"show all\"\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show all')\n\t\t\t.on('click', () => {\n\t\t\t\ttip.hide()\n\t\t\t\tmcset.categoryhidden = {}\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\t}\n}\n\nfunction getter_pfrequency(m, tk) {\n\t/*\n\tget population frequency\n\tfor multi-sample vcf\n\tdo not work for variant-only vcf\n\t*/\n\tif (!m.vcfid) return ['.vcfid missing']\n\tif (!m.sampledata) return ['.sampledata missing']\n\tconst v = tk.ds.id2vcf[m.vcfid]\n\tif (!v) return ['no vcf']\n\tif (!v.samples || v.samples.length == 0) return ['vcf no samples']\n\t/*\n\tonly count samples without .gtallref\n\t*/\n\tlet count = 0\n\tfor (const s of m.sampledata) {\n\t\tif (!s.gtallref) count++\n\t}\n\treturn [null, count / v.samples.length]\n}\n\nfunction showlegend_populationfrequencyfilter(tk, block) {\n\t/*\n\thardcoded frequency filter for multi-sample vcf\n\t*/\n\tif (!tk.populationfrequencyfilter) return\n\n\tfor (const o of tk.populationfrequencyfilter.lst) {\n\t\to.count = 0\n\t}\n\n\tfor (const m of tk.mlst) {\n\t\tconst [err, f] = getter_pfrequency(m, tk)\n\t\tif (err) {\n\t\t\tcontinue\n\t\t}\n\t\tfor (const o of tk.populationfrequencyfilter.lst) {\n\t\t\tif (f < o.value) {\n\t\t\t\to.count++\n\t\t\t}\n\t\t}\n\t}\n\n\ttk.populationfrequencyfilter.holder.selectAll('*').remove()\n\n\tfor (const o of tk.populationfrequencyfilter.lst) {\n\t\tconst cell = tk.populationfrequencyfilter.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '10px')\n\t\t\t.attr('class', 'sja_clb')\n\t\t\t.on('click', () => {\n\t\t\t\t// apply or cancel filter\n\t\t\t\tif (tk.populationfrequencyfilter.cutoff == o.value) {\n\t\t\t\t\tdelete tk.populationfrequencyfilter.cutoff\n\t\t\t\t} else {\n\t\t\t\t\ttk.populationfrequencyfilter.cutoff = o.value\n\t\t\t\t}\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\n\t\tif (tk.populationfrequencyfilter.cutoff == o.value) {\n\t\t\tcell.style('border-bottom', 'solid 2px #ccc').style('background-color', '#f1f1f1')\n\t\t}\n\n\t\t// dot\n\t\tcell\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t.style('padding', '1px 5px')\n\t\t\t.style('background-color', '#ccc')\n\t\t\t.style('color', 'white')\n\t\t\t.html(o.count > 1 ? o.count : '&nbsp;')\n\t\t\t.style('margin-right', '5px')\n\t\t// label\n\t\tcell.append('span').text('< ' + o.value)\n\t}\n}\n\nfunction showlegend_sampleattribute(tk, block) {\n\t/*\n\t */\n\tif (!tk.ds || !tk.ds.cohort || !tk.ds.cohort.sampleattribute) return\n\tif (!tk.ds.cohort.annotation) return '.ds.cohort.annotation missing'\n\tif (!tk.ds.cohort.key4annotation) return '.ds.cohort.key4annotation missing'\n\n\tconst smat = tk.ds.cohort.sampleattribute\n\n\tif (!smat.lst) return '.lst missing'\n\tif (!smat.holder) return '.holder missing'\n\n\tsmat.holder.selectAll('*').remove()\n\n\tif (tk.mlst.length == 0) {\n\t\treturn\n\t}\n\tfor (const attr of smat.lst) {\n\t\tif (!attr.k) return '.k missing for an attribute'\n\t\tif (!attr.hiddenvalues) attr.hiddenvalues = new Set()\n\t}\n\n\tconst runtimelst = []\n\t// collect keys with any valid samples\n\n\t/*\n\tFIXME \n\tshadow vcf, use slim matrix to map variant to sample list\n\t*/\n\tif (tk.mlst[0].sampledata) {\n\t\t/*\n\t\tmulti-sample vcf\n\t\t*/\n\t\tfor (const attr of smat.lst) {\n\t\t\tlet samplecount = 0\n\t\t\tconst value2count = new Map()\n\t\t\tfor (const m of tk.mlst) {\n\t\t\t\tif (!m.sampledata) continue\n\n\t\t\t\tfor (const s0 of m.sampledata) {\n\t\t\t\t\tconst k4a = s0.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\t\t\tif (!k4a) continue\n\n\t\t\t\t\tconst o = tk.ds.cohort.annotation[k4a]\n\t\t\t\t\tif (!o) continue\n\n\t\t\t\t\tconst value = o[attr.k]\n\t\t\t\t\tif (value == undefined) continue\n\n\t\t\t\t\tsamplecount++\n\n\t\t\t\t\tif (!value2count.has(value)) {\n\t\t\t\t\t\tvalue2count.set(value, 0)\n\t\t\t\t\t}\n\t\t\t\t\tvalue2count.set(value, value2count.get(value) + 1)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (samplecount == 0) {\n\t\t\t\t// skip this key\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\truntimelst.push({\n\t\t\t\tsamplecount: samplecount,\n\t\t\t\tkey: attr,\n\t\t\t\tlst: [...value2count]\n\t\t\t\t\t.sort((a, b) => b[1] - a[1])\n\t\t\t\t\t.map(i => {\n\t\t\t\t\t\treturn { value: i[0], count: i[1] }\n\t\t\t\t\t})\n\t\t\t})\n\t\t}\n\t} else {\n\t\t/*\n\t\teach m is one case\n\t\tretrieved from db\n\t\t*/\n\t\tfor (const attr of smat.lst) {\n\t\t\tlet samplecount = 0\n\t\t\tconst value2count = new Map()\n\t\t\tfor (const m of tk.mlst) {\n\t\t\t\tconst k4a = m[tk.ds.cohort.key4annotation]\n\t\t\t\tif (!k4a) continue\n\n\t\t\t\tconst o = tk.ds.cohort.annotation[k4a]\n\t\t\t\tif (!o) continue\n\n\t\t\t\tconst value = o[attr.k]\n\t\t\t\tif (value == undefined) continue\n\n\t\t\t\tsamplecount++\n\n\t\t\t\tif (!value2count.has(value)) {\n\t\t\t\t\tvalue2count.set(value, 0)\n\t\t\t\t}\n\t\t\t\tvalue2count.set(value, value2count.get(value) + 1)\n\t\t\t}\n\t\t\tif (samplecount == 0) {\n\t\t\t\t// skip this key\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\truntimelst.push({\n\t\t\t\tsamplecount: samplecount,\n\t\t\t\tkey: attr,\n\t\t\t\tlst: [...value2count]\n\t\t\t\t\t.sort((a, b) => b[1] - a[1])\n\t\t\t\t\t.map(i => {\n\t\t\t\t\t\treturn { value: i[0], count: i[1] }\n\t\t\t\t\t})\n\t\t\t})\n\t\t}\n\t}\n\n\tif (runtimelst.length == 0) {\n\t\t// no keys are used to annotate current samples\n\t\t// disable filtering\n\t\tdelete smat.runtimelst\n\t\treturn\n\t}\n\t// activate filtering\n\tsmat.runtimelst = runtimelst\n\n\tconst table = smat.holder.append('table').style('border-spacing', '5px')\n\n\tfor (const attr of runtimelst) {\n\t\t/*\n\t\t.samplecount\n\t\t.key\n\t\t.lst\n\t\t*/\n\n\t\tconst tr = table.append('tr')\n\n\t\t// label of key\n\t\ttr.append('td')\n\t\t\t.style('color', '#858585')\n\t\t\t.style('text-align', 'right')\n\t\t\t.text(attr.key.label || attr.key.k)\n\n\t\tconst td = tr.append('td')\n\n\t\t// values of this key\n\t\tfor (const value of attr.lst) {\n\t\t\t/*\n\t\t\t.value\n\t\t\t.count\n\t\t\t*/\n\t\t\tconst cell = td\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '5px')\n\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tsmat.tip.showunder(cell.node())\n\t\t\t\t\tlegendmenu_sampleattribute(value, attr, smat.tip, tk, block)\n\t\t\t\t})\n\t\t\t// dot\n\t\t\tcell\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t.style('padding', '1px 3px')\n\t\t\t\t.style('background-color', '#858585')\n\t\t\t\t.style('color', 'white')\n\t\t\t\t.html(value.count > 1 ? value.count : '&nbsp;')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t// label\n\t\t\tconst lab = cell.append('span').text(value.value)\n\t\t\tif (attr.key.hiddenvalues.has(value.value)) {\n\t\t\t\tlab.style('text-decoration', 'line-through')\n\t\t\t}\n\t\t}\n\t}\n\treturn null\n}\n\nfunction legendmenu_sampleattribute(thisvalue, thisattr, tip, tk, block) {\n\t/*\n\tvalue\n\t.hidden\n\t*/\n\ttip.clear()\n\n\ttip.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show alone')\n\t\t.on('click', () => {\n\t\t\ttip.hide()\n\t\t\tfor (const value of thisattr.lst) {\n\t\t\t\tthisattr.key.hiddenvalues.add(value.value)\n\t\t\t}\n\t\t\tthisattr.key.hiddenvalues.delete(thisvalue.value)\n\t\t\tdstkrender(tk, block)\n\t\t})\n\tif (thisattr.key.hiddenvalues.has(thisvalue.value)) {\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show')\n\t\t\t.on('click', () => {\n\t\t\t\ttip.hide()\n\t\t\t\tthisattr.key.hiddenvalues.delete(thisvalue.value)\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\t} else {\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.html('<div style=\"display:inline-block;width:25px\">&times;</div> hide')\n\t\t\t.on('click', () => {\n\t\t\t\ttip.hide()\n\t\t\t\tthisattr.key.hiddenvalues.add(thisvalue.value)\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\t}\n\n\tif (thisattr.key.hiddenvalues.size > 1) {\n\t\t// more than 1 attribute is hidden, make \"show all\"\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show all')\n\t\t\t.on('click', () => {\n\t\t\t\ttip.hide()\n\t\t\t\tthisattr.key.hiddenvalues.clear()\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\t}\n}\n\nexport function mlst_pretreat(tk, block, originhidden) {\n\t/*\n\tused both in skewer & numeric\n\tno change to tk.mlst, but return a subset where they:\n\t- inside view range\n\t- pass filter\n\t\t- mclass, morigin\n\t\t- vcf info\n\t\t- population freq\n\t\t- sample annotation\n\tthen:\n\t- calculate m.__x by mapping coord to view range\n\t- update tk labels\n\t*/\n\n\tlet nogenomicpos = 0\n\tlet nochr = 0\n\tlet unmapped = []\n\tlet usemlst = [] // usable after filtering, for updating stats\n\n\tfor (const m of tk.mlst) {\n\t\tdelete m.__x\n\n\t\t/******************\n\t\t__filter__\n\t\t- by mclass/morigin\n\t\t\tblock.legend.mclasses(?).hidden\n\t\t- by vcf INFO\n\t\t\ttk.vcfinfofilter.lst[?]\n\t\t\t\tfor categorical, use categoryhidden\n\t\t\t\tfor numerical, use .numericCutoff\n\t\t- by vcf populationfrequencyfilter\n\t\t\tfor multi-sample vcf\n\t\t*******************/\n\n\t\tif (block.legend && block.legend.mclasses.has(m.class) && block.legend.mclasses.get(m.class).hidden) {\n\t\t\tcontinue\n\t\t}\n\t\tif (block.legend && block.legend.morigins.has(m.origin) && block.legend.morigins.get(m.origin).hidden) {\n\t\t\tcontinue\n\t\t}\n\t\tif (m.origin && originhidden.has(m.origin)) {\n\t\t\tcontinue\n\t\t}\n\t\tif (block.gmmode == common.gmmode.protein && block.usegm.codingstart && block.usegm.codingstop) {\n\t\t\t// in protein view, exclude those out of cds, e.g. utr ones\n\t\t\t// this may be risky as those p53 utr SVs are no longer visible\n\t\t\tif (m.pos < block.usegm.codingstart || m.pos > block.usegm.codingstop) continue\n\t\t}\n\t\tif (tk.vcfinfofilter) {\n\t\t\tlet hidden = false\n\t\t\tfor (const mcset of tk.vcfinfofilter.lst) {\n\t\t\t\tconst [err, vlst] = getter_mcset_key(mcset, m)\n\t\t\t\tif (err) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst v2 = vlst == undefined ? [vcfnotannotated_label] : vlst\n\n\t\t\t\tif (mcset.numericCutoff != undefined) {\n\t\t\t\t\t// numerical value, filter\n\t\t\t\t\t// only use the first value from vlst[]\n\t\t\t\t\tconst v3 = Number.parseFloat(v2[0])\n\n\t\t\t\t\tif (Number.isNaN(v3)) {\n\t\t\t\t\t\t// what\n\t\t\t\t\t\thidden = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\n\t\t\t\t\tif (mcset.numericCutoffSide == '<') {\n\t\t\t\t\t\tif (v3 >= mcset.numericCutoff) {\n\t\t\t\t\t\t\thidden = true\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (mcset.numericCutoffSide == '>') {\n\t\t\t\t\t\tif (v3 <= mcset.numericCutoff) {\n\t\t\t\t\t\t\thidden = true\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else if (mcset.categoryhidden) {\n\t\t\t\t\t/* categorical\n\t\t\t\t\tsince an INFO field may contain multiple values, if any of the value is not hidden, then the variant should not be hidden\n\t\t\t\t\t*/\n\t\t\t\t\tlet onevaluenothidden = false\n\t\t\t\t\tfor (const v of v2) {\n\t\t\t\t\t\tif (!mcset.categoryhidden[v]) {\n\t\t\t\t\t\t\tonevaluenothidden = true\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (!onevaluenothidden) {\n\t\t\t\t\t\t// all values are hidden\n\t\t\t\t\t\thidden = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (hidden) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\tif (tk.populationfrequencyfilter && tk.populationfrequencyfilter.cutoff) {\n\t\t\tconst [err, f] = getter_pfrequency(m, tk)\n\t\t\tif (err) {\n\t\t\t\t// still keep??\n\t\t\t} else {\n\t\t\t\tif (f > tk.populationfrequencyfilter.cutoff) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (\n\t\t\ttk.ds &&\n\t\t\ttk.ds.cohort &&\n\t\t\ttk.ds.cohort.annotation &&\n\t\t\ttk.ds.cohort.key4annotation &&\n\t\t\ttk.ds.cohort.sampleattribute &&\n\t\t\ttk.ds.cohort.sampleattribute.runtimelst\n\t\t) {\n\t\t\t/*\n\t\t\tsample attribute filtering can be applied\n\t\t\ttwo ways of getting annotation for the current sample\n\t\t\t*/\n\n\t\t\tlet hiddenattrcount = 0\n\t\t\tfor (const i of tk.ds.cohort.sampleattribute.runtimelst) {\n\t\t\t\tif (i.key && i.key.hiddenvalues) {\n\t\t\t\t\thiddenattrcount += i.key.hiddenvalues.size\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (hiddenattrcount > 0) {\n\t\t\t\t// there are indeed hidden attributes, so commence filtering\n\t\t\t\tif (tk.ds.vcfcohorttrack) {\n\t\t\t\t\t/*\n\t\t\t\t\tslim matrix\n\t\t\t\t\t*/\n\t\t\t\t} else if (m.sampledata) {\n\t\t\t\t\t/*\n\t\t\t\t\tloaded from multi-sample vcf\n\t\t\t\t\t*/\n\t\t\t\t\tlet usesamples = 0\n\t\t\t\t\tfor (const s0 of m.sampledata) {\n\t\t\t\t\t\t/*\n\t\t\t\t\t\tfor this sample to be considered, it must have the alt allele\n\t\t\t\t\t\t*/\n\t\t\t\t\t\tif (!common.alleleInGenotypeStr(s0.genotype, m.alt)) {\n\t\t\t\t\t\t\t// this sample does not have alt allele\n\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tconst k4a = s0.sampleobj[tk.ds.cohort.key4annotation]\n\t\t\t\t\t\tif (k4a) {\n\t\t\t\t\t\t\tconst sanno = tk.ds.cohort.annotation[k4a]\n\t\t\t\t\t\t\tif (sanno) {\n\t\t\t\t\t\t\t\t// this sample has valid annotation\n\t\t\t\t\t\t\t\tlet hidden = false\n\t\t\t\t\t\t\t\tfor (const attr of tk.ds.cohort.sampleattribute.runtimelst) {\n\t\t\t\t\t\t\t\t\tconst thisvalue = sanno[attr.key.k]\n\t\t\t\t\t\t\t\t\tif (thisvalue != undefined) {\n\t\t\t\t\t\t\t\t\t\t// this sample is annotated by this key\n\t\t\t\t\t\t\t\t\t\tif (attr.key.hiddenvalues.has(thisvalue)) {\n\t\t\t\t\t\t\t\t\t\t\t// annotation value of this sample is hidden\n\t\t\t\t\t\t\t\t\t\t\thidden = true\n\t\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (hidden) {\n\t\t\t\t\t\t\t\t\t// this is a hidden sample\n\t\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tusesamples++\n\t\t\t\t\t}\n\t\t\t\t\tif (usesamples == 0) {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t/*\n\t\t\t\t\tm loaded from db, per sample case\n\t\t\t\t\t*/\n\t\t\t\t\tconst k4a = m[tk.ds.cohort.key4annotation]\n\t\t\t\t\tif (k4a) {\n\t\t\t\t\t\tconst sanno = tk.ds.cohort.annotation[k4a]\n\t\t\t\t\t\tif (sanno) {\n\t\t\t\t\t\t\t// this sample has valid annotation\n\t\t\t\t\t\t\tlet hidden = false\n\t\t\t\t\t\t\tfor (const attr of tk.ds.cohort.sampleattribute.runtimelst) {\n\t\t\t\t\t\t\t\tconst thisvalue = sanno[attr.key.k]\n\t\t\t\t\t\t\t\tif (thisvalue != undefined) {\n\t\t\t\t\t\t\t\t\t// this sample is annotated by this key\n\t\t\t\t\t\t\t\t\tif (attr.key.hiddenvalues.has(thisvalue)) {\n\t\t\t\t\t\t\t\t\t\t// annotation value of this sample is hidden\n\t\t\t\t\t\t\t\t\t\thidden = true\n\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tif (hidden) {\n\t\t\t\t\t\t\t\t// this is a hidden sample\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t////////////   __filter__ ends\n\n\t\tif (!m.chr) {\n\t\t\tnochr++\n\t\t\tcontinue\n\t\t}\n\t\tif (!Number.isInteger(m.pos)) {\n\t\t\tnogenomicpos++\n\t\t\tcontinue\n\t\t}\n\t\tconst hits = block.seekcoord(m.chr, m.pos)\n\t\tif (hits.length == 0) {\n\t\t\tunmapped.push(m)\n\t\t\tcontinue\n\t\t}\n\t\tif (hits.length == 1) {\n\t\t\tm.__x = hits[0].x\n\t\t} else {\n\t\t\t// hit at multiple regions, still use first hit as following code is not finished\n\t\t\tm.__x = hits[0].x\n\n\t\t\t// see if to keep one or all\n\t\t\t/*\n\t\t\tlet usehitidx=-1\n\t\t\tfor(let i=0; i<hits.length; i++) {\n\t\t\t\tif(block.rglst[hits[i].ridx].keepthis) {\n\t\t\t\t\tusehitidx=i\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif(usehitidx==-1) {\n\t\t\t\t// no preference, duplicate mlst for all positions\n\t\t\t\tconsole.error('use all position: not done yet')\n\t\t\t} else {\n\t\t\t\t// use selected position\n\t\t\t\tm.usehitidx=usehitidx\n\t\t\t\tm.__x=hits[usehitidx].x\n\t\t\t}\n\t\t\t*/\n\t\t}\n\n\t\tif (m.__x < -1 || m.__x > block.width + 1) {\n\t\t\t// out of view range\n\t\t\tcontinue\n\t\t}\n\n\t\tusemlst.push(m)\n\t}\n\n\tconst collectleftlabw = []\n\ttk.tklabel.each(function () {\n\t\tcollectleftlabw.push(this.getBBox().width)\n\t})\n\n\t// ************* update stats label TODO should be a standalone func\n\tif (usemlst.length == 0) {\n\t\t// hide label\n\t\ttk.label_mcount.text('')\n\t} else {\n\t\ttk.label_mcount\n\t\t\t.text(\n\t\t\t\tusemlst.length < tk.mlst.length\n\t\t\t\t\t? usemlst.length + ' of ' + tk.mlst.length + ' ' + tk.itemlabelname + 's'\n\t\t\t\t\t: usemlst.length + ' ' + tk.itemlabelname + (usemlst.length > 1 ? 's' : '')\n\t\t\t)\n\t\t\t.each(function () {\n\t\t\t\tcollectleftlabw.push(this.getBBox().width)\n\t\t\t})\n\t}\n\tif (tk.label_stratify) {\n\t\tfor (const strat of tk.label_stratify) {\n\t\t\t// get number of ?? for each strat method\n\t\t\tlet itemcount\n\t\t\tif (strat.bycohort) {\n\t\t\t\tconst set = new Set()\n\t\t\t\tfor (const m of usemlst) {\n\t\t\t\t\tlet key = ''\n\t\t\t\t\tfor (const level of tk.ds.cohort.levels) {\n\t\t\t\t\t\tconst v = m[level.k]\n\t\t\t\t\t\tif (v) {\n\t\t\t\t\t\t\tkey += v\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tset.add(key)\n\t\t\t\t}\n\t\t\t\titemcount = set.size\n\t\t\t} else {\n\t\t\t\tconst set = new Set()\n\t\t\t\tfor (const m of usemlst) {\n\t\t\t\t\tlet key = m[strat.attr1.k]\n\t\t\t\t\tif (!key) continue\n\t\t\t\t\tif (strat.attr2) {\n\t\t\t\t\t\tconst v2 = m[strat.attr2.k]\n\t\t\t\t\t\tif (v2) {\n\t\t\t\t\t\t\tkey += v2\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (strat.attr3) {\n\t\t\t\t\t\tconst v3 = m[strat.attr3.k]\n\t\t\t\t\t\tif (v3) {\n\t\t\t\t\t\t\tkey += v3\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tset.add(key)\n\t\t\t\t}\n\t\t\t\titemcount = set.size\n\t\t\t}\n\t\t\tif (itemcount == 0) {\n\t\t\t\tstrat.svglabel.text('')\n\t\t\t} else {\n\t\t\t\tstrat.svglabel.text(itemcount + ' ' + strat.label + (itemcount > 1 ? 's' : '')).each(function () {\n\t\t\t\t\tcollectleftlabw.push(this.getBBox().width)\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\ttk.leftLabelMaxwidth = Math.max(...collectleftlabw)\n\t// ************ done labels\n\n\tif (nogenomicpos + nochr > 0) {\n\t\tblock.tkerror(tk, nogenomicpos + nochr + ' items have no chromosome or genomic position')\n\t}\n\tif (unmapped.length) {\n\t\tconsole.error(unmapped.length + ' items not mapped to any region')\n\t\tfor (const m of unmapped) console.log(m)\n\t}\n\n\treturn usemlst\n}\n\nexport function tkdata_update_x(tk, block) {\n\t/*\n\tcall when panned in gmmode,\n\tno re-requesting data\n\tno re-rendering\n\tonly update skewer x position\n\t*/\n\n\tfor (const d of tk.data) {\n\t\tif (d.isbin) {\n\t\t\tlet sumx = 0\n\t\t\tfor (const m of d.mlst) {\n\t\t\t\tconst hits = block.seekcoord(m.chr, m.pos)\n\t\t\t\tif (m.usehitidx != undefined && hits[m.usehitidx]) {\n\t\t\t\t\tsumx += hits[m.usehitidx].x\n\t\t\t\t} else if (hits.length == 1) {\n\t\t\t\t\tsumx += hits[0].x\n\t\t\t\t} else {\n\t\t\t\t\tconsole.log('cannot map item')\n\t\t\t\t\tconsole.log(m)\n\t\t\t\t}\n\t\t\t}\n\t\t\td.x0 = sumx / d.mlst.length\n\t\t\td.x = d.x0 + (d.xoffset != undefined ? d.xoffset : 0)\n\t\t} else {\n\t\t\tconst hits = block.seekcoord(d.chr, d.pos)\n\t\t\tif (hits.length > 0) {\n\t\t\t\td.x0 = hits[0].x\n\t\t\t\td.x = d.x0 + (d.xoffset != undefined ? d.xoffset : 0)\n\t\t\t} else {\n\t\t\t\tconsole.log('cannot map group of item')\n\t\t\t\tconsole.log(d)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function done_tknodata(tk, block) {\n\t/*\n\tno data loaded for track\n\tset track height by # of controllers\n\tin case of hlaachange, create new track and show\n\t*/\n\ttk.height_main = tk.toppad + block.labelfontsize + tk.bottompad\n\tif (tk.label_mcount && tk.label_mcount.text().length > 0) {\n\t\ttk.height_main += tk.labyspace + block.labelfontsize\n\t}\n\tif (tk.label_stratify) {\n\t\tfor (const strat of tk.label_stratify) {\n\t\t\tif (strat.svglabel.text().length > 0) {\n\t\t\t\ttk.height_main += tk.labyspace + block.labelfontsize\n\t\t\t}\n\t\t}\n\t}\n\n\t/*\n\tremove previous message in case of panning in gmmode\n\t*/\n\ttk.glider.selectAll('*').remove()\n\ttk.leftaxis.selectAll('*').remove()\n\n\tif (tk.viewrangeupperlimit_above) {\n\t\t// went beyond range\n\t\tblock.tkerror(tk, tk.name + ': zoom in under ' + common.bplen(tk.viewrangeupperlimit) + ' to view data')\n\t} else {\n\t\tlet context\n\t\tif (!tk.skewer.data || tk.skewer.data.length == 0) {\n\t\t\tif (block.pannedpx != undefined || block.zoomedin == true) {\n\t\t\t\tcontext = 'view range'\n\t\t\t} else if (block.usegm && block.gmmode != 'genomic') {\n\t\t\t\tcontext = block.usegm.name || block.usegm.isoform\n\t\t\t}\n\t\t}\n\t\tblock.tkerror(tk, tk.name + ': no mutation in ' + context)\n\t}\n\n\tif (tk.hlaachange) {\n\t\thlaachange_addnewtrack(tk, block)\n\t\tdelete tk.hlaachange\n\t}\n}\n\nfunction may_print_stratifycountfromserver(dat, tk) {\n\t/*\n\tdataset may be equipped to compute stratify category item count at server\n\t*/\n\tif (!dat.stratifycount) return\n\tfor (const [label, count] of dat.stratifycount) {\n\t\tconst strat = tk.label_stratify.find(i => i.label == label)\n\t\tif (!strat) {\n\t\t\tconsole.error('unknown strat label: ' + label)\n\t\t\tcontinue\n\t\t}\n\t\tstrat.servercount = count\n\t}\n}\n", "import * as common from '#shared/common.js'\nimport * as client from './client'\nimport { dstkrender } from './block.ds'\nimport * as coord from './coord'\n\n/*\n\nhardcoded legend for common.mclass, common.morigin\ndo not belong to specific tk but for all tk of ds type\n\nfunctions:\n\n\tlegend_newrow( holder, label )\n\tlegend_mclass()\n\tlegend_morigin()\n\n*/\n\nconst tip = new client.Menu({ padding: '0px' })\n\nexport function legend_newrow(block, label) {\n\tconst tr = block.legend.holder.append('tr')\n\tconst td0 = tr\n\t\t.append('td')\n\t\t.text(label)\n\t\t.style('padding-right', '10px')\n\t\t.style('text-align', 'right')\n\t\t//.style('vertical-align','top')\n\t\t//.style('color',block.legend.legendcolor)\n\t\t//.style('font-weight','bold')\n\t\t.style('color', '#555')\n\t\t.style('border-right', 'solid 1px ' + block.legend.legendcolor)\n\tconst td = tr.append('td')\n\treturn [tr, td, td0]\n}\n\nexport function legend_mclass(block) {\n\tif (!block.legend) {\n\t\treturn\n\t}\n\tconst hidden = new Set()\n\tfor (const [c, obj] of block.legend.mclasses) {\n\t\tif (obj.hidden) {\n\t\t\thidden.add(c)\n\t\t}\n\t}\n\tconst map = new Map()\n\tfor (const t of block.tklst) {\n\t\tif (t.hidden || t.type != client.tkt.ds) continue\n\t\tif (!t.mlst) {\n\t\t\t// maybe mlst not loaded yet\n\t\t\tcontinue\n\t\t}\n\t\tfor (const m of t.mlst) {\n\t\t\tif (m.class) {\n\t\t\t\tif (!map.has(m.class)) {\n\t\t\t\t\tmap.set(m.class, { count: 0 })\n\t\t\t\t}\n\t\t\t\tmap.get(m.class).count++\n\t\t\t}\n\t\t}\n\t}\n\tconst slst = []\n\tfor (const [c, obj] of map) {\n\t\tif (hidden.has(c)) {\n\t\t\tmap.get(c).hidden = true\n\t\t}\n\t\tslst.push({ key: c, count: obj.count })\n\t}\n\tblock.legend.mclasses = map\n\tif (map.size == 0) {\n\t\tblock.legend.tr_mclass.style('display', 'none')\n\t\treturn\n\t}\n\tblock.legend.tr_mclass.style('display', 'table-row')\n\tslst.sort((a, b) => b.count - a.count)\n\tblock.legend.td_mclass.selectAll('*').remove()\n\tfor (const e of slst) {\n\t\tconst butt = block.legend.td_mclass\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('padding', block.legend.vpad + ' 20px ' + block.legend.vpad + ' 0px')\n\t\t\t.classed('sja_clb', true)\n\t\t\t.on('click', () => {\n\t\t\t\ttip.clear()\n\t\t\t\ttip.showunder(butt.node())\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show alone')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\tfor (const obj of block.legend.mclasses.values()) {\n\t\t\t\t\t\t\tobj.hidden = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tblock.legend.mclasses.get(e.key).hidden = false\n\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\tif (block.legend.mclasses.get(e.key).hidden) {\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\t\tblock.legend.mclasses.get(e.key).hidden = false\n\t\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t} else {\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&times;</div> hide')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\t\tblock.legend.mclasses.get(e.key).hidden = true\n\t\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tif (hidden.size > 1) {\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show all')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\t\tfor (const obj of block.legend.mclasses.values()) {\n\t\t\t\t\t\t\t\tobj.hidden = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tconst div2 = tip.d.append('div').style('margin', '20px')\n\t\t\t\tdiv2\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.text(common.mclass[e.key].label.toUpperCase())\n\t\t\t\t\t.style('color', common.mclass[e.key].color)\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\tdiv2\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.html(common.mclass[e.key].desc)\n\t\t\t\t\t.style('color', '#858585')\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t.style('width', '210px')\n\t\t\t\t// end of click\n\t\t\t})\n\t\tbutt\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('background-color', common.mclass[e.key].color)\n\t\t\t.style('margin-right', '5px')\n\t\t\t.style('border-radius', '15px')\n\t\t\t.style('padding', '4px 8px')\n\t\t\t.style('color', 'white')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text(e.count)\n\t\tconst lab = butt\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', common.mclass[e.key].color)\n\t\t\t.text(common.mclass[e.key].label)\n\t\tif (hidden.has(e.key)) {\n\t\t\tlab.style('text-decoration', 'line-through')\n\t\t}\n\t}\n}\n\nexport function legend_morigin(block) {\n\tif (!block.legend) {\n\t\treturn\n\t}\n\tconst hidden = new Set()\n\tfor (const [c, obj] of block.legend.morigins) {\n\t\tif (obj.hidden) {\n\t\t\thidden.add(c)\n\t\t}\n\t}\n\tconst map = new Map()\n\tfor (const t of block.tklst) {\n\t\tif (t.hidden || t.type != client.tkt.ds) continue\n\t\tif (!t.mlst) {\n\t\t\tcontinue\n\t\t}\n\t\tfor (const m of t.mlst) {\n\t\t\tif (!m.origin) continue\n\t\t\tif (!map.has(m.origin)) {\n\t\t\t\t// adding new entry to the origin legend\n\t\t\t\t/*\n\t\t\t\ttricky alert\n\t\t\t\tby default, common.morigin has some item hidden\n\t\t\t\tso whatever is set hidden there, effect will be applicable here\n\t\t\t\tand when user clicks \"Show only\" or \"Show\" option in the morigin menu\n\t\t\t\tit will forever abolish the .hidden of that item in common.morigin\n\t\t\t\t*/\n\t\t\t\tlet hidebydefault = false\n\t\t\t\tif (common.morigin[m.origin] && common.morigin[m.origin].hidden) {\n\t\t\t\t\t// this type is hidden by default\n\t\t\t\t\thidebydefault = true\n\t\t\t\t\thidden.add(m.origin)\n\t\t\t\t}\n\t\t\t\tmap.set(m.origin, { count: 0, hidden: hidebydefault })\n\t\t\t}\n\t\t\tmap.get(m.origin).count++\n\t\t}\n\t}\n\tconst slst = []\n\tfor (const [c, obj] of map) {\n\t\tif (hidden.has(c)) {\n\t\t\tmap.get(c).hidden = true\n\t\t}\n\t\tslst.push({ key: c, count: obj.count })\n\t}\n\tblock.legend.morigins = map\n\tif (map.size == 0) {\n\t\tblock.legend.tr_morigin.style('display', 'none')\n\t\treturn\n\t}\n\tblock.legend.tr_morigin.style('display', 'table-row')\n\tslst.sort((a, b) => b.count - a.count)\n\tblock.legend.td_morigin.selectAll('*').remove()\n\tfor (const e of slst) {\n\t\tconst butt = block.legend.td_morigin\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('padding', block.legend.vpad + ' 20px ' + block.legend.vpad + ' 0px')\n\t\t\t.classed('sja_clb', true)\n\t\t\t.on('click', () => {\n\t\t\t\ttip.clear()\n\t\t\t\ttip.showunder(butt.node())\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show alone')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\tfor (const obj of block.legend.morigins.values()) {\n\t\t\t\t\t\t\tobj.hidden = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tblock.legend.morigins.get(e.key).hidden = false\n\t\t\t\t\t\t/*\n\t\t\t\t\t\ttricky alert\n\t\t\t\t\t\tabolish .hidden from common.morigin\n\t\t\t\t\t\tin case when .hidden is set by default, the variants of this origin can show\n\t\t\t\t\t\t*/\n\t\t\t\t\t\tcommon.morigin[e.key].hidden = false\n\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\tif (block.legend.morigins.get(e.key).hidden) {\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\t\tblock.legend.morigins.get(e.key).hidden = false\n\t\t\t\t\t\t\t/*\n\t\t\t\t\t\t\ttricky alert\n\t\t\t\t\t\t\tsee above\n\t\t\t\t\t\t\t*/\n\t\t\t\t\t\t\tcommon.morigin[e.key].hidden = false\n\t\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t} else {\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&times;</div> hide')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\t\tblock.legend.morigins.get(e.key).hidden = true\n\t\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tif (hidden.size > 1) {\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.html('<div style=\"display:inline-block;width:25px\">&#10003;</div> show all')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\tblock.pannedpx = undefined // make sure\n\t\t\t\t\t\t\tfor (const obj of block.legend.morigins.values()) {\n\t\t\t\t\t\t\t\tobj.hidden = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tfor (const t of block.tklst) {\n\t\t\t\t\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\t\t\t\t\tdstkrender(t, block)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tconst div2 = tip.d.append('div').style('margin', '20px')\n\t\t\t\tdiv2\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.text(common.morigin[e.key].label.toUpperCase())\n\t\t\t\t\t.style('color', common.morigin[e.key].color)\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\tdiv2\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.html(common.morigin[e.key].desc)\n\t\t\t\t\t.style('color', '#858585')\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t.style('width', '210px')\n\t\t\t\t// end of click\n\t\t\t})\n\t\tbutt\n\t\t\t.append('svg')\n\t\t\t.style('margin-right', '5px')\n\t\t\t.attr('width', 19) // hardcoded legend w/h\n\t\t\t.attr('height', 19)\n\t\t\t.html(common.morigin[e.key].legend)\n\t\tconst lab = butt\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', '#858585')\n\t\t\t.text(common.morigin[e.key].label + ', ' + e.count)\n\t\tif (hidden.has(e.key)) {\n\t\t\tlab.style('text-decoration', 'line-through')\n\t\t}\n\t}\n}\n"],
-  "mappings": 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-}