@sjcrh/proteinpaint-client 2.221.0 → 2.223.0

package/dist/block.mds.svcnv-53DTOPBC.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/block.mds.svcnv.samplematrix.js", "../src/block.mds.svcnv.clickitem.js", "../src/block.mds.svcnv.legend.js", "../src/block.mds.svcnv.single.js", "../src/block.mds.svcnv.addcolumn.js", "../src/block.mds.svcnv.js"],
-  "sourcesContent": ["import * as common from '#shared/common.js'\nimport * as client from './client'\nimport { escapeHtml } from '#dom'\nimport { string2pos, invalidcoord } from './coord'\nimport { getsjcharts } from './getsjcharts'\n\n/*\n\n********************** EXPORTED\nmay_show_samplematrix_button\ncreatebutton_addfeature\ncreatenewmatrix_withafeature\n\n********************** INTERNAL\naddnewfeature_nosamplefilter\n\n\ncreated smat is stored in tk.samplematrices[]\n\ncreatebutton_addfeature():\n\tlaunches smat by a mutation, creates a feature\n\tsubsequent selection of new mutations will add features to this same smat\n\teach feature is limited to that type of mutation\n\tdoes not restrict samples\n\tthere should only be one such matrix\n\nclicking Matrix view on sample group label\n\tlaunches a smat including all types of mutation\n\trestrict samples to the group\n\tone matrix can be created for each sample group\n\tofficial only\n\neach time creating either matrix, must find out if it has already existed in samplematrices[]\ncurrently a hardcoded method of telling that is through limitsamplebyeitherannotation\n\tif this attr exists, it belongs to one of sample group\n\totherwise, it is first type\n\n\n\nhardcoded keys to identify tracks in querykey2tracks of a custom dataset\nonly used to correlate feature.querykey to its track in smat.querykey2tracks\ntheir literal value won't be used in server\n\nthis requires that, in custom dataset,\n\t*** there can be only 1 track of each type ***\n\te.g. there cannot be two svcnv tracks...\n\n*/\n\nexport const customkey_svcnv = 'svcnv'\nexport const customkey_vcf = 'vcf'\nexport const customkey_expression = 'expression'\n\nexport function createbutton_addfeature(p) {\n\t/*\n\tcreate a button for adding feature to samplematrix\n\tthe feature is underlied by m (m.dt for datatype)\n\n\tno sample filter: this feature does not restrict samples to a group\n\t*/\n\n\tconst { m, tk, block, holder } = p\n\n\tif (!m) return\n\n\tif (m.dt == common.dtcnv || m.dt == common.dtloh) {\n\t\t/*\n\t\tserver has 10mb range limit hardcoded\n\t\tto avoid embarrassment, do not show button when out of limit\n\t\t*/\n\t\tif (m.stop - m.start >= 10000000) {\n\t\t\treturn\n\t\t}\n\t}\n\n\t// generate new feature beforehand\n\tlet nf\n\n\tswitch (m.dt) {\n\t\tcase common.dtcnv:\n\t\t\tnf = {\n\t\t\t\tiscnv: 1,\n\t\t\t\tlabel: m.chr + ' ' + common.bplen(m.stop - m.start) + ' CNV',\n\t\t\t\tquerykey: tk.iscustom ? customkey_svcnv : tk.querykey,\n\t\t\t\tchr: m.chr,\n\t\t\t\tstart: m.start,\n\t\t\t\tstop: m.stop,\n\t\t\t\tvaluecutoff: tk.valueCutoff,\n\t\t\t\tfocalsizelimit: tk.bplengthUpperLimit,\n\t\t\t\tcolorgain: tk.cnvcolor.gain.str,\n\t\t\t\tcolorloss: tk.cnvcolor.loss.str\n\t\t\t}\n\t\t\tbreak\n\t\tcase common.dtloh:\n\t\t\tnf = {\n\t\t\t\tisloh: 1,\n\t\t\t\tlabel: m.chr + ' ' + common.bplen(m.stop - m.start) + ' LOH',\n\t\t\t\tquerykey: tk.iscustom ? customkey_svcnv : tk.querykey,\n\t\t\t\tchr: m.chr,\n\t\t\t\tstart: m.start,\n\t\t\t\tstop: m.stop,\n\t\t\t\tvaluecutoff: tk.segmeanValueCutoff,\n\t\t\t\tfocalsizelimit: tk.lohLengthUpperLimit,\n\t\t\t\tcolor: tk.cnvcolor.loh.str\n\t\t\t}\n\t\t\tbreak\n\t\tcase common.dtgeneexpression:\n\t\t\tif (!tk.gene2coord) {\n\t\t\t\tholder.text('tk.gene2coord missing')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst tmp = tk.gene2coord[m.genename]\n\t\t\tif (!tmp) {\n\t\t\t\tholder.text('No position for ' + m.genename)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tnf = {\n\t\t\t\tisgenevalue: 1,\n\t\t\t\tquerykey: tk.iscustom ? customkey_expression : tk.checkexpressionrank.querykey,\n\t\t\t\tgenename: m.genename,\n\t\t\t\tlabel: m.genename + ' expression',\n\t\t\t\tchr: tmp.chr,\n\t\t\t\tstart: tmp.start,\n\t\t\t\tstop: tmp.stop\n\t\t\t}\n\t\t\tbreak\n\t\tcase common.dtsnvindel:\n\t\t\tnf = {\n\t\t\t\tisvcf: 1,\n\t\t\t\tquerykey: tk.iscustom ? customkey_vcf : tk.checkvcf.querykey,\n\t\t\t\tlabel: 'Mutation at ' + m.chr + ':' + m.pos,\n\t\t\t\tchr: m.chr,\n\t\t\t\tstart: m.pos,\n\t\t\t\tstop: m.pos\n\t\t\t}\n\t\t\tbreak\n\t\tcase common.dtitd:\n\t\t\tnf = {\n\t\t\t\tisitd: 1,\n\t\t\t\tquerykey: tk.iscustom ? customkey_svcnv : tk.querykey,\n\t\t\t\tlabel: 'ITD at ' + m.chr + ':' + (m.start + 1) + '-' + (m.stop + 1),\n\t\t\t\tchr: m.chr,\n\t\t\t\tstart: m.start,\n\t\t\t\tstop: m.stop\n\t\t\t}\n\t\t\tbreak\n\t\tcase common.dtsv:\n\t\tcase common.dtfusionrna:\n\t\t\t// TODO hardcoded range +/- 1k\n\t\t\tnf = {\n\t\t\t\tissvfusion: 1,\n\t\t\t\tquerykey: tk.iscustom ? customkey_svcnv : tk.querykey,\n\t\t\t\tlabel: 'SV/fusion around ' + m._chr + ':' + (m._pos + 1),\n\t\t\t\tchr: m._chr,\n\t\t\t\tstart: Math.max(0, m._pos - 1000),\n\t\t\t\tstop: m._pos + 1000\n\t\t\t}\n\t\t\tbreak\n\t\tdefault:\n\t\t\tconsole.log('createbutton_addfeature: unknown dt')\n\t\t\treturn\n\t}\n\n\tconst button = holder\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Add feature: ' + nf.label)\n\t\t.on('click', () => {\n\t\t\tif (p.pane) {\n\t\t\t\t// close old pane\n\t\t\t\tp.pane.pane.remove()\n\t\t\t}\n\n\t\t\taddnewfeature_nosamplefilter(nf, tk, block)\n\t\t})\n}\n\nfunction addnewfeature_nosamplefilter(nf, tk, block) {\n\t/*\n\twill generate a matrix without sample filtering\n\tif the matrix does not exist, create it;\n\totherwise, add the new feature to it\n\n\t*/\n\n\tconst smat = tk.samplematrices.find(i => !i.limitsamplebyeitherannotation) // hardcoded to use this attribute to tell\n\n\tif (!smat) {\n\t\tcreatenewmatrix_withafeature({\n\t\t\tfeature: nf,\n\t\t\ttk: tk,\n\t\t\tblock: block\n\t\t})\n\t\treturn\n\t}\n\n\t// already exists\n\tif (smat._pane.pane.style('display') == 'none') {\n\t\t// show first\n\t\tclient.appear(smat._pane.pane)\n\t}\n\n\tsmat.addnewfeature_update(nf)\n}\n\nexport async function createnewmatrix_withafeature(_p) {\n\t// create new instance\n\tconst { feature, tk, block, limitsamplebyeitherannotation, limitbysamplesetgroup } = _p\n\n\tconst pane = client.newpane({\n\t\tx: 100,\n\t\ty: 100,\n\t\tclose: () => {\n\t\t\tclient.flyindi(pane.pane, tk.config_handle)\n\t\t\tpane.pane.style('display', 'none')\n\t\t}\n\t})\n\n\tif (limitsamplebyeitherannotation) {\n\t\t// from matrix view of a sample group\n\t\tconst a = limitsamplebyeitherannotation[0]\n\t\tif (a) {\n\t\t\tpane.header.html(\n\t\t\t\t'<span style=\"font-size:.8em;opacity:.5\">' + escapeHtml(tk.name) + '</span> ' + escapeHtml(a.value)\n\t\t\t)\n\t\t}\n\t} else if (limitbysamplesetgroup) {\n\t\tpane.header.html(\n\t\t\t'<span style=\"font-size:.8em;opacity:.5\">' +\n\t\t\t\tescapeHtml(tk.name) +\n\t\t\t\t'</span> ' +\n\t\t\t\tescapeHtml(limitbysamplesetgroup.name)\n\t\t)\n\t} else {\n\t\tpane.header.text(tk.name)\n\t}\n\n\tconst arg = {\n\t\tdebugmode: block.debugmode,\n\t\tgenome: block.genome,\n\t\tfeatures: [feature],\n\t\thostURL: block.hostURL,\n\t\tlimitsamplebyeitherannotation,\n\t\tlimitbysamplesetgroup,\n\t\tjwt: block.jwt,\n\t\tholder: pane.body.append('div').style('margin', '20px')\n\t}\n\n\tif (tk.iscustom) {\n\t\targ.iscustom = 1\n\t\targ.querykey2tracks = {}\n\t\targ.querykey2tracks[customkey_svcnv] = {\n\t\t\ttype: common.tkt.mdssvcnv,\n\t\t\tfile: tk.file,\n\t\t\turl: tk.url,\n\t\t\tindexURL: tk.indexURL\n\t\t}\n\t\tif (tk.checkexpressionrank) {\n\t\t\t/*\n\t\t\tgene expression track file \"type\" is only temporary,\n\t\t\tsince in mds.queries, this data is not regarded as a track, thus has no type\n\t\t\tadd type here so server code won't break\n\t\t\t*/\n\t\t\targ.querykey2tracks[customkey_expression] = {\n\t\t\t\ttype: common.tkt.mdsexpressionrank\n\t\t\t}\n\t\t\tfor (const k in tk.checkexpressionrank) {\n\t\t\t\targ.querykey2tracks[customkey_expression][k] = tk.checkexpressionrank[k]\n\t\t\t}\n\t\t}\n\t\tif (tk.checkvcf) {\n\t\t\t// hardcoded one single vcf file\n\t\t\targ.querykey2tracks[customkey_vcf] = {\n\t\t\t\ttype: common.tkt.mdsvcf\n\t\t\t}\n\t\t\tfor (const k in tk.checkvcf) {\n\t\t\t\tif (k == 'stringifiedObj') continue\n\t\t\t\targ.querykey2tracks[customkey_vcf][k] = tk.checkvcf[k]\n\t\t\t}\n\t\t}\n\t} else {\n\t\t// official\n\t\targ.dslabel = tk.mds.label\n\t}\n\n\t// dynamic import works with static values, not expressions\n\tif (window.location.search.includes('smx=3')) {\n\t\targ.client = client\n\t\targ.common = common\n\t\targ.string2pos = string2pos\n\t\targ.invalidcoord = invalidcoord\n\t\targ.block = import('./block.js')\n\t\tconst sjcharts = await getsjcharts()\n\t\tsjcharts.dthm(arg).then(m => {\n\t\t\tm._pane = pane\n\t\t\ttk.samplematrices.push(m)\n\t\t})\n\t} else {\n\t\timport('./samplematrix').then(_ => {\n\t\t\tconst m = new _.Samplematrix(arg)\n\t\t\tm._pane = pane\n\t\t\ttk.samplematrices.push(m)\n\t\t})\n\t}\n}\n\nexport function may_show_samplematrix_button(tk, block) {\n\t/*\n\tif samplematrix is hidden, show button in config menu\n\t*/\n\tif (!tk.samplematrices || tk.samplematrices.length == 0) return\n\n\tconst table = tk.tkconfigtip.d.append('table').style('margin-bottom', '5px')\n\n\tfor (const m of tk.samplematrices) {\n\t\tconst tr = table.append('tr')\n\n\t\t{\n\t\t\t// name\n\n\t\t\tconst words = []\n\t\t\tif (m.limitsamplebyeitherannotation) {\n\t\t\t\t// by sample group\n\t\t\t\tconst a = m.limitsamplebyeitherannotation[0]\n\t\t\t\twords.push(a.value)\n\t\t\t} else if (m.limitbysamplesetgroup) {\n\t\t\t\twords.push(m.limitbysamplesetgroup.name)\n\t\t\t} else {\n\t\t\t\t// general\n\t\t\t\twords.push('Any sample')\n\t\t\t}\n\t\t\tconst c = m.features.length\n\t\t\twords.push(c + ' feature' + (c > 1 ? 's' : ''))\n\n\t\t\twords.push(m.samples.length + ' samples')\n\n\t\t\tconst div = tr\n\t\t\t\t.append('td')\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.style('border', 'solid 1px #ededed')\n\t\t\t\t.text(words.join(', '))\n\t\t\tif (m._pane.pane.style('display') == 'none') {\n\t\t\t\tdiv.style('border-color', 'black')\n\t\t\t}\n\t\t\tdiv.on('click', () => {\n\t\t\t\tif (m._pane.pane.style('display') == 'none') {\n\t\t\t\t\tclient.appear(m._pane.pane)\n\t\t\t\t\tclient.flyindi(div, m._pane.pane)\n\t\t\t\t\tdiv.style('border-color', '#ededed')\n\t\t\t\t} else {\n\t\t\t\t\tclient.flyindi(m._pane.pane, div)\n\t\t\t\t\tclient.disappear(m._pane.pane)\n\t\t\t\t\tdiv.style('border-color', 'black')\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\t{\n\t\t\t// remove\n\t\t\ttr.append('td')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.html('&times;')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttr.remove()\n\t\t\t\t\tm._pane.pane.remove()\n\t\t\t\t\tfor (const [i, m2] of tk.samplematrices.entries()) {\n\t\t\t\t\t\tif (m.limitsamplebyeitherannotation) {\n\t\t\t\t\t\t\tif (m2.limitsamplebyeitherannotation) {\n\t\t\t\t\t\t\t\tconst a = m.limitsamplebyeitherannotation[0]\n\t\t\t\t\t\t\t\tconst b = m2.limitsamplebyeitherannotation[0]\n\t\t\t\t\t\t\t\tif (a.key == b.key && a.value == b.value) {\n\t\t\t\t\t\t\t\t\ttk.samplematrices.splice(i, 1)\n\t\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (!m2.limitsamplebyeitherannotation) {\n\t\t\t\t\t\t\t\ttk.samplematrices.splice(i, 1)\n\t\t\t\t\t\t\t\treturn\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}\n\t}\n}\n", "import { select as d3select } from 'd3-selection'\nimport { axisTop } from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\nimport * as client from './client'\nimport { escapeHtml } from '#dom'\nimport * as common from '#shared/common.js'\nimport {\n\tloadTk,\n\tfocus_singlesample,\n\tdedup_sv,\n\titemname_svfusion,\n\tmulti_sample_addhighlight,\n\tmulti_sample_removehighlight\n} from './block.mds.svcnv'\nimport {\n\tcreatebutton_addfeature,\n\tcreatenewmatrix_withafeature,\n\tcustomkey_svcnv,\n\tcustomkey_vcf\n} from './block.mds.svcnv.samplematrix'\nimport { getsjcharts } from './getsjcharts'\nimport { debounce } from 'debounce'\n\n/*\n\n********************** EXPORTED\nclick_multi_singleitem\ntooltip_singleitem\nclick_multi_vcfdense\ntooltip_multi_vcfdense\nclick_multi_svdense\ntooltip_multi_svdense\ntooltip_samplegroup\nclick_samplegroup_showmenu\nclick_samplegroup_showtable\nmay_add_sampleannotation\nsvchr2html\nsvcoord2html\ndetailtable_singlesample\nmake_svgraph\nmay_allow_samplesearch\n\n********************** INTERNAL\nprinter_snvindel\nmay_show_matrixbutton\nmay_createbutton_survival_grouplab\nmatrix_view()\n\n\n*/\n\nexport async function may_allow_samplesearch(tk, block) {\n\t/*\n\tfor official track, allow search for sample\n\n\tcreate a search box for finding samples\n\n\tsingle or multi\n\n\tmay query server to see if is allowed\n\t*/\n\tif (tk.iscustom) return\n\tif (tk.singlesample) return\n\n\tconst row = tk.tkconfigtip.d.append('div').style('margin-bottom', '15px')\n\tconst input = row.append('input').attr('size', 20).attr('placeholder', 'Find sample')\n\tconst showdiv = row.append('div').style('margin-top', '10px')\n\n\tinput.on('keyup', debounce(samplesearch, 300))\n\n\tasync function samplesearch() {\n\t\tshowdiv.selectAll('*').remove()\n\n\t\tconst str = input.property('value').trim()\n\t\tif (!str) return\n\n\t\tconst par = {\n\t\t\tgenome: block.genome.name,\n\t\t\tdslabel: tk.mds.label,\n\t\t\tquerykey: tk.querykey,\n\t\t\tfindsamplename: str\n\t\t}\n\t\ttry {\n\t\t\tconst data = await client.dofetch('mdssvcnv', par)\n\n\t\t\tif (data.error) throw data.error\n\t\t\tif (!data.result) return\n\t\t\tfor (const sample of data.result) {\n\t\t\t\tconst cell = showdiv.append('div')\n\t\t\t\tcell.append('span').text(sample.name)\n\n\t\t\t\tif (sample.grouplabel) {\n\t\t\t\t\tcell.append('span').style('margin-left', '10px').style('font-size', '.7em').text(sample.grouplabel)\n\t\t\t\t}\n\n\t\t\t\tif (sample.num_assay_tracks) {\n\t\t\t\t\tcell\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\t\t.style('background', '#bbb')\n\t\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t\t.style('border-radius', '3px')\n\t\t\t\t\t\t.text(sample.num_assay_tracks + ' track' + (sample.num_assay_tracks > 1 ? 's' : ''))\n\t\t\t\t}\n\n\t\t\t\tif (sample.disco) {\n\t\t\t\t\tcell\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\t\t.style('background', '#bbb')\n\t\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t\t.style('border-radius', '3px')\n\t\t\t\t\t\t.text('Genome view')\n\t\t\t\t}\n\t\t\t\tif (sample.mutation_signature) {\n\t\t\t\t\tcell\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\t\t.style('background', '#bbb')\n\t\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t\t.style('border-radius', '3px')\n\t\t\t\t\t\t.text('Mutation signature')\n\t\t\t\t}\n\n\t\t\t\tcell.attr('class', 'sja_menuoption').on('click', () => {\n\t\t\t\t\ttk.tkconfigtip.hide()\n\n\t\t\t\t\tconst tabs = []\n\n\t\t\t\t\taddtab_sampleview(tabs, {\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tblock: block,\n\t\t\t\t\t\tsample: {\n\t\t\t\t\t\t\tsamplename: sample.name\n\t\t\t\t\t\t},\n\t\t\t\t\t\tsamplegroup: { attributes: sample.attributes }\n\t\t\t\t\t})\n\n\t\t\t\t\tmayaddtab_disco(tabs, {\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tblock: block,\n\t\t\t\t\t\tsample: {\n\t\t\t\t\t\t\tsamplename: sample.name\n\t\t\t\t\t\t}\n\t\t\t\t\t\t//samplegroup: {attributes: sample.attributes}\n\t\t\t\t\t})\n\t\t\t\t\tmayaddtab_genome(tabs, {\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tblock: block,\n\t\t\t\t\t\tsample: {\n\t\t\t\t\t\t\tsamplename: sample.name\n\t\t\t\t\t\t}\n\t\t\t\t\t\t//samplegroup: {attributes: sample.attributes}\n\t\t\t\t\t})\n\t\t\t\t\tmayaddtab_mutationsignature(tabs, sample.name, tk, block)\n\n\t\t\t\t\tif (sample.attr && tk.sampleAttribute && tk.sampleAttribute.attributes) {\n\t\t\t\t\t\ttabs.push({\n\t\t\t\t\t\t\tlabel: 'Attributes',\n\t\t\t\t\t\t\tcallback: div => {\n\t\t\t\t\t\t\t\tfor (const attr of sample.attr) {\n\t\t\t\t\t\t\t\t\tconst a = tk.sampleAttribute.attributes[attr.k]\n\t\t\t\t\t\t\t\t\tif (a) attr.k = a.label\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tclient.make_table_2col(div, sample.attr)\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\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\t\t\t\tpane.header.text(sample.name)\n\t\t\t\t\tclient.tab2box(pane.body.style('padding-top', '10px'), tabs)\n\t\t\t\t})\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tclient.sayerror(showdiv, err.message || err)\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t}\n\t}\n}\n\nexport function click_samplegroup_showmenu(samplegroup, tk, block) {\n\t/*\n\tofficial only, multi-sample\n\tdense or full\n\tclick sample group label in track display to show menu\n\tthis group must already has been shown\n\t*/\n\n\tif (tk.sampleset) return sampleset_showgrpmenu(samplegroup, tk, block)\n\n\tif (tk.iscustom) return\n\n\tif (!samplegroup.attributes) {\n\t\t// no attributes[], maybe unannotated samples, do not show menu for the moment\n\t\treturn\n\t}\n\n\tconst printerror = msg => client.sayerror(tk.tip2.d, msg)\n\n\tif (!tk.sampleAttribute) return printerror('tk.sampleAttribute missing')\n\tif (!tk.sampleAttribute.attributes) return printerror('tk.sampleAttribute.attributes{} missing')\n\n\ttk.tip2.d.append('div').style('margin', '4px 10px').style('font-size', '.7em').text(samplegroup.name)\n\n\ttk.tip2.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Hide')\n\t\t.on('click', () => {\n\t\t\ttk.tip2.clear()\n\t\t\tconst err = samplegroup_setShowhide(samplegroup, tk, true)\n\t\t\tif (err) {\n\t\t\t\t//return printerror(err)\n\t\t\t}\n\t\t\ttk.tip2.hide()\n\t\t\tloadTk(tk, block)\n\t\t})\n\n\ttk.tip2.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Show only')\n\t\t.on('click', () => {\n\t\t\ttk.tip2.clear()\n\t\t\tfor (const g of tk._data) {\n\t\t\t\tconst err = samplegroup_setShowhide(g, tk, true)\n\t\t\t\tif (err) {\n\t\t\t\t\t//return printerror(err)\n\t\t\t\t}\n\t\t\t}\n\t\t\tsamplegroup_setShowhide(samplegroup, tk, false)\n\t\t\ttk.tip2.hide()\n\t\t\tloadTk(tk, block)\n\t\t})\n\n\t{\n\t\t/*\n\t\tunder the same driver attribute, any other groups are hidden?\n\t\tif so, allow to show all\n\t\t*/\n\t\tconst [err, attr, attrR] = samplegroup_getdriverattribute(samplegroup, tk)\n\t\tif (err) {\n\t\t\t// do not abort -- unannotated group of sample won't have .attributes[]\n\t\t\t// return printerror(err)\n\t\t} else if (attrR.hiddenvalues.size > 0) {\n\t\t\t// has other hidden groups\n\t\t\ttk.tip2.d\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.text('Show all')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\tattrR.hiddenvalues.clear()\n\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t})\n\t\t}\n\t}\n\n\ttk.tip2.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Table view')\n\t\t.on('click', () => {\n\t\t\ttk.tip2.hide()\n\t\t\tclick_samplegroup_showtable(samplegroup, tk, block)\n\t\t})\n\n\ttk.tip2.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Matrix view')\n\t\t.on('click', () => {\n\t\t\ttk.tip2.hide()\n\t\t\tmatrix_view(tk, block, samplegroup)\n\t\t})\n\n\tmay_show_matrixbutton(samplegroup, tk, block)\n\n\tmay_createbutton_survival_grouplab({\n\t\ttk,\n\t\tblock,\n\t\tsamplegroup,\n\t\tholder: tk.tip2.d\n\t})\n\n\tmay_createbutton_assayAvailability(tk, block, tk.tip2.d, samplegroup)\n}\n\nfunction sampleset_showgrpmenu(grp, tk, block) {\n\t// display menu for a group of sampleset\n\t// for both official and custom tracks\n\ttk.tip2.d.append('div').style('margin', '4px 10px').style('font-size', '.7em').text(grp.name)\n\ttk.tip2.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Table view')\n\t\t.on('click', () => {\n\t\t\ttk.tip2.hide()\n\t\t\tclick_samplegroup_showtable(grp, tk, block)\n\t\t})\n\ttk.tip2.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Matrix view')\n\t\t.on('click', () => {\n\t\t\ttk.tip2.hide()\n\t\t\tmatrix_view(tk, block, grp)\n\t\t})\n}\n\nfunction matrix_view(tk, block, samplegroup) {\n\t/*\n\tin group-less track (custom or official lacking config)\n\tsamplegroup will not be given, use all samples\n\t*/\n\n\tconst r = block.rglst[block.startidx]\n\tconst feature = {\n\t\tismutation: 1,\n\t\twidth: 60,\n\t\tchr: r.chr,\n\t\tstart: r.start,\n\t\tstop: r.stop,\n\t\tcnv: {\n\t\t\tvaluecutoff: tk.valueCutoff,\n\t\t\tfocalsizelimit: tk.bplengthUpperLimit\n\t\t},\n\t\tloh: {\n\t\t\tvaluecutoff: tk.segmeanValueCutoff,\n\t\t\tfocalsizelimit: tk.lohLengthUpperLimit\n\t\t},\n\t\titd: {},\n\t\tsv: {},\n\t\tfusion: {},\n\t\tsnvindel: {\n\t\t\texcludeclasses: {}\n\t\t}\n\t}\n\n\tif (tk.legend_mclass && tk.legend_mclass.hiddenvalues) {\n\t\t// hidden class and dt\n\t\tfor (const v of tk.legend_mclass.hiddenvalues) {\n\t\t\tif (typeof v == 'string') {\n\t\t\t\tfeature.snvindel.excludeclasses[v] = 1\n\t\t\t} else {\n\t\t\t\tif (v == common.dtcnv) {\n\t\t\t\t\tfeature.cnv.hidden = 1\n\t\t\t\t} else if (v == common.dtloh) {\n\t\t\t\t\tfeature.loh.hidden = 1\n\t\t\t\t} else if (v == common.dtitd) {\n\t\t\t\t\tfeature.itd.hidden = 1\n\t\t\t\t} else if (v == common.dtsv) {\n\t\t\t\t\tfeature.sv.hidden = 1\n\t\t\t\t} else if (v == common.dtfusionrna) {\n\t\t\t\t\tfeature.fusion.hidden = 1\n\t\t\t\t} else {\n\t\t\t\t\tconsole.error('unknown hidden dt?? ' + v)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// label, try to use expression gene name\n\tif (tk.showinggene) {\n\t\tfeature.label = tk.showinggene\n\t} else {\n\t\tfeature.label = r.chr + ':' + r.start + '-' + r.stop\n\t}\n\n\tconst smat_arg = { tk, block, feature }\n\n\tfeature.querykeylst = []\n\n\tif (tk.iscustom) {\n\t\tif (tk.file || tk.url) feature.querykeylst.push(customkey_svcnv)\n\t\tif (tk.checkvcf) feature.querykeylst.push(customkey_vcf)\n\t} else if (tk.querykey) {\n\t\tfeature.querykeylst.push(tk.querykey)\n\t\tif (tk.checkvcf) feature.querykeylst.push(tk.checkvcf.querykey)\n\t}\n\n\tif (tk.sampleset) {\n\t\t// the group is from sampleset\n\t\tfor (const m of tk.samplematrices) {\n\t\t\tif (m.limitbysamplesetgroup && m.limitbysamplesetgroup.name == samplegroup.name) {\n\t\t\t\tclient.appear(m._pane.pane)\n\t\t\t\tm.addnewfeature_update(feature)\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\t\tsmat_arg.limitbysamplesetgroup = {\n\t\t\tname: samplegroup.name,\n\t\t\tsamples: JSON.parse(JSON.stringify(tk.sampleset.find(i => i.name == samplegroup.name).samples))\n\t\t}\n\t} else if (samplegroup.attributes) {\n\t\t// attribute that defines this group of samples\n\t\tconst attr = samplegroup.attributes[samplegroup.attributes.length - 1]\n\t\tfor (const m of tk.samplematrices) {\n\t\t\tif (m.limitsamplebyeitherannotation) {\n\t\t\t\t// hardcoded to use first attr\n\t\t\t\tconst a = m.limitsamplebyeitherannotation[0]\n\t\t\t\tif (a && a.key == attr.k && a.value == attr.kvalue) {\n\t\t\t\t\t// found the smat of this sample group\n\t\t\t\t\tclient.appear(m._pane.pane)\n\t\t\t\t\tm.addnewfeature_update(feature)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tsmat_arg.limitsamplebyeitherannotation = [\n\t\t\t{\n\t\t\t\tkey: attr.k,\n\t\t\t\tvalue: attr.kvalue\n\t\t\t}\n\t\t]\n\t}\n\n\t// create new smat\n\tcreatenewmatrix_withafeature(smat_arg)\n}\n\nfunction samplegroup_getdriverattribute(g, tk) {\n\tif (!g.attributes) return ['.attributes[] missing for group ' + g.name]\n\tif (g.attributes.length == 0) return ['.attributes[] zero length for group ' + g.name]\n\tconst attribute = g.attributes[g.attributes.length - 1]\n\t/*\n\t.k\n\t.kvalue\n\t.full\n\t.fullvalue\n\n\tuse this attribute to set this group to hidden in tk.sampleAttribute \n\t*/\n\tconst attrRegister = tk.sampleAttribute.attributes[attribute.k]\n\tif (!attrRegister) return ['\"' + attribute.k + '\" not registered in sampleAttribute for group ' + g.name]\n\treturn [null, attribute, attrRegister]\n}\n\nfunction samplegroup_setShowhide(g, tk, tohide) {\n\tconst [err, attr, attrR] = samplegroup_getdriverattribute(g, tk)\n\tif (err) return err\n\tif (tohide) {\n\t\tattrR.hiddenvalues.add(attr.kvalue)\n\t} else {\n\t\tattrR.hiddenvalues.delete(attr.kvalue)\n\t}\n\treturn null\n}\n\nexport function tooltip_samplegroup(g, tk) {\n\tconst d = tk.tktip.clear().d.append('div')\n\n\tif (g.attributes) {\n\t\t// official only\n\t\tfor (const a of g.attributes) {\n\t\t\td.append('div').html(\n\t\t\t\tescapeHtml(a.kvalue) +\n\t\t\t\t\t(a.fullvalue ? ' <span style=\"opacity:.5;font-size:.8em;\">' + escapeHtml(a.fullvalue) + '</span>' : '')\n\t\t\t)\n\t\t}\n\t} else if (g.name) {\n\t\td.append('div').text(g.name)\n\t}\n\n\tconst html = [g.samples.length + ' sample' + (g.samples.length > 1 ? 's' : '')]\n\tif (g.sampletotalnum)\n\t\thtml.push(g.sampletotalnum + ' samples total, ' + Math.ceil((100 * g.samples.length) / g.sampletotalnum) + '%')\n\tif (tk.sampleset) {\n\t\t// full list of samples registered in tk.sampleset\n\t\tconst s = tk.sampleset.find(i => i.name == g.name)\n\t\tif (s) {\n\t\t\thtml.push(s.samples.length + ' samples total, ' + Math.ceil((100 * g.samples.length) / s.samples.length) + '%')\n\t\t}\n\t}\n\ttk.tktip.d.append('div').style('margin-top', '10px').style('color', '#858585').html(html.join('<br>'))\n\n\ttk.tktip.show(event.clientX, event.clientY)\n}\n\nexport function click_samplegroup_showtable(samplegroup, tk, block) {\n\t/*\n\tshow a table\n\tmulti-sample\n\tonly for native track: no group for custom track for lack of annotation\n\t*/\n\tconst pane = client.newpane({ x: event.clientX + 100, y: Math.max(100, event.clientY - 100) })\n\tpane.header.html(escapeHtml(samplegroup.name) + ' <span style=\"font-size:.7em\">' + escapeHtml(tk.name) + '</span>')\n\n\tif (samplegroup.samples.length == 1) {\n\t\t// one sample\n\n\t\tconst sample = samplegroup.samples[0]\n\n\t\tconst table = pane.body.append('table').style('margin', '10px').style('border-spacing', '4px')\n\n\t\t{\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('Sample').style('opacity', 0.5)\n\t\t\ttr.append('td').text(sample.samplename)\n\t\t}\n\t\tif (sample.sampletype) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('Sample type').style('opacity', 0.5)\n\t\t\ttr.append('td').text(sample.sampletype)\n\t\t}\n\n\t\tconst [cnvlst, svlst, lohlst, itdlst, vcflst, cnvlst0, svlst0, lohlst0, itdlst0, vcflst0] =\n\t\t\tsortitemsbytype_onesample(sample.samplename, sample.items, tk)\n\n\t\tif (cnvlst.length) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('CNV').style('opacity', 0.5)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let i = 0; i < cnvlst.length; i++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(cnvlst[i])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: cnvlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: cnvlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (svlst.length) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('SV').style('opacity', 0.5)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let i = 0; i < svlst.length; i++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(svlst[i])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: svlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: svlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (lohlst.length) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('LOH').style('opacity', 0.5)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let i = 0; i < lohlst.length; i++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(lohlst[i])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: lohlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: lohlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (itdlst.length) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('ITD').style('opacity', 0.5)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let i = 0; i < itdlst.length; i++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(itdlst[i])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: itdlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: itdlst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (vcflst.length) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('SNV/indel').style('opacity', 0.5)\n\t\t\tconst td = tr.append('td')\n\n\t\t\tfor (let i = 0; i < vcflst.length; i++) {\n\t\t\t\tconst ms = vcflst0[i].sampledata.find(j => j.sampleobj.name == sample.samplename)\n\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(vcflst[i])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: vcflst0[i],\n\t\t\t\t\t\t\tm_sample: ms,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: vcflst0[i],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tm_sample: ms,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn\n\t}\n\n\t// multiple samples\n\tconst table = pane.body.append('table').style('border-spacing', '2px').style('margin', '20px')\n\n\tconst hassampletype = samplegroup.samples.find(i => i.sampletype)\n\n\t// header\n\tconst tr = table.append('tr')\n\ttr.append('td').text('Sample').style('opacity', 0.5)\n\tif (hassampletype) {\n\t\ttr.append('td').text('Sample type').style('opacity', 0.5)\n\t}\n\ttr.append('td').text('CNV').style('opacity', 0.5)\n\ttr.append('td').text('SV').style('opacity', 0.5)\n\ttr.append('td').text('LOH').style('opacity', 0.5)\n\ttr.append('td').text('ITD').style('opacity', 0.5)\n\n\tif (tk.data_vcf) {\n\t\ttr.append('td').text('SNV/indel').style('opacity', 0.5)\n\t}\n\n\tfor (const [i, sample] of samplegroup.samples.entries()) {\n\t\tconst tr = table.append('tr')\n\n\t\tif (!(i % 2)) {\n\t\t\ttr.style('background', '#f1f1f1')\n\t\t}\n\n\t\ttr.append('td').text(sample.samplename)\n\n\t\tif (hassampletype) {\n\t\t\ttr.append('td').text(sample.sampletype || '')\n\t\t}\n\n\t\tconst [cnvlst, svlst, lohlst, itdlst, vcflst, cnvlst0, svlst0, lohlst0, itdlst0, vcflst0] =\n\t\t\tsortitemsbytype_onesample(sample.samplename, sample.items, tk)\n\n\t\t{\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let j = 0; j < cnvlst.length; j++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(cnvlst[j])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: cnvlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: cnvlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\t{\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let j = 0; j < svlst.length; j++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(svlst[j])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: svlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: svlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\t{\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let j = 0; j < lohlst.length; j++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(lohlst[j])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: lohlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: lohlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\t{\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let j = 0; j < itdlst.length; j++) {\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(itdlst[j])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: itdlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: itdlst0[j],\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tif (tk.data_vcf) {\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (let j = 0; j < vcflst.length; j++) {\n\t\t\t\tconst ms = vcflst0[j].sampledata.find(k => k.sampleobj.name == sample.samplename)\n\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.html(vcflst[j])\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: vcflst0[j],\n\t\t\t\t\t\t\tm_sample: ms,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: vcflst0[j],\n\t\t\t\t\t\t\tm_sample: ms,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function tooltip_multi_svdense(g, tk, block) {\n\t/*\n\tmulti-sample\n\tofficial or custom\n\tdense mode\n\tmouse over a dot\n\t*/\n\n\tif (g.items.length == 1) {\n\t\tconst sv = g.items[0]\n\t\ttooltip_singleitem({\n\t\t\titem: sv,\n\t\t\tsample: sv._sample,\n\t\t\tsamplegroup: sv._samplegroup,\n\t\t\ttk: tk,\n\t\t\tblock: block\n\t\t})\n\t\treturn\n\t}\n\n\ttk.tktip.clear()\n\n\tlet grouplabel = 'Group'\n\tif (tk.groupsamplebyattr && tk.groupsamplebyattr.attrlst) {\n\t\t// passed from mds.query\n\t\tgrouplabel = tk.groupsamplebyattr.attrlst[tk.groupsamplebyattr.attrlst.length - 1].label\n\t}\n\n\tconst lst = [\n\t\t{\n\t\t\tk: grouplabel,\n\t\t\tv: g.name\n\t\t}\n\t]\n\n\tlet svnum = 0,\n\t\tfusionnum = 0\n\tfor (const i of g.items) {\n\t\tif (i.dt == common.dtsv) svnum++\n\t\telse if (i.dt == common.dtfusionrna) fusionnum++\n\t}\n\n\tif (svnum) lst.push({ k: '# of SV', v: svnum })\n\tif (fusionnum) lst.push({ k: '# of fusion', v: fusionnum })\n\n\tclient.make_table_2col(tk.tktip.d, lst)\n\ttk.tktip.show(event.clientX, event.clientY)\n}\n\nexport function click_multi_svdense(g, tk, block) {\n\t/*\n\tmulti-sample\n\tnative/custom\n\tdense\n\tclicking on a ball representing density of sv breakend\n\t*/\n\tif (g.items.length == 1) {\n\t\tconst sv = g.items[0]\n\t\tclick_multi_singleitem({\n\t\t\titem: sv,\n\t\t\tsample: sv._sample,\n\t\t\tsamplegroup: sv._samplegroup,\n\t\t\ttk: tk,\n\t\t\tblock: block\n\t\t})\n\t\treturn\n\t}\n\n\tconst pane = client.newpane({ x: event.clientX, y: event.clientY })\n\tpane.header.html(escapeHtml(g.name) + ' <span style=\"font-size:.8em\">' + escapeHtml(tk.name) + '</span>')\n\n\tconst sample2lst = new Map()\n\tfor (const i of g.items) {\n\t\tif (!sample2lst.has(i.sample)) {\n\t\t\tsample2lst.set(i.sample, {\n\t\t\t\tsv: [],\n\t\t\t\tfusion: []\n\t\t\t})\n\t\t}\n\t\tif (i.dt == common.dtsv) {\n\t\t\tsample2lst.get(i.sample).sv.push(i)\n\t\t} else if (i.dt == common.dtfusionrna) {\n\t\t\tsample2lst.get(i.sample).fusion.push(i)\n\t\t}\n\t}\n\n\tconst table = pane.body.append('table').style('border-spacing', '2px').style('margin', '10px')\n\n\tconst tr = table.append('tr')\n\ttr.append('td').text('Sample').style('font-size', '.8em').style('opacity', 0.5)\n\ttr.append('td').text('SV').style('font-size', '.8em').style('opacity', 0.5)\n\ttr.append('td').text('RNA fusion').style('font-size', '.8em').style('opacity', 0.5)\n\n\tlet j = 0\n\tfor (const [sample, so] of sample2lst) {\n\t\tconst tr = table.append('tr')\n\t\tif (!(j++ % 2)) {\n\t\t\ttr.style('background', '#f1f1f1')\n\t\t}\n\n\t\ttr.append('td').text(sample)\n\n\t\tconst td1 = tr.append('td')\n\t\tfor (const i of so.sv) {\n\t\t\tconst breakpoint = svcoord2html(i, tk)\n\n\t\t\ttd1\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t.html(\n\t\t\t\t\ti.cytogeneticname\n\t\t\t\t\t\t? escapeHtml(i.cytogeneticname) + ' <span style=\"font-size:.7em\">' + breakpoint + '</span>'\n\t\t\t\t\t\t: breakpoint\n\t\t\t\t)\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\titem: i,\n\t\t\t\t\t\tsample: i._sample,\n\t\t\t\t\t\tsamplegroup: i._samplegroup,\n\t\t\t\t\t\ttk: tk\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\tmulti_sample_removehighlight(i._sample)\n\t\t\t\t})\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\titem: i,\n\t\t\t\t\t\tsample: i._sample,\n\t\t\t\t\t\tsamplegroup: i._samplegroup,\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tblock: block\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\n\t\tconst td2 = tr.append('td')\n\t\tfor (const i of so.fusion) {\n\t\t\ttd2\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t.html(escapeHtml(itemname_svfusion(i)) + ' <span style=\"font-size:.7em\">' + svcoord2html(i, tk) + '</span>')\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\titem: i,\n\t\t\t\t\t\tsample: i._sample,\n\t\t\t\t\t\tsamplegroup: i._samplegroup,\n\t\t\t\t\t\ttk: tk\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\tmulti_sample_removehighlight(i._sample)\n\t\t\t\t})\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\titem: i,\n\t\t\t\t\t\tsample: i._sample,\n\t\t\t\t\t\tsamplegroup: i._samplegroup,\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tblock: block\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\t}\n}\n\nexport function click_multi_vcfdense(g, tk, block) {\n\t/*\n\tmulti-sample\n\tnative/custom\n\tdense\n\tclick on a dot representing some snvindel or itd, of same type\n\tg is a list of variants of the same class, shown as a dot\n\t*/\n\n\tconst pane = client.newpane({ x: event.clientX, y: event.clientY })\n\tpane.header.text(tk.name)\n\n\tif (g.items.length == 1) {\n\t\t// only one variant\n\t\tconst m = g.items[0]\n\n\t\tconst butrow = pane.body.append('div').style('margin', '10px')\n\n\t\tif (m.dt == common.dtsnvindel) {\n\t\t\tif (m.sampledata.length == 1) {\n\t\t\t\t// in a single sample\n\t\t\t\tpane.pane.remove()\n\t\t\t\t// sample/group should always be found\n\t\t\t\tconst [sample, samplegroup] = findsamplegroup_byvcf({\n\t\t\t\t\tm: m,\n\t\t\t\t\tm_sample: m.sampledata[0],\n\t\t\t\t\ttk: tk\n\t\t\t\t})\n\t\t\t\tconst ms = m.sampledata[0]\n\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\titem: m,\n\t\t\t\t\tm_sample: m.sampledata[0],\n\t\t\t\t\tsample: sample,\n\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\ttk: tk,\n\t\t\t\t\tblock: block\n\t\t\t\t})\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// one snv, in multiple samples\n\t\t\t/*\n\t\t\tcreatebutton_addfeature( {\n\t\t\t\tm:m,\n\t\t\t\tholder:butrow,\n\t\t\t\ttk:tk,\n\t\t\t\tblock:block,\n\t\t\t\tpane: pane\n\t\t\t})\n\n\t\t\tmay_createbutton_survival_onemutation({\n\t\t\t\tholder: butrow,\n\t\t\t\ttk: tk,\n\t\t\t\tblock: block,\n\t\t\t\tm: m,\n\t\t\t\tsample: {\n\t\t\t\t\tsamplename: m.sampledata[0].sampleobj.name\n\t\t\t\t}\n\t\t\t})\n\t\t\t*/\n\n\t\t\tconst lst = printer_snvindel(m, tk)\n\t\t\tconst table = client.make_table_2col(pane.body, lst)\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').text('Samples').style('opacity', 0.5).attr('colspan', 2)\n\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (const sm of m.sampledata) {\n\t\t\t\tconst [sample, samplegroup] = findsamplegroup_byvcf({\n\t\t\t\t\tm: m,\n\t\t\t\t\tm_sample: sm,\n\t\t\t\t\ttk: tk\n\t\t\t\t})\n\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.text(sm.sampleobj.name)\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\tm_sample: sm,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\tm_sample: sm,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t\tmay_findmatchingsnp_printintable(m, block, table)\n\t\t} else {\n\t\t\tthrow 'Unknown dt: ' + m.dt\n\t\t}\n\t\treturn\n\t}\n\n\t/* multiple variants\n\tlist samples for each variant\n\t*/\n\n\tconst table = pane.body.append('table').style('margin-top', '10px').style('border-spacing', '4px')\n\n\tfor (const m of g.items) {\n\t\tconst tr = table.append('tr')\n\n\t\t// col 1: mutation name\n\t\ttr.append('td')\n\t\t\t.text(m.mname)\n\t\t\t.style('color', common.mclass[m.class].color)\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('vertical-align', 'top')\n\t\t// createbutton_addfeature\n\n\t\t// col 2\n\t\t{\n\t\t\tconst td = tr.append('td')\n\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\ttd.style('opacity', '.5')\n\t\t\t\t\t.text(m.ref + ' > ' + m.alt)\n\t\t\t\t\t.style('vertical-align', 'top')\n\t\t\t}\n\t\t}\n\n\t\t// col 3\n\t\t{\n\t\t\tconst td = tr.append('td')\n\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\t// show each sample\n\n\t\t\t\tfor (const m_sample of m.sampledata) {\n\t\t\t\t\tconst [s, sg] = findsamplegroup_byvcf({\n\t\t\t\t\t\tm: m,\n\t\t\t\t\t\tm_sample: m_sample,\n\t\t\t\t\t\ttk: tk\n\t\t\t\t\t})\n\t\t\t\t\ttd.append('div')\n\t\t\t\t\t\t.text(m_sample.sampleobj.name)\n\t\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\t\tm_sample: m_sample,\n\t\t\t\t\t\t\t\tsample: s,\n\t\t\t\t\t\t\t\tsamplegroup: sg,\n\t\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\tmulti_sample_removehighlight(s)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\t\tm_sample: m_sample,\n\t\t\t\t\t\t\t\tsample: s,\n\t\t\t\t\t\t\t\tsamplegroup: sg,\n\t\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconsole.error('unknown dt: ' + m.dt)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function tooltip_multi_vcfdense(g, tk, block) {\n\t/*\n\tmulti-sample\n\tofficial or custom\n\tdense mode\n\tmouseover a dot\n\t*/\n\ttk.tktip.clear()\n\n\tif (g.items.length == 1) {\n\t\t// single variant\n\t\tconst m = g.items[0]\n\n\t\tif (m.dt == common.dtsnvindel) {\n\t\t\tif (m.sampledata.length == 1) {\n\t\t\t\t// in just one sample\n\t\t\t\tconst [sample, samplegroup] = findsamplegroup_byvcf({\n\t\t\t\t\tm: m,\n\t\t\t\t\tm_sample: m.sampledata[0],\n\t\t\t\t\ttk: tk\n\t\t\t\t})\n\t\t\t\ttooltip_singleitem({\n\t\t\t\t\titem: m,\n\t\t\t\t\tm_sample: m.sampledata[0],\n\t\t\t\t\tsample: sample,\n\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\ttk: tk,\n\t\t\t\t\tblock: block\n\t\t\t\t})\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// multiple samples have this variant\n\t\t\tconst lst = printer_snvindel(m, tk)\n\t\t\tlst.push({\n\t\t\t\tk: 'Samples',\n\t\t\t\tv:\n\t\t\t\t\tm.sampledata.length > 10\n\t\t\t\t\t\t? m.sampledata\n\t\t\t\t\t\t\t\t.slice(0, 6)\n\t\t\t\t\t\t\t\t.map(i => i.sampleobj.name)\n\t\t\t\t\t\t\t\t.join('<br>') +\n\t\t\t\t\t\t  '<br><i>... and ' +\n\t\t\t\t\t\t  (m.sampledata.length - 6) +\n\t\t\t\t\t\t  ' more samples</i>'\n\t\t\t\t\t\t: m.sampledata.map(i => i.sampleobj.name).join('<br>')\n\t\t\t})\n\n\t\t\tconst table = client.make_table_2col(tk.tktip.d, lst)\n\n\t\t\t// mds may indicate whether to perform snp/clinvar checking\n\t\t\tmay_findmatchingsnp_printintable(m, block, table)\n\n\t\t\ttk.tktip.show(event.clientX, event.clientY)\n\t\t} else {\n\t\t\tthrow 'unknown dt: ' + m.dt\n\t\t}\n\t\treturn\n\t}\n\n\t// multiple variants, of same class\n\ttk.tktip.d\n\t\t.append('div')\n\t\t.style('font-size', '.7em')\n\t\t.style('margin-bottom', '5px')\n\t\t.text(g.items.length + ' ' + common.mclass[g.items[0].class].label + ' mutations, ' + g.samplecount + ' samples')\n\tconst table = tk.tktip.d.append('table').style('border-spacing', '3px')\n\tfor (const m of g.items) {\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').style('color', common.mclass[m.class].color).style('font-weight', 'bold').text(m.mname)\n\n\t\ttr.append('td')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('opacity', '.5')\n\t\t\t.text(m.ref + ' > ' + m.alt)\n\n\t\tconst td = tr.append('td').style('font-size', '.7em')\n\n\t\tif (m.dt == common.dtsnvindel) {\n\t\t\ttd.text(m.sampledata.length == 1 ? m.sampledata[0].sampleobj.name : '(' + m.sampledata.length + ' samples)')\n\t\t} else {\n\t\t\ttd.text('unknown dt: ' + m.dt)\n\t\t}\n\t}\n\n\ttk.tktip.show(event.clientX, event.clientY)\n}\n\nexport async function click_multi_singleitem(p) {\n\t/*\n\tclick on a single item, of any type\n\tlaunch a panel to show details\n\tonly in multi-sample mode, not in single-sample\n\tfor official or custom tracks\n\n\n\tp {}\n\t.item\n\t.sample\n\t.samplegroup\n\t.tk\n\t.block\n\n\tif item is snvindel, will have:\n\t\t.m_sample\n\t*/\n\n\tconst pane = client.newpane({ x: event.clientX, y: event.clientY })\n\tpane.header.text(p.tk.name)\n\n\tconst tabs = []\n\ttabs.push({\n\t\tlabel: 'Details',\n\t\tcallback: div => {\n\t\t\tp.holder = div\n\t\t\tdetailtable_singlesample(p)\n\t\t}\n\t})\n\n\taddtab_sampleview(tabs, p)\n\tmayaddtab_svgraph(tabs, p)\n\tmayaddtab_disco(tabs, p)\n\tmayaddtab_genome(tabs, p)\n\t/*\n\tcreatebutton_addfeature( {\n\t\tm: p.item,\n\t\tholder:buttonrow,\n\t\ttk: p.tk,\n\t\tblock: p.block,\n\t\tpane: pane\n\t})\n\t*/\n\tmayaddtab_mutationsignature(tabs, p.sample.samplename, p.tk, p.block)\n\tmayaddtab_survival_onemutation(tabs, {\n\t\ttk: p.tk,\n\t\tblock: p.block,\n\t\tm: p.item,\n\t\tsample: p.sample\n\t})\n\tmayaddtab_fimo(tabs, {\n\t\ttk: p.tk,\n\t\tblock: p.block,\n\t\tm: p.item,\n\t\tsample: p.sample,\n\t\tsamplegroup: p.samplegroup\n\t})\n\n\tclient.tab2box(pane.body.style('padding-top', '10px'), tabs)\n}\n\nexport function tooltip_singleitem(p) {\n\t/*\n\tmulti-sample\n\tmouse over an item\n\t*/\n\n\tmulti_sample_addhighlight(p.sample)\n\n\tp.holder = p.tk.tktip.clear().d\n\n\tdetailtable_singlesample(p)\n\n\t// show tip after content is made\n\tp.tk.tktip.show(event.clientX, event.clientY)\n}\n\nexport function detailtable_singlesample(p) {\n\t/*\n\tmulti or single\n\ta table to indicate basic info about an item from a sample\n\n\t.item\n\t.sample {}\n\t\t.samplename\n\t.samplegroup {}\n\t\t.name\n\t.tk\n\t*/\n\tconst lst = []\n\n\tif (p.sample) {\n\t\tlst.push({\n\t\t\tk: 'Sample',\n\t\t\tv: p.sample.samplename\n\t\t})\n\n\t\tmay_add_sampleannotation(p.sample.samplename, p.tk, lst)\n\t} else {\n\t\t// if in single-sample mode, won't have p.sample\n\t}\n\n\tconst m = p.item\n\n\t// mutation-level attributes\n\tlet mattr\n\n\tif (m.dt == common.dtitd) {\n\t\tlst.push({\n\t\t\tk: 'ITD',\n\t\t\tv: m.chr + ':' + (m.start + 1) + '-' + (m.stop + 1)\n\t\t})\n\n\t\tif (m.gene || m.isoform) {\n\t\t\tconst t = []\n\t\t\tif (m.gene) t.push(m.gene)\n\t\t\tif (m.isoform) t.push(m.isoform)\n\t\t\tlst.push({ k: 'Gene', v: t.join(', ') })\n\t\t}\n\n\t\tif (m.rnaduplength) {\n\t\t\tlst.push({ k: 'RNA duplicated', v: m.rnaduplength + ' bp' })\n\t\t}\n\t\tif (m.aaduplength) {\n\t\t\tlst.push({ k: 'AA duplicated', v: m.aaduplength + ' aa' })\n\t\t}\n\n\t\tmattr = m.mattr\n\t} else if (m.dt == common.dtcnv || m.dt == common.dtloh) {\n\t\tif (m.dt == common.dtloh) {\n\t\t\tlst.push({\n\t\t\t\tk: 'LOH seg.mean',\n\t\t\t\tv: m.segmean.toFixed(2)\n\t\t\t})\n\t\t} else {\n\t\t\tlst.push({\n\t\t\t\tk: 'CNV log2(ratio)',\n\t\t\t\tv:\n\t\t\t\t\t'<span style=\"padding:0px 4px;background:' +\n\t\t\t\t\t(m.value > 0 ? p.tk.cnvcolor.gain.str : p.tk.cnvcolor.loss.str) +\n\t\t\t\t\t';color:white;\">' +\n\t\t\t\t\tm.value.toFixed(2) +\n\t\t\t\t\t'</span>'\n\t\t\t})\n\t\t\tlst.push({\n\t\t\t\tk: 'Copy number',\n\t\t\t\tv: (2 * Math.pow(2, m.value)).toFixed(2)\n\t\t\t})\n\t\t}\n\n\t\tlst.push({\n\t\t\tk: 'Position',\n\t\t\tv:\n\t\t\t\tm.chr +\n\t\t\t\t':' +\n\t\t\t\t(m.start + 1) +\n\t\t\t\t'-' +\n\t\t\t\t(m.stop + 1) +\n\t\t\t\t' <span style=\"font-size:.7em\">' +\n\t\t\t\tcommon.bplen(m.stop - m.start) +\n\t\t\t\t'</span>'\n\t\t})\n\n\t\tmattr = m.mattr\n\t} else if (m.dt == common.dtsv || m.dt == common.dtfusionrna) {\n\t\t{\n\t\t\tlst.push({\n\t\t\t\tk: m.dt == common.dtsv ? 'SV' : 'RNA fusion',\n\t\t\t\tv: escapeHtml(itemname_svfusion(m)) + ' <span style=\"font-size:.7em\">' + svcoord2html(m, p.tk) + '</span>'\n\t\t\t})\n\t\t}\n\n\t\tif (m.clipreadA || m.clipreadB) {\n\t\t\tlst.push({\n\t\t\t\tk: '# clip reads',\n\t\t\t\tv:\n\t\t\t\t\t'<span style=\"font-size:.7em;opacity:.7\">A CLIP / TOTAL</span> ' +\n\t\t\t\t\t(Number.isInteger(m.clipreadA) ? m.clipreadA : '?') +\n\t\t\t\t\t' / ' +\n\t\t\t\t\t(Number.isInteger(m.totalreadA) ? m.totalreadA : '?') +\n\t\t\t\t\t'<br>' +\n\t\t\t\t\t'<span style=\"font-size:.7em;opacity:.7\">B CLIP / TOTAL</span> ' +\n\t\t\t\t\t(Number.isInteger(m.clipreadB) ? m.clipreadB : '?') +\n\t\t\t\t\t' / ' +\n\t\t\t\t\t(Number.isInteger(m.totalreadB) ? m.totalreadB : '?')\n\t\t\t})\n\t\t}\n\n\t\tmattr = m.mattr\n\t} else if (m.dt == common.dtsnvindel) {\n\t\tconst tmp = printer_snvindel(m, p.tk)\n\t\tfor (const l of tmp) lst.push(l)\n\n\t\tif (p.m_sample) {\n\t\t\t/*\n\t\t\tm_sample as from m.sampledata[]\n\n\t\t\tin vcf item, mutation-level attributes are in Formats\n\t\t\tcollect them for showing later\n\t\t\t*/\n\t\t\tmattr = {}\n\n\t\t\tconst formats = p.tk.checkvcf ? p.tk.checkvcf.format : null // format registry\n\n\t\t\tfor (const formatfield in p.m_sample) {\n\t\t\t\tif (formatfield == 'sampleobj') {\n\t\t\t\t\t// skip hardcoded attribute\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\t/*\n\t\t\t\tif this format field could be mutation signature\n\t\t\t\t*/\n\t\t\t\tif (p.tk.mds && p.tk.mds.mutation_signature) {\n\t\t\t\t\tconst sigset = p.tk.mds.mutation_signature.sets[formatfield]\n\t\t\t\t\tif (sigset) {\n\t\t\t\t\t\t// this format field is a signature\n\t\t\t\t\t\tconst key = p.m_sample[formatfield]\n\t\t\t\t\t\tconst v = sigset.signatures[key]\n\t\t\t\t\t\t// quick fix that there may be \"nodata\" as the decoy for indel\n\t\t\t\t\t\tif (!v.nodata) {\n\t\t\t\t\t\t\tconst label = v ? v.name : 'Unknown (' + key + ')'\n\t\t\t\t\t\t\tconst color = v ? v.color : 'black'\n\t\t\t\t\t\t\tlst.push({\n\t\t\t\t\t\t\t\tk: sigset.name,\n\t\t\t\t\t\t\t\tv: '<span style=\"background:' + color + '\">&nbsp;&nbsp;&nbsp;</span> ' + label\n\t\t\t\t\t\t\t})\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}\n\n\t\t\t\tif (p.tk.mutationAttribute && p.tk.mutationAttribute.attributes) {\n\t\t\t\t\t// has it; test whether this format is actually attribute\n\t\t\t\t\tif (p.tk.mutationAttribute.attributes[formatfield]) {\n\t\t\t\t\t\tmattr[formatfield] = p.m_sample[formatfield]\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\t/*\n\t\t\t\tthis format field is not declared in mds.mutationAttribute\n\t\t\t\tconfusing here\n\t\t\t\te.g. allele count\n\t\t\t\t*/\n\n\t\t\t\tconst formatdesc = formats ? formats[formatfield] : null\n\n\t\t\t\tif (formatdesc) {\n\t\t\t\t\t// if the FORMAT has per-allele value, like AD in vcf 4.2+\n\t\t\t\t\tlet isperallelevalue = formatdesc.Number == 'R' || formatdesc.Number == 'A'\n\t\t\t\t\tif (!isperallelevalue) {\n\t\t\t\t\t\tif (formatfield == 'AD') {\n\t\t\t\t\t\t\t// vcf 4.1 has AD as '.'\n\t\t\t\t\t\t\tisperallelevalue = true\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\tif (isperallelevalue) {\n\t\t\t\t\t\t// per allele value\n\n\t\t\t\t\t\tconst alleles = []\n\t\t\t\t\t\tconst values = []\n\t\t\t\t\t\tlet altvalue\n\n\t\t\t\t\t\t// add alt first\n\t\t\t\t\t\tfor (const ale in p.m_sample[formatfield]) {\n\t\t\t\t\t\t\tif (ale == m.ref) continue\n\t\t\t\t\t\t\talleles.push(ale)\n\t\t\t\t\t\t\taltvalue = p.m_sample[formatfield][ale]\n\t\t\t\t\t\t\tvalues.push(altvalue)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// add ref after alt\n\t\t\t\t\t\tconst refvalue = p.m_sample[formatfield][m.ref]\n\t\t\t\t\t\tif (refvalue != undefined) {\n\t\t\t\t\t\t\talleles.push(m.ref)\n\t\t\t\t\t\t\tvalues.push(refvalue)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tlet barsvg\n\t\t\t\t\t\tif (refvalue + altvalue > 0) {\n\t\t\t\t\t\t\tbarsvg = client.fillbar(null, { f: altvalue / (altvalue + refvalue) })\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tlst.push({\n\t\t\t\t\t\t\tk: formatfield,\n\t\t\t\t\t\t\tv:\n\t\t\t\t\t\t\t\t(barsvg ? barsvg + ' ' : '') +\n\t\t\t\t\t\t\t\t'<span style=\"font-size:.8em;opacity:.5\">' +\n\t\t\t\t\t\t\t\talleles.join(' / ') +\n\t\t\t\t\t\t\t\t'</span> ' +\n\t\t\t\t\t\t\t\tvalues.join(' / ') +\n\t\t\t\t\t\t\t\t(formatdesc.Description\n\t\t\t\t\t\t\t\t\t? ' <span style=\"font-size:.7em;opacity:.5\">' + formatdesc.Description + '</span>'\n\t\t\t\t\t\t\t\t\t: '')\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}\n\n\t\t\t\tlst.push({\n\t\t\t\t\tk: formatfield,\n\t\t\t\t\tv: p.m_sample[formatfield]\n\t\t\t\t})\n\t\t\t}\n\t\t\t// mutation attributes are FORMAT in vcf, already shown above\n\t\t}\n\t} else {\n\t\tlst.push({ k: 'Unknown dt!!', v: m.dt })\n\t}\n\n\tif (mattr) {\n\t\t// show mutation-level attributes, won't do here for vcf stuff\n\t\tfor (const key in mattr) {\n\t\t\tconst attr = p.tk.mutationAttribute ? p.tk.mutationAttribute.attributes[key] : null\n\t\t\tconst vstr = mattr[key]\n\n\t\t\tif (attr) {\n\t\t\t\tif (attr.appendto_link) {\n\t\t\t\t\t// quick fix for pmid\n\n\t\t\t\t\tif (!vstr) {\n\t\t\t\t\t\t// no value\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tk: attr.label,\n\t\t\t\t\t\tv: vstr\n\t\t\t\t\t\t\t.split(',')\n\t\t\t\t\t\t\t.map(id => '<a target=_blank href=' + attr.appendto_link + id + '>' + id + '</a>')\n\t\t\t\t\t\t\t.join(' ')\n\t\t\t\t\t})\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tif (attr.values) {\n\t\t\t\t\t// values is optional\n\t\t\t\t\tconst vv = attr.values[vstr]\n\t\t\t\t\tif (vv) {\n\t\t\t\t\t\tlst.push({\n\t\t\t\t\t\t\tk: attr.label,\n\t\t\t\t\t\t\tv:\n\t\t\t\t\t\t\t\tescapeHtml(vv.name) +\n\t\t\t\t\t\t\t\t(vv.label ? ' <span style=\"font-size:.7em;opacity:.5\">' + escapeHtml(vv.label) + '</span>' : '')\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}\n\n\t\t\t\t// no attr.values{} or unregistered value\n\t\t\t\tlst.push({\n\t\t\t\t\tk: attr.label,\n\t\t\t\t\tv: vstr\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\tlst.push({\n\t\t\t\t\tk: key,\n\t\t\t\t\tv: vstr\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\tmayaddexpressionrank(p, lst)\n\n\tconst table = client.make_table_2col(p.holder, lst)\n\n\tif (m.dt == common.dtsnvindel) {\n\t\tmay_findmatchingsnp_printintable(m, p.block, table)\n\t}\n}\n\nfunction mayaddexpressionrank(p, lines) {\n\tconst tk = p.tk\n\tif (!tk) return\n\tconst sample = p.sample\n\tif (!sample) return\n\tif (!sample.expressionrank) return\n\n\t// one gene per row\n\tconst rows = []\n\n\tfor (const genename in sample.expressionrank) {\n\t\tconst v = sample.expressionrank[genename]\n\t\tconst lst = [\n\t\t\t'<tr>' +\n\t\t\t\t'<td><b>' +\n\t\t\t\tgenename +\n\t\t\t\t'</b></td>' +\n\t\t\t\t'<td>&nbsp;<span style=\"font-size:.7em\">RANK</span> ' +\n\t\t\t\tclient.ranksays(v.rank) +\n\t\t\t\t'</td>' +\n\t\t\t\t'<td>&nbsp;<span style=\"font-size:.7em\">' +\n\t\t\t\ttk.gecfg.datatype +\n\t\t\t\t'</span> ' +\n\t\t\t\tv.value +\n\t\t\t\t'</td>' +\n\t\t\t\t'<td>'\n\t\t]\n\n\t\tif (v.estat) {\n\t\t\tif (v.estat.ase_uncertain) {\n\t\t\t\tlst.push(\n\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\ttk.gecfg.ase.color_uncertain +\n\t\t\t\t\t\t';color:white\">ASE uncertain</span>'\n\t\t\t\t)\n\t\t\t} else if (v.estat.ase_biallelic) {\n\t\t\t\tlst.push(\n\t\t\t\t\t'<span style=\"padding:0px 5px;background:' + tk.gecfg.ase.color_biallelic + ';color:white\">Bi-allelic</span>'\n\t\t\t\t)\n\t\t\t} else if (v.estat.ase_monoallelic) {\n\t\t\t\tlst.push(\n\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\ttk.gecfg.ase.color_monoallelic +\n\t\t\t\t\t\t';color:white\">Mono-allelic</span>'\n\t\t\t\t)\n\t\t\t}\n\t\t\tif (v.estat.outlier) {\n\t\t\t\tlst.push(\n\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\ttk.gecfg.outlier.color_outlier +\n\t\t\t\t\t\t';color:white\">Outlier HIGH</span>'\n\t\t\t\t)\n\t\t\t} else if (v.estat.outlier_asehigh) {\n\t\t\t\tlst.push(\n\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\ttk.gecfg.outlier.color_outlier_asehigh +\n\t\t\t\t\t\t';color:white\">ASE HIGH</span>'\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\n\t\tlst.push('</td></tr>')\n\t\trows.push(lst.join(''))\n\t}\n\n\tif (tk.gecfg && tk.gecfg.fixed) {\n\t\tfor (const fgene of tk.gecfg.fixed) {\n\t\t\tif (fgene.sample2rank && fgene.sample2rank[sample.samplename]) {\n\t\t\t\tconst v = fgene.sample2rank[sample.samplename]\n\t\t\t\tconst lst = [\n\t\t\t\t\t'<tr>' +\n\t\t\t\t\t\t'<td><b>' +\n\t\t\t\t\t\tfgene.gene +\n\t\t\t\t\t\t'</b></td>' +\n\t\t\t\t\t\t'<td>&nbsp;<span style=\"font-size:.7em\">RANK</span> ' +\n\t\t\t\t\t\tclient.ranksays(v.rank) +\n\t\t\t\t\t\t'</td>' +\n\t\t\t\t\t\t'<td>&nbsp;<span style=\"font-size:.7em\">' +\n\t\t\t\t\t\ttk.gecfg.datatype +\n\t\t\t\t\t\t'</span> ' +\n\t\t\t\t\t\tv.value +\n\t\t\t\t\t\t'</td>' +\n\t\t\t\t\t\t'<td>'\n\t\t\t\t]\n\n\t\t\t\tif (v.estat) {\n\t\t\t\t\tif (v.estat.ase_uncertain) {\n\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\t\t\ttk.gecfg.ase.color_uncertain +\n\t\t\t\t\t\t\t\t';color:white\">ASE uncertain</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t} else if (v.estat.ase_biallelic) {\n\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\t\t\ttk.gecfg.ase.color_biallelic +\n\t\t\t\t\t\t\t\t';color:white\">Bi-allelic</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t} else if (v.estat.ase_monoallelic) {\n\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\t\t\ttk.gecfg.ase.color_monoallelic +\n\t\t\t\t\t\t\t\t';color:white\">Mono-allelic</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t}\n\t\t\t\t\tif (v.estat.outlier) {\n\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\t\t\ttk.gecfg.outlier.color_outlier +\n\t\t\t\t\t\t\t\t';color:white\">Outlier HIGH</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t} else if (v.estat.outlier_asehigh) {\n\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t'<span style=\"padding:0px 5px;background:' +\n\t\t\t\t\t\t\t\ttk.gecfg.outlier.color_outlier_asehigh +\n\t\t\t\t\t\t\t\t';color:white\">ASE HIGH</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tlst.push('</td></tr>')\n\t\t\t\trows.push(lst.join(''))\n\t\t\t}\n\t\t}\n\t}\n\n\tif (rows.length) {\n\t\tlines.push({\n\t\t\tk: 'Expression',\n\t\t\tv: '<table style=\"font-size:.9em\">' + rows.join('') + '</table>'\n\t\t})\n\t}\n}\n\nfunction printer_snvindel(m, tk) {\n\t/*\n\tshow attributes for a single variant\n\tmay show INFO if they are used for filtering\n\t*/\n\n\tconst lst = []\n\n\t{\n\t\t// somehow mname may be abscent from vep annotation\n\t\tconst _c = common.mclass[m.class]\n\t\tlst.push({\n\t\t\tk: 'Mutation',\n\t\t\tv:\n\t\t\t\t(m.mname ? '<span style=\"color:' + _c.color + '\">' + m.mname + '</span>' : '') +\n\t\t\t\t' <span style=\"font-size:.7em\">' +\n\t\t\t\t_c.label +\n\t\t\t\t'</span>'\n\t\t})\n\t}\n\n\t{\n\t\tconst phrases = []\n\t\tif (m.gene) phrases.push(m.gene)\n\t\tif (m.isoform) phrases.push(m.isoform)\n\t\tif (phrases.length) {\n\t\t\tlst.push({\n\t\t\t\tk: 'Gene',\n\t\t\t\tv: phrases.join(' ')\n\t\t\t})\n\t\t}\n\t}\n\n\tlst.push({\n\t\tk: 'Position',\n\t\tv: m.chr + ':' + (m.pos + 1)\n\t})\n\tlst.push({\n\t\tk: 'Alleles',\n\t\tv: '<span style=\"font-size:.8em;opacity:.5\">REF/ALT</span> ' + m.ref + ' / ' + m.alt\n\t})\n\n\tif (tk && tk.alleleAttribute && tk.alleleAttribute.attributes) {\n\t\tfor (const key in tk.alleleAttribute.attributes) {\n\t\t\tconst attr = tk.alleleAttribute.attributes[key]\n\t\t\tlst.push({\n\t\t\t\tk: attr.label,\n\t\t\t\tv: m.altinfo ? m.altinfo[key] : ''\n\t\t\t})\n\t\t}\n\t}\n\n\tif (tk && tk.locusAttribute && tk.locusAttribute.attributes) {\n\t\tfor (const key in tk.locusAttribute.attributes) {\n\t\t\tconst attr = tk.locusAttribute.attributes[key]\n\n\t\t\tconst vstr = m.info ? m.info[key] : ''\n\n\t\t\t// locus attribute support adding hyper links\n\t\t\tif (attr.appendto_link) {\n\t\t\t\tif (!vstr) {\n\t\t\t\t\t// no value, do not add link\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tlst.push({\n\t\t\t\t\tk: attr.label,\n\t\t\t\t\tv: vstr\n\t\t\t\t\t\t.split(',')\n\t\t\t\t\t\t.map(id => '<a target=_blank href=' + attr.appendto_link + id + '>' + id + '</a>')\n\t\t\t\t\t\t.join(' ')\n\t\t\t\t})\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tlst.push({\n\t\t\t\tk: attr.label,\n\t\t\t\tv: m.info ? m.info[key] : ''\n\t\t\t})\n\t\t}\n\t}\n\n\treturn lst\n}\n\nfunction findsamplegroup_byvcf(p) {\n\t/*\n\t.m\n\t.m_sample\n\tp.tk\n\t*/\n\n\tlet samplename\n\tif (p.m.dt == common.dtsnvindel) {\n\t\tif (!p.m_sample) throw 'm_sample missing'\n\t\tsamplename = p.m_sample.sampleobj.name\n\t} else {\n\t\tthrow 'unknown dt'\n\t}\n\n\tfor (const g of p.tk._data) {\n\t\tfor (const sample of g.samples) {\n\t\t\tif (sample.samplename == samplename) {\n\t\t\t\treturn [sample, g]\n\t\t\t}\n\t\t}\n\t}\n\treturn [-1, -1]\n}\n\nexport function svchr2html(chr, tk) {\n\t// only for multi-sample, full mode\n\tif (tk.legend_svchrcolor.interchrs.has(chr)) {\n\t\treturn (\n\t\t\t'<span style=\"background:' +\n\t\t\ttk.legend_svchrcolor.colorfunc(chr) +\n\t\t\t';font-weight:bold;padding:0px 5px;color:white\">' +\n\t\t\tescapeHtml(chr) +\n\t\t\t'</span>'\n\t\t)\n\t}\n\treturn escapeHtml(chr)\n}\n\nexport function svcoord2html(i, tk) {\n\treturn (\n\t\tsvchr2html(i.chrA, tk) +\n\t\t':' +\n\t\tescapeHtml(i.posA) +\n\t\t(i.strandA ? ':' + escapeHtml(i.strandA) : '') +\n\t\t' &raquo; ' +\n\t\tsvchr2html(i.chrB, tk) +\n\t\t':' +\n\t\tescapeHtml(i.posB) +\n\t\t(i.strandB ? ':' + escapeHtml(i.strandB) : '')\n\t)\n}\n\nfunction sortitemsbytype_onesample(samplename, lst, tk) {\n\t/*\n\tmulti-sample\n\tdense or full\n\tfor one sample, to show its mutation data in table, grouped by type\n\t*/\n\n\tconst cnvlst = [], // html\n\t\tsvlst = [],\n\t\tlohlst = [],\n\t\titdlst = [],\n\t\tvcflst = [],\n\t\tcnvlst0 = [], // actual objects\n\t\tsvlst0 = [],\n\t\tlohlst0 = [],\n\t\titdlst0 = [],\n\t\tvcflst0 = []\n\n\t{\n\t\t// treat sv/fusion first: dedup breakends\n\t\tconst breakends = lst.filter(i => i.dt == common.dtsv || i.dt == common.dtfusionrna)\n\t\tconst deduped = dedup_sv(breakends)\n\t\tfor (const i of deduped) {\n\t\t\tsvlst.push(\n\t\t\t\t'<div style=\"white-space:nowrap\">' +\n\t\t\t\t\tescapeHtml(itemname_svfusion(i)) +\n\t\t\t\t\t' <span style=\"font-size:.7em\">' +\n\t\t\t\t\tsvcoord2html(i, tk) +\n\t\t\t\t\t'</span>' +\n\t\t\t\t\t(i.dt == common.dtfusionrna ? ' <span style=\"font-size:.7em\">(RNA fusion)</span>' : '') +\n\t\t\t\t\t'</div>'\n\t\t\t)\n\t\t\tsvlst0.push(i)\n\t\t}\n\t}\n\n\tfor (const i of lst) {\n\t\tif (i.dt == common.dtsv || i.dt == common.dtfusionrna) continue\n\n\t\tif (i.dt == common.dtloh) {\n\t\t\tlohlst.push(\n\t\t\t\t'<div style=\"white-space:nowrap\">' +\n\t\t\t\t\tescapeHtml(i.chr) +\n\t\t\t\t\t':' +\n\t\t\t\t\t(i.start + 1) +\n\t\t\t\t\t'-' +\n\t\t\t\t\t(i.stop + 1) +\n\t\t\t\t\t' <span style=\"font-size:.8em\">' +\n\t\t\t\t\tcommon.bplen(i.stop - i.start) +\n\t\t\t\t\t' seg.mean: ' +\n\t\t\t\t\tescapeHtml(i.segmean) +\n\t\t\t\t\t'</span>'\n\t\t\t)\n\t\t\tlohlst0.push(i)\n\t\t} else if (i.dt == common.dtcnv) {\n\t\t\tcnvlst.push(\n\t\t\t\t'<div style=\"white-space:nowrap\">' +\n\t\t\t\t\tescapeHtml(i.chr) +\n\t\t\t\t\t':' +\n\t\t\t\t\t(i.start + 1) +\n\t\t\t\t\t'-' +\n\t\t\t\t\t(i.stop + 1) +\n\t\t\t\t\t' <span style=\"font-size:.8em\">' +\n\t\t\t\t\tcommon.bplen(i.stop - i.start) +\n\t\t\t\t\t'</span>' +\n\t\t\t\t\t' <span style=\"background:' +\n\t\t\t\t\t(i.value > 0 ? tk.cnvcolor.gain.str : tk.cnvcolor.loss.str) +\n\t\t\t\t\t';font-size:.8em;color:white\">&nbsp;' +\n\t\t\t\t\tescapeHtml(i.value) +\n\t\t\t\t\t'&nbsp;</span>' +\n\t\t\t\t\t'</div>'\n\t\t\t)\n\t\t\tcnvlst0.push(i)\n\t\t} else if (i.dt == common.dtitd) {\n\t\t\titdlst.push(\n\t\t\t\t'<div style=\"white-space:nowrap\">' +\n\t\t\t\t\tescapeHtml(i.chr) +\n\t\t\t\t\t':' +\n\t\t\t\t\t(i.start + 1) +\n\t\t\t\t\t'-' +\n\t\t\t\t\t(i.stop + 1) +\n\t\t\t\t\t(i.rnaduplength ? ', ' + escapeHtml(i.rnaduplength) + ' bp duplicated in RNA' : '') +\n\t\t\t\t\t(i.aaduplength ? ', ' + escapeHtml(i.aaduplength) + ' AA duplicated' : '') +\n\t\t\t\t\t'</div>'\n\t\t\t)\n\t\t\titdlst0.push(i)\n\t\t} else {\n\t\t\tthrow 'unknown dt: ' + i.dt\n\t\t}\n\t}\n\n\tif (tk.data_vcf) {\n\t\tfor (const m of tk.data_vcf) {\n\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\tif (m.sampledata.find(s => s.sampleobj.name == samplename)) {\n\t\t\t\t\tconst c = common.mclass[m.class]\n\t\t\t\t\tvcflst.push(\n\t\t\t\t\t\t'<div style=\"white-space:nowrap\">' +\n\t\t\t\t\t\t\t'<span style=\"color:' +\n\t\t\t\t\t\t\tc.color +\n\t\t\t\t\t\t\t';font-weight:bold\">' +\n\t\t\t\t\t\t\tescapeHtml(m.mname) +\n\t\t\t\t\t\t\t'</span> ' +\n\t\t\t\t\t\t\t'<span style=\"font-size:.7em\">' +\n\t\t\t\t\t\t\tc.label +\n\t\t\t\t\t\t\t'</span></div>'\n\t\t\t\t\t)\n\t\t\t\t\tvcflst0.push(m)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow 'unknown dt: ' + m.dt\n\t\t\t}\n\t\t}\n\t}\n\n\treturn [cnvlst, svlst, lohlst, itdlst, vcflst, cnvlst0, svlst0, lohlst0, itdlst0, vcflst0]\n}\n\nfunction may_show_matrixbutton(samplegroup, tk, block) {\n\t/*\n\tin sample group name menu, may add a button for showing pre-configured samplematrix for this group\n\tannotationsampleset2matrix has one key\n\t*/\n\tif (!tk.mds || !tk.mds.annotationsampleset2matrix) return\n\tif (!samplegroup.attributes) return\n\n\t// from attributes of this group, find one using that key\n\tconst attr = samplegroup.attributes.find(i => i.k == tk.mds.annotationsampleset2matrix.key)\n\tif (!attr) return\n\n\t// and the value of the attribute for this group should have corresponding item\n\tconst valueitem = tk.mds.annotationsampleset2matrix.groups[attr.kvalue]\n\tif (!valueitem) return\n\n\tif (!valueitem.groups) return // should not happen\n\n\t// this group will have 1 or more subgroups, each is one study group or subtype\n\tfor (const group of valueitem.groups) {\n\t\tif (!group.name || !group.matrixconfig) continue\n\n\t\ttk.tip2.d\n\t\t\t.append('div')\n\t\t\t.html(escapeHtml(group.name) + ' <span style=\"font-size:.8em;opacity:.5\">SUMMARY</span>')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.on('click', () => {\n\t\t\t\ttk.tip2.hide()\n\n\t\t\t\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\t\t\tpane.header.text(group.name + ' summary')\n\n\t\t\t\tconst arg = {\n\t\t\t\t\tdslabel: tk.mds.label,\n\t\t\t\t\tdebugmode: block.debugmode,\n\t\t\t\t\tgenome: block.genome,\n\t\t\t\t\thostURL: block.hostURL,\n\t\t\t\t\tjwt: block.jwt,\n\t\t\t\t\tholder: pane.body.append('div').style('margin', '20px')\n\t\t\t\t}\n\n\t\t\t\tfor (const k in group.matrixconfig) {\n\t\t\t\t\targ[k] = group.matrixconfig[k]\n\t\t\t\t}\n\n\t\t\t\timport('./samplematrix').then(_ => {\n\t\t\t\t\tnew _.Samplematrix(arg)\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n\nexport function may_add_sampleannotation(samplename, tk, lst) {\n\tif (!tk.sampleAttribute) return\n\tif (!tk.sampleAttribute.attributes || !tk.sampleAttribute.samples) return\n\n\t// should only be available in multi-sample, official tk\n\n\tconst anno = tk.sampleAttribute.samples[samplename]\n\tif (!anno) return\n\n\t// show annotation for this sample\n\tfor (const key in anno) {\n\t\t// config about this key\n\t\tconst keycfg = tk.sampleAttribute.attributes[key] || {}\n\n\t\tconst value = anno[key]\n\n\t\tif (value == undefined) continue\n\n\t\tlet printvalue = value\n\t\tif (keycfg.values) {\n\t\t\tconst o = keycfg.values[value]\n\t\t\tif (o && o.name) {\n\t\t\t\tprintvalue = o.name\n\t\t\t}\n\t\t}\n\n\t\tlst.push({\n\t\t\tk: keycfg.label || key,\n\t\t\tv: printvalue\n\t\t})\n\t}\n}\n\nfunction mayaddtab_svgraph(tabs, p) {\n\tif (!p.item) return\n\tif (p.item.dt != common.dtsv && p.item.dt != common.dtfusionrna) return\n\ttabs.push({\n\t\tlabel: 'Fusion graph',\n\t\tcallback: async div => {\n\t\t\tconst wait = client.tab_wait(div)\n\t\t\tawait make_svgraph(p, div)\n\t\t\twait.remove()\n\t\t}\n\t})\n}\n\nexport async function make_svgraph(p, holder) {\n\tconst svpair = {\n\t\ta: {\n\t\t\tchr: p.item.chrA,\n\t\t\tposition: p.item.posA,\n\t\t\tstrand: p.item.strandA\n\t\t},\n\t\tb: {\n\t\t\tchr: p.item.chrB,\n\t\t\tposition: p.item.posB,\n\t\t\tstrand: p.item.strandB\n\t\t}\n\t}\n\n\tconst wait = holder.append('div')\n\n\ttry {\n\t\t// may use isoform supplied along with the data!!\n\n\t\t{\n\t\t\twait.text('Loading gene at ' + svpair.a.chr + ':' + svpair.a.position + ' ...')\n\t\t\tconst lst = await getisoform(p, svpair.a.chr, svpair.a.position)\n\t\t\tconst useone = lst.find(i => i.isdefault) || lst[0]\n\t\t\tif (useone) {\n\t\t\t\tsvpair.a.name = useone.name\n\t\t\t\tsvpair.a.gm = { isoform: useone.isoform }\n\t\t\t}\n\t\t}\n\t\t{\n\t\t\twait.text('Loading gene at ' + svpair.b.chr + ':' + svpair.b.position + ' ...')\n\t\t\tconst lst = await getisoform(p, svpair.b.chr, svpair.b.position)\n\t\t\tconst useone = lst.find(i => i.isdefault) || lst[0]\n\t\t\tif (useone) {\n\t\t\t\tsvpair.b.name = useone.name\n\t\t\t\tsvpair.b.gm = { isoform: useone.isoform }\n\t\t\t}\n\t\t}\n\n\t\twait.remove()\n\n\t\tconst svarg = {\n\t\t\t//jwt: p.block.jwt,\n\t\t\t//hostURL: p.block.hostURL,\n\t\t\tpairlst: [svpair],\n\t\t\tgenome: p.block.genome,\n\t\t\tholder: holder\n\t\t}\n\t\timport('./svgraph').then(_ => {\n\t\t\t_.default(svarg)\n\t\t})\n\t} catch (e) {\n\t\tif (e.stack) console.log(e.stack)\n\t\twait.text('Error: ' + (e.message || e))\n\t}\n}\n\nfunction getisoform(p, chr, pos) {\n\treturn client.dofetch3(`isoformbycoord?genome=${p.block.genome.name}&chr=${chr}&pos=${pos}`).then(data => {\n\t\tif (data.error) throw data.error\n\t\treturn data.lst\n\t})\n}\n\nasync function may_findmatchingsnp_printintable(m, block, table) {\n\tif (!block || !block.genome || !block.genome.hasSNP) return\n\tconst tr = table.append('tr')\n\ttr.append('td').attr('colspan', 2).text('dbSNP').style('opacity', 0.4).style('padding', '3px')\n\tconst td = tr.append('td')\n\tconst wait = td.append('div').text('Loading...')\n\ttry {\n\t\tconst hits = await client.may_findmatchingsnp(m.chr, [m.pos], block.genome, [m.ref, m.altstr])\n\t\tif (!hits || hits.length == 0) {\n\t\t\twait.text('No match')\n\t\t\treturn\n\t\t}\n\t\twait.remove()\n\t\tfor (const s of hits) {\n\t\t\tconst row = td.append('div')\n\t\t\tclient.snp_printhtml(s, row)\n\t\t}\n\t} catch (e) {\n\t\twait.text(e.message || e)\n\t}\n}\n\nfunction createbutton_focus(buttonrow, div, p, defaultshow) {\n\t// click focus button to show block in holder\n\tlet blocknotshown = !defaultshow\n\tconst holder = div\n\t\t.append('div')\n\t\t.style('margin', '10px')\n\t\t.style('display', defaultshow ? 'block' : 'none')\n\n\t// focus button\n\tbuttonrow\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Focus')\n\t\t.on('click', () => {\n\t\t\tif (holder.style('display') == 'none') {\n\t\t\t\tclient.appear(holder)\n\t\t\t} else {\n\t\t\t\tclient.disappear(holder)\n\t\t\t}\n\n\t\t\tif (blocknotshown) {\n\t\t\t\tblocknotshown = false\n\t\t\t\tfocus_singlesample({\n\t\t\t\t\tholder: holder,\n\t\t\t\t\tm: p.item,\n\t\t\t\t\tsample: p.sample,\n\t\t\t\t\tsamplegroup: p.samplegroup,\n\t\t\t\t\ttk: p.tk,\n\t\t\t\t\tblock: p.block\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\n\tif (defaultshow) {\n\t\tfocus_singlesample({\n\t\t\tholder: holder,\n\t\t\tm: p.item,\n\t\t\tsample: p.sample,\n\t\t\tsamplegroup: p.samplegroup,\n\t\t\ttk: p.tk,\n\t\t\tblock: p.block\n\t\t})\n\t}\n}\n\nfunction addtab_sampleview(tabs, p) {\n\ttabs.push({\n\t\tlabel: 'Sample View',\n\t\tcallback: div => {\n\t\t\tfocus_singlesample({\n\t\t\t\tholder: div,\n\t\t\t\tm: p.item,\n\t\t\t\tsample: p.sample,\n\t\t\t\tsamplegroup: p.samplegroup,\n\t\t\t\ttk: p.tk,\n\t\t\t\tblock: p.block\n\t\t\t})\n\t\t}\n\t})\n}\n\nfunction mayaddtab_genome(tabs, p) {\n\t/*\nif the sample has a single vcf file\nwill allow genome view\nalso allow if there is no vcf query at all\nshow entirety of each chr, and the mds single sample track\n\nmay allow for custom track without vcf\n*/\n\tif (!p.tk.mds) return\n\ttabs.push({\n\t\tlabel: 'Genome',\n\t\tcallback: async div => {\n\t\t\tconst wait = client.tab_wait(div)\n\t\t\ttry {\n\t\t\t\tconst data = await client.dofetch('mdssvcnv', {\n\t\t\t\t\tgenome: p.block.genome.name,\n\t\t\t\t\tdslabel: p.tk.mds.label,\n\t\t\t\t\tquerykey: p.tk.mds.querykey,\n\t\t\t\t\tifsamplehasvcf: p.sample.samplename\n\t\t\t\t})\n\t\t\t\tif (data.no) return\n\t\t\t\t// has single-sample vcf\n\t\t\t\tlet maxbp = 0\n\t\t\t\tfor (const chr in p.block.genome.majorchr) {\n\t\t\t\t\tmaxbp = Math.max(maxbp, p.block.genome.majorchr[chr])\n\t\t\t\t}\n\n\t\t\t\tfor (const chr in p.block.genome.majorchr) {\n\t\t\t\t\tconst chrdiv = div.append('div').style('display', 'inline-block')\n\t\t\t\t\tconst t = {}\n\n\t\t\t\t\tif (p.tk.iscustom) {\n\t\t\t\t\t\t// TODO\n\t\t\t\t\t} else {\n\t\t\t\t\t\tt.fixname = chr.toUpperCase()\n\t\t\t\t\t\tt.mds = p.tk.mds\n\t\t\t\t\t\tt.querykey = p.tk.querykey\n\t\t\t\t\t\tt.singlesample = {\n\t\t\t\t\t\t\tname: p.sample.samplename,\n\t\t\t\t\t\t\twaterfall: { inuse: 1 }\n\t\t\t\t\t\t}\n\t\t\t\t\t\tfor (const k in p.tk.mds.queries[p.tk.querykey]) {\n\t\t\t\t\t\t\tif (k == 'bplengthUpperLimit' || k == 'valueCutoff') {\n\t\t\t\t\t\t\t\t// do not use default\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tt[k] = p.tk.mds.queries[p.tk.querykey][k]\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tp.block.newblock({\n\t\t\t\t\t\tfoldlegend: true,\n\t\t\t\t\t\thide_mdsHandleHolder: 1,\n\t\t\t\t\t\twidth: Math.ceil((900 * p.block.genome.majorchr[chr]) / maxbp),\n\t\t\t\t\t\tholder: chrdiv,\n\t\t\t\t\t\tblock: 1,\n\t\t\t\t\t\tchr: chr,\n\t\t\t\t\t\tstart: 0,\n\t\t\t\t\t\tstop: p.block.genome.majorchr[chr],\n\t\t\t\t\t\ttklst: [t]\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Error: ' + (e.message || e))\n\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction mayaddtab_disco(tabs, p) {\n\tif (!p.tk.mds || !p.tk.mds.singlesamplemutationjson) return\n\t/*\n\tis official dataset, and equipped with single-sample files\n\tclick button to retrieve all mutations and show in disco plot\n\t*/\n\ttabs.push({\n\t\tlabel: 'Disco plot',\n\t\tcallback: async div => {\n\t\t\tconst wait = client.tab_wait(div)\n\t\t\ttry {\n\t\t\t\tconst sjcharts = await getsjcharts()\n\n\t\t\t\tconst arg = {\n\t\t\t\t\tgenome: p.block.genome.name,\n\t\t\t\t\tdslabel: p.tk.mds.label,\n\t\t\t\t\tquerykey: p.tk.querykey,\n\t\t\t\t\tgetsample4disco: p.sample.samplename\n\t\t\t\t}\n\t\t\t\tconst data = await client.dofetch('/mdssvcnv', arg)\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tif (!data.text) throw '.text missing'\n\n\t\t\t\tconst disco_arg = {\n\t\t\t\t\tsampleName: p.sample.samplename,\n\t\t\t\t\tdata: JSON.parse(data.text)\n\t\t\t\t}\n\n\t\t\t\tif (p.tk.mds.mutation_signature) {\n\t\t\t\t\tlet hassig = false\n\t\t\t\t\tfor (const k in p.tk.mds.mutation_signature.sets) {\n\t\t\t\t\t\tfor (const m of disco_arg.data) {\n\t\t\t\t\t\t\tif (m[k]) {\n\t\t\t\t\t\t\t\thassig = k\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\tif (hassig) break\n\t\t\t\t\t}\n\t\t\t\t\tif (hassig) {\n\t\t\t\t\t\tconst o = p.tk.mds.mutation_signature.sets[hassig]\n\t\t\t\t\t\tdisco_arg.mutation_signature = {\n\t\t\t\t\t\t\tkey: hassig,\n\t\t\t\t\t\t\tname: o.name,\n\t\t\t\t\t\t\tsignatures: o.signatures\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tconst renderer = await sjcharts.dtDisco({\n\t\t\t\t\tchromosomeType: p.block.genome.name,\n\t\t\t\t\tmajorchr: p.block.genome.majorchr,\n\t\t\t\t\tholderSelector: div,\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tshowControls: false,\n\t\t\t\t\t\tselectedSamples: []\n\t\t\t\t\t},\n\t\t\t\t\tcallbacks: {\n\t\t\t\t\t\tgeneLabelClick: {\n\t\t\t\t\t\t\ttype: 'genomepaint',\n\t\t\t\t\t\t\thostURL: p.block.hostURL,\n\t\t\t\t\t\t\tgenome: p.block.genome.name,\n\t\t\t\t\t\t\tdslabel: p.tk.mds.label,\n\t\t\t\t\t\t\tsample: p.sample.samplename\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\trenderer.main(disco_arg)\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Error: ' + (e.message || e))\n\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction mayaddtab_mutationsignature(tabs, samplename, tk, block) {\n\tif (tk.iscustom || !tk.mds || !tk.mds.mutation_signature) return\n\ttabs.push({\n\t\tlabel: 'Mutation signature',\n\t\tcallback: async div => {\n\t\t\tconst wait = client.tab_wait(div)\n\t\t\ttry {\n\t\t\t\tconst data = await client.dofetch('mdssamplesignature', {\n\t\t\t\t\tsample: samplename,\n\t\t\t\t\tgenome: block.genome.name,\n\t\t\t\t\tdslabel: tk.mds.label\n\t\t\t\t})\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tif (!data.lst) throw '.lst[] missing'\n\t\t\t\tif (data.lst.length == 0) {\n\t\t\t\t\twait.text('No mutation signature for this sample.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tfor (const s of data.lst) {\n\t\t\t\t\tconst ss = tk.mds.mutation_signature.sets[s.key]\n\t\t\t\t\tconst d2 = div.append('div').style('margin-bottom', '20px')\n\t\t\t\t\td2.append('div').text(ss.name)\n\t\t\t\t\td2.append('div').text(s.valuename)\n\t\t\t\t\tconst svg = d2.append('svg')\n\t\t\t\t\tconst fontsize = 14,\n\t\t\t\t\t\trowh = 16,\n\t\t\t\t\t\tbarw = 250,\n\t\t\t\t\t\tpad = 20,\n\t\t\t\t\t\trowspace = 2,\n\t\t\t\t\t\tlabelspace = 6,\n\t\t\t\t\t\taxish = 5\n\t\t\t\t\tconst maxv = s.annotation[0].v\n\t\t\t\t\t//const minv = s.annotation[s.annotation.length-1].v\n\t\t\t\t\tconst minv = 0 // hardcode the #mutation per mb minimum value as 0\n\t\t\t\t\tconst scale = scaleLinear().domain([minv, maxv]).range([0, barw])\n\t\t\t\t\tlet labelw = 0\n\t\t\t\t\tfor (const i of s.annotation) {\n\t\t\t\t\t\tsvg\n\t\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t\t\t.text(ss.signatures[i.k].name)\n\t\t\t\t\t\t\t.each(function () {\n\t\t\t\t\t\t\t\tlabelw = Math.max(labelw, this.getBBox().width)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.remove()\n\t\t\t\t\t}\n\t\t\t\t\tconst g = svg\n\t\t\t\t\t\t.append('g')\n\t\t\t\t\t\t.attr('transform', 'translate(' + (pad + labelw + labelspace) + ',' + (pad + axish + rowspace) + ')')\n\t\t\t\t\tfor (const [i, a] of s.annotation.entries()) {\n\t\t\t\t\t\tconst row = g.append('g').attr('transform', 'translate(0,' + (rowh + rowspace) * i + ')')\n\t\t\t\t\t\trow\n\t\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t\t\t.attr('x', -labelspace)\n\t\t\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t\t\t.text(ss.signatures[a.k].name)\n\t\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\trow\n\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t.attr('width', Math.max(1, scale(a.v)))\n\t\t\t\t\t\t\t.attr('height', rowh)\n\t\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t\t.attr('fill', ss.signatures[a.k].color)\n\t\t\t\t\t}\n\n\t\t\t\t\tclient.axisstyle({\n\t\t\t\t\t\taxis: g\n\t\t\t\t\t\t\t.append('g')\n\t\t\t\t\t\t\t.attr('transform', 'translate(0,-' + rowspace + ')')\n\t\t\t\t\t\t\t.call(axisTop().scale(scale).ticks(4)),\n\t\t\t\t\t\tshowline: 1,\n\t\t\t\t\t\tfontsize: fontsize - 2\n\t\t\t\t\t})\n\n\t\t\t\t\tsvg\n\t\t\t\t\t\t.attr('width', pad + labelw + labelspace + barw + pad)\n\t\t\t\t\t\t.attr('height', pad + axish + rowspace + (rowh + rowspace) * s.annotation.length + pad)\n\t\t\t\t}\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Error: ' + (e.message || e))\n\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction mayaddtab_fimo(tabs, arg) {\n\t/*\nmay create a tf motif find button for mutation\n*/\n\tif (!arg.tk || !arg.block || !arg.block.genome || !arg.block.genome.fimo_motif) return\n\tif (!arg.m || arg.m.dt != common.dtsnvindel) return\n\ttabs.push({\n\t\tlabel: 'TF motif',\n\t\tcallback: async div => {\n\t\t\tconst wait = client.tab_wait(div)\n\t\t\ttry {\n\t\t\t\t// generate fimo query param\n\t\t\t\tconst fimoarg = {\n\t\t\t\t\tgenome: arg.block.genome,\n\t\t\t\t\tdiv: div,\n\t\t\t\t\tm: {\n\t\t\t\t\t\tchr: arg.m.chr,\n\t\t\t\t\t\tpos: arg.m.pos + 1, // 1 based\n\t\t\t\t\t\tref: arg.m.ref,\n\t\t\t\t\t\talt: arg.m.alt\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// if fpkm is available and how to query\n\t\t\t\tif (arg.tk.iscustom) {\n\t\t\t\t\tif (arg.tk.checkexpressionrank) {\n\t\t\t\t\t\tfimoarg.factor_profiles = [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tisgenevalue: 1,\n\t\t\t\t\t\t\t\tname: 'Gene ' + arg.tk.gecfg.datatype,\n\t\t\t\t\t\t\t\tfile: arg.tk.checkexpressionrank.file,\n\t\t\t\t\t\t\t\turl: arg.tk.checkexpressionrank.url,\n\t\t\t\t\t\t\t\tindexURL: arg.tk.checkexpressionrank.indexURL\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\n\t\t\t\t\t\tif (arg.sample) {\n\t\t\t\t\t\t\tfimoarg.factor_profiles.push({\n\t\t\t\t\t\t\t\tisgenevalueonesample: 1,\n\t\t\t\t\t\t\t\tname: arg.sample.samplename + ' ' + arg.tk.gecfg.datatype,\n\t\t\t\t\t\t\t\tsamplename: arg.sample.samplename,\n\t\t\t\t\t\t\t\tfile: arg.tk.checkexpressionrank.file,\n\t\t\t\t\t\t\t\turl: arg.tk.checkexpressionrank.url,\n\t\t\t\t\t\t\t\tindexURL: arg.tk.checkexpressionrank.indexURL\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} else {\n\t\t\t\t\t// native\n\t\t\t\t\tif (arg.tk.checkexpressionrank) {\n\t\t\t\t\t\tconst fpro = {\n\t\t\t\t\t\t\tisgenevalue: 1,\n\t\t\t\t\t\t\tdatatype: arg.tk.checkexpressionrank.datatype,\n\t\t\t\t\t\t\tquerykey: arg.tk.checkexpressionrank.querykey,\n\t\t\t\t\t\t\tmdslabel: arg.tk.mds.label\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (arg.samplegroup) {\n\t\t\t\t\t\t\tif (arg.samplegroup.attributes) {\n\t\t\t\t\t\t\t\t// restrict expression to a group\n\t\t\t\t\t\t\t\tfpro.name = arg.samplegroup.name + ' ' + arg.tk.gecfg.datatype\n\t\t\t\t\t\t\t\tfpro.samplegroup_attrlst = arg.samplegroup.attributes\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (!fpro.name) {\n\t\t\t\t\t\t\tfpro.name = 'Gene ' + arg.tk.gecfg.datatype\n\t\t\t\t\t\t}\n\t\t\t\t\t\tfimoarg.factor_profiles = [fpro]\n\n\t\t\t\t\t\tif (arg.sample) {\n\t\t\t\t\t\t\tfimoarg.factor_profiles.push({\n\t\t\t\t\t\t\t\tisgenevalueonesample: 1,\n\t\t\t\t\t\t\t\tname: arg.sample.samplename + ' ' + arg.tk.gecfg.datatype,\n\t\t\t\t\t\t\t\tsamplename: arg.sample.samplename,\n\t\t\t\t\t\t\t\tdatatype: arg.tk.checkexpressionrank.datatype,\n\t\t\t\t\t\t\t\tquerykey: arg.tk.checkexpressionrank.querykey,\n\t\t\t\t\t\t\t\tmdslabel: arg.tk.mds.label\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\tconst _ = await import('./mds.fimo')\n\t\t\t\tawait _.init(fimoarg)\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Error: ' + (e.message || e))\n\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction mayaddtab_survival_onemutation(tabs, arg) {\n\t/*\nmay create a 'survival plot' button and use one mutation to divide samples\nholder\ntk\nblock\n*/\n\tif (!arg.tk.mds || !arg.tk.mds.survivalplot) return\n\ttabs.push({\n\t\tlabel: 'Survival',\n\t\tcallback: async div => {\n\t\t\tconst wait = client.tab_wait(div)\n\t\t\ttry {\n\t\t\t\tconst m = arg.m\n\t\t\t\t// sample dividing rules\n\t\t\t\tconst st = {\n\t\t\t\t\tmutation: 1\n\t\t\t\t}\n\n\t\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\t\t// default to use this specific mutation\n\t\t\t\t\tst.chr = m.chr\n\t\t\t\t\tst.start = m.pos\n\t\t\t\t\tst.stop = m.pos\n\t\t\t\t\tst.snvindel = {\n\t\t\t\t\t\tname: (m.gene ? m.gene + ' ' : '') + m.mname,\n\t\t\t\t\t\tref: m.ref,\n\t\t\t\t\t\talt: m.alt\n\t\t\t\t\t}\n\t\t\t\t} else if (m.dt == common.dtcnv) {\n\t\t\t\t\tst.chr = m.chr\n\t\t\t\t\tst.start = m.start\n\t\t\t\t\tst.stop = m.stop\n\t\t\t\t\tst.cnv = {\n\t\t\t\t\t\tfocalsizelimit: arg.tk.bplengthUpperLimit,\n\t\t\t\t\t\tvaluecutoff: arg.tk.valueCutoff\n\t\t\t\t\t}\n\t\t\t\t} else if (m.dt == common.dtloh) {\n\t\t\t\t\tst.chr = m.chr\n\t\t\t\t\tst.start = m.start\n\t\t\t\t\tst.stop = m.stop\n\t\t\t\t\tst.loh = {\n\t\t\t\t\t\tfocalsizelimit: arg.tk.lohLengthUpperLimit,\n\t\t\t\t\t\tvaluecutoff: arg.tk.segmeanValueCutoff\n\t\t\t\t\t}\n\t\t\t\t} else if (m.dt == common.dtsv) {\n\t\t\t\t\tst.chr = m._chr\n\t\t\t\t\tst.start = m._pos\n\t\t\t\t\tst.stop = m._pos\n\t\t\t\t\tst.sv = {}\n\t\t\t\t} else if (m.dt == common.dtfusionrna) {\n\t\t\t\t\tst.chr = m._chr\n\t\t\t\t\tst.start = m._pos\n\t\t\t\t\tst.stop = m._pos\n\t\t\t\t\tst.fusion = {}\n\t\t\t\t} else if (m.dt == common.dtitd) {\n\t\t\t\t\tst.chr = m.chr\n\t\t\t\t\tst.start = m.start\n\t\t\t\t\tst.stop = m.stop\n\t\t\t\t\tst.itd = {}\n\t\t\t\t}\n\n\t\t\t\tconst plot = {\n\t\t\t\t\trenderplot: 1, // instruct the plot to be rendered, no wait\n\t\t\t\t\tsamplerule: {\n\t\t\t\t\t\tfull: {},\n\t\t\t\t\t\tset: st\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tif (arg.tk.mds.survivalplot.samplegroupattrlst && arg.sample) {\n\t\t\t\t\t// the survivalplot has samplegrouping, and there is a single sample\n\t\t\t\t\t// will just use the first attribute\n\t\t\t\t\tconst attr = arg.tk.mds.survivalplot.samplegroupattrlst[0]\n\t\t\t\t\tconst sampleanno = arg.tk.sampleAttribute ? arg.tk.sampleAttribute.samples[arg.sample.samplename] : null\n\t\t\t\t\tif (sampleanno) {\n\t\t\t\t\t\tconst v = sampleanno[attr.key]\n\t\t\t\t\t\tif (v) {\n\t\t\t\t\t\t\tplot.samplerule.full.byattr = 1\n\t\t\t\t\t\t\tplot.samplerule.full.key = attr.key\n\t\t\t\t\t\t\tplot.samplerule.full.value = v\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// do not set rule for sample-full\n\t\t\t\t}\n\n\t\t\t\tconst _ = await import('./mds.survivalplot')\n\t\t\t\tawait _.init(\n\t\t\t\t\t{\n\t\t\t\t\t\tgenome: arg.block.genome,\n\t\t\t\t\t\tmds: arg.tk.mds,\n\t\t\t\t\t\tplotlist: [plot]\n\t\t\t\t\t},\n\t\t\t\t\tdiv,\n\t\t\t\t\targ.block.debugmode\n\t\t\t\t)\n\t\t\t\twait.remove()\n\t\t\t} catch (e) {\n\t\t\t\twait.text('Error: ' + (e.message || e))\n\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction may_createbutton_survival_grouplab(arg) {\n\t/*\nin multi-sample mode, either dense or expanded\nclick on group label to show button\nuse current range for finding mutations\nobserve those in legend_mclass.hiddenvalues\n\nholder\ntk\nblock\nsamplegroup\n\t.attributes\n*/\n\tif (!arg.tk.mds || !arg.tk.mds.survivalplot) {\n\t\treturn\n\t}\n\n\targ.holder\n\t\t.append('div')\n\t\t.text('Survival plot')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.on('click', () => {\n\t\t\targ.tk.tip2.hide()\n\n\t\t\tconst m = arg.m\n\n\t\t\t// sample dividing rules\n\t\t\tconst st = {\n\t\t\t\tmutation: 1\n\t\t\t}\n\t\t\t// get look range\n\t\t\t{\n\t\t\t\tconst lst = arg.block.rglst\n\t\t\t\tst.chr = lst[arg.block.startidx].chr\n\t\t\t\tconst a = lst[arg.block.startidx].start\n\t\t\t\tconst b = lst[arg.block.stopidx].stop\n\t\t\t\tst.start = Math.min(a, b)\n\t\t\t\tst.stop = Math.max(a, b)\n\t\t\t}\n\n\t\t\tst.snvindel = {\n\t\t\t\thiddenclass: {}\n\t\t\t}\n\n\t\t\t// hiddenvalues is a mix of dt and mclass\n\t\t\t{\n\t\t\t\t// check mclass first\n\t\t\t\tlet hashiddensnv = false\n\t\t\t\tfor (const c of arg.tk.legend_mclass.hiddenvalues) {\n\t\t\t\t\tif (typeof c == 'string') {\n\t\t\t\t\t\tst.snvindel.hiddenclass[c] = 1\n\t\t\t\t\t\thashiddensnv = true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!hashiddensnv) {\n\t\t\t\t\tdelete st.snvindel.hiddenclass\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (!arg.tk.legend_mclass.hiddenvalues.has(common.dtcnv)) {\n\t\t\t\tst.cnv = {\n\t\t\t\t\tfocalsizelimit: arg.tk.bplengthUpperLimit,\n\t\t\t\t\tvaluecutoff: arg.tk.valueCutoff\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!arg.tk.legend_mclass.hiddenvalues.has(common.dtloh)) {\n\t\t\t\tst.loh = {\n\t\t\t\t\tfocalsizelimit: arg.tk.lohLengthUpperLimit,\n\t\t\t\t\tvaluecutoff: arg.tk.segmeanValueCutoff\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!arg.tk.legend_mclass.hiddenvalues.has(common.dtsv)) {\n\t\t\t\tst.sv = {}\n\t\t\t}\n\t\t\tif (!arg.tk.legend_mclass.hiddenvalues.has(common.dtfusionrna)) {\n\t\t\t\tst.fusion = {}\n\t\t\t}\n\t\t\tif (!arg.tk.legend_mclass.hiddenvalues.has(common.dtitd)) {\n\t\t\t\tst.itd = {}\n\t\t\t}\n\n\t\t\tconst plot = {\n\t\t\t\trenderplot: 1, // instruct the plot to be rendered, no wait\n\t\t\t\tsamplerule: {\n\t\t\t\t\tfull: {},\n\t\t\t\t\tset: st\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t/*\n\t\tsamplegroup.attributes[] can be more than 1\n\t\tbut samplerule.full only works for 1\n\t\t*/\n\t\t\tconst attr = arg.samplegroup.attributes[arg.samplegroup.attributes.length - 1]\n\t\t\tplot.samplerule.full = {\n\t\t\t\tbyattr: 1,\n\t\t\t\tkey: attr.k,\n\t\t\t\tvalue: attr.kvalue\n\t\t\t}\n\n\t\t\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\t\tpane.header.text('Survival plot')\n\n\t\t\timport('./mds.survivalplot').then(_ => {\n\t\t\t\t_.init(\n\t\t\t\t\t{\n\t\t\t\t\t\tgenome: arg.block.genome,\n\t\t\t\t\t\tmds: arg.tk.mds,\n\t\t\t\t\t\tplotlist: [plot]\n\t\t\t\t\t},\n\t\t\t\t\tpane.body,\n\t\t\t\t\targ.block.debugmode\n\t\t\t\t)\n\t\t\t})\n\t\t})\n}\n\nfunction may_createbutton_assayAvailability(tk, block, holder, samplegroup) {\n\tif (!tk.mds || !tk.mds.assayAvailability) return\n\n\tholder\n\t\t.append('div')\n\t\t.text('Assay summary')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.on('click', async () => {\n\t\t\ttk.tip2.clear()\n\t\t\tconst wait = tk.tip2.d.append('div').style('margin', '10px').text('Loading...')\n\t\t\tconst par = {\n\t\t\t\tgenome: block.genome.name,\n\t\t\t\tdslabel: tk.mds.label,\n\t\t\t\tquerykey: tk.querykey,\n\t\t\t\tassaymap: 1\n\t\t\t}\n\t\t\tif (samplegroup.attributes) {\n\t\t\t\t// hardcoded to use the last item, to be replaced by termdb\n\t\t\t\tconst k = samplegroup.attributes[samplegroup.attributes.length - 1]\n\t\t\t\tpar.key = k.k\n\t\t\t\tpar.value = k.kvalue\n\t\t\t}\n\t\t\tconst data = await client.dofetch('mdssvcnv', par)\n\t\t\tif (data.error) {\n\t\t\t\twait.text('Error: ' + data.error)\n\t\t\t\treturn\n\t\t\t}\n\t\t\twait.remove()\n\t\t\tinitui_partition({\n\t\t\t\tdata,\n\t\t\t\tpar,\n\t\t\t\tdiv: tk.tip2.d.append('div').style('margin', '10px'),\n\t\t\t\tboxtip: tk.tktip,\n\t\t\t\theadlabel: samplegroup.name\n\t\t\t})\n\t\t\ttk.tip2.d\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.text('Drag and move a sequencing type label up/down to change order.')\n\t\t\tif (samplegroup.attributes) {\n\t\t\t\t// quick fix to show full labels\n\t\t\t\tconst d = tk.tip2.d.append('div').style('margin', '20px 10px 10px 10px').style('opacity', 0.7)\n\t\t\t\tfor (const a of samplegroup.attributes) {\n\t\t\t\t\td.append('div').text(a.kvalue + (a.fullvalue ? ': ' + a.fullvalue : ''))\n\t\t\t\t}\n\t\t\t}\n\t\t})\n}\n\nfunction initui_partition(opts) {\n\t// quick fix\n\t// call when menu option is clicked, render map with all assay types, and checkboxes for each\n\n\tconst plot = {\n\t\theadlabel: opts.headlabel,\n\t\tpar: opts.par,\n\t\trows: [], // for moving rows\n\t\thidetermid: new Set(),\n\t\tsvg: opts.div.append('svg')\n\t}\n\n\tplot_partition(plot, opts.data)\n\n\t// make one checkbox for each term\n\tconst div = opts.div.append('div').append('div').style('display', 'inline')\n\tfor (const term of opts.data.terms) {\n\t\tconst cell = div\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin-right', '15px')\n\t\t\t.style('white-space', 'nowrap')\n\t\tconst label = cell.append('label')\n\t\tlabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.property('checked', true)\n\t\t\t.on('change', async event => {\n\t\t\t\tif (event.target.checked) {\n\t\t\t\t\tplot.hidetermid.delete(term.id)\n\t\t\t\t\tif (plot.par.termidorder && !plot.par.termidorder.includes(term.id)) {\n\t\t\t\t\t\tplot.par.termidorder.push(term.id)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tplot.hidetermid.add(term.id)\n\t\t\t\t}\n\t\t\t\tplot.par.skip_termids = [...plot.hidetermid]\n\t\t\t\tconst data = await client.dofetch('mdssvcnv', plot.par)\n\t\t\t\tplot_partition(plot, data)\n\t\t\t})\n\t\tlabel.append('span').text(term.name).style('padding-left', '5px')\n\t}\n}\n\nfunction plot_partition(plot, data) {\n\tconst toppad = 20, // leave enough space for header in graphg\n\t\tbottompad = 5,\n\t\thpad = 5,\n\t\trowheight = 25,\n\t\tfontsize = 16,\n\t\trowspace = 1,\n\t\tlabxspace = 10,\n\t\tsymbolpxwidth = 15\n\n\t// clear existing plot\n\tplot.rows = []\n\tplot.svg.selectAll('*').remove()\n\n\tlet maxsymbolcount = 0\n\tfor (const t of data.terms) {\n\t\tconst b = t.blocks[t.blocks.length - 1]\n\t\tmaxsymbolcount = Math.max(maxsymbolcount, b.x + b.symbolwidth)\n\t}\n\tconst termwidth = symbolpxwidth * maxsymbolcount\n\n\tconst graphg = plot.svg.append('g')\n\n\t// header\n\tgraphg\n\t\t.append('rect')\n\t\t.attr('width', termwidth)\n\t\t.attr('height', data.terms.length * (rowheight + rowspace) - rowspace)\n\t\t.attr('stroke', '#858585')\n\t\t.attr('fill', 'none')\n\t{\n\t\tlet headlabw\n\t\tconst text = graphg\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('font-size', fontsize - 2)\n\t\t\t.attr('y', -5)\n\t\t\t.text((plot.headlabel ? plot.headlabel + ', ' : '') + 'n=' + data.totalsample)\n\t\t\t.each(function () {\n\t\t\t\theadlabw = this.getBBox().width\n\t\t\t})\n\t\ttext.attr('x', termwidth / 2 - (headlabw > termwidth ? (headlabw - termwidth) / 2 : 0))\n\t}\n\n\tlet maxlabelw = 0\n\tlet y = 0\n\tfor (const term of data.terms) {\n\t\tconst rowg = graphg.append('g').attr('transform', 'translate(0,' + y + ')')\n\t\t// tick\n\t\trowg\n\t\t\t.append('line')\n\t\t\t.attr('stroke', '#858585')\n\t\t\t.attr('x1', -6)\n\t\t\t.attr('y1', rowheight / 2)\n\t\t\t.attr('y2', rowheight / 2)\n\t\tconst thisrow = {\n\t\t\tid: term.id,\n\t\t\ty,\n\t\t\trowg\n\t\t}\n\t\tplot.rows.push(thisrow)\n\t\tthisrow.svglabel = rowg\n\t\t\t.append('text')\n\t\t\t.text(term.name + ', n=' + term.samplecount)\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('x', -labxspace)\n\t\t\t.attr('y', rowheight / 2)\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.each(function () {\n\t\t\t\tmaxlabelw = Math.max(maxlabelw, this.getBBox().width)\n\t\t\t})\n\t\t\t.on('mousedown', event => {\n\t\t\t\tevent.preventDefault()\n\t\t\t\tthisrow.moving = true\n\t\t\t\tconst b = d3select(document.body)\n\t\t\t\tlet my0 = event.clientY\n\t\t\t\tlet deltay\n\t\t\t\tlet nochange = true\n\t\t\t\tb.on('mousemove', event => {\n\t\t\t\t\tconst my = event.clientY\n\t\t\t\t\tdeltay = my - my0\n\t\t\t\t\tconst rowidx = plot.rows.findIndex(i => i.id == thisrow.id)\n\t\t\t\t\tif (deltay < 0) {\n\t\t\t\t\t\tif (rowidx > 0 && -deltay >= rowheight - 2) {\n\t\t\t\t\t\t\tplot.rows.splice(rowidx, 1)\n\t\t\t\t\t\t\tplot.rows.splice(rowidx - 1, 0, thisrow)\n\t\t\t\t\t\t\treorderRows()\n\t\t\t\t\t\t\tdeltay = 0\n\t\t\t\t\t\t\tmy0 = my\n\t\t\t\t\t\t\tnochange = false\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (rowidx < plot.rows.length - 1 && deltay >= rowheight - 2) {\n\t\t\t\t\t\t\tplot.rows.splice(rowidx, 1)\n\t\t\t\t\t\t\tplot.rows.splice(rowidx + 1, 0, thisrow)\n\t\t\t\t\t\t\treorderRows()\n\t\t\t\t\t\t\tdeltay = 0\n\t\t\t\t\t\t\tmy0 = my\n\t\t\t\t\t\t\tnochange = false\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\trowg.attr('transform', 'translate(0,' + (thisrow.y + deltay) + ')')\n\t\t\t\t})\n\t\t\t\tb.on('mouseup', async () => {\n\t\t\t\t\tb.on('mousemove', null).on('mouseup', null)\n\t\t\t\t\tdelete thisrow.moving\n\t\t\t\t\treorderRows()\n\t\t\t\t\tif (nochange) return\n\t\t\t\t\tthisrow.svglabel.text('Loading...')\n\t\t\t\t\tplot.par.termidorder = plot.rows.map(i => i.id)\n\t\t\t\t\tplot.par.skip_termids = [...plot.hidetermid]\n\t\t\t\t\tconst data = await client.dofetch('mdssvcnv', plot.par)\n\t\t\t\t\tplot_partition(plot, data)\n\t\t\t\t})\n\t\t\t})\n\n\t\tlet x = 0\n\t\tfor (const b of term.blocks) {\n\t\t\tif (0) {\n\t\t\t\t// width to scale\n\t\t\t\tconst w = b.samplecount * sf\n\t\t\t\tif (b.value) {\n\t\t\t\t\t// this block is for samples annotated to this term\n\t\t\t\t\tconst box = rowg\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('fill', b.color)\n\t\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t\t.attr('width', Math.max(1, w))\n\t\t\t\t\t\t.attr('height', rowheight)\n\t\t\t\t\tlet numwidth\n\t\t\t\t\tconst text = rowg\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(b.samplecount)\n\t\t\t\t\t\t.attr('font-size', fontsize - 2)\n\t\t\t\t\t\t.each(function () {\n\t\t\t\t\t\t\tnumwidth = this.getBBox().width\n\t\t\t\t\t\t})\n\t\t\t\t\tif (numwidth < w) {\n\t\t\t\t\t\ttext\n\t\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t\t.attr('x', x + w / 2)\n\t\t\t\t\t\t\t.attr('y', rowheight / 2)\n\t\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// not enough width to print width\n\t\t\t\t\t\ttext.remove()\n\t\t\t\t\t\tbox\n\t\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\t\tbox.attr('fill', 'black')\n\t\t\t\t\t\t\t\topts.boxtip\n\t\t\t\t\t\t\t\t\t.clear()\n\t\t\t\t\t\t\t\t\t.showunder(event.target)\n\t\t\t\t\t\t\t\t\t.d.append('div')\n\t\t\t\t\t\t\t\t\t.html(b.samplecount + ' <span style=\"font-size:.7em\">' + escapeHtml(term.name) + '</span>')\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\tbox.attr('fill', b.color)\n\t\t\t\t\t\t\t\topts.boxtip.hide()\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tx += w\n\t\t\t} else {\n\t\t\t\t// symbolic, print count\n\t\t\t\tconst w = b.symbolwidth * symbolpxwidth\n\t\t\t\tconst x = b.x * symbolpxwidth\n\t\t\t\tif (!b.isgap) {\n\t\t\t\t\tconst box = rowg.append('rect').attr('fill', b.color).attr('x', x).attr('width', w).attr('height', rowheight)\n\t\t\t\t\trowg\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(b.samplecount)\n\t\t\t\t\t\t.attr('font-size', fontsize - 2)\n\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t.attr('x', x + w / 2)\n\t\t\t\t\t\t.attr('y', rowheight / 2)\n\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\ty += rowheight + rowspace\n\t}\n\tgraphg.attr('transform', 'translate(' + (hpad + maxlabelw + labxspace) + ',' + toppad + ')')\n\tplot.svg\n\t\t.attr('width', hpad * 2 + maxlabelw + labxspace + termwidth)\n\t\t.attr('height', toppad + (rowheight + rowspace) * data.terms.length + bottompad)\n\n\tfunction reorderRows() {\n\t\tlet y = 0\n\t\tfor (const t of plot.rows) {\n\t\t\tif (!t.moving) t.rowg.transition().attr('transform', 'translate(0,' + y + ')')\n\t\t\tt.y = y\n\t\t\ty += rowheight + rowspace\n\t\t}\n\t}\n}\n", "import { scaleOrdinal } from 'd3-scale'\nimport { schemeCategory20 } from '#common/legacy-d3-polyfill'\nimport * as client from './client'\nimport { legend_newrow } from './block.legend'\nimport * as common from '#shared/common.js'\nimport { loadTk } from './block.mds.svcnv'\nimport { rgb as d3rgb } from 'd3-color'\n\n/*\n*********** exported:\n\nmakeTk_legend\nupdate_legend\nupdateLegend_singleSample\nupdateLegend_multiSample\n\n\n*********** internal:\nmay_legend_svchr\nmay_legend_mclass\nmay_legend_attribute\nmay_legend_signature_singlesample\n*/\n\nconst fontsize = 14\nconst xpad = 15\nconst barh = 20\n\nexport function makeTk_legend(block, tk) {\n\t/*\n\tonly run once, to initialize legend\n\tfor all cases:\n\t\tsingle- and multi-sample\n\t\tofficial and custom track\n\t*/\n\n\tconst [tr, td] = legend_newrow(block, tk.name)\n\ttk.tr_legend = tr\n\ttk.td_legend = td\n\n\tconst table = td.append('table').style('border-spacing', '5px')\n\n\ttk.legend_table = table\n\t// track hideable rows that are non-mutation attr\n\ttk.legend_hideable = []\n\n\tcreate_mclass(tk)\n\n\tif (!tk.nocnvlohsv) {\n\t\t// has svcnv file\n\t\tcreate_cnv(tk, block)\n\t\tcreate_loh(tk)\n\t\tcreate_svchrcolor(tk)\n\t}\n\n\tcreate_mutationsignature_single(tk)\n\n\tcreate_sampleAttribute(tk)\n\n\tcreate_mutationAttribute(tk)\n\n\tif (tk.alleleAttribute) create_vcfAttribute(tk.alleleAttribute, tk, block)\n\tif (tk.locusAttribute) create_vcfAttribute(tk.locusAttribute, tk, block)\n\n\ttk.legend_more_row = table.append('tr')\n\ttk.legend_more_label = tk.legend_more_row.append('td').style('text-align', 'right').append('span')\n\t// blank cell for now since hidden legend items\n\t// are displayed in pop-down menu, not in this row\n\ttk.legend_more_row.append('td')\n}\n\nexport function update_legend(tk, block) {\n\t/*\n\tfor all cases\n\t*/\n\tmay_legend_svchr(tk)\n\tmay_legend_mclass(tk, block)\n\tif (tk.singlesample) {\n\t\t// only do above for single sample case\n\t\tmay_legend_signature_singlesample(tk, block)\n\t\treturn\n\t}\n\t// is multi-sample: also do following\n\tmay_legend_attribute(tk, block)\n}\n\n// helpers\n\nfunction create_mclass(tk) {\n\t/*\n\tlist all mutation classes\n\tattribute may have already been created with customization\n\t*/\n\tif (!tk.legend_mclass) tk.legend_mclass = {}\n\tif (!tk.legend_mclass.hiddenvalues) tk.legend_mclass.hiddenvalues = new Set()\n\n\ttk.legend_mclass.hidden = false\n\n\ttk.legend_mclass.row = tk.legend_table.append('tr')\n\n\ttk.legend_mclass.row.append('td').style('text-align', 'right').style('opacity', 0.5).text('Mutation')\n\ttk.legend_mclass.holder = tk.legend_mclass.row.append('td')\n\ttk.legend_hideable.push(tk.legend_mclass)\n}\n\nfunction create_cnv(tk, block) {\n\t/*\n\tcnv log ratio color scale\n\n\t*/\n\n\tconst leftpad = 50\n\n\t//// cnv color scale\n\n\ttk.cnvcolor.cnvlegend = {\n\t\taxistickh: 4,\n\t\tbarw: 55\n\t}\n\n\ttk.cnvcolor.cnvlegend.row = tk.legend_table.append('tr')\n\ttk.cnvcolor.cnvlegend.row.append('td').style('text-align', 'right').style('opacity', 0.5).text('CNV log2(ratio)')\n\ttk.legend_hideable.push(tk.cnvcolor.cnvlegend)\n\n\tconst btn = tk.cnvcolor.cnvlegend.row\n\t\t.append('td')\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.attr('class', 'sja_clb')\n\t\t.style('padding', '0px')\n\t\t.on('click', () => {\n\t\t\t// quick fix to allow to show only gain or loss\n\t\t\ttk.tkconfigtip.clear().showunder(btn.node())\n\t\t\t{\n\t\t\t\tconst lab = tk.tkconfigtip.d.append('div').append('label')\n\t\t\t\tlab\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t\t.property('checked', !tk.hide_cnvgain)\n\t\t\t\t\t.on('change', () => {\n\t\t\t\t\t\ttk.hide_cnvgain = !tk.hide_cnvgain\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t})\n\t\t\t\tlab.append('span').html('&nbsp;Show copy number gain')\n\t\t\t}\n\t\t\t{\n\t\t\t\tconst lab = tk.tkconfigtip.d.append('div').style('margin-top', '10px').append('label')\n\t\t\t\tlab\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t\t.property('checked', !tk.hide_cnvloss)\n\t\t\t\t\t.on('change', () => {\n\t\t\t\t\t\ttk.hide_cnvloss = !tk.hide_cnvloss\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t})\n\t\t\t\tlab.append('span').html('&nbsp;Show copy number loss')\n\t\t\t}\n\t\t})\n\n\tconst svg = btn\n\t\t.append('svg')\n\t\t.attr('width', (leftpad + tk.cnvcolor.cnvlegend.barw) * 2)\n\t\t.attr('height', fontsize + tk.cnvcolor.cnvlegend.axistickh + barh)\n\n\ttk.cnvcolor.cnvlegend.svg = svg\n\n\ttk.cnvcolor.cnvlegend.nodatadiv = btn\n\t\t.append('div')\n\t\t.text('no data')\n\t\t.style('opacity', 0.3)\n\t\t.style('padding-left', '10px')\n\n\ttk.cnvcolor.cnvlegend.axisg = svg\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + leftpad + ',' + (fontsize + tk.cnvcolor.cnvlegend.axistickh) + ')')\n\n\tconst gain_id = Math.random().toString()\n\tconst loss_id = Math.random().toString()\n\n\tconst defs = svg.append('defs')\n\t{\n\t\t// loss\n\t\tconst grad = defs.append('linearGradient').attr('id', loss_id)\n\t\ttk.cnvcolor.cnvlegend.loss_stop = grad.append('stop').attr('offset', '0%').attr('stop-color', tk.cnvcolor.loss.str)\n\t\tgrad.append('stop').attr('offset', '100%').attr('stop-color', 'white')\n\t}\n\t{\n\t\t// gain\n\t\tconst grad = defs.append('linearGradient').attr('id', gain_id)\n\t\tgrad.append('stop').attr('offset', '0%').attr('stop-color', 'white')\n\t\ttk.cnvcolor.cnvlegend.gain_stop = grad\n\t\t\t.append('stop')\n\t\t\t.attr('offset', '100%')\n\t\t\t.attr('stop-color', tk.cnvcolor.gain.str)\n\t}\n\n\tsvg\n\t\t.append('rect')\n\t\t.attr('x', leftpad)\n\t\t.attr('y', fontsize + tk.cnvcolor.cnvlegend.axistickh)\n\t\t.attr('width', tk.cnvcolor.cnvlegend.barw)\n\t\t.attr('height', barh)\n\t\t.attr('fill', 'url(#' + loss_id + ')')\n\n\tsvg\n\t\t.append('rect')\n\t\t.attr('x', leftpad + tk.cnvcolor.cnvlegend.barw)\n\t\t.attr('y', fontsize + tk.cnvcolor.cnvlegend.axistickh)\n\t\t.attr('width', tk.cnvcolor.cnvlegend.barw)\n\t\t.attr('height', barh)\n\t\t.attr('fill', 'url(#' + gain_id + ')')\n\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', leftpad - 5)\n\t\t.attr('y', fontsize + tk.cnvcolor.cnvlegend.axistickh + barh / 2)\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('text-anchor', 'end')\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('fill', 'black')\n\t\t.text('Loss')\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', leftpad + tk.cnvcolor.cnvlegend.barw * 2 + 5)\n\t\t.attr('y', fontsize + tk.cnvcolor.cnvlegend.axistickh + barh / 2)\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('fill', 'black')\n\t\t.text('Gain')\n}\n\nfunction create_loh(tk) {\n\tif (tk.mds && tk.mds.queries && tk.mds.queries[tk.querykey] && tk.mds.queries[tk.querykey].no_loh) {\n\t\t// quick dirty\n\t\treturn\n\t}\n\n\t//// loh color legend\n\n\tconst leftpad = 20\n\n\ttk.cnvcolor.lohlegend = {\n\t\taxistickh: 4,\n\t\tbarw: 55\n\t}\n\n\ttk.cnvcolor.lohlegend.row = tk.legend_table.append('tr')\n\ttk.cnvcolor.lohlegend.row.append('td').style('text-align', 'right').style('opacity', 0.5).text('LOH seg.mean')\n\ttk.legend_hideable.push(tk.cnvcolor.lohlegend)\n\n\tconst td = tk.cnvcolor.lohlegend.row.append('td')\n\n\tconst svg = td\n\t\t.append('svg')\n\t\t.attr('width', (leftpad + tk.cnvcolor.lohlegend.barw) * 2)\n\t\t.attr('height', fontsize + tk.cnvcolor.lohlegend.axistickh + barh)\n\n\ttk.cnvcolor.lohlegend.svg = svg\n\ttk.cnvcolor.lohlegend.nodatadiv = td.append('div').text('no data').style('opacity', 0.3).style('padding-left', '10px')\n\n\ttk.cnvcolor.lohlegend.axisg = svg\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + leftpad + ',' + (fontsize + tk.cnvcolor.lohlegend.axistickh) + ')')\n\n\tconst loh_id = Math.random().toString()\n\n\tconst defs = svg.append('defs')\n\t{\n\t\tconst grad = defs.append('linearGradient').attr('id', loh_id)\n\t\tgrad.append('stop').attr('offset', '0%').attr('stop-color', 'white')\n\t\ttk.cnvcolor.lohlegend.loh_stop = grad.append('stop').attr('offset', '100%').attr('stop-color', tk.cnvcolor.loh.str)\n\t}\n\n\tsvg\n\t\t.append('rect')\n\t\t.attr('x', leftpad)\n\t\t.attr('y', fontsize + tk.cnvcolor.lohlegend.axistickh)\n\t\t.attr('width', tk.cnvcolor.lohlegend.barw)\n\t\t.attr('height', barh)\n\t\t.attr('fill', 'url(#' + loh_id + ')')\n}\n\nfunction create_svchrcolor(tk) {\n\tconst row = tk.legend_table.append('tr').style('display', 'none') // default hide\n\n\ttk.legend_svchrcolor = {\n\t\trow: row,\n\t\tinterchrs: new Set(),\n\t\tcolorfunc: scaleOrdinal(schemeCategory20),\n\t\thidden: true\n\t}\n\trow.append('td').style('text-align', 'right').style('opacity', 0.5).text('SV chromosome')\n\ttk.legend_svchrcolor.holder = row.append('td')\n\ttk.legend_hideable.push(tk.legend_svchrcolor)\n}\n\nfunction create_sampleAttribute(tk) {\n\tif (tk.singlesample) return\n\tif (!tk.sampleAttribute) return\n\t/*\n\tofficial only\n\tsampleAttribute is copied over from mds.queries\n\tinitiate attributes used for filtering & legend display\n\t*/\n\tfor (const key in tk.sampleAttribute.attributes) {\n\t\tconst attr = tk.sampleAttribute.attributes[key]\n\t\tif (!attr.filter) {\n\t\t\t// not a filter\n\t\t\tcontinue\n\t\t}\n\n\t\t// do not override customization from embedding\n\t\tif (!attr.hiddenvalues || !(attr.hiddenvalues instanceof Set)) {\n\t\t\tattr.hiddenvalues = new Set()\n\t\t\t// k: key in mutationAttribute.attributes{}\n\t\t}\n\n\t\tattr.value2count = new Map()\n\t\t/*\n\t\tk: key\n\t\tv: {\n\t\t\ttotalitems: INT\n\t\t\tdt2count: Map( dt => count )\n\t\t}\n\t\t*/\n\n\t\tattr.legendrow = tk.legend_table.append('tr')\n\t\tattr.legendcell = attr.legendrow.append('td').style('text-align', 'right').style('opacity', 0.5).text(attr.label)\n\n\t\tattr.legendholder = attr.legendrow.append('td')\n\t}\n}\n\nfunction create_mutationsignature_single(tk) {\n\tif (!tk.singlesample) return\n\tif (!tk.mds || !tk.mds.mutation_signature) return\n\t/* dataset has mutation signature\n\twill create legend for this track\n\tbut does not know if this sample has signature or not\n\tso the legend <tr> remains hidden\n\tand only show if it has signature for data in view range\n\n\talso one sample could have mutation from more than one set of signature\n\tthus, one legend <tr> should be shown for each signature set\n\n\t*/\n\ttk.mutation_signature_legend = {\n\t\tsets: {}\n\t}\n\tfor (const k in tk.mds.mutation_signature.sets) {\n\t\tconst tr = tk.legend_table.append('tr').style('display', 'none')\n\n\t\ttr.append('td').text(tk.mds.mutation_signature.sets[k].name).style('text-align', 'right').style('opacity', 0.5)\n\n\t\tconst td = tr.append('td')\n\t\tconst table = td.append('table').style('border-spacing', '0px').style('margin', '10px')\n\n\t\ttk.mutation_signature_legend.sets[k] = {\n\t\t\ttr: tr,\n\t\t\ttd: td,\n\t\t\ttable: table\n\t\t}\n\t}\n}\n\nfunction create_mutationAttribute(tk) {\n\tif (tk.singlesample) return\n\tif (!tk.mutationAttribute) return\n\t/*\n\tofficial only\n\tmutationAttribute is copied over from mds.queries\n\tinitiate attributes used for filtering & legend display\n\t*/\n\tfor (const key in tk.mutationAttribute.attributes) {\n\t\tconst attr = tk.mutationAttribute.attributes[key]\n\t\tif (!attr.filter) {\n\t\t\t// not a filter\n\t\t\tcontinue\n\t\t}\n\t\tattr.hiddenvalues = new Set()\n\t\t// k: key in mutationAttribute.attributes{}\n\n\t\tattr.value2count = new Map()\n\t\t/*\n\t\tk: key\n\t\tv: {\n\t\t\ttotalitems: INT\n\t\t\tdt2count: Map( dt => count )\n\t\t}\n\t\t*/\n\n\t\tattr.legendrow = tk.legend_table.append('tr')\n\t\tattr.legendcell = attr.legendrow.append('td').style('text-align', 'right').style('opacity', 0.5).text(attr.label)\n\n\t\tattr.legendholder = attr.legendrow.append('td')\n\t}\n}\n\nfunction create_vcfAttribute(attrSet, tk, block) {\n\t// for both alleleAttribute and locusAttribute\n\t/*\n\tofficial only\n\talleleAttribute/locusAttribute is copied over from mds.queries\n\tinitiate attributes used for filtering & legend display\n\t*/\n\tfor (const key in attrSet.attributes) {\n\t\tconst attr = attrSet.attributes[key]\n\t\tif (!attr.filter) {\n\t\t\t// not a filter\n\t\t\tcontinue\n\t\t}\n\n\t\tattr.legendrow = tk.legend_table.append('tr')\n\t\tattr.legendcell = attr.legendrow.append('td').style('text-align', 'right').style('opacity', 0.5).text(attr.label)\n\n\t\tattr.legendholder = attr.legendrow.append('td')\n\n\t\tif (attr.isnumeric) {\n\t\t\t/*\n\t\t\tnumeric cutoff with options:\n\t\t\t<= no greater than\n\t\t\t>= no smaller than\n\t\t\tx  do not use\n\t\t\t*/\n\n\t\t\tconst select = attr.legendholder\n\t\t\t\t.append('select')\n\t\t\t\t.style('margin', '0px 10px 0px 10px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tconst value = select.property('value')\n\n\t\t\t\t\tif (value == 'x') {\n\t\t\t\t\t\tattr.disable = true\n\t\t\t\t\t} else {\n\t\t\t\t\t\tdelete attr.disable\n\t\t\t\t\t\tattr.keeplowerthan = value == '<'\n\t\t\t\t\t}\n\n\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t})\n\n\t\t\tconst lowerthan = select.append('option').attr('value', '<').property('text', '\u2264')\n\n\t\t\tconst higherthan = select.append('option').attr('value', '>').property('text', '\u2265')\n\n\t\t\tconst disable = select.append('option').attr('value', 'x').property('text', 'X')\n\n\t\t\tif (attr.disable) {\n\t\t\t\tdisable.property('selected', 1)\n\t\t\t} else if (attr.keeplowerthan) {\n\t\t\t\tlowerthan.property('selected', 1)\n\t\t\t} else {\n\t\t\t\thigherthan.property('selected', 1)\n\t\t\t}\n\n\t\t\tattr.legendholder\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'number')\n\t\t\t\t.style('width', '50px')\n\t\t\t\t.property('value', attr.cutoffvalue)\n\t\t\t\t.on('keyup', event => {\n\t\t\t\t\tif (event.key != 'Enter') return\n\t\t\t\t\tattr.cutoffvalue = event.target.valueAsNumber\n\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t})\n\t\t} else {\n\t\t\t// categorical\n\t\t\tattr.hiddenvalues = new Set()\n\t\t\t// k: key in mutationAttribute.attributes{}\n\n\t\t\tattr.value2count = new Map()\n\t\t\t/*\n\t\t\tk: key\n\t\t\tv: {\n\t\t\t\ttotalitems: INT\n\t\t\t\tdt2count: Map( dt => count )\n\t\t\t}\n\t\t\t*/\n\n\t\t\tattr.legendrow = tk.legend_table.append('tr')\n\t\t\tattr.legendcell = attr.legendrow.append('td').style('text-align', 'right').style('opacity', 0.5).text(attr.label)\n\n\t\t\tattr.legendholder = attr.legendrow.append('td')\n\t\t}\n\t}\n}\n\nfunction may_legend_svchr(tk) {\n\tif (!tk.legend_svchrcolor) {\n\t\t// not there when there is no svcnv file\n\t\treturn\n\t}\n\n\ttk.legend_svchrcolor.holder.selectAll('*').remove()\n\tif (tk.legend_svchrcolor.interchrs.size == 0) return\n\ttk.legend_svchrcolor.row.style('display', 'table-row')\n\tfor (const chr of tk.legend_svchrcolor.interchrs) {\n\t\tconst color = tk.legend_svchrcolor.colorfunc(chr)\n\t\tconst d = tk.legend_svchrcolor.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin', '3px 10px 3px 0px')\n\t\td.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('border-radius', '10px')\n\t\t\t.style('padding', '0px 10px')\n\t\t\t.style('border', 'solid 1px ' + color)\n\t\t\t.style('color', color)\n\t\t\t.style('font-size', '.9em')\n\t\t\t.text(chr)\n\t}\n}\n\nfunction may_legend_mclass(tk, block) {\n\t/*\n\tfull or dense\n\tnative or custom\n\tsingle or multi-sample\n\talways shown! both snvindel class & dt included (cnv/loh/sv/fusion/itd)\n\t*/\n\n\tif (!tk.legend_mclass || !tk.legend_mclass.holder) return\n\n\ttk.legend_mclass.holder.selectAll('*').remove()\n\n\tconst classes = new Map()\n\t/*\n\tk: class\n\tv: {cname, count}\n\tif is snvindel class, key is class code e.g. \"M\"\n\tif not, key is dt\n\t*/\n\n\t// vcf classes\n\tif (tk.data_vcf) {\n\t\tfor (const m of tk.data_vcf) {\n\t\t\tif (!classes.has(m.class)) {\n\t\t\t\tclasses.set(m.class, {\n\t\t\t\t\tisvcf: 1,\n\t\t\t\t\tcname: m.class,\n\t\t\t\t\tcount: 0\n\t\t\t\t})\n\t\t\t}\n\t\t\tclasses.get(m.class).count++\n\t\t}\n\t}\n\t// non-vcf classes\n\tif (tk.singlesample) {\n\t\tif (tk.data) {\n\t\t\tfor (const i of tk.data) {\n\t\t\t\tif (!classes.has(i.dt)) {\n\t\t\t\t\tclasses.set(i.dt, {\n\t\t\t\t\t\tdt: i.dt,\n\t\t\t\t\t\tcount: 0\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tclasses.get(i.dt).count++\n\t\t\t}\n\t\t}\n\t} else if (tk._data) {\n\t\tfor (const g of tk._data) {\n\t\t\tfor (const s of g.samples) {\n\t\t\t\tfor (const i of s.items) {\n\t\t\t\t\tif (!classes.has(i.dt)) {\n\t\t\t\t\t\tclasses.set(i.dt, {\n\t\t\t\t\t\t\tdt: i.dt,\n\t\t\t\t\t\t\tcount: 0\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\tclasses.get(i.dt).count++\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst classlst = [...classes.values()]\n\tclasslst.sort((i, j) => j.count - i.count)\n\ttk.legend_mclass.total_count = classlst.reduce((a, b) => a + b.count, 0)\n\n\tfor (const c of classlst) {\n\t\tlet key,\n\t\t\tlabel,\n\t\t\tdesc,\n\t\t\tcolor = '#858585'\n\n\t\tif (c.dt) {\n\t\t\tkey = c.dt\n\t\t\tlabel = common.dt2label[c.dt]\n\t\t\tif (c.dt == common.dtcnv) desc = 'Copy number variation.'\n\t\t\telse if (c.dt == common.dtloh) desc = 'Loss of heterozygosity.'\n\t\t\telse if (c.dt == common.dtitd) {\n\t\t\t\tcolor = common.mclass[common.mclassitd].color\n\t\t\t\tdesc = 'Internal tandem duplication.'\n\t\t\t} else if (c.dt == common.dtsv) desc = 'Structural variation of DNA.'\n\t\t\telse if (c.dt == common.dtfusionrna) desc = 'Fusion gene from RNA-seq.'\n\t\t} else {\n\t\t\tkey = c.cname\n\t\t\tlabel = common.mclass[c.cname].label\n\t\t\tcolor = common.mclass[c.cname].color\n\t\t\tdesc = common.mclass[c.cname].desc\n\t\t}\n\n\t\tconst cell = tk.legend_mclass.holder\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_clb')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.on('click', () => {\n\t\t\t\ttk.tip2\n\t\t\t\t\t.clear()\n\t\t\t\t\t.d.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.text('Hide')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\ttk.legend_mclass.hiddenvalues.add(key)\n\t\t\t\t\t\tapplychange()\n\t\t\t\t\t})\n\n\t\t\t\ttk.tip2.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.text('Show only')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tfor (const c2 of classes.keys()) {\n\t\t\t\t\t\t\ttk.legend_mclass.hiddenvalues.add(c2)\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttk.legend_mclass.hiddenvalues.delete(key)\n\t\t\t\t\t\tapplychange()\n\t\t\t\t\t})\n\n\t\t\t\tif (tk.legend_mclass.hiddenvalues.size) {\n\t\t\t\t\ttk.tip2.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.text('Show all')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\ttk.legend_mclass.hiddenvalues.clear()\n\t\t\t\t\t\t\tapplychange()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\ttk.tip2.d.append('div').style('padding', '10px').style('font-size', '.8em').style('width', '150px').text(desc)\n\n\t\t\t\ttk.tip2.showunder(cell.node())\n\t\t\t})\n\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('background', color)\n\t\t\t.html(c.count > 1 ? c.count : '&nbsp;')\n\t\tcell\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', color)\n\t\t\t.html('&nbsp;' + label)\n\t}\n\n\t// hidden\n\tfor (const key of tk.legend_mclass.hiddenvalues) {\n\t\ttk.legend_mclass.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.attr('class', 'sja_clb')\n\t\t\t.style('text-decoration', 'line-through')\n\t\t\t.text(Number.isInteger(key) ? common.dt2label[key] : common.mclass[key].label)\n\t\t\t.on('click', () => {\n\t\t\t\ttk.legend_mclass.hiddenvalues.delete(key)\n\t\t\t\tapplychange()\n\t\t\t})\n\t}\n\n\tif (tk.vcfrangelimit) {\n\t\t// range too big for vcf, no vcf data\n\t\ttk.legend_mclass.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.text('Zoom in under ' + common.bplen(tk.vcfrangelimit) + ' to view SNV/indel data')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style('margin', '10px')\n\t}\n\n\tconst applychange = () => {\n\t\ttk.tip2.hide()\n\t\tloadTk(tk, block)\n\t}\n}\n\nfunction may_legend_signature_singlesample(tk, block) {\n\t/*\n\tonly for single sample\n\tif mds has signature\n\t*/\n\n\tif (!tk.mds || !tk.mds.mutation_signature) return\n\n\t// dataset is equipped with signature, but the sample may not have it, or there may not be any variants from view range\n\t// still need to clear legend\n\tfor (const k in tk.mutation_signature_legend.sets) {\n\t\ttk.mutation_signature_legend.sets[k].tr.style('display', 'none')\n\t}\n\n\tif (!tk.data_vcf) {\n\t\t// currently signature data all come from vcf\n\t\treturn\n\t}\n\n\tconst set2signatures = new Map()\n\n\tfor (const m of tk.data_vcf) {\n\t\tif (m.x == undefined) continue\n\t\tif (!m.sampledata || !m.sampledata[0]) continue\n\t\tfor (const k in tk.mds.mutation_signature.sets) {\n\t\t\tconst v = m.sampledata[0][k]\n\t\t\tif (v == undefined) continue\n\t\t\tconst obj = tk.mds.mutation_signature.sets[k].signatures[v]\n\t\t\tif (obj) {\n\t\t\t\t// has a valid signature for this set\n\t\t\t\t// but will not count the 'no data' placeholder\n\t\t\t\tif (obj.nodata) continue\n\t\t\t\tif (!set2signatures.has(k)) set2signatures.set(k, new Map())\n\t\t\t\tset2signatures.get(k).set(v, 1 + (set2signatures.get(k).get(v) || 0))\n\t\t\t}\n\t\t}\n\t}\n\n\tfor (const [k, o1] of set2signatures) {\n\t\tconst leg = tk.mutation_signature_legend.sets[k]\n\t\t// turn on this tr\n\t\tleg.tr.style('display', 'table-row')\n\t\tleg.table.selectAll('*').remove()\n\n\t\tconst lst = [...o1].sort((i, j) => j[1] - i[1])\n\t\tfor (const [v, count] of lst) {\n\t\t\tconst obj = tk.mds.mutation_signature.sets[k].signatures[v]\n\n\t\t\tconst tr = leg.table.append('tr')\n\t\t\ttr.append('td')\n\t\t\t\t.style('background', obj.color)\n\t\t\t\t.style('padding', '0px 4px')\n\t\t\t\t.style('color', 'white')\n\t\t\t\t.style('text-align', 'right')\n\t\t\t\t.html(count > 1 ? count : '')\n\t\t\tconst c = d3rgb(obj.color)\n\t\t\ttr.append('td')\n\t\t\t\t.html('&nbsp;' + obj.name)\n\t\t\t\t.style('background', 'rgba(' + c.r + ',' + c.g + ',' + c.b + ',.2)')\n\t\t\t\t.style('opacity', 0.6)\n\t\t}\n\t}\n}\n\nfunction may_legend_attribute(tk, block) {\n\tif (tk.singlesample) {\n\t\t// multi-sample only\n\t\treturn\n\t}\n\n\t// collects attributes that are selected to be hidden\n\tconst hiddenAttributes = []\n\n\t/*\n\tofficial-only, multi-sample\n\tfiltering by mutation attribute is done on server\n\t*/\n\tfor (const attrGrp of ['sampleAttribute', 'mutationAttribute', 'locusAttribute']) {\n\t\tif (!tk[attrGrp]) continue\n\n\t\t// clear\n\t\tfor (const key in tk[attrGrp].attributes) {\n\t\t\tconst attr = tk[attrGrp].attributes[key]\n\t\t\tif (!attr.filter) continue\n\t\t\tattr.value2count.clear()\n\t\t}\n\n\t\t// count\n\t\tif (attrGrp == 'sampleAttribute') {\n\t\t\tfor (const key in tk.sampleAttribute.attributes) {\n\t\t\t\tfor (const sample in tk.sampleAttribute.samples) {\n\t\t\t\t\tcount_sampleAttribute(key, tk.sampleAttribute.attributes[key], tk.sampleAttribute.samples[sample])\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\tif (tk._data) {\n\t\t\t\tfor (const g of tk._data) {\n\t\t\t\t\tfor (const s of g.samples) {\n\t\t\t\t\t\tfor (const i of s.items) {\n\t\t\t\t\t\t\t// won't count if i.mattr is undefined\n\t\t\t\t\t\t\tcount_mutationAttribute(i.mattr, tk, i.dt)\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\tif (tk.data_vcf) {\n\t\t\t\tfor (const m of tk.data_vcf) {\n\t\t\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\t\t\tif (m.sampledata) {\n\t\t\t\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\t\t\t\tcount_mutationAttribute(s, tk, m.dt)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (m.info) {\n\t\t\t\t\t\t\tcount_locusAttribute(tk, m)\n\t\t\t\t\t\t}\n\t\t\t\t\t\t// TODO altinfo may be supported in the same way?\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconsole.error('unknown dt: ' + m.dt)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// show legend\n\t\tfor (const key in tk[attrGrp].attributes) {\n\t\t\tconst attr = tk[attrGrp].attributes[key]\n\t\t\tif (!attr.filter) continue\n\n\t\t\tattr.legendcell.classed('sja_hideable_legend', true).on('click', () => {\n\t\t\t\ttk.tip2.hide()\n\t\t\t\tattr.hidden = 1\n\t\t\t\ttk.legend_more_row.style('display', 'table-row')\n\t\t\t\tclient.flyindi(attr.legendcell, tk.legend_more_label)\n\t\t\t\tattr.legendrow.transition().delay(500).style('display', 'none')\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tmay_legend_attribute(tk, block)\n\t\t\t\t}, 500)\n\t\t\t})\n\n\t\t\tif (attr.hidden) {\n\t\t\t\t// this attribute is hidden\n\t\t\t\tattr.legendrow.style('display', 'none')\n\t\t\t\thiddenAttributes.push(attr)\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\t// this attribute is not hidden\n\n\t\t\tif (attr.value2count.size + attr.hiddenvalues.size == 0) {\n\t\t\t\t// no value after counting, no hidden value either: no data for this attribute\n\t\t\t\tattr.legendrow.style('display', 'none')\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\t// this attribute is shown\n\t\t\tattr.legendrow.style('display', 'table-row')\n\n\t\t\tattr.legendholder.selectAll('*').remove()\n\n\t\t\tconst lst = [...attr.value2count]\n\t\t\tlst.sort((i, j) => j[1].totalitems - i[1].totalitems)\n\n\t\t\tfor (const [valuestr, _o] of lst) {\n\t\t\t\tconst printstr = attr.values[valuestr] ? attr.values[valuestr].name : valuestr\n\n\t\t\t\tconst cell = attr.legendholder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\ttk.tip2.clear()\n\n\t\t\t\t\t\tif (attr.hiddenvalues.has(valuestr)) {\n\t\t\t\t\t\t\ttk.tip2.d\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t\t.text('Show')\n\t\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\t\t\t\t\tattr.hiddenvalues.delete(valuestr)\n\t\t\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\ttk.tip2.d\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t\t.text('Hide')\n\t\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\t\t\t\t\tattr.hiddenvalues.add(valuestr)\n\t\t\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttk.tip2.d\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t.text('Show only')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\t\t\t\tfor (const [vstr, c] of lst) {\n\t\t\t\t\t\t\t\t\tattr.hiddenvalues.add(vstr)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tattr.hiddenvalues.delete(valuestr)\n\t\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\tif (attr.hiddenvalues.size) {\n\t\t\t\t\t\t\ttk.tip2.d\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t\t.text('Show all')\n\t\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\t\t\t\t\tattr.hiddenvalues.clear()\n\t\t\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// label for this value?\n\t\t\t\t\t\tif (attr.values[valuestr] && attr.values[valuestr].label) {\n\t\t\t\t\t\t\ttk.tip2.d\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.text(attr.values[valuestr].label)\n\t\t\t\t\t\t\t\t.style('opacity', 0.5)\n\t\t\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// show by-dt count\n\t\t\t\t\t\tif (_o.dt2count) {\n\t\t\t\t\t\t\tconst lst2 = [..._o.dt2count]\n\t\t\t\t\t\t\tlst2.sort((i, j) => j[1] - i[1])\n\n\t\t\t\t\t\t\tconst table = tk.tip2.d\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('margin', '5px')\n\t\t\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t\t\t.style('opacity', 0.8)\n\t\t\t\t\t\t\t\t.style('border-spacing', '4px')\n\t\t\t\t\t\t\tfor (const [dt, count] of lst2) {\n\t\t\t\t\t\t\t\tconst tr = table.append('tr')\n\t\t\t\t\t\t\t\ttr.append('td').text(common.dt2label[dt])\n\t\t\t\t\t\t\t\ttr.append('td').text(count)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttk.tip2.showunder(cell.node())\n\t\t\t\t\t})\n\n\t\t\t\tconst color =\n\t\t\t\t\tattrGrp == 'sampleAttribute' && tk.legend_samplegroups && tk.legend_samplegroups.color(valuestr)\n\t\t\t\t\t\t? tk.legend_samplegroups.color(valuestr)\n\t\t\t\t\t\t: '#858585'\n\n\t\t\t\tcell\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t\t.style('background', color)\n\t\t\t\t\t.text(_o.totalitems)\n\t\t\t\tcell.append('span').html('&nbsp;' + printstr)\n\t\t\t}\n\n\t\t\tif (attr.hiddenvalues.size) {\n\t\t\t\t// this attribute has hidden values, show with strike-through\n\t\t\t\tfor (const valuestr of attr.hiddenvalues) {\n\t\t\t\t\tconst printstr = attr.values[valuestr] && attr.values[valuestr].name ? attr.values[valuestr].name : valuestr\n\n\t\t\t\t\tattr.legendholder\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_clb')\n\t\t\t\t\t\t.style('text-decoration', 'line-through')\n\t\t\t\t\t\t.text(printstr)\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tattr.hiddenvalues.delete(valuestr)\n\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tmay_process_hideable_rows(tk, block, hiddenAttributes)\n}\n\nfunction may_process_hideable_rows(tk, block, hiddenAttributes) {\n\t// handle non-mutation attribute\n\tlet numHiddenRows = 0\n\tfor (const hideable of tk.legend_hideable) {\n\t\thideable.row\n\t\t\t.select('td')\n\t\t\t.classed('sja_hideable_legend', true)\n\t\t\t.on('click', () => {\n\t\t\t\ttk.tip2.hide()\n\t\t\t\thideable.hidden = 1\n\t\t\t\ttk.legend_more_row.style('display', 'table-row')\n\t\t\t\tclient.flyindi(hideable.row.select('td'), tk.legend_more_label)\n\t\t\t\thideable.row.transition().delay(500).style('display', 'none')\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tmay_legend_attribute(tk, block)\n\t\t\t\t}, 500)\n\t\t\t})\n\n\t\thideable.row.style('display', hideable.hidden ? 'none' : 'table-row')\n\t\tif (hideable.hidden) {\n\t\t\tnumHiddenRows++\n\t\t}\n\t}\n\n\tif (!hiddenAttributes.length && !numHiddenRows) {\n\t\ttk.legend_more_row.style('display', 'none')\n\t} else {\n\t\ttk.legend_more_row.style('display', 'table-row')\n\t\ttk.legend_more_label.selectAll('*').remove()\n\n\t\tconst btn = tk.legend_more_label\n\t\t\t.attr('class', 'sja_legend_more_btn')\n\t\t\t.html('MORE...')\n\t\t\t.on('click', () => {\n\t\t\t\ttk.tip2.clear()\n\n\t\t\t\tfor (const hideable of tk.legend_hideable) {\n\t\t\t\t\tif (!hideable.hidden) continue\n\t\t\t\t\tconst div = tk.tip2.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.on('click', () => {\n\t\t\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\t\t\thideable.hidden = 0\n\t\t\t\t\t\t\tmay_legend_attribute(tk, block)\n\t\t\t\t\t\t})\n\n\t\t\t\t\tif (hideable.hidden && hideable.total_count) {\n\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t\t\t\t.style('background', '#858585')\n\t\t\t\t\t\t\t.text(hideable.total_count)\n\t\t\t\t\t}\n\n\t\t\t\t\tdiv.append('span').html('&nbsp;' + hideable.row.node().firstChild.innerHTML)\n\t\t\t\t}\n\n\t\t\t\tfor (const attr of hiddenAttributes) {\n\t\t\t\t\tif (!attr.hidden) continue\n\t\t\t\t\tconst total = [...attr.value2count.values()].reduce((a, b) => a + b.totalitems, 0)\n\t\t\t\t\tconst div = tk.tip2.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.on('click', () => {\n\t\t\t\t\t\t\ttk.tip2.hide()\n\t\t\t\t\t\t\tattr.hidden = 0\n\t\t\t\t\t\t\tmay_legend_attribute(tk, block)\n\t\t\t\t\t\t})\n\n\t\t\t\t\tdiv\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('background', '#858585')\n\t\t\t\t\t\t.text(total)\n\n\t\t\t\t\tdiv.append('span').html('&nbsp;' + attr.label)\n\t\t\t\t}\n\n\t\t\t\ttk.tip2.showunder(btn.node())\n\t\t\t})\n\t}\n}\n\nfunction count_sampleAttribute(key, attr, sample) {\n\tif (!(key in sample)) return\n\n\tif (!attr.filter) return // not a filter\n\n\tconst value = sample[key]\n\tif (!attr.value2count.has(value)) {\n\t\tattr.value2count.set(value, {\n\t\t\ttotalitems: 0\n\t\t})\n\t}\n\tattr.value2count.get(value).totalitems++\n\tif (!attr.values) {\n\t\tattr.values = {}\n\t}\n\tif (!attr.values[value]) {\n\t\tattr.values[value] = {\n\t\t\tname: value,\n\t\t\tlabel: value\n\t\t}\n\t}\n}\n\nfunction count_mutationAttribute(mattr, tk, itemdt) {\n\tif (!mattr) {\n\t\t// the item does not have mattr, do not count\n\t\treturn\n\t}\n\tif (!tk.mutationAttribute) return\n\n\tfor (const key in tk.mutationAttribute.attributes) {\n\t\tconst attr = tk.mutationAttribute.attributes[key]\n\t\tif (!attr.filter) continue\n\n\t\tconst value = mattr[key]\n\n\t\tif (value == undefined) {\n\t\t\t// not annotated, do not count\n\t\t\tcontinue\n\t\t}\n\n\t\t/*\n\t\tno longer acknowledge unannotated values\n\t\tif( value==undefined ) {\n\t\t\t// this item is not annotated, change its label to hardcoded\n\t\t\tvalue = common.not_annotated\n\t\t}\n\t\t*/\n\n\t\t// even if this value is not cataloged in attr.values{}, still record it for displaying\n\t\tif (!attr.value2count.has(value)) {\n\t\t\tattr.value2count.set(value, {\n\t\t\t\ttotalitems: 0,\n\t\t\t\tdt2count: new Map()\n\t\t\t})\n\t\t}\n\t\tattr.value2count.get(value).totalitems++\n\n\t\tif (!attr.value2count.get(value).dt2count.has(itemdt)) {\n\t\t\tattr.value2count.get(value).dt2count.set(itemdt, 0)\n\t\t}\n\n\t\tattr.value2count.get(value).dt2count.set(itemdt, attr.value2count.get(value).dt2count.get(itemdt) + 1)\n\t}\n}\n\nfunction count_locusAttribute(tk, m) {\n\tif (!tk.locusAttribute) return\n\n\tfor (const key in tk.locusAttribute.attributes) {\n\t\tconst attr = tk.locusAttribute.attributes[key]\n\t\tif (!attr.filter) continue\n\n\t\tconst _value = m.info[key]\n\n\t\tif (_value == undefined) continue // not annotated, do not count\n\n\t\t// quick fix! should refer to info field definition\n\t\tlet value\n\t\tif (Array.isArray(_value)) {\n\t\t\tvalue = _value[0]\n\t\t\tif (value == '.') continue\n\t\t} else {\n\t\t\tvalue = _value\n\t\t}\n\n\t\tif (attr.hiddenvalues.has(value)) continue\n\n\t\t// even if this value is not cataloged in attr.values{}, still record it for displaying\n\t\tif (!attr.value2count.has(value)) {\n\t\t\tattr.value2count.set(value, {\n\t\t\t\ttotalitems: 0,\n\t\t\t\tdt2count: new Map()\n\t\t\t})\n\t\t}\n\t\tattr.value2count.get(value).totalitems++\n\n\t\tif (!attr.value2count.get(value).dt2count.has(m.dt)) {\n\t\t\tattr.value2count.get(value).dt2count.set(m.dt, 0)\n\t\t}\n\n\t\tattr.value2count.get(value).dt2count.set(m.dt, attr.value2count.get(value).dt2count.get(m.dt) + 1)\n\t}\n}\n", "import * as client from './client'\nimport * as common from '#shared/common.js'\nimport { scaleLinear, scaleLog } from 'd3-scale'\nimport { axisRight } from 'd3-axis'\nimport { tooltip_singleitem, svcoord2html, make_svgraph, detailtable_singlesample } from './block.mds.svcnv.clickitem'\nimport {\n\tmap_cnv,\n\tlabelspace,\n\tdraw_colorscale_cnv,\n\tdraw_colorscale_loh,\n\tintrasvcolor,\n\ttrackclear,\n\titemname_svfusion,\n\tvcfvariantisgermline\n} from './block.mds.svcnv'\nimport { update_legend } from './block.mds.svcnv.legend'\n\nexport function render_singlesample(tk, block) {\n\t/*\n\tsingle-sample mode\n\tmay not have any data!\n\tsv/fusion with both feet in view range as legged\n\tcnv & loh & snvindel & itd as stack bars\n\t*/\n\n\ttrackclear(tk)\n\n\tconst svlst = []\n\tconst cnvlst = []\n\tconst lohlst = []\n\tconst itdlst = []\n\tconst id2sv = {} // must dedup sv, tell by breakpoint position\n\n\tconst usecopynumber = false // but not logratio\n\n\tlet gainmaxvalue = 0, // for cnv logratio\n\t\tlossmaxvalue = 0,\n\t\tcopynumbermax = 0, // for copy number converted from logratio, instead of logratio\n\t\tsegmeanmax = 0\n\n\tif (tk.data) {\n\t\t// divide cnv/loh/sv/itd data into holders\n\n\t\tfor (const item of tk.data) {\n\t\t\tif (item.dt == common.dtfusionrna || item.dt == common.dtsv) {\n\t\t\t\t// sv\n\n\t\t\t\tconst id = item.chrA + '.' + item.posA + '.' + item.chrB + '.' + item.posB + '.' + item.dt\n\n\t\t\t\tif (!id2sv[id]) {\n\t\t\t\t\tmap_sv(item, block)\n\t\t\t\t\tif (item.x0 || item.x1) {\n\t\t\t\t\t\tid2sv[id] = 1\n\t\t\t\t\t\tsvlst.push(item)\n\t\t\t\t\t\tif (item.chrA != item._chr) {\n\t\t\t\t\t\t\ttk.legend_svchrcolor.interchrs.add(item.chrA)\n\t\t\t\t\t\t\ttk.legend_svchrcolor.colorfunc(item.chrA)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (item.chrB != item._chr) {\n\t\t\t\t\t\t\ttk.legend_svchrcolor.interchrs.add(item.chrB)\n\t\t\t\t\t\t\ttk.legend_svchrcolor.colorfunc(item.chrB)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\t// cnv, loh, itd\n\n\t\t\tmap_cnv(item, tk, block)\n\t\t\tif (item.x1 == undefined || item.x2 == undefined) {\n\t\t\t\tconsole.log('unmappable: ' + item.chr + ' ' + item.start + ' ' + item.stop)\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (item.dt == common.dtloh) {\n\t\t\t\t// loh\n\t\t\t\tsegmeanmax = Math.max(segmeanmax, item.segmean)\n\t\t\t\tlohlst.push(item)\n\t\t\t} else if (item.dt == common.dtcnv) {\n\t\t\t\t// cnv\n\t\t\t\tif (usecopynumber) {\n\t\t\t\t\tconst v = 2 * Math.pow(2, item.value)\n\t\t\t\t\tcopynumbermax = Math.max(copynumbermax, v)\n\t\t\t\t} else {\n\t\t\t\t\t// item.value is log2 ratio by default\n\t\t\t\t\tif (item.value > 0) {\n\t\t\t\t\t\tgainmaxvalue = Math.max(gainmaxvalue, item.value)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlossmaxvalue = Math.min(lossmaxvalue, item.value)\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tcnvlst.push(item)\n\t\t\t} else if (item.dt == common.dtitd) {\n\t\t\t\titdlst.push(item)\n\t\t\t}\n\t\t}\n\n\t\tif (cnvlst.length) {\n\t\t\ttk.cnvcolor.cnvmax = Math.max(gainmaxvalue, -lossmaxvalue)\n\t\t\tdraw_colorscale_cnv(tk)\n\t\t}\n\n\t\tif (lohlst.length) {\n\t\t\ttk.cnvcolor.segmeanmax = segmeanmax\n\t\t\tdraw_colorscale_loh(tk)\n\t\t}\n\t}\n\n\t// sv on top\n\tconst svheight = render_singlesample_sv(group_sv(svlst), tk, block)\n\n\t/*\n\tstack bar plot on bottom:\n\t\tcnv, itd, loh as bars\n\t\tsnvindel: show label\n\t*/\n\ttk.cnv_g.attr('transform', 'translate(0,' + svheight + ')')\n\n\ttk.waterfall.axisgg.attr('transform', 'translate(0,' + svheight + ')')\n\n\tconst items = [...cnvlst, ...lohlst, ...itdlst] // stack bar items\n\tif (tk.data_vcf) {\n\t\tfor (const m of tk.data_vcf) {\n\t\t\tif (m.x != undefined) {\n\t\t\t\titems.push(m)\n\t\t\t}\n\t\t}\n\t}\n\n\tconst stackploth = render_singlesample_stack(items, tk, block)\n\n\ttk.height_main = tk.toppad + svheight + stackploth + tk.bottompad\n\n\tupdate_legend(tk, block)\n}\n\nfunction group_sv(lst) {\n\t/*\n\tsv/fusion will be merged\n\n\tfor group of sv with both ends mapped, their ends are close enough within a bin\n\n\tfor group of sv with only one mapped end, no matter which, that end for each is within a bin\n\n\n\tinput:\n\t.x0 .x1 could be undefined\n\t.chrA .chrB\n\t.posA .posB\n\n\toutput will add .lst[ {original} ]\n\t*/\n\tconst newlst = []\n\n\tconst pxbinsize = 8 // bin pixel size\n\n\tfor (let i = 0; i < lst.length; i++) {\n\t\tconst si = lst[i]\n\t\tif (si.__claimed) continue\n\n\t\tconst thisgroup = {\n\t\t\tx0: si.x0,\n\t\t\tx1: si.x1,\n\t\t\t_chr: si._chr,\n\t\t\tchrA: si.chrA,\n\t\t\tchrB: si.chrB,\n\t\t\tposA: si.posA,\n\t\t\tposB: si.posB,\n\t\t\tlst: [si]\n\t\t}\n\n\t\tfor (let j = i + 1; j < lst.length; j++) {\n\t\t\tconst sj = lst[j]\n\t\t\tif (sj.__claimed) continue\n\n\t\t\tconst isoneend = sj.x0 == undefined || sj.x1 == undefined\n\n\t\t\tif (si.x0 != undefined && si.x1 != undefined) {\n\t\t\t\t// two ends\n\n\t\t\t\tif (isoneend) continue\n\n\t\t\t\tif (Math.abs(sj.x0 - si.x0) <= pxbinsize && Math.abs(sj.x1 - si.x1) <= pxbinsize) {\n\t\t\t\t\tthisgroup.lst.push(sj)\n\t\t\t\t\tsj.__claimed = true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// one end\n\t\t\t\tif (!isoneend) continue\n\t\t\t\tconst end_i = si.x0 == undefined ? si.x1 : si.x0\n\t\t\t\tconst end_j = sj.x0 == undefined ? sj.x1 : sj.x0\n\t\t\t\tif (Math.abs(end_i - end_j) <= pxbinsize) {\n\t\t\t\t\tthisgroup.lst.push(sj)\n\t\t\t\t\tsj.__claimed = true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tnewlst.push(thisgroup)\n\t}\n\n\tfor (const s of lst) delete s.__claimed\n\n\treturn newlst\n}\n\nfunction getcolor_snvindel(m, tk) {\n\tif (tk.mds && tk.mds.mutation_signature) {\n\t\tif (m.sampledata && m.sampledata[0]) {\n\t\t\t// which signature set this sample has\n\t\t\tfor (const setkey in tk.mds.mutation_signature.sets) {\n\t\t\t\tconst v = m.sampledata[0][setkey]\n\t\t\t\tif (v) {\n\t\t\t\t\treturn tk.mds.mutation_signature.sets[setkey].signatures[v].color\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\treturn common.mclass[m.class].color\n}\n\nfunction render_singlesample_stack(items, tk, block, svheight) {\n\tif (items.length == 0) return 0\n\n\t/*\n\tstack for cnv/loh/snvindel/itd\n\tall in items[]\n\t*/\n\n\tconst stackheight = 12 // hardcoded\n\tconst stackspace = 1\n\n\tlet waterfall_shown = false\n\n\tif (tk.waterfall.inuse) {\n\t\t/* has waterfall, only show snvindel\n\t\tsegment items still in stack plot\n\t\t*/\n\t\tconst snvindels = items.filter(m => m.dt == common.dtsnvindel)\n\t\tif (snvindels.length > 1) {\n\t\t\tif (plot_waterfall(snvindels, tk, block)) {\n\t\t\t\twaterfall_shown = true\n\t\t\t}\n\t\t}\n\t}\n\n\tif (!waterfall_shown) {\n\t\t/* no waterfall\n\t\tprep & pre-render snvindel\n\t\t*/\n\n\t\ttk.waterfall.axisg.selectAll('*').remove()\n\t\ttk.waterfall.lab1.text('')\n\t\ttk.waterfall.lab2.text('')\n\t\ttk.waterfall.lab3.text('')\n\n\t\tfor (const m of items) {\n\t\t\tif (m.dt != common.dtsnvindel) continue\n\n\t\t\tconst g = tk.cnv_g.append('g')\n\t\t\tm._p = {\n\t\t\t\tg: g\n\t\t\t}\n\t\t\t/* for later use:\n\t\t\tstackw\n\t\t\tstackx\n\t\t\tg_x\n\t\t\t*/\n\n\t\t\tconst color = getcolor_snvindel(m, tk)\n\n\t\t\t/////////////////////////////////// label is the same for snvindel/itd\n\t\t\t// mouseover event not on label but on cover box\n\t\t\tconst lab = g\n\t\t\t\t.append('text')\n\t\t\t\t.attr('font-size', stackheight)\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.text(m.mname)\n\n\t\t\tlet labelw\n\t\t\tlab.each(function () {\n\t\t\t\tlabelw = this.getBBox().width\n\t\t\t})\n\n\t\t\tconst bgbox = g\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', -stackheight / 2)\n\t\t\t\t.attr('y', -stackheight / 2)\n\t\t\t\t.attr('width', stackheight)\n\t\t\t\t.attr('height', stackheight)\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.attr('fill-opacity', 0)\n\n\t\t\tlet fgline1, fgline2\n\n\t\t\tif (m.sampledata && vcfvariantisgermline(m.sampledata[0], tk)) {\n\t\t\t\tfgline1 = g\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('y1', 1 - stackheight / 2)\n\t\t\t\t\t.attr('y2', stackheight / 2 - 1)\n\t\t\t\tfgline2 = g\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('x1', 1 - stackheight / 2)\n\t\t\t\t\t.attr('x2', stackheight / 2 - 1)\n\t\t\t} else {\n\t\t\t\tfgline1 = g\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('x1', 1 - stackheight / 2)\n\t\t\t\t\t.attr('x2', stackheight / 2 - 1)\n\t\t\t\t\t.attr('y1', 1 - stackheight / 2)\n\t\t\t\t\t.attr('y2', stackheight / 2 - 1)\n\t\t\t\tfgline2 = g\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t\t.attr('x1', 1 - stackheight / 2)\n\t\t\t\t\t.attr('x2', stackheight / 2 - 1)\n\t\t\t\t\t.attr('y1', stackheight / 2 - 1)\n\t\t\t\t\t.attr('y2', 1 - stackheight / 2)\n\t\t\t}\n\n\t\t\t// to cover both cross & label, will be placed after deciding whether label is on left/right\n\t\t\tm._p.cover = g\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('y', -stackheight / 2)\n\t\t\t\t.attr('width', stackheight + labelspace + labelw)\n\t\t\t\t.attr('height', stackheight)\n\t\t\t\t.attr('fill', 'white')\n\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\tbgbox.attr('fill-opacity', 1)\n\t\t\t\t\tfgline1.attr('stroke', 'white')\n\t\t\t\t\tfgline2.attr('stroke', 'white')\n\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\titem: m,\n\t\t\t\t\t\tm_sample: m.sampledata[0],\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tblock: block\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\tbgbox.attr('fill-opacity', 0)\n\t\t\t\t\tfgline1.attr('stroke', color)\n\t\t\t\t\tfgline2.attr('stroke', color)\n\t\t\t\t})\n\n\t\t\t//////////////////////////////// set position for text label & cover\n\n\t\t\tm._p.stackw = stackheight + 5 + labelw\n\n\t\t\tif (block.width - m.x > labelw + labelspace + stackheight / 2) {\n\t\t\t\t// label on right\n\t\t\t\tm._p.stackx = m.x - stackheight / 2\n\t\t\t\tm._p.g_x = stackheight / 2\n\t\t\t\tlab.attr('x', stackheight / 2 + labelspace)\n\t\t\t\tm._p.cover.attr('x', -stackheight / 2)\n\t\t\t} else {\n\t\t\t\t// label on left\n\t\t\t\tm._p.stackx = m.x - stackheight / 2 - labelspace - labelw\n\t\t\t\tm._p.g_x = stackheight / 2 + labelspace + labelw\n\t\t\t\tlab.attr('x', -stackheight / 2 - labelspace).attr('text-anchor', 'end')\n\t\t\t\tm._p.cover.attr('x', -labelw - labelspace - stackheight / 2)\n\t\t\t}\n\t\t}\n\t}\n\n\titems.sort((i, j) => {\n\t\tconst xi = i._p ? i._p.stackx : Math.min(i.x1, i.x2)\n\t\tconst xj = j._p ? j._p.stackx : Math.min(j.x1, j.x2)\n\t\treturn xi - xj\n\t})\n\n\tconst stacks = [0]\n\tfor (const item of items) {\n\t\tif (waterfall_shown && item.dt == common.dtsnvindel) continue\n\t\t/*\n\t\tmust delete\n\t\t*/\n\t\tdelete item.stack\n\n\t\tconst itemstart = item._p ? item._p.stackx : Math.min(item.x1, item.x2)\n\t\tconst itemwidth = item._p ? item._p.stackw : Math.abs(item.x1 - item.x2)\n\n\t\tfor (let i = 0; i < stacks.length; i++) {\n\t\t\tif (stacks[i] <= itemstart) {\n\t\t\t\tstacks[i] = itemstart + itemwidth\n\t\t\t\titem.stack = i\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (item.stack == undefined) {\n\t\t\titem.stack = stacks.length\n\t\t\tstacks.push(itemstart + itemwidth)\n\t\t}\n\t}\n\n\tconst yoff = waterfall_shown ? tk.waterfall.axisheight + tk.waterfall.bottompad : 0\n\n\tfor (const item of items) {\n\t\tif (item.dt == common.dtloh || item.dt == common.dtcnv || item.dt == common.dtitd) {\n\t\t\tlet color\n\n\t\t\tif (item.dt == common.dtloh) {\n\t\t\t\tcolor =\n\t\t\t\t\t'rgba(' +\n\t\t\t\t\ttk.cnvcolor.loh.r +\n\t\t\t\t\t',' +\n\t\t\t\t\ttk.cnvcolor.loh.g +\n\t\t\t\t\t',' +\n\t\t\t\t\ttk.cnvcolor.loh.b +\n\t\t\t\t\t',' +\n\t\t\t\t\titem.segmean / tk.cnvcolor.segmeanmax +\n\t\t\t\t\t')'\n\t\t\t} else if (item.dt == common.dtcnv) {\n\t\t\t\tif (item.value > 0) {\n\t\t\t\t\tcolor =\n\t\t\t\t\t\t'rgba(' +\n\t\t\t\t\t\ttk.cnvcolor.gain.r +\n\t\t\t\t\t\t',' +\n\t\t\t\t\t\ttk.cnvcolor.gain.g +\n\t\t\t\t\t\t',' +\n\t\t\t\t\t\ttk.cnvcolor.gain.b +\n\t\t\t\t\t\t',' +\n\t\t\t\t\t\titem.value / tk.cnvcolor.cnvmax +\n\t\t\t\t\t\t')'\n\t\t\t\t} else {\n\t\t\t\t\tcolor =\n\t\t\t\t\t\t'rgba(' +\n\t\t\t\t\t\ttk.cnvcolor.loss.r +\n\t\t\t\t\t\t',' +\n\t\t\t\t\t\ttk.cnvcolor.loss.g +\n\t\t\t\t\t\t',' +\n\t\t\t\t\t\ttk.cnvcolor.loss.b +\n\t\t\t\t\t\t',' +\n\t\t\t\t\t\t-item.value / tk.cnvcolor.cnvmax +\n\t\t\t\t\t\t')'\n\t\t\t\t}\n\t\t\t} else if (item.dt == common.dtitd) {\n\t\t\t\tcolor = common.mclass[common.mclassitd].color\n\t\t\t}\n\n\t\t\ttk.cnv_g\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', Math.min(item.x1, item.x2))\n\t\t\t\t.attr('y', yoff + (stackheight + stackspace) * item.stack)\n\t\t\t\t.attr('width', Math.max(1, Math.abs(item.x2 - item.x1)))\n\t\t\t\t.attr('height', stackheight)\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t.attr('stroke', 'none')\n\t\t\t\t.attr('class', 'sja_aa_skkick')\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\titem: item,\n\t\t\t\t\t\ttk: tk\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t})\n\t\t\tcontinue\n\t\t}\n\n\t\tif (item.dt == common.dtsnvindel && !waterfall_shown) {\n\t\t\titem._p.g.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(item._p.stackx + item._p.g_x) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(stackheight / 2 + (stackheight + stackspace) * item.stack) +\n\t\t\t\t\t')'\n\t\t\t)\n\t\t\tcontinue\n\t\t}\n\t}\n\n\treturn yoff + stacks.length * (stackheight + stackspace) - stackspace\n}\n\nfunction plot_waterfall(snvindels, tk, block) {\n\t/*\nwaterfall only plots snvindel, not breakpoint\nplot them in cnv_g, axis shown in .waterfall.axisgg{}\n*/\n\n\t// first item has no dist\n\tsnvindels[0].water = {\n\t\th: tk.waterfall.axisheight\n\t}\n\n\tlet maxdist = 0\n\tfor (let i = 1; i < snvindels.length; i++) {\n\t\tconst m = snvindels[i]\n\t\tif (m.chr != snvindels[i - 1].chr) {\n\t\t\t// saw a new chr; snv from subpanel could be in different chr\n\t\t\tm.water = {\n\t\t\t\th: tk.waterfall.axisheight\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\t\tm.water = {\n\t\t\tbpdist: m.pos - snvindels[i - 1].pos\n\t\t}\n\t\tmaxdist = Math.max(maxdist, m.water.bpdist)\n\t}\n\n\tif (maxdist < 2) {\n\t\t// cannot draw\n\t\treturn false\n\t}\n\n\t// show axis\n\tclient.axisstyle({\n\t\taxis: tk.waterfall.axisg.call(\n\t\t\taxisRight()\n\t\t\t\t.ticks(3, '.0f')\n\t\t\t\t.scale(scaleLog().domain([1, maxdist]).range([tk.waterfall.axisheight, 0]))\n\t\t),\n\t\tcolor: 'black',\n\t\tshowline: 1\n\t})\n\ttk.waterfall.lab1.text('Log10').attr('y', tk.waterfall.axisheight / 2 - 14)\n\ttk.waterfall.lab2.text('intermutation').attr('y', tk.waterfall.axisheight / 2)\n\ttk.waterfall.lab3.text('distance').attr('y', tk.waterfall.axisheight / 2 + 14)\n\n\tfor (let i = 1; i < snvindels.length; i++) {\n\t\tconst m = snvindels[i]\n\t\tif (m.water.h) {\n\t\t\t// already set\n\t\t\tcontinue\n\t\t}\n\t\tif (m.water.bpdist == 0) {\n\t\t\tm.water.h = 0\n\t\t} else {\n\t\t\tm.water.h = (Math.log10(m.water.bpdist) * tk.waterfall.axisheight) / Math.log10(maxdist)\n\t\t}\n\t}\n\n\t// repetition of code\n\n\tconst stackheight = 12 // hardcoded\n\tconst stackspace = 1\n\tfor (const m of snvindels) {\n\t\tconst g = tk.cnv_g\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(' + m.x + ',' + (tk.waterfall.axisheight - m.water.h) + ')')\n\n\t\tconst color = getcolor_snvindel(m, tk)\n\n\t\tconst bgbox = g\n\t\t\t.append('rect')\n\t\t\t.attr('x', -stackheight / 2)\n\t\t\t.attr('y', -stackheight / 2)\n\t\t\t.attr('width', stackheight)\n\t\t\t.attr('height', stackheight)\n\t\t\t.attr('fill', color)\n\t\t\t.attr('fill-opacity', 0)\n\n\t\tlet fgline1, fgline2\n\n\t\tif (m.sampledata && vcfvariantisgermline(m.sampledata[0], tk)) {\n\t\t\tfgline1 = g\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t.attr('y1', 1 - stackheight / 2)\n\t\t\t\t.attr('y2', stackheight / 2 - 1)\n\t\t\tfgline2 = g\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t.attr('x1', 1 - stackheight / 2)\n\t\t\t\t.attr('x2', stackheight / 2 - 1)\n\t\t} else {\n\t\t\tfgline1 = g\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t.attr('x1', 1 - stackheight / 2)\n\t\t\t\t.attr('x2', stackheight / 2 - 1)\n\t\t\t\t.attr('y1', 1 - stackheight / 2)\n\t\t\t\t.attr('y2', stackheight / 2 - 1)\n\t\t\tfgline2 = g\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('stroke-width', 2)\n\t\t\t\t.attr('x1', 1 - stackheight / 2)\n\t\t\t\t.attr('x2', stackheight / 2 - 1)\n\t\t\t\t.attr('y1', stackheight / 2 - 1)\n\t\t\t\t.attr('y2', 1 - stackheight / 2)\n\t\t}\n\n\t\t// to cover both cross & label, will be placed after deciding whether label is on left/right\n\t\tg.append('rect')\n\t\t\t.attr('y', -stackheight / 2)\n\t\t\t.attr('x', -stackheight / 2)\n\t\t\t.attr('width', stackheight)\n\t\t\t.attr('height', stackheight)\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.on('mouseover', () => {\n\t\t\t\tbgbox.attr('fill-opacity', 1)\n\t\t\t\tfgline1.attr('stroke', 'white')\n\t\t\t\tfgline2.attr('stroke', 'white')\n\t\t\t\ttooltip_singleitem({\n\t\t\t\t\titem: m,\n\t\t\t\t\tm_sample: m.sampledata[0],\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\t.on('mouseout', () => {\n\t\t\t\ttk.tktip.hide()\n\t\t\t\tbgbox.attr('fill-opacity', 0)\n\t\t\t\tfgline1.attr('stroke', color)\n\t\t\t\tfgline2.attr('stroke', color)\n\t\t\t})\n\t\tdelete m.water\n\t}\n\treturn true // successfully drawn\n}\n\nfunction horiplace(lst, width) {\n\t/*\n\tj._x: ideal position\n\tj.x:  shifted position\n\t*/\n\n\tlst.forEach(i => (i.tox = i._x))\n\tconst todo = lst\n\n\ttodo.sort((a, b) => {\n\t\treturn a.tox - b.tox\n\t})\n\n\t// push all to left\n\t// set initial x for all for shifting\n\tlet cumx = todo.length == 0 ? 0 : todo[0].radius\n\tfor (const i of todo) {\n\t\ti.x = cumx + i.radius\n\t\tcumx += i.radius * 2\n\t}\n\n\tfor (let i = 0; i < todo.length; i++) {\n\t\twhile (1) {\n\t\t\tlet currsum = 0,\n\t\t\t\tnewsum = 0\n\t\t\tfor (let j = i; j < todo.length; j++) {\n\t\t\t\tconst k = todo[j]\n\t\t\t\t// detect conditions to stop\n\t\t\t\tif (j > 0) {\n\t\t\t\t\tconst prev = todo[j - 1]\n\t\t\t\t\tif (prev.x + prev.radius <= k.x - k.radius) {\n\t\t\t\t\t\t// not overlapping with previous\n\t\t\t\t\t\tif (k.x >= k.tox) {\n\t\t\t\t\t\t\t// so it can stop\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 {\n\t\t\t\t\tif (k.x >= k.tox) {\n\t\t\t\t\t\t// the first one, it can stop too\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tconst z = todo[todo.length - 1]\n\t\t\t\tif (z.x + z.radius >= width) {\n\t\t\t\t\t// last one out of range\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcurrsum += Math.abs(k.x - k.tox)\n\t\t\t\tk.x++\n\t\t\t\tnewsum += Math.abs(k.x - k.tox)\n\t\t\t}\n\t\t\tif (newsum < currsum) {\n\t\t\t} else {\n\t\t\t\t// reject\n\t\t\t\tfor (let j = i; j < todo.length; j++) {\n\t\t\t\t\ttodo[j].x--\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\ttodo.forEach(i => delete i.tox)\n}\n\nfunction render_singlesample_sv(svlst, tk, block) {\n\tif (svlst.length == 0) return 0\n\n\tlet sf_discradius\n\t{\n\t\tlet maxcount = 1\n\t\tfor (const j of svlst) maxcount = Math.max(maxcount, j.lst.length)\n\n\t\tlet mrd = 0 // max radius\n\t\tconst w = Math.pow(tk.discradius, 2) * Math.PI // unit area\n\n\t\t/*\n\t\tif(maxcount==1) {\n\t\t\tmrd=w\n\t\t} else if(maxcount<=2) {\n\t\t\tmrd=w * 1.4\n\t\t} else if(maxcount<=3) {\n\t\t\tmrd=w * 1.7\n\t\t} else if(maxcount<=5) {\n\t\t\tmrd=w * 2\n\t\t} else if(maxcount<=8) {\n\t\t\tmrd=w * 3\n\t\t} else {\n\t\t\tmrd=w * 4\n\t\t}\n\n\t\tsf_discradius=scaleLinear()\n\t\t\t.domain([1,\n\t\t\t\tmaxcount*.5+.1,\n\t\t\t\tmaxcount*.6+.1,\n\t\t\t\tmaxcount*.7+.1,\n\t\t\t\tmaxcount*.8+.1,\n\t\t\t\tmaxcount])\n\t\t\t.range([w,\n\t\t\t\tw+(mrd-w)*.8,\n\t\t\t\tw+(mrd-w)*.85,\n\t\t\t\tw+(mrd-w)*.9,\n\t\t\t\tw+(mrd-w)*.95,\n\t\t\t\tmrd])\n\t\t\t\t*/\n\n\t\tconst s = scaleLinear()\n\t\tif (maxcount == 1) {\n\t\t\ts.domain([1, 1]).range([w, w])\n\t\t} else if (maxcount == 2) {\n\t\t\ts.domain([1, 2]).range([w, w * 1.3])\n\t\t} else if (maxcount == 3) {\n\t\t\ts.domain([1, 3]).range([w, w * 1.6])\n\t\t} else if (maxcount == 4) {\n\t\t\ts.domain([1, 4]).range([w, w * 1.8])\n\t\t} else if (maxcount == 6) {\n\t\t\ts.domain([1, 6]).range([w, w * 2])\n\t\t} else if (maxcount == 10) {\n\t\t\ts.domain([1, 10]).range([w, w * 3])\n\t\t} else {\n\t\t\ts.domain([1, maxcount]).range([w, w * 4])\n\t\t}\n\t\tsf_discradius = s\n\t}\n\n\t// clean sv\n\n\tlet maxradius = 0\n\n\tfor (const i of svlst) {\n\t\ti.radius = Math.sqrt(sf_discradius(i.lst.length) / Math.PI)\n\t\tmaxradius = Math.max(i.radius, maxradius)\n\n\t\tif (i.x0 != undefined && i.x1 != undefined) {\n\t\t\tif (i.x0 > i.x1) {\n\t\t\t\t// x0 maybe bigger than x1\n\t\t\t\tconst a = i.x1\n\t\t\t\ti.x1 = i.x0\n\t\t\t\ti.x0 = a\n\t\t\t}\n\t\t\ti._x = (i.x0 + i.x1) / 2\n\t\t} else {\n\t\t\ti._x = i.x0 || i.x1\n\t\t}\n\t\ti.x = i._x\n\t}\n\n\t/*\n\tradius for all items have been set\n\tsum up height for subtrack\n\tif sv has both x0/x1 will show both legs, will be higher, else lower\n\t*/\n\tconst svheight =\n\t\tmaxradius * 2 + // ball diameter\n\t\tmaxradius * 2 + // raise height\n\t\t(svlst.find(s => s.x0 && s.x1) ? tk.legheight : 0)\n\n\ttk.svvcf_g.attr('transform', 'translate(0,' + (svheight - 0) + ')')\n\n\tconst entirewidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0)\n\n\t//horiplace( svlst, entirewidth )\n\n\tfor (const sv of svlst) {\n\t\tconst doubleleg = sv.x0 && sv.x1\n\n\t\tconst thislegheight = tk.legheight * (doubleleg ? 1 : 0)\n\t\tconst raiseheight = sv.lst.length == 1 ? sv.radius : sv.radius * 2\n\n\t\tconst g = tk.svvcf_g.append('g').attr('transform', 'translate(' + sv.x + ',-' + (thislegheight + raiseheight) + ')')\n\n\t\tconst otherchr = sv.chrA == sv._chr ? sv.chrB : sv.chrA\n\t\tconst color = otherchr == sv._chr ? intrasvcolor : tk.legend_svchrcolor.colorfunc(otherchr)\n\n\t\tg.append('circle').attr('r', sv.radius).attr('cy', -sv.radius).attr('fill', color).attr('stroke', 'white')\n\n\t\tif (sv.lst.length > 1) {\n\t\t\tconst s = sv.radius * 1.5\n\t\t\tconst text = sv.lst.length.toString()\n\t\t\tconst fontsize = Math.min(s / (text.length * client.textlensf), s)\n\t\t\tg.append('text')\n\t\t\t\t.text(text)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('fill', 'white')\n\t\t\t\t.attr('y', -sv.radius)\n\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t.attr('font-family', client.font)\n\t\t}\n\n\t\t// cover\n\t\tg.append('circle')\n\t\t\t.attr('r', sv.radius)\n\t\t\t.attr('cy', -sv.radius)\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('stroke', color)\n\t\t\t.attr('stroke-opacity', 0)\n\t\t\t.attr('class', 'sja_aa_disckick')\n\t\t\t.on('mouseover', event => {\n\t\t\t\tif (sv.lst.length == 1) {\n\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\titem: sv.lst[0],\n\t\t\t\t\t\ttk: tk\n\t\t\t\t\t})\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttooltip_multi_sv(sv.lst, tk, event)\n\t\t\t})\n\t\t\t.on('mouseout', () => tk.tktip.hide())\n\t\t\t.on('click', event => {\n\t\t\t\tif (sv.lst.length == 1) {\n\t\t\t\t\tconst m = sv.lst[0]\n\t\t\t\t\tconst pane = client.newpane({ x: event.clientX, y: event.clientY })\n\t\t\t\t\tpane.header.text(m.sample)\n\t\t\t\t\tpane.body.style('margin-top', '10px')\n\n\t\t\t\t\t// 1 - may split button\n\t\t\t\t\tconst [chr, otherpos] = get_split_coord(m, block)\n\t\t\t\t\tif (chr) {\n\t\t\t\t\t\t// will split\n\t\t\t\t\t\tconst row = pane.body.append('div').style('margin-bottom', '5px')\n\t\t\t\t\t\trow\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t\t.text('Add new panel at ' + chr.name + ':' + otherpos)\n\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\trow.remove()\n\t\t\t\t\t\t\t\tsplit_panel(chr, otherpos, block)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\n\t\t\t\t\t// 2 - svgraph\n\t\t\t\t\tmake_svgraph(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t\t//tk: tk,\n\t\t\t\t\t\t},\n\t\t\t\t\t\tpane.body.append('div')\n\t\t\t\t\t)\n\n\t\t\t\t\t// 3 - detail table\n\t\t\t\t\tdetailtable_singlesample({\n\t\t\t\t\t\titem: m,\n\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\tholder: pane.body.append('div')\n\t\t\t\t\t})\n\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tpanel_multi_sv(sv.lst, tk, block, event)\n\t\t\t})\n\n\t\tif (doubleleg) {\n\t\t\tg.append('line').attr('stroke', color).attr('y2', raiseheight).attr('shape-rendering', 'crispEdges')\n\t\t\tg.append('line') // right leg\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('x2', (sv.x1 - sv.x0) / 2 - (sv.x - sv._x))\n\t\t\t\t.attr('y1', raiseheight)\n\t\t\t\t.attr('y2', raiseheight + thislegheight)\n\t\t\tg.append('line') // left leg\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('x2', -(sv.x1 - sv.x0) / 2 - (sv.x - sv._x))\n\t\t\t\t.attr('y1', raiseheight)\n\t\t\t\t.attr('y2', raiseheight + thislegheight)\n\t\t} else {\n\t\t\tg.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('y2', raiseheight + thislegheight)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t}\n\t}\n\treturn svheight\n}\n\nfunction get_split_coord(sv, block) {\n\tlet otherchr\n\tlet otherpos\n\tif (sv._chr != sv.chrA) {\n\t\totherchr = sv.chrA\n\t\totherpos = sv.posA\n\t} else if (sv._chr != sv.chrB) {\n\t\totherchr = sv.chrB\n\t\totherpos = sv.posB\n\t}\n\tif (!otherchr) return [null]\n\tconst chr = block.genome.chrlookup[otherchr.toUpperCase()]\n\tif (!chr) {\n\t\tblock.error('Invalid chr name: ' + otherchr)\n\t\treturn [null]\n\t}\n\n\t// see if this chr already exists...\n\tfor (const p of block.subpanels) {\n\t\tif (p.chr == otherchr) {\n\t\t\treturn [null]\n\t\t}\n\t}\n\treturn [chr, otherpos]\n}\n\nfunction split_panel(chr, otherpos, block) {\n\tconst span = 10000\n\tconst p = {\n\t\tchr: chr.name,\n\t\tstart: Math.max(0, otherpos - span),\n\t\tstop: Math.min(chr.len, otherpos + span),\n\t\twidth: 600,\n\t\tleftpad: 10,\n\t\tleftborder: 'rgba(50,50,50,.1)'\n\t}\n\tp.exonsf = p.width / (p.stop - p.start)\n\tblock.init_coord_subpanel(p)\n\tblock.subpanels.push(p)\n\tblock.ifbusy()\n}\n\nfunction map_sv(sv, block) {\n\tconst lst1 = block.seekcoord(sv.chrA, sv.posA)\n\tfor (const r of lst1) {\n\t\tif (r.ridx != undefined) {\n\t\t\t// in main, if outside won't show this end\n\t\t\tif (r.x > 0 && r.x < block.width) {\n\t\t\t\tsv.x0 = r.x\n\t\t\t\tbreak\n\t\t\t}\n\t\t} else if (r.subpanelidx != undefined) {\n\t\t\tsv.x0 = r.x\n\t\t}\n\t}\n\tconst lst2 = block.seekcoord(sv.chrB, sv.posB)\n\tfor (const r of lst2) {\n\t\tif (r.ridx != undefined) {\n\t\t\t// in main, if outside won't show this end\n\t\t\tif (r.x > 0 && r.x < block.width) {\n\t\t\t\tsv.x1 = r.x\n\t\t\t\tbreak\n\t\t\t}\n\t\t} else if (r.subpanelidx != undefined) {\n\t\t\tsv.x1 = r.x\n\t\t}\n\t}\n}\n\nfunction tooltip_multi_sv(lst, tk, event) {\n\ttk.tktip.clear()\n\tshowtable_multi_sv(lst, tk.tktip.d, tk)\n\ttk.tktip.show(event.clientX, event.clientY)\n}\n\nfunction panel_multi_sv(lst, tk, block, event) {\n\tconst pane = client.newpane({ x: event.clientX, y: event.clientY })\n\tshowtable_multi_sv(lst, pane.body, tk)\n}\n\nfunction showtable_multi_sv(lst, holder, tk) {\n\tconst table = holder.append('table')\n\tfor (const i of lst) {\n\t\tconst tr = table.append('tr')\n\n\t\ttr.append('td')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.text(i.dt == common.dtsv ? 'SV' : 'Fusion')\n\n\t\ttr.append('td').text(itemname_svfusion(i))\n\t\ttr.append('td').style('font-size', '.8em').html(svcoord2html(i, tk))\n\t}\n}\n", "import * as client from './client'\nimport { axisTop } from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\nimport * as common from '#shared/common.js'\nimport * as expressionstat from './block.mds.expressionstat'\nimport { may_add_sampleannotation } from './block.mds.svcnv.clickitem'\nimport { createbutton_addfeature } from './block.mds.svcnv.samplematrix'\nimport { gene_searchbox } from './gene'\nimport {\n\tfocus_singlesample,\n\tcoverbarcolor_silent,\n\tmulti_sample_addhighlight,\n\tmulti_sample_removehighlight,\n\tmulti_expressionstatus_ase_outlier\n} from './block.mds.svcnv'\n\n/*\n\n********************** EXPORTED\nrender_multi_genebar\n\tgenebarconfig_fixed\n\n********************** INTERNAL\nmulti_show_geneboxplot\ngenebar_printtooltip\naddcolumn_autogene\naddcolumn_fixedgene\n\tgenebarconfig_auto\n\t\tfindgene4fix\naddcolumn_attr\nmayadd_survivaloption\n\n\nadd columns\ncolumn could be gene expression rank and sample attribute\n\n*/\n\nexport function render_multi_genebar(tk, block) {\n\t/*\n\tmulti-sample\n\tnative or custom\n\tdense or full\n\n\t*/\n\n\t// it may have been cleared in trunk, but local func could still call to re-render\n\ttk.cnvrightg.selectAll('*').remove()\n\n\tconst attrlst = [] // list of sample attributes to show alongside expression\n\n\t// TODO support categorical attributes\n\n\tif (tk.sampleAttribute && tk.sampleAttribute.attributes && tk.sampleAttribute.samples) {\n\t\tfor (const attrkey in tk.sampleAttribute.attributes) {\n\t\t\tconst attr = tk.sampleAttribute.attributes[attrkey]\n\t\t\tif (!attr.showintrack) continue\n\n\t\t\tconst attrobj = {\n\t\t\t\tkey: attrkey,\n\t\t\t\tlabel: attr.label,\n\t\t\t\tmin: null,\n\t\t\t\tmax: null\n\t\t\t}\n\t\t\t// determine min/max\n\t\t\tfor (const g of tk.samplegroups) {\n\t\t\t\tfor (const s of g.samples) {\n\t\t\t\t\tconst v0 = tk.sampleAttribute.samples[s.samplename]\n\t\t\t\t\tif (!v0) continue\n\t\t\t\t\tconst v = v0[attrkey]\n\t\t\t\t\tif (Number.isNaN(v)) continue\n\t\t\t\t\tif (attrobj.min == null) {\n\t\t\t\t\t\tattrobj.min = attrobj.max = v\n\t\t\t\t\t} else {\n\t\t\t\t\t\tattrobj.min = Math.min(attrobj.min, v)\n\t\t\t\t\t\tattrobj.max = Math.max(attrobj.max, v)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tattrlst.push(attrobj)\n\t\t}\n\t}\n\n\t/*\n\tthree types of columns\n\t1. auto gene, single, changes as you scroll\n\t2. fixed genes, 0-multi\n\t3. sample attr\n\t*/\n\n\tconst genes_auto = new Set() // names of auto gene, will choose one\n\n\tif (tk._data) {\n\t\tfor (const g of tk._data) {\n\t\t\tif (!g.samples) continue\n\t\t\tfor (const s of g.samples) {\n\t\t\t\tif (!s.expressionrank) continue\n\n\t\t\t\tfor (const gene in s.expressionrank) {\n\t\t\t\t\tgenes_auto.add(gene)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst genes_fixed = tk.gecfg ? tk.gecfg.fixed : []\n\n\tlet autogenename\n\tif (tk.selectedgene && genes_auto.has(tk.selectedgene)) {\n\t\tautogenename = tk.selectedgene\n\t} else {\n\t\tautogenename = [...genes_auto][0]\n\t}\n\n\tif (autogenename) {\n\t\t// has got one name, check if it is in fixed\n\t\tfor (const gf of genes_fixed) {\n\t\t\tif (autogenename == gf.gene) {\n\t\t\t\t// same, won't show auto\n\t\t\t\tautogenename = undefined\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\n\t/*\n\tquick fix\n\texpose the name of first showing gene to smat task in Matrix view\n\t*/\n\tif (autogenename) {\n\t\ttk.showinggene = autogenename\n\t} else if (genes_fixed[0]) {\n\t\ttk.showinggene = genes_fixed[0].name\n\t}\n\n\t// any gene has ase info? if so, tooltip will show 'no info' for those missing\n\t// otherwise won't indicate ase status\n\tlet anygenehasase = false\n\tfor (const g of tk.samplegroups) {\n\t\tfor (const s of g.samples) {\n\t\t\tif (s.expressionrank) {\n\t\t\t\tfor (const n in s.expressionrank) {\n\t\t\t\t\tif (s.expressionrank[n].ase) {\n\t\t\t\t\t\tanygenehasase = true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// initiate columnbars holder\n\tfor (const g of tk.samplegroups) {\n\t\tfor (const s of g.samples) {\n\t\t\ts.columnbars = []\n\t\t}\n\t}\n\n\tlet column_xoff = 0\n\n\tcolumn_xoff += addcolumn_autogene(autogenename, genes_auto, tk, block)\n\n\tfor (const fixedgene of genes_fixed) {\n\t\t/***********\n\t\tone column for each fixed gene\n\t\t.gene str\n\t\t.sample2rank{}\n\t\t*/\n\n\t\tcolumn_xoff += addcolumn_fixedgene(fixedgene, tk, block, column_xoff)\n\t}\n\n\t// one column for each sample attribute\n\tfor (const attr of attrlst) {\n\t\tcolumn_xoff += addcolumn_attr(attr, tk, block, column_xoff)\n\t}\n\n\t/* sloppy\n\tshould await for data to be loaded for all fixed genes\n\t*/\n\tif (tk.gecfg && tk.gecfg.fixed_pend) {\n\t\tconst i = tk.gecfg.fixed_pend.shift()\n\t\tif (tk.gecfg.fixed_pend.length == 0) {\n\t\t\tdelete tk.gecfg.fixed_pend\n\t\t}\n\t\t// not using predefined position\n\t\tfindgene4fix(i.gene, tk, block)\n\t}\n\n\t// adjust block right width\n\ttk.rightheadw_tk = column_xoff\n\tblock.rightheadw = 0\n\tfor (const t of block.tklst) {\n\t\tblock.rightheadw = Math.max(block.rightheadw, t.rightheadw_tk)\n\t}\n\tblock.blocksetw()\n\n\tconst axispad = 0\n\tconst labelpad = 3\n\tconst ticksize = 5\n\tconst fontsize = 12\n\n\treturn fontsize + fontsize + labelpad + ticksize + axispad\n}\n\nfunction multi_show_geneboxplot(arg) {\n\t/*\n\tmulti-sample\n\tfor a given gene, show expression across all samples\n\tif the gecfg are configured to group samples by attribute, will show boxplot for each group\n\t*/\n\n\tconst { gene, samplename, value, tk, block } = arg\n\n\tconst pane = client.newpane({ x: window.innerWidth / 2, y: 100 })\n\tpane.header.text(gene + ' ' + tk.gecfg.datatype + ' from ' + tk.name)\n\tconst c = tk.gene2coord[gene]\n\tif (!c) {\n\t\tpane.body.text('No coordinate for ' + gene)\n\t\treturn\n\t}\n\n\tconst p = {\n\t\tgene: gene,\n\t\tchr: c.chr,\n\t\tstart: c.start,\n\t\tstop: c.stop,\n\t\tholder: pane.body,\n\t\tblock: block,\n\t\tgenome: block.genome,\n\t\t//jwt: block.jwt,\n\t\t//hostURL: block.hostURL,\n\t\tsample: samplename ? { name: samplename, value: value } : null,\n\t\t// if sampleset is defined for custom dataset, allow to show boxplot at exp panel\n\t\tsampleset: tk.sampleset\n\t}\n\n\t// expression\n\tif (tk.iscustom) {\n\t\tfor (const k in tk.checkexpressionrank) {\n\t\t\tp[k] = tk.checkexpressionrank[k]\n\t\t}\n\t} else {\n\t\tconst e = tk.mds.queries[tk.querykey].checkexpressionrank\n\t\tp.dslabel = tk.mds.label\n\t\tp.querykey = e.querykey\n\t\tp.boxplotgroupers = e.boxplotgroupers\n\t}\n\t// svcnv\n\tp.color = {\n\t\tcnvgain: tk.cnvcolor.gain.str,\n\t\tcnvloss: tk.cnvcolor.loss.str,\n\t\tsv: 'black'\n\t}\n\tif (tk.iscustom) {\n\t\tp.svcnv = {\n\t\t\tiscustom: 1,\n\t\t\tfile: tk.file,\n\t\t\turl: tk.url,\n\t\t\tindexURL: tk.indexURL\n\t\t}\n\t} else {\n\t\tp.svcnv = {\n\t\t\tdslabel: tk.mds.label,\n\t\t\tquerykey: tk.querykey\n\t\t}\n\t}\n\tp.svcnv.valueCutoff = tk.valueCutoff\n\tp.svcnv.bplengthUpperLimit = tk.bplengthUpperLimit\n\n\tp.clicksample = (thissample, group, plot) => {\n\t\t// click outlier sample to launch browser and show sv/cnv+expression rank for single sample\n\t\tconst sample = {\n\t\t\tsamplename: thissample.sample\n\t\t}\n\n\t\tlet samplegroup\n\t\tif (group) {\n\t\t\tsamplegroup = {\n\t\t\t\tattributes: group.attributes\n\t\t\t}\n\t\t}\n\n\t\tconst tk2 = {} // build a svcnv track\n\n\t\tfor (const k in plot.svcnv) {\n\t\t\ttk2[k] = plot.svcnv[k]\n\t\t}\n\n\t\tif (plot.svcnv.iscustom) {\n\t\t\ttk2.checkexpressionrank = {\n\t\t\t\tfile: plot.file,\n\t\t\t\turl: plot.url,\n\t\t\t\tindexURL: plot.indexURL,\n\t\t\t\tdatatype: plot.gecfg.datatype\n\t\t\t}\n\t\t} else {\n\t\t\ttk2.mds = plot.block.genome.datasets[plot.svcnv.dslabel]\n\t\t}\n\t\tfocus_singlesample({\n\t\t\tm: {\n\t\t\t\tdt: common.dtcnv,\n\t\t\t\tchr: plot.chr,\n\t\t\t\tstart: plot.start,\n\t\t\t\tstop: plot.stop\n\t\t\t},\n\t\t\tsample: sample,\n\t\t\tsamplegroup: samplegroup,\n\t\t\ttk: tk2,\n\t\t\tblock: plot.block\n\t\t})\n\t}\n\timport('./block.mds.geneboxplot').then(_ => {\n\t\t_.init(p)\n\t})\n}\n\nfunction addcolumn_autogene(autogenename, genes_auto, tk, block) {\n\t/*\n\treturn width of column to indicate whether a column is drawn or not\n\t*/\n\n\t// TODO enable column-specific width config\n\n\t// hardcoded bar width for expression rank\n\tconst expbarwidth = 80\n\t// hardcoded bar width for numeric attribute\n\tconst numattrbarwidth = 80\n\tconst xspace = 15\n\n\t// axis label\n\tconst axispad = 0\n\tconst labelpad = 3\n\tconst ticksize = 5\n\tconst fontsize = 12\n\n\t////// column 1 is for auto gene\n\tif (autogenename) {\n\t\tlet minvalue = 0\n\t\tlet maxvalue = 100 // hardcoded rank\n\n\t\tfor (const g of tk.samplegroups) {\n\t\t\tlet y = g.y\n\n\t\t\tfor (const s of g.samples) {\n\t\t\t\tconst row = tk.cnvrightg.append('g').attr('transform', 'translate(0,' + y + ')')\n\n\t\t\t\tif (s.expressionrank) {\n\t\t\t\t\tconst v = s.expressionrank[autogenename]\n\t\t\t\t\tif (v != undefined) {\n\t\t\t\t\t\tconst bar = row\n\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t.attr('fill', expressionstat.ase_color(v, tk.gecfg)) // bar color set by ase status\n\t\t\t\t\t\t\t.attr('width', (expbarwidth * v.rank) / maxvalue)\n\t\t\t\t\t\t\t.attr('height', s.height)\n\t\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\n\t\t\t\t\t\tif (0 && tk.isfull && v.estat) {\n\t\t\t\t\t\t\t// only show dots for outlier status in full, not dense\n\t\t\t\t\t\t\tif (v.estat.outlier) {\n\t\t\t\t\t\t\t\trow\n\t\t\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t\t\t.attr('cx', expbarwidth)\n\t\t\t\t\t\t\t\t\t.attr('cy', s.height / 2)\n\t\t\t\t\t\t\t\t\t.attr('r', s.height / 2)\n\t\t\t\t\t\t\t\t\t.attr('fill', tk.gecfg.outlier.color_outlier)\n\t\t\t\t\t\t\t} else if (v.estat.outlier_asehigh) {\n\t\t\t\t\t\t\t\trow\n\t\t\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t\t\t.attr('cx', expbarwidth)\n\t\t\t\t\t\t\t\t\t.attr('cy', s.height / 2)\n\t\t\t\t\t\t\t\t\t.attr('r', s.height / 2)\n\t\t\t\t\t\t\t\t\t.attr('fill', tk.gecfg.outlier.color_outlier_asehigh)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tconst cover = row\n\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t.attr('fill', coverbarcolor_silent)\n\t\t\t\t\t\t\t.attr('fill-opacity', 0.1)\n\t\t\t\t\t\t\t.attr('width', expbarwidth)\n\t\t\t\t\t\t\t.attr('height', s.height)\n\n\t\t\t\t\t\tif (tk.isfull) {\n\t\t\t\t\t\t\ts.columnbars.push(cover)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tcover\n\t\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\t\ttk.tktip.clear()\n\n\t\t\t\t\t\t\t\tgenebar_printtooltip(autogenename, v, s, tk.tktip.d, tk)\n\n\t\t\t\t\t\t\t\ttk.tktip.show(event.clientX, event.clientY)\n\n\t\t\t\t\t\t\t\tmulti_sample_addhighlight(s)\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\tmulti_sample_removehighlight(s)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tmulti_show_geneboxplot({\n\t\t\t\t\t\t\t\t\tgene: autogenename,\n\t\t\t\t\t\t\t\t\tsamplename: s.samplename,\n\t\t\t\t\t\t\t\t\tvalue: v.value,\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})\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\t// done this sample\n\t\t\t\ty += s.height + tk.rowspace\n\t\t\t}\n\n\t\t\t// done this group\n\t\t}\n\n\t\tconst headg = tk.cnvrightg.append('g').attr('transform', 'translate(0,-' + axispad + ')')\n\n\t\tclient.axisstyle({\n\t\t\taxis: headg.append('g').call(\n\t\t\t\taxisTop()\n\t\t\t\t\t.scale(scaleLinear().domain([minvalue, maxvalue]).range([0, expbarwidth]))\n\t\t\t\t\t.tickValues([0, maxvalue])\n\t\t\t\t\t.tickSize(ticksize)\n\t\t\t),\n\t\t\tfontsize: fontsize,\n\t\t\tshowline: 1\n\t\t})\n\n\t\theadg\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('x', expbarwidth / 2)\n\t\t\t.attr('y', -(fontsize + labelpad + ticksize + axispad))\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.text(autogenename + ' ' + 'rank')\n\t\t\t.attr('class', 'sja_clbtext2')\n\t\t\t.on('click', () => {\n\t\t\t\tgenebarconfig_auto(autogenename, genes_auto, tk, block)\n\t\t\t})\n\n\t\t// done column for auto gene\n\t\treturn expbarwidth + xspace\n\t}\n\n\t/* no auto gene name\n\t1. no expression track\n\t2. no gene in view range\n\t3. view range beyond limit\n\t*/\n\n\tif (tk.gecfg) {\n\t\t// indeed has expression track\n\t\t// here should show button for querying gene\n\n\t\tconst g = tk.cnvrightg\n\n\t\tg.append('text')\n\t\t\t.attr('class', 'sja_clbtext2')\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('font-size', 14)\n\t\t\t.text('ADD GENE')\n\t\t\t.on('click', event => {\n\t\t\t\tfindgene4fix_searchui(tk.tkconfigtip.clear().d, tk, block)\n\t\t\t\ttk.tkconfigtip.showunder(event.target)\n\t\t\t})\n\n\t\tif (tk.expressionrangelimit) {\n\t\t\t// too big to do it\n\t\t\tconst h = 15\n\t\t\tlet y = 20\n\t\t\tg.append('text').text('Zoom in').attr('y', y).attr('font-size', 12)\n\t\t\ty += h\n\t\t\tg.append('text').text('under').attr('y', y).attr('font-size', 12)\n\t\t\ty += h\n\t\t\tg.append('text').text(common.bplen(tk.expressionrangelimit)).attr('y', y).attr('font-size', 12)\n\t\t\ty += h\n\t\t\tg.append('text').text('to show').attr('y', y).attr('font-size', 12)\n\t\t\ty += h\n\t\t\tg.append('text').text('gene exp').attr('y', y).attr('font-size', 12)\n\t\t\t/*\n\t\t\ty+=h\n\t\t\tg.append('text').text('automatically').attr('y',y).attr('font-size',12)\n\t\t\t*/\n\t\t}\n\n\t\treturn expbarwidth + xspace\n\t}\n\n\t// no expression track, won't draw column\n\treturn 0\n}\n\nfunction addcolumn_fixedgene(fixedgene, tk, block, column_xoff) {\n\t/*\n\t */\n\n\t// surely the coord of this fixed gene is not in cache\n\tif (!tk.gene2coord) tk.gene2coord = {}\n\ttk.gene2coord[fixedgene.gene] = {\n\t\tchr: fixedgene.chr,\n\t\tstart: fixedgene.start,\n\t\tstop: fixedgene.stop\n\t}\n\n\t// TODO enable column-specific width config\n\n\t// hardcoded bar width for expression rank\n\tconst expbarwidth = 80\n\t// hardcoded bar width for numeric attribute\n\tconst numattrbarwidth = 80\n\tconst xspace = 15\n\n\t// axis label\n\tconst axispad = 0\n\tconst labelpad = 3\n\tconst ticksize = 5\n\tconst fontsize = 12\n\n\tlet minvalue = 0,\n\t\tmaxvalue = 100 // still rank\n\n\tfor (const g of tk.samplegroups) {\n\t\tlet y = g.y\n\n\t\tfor (const s of g.samples) {\n\t\t\tconst row = tk.cnvrightg.append('g').attr('transform', 'translate(' + column_xoff + ',' + y + ')')\n\n\t\t\tconst v = fixedgene.sample2rank[s.samplename]\n\t\t\tif (v) {\n\t\t\t\tconst bar = row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', expressionstat.ase_color(v, tk.gecfg)) // bar color set by ase status\n\t\t\t\t\t.attr('width', (expbarwidth * v.rank) / maxvalue)\n\t\t\t\t\t.attr('height', s.height)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\n\t\t\t\tif (tk.isfull && v.estat) {\n\t\t\t\t\t// only show dots for outlier status in full, not dense\n\t\t\t\t\tif (v.estat.outlier) {\n\t\t\t\t\t\trow\n\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t.attr('cx', expbarwidth)\n\t\t\t\t\t\t\t.attr('cy', s.height / 2)\n\t\t\t\t\t\t\t.attr('r', s.height / 2)\n\t\t\t\t\t\t\t.attr('fill', tk.gecfg.outlier.color_outlier)\n\t\t\t\t\t} else if (v.estat.outlier_asehigh) {\n\t\t\t\t\t\trow\n\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t.attr('cx', expbarwidth)\n\t\t\t\t\t\t\t.attr('cy', s.height / 2)\n\t\t\t\t\t\t\t.attr('r', s.height / 2)\n\t\t\t\t\t\t\t.attr('fill', tk.gecfg.outlier.color_outlier_asehigh)\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tconst cover = row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', coverbarcolor_silent)\n\t\t\t\t\t.attr('fill-opacity', 0.1)\n\t\t\t\t\t.attr('width', expbarwidth)\n\t\t\t\t\t.attr('height', s.height)\n\n\t\t\t\tif (tk.isfull) {\n\t\t\t\t\ts.columnbars.push(cover)\n\t\t\t\t}\n\n\t\t\t\tcover\n\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\ttk.tktip.clear()\n\n\t\t\t\t\t\tconst lst = [{ k: 'Sample', v: s.samplename }]\n\t\t\t\t\t\tmay_add_sampleannotation(s.samplename, tk, lst)\n\n\t\t\t\t\t\tlst.push({\n\t\t\t\t\t\t\tk: fixedgene.gene + ' rank',\n\t\t\t\t\t\t\tv: client.ranksays(v.rank)\n\t\t\t\t\t\t})\n\t\t\t\t\t\tlst.push({\n\t\t\t\t\t\t\tk: fixedgene.gene + ' ' + tk.gecfg.datatype,\n\t\t\t\t\t\t\tv: v.value\n\t\t\t\t\t\t})\n\n\t\t\t\t\t\tconst table = client.make_table_2col(tk.tktip.d, lst)\n\n\t\t\t\t\t\texpressionstat.showsingleitem_table(v, tk.gecfg, table)\n\n\t\t\t\t\t\ttk.tktip.show(event.clientX, event.clientY)\n\n\t\t\t\t\t\tmulti_sample_addhighlight(s)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(s)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tmulti_show_geneboxplot({\n\t\t\t\t\t\t\tgene: fixedgene.gene,\n\t\t\t\t\t\t\tsamplename: s.samplename,\n\t\t\t\t\t\t\tvalue: v.value,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\n\t\t\t// done this sample\n\t\t\ty += s.height + tk.rowspace\n\t\t}\n\t\t// done this group\n\t}\n\n\tconst headg = tk.cnvrightg.append('g').attr('transform', 'translate(' + column_xoff + ',-' + axispad + ')')\n\n\tclient.axisstyle({\n\t\taxis: headg.append('g').call(\n\t\t\taxisTop()\n\t\t\t\t.scale(scaleLinear().domain([minvalue, maxvalue]).range([0, expbarwidth]))\n\t\t\t\t.tickValues([minvalue, maxvalue])\n\t\t\t\t.tickSize(ticksize)\n\t\t),\n\t\tfontsize: fontsize,\n\t\tshowline: 1\n\t})\n\n\t// special looking header compared to auto genes\n\n\theadg\n\t\t.append('text')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('x', expbarwidth / 2)\n\t\t.attr('y', -(fontsize + labelpad + ticksize + axispad))\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', fontsize)\n\t\t.attr('fill', 'black')\n\t\t.attr('class', 'sja_clbtext2')\n\t\t.text(fixedgene.gene + ' rank')\n\t\t.on('click', event => {\n\t\t\tgenebarconfig_fixed(fixedgene, tk, block)\n\t\t\ttk.tkconfigtip.showunder(event.target)\n\t\t})\n\n\treturn expbarwidth + xspace\n}\n\nfunction addcolumn_attr(attr, tk, block, column_xoff) {\n\t// TODO enable column-specific width config\n\n\t// hardcoded bar width for expression rank\n\tconst expbarwidth = 80\n\t// hardcoded bar width for numeric attribute\n\tconst numattrbarwidth = 80\n\tconst xspace = 15\n\n\t// axis label\n\tconst axispad = 0\n\tconst labelpad = 3\n\tconst ticksize = 5\n\tconst fontsize = 12\n\n\tfor (const g of tk.samplegroups) {\n\t\tlet y = g.y\n\n\t\tfor (const s of g.samples) {\n\t\t\tconst row = tk.cnvrightg.append('g').attr('transform', 'translate(' + column_xoff + ',' + y + ')')\n\n\t\t\t// TODO support categorical attr and detect type\n\n\t\t\tconst v0 = tk.sampleAttribute.samples[s.samplename]\n\t\t\tif (v0) {\n\t\t\t\tconst v = v0[attr.key]\n\t\t\t\tif (!Number.isNaN(v)) {\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('x', 0)\n\t\t\t\t\t\t.attr('width', Math.max(1, (numattrbarwidth * (v - attr.min)) / (attr.max - attr.min)))\n\t\t\t\t\t\t.attr('height', s.height)\n\t\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('x', 0)\n\t\t\t\t\t\t.attr('width', numattrbarwidth)\n\t\t\t\t\t\t.attr('height', s.height)\n\t\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t\t\t\t.attr('fill-opacity', 0.1)\n\t\t\t\t\tconst cover = row\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('fill', coverbarcolor_silent)\n\t\t\t\t\t\t.attr('fill-opacity', 0.1)\n\t\t\t\t\t\t.attr('width', numattrbarwidth)\n\t\t\t\t\t\t.attr('height', s.height)\n\n\t\t\t\t\ts.columnbars.push(cover)\n\n\t\t\t\t\tcover\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\ttk.tktip.clear()\n\n\t\t\t\t\t\t\tconst lst = [{ k: 'Sample', v: s.samplename }]\n\t\t\t\t\t\t\tmay_add_sampleannotation(s.samplename, tk, lst)\n\t\t\t\t\t\t\tclient.make_table_2col(tk.tktip.d, lst)\n\n\t\t\t\t\t\t\ttk.tktip.show(event.clientX, event.clientY)\n\n\t\t\t\t\t\t\tmulti_sample_addhighlight(s)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\t\tmulti_sample_removehighlight(s)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// done this sample\n\t\t\ty += s.height + tk.rowspace\n\t\t}\n\n\t\t// done this group\n\t}\n\n\tconst headg = tk.cnvrightg.append('g').attr('transform', 'translate(' + column_xoff + ',-' + axispad + ')')\n\n\t// if is numeric type\n\tclient.axisstyle({\n\t\taxis: headg\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(0,0)')\n\t\t\t.call(\n\t\t\t\taxisTop()\n\t\t\t\t\t.scale(scaleLinear().domain([attr.min, attr.max]).range([0, numattrbarwidth]))\n\t\t\t\t\t.ticks(3)\n\t\t\t),\n\t\tfontsize: fontsize,\n\t\tshowline: 1\n\t})\n\n\tconst text = headg\n\t\t.append('text')\n\t\t.attr('x', numattrbarwidth / 2)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('y', -(fontsize + labelpad + ticksize + axispad))\n\t\t.attr('font-family', client.font)\n\t\t.attr('font-size', fontsize)\n\t\t.text(attr.label)\n\n\t// TODO click for menu\n\n\treturn expbarwidth + xspace\n}\n\nfunction genebarconfig_auto(usegene, genes, tk, block) {\n\t/*\n\tfor auto gene\n\tusegene: str\n\tgenes:\n\t*/\n\n\ttk.tkconfigtip.clear()\n\n\tconst holder = tk.tkconfigtip.d\n\t/*\n\tcreatebutton_addfeature({\n\t\tm: {\n\t\t\tdt: common.dtgeneexpression,\n\t\t\tgenename: usegene,\n\t\t},\n\t\tholder: holder.append('div').style('margin-bottom','10px'),\n\t\ttk: tk,\n\t\tblock: block\n\t})\n\t*/\n\n\tfindgene4fix_searchui(holder, tk, block)\n\n\tif (genes.size > 1) {\n\t\t// more than one gene\n\t\tconst scrollholder = holder.append('div').style('margin-bottom', '15px')\n\t\tif (genes.size > 8) {\n\t\t\tscrollholder\n\t\t\t\t.style('height', '200px')\n\t\t\t\t.style('padding', '15px')\n\t\t\t\t.style('overflow-y', 'scroll')\n\t\t\t\t.style('resize', 'vertical')\n\t\t}\n\t\tconst id0 = Math.random().toString()\n\t\tfor (const gene of genes) {\n\t\t\tconst row = scrollholder.append('div')\n\t\t\tconst id = Math.random().toString()\n\t\t\tconst r = row\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'radio')\n\t\t\t\t.attr('id', id)\n\t\t\t\t.attr('name', id0)\n\t\t\t\t.on('change', () => {\n\t\t\t\t\ttk.tkconfigtip.hide()\n\t\t\t\t\ttk.selectedgene = gene\n\t\t\t\t\trender_multi_genebar(tk, block)\n\t\t\t\t})\n\t\t\tif (gene == usegene) r.attr('checked', 1)\n\t\t\trow\n\t\t\t\t.append('label')\n\t\t\t\t.attr('for', id)\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t.html('&nbsp;' + gene)\n\t\t}\n\t}\n\n\tmayadd_boxplotbutton(holder, usegene, tk, block)\n\n\tif (tk.mds) {\n\t\t/*\n\t\tauto gene should be in tk.gene2coord\n\t\t*/\n\t\tmayadd_survivaloption(\n\t\t\tholder,\n\t\t\t{\n\t\t\t\tgene: usegene,\n\t\t\t\tchr: tk.gene2coord[usegene].chr,\n\t\t\t\tstart: tk.gene2coord[usegene].start,\n\t\t\t\tstop: tk.gene2coord[usegene].stop\n\t\t\t},\n\t\t\ttk,\n\t\t\tblock\n\t\t)\n\t}\n\n\tmayadd_aseohe(holder, tk, block)\n\n\ttk.tkconfigtip.showunder(event.target)\n}\n\nexport function genebarconfig_fixed(fixedgene, tk, block) {\n\ttk.tkconfigtip.clear()\n\n\tmayadd_boxplotbutton(tk.tkconfigtip.d, fixedgene.gene, tk, block)\n\n\tmayadd_survivaloption(tk.tkconfigtip.d, fixedgene, tk, block)\n\n\ttk.tkconfigtip.d\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('Remove')\n\t\t.on('click', () => {\n\t\t\ttk.tkconfigtip.hide()\n\n\t\t\tconst idx = tk.gecfg.fixed.findIndex(i => i.gene == fixedgene.gene)\n\t\t\tif (idx == -1) {\n\t\t\t\t/*\n\t\t\t\tthis gene is not found as a fixed gene\n\t\t\t\tremove function should not do anything\n\t\t\t\tthis because fixed gene config is hijacked by cases\n\t\t\t\tsuch as when there's no mutation data for a gene in view range\n\t\t\t\tstill allows to show this menu for that gene\n\t\t\t\t*/\n\t\t\t\treturn\n\t\t\t}\n\t\t\ttk.gecfg.fixed.splice(idx, 1)\n\t\t\trender_multi_genebar(tk, block)\n\t\t})\n}\n\nfunction mayadd_aseohe(holder, tk, block) {\n\tif (!tk.gecfg || tk.gecfg.no_ase) return\n\tholder\n\t\t.append('div')\n\t\t.text('Customize ASE parameters')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.on('click', () => {\n\t\t\tholder.selectAll('*').remove()\n\t\t\texpressionstat.ui_config(holder, tk.gecfg, tk, () => {\n\t\t\t\ttk.tkconfigtip.hide()\n\t\t\t\tmulti_expressionstatus_ase_outlier(tk)\n\t\t\t\trender_multi_genebar(tk, block)\n\t\t\t})\n\t\t})\n}\n\nfunction mayadd_survivaloption(holder, gene, tk, block) {\n\tif (!tk.mds || !tk.mds.survivalplot) return\n\tholder\n\t\t.append('div')\n\t\t.text('Survival plot by ' + gene.gene + ' ' + tk.gecfg.datatype)\n\t\t.attr('class', 'sja_menuoption')\n\t\t.on('click', () => {\n\t\t\ttk.tkconfigtip.hide()\n\n\t\t\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\t\tpane.header.text('Survival plot by ' + gene.gene + ' ' + tk.gecfg.datatype)\n\t\t\tconst arg = {\n\t\t\t\tgenome: block.genome,\n\t\t\t\tmds: tk.mds,\n\t\t\t\tplotlist: [\n\t\t\t\t\t{\n\t\t\t\t\t\trenderplot: 1,\n\t\t\t\t\t\tsamplerule: {\n\t\t\t\t\t\t\tset: {\n\t\t\t\t\t\t\t\tgeneexpression: 1,\n\t\t\t\t\t\t\t\tbymedian: 1,\n\t\t\t\t\t\t\t\tgene: gene.gene,\n\t\t\t\t\t\t\t\tchr: gene.chr,\n\t\t\t\t\t\t\t\tstart: gene.start,\n\t\t\t\t\t\t\t\tstop: gene.stop\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\n\t\t\timport('./mds.survivalplot').then(_ => {\n\t\t\t\t_.init(arg, pane.body, block.debugmode)\n\t\t\t})\n\t\t})\n}\n\n////////////// find a gene and use as fixed\n\nfunction findgene4fix_searchui(holder, tk, block) {\n\t// for auto gene column, show\n\tgene_searchbox({\n\t\tdiv: holder,\n\t\tgenome: block.genome.name,\n\t\ttip: tk.tip2,\n\t\tcallback: genename => {\n\t\t\tfindgene4fix(genename, tk, block)\n\t\t}\n\t})\n}\n\nasync function findgene4fix(name, tk, block, norender) {\n\ttk.tkconfigtip.clear()\n\n\tconst wait = tk.tkconfigtip.d.append('div').text('Searching for ' + name + ' ...')\n\n\ttry {\n\t\tconst data1 = await client.dofetch3('genelookup', { body: { genome: block.genome.name, input: name, deep: 1 } })\n\n\t\tif (data1.error) throw data1.error\n\t\tif (!data1.gmlst) throw '.gmlst[] missing'\n\n\t\t// simply use first gm for coordinate...\n\t\tconst gm = data1.gmlst[0]\n\n\t\twait.text('Loading ' + tk.gecfg.datatype + ' for ' + gm.name + ' ...')\n\n\t\tconst data2 = await findgene4fix_getsamplevalue(gm, tk, block)\n\n\t\tif (data2.error) throw data2.error\n\n\t\tconst fixedgene = {\n\t\t\tgene: name,\n\t\t\tchr: gm.chr,\n\t\t\tstart: gm.start,\n\t\t\tstop: gm.stop\n\t\t}\n\n\t\tif (!data2.sample2rank) throw '.sample2rank{} missing'\n\t\tfor (const sample in data2.sample2rank) {\n\t\t\texpressionstat.measure(data2.sample2rank[sample], tk.gecfg)\n\t\t}\n\t\tfixedgene.sample2rank = data2.sample2rank\n\n\t\ttk.gecfg.fixed.push(fixedgene)\n\n\t\ttk.tkconfigtip.hide()\n\n\t\tif (norender) {\n\t\t\t// upon init and add genes from custom param, won't render until exp data is loaded for each pending fixed gene then render just once\n\t\t} else {\n\t\t\trender_multi_genebar(tk, block)\n\t\t}\n\t} catch (err) {\n\t\tif (err.stack) console.log(err.stack)\n\t\twait.text('Error: ' + (err.message ? err.message : err))\n\t}\n}\n\nfunction findgene4fix_getsamplevalue(gm, tk, block) {\n\tconst arg = {\n\t\tgenome: block.genome.name,\n\t\tgetexpression4gene: {\n\t\t\tchr: gm.chr,\n\t\t\tstart: gm.start,\n\t\t\tstop: gm.stop,\n\t\t\tname: gm.name\n\t\t}\n\t}\n\n\tif (tk.iscustom) {\n\t\targ.iscustom = 1\n\t\tconst c = tk.checkexpressionrank\n\t\tif (c) {\n\t\t\targ.checkexpressionrank = {\n\t\t\t\tfile: c.file,\n\t\t\t\turl: c.url,\n\t\t\t\tindexURL: c.indexURL\n\t\t\t}\n\t\t}\n\n\t\tif (tk.checkvcf) {\n\t\t\targ.checkvcf = tk.checkvcf.stringifiedObj\n\t\t}\n\t} else {\n\t\targ.dslabel = tk.mds.label\n\t\targ.querykey = tk.querykey\n\t}\n\n\treturn client.dofetch('mdssvcnv', arg)\n}\n\nfunction genebar_printtooltip(genename, v, s, holder, tk) {\n\tconst lst = [{ k: 'Sample', v: s.samplename }]\n\tmay_add_sampleannotation(s.samplename, tk, lst)\n\n\tlst.push({\n\t\tk: genename + ' rank',\n\t\tv: client.ranksays(v.rank)\n\t})\n\tlst.push({\n\t\tk: genename + ' ' + tk.gecfg.datatype,\n\t\tv: v.value\n\t})\n\tconst table = client.make_table_2col(holder, lst)\n\texpressionstat.showsingleitem_table(v, tk.gecfg, table)\n}\n\nfunction mayadd_boxplotbutton(holder, usegene, tk, block) {\n\tholder\n\t\t.append('div')\n\t\t.text(usegene + ' ' + tk.gecfg.datatype + ' boxplot')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.on('click', () => {\n\t\t\ttk.tkconfigtip.hide()\n\t\t\tmulti_show_geneboxplot({\n\t\t\t\tgene: usegene,\n\t\t\t\ttk: tk,\n\t\t\t\tblock: block\n\t\t\t})\n\t\t})\n}\n", "import * as client from './client'\nimport { rgb as d3rgb } from 'd3-color'\nimport { axisTop, axisLeft, axisRight } from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\nimport * as common from '#shared/common.js'\nimport * as expressionstat from './block.mds.expressionstat'\nimport {\n\ttooltip_singleitem,\n\tclick_multi_singleitem,\n\ttooltip_multi_vcfdense,\n\tclick_multi_vcfdense,\n\ttooltip_multi_svdense,\n\tclick_multi_svdense,\n\ttooltip_samplegroup,\n\tclick_samplegroup_showtable,\n\tclick_samplegroup_showmenu,\n\tmay_add_sampleannotation,\n\tmay_allow_samplesearch\n} from './block.mds.svcnv.clickitem'\nimport { makeTk_legend, update_legend } from './block.mds.svcnv.legend'\nimport { render_singlesample } from './block.mds.svcnv.single'\nimport { createbutton_addfeature, may_show_samplematrix_button } from './block.mds.svcnv.samplematrix'\nimport { render_multi_genebar, genebarconfig_fixed } from './block.mds.svcnv.addcolumn'\nimport { vcfparsemeta } from '#shared/vcf.js'\n\n/*\nJUMP __multi __maketk __sm\n\nmakeTk\n\tapply_customization_oninit\nloadTk\n\tloadTk_do\n\t\taddLoadParameter\nmay_showgeneexp_nomutationdata\nrender_samplegroups\n\tprep_samplegroups\n\trender_multi_vcfdense\n\trender_multi_svdense\n\trender_multi_cnvloh\n\t\trender_multi_cnvloh_stackeachsample\n\t\t** focus_singlesample\nconfigPanel()\nmulti_sample_addhighlight\nmulti_sample_removehighlight\n\n\nmodes:\n\n\tdriven by svcnv file, sv-cnv-vcf-fpkm ranking\n\n\t\tmulti-sample:\n\t\t\tone row per sample\n\t\t\ttwo forms:\n\t\t\t\tdense\n\t\t\t\t\tsv breakpoint density in separate track\n\t\t\t\t\tcnv shown densily\n\t\t\t\tfull\n\t\t\t\t\tcnv & sv shown together at sample-level\n\n\t\tsampleset:\n\t\t\tcustom set of samples, in groups\n\n\t\tsingle-sample:\n\t\t\tshow cnv & sv data from a single sample\n\t\t\tindicated by tk.singlesample {name:\"samplename\"}\n\t\t\tspawn from sample group, mode won't mutate\n\t\t\tfpkm ranking shown as independent track\n\n\tase mode, driven by vcf file and supplemented by rna bam files\n\t\talways multi-sample\n\t\talways cohort\n\n\nsv/cnv/loh data mixed in same file, sv has _chr and _pos which are indexing fields, along with chrA/posA/chrB/posB\nfpkm data in one file, fpkm may contain Yu's results on ASE/outlier\n\ncustom vcf handling:\n\tmulti-sample\n\tsingle-sample\n\n!!!!!!!!!!!Task-specific temporary fixes!!!!!!!!!!!\nmaysortsamplesingroupbydt\n*/\n\nconst labyspace = 5\nexport const intrasvcolor = '#858585' // inter-chr sv color is defined on the fly\nconst cnvhighlightcolor = '#E8FFFF'\nexport const coverbarcolor_silent = '#222'\nexport const coverbarcolor_active = '#ED8600'\n\nconst minlabfontsize = 7\nconst minsvradius = 5\nconst svdensitynogroupcolor = '#aaa'\nconst leftlabelticksize = 5\n\nconst hardcode_cellline = 'CELLLINE'\nconst novalue_max_cnvloh = 0 // for max scale of log2ratio and segmean, if there is no cnv or loh data in view range\n\n// x space between label and box/circle\nexport const labelspace = 5 // when label is shown outside of box, the space between them\n\nconst stackheightscale = scaleLinear().domain([1, 3, 5, 10]).range([8, 4, 2, 1])\n\nexport function loadTk(tk, block) {\n\t/*\n\tworks for both multi- and single-sample modes\n\t*/\n\n\tblock.tkcloakon(tk)\n\tblock.block_setheight()\n\n\tif (tk.uninitialized) {\n\t\tmakeTk(tk, block)\n\t\tdelete tk.uninitialized\n\t}\n\n\tPromise.resolve()\n\t\t.then(() => {\n\t\t\treturn loadTk_mayinitiatecustomvcf(tk, block)\n\t\t})\n\t\t.then(() => {\n\t\t\t/*\n\t\tif error, throw error\n\t\tif no data, throw {nodata:1}\n\t\telse, set tk height and quiet\n\t\t*/\n\t\t\treturn loadTk_do(tk, block)\n\t\t})\n\t\t.catch(err => {\n\t\t\ttk.height_main = 50\n\n\t\t\tif (err.nodata) {\n\t\t\t\t/*\n\t\t\tcentral place to handle \"no data\", no mutation data in any sample\n\t\t\tfor both single/multi-sample\n\t\t\t*/\n\t\t\t\ttrackclear(tk)\n\t\t\t\t// remove old data so the legend can update properly\n\t\t\t\tdelete tk.data_vcf\n\t\t\t\tif (tk.singlesample) {\n\t\t\t\t\tdelete tk.data\n\t\t\t\t} else {\n\t\t\t\t\t// multi\n\t\t\t\t\tdelete tk._data\n\t\t\t\t\tdelete tk.samplegroups\n\t\t\t\t\tmay_showgeneexp_nomutationdata(tk, block)\n\t\t\t\t}\n\t\t\t\tupdate_legend(tk, block)\n\t\t\t\treturn { error: tk.name + ': no data in view range' }\n\t\t\t}\n\n\t\t\tif (err.stack) console.error(err.stack)\n\t\t\treturn { error: err.message }\n\t\t})\n\t\t.then(_final => {\n\t\t\tblock.tkcloakoff(tk, { error: _final.error })\n\t\t\tblock.block_setheight()\n\t\t\tblock.setllabel()\n\t\t})\n}\n\nfunction may_showgeneexp_nomutationdata(tk, block) {\n\t/*\n\tmulti-sample\n\tno mutation data in view range, thus no .samplegroup\n\tbut still may be genes with expression, as in .gene2coord\n\tneed to indicate them\n\t*/\n\tconst genenames = []\n\tif (tk.gene2coord) {\n\t\tfor (const gene in tk.gene2coord) genenames.push(gene)\n\t}\n\tif (genenames.length == 0) return\n\n\tif (!tk.gecfg) {\n\t\tconsole.error('but .gecfg is missing')\n\t\treturn\n\t}\n\n\t// must reset cnvrightg y pos since it will be shifted if there was data previously\n\ttk.cnvrightg.attr('transform', 'translate(0,' + (4 + tk.height_main / 2) + ')')\n\n\tconst text = tk.cnvrightg.append('text').attr('font-size', 12).attr('class', 'sja_clbtext2')\n\n\tif (genenames.length == 1) {\n\t\t/*\n\t\tjust one gene in view range\n\t\tpretend it to be fixed gene\n\t\tand show the menu option\n\t\t*/\n\n\t\ttext.text(genenames[0]).on('click', event => {\n\t\t\tconst c = tk.gene2coord[genenames[0]]\n\t\t\tgenebarconfig_fixed(\n\t\t\t\t{\n\t\t\t\t\tgene: genenames[0],\n\t\t\t\t\tchr: c.chr,\n\t\t\t\t\tstart: c.start,\n\t\t\t\t\tstop: c.stop\n\t\t\t\t},\n\t\t\t\ttk,\n\t\t\t\tblock\n\t\t\t)\n\t\t\ttk.tkconfigtip.showunder(event.target)\n\t\t})\n\t\treturn\n\t}\n\n\t/*\n\tmultiple genes in view range\n\tallow to select one gene and show menu like above\n\t*/\n\n\ttext.text('Select gene').on('click', () => {\n\t\ttk.tkconfigtip.clear().showunder(text.node())\n\t\tfor (const gene of genenames) {\n\t\t\ttk.tkconfigtip.d\n\t\t\t\t.append('div')\n\t\t\t\t.text(gene)\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst c = tk.gene2coord[gene]\n\t\t\t\t\tgenebarconfig_fixed(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tgene: gene,\n\t\t\t\t\t\t\tchr: c.chr,\n\t\t\t\t\t\t\tstart: c.start,\n\t\t\t\t\t\t\tstop: c.stop\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttk,\n\t\t\t\t\t\tblock\n\t\t\t\t\t)\n\t\t\t\t})\n\t\t}\n\t})\n}\n\nfunction loadTk_mayinitiatecustomvcf(tk, block) {\n\tif (!tk.iscustom) return\n\n\tif (tk.checkvcf && !tk.checkvcf.stringifiedObj) {\n\t\t// driven by svcnv file\n\t\t// load vcf meta keep on client for parsing vcf data\n\t\tconst arg = ['genome=' + block.genome.name]\n\t\tif (tk.checkvcf.file) {\n\t\t\targ.push('file=' + tk.checkvcf.file)\n\t\t} else {\n\t\t\targ.push('url=' + tk.checkvcf.url)\n\t\t\tif (tk.checkvcf.indexURL) arg.push('indexURL=' + tk.checkvcf.indexURL)\n\t\t}\n\t\treturn client.dofetch2('vcfheader?' + arg.join('&')).then(data => {\n\t\t\tif (!data) throw { message: 'server error!' }\n\t\t\tif (data.error) throw { message: data.error }\n\n\t\t\tconst [info, format, samples, errs] = vcfparsemeta(data.metastr.split('\\n'))\n\t\t\tif (errs) throw { message: 'Error parsing VCF meta lines: ' + errs.join('; ') }\n\t\t\ttk.checkvcf.info = info\n\t\t\ttk.checkvcf.format = format\n\t\t\ttk.checkvcf.samples = samples\n\t\t\ttk.checkvcf.nochr = data.nochr\n\t\t\ttk.checkvcf.stringifiedObj = JSON.stringify(tk.checkvcf)\n\t\t})\n\t}\n}\n\nfunction loadTk_do(tk, block) {\n\tconst par = {\n\t\t//jwt:block.jwt,\n\t\tgenome: block.genome.name,\n\t\trglst: block.tkarg_maygm(tk)\n\t}\n\n\tif (block.subpanels.length == tk.subpanels.length) {\n\t\t/*\n\t\tmust wait when subpanels are added to tk\n\t\tthis is only done when block finishes loading data for main tk\n\t\t*/\n\t\tfor (const [idx, r] of block.subpanels.entries()) {\n\t\t\tpar.rglst.push({\n\t\t\t\tchr: r.chr,\n\t\t\t\tstart: r.start,\n\t\t\t\tstop: r.stop,\n\t\t\t\twidth: r.width,\n\t\t\t\texonsf: r.exonsf,\n\t\t\t\tsubpanelidx: idx\n\t\t\t})\n\t\t}\n\t}\n\n\taddLoadParameter(par, tk)\n\n\treturn client.dofetch('/mdssvcnv', par).then(data => {\n\t\t// throw errors\n\n\t\tif (data.error) throw { message: data.error }\n\n\t\t/*\n\t\tmust keep the loaded \"raw\" data in _data_vcf, so it can later apply class filter without having to reload from server\n\t\ton serverside, the \"class\" won't be parsed out from csq, without gmmode/isoform info of the client\n\t\t*/\n\t\ttk._data_vcf = data.data_vcf\n\n\t\ttk.vcfrangelimit = data.vcfrangelimit // range too big\n\t\tvcfdata_prep(tk, block) // data for display is now in tk.data_vcf[]\n\n\t\tmay_map_vcf(tk, block)\n\n\t\tif (tk.singlesample) {\n\t\t\tif (!data.lst || data.lst.length == 0) {\n\t\t\t\t// no cnv/sv\n\t\t\t\tif (!tk.data_vcf || tk.data_vcf.length == 0) {\n\t\t\t\t\t// no vcf, nothing to show\n\t\t\t\t\tthrow { nodata: 1 }\n\t\t\t\t}\n\t\t\t}\n\t\t\ttk.data = data.lst\n\t\t} else {\n\t\t\t// multi-sample\n\n\t\t\t/*\n\t\t\tkeep gene expression info,\n\t\t\tso even if no sample with mutation in view range, still be able to indicate available of gene expression\n\t\t\t*/\n\t\t\ttk.gene2coord = data.gene2coord\n\t\t\ttk.expressionrangelimit = data.expressionrangelimit\n\n\t\t\t// now samplegroups contains samples with any data type (cnv, sv, vcf), no matter dense or full\n\t\t\tif (!data.samplegroups || data.samplegroups.length == 0) {\n\t\t\t\tthrow { nodata: 1 }\n\t\t\t}\n\t\t\ttk._data = data.samplegroups\n\n\t\t\tif (tk.sampleAttribute) {\n\t\t\t\tif (data.sampleannotation) {\n\t\t\t\t\ttk.sampleAttribute.samples = data.sampleannotation\n\t\t\t\t} else {\n\t\t\t\t\ttk.sampleAttribute.samples = {}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// preps common to both single and multi sample\n\t\tif (tk.legend_svchrcolor) {\n\t\t\ttk.legend_svchrcolor.interchrs.clear()\n\t\t\ttk.legend_svchrcolor.row.style('display', 'none')\n\t\t}\n\n\t\tif (tk.singlesample) {\n\t\t\trender_singlesample(tk, block)\n\t\t} else {\n\t\t\trender_samplegroups(tk, block)\n\t\t}\n\t\treturn {}\n\t})\n}\n\nexport function trackclear(tk) {\n\tif (tk.singlesample) {\n\t\ttk.waterfall.axisg.selectAll('*').remove()\n\t\ttk.waterfall.lab1.text('')\n\t\ttk.waterfall.lab2.text('')\n\t\ttk.waterfall.lab3.text('')\n\t\ttk.svvcf_g.selectAll('*').remove()\n\t\ttk.cnv_g.selectAll('*').remove()\n\t\tif (tk.cnvcolor.cnvlegend) tk.cnvcolor.cnvlegend.row.style('display', 'none')\n\t\tif (tk.cnvcolor.lohlegend) tk.cnvcolor.lohlegend.row.style('display', 'none')\n\t\treturn\n\t}\n\ttk.cnvleftg.selectAll('*').remove()\n\ttk.vcfdensitylabelg.selectAll('*').remove()\n\ttk.vcfdensityg.selectAll('*').remove()\n\ttk.svdensitylabelg.selectAll('*').remove()\n\ttk.svdensityg.selectAll('*').remove()\n\ttk.cnvmidg.selectAll('*').remove()\n\ttk.cnvrightg.selectAll('*').remove()\n\ttk.config_handle.transition().attr('text-anchor', 'start').attr('x', 0)\n}\n\nfunction addLoadParameter(par, tk) {\n\tif (tk.iscustom) {\n\t\tpar.iscustom = 1\n\t\tpar.file = tk.file\n\t\tpar.url = tk.url\n\t\tpar.indexURL = tk.indexURL\n\n\t\tif (tk.checkexpressionrank) {\n\t\t\tpar.checkexpressionrank = {}\n\t\t\tfor (const k in tk.checkexpressionrank) {\n\t\t\t\tpar.checkexpressionrank[k] = tk.checkexpressionrank[k]\n\t\t\t}\n\t\t}\n\n\t\tif (tk.checkvcf) {\n\t\t\tpar.checkvcf = tk.checkvcf.stringifiedObj\n\t\t}\n\t} else {\n\t\tpar.dslabel = tk.mds.label\n\t\tpar.querykey = tk.querykey\n\t}\n\n\tif (tk.getallsamples) {\n\t\tpar.getallsamples = true\n\t}\n\n\t// cnv\n\tif (tk.sampleset) par.sampleset = tk.sampleset\n\tif (tk.valueCutoff) par.valueCutoff = tk.valueCutoff\n\tif (Number.isInteger(tk.bplengthUpperLimit)) par.bplengthUpperLimit = tk.bplengthUpperLimit\n\tif (tk.showonlycnvwithsv) par.showonlycnvwithsv = 1\n\tpar.hide_cnvgain = tk.hide_cnvgain\n\tpar.hide_cnvloss = tk.hide_cnvloss\n\n\t// loh\n\tif (tk.segmeanValueCutoff) par.segmeanValueCutoff = tk.segmeanValueCutoff\n\tif (Number.isInteger(tk.lohLengthUpperLimit)) par.lohLengthUpperLimit = tk.lohLengthUpperLimit\n\n\tif (tk.singlesample) {\n\t\t// single sample\n\t\tpar.singlesample = tk.singlesample.name\n\t} else {\n\t\t// multi sample\n\t\t// here are things not to be applied to single sample\n\t\tif (tk.sampleAttribute) {\n\t\t\t// mutation attribute applicable to all data types\n\t\t\tconst key2value = {}\n\t\t\tlet hashidden = false\n\t\t\tfor (const key in tk.sampleAttribute.attributes) {\n\t\t\t\tconst attr = tk.sampleAttribute.attributes[key]\n\t\t\t\tif (attr.hiddenvalues && attr.hiddenvalues.size) {\n\t\t\t\t\tkey2value[key] = [...attr.hiddenvalues]\n\t\t\t\t\thashidden = true\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (hashidden) {\n\t\t\t\tpar.hiddensampleattr = key2value\n\t\t\t}\n\t\t}\n\t}\n\n\tif (tk.mutationAttribute) {\n\t\t// mutation attribute applicable to all data types\n\t\tconst key2value = {}\n\t\tlet hashidden = false\n\t\tfor (const key in tk.mutationAttribute.attributes) {\n\t\t\tconst attr = tk.mutationAttribute.attributes[key]\n\t\t\tif (attr.hiddenvalues && attr.hiddenvalues.size) {\n\t\t\t\tkey2value[key] = [...attr.hiddenvalues]\n\t\t\t\thashidden = true\n\t\t\t}\n\t\t}\n\t\tif (hashidden) {\n\t\t\tpar.hiddenmattr = key2value\n\t\t}\n\t}\n\n\tif (tk.alleleAttribute) {\n\t\t// mutation attribute applicable to all data types\n\t\tconst key2value = {}\n\t\tlet hashidden = false\n\t\tfor (const key in tk.alleleAttribute.attributes) {\n\t\t\tconst attr = tk.alleleAttribute.attributes[key]\n\t\t\tif (attr.disable) continue\n\t\t\tif (attr.isnumeric) {\n\t\t\t\tif (Number.isFinite(attr.cutoffvalue)) {\n\t\t\t\t\tkey2value[key] = {\n\t\t\t\t\t\tcutoffvalue: attr.cutoffvalue,\n\t\t\t\t\t\tkeeplowerthan: attr.keeplowerthan\n\t\t\t\t\t}\n\t\t\t\t\thashidden = true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// categorical\n\t\t\t\tif (attr.hiddenvalues && attr.hiddenvalues.size) {\n\t\t\t\t\tkey2value[key] = [...attr.hiddenvalues]\n\t\t\t\t\thashidden = true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (hashidden) {\n\t\t\tpar.filteralleleattr = key2value\n\t\t}\n\t}\n\tif (tk.locusAttribute) {\n\t\t// mutation attribute applicable to all data types\n\t\tconst key2value = {}\n\t\tlet hashidden = false\n\t\tfor (const key in tk.locusAttribute.attributes) {\n\t\t\tconst attr = tk.locusAttribute.attributes[key]\n\t\t\tif (attr.disable) continue\n\t\t\tif (attr.isnumeric) {\n\t\t\t\tif (Number.isFinite(attr.cutoffvalue)) {\n\t\t\t\t\tkey2value[key] = {\n\t\t\t\t\t\tcutoffvalue: attr.cutoffvalue,\n\t\t\t\t\t\tkeeplowerthan: attr.keeplowerthan\n\t\t\t\t\t}\n\t\t\t\t\thashidden = true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// categorical\n\t\t\t\tif (attr.hiddenvalues && attr.hiddenvalues.size) {\n\t\t\t\t\tkey2value[key] = [...attr.hiddenvalues]\n\t\t\t\t\thashidden = true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (hashidden) {\n\t\t\tpar.filterlocusattr = key2value\n\t\t}\n\t}\n\n\t{\n\t\t// from mclass.hidden, only dt are used for filtering, vcf class currently filter on client\n\t\tconst hiddendt = []\n\t\tfor (const k of tk.legend_mclass.hiddenvalues) {\n\t\t\tif (Number.isInteger(k)) hiddendt.push(k)\n\t\t}\n\t\tif (hiddendt.length) {\n\t\t\tpar.hiddendt = hiddendt\n\t\t}\n\t}\n}\n\n/////////////////////// __multi\n\nfunction render_samplegroups(tk, block) {\n\t/*\n\tmulti-sample\n\tdense or full\n\n\ta sample should have 1 or more of cnv/sv/loh/itd/snvindel, cannot be empty\n\tsv that are fully in view range will be shown as 2 circles\n\tone sample per row, equal row height\n\tfor dense/full\n\n\tdraw stack items first (cnv/loh/itd); then sv; then vcf\n\n\tin dense mode, sv won't involve in tk.samplegroups\n\tneed sv in separate list for dense plot\n\t*/\n\n\ttrackclear(tk)\n\n\t// track labels will include both bold label and version label\n\tlet labelheight = block.labelfontsize\n\tif (tk.versionlabel) labelheight += block.labelfontsize\n\n\tconst [groups, svlst4dense] = prep_samplegroups(tk, block)\n\n\ttk.samplegroups = groups\n\n\t/*\n\tif dense, draw vcf density and return height; otherwise variants are dispersed among samplegroup and won't affect tk height\n\twhen view range is too big, won't draw but show a message\n\twhich will take vertical space, the height of which will also be returned\n\t*/\n\tconst vcfdensityheight = render_multi_vcfdense(tk, block)\n\n\t// likewise for sv\n\tconst svdensityheight = render_multi_svdense(svlst4dense, tk, block)\n\n\t// for each sample group, draw cnv bars, will draw sv and vcf if in full mode\n\tconst cnvheight = render_multi_cnvloh(tk, block)\n\n\tmulti_expressionstatus_ase_outlier(tk)\n\n\tconst genebaraxisheight = render_multi_genebar(tk, block)\n\n\t// padding between sv/vcf, if both drawn\n\tconst vcfsvpad = vcfdensityheight && svdensityheight ? 3 : 0\n\n\t// track top blank height\n\tlet hpad = Math.max(labelheight, vcfdensityheight + svdensityheight + vcfsvpad, genebaraxisheight)\n\n\t// may increase hpad: don't allow tk label to overlap with density plot label\n\tif (vcfdensityheight) {\n\t\thpad += Math.max(0, labelheight + 8 - (hpad - svdensityheight - vcfsvpad - vcfdensityheight / 2))\n\t} else if (svdensityheight) {\n\t\thpad += Math.max(0, labelheight + 8 - (hpad - svdensityheight / 2))\n\t}\n\n\t// adjust config handle position by top blank height\n\tif (genebaraxisheight == 0 || hpad > genebaraxisheight + 3 + block.labelfontsize) {\n\t\t// enough space for label to be in usual place\n\t\ttk.config_handle.transition().attr('text-anchor', 'start').attr('x', 0)\n\t} else {\n\t\ttk.config_handle.transition().attr('text-anchor', 'end').attr('x', -block.rpad)\n\t}\n\n\ttk.cnvleftg.transition().attr('transform', 'translate(0,' + hpad + ')')\n\ttk.cnvmidg.transition().attr('transform', 'translate(0,' + hpad + ')')\n\ttk.vcfdensityg.transition().attr('transform', 'translate(0,' + (hpad - svdensityheight - vcfsvpad) + ')')\n\ttk.svdensityg.transition().attr('transform', 'translate(0,' + hpad + ')')\n\ttk.cnvrightg.transition().attr('transform', 'translate(0,' + hpad + ')')\n\n\t{\n\t\t// if showing density plots, put labels on left of density track\n\t\tconst color = '#858585'\n\t\tif (vcfdensityheight && tk.data_vcf) {\n\t\t\tlet c_snvindel = 0\n\n\t\t\tfor (const m of tk.data_vcf) {\n\t\t\t\tif (m.x == undefined) continue\n\t\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\t\tc_snvindel += m.sampledata.length\n\t\t\t\t} else {\n\t\t\t\t\tconsole.error('unknown dt from data_vcf')\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tconst phrases = []\n\t\t\tif (c_snvindel) phrases.push(c_snvindel + ' SNV/indel' + (c_snvindel > 1 ? 's' : ''))\n\n\t\t\ttk.vcfdensitylabelg\n\t\t\t\t.attr('transform', 'translate(0,' + (hpad - vcfdensityheight - vcfsvpad - svdensityheight) + ')')\n\t\t\t\t.append('text')\n\t\t\t\t.text(phrases.join(', '))\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('x', block.tkleftlabel_xshift)\n\t\t\t\t.attr('y', vcfdensityheight / 2)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('font-size', Math.min(block.labelfontsize, vcfdensityheight) - 1)\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.each(function () {\n\t\t\t\t\ttk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width)\n\t\t\t\t})\n\n\t\t\ttk.vcfdensitylabelg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('y2', vcfdensityheight)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\ttk.vcfdensitylabelg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t.attr('x1', -leftlabelticksize)\n\t\t\t\t.attr('y1', vcfdensityheight / 2)\n\t\t\t\t.attr('y2', vcfdensityheight / 2)\n\t\t\ttk.vcfdensitylabelg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('stroke-width', 1)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t.attr('stroke-dasharray', '1,3')\n\t\t\t\t.attr('x2', block.width)\n\t\t\t\t.attr('y1', vcfdensityheight)\n\t\t\t\t.attr('y2', vcfdensityheight)\n\t\t}\n\n\t\tif (svdensityheight) {\n\t\t\ttk.svdensitylabelg\n\t\t\t\t.attr('transform', 'translate(0,' + (hpad - svdensityheight) + ')')\n\t\t\t\t.append('text')\n\t\t\t\t.text(svlst4dense.length + ' SV breakpoint' + (svlst4dense.length > 1 ? 's' : ''))\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('x', block.tkleftlabel_xshift)\n\t\t\t\t.attr('y', svdensityheight / 2)\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('font-size', Math.min(block.labelfontsize, svdensityheight) - 1)\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.each(function () {\n\t\t\t\t\ttk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width)\n\t\t\t\t})\n\t\t\ttk.svdensitylabelg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('y2', svdensityheight)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\ttk.svdensitylabelg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t.attr('x1', -leftlabelticksize)\n\t\t\t\t.attr('y1', svdensityheight / 2)\n\t\t\t\t.attr('y2', svdensityheight / 2)\n\t\t\ttk.svdensitylabelg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('stroke-width', 1)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t.attr('stroke-dasharray', '1,3')\n\t\t\t\t.attr('x2', block.width)\n\t\t\t\t.attr('y1', svdensityheight)\n\t\t\t\t.attr('y2', svdensityheight)\n\t\t}\n\t}\n\n\ttk.height_main = tk.toppad + hpad + cnvheight + tk.bottompad\n\n\tupdate_legend(tk, block)\n}\n\nfunction render_multi_vcfdense(tk, block) {\n\t/*\n\tmulti-sample\n\tnative/custom\n\tdense\n\t*/\n\tif (tk.vcfrangelimit) {\n\t\ttk.vcfdensityg\n\t\t\t.append('text')\n\t\t\t.text('Zoom in under ' + common.bplen(tk.vcfrangelimit) + ' to show SNV/indel density')\n\t\t\t.attr('font-size', block.labelfontsize)\n\t\t\t.attr('font-family', client.font)\n\t\treturn block.labelfontsize\n\t}\n\tif (!tk.isdense) return 0\n\n\tif (!tk.data_vcf || tk.data_vcf.length == 0) return 0\n\n\tconst bins = render_multi_vcfdense_2bins(tk, block)\n\n\t// group m in each bin by class\n\tfor (const b of bins) {\n\t\tif (b.lst.length == 0) continue\n\t\tconst name2group = new Map()\n\t\t// k: mclass key\n\t\t// v: mlst[]\n\n\t\tfor (const m of b.lst) {\n\t\t\tif (!name2group.has(m.class)) {\n\t\t\t\tname2group.set(m.class, [])\n\t\t\t}\n\t\t\tname2group.get(m.class).push(m)\n\t\t}\n\n\t\tconst lst = []\n\t\tfor (const [classname, mlst] of name2group) {\n\t\t\tlet samplecount = 0 // total # of samples in this group\n\t\t\tfor (const m of mlst) {\n\t\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\t\tsamplecount += m.sampledata.length\n\t\t\t\t} else {\n\t\t\t\t\tconsole.error('unknown dt')\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tlst.push({\n\t\t\t\tname: common.mclass[classname].label,\n\t\t\t\titems: mlst,\n\t\t\t\tcolor: common.mclass[classname].color,\n\t\t\t\tsamplecount: samplecount\n\t\t\t})\n\t\t}\n\t\tlst.sort((i, j) => j.samplecount - i.samplecount)\n\t\tb.groups = lst\n\t}\n\n\tlet maxcount = 0 // per group\n\tfor (const b of bins) {\n\t\tif (!b.groups) continue\n\t\tfor (const g of b.groups) {\n\t\t\tmaxcount = Math.max(maxcount, g.samplecount)\n\t\t}\n\t}\n\n\tlet maxheight = 0 // of all bins\n\t{\n\t\tconst radius = 4\n\t\tlet mrd = 0 // max radius\n\t\tconst w = Math.pow(radius, 2) * Math.PI // unit area\n\t\tif (maxcount <= 3) {\n\t\t\tmrd = w * maxcount * 0.9\n\t\t} else if (maxcount <= 10) {\n\t\t\tmrd = w * 5\n\t\t} else if (maxcount <= 100) {\n\t\t\tmrd = w * 7\n\t\t} else {\n\t\t\tmrd = w * 10\n\t\t}\n\t\tconst sf_discradius = scaleLinear()\n\t\t\t.domain([1, maxcount * 0.5 + 0.1, maxcount * 0.6 + 0.1, maxcount * 0.7 + 0.1, maxcount * 0.8 + 0.1, maxcount])\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\n\t\t// note: must count # of samples in each mutation for radius & offset\n\t\tfor (const bin of bins) {\n\t\t\tif (!bin.groups) continue\n\n\t\t\tfor (const g of bin.groups) {\n\t\t\t\t// group dot radius determined by total number of samples in each mutation, not # of mutations\n\n\t\t\t\tg.radius = Math.sqrt(sf_discradius(g.samplecount) / Math.PI)\n\t\t\t}\n\n\t\t\t// offset of a bin determined by the total number of samples\n\t\t\t// count again for the bin\n\t\t\tconst totalnum = bin.groups.reduce((i, j) => j.samplecount + i, 0)\n\n\t\t\tbin.offset = Math.sqrt(sf_discradius(totalnum) / Math.PI)\n\n\t\t\tconst sumheight = bin.groups.reduce((i, j) => i + j.radius * 2, 0)\n\n\t\t\tmaxheight = Math.max(maxheight, bin.offset + sumheight)\n\t\t}\n\t}\n\n\tfor (const b of bins) {\n\t\tif (!b.groups) continue\n\n\t\tconst g = tk.vcfdensityg.append('g').attr('transform', 'translate(' + b.x + ',0)')\n\n\t\tlet y = b.offset\n\n\t\tfor (const grp of b.groups) {\n\t\t\t/*\n\t\t\tone dot for each group\n\n\t\t\t.name\n\t\t\t.items[]\n\t\t\t.radius\n\t\t\t.color\n\t\t\t.samplecount\n\t\t\t*/\n\n\t\t\ty += grp.radius\n\t\t\tg.append('circle').attr('cy', -y).attr('r', grp.radius).attr('fill', grp.color).attr('stroke', 'white')\n\n\t\t\tif (grp.radius >= 8) {\n\t\t\t\t// big enough dot, show # of items\n\t\t\t\tconst s = grp.radius * 1.5\n\t\t\t\tconst text = grp.samplecount.toString()\n\t\t\t\tconst fontsize = Math.min(s / (text.length * client.textlensf), s)\n\n\t\t\t\tg.append('text')\n\t\t\t\t\t.text(text)\n\t\t\t\t\t.attr('y', -y)\n\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', 'white')\n\t\t\t}\n\n\t\t\tg.append('circle')\n\t\t\t\t.attr('cy', -y)\n\t\t\t\t.attr('r', grp.radius)\n\t\t\t\t.attr('fill', 'white')\n\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t.attr('stroke', grp.color)\n\t\t\t\t.attr('stroke-opacity', 0)\n\t\t\t\t.attr('class', 'sja_aa_disckick')\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\ttooltip_multi_vcfdense(grp, tk, block)\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t})\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tclick_multi_vcfdense(grp, tk, block)\n\t\t\t\t})\n\t\t\ty += grp.radius\n\t\t}\n\t\tg.append('line').attr('y2', -b.offset).attr('stroke', b.groups[0].color)\n\t}\n\treturn maxheight\n}\n\nfunction render_multi_vcfdense_2bins(tk, block) {\n\tif (block.exonsf >= 3) {\n\t\t// group by basepairs\n\t\tconst bp2lst = new Map()\n\t\tfor (const m of tk.data_vcf) {\n\t\t\tif (m.x == undefined) continue\n\t\t\tif (!bp2lst.has(m.pos)) {\n\t\t\t\tbp2lst.set(m.pos, {\n\t\t\t\t\tx: m.x,\n\t\t\t\t\tlst: []\n\t\t\t\t})\n\t\t\t}\n\t\t\tbp2lst.get(m.pos).lst.push(m)\n\t\t}\n\t\tconst bins = []\n\t\tfor (const b of bp2lst.values()) {\n\t\t\tbins.push(b)\n\t\t}\n\t\treturn bins\n\t}\n\n\t// fixed pixel width\n\tconst binw = 10 // pixel\n\tconst bins = []\n\tlet x = 0\n\twhile (x < block.width) {\n\t\tbins.push({\n\t\t\tx1: x,\n\t\t\tx2: x + binw,\n\t\t\tx: x + binw / 2,\n\t\t\tlst: []\n\t\t})\n\t\tx += binw\n\t}\n\tx = block.width\n\tfor (const p of block.subpanels) {\n\t\tx += p.leftpad\n\t\tlet b = 0\n\t\twhile (b < p.width) {\n\t\t\tbins.push({\n\t\t\t\tx1: x + b,\n\t\t\t\tx2: x + b + binw,\n\t\t\t\tlst: []\n\t\t\t})\n\t\t\tb += binw\n\t\t}\n\t\tx += p.width\n\t}\n\n\t// m to bins\n\tfor (const m of tk.data_vcf) {\n\t\tif (m.x == undefined) {\n\t\t\t// unmapped\n\t\t\tcontinue\n\t\t}\n\t\tfor (const b of bins) {\n\t\t\tif (b.x1 <= m.x && b.x2 >= m.x) {\n\t\t\t\tb.lst.push(m)\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\treturn bins\n}\n\nfunction render_multi_svdense(svlst, tk, block) {\n\t/*\n\tmulti-sample\n\tnative/custom\n\tdense\n\tlist of sv provided\n\tTODO change disc color to sv type\n\t*/\n\tif (!tk.isdense || svlst.length == 0) return 0\n\n\tconst tmpbins = render_multi_svdense_2bins(svlst, tk, block)\n\n\t// since sv are breakends, one sv with both ends may be in the same bin, so much dedup\n\tconst bins = []\n\tfor (const b of tmpbins) {\n\t\tif (b.lst.length == 0) continue\n\t\tconst b2 = {}\n\t\tfor (const k in b) {\n\t\t\tb2[k] = b[k]\n\t\t}\n\n\t\tb2.lst = dedup_sv(b.lst)\n\n\t\tbins.push(b2)\n\t}\n\n\t// group items in each bin\n\tfor (const b of bins) {\n\t\tconst name2group = new Map()\n\t\tconst nonamelst = []\n\t\tfor (const i of b.lst) {\n\t\t\tif (i._samplegroup.name) {\n\t\t\t\tif (!name2group.has(i._samplegroup.name)) {\n\t\t\t\t\tname2group.set(i._samplegroup.name, [])\n\t\t\t\t}\n\t\t\t\tname2group.get(i._samplegroup.name).push(i)\n\t\t\t} else {\n\t\t\t\tnonamelst.push(i)\n\t\t\t}\n\t\t}\n\t\tconst lst = []\n\t\tif (nonamelst.length) {\n\t\t\tlst.push({\n\t\t\t\titems: nonamelst,\n\t\t\t\tcolor: svdensitynogroupcolor\n\t\t\t})\n\t\t}\n\t\tfor (const [name, items] of name2group) {\n\t\t\tlst.push({\n\t\t\t\tname: name,\n\t\t\t\titems: items,\n\t\t\t\tcolor: tk.legend_samplegroup ? tk.legend_samplegroup.color(name) : '#aaa'\n\t\t\t})\n\t\t}\n\t\tlst.sort((i, j) => j.items.length - i.items.length)\n\t\tb.groups = lst\n\t}\n\n\tlet maxcount = 0 // per group\n\tfor (const b of bins) {\n\t\tfor (const g of b.groups) {\n\t\t\tmaxcount = Math.max(maxcount, g.items.length)\n\t\t}\n\t}\n\n\tlet maxheight = 0 // of all bins\n\t{\n\t\tconst radius = 4\n\t\tlet mrd = 0 // max radius\n\t\tconst w = Math.pow(radius, 2) * Math.PI // unit area\n\t\tif (maxcount <= 3) {\n\t\t\tmrd = w * maxcount * 0.9\n\t\t} else if (maxcount <= 10) {\n\t\t\tmrd = w * 5\n\t\t} else if (maxcount <= 100) {\n\t\t\tmrd = w * 7\n\t\t} else {\n\t\t\tmrd = w * 10\n\t\t}\n\t\tconst sf_discradius = scaleLinear()\n\t\t\t.domain([1, maxcount * 0.5 + 0.1, maxcount * 0.6 + 0.1, maxcount * 0.7 + 0.1, maxcount * 0.8 + 0.1, maxcount])\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\tfor (const b of bins) {\n\t\t\tif (!b.groups) continue\n\t\t\tfor (const g of b.groups) {\n\t\t\t\tg.radius = Math.sqrt(sf_discradius(g.items.length) / Math.PI)\n\t\t\t}\n\t\t\t// offset of a bin determined by the total number of items\n\t\t\tb.offset = Math.sqrt(sf_discradius(b.lst.length) / Math.PI)\n\t\t\tconst h = b.groups.reduce((i, j) => i + j.radius * 2, 0)\n\t\t\tmaxheight = Math.max(maxheight, b.offset + h)\n\t\t}\n\t}\n\n\tfor (const b of bins) {\n\t\tconst g = tk.svdensityg.append('g').attr('transform', 'translate(' + b.x + ',0)')\n\n\t\tlet y = b.offset\n\n\t\tfor (const grp of b.groups) {\n\t\t\t// one dot for each group\n\n\t\t\ty += grp.radius\n\t\t\tg.append('circle').attr('cy', -y).attr('r', grp.radius).attr('fill', grp.color).attr('stroke', 'white')\n\n\t\t\tif (grp.radius >= 8) {\n\t\t\t\t// big enough dot, show # of items\n\t\t\t\tconst s = grp.radius * 1.5\n\t\t\t\tconst text = grp.items.length.toString()\n\t\t\t\tconst fontsize = Math.min(s / (text.length * client.textlensf), s)\n\n\t\t\t\tg.append('text')\n\t\t\t\t\t.text(text)\n\t\t\t\t\t.attr('y', -y)\n\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', 'white')\n\t\t\t}\n\n\t\t\t// cover\n\t\t\tg.append('circle')\n\t\t\t\t.attr('cy', -y)\n\t\t\t\t.attr('r', grp.radius)\n\t\t\t\t.attr('fill', 'white')\n\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t.attr('stroke', grp.color)\n\t\t\t\t.attr('stroke-opacity', 0)\n\t\t\t\t.attr('class', 'sja_aa_disckick')\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\ttooltip_multi_svdense(grp, tk, block)\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t})\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tclick_multi_svdense(grp, tk, block)\n\t\t\t\t})\n\t\t\ty += grp.radius\n\t\t}\n\t\tg.append('line').attr('y2', -b.offset).attr('stroke', b.groups[0].color)\n\t}\n\treturn maxheight\n}\n\nfunction render_multi_svdense_2bins(svlst, tk, block) {\n\t// repetitive\n\tif (block.exonsf >= 3) {\n\t\t// group by basepairs\n\t\tconst bp2lst = new Map()\n\t\tfor (const m of svlst) {\n\t\t\tif (m.x == undefined) continue\n\t\t\tif (!bp2lst.has(m._pos)) {\n\t\t\t\tbp2lst.set(m._pos, {\n\t\t\t\t\tx: m.x,\n\t\t\t\t\tlst: []\n\t\t\t\t})\n\t\t\t}\n\t\t\tbp2lst.get(m._pos).lst.push(m)\n\t\t}\n\t\tconst bins = []\n\t\tfor (const b of bp2lst.values()) {\n\t\t\tbins.push(b)\n\t\t}\n\t\treturn bins\n\t}\n\n\t// list of bins\n\tconst binw = 10 // pixel\n\tconst tmpbins = []\n\tlet x = 0\n\twhile (x < block.width) {\n\t\ttmpbins.push({\n\t\t\tx1: x,\n\t\t\tx2: x + binw,\n\t\t\tx: x + binw / 2,\n\t\t\tlst: []\n\t\t})\n\t\tx += binw\n\t}\n\n\tx = block.width\n\tfor (const p of block.subpanels) {\n\t\tx += p.leftpad\n\t\tlet b = 0\n\t\twhile (b < p.width) {\n\t\t\ttmpbins.push({\n\t\t\t\tx1: x + b,\n\t\t\t\tx2: x + b + binw,\n\t\t\t\tlst: []\n\t\t\t})\n\t\t\tb += binw\n\t\t}\n\t\tx += p.width\n\t}\n\n\t// sv to bins\n\tfor (const sv of svlst) {\n\t\tfor (const b of tmpbins) {\n\t\t\tif (b.x1 <= sv.x && b.x2 >= sv.x) {\n\t\t\t\tb.lst.push(sv)\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\treturn tmpbins\n}\n\nfunction render_multi_cnvloh(tk, block) {\n\t/*\n\tdraws sample rows, each contain cnv & loh segments\n\tin full mode, include vcf data as well\n\n\tmulti-sample\n\tofficial or custom\n\tfull or dense\n\n\tin full mode:\n\t\tsample/group height determined on the fly\n\t\tfor each sample, gather all stackable items: cnv/loh/itd\n\t\tthen do stacking, generate item.stack_y and obtain height for this sample\n\t\tthen commence rendering\n\n\tin dense mode:\n\t\tall samples have equal height, 1 pixel hardcoded\n\t*/\n\n\t{\n\t\t// get value cutoff for varying color of cnv or loh segments\n\n\t\tconst gain = [], // log2ratio values\n\t\t\tloss = [],\n\t\t\tsegmean = [] // segmean values\n\n\t\tfor (const g of tk.samplegroups) {\n\t\t\tfor (const s of g.samples) {\n\t\t\t\tfor (const i of s.items) {\n\t\t\t\t\tif (i.dt == common.dtloh) {\n\t\t\t\t\t\tsegmean.push(i.segmean)\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tif (i.dt == common.dtcnv) {\n\t\t\t\t\t\tif (i.value > 0) gain.push(i.value)\n\t\t\t\t\t\telse loss.push(-i.value)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst gainmaxvalue = common.getMax_byiqr(gain, novalue_max_cnvloh)\n\t\tconst lossmaxvalue = -common.getMax_byiqr(loss, novalue_max_cnvloh)\n\t\ttk.cnvcolor.cnvmax = Math.max(gainmaxvalue, -lossmaxvalue)\n\n\t\tif (segmean.length) {\n\t\t\ttk.cnvcolor.segmeanmax = Math.max(...segmean)\n\t\t} else {\n\t\t\ttk.cnvcolor.segmeanmax = novalue_max_cnvloh\n\t\t}\n\t}\n\n\tlet groupspace // vertical spacing between groups\n\tif (tk.isdense) {\n\t\ttk.rowspace = 0\n\t\tgroupspace = 4\n\t} else if (tk.isfull) {\n\t\ttk.rowspace = 1\n\t\tgroupspace = 10\n\t}\n\n\t// for width of background bar of each sample\n\tconst entirewidth = block.width + block.subpanels.reduce((i, j) => i + j.width + j.leftpad, 0)\n\n\trender_multi_cnvloh_stackeachsample(tk, block) // in each sample, process stackable items\n\n\t// sample height are set, but it doesn't set group height, because group height needs rowspace which is set above\n\tfor (const g of tk.samplegroups) {\n\t\tg.height = tk.rowspace * (g.samples.length - 1) + g.samples.reduce((i, j) => j.height + i, 0)\n\t}\n\n\tconst grouplabelfontsize = block.labelfontsize - (tk.isfull ? 0 : 1)\n\n\tlet yoff = groupspace\n\n\tfor (const [groupidx, samplegroup] of tk.samplegroups.entries()) {\n\t\t/*\n\t\tfor each group (custom track has just 1)\n\t\t*/\n\n\t\t// a group may have just 1 sample so height is smaller than label font size, need to have a ypad\n\t\tlet thisgroupypad = 0\n\t\tif (samplegroup.height < grouplabelfontsize) {\n\t\t\tthisgroupypad = (grouplabelfontsize - samplegroup.height) / 2\n\t\t}\n\n\t\tif (samplegroup.name) {\n\t\t\t// the group's got a name, show name and border lines\n\t\t\tconst color = tk.legend_samplegroup ? tk.legend_samplegroup.color(samplegroup.name) : '#0A7FA6'\n\n\t\t\tconst glabellst = [samplegroup.name + ' (' + samplegroup.samples.length]\n\t\t\tif (samplegroup.sampletotalnum)\n\t\t\t\tglabellst.push(', ' + Math.ceil((100 * samplegroup.samples.length) / samplegroup.sampletotalnum) + '%')\n\t\t\tif (tk.sampleset) {\n\t\t\t\tconst s = tk.sampleset.find(i => i.name == samplegroup.name)\n\t\t\t\tif (s) glabellst.push(', ' + Math.ceil((100 * samplegroup.samples.length) / s.samples.length) + '%')\n\t\t\t}\n\t\t\tglabellst.push(')')\n\n\t\t\ttk.cnvleftg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('font-size', grouplabelfontsize)\n\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t.attr('y', yoff + thisgroupypad + samplegroup.height / 2)\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.attr('x', block.tkleftlabel_xshift)\n\t\t\t\t.text(glabellst.join(''))\n\t\t\t\t.each(function () {\n\t\t\t\t\ttk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width)\n\t\t\t\t})\n\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\ttooltip_samplegroup(samplegroup, tk)\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t})\n\t\t\t\t.on('click', event => {\n\t\t\t\t\ttk.tip2.clear()\n\t\t\t\t\tclick_samplegroup_showmenu(samplegroup, tk, block)\n\t\t\t\t\ttk.tip2.showunder(event.target)\n\t\t\t\t})\n\n\t\t\t// v span\n\t\t\ttk.cnvleftg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('y1', yoff + thisgroupypad)\n\t\t\t\t.attr('y2', yoff + thisgroupypad + samplegroup.height)\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\n\t\t\t// tick\n\t\t\ttk.cnvleftg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('y1', yoff + thisgroupypad + samplegroup.height / 2)\n\t\t\t\t.attr('y2', yoff + thisgroupypad + samplegroup.height / 2)\n\t\t\t\t.attr('x2', -leftlabelticksize)\n\t\t\t\t.attr('stroke', color)\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t}\n\n\t\tlet yoff1 = yoff + thisgroupypad\n\t\tsamplegroup.y = yoff1\n\n\t\tfor (const sample of samplegroup.samples) {\n\t\t\t/*\n\t\t\tfor each sample from this group\n\t\t\t*/\n\n\t\t\t// if to draw sample name\n\n\t\t\tif (!samplegroup.name && sample.samplename && sample.height >= minlabfontsize) {\n\t\t\t\t// show sample name there is no group name, and tall enough, no matter if custom/native/sampleset\n\t\t\t\tsample.svglabel = tk.cnvleftg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(sample.samplename)\n\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t.attr('x', -5)\n\t\t\t\t\t.attr('y', yoff1 + sample.height / 2)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('font-size', Math.min(15, Math.max(minlabfontsize, sample.height + 1)))\n\t\t\t\t\t.each(function () {})\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\tmulti_sample_addhighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\ttk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, sample.svglabel.node().getBBox().width)\n\t\t\t}\n\n\t\t\t// container for all the browser track elements\n\t\t\tconst g = tk.cnvmidg.append('g').attr('transform', 'translate(0,' + yoff1 + ')')\n\n\t\t\tif (tk.isfull) {\n\t\t\t\tsample.blockbg = g\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('width', entirewidth)\n\t\t\t\t\t.attr('height', sample.height)\n\t\t\t\t\t.attr('fill', coverbarcolor_active)\n\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\tmulti_sample_addhighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t}\n\n\t\t\t/*\n\t\t\tjinghui nbl cell line mixed into st/nbl\n\t\t\t*/\n\t\t\tif (tk.isfull && sample.sampletype == hardcode_cellline) {\n\t\t\t\tg.append('rect')\n\t\t\t\t\t.attr('x', -5)\n\t\t\t\t\t.attr('y', 0)\n\t\t\t\t\t.attr('width', 5)\n\t\t\t\t\t.attr('height', sample.height)\n\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t}\n\n\t\t\t/*\n\t\t\tdraw cnv/loh/itd bars, before all others\n\t\t\t*/\n\t\t\tfor (const item of sample.items) {\n\t\t\t\tif (item.dt != common.dtcnv && item.dt != common.dtloh && item.dt != common.dtitd) continue\n\n\t\t\t\t// segment color set by numeric value against a cutoff\n\t\t\t\tlet color\n\t\t\t\tif (item.dt == common.dtloh) {\n\t\t\t\t\tif (item.segmean >= tk.cnvcolor.segmeanmax) {\n\t\t\t\t\t\tcolor = tk.cnvcolor.loh.str\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcolor =\n\t\t\t\t\t\t\t'rgba(' +\n\t\t\t\t\t\t\ttk.cnvcolor.loh.r +\n\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\ttk.cnvcolor.loh.g +\n\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\ttk.cnvcolor.loh.b +\n\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t(item.segmean / tk.cnvcolor.segmeanmax).toFixed(2) +\n\t\t\t\t\t\t\t')'\n\t\t\t\t\t}\n\t\t\t\t} else if (item.dt == common.dtcnv) {\n\t\t\t\t\t// cnv\n\t\t\t\t\tif (item.value > 0) {\n\t\t\t\t\t\tif (item.value >= tk.cnvcolor.cnvmax) {\n\t\t\t\t\t\t\tcolor = tk.cnvcolor.gain.str\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tcolor =\n\t\t\t\t\t\t\t\t'rgba(' +\n\t\t\t\t\t\t\t\ttk.cnvcolor.gain.r +\n\t\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t\ttk.cnvcolor.gain.g +\n\t\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t\ttk.cnvcolor.gain.b +\n\t\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t\t(item.value / tk.cnvcolor.cnvmax).toFixed(2) +\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\tif (item.value <= -tk.cnvcolor.cnvmax) {\n\t\t\t\t\t\t\tcolor = tk.cnvcolor.loss.str\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tcolor =\n\t\t\t\t\t\t\t\t'rgba(' +\n\t\t\t\t\t\t\t\ttk.cnvcolor.loss.r +\n\t\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t\ttk.cnvcolor.loss.g +\n\t\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t\ttk.cnvcolor.loss.b +\n\t\t\t\t\t\t\t\t',' +\n\t\t\t\t\t\t\t\t(-item.value / tk.cnvcolor.cnvmax).toFixed(2) +\n\t\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} else if (item.dt == common.dtitd) {\n\t\t\t\t\tcolor = common.mclass[common.mclassitd].color\n\t\t\t\t}\n\n\t\t\t\tg.append('rect')\n\t\t\t\t\t.attr('x', Math.min(item.x1, item.x2))\n\t\t\t\t\t.attr('y', item.stack_y)\n\t\t\t\t\t.attr('width', Math.max(1, Math.abs(item.x1 - item.x2)))\n\t\t\t\t\t.attr('height', item.stack_h)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t.attr('stroke', 'none')\n\t\t\t\t\t.attr('class', 'sja_aa_skkick')\n\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: item,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t// FIXME prevent click while dragging\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: item,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\n\t\t\t/*\n\t\t\tdraw sv/fusion circles, appears here in full mode, not in dense\n\t\t\t*/\n\t\t\tfor (const item of sample.items) {\n\t\t\t\tif (item.dt != common.dtsv && item.dt != common.dtfusionrna) continue\n\n\t\t\t\tconst otherchr = item.chrA == item._chr ? item.chrB : item.chrA\n\n\t\t\t\tconst color = otherchr == item._chr ? intrasvcolor : tk.legend_svchrcolor.colorfunc(otherchr)\n\n\t\t\t\tconst m_g = g.append('g').attr('transform', 'translate(' + item.x + ',' + sample.height / 2 + ')')\n\n\t\t\t\tconst w = sample.crossboxw\n\t\t\t\tlet coverstart = -w / 2,\n\t\t\t\t\tcoverwidth = w\n\n\t\t\t\tconst circle = m_g\n\t\t\t\t\t.append('circle')\n\t\t\t\t\t.attr('r', Math.min(5, Math.max(minsvradius, 1 + sample.height / 2)))\n\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t.attr('stroke', color)\n\n\t\t\t\t// whether to draw label is solely dependent on the flags\n\t\t\t\tif (item.labonleft) {\n\t\t\t\t\tm_g\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(itemname_svfusion(item))\n\t\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t.attr('font-size', w + 2)\n\t\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t\t.attr('x', -w / 2 - labelspace)\n\t\t\t\t\tcoverstart = -w / 2 - labelspace - item.labelwidth\n\t\t\t\t\tcoverwidth = w + labelspace + item.labelwidth\n\t\t\t\t} else if (item.labonright) {\n\t\t\t\t\tm_g\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(itemname_svfusion(item))\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t.attr('font-size', w + 2)\n\t\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t\t.attr('x', w / 2 + labelspace)\n\t\t\t\t\tcoverwidth = w + labelspace + item.labelwidth\n\t\t\t\t}\n\n\t\t\t\t// mouseover cover\n\t\t\t\tm_g\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('x', coverstart)\n\t\t\t\t\t.attr('y', -w / 2)\n\t\t\t\t\t.attr('width', coverwidth)\n\t\t\t\t\t.attr('height', w)\n\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\tcircle.attr('fill-opacity', 1)\n\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\titem: item,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\tcircle.attr('fill-opacity', 0)\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\titem: item,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\tsamplegroup: samplegroup,\n\t\t\t\t\t\t\ttk: tk,\n\t\t\t\t\t\t\tblock: block\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\n\t\t\t/*\n\t\t\tif in full mode (not dense), draw crosses for snv/indel\n\t\t\t*/\n\t\t\tif (tk.isfull && tk.data_vcf) {\n\t\t\t\tfor (const m of tk.data_vcf) {\n\t\t\t\t\tif (m.dt != common.dtsnvindel) continue\n\t\t\t\t\tif (m.x == undefined) continue\n\t\t\t\t\tif (!m.sampledata) continue\n\n\t\t\t\t\tconst w = sample.crossboxw\n\n\t\t\t\t\t//const color = common.mclass[m.class].color\n\t\t\t\t\tconst color = multi_snvindelcolor(tk, m, sample)\n\n\t\t\t\t\tfor (const ms of m.sampledata) {\n\t\t\t\t\t\tif (ms.sampleobj.name != sample.samplename) continue\n\n\t\t\t\t\t\t// a variant from this sample\n\n\t\t\t\t\t\tconst m_g = g.append('g').attr('transform', 'translate(' + m.x + ',' + sample.height / 2 + ')')\n\n\t\t\t\t\t\tconst bgbox = m_g\n\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t.attr('x', -w / 2 - 1)\n\t\t\t\t\t\t\t.attr('y', -w / 2 - 1)\n\t\t\t\t\t\t\t.attr('width', w + 2)\n\t\t\t\t\t\t\t.attr('height', w + 2)\n\t\t\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t\t\t.attr('fill-opacity', 0)\n\n\t\t\t\t\t\tlet bgline1, bgline2, fgline1, fgline2\n\n\t\t\t\t\t\tif (vcfvariantisgermline(ms, tk)) {\n\t\t\t\t\t\t\t// germline: 1 |  2 --\n\t\t\t\t\t\t\tbgline1 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t\t\t\t\t.attr('stroke-width', 3)\n\t\t\t\t\t\t\t\t.attr('y1', -w / 2 - 1)\n\t\t\t\t\t\t\t\t.attr('y2', w / 2 + 1)\n\t\t\t\t\t\t\tbgline2 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t\t\t\t\t.attr('stroke-width', 3)\n\t\t\t\t\t\t\t\t.attr('x1', -w / 2 - 1)\n\t\t\t\t\t\t\t\t.attr('x2', w / 2 + 1)\n\t\t\t\t\t\t\tfgline1 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t\t\t\t.attr('stroke-width', 1.5)\n\t\t\t\t\t\t\t\t.attr('y1', -w / 2 - 1)\n\t\t\t\t\t\t\t\t.attr('y2', w / 2 + 1)\n\t\t\t\t\t\t\tfgline2 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t\t\t\t.attr('stroke-width', 1.5)\n\t\t\t\t\t\t\t\t.attr('x1', -w / 2 - 1)\n\t\t\t\t\t\t\t\t.attr('x2', w / 2 + 1)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// somatic or not specified: 1 \\  2 /\n\t\t\t\t\t\t\tbgline1 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t\t\t\t\t.attr('stroke-width', 3)\n\t\t\t\t\t\t\t\t.attr('x1', -w / 2)\n\t\t\t\t\t\t\t\t.attr('x2', w / 2)\n\t\t\t\t\t\t\t\t.attr('y1', -w / 2)\n\t\t\t\t\t\t\t\t.attr('y2', w / 2)\n\t\t\t\t\t\t\tbgline2 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t\t\t\t\t.attr('stroke-width', 3)\n\t\t\t\t\t\t\t\t.attr('x1', -w / 2)\n\t\t\t\t\t\t\t\t.attr('x2', w / 2)\n\t\t\t\t\t\t\t\t.attr('y1', w / 2)\n\t\t\t\t\t\t\t\t.attr('y2', -w / 2)\n\t\t\t\t\t\t\tfgline1 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t\t\t\t.attr('stroke-width', 1.5)\n\t\t\t\t\t\t\t\t.attr('x1', -w / 2)\n\t\t\t\t\t\t\t\t.attr('x2', w / 2)\n\t\t\t\t\t\t\t\t.attr('y1', -w / 2)\n\t\t\t\t\t\t\t\t.attr('y2', w / 2)\n\t\t\t\t\t\t\tfgline2 = m_g\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('stroke', color)\n\t\t\t\t\t\t\t\t.attr('stroke-width', 1.5)\n\t\t\t\t\t\t\t\t.attr('x1', -w / 2)\n\t\t\t\t\t\t\t\t.attr('x2', w / 2)\n\t\t\t\t\t\t\t\t.attr('y1', w / 2)\n\t\t\t\t\t\t\t\t.attr('y2', -w / 2)\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tlet coverstart = -w / 2,\n\t\t\t\t\t\t\tcoverwidth = w\n\n\t\t\t\t\t\tif (ms.sampleobj.labonleft) {\n\t\t\t\t\t\t\tm_g\n\t\t\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t\t\t.text(m.mname)\n\t\t\t\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t\t\t.attr('font-size', sample.crossboxw + 2)\n\t\t\t\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t\t\t\t.attr('x', -w / 2 - labelspace)\n\t\t\t\t\t\t\tcoverstart = -w / 2 - labelspace - ms.sampleobj.labelwidth\n\t\t\t\t\t\t\tcoverwidth = w + labelspace + ms.sampleobj.labelwidth\n\t\t\t\t\t\t} else if (ms.sampleobj.labonright) {\n\t\t\t\t\t\t\tm_g\n\t\t\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t\t\t.text(m.mname)\n\t\t\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t\t\t.attr('font-size', sample.crossboxw + 2)\n\t\t\t\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t\t\t\t.attr('x', w / 2 + labelspace)\n\t\t\t\t\t\t\tcoverwidth = w + labelspace + ms.sampleobj.labelwidth\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// mouseover cover\n\t\t\t\t\t\tm_g\n\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t.attr('x', coverstart)\n\t\t\t\t\t\t\t.attr('y', -w / 2)\n\t\t\t\t\t\t\t.attr('width', coverwidth)\n\t\t\t\t\t\t\t.attr('height', w)\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', () => {\n\t\t\t\t\t\t\t\tbgbox.attr('fill-opacity', 1)\n\t\t\t\t\t\t\t\tbgline1.attr('stroke-opacity', 0)\n\t\t\t\t\t\t\t\tbgline2.attr('stroke-opacity', 0)\n\t\t\t\t\t\t\t\tfgline1.attr('stroke', 'white')\n\t\t\t\t\t\t\t\tfgline2.attr('stroke', 'white')\n\n\t\t\t\t\t\t\t\ttooltip_singleitem({\n\t\t\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\t\t\tm_sample: ms,\n\t\t\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\t\t\tsamplegroup: samplegroup,\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})\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\tbgbox.attr('fill-opacity', 0)\n\t\t\t\t\t\t\t\tbgline1.attr('stroke-opacity', 1)\n\t\t\t\t\t\t\t\tbgline2.attr('stroke-opacity', 1)\n\t\t\t\t\t\t\t\tfgline1.attr('stroke', color)\n\t\t\t\t\t\t\t\tfgline2.attr('stroke', color)\n\t\t\t\t\t\t\t\tmulti_sample_removehighlight(sample)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tclick_multi_singleitem({\n\t\t\t\t\t\t\t\t\titem: m,\n\t\t\t\t\t\t\t\t\tm_sample: ms,\n\t\t\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\t\t\tsamplegroup: samplegroup,\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})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t/*** done all items for this sample ***/\n\t\t\tyoff1 += sample.height + tk.rowspace\n\t\t}\n\n\t\t/*** done a group ***/\n\t\tyoff += samplegroup.height + thisgroupypad * 2 + groupspace\n\t}\n\n\tif (!tk.nocnvlohsv) {\n\t\tif (tk.cnvcolor.cnvmax == novalue_max_cnvloh) {\n\t\t\t// hide svg and show 'nodata'\n\t\t\ttk.cnvcolor.cnvlegend.svg.style('display', 'none')\n\t\t\ttk.cnvcolor.cnvlegend.nodatadiv.style('display', 'block')\n\t\t} else {\n\t\t\t// hide 'nodata' and show svg\n\t\t\ttk.cnvcolor.cnvlegend.svg.style('display', 'block')\n\t\t\ttk.cnvcolor.cnvlegend.nodatadiv.style('display', 'none')\n\t\t\tdraw_colorscale_cnv(tk)\n\t\t}\n\n\t\tif (tk.cnvcolor.segmeanmax == novalue_max_cnvloh) {\n\t\t\tif (tk.cnvcolor.lohlegend) {\n\t\t\t\t// hide svg and show 'nodata'\n\t\t\t\ttk.cnvcolor.lohlegend.svg.style('display', 'none')\n\t\t\t\ttk.cnvcolor.lohlegend.nodatadiv.style('display', 'block')\n\t\t\t}\n\t\t} else {\n\t\t\t// hide 'nodata' and show svg\n\t\t\ttk.cnvcolor.lohlegend.svg.style('display', 'block')\n\t\t\ttk.cnvcolor.lohlegend.nodatadiv.style('display', 'none')\n\t\t\tdraw_colorscale_loh(tk)\n\t\t}\n\t}\n\n\treturn yoff\n}\n\nfunction multi_snvindelcolor(tk, m, sample) {\n\t/*\nin multi-sample mode, snvindel drawn as x or +\ndecide the color\nm{}\nsample{}\n\t.samplename\n*/\n\treturn common.mclass[m.class].color\n}\n\nexport function multi_sample_addhighlight(sample) {\n\tif (!sample) return\n\t// one of tk.samplegroup[].sample[]\n\tif (sample.svglabel) sample.svglabel.attr('fill', coverbarcolor_active)\n\tif (sample.blockbg) sample.blockbg.attr('fill-opacity', 0.1)\n\tif (sample.columnbars) {\n\t\tfor (const b of sample.columnbars) {\n\t\t\tb.attr('fill', coverbarcolor_active)\n\t\t}\n\t}\n}\n\nexport function multi_sample_removehighlight(sample) {\n\tif (!sample) return\n\t// one of tk.samplegroup[].sample[]\n\tif (sample.svglabel) sample.svglabel.attr('fill', coverbarcolor_silent)\n\tif (sample.blockbg) sample.blockbg.attr('fill-opacity', 0)\n\tif (sample.columnbars) {\n\t\tfor (const b of sample.columnbars) {\n\t\t\tb.attr('fill', coverbarcolor_silent)\n\t\t}\n\t}\n}\n\nfunction render_multi_cnvloh_stackeachsample(tk, block) {\n\t/*\n\tcalled by render_multi_cnvloh()\n\tfor each sample, set .height\n\tfor each stackable item (cnv/loh/itd), set .stack_y, .stack_h\n\n\tfor vcf/fusion/sv, check if can show label for each\n\t*/\n\tif (!tk.samplegroups || tk.samplegroups.length == 0) return\n\n\tif (tk.isdense) {\n\t\t// no stacking in dense mode, itd won't go into .items[]\n\t\tfor (const g of tk.samplegroups) {\n\t\t\tfor (const s of g.samples) {\n\t\t\t\ts.height = 1 // hardcoded\n\t\t\t\tfor (const i of s.items) {\n\t\t\t\t\tif (i.dt == common.dtcnv || i.dt == common.dtloh || i.dt == common.dtitd) {\n\t\t\t\t\t\ti.stack_y = 0\n\t\t\t\t\t\ti.stack_h = 1\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn\n\t}\n\n\t/*\n\tbefore commencing, delete prior label-drawing flags from vcf sampleobj\n\tthis can happen when toggling label show/hide without reloading data\n\t*/\n\tfor (const g of tk.samplegroups) {\n\t\tfor (const s of g.samples) {\n\t\t\tfor (const i of s.items) {\n\t\t\t\tif (i.dt == common.dtsv || i.dt == common.dtfusionrna) {\n\t\t\t\t\tdelete i.labonleft\n\t\t\t\t\tdelete i.labonright\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tif (tk.data_vcf) {\n\t\tfor (const m of tk.data_vcf) {\n\t\t\tif (m.sampledata) {\n\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\tif (s.sampleobj) {\n\t\t\t\t\t\tdelete s.sampleobj.labonleft\n\t\t\t\t\t\tdelete s.sampleobj.labonright\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// full width\n\tconst blockwidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0)\n\n\t// full mode\n\tfor (const g of tk.samplegroups) {\n\t\tfor (const s of g.samples) {\n\t\t\t// for this sample, gather stackable items\n\t\t\tconst items = []\n\t\t\tfor (const i of s.items) {\n\t\t\t\tif (i.dt == common.dtcnv || i.dt == common.dtloh || i.dt == common.dtitd) {\n\t\t\t\t\tif (i.x1 != undefined && i.x2 != undefined) {\n\t\t\t\t\t\ti._boxstart = Math.min(i.x1, i.x2)\n\t\t\t\t\t\ti._boxwidth = Math.abs(i.x2 - i.x1)\n\t\t\t\t\t\titems.push(i)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tdostack(s, items)\n\n\t\t\ts.crossboxw = Math.min(8, s.height) // determines label font size\n\n\t\t\t// after stacking, decide if to draw label for pointy items\n\n\t\t\t/*\n\t\t\tcollect pointy items of this sample, sv/fusion/snv\n\t\t\tmust collect all, even if its name is hidden or doesn't have a name, in order for collision detection to work\n\t\t\t*/\n\t\t\tconst pointitems = []\n\n\t\t\tfor (const i of s.items) {\n\t\t\t\tif (i.dt == common.dtfusionrna) {\n\t\t\t\t\tif (i.x == undefined) continue\n\t\t\t\t\tconst item = {\n\t\t\t\t\t\tdt: i.dt,\n\t\t\t\t\t\tx: i.x,\n\t\t\t\t\t\tobj: i\n\t\t\t\t\t}\n\t\t\t\t\tif (tk.multihidelabel_fusion) {\n\t\t\t\t\t\t// no show\n\t\t\t\t\t} else {\n\t\t\t\t\t\titem.name = itemname_svfusion(i)\n\t\t\t\t\t}\n\t\t\t\t\tpointitems.push(item)\n\t\t\t\t} else if (i.dt == common.dtsv) {\n\t\t\t\t\tif (i.x == undefined) continue\n\t\t\t\t\tconst item = {\n\t\t\t\t\t\tdt: i.dt,\n\t\t\t\t\t\tx: i.x,\n\t\t\t\t\t\tobj: i\n\t\t\t\t\t}\n\t\t\t\t\tif (tk.multihidelabel_sv) {\n\t\t\t\t\t\t// no show\n\t\t\t\t\t} else {\n\t\t\t\t\t\titem.name = itemname_svfusion(i)\n\t\t\t\t\t}\n\t\t\t\t\tpointitems.push(item)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (tk.data_vcf) {\n\t\t\t\t// collect vcf items for this sample\n\t\t\t\tfor (const m of tk.data_vcf) {\n\t\t\t\t\tif (m.dt != common.dtsnvindel || m.x == undefined || !m.sampledata) continue\n\t\t\t\t\tconst m_sample = m.sampledata.find(i => i.sampleobj.name == s.samplename)\n\t\t\t\t\tif (m_sample) {\n\t\t\t\t\t\tconst item = {\n\t\t\t\t\t\t\tdt: m.dt,\n\t\t\t\t\t\t\tx: m.x,\n\t\t\t\t\t\t\tobj: m_sample.sampleobj\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (tk.multihidelabel_vcf) {\n\t\t\t\t\t\t\t// no show\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\titem.name = m.mname\n\t\t\t\t\t\t}\n\t\t\t\t\t\tpointitems.push(item)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (pointitems.length > 0) {\n\t\t\t\tpointitems.sort((i, j) => i.x - j.x)\n\n\t\t\t\tfor (let pidx = 0; pidx < pointitems.length; pidx++) {\n\t\t\t\t\t/*\n\t\t\t\t\tdt, x, name, obj\n\t\t\t\t\tfor each item, decide if/where to show label\n\t\t\t\t\t*/\n\n\t\t\t\t\tconst pi = pointitems[pidx]\n\n\t\t\t\t\tif (!pi.name) {\n\t\t\t\t\t\t// no name\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\n\t\t\t\t\tlet labw\n\t\t\t\t\ttk.g\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(pi.name)\n\t\t\t\t\t\t.attr('font-size', s.crossboxw + 2)\n\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t.each(function () {\n\t\t\t\t\t\t\tlabw = this.getBBox().width\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.remove()\n\n\t\t\t\t\tlabw += s.crossboxw / 2 + labelspace\n\n\t\t\t\t\tlet nleft = false,\n\t\t\t\t\t\tnright = false\n\n\t\t\t\t\tif (labw > pi.x) {\n\t\t\t\t\t\t// no space on left\n\t\t\t\t\t\tnleft = true\n\t\t\t\t\t} else if (labw > blockwidth - pi.x) {\n\t\t\t\t\t\t// no space on right\n\t\t\t\t\t\tnright = true\n\t\t\t\t\t}\n\n\t\t\t\t\t// test segment items\n\t\t\t\t\tfor (const i of s.items) {\n\t\t\t\t\t\tif (nleft && nright) break\n\n\t\t\t\t\t\tif (i.dt == common.dtcnv || i.dt == common.dtloh || i.dt == common.dtitd) {\n\t\t\t\t\t\t\tif (i.x1 == undefined || i.x2 == undefined) continue\n\t\t\t\t\t\t\tconst x1 = Math.min(i.x1, i.x2)\n\t\t\t\t\t\t\tconst x2 = Math.max(i.x1, i.x2)\n\n\t\t\t\t\t\t\tif (x1 < pi.x) {\n\t\t\t\t\t\t\t\tif (x2 < pi.x) {\n\t\t\t\t\t\t\t\t\tif (labw > pi.x - x2) {\n\t\t\t\t\t\t\t\t\t\tnleft = true\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\tnleft = true\n\t\t\t\t\t\t\t\t\tnright = true\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\tif (labw > x1 - pi.x) {\n\t\t\t\t\t\t\t\t\tnright = true\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\n\t\t\t\t\tif (nleft && nright) {\n\t\t\t\t\t\t// cannot show label\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\n\t\t\t\t\tif (!nleft) {\n\t\t\t\t\t\t// check previous item for putting label on left\n\t\t\t\t\t\tfor (let pidx2 = pidx - 1; pidx2 >= 0; pidx2--) {\n\t\t\t\t\t\t\tconst pi0 = pointitems[pidx2]\n\t\t\t\t\t\t\tif (pi0.x == pi.x) {\n\t\t\t\t\t\t\t\t// possible, avoid label overlap\n\t\t\t\t\t\t\t\tif (pi0.obj.labonleft) {\n\t\t\t\t\t\t\t\t\tnleft = true\n\t\t\t\t\t\t\t\t} else if (pi0.obj.labonright) {\n\t\t\t\t\t\t\t\t\tnright = true\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t// do not prohibit\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\tif (labw > pi.x - pi0.x - (pi0.obj.labonright ? pi0.obj.labelwidth : 0)) {\n\t\t\t\t\t\t\t\t\tnleft = true\n\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t// good space\n\t\t\t\t\t\t\t\t\tbreak\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\n\t\t\t\t\tif (nleft && nright) continue\n\n\t\t\t\t\tif (!nright) {\n\t\t\t\t\t\t// check rest of items for putting label on right\n\t\t\t\t\t\tfor (let pidx2 = pidx + 1; pidx2 < pointitems.length; pidx2++) {\n\t\t\t\t\t\t\tconst pi2 = pointitems[pidx2]\n\n\t\t\t\t\t\t\tif (pi2.x == pi.x) {\n\t\t\t\t\t\t\t\t// do not prohibit\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tif (labw > pi2.x - pi.x) {\n\t\t\t\t\t\t\t\t\tnright = true\n\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t// allow label on right\n\t\t\t\t\t\t\t\t\tbreak\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\n\t\t\t\t\tif (nleft && nright) continue\n\n\t\t\t\t\tif (nleft) {\n\t\t\t\t\t\tif (!nright) {\n\t\t\t\t\t\t\tpi.obj.labonright = true\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (nright) {\n\t\t\t\t\t\t\tpi.obj.labonleft = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tpi.obj.labonright = true // on right first\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\tif (pi.obj.labonleft || pi.obj.labonright) {\n\t\t\t\t\t\tpi.obj.labelwidth = labw\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function itemname_svfusion(i) {\n\tif (i.cytogeneticname) return i.cytogeneticname\n\treturn (i.geneA || i.chrA) + ' > ' + (i.geneB || i.chrB)\n}\n\nfunction dostack(sample, items) {\n\t// set sample.height\n\n\tif (items.length == 0) {\n\t\t// this sample has no stackable item, but it must have other pointy items\n\t\t// still set height\n\t\tsample.height = 8\n\t\treturn\n\t}\n\n\t// stack\n\n\titems.sort((i, j) => i._boxstart - j._boxstart)\n\n\tconst stacks = []\n\tfor (const m of items) {\n\t\tfor (let i = 0; i < stacks.length; i++) {\n\t\t\tif (stacks[i] < m._boxstart) {\n\t\t\t\tm._stacki = i\n\t\t\t\tstacks[i] = m._boxstart + m._boxwidth\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (m._stacki == undefined) {\n\t\t\tm._stacki = stacks.length\n\t\t\tstacks.push(m._boxstart + m._boxwidth)\n\t\t}\n\t}\n\n\tlet stackheight = stackheightscale(stacks.length)\n\tif (stackheight < 1) {\n\t\t// simpleminded scaling can make it negative\n\t\tstackheight = 1\n\t}\n\n\t// no spacing between stacks!!\n\n\tfor (const i of items) {\n\t\ti.stack_y = i._stacki * stackheight\n\t\ti.stack_h = stackheight\n\t\tdelete i._stacki\n\t\tdelete i._boxstart\n\t\tdelete i._boxwidth\n\t}\n\n\tsample.height = stackheight * stacks.length\n}\n\nexport function multi_expressionstatus_ase_outlier(tk) {\n\t/*\n\tmulti-sample\n\tfor all genes\n\tcalculate expression status including ase and outlier, using Yu's data & method\n\tonly do this when getting new data, or changing cutoffs\n\n\tshould process _data, since in dense mode, .samplegroups[] will not contain sv-only samples\n\t*/\n\t//if(!tk.samplegroups) return\n\tif (!tk._data) return\n\tif (!tk.gecfg) return\n\tif (tk.gecfg.no_ase) return\n\tfor (const g of tk._data) {\n\t\tif (!g.samples) continue\n\t\tfor (const s of g.samples) {\n\t\t\tif (!s.expressionrank) continue\n\t\t\tfor (const gene in s.expressionrank) {\n\t\t\t\tconst v = s.expressionrank[gene]\n\t\t\t\texpressionstat.measure(v, tk.gecfg)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function draw_colorscale_cnv(tk) {\n\ttk.cnvcolor.cnvlegend.row.style('display', 'table-row')\n\tclient.axisstyle({\n\t\taxis: tk.cnvcolor.cnvlegend.axisg.call(\n\t\t\taxisTop()\n\t\t\t\t.scale(\n\t\t\t\t\tscaleLinear()\n\t\t\t\t\t\t.domain([-tk.cnvcolor.cnvmax, 0, tk.cnvcolor.cnvmax])\n\t\t\t\t\t\t.range([0, tk.cnvcolor.cnvlegend.barw, tk.cnvcolor.cnvlegend.barw * 2])\n\t\t\t\t)\n\t\t\t\t.tickValues([-tk.cnvcolor.cnvmax, 0, tk.cnvcolor.cnvmax])\n\t\t\t\t.tickSize(tk.cnvcolor.cnvlegend.axistickh)\n\t\t)\n\t})\n}\n\nexport function draw_colorscale_loh(tk) {\n\tif (!tk.cnvcolor.lohlegend) return\n\n\ttk.cnvcolor.lohlegend.row.style('display', 'table-row')\n\tclient.axisstyle({\n\t\taxis: tk.cnvcolor.lohlegend.axisg.call(\n\t\t\taxisTop()\n\t\t\t\t.scale(scaleLinear().domain([0, tk.cnvcolor.segmeanmax]).range([0, tk.cnvcolor.lohlegend.barw]))\n\t\t\t\t.tickValues([0, tk.cnvcolor.segmeanmax])\n\t\t\t\t.tickSize(tk.cnvcolor.lohlegend.axistickh)\n\t\t)\n\t})\n}\n\nexport async function focus_singlesample(p) {\n\t/*\n\tmulti-sample\n\tnative or custom\n\tlaunch a new block instance, show sv-cnv-vcf-expression track in single-sample mode,\n\tview range determined by cnv or sv\n\tif vcf, will use block view range\n\n\t.m\n\t.sample\n\t\t.samplename\n\t\t.sampletype\n\t.samplegroup\n\t\t.attributes[]\n\t.tk\n\t.block\n\t*/\n\n\tconst { m, sample, samplegroup, tk, block } = p\n\n\tlet holder\n\n\tif (p.holder) {\n\t\tholder = p.holder\n\t} else {\n\t\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\tholder = pane.body\n\t}\n\n\tconst assaytkbuttondiv = holder.append('div')\n\n\t// for launching block\n\tconst arg = {\n\t\tstyle: {\n\t\t\tmargin: '0px'\n\t\t},\n\n\t\t// this is to hide green button in sub block\n\t\t//hide_mdsHandleHolder:1,\n\n\t\ttklst: [],\n\t\tholder,\n\t\tsubpanels: []\n\t}\n\n\tclient.first_genetrack_tolist(block.genome, arg.tklst)\n\n\t// should also root out error when showing that\n\n\t// expression rank\n\tif (tk.iscustom) {\n\t\tif (tk.checkexpressionrank) {\n\t\t\tconst et = {\n\t\t\t\ttype: client.tkt.mdsexpressionrank,\n\t\t\t\tname: sample.samplename + ' expression rank',\n\t\t\t\tsample: sample.samplename,\n\t\t\t\tiscustom: 1\n\t\t\t}\n\t\t\tfor (const k in tk.checkexpressionrank) {\n\t\t\t\tet[k] = tk.checkexpressionrank[k]\n\t\t\t}\n\t\t\targ.tklst.push(et)\n\t\t}\n\t\t// other assay tracks\n\t\tif (tk.sample2assaytrack && tk.sample2assaytrack[sample.samplename]) {\n\t\t\tfor (const t of tk.sample2assaytrack[sample.samplename]) {\n\t\t\t\targ.tklst.push(t)\n\t\t\t}\n\t\t}\n\t} else if (tk.mds && tk.mds.queries[tk.querykey].checkexpressionrank) {\n\t\t// official mds\n\n\t\tif (samplegroup) {\n\t\t\tconst et = {\n\t\t\t\ttype: client.tkt.mdsexpressionrank,\n\t\t\t\tname: sample.samplename + ' expression rank',\n\t\t\t\tdslabel: tk.mds.label,\n\t\t\t\tquerykey: tk.mds.queries[tk.querykey].checkexpressionrank.querykey,\n\t\t\t\tsample: sample.samplename,\n\t\t\t\tattributes: samplegroup.attributes\n\t\t\t}\n\t\t\targ.tklst.push(et)\n\t\t} else {\n\t\t\t// in dense mode, vcf samples may not have group\n\t\t}\n\t}\n\n\t// add sv-cnv-vcf track in single-sample mode\n\tconst t2 = {\n\t\tbplengthUpperLimit: 0, // sample view to show all cnvs by default, not just focal\n\t\tvalueCutoff: tk.valueCutoff,\n\t\tlohLengthUpperLimit: tk.lohLengthUpperLimit,\n\t\tsegmeanValueCutoff: tk.segmeanValueCutoff,\n\t\tsinglesample: {\n\t\t\tname: sample.samplename\n\t\t}\n\t}\n\tif (tk.iscustom) {\n\t\tt2.type = client.tkt.mdssvcnv\n\t\tt2.file = tk.file\n\t\tt2.url = tk.url\n\t\tt2.indexURL = tk.indexURL\n\t\tt2.iscustom = true\n\t\tt2.legend_vorigin = tk.legend_vorigin\n\t} else {\n\t\t// official\n\t\tt2.mds = tk.mds\n\t\tt2.querykey = tk.querykey\n\t\tfor (const k in tk.mds.queries[tk.querykey]) {\n\t\t\tif (k == 'bplengthUpperLimit' || k == 'valueCutoff') {\n\t\t\t\t// do not use default\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tt2[k] = tk.mds.queries[tk.querykey][k]\n\t\t}\n\t}\n\n\t// custom vcf track to be declared in t2\n\tif (tk.iscustom && tk.checkvcf) {\n\t\tt2.checkvcf = tk.checkvcf\n\t}\n\n\targ.tklst.push(t2)\n\n\tif (m) {\n\t\tif (m.dt == common.dtcnv || m.dt == common.dtloh) {\n\t\t\tconst span = Math.ceil((m.stop - m.start) / 2)\n\t\t\targ.chr = m.chr\n\t\t\targ.start = Math.max(0, m.start - span)\n\t\t\targ.stop = Math.min(block.genome.chrlookup[m.chr.toUpperCase()].len, m.stop + span)\n\t\t} else if (m.dt == common.dtsv || m.dt == common.dtfusionrna) {\n\t\t\tif (m.chrA == m.chrB) {\n\t\t\t\tconst span = Math.ceil(Math.abs(m.posA - m.posB) / 4)\n\t\t\t\targ.chr = m.chrA\n\t\t\t\targ.start = Math.max(0, Math.min(m.posA, m.posB) - span)\n\t\t\t\targ.stop = Math.min(block.genome.chrlookup[m.chrA.toUpperCase()].len, Math.max(m.posA, m.posB) + span)\n\t\t\t} else {\n\t\t\t\tconst span = 10000\n\t\t\t\targ.chr = m.chrA\n\t\t\t\targ.start = Math.max(0, m.posA - span)\n\t\t\t\targ.stop = Math.min(block.genome.chrlookup[m.chrA.toUpperCase()].len, m.posA + span)\n\t\t\t\targ.subpanels.push({\n\t\t\t\t\tchr: m.chrB,\n\t\t\t\t\tstart: Math.max(0, m.posB - span),\n\t\t\t\t\tstop: Math.min(block.genome.chrlookup[m.chrB.toUpperCase()].len, m.posB + span),\n\t\t\t\t\twidth: 600,\n\t\t\t\t\tleftpad: 10,\n\t\t\t\t\tleftborder: 'rgba(50,50,50,.1)'\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\tif (!arg.chr) {\n\t\t// no view range set\n\t\tconst r = block.tkarg_maygm(tk)[0]\n\n\t\tif (m && m.dt == common.dtsnvindel) {\n\t\t\t// is snvindel\n\n\t\t\tconst span = 10000 // hardcoded\n\n\t\t\tif (span < r.stop - r.start) {\n\t\t\t\t// current view range is bigger than span, use span\n\t\t\t\targ.chr = m.chr\n\t\t\t\targ.start = Math.max(0, m.pos - span)\n\t\t\t\targ.stop = Math.min(block.genome.chrlookup[m.chr.toUpperCase()].len, m.pos + span)\n\t\t\t}\n\t\t}\n\n\t\tif (!arg.chr) {\n\t\t\t// is not snvindel\n\n\t\t\targ.chr = r.chr\n\t\t\targ.start = r.start\n\t\t\targ.stop = r.stop\n\t\t}\n\t}\n\n\tlet assaytklst\n\n\tif (!tk.iscustom) {\n\t\t// official track\n\t\t// get sample-level track from serverside dataset config\n\t\tconst data = await client.dofetch2('mdssvcnv', {\n\t\t\tmethod: 'POST',\n\t\t\tbody: JSON.stringify({\n\t\t\t\tgenome: block.genome.name,\n\t\t\t\tdslabel: tk.mds.label,\n\t\t\t\tquerykey: tk.querykey,\n\t\t\t\tgettrack4singlesample: sample.samplename\n\t\t\t})\n\t\t})\n\t\tif (data.error) throw data.error\n\t\tif (data.tracks) {\n\t\t\t// important: must duplicate as block init will erase the .hidden tag\n\t\t\tassaytklst = data.tracks\n\t\t\tfor (const t of data.tracks) {\n\t\t\t\targ.tklst.push(JSON.parse(JSON.stringify(t)))\n\t\t\t}\n\t\t}\n\t}\n\tconst bb = block.newblock(arg)\n\n\tif (m) {\n\t\tif (m.dt == common.dtcnv || m.dt == common.dtloh) {\n\t\t\tbb.addhlregion(m.chr, m.start, m.stop, cnvhighlightcolor)\n\t\t}\n\t}\n\tif (assaytklst) {\n\t\t// display buttons for toggling each assay track\n\t\tassaytkbuttondiv\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin', '0px 10px 20px 10px')\n\t\t\t.append('div')\n\t\t\t.style('margin-bottom', '3px')\n\t\t\t.text('Show/hide available assay tracks for ' + sample.samplename)\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('opacity', 0.5)\n\t\tconst d = assaytkbuttondiv.append('div').style('border', 'solid 1px #ccc').style('border-radius', '7px')\n\t\tfor (const t of assaytklst) {\n\t\t\tconst label = d\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.append('label')\n\t\t\tlabel\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.style('margin-right', '3px')\n\t\t\t\t.property('checked', !t.hidden)\n\t\t\t\t.on('change', event => {\n\t\t\t\t\tif (event.target.checked) {\n\t\t\t\t\t\tbb.turnOnTrack(t)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tbb.turnOffTrack(t)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\tlabel.append('span').text(t.name)\n\t\t}\n\t}\n}\n\nfunction prep_samplegroups(tk, block) {\n\t/*\n\tmulti-sample\n\tfrom tk._data, prepare samplegroups for plotting\n\tmap sv/cnv/loh/itd to view range, exclude unmappable items\n\t*/\n\n\tif (!tk._data) {\n\t\t// could be that all dt are hidden\n\t\treturn [[], []]\n\t}\n\n\tconst svlst4dense = []\n\n\tlet plotgroups = []\n\n\tfor (const samplegroup of tk._data) {\n\t\tconst g2 = {}\n\t\tfor (const k in samplegroup) g2[k] = samplegroup[k]\n\t\tg2.samples = []\n\n\t\tfor (const sample of samplegroup.samples) {\n\t\t\tconst s2 = {}\n\t\t\tfor (const k in sample) s2[k] = sample[k]\n\t\t\ts2.items = []\n\n\t\t\tfor (const item of sample.items) {\n\t\t\t\tif (item.dt == common.dtsv || item.dt == common.dtfusionrna) {\n\t\t\t\t\t// sv\n\t\t\t\t\tmap_sv_2(item, block)\n\t\t\t\t\tif (item.x == undefined) {\n\t\t\t\t\t\tconsole.log('unmappable sv: ' + item._chr + ' ' + item._pos)\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\n\t\t\t\t\tif (item.chrA != item._chr) {\n\t\t\t\t\t\ttk.legend_svchrcolor.interchrs.add(item.chrA)\n\t\t\t\t\t\ttk.legend_svchrcolor.colorfunc(item.chrA)\n\t\t\t\t\t}\n\t\t\t\t\tif (item.chrB != item._chr) {\n\t\t\t\t\t\ttk.legend_svchrcolor.interchrs.add(item.chrB)\n\t\t\t\t\t\ttk.legend_svchrcolor.colorfunc(item.chrB)\n\t\t\t\t\t}\n\n\t\t\t\t\tif (tk.isdense) {\n\t\t\t\t\t\tconst i = {\n\t\t\t\t\t\t\t_samplegroup: samplegroup,\n\t\t\t\t\t\t\t_sample: sample\n\t\t\t\t\t\t}\n\t\t\t\t\t\tfor (const k in item) {\n\t\t\t\t\t\t\ti[k] = item[k]\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsvlst4dense.push(i)\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\n\t\t\t\t\t// not dense\n\t\t\t\t\ts2.items.push(item)\n\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\t// cnv, loh, itd\n\t\t\t\tmap_cnv(item, tk, block)\n\t\t\t\tif (item.x1 == undefined || item.x2 == undefined) {\n\t\t\t\t\tconsole.log('unmappable stack item: ', item)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\ts2.items.push(item)\n\t\t\t}\n\n\t\t\tif (s2.items.length == 0) {\n\t\t\t\t/*\n\t\t\t\tno cnv/sv/loh for this sample, may drop it\n\t\t\t\thowever if vcf is in full mode, must check if this sample has vcf data\n\t\t\t\tsince vcf data is not bundled in items[]\n\t\t\t\t*/\n\t\t\t\tif (tk.isfull && tk.data_vcf) {\n\t\t\t\t\tlet samplehasvcf = false\n\n\t\t\t\t\tfor (const m of tk.data_vcf) {\n\t\t\t\t\t\tif (samplehasvcf) break\n\t\t\t\t\t\tif (m.x == undefined) continue\n\n\t\t\t\t\t\tif (m.dt == common.dtsnvindel) {\n\t\t\t\t\t\t\tif (!m.sampledata) continue\n\t\t\t\t\t\t\tfor (const s of m.sampledata) {\n\t\t\t\t\t\t\t\tif (s.sampleobj.name == sample.samplename) {\n\t\t\t\t\t\t\t\t\tsamplehasvcf = true\n\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t}\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}\n\n\t\t\t\t\tif (!samplehasvcf) {\n\t\t\t\t\t\t// this sample has no vcf either\n\t\t\t\t\t\tif (if_getallsamples(tk)) {\n\t\t\t\t\t\t\t// QUICK FIX!!!!\n\t\t\t\t\t\t\t// when this is set, will keep samples with empty .items[]\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tif (if_getallsamples(tk)) {\n\t\t\t\t\t\t// QUICK FIX!!!!\n\t\t\t\t\t\t// when this is set, will keep samples with empty .items[]\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tg2.samples.push(s2)\n\t\t}\n\t\tif (g2.samples.length == 0) continue\n\n\t\t// only for tal1 figure\n\t\t//maysortsamplesingroupbydt(g2)\n\n\t\tplotgroups.push(g2)\n\t}\n\n\tif (tk.groupsamplebyattr) {\n\t\tconst sortgroupby = tk.groupsamplebyattr.sortgroupby\n\t\tif (sortgroupby && sortgroupby.key && sortgroupby.order) {\n\t\t\t// sort groups, may be available for official track\n\t\t\tconst lst = []\n\t\t\tfor (const value of sortgroupby.order) {\n\t\t\t\tfor (const g of plotgroups) {\n\t\t\t\t\tif (!g.attributes) continue\n\t\t\t\t\tfor (const at of g.attributes) {\n\t\t\t\t\t\tif (at.k == sortgroupby.key && at.kvalue == value) {\n\t\t\t\t\t\t\t// is one\n\t\t\t\t\t\t\tg._sorted = 1\n\t\t\t\t\t\t\tlst.push(g)\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}\n\t\t\tfor (const g of plotgroups) {\n\t\t\t\tif (!g._sorted) lst.push(g)\n\t\t\t}\n\t\t\tfor (const g of lst) delete g._sorted\n\t\t\tplotgroups = lst\n\t\t}\n\t}\n\tif (tk.sampleset) {\n\t\t//sort plotgroups in same order as tk.sampleset\n\t\tconst sortOrder = tk.sampleset.map(i => i.name)\n\t\tplotgroups.sort((a, b) => {\n\t\t\tif (sortOrder.indexOf(a.name) > sortOrder.indexOf(b.name)) return 1\n\t\t\telse return -1\n\t\t})\n\t\t// for each group, sort samples by the order given\n\t\tfor (const sampleset of tk.sampleset) {\n\t\t\tconst plotgroup = plotgroups.find(pg => pg.name == sampleset.name)\n\t\t\tif (!plotgroup || !plotgroup.samples) continue\n\t\t\tconst foundsamples = []\n\t\t\tfor (const name of sampleset.samples) {\n\t\t\t\tconst s = plotgroup.samples.find(j => j.samplename == name)\n\t\t\t\tif (s) {\n\t\t\t\t\tfoundsamples.push(s)\n\t\t\t\t}\n\t\t\t}\n\t\t\tplotgroup.samples = foundsamples\n\t\t}\n\t}\n\treturn [plotgroups, svlst4dense]\n}\n\nfunction if_getallsamples(tk) {\n\t// QUICK FIX\n\tif (!tk.getallsamples) return false\n\tif (tk.iscustom) return true\n\tif (tk.mds && tk.mds.allow_getallsamples) return true\n\treturn false\n}\n\nfunction maysortsamplesingroupbydt(g) {\n\t/*\n\ttemporary, only for making tal1 figure\n\tby default samples are ordered by the first genomic position of their mutations\n\n\targ: a group with .samples[ {} ]\n\t*/\n\tconst cnv = []\n\tconst fusioninter = []\n\tconst fusionintra = []\n\tconst rest = []\n\tfor (const s of g.samples) {\n\t\tif (s.items.find(m => m.dt == common.dtcnv && m.start < 47720000 && m.stop > 47720000)) {\n\t\t\t// skip tiny cnvs not overlapping with stil promoter\n\t\t\tcnv.push(s)\n\t\t\tcontinue\n\t\t}\n\t\t{\n\t\t\tconst m = s.items.find(m => m.dt == common.dtfusionrna || m.dt == common.dtsv)\n\t\t\tif (m) {\n\t\t\t\tif (m.chrA == m.chrB) {\n\t\t\t\t\t// intra-chr\n\t\t\t\t\tif (m.posA < 48000000 && m.posB < 48000000) {\n\t\t\t\t\t\tcnv.push(s)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tfusionintra.push(s)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// inter-chr\n\t\t\t\t\tfusioninter.push(s)\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\trest.push(s)\n\t}\n\n\tg.samples = [...cnv, ...fusionintra, ...fusioninter, ...rest]\n}\n\n////////////////////// __multi ends\n\n/////////////  __maketk\n\nfunction copy_attributes(from, to) {\n\t// from mds.mutationAttribute to tk.mutationAttribute\n\tfor (const k in from) {\n\t\tto[k] = from[k]\n\t}\n\tif (from.attributes) {\n\t\tto.attributes = {}\n\t\tfor (const m in from.attributes) {\n\t\t\tto.attributes[m] = {}\n\t\t\tfor (const n in from.attributes[m]) {\n\t\t\t\tto.attributes[m][n] = from.attributes[m][n]\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction makeTk(tk, block) {\n\t/*\nfor both multi- and single-sample\n*/\n\n\tif (tk.mds) {\n\t\t/*\n\t\tin ds.js, these attributes belong to mds, but not the svcnv query track,\n\t\tmeant to be applied to all tracks of this mds\n\t\tpreviously, on client, these two attributes were recorded on the svcnv track object\n\t\tnow they reside in the mds registry object of genome\n\t\thowever, they are still copied to tk object so that all the code will work!!\n\n\t\ttk.mutationAttribute = tk.mds.mutationAttribute\n\t\ttk.sampleAttribute = tk.mds.sampleAttribute\n\t\ttk.locusAttribute = tk.mds.locusAttribute\n\t\ttk.alleleAttribute = tk.mds.alleleAttribute\n\t\t*/\n\n\t\tif (tk.mds.mutationAttribute) {\n\t\t\ttk.mutationAttribute = {}\n\t\t\tcopy_attributes(tk.mds.mutationAttribute, tk.mutationAttribute)\n\t\t}\n\t\tif (tk.mds.sampleAttribute) {\n\t\t\ttk.sampleAttribute = {}\n\t\t\tcopy_attributes(tk.mds.sampleAttribute, tk.sampleAttribute)\n\t\t}\n\t\tif (tk.mds.locusAttribute) {\n\t\t\ttk.locusAttribute = {}\n\t\t\tcopy_attributes(tk.mds.locusAttribute, tk.locusAttribute)\n\t\t}\n\t\tif (tk.mds.alleleAttribute) {\n\t\t\ttk.alleleAttribute = {}\n\t\t\tcopy_attributes(tk.mds.alleleAttribute, tk.alleleAttribute)\n\t\t}\n\n\t\ttk.nocnvlohsv = true\n\t\ttk.isdense = true\n\t\ttk.isfull = false\n\t\tif (tk.mds.queries) {\n\t\t\tfor (const k in tk.mds.queries) {\n\t\t\t\tconst t = tk.mds.queries[k]\n\t\t\t\tif (t.type == common.tkt.mdssvcnv) {\n\t\t\t\t\t// mds has a svcnv track\n\t\t\t\t\tdelete tk.nocnvlohsv\n\t\t\t\t\tif (t.isfull) {\n\t\t\t\t\t\ttk.isfull = true\n\t\t\t\t\t\ttk.isdense = false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} else if (tk.iscustom) {\n\t\tif (!tk.file && !tk.url) {\n\t\t\t// custom track without svcnv file\n\t\t\t// do not show legend and config for cnv loh sv fusion\n\t\t\ttk.nocnvlohsv = true\n\t\t}\n\t}\n\n\t/*\n\tmust do this first\n\tit may set singlesample{} as is defined in datasetqueries of embedding call\n\t*/\n\tapply_customization_oninit(tk, block)\n\n\tif (tk.singlesample) {\n\t\t// single-sample\n\n\t\ttk.waterfall = {\n\t\t\tinuse: false,\n\t\t\taxisheight: 100,\n\t\t\tbottompad: 10,\n\t\t\taxisgg: tk.gleft.append('g')\n\t\t}\n\t\tif (tk.singlesample.waterfall) {\n\t\t\t// default setting sneaked in from embedding call\n\t\t\ttk.waterfall.inuse = tk.singlesample.waterfall.inuse\n\t\t}\n\n\t\ttk.waterfall.axisg = tk.waterfall.axisgg.append('g')\n\t\ttk.waterfall.lab1 = tk.waterfall.axisgg\n\t\t\t.append('text')\n\t\t\t.attr('font-size', 13)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('x', -10)\n\t\ttk.waterfall.lab2 = tk.waterfall.axisgg\n\t\t\t.append('text')\n\t\t\t.attr('font-size', 13)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('x', -10)\n\t\ttk.waterfall.lab3 = tk.waterfall.axisgg\n\t\t\t.append('text')\n\t\t\t.attr('font-size', 13)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('x', -10)\n\t} else {\n\t\t// in multi-sample\n\n\t\ttk.samplematrices = []\n\n\t\t// allow hidding some labels\n\t\t// do not override config from native dataset\n\t\tif (tk.multihidelabel_vcf == undefined) {\n\t\t\ttk.multihidelabel_vcf = true\n\t\t}\n\t\tif (tk.multihidelabel_fusion == undefined) {\n\t\t\ttk.multihidelabel_fusion = true\n\t\t}\n\t\tif (tk.multihidelabel_sv == undefined) {\n\t\t\ttk.multihidelabel_sv = true\n\t\t}\n\t}\n\n\t// if not set, will set default mode here\n\tif (!tk.singlesample && !tk.isdense && !tk.isfull) {\n\t\tif (tk.iscustom) {\n\t\t\ttk.isdense = false\n\t\t\ttk.isfull = true\n\t\t} else {\n\t\t\ttk.isdense = true\n\t\t\ttk.isfull = false\n\t\t\tif (tk.showfullmode) {\n\t\t\t\ttk.isdense = false\n\t\t\t\ttk.isfull = true\n\t\t\t}\n\t\t}\n\t}\n\n\ttk.tip2 = new client.Menu({ padding: '0px' })\n\n\tif (tk.singlesample) {\n\t\t// set default values\n\t\tif (!tk.midpad) tk.midpad = 3\n\t\tif (!tk.stem1) {\n\t\t\ttk.stem1 = 10\n\t\t\ttk.stem2 = 0\n\t\t\ttk.stem3 = 5\n\t\t}\n\t\tif (!tk.legheight) tk.legheight = 40\n\t\tif (!tk.discradius) tk.discradius = 8\n\t\tif (!tk.valueCutoff) tk.valueCutoff = 0.2\n\t\t// length limit could be 0\n\t\tif (!Number.isInteger(tk.bplengthUpperLimit)) tk.bplengthUpperLimit = 2000000\n\t\tif (!Number.isInteger(tk.lohLengthUpperLimit)) tk.lohLengthUpperLimit = 2000000\n\t\tif (!tk.segmeanValueCutoff) tk.segmeanValueCutoff = 0.1\n\n\t\tif (tk.fixname) {\n\t\t\ttk.name = tk.fixname\n\t\t\ttk.tklabel.text(tk.name)\n\t\t\tdelete tk.fixname\n\t\t} else {\n\t\t\ttk.tklabel.text((tk.name ? tk.name + ', ' : '') + tk.singlesample.name)\n\t\t}\n\n\t\t// tklabel name updated, must do below\n\t\ttk.leftLabelMaxwidth = tk.tklabel.node().getBBox().width\n\t\tblock.setllabel()\n\n\t\ttk.svvcf_g = tk.glider.append('g') // show sv as lollipops\n\t\ttk.cnv_g = tk.glider.append('g') // show cnv/loh as bed track\n\t} else {\n\t\t// multi-sample\n\t\tif (tk.mds && tk.mds.version && tk.mds.version.label) {\n\t\t\ttk.versionlabel = block.maketklefthandle(tk, block.labelfontsize).text(tk.mds.version.label)\n\t\t\tif (tk.mds.version.link) {\n\t\t\t\ttk.versionlabel.on('click', () => {\n\t\t\t\t\twindow.open(tk.mds.version.link)\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\ttk.cnvleftg = tk.gleft.append('g')\n\t\ttk.vcfdensityg = tk.glider.append('g')\n\t\ttk.vcfdensitylabelg = tk.gleft.append('g')\n\t\ttk.svdensityg = tk.glider.append('g')\n\t\ttk.svdensitylabelg = tk.gleft.append('g')\n\t\ttk.cnvmidg = tk.glider.append('g')\n\t\ttk.cnvrightg = tk.gright.append('g')\n\t}\n\n\ttk.cnvcolor = {}\n\t{\n\t\tconst t = d3rgb(tk.gaincolor)\n\t\ttk.cnvcolor.gain = {\n\t\t\tstr: tk.gaincolor,\n\t\t\tr: t.r,\n\t\t\tg: t.g,\n\t\t\tb: t.b\n\t\t}\n\t\tdelete tk.gaincolor\n\t}\n\t{\n\t\tconst t = d3rgb(tk.losscolor)\n\t\ttk.cnvcolor.loss = {\n\t\t\tstr: tk.losscolor,\n\t\t\tr: t.r,\n\t\t\tg: t.g,\n\t\t\tb: t.b\n\t\t}\n\t\tdelete tk.losscolor\n\t}\n\t{\n\t\tconst t = d3rgb(tk.lohcolor)\n\t\ttk.cnvcolor.loh = {\n\t\t\tstr: tk.lohcolor,\n\t\t\tr: t.r,\n\t\t\tg: t.g,\n\t\t\tb: t.b\n\t\t}\n\t\tdelete tk.lohcolor\n\t}\n\n\tif (tk.iscustom) {\n\t\t// default value for naive custom track\n\t\tif (tk.valueCutoff == undefined) tk.valueCutoff = 0.2\n\t\tif (tk.bplengthUpperLimit == undefined) tk.bplengthUpperLimit = 2000000\n\t\tif (tk.segmeanValueCutoff == undefined) tk.segmeanValueCutoff = 0.1\n\t\tif (tk.lohLengthUpperLimit == undefined) tk.lohLengthUpperLimit = 2000000\n\t}\n\n\t// config\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\tconfigPanel(tk, block)\n\t})\n\n\tmakeTk_legend(block, tk)\n\n\t// gene expression config\n\t// make sure do not overwrite gecfg from custom setting\n\n\tlet hasexpression = false\n\tif (tk.iscustom) {\n\t\t// custom\n\t\tif (tk.checkexpressionrank) {\n\t\t\thasexpression = true\n\t\t\tif (!tk.gecfg) tk.gecfg = {}\n\t\t\ttk.gecfg.datatype = tk.checkexpressionrank.datatype\n\t\t}\n\t} else {\n\t\t// official\n\t\tif (tk.mds.queries[tk.querykey].checkexpressionrank) {\n\t\t\thasexpression = true\n\t\t\tconst cp = tk.mds.queries[tk.mds.queries[tk.querykey].checkexpressionrank.querykey]\n\t\t\tif (tk.gecfg && tk.gecfg.fixed_pend) {\n\t\t\t\t// copy over custom settings\n\t\t\t\tcp.fixed_pend = tk.gecfg.fixed_pend\n\t\t\t}\n\t\t\ttk.gecfg = cp\n\t\t}\n\t}\n\tif (hasexpression) {\n\t\t/* inherit configs from official tk, if not, rebuild\n\t\tthis can make sure the same configurations are also available under the dataset.queries.genefpkm\n\t\tallowing it to be shared for boxplots etc.\n\t\t*/\n\t\tif (!tk.gecfg) tk.gecfg = {}\n\n\t\tif (!tk.gecfg.fixed) {\n\t\t\t/*\n\t\t\tupon initing multi-sample view, fixed[] is added\n\t\t\twhen launching a single-sample from multi, makeTk will be called again\n\t\t\tsince gecfg is referencing the original object but not a duplicate, must not overwrite fixed[]\n\t\t\tshould really be a duplicate object instead\n\t\t\t*/\n\t\t\ttk.gecfg.fixed = []\n\t\t}\n\n\t\tif (!tk.gecfg.no_ase) {\n\t\t\texpressionstat.init_config(tk.gecfg)\n\t\t}\n\t}\n\n\t// end of makeTk\n}\n\nfunction apply_customization_oninit(tk, block) {\n\t/*\n\tcustomization attr from embedding\n\teither native or custom track\n\tcopy them to attributes\n\twill override some previous settings\n\n\tfor filtering attributes, must do it before initiating legend\n\tbecause novel keys will be added anew\n\t*/\n\n\t// if is custom, the \"customization\" will be tk itself\n\n\tconst c = tk.iscustom ? tk : tk.customization\n\n\tif (!c) return\n\n\tif (c.singlesample) {\n\t\t/*\n\t\tthis method will pop up panel and show all associated tracks, not in use now\n\n\t\tconst s = c.singlesample\n\t\tfocus_singlesample({\n\t\t\tsample: { samplename: s.name },\n\t\t\tsamplegroup: { attributes: s.attributes },\n\t\t\ttk: tk,\n\t\t\tblock: block,\n\t\t})\n\t\t*/\n\n\t\t// for now, simply turn the mds track into single-sample mode\n\t\ttk.singlesample = c.singlesample\n\t} else if (c.sampleset) {\n\t\ttk.sampleset = c.sampleset\n\t}\n\n\t// rest are multi-sample\n\ttk.hide_cnvgain = c.hide_cnvgain\n\ttk.hide_cnvloss = c.hide_cnvloss\n\n\tif (c.isfull) {\n\t\ttk.isdense = false\n\t\ttk.isfull = true\n\t} else if (c.isdense) {\n\t\ttk.isdense = true\n\t\ttk.isfull = false\n\t}\n\n\tif (c.sampleAttribute) {\n\t\tif (!tk.sampleAttribute) tk.sampleAttribute = {}\n\t\tif (!tk.sampleAttribute.attributes) tk.sampleAttribute.attributes = {}\n\t\tfor (const k in c.sampleAttribute) {\n\t\t\tconst cust = c.sampleAttribute[k]\n\t\t\tif (!tk.sampleAttribute.attributes[k]) {\n\t\t\t\t// a customized attribute is not found in registry, allow it\n\t\t\t\ttk.sampleAttribute.attributes[k] = {\n\t\t\t\t\tlabel: k\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst attr = tk.sampleAttribute.attributes[k]\n\t\t\tif (!attr.hiddenvalues) attr.hiddenvalues = new Set()\n\t\t\tif (cust.hiddenvalues) {\n\t\t\t\tfor (const v of cust.hiddenvalues) attr.hiddenvalues.add(v)\n\t\t\t}\n\t\t}\n\t}\n\n\ttk.legend_mclass = {\n\t\thiddenvalues: new Set()\n\t}\n\tif (c.vcf) {\n\t\tif (c.vcf.hiddenclass) {\n\t\t\tfor (const m of c.vcf.hiddenclass) tk.legend_mclass.hiddenvalues.add(m)\n\t\t}\n\t}\n\tif (c.cnv) {\n\t\tif (c.cnv.hidden) tk.legend_mclass.hiddenvalues.add(common.dtcnv)\n\t\tif (Number.isInteger(c.cnv.upperlengthlimit)) tk.bplengthUpperLimit = c.cnv.upperlengthlimit\n\t}\n\tif (c.loh) {\n\t\tif (c.loh.hidden) tk.legend_mclass.hiddenvalues.add(common.dtloh)\n\t\tif (Number.isInteger(c.loh.upperlengthlimit)) tk.lohLengthUpperLimit = c.loh.upperlengthlimit\n\t}\n\tif (c.fusion) {\n\t\tif (c.fusion.hidden) tk.legend_mclass.hiddenvalues.add(common.dtfusionrna)\n\t}\n\tif (c.sv) {\n\t\tif (c.sv.hidden) tk.legend_mclass.hiddenvalues.add(common.dtsv)\n\t}\n\tif (c.itd) {\n\t\tif (c.itd.hidden) tk.legend_mclass.hiddenvalues.add(common.dtitd)\n\t}\n\tif (c.fixedgeneexpression) {\n\t\tif (!tk.gecfg) tk.gecfg = {}\n\t\ttk.gecfg.fixed_pend = c.fixedgeneexpression\n\t}\n}\n\nfunction multi_changemode(tk, block) {\n\ttk.tkconfigtip.hide()\n\tif (tk.mode_radio_1.property('checked')) {\n\t\ttk.isdense = true\n\t\ttk.isfull = false\n\t} else if (tk.mode_radio_2.property('checked')) {\n\t\ttk.isdense = false\n\t\ttk.isfull = true\n\t}\n\n\tif (!tk._data) {\n\t\t// no data\n\t\treturn\n\t}\n\n\trender_samplegroups(tk, block)\n\tblock.block_setheight()\n\tblock.setllabel()\n}\n\nfunction configPanel(tk, block) {\n\ttk.tkconfigtip.clear()\n\n\tmay_show_samplematrix_button(tk, block)\n\n\tmay_allow_modeswitch(tk, block)\n\n\tmay_allow_samplesearch(tk, block)\n\n\tmakeoption_sampleset(tk, block)\n\n\tmay_allow_showhidelabel_multi(tk, block)\n\n\tmay_allow_togglewaterfall_single(tk, block)\n\n\tconfigPanel_cnvloh(tk, block)\n\n\ttk.tkconfigtip.showunder(tk.config_handle.node())\n}\n\nfunction makeoption_sampleset(tk, block) {\n\tif (tk.singlesample) return\n\tconst row = tk.tkconfigtip.d.append('div').style('margin-bottom', '25px')\n\tif (tk.sampleset) {\n\t\trow\n\t\t\t.append('span')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('padding-right', '10px')\n\t\t\t.text('Restricted to ' + tk.sampleset.reduce((i, j) => i + j.samples.length, 0) + ' samples')\n\t\trow\n\t\t\t.append('button')\n\t\t\t.text('Edit')\n\t\t\t.on('click', () => {\n\t\t\t\tshowinput_sampleset(tk, block)\n\t\t\t})\n\t\trow\n\t\t\t.append('button')\n\t\t\t.text('Remove')\n\t\t\t.on('click', () => {\n\t\t\t\ttk.tkconfigtip.hide()\n\t\t\t\tdelete tk.sampleset\n\t\t\t\tloadTk(tk, block)\n\t\t\t})\n\t\treturn\n\t}\n\t// allow to enter sampleset\n\trow\n\t\t.append('button')\n\t\t.text('Use a sample list')\n\t\t.on('click', () => {\n\t\t\tshowinput_sampleset(tk, block)\n\t\t})\n\n\t// QUICKFIX\n\t// ways to inhibit this button: when sampleset is in use; or if official dataset doesn't say this is allowed\n\t// while not using sampleset, check condition if to allow to show all samples\n\tif (tk.iscustom || (tk.mds && tk.mds.allow_getallsamples)) {\n\t\trow\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.text(tk.getallsamples ? 'Only show samples with variants' : 'Show all samples')\n\t\t\t.on('click', () => {\n\t\t\t\ttk.getallsamples = !tk.getallsamples\n\t\t\t\ttk.tkconfigtip.hide()\n\t\t\t\tloadTk(tk, block)\n\t\t\t})\n\t}\n}\n\nfunction showinput_sampleset(tk, block) {\n\t// for editing existing set or create new\n\ttk.tkconfigtip.clear()\n\tconst d = tk.tkconfigtip.d.append('div')\n\tconst ta = d\n\t\t.append('textarea')\n\t\t.attr('placeholder', 'One sample per row. Each row has sample and optional group name, joined by space or tab.')\n\tif (tk.sampleset) {\n\t\tconst lst = []\n\t\tfor (const l of tk.sampleset) {\n\t\t\tfor (const s of l.samples) {\n\t\t\t\tlst.push(s + ' ' + l.name)\n\t\t\t}\n\t\t}\n\t\tta.property('value', lst.join('\\n')).style('width', '250px').style('height', '200px')\n\t} else {\n\t\tta.style('width', '200px').style('height', '100px')\n\t}\n\td.append('button')\n\t\t.text('Submit')\n\t\t.style('display', 'block')\n\t\t.on('click', () => {\n\t\t\tconst lst = ta.property('value').trim().split('\\n')\n\t\t\tif (lst.length == 0) return\n\t\t\tconst g2l = new Map()\n\t\t\tconst samplesnogrp = []\n\t\t\tfor (const line of lst) {\n\t\t\t\tconst [sample, group] = line.split(/[\\s\\t]/)\n\t\t\t\tif (!sample) continue\n\t\t\t\tif (!group) {\n\t\t\t\t\tsamplesnogrp.push(sample)\n\t\t\t\t} else {\n\t\t\t\t\tif (!g2l.has(group)) g2l.set(group, [])\n\t\t\t\t\tg2l.get(group).push(sample)\n\t\t\t\t}\n\t\t\t}\n\t\t\ttk.sampleset = []\n\t\t\tfor (const [name, samples] of g2l) {\n\t\t\t\ttk.sampleset.push({ name, samples })\n\t\t\t}\n\t\t\tif (samplesnogrp.length) {\n\t\t\t\tconst g = { samples: samplesnogrp }\n\t\t\t\t// has samples without group name, if there are others with group name, use default, otherwise use none\n\t\t\t\tif (g2l.size) {\n\t\t\t\t\tg.name = 'Unnamed group'\n\t\t\t\t}\n\t\t\t\ttk.sampleset.push(g)\n\t\t\t}\n\t\t\ttk.tkconfigtip.hide()\n\t\t\tloadTk(tk, block)\n\t\t})\n}\n\nfunction may_allow_togglewaterfall_single(tk, block) {\n\t/*\nin single sample, when snvindel has more than 1, may show as waterfall\nthe cutoff \"1\" may be configurable\n*/\n\tif (!tk.singlesample) return\n\n\tconst row = tk.tkconfigtip.d.append('div').style('margin-bottom', '15px')\n\n\tif (!tk.data_vcf || tk.data_vcf.length < 2) {\n\t\t// not enough snvindel\n\t\trow.style('opacity', 0.5).text('No waterfall plot: not enough SNV/indels')\n\t\treturn\n\t}\n\n\tconst id = Math.random()\n\trow\n\t\t.append('input')\n\t\t.attr('type', 'checkbox')\n\t\t.attr('id', id)\n\t\t.property('checked', tk.waterfall.inuse)\n\t\t.on('change', event => {\n\t\t\ttk.waterfall.inuse = event.target.checked\n\t\t\trender_singlesample(tk, block)\n\t\t\tblock.block_setheight()\n\t\t})\n\trow.append('label').attr('for', id).html('&nbsp;use Waterfall plot for SNV/indels')\n}\n\nfunction configPanel_cnvloh(tk, block) {\n\tif (tk.nocnvlohsv) return\n\n\tconst holder = tk.tkconfigtip.d\n\t/*\n\t// filter cnv with sv\n\t{\n\t\t// do not use!!! see notes on server\n\t\tconst row=holder.append('div').style('margin-bottom','15px')\n\t\tconst id = Math.random().toString()\n\t\trow.append('input')\n\t\t\t.attr('type','checkbox')\n\t\t\t.attr('id', id)\n\t\t\t.property( 'checked', tk.showonlycnvwithsv )\n\t\t\t.on('change',(event)=>{\n\t\t\t\ttk.showonlycnvwithsv = event.target.checked\n\t\t\t\tloadTk(tk, block)\n\t\t\t})\n\t\trow.append('label')\n\t\t\t.attr('for',id)\n\t\t\t.html('&nbsp;Show only CNV with SV support')\n\t\trow.append('div')\n\t\t\t.style('font-size','.7em').style('color','#858585')\n\t\t\t.html('SV breakpoint must be inside a CNV or within its 1 Kb flanking.')\n\t}\n\t*/\n\n\t// cnv log2 ratio\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').html('CNV log2(ratio) cutoff&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.property('value', tk.valueCutoff || 0)\n\t\t\t.attr('type', 'number')\n\t\t\t.style('width', '50px')\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tlet v = Number.parseFloat(event.target.value)\n\t\t\t\tif (!v || v < 0) {\n\t\t\t\t\t// invalid value, set to 0 to cancel\n\t\t\t\t\tv = 0\n\t\t\t\t}\n\t\t\t\tif (v == 0) {\n\t\t\t\t\tif (tk.valueCutoff) {\n\t\t\t\t\t\t// cutoff has been set, cancel and refetch data\n\t\t\t\t\t\ttk.valueCutoff = 0\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// cutoff has not been set, do nothing\n\t\t\t\t\t}\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// set cutoff\n\t\t\t\tif (tk.valueCutoff) {\n\t\t\t\t\t// cutoff has been set\n\t\t\t\t\tif (tk.valueCutoff == v) {\n\t\t\t\t\t\t// same as current cutoff, do nothing\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// set new cutoff\n\t\t\t\t\t\ttk.valueCutoff = v\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// cutoff has not been set\n\t\t\t\t\ttk.valueCutoff = v\n\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t}\n\t\t\t})\n\t\trow\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('color', '#858585')\n\t\t\t.html(\n\t\t\t\t'Only show CNV with absolute log2(ratio) no less than cutoff.<br>Set to 0 to show all. Press ENTER to update.'\n\t\t\t)\n\t}\n\n\t// focal cnv\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').html('CNV segment size limit&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.property('value', tk.bplengthUpperLimit || 0)\n\t\t\t.attr('type', 'number')\n\t\t\t.style('width', '80px')\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tlet v = Number.parseInt(event.target.value)\n\t\t\t\tif (!v || v < 0) {\n\t\t\t\t\t// invalid value, set to 0 to cancel\n\t\t\t\t\tv = 0\n\t\t\t\t}\n\t\t\t\tif (v == 0) {\n\t\t\t\t\tif (tk.bplengthUpperLimit) {\n\t\t\t\t\t\t// cutoff has been set, cancel and refetch data\n\t\t\t\t\t\ttk.bplengthUpperLimit = 0\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// cutoff has not been set, do nothing\n\t\t\t\t\t}\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// set cutoff\n\t\t\t\tif (tk.bplengthUpperLimit) {\n\t\t\t\t\t// cutoff has been set\n\t\t\t\t\tif (tk.bplengthUpperLimit == v) {\n\t\t\t\t\t\t// same as current cutoff, do nothing\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// set new cutoff\n\t\t\t\t\t\ttk.bplengthUpperLimit = v\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// cutoff has not been set\n\t\t\t\t\ttk.bplengthUpperLimit = v\n\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t}\n\t\t\t})\n\t\trow.append('span').text('bp')\n\t\trow\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('color', '#858585')\n\t\t\t.html('Limit the CNV segment length to show only focal events.<br>Set to 0 to show all. Press ENTER to update.')\n\t}\n\n\t// cnv color\n\t{\n\t\tconst row = holder.append('div')\n\t\trow.append('span').html('Copy number gain&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', tk.cnvcolor.gain.str)\n\t\t\t.on('change', event => {\n\t\t\t\ttk.cnvcolor.gain.str = event.target.value\n\t\t\t\tconst c = d3rgb(tk.cnvcolor.gain.str)\n\t\t\t\ttk.cnvcolor.gain.r = c.r\n\t\t\t\ttk.cnvcolor.gain.g = c.g\n\t\t\t\ttk.cnvcolor.gain.b = c.b\n\t\t\t\ttk.cnvcolor.cnvlegend.gain_stop.attr('stop-color', tk.cnvcolor.gain.str)\n\t\t\t\tif (tk.singlesample) {\n\t\t\t\t\trender_singlesample(tk, block)\n\t\t\t\t} else {\n\t\t\t\t\trender_samplegroups(tk, block)\n\t\t\t\t}\n\t\t\t})\n\t\trow.append('span').html('&nbsp;&nbsp;loss&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', tk.cnvcolor.loss.str)\n\t\t\t.on('change', event => {\n\t\t\t\ttk.cnvcolor.loss.str = event.target.value\n\t\t\t\tconst c = d3rgb(tk.cnvcolor.loss.str)\n\t\t\t\ttk.cnvcolor.loss.r = c.r\n\t\t\t\ttk.cnvcolor.loss.g = c.g\n\t\t\t\ttk.cnvcolor.loss.b = c.b\n\t\t\t\ttk.cnvcolor.cnvlegend.loss_stop.attr('stop-color', tk.cnvcolor.loss.str)\n\t\t\t\tif (tk.singlesample) {\n\t\t\t\t\trender_singlesample(tk, block)\n\t\t\t\t} else {\n\t\t\t\t\trender_samplegroups(tk, block)\n\t\t\t\t}\n\t\t\t})\n\t}\n\n\tif (tk.cnvcolor.lohlegend) {\n\t\tholder.append('hr').style('margin', '20px')\n\n\t\t// loh segmean cutoff\n\t\t{\n\t\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\t\trow.append('span').html('LOH seg.mean cutoff&nbsp;')\n\t\t\trow\n\t\t\t\t.append('input')\n\t\t\t\t.property('value', tk.segmeanValueCutoff || 0)\n\t\t\t\t.attr('type', 'number')\n\t\t\t\t.style('width', '50px')\n\t\t\t\t.on('keyup', event => {\n\t\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\t\tlet v = Number.parseFloat(event.target.value)\n\t\t\t\t\tif (!v || v < 0) {\n\t\t\t\t\t\t// invalid value, set to 0 to cancel\n\t\t\t\t\t\tv = 0\n\t\t\t\t\t}\n\t\t\t\t\tif (v == 0) {\n\t\t\t\t\t\tif (tk.segmeanValueCutoff) {\n\t\t\t\t\t\t\t// cutoff has been set, cancel and refetch data\n\t\t\t\t\t\t\ttk.segmeanValueCutoff = 0\n\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// cutoff has not been set, do nothing\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\t// set cutoff\n\t\t\t\t\tif (tk.segmeanValueCutoff) {\n\t\t\t\t\t\t// cutoff has been set\n\t\t\t\t\t\tif (tk.segmeanValueCutoff == v) {\n\t\t\t\t\t\t\t// same as current cutoff, do nothing\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// set new cutoff\n\t\t\t\t\t\t\ttk.segmeanValueCutoff = v\n\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// cutoff has not been set\n\t\t\t\t\t\ttk.segmeanValueCutoff = v\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('color', '#858585')\n\t\t\t\t.html('Only show LOH with seg.mean no less than cutoff.<br>Set to 0 to show all. Press ENTER to update.')\n\t\t}\n\n\t\t// focal loh\n\t\t{\n\t\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\t\trow.append('span').html('LOH segment size limit&nbsp;')\n\t\t\trow\n\t\t\t\t.append('input')\n\t\t\t\t.property('value', tk.lohLengthUpperLimit || 0)\n\t\t\t\t.attr('type', 'number')\n\t\t\t\t.style('width', '80px')\n\t\t\t\t.on('keyup', event => {\n\t\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\t\tlet v = Number.parseInt(event.target.value)\n\t\t\t\t\tif (!v || v < 0) {\n\t\t\t\t\t\t// invalid value, set to 0 to cancel\n\t\t\t\t\t\tv = 0\n\t\t\t\t\t}\n\t\t\t\t\tif (v == 0) {\n\t\t\t\t\t\tif (tk.lohLengthUpperLimit) {\n\t\t\t\t\t\t\t// cutoff has been set, cancel and refetch data\n\t\t\t\t\t\t\ttk.lohLengthUpperLimit = 0\n\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// cutoff has not been set, do nothing\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\t// set cutoff\n\t\t\t\t\tif (tk.lohLengthUpperLimit) {\n\t\t\t\t\t\t// cutoff has been set\n\t\t\t\t\t\tif (tk.lohLengthUpperLimit == v) {\n\t\t\t\t\t\t\t// same as current cutoff, do nothing\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// set new cutoff\n\t\t\t\t\t\t\ttk.lohLengthUpperLimit = v\n\t\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// cutoff has not been set\n\t\t\t\t\t\ttk.lohLengthUpperLimit = v\n\t\t\t\t\t\tloadTk(tk, block)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\trow.append('span').text('bp')\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('color', '#858585')\n\t\t\t\t.html('Limit the LOH segment length to show only focal events.<br>Set to 0 to show all. Press ENTER to update.')\n\t\t}\n\n\t\t// loh color\n\t\t{\n\t\t\tconst row = holder.append('div').style('margin-bottom', '1px')\n\t\t\trow.append('span').html('LOH color&nbsp;')\n\t\t\trow\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.property('value', tk.cnvcolor.loh.str)\n\t\t\t\t.on('change', event => {\n\t\t\t\t\ttk.cnvcolor.loh.str = event.target.value\n\t\t\t\t\tconst c = d3rgb(tk.cnvcolor.loh.str)\n\t\t\t\t\ttk.cnvcolor.loh.r = c.r\n\t\t\t\t\ttk.cnvcolor.loh.g = c.g\n\t\t\t\t\ttk.cnvcolor.loh.b = c.b\n\t\t\t\t\ttk.cnvcolor.lohlegend.loh_stop.attr('stop-color', tk.cnvcolor.loh.str)\n\t\t\t\t\tif (tk.singlesample) {\n\t\t\t\t\t\trender_singlesample(tk, block)\n\t\t\t\t\t} else {\n\t\t\t\t\t\trender_samplegroups(tk, block)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t}\n\t}\n\n\t// end of config\n}\n\nfunction may_allow_modeswitch(tk, block) {\n\t// only for multi-sample\n\tif (tk.singlesample) return\n\n\tconst div = tk.tkconfigtip.d\n\t\t.append('div')\n\t\t.style('background', '#FAF9DE')\n\t\t.style('margin-bottom', '20px')\n\t\t.style('padding', '15px')\n\n\tconst id1 = Math.random().toString()\n\tconst id2 = Math.random().toString()\n\tconst name = Math.random().toString()\n\tconst row1 = div.append('div').style('margin-bottom', '5px')\n\ttk.mode_radio_1 = row1\n\t\t.append('input')\n\t\t.attr('type', 'radio')\n\t\t.attr('id', id1)\n\t\t.attr('name', name)\n\t\t.property('checked', tk.isdense)\n\t\t.on('change', () => {\n\t\t\tmulti_changemode(tk, block)\n\t\t})\n\trow1\n\t\t.append('label')\n\t\t.attr('for', id1)\n\t\t.attr('class', 'sja_clbtext')\n\t\t.html(\n\t\t\t'&nbsp;Dense <span style=\"font-size:.7em;color:#858585;\">Showing densities of SV breakpoints and SNV/indels, over all samples</span>'\n\t\t)\n\n\tconst row2 = div.append('div')\n\ttk.mode_radio_2 = row2\n\t\t.append('input')\n\t\t.attr('type', 'radio')\n\t\t.attr('id', id2)\n\t\t.attr('name', name)\n\t\t.property('checked', tk.isfull)\n\t\t.on('change', () => {\n\t\t\tmulti_changemode(tk, block)\n\t\t})\n\trow2\n\t\t.append('label')\n\t\t.attr('for', id2)\n\t\t.attr('class', 'sja_clbtext')\n\t\t.html('&nbsp;Expanded <span style=\"font-size:.7em;color:#858585;\">Showing SV/SNV/indel for each sample</span>')\n}\n\nfunction may_allow_showhidelabel_multi(tk, block) {\n\t// only for multi-sample\n\tif (tk.singlesample) return\n\ttk.tkconfigtip.d\n\t\t.append('div')\n\t\t.style('margin-bottom', '5px')\n\t\t.text('Show text labels in expanded mode')\n\t\t.style('opacity', 0.5)\n\n\tconst row = tk.tkconfigtip.d.append('div').style('margin-bottom', '20px')\n\t{\n\t\t// TODO if no vcf tk, do not show it\n\t\tconst id = Math.random().toString()\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.attr('id', id)\n\t\t\t.property('checked', !tk.multihidelabel_vcf)\n\t\t\t.on('change', () => {\n\t\t\t\ttk.multihidelabel_vcf = !tk.multihidelabel_vcf\n\t\t\t\trender_samplegroups(tk, block)\n\t\t\t})\n\t\trow.append('label').attr('for', id).attr('class', 'sja_clbtext').html('&nbsp;SNV/indel')\n\t}\n\n\tif (!tk.nocnvlohsv) {\n\t\t{\n\t\t\tconst id = Math.random().toString()\n\t\t\trow\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.style('margin-left', '20px')\n\t\t\t\t.attr('id', id)\n\t\t\t\t.property('checked', !tk.multihidelabel_sv)\n\t\t\t\t.on('change', () => {\n\t\t\t\t\ttk.multihidelabel_sv = !tk.multihidelabel_sv\n\t\t\t\t\trender_samplegroups(tk, block)\n\t\t\t\t})\n\t\t\trow.append('label').attr('for', id).attr('class', 'sja_clbtext').html('&nbsp;DNA SV')\n\t\t}\n\t\t{\n\t\t\tconst id = Math.random().toString()\n\t\t\trow\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.style('margin-left', '20px')\n\t\t\t\t.attr('id', id)\n\t\t\t\t.property('checked', !tk.multihidelabel_fusion)\n\t\t\t\t.on('change', () => {\n\t\t\t\t\ttk.multihidelabel_fusion = !tk.multihidelabel_fusion\n\t\t\t\t\trender_samplegroups(tk, block)\n\t\t\t\t})\n\t\t\trow.append('label').attr('for', id).attr('class', 'sja_clbtext').html('&nbsp;RNA fusion')\n\t\t}\n\t}\n}\n\n/////////////  __maketk ENDS\n\nexport function map_cnv(item, tk, block) {\n\t/*\n\tcnv, loh, itd\n\t*/\n\tconst main = block.tkarg_maygm(tk)[0]\n\n\tif (item.chr == main.chr && Math.max(item.start, main.start) < Math.min(item.stop, main.stop)) {\n\t\titem.x1 = block.seekcoord(item.chr, Math.max(item.start, main.start))[0].x\n\t\t// in case item.stop is beyond chr length,\n\t\t// main.stop has to -1 to allow it to work with seekcoord\n\t\titem.x2 = block.seekcoord(item.chr, Math.min(item.stop, main.stop - 1))[0].x\n\t}\n\n\tlet x = block.width\n\tfor (const p of block.subpanels) {\n\t\tx += p.leftpad\n\t\tif (item.chr == p.chr && Math.max(item.start, p.start) < Math.min(item.stop, p.stop)) {\n\t\t\tconst x1 = x + (Math.max(item.start, p.start) - p.start) * p.exonsf\n\t\t\tconst x2 = x + (Math.min(item.stop, p.stop) - p.start) * p.exonsf\n\t\t\tif (item.x1 == undefined) {\n\t\t\t\titem.x1 = x1\n\t\t\t\titem.x2 = x2\n\t\t\t} else {\n\t\t\t\titem.x2 = x2\n\t\t\t}\n\t\t}\n\t\tx += p.width\n\t}\n\n\tif (item.x1 != undefined && block.gmmode && block.gmmode != common.gmmode.genomic) {\n\t\t// mapped item, in gmmode, may adjust\n\n\t\tconst pxw = block.width + block.subpanels.reduce((i, j) => j.width + j.leftpad, 0)\n\n\t\tif (item.x1 < item.x2) {\n\t\t\tif (item.x2 < 0 || item.x1 > pxw) {\n\t\t\t\t// out of range\n\t\t\t\titem.x1 = undefined\n\t\t\t\titem.x2 = undefined\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (item.x1 < 0) {\n\t\t\t\titem.x1 = 0\n\t\t\t}\n\t\t\tif (item.x2 > pxw) {\n\t\t\t\titem.x2 = pxw\n\t\t\t}\n\t\t} else if (item.x1 > item.x2) {\n\t\t\t// reversed\n\t\t\tif (item.x1 < 0 || item.x2 > pxw) {\n\t\t\t\t// out of range\n\t\t\t\titem.x1 = undefined\n\t\t\t\titem.x2 = undefined\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (item.x2 < 0) {\n\t\t\t\titem.x2 = 0\n\t\t\t}\n\t\t\tif (item.x1 > pxw) {\n\t\t\t\titem.x1 = pxw\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction map_sv_2(item, block) {\n\tconst lst = block.seekcoord(item._chr, item._pos)\n\tfor (const r of lst) {\n\t\tif (r.ridx != undefined) {\n\t\t\t// in main, if outside won't show this end\n\t\t\tif (r.x > 0 && r.x < block.width) {\n\t\t\t\titem.x = r.x\n\t\t\t\tbreak\n\t\t\t}\n\t\t} else if (r.subpanelidx != undefined) {\n\t\t\titem.x = r.x\n\t\t}\n\t}\n}\n\nfunction may_map_vcf(tk, block) {\n\t// map to view range: snvindel, itd\n\tif (!tk.data_vcf) return\n\tfor (const m of tk.data_vcf) {\n\t\tif (m.dt == common.dtsnvindel) {\n\t\t\tm._chr = m.chr\n\t\t\tm._pos = m.pos\n\t\t\tmap_sv_2(m, block)\n\t\t\tif (m.x == undefined) {\n\t\t\t\tconsole.log('snvindel unmapped: ' + m.chr + ':' + m.pos)\n\t\t\t} else {\n\t\t\t\tdelete m._chr\n\t\t\t\tdelete m._pos\n\t\t\t}\n\t\t} else {\n\t\t\tconsole.error('may_map_vcf: unknown dt')\n\t\t}\n\t}\n}\n\nfunction vcfdata_prep(tk, block) {\n\t/*\n\t_data_vcf returned by server\n\twill be filtered to data_vcf for display\n\tchanging mclass filtering option won't call this, will reload all datatypes from server, sorry about the trouble\n\t*/\n\tif (!tk._data_vcf || tk._data_vcf.length == 0) {\n\t\ttk.data_vcf = null\n\t\treturn\n\t}\n\n\tconst mlst = tk._data_vcf\n\n\ttk.data_vcf = []\n\n\tfor (const m of mlst) {\n\t\tif (m.dt == common.dtsnvindel) {\n\t\t\tcommon.vcfcopymclass(m, block)\n\t\t} else {\n\t\t\tthrow 'unknown dt ' + m.dt\n\t\t}\n\t\tif (!tk.legend_mclass.hiddenvalues.has(m.class)) {\n\t\t\ttk.data_vcf.push(m)\n\t\t}\n\t}\n}\n\nexport function dedup_sv(lst) {\n\t/* sv are breakends\n\tdedup\n\t*/\n\tconst key2sv = new Map()\n\tfor (const i of lst) {\n\t\tkey2sv.set(\n\t\t\ti.sample + '.' + i.chrA + '.' + i.posA + '.' + i.strandA + '.' + i.chrB + '.' + i.posB + '.' + i.strandB,\n\t\t\ti\n\t\t)\n\t}\n\treturn [...key2sv.values()]\n}\n\nexport function vcfvariantisgermline(ms, tk) {\n\t/*\n\tharcode: either somatic or germline\n\tms as an item from tk.data_vcf[].sampledata[]\n\ttk\n\t*/\n\n\tif (!ms) return false\n\n\tif (tk.legend_vorigin && tk.legend_vorigin.key) {\n\t\tconst v = ms[tk.legend_vorigin.key]\n\t\tif (v) {\n\t\t\tif (v.toLowerCase() == tk.legend_vorigin.germline) return true\n\t\t}\n\t}\n\treturn false\n}\n"],
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