@sjcrh/proteinpaint-client 2.217.1-0 → 2.218.0

package/dist/svmr-45YJKRQP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/svmr.unload.js", "../src/svmr.c.js", "../src/svmr.js"],
+  "sourcesContent": ["import { genomic2gm } from './coord'\nimport {\n\tdtitd,\n\tdtdel,\n\tdtfusionrna,\n\tdtnloss,\n\tdtcloss,\n\tmclassitd,\n\tmclassnloss,\n\tmclasscloss,\n\tmclassfusionrna\n} from '#shared/common.js'\nimport { newpane, export_data } from './client'\n\nexport function svmr_export_json(svmr, hqonly) {\n\tvar rows = []\n\tfor (const sample of svmr.samples) {\n\t\tfor (const egg of sample.egglst) {\n\t\t\tfor (const eg of egg.lst) {\n\t\t\t\tif (eg.ismsg) {\n\t\t\t\t\tconst lst = eg.lst.map(evt => evt.lst[0])\n\t\t\t\t\tif (hqonly) {\n\t\t\t\t\t\tlet hashq = false\n\t\t\t\t\t\tfor (const i of lst) {\n\t\t\t\t\t\t\tif (i.rating == 'Major') hashq = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (hashq) {\n\t\t\t\t\t\t\trows.push(lst)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\trows.push(lst)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\tfor (const p of evt.lst) {\n\t\t\t\t\t\t\tif (hqonly) {\n\t\t\t\t\t\t\t\tif (p.rating == 'Major') rows.push([p])\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\trows.push([p])\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tconst lines = [],\n\t\te_itd = [],\n\t\te_nloss = [],\n\t\te_closs = []\n\tfor (const row of rows) {\n\t\tif (row.length == 1 && row[0].usepair) {\n\t\t\tconst p = row[0]\n\t\t\tif (p.isitd) {\n\t\t\t\tconst u = p.usepair\n\t\t\t\tconst gm = svmr.genome.isoformmatch(u.a.isoform, p.chrA, p.posA)\n\t\t\t\tif (!gm) {\n\t\t\t\t\te_itd.push(p.sample + ' ' + p.geneA + ' ITD (' + p.rating + '): no gene model found for ' + u.a.isoform)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst exonbp1 = genomic2gm(p.posA, gm).rnapos\n\t\t\t\tconst exonbp2 = genomic2gm(p.posB, gm).rnapos\n\t\t\t\tif (exonbp1 <= exonbp2) {\n\t\t\t\t\te_itd.push(p.sample + ' ' + p.geneA + ' ITD (' + p.rating + '): negative duplication length')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst itd = {\n\t\t\t\t\ttypecode: dtitd,\n\t\t\t\t\tgene: p.geneA,\n\t\t\t\t\tisoform: u.a.isoform,\n\t\t\t\t\trating: p.rating,\n\t\t\t\t\tscore: p.score,\n\t\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\t\trnaposition: exonbp2,\n\t\t\t\t\trnaduplength: exonbp1 - exonbp2 + 1,\n\t\t\t\t\ta: {\n\t\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\t\tposition: p.posA,\n\t\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\t\ttotalreads: p.totalreadsA,\n\t\t\t\t\t\tmatch: p.matchA,\n\t\t\t\t\t\trepeat: p.repeatA\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\t\tposition: p.posB,\n\t\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\t\ttotalreads: p.totalreadsB,\n\t\t\t\t\t\tmatch: p.matchB,\n\t\t\t\t\t\trepeat: p.repeatB\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// interstitial\n\t\t\t\tlet aalen = 0,\n\t\t\t\t\tbplen = 0\n\t\t\t\tif (u.a.contigaa && u.b.contigaa) {\n\t\t\t\t\taalen = u.b.contigaa - u.a.contigaa - 1\n\t\t\t\t}\n\t\t\t\tif (u.a.contigbp && u.b.contigbp) {\n\t\t\t\t\tbplen = u.b.contigbp - u.a.contigbp - 1\n\t\t\t\t}\n\t\t\t\tif (aalen > 0) {\n\t\t\t\t\titd.interstitial = { aalen: aalen }\n\t\t\t\t}\n\t\t\t\tif (bplen > 0) {\n\t\t\t\t\tif (!itd.interstitial) itd.interstitial = {}\n\t\t\t\t\titd.interstitial.bplen = bplen\n\t\t\t\t}\n\t\t\t\tlines.push([p.sample, p.geneA, p.usepair.a.isoform, JSON.stringify(itd)])\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (p.isnloss) {\n\t\t\t\tconst p2 = p.usepair.b\n\t\t\t\tif (!p2.isoform) {\n\t\t\t\t\te_nloss.push(p.sample + ' ' + p.geneB + ' NLoss (' + p.rating + '): no isoform')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst gm = svmr.genome.isoformmatch(p2.isoform, p.chrB, p.posB)\n\t\t\t\tif (!gm) {\n\t\t\t\t\te_nloss.push(p.sample + ' ' + p.geneB + ' NLoss (' + p.rating + '): no gene model found for ' + p2.isoform)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst exonbp = genomic2gm(p.posB, gm).rnapos\n\t\t\t\tconst pp = {\n\t\t\t\t\ttypecode: dtnloss,\n\t\t\t\t\tgene: p.geneB,\n\t\t\t\t\tisoform: p2.isoform,\n\t\t\t\t\trating: p.rating,\n\t\t\t\t\tscore: p.score,\n\t\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\t\trnaposition: exonbp,\n\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\tposition: p.posB,\n\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\tmatch: p.matchB,\n\t\t\t\t\trepeat: p.repeatB,\n\t\t\t\t\tpartner: {\n\t\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\t\tposition: p.posA,\n\t\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\t\tmatch: p.matchA,\n\t\t\t\t\t\trepeat: p.repeatA\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (p.geneA) {\n\t\t\t\t\tpp.partner.gene = p.geneA\n\t\t\t\t}\n\t\t\t\tif (p.usepair.a.isoform) {\n\t\t\t\t\tpp.partner.isoform = p.usepair.a.isoform\n\t\t\t\t}\n\t\t\t\tlines.push([p.sample, p.geneB, p2.isoform, JSON.stringify(pp)])\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (p.iscloss) {\n\t\t\t\tconst p2 = p.usepair.a\n\t\t\t\tif (!p2.isoform) {\n\t\t\t\t\te_nloss.push(p.sample + ' ' + p.geneA + ' CLoss (' + p.rating + '): no isoform')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst gm = svmr.genome.isoformmatch(p2.isoform, p.chrA, p.posA)\n\t\t\t\tif (!gm) {\n\t\t\t\t\te_nloss.push(p.sample + ' ' + p.geneA + ' CLoss (' + p.rating + '): no gene model found by ' + p2.isoform)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst exonbp = genomic2gm(p.posA, gm).rnapos\n\t\t\t\tconst pp = {\n\t\t\t\t\ttypecode: dtcloss,\n\t\t\t\t\tgene: p.geneA,\n\t\t\t\t\tisoform: p2.isoform,\n\t\t\t\t\trating: p.rating,\n\t\t\t\t\tscore: p.score,\n\t\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\t\trnaposition: exonbp,\n\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\tposition: p.posA,\n\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\tmatch: p.matchA,\n\t\t\t\t\trepeat: p.repeatA,\n\t\t\t\t\tpartner: {\n\t\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\t\tposition: p.posB,\n\t\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\t\tmatch: p.matchB,\n\t\t\t\t\t\trepeat: p.repeatB\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (p.geneB) {\n\t\t\t\t\tpp.partner.gene = p.geneB\n\t\t\t\t}\n\t\t\t\tif (p.usepair.b.isoform) {\n\t\t\t\t\tpp.partner.isoform = p.usepair.b.isoform\n\t\t\t\t}\n\t\t\t\tlines.push([p.sample, p.geneA, p2.isoform, JSON.stringify(pp)])\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\tconst genes = new Set(),\n\t\t\tisoforms = new Set(),\n\t\t\tcleanup = []\n\t\tfor (const p of row) {\n\t\t\tif (p.geneA) genes.add(p.geneA)\n\t\t\tif (p.geneB) genes.add(p.geneB)\n\t\t\tif (p.usepair) {\n\t\t\t\tif (p.usepair.a.isoform) isoforms.add(p.usepair.a.isoform)\n\t\t\t\tif (p.usepair.b.isoform) isoforms.add(p.usepair.b.isoform)\n\t\t\t}\n\t\t\tconst clean = {\n\t\t\t\ttype: p.type,\n\t\t\t\ttype2: p.type2,\n\t\t\t\trating: p.rating,\n\t\t\t\tscore: p.score,\n\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\ta: {\n\t\t\t\t\tname: p.geneA,\n\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\tposition: p.posA,\n\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\tfeature: p.featureA,\n\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\tcontiglen: p.matchA,\n\t\t\t\t\trepeatscore: p.repeatA\n\t\t\t\t},\n\t\t\t\tb: {\n\t\t\t\t\tname: p.geneB,\n\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\tposition: p.posB,\n\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\tfeature: p.featureB,\n\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\tcontiglen: p.matchB,\n\t\t\t\t\trepeatscore: p.repeatB\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (p.usepair) {\n\t\t\t\tconst u = p.usepair\n\t\t\t\tclean.frame = u.frame\n\t\t\t\tif (u.a.isoform) {\n\t\t\t\t\tclean.a.isoform = u.a.isoform\n\t\t\t\t}\n\t\t\t\tif (u.b.isoform) {\n\t\t\t\t\tclean.b.isoform = u.b.isoform\n\t\t\t\t}\n\t\t\t\t/*\n\t\t\t\tclean.a.exon=u.a.exon\n\t\t\t\tclean.b.exon=u.b.exon\n\t\t\t\tclean.a.codon=u.a.codon\n\t\t\t\tclean.b.codon=u.b.codon\n\t\t\t\t*/\n\t\t\t\t// interstitial\n\t\t\t\tlet aalen = 0,\n\t\t\t\t\tbplen = 0\n\t\t\t\tif (u.a.contigaa && u.b.contigaa) {\n\t\t\t\t\taalen = u.b.contigaa - u.a.contigaa - 1\n\t\t\t\t}\n\t\t\t\tif (u.a.contigbp && u.b.contigbp) {\n\t\t\t\t\tbplen = u.b.contigbp - u.a.contigbp - 1\n\t\t\t\t}\n\t\t\t\tif (aalen > 0) {\n\t\t\t\t\tclean.interstitial = { aalen: aalen }\n\t\t\t\t}\n\t\t\t\tif (bplen > 0) {\n\t\t\t\t\tif (!clean.interstitial) clean.interstitial = {}\n\t\t\t\t\tclean.interstitial.bplen = bplen\n\t\t\t\t}\n\t\t\t}\n\t\t\tcleanup.push(clean)\n\t\t}\n\t\tconst genenames = [...genes]\n\t\tconst isoformnames = [...isoforms]\n\t\tlines.push([\n\t\t\trow[0].sample,\n\t\t\tgenenames.length ? genenames.join(',') : 'none',\n\t\t\tisoformnames.length ? isoformnames.join(',') : 'none',\n\t\t\tJSON.stringify(cleanup)\n\t\t])\n\t}\n\tif (e_itd.length) {\n\t\tsvmr.err(e_itd.join('<br>'))\n\t}\n\tif (e_nloss.length) {\n\t\tsvmr.err(e_nloss.join('<br>'))\n\t}\n\tif (e_closs.length) {\n\t\tsvmr.err(e_closs.join('<br>'))\n\t}\n\texport_data('Fusion data from ' + svmr.filename, [{ text: lines.map(i => i.join('\\t')).join('\\n') }])\n}\n\nexport function svmr_2pp(svmr, hqonly) {\n\tconst rows = []\n\tfor (const sample of svmr.samples) {\n\t\tfor (const egg of sample.egglst) {\n\t\t\tfor (const eg of egg.lst) {\n\t\t\t\tif (eg.ismsg) {\n\t\t\t\t\tconst lst = eg.lst.map(evt => evt.lst[0])\n\t\t\t\t\tif (hqonly) {\n\t\t\t\t\t\tlet hashq = false\n\t\t\t\t\t\tfor (const i of lst) {\n\t\t\t\t\t\t\tif (i.rating == 'Major') hashq = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (hashq) {\n\t\t\t\t\t\t\trows.push(lst)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\trows.push(lst)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\tfor (const p of evt.lst) {\n\t\t\t\t\t\t\tif (hqonly) {\n\t\t\t\t\t\t\t\tif (p.rating == 'Major') rows.push([p])\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\trows.push([p])\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tconst genes = {},\n\t\t// k: symbol, original case, will be converted to upper case later\n\t\te_itd = [],\n\t\te_nloss = [],\n\t\te_closs = []\n\tfor (const row of rows) {\n\t\tif (row.length == 1 && row[0].usepair) {\n\t\t\tconst p = row[0]\n\t\t\tif (p.isitd) {\n\t\t\t\tif (!p.geneA) {\n\t\t\t\t\te_itd.push(p.sample + ' ITD (' + p.rating + '): no gene name??')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst u = p.usepair\n\t\t\t\tconst gm = svmr.genome.isoformmatch(u.a.isoform, p.chrA, p.posA)\n\t\t\t\tif (!gm) {\n\t\t\t\t\te_itd.push(p.sample + ' ' + p.geneA + ' ITD (' + p.rating + '): no gene model found for ' + u.a.isoform)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst exonbp1 = genomic2gm(p.posA, gm).rnapos\n\t\t\t\tconst exonbp2 = genomic2gm(p.posB, gm).rnapos\n\t\t\t\tif (exonbp1 <= exonbp2) {\n\t\t\t\t\te_itd.push(p.sample + ' ' + p.geneA + ' ITD (' + p.rating + '): negative duplication length')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst itd = {\n\t\t\t\t\tdt: dtitd,\n\t\t\t\t\tclass: mclassitd,\n\t\t\t\t\tmname: 'ITD',\n\t\t\t\t\tgene: p.geneA,\n\t\t\t\t\tsample: p.sample,\n\t\t\t\t\tisoform: u.a.isoform,\n\t\t\t\t\trating: p.rating,\n\t\t\t\t\tscore: p.score,\n\t\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\t\trnaposition: exonbp2,\n\t\t\t\t\trnaduplength: exonbp1 - exonbp2 + 1,\n\t\t\t\t\ta: {\n\t\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\t\tposition: p.posA,\n\t\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\t\ttotalreads: p.totalreadsA,\n\t\t\t\t\t\tmatch: p.matchA,\n\t\t\t\t\t\trepeat: p.repeatA\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\t\tposition: p.posB,\n\t\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\t\ttotalreads: p.totalreadsB,\n\t\t\t\t\t\tmatch: p.matchB,\n\t\t\t\t\t\trepeat: p.repeatB\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// interstitial\n\t\t\t\tlet aalen = 0,\n\t\t\t\t\tbplen = 0\n\t\t\t\tif (u.a.contigaa && u.b.contigaa) {\n\t\t\t\t\taalen = u.b.contigaa - u.a.contigaa - 1\n\t\t\t\t}\n\t\t\t\tif (u.a.contigbp && u.b.contigbp) {\n\t\t\t\t\tbplen = u.b.contigbp - u.a.contigbp - 1\n\t\t\t\t}\n\t\t\t\tif (aalen > 0) {\n\t\t\t\t\titd.interstitial = { aalen: aalen }\n\t\t\t\t}\n\t\t\t\tif (bplen > 0) {\n\t\t\t\t\tif (!itd.interstitial) itd.interstitial = {}\n\t\t\t\t\titd.interstitial.bplen = bplen\n\t\t\t\t}\n\t\t\t\tif (!(p.geneA in genes)) {\n\t\t\t\t\tgenes[p.geneA] = []\n\t\t\t\t}\n\t\t\t\tgenes[p.geneA].push(itd)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (p.isnloss) {\n\t\t\t\tif (!p.geneB) {\n\t\t\t\t\te_nloss.push(p.sample + ' NLoss (' + p.rating + '): no geneB')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst p2 = p.usepair.b\n\t\t\t\tif (!p2.isoform) {\n\t\t\t\t\te_nloss.push(p.sample + ' ' + p.geneB + ' NLoss (' + p.rating + '): no isoform')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst gm = svmr.genome.isoformmatch(p2.isoform, p.chrB, p.posB)\n\t\t\t\tif (!gm) {\n\t\t\t\t\te_nloss.push(p.sample + ' ' + p.geneB + ' NLoss (' + p.rating + '): no gene model found for ' + p2.isoform)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst exonbp = genomic2gm(p.posB, gm).rnapos\n\t\t\t\tconst pp = {\n\t\t\t\t\tdt: dtnloss,\n\t\t\t\t\tclass: mclassnloss,\n\t\t\t\t\tmname: 'N-loss',\n\t\t\t\t\tgene: p.geneB,\n\t\t\t\t\tsample: p.sample,\n\t\t\t\t\tisoform: p2.isoform,\n\t\t\t\t\trating: p.rating,\n\t\t\t\t\tscore: p.score,\n\t\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\t\trnaposition: exonbp,\n\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\tposition: p.posB,\n\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\tmatch: p.matchB,\n\t\t\t\t\trepeat: p.repeatB,\n\t\t\t\t\tpartner: {\n\t\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\t\tposition: p.posA,\n\t\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\t\tmatch: p.matchA,\n\t\t\t\t\t\trepeat: p.repeatA\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (p.geneA) {\n\t\t\t\t\tpp.partner.gene = p.geneA\n\t\t\t\t}\n\t\t\t\tif (p.usepair.a.isoform) {\n\t\t\t\t\tpp.partner.isoform = p.usepair.a.isoform\n\t\t\t\t}\n\t\t\t\tif (!(p.geneB in genes)) {\n\t\t\t\t\tgenes[p.geneB] = []\n\t\t\t\t}\n\t\t\t\tgenes[p.geneB].push(pp)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (p.iscloss) {\n\t\t\t\tif (!p.geneA) {\n\t\t\t\t\te_closs.push(p.sample + ' CLoss (' + p.rating + '): no geneA')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst p2 = p.usepair.a\n\t\t\t\tif (!p2.isoform) {\n\t\t\t\t\te_closs.push(p.sample + ' ' + p.geneA + ' CLoss (' + p.rating + '): no isoform')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst gm = svmr.genome.isoformmatch(p2.isoform, p.chrA, p.posA)\n\t\t\t\tif (!gm) {\n\t\t\t\t\te_closs.push(p.sample + ' ' + p.geneA + ' CLoss (' + p.rating + '): no gene model found by ' + p2.isoform)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst exonbp = genomic2gm(p.posA, gm).rnapos\n\t\t\t\tconst pp = {\n\t\t\t\t\tdt: dtcloss,\n\t\t\t\t\tclass: mclasscloss,\n\t\t\t\t\tmname: 'C-loss',\n\t\t\t\t\tgene: p.geneA,\n\t\t\t\t\tsample: p.sample,\n\t\t\t\t\tisoform: p2.isoform,\n\t\t\t\t\trating: p.rating,\n\t\t\t\t\tscore: p.score,\n\t\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\t\trnaposition: exonbp,\n\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\tposition: p.posA,\n\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\tmatch: p.matchA,\n\t\t\t\t\trepeat: p.repeatA,\n\t\t\t\t\tpartner: {\n\t\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\t\tposition: p.posB,\n\t\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\t\tmatch: p.matchB,\n\t\t\t\t\t\trepeat: p.repeatB\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (p.geneB) {\n\t\t\t\t\tpp.partner.gene = p.geneB\n\t\t\t\t}\n\t\t\t\tif (p.usepair.b.isoform) {\n\t\t\t\t\tpp.partner.isoform = p.usepair.b.isoform\n\t\t\t\t}\n\t\t\t\tif (!(p.geneA in genes)) {\n\t\t\t\t\tgenes[p.geneA] = []\n\t\t\t\t}\n\t\t\t\tgenes[p.geneA].push(pp)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\t// regular fusions\n\t\tconst gene2isoform = new Map() // gene -> isoform\n\t\tconst cleanup = []\n\t\tfor (const p of row) {\n\t\t\tif (p.geneA) {\n\t\t\t\tif (!gene2isoform.has(p.geneA)) gene2isoform.set(p.geneA, new Set())\n\t\t\t\tif (p.usepair) {\n\t\t\t\t\tif (p.usepair.a.isoform) gene2isoform.get(p.geneA).add(p.usepair.a.isoform)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (p.geneB) {\n\t\t\t\tif (!gene2isoform.has(p.geneB)) gene2isoform.set(p.geneB, new Set())\n\t\t\t\tif (p.usepair) {\n\t\t\t\t\tif (p.usepair.b.isoform) gene2isoform.get(p.geneB).add(p.usepair.b.isoform)\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst clean = {\n\t\t\t\ttype: p.type,\n\t\t\t\ttype2: p.type2,\n\t\t\t\trating: p.rating,\n\t\t\t\tscore: p.score,\n\t\t\t\tfunctioneffect: p.functioneffect,\n\t\t\t\ta: {\n\t\t\t\t\tname: p.geneA,\n\t\t\t\t\tchr: p.chrA,\n\t\t\t\t\tposition: p.posA,\n\t\t\t\t\tstrand: p.ortA,\n\t\t\t\t\tratio: p.ratioA,\n\t\t\t\t\tfeature: p.featureA,\n\t\t\t\t\tchimericreads: p.readsA,\n\t\t\t\t\tcontiglen: p.matchA,\n\t\t\t\t\trepeatscore: p.repeatA\n\t\t\t\t},\n\t\t\t\tb: {\n\t\t\t\t\tname: p.geneB,\n\t\t\t\t\tchr: p.chrB,\n\t\t\t\t\tposition: p.posB,\n\t\t\t\t\tstrand: p.ortB,\n\t\t\t\t\tratio: p.ratioB,\n\t\t\t\t\tfeature: p.featureB,\n\t\t\t\t\tchimericreads: p.readsB,\n\t\t\t\t\tcontiglen: p.matchB,\n\t\t\t\t\trepeatscore: p.repeatB\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (p.usepair) {\n\t\t\t\tconst u = p.usepair\n\t\t\t\tclean.frame = u.frame\n\t\t\t\tif (u.a.isoform) {\n\t\t\t\t\tclean.a.isoform = u.a.isoform\n\t\t\t\t}\n\t\t\t\tif (u.b.isoform) {\n\t\t\t\t\tclean.b.isoform = u.b.isoform\n\t\t\t\t}\n\t\t\t\t/*\n\t\t\t\tclean.a.exon=u.a.exon\n\t\t\t\tclean.b.exon=u.b.exon\n\t\t\t\tclean.a.codon=u.a.codon\n\t\t\t\tclean.b.codon=u.b.codon\n\t\t\t\t*/\n\t\t\t\t// interstitial\n\t\t\t\tlet aalen = 0,\n\t\t\t\t\tbplen = 0\n\t\t\t\tif (u.a.contigaa && u.b.contigaa) {\n\t\t\t\t\taalen = u.b.contigaa - u.a.contigaa - 1\n\t\t\t\t}\n\t\t\t\tif (u.a.contigbp && u.b.contigbp) {\n\t\t\t\t\tbplen = u.b.contigbp - u.a.contigbp - 1\n\t\t\t\t}\n\t\t\t\tif (aalen > 0) {\n\t\t\t\t\tclean.interstitial = { aalen: aalen }\n\t\t\t\t}\n\t\t\t\tif (bplen > 0) {\n\t\t\t\t\tif (!clean.interstitial) clean.interstitial = {}\n\t\t\t\t\tclean.interstitial.bplen = bplen\n\t\t\t\t}\n\t\t\t}\n\t\t\tcleanup.push(clean)\n\t\t}\n\t\tfor (const [genename, iset] of gene2isoform) {\n\t\t\tfor (const isoform of iset) {\n\t\t\t\tif (!(genename in genes)) {\n\t\t\t\t\tgenes[genename] = []\n\t\t\t\t}\n\t\t\t\tconst pp = {\n\t\t\t\t\tdt: dtfusionrna,\n\t\t\t\t\tclass: mclassfusionrna,\n\t\t\t\t\tsample: row[0].sample,\n\t\t\t\t\tisoform: isoform,\n\t\t\t\t\tpairlst: duplicate(cleanup)\n\t\t\t\t}\n\t\t\t\t// functional effect is offered on individual breakpoints which does not make sense, should be placed on the entire product\n\t\t\t\tfor (const i of cleanup) {\n\t\t\t\t\tif (i.functioneffect) {\n\t\t\t\t\t\tpp.functioneffect = i.functioneffect\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tgenes[genename].push(pp)\n\t\t\t}\n\t\t}\n\t}\n\tif (e_itd.length) {\n\t\tsvmr.err(e_itd.join('<br>'))\n\t}\n\tif (e_nloss.length) {\n\t\tsvmr.err(e_nloss.join('<br>'))\n\t}\n\tif (e_closs.length) {\n\t\tsvmr.err(e_closs.join('<br>'))\n\t}\n\tlet genecount = 0,\n\t\tgenesup = {}\n\tfor (const k in genes) {\n\t\tgenecount++\n\t\tgenesup[k.toUpperCase()] = genes[k]\n\t}\n\tif (genecount == 0) {\n\t\talert('No data can be added.')\n\t\treturn\n\t}\n\t// to datasets\n\tlet ds = null\n\tfor (const n in svmr.genome.datasets) {\n\t\tif (svmr.genome.datasets[n].svmrid == svmr.id) {\n\t\t\tds = svmr.genome.datasets[n]\n\t\t\tbreak\n\t\t}\n\t}\n\tif (ds) {\n\t\t// update existing\n\t\tds.bulkdata = genesup\n\t} else {\n\t\t// create new\n\t\tds = {\n\t\t\tlabel: svmr.filename,\n\t\t\tsvmrid: svmr.id,\n\t\t\tbulkdata: genesup\n\t\t}\n\t\tsvmr.genome.datasets[svmr.filename] = ds\n\t}\n\tif (svmr.cohort) {\n\t\tsvmr.cohortpane.pane.remove()\n\t} else {\n\t\tsvmr.cohort = {\n\t\t\tname: svmr.filename,\n\t\t\tgenome: svmr.genome,\n\t\t\tshow_genetable: 1,\n\t\t\tjwt: svmr.jwt,\n\t\t\tdsset: {}\n\t\t}\n\t\tsvmr.cohort.dsset[svmr.filename] = ds\n\t}\n\tconst pane = newpane({ x: 200, y: 200 })\n\n\timport('./tp.ui').then(p => {\n\t\tp.default(svmr.cohort, pane.body, svmr.hostURL)\n\t\tsvmr.cohortpane = pane\n\t})\n}\n\nexport function svmr_export_text(svmr, hqonly) {\n\tconst rows = []\n\tconst headerlst = svmr.atlst.map(i => i.label)\n\t// new fields\n\theaderlst.push('transcript_nbr')\n\theaderlst.push('breakpoint_nbr')\n\theaderlst.push('functionalClass')\n\tfor (const sample of svmr.samples) {\n\t\tconst whole = []\n\t\tfor (const egg of sample.egglst) {\n\t\t\tfor (const eg of egg.lst) {\n\t\t\t\tif (eg.ismsg) {\n\t\t\t\t\tconst lst = eg.lst.map(evt => evt.lst[0])\n\t\t\t\t\tif (hqonly) {\n\t\t\t\t\t\tlet hashq = false\n\t\t\t\t\t\tfor (const i of lst) {\n\t\t\t\t\t\t\tif (i.rating == 'Major') hashq = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (hashq) {\n\t\t\t\t\t\t\twhole.push(lst)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\twhole.push(lst)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\tfor (const p of evt.lst) {\n\t\t\t\t\t\t\tif (hqonly) {\n\t\t\t\t\t\t\t\tif (p.rating == 'Major') whole.push([p])\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\twhole.push([p])\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tfor (let gid = 0; gid < whole.length; gid++) {\n\t\t\tfor (let prodid = 0; prodid < whole[gid].length; prodid++) {\n\t\t\t\tlet prod = whole[gid][prodid]\n\t\t\t\tconst frame = [],\n\t\t\t\t\ta_isoform = [],\n\t\t\t\t\ta_codon = [],\n\t\t\t\t\ta_exon = [],\n\t\t\t\t\ta_anchor = [],\n\t\t\t\t\ta_contigaa = [],\n\t\t\t\t\ta_contigbp = [],\n\t\t\t\t\tb_isoform = [],\n\t\t\t\t\tb_codon = [],\n\t\t\t\t\tb_exon = [],\n\t\t\t\t\tb_anchor = [],\n\t\t\t\t\tb_contigaa = [],\n\t\t\t\t\tb_contigbp = []\n\t\t\t\tfor (const p of prod.pairs) {\n\t\t\t\t\tframe.push(p.frame)\n\t\t\t\t\ta_isoform.push(p.a.isoform)\n\t\t\t\t\tb_isoform.push(p.b.isoform)\n\t\t\t\t\tlet v = p.a.codon\n\t\t\t\t\ta_codon.push(Number.isNaN(v) ? '' : v)\n\t\t\t\t\tv = p.b.codon\n\t\t\t\t\tb_codon.push(Number.isNaN(v) ? '' : v)\n\t\t\t\t\tv = p.a.exon\n\t\t\t\t\ta_exon.push(Number.isNaN(v) ? '' : v)\n\t\t\t\t\tv = p.b.exon\n\t\t\t\t\tb_exon.push(Number.isNaN(v) ? '' : v)\n\t\t\t\t\ta_anchor.push(p.a.anchor ? p.a.anchor : '')\n\t\t\t\t\tb_anchor.push(p.b.anchor ? p.b.anchor : '')\n\t\t\t\t\tv = p.a.contigaa\n\t\t\t\t\ta_contigaa.push(v == undefined ? '' : v)\n\t\t\t\t\tv = p.b.contigaa\n\t\t\t\t\tb_contigaa.push(v == undefined ? '' : v)\n\t\t\t\t\tv = p.a.contigbp\n\t\t\t\t\ta_contigbp.push(v == undefined ? '' : v)\n\t\t\t\t\tv = p.b.contigbp\n\t\t\t\t\tb_contigbp.push(v == undefined ? '' : v)\n\t\t\t\t}\n\t\t\t\tconst row = []\n\t\t\t\tfor (const i of svmr.atlst) {\n\t\t\t\t\tswitch (i.key) {\n\t\t\t\t\t\tcase 'lstframe':\n\t\t\t\t\t\t\trow.push(frame.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t// A\n\t\t\t\t\t\tcase 'lstisoforma':\n\t\t\t\t\t\t\trow.push(a_isoform.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstisoformacodon':\n\t\t\t\t\t\t\trow.push(a_codon.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstisoformaexon':\n\t\t\t\t\t\t\trow.push(a_exon.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstisoformaanchor':\n\t\t\t\t\t\t\trow.push(a_anchor.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstcontigaaA':\n\t\t\t\t\t\t\trow.push(a_contigaa.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstcontigbpA':\n\t\t\t\t\t\t\trow.push(a_contigbp.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t// B\n\t\t\t\t\t\tcase 'lstisoformb':\n\t\t\t\t\t\t\trow.push(b_isoform.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstisoformbcodon':\n\t\t\t\t\t\t\trow.push(b_codon.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstisoformbexon':\n\t\t\t\t\t\t\trow.push(b_exon.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstisoformbanchor':\n\t\t\t\t\t\t\trow.push(b_anchor.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstcontigaaB':\n\t\t\t\t\t\t\trow.push(b_contigaa.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase 'lstcontigbpB':\n\t\t\t\t\t\t\trow.push(b_contigbp.join(','))\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tdefault:\n\t\t\t\t\t\t\trow.push(prod[i.key])\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// new field - multi seg group\n\t\t\t\trow.push(gid + 1)\n\t\t\t\trow.push(prodid + 1)\n\t\t\t\t// new field - function effect\n\t\t\t\trow.push(prod.functioneffect ? prod.functioneffect : '')\n\t\t\t\trows.push(row)\n\t\t\t}\n\t\t}\n\t}\n\texport_data('Fusion data from ' + svmr.filename, [{ text: headerlst.join('\\t') + '\\n' + rows.join('\\n') }])\n}\n\nfunction duplicate(i) {\n\tconst lst = []\n\tfor (const j of i) {\n\t\tconst k = {}\n\t\tfor (const n in j) k[n] = j[n]\n\t\tk.a = {}\n\t\tfor (const n in j.a) k.a[n] = j.a[n]\n\t\tk.b = {}\n\t\tfor (const n in j.b) k.b[n] = j.b[n]\n\t\tif (j.interstitial) {\n\t\t\tk.interstitial = {}\n\t\t\tfor (const n in j.interstitial) k.interstitial[n] = j.interstitial[n]\n\t\t}\n\t\tlst.push(k)\n\t}\n\treturn lst\n}\n", "import { select as d3select } from 'd3-selection'\nimport * as client from './client'\nimport { genomic2gm } from './coord'\nimport { bplen as bplength } from '#shared/common.js'\nimport * as unload from './svmr.unload'\nimport { scaleLinear } from 'd3-scale'\nimport { axisTop } from 'd3-axis'\nimport { Menu } from '../dom/menu'\n\nconst genomelimit = 10000 // bp distance\nconst knownprod_c = '#A702C4'\nconst tip = new Menu()\n\nexport default class {\n\tconstructor(genome, atlst, items, filename, holder, hostURL, jwt) {\n\t\twindow.svmr = this\n\n\t\tthis.hostURL = hostURL\n\t\tthis.jwt = jwt\n\t\tthis.id = Math.random()\n\t\tthis.items = items\n\t\tthis.genome = genome\n\t\tthis.filename = filename\n\t\tthis.atlst = atlst\n\t\t;(this.cf_repeat = 0.7), (this.cf_reads = 2)\n\t\tthis.cf_match = 40\n\t\tthis.cf_ratio = 0.01\n\t\tthis.expression = {}\n\t\tthis.samples = []\n\t\tthis.genelst = []\n\t\tthis.elab2sample = {} // for detecting recurrence, only when geneA/B are valid\n\n\t\tif (!holder) {\n\t\t\tconst pane = client.newpane({ x: 100, y: 100, toshrink: true })\n\t\t\tpane.header.append('span').style('color', '#858585').style('font-size', '.7em').html('Fusion Editor&nbsp;')\n\t\t\tpane.header.append('span').text(filename)\n\t\t\tholder = pane.body\n\t\t}\n\t\tthis.holder = holder\n\t\tthis.errdiv = holder.append('div').style('width', '500px').style('margin', '10px')\n\t\tconst butrow = holder.append('div').style('margin', '20px').style('padding', '0px')\n\t\tthis.buttgene = butrow\n\t\t\t.append('button')\n\t\t\t.text('Loading genes')\n\t\t\t.on('click', () => {\n\t\t\t\tif (genediv.style('display') == 'none') {\n\t\t\t\t\tclient.appear(genediv)\n\t\t\t\t} else {\n\t\t\t\t\tclient.disappear(genediv)\n\t\t\t\t}\n\t\t\t})\n\t\tthis.buttsample = butrow\n\t\t\t.append('button')\n\t\t\t.text('Loading samples')\n\t\t\t.on('click', () => {\n\t\t\t\tif (this.ul.style('display') == 'none') {\n\t\t\t\t\tclient.appear(this.ul)\n\t\t\t\t} else {\n\t\t\t\t\tclient.disappear(this.ul)\n\t\t\t\t}\n\t\t\t})\n\t\tbutrow\n\t\t\t.append('button')\n\t\t\t.text('Gene expression')\n\t\t\t.on('click', () => {\n\t\t\t\tif (this.expression.div.style('display') == 'none') {\n\t\t\t\t\tclient.appear(this.expression.div)\n\t\t\t\t} else {\n\t\t\t\t\tclient.disappear(this.expression.div)\n\t\t\t\t}\n\t\t\t})\n\t\tbutrow\n\t\t\t.append('button')\n\t\t\t.text('Parameter cutoff')\n\t\t\t.on('click', () => {\n\t\t\t\tif (cutoffdiv.style('display') == 'none') {\n\t\t\t\t\tclient.appear(cutoffdiv)\n\t\t\t\t} else {\n\t\t\t\t\tclient.disappear(cutoffdiv)\n\t\t\t\t}\n\t\t\t})\n\t\tbutrow\n\t\t\t.append('button')\n\t\t\t.text('Legend')\n\t\t\t.on('click', () => {\n\t\t\t\tif (legenddiv.style('display') == 'none') {\n\t\t\t\t\tclient.appear(legenddiv)\n\t\t\t\t} else {\n\t\t\t\t\tclient.disappear(legenddiv)\n\t\t\t\t}\n\t\t\t})\n\t\tbutrow\n\t\t\t.append('button')\n\t\t\t.style('margin-right', '20px')\n\t\t\t.text('Export data')\n\t\t\t.on('click', event => {\n\t\t\t\t// in fact, using Major instead of HQ\n\t\t\t\tlet single_hq = 0,\n\t\t\t\t\tmulti_hq = 0,\n\t\t\t\t\tsingle_nhq = 0,\n\t\t\t\t\tmulti_nhq = 0,\n\t\t\t\t\titd_hq = 0,\n\t\t\t\t\titd_nhq = 0,\n\t\t\t\t\ttrunc_hq = 0,\n\t\t\t\t\ttrunc_nhq = 0\n\t\t\t\tfor (const sample of this.samples) {\n\t\t\t\t\tfor (const egg of sample.egglst) {\n\t\t\t\t\t\tfor (const eg of egg.lst) {\n\t\t\t\t\t\t\tif (eg.ismsg) {\n\t\t\t\t\t\t\t\tlet hashq = false\n\t\t\t\t\t\t\t\tfor (const i of eg.lst) {\n\t\t\t\t\t\t\t\t\tif (i.rating == 'Major') hashq = true\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (hashq) multi_hq++\n\t\t\t\t\t\t\t\telse multi_nhq++\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\t\t\t\tfor (const p of evt.lst) {\n\t\t\t\t\t\t\t\t\t\tif (p.rating == 'Major') {\n\t\t\t\t\t\t\t\t\t\t\tif (p.isitd) itd_hq++\n\t\t\t\t\t\t\t\t\t\t\telse if (p.iscloss || p.isnloss) trunc_hq++\n\t\t\t\t\t\t\t\t\t\t\telse single_hq++\n\t\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\t\tif (p.isitd) itd_nhq++\n\t\t\t\t\t\t\t\t\t\t\telse if (p.iscloss || p.isnloss) trunc_nhq++\n\t\t\t\t\t\t\t\t\t\t\telse single_nhq++\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tconst d0 = tip.clear().showunder(event.target).d.append('div')\n\t\t\t\tconst table = d0.append('table').style('border-spacing', '10px').style('border-collapse', 'separate')\n\t\t\t\tlet tr = table.append('tr').style('color', '#858585')\n\t\t\t\ttr.append('td')\n\t\t\t\ttr.append('td').text('2-gene fusion')\n\t\t\t\ttr.append('td').text('Multi-gene fusion')\n\t\t\t\ttr.append('td').text('ITD')\n\t\t\t\ttr.append('td').text('Truncation')\n\t\t\t\ttr = table.append('tr')\n\t\t\t\ttr.append('td').text('Major').style('color', '#858585').style('text-align', 'right')\n\t\t\t\ttr.append('td').text(single_hq)\n\t\t\t\ttr.append('td').text(multi_hq)\n\t\t\t\ttr.append('td').text(itd_hq)\n\t\t\t\ttr.append('td').text(trunc_hq)\n\t\t\t\ttr = table.append('tr')\n\t\t\t\ttr.append('td').text('not Major').style('color', '#858585').style('text-align', 'right')\n\t\t\t\ttr.append('td').text(single_nhq)\n\t\t\t\ttr.append('td').text(multi_nhq)\n\t\t\t\ttr.append('td').text(itd_nhq)\n\t\t\t\ttr.append('td').text(trunc_nhq)\n\t\t\t\tlet dd = d0.append('div').style('margin', '10px').text('Export fusions labeled as \"Major\"')\n\t\t\t\tdd.append('button')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.text('Tabular format')\n\t\t\t\t\t.on('click', () => unload.svmr_export_text(this, true))\n\t\t\t\tdd.append('button')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.text('JSON format')\n\t\t\t\t\t.on('click', () => unload.svmr_export_json(this, true))\n\t\t\t\tdd.append('button')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.text('View in ProteinPaint')\n\t\t\t\t\t.on('click', () => unload.svmr_2pp(this, true))\n\t\t\t\tdd = d0.append('div').style('margin', '10px').text('Export all fusions')\n\t\t\t\tdd.append('button')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.text('Tabular format')\n\t\t\t\t\t.on('click', () => unload.svmr_export_text(this, false))\n\t\t\t\tdd.append('button')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.text('JSON format')\n\t\t\t\t\t.on('click', () => unload.svmr_export_json(this, false))\n\t\t\t\tdd.append('button')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.text('View in ProteinPaint')\n\t\t\t\t\t.on('click', () => unload.svmr_2pp(this, false))\n\t\t\t})\n\t\tbutrow\n\t\t\t.append('a')\n\t\t\t.attr('target', '_blank')\n\t\t\t.attr('href', 'https://docs.google.com/document/d/1DRVzE_WenG490eRYB7VGFOygtSqtF5L97rhK0HOUCNY/edit?usp=sharing')\n\t\t\t.text('Help')\n\t\t// expression\n\t\tthis.expression.div = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin', '20px')\n\t\t\t.style('padding', '20px')\n\t\t\t.style('border', 'dashed 1px #bbb')\n\t\tthis.expression.prediv = this.expression.div.append('div')\n\t\tthis.expression.prediv\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px')\n\t\t\t.text('Load a file that includes gene expression data for current samples.')\n\t\tthis.expression.prediv\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px 5px 10px 5px')\n\t\t\t.style('font-size', '80%')\n\t\t\t.text('The first 3 columns of the file should be: 1) gene name, 2) expression value, 3) sample name')\n\t\tthis.expression.input = this.expression.prediv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'file')\n\t\t\t.on('change', event => {\n\t\t\t\tloadexpression(this, event.target.files[0])\n\t\t\t})\n\t\tthis.expression.presays = this.expression.prediv.append('span').style('padding-left', '20px')\n\t\tthis.expression.afterdiv = this.expression.div.append('div').style('display', 'none')\n\t\t// gene table\n\t\tconst genediv = holder.append('div').style('display', 'none').style('margin', '20px')\n\t\tlet d0 = genediv.append('div').style('display', 'inline-block').style('border', 'dashed 1px #bbb')\n\t\tthis.genefilter = d0.append('div').style('background-color', '#ededed').style('padding', '10px 20px')\n\t\tlet d01 = d0\n\t\t\t.append('div')\n\t\t\t.style('padding', '10px 20px')\n\t\t\t.style('overflow-y', 'scroll')\n\t\t\t.style('resize', 'vertical')\n\t\t\t.style('height', '300px')\n\t\td01\n\t\t\t.append('div')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('font-size', '70%')\n\t\t\t.text('Not included: read-through and intergenic events (including one or both sides).')\n\t\tthis.genetable = d01.append('table')\n\t\t// cutoff\n\t\tconst cutoffdiv = holder.append('div').style('display', 'none').style('margin', '20px')\n\t\td0 = cutoffdiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '20px')\n\t\t\t.style('border', 'solid 1px #ededed')\n\t\td0.append('span').style('padding', '0px 10px').text('Alert if:')\n\t\td01 = d0.append('span').style('padding', '0px 10px')\n\t\td01.append('span').html('chimeric reads &le;&nbsp;')\n\t\td01\n\t\t\t.append('input')\n\t\t\t.attr('size', 3)\n\t\t\t.property('value', this.cf_reads)\n\t\t\t.on('change', event => {\n\t\t\t\tconst v = Number.parseInt(event.target.value)\n\t\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.cf_reads = v\n\t\t\t})\n\t\td01 = d0.append('span').style('padding', '0px 10px')\n\t\td01.append('span').html('repeat score &ge;&nbsp;')\n\t\td01\n\t\t\t.append('input')\n\t\t\t.attr('size', 3)\n\t\t\t.property('value', this.cf_repeat)\n\t\t\t.on('change', event => {\n\t\t\t\tconst v = Number.parseFloat(event.target.value)\n\t\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.cf_repeat = v\n\t\t\t})\n\t\td01 = d0.append('span').style('padding', '0px 10px')\n\t\td01.append('span').html('contig bp length &le;&nbsp;')\n\t\td01\n\t\t\t.append('input')\n\t\t\t.attr('size', 3)\n\t\t\t.property('value', this.cf_match)\n\t\t\t.on('change', event => {\n\t\t\t\tconst v = Number.parseInt(event.target.value)\n\t\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.cf_match = v\n\t\t\t})\n\t\td01 = d0.append('span').style('padding', '0px 10px')\n\t\td01.append('span').html('ratio &le;&nbsp;')\n\t\td01\n\t\t\t.append('input')\n\t\t\t.attr('size', 3)\n\t\t\t.property('value', this.cf_ratio)\n\t\t\t.on('change', event => {\n\t\t\t\tconst v = Number.parseFloat(event.target.value)\n\t\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.cf_ratio = v\n\t\t\t})\n\t\t// legend\n\t\tconst legenddiv = holder.append('div').style('display', 'none').style('margin', '20px')\n\t\tvar h = 16\n\t\tlegenddiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '10px')\n\t\t\t.style('border', 'solid 1px #ededed')\n\t\t\t.html(\n\t\t\t\t'<table style=\"margin:20px\">' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;font-size:80%;color:white;background-color:' +\n\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t';padding:2px 5px\">IN</div></td><td>In-frame fusion</td></tr>' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;font-size:80%;color:white;background-color:' +\n\t\t\t\t\tclient.coloroutframe +\n\t\t\t\t\t';padding:2px 5px\">O</div></td><td>Out-of-frame fusion</td></tr>' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;font-size:80%;color:black;border:solid 1px black;padding:1px 3px\">?</div></td><td>Intergenic fusion, or gene isoform not specified</td></tr>' +\n\t\t\t\t\t'</table>' +\n\t\t\t\t\t'<table style=\"margin:20px\">' +\n\t\t\t\t\t'<tr><td>chr5 <span style=\"border:solid 1px black;padding:0px 10px;\"></span>' +\n\t\t\t\t\t'-' +\n\t\t\t\t\t'<span style=\"border:solid 1px black;padding:0px 10px;\"></span> chr5</td>' +\n\t\t\t\t\t'<td>Intra-chromosomal breakpoints</td></tr>' +\n\t\t\t\t\t'<tr><td><span style=\"color:red\">chr5</span> <span style=\"border:solid 1px black;padding:0px 10px;\"></span>' +\n\t\t\t\t\t'-' +\n\t\t\t\t\t'<span style=\"border:solid 1px black;padding:0px 10px;\"></span> <span style=\"color:red\">chr10</span></td>' +\n\t\t\t\t\t'<td>Inter-chromosomal breakpoints</td></tr>' +\n\t\t\t\t\t'</tr></table>' +\n\t\t\t\t\t'<table style=\"margin:20px\">' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%\">geneA</div>' +\n\t\t\t\t\t'-' +\n\t\t\t\t\t'<div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%\">geneB</div>' +\n\t\t\t\t\t'</td><td>Neither geneA nor geneB is known fusion partner</td>' +\n\t\t\t\t\t'</tr>' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;\">geneA</div>' +\n\t\t\t\t\t'-' +\n\t\t\t\t\t'<div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%\">geneB</div>' +\n\t\t\t\t\t'</td><td>GeneA is a known fusion partner</td>' +\n\t\t\t\t\t'</tr>' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;\">geneA</div>' +\n\t\t\t\t\t'-' +\n\t\t\t\t\t'<div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;\">geneB</div>' +\n\t\t\t\t\t'</td><td>Both genes are known fusion partners, but they do not make a known fusion product.</td>' +\n\t\t\t\t\t'</tr>' +\n\t\t\t\t\t'<tr><td><div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;color:' +\n\t\t\t\t\tknownprod_c +\n\t\t\t\t\t'\">geneA</div>' +\n\t\t\t\t\t'-' +\n\t\t\t\t\t'<div style=\"display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;color:' +\n\t\t\t\t\tknownprod_c +\n\t\t\t\t\t'\">geneB</div>' +\n\t\t\t\t\t'</td><td>A known fusion product</td>' +\n\t\t\t\t\t'</tr>' +\n\t\t\t\t\t'</table>' +\n\t\t\t\t\t'<table style=\"margin:20px\">' +\n\t\t\t\t\t'<tr><td><div style=\"width:40px;height:16px;position:relative;\">' +\n\t\t\t\t\t'<div style=\"position:absolute;right:0px;top:0px;width:20px;height:16px;background-color:' +\n\t\t\t\t\tclient.colorbgleft +\n\t\t\t\t\t'\"></div>' +\n\t\t\t\t\t'<div style=\"position:absolute;border:solid 1px black;width:100%;height:15px\"></div>' +\n\t\t\t\t\t'</div>' +\n\t\t\t\t\t'</td>' +\n\t\t\t\t\t'<td>ratioA: for geneA, the ratio of chimeric reads over total reads</td></tr>' +\n\t\t\t\t\t'<tr><td><div style=\"width:40px;height:16px;position:relative;\">' +\n\t\t\t\t\t'<div style=\"position:absolute;left:0px;top:0px;width:20px;height:16px;background-color:' +\n\t\t\t\t\tclient.colorbgright +\n\t\t\t\t\t'\"></div>' +\n\t\t\t\t\t'<div style=\"position:absolute;border:solid 1px black;width:100%;height:15px\"></div>' +\n\t\t\t\t\t'</div>' +\n\t\t\t\t\t'</td>' +\n\t\t\t\t\t'<td>ratioB: for geneB, the ratio of chimeric reads over total reads</td></tr>' +\n\t\t\t\t\t'<tr><td><div style=\"width:40px;height:16px;border:solid 1px red;\"></div></td><td>Antisense (reported strand is on the opposite of gene strand)</td></tr>' +\n\t\t\t\t\t'</table>'\n\t\t\t)\n\n\t\tthis.ul = holder.append('ul') // root of tree\n\n\t\t/*\nthis.hassample=false\nfor(const i of atlst) {\n\tif(i.key=='sample') {\n\t\tthis.hassample=true\n\t}\n}\n*/\n\n\t\tthis.step_isoform(items)\n\t}\n\t// end of constructor\n\n\terr(m) {\n\t\tclient.sayerror(this.errdiv, m)\n\t}\n\n\tstep_isoform(items) {\n\t\t// get isoform info ready before showing table\n\t\tconst newset = new Set()\n\t\tfor (const item of items) {\n\t\t\tfor (const i of item.pairs) {\n\t\t\t\tlet n = i.a.isoform\n\t\t\t\tif (n && !this.genome.isoformcache.has(n.toUpperCase())) {\n\t\t\t\t\tnewset.add(n)\n\t\t\t\t}\n\t\t\t\tn = i.b.isoform\n\t\t\t\tif (n && !this.genome.isoformcache.has(n.toUpperCase())) {\n\t\t\t\t\tnewset.add(n)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (newset.size == 0) {\n\t\t\tthis.step_eat(items)\n\t\t\treturn\n\t\t}\n\t\tconst newisoform = []\n\t\tfor (const n of newset) {\n\t\t\tnewisoform.push(n)\n\t\t}\n\t\tconst wait = this.holder\n\t\t\t.append('div')\n\t\t\t.style('margin', '20px')\n\t\t\t.text('Loading ' + newset.size + ' isoforms ...')\n\n\t\t// FIXME query small amount of isoforms at a time\n\n\t\tfetch(\n\t\t\tnew Request(this.hostURL + '/isoformlst', {\n\t\t\t\tmethod: 'POST',\n\t\t\t\theaders: { 'content-type': 'application/json' },\n\t\t\t\tbody: JSON.stringify({ genome: this.genome.name, lst: newisoform, jwt: this.jwt })\n\t\t\t})\n\t\t)\n\t\t\t.then(data => {\n\t\t\t\treturn data.json()\n\t\t\t})\n\t\t\t.then(data => {\n\t\t\t\tif (data.error) throw { message: 'Cannot load isoforms: ' + data.error }\n\t\t\t\twait.remove()\n\t\t\t\tfor (const ilst of data.lst) {\n\t\t\t\t\tif (ilst[0]) {\n\t\t\t\t\t\tthis.genome.isoformcache.set(ilst[0].isoform, ilst)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// invalid isoforms\n\t\t\t\tconst isoformErr = []\n\t\t\t\tfor (const k of newset) {\n\t\t\t\t\tif (!this.genome.isoformcache.has(k.toUpperCase())) {\n\t\t\t\t\t\tisoformErr.push(k)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (isoformErr.length) {\n\t\t\t\t\tthis.err(\n\t\t\t\t\t\tisoformErr.length + ' invalid isoform' + (isoformErr.length > 1 ? 's' : '') + ': ' + isoformErr.join(', ')\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\tthis.step_eat(items)\n\t\t\t})\n\t\t\t.catch(err => {\n\t\t\t\tthis.err(err.message)\n\t\t\t\tif (err.stack) console.log(err.stack)\n\t\t\t})\n\t}\n\n\tstep_eat(items) {\n\t\t// call after all isoforms loaded\n\t\tfor (const prod of items) {\n\t\t\tprod.hook = {}\n\t\t\t// set .usepair for product using default isoform\n\t\t\tlet use = null\n\t\t\tfor (const p of prod.pairs) {\n\t\t\t\tlet gm = this.genome.isoformmatch(p.a.isoform, prod.chrA, prod.posA)\n\t\t\t\tif (gm) {\n\t\t\t\t\t// replaces old geneA label!\n\t\t\t\t\tprod.geneA = gm.name\n\t\t\t\t\tp.a.isdefault = gm.isdefault\n\t\t\t\t\tif (Number.isNaN(p.a.codon) || p.a.codon < 0) {\n\t\t\t\t\t\tp.a.codon = undefined\n\t\t\t\t\t\tconst a = genomic2gm(prod.posA, gm)\n\t\t\t\t\t\tif (a.atupstream) {\n\t\t\t\t\t\t\tp.a.atupstream = a.atupstream\n\t\t\t\t\t\t} else if (a.atdownstream) {\n\t\t\t\t\t\t\tp.a.atdownstream = a.atdownstream\n\t\t\t\t\t\t} else if (a.atutr3) {\n\t\t\t\t\t\t\tp.a.atutr3 = a.atutr3\n\t\t\t\t\t\t} else if (a.atutr5) {\n\t\t\t\t\t\t\tp.a.atutr5 = a.atutr5\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tp.a.codon = a.codon\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tgm = this.genome.isoformmatch(p.b.isoform, prod.chrB, prod.posB)\n\t\t\t\tif (gm) {\n\t\t\t\t\tprod.geneB = gm.name\n\t\t\t\t\tp.b.isdefault = gm.isdefault\n\t\t\t\t\tif (Number.isNaN(p.b.codon) || p.b.codon < 0) {\n\t\t\t\t\t\tp.b.codon = undefined\n\t\t\t\t\t\tconst a = genomic2gm(prod.posB, gm)\n\t\t\t\t\t\tif (a.atupstream) {\n\t\t\t\t\t\t\tp.b.atupstream = a.atupstream\n\t\t\t\t\t\t} else if (a.atdownstream) {\n\t\t\t\t\t\t\tp.b.atdownstream = a.atdownstream\n\t\t\t\t\t\t} else if (a.atutr3) {\n\t\t\t\t\t\t\tp.b.atutr3 = a.atutr3\n\t\t\t\t\t\t} else if (a.atutr5) {\n\t\t\t\t\t\t\tp.b.atutr5 = a.atutr5\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tp.b.codon = a.codon\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (p.a.isdefault && p.b.isdefault) {\n\t\t\t\t\tif (!use) {\n\t\t\t\t\t\t// none selected yet\n\t\t\t\t\t\tuse = p\n\t\t\t\t\t}\n\t\t\t\t\tif (p.inframe) {\n\t\t\t\t\t\t// in-frame, must choose, may override previous selected out-of frame pair\n\t\t\t\t\t\tuse = p\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (use) {\n\t\t\t\tprod.usepair = use\n\t\t\t} else {\n\t\t\t\tprod.notes.push('No preferred isoform pair')\n\t\t\t\tprod.usepair = prod.pairs[0] // could be undefined\n\t\t\t}\n\t\t\tif (prod.usepair) {\n\t\t\t\tprod.usepair.inuse = true\n\t\t\t}\n\t\t\t// geneA/B label ready\n\t\t\tprod.eventlabel = (prod.geneA ? prod.geneA : prod.chrA) + '-' + (prod.geneB ? prod.geneB : prod.chrB)\n\t\t}\n\t\t// group by sample\n\t\t// prod.sample is attacker-reachable data (fusioneditor upload/runpp arg); use\n\t\t// null-prototype objects so a sample name of \"__proto__\" cannot pollute Object.prototype\n\t\tconst tmp = Object.create(null)\n\t\tconst sampleless = Object.create(null)\n\t\tlet hassampleless = false\n\t\tfor (const prod of items) {\n\t\t\tlet n = prod.sample\n\t\t\tif (n) {\n\t\t\t\tif (!(n in tmp)) {\n\t\t\t\t\ttmp[n] = {}\n\t\t\t\t}\n\t\t\t\tif (!(prod.eventlabel in tmp[n])) {\n\t\t\t\t\ttmp[n][prod.eventlabel] = []\n\t\t\t\t}\n\t\t\t\ttmp[n][prod.eventlabel].push(prod)\n\t\t\t} else {\n\t\t\t\thassampleless = true\n\t\t\t\tif (!(prod.eventlabel in sampleless)) {\n\t\t\t\t\tsampleless[prod.eventlabel] = []\n\t\t\t\t}\n\t\t\t\tsampleless[prod.eventlabel].push(prod)\n\t\t\t}\n\t\t}\n\t\tfor (const sn in tmp) {\n\t\t\tthis.samples.push({\n\t\t\t\tname: sn,\n\t\t\t\tevents: tmp[sn]\n\t\t\t})\n\t\t}\n\t\tif (hassampleless) {\n\t\t\tthis.samples.push({\n\t\t\t\tname: 'No name',\n\t\t\t\tevents: sampleless\n\t\t\t})\n\t\t}\n\t\tthis.buttsample.text(this.samples.length + ' sample' + (this.samples.length > 1 ? 's' : ''))\n\t\t// \"samples\" done\n\t\t// fill in event-to-sample recurrence\n\t\tfor (const sample of this.samples) {\n\t\t\t// register event label to sample mapping\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\tif (!(elab in this.elab2sample)) {\n\t\t\t\t\tthis.elab2sample[elab] = []\n\t\t\t\t}\n\t\t\t\tthis.elab2sample[elab].push(sample)\n\t\t\t}\n\t\t}\n\t\t// foreach sample, gene to event\n\t\tfor (const sample of this.samples) {\n\t\t\tsample.gene2events = {}\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\tfor (const prod of sample.events[elab]) {\n\t\t\t\t\tconst a = prod.geneA\n\t\t\t\t\tif (a) {\n\t\t\t\t\t\tif (!(a in sample.gene2events)) {\n\t\t\t\t\t\t\tsample.gene2events[a] = {}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsample.gene2events[a][elab] = 1\n\t\t\t\t\t}\n\t\t\t\t\tconst b = prod.geneB\n\t\t\t\t\tif (b) {\n\t\t\t\t\t\tif (!(b in sample.gene2events)) {\n\t\t\t\t\t\t\tsample.gene2events[b] = {}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsample.gene2events[b][elab] = 1\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tfor (const sample of this.samples) {\n\t\t\t/* group - multi-seg */\n\t\t\tconst newholder = []\n\t\t\t// multiple rounds, one rating grade each time\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\tfor (const prod of sample.events[elab]) {\n\t\t\t\t\tif (prod.rating == 'HQ') msjoin(prod, newholder)\n\t\t\t\t}\n\t\t\t}\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\tfor (const prod of sample.events[elab]) {\n\t\t\t\t\tif (prod.rating == 'LQ') msjoin(prod, newholder)\n\t\t\t\t}\n\t\t\t}\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\tfor (const prod of sample.events[elab]) {\n\t\t\t\t\tif (prod.rating == 'RT') msjoin(prod, newholder)\n\t\t\t\t}\n\t\t\t}\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\tfor (const prod of sample.events[elab]) {\n\t\t\t\t\tif (prod.rating == 'bad') msjoin(prod, newholder)\n\t\t\t\t}\n\t\t\t}\n\t\t\t// assign id to multi-seg groups\n\t\t\tlet msgid = 0\n\t\t\tconst msglst = [] // multi-seg groups only\n\t\t\tfor (const lst of newholder) {\n\t\t\t\tif (lst.length > 1) {\n\t\t\t\t\tfor (const prod of lst) {\n\t\t\t\t\t\tprod.msgid = msgid\n\t\t\t\t\t}\n\t\t\t\t\tmsgid++\n\t\t\t\t\tmsglst.push(lst)\n\t\t\t\t}\n\t\t\t}\n\t\t\t/* rating grades */\n\t\t\tconst hqin = [], // in frame\n\t\t\t\thqt = [], // truncation, including not in-frame fusion\n\t\t\t\thqo = [], // others\n\t\t\t\tlqin = [],\n\t\t\t\tlqt = [],\n\t\t\t\tlqo = [],\n\t\t\t\trtin = [],\n\t\t\t\trtt = [],\n\t\t\t\trto = [],\n\t\t\t\tbadin = [],\n\t\t\t\tbadt = [],\n\t\t\t\tbado = []\n\t\t\t// stuff multi-seg into grades\n\t\t\tfor (const msg of msglst) {\n\t\t\t\tconst thisset = []\n\t\t\t\t// survey through all events in a group, find the highest grade, assign this group to that grade\n\t\t\t\tlet hqin3 = false,\n\t\t\t\t\thqt3 = false,\n\t\t\t\t\thqo3 = false,\n\t\t\t\t\tlqin3 = false,\n\t\t\t\t\tlqt3 = false,\n\t\t\t\t\tlqo3 = false,\n\t\t\t\t\trtin3 = false,\n\t\t\t\t\trtt3 = false,\n\t\t\t\t\trto3 = false,\n\t\t\t\t\tbadin3 = false,\n\t\t\t\t\tbadt3 = false,\n\t\t\t\t\tbado3 = false\n\t\t\t\tfor (const prod of msg) {\n\t\t\t\t\tthisset.push({ label: prod.eventlabel, lst: [prod] })\n\t\t\t\t\tconst pair = prod.usepair\n\t\t\t\t\tif (prod.rating == 'HQ') {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) hqin3 = true\n\t\t\t\t\t\t\telse hqt3 = true\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\thqt3 = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\thqo3 = true\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (prod.rating == 'LQ') {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) lqin3 = true\n\t\t\t\t\t\t\telse lqt3 = true\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\tlqt3 = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tlqo3 = true\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (prod.rating == 'RT') {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) rtin3 = true\n\t\t\t\t\t\t\telse rtt3 = true\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\trtt3 = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\trto3 = true\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) badin3 = true\n\t\t\t\t\t\t\telse badt3 = true\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\tbadt3 = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tbado3 = true\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// must only assign after going through all events\n\t\t\t\tif (hqin3) {\n\t\t\t\t\thqin.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (hqt3) {\n\t\t\t\t\thqt.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (hqo3) {\n\t\t\t\t\thqo.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (lqin3) {\n\t\t\t\t\tlqin.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (lqt3) {\n\t\t\t\t\tlqt.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (lqo3) {\n\t\t\t\t\tlqo.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (rtin3) {\n\t\t\t\t\trtin.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (rtt3) {\n\t\t\t\t\trtt.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (rto3) {\n\t\t\t\t\trto.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (badin3) {\n\t\t\t\t\tbadin.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (badt3) {\n\t\t\t\t\tbadt.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else if (bado3) {\n\t\t\t\t\tbado.push({ label: '', lst: thisset, ismsg: true })\n\t\t\t\t} else {\n\t\t\t\t\tconsole.log('multi-seg group unclassfied? ' + key)\n\t\t\t\t}\n\t\t\t}\n\t\t\t/* group - reciprocal gene pairs */\n\t\t\tconst genepairs = {}\n\t\t\t// k: master label, A-B, equivalent with B-A\n\t\t\t// v: {}\n\t\t\t//   k: actual label\n\t\t\t//   v: prod lst\n\t\t\tfor (const elab in sample.events) {\n\t\t\t\t// to hold non-gene-pair products\n\t\t\t\tconst hqin2 = [],\n\t\t\t\t\thqt2 = [],\n\t\t\t\t\thqo2 = [],\n\t\t\t\t\tlqin2 = [],\n\t\t\t\t\tlqt2 = [],\n\t\t\t\t\tlqo2 = [],\n\t\t\t\t\trtin2 = [],\n\t\t\t\t\trtt2 = [],\n\t\t\t\t\trto2 = [],\n\t\t\t\t\tbadin2 = [],\n\t\t\t\t\tbadt2 = [],\n\t\t\t\t\tbado2 = []\n\t\t\t\tfor (const prod of sample.events[elab]) {\n\t\t\t\t\tif (prod.msgid != undefined) {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tif (prod.geneA && prod.geneB) {\n\t\t\t\t\t\tconst key = prod.geneA + '-' + prod.geneB // A/B key\n\t\t\t\t\t\tlet hash = genepairs[key]\n\t\t\t\t\t\tif (!hash) {\n\t\t\t\t\t\t\t// B/A key to match reciprocal event\n\t\t\t\t\t\t\tconst key2 = prod.geneB + '-' + prod.geneA\n\t\t\t\t\t\t\thash = genepairs[key2]\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (hash) {\n\t\t\t\t\t\t\t// is such hash\n\t\t\t\t\t\t\tif (!(key in hash)) {\n\t\t\t\t\t\t\t\thash[key] = []\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\thash[key].push(prod)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tgenepairs[key] = {}\n\t\t\t\t\t\t\tgenepairs[key][key] = [prod]\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\t// not a gene pair\n\t\t\t\t\tvar pair = prod.usepair\n\t\t\t\t\t// directly to holder\n\t\t\t\t\tif (prod.rating == 'HQ') {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) hqin2.push(prod)\n\t\t\t\t\t\t\telse hqt2.push(prod)\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\thqt2.push(prod)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\thqo2.push(prod)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (prod.rating == 'LQ') {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) lqin2.push(prod)\n\t\t\t\t\t\t\telse lqt2.push(prod)\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\tlqt2.push(prod)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tlqo2.push(prod)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (prod.rating == 'RT') {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) rtin2.push(prod)\n\t\t\t\t\t\t\telse rtt2.push(prod)\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\trtt2.push(prod)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\trto2.push(prod)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\tif (pair.inframe) badin2.push(prod)\n\t\t\t\t\t\t\telse badt2.push(prod)\n\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\tbadt2.push(prod)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tbado2.push(prod)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// fill-in any non-gene-pairs\n\t\t\t\tif (hqin2.length > 0) {\n\t\t\t\t\thqin.push({ label: elab, lst: [{ label: elab, lst: hqin2 }] })\n\t\t\t\t} else if (hqt2.length > 0) {\n\t\t\t\t\thqt.push({ label: elab, lst: [{ label: elab, lst: hqt2 }] })\n\t\t\t\t} else if (hqo2.length > 0) {\n\t\t\t\t\thqo.push({ label: elab, lst: [{ label: elab, lst: hqo2 }] })\n\t\t\t\t} else if (lqin2.length > 0) {\n\t\t\t\t\tlqin.push({ label: elab, lst: [{ label: elab, lst: lqin2 }] })\n\t\t\t\t} else if (lqt2.length > 0) {\n\t\t\t\t\tlqt.push({ label: elab, lst: [{ label: elab, lst: lqt2 }] })\n\t\t\t\t} else if (lqo2.length > 0) {\n\t\t\t\t\tlqo.push({ label: elab, lst: [{ label: elab, lst: lqo2 }] })\n\t\t\t\t} else if (rtin2.length > 0) {\n\t\t\t\t\trtin.push({ label: elab, lst: [{ label: elab, lst: rtin2 }] })\n\t\t\t\t} else if (rtt2.length > 0) {\n\t\t\t\t\trtt.push({ label: elab, lst: [{ label: elab, lst: rtt2 }] })\n\t\t\t\t} else if (rto2.length > 0) {\n\t\t\t\t\trto.push({ label: elab, lst: [{ label: elab, lst: rto2 }] })\n\t\t\t\t} else if (badin2.length > 0) {\n\t\t\t\t\tbadin.push({ label: elab, lst: [{ label: elab, lst: badin2 }] })\n\t\t\t\t} else if (badt2.length > 0) {\n\t\t\t\t\tbadt.push({ label: elab, lst: [{ label: elab, lst: badt2 }] })\n\t\t\t\t} else if (bado2.length > 0) {\n\t\t\t\t\tbado.push({ label: elab, lst: [{ label: elab, lst: bado2 }] })\n\t\t\t\t}\n\t\t\t}\n\t\t\t// for group of gene pairs, assign to rating grades\n\t\t\tfor (const key in genepairs) {\n\t\t\t\tlet hqin3 = false,\n\t\t\t\t\thqt3 = false,\n\t\t\t\t\thqo3 = false,\n\t\t\t\t\tlqin3 = false,\n\t\t\t\t\tlqt3 = false,\n\t\t\t\t\tlqo3 = false,\n\t\t\t\t\trtin3 = false,\n\t\t\t\t\trtt3 = false,\n\t\t\t\t\trto3 = false,\n\t\t\t\t\tbadin3 = false,\n\t\t\t\t\tbadt3 = false,\n\t\t\t\t\tbado3 = false\n\t\t\t\tconst thisset = []\n\t\t\t\tfor (const elab in genepairs[key]) {\n\t\t\t\t\tconst prodlst = genepairs[key][elab]\n\t\t\t\t\tif (prodlst.length == 1) {\n\t\t\t\t\t\tif (prodlst[0].msgid != undefined) {\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\tthisset.push({ label: elab, lst: prodlst })\n\t\t\t\t\tfor (const prod of prodlst) {\n\t\t\t\t\t\tconst pair = prod.usepair\n\t\t\t\t\t\tif (prod.rating == 'HQ') {\n\t\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\t\tif (pair.inframe) hqin3 = true\n\t\t\t\t\t\t\t\telse hqt3 = true\n\t\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\t\thqt3 = true\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\thqo3 = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else if (prod.rating == 'LQ') {\n\t\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\t\tif (pair.inframe) lqin3 = true\n\t\t\t\t\t\t\t\telse lqt3 = true\n\t\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\t\tlqt3 = true\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tlqo3 = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else if (prod.rating == 'RT') {\n\t\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\t\tif (pair.inframe) rtin3 = true\n\t\t\t\t\t\t\t\telse rtt3 = true\n\t\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\t\trtt3 = true\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\trto3 = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (pair) {\n\t\t\t\t\t\t\t\tif (pair.inframe) badin3 = true\n\t\t\t\t\t\t\t\telse badt3 = true\n\t\t\t\t\t\t\t} else if (prod.isnloss || prod.iscloss) {\n\t\t\t\t\t\t\t\tbadt3 = true\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tbado3 = true\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (hqin3) {\n\t\t\t\t\thqin.push({ label: key, lst: thisset })\n\t\t\t\t} else if (hqt3) {\n\t\t\t\t\thqt.push({ label: key, lst: thisset })\n\t\t\t\t} else if (hqo3) {\n\t\t\t\t\thqo.push({ label: key, lst: thisset })\n\t\t\t\t} else if (lqin3) {\n\t\t\t\t\tlqin.push({ label: key, lst: thisset })\n\t\t\t\t} else if (lqt3) {\n\t\t\t\t\tlqt.push({ label: key, lst: thisset })\n\t\t\t\t} else if (lqo3) {\n\t\t\t\t\tlqo.push({ label: key, lst: thisset })\n\t\t\t\t} else if (rtin3) {\n\t\t\t\t\trtin.push({ label: key, lst: thisset })\n\t\t\t\t} else if (rtt3) {\n\t\t\t\t\trtt.push({ label: key, lst: thisset })\n\t\t\t\t} else if (rto3) {\n\t\t\t\t\trto.push({ label: key, lst: thisset })\n\t\t\t\t} else if (badin3) {\n\t\t\t\t\tbadin.push({ label: key, lst: thisset })\n\t\t\t\t} else if (badt3) {\n\t\t\t\t\tbadt.push({ label: key, lst: thisset })\n\t\t\t\t} else if (bado3) {\n\t\t\t\t\tbado.push({ label: key, lst: thisset })\n\t\t\t\t}\n\t\t\t}\n\t\t\tsample.egglst = []\n\t\t\tsample.hqincount = 0\n\t\t\tsample.lqincount = 0\n\t\t\tif (hqin.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'HQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';color:white;padding:1px 3px;font-size:80%;\">in-frame&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: hqin\n\t\t\t\t})\n\t\t\t\tsample.hqincount = hqin.reduce((i, j) => i + j.lst.length, 0)\n\t\t\t}\n\t\t\tif (hqt.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'HQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:#E3C3C8;padding:1px 3px;font-size:80%;\">truncation</span>',\n\t\t\t\t\tlst: hqt\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (hqo.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'HQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:#ccc;padding:1px 3px;font-size:80%;\">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: hqo\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (lqin.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'LQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';color:white;padding:1px 3px;font-size:80%;\">in-frame&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: lqin\n\t\t\t\t})\n\t\t\t\tsample.lqincount = lqin.reduce((i, j) => i + j, 0)\n\t\t\t}\n\t\t\tif (lqt.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'LQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:#E3C3C8;padding:1px 3px;font-size:80%;\">truncation</span>',\n\t\t\t\t\tlst: lqt\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (lqo.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'LQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:#ccc;padding:1px 3px;font-size:80%;\">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: lqo\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (rtin.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'Read-through <span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';color:white;padding:1px 3px;font-size:80%;\">in-frame&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: rtin\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (rtt.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'Read-through <span style=\"background-color:#E3C3C8;padding:1px 3px;font-size:80%;\">truncation</span>',\n\t\t\t\t\tlst: rtt\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (rto.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'Read-through <span style=\"background-color:#ccc;padding:1px 3px;font-size:80%;\">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: rto\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (badin.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'Bad&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';color:white;padding:1px 3px;font-size:80%;\">in-frame</span>',\n\t\t\t\t\tlst: badin\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (badt.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'Bad&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:#E3C3C8;padding:1px 3px;font-size:80%;\">truncation</span>',\n\t\t\t\t\tlst: badt\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (bado.length) {\n\t\t\t\tsample.egglst.push({\n\t\t\t\t\thtmlab:\n\t\t\t\t\t\t'Bad&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style=\"background-color:#ccc;padding:1px 3px;font-size:80%;\">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',\n\t\t\t\t\tlst: bado\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\t// sort samples\n\t\tthis.samples.sort((a, b) => {\n\t\t\tif (a.hqincount == b.hqincount) {\n\t\t\t\treturn b.lqincount - a.lqincount\n\t\t\t}\n\t\t\treturn b.hqincount - a.hqincount\n\t\t})\n\t\t// for each sample\n\t\tfor (const sample of this.samples) {\n\t\t\t// for each egg (rating grade)\n\t\t\tfor (const egg of sample.egglst) {\n\t\t\t\t// for each event group in an egg\n\t\t\t\tfor (const eg of egg.lst) {\n\t\t\t\t\t// for each event\n\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\t// sort products in an event\n\t\t\t\t\t\tevt.lst.sort((a, b) => {\n\t\t\t\t\t\t\tconst pa = a.usepair,\n\t\t\t\t\t\t\t\tpb = b.usepair\n\t\t\t\t\t\t\tif (pa) {\n\t\t\t\t\t\t\t\tif (pb) {\n\t\t\t\t\t\t\t\t\tif (pa.inframe) {\n\t\t\t\t\t\t\t\t\t\tif (!pb.inframe) {\n\t\t\t\t\t\t\t\t\t\t\treturn -1\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\tif (pb.inframe) {\n\t\t\t\t\t\t\t\t\t\t\treturn 1\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\treturn -1\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 (pb) {\n\t\t\t\t\t\t\t\t\treturn 1\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\treturn b.score - a.score\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// sort groups in an egg/rating grade\n\t\t\t\tegg.lst.sort((a, b) => {\n\t\t\t\t\t// by max score of products for each event group\n\t\t\t\t\tif (a.lst.length != b.lst.length) {\n\t\t\t\t\t\treturn b.lst.length - a.lst.length\n\t\t\t\t\t}\n\t\t\t\t\tlet scorea = 0\n\t\t\t\t\tfor (const evta of a.lst) {\n\t\t\t\t\t\tfor (const prod of evta.lst) {\n\t\t\t\t\t\t\tscorea = Math.max(scorea, prod.score)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tlet scoreb = 0\n\t\t\t\t\tfor (const evtb of b.lst) {\n\t\t\t\t\t\tfor (const prod of evtb.lst) {\n\t\t\t\t\t\t\tscoreb = Math.max(scoreb, prod.score)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\treturn scoreb - scorea\n\t\t\t\t})\n\t\t\t}\n\t\t\t// assign product id for editing\n\t\t\tlet prodid = 1\n\t\t\tfor (const egg of sample.egglst) {\n\t\t\t\tfor (const eg of egg.lst) {\n\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\tfor (const prod of evt.lst) {\n\t\t\t\t\t\t\tprod.prodid = prodid++\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.step_gene()\n\t\tthis.step_table()\n\t}\n\tdogenefilter() {\n\t\tlet va = this.gui.inputa.property('value')\n\t\tlet vb = this.gui.inputb.property('value')\n\t\tif (va.length + vb.length == 0) {\n\t\t\tthis.gui.says.text(\n\t\t\t\t'Showing ' + (this.genelst.length > 100 ? 100 : 'all') + ' of ' + this.genelst.length + ' pairs'\n\t\t\t)\n\t\t\tthis.geneshow(this.genelst.length > 100 ? this.genelst.slice(0, 100) : this.genelst)\n\t\t\treturn\n\t\t}\n\t\tva = va.length == 0 ? null : va.toLowerCase()\n\t\tvb = vb.length == 0 ? null : vb.toLowerCase()\n\t\tconst uselst = []\n\t\tfor (const g of this.genelst) {\n\t\t\tif (va) {\n\t\t\t\tif (!g.a) continue\n\t\t\t\tif (g.a.toLowerCase().indexOf(va) == -1) continue\n\t\t\t}\n\t\t\tif (vb) {\n\t\t\t\tif (!g.b) continue\n\t\t\t\tif (g.b.toLowerCase().indexOf(vb) == -1) continue\n\t\t\t}\n\t\t\tuselst.push(g)\n\t\t}\n\t\tthis.gui.says.text('Showing ' + Math.min(100, uselst.length) + ' of ' + this.genelst.length + ' pairs')\n\t\tthis.geneshow(uselst.length > 100 ? uselst.slice(0, 100) : uselst)\n\t}\n\tgeneshow(lst) {\n\t\tthis.genetable.selectAll('*').remove()\n\t\tconst tr = this.genetable.append('tr').style('background-color', '#ededed').style('font-size', '.8em')\n\t\ttr.append('td').text('gene A')\n\t\ttr.append('td').text('gene B')\n\t\ttr.append('td').text('# sample')\n\t\ttr.append('td').text('rating')\n\t\tfor (const evt of lst) {\n\t\t\tlet color1 = 'black',\n\t\t\t\tcolor2 = 'black',\n\t\t\t\tweight1,\n\t\t\t\tweight2\n\t\t\tif (evt.ainter) {\n\t\t\t\tcolor1 = '#aaa'\n\t\t\t\tweight1 = 'normal'\n\t\t\t} else {\n\t\t\t\tconst a = evt.samples[0].prodlst[0].hlgene\n\t\t\t\tif (a == 1 || a == 3 || a == 4) weight1 = 'bold'\n\t\t\t\tif (a == 4) color1 = knownprod_c\n\t\t\t}\n\t\t\tif (evt.binter) {\n\t\t\t\tcolor2 = '#aaa'\n\t\t\t\tweight2 = 'normal'\n\t\t\t} else {\n\t\t\t\tconst a = evt.samples[0].prodlst[0].hlgene\n\t\t\t\tif (a == 2 || a == 3 || a == 4) weight2 = 'bold'\n\t\t\t\tif (a == 4) color2 = knownprod_c\n\t\t\t}\n\t\t\tconst tr = this.genetable.append('tr').attr('class', 'sja_clb')\n\t\t\ttr.append('td').text(evt.a).style('color', color1).style('font-weight', weight1)\n\t\t\ttr.append('td').text(evt.b).style('color', color2).style('font-weight', weight2)\n\t\t\tconst td = tr.append('td').text(evt.samples.length)\n\t\t\ttr.on('click', () => {\n\t\t\t\tconst p = tr.node().getBoundingClientRect()\n\t\t\t\tconst pane2 = client.newpane({ x: p.left + p.width + 10, y: p.top })\n\t\t\t\tpane2.header.text(evt.a + ' - ' + evt.b)\n\t\t\t\tconst table = pane2.body.append('table')\n\t\t\t\tfor (const sample of evt.samples) {\n\t\t\t\t\tconst tr = table.append('tr')\n\t\t\t\t\ttr.append('td').style('vertical-align', 'top').style('padding-top', '5px').text(sample.name)\n\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\tfor (const prod of sample.prodlst) {\n\t\t\t\t\t\tconst logo = this.eventlogo([prod], td)\n\t\t\t\t\t\tlogo.style('position', 'relative')\n\t\t\t\t\t\tlogo\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t\t\t.style('width', '100%')\n\t\t\t\t\t\t\t.style('height', '100%')\n\t\t\t\t\t\t\t.style('top', '0px')\n\t\t\t\t\t\t\t.style('left', '0px')\n\t\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\t\t\ttip.clear().show(p.left + p.width - 2, p.top - 30)\n\t\t\t\t\t\t\t\tthis.showsvpairs({\n\t\t\t\t\t\t\t\t\tprodlst: [prod],\n\t\t\t\t\t\t\t\t\tholder: tip.d.append('div'),\n\t\t\t\t\t\t\t\t\tnodetail: true,\n\t\t\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\t\t\teglst: null,\n\t\t\t\t\t\t\t\t\tshowothersample: false\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('click', event => {\n\t\t\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\t\t\tconst pane = client.newpane({ x: p.left + p.width + 40, y: p.top - 60 })\n\t\t\t\t\t\t\t\tpane.header.text(sample.name)\n\t\t\t\t\t\t\t\tthis.showsvpairs({\n\t\t\t\t\t\t\t\t\tprodlst: [prod],\n\t\t\t\t\t\t\t\t\tholder: pane.body\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\t\t\tconst hash = {}\n\t\t\tfor (const smp of evt.samples) {\n\t\t\t\tconst hash2 = {}\n\t\t\t\tfor (const p of smp.prodlst) {\n\t\t\t\t\thash2[p.rating] = 1\n\t\t\t\t}\n\t\t\t\tfor (var n in hash2) {\n\t\t\t\t\tif (!(n in hash)) {\n\t\t\t\t\t\thash[n] = 0\n\t\t\t\t\t}\n\t\t\t\t\thash[n]++\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst lst = []\n\t\t\tfor (const smp of ['HQ', 'LQ', 'RT', 'bad']) {\n\t\t\t\tif (hash[smp]) {\n\t\t\t\t\tlst.push(\n\t\t\t\t\t\t'<span style=\"border-radius:6px;background-color:#ededed;padding:1px 6px;font-size:80%\">' +\n\t\t\t\t\t\t\tsmp +\n\t\t\t\t\t\t\t(hash[smp] > 1 ? ' <span style=\"font-size:80%\">' + hash[smp] + '</span>' : '') +\n\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t\ttr.append('td').html(lst.join(' '))\n\t\t}\n\t}\n\tstep_gene() {\n\t\tthis.gui = {}\n\t\tthis.genefilter.append('span').text('Filter:')\n\t\tthis.gui.inputa = this.genefilter\n\t\t\t.append('input')\n\t\t\t.attr('size', 7)\n\t\t\t.attr('placeholder', 'gene A')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.on('keyup', () => this.dogenefilter())\n\t\tthis.gui.inputb = this.genefilter\n\t\t\t.append('input')\n\t\t\t.attr('size', 7)\n\t\t\t.attr('placeholder', 'gene B')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.on('keyup', () => this.dogenefilter())\n\t\tthis.genefilter\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.text('Reset')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.gui.inputa.property('value', '')\n\t\t\t\tthis.gui.inputb.property('value', '')\n\t\t\t\tthis.dogenefilter()\n\t\t\t})\n\t\tthis.gui.says = this.genefilter.append('span').style('padding-left', '20px')\n\t\tconst events = {}\n\t\tconst genes = new Set()\n\t\tfor (const sample of this.samples) {\n\t\t\tfor (const k in sample.events) {\n\t\t\t\tfor (const prod of sample.events[k]) {\n\t\t\t\t\t// exclude events from showing in gene table\n\t\t\t\t\tif (!prod.geneA || !prod.geneB) continue\n\t\t\t\t\tif (prod.rating == 'RT') continue\n\t\t\t\t\tif (prod.geneA) {\n\t\t\t\t\t\tgenes.add(prod.geneA)\n\t\t\t\t\t}\n\t\t\t\t\tif (prod.geneB) {\n\t\t\t\t\t\tgenes.add(prod.geneB)\n\t\t\t\t\t}\n\t\t\t\t\tconst n = (prod.geneA ? prod.geneA : '<' + prod.chrA) + ' - ' + (prod.geneB ? prod.geneB : '<' + prod.chrB)\n\t\t\t\t\tif (!(n in events)) {\n\t\t\t\t\t\t// sample.name (an attacker/user-reachable sample name) indexes this\n\t\t\t\t\t\t// nested bucket, so it must not inherit from Object.prototype\n\t\t\t\t\t\tevents[n] = Object.create(null)\n\t\t\t\t\t}\n\t\t\t\t\tif (!(sample.name in events[n])) {\n\t\t\t\t\t\tevents[n][sample.name] = []\n\t\t\t\t\t}\n\t\t\t\t\tevents[n][sample.name].push(prod)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.buttgene.text(genes.size + ' gene' + (genes.size > 1 ? 's' : ''))\n\t\tfor (const k in events) {\n\t\t\tconst tmp = k.split(' - ')\n\t\t\tconst evt = { samples: [] }\n\t\t\tif (tmp[0][0] == '<') {\n\t\t\t\tevt.a = tmp[0].slice(1, tmp[0].length)\n\t\t\t\tevt.ainter = true\n\t\t\t} else {\n\t\t\t\tevt.a = tmp[0]\n\t\t\t}\n\t\t\tif (tmp[1][0] == '<') {\n\t\t\t\tevt.b = tmp[1].slice(1, tmp[1].length)\n\t\t\t\tevt.binter = true\n\t\t\t} else {\n\t\t\t\tevt.b = tmp[1]\n\t\t\t}\n\t\t\tfor (const sn in events[k]) {\n\t\t\t\tevt.samples.push({ name: sn, prodlst: events[k][sn] })\n\t\t\t}\n\t\t\tthis.genelst.push(evt)\n\t\t}\n\t\tthis.genelst.sort((a, b) => {\n\t\t\t// sort by hq count\n\t\t\tlet ca = 0\n\t\t\tfor (const s of a.samples) {\n\t\t\t\tfor (const p of s.prodlst) {\n\t\t\t\t\tif (p.rating == 'HQ') ca++\n\t\t\t\t}\n\t\t\t}\n\t\t\tlet cb = 0\n\t\t\tfor (const s of b.samples) {\n\t\t\t\tfor (const p of s.prodlst) {\n\t\t\t\t\tif (p.rating == 'HQ') cb++\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn cb - ca\n\t\t})\n\t\tthis.dogenefilter()\n\t}\n\tstep_table() {\n\t\tthis.eggbar = []\n\t\tthis.ul.selectAll('*').remove()\n\t\tfor (const sample of this.samples) {\n\t\t\tthis.ul.append('li').style('font-weight', 'bold').style('color', '#545454').text(sample.name)\n\t\t\tsample.ul = this.ul.append('ul').style('margin-bottom', '10px')\n\t\t\tthis.showsample(sample)\n\t\t}\n\t}\n\tshowsample(sample) {\n\t\tsample.ul.selectAll('*').remove()\n\t\tfor (const egg of sample.egglst) {\n\t\t\t// one egg: rating grade\n\t\t\t// count number of events\n\t\t\tconst evtnum = egg.lst.reduce((i, j) => i + j.lst.length, 0)\n\t\t\tconst li = sample.ul.append('li')\n\t\t\tconst bar = li\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_clb2')\n\t\t\t\t.html(egg.htmlab + ' ' + evtnum)\n\t\t\tbar.on('click', () => {\n\t\t\t\tfor (const bar0 of this.eggbar) {\n\t\t\t\t\tbar0.style('background-color', '')\n\t\t\t\t}\n\t\t\t\tbar.style('background-color', 'yellow')\n\t\t\t\tconst next = d3select(li.node().nextSibling)\n\t\t\t\tif (next.style('display') == 'none') {\n\t\t\t\t\tclient.appear(next)\n\t\t\t\t\tegg.isopen = true\n\t\t\t\t} else {\n\t\t\t\t\tclient.disappear(next)\n\t\t\t\t\tegg.isopen = false\n\t\t\t\t}\n\t\t\t})\n\t\t\tthis.eggbar.push(bar)\n\t\t\tconst div = sample.ul.append('div').style('margin', '10px')\n\t\t\tthis.showevents(sample, egg.lst, div)\n\t\t}\n\t}\n\n\tshowevents(sample, eglst, holder) {\n\t\tconst svg = holder.append('svg')\n\t\tlet rowh = 22,\n\t\t\trowh2 = 15,\n\t\t\trows = 13,\n\t\t\tfontsize = rowh - 3,\n\t\t\tfontsizeframe = 14,\n\t\t\tfontsizefeature = 10,\n\t\t\thpad0 = 20,\n\t\t\thpad = 10,\n\t\t\tvpad = 10,\n\t\t\tgvpad = 10,\n\t\t\tchrAw = 60,\n\t\t\tchrBw = 60,\n\t\t\ts1 = 10,\n\t\t\ts2 = 10,\n\t\t\ts3 = 10,\n\t\t\ts4 = 10,\n\t\t\ts5 = 5,\n\t\t\ts6 = 15,\n\t\t\ts7 = 13,\n\t\t\teventlogow = 0,\n\t\t\tetw = 25,\n\t\t\tgenesp = 12,\n\t\t\tgeneAw = 0,\n\t\t\tgeneBw = 0,\n\t\t\trecurw = 0,\n\t\t\tgraphheight = 0\n\t\tfor (const eg of eglst) {\n\t\t\tgraphheight += rows\n\t\t\tif (eg.lst.length == 1) {\n\t\t\t\tgraphheight += rowh\n\t\t\t} else {\n\t\t\t\tgraphheight += vpad * 2 + (rowh + rows) * eg.lst.length + (rowh2 + rows) * (eg.lst.length - 1) + gvpad\n\t\t\t}\n\t\t\tfor (const evt of eg.lst) {\n\t\t\t\tevt.svg = {} // tmp obj for rendering\n\t\t\t\tconst prodlst = evt.lst\n\t\t\t\tconst prod = prodlst[0]\n\t\t\t\tlet labA, labB\n\t\t\t\tif (prod.geneA) {\n\t\t\t\t\tconst t = prod.geneA.split(',')\n\t\t\t\t\tif (t.length > 2) {\n\t\t\t\t\t\tlabA = t[0] + ',' + t[1] + '...'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlabA = prod.geneA\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tlabA = ''\n\t\t\t\t}\n\t\t\t\tif (prod.geneB) {\n\t\t\t\t\tconst t = prod.geneB.split(',')\n\t\t\t\t\tif (t.length > 2) {\n\t\t\t\t\t\tlabB = t[0] + ',' + t[1] + '...'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlabB = prod.geneB\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tlabB = ''\n\t\t\t\t}\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(labA)\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', 'Courier')\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tgeneAw = Math.max(geneAw, this.getBBox().width)\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(labB)\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', 'Courier')\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tgeneBw = Math.max(geneBw, this.getBBox().width)\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\t// event logo\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.rating)\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', 'Courier')\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tevt.svg.ratingw = this.getBBox().width\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tevt.svg.framew = 22 // fixed\n\t\t\t\tevt.svg.typew = 60 // fixed\n\t\t\t\tif (prod.usepair) {\n\t\t\t\t\tevt.svg.frameword = prod.usepair.inframe ? 'IN' : 'O'\n\t\t\t\t} else {\n\t\t\t\t\tevt.svg.frameword = '?'\n\t\t\t\t}\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.featureA)\n\t\t\t\t\t.attr('font-size', fontsizefeature)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tevt.svg.featurew = this.getBBox().width\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.featureB)\n\t\t\t\t\t.attr('font-size', fontsizefeature)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tevt.svg.featurew = Math.max(evt.svg.featurew, this.getBBox().width)\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(Math.floor(prod.score))\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.each(function () {\n\t\t\t\t\t\tevt.svg.scorew = this.getBBox().width\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tevt.svg.logow = evt.svg.ratingw + evt.svg.framew + evt.svg.typew + evt.svg.featurew + evt.svg.scorew + s5 * 6\n\t\t\t\teventlogow = Math.max(eventlogow, evt.svg.logow + (prodlst.length > 1 ? s4 + etw : 0))\n\t\t\t\tif (prod.geneA && prod.geneB) {\n\t\t\t\t\tconst slst = this.elab2sample[evt.label]\n\t\t\t\t\tif (!slst) {\n\t\t\t\t\t\tevt.svg.recurtext = 'Recurrence check error'\n\t\t\t\t\t\tevt.svg.recurtextcolor = 'red'\n\t\t\t\t\t} else if (slst.length == 1) {\n\t\t\t\t\t\tevt.svg.recurtext = 'No recurrence'\n\t\t\t\t\t\tevt.svg.recurtextcolor = '#aaaaaa'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tevt.svg.hasrecurrence = true\n\t\t\t\t\t\tevt.svg.recurtext = 'In ' + slst.length + ' samples'\n\t\t\t\t\t\tevt.svg.recurtextcolor = 'black'\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tevt.svg.recurtext = 'Unknown recurrence'\n\t\t\t\t\tevt.svg.recurtextcolor = '#aaaaaa'\n\t\t\t\t}\n\t\t\t\tsvg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(evt.svg.recurtext)\n\t\t\t\t\t.attr('font-size', fontsize - 4)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tevt.svg.recurw = this.getBBox().width\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\trecurw = Math.max(recurw, evt.svg.recurw)\n\t\t\t}\n\t\t}\n\t\tgeneAw += 10\n\t\tgeneBw += 10\n\t\tgraphheight += rows\n\t\tlet ghandlew = 100\n\t\tlet roww =\n\t\t\tchrAw +\n\t\t\ts1 +\n\t\t\trowh +\n\t\t\ts7 +\n\t\t\tgeneAw +\n\t\t\tgenesp +\n\t\t\ts2 +\n\t\t\tgenesp +\n\t\t\tgeneBw +\n\t\t\ts7 +\n\t\t\trowh +\n\t\t\ts1 +\n\t\t\tchrBw +\n\t\t\ts3 +\n\t\t\teventlogow +\n\t\t\ts6 +\n\t\t\trecurw\n\t\t/****************************** render */\n\t\tsvg.attr('width', hpad0 * 2 + hpad * 2 + roww + ghandlew).attr('height', graphheight)\n\t\tconst g = svg.append('g').attr('transform', 'translate(' + hpad0 + ',0)')\n\t\tlet y = 0\n\t\tfor (const eg of eglst) {\n\t\t\ty += rows\n\t\t\tconst g_eg = g.append('g').attr('transform', 'translate(0,' + y + ')')\n\t\t\tconst groupheight =\n\t\t\t\t(rowh + rows) * eg.lst.length -\n\t\t\t\trows +\n\t\t\t\t(eg.lst.length > 1 ? vpad * 2 : 0) +\n\t\t\t\t(eg.lst.length > 1 ? (rowh2 + rows) * (eg.lst.length - 1) : 0)\n\t\t\tif (eg.lst.length > 1) {\n\t\t\t\t// group box\n\t\t\t\tg_eg\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t.attr('stroke-dasharray', eg.ismsg ? 'none' : '2,3')\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.attr('width', roww + hpad * 2)\n\t\t\t\t\t.attr('height', groupheight)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\tif (eg.ismsg) {\n\t\t\t\t\tconst g2 = g_eg.append('g').attr('transform', 'translate(' + (roww + hpad * 2) + ',0)')\n\t\t\t\t\tg2.append('rect')\n\t\t\t\t\t\t.attr('width', ghandlew)\n\t\t\t\t\t\t.attr('height', rowh)\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\tg2.append('text')\n\t\t\t\t\t\t.text('multi-seg')\n\t\t\t\t\t\t.attr('x', 10)\n\t\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t\t.attr('font-size', rowh - 6)\n\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\tg2.append('rect')\n\t\t\t\t\t\t.attr('width', ghandlew)\n\t\t\t\t\t\t.attr('height', rowh)\n\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\t\tconst joinlst = []\n\t\t\t\t\t\t\tconst idlst = []\n\t\t\t\t\t\t\tfor (const evt of eg.lst) {\n\t\t\t\t\t\t\t\tconst prod = evt.lst[0]\n\t\t\t\t\t\t\t\tidlst.push(prod.prodid)\n\t\t\t\t\t\t\t\tconst p = {\n\t\t\t\t\t\t\t\t\ta: {\n\t\t\t\t\t\t\t\t\t\tchr: prod.chrA,\n\t\t\t\t\t\t\t\t\t\tposition: prod.posA,\n\t\t\t\t\t\t\t\t\t\tstrand: prod.ortA,\n\t\t\t\t\t\t\t\t\t\tname: prod.geneA ? prod.geneA : prod.chrA,\n\t\t\t\t\t\t\t\t\t\tratio: prod.ratioA.toFixed(2),\n\t\t\t\t\t\t\t\t\t\tfeature: prod.featureA,\n\t\t\t\t\t\t\t\t\t\tcontiglen: prod.matchA,\n\t\t\t\t\t\t\t\t\t\tchimericreads: prod.readsA,\n\t\t\t\t\t\t\t\t\t\trepeatscore: prod.repeatA\n\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\tb: {\n\t\t\t\t\t\t\t\t\t\tchr: prod.chrB,\n\t\t\t\t\t\t\t\t\t\tposition: prod.posB,\n\t\t\t\t\t\t\t\t\t\tstrand: prod.ortB,\n\t\t\t\t\t\t\t\t\t\tname: prod.geneB ? prod.geneB : prod.chrB,\n\t\t\t\t\t\t\t\t\t\tratio: prod.ratioB.toFixed(2),\n\t\t\t\t\t\t\t\t\t\tfeature: prod.featureB,\n\t\t\t\t\t\t\t\t\t\tcontiglen: prod.matchB,\n\t\t\t\t\t\t\t\t\t\tchimericreads: prod.readsB,\n\t\t\t\t\t\t\t\t\t\trepeatscore: prod.repeatB\n\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\trating: prod.rating,\n\t\t\t\t\t\t\t\t\tscore: Math.ceil(prod.score)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (prod.usepair) {\n\t\t\t\t\t\t\t\t\tp.inframe = prod.usepair.inframe\n\t\t\t\t\t\t\t\t\tconst x = prod.usepair.a\n\t\t\t\t\t\t\t\t\tp.a.gm = this.genome.isoformmatch(x.isoform, p.a.chr, p.a.position)\n\t\t\t\t\t\t\t\t\tp.a.codon = x.codon\n\t\t\t\t\t\t\t\t\tp.a.exon = x.exon\n\t\t\t\t\t\t\t\t\tp.a.atupstream = x.atupstream\n\t\t\t\t\t\t\t\t\tp.a.atdownstream = x.atdownstream\n\t\t\t\t\t\t\t\t\tp.a.atutr5 = x.atutr5\n\t\t\t\t\t\t\t\t\tp.a.atutr3 = x.atutr3\n\t\t\t\t\t\t\t\t\tconst y = prod.usepair.b\n\t\t\t\t\t\t\t\t\tp.b.gm = this.genome.isoformmatch(y.isoform, p.b.chr, p.b.position)\n\t\t\t\t\t\t\t\t\tp.b.codon = y.codon\n\t\t\t\t\t\t\t\t\tp.b.exon = y.exon\n\t\t\t\t\t\t\t\t\tp.b.atupstream = y.atupstream\n\t\t\t\t\t\t\t\t\tp.b.atdownstream = y.atdownstream\n\t\t\t\t\t\t\t\t\tp.b.atutr5 = y.atutr5\n\t\t\t\t\t\t\t\t\tp.b.atutr3 = y.atutr3\n\t\t\t\t\t\t\t\t\t// interstitial\n\t\t\t\t\t\t\t\t\tlet aalen = 0,\n\t\t\t\t\t\t\t\t\t\tbplen = 0\n\t\t\t\t\t\t\t\t\tif (x.contigaa && y.contigaa) {\n\t\t\t\t\t\t\t\t\t\taalen = y.contigaa - x.contigaa - 1\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tif (x.contigbp && y.contigbp) {\n\t\t\t\t\t\t\t\t\t\tbplen = y.contigbp - x.contigbp - 1\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tif (aalen) {\n\t\t\t\t\t\t\t\t\t\tp.interstitial = { aalen: aalen }\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\tif (bplen) {\n\t\t\t\t\t\t\t\t\t\tif (!p.interstitial) p.interstitial = {}\n\t\t\t\t\t\t\t\t\t\tp.interstitial.bplen = bplen\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tjoinlst.push(p)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\t\tconst pane = client.newpane({ x: p.left + 10, y: p.top + p.height + 10 })\n\t\t\t\t\t\t\tconst div = pane.body.append('div').style('margin', '10px')\n\t\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t\t\t.style('padding-right', '20px')\n\t\t\t\t\t\t\t\t.text('Product id: ' + idlst.join(', '))\n\t\t\t\t\t\t\t// break msg\n\t\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t\t.style('margin-right', '10px')\n\t\t\t\t\t\t\t\t.text('Break')\n\t\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\t\t// find array index of group eg\n\t\t\t\t\t\t\t\t\tconst eg2id = eg.lst.map(j => j.lst[0].prodid)\n\t\t\t\t\t\t\t\t\tlet idx = 0\n\t\t\t\t\t\t\t\t\tfor (; idx < eglst.length; idx++) {\n\t\t\t\t\t\t\t\t\t\tconst eg2 = eglst[idx]\n\t\t\t\t\t\t\t\t\t\tif (eg2.ismsg) {\n\t\t\t\t\t\t\t\t\t\t\tconst eg22id = eg2.lst.map(j => j.lst[0].prodid)\n\t\t\t\t\t\t\t\t\t\t\tif (eg22id.join(',') == eg2id.join(',')) {\n\t\t\t\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t// break group\n\t\t\t\t\t\t\t\t\tdelete eg.ismsg\n\t\t\t\t\t\t\t\t\tconst oldlst = eg.lst\n\t\t\t\t\t\t\t\t\teg.lst = [eg.lst[0]]\n\t\t\t\t\t\t\t\t\tfor (let j = 1; j < oldlst.length; j++) {\n\t\t\t\t\t\t\t\t\t\teglst.splice(idx, 0, {\n\t\t\t\t\t\t\t\t\t\t\tlabel: '',\n\t\t\t\t\t\t\t\t\t\t\tlst: [oldlst[j]]\n\t\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t// remake graph\n\t\t\t\t\t\t\t\t\tsvg.remove()\n\t\t\t\t\t\t\t\t\tthis.showevents(sample, eglst, holder)\n\t\t\t\t\t\t\t\t\t// done\n\t\t\t\t\t\t\t\t\tpane.pane.remove()\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t// edit msg\n\t\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t\t.text('Edit')\n\t\t\t\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\t\t\t\tconst inputdom = document.createElement('input')\n\t\t\t\t\t\t\t\t\tdiv.node().insertBefore(inputdom, event.target)\n\t\t\t\t\t\t\t\t\tconst buttdom = document.createElement('button')\n\t\t\t\t\t\t\t\t\tdiv.node().insertBefore(buttdom, event.target)\n\t\t\t\t\t\t\t\t\tdiv.node().removeChild(event.target)\n\t\t\t\t\t\t\t\t\tinputdom.focus()\n\t\t\t\t\t\t\t\t\tconst input = d3select(inputdom)\n\t\t\t\t\t\t\t\t\tconst butt = d3select(buttdom)\n\t\t\t\t\t\t\t\t\tinput.attr('size', 10).style('margin', '0px 10px').property('value', idlst.join(','))\n\t\t\t\t\t\t\t\t\tbutt.text('Apply').on('click', () => {\n\t\t\t\t\t\t\t\t\t\tconst lst0 = inputdom.value.trim().split(',')\n\t\t\t\t\t\t\t\t\t\tconst goodid = []\n\t\t\t\t\t\t\t\t\t\tfor (const s of lst0) {\n\t\t\t\t\t\t\t\t\t\t\tif (!s) continue\n\t\t\t\t\t\t\t\t\t\t\tconst j = Number.parseInt(s)\n\t\t\t\t\t\t\t\t\t\t\tif (Number.isNaN(j)) return alert('invalid id: ' + s)\n\t\t\t\t\t\t\t\t\t\t\tif (this.prodidisinvalid(j, sample)) return alert('invalid id ' + j)\n\t\t\t\t\t\t\t\t\t\t\tgoodid.push(j)\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\tif (goodid.length <= 1) return alert('must be at least 2 products')\n\t\t\t\t\t\t\t\t\t\tconst newevtlst = []\n\t\t\t\t\t\t\t\t\t\tfor (const id of goodid) {\n\t\t\t\t\t\t\t\t\t\t\tconst lookprod = this.extractprod(id, sample)\n\t\t\t\t\t\t\t\t\t\t\tif (lookprod) {\n\t\t\t\t\t\t\t\t\t\t\t\tnewevtlst.push({ label: lookprod.eventlabel, lst: [lookprod] })\n\t\t\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\t\t\treturn alert('unknown product id ' + id)\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\tif (newevtlst.length <= 1) return alert('less than 2 products cannot make a group')\n\t\t\t\t\t\t\t\t\t\teglst.unshift({ lst: newevtlst, ismsg: true })\n\t\t\t\t\t\t\t\t\t\t// remake entire sample\n\t\t\t\t\t\t\t\t\t\tthis.showsample(sample)\n\t\t\t\t\t\t\t\t\t\t// done\n\t\t\t\t\t\t\t\t\t\tpane.pane.remove()\n\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tsvtable({\n\t\t\t\t\t\t\t\tsamplelst: [\n\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\tpairlst: joinlst\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\t\tnosample: true,\n\t\t\t\t\t\t\t\tholder: pane.body\n\t\t\t\t\t\t\t})\n\n\t\t\t\t\t\t\tconst par = {\n\t\t\t\t\t\t\t\tpairlst: joinlst,\n\t\t\t\t\t\t\t\tgenome: this.genome,\n\t\t\t\t\t\t\t\tholder: pane.body,\n\t\t\t\t\t\t\t\thostURL: this.hostURL,\n\t\t\t\t\t\t\t\tjwt: this.jwt\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\timport('./svgraph').then(p => {\n\t\t\t\t\t\t\t\tp.default(par)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\t// end of event group business\n\t\t\t}\n\t\t\tconst g_rows = g_eg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', 'translate(' + hpad + ',' + (eg.lst.length > 1 ? vpad : 0) + ')')\n\t\t\tlet y1 = 0\n\t\t\tlet evtid = 0\n\t\t\tconst bgcolor = '#ededed'\n\t\t\t// collect event labels in this group, for subtracting out *this event* when showing external events\n\t\t\tconst elabhash = {}\n\t\t\tfor (const e of eg.lst) {\n\t\t\t\telabhash[e.label] = 1\n\t\t\t}\n\t\t\t// collect shown gene names, shown genes won't display tips (ext events) to avoid duplication\n\t\t\tconst showngenenotip = {}\n\t\t\tfor (const evt of eg.lst) {\n\t\t\t\tconst prodlst = evt.lst\n\t\t\t\tconst prod = prodlst[0]\n\t\t\t\tconst thispair = prod.usepair\n\t\t\t\tif (eg.lst.length > 1 && evtid > 0) {\n\t\t\t\t\t// marker in-the-middle row inside a group\n\t\t\t\t\tconst g_row = g_rows\n\t\t\t\t\t\t.append('g')\n\t\t\t\t\t\t.attr('transform', 'translate(' + (chrAw + s1 + rowh + s7 + geneAw + genesp + s2 / 2) + ',' + y1 + ')')\n\t\t\t\t\tconst text = g_row\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.attr('fill', '#858585')\n\t\t\t\t\t\t.attr('font-size', rowh2)\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t.attr('y', rowh2 / 2)\n\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\tif (eg.ismsg) {\n\t\t\t\t\t\ttext.text(prod.mswhat ? prod.mswhat : 'No connection detail')\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttext.text('Reciprocal')\n\t\t\t\t\t}\n\t\t\t\t\ty1 += rowh2 + rows\n\t\t\t\t}\n\t\t\t\tconst textcolor = prod.chrA == prod.chrB ? 'black' : client.colorctx\n\t\t\t\tconst g_row = g_rows.append('g').attr('transform', 'translate(0,' + y1 + ')')\n\t\t\t\t// chr a\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.chrA)\n\t\t\t\t\t.attr('x', chrAw)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('font-size', fontsize - 4)\n\t\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t.attr('fill', textcolor)\n\t\t\t\tconst extevt = { a: null, b: null }\n\t\t\t\tif (prod.geneA) {\n\t\t\t\t\tif (prod.geneA in showngenenotip) {\n\t\t\t\t\t\tshowngenenotip[prod.geneA] = 1\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconst lst = []\n\t\t\t\t\t\tfor (const elab in sample.gene2events[prod.geneA]) {\n\t\t\t\t\t\t\tif (!(elab in elabhash)) {\n\t\t\t\t\t\t\t\tlst.push(elab)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (lst.length > 0) {\n\t\t\t\t\t\t\textevt.a = { lst: lst }\n\t\t\t\t\t\t\t// gene a tip\n\t\t\t\t\t\t\textevt.a.circle = g_row\n\t\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t\t\t\t.attr('cx', chrAw + s1 + rowh / 2)\n\t\t\t\t\t\t\t\t.attr('cy', rowh / 2)\n\t\t\t\t\t\t\t\t.attr('r', rowh / 2)\n\t\t\t\t\t\t\tif (lst.length > 1) {\n\t\t\t\t\t\t\t\textevt.a.text = g_row\n\t\t\t\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t\t\t\t.text(lst.length)\n\t\t\t\t\t\t\t\t\t.attr('x', chrAw + s1 + rowh / 2)\n\t\t\t\t\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t\t\t\t.attr('font-size', rowh2)\n\t\t\t\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tg_row\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('x1', chrAw + s1 + rowh)\n\t\t\t\t\t\t\t\t.attr('x2', chrAw + s1 + rowh + s7)\n\t\t\t\t\t\t\t\t.attr('y1', rowh / 2)\n\t\t\t\t\t\t\t\t.attr('y2', rowh / 2)\n\t\t\t\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// ratio a\n\t\t\t\tg_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', client.colorbgleft)\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + (geneAw + genesp) * (1 - prod.ratioA))\n\t\t\t\t\t.attr('width', (geneAw + genesp) * prod.ratioA)\n\t\t\t\t\t.attr('height', rowh)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\tlet antisense = false\n\t\t\t\tif (thispair) {\n\t\t\t\t\tconst thisn = thispair.a.isoform\n\t\t\t\t\tif (thisn) {\n\t\t\t\t\t\tconst _gm = this.genome.isoformmatch(thisn, prod.chrA, prod.posA)\n\t\t\t\t\t\tif (_gm && _gm.strand != prod.ortA) {\n\t\t\t\t\t\t\t// gene a antisense\n\t\t\t\t\t\t\tantisense = true\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// gene a box\n\t\t\t\tconst boxa = g_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.attr('stroke', antisense ? 'red' : 'black')\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7)\n\t\t\t\t\t.attr('width', geneAw + genesp)\n\t\t\t\t\t.attr('height', rowh)\n\t\t\t\t// name a\n\t\t\t\tlet labA\n\t\t\t\tif (prod.geneA) {\n\t\t\t\t\tconst t = prod.geneA.split(',')\n\t\t\t\t\tif (t.length > 2) {\n\t\t\t\t\t\tlabA = t[0] + ',' + t[1] + '...'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlabA = prod.geneA\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tlabA = ''\n\t\t\t\t}\n\t\t\t\t// gene a label\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(labA)\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + geneAw)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', 'Courier')\n\t\t\t\t\t.attr(\n\t\t\t\t\t\t'font-weight',\n\t\t\t\t\t\tprod.hlgene ? (prod.hlgene == 1 || prod.hlgene == 3 || prod.hlgene == 4 ? 'bold' : 'normal') : 'normal'\n\t\t\t\t\t)\n\t\t\t\t\t.attr('fill', prod.hlgene ? (prod.hlgene == 4 ? knownprod_c : '#545454') : '#545454')\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// a-b conn\n\t\t\t\tg_row\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('x1', chrAw + s1 + rowh + s7 + geneAw + genesp)\n\t\t\t\t\t.attr('x2', chrAw + s1 + rowh + s7 + geneAw + genesp + s2)\n\t\t\t\t\t.attr('y1', rowh / 2)\n\t\t\t\t\t.attr('y2', rowh / 2)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t// ratio b\n\t\t\t\tg_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', client.colorbgright)\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + geneAw + genesp + s2)\n\t\t\t\t\t.attr('width', (genesp + geneBw) * prod.ratioB)\n\t\t\t\t\t.attr('height', rowh)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\tantisense = false\n\t\t\t\tif (thispair) {\n\t\t\t\t\tconst thisn = thispair.b.isoform\n\t\t\t\t\tif (thisn) {\n\t\t\t\t\t\tconst _gm = this.genome.isoformmatch(thisn, prod.chrB, prod.posB)\n\t\t\t\t\t\tif (_gm && _gm.strand != prod.ortB) {\n\t\t\t\t\t\t\t// gene b antisense\n\t\t\t\t\t\t\tantisense = true\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// gene b box\n\t\t\t\tconst boxb = g_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.attr('stroke', antisense ? 'red' : 'black')\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + geneAw + genesp + s2)\n\t\t\t\t\t.attr('width', geneBw + genesp)\n\t\t\t\t\t.attr('height', rowh)\n\t\t\t\t// name b\n\t\t\t\tlet labB\n\t\t\t\tif (prod.geneB) {\n\t\t\t\t\tlet t = prod.geneB.split(',')\n\t\t\t\t\tif (t.length > 2) {\n\t\t\t\t\t\tlabB = t[0] + ',' + t[1] + '...'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlabB = prod.geneB\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tlabB = ''\n\t\t\t\t}\n\t\t\t\t// gene b label\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(labB)\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('font-size', fontsize)\n\t\t\t\t\t.attr('font-family', 'Courier')\n\t\t\t\t\t.attr(\n\t\t\t\t\t\t'font-weight',\n\t\t\t\t\t\tprod.hlgene ? (prod.hlgene == 2 || prod.hlgene == 3 || prod.hlgene == 4 ? 'bold' : 'normal') : 'normal'\n\t\t\t\t\t)\n\t\t\t\t\t.attr('fill', prod.hlgene ? (prod.hlgene == 4 ? knownprod_c : '#545454') : '#545454')\n\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\tif (prod.geneB) {\n\t\t\t\t\tif (prod.geneB in showngenenotip) {\n\t\t\t\t\t} else {\n\t\t\t\t\t\tshowngenenotip[prod.geneB] = 1\n\t\t\t\t\t\tconst lst = []\n\t\t\t\t\t\tfor (const elab in sample.gene2events[prod.geneB]) {\n\t\t\t\t\t\t\tif (!(elab in elabhash)) {\n\t\t\t\t\t\t\t\tlst.push(elab)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (lst.length > 0) {\n\t\t\t\t\t\t\textevt.b = { lst: lst }\n\t\t\t\t\t\t\t// gene b tip\n\t\t\t\t\t\t\textevt.b.circle = g_row\n\t\t\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t\t\t\t.attr('cx', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh / 2)\n\t\t\t\t\t\t\t\t.attr('cy', rowh / 2)\n\t\t\t\t\t\t\t\t.attr('r', rowh / 2)\n\t\t\t\t\t\t\tif (lst.length > 1) {\n\t\t\t\t\t\t\t\textevt.b.text = g_row\n\t\t\t\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t\t\t\t.text(lst.length)\n\t\t\t\t\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh / 2)\n\t\t\t\t\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t\t\t\t.attr('font-size', rowh2)\n\t\t\t\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tg_row\n\t\t\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t\t\t.attr('x1', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw)\n\t\t\t\t\t\t\t\t.attr('x2', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7)\n\t\t\t\t\t\t\t\t.attr('y1', rowh / 2)\n\t\t\t\t\t\t\t\t.attr('y2', rowh / 2)\n\t\t\t\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// chr b\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.chrB)\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh + s1)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('font-size', fontsize - 4)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\t.attr('fill', textcolor)\n\t\t\t\t// event logo\n\t\t\t\tlet x = chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh + s1 + chrBw + s3\n\t\t\t\tconst x0 = x\n\t\t\t\tconst logobg = g_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t.attr('stroke', '#858585')\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', -1.5)\n\t\t\t\t\t.attr('width', evt.svg.logow)\n\t\t\t\t\t.attr('height', rowh + 2)\n\t\t\t\t\t.attr('rx', 5)\n\t\t\t\t\t.attr('ry', 5)\n\t\t\t\tx += s5\n\t\t\t\tprod.hook.mainRating = g_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.rating)\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', '#858585')\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tx += evt.svg.ratingw + s5\n\t\t\t\tprod.hook.mainFrame = {}\n\t\t\t\tprod.hook.mainFrame.bg = g_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('x', x + 1)\n\t\t\t\t\t.attr('y', 3)\n\t\t\t\t\t.attr('width', evt.svg.framew)\n\t\t\t\t\t.attr('height', rowh - 7)\n\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\tif (prod.usepair) {\n\t\t\t\t\tprod.hook.mainFrame.bg.attr('fill', prod.usepair.inframe ? client.colorinframe : client.coloroutframe)\n\t\t\t\t} else {\n\t\t\t\t\tprod.hook.mainFrame.bg.attr('fill', 'none').attr('stroke', 'black')\n\t\t\t\t}\n\t\t\t\tprod.hook.mainFrame.text = g_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(evt.svg.frameword)\n\t\t\t\t\t.attr('font-size', fontsizeframe)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', prod.usepair ? 'white' : 'black')\n\t\t\t\t\t.attr('x', x + 1 + evt.svg.framew / 2)\n\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tx += evt.svg.framew + s5\n\t\t\t\tprod.hook.mainType = g_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.type2)\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', '#858585')\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tx += evt.svg.typew + s5\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.featureA)\n\t\t\t\t\t.attr('font-size', fontsizefeature)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', rowh / 4)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(prod.featureB)\n\t\t\t\t\t.attr('font-size', fontsizefeature)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', (rowh * 3) / 4)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tx += evt.svg.featurew + s5\n\t\t\t\tg_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(Math.floor(prod.score))\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', '#858585')\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tx += evt.svg.scorew + s5 + s4\n\t\t\t\t// logo kick\n\t\t\t\tg_row\n\t\t\t\t\t.append('rect')\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.attr('stroke', 'none')\n\t\t\t\t\t.attr('x', x0)\n\t\t\t\t\t.attr('y', -1.5)\n\t\t\t\t\t.attr('width', evt.svg.logow)\n\t\t\t\t\t.attr('height', rowh + 2)\n\t\t\t\t\t.on('mouseover', () => {\n\t\t\t\t\t\tlogobg.attr('stroke-width', '2')\n\t\t\t\t\t\tconst d = tip.clear().showunder(logobg.node()).d.append('div')\n\t\t\t\t\t\tthis.prodstat(prod, d)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\tlogobg.attr('stroke-width', '1')\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t})\n\t\t\t\tif (prodlst.length > 1) {\n\t\t\t\t\tconst logobg2 = g_row\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t\t.attr('stroke', '#858585')\n\t\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t\t.attr('y', 3.5)\n\t\t\t\t\t\t.attr('width', etw)\n\t\t\t\t\t\t.attr('height', rowh - 4)\n\t\t\t\t\t\t.attr('rx', 5)\n\t\t\t\t\t\t.attr('ry', 5)\n\t\t\t\t\tg_row\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(prodlst.length - 1)\n\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t.attr('font-size', fontsizefeature)\n\t\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t\t.attr('x', x + etw / 2)\n\t\t\t\t\t\t.attr('y', 3.5 + (rowh - 3.5) / 2)\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t\tg_row\n\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t\t.attr('y', 3.5)\n\t\t\t\t\t\t.attr('width', etw)\n\t\t\t\t\t\t.attr('height', rowh - 4)\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\tlogobg2.attr('stroke-width', '2')\n\t\t\t\t\t\t\tconst table = tip\n\t\t\t\t\t\t\t\t.clear()\n\t\t\t\t\t\t\t\t.showunder(event.target)\n\t\t\t\t\t\t\t\t.d.append('table')\n\t\t\t\t\t\t\t\t.style('border-spacing', '10px')\n\t\t\t\t\t\t\t\t.style('border-collapse', 'separate')\n\t\t\t\t\t\t\tconst tr1 = table.append('tr')\n\t\t\t\t\t\t\tconst tr2 = table.append('tr')\n\t\t\t\t\t\t\tfor (var k = 1; k < prodlst.length; k++) {\n\t\t\t\t\t\t\t\tthis.eventlogo([prodlst[k]], tr1.append('td'))\n\t\t\t\t\t\t\t\tthis.prodstat(prodlst[k], tr2.append('td'))\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\tlogobg2.attr('stroke-width', '1')\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\t// recurrence\n\t\t\t\tx =\n\t\t\t\t\tchrAw +\n\t\t\t\t\ts1 +\n\t\t\t\t\trowh +\n\t\t\t\t\ts7 +\n\t\t\t\t\tgeneAw +\n\t\t\t\t\tgenesp +\n\t\t\t\t\ts2 +\n\t\t\t\t\tgenesp +\n\t\t\t\t\tgeneBw +\n\t\t\t\t\ts7 +\n\t\t\t\t\trowh +\n\t\t\t\t\ts1 +\n\t\t\t\t\tchrBw +\n\t\t\t\t\ts3 +\n\t\t\t\t\teventlogow +\n\t\t\t\t\ts6\n\t\t\t\tconst text = g_row\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(evt.svg.recurtext)\n\t\t\t\t\t.attr('font-size', fontsize - 4)\n\t\t\t\t\t.attr('font-family', client.font)\n\t\t\t\t\t.attr('fill', evt.svg.recurtextcolor)\n\t\t\t\t\t.attr('x', x)\n\t\t\t\t\t.attr('y', rowh / 2)\n\t\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\tif (evt.svg.hasrecurrence) {\n\t\t\t\t\ttext\n\t\t\t\t\t\t.attr('class', 'sja_svgtext2')\n\t\t\t\t\t\t.on('mouseover', event => {\n\t\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\t\ttip.clear().show(p.left + p.width + 10, p.top - 15)\n\t\t\t\t\t\t\tconst slst = this.elab2sample[evt.label]\n\t\t\t\t\t\t\tconst dd = tip.d\n\t\t\t\t\t\t\tdd.append('div')\n\t\t\t\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t\t\t\t.style('color', '#aaa')\n\t\t\t\t\t\t\t\t.text('This fusion is recurrent in other samples:')\n\t\t\t\t\t\t\tconst table = dd.append('table').style('border-spacing', '10px').style('border-collapse', 'separate')\n\t\t\t\t\t\t\tfor (const s of slst) {\n\t\t\t\t\t\t\t\tif (s.name == sample.name) {\n\t\t\t\t\t\t\t\t\t// self, no show\n\t\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tconst tr = table.append('tr')\n\t\t\t\t\t\t\t\ttr.append('td').style('font-weight', 'bold').style('color', '#858585').text(s.name)\n\t\t\t\t\t\t\t\tthis.eventlogo(s.events[evt.label], tr.append('td'))\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('mouseout', () => tip.hide())\n\t\t\t\t}\n\t\t\t\t// row kick\n\t\t\t\tg_row\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('x', chrAw + s1 + rowh + s7)\n\t\t\t\t\t.attr('width', geneAw + genesp + s2 + genesp + geneBw)\n\t\t\t\t\t.attr('height', rowh)\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', event => {\n\t\t\t\t\t\tboxa.attr('stroke-width', 2)\n\t\t\t\t\t\tboxb.attr('stroke-width', 2)\n\t\t\t\t\t\t/* old behavior to remember the one under highlight and not to re-show tip on it\n\t\t\t\t\t\tif (evt.inview) return\n\t\t\t\t\t\tfor (const eg2 of eglst) {\n\t\t\t\t\t\t\tfor (const e2 of eg2.lst) {\n\t\t\t\t\t\t\t\te2.inview = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tevt.inview = true\n\t\t\t\t\t\td3select(document.body).on('mousedown', () => (evt.inview = false))\n\t\t\t\t\t\t*/\n\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\ttip.clear().show(p.left + p.width + s7 / 2, p.top - 30)\n\t\t\t\t\t\tthis.showsvpairs({\n\t\t\t\t\t\t\tprodlst: evt.lst,\n\t\t\t\t\t\t\tholder: tip.d,\n\t\t\t\t\t\t\tnodetail: true,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\teglst: eglst,\n\t\t\t\t\t\t\tshowothersample: true\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\ttip.hide()\n\t\t\t\t\t\tboxa.attr('stroke-width', 1)\n\t\t\t\t\t\tboxb.attr('stroke-width', 1)\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tif (evt.inclick) {\n\t\t\t\t\t\t\t// shake\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tevt.inclick = true\n\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\tconst pane3 = client.newpane({\n\t\t\t\t\t\t\tx: p.left + p.width + s7 + rowh + s1 + chrBw + s3 + eventlogow + s6 + recurw + 5,\n\t\t\t\t\t\t\ty: p.top - 100,\n\t\t\t\t\t\t\tclose: function () {\n\t\t\t\t\t\t\t\tevt.inclick = false\n\t\t\t\t\t\t\t\tpane3.pane.remove()\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t\tconst prod = evt.lst[0]\n\t\t\t\t\t\tpane3.header.html(\n\t\t\t\t\t\t\t'<span style=\"padding:2px 4px;background-color:' +\n\t\t\t\t\t\t\t\tclient.colorbgleft +\n\t\t\t\t\t\t\t\t';\">' +\n\t\t\t\t\t\t\t\t(prod.geneA ? prod.geneA : prod.chrA) +\n\t\t\t\t\t\t\t\t'</span>' +\n\t\t\t\t\t\t\t\t'<span style=\"padding:2px 4px;background-color:' +\n\t\t\t\t\t\t\t\tclient.colorbgright +\n\t\t\t\t\t\t\t\t';\">' +\n\t\t\t\t\t\t\t\t(prod.geneB ? prod.geneB : prod.chrB) +\n\t\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t)\n\t\t\t\t\t\tthis.showsvpairs({\n\t\t\t\t\t\t\tprodlst: evt.lst,\n\t\t\t\t\t\t\tholder: pane3.body\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t// external events for a, kick\n\t\t\t\tif (extevt.a) {\n\t\t\t\t\tg_row\n\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t.attr('cx', chrAw + s1 + rowh / 2)\n\t\t\t\t\t\t.attr('cy', rowh / 2)\n\t\t\t\t\t\t.attr('r', rowh / 2)\n\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t.on('mouseover', event => this.extevt_mover(extevt.a, event.target, sample))\n\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\tthis.extevt_mo(extevt.a)\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\t\tthis.extevt_c(extevt.a, event.target, sample)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tif (extevt.b) {\n\t\t\t\t\tg_row\n\t\t\t\t\t\t.append('circle')\n\t\t\t\t\t\t.attr('cx', chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh / 2)\n\t\t\t\t\t\t.attr('cy', rowh / 2)\n\t\t\t\t\t\t.attr('r', rowh / 2)\n\t\t\t\t\t\t.attr('fill', 'white')\n\t\t\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t\t\t.on('mouseover', event => this.extevt_mover(extevt.b, event.target, sample))\n\t\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\t\tthis.extevt_mo(extevt.b)\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('click', event => this.extevt_c(extevt.b, event.target, sample))\n\t\t\t\t}\n\t\t\t\ty1 += rowh + rows\n\t\t\t\tevtid++\n\t\t\t}\n\t\t\ty += groupheight + (eg.lst.length > 1 ? gvpad : 0)\n\t\t}\n\t\tholder.style('display', 'none')\n\t}\n\n\textevt_mover(ext, dom, sample) {\n\t\text.circle.attr('fill', '#858585')\n\t\tif (ext.text) {\n\t\t\text.text.attr('fill', 'white')\n\t\t}\n\t\ttip.clear().showunder(dom)\n\t\ttip.d.append('div').style('margin', '10px').style('color', '#aaa').text('Associated fusions from this sample:')\n\t\tthis.extevt_table(ext.lst, tip.d, sample)\n\t}\n\textevt_mo(ext) {\n\t\text.circle.attr('fill', 'white')\n\t\tif (ext.text) {\n\t\t\text.text.attr('fill', 'black')\n\t\t}\n\t}\n\textevt_c(ext, dom, sample) {\n\t\tconst p = dom.getBoundingClientRect()\n\t\tconst pane = client.newpane({ x: p.left, y: p.top + p.height + 10 })\n\t\tthis.extevt_table(ext.lst, pane.body, sample)\n\t}\n\textevt_table(lst, holder, sample) {\n\t\tconst table = holder.append('table').style('border-spacing', '10px').style('border-collapse', 'separate')\n\t\tfor (const elab of lst) {\n\t\t\tconst tr = table.append('tr')\n\t\t\tconst prodlst = sample.events[elab]\n\t\t\tif (!prodlst) {\n\t\t\t\ttr.append('<td colspan=2 style=\"color:red\">No products found for ' + elab + '</td>')\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst prod = prodlst[0]\n\t\t\ttr.append('td')\n\t\t\t\t.style('text-align', 'right')\n\t\t\t\t.text(prod.geneA ? prod.geneA : prod.chrA)\n\t\t\ttr.append('td').text(prod.geneB ? prod.geneB : prod.chrB)\n\t\t\tthis.eventlogo(prodlst, tr.append('td'))\n\t\t}\n\t}\n\teventlogo(prodlst, holder) {\n\t\tconst d = holder.append('div')\n\t\tif (!prodlst || prodlst.length == 0) {\n\t\t\td.style('color', 'red').text('No products')\n\t\t} else {\n\t\t\tconst p = prodlst[0]\n\t\t\td.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '2px 4px')\n\t\t\t\t.style('border', 'solid 1px #858585')\n\t\t\t\t.style('border-radius', '5px')\n\t\t\t\t.html(\n\t\t\t\t\tp.rating +\n\t\t\t\t\t\t'&nbsp;' +\n\t\t\t\t\t\t'<span style=\"font-size:70%;vertical-align:2px;' +\n\t\t\t\t\t\t(p.usepair\n\t\t\t\t\t\t\t? p.usepair.inframe\n\t\t\t\t\t\t\t\t? 'padding:2px 4px;background-color:' + client.colorinframe + ';color:white;\">IN'\n\t\t\t\t\t\t\t\t: 'padding:2px 4px;background-color:' + client.coloroutframe + ';color:white;\">O'\n\t\t\t\t\t\t\t: 'padding:1px 3px;border:solid 1px black;background-color:white;color:black;\">?') +\n\t\t\t\t\t\t'</span>' +\n\t\t\t\t\t\t'&nbsp;<span style=\"color:#858585\">' +\n\t\t\t\t\t\tp.type2 +\n\t\t\t\t\t\t'</span>&nbsp;' +\n\t\t\t\t\t\t'<div style=\"display:inline-block;font-size:70%;line-height:.9\">' +\n\t\t\t\t\t\tp.featureA +\n\t\t\t\t\t\t'<br>' +\n\t\t\t\t\t\tp.featureB +\n\t\t\t\t\t\t'</div>' +\n\t\t\t\t\t\t'&nbsp;' +\n\t\t\t\t\t\tMath.floor(p.score)\n\t\t\t\t)\n\t\t\tif (prodlst.length > 1) {\n\t\t\t\td.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\t.style('padding', '2px 4px')\n\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t.style('border', 'solid 1px #858585')\n\t\t\t\t\t.style('border-radius', 5)\n\t\t\t\t\t.text(prodlst.length - 1)\n\t\t\t}\n\t\t}\n\t\treturn d\n\t}\n\n\tprodstat(prod, holder) {\n\t\tholder.append('p').text('Product id: ' + prod.prodid)\n\t\tconst alertcolor = '#FFb3b3',\n\t\t\tbg = '#f1f1f1'\n\t\tconst table = holder.append('table').style('border-spacing', '8px').style('border-collapse', 'separate')\n\t\tlet tr = table.append('tr')\n\t\ttr.append('td')\n\t\ttr.append('td')\n\t\t\t.style('background-color', bg)\n\t\t\t.text(prod.geneA ? prod.geneA : prod.chrA)\n\t\ttr.append('td')\n\t\t\t.style('background-color', bg)\n\t\t\t.text(prod.geneB ? prod.geneB : prod.chrB)\n\t\ttr = table.append('tr')\n\t\ttr.append('td').style('font-size', '80%').style('background-color', bg).text('chimeric reads')\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.readsA <= this.cf_reads ? alertcolor : '')\n\t\t\t.text(prod.readsA)\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.readsB <= this.cf_reads ? alertcolor : '')\n\t\t\t.text(prod.readsB)\n\t\ttr = table.append('tr')\n\t\ttr.append('td').style('font-size', '80%').style('background-color', bg).text('ratio')\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.ratioA <= this.cf_ratio ? alertcolor : '')\n\t\t\t.text(Math.ceil(prod.ratioA * 100) + '%')\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.ratioB <= this.cf_ratio ? alertcolor : '')\n\t\t\t.text(Math.ceil(prod.ratioB * 100) + '%')\n\t\ttr = table.append('tr')\n\t\ttr.append('td').style('font-size', '80%').style('background-color', bg).text('contig length')\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.matchA <= this.cf_match ? alertcolor : '')\n\t\t\t.text(prod.matchA + ' bp')\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.matchB <= this.cf_match ? alertcolor : '')\n\t\t\t.text(prod.matchB + ' bp')\n\t\ttr = table.append('tr')\n\t\ttr.append('td').style('font-size', '80%').style('background-color', bg).text('repeat score')\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.repeatA >= this.cf_repeat ? alertcolor : '')\n\t\t\t.text(prod.repeatA)\n\t\ttr.append('td')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('background-color', prod.repeatB >= this.cf_repeat ? alertcolor : '')\n\t\t\t.text(prod.repeatB)\n\t}\n\n\tshowsvpairs(arg) {\n\t\t// individual pairs show separately\n\t\tconst table = arg.holder.append('table').style('border-spacing', '10px').style('border-collapse', 'separate')\n\t\tconst tr = table.append('tr')\n\t\tconst _tr = table.append('tr')\n\t\tconst expressiontd = _tr.append('td').attr('colspan', arg.prodlst.length)\n\t\tconst tr2 = table.append('tr')\n\t\t// collect genes for showing expression\n\t\tconst geneset = new Set()\n\t\tfor (const prod of arg.prodlst) {\n\t\t\tif (prod.geneA) {\n\t\t\t\tgeneset.add(prod.geneA)\n\t\t\t}\n\t\t\tif (prod.geneB) {\n\t\t\t\tgeneset.add(prod.geneB)\n\t\t\t}\n\t\t\tconst td = tr.append('td').style('vertical-align', 'top')\n\t\t\t// edit function\n\t\t\tif (arg.nodetail) {\n\t\t\t\tconst div = td.append('div')\n\t\t\t\tdiv\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('padding-right', '20px')\n\t\t\t\t\t.text('Product id: ' + prod.prodid)\n\t\t\t\tconst ratingsl = div\n\t\t\t\t\t.append('select')\n\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tconst sl = event.target\n\t\t\t\t\t\tconst newv = sl.options[sl.selectedIndex].innerHTML\n\t\t\t\t\t\tprod.rating = newv\n\t\t\t\t\t\tif (prod.hook.mainRating) {\n\t\t\t\t\t\t\tprod.hook.mainRating.text(newv)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (prod.hook.lessRating) {\n\t\t\t\t\t\t\tprod.hook.lessRating.text(newv)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\tconst framesl = div\n\t\t\t\t\t.append('select')\n\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tconst sl = event.target\n\t\t\t\t\t\tconst inframe = sl.options[sl.selectedIndex].innerHTML == 'in-frame'\n\t\t\t\t\t\tprod.usepair.inframe = inframe\n\t\t\t\t\t\tif (prod.hook.mainFrame) {\n\t\t\t\t\t\t\tprod.hook.mainFrame.text.text(inframe ? 'IN' : 'O')\n\t\t\t\t\t\t\tprod.hook.mainFrame.bg.attr('fill', inframe ? client.colorinframe : client.coloroutframe)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (prod.hook.lessFrame) {\n\t\t\t\t\t\t\tprod.hook.lessFrame.html(\n\t\t\t\t\t\t\t\tinframe\n\t\t\t\t\t\t\t\t\t? '<span style=\"background-color:' +\n\t\t\t\t\t\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t\t\t\t\t\t';color:white;padding:2px 3px;font-size:80%;white-space:nowrap\">In frame</span>'\n\t\t\t\t\t\t\t\t\t: '<span style=\"background-color:' +\n\t\t\t\t\t\t\t\t\t\t\tclient.coloroutframe +\n\t\t\t\t\t\t\t\t\t\t\t';color:white;padding:2px 3px;font-size:80%;white-space:nowrap\">Out of frame</span>'\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\tconst typesl = div\n\t\t\t\t\t.append('select')\n\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tconst sl = event.target\n\t\t\t\t\t\tconst i = sl.selectedIndex\n\t\t\t\t\t\tconst newv = sl.options[i].innerHTML\n\t\t\t\t\t\tprod.type2 = newv\n\t\t\t\t\t\tif (prod.hook.mainType) {\n\t\t\t\t\t\t\tprod.hook.mainType.text(newv)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tprod.iscloss = i == 0\n\t\t\t\t\t\tprod.isnloss = i == 1\n\t\t\t\t\t\tprod.isfusion = i == 2\n\t\t\t\t\t\tprod.isitd = i == 3\n\t\t\t\t\t\tprod.isuptss = i == 4\n\t\t\t\t\t\tprod.isother = i == 5\n\t\t\t\t\t})\n\t\t\t\tconst effectsl = div\n\t\t\t\t\t.append('select')\n\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tconst sl = event.target\n\t\t\t\t\t\tconst newv = sl.options[sl.selectedIndex].innerHTML\n\t\t\t\t\t\tprod.functioneffect = newv\n\t\t\t\t\t})\n\t\t\t\tdiv\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.text('Create group')\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tlet dnew = document.createElement('div')\n\t\t\t\t\t\tdiv.node().insertBefore(dnew, event.target)\n\t\t\t\t\t\td3select(event.target).remove()\n\t\t\t\t\t\tdnew = d3select(dnew)\n\t\t\t\t\t\tdnew.style('display', 'inline-block')\n\t\t\t\t\t\tif (!arg.eglst) {\n\t\t\t\t\t\t\t// this is showing recurrent event from other samples, not able to dig up eglst\n\t\t\t\t\t\t\tdnew.text('Cannot do it here: please go to sample ' + arg.sample.name)\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tdnew\n\t\t\t\t\t\t\t.append('input')\n\t\t\t\t\t\t\t.attr('size', 10)\n\t\t\t\t\t\t\t.property('value', prod.prodid + ',')\n\t\t\t\t\t\tdnew\n\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t.style('margin', '0px 10px')\n\t\t\t\t\t\t\t.text('Apply')\n\t\t\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\t\t\tconst lst0 = event.target.previousSibling.value.trim().split(',')\n\t\t\t\t\t\t\t\tconst goodid = []\n\t\t\t\t\t\t\t\tfor (const i of lst0) {\n\t\t\t\t\t\t\t\t\tconst j = Number.parseInt(i)\n\t\t\t\t\t\t\t\t\tif (Number.isNaN(j)) return alert('invalid id ' + i)\n\t\t\t\t\t\t\t\t\tif (this.prodidisinvalid(j, arg.sample)) return alert('invalid id ' + j)\n\t\t\t\t\t\t\t\t\tgoodid.push(j)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (goodid.length <= 1) return alert('need at least 2 id')\n\t\t\t\t\t\t\t\tconst newevtlst = []\n\t\t\t\t\t\t\t\tfor (const i of goodid) {\n\t\t\t\t\t\t\t\t\tconst thisprod = this.extractprod(i, arg.sample)\n\t\t\t\t\t\t\t\t\tif (thisprod) {\n\t\t\t\t\t\t\t\t\t\tnewevtlst.push({ label: thisprod.eventlabel, lst: [thisprod] })\n\t\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\t\treturn alert('invalid id ' + i)\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tif (newevtlst.length <= 1) return alert('less than 2 products cannot make a group')\n\t\t\t\t\t\t\t\targ.eglst.unshift({ lst: newevtlst, ismsg: true })\n\t\t\t\t\t\t\t\t// remake entire sample\n\t\t\t\t\t\t\t\tthis.showsample(arg.sample)\n\t\t\t\t\t\t\t\t// done\n\t\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t// <select>\n\t\t\t\tratingsl.append('option').text('HQ')\n\t\t\t\tratingsl.append('option').text('LQ')\n\t\t\t\tratingsl.append('option').text('RT')\n\t\t\t\tratingsl.append('option').text('bad')\n\t\t\t\tratingsl.append('option').text('Major')\n\t\t\t\tswitch (prod.rating) {\n\t\t\t\t\tcase 'HQ':\n\t\t\t\t\t\tratingsl.property('selectedindex', 0)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'LQ':\n\t\t\t\t\t\tratingsl.property('selectedIndex', 1)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'RT':\n\t\t\t\t\t\tratingsl.property('selectedIndex', 2)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'bad':\n\t\t\t\t\t\tratingsl.property('selectedIndex', 3)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'Major':\n\t\t\t\t\t\tratingsl.property('selectedIndex', 4)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tdefault:\n\t\t\t\t\t\talert('unknown rating: ' + prod.rating)\n\t\t\t\t}\n\t\t\t\tframesl.append('option').text('in-frame')\n\t\t\t\tframesl.append('option').text('out-of-frame')\n\t\t\t\tif (!prod.usepair) {\n\t\t\t\t\tframesl.attr('disabled', 1)\n\t\t\t\t} else {\n\t\t\t\t\tframesl.property('selectedIndex', prod.usepair.inframe ? 0 : 1)\n\t\t\t\t}\n\t\t\t\ttypesl.append('option').text('CLoss')\n\t\t\t\ttypesl.append('option').text('NLoss')\n\t\t\t\ttypesl.append('option').text('Fusion')\n\t\t\t\ttypesl.append('option').text('ITD')\n\t\t\t\ttypesl.append('option').text('upTSS')\n\t\t\t\ttypesl.append('option').text('other')\n\t\t\t\tif (prod.iscloss) {\n\t\t\t\t\ttypesl.property('selectedIndex', 0)\n\t\t\t\t} else if (prod.isnloss) {\n\t\t\t\t\ttypesl.property('selectedIndex', 1)\n\t\t\t\t} else if (prod.isfusion) {\n\t\t\t\t\ttypesl.property('selectedIndex', 2)\n\t\t\t\t} else if (prod.isitd) {\n\t\t\t\t\ttypesl.property('selectedIndex', 3)\n\t\t\t\t} else if (prod.isuptss) {\n\t\t\t\t\ttypesl.property('selectedIndex', 4)\n\t\t\t\t} else if (prod.isother) {\n\t\t\t\t\ttypesl.property('selectedIndex', 5)\n\t\t\t\t} else {\n\t\t\t\t\talert('unknown type2: ' + prod.type2)\n\t\t\t\t}\n\t\t\t\t// <select> done\n\t\t\t\teffectsl.append('option').text('unknown effect')\n\t\t\t\teffectsl.append('option').text('fusion gene')\n\t\t\t\teffectsl.append('option').text('truncation, activated oncogene')\n\t\t\t\teffectsl.append('option').text('truncation, loss-of-function')\n\t\t\t\teffectsl.append('option').text('truncation, no consequence')\n\t\t\t\teffectsl.append('option').text('ITD')\n\t\t\t\tswitch (prod.functioneffect) {\n\t\t\t\t\tcase undefined:\n\t\t\t\t\t\teffectsl.property('selectedIndex', 0)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'fusion gene':\n\t\t\t\t\t\teffectsl.property('selectedIndex', 1)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'truncation, activated oncogene':\n\t\t\t\t\t\teffectsl.property('selectedIndex', 2)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'truncation, loss-of-function':\n\t\t\t\t\t\teffectsl.property('selectedIndex', 3)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'truncation, no consequence':\n\t\t\t\t\t\teffectsl.property('selectedIndex', 4)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 'ITD':\n\t\t\t\t\t\teffectsl.property('selectedIndex', 5)\n\t\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst p = {\n\t\t\t\ta: {\n\t\t\t\t\tchr: prod.chrA,\n\t\t\t\t\tposition: prod.posA,\n\t\t\t\t\tstrand: prod.ortA,\n\t\t\t\t\tname: prod.geneA ? prod.geneA : prod.chrA,\n\t\t\t\t\tratio: prod.ratioA.toFixed(2),\n\t\t\t\t\tfeature: prod.featureA,\n\t\t\t\t\tcontiglen: prod.matchA,\n\t\t\t\t\tchimericreads: prod.readsA,\n\t\t\t\t\trepeatscore: prod.repeatA\n\t\t\t\t},\n\t\t\t\tb: {\n\t\t\t\t\tchr: prod.chrB,\n\t\t\t\t\tposition: prod.posB,\n\t\t\t\t\tstrand: prod.ortB,\n\t\t\t\t\tname: prod.geneB ? prod.geneB : prod.chrB,\n\t\t\t\t\tratio: prod.ratioB.toFixed(2),\n\t\t\t\t\tfeature: prod.featureB,\n\t\t\t\t\tcontiglen: prod.matchB,\n\t\t\t\t\tchimericreads: prod.readsB,\n\t\t\t\t\trepeatscore: prod.repeatB\n\t\t\t\t},\n\t\t\t\trating: prod.rating,\n\t\t\t\tscore: Math.ceil(prod.score),\n\t\t\t\toriginalprod: prod\n\t\t\t}\n\t\t\tif (prod.usepair) {\n\t\t\t\tp.inframe = prod.usepair.inframe\n\t\t\t\tconst x = prod.usepair.a\n\t\t\t\tp.a.gm = this.genome.isoformmatch(x.isoform, prod.chrA, prod.posA)\n\t\t\t\tp.a.codon = x.codon\n\t\t\t\tp.a.exon = x.exon\n\t\t\t\tp.a.atupstream = x.atupstream\n\t\t\t\tp.a.atdownstream = x.atdownstream\n\t\t\t\tp.a.atutr5 = x.atutr5\n\t\t\t\tp.a.atutr3 = x.atutr3\n\t\t\t\tconst y = prod.usepair.b\n\t\t\t\tp.b.gm = this.genome.isoformmatch(y.isoform, prod.chrB, prod.posB)\n\t\t\t\tp.b.codon = y.codon\n\t\t\t\tp.b.exon = y.exon\n\t\t\t\tp.b.atupstream = y.atupstream\n\t\t\t\tp.b.atdownstream = y.atdownstream\n\t\t\t\tp.b.atutr5 = y.atutr5\n\t\t\t\tp.b.atutr3 = y.atutr3\n\t\t\t\t// interstitial\n\t\t\t\tlet aalen = 0,\n\t\t\t\t\tbplen = 0\n\t\t\t\tif (x.contigaa && y.contigaa) {\n\t\t\t\t\taalen = y.contigaa - x.contigaa - 1\n\t\t\t\t}\n\t\t\t\tif (x.contigbp && y.contigbp) {\n\t\t\t\t\tbplen = y.contigbp - x.contigbp - 1\n\t\t\t\t}\n\t\t\t\tif (aalen) {\n\t\t\t\t\tp.interstitial = { aalen: aalen }\n\t\t\t\t}\n\t\t\t\tif (bplen) {\n\t\t\t\t\tif (!p.interstitial) p.interstitial = {}\n\t\t\t\t\tp.interstitial.bplen = bplen\n\t\t\t\t}\n\t\t\t}\n\t\t\tsvtable({\n\t\t\t\tsamplelst: [\n\t\t\t\t\t{\n\t\t\t\t\t\tpairlst: [p]\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\tnosample: true,\n\t\t\t\tholder: td\n\t\t\t})\n\n\t\t\tconst par = {\n\t\t\t\tpairlst: [p],\n\t\t\t\tgenome: this.genome,\n\t\t\t\tholder: td,\n\t\t\t\tquiet: true,\n\t\t\t\thostURL: this.hostURL,\n\t\t\t\tjwt: this.jwt\n\t\t\t}\n\t\t\timport('./svgraph').then(p => {\n\t\t\t\tp.default(par)\n\t\t\t})\n\n\t\t\tif (!arg.nodetail) {\n\t\t\t\tconst td = tr2.append('td').style('font-size', '.8em').style('vertical-align', 'top')\n\t\t\t\t// custom attributes\n\t\t\t\tconst lst = []\n\t\t\t\tfor (const at of this.atlst) {\n\t\t\t\t\tif (!at.custom) continue\n\t\t\t\t\tconst v = prod[at.key]\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tk: at.label,\n\t\t\t\t\t\tv: v == undefined ? '' : v\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tclient.make_table_2col(td, lst, 25)\n\t\t\t\t// isoform pairs\n\t\t\t\tprod.pairs.sort((a, b) => {\n\t\t\t\t\tif (a.inuse) return -1\n\t\t\t\t\tif (b.inuse) return 1\n\t\t\t\t\treturn 0\n\t\t\t\t})\n\t\t\t\tconst table0 = td.append('table')\n\t\t\t\tfor (const pair of prod.pairs) {\n\t\t\t\t\tconst tr = table0.append('tr')\n\t\t\t\t\ttr.append('td').html(\n\t\t\t\t\t\t(pair.inframe ? 'in-frame' : 'out-of-frame') +\n\t\t\t\t\t\t\t'<div style=\"font-size:70%\">frame code: ' +\n\t\t\t\t\t\t\tpair.frame +\n\t\t\t\t\t\t\t'</div>'\n\t\t\t\t\t)\n\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\tconst table = td\n\t\t\t\t\t\t.append('table')\n\t\t\t\t\t\t.style('margin-bottom', '20px')\n\t\t\t\t\t\t.style('border', pair.inuse ? 'solid 1px black' : '')\n\t\t\t\t\t\t.style('border-spacing', '10px')\n\t\t\t\t\t\t.style('border-collapse', 'separate')\n\t\t\t\t\tlet _tr = table.append('tr').style('color', '#858585').style('font-size', '.7em')\n\t\t\t\t\t_tr.append('td').text('gene')\n\t\t\t\t\t_tr.append('td').text('isoform')\n\t\t\t\t\t_tr.append('td').text('gene position')\n\t\t\t\t\t_tr.append('td').text('exon')\n\t\t\t\t\t_tr.append('td').text('anchor')\n\t\t\t\t\t_tr.append('td').text('contig AA')\n\t\t\t\t\t_tr.append('td').text('contig bp')\n\t\t\t\t\tconst tr1 = table.append('tr')\n\t\t\t\t\tconst tr2 = table.append('tr')\n\t\t\t\t\ttr1.append('td').text(prod.geneA ? prod.geneA : prod.chrA)\n\t\t\t\t\ttr2.append('td').text(prod.geneB ? prod.geneB : prod.chrB)\n\t\t\t\t\ttr1.append('td').text(pair.a.isoform ? pair.a.isoform : '')\n\t\t\t\t\ttr2.append('td').text(pair.b.isoform ? pair.b.isoform : '')\n\t\t\t\t\ttr1\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.text(\n\t\t\t\t\t\t\tpair.a.isoform\n\t\t\t\t\t\t\t\t? pair.a.codon != undefined\n\t\t\t\t\t\t\t\t\t? 'codon: ' + pair.a.codon\n\t\t\t\t\t\t\t\t\t: pair.a.atutr5\n\t\t\t\t\t\t\t\t\t? \"5' UTR\"\n\t\t\t\t\t\t\t\t\t: pair.a.atutr3\n\t\t\t\t\t\t\t\t\t? \"3' UTR\"\n\t\t\t\t\t\t\t\t\t: pair.a.atupstream\n\t\t\t\t\t\t\t\t\t? 'upstream'\n\t\t\t\t\t\t\t\t\t: 'downstream'\n\t\t\t\t\t\t\t\t: ''\n\t\t\t\t\t\t)\n\t\t\t\t\ttr2\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.text(\n\t\t\t\t\t\t\tpair.b.isoform\n\t\t\t\t\t\t\t\t? pair.b.codon != undefined\n\t\t\t\t\t\t\t\t\t? 'codon: ' + pair.b.codon\n\t\t\t\t\t\t\t\t\t: pair.b.atutr5\n\t\t\t\t\t\t\t\t\t? \"5' UTR\"\n\t\t\t\t\t\t\t\t\t: pair.b.atutr3\n\t\t\t\t\t\t\t\t\t? \"3' UTR\"\n\t\t\t\t\t\t\t\t\t: pair.b.atupstream\n\t\t\t\t\t\t\t\t\t? 'upstream'\n\t\t\t\t\t\t\t\t\t: 'downstream'\n\t\t\t\t\t\t\t\t: ''\n\t\t\t\t\t\t)\n\t\t\t\t\ttr1.append('td').text(pair.a.exon ? pair.a.exon : '')\n\t\t\t\t\ttr2.append('td').text(pair.b.exon ? pair.b.exon : '')\n\t\t\t\t\ttr1.append('td').text(pair.a.anchor ? pair.a.anchor : '')\n\t\t\t\t\ttr2.append('td').text(pair.b.anchor ? pair.b.anchor : '')\n\t\t\t\t\ttr1\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.html(pair.a.contigaa ? '<span style=\"color:#858585;font-size:70%\">ends at</span> ' + pair.a.contigaa : '?')\n\t\t\t\t\ttr2\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\tpair.b.contigaa ? '<span style=\"color:#858585;font-size:70%\">starts at</span> ' + pair.b.contigaa : '?'\n\t\t\t\t\t\t)\n\t\t\t\t\ttr1\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.html(pair.a.contigbp ? '<span style=\"color:#858585;font-size:70%\">ends at</span> ' + pair.a.contigbp : '?')\n\t\t\t\t\ttr2\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\tpair.b.contigbp ? '<span style=\"color:#858585;font-size:70%\">starts at</span> ' + pair.b.contigbp : '?'\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (!arg.sample) {\n\t\t\t// the current sample is not provided, won't try to find out samples with recurrent events\n\t\t\treturn\n\t\t}\n\t\tconst thislab = arg.prodlst[0].eventlabel\n\t\tconst samplelst = this.elab2sample[thislab]\n\t\tconst othersample = []\n\t\tif (samplelst) {\n\t\t\tfor (const s of samplelst) {\n\t\t\t\tif (s.name != arg.sample.name) othersample.push(s)\n\t\t\t}\n\t\t}\n\t\tif (arg.showothersample && othersample.length > 0) {\n\t\t\targ.holder\n\t\t\t\t.append('button')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('margin', '20px')\n\t\t\t\t.text('Show in ' + othersample.length + ' other sample' + (othersample.length > 1 ? 's' : ''))\n\t\t\t\t.on('click', event => {\n\t\t\t\t\td3select(event.target).remove()\n\t\t\t\t\tfor (const sample of othersample) {\n\t\t\t\t\t\tconst prodlst = sample.events[thislab]\n\t\t\t\t\t\tif (!prodlst) {\n\t\t\t\t\t\t\targ.holder\n\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t.style('margin', '20px')\n\t\t\t\t\t\t\t\t.style('color', 'red')\n\t\t\t\t\t\t\t\t.text('Error: no products for this event in ' + sample.name)\n\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t}\n\t\t\t\t\t\tconst table = arg.holder.append('table').style('margin-top', '20px').style('border', 'solid 1px #ccc')\n\t\t\t\t\t\tconst tr = table.append('tr')\n\t\t\t\t\t\ttr.append('td').text(sample.name)\n\t\t\t\t\t\tconst td = tr.append('td')\n\t\t\t\t\t\tthis.showsvpairs({\n\t\t\t\t\t\t\tprodlst: prodlst,\n\t\t\t\t\t\t\tholder: td,\n\t\t\t\t\t\t\tnodetail: true,\n\t\t\t\t\t\t\tsample: sample,\n\t\t\t\t\t\t\t// FIXME: eglst info is hidden somewhere in sample.egglst\n\t\t\t\t\t\t\teglst: null\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t}\n\t\tif (this.expression.genes && geneset.size > 0) {\n\t\t\tconst table = expressiontd.append('table')\n\t\t\tconst tr = table.append('tr')\n\t\t\tfor (const gene of geneset) {\n\t\t\t\tconst expd = this.expression.genes[gene]\n\t\t\t\tif (expd) {\n\t\t\t\t\tconst div = tr\n\t\t\t\t\t\t.append('td')\n\t\t\t\t\t\t.style('vertical-align', 'top')\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.style('margin-right', '20px')\n\t\t\t\t\t\t.style('border', 'solid 1px #ccc')\n\t\t\t\t\tdiv.append('div').style('background-color', '#ededed').style('padding', '10px').text(gene)\n\t\t\t\t\tif (arg.sample) {\n\t\t\t\t\t\tfor (const v of expd) {\n\t\t\t\t\t\t\tif (v.sample == arg.sample.name) {\n\t\t\t\t\t\t\t\tv.ishighlight = true\n\t\t\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t\t\t.style('padding', '10px')\n\t\t\t\t\t\t\t\t\t.style('font-size', '70%')\n\t\t\t\t\t\t\t\t\t.html('Expression in ' + arg.sample.name + ': <span style=\"font-size:150%\">' + v.value + '</span>')\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tv.ishighlight = false\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\tshowgenevalues({\n\t\t\t\t\t\tdata: this.expression.genes[gene],\n\t\t\t\t\t\tholder: div.append('div').style('margin', '10px'),\n\t\t\t\t\t\twidth: 200,\n\t\t\t\t\t\theight: 200,\n\t\t\t\t\t\tnamename: 'sample'\n\t\t\t\t\t})\n\t\t\t\t} else {\n\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t\t\t.text('No expression data for ' + gene + '</td>')\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tprodidisinvalid(id, sample) {\n\t\tfor (const egg of sample.egglst) {\n\t\t\tfor (const eg of egg.lst) {\n\t\t\t\tfor (const e of eg.lst) {\n\t\t\t\t\tfor (const p of e.lst) {\n\t\t\t\t\t\tif (p.prodid == id) return false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn true\n\t}\n\n\textractprod(id, sample) {\n\t\tlet prod = null\n\t\tfor (let n = 0; n < sample.egglst.length; n++) {\n\t\t\tconst _egg = sample.egglst[n]\n\t\t\tfor (let j = 0; j < _egg.lst.length; j++) {\n\t\t\t\tconst _eg = _egg.lst[j]\n\t\t\t\tfor (let k = 0; k < _eg.lst.length; k++) {\n\t\t\t\t\tconst _evt = _eg.lst[k]\n\t\t\t\t\tfor (let p = 0; p < _evt.lst.length; p++) {\n\t\t\t\t\t\tconst p2 = _evt.lst[p]\n\t\t\t\t\t\tif (p2.prodid == id) {\n\t\t\t\t\t\t\tprod = p2\n\t\t\t\t\t\t\t_evt.lst.splice(p, 1)\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (prod) {\n\t\t\t\t\t\tif (_evt.lst.length == 0) {\n\t\t\t\t\t\t\t_eg.lst.splice(k, 1)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (prod) {\n\t\t\t\t\tif (_eg.lst.length == 0) {\n\t\t\t\t\t\t_egg.lst.splice(j, 1)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (_eg.ismsg && _eg.lst.length == 1) {\n\t\t\t\t\t\t\tdelete _eg.ismsg\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (prod) {\n\t\t\t\tif (_egg.lst.length == 0) {\n\t\t\t\t\tsample.egglst.splice(n, 1)\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\treturn prod\n\t}\n\t// end of class\n}\n\nfunction msjoin(prod, newholder) {\n\tif (prod.isitd) return\n\tif (prod.sv_ort == '?') return\n\tvar single = true\n\tvar thispair = prod.usepair\n\tfor (var i = 0; i < newholder.length; i++) {\n\t\tvar tmplst = newholder[i]\n\t\t// test head\n\t\tvar prod2 = tmplst[0]\n\t\tif (prod.chrB == prod2.chrA && prod.ortB == prod2.ortA) {\n\t\t\tif (testreadcount(prod, prod2)) {\n\t\t\t\t// compare isoform/codon position\n\t\t\t\tvar thatpair = prod2.usepair\n\t\t\t\tif (thispair && thatpair && thispair.b.isoform && thispair.b.isoform == thatpair.a.isoform) {\n\t\t\t\t\tvar p1 = thispair.b\n\t\t\t\t\tvar p2 = thatpair.a\n\t\t\t\t\tvar ahead = false\n\t\t\t\t\tif (p1.atutr5) {\n\t\t\t\t\t\tif (p2.codon != undefined) {\n\t\t\t\t\t\t\tahead = true\n\t\t\t\t\t\t\tprod2.mswhat = \"5' UTR to coding region\"\n\t\t\t\t\t\t} else if (p2.atutr3) {\n\t\t\t\t\t\t\tahead = true\n\t\t\t\t\t\t\tprod2.mswhat = \"5' UTR to 3' UTR\"\n\t\t\t\t\t\t} else if (p2.atutr5 && p1.atutr5.off < p2.atutr5.off) {\n\t\t\t\t\t\t\tahead = true\n\t\t\t\t\t\t\tprod2.mswhat = p2.atutr5.off - p1.atutr5.off + \" bp apart in 5' UTR\"\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (p1.atutr3) {\n\t\t\t\t\t\tif (p2.atutr3 && p1.atutr3.off < p2.atutr3.off) {\n\t\t\t\t\t\t\tahead = true\n\t\t\t\t\t\t\tprod2.mswhat = p2.atutr3.off - p1.atutr3.off + \" bp apart in 3' UTR\"\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (p1.codon != undefined) {\n\t\t\t\t\t\tif (p2.codon != undefined && p2.codon > p1.codon) {\n\t\t\t\t\t\t\tahead = true\n\t\t\t\t\t\t\tprod2.mswhat = p2.codon - p1.codon + ' aa apart in protein'\n\t\t\t\t\t\t} else if (p2.atutr3) {\n\t\t\t\t\t\t\tahead = true\n\t\t\t\t\t\t\tprod2.mswhat = \"coding region to 3' UTR\"\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (ahead) {\n\t\t\t\t\t\ttmplst.unshift(prod)\n\t\t\t\t\t\tsingle = false\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// compare by genomic pos, if upstream of head\n\t\t\t\tvar dst = prod2.posA - prod.posB\n\t\t\t\tif ((prod.ortB == '+' && dst > 0 && dst < genomelimit) || (prod.ortB == '-' && dst < 0 && -dst < genomelimit)) {\n\t\t\t\t\tprod2.mswhat = Math.abs(dst) + ' bp apart on genome'\n\t\t\t\t\ttmplst.unshift(prod)\n\t\t\t\t\tsingle = false\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t// test tail\n\t\tprod2 = tmplst[tmplst.length - 1]\n\t\tif (prod.chrA == prod2.chrB && prod.ortA == prod2.ortB) {\n\t\t\tif (testreadcount(prod2, prod)) {\n\t\t\t\tvar thatpair = prod2.usepair\n\t\t\t\tif (thispair && thatpair && thispair.a.isoform && thispair.a.isoform == thatpair.b.isoform) {\n\t\t\t\t\tvar p1 = thatpair.b\n\t\t\t\t\tvar p2 = thispair.a\n\t\t\t\t\tvar behind = false\n\t\t\t\t\tif (p1.atutr5) {\n\t\t\t\t\t\tif (p2.codon != undefined) {\n\t\t\t\t\t\t\tbehind = true\n\t\t\t\t\t\t\tprod.mswhat = \"5' UTR to coding region\"\n\t\t\t\t\t\t} else if (p2.atutr3) {\n\t\t\t\t\t\t\tbehind = true\n\t\t\t\t\t\t\tprod.mswhat = \"5' UTR to 3' UTR\"\n\t\t\t\t\t\t} else if (p2.atutr5 && p1.atutr5.off < p2.atutr5.off) {\n\t\t\t\t\t\t\tbehind = true\n\t\t\t\t\t\t\tprod.mswhat = p2.atutr5.off - p1.atutr5.off + \" bp apart in 5' UTR\"\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (p1.atutr3) {\n\t\t\t\t\t\tif (p2.atutr3 && p1.atutr3.off < p2.atutr3.off) {\n\t\t\t\t\t\t\tbehind = true\n\t\t\t\t\t\t\tprod.mswhat = p2.atutr3.off - p1.atutr3.off + \" bp apart in 3' UTR\"\n\t\t\t\t\t\t}\n\t\t\t\t\t} else if (p1.codon != undefined) {\n\t\t\t\t\t\tif (p2.codon != undefined && p2.codon > p1.codon) {\n\t\t\t\t\t\t\tbehind = true\n\t\t\t\t\t\t\tprod.mswhat = p2.codon - p1.codon + ' aa apart in protein'\n\t\t\t\t\t\t} else if (p2.atutr3) {\n\t\t\t\t\t\t\tbehind = true\n\t\t\t\t\t\t\tprod.mswhat = \"coding region to 3' UTR\"\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (behind) {\n\t\t\t\t\t\ttmplst.push(prod)\n\t\t\t\t\t\tsingle = false\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// if downstream of tail\n\t\t\t\tvar dst = prod.posA - prod2.posB\n\t\t\t\tif (prod.ortA == '+' && dst > 0 && dst < genomelimit && prod.ortA == '-' && dst < 0 && -dst < genomelimit) {\n\t\t\t\t\tprod.mswhat = Math.abs(dst) + ' bp apart on genome'\n\t\t\t\t\ttmplst.push(prod)\n\t\t\t\t\tsingle = false\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tif (single) {\n\t\tnewholder.push([prod])\n\t}\n\tfunction testreadcount(p1, p2) {\n\t\tif (!p1.usepair || !p1.usepair.inframe) return false\n\t\tif (!p2.usepair || !p2.usepair.inframe) return false\n\t\t// Another problem is too many multi-seg. Please use read count to filter out some artifacts. Following is an artifact multi-seg LINC00598- PLXNB2-MUC4. The number of reads are not comparable for these two segments. We should not connect these two. I suggest using 5 fold as threshold to connect segments.\n\t\tif (p1.readsB == 0 || p2.readsA == 0) return false\n\t\tvar fold = p1.readsB / p2.readsA\n\t\treturn fold >= 0.2 && fold <= 5\n\t}\n}\n\nfunction svtable(arg) {\n\t// sample level events\n\tconst table = arg.holder.append('table').style('border-spacing', '10px').style('border-collapse', 'separate')\n\tconst htr = table.append('tr').style('font-size', '70%').style('color', '#858585')\n\tconst fields = [\n\t\t{ label: 'Feature', hide: true, get: a => a.feature },\n\t\t{ label: 'Ratio', hide: true, get: a => Math.ceil(a.ratio * 100) + '%' },\n\t\t{ label: 'Chimeric<br>reads', hide: true, get: a => a.chimericreads },\n\t\t{ label: 'Contig<br>length', hide: true, get: a => a.contiglen },\n\t\t{ label: 'Repeat<br>score', hide: true, get: a => a.repeatscore },\n\t\t{ label: 'Cicero<br>score', hide: true, atpair: true, get: a => a.score },\n\t\t{ label: 'Cicero<br>rating', israting: true, hide: true, atpair: true, get: a => a.rating }\n\t]\n\tfor (const sample of arg.samplelst) {\n\t\tfor (const p of sample.pairlst) {\n\t\t\tif (p.a.feature || p.b.feature) fields[0].hide = false\n\t\t\tif (typeof p.a.ratio == 'number' || typeof (p.b.ratio == 'number')) fields[1].hide = false\n\t\t\tif (typeof p.a.chimericreads == 'number' || typeof p.b.chimericreads == 'number') fields[2].hide = false\n\t\t\tif (typeof p.a.contiglen == 'number' || typeof p.b.contiglen == 'number') fields[3].hide = false\n\t\t\tif (typeof p.a.repeatscore == 'number' || typeof p.b.repeatscore == 'number') fields[4].hide = false\n\t\t\tif (typeof p.score == 'number') fields[5].hide = false\n\t\t\tif (p.rating) fields[6].hide = false\n\t\t}\n\t}\n\t// header\n\tif (!arg.nosample) {\n\t\thtr.append('td')\n\t}\n\thtr.append('td') // gene\n\thtr.append('td') // frame\n\thtr.append('td').html('Genomic<br>position') // coord\n\thtr.append('td').html('Genomic<br>dist.') //\n\tfor (const f of fields) {\n\t\tif (f.hide) return\n\t\thtr.append('td').html(f.label)\n\t}\n\tfor (const sample of arg.samplelst) {\n\t\tlet tr = table.append('tr')\n\t\tif (!arg.nosample) {\n\t\t\tconst td = tr.append('td').text(sample.sample)\n\t\t\tif (sample.pairlst.length > 1) {\n\t\t\t\ttd.attr('rowspan', sample.pairlst.length)\n\t\t\t}\n\t\t}\n\t\tfor (let i = 0; i < sample.pairlst.length; i++) {\n\t\t\tif (i > 0) {\n\t\t\t\t// new\n\t\t\t\ttr = table.append('tr')\n\t\t\t}\n\t\t\tconst pair = sample.pairlst[i]\n\t\t\t// gene\n\t\t\ttr.append('td')\n\t\t\t\t.style('text-align', 'right')\n\t\t\t\t.html(\n\t\t\t\t\t'<span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorbgleft +\n\t\t\t\t\t\t';padding:2px 3px;font-size:80%\">' +\n\t\t\t\t\t\tpair.a.name +\n\t\t\t\t\t\t'</span>' +\n\t\t\t\t\t\t'<span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorbgright +\n\t\t\t\t\t\t';padding:2px 3px;font-size:80%\">' +\n\t\t\t\t\t\tpair.b.name +\n\t\t\t\t\t\t'</span>'\n\t\t\t\t)\n\t\t\t// frame\n\t\t\tconst td = tr.append('td')\n\t\t\tif (pair.originalprod && pair.originalprod.hook.lessFrame) {\n\t\t\t\tpair.originalprod.hook.lessFrame = td\n\t\t\t}\n\t\t\tif (pair.inframe) {\n\t\t\t\ttd.html(\n\t\t\t\t\t'<span style=\"background-color:' +\n\t\t\t\t\t\tclient.colorinframe +\n\t\t\t\t\t\t';color:white;padding:2px 3px;font-size:80%;white-space:nowrap\">In frame</span>'\n\t\t\t\t)\n\t\t\t} else {\n\t\t\t\tif (pair.a.gm || pair.b.gm) {\n\t\t\t\t\ttd.html(\n\t\t\t\t\t\t'<span style=\"background-color:#858585;color:white;padding:2px 3px;font-size:80%;white-space:nowrap\">Out of frame</span>'\n\t\t\t\t\t)\n\t\t\t\t} else {\n\t\t\t\t\ttd.html(\n\t\t\t\t\t\t'<span style=\"border:solid 1px #858585;color:#858585;padding:1px 2px;font-size:80%;white-space:nowrap\">no gene ?</span>'\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t\t// coord\n\t\t\ttr.append('td').html(\n\t\t\t\t'<div style=\"background-color:' +\n\t\t\t\t\tclient.colorbgleft +\n\t\t\t\t\t';padding:1px 3px;font-size:70%;white-space:nowrap\">' +\n\t\t\t\t\tpair.a.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\tpair.a.position +\n\t\t\t\t\t' ' +\n\t\t\t\t\tpair.a.strand +\n\t\t\t\t\t'</div>' +\n\t\t\t\t\t'<div style=\"background-color:' +\n\t\t\t\t\tclient.colorbgright +\n\t\t\t\t\t';padding:1px 3px;font-size:70%;white-space:nowrap\">' +\n\t\t\t\t\tpair.b.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\tpair.b.position +\n\t\t\t\t\t' ' +\n\t\t\t\t\tpair.b.strand +\n\t\t\t\t\t'</div>'\n\t\t\t)\n\t\t\t// dist\n\t\t\ttr.append('td').html(\n\t\t\t\tpair.a.chr == pair.b.chr\n\t\t\t\t\t? bplength(Math.abs(pair.a.position - pair.b.position))\n\t\t\t\t\t: '<span style=\"color:' + client.colorctx + '\">CTX</span>'\n\t\t\t)\n\t\t\tfor (const f of fields) {\n\t\t\t\tif (f.hide) continue\n\t\t\t\tconst td = tr.append('td')\n\t\t\t\tif (f.israting && pair.originalprod && pair.originalprod.hook.lessRating) {\n\t\t\t\t\tpair.originalprod.hook.lessRating = td\n\t\t\t\t}\n\t\t\t\tif (f.atpair) {\n\t\t\t\t\ttd.text(f.get(pair))\n\t\t\t\t} else {\n\t\t\t\t\ttd.html(\n\t\t\t\t\t\t'<span style=\"background-color:' +\n\t\t\t\t\t\t\tclient.colorbgleft +\n\t\t\t\t\t\t\t';padding:2px 3px;font-size:80%\">' +\n\t\t\t\t\t\t\tf.get(pair.a) +\n\t\t\t\t\t\t\t'</span>' +\n\t\t\t\t\t\t\t'<span style=\"background-color:' +\n\t\t\t\t\t\t\tclient.colorbgright +\n\t\t\t\t\t\t\t';padding:2px 3px;font-size:80%\">' +\n\t\t\t\t\t\t\tf.get(pair.b) +\n\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction loadexpression(svmr, file) {\n\tconst genes = {}\n\tconst ep = svmr.expression\n\tep.genes = genes\n\tconst reader = new FileReader()\n\tconst chunksize = 4096\n\tlet chunks = []\n\tlet offset = 0\n\treader.onloadend = e => {\n\t\tif (e.target.readyState != FileReader.DONE) return\n\t\tconst chunk = e.target.result\n\t\tchunks.push(chunk)\n\t\tconst isend = offset >= file.size\n\t\tprocess(isend)\n\t\tif (isend) {\n\t\t\tdone()\n\t\t} else {\n\t\t\toffset += chunksize\n\t\t\tep.presays.text('Reading file: ' + Math.ceil((offset / file.size) * 100) + '%')\n\t\t\treader.readAsText(file.slice(offset, offset + chunksize))\n\t\t}\n\t}\n\treader.readAsText(file.slice(0, chunksize))\n\tconst hg = {},\n\t\ths = {}\n\tlet good = 0,\n\t\tbad = 0\n\tfunction process(isend) {\n\t\tconst lines = chunks.join('').split('\\n')\n\t\tfor (let i = 0; i < lines.length - 1 - (isend ? 0 : 1); i++) {\n\t\t\tconst l = lines[i].split('\\t')\n\t\t\tif (l.length == 3) {\n\t\t\t\tconst v = Number.parseFloat(l[1])\n\t\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t\tbad++\n\t\t\t\t} else {\n\t\t\t\t\tgood++\n\t\t\t\t\thg[l[0]] = 1\n\t\t\t\t\ths[l[2]] = 1\n\t\t\t\t\tif (!(l[0] in genes)) {\n\t\t\t\t\t\tgenes[l[0]] = []\n\t\t\t\t\t}\n\t\t\t\t\tgenes[l[0]].push({\n\t\t\t\t\t\tsample: l[2],\n\t\t\t\t\t\tvalue: v\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tbad++\n\t\t\t}\n\t\t}\n\t\tif (!isend) {\n\t\t\tchunks = [lines[lines.length - 1]]\n\t\t}\n\t}\n\tfunction done() {\n\t\tlet genec = 0\n\t\tfor (const n in hg) genec++\n\t\tlet samplec = 0\n\t\tfor (const n in hs) samplec++\n\t\tclient.disappear(ep.prediv)\n\t\tclient.appear(ep.afterdiv)\n\t\tep.afterdiv.selectAll('*').remove()\n\t\tep.afterdiv\n\t\t\t.append('div')\n\t\t\t.text(\n\t\t\t\t'Expression data loaded for ' +\n\t\t\t\t\tgenec +\n\t\t\t\t\t' genes, ' +\n\t\t\t\t\tsamplec +\n\t\t\t\t\t' samples, ' +\n\t\t\t\t\tgood +\n\t\t\t\t\t' data points' +\n\t\t\t\t\t(bad > 0 ? ', ' + bad + ' bad lines' : '')\n\t\t\t)\n\t\tep.afterdiv\n\t\t\t.append('button')\n\t\t\t.text('Delete')\n\t\t\t.style('margin', '20px')\n\t\t\t.on('click', () => {\n\t\t\t\tdelete ep.genes\n\t\t\t\tep.prediv.node().removeChild(ep.input.node())\n\t\t\t\tep.input = ep.prediv\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'file')\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tloadexpression(svmr, event.target.files[0])\n\t\t\t\t\t})\n\t\t\t\tep.presays.text('')\n\t\t\t\tclient.disappear(ep.afterdiv)\n\t\t\t\tclient.appear(ep.prediv)\n\t\t\t})\n\t}\n}\n\nfunction showgenevalues(arg) {\n\t// arg.data: [ {sample:'xx', patient:, sampletype:, value:10.4}, ... ]\n\tconst hlcolor = 'red'\n\targ.data.sort((a, b) => {\n\t\treturn b.value - a.value\n\t})\n\tlet width = arg.width ? arg.width : 400,\n\t\theight = arg.height ? arg.height : 400\n\tlet maxv = 0\n\tfor (const v of arg.data) {\n\t\tmaxv = Math.max(maxv, v.value)\n\t}\n\tlet dotr // radius\n\tconst xscale = scaleLinear().domain([0, maxv])\n\tconst svg = arg.holder.append('svg')\n\tconst axisg = svg.append('g')\n\tconst dotg = svg.append('g')\n\tconst dotset = dotg.selectAll().data(arg.data).enter().append('g')\n\tconst dotcir = dotset\n\t\t.append('circle')\n\t\t.attr('fill', 'white')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('stroke', d => (d.ishighlight ? hlcolor : 'black'))\n\t\t.attr('stroke-opacity', d => (d.ishighlight ? 0.7 : 0.2))\n\t\t.on('mouseover', (event, d) => {\n\t\t\tevent.target.setAttribute('transform', 'scale(1.5)')\n\t\t\tdrag\n\t\t\t\t.text((d.sample ? d.sample : d.patient + ' ' + d.sampletype) + ' ' + d.value)\n\t\t\t\t.attr('fill', d.ishighlight ? hlcolor : 'black')\n\t\t})\n\t\t.on('mouseout', (event, d) => {\n\t\t\tevent.target.setAttribute('transform', 'scale(1)')\n\t\t\tdrag.text('drag to resize').attr('fill', 'black')\n\t\t})\n\tconst drag = svg\n\t\t.append('text')\n\t\t.text('drag to resize')\n\t\t.attr('font-size', 12)\n\t\t.attr('class', 'sja_svgtext')\n\t\t.attr('font-family', client.font)\n\t\t.attr('text-anchor', 'end')\n\t\t.on('mousedown', event => {\n\t\t\tevent.preventDefault()\n\t\t\tconst x0 = event.clientX,\n\t\t\t\ty0 = event.clientY,\n\t\t\t\twidth0 = width,\n\t\t\t\theight0 = height\n\t\t\tconst b = d3select(document.body)\n\t\t\tb.on('mousemove', () => {\n\t\t\t\twidth = width0 + event.clientX - x0\n\t\t\t\theight = height0 + event.clientY - y0\n\t\t\t\tsizing()\n\t\t\t}).on('mouseup', () => {\n\t\t\t\tb.on('mousemove', null).on('mouseup', null)\n\t\t\t})\n\t\t})\n\tfunction sizing() {\n\t\tdotr = Math.max(5, Math.min(width, height) / 40)\n\t\tconst fontsize = Math.min(18, Math.max(12, dotr * 2)),\n\t\t\tticksize = 5,\n\t\t\taxish = fontsize + ticksize + 5,\n\t\t\taxispad = dotr + 5,\n\t\t\twidth2 = dotr * 3\n\t\txscale.range([0, width])\n\t\tsvg.attr('width', dotr * 2 + width + width2).attr('height', axish + axispad + height + dotr * 2)\n\t\tclient.axisstyle({\n\t\t\taxis: axisg.attr('transform', 'translate(' + dotr * 2 + ',' + axish + ')').call(\n\t\t\t\taxisTop()\n\t\t\t\t\t.scale(xscale)\n\t\t\t\t\t.ticks(Math.min(10, Math.ceil(width / 50)))\n\t\t\t),\n\t\t\tfontsize: fontsize,\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t\tdotg.attr('transform', 'translate(' + dotr * 2 + ',' + (axish + axispad) + ')')\n\t\tdotset.attr('transform', (d, i) => {\n\t\t\treturn 'translate(' + xscale(d.value) + ',' + (height * i) / arg.data.length + ')'\n\t\t})\n\t\tdotcir.attr('r', d => {\n\t\t\treturn dotr * (d.ishighlight ? 1.5 : 1)\n\t\t})\n\t\tdrag\n\t\t\t.attr('font-size', fontsize)\n\t\t\t.attr('x', dotr * 2 + width + width2 - 5)\n\t\t\t.attr('y', axish + axispad + height + dotr * 2 - 5)\n\t}\n\tsizing()\n\t/*\n\tthis.highlighttoggle=function(sample) {\n\t\tif(!sample) return\n\t\tvar thisd=null\n\t\tdotcir.attr('transform',function(d){\n\t\t\tif(d.sample==sample) {\n\t\t\t\tthisd=d\n\t\t\t\treturn 'scale(1.5)'\n\t\t\t}\n\t\t\treturn 'scale(1)'\n\t\t})\n\t\tif(thisd) {\n\t\t\tdrag.text(thisd.sample+' '+thisd.value)\n\t\t} else {\n\t\t\tdrag.text('drag to resize')\n\t\t}\n\t}\n\t*/\n\treturn this\n}\n", "import { select as d3select } from 'd3-selection'\nimport * as client from './client'\nimport { genomic2gm } from './coord'\nimport { bplen as bplength } from '#shared/common.js'\nimport Svmr from './svmr.c'\n\nexport function svmrparseinput(arg, sayerror, genome, holder, hostURL, jwt) {\n\tif (!arg.dataname) {\n\t\targ.dataname = 'Unnamed dataset'\n\t}\n\tif (arg.input) {\n\t\tconst [e, header, items] = svmrparseraw(arg.input, genome)\n\t\tif (e) {\n\t\t\tsayerror('Fusion Editor input error: ' + e)\n\t\t\treturn\n\t\t}\n\t\tsvmrlaunch(genome, header, items, arg.dataname, holder, hostURL, jwt)\n\t\treturn\n\t}\n\tif (!arg.urls) {\n\t\tsayerror('neither .input:\"\" or .urls:[] is provided for Fusion Editor')\n\t\treturn\n\t}\n\tif (!Array.isArray(arg.urls)) {\n\t\tsayerror('fusioneditor.urls[] should be an array of URL strings')\n\t\treturn\n\t}\n\tif (arg.urls.length == 0) {\n\t\tsayerror('fusioneditor.urls[] is empty')\n\t\treturn\n\t}\n\tconst wait = holder\n\t\t.append('div')\n\t\t.style('margin', '20px')\n\t\t.style('color', '#aaa')\n\t\t.style('font-size', '1.5em')\n\t\t.text('Loading fusion gene data ...')\n\n\tconst tasks = []\n\n\targ.urls.forEach(url => {\n\t\ttasks.push(\n\t\t\tfetch(\n\t\t\t\tnew Request(hostURL + '/urltextfile', {\n\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\theaders: { 'content-type': 'application/json' },\n\t\t\t\t\tbody: JSON.stringify({ url: url, jwt: jwt })\n\t\t\t\t})\n\t\t\t)\n\t\t\t\t.then(data => {\n\t\t\t\t\treturn data.json()\n\t\t\t\t})\n\t\t\t\t.then(data => {\n\t\t\t\t\tif (data.error) throw { message: 'Error with ' + url + ': ' + data.error }\n\t\t\t\t\treturn { data: data.text, url: url }\n\t\t\t\t})\n\t\t)\n\t})\n\n\tPromise.all(tasks)\n\t\t.then(data => {\n\t\t\twait.remove()\n\t\t\tif (data.length == 0) {\n\t\t\t\tsayerror('No data retrieved from fusioneditor.urls')\n\t\t\t\treturn\n\t\t\t}\n\t\t\t// begin with parsing the first file and initialize holders\n\t\t\tconst [e, header, items] = svmrparseraw(data[0].data, genome)\n\t\t\tif (e) {\n\t\t\t\tsayerror('Error parsing fusion gene data in file ' + data[0].url)\n\t\t\t\treturn\n\t\t\t}\n\t\t\t// first file parsed, proceed with more\n\t\t\tfor (let i = 1; i < data.length; i++) {\n\t\t\t\tconst [e, header2, items2] = svmrparseraw(data[i].data, genome)\n\t\t\t\tif (e) {\n\t\t\t\t\tsayerror('Error parsing fusion gene data in file ' + data[i].url)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tfor (const j of items2) {\n\t\t\t\t\titems.push(j)\n\t\t\t\t}\n\t\t\t\t// anything new in header2 will be added to header\n\t\t\t\tfor (const h of header2) {\n\t\t\t\t\tlet notfound = true\n\t\t\t\t\tfor (const h2 of header) {\n\t\t\t\t\t\tif (h2.key == h.key) {\n\t\t\t\t\t\t\tnotfound = false\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (notfound) {\n\t\t\t\t\t\theader.push(h)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (items.length == 0) {\n\t\t\t\tsayerror('No fusion genes parsed from fusioneditor')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tsvmrlaunch(genome, header, items, arg.dataname, holder, hostURL, jwt)\n\t\t})\n\t\t.catch(err => {\n\t\t\twait.remove()\n\t\t\tsayerror(err.message)\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t})\n}\n\nexport function svmrui(dlst, genomes, hostURL, jwt) {\n\tconst [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = dlst\n\tinputdiv\n\t\t.append('div')\n\t\t.style('margin-top', '20px')\n\t\t.html(\n\t\t\t'<p>Please upload CICERO output as a text file. ' +\n\t\t\t\t'See <a href=https://docs.google.com/document/d/1jkVYRPIJpkWvA9vqtahRlNn63Hk5DehjHbF_BH9k7Rs/edit?usp=sharing target=_blank>file format</a>.</p>' +\n\t\t\t\t'<p>See <a href=https://docs.google.com/document/d/1DRVzE_WenG490eRYB7VGFOygtSqtF5L97rhK0HOUCNY/edit?usp=sharing target=_blank>function usage</a>.</p>'\n\t\t)\n\tinputdiv\n\t\t.append('p')\n\t\t.html('<a href=https://proteinpaint.stjude.org/ppdemo/hg19/fusion/cicero.output target=_blank>Example file</a>')\n\tfunction cmt(t, red) {\n\t\tsaydiv.style('color', red ? 'red' : 'black').text(t)\n\t}\n\tconst fileui = () => {\n\t\tfilediv.selectAll('*').remove()\n\t\tconst input = filediv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'file')\n\t\t\t.on('change', event => {\n\t\t\t\tconst file = event.target.files[0]\n\t\t\t\tif (!file) {\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!file.size) {\n\t\t\t\t\tcmt('Invalid file ' + file.name)\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst reader = new FileReader()\n\t\t\t\treader.onload = event => {\n\t\t\t\t\tconst usegenome = gselect.options[gselect.selectedIndex].innerHTML\n\t\t\t\t\tconst genomeobj = genomes[usegenome]\n\t\t\t\t\tconst [err, header, items] = svmrparseraw(event.target.result, genomeobj)\n\t\t\t\t\tif (err) {\n\t\t\t\t\t\tcmt(err, 1)\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tsvmrlaunch(genomeobj, header, items, file.name, visualdiv, hostURL, jwt)\n\t\t\t\t\tfilediv.remove()\n\t\t\t\t\tinputdiv.remove()\n\t\t\t\t}\n\t\t\t\treader.onerror = function () {\n\t\t\t\t\tcmt('Error reading file ' + file.name, 1)\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\treader.readAsText(file, 'utf8')\n\t\t\t})\n\n\t\tsetTimeout(() => input.node().focus(), 1100)\n\t}\n\tfileui()\n}\n\nexport function svmrlaunch(genome, header, items, filename, holder, hostURL, jwt) {\n\tnew Svmr(genome, header, items, filename, holder, hostURL, jwt)\n}\n\nexport function svmrparseraw(raw, genome) {\n\tconst lines = raw.trim().split('\\n')\n\tconst [err, header] = parseheader(lines[0])\n\tif (err) {\n\t\treturn ['File header error: ' + err]\n\t}\n\tconst skipword = lines[0].split('\\t')[0]\n\tconst items = []\n\tconst badlines = []\n\tfor (let i = 1; i < lines.length; i++) {\n\t\tconst line = lines[i]\n\t\tif (line == '') continue\n\t\tif (line[0] == '#') continue\n\t\tconst lst = line.trim().split('\\t')\n\t\tif (lst[0] == skipword) continue\n\t\t// m is a product\n\t\tconst m = {\n\t\t\tnotes: [] // collect notes\n\t\t}\n\t\tfor (let j = 0; j < header.length; j++) {\n\t\t\tif (lst[j] !== undefined && lst[j].includes('\"'))\n\t\t\t\treturn ['Input file has  invalid character \" e.g. \"NM_001007565\"']\n\t\t\tm[header[j].key] = lst[j]\n\t\t}\n\t\tif (!m.rating) {\n\t\t\tbadlines.push([i, 'rating unspecified', lst])\n\t\t\tcontinue\n\t\t}\n\t\tlet s = m.rating\n\t\tif (s.toLowerCase() == 'major') {\n\t\t\tm.rating = 'HQ'\n\t\t\ts = 'HQ'\n\t\t}\n\t\tif (s != 'HQ' && s != 'LQ' && s != 'RT' && s != 'bad') {\n\t\t\tbadlines.push([i, 'invalid rating: ' + m.rating, lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (!m.chrA) {\n\t\t\tbadlines.push([i, 'missing chrA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (!genome.chrlookup[m.chrA.toUpperCase()]) {\n\t\t\tbadlines.push([i, 'invalid chrA: ' + m.chrA, lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (!m.chrB) {\n\t\t\tbadlines.push([i, 'missing chrB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (!genome.chrlookup[m.chrB.toUpperCase()]) {\n\t\t\tbadlines.push([i, 'invalid chrB: ' + m.chrB, lst])\n\t\t\tcontinue\n\t\t}\n\t\ts = m.posA\n\t\tif (!s) {\n\t\t\tbadlines.push([i, 'missing posA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tlet v = Number.parseInt(s)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid posA: ' + s, lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (v < 0 || v >= genome.chrlookup[m.chrA.toUpperCase()]) {\n\t\t\tbadlines.push([i, 'invalid posA: ' + s, lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.posA = v\n\t\ts = m.posB\n\t\tif (!s) {\n\t\t\tbadlines.push([i, 'missing posB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseInt(s)\n\t\tif (isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid posB: ' + s, lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (v < 0 || v >= genome.chrlookup[m.chrB.toUpperCase()]) {\n\t\t\tbadlines.push([i, 'invalid posB: ' + s, lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.posB = v\n\t\tif (!m.ratioA) {\n\t\t\tbadlines.push([i, 'missing ratioA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseFloat(m.ratioA)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for ratioA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (v > 1) {\n\t\t\tbadlines.push([i, 'ratioA > 100%', lst])\n\t\t\tv = 1\n\t\t}\n\t\tm.ratioA = v\n\t\tif (!m.ratioB) {\n\t\t\tbadlines.push([i, 'missing ratioB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseFloat(m.ratioB)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for ratioB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (v > 1) {\n\t\t\tbadlines.push([i, 'ratioB > 100%', lst])\n\t\t\tv = 1\n\t\t}\n\t\tm.ratioB = v\n\t\tif (!m.score) {\n\t\t\tbadlines.push([i, 'missing score', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseFloat(m.score)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for score', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.score = v\n\n\t\tif (!m.readsA) {\n\t\t\tbadlines.push([i, 'readsA missing', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseInt(m.readsA)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for readsA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.readsA = v\n\t\tif (!m.readsB) {\n\t\t\tbadlines.push([i, 'readsB missing', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseInt(m.readsB)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for readsB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.readsB = v\n\n\t\tif (!m.matchA) {\n\t\t\tbadlines.push([i, 'matchA missing', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseInt(m.matchA)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for matchA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.matchA = v\n\t\tif (!m.matchB) {\n\t\t\tbadlines.push([i, 'matchB missing', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseInt(m.matchB)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for matchB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.matchB = v\n\n\t\tif (!m.repeatA) {\n\t\t\tbadlines.push([i, 'repeatA missing', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseFloat(m.repeatA)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for repeatA', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.repeatA = v\n\t\tif (!m.repeatB) {\n\t\t\tbadlines.push([i, 'repeatB missing', lst])\n\t\t\tcontinue\n\t\t}\n\t\tv = Number.parseFloat(m.repeatB)\n\t\tif (Number.isNaN(v)) {\n\t\t\tbadlines.push([i, 'invalid value for repeatB', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm.repeatB = v\n\n\t\tif (m.type2) {\n\t\t\tswitch (m.type2.toLowerCase()) {\n\t\t\t\tcase 'closs':\n\t\t\t\t\tm.iscloss = true\n\t\t\t\t\tbreak\n\t\t\t\tcase 'nloss':\n\t\t\t\t\tm.isnloss = true\n\t\t\t\t\tbreak\n\t\t\t\tcase 'fusion':\n\t\t\t\t\tm.isfusion = true\n\t\t\t\t\tbreak\n\t\t\t\tcase 'itd':\n\t\t\t\t\tm.isitd = true\n\t\t\t\t\tbreak\n\t\t\t\tcase 'other':\n\t\t\t\t\tm.isother = true\n\t\t\t\t\tbreak\n\t\t\t\tcase 'uptss':\n\t\t\t\t\tm.isuptss = true\n\t\t\t\t\tbreak\n\t\t\t\tdefault:\n\t\t\t\t\tbadlines.push([i, 'unknown type2: ' + m.type2, lst])\n\t\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\t// A B names\n\t\tif (m.geneA == '' || m.geneA == 'NA') {\n\t\t\tm.geneA = null\n\t\t}\n\t\tif (m.geneB == '' || m.geneB == 'NA') {\n\t\t\tm.geneB = null\n\t\t}\n\t\tif (m.featureA == 'intergenic') m.geneA = null\n\t\tif (m.featureB == 'intergenic') m.geneB = null\n\t\t// validate isoform pairs\n\t\tconst isoforma = m.lstisoforma ? m.lstisoforma.toUpperCase().split(',') : [],\n\t\t\tisoformb = m.lstisoformb ? m.lstisoformb.toUpperCase().split(',') : [],\n\t\t\tcodona = m.lstisoformacodon ? m.lstisoformacodon.split(',') : [],\n\t\t\tcodonb = m.lstisoformbcodon ? m.lstisoformbcodon.split(',') : [],\n\t\t\tframe = m.lstframe ? m.lstframe.split(',') : []\n\t\tlet exona = null,\n\t\t\texonb = null,\n\t\t\tanchora = null,\n\t\t\tanchorb = null,\n\t\t\tcontigaaA = null,\n\t\t\tcontigaaB = null,\n\t\t\tcontigbpA = null,\n\t\t\tcontigbpB = null\n\t\tif (m.lstisoformaexon) exona = m.lstisoformaexon.split(',')\n\t\tif (m.lstisoformbexon) exonb = m.lstisoformbexon.split(',')\n\t\tif (m.lstisoformaanchor) anchora = m.lstisoformaanchor.split(',')\n\t\tif (m.lstisoformbanchor) anchorb = m.lstisoformbanchor.split(',')\n\t\tif (m.lstcontigaaA) contigaaA = m.lstcontigaaA.split(',')\n\t\tif (m.lstcontigaaB) contigaaB = m.lstcontigaaB.split(',')\n\t\tif (m.lstcontigbpA) contigbpA = m.lstcontigbpA.split(',')\n\t\tif (m.lstcontigbpB) contigbpB = m.lstcontigbpB.split(',')\n\t\tconst paircount = Math.max(isoforma.length, isoformb.length, codona.length, codonb.length, frame.length)\n\t\t// good one, make pairs\n\t\tm.pairs = []\n\t\tfor (let j = 0; j < paircount; j++) {\n\t\t\tconst pair = {\n\t\t\t\ta: {\n\t\t\t\t\tisoform: isoforma[j] && isoforma[j].length > 0 ? isoforma[j] : null,\n\t\t\t\t\texon: exona ? Number.parseInt(exona[j]) : NaN,\n\t\t\t\t\tcodon: codona[j] ? Number.parseInt(codona[j]) : NaN,\n\t\t\t\t\tanchor: anchora ? anchora[j] : undefined\n\t\t\t\t},\n\t\t\t\tb: {\n\t\t\t\t\tisoform: isoformb[j] && isoformb[j].length > 0 ? isoformb[j] : null,\n\t\t\t\t\texon: exonb ? Number.parseInt(exonb[j]) : NaN,\n\t\t\t\t\tcodon: codonb[j] ? Number.parseInt(codonb[j]) : NaN,\n\t\t\t\t\tanchor: anchorb ? anchorb[j] : undefined\n\t\t\t\t},\n\t\t\t\tframe: frame[j],\n\t\t\t\tinframe: frame[j] == '1' || frame[j] == '2'\n\t\t\t}\n\t\t\tif (m.isuptss) {\n\t\t\t\tpair.inframe = true\n\t\t\t}\n\t\t\tlet aaa = NaN,\n\t\t\t\taab = NaN,\n\t\t\t\tbpa = NaN,\n\t\t\t\tbpb = NaN\n\t\t\tif (contigaaA && contigaaA[j]) aaa = Number.parseInt(contigaaA[j])\n\t\t\tif (contigaaB && contigaaB[j]) aab = Number.parseInt(contigaaB[j])\n\t\t\tif (contigbpA && contigbpA[j]) bpa = Number.parseInt(contigbpA[j])\n\t\t\tif (contigbpB && contigbpB[j]) bpb = Number.parseInt(contigbpB[j])\n\t\t\tif (!Number.isNaN(aaa) && !Number.isNaN(aab)) {\n\t\t\t\tpair.a.contigaa = aaa\n\t\t\t\tpair.b.contigaa = aab\n\t\t\t}\n\t\t\tif (!Number.isNaN(bpa) && !Number.isNaN(bpb)) {\n\t\t\t\tpair.a.contigbp = bpa\n\t\t\t\tpair.b.contigbp = bpb\n\t\t\t}\n\t\t\tm.pairs.push(pair)\n\t\t}\n\t\tif (m.exception) {\n\t\t\tm.notes.push(m.exception)\n\t\t}\n\t\tif (m.hlgene) {\n\t\t\tconst v = Number.parseInt(m.hlgene)\n\t\t\tif (Number.isNaN(v) || (v != 0 && v != 1 && v != 2 && v != 3 && v != 4)) {\n\t\t\t\tbadlines.push([i, 'invalid value for highlight gene flag: ' + m.hlgene, lst])\n\t\t\t\tdelete m.hlgene\n\t\t\t} else {\n\t\t\t\tm.hlgene = v\n\t\t\t}\n\t\t}\n\t\titems.push(m)\n\t}\n\tif (badlines.length > 0) {\n\t\tconst hlst = header.map(i => i.key)\n\t\tclient.bulk_badline(hlst, badlines)\n\t}\n\tif (items.length == 0) {\n\t\treturn ['No data loaded']\n\t}\n\treturn [null, header, items]\n}\n\nfunction parseheader(line) {\n\tconst original = line.trim().split('\\t')\n\tif (original.length <= 1) return ['invalid file header']\n\tconst header = []\n\tconst lower = []\n\tfor (const i of original) {\n\t\tlower.push(i.toLowerCase())\n\t\theader.push({\n\t\t\tlabel: i,\n\t\t\tkey: i.toLowerCase(),\n\t\t\tcustom: true\n\t\t})\n\t}\n\tconst htry = (...arg) => {\n\t\tfor (const s of arg) {\n\t\t\tconst i = lower.indexOf(s)\n\t\t\tif (i != -1) return i\n\t\t}\n\t\treturn -1\n\t}\n\t// A\n\tlet i = htry('genea')\n\tif (i == -1) return ['geneA missing']\n\theader[i].key = 'geneA'\n\tdelete header[i].custom\n\ti = htry('chra')\n\tif (i == -1) return ['chrA missing']\n\theader[i].key = 'chrA'\n\tdelete header[i].custom\n\ti = htry('posa')\n\tif (i == -1) return ['posA missing']\n\theader[i].key = 'posA'\n\tdelete header[i].custom\n\ti = htry('orta')\n\tif (i == -1) return ['ortA missing']\n\theader[i].key = 'ortA'\n\tdelete header[i].custom\n\ti = htry('featurea')\n\tif (i == -1) return ['featureA missing']\n\theader[i].key = 'featureA'\n\tdelete header[i].custom\n\ti = htry('ratioa')\n\tif (i == -1) return ['ratioA missing']\n\theader[i].key = 'ratioA'\n\tdelete header[i].custom\n\ti = htry('readsa')\n\tif (i == -1) return ['readsA missing']\n\theader[i].key = 'readsA'\n\tdelete header[i].custom\n\ti = htry('sv_refseqa_aa_index')\n\tif (i != -1) {\n\t\theader[i].key = 'lstcontigaaA'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('sv_refseqa_contig_index')\n\tif (i != -1) {\n\t\theader[i].key = 'lstcontigbpA'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('total_readsa')\n\tif (i != -1) {\n\t\theader[i].key = 'totalreadsA'\n\t\tdelete header[i].custom\n\t}\n\n\t// B\n\ti = htry('geneb')\n\tif (i == -1) return ['geneB missing']\n\theader[i].key = 'geneB'\n\tdelete header[i].custom\n\ti = htry('chrb')\n\tif (i == -1) return ['chrB missing']\n\theader[i].key = 'chrB'\n\tdelete header[i].custom\n\ti = htry('posb')\n\tif (i == -1) return ['posB missing']\n\theader[i].key = 'posB'\n\tdelete header[i].custom\n\ti = htry('ortb')\n\tif (i == -1) return ['ortB missing']\n\theader[i].key = 'ortB'\n\tdelete header[i].custom\n\ti = htry('featureb')\n\tif (i == -1) return ['featureB missing']\n\theader[i].key = 'featureB'\n\tdelete header[i].custom\n\ti = htry('ratiob')\n\tif (i == -1) return ['ratioB missing']\n\theader[i].key = 'ratioB'\n\tdelete header[i].custom\n\ti = htry('readsb')\n\tif (i == -1) return ['readsB missing']\n\theader[i].key = 'readsB'\n\tdelete header[i].custom\n\ti = htry('sv_refseqb_aa_index')\n\tif (i != -1) {\n\t\theader[i].key = 'lstcontigaaB'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('sv_refseqb_contig_index')\n\tif (i != -1) {\n\t\theader[i].key = 'lstcontigbpB'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('total_readsb')\n\tif (i != -1) {\n\t\theader[i].key = 'totalreadsB'\n\t\tdelete header[i].custom\n\t}\n\t// others\n\ti = htry('sv_inframe', 'frame')\n\tif (i == -1) return ['sv_inframe missing']\n\theader[i].key = 'lstframe'\n\tdelete header[i].custom\n\ti = htry('sv_refseqa')\n\tif (i == -1) return ['sv_refseqA missing']\n\theader[i].key = 'lstisoforma'\n\tdelete header[i].custom\n\n\ti = htry('sv_refseqa_codon')\n\t//if(i==-1) return ['sv_refseqA_codon missing']\n\t//header[i].key='lstisoformacodon'\n\tif (i != -1) {\n\t\theader[i].key = 'lstisoformacodon'\n\t}\n\n\ti = htry('sv_refseqb_codon')\n\t//if(i==-1) return ['sv_refseqB_codon missing']\n\t//header[i].key='lstisoformbcodon'\n\tif (i != -1) {\n\t\theader[i].key = 'lstisoformbcodon'\n\t}\n\n\ti = htry('score')\n\tif (i == -1) return ['score missing']\n\theader[i].key = 'score'\n\tdelete header[i].custom\n\ti = htry('sv_refseqb')\n\tif (i == -1) return ['sv_refseqB missing']\n\theader[i].key = 'lstisoformb'\n\tdelete header[i].custom\n\ti = htry('rating')\n\tif (i == -1) return ['rating missing']\n\theader[i].key = 'rating'\n\tdelete header[i].custom\n\n\ti = htry('matcha')\n\tif (i == -1) return ['matchA missing']\n\theader[i].key = 'matchA'\n\tdelete header[i].custom\n\ti = htry('matchb')\n\tif (i == -1) return ['matchB missing']\n\theader[i].key = 'matchB'\n\tdelete header[i].custom\n\ti = htry('repeata')\n\tif (i == -1) return ['repeatA missing']\n\theader[i].key = 'repeatA'\n\tdelete header[i].custom\n\ti = htry('repeatb')\n\tif (i == -1) return ['repeatB missing']\n\theader[i].key = 'repeatB'\n\tdelete header[i].custom\n\n\ti = htry('functional effect')\n\tif (i == -1) return ['functional effect missing']\n\theader[i].key = 'type2'\n\tdelete header[i].custom\n\n\t// may need to support other fusion builder format, so keep optional fields\n\ti = htry('sample')\n\tif (i != -1) {\n\t\theader[i].key = 'sample'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('sv_processing_exception')\n\tif (i != -1) {\n\t\theader[i].key = 'exception'\n\t}\n\ti = htry('medal')\n\tif (i != -1) {\n\t\theader[i].key = 'hlgene'\n\t}\n\ti = htry('sv_refseqa_exon')\n\tif (i != -1) {\n\t\theader[i].key = 'lstisoformaexon'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('sv_refseqb_exon')\n\tif (i != -1) {\n\t\theader[i].key = 'lstisoformbexon'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('sv_refseqa_anchor_type')\n\tif (i != -1) {\n\t\theader[i].key = 'lstisoformaanchor'\n\t\tdelete header[i].custom\n\t}\n\ti = htry('sv_refseqb_anchor_type')\n\tif (i != -1) {\n\t\theader[i].key = 'lstisoformbanchor'\n\t\tdelete header[i].custom\n\t}\n\treturn [null, header]\n}\n"],
+  "mappings": 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+}