@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

package/dist/block-OO2NLGUP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/block.js", "../src/block.tk.bam.adaptor.js", "../src/block.tk.pgv.adaptor.js", "../src/block.tk.ld.adaptor.js", "../src/block.tk.junction.adaptor.js", "../src/block.tk.bampile.js", "../src/block.tk.aicheck.adaptor.js", "../src/block.tk.bigwigstranded.js", "../src/block.tk.bedj.js", "../src/block.tk.usegm.js", "../src/block.tk.hicstraw.adaptor.ts", "../src/block.tk.ase.adaptor.js", "../src/block.mds.junction.adaptor.js", "../src/block.mds.svcnv.adaptor.js", "../src/block.mds.expressionrank.adaptor.js", "../mds3/adaptor.js", "../src/block.tk.bedgraphdot.adaptor.js", "../src/block.ds.maketk.js"],
+  "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport { select as d3select, selectAll as d3selectAll, pointer } from 'd3-selection'\nimport { format as d3format } from 'd3-format'\nimport { axisTop, axisLeft } from 'd3-axis'\nimport { debounce } from 'debounce'\nimport * as client from './client'\nimport { axisstyle, Menu, newSandboxDiv, sayerror, appear, disappear, isoformSelect, allgm2sum, sketchGene, sketchSplicerna, sketchRna, sketchProtein2 } from '#dom'\nimport { dofetch3 } from '../common/dofetch'\nimport * as common from '#shared/common.js'\nimport * as coord from './coord'\nimport vcf2dstk from './vcf.tkconvert'\nimport blockinit from './block.init'\nimport * as Legend from './block.legend'\nimport { string2snp } from '#common/snp'\n\n// track types\nimport { bamfromtemplate, bammaketk, bamload } from './block.tk.bam.adaptor'\nimport { pgvfromtemplate, pgvmaketk, pgvload } from './block.tk.pgv.adaptor'\nimport { ldfromtemplate, ldmaketk, ldload } from './block.tk.ld.adaptor'\nimport { junctionfromtemplate, junctionmaketk, junctionload } from './block.tk.junction.adaptor'\nimport { bampilefromtemplate, bampilemaketk, bampileload } from './block.tk.bampile'\nimport { bigwigfromtemplate, bigwigmaketk, bigwigload, bigwigloadsubpanel } from './block.tk.bigwig'\nimport { aicheckfromtemplate, aicheckmaketk, aicheckload, aicheckloadsubpanel } from './block.tk.aicheck.adaptor'\nimport {\n\tbigwigstrandedfromtemplate,\n\tbigwigstrandedmaketk,\n\tbigwigstrandedload,\n\tbigwigstrandedloadsubpanel\n} from './block.tk.bigwigstranded'\nimport { bedjfromtemplate, bedjmaketk, bedjload, bedjloadsubpanel } from './block.tk.bedj'\nimport { gmtkfromtemplate, gmtkmaketk, gmtkrender } from './block.tk.usegm'\nimport { hicstrawfromtemplate, hicstrawmaketk, hicstrawload } from './block.tk.hicstraw.adaptor'\nimport { asefromtemplate, asemaketk, aseload } from './block.tk.ase.adaptor'\n\nimport { mdsjunctionfromtemplate, mdsjunctionmaketk, mdsjunctionload } from './block.mds.junction.adaptor'\nimport { mdssvcnvfromtemplate, mdssvcnvmaketk, mdssvcnvload } from './block.mds.svcnv.adaptor'\nimport {\n\tmdsexpressionrankfromtemplate,\n\tmdsexpressionrankmaketk,\n\tmdsexpressionrankload\n} from './block.mds.expressionrank.adaptor'\nimport { mds3_fromtemplate, mds3_maketk, mds3_load } from '../mds3/adaptor'\nimport { bedgraphdot_fromtemplate, bedgraphdot_maketk, bedgraphdot_load } from './block.tk.bedgraphdot.adaptor'\n\n/* non-standard handler for legacy dataset\ncan delete when migrated to mds3\n*/\nimport * as blockds from './block.ds'\nimport dsmaketk from './block.ds.maketk'\n\n// dummy\n\n/* \ncallbacks from constructor options\n- onloadalltk\n- onloadalltk_always\n- onCoordinateChange\n- onpanning\n- onsetheight\n- onAddRemoveTk\n\n**************** METHODS\nupdateruler()\nmoremenu()\n**************** helper\nmakecoordinput()\n\n*/\n\nconst basecolorunknown = '#858585'\nconst baseheight = 16\nconst ntpxwidth = 20 // max allowed pixel width for a nt\nconst hlregioncolor = '#ccffff' // default color\nconst rulergrabzindex = 1000\nconst headerTip = new Menu()\n\nlet blockId = 1\n\nexport class Block {\n\tconstructor(arg) {\n\t\t/*** NOTE: This block instance is returned when calling runproteinpaint({block: true, ....}) ***/\n\n\t\t// assign a blockId to help in targeted DOM selection, in testing and maybe live usage.\n\t\tthis.blockId = blockId++\n\n\t\tthis.mclassOverride = arg.mclassOverride // allow tracks to access it to render legend\n\n\t\t// temp fix, to use in dofetch( {serverData} )\n\t\tthis.cache = {}\n\n\t\tif (arg.debugmode) {\n\t\t\twindow.bb = this\n\t\t\tthis.debugmode = true\n\t\t}\n\n\t\tthis.hostURL = sessionStorage.getItem('hostURL') // NO NEED for these after replacing fetch() with dofetch\n\t\tthis.jwt = sessionStorage.getItem('jwt')\n\n\t\tif (!arg.style) {\n\t\t\targ.style = {}\n\t\t}\n\t\tif (arg.style.margin == undefined) {\n\t\t\targ.style.margin = '20px'\n\t\t}\n\t\tif (arg.cohort) {\n\t\t\tthis.cohort = arg.cohort\n\t\t}\n\t\tthis.busy = true\n\n\t\t//////////////////////////////////////////\n\t\t//////// attach particular configurations\n\t\tif (arg.hidedatasetexpression) this.hidedatasetexpression = arg.hidedatasetexpression\n\t\tif (arg.variantPageCall_snv) this.variantPageCall_snv = arg.variantPageCall_snv\n\t\tif (arg.samplecart) this.samplecart = arg.samplecart\n\n\t\tthis.pannedpx = undefined\n\t\tthis.zoomedin = false\n\t\tthis.resized = false\n\n\t\tif (!arg.hidegenelegend) {\n\t\t\tthis.legend = {\n\t\t\t\tmclasses: new Map(), // two special legend that cover all dstk on display\n\t\t\t\tmorigins: new Map(),\n\t\t\t\tlegendcolor: '#7D6836',\n\t\t\t\theadtextcolor: '#555',\n\t\t\t\tvpad: '5px'\n\t\t\t}\n\t\t}\n\n\t\tthis.ctrl = {}\n\t\tthis.ds2handle = {}\n\t\tthis.ownds = {} // compared to genome.datasets\n\t\tthis.rglst = []\n\t\tthis.tklst = []\n\n\t\t// special effects\n\t\tthis.rotated = arg.rotated\n\t\tthis.showreverse = arg.showreverse // effect on pan\n\n\t\t////////////////////////////////\n\t\t// callbacks\n\t\tthis.onloadalltk = []\n\t\tthis.onloadalltk_always = arg.onloadalltk_always\n\t\tthis.onpanning = arg.onpanning\n\t\tthis.onsetheight = arg.onsetheight\n\t\tif (arg.onAddRemoveTk) {\n\t\t\tif (typeof arg.onAddRemoveTk != 'function') throw 'onAddRemoveTk() not function'\n\t\t\tthis.onAddRemoveTk = arg.onAddRemoveTk\n\t\t}\n\t\tthis.onCoordinateChange = arg.onCoordinateChange // argument is the rglst[]\n\n\t\tthis.exonsf = 1 // # pixel per basepair\n\n\t\tthis.labelfontsize = 14\n\t\tthis.tkleftlabel_xshift = -10\n\t\tthis.genome = arg.genome\n\t\tthis.holder0 = arg.holder\n\t\tthis.errdiv = arg.holder.append('div')\n\n\t\tthis.blocktip = new Menu({ padding: '0px' })\n\t\t/* used at:\n\t\told official ds handle, mouse over for \"About\" menu\n\t\tmds handle, click to show list of contents\n\t\tzoom buttons, mouse over for list of subpanels\n\t*/\n\t\tthis.tip = new Menu({ padding: '0px' })\n\n\t\tif (!this.genome) {\n\t\t\tthis.error('no genome')\n\t\t\treturn\n\t\t}\n\n\t\t// the main block width, not including subpanels\n\t\tif (arg.width) {\n\t\t\tthis.width = arg.width\n\t\t} else {\n\t\t\tconst minwidth = 800\n\t\t\tconst w = arg.holder.node().getBoundingClientRect().width\n\t\t\tthis.width = ntpxwidth * Math.ceil(Math.max(w * 0.63, minwidth) / ntpxwidth)\n\n\t\t\t// !!! TEMP !!!\n\t\t\t// hardcoded method to detect legacy ds with floating exp panel, to make room for the panels; delete after pediatric legacy ds is retired\n\t\t\tif (arg.datasetlst?.includes('pediatric')) this.width -= 100\n\t\t}\n\n\t\tif (arg.usegm) {\n\t\t\tthis.usegm = arg.usegm\n\t\t\tif (!this.usegm.pdomains) {\n\t\t\t\t// when it didn't go through block.init\n\t\t\t\tthis.usegm.pdomains = []\n\t\t\t}\n\t\t\tthis.allgm = arg.allgm\n\t\t\tif (!this.allgm) {\n\t\t\t\tthis.allgm = [arg.usegm]\n\t\t\t}\n\t\t\tif (!arg.tklst) {\n\t\t\t\targ.tklst = []\n\t\t\t}\n\n\t\t\tconst gmtk = arg.tklst.find(i => i.type == client.tkt.usegm)\n\t\t\tif (gmtk) {\n\t\t\t\t/*\n\t\t\t\ta track obj by type=\"usegm\" already exists\n\t\t\t\toverride gene name of this tk, and do not add a new \"gmtk\" obj to arg.tklst[]\n\t\t\t\t*/\n\t\t\t\tgmtk.name = arg.usegm.name\n\t\t\t} else {\n\t\t\t\t// no \"usegm\" track exists in arg.tklst[], create new object\n\t\t\t\targ.tklst.push({\n\t\t\t\t\ttype: client.tkt.usegm,\n\t\t\t\t\tname: arg.usegm.name,\n\t\t\t\t\t//model:arg.usegm,\n\t\t\t\t\tstackheight: arg.gmstackheight\n\t\t\t\t})\n\t\t\t}\n\t\t} else if (arg.rglst) {\n\t\t\tfor (const r of arg.rglst) {\n\t\t\t\tthis.rglst.push({\n\t\t\t\t\tchr: r.chr,\n\t\t\t\t\tbstart: r.start,\n\t\t\t\t\tbstop: r.stop,\n\t\t\t\t\tstart: r.start,\n\t\t\t\t\tstop: r.stop,\n\t\t\t\t\treverse: r.reverse\n\t\t\t\t})\n\t\t\t}\n\t\t\tthis.regionspace = 10\n\t\t} else {\n\t\t\t// single region\n\t\t\tconst e = coord.invalidcoord(this.genome, arg.chr, arg.start, arg.stop)\n\t\t\tif (e) {\n\t\t\t\tthis.error(e)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst _chr = this.genome.chrlookup[arg.chr.toUpperCase()]\n\t\t\tconst minspan = Math.ceil(this.width / ntpxwidth) //200\n\t\t\tif (arg.stop - arg.start < minspan) {\n\t\t\t\tconst h = Math.ceil(minspan / 2)\n\t\t\t\tconst m = Math.floor((arg.start + arg.stop) / 2)\n\t\t\t\targ.start = m - h\n\t\t\t\targ.stop = m + h\n\t\t\t}\n\t\t\tthis.rglst = [\n\t\t\t\t{\n\t\t\t\t\tchr: _chr.name,\n\t\t\t\t\tbstart: 0,\n\t\t\t\t\tbstop: _chr.len,\n\t\t\t\t\tstart: arg.start,\n\t\t\t\t\tstop: arg.stop,\n\t\t\t\t\treverse: this.showreverse\n\t\t\t\t}\n\t\t\t]\n\t\t\tthis.regionspace = 0\n\t\t}\n\t\tthis.startidx = 0\n\t\tthis.stopidx = this.rglst.length - 1\n\n\t\t// TODO allow svgholder for embedding into an existing svg\n\n\t\tthis.holder = arg.holder\n\t\t\t.append('div')\n\t\t\t.style('margin', arg.style.margin)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.attr('class', 'sja_Block_div')\n\t\tif (!arg.nobox) {\n\t\t\tthis.holder.style('border', 'solid 1px #ccc')\n\t\t}\n\t\tif (arg.bgcolor) {\n\t\t\tthis.holder.style('background-color', arg.bgcolor)\n\t\t}\n\n\t\tif (this.genome.hasIdeogram) {\n\t\t\tthis.initIdeogram(arg)\n\t\t\t// creates this.ideogram{}\n\t\t}\n\n\t\tlet butrow\n\t\tif (!arg.butrowbottom) {\n\t\t\tbutrow = this.holder.append('div')\n\t\t}\n\t\t{\n\t\t\tconst inlinediv = this.holder\n\t\t\t\t.append('div') // contains svg and resize button\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\tthis.svg = inlinediv\n\t\t\t\t.append('svg')\n\t\t\t\t.attr('data-testid', 'sjpp_block_svg')\n\t\t\t\t.on('mousedown', event => {\n\t\t\t\t\tevent.preventDefault()\n\t\t\t\t})\n\t\t\tif (!arg.noresize) {\n\t\t\t\tthis.resizewidthbutton = inlinediv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.text('drag to resize')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t.style('bottom', '-5px') // push down enough not to touch protein bar\n\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t.on('mousedown', event => {\n\t\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\t\tconst x = event.clientX\n\t\t\t\t\t\tconst body = d3select(document.body)\n\t\t\t\t\t\tbody.on('mousemove', event => {\n\t\t\t\t\t\t\tthis.resizewidthbutton.style('right', this.rpad + this.rightheadw + x - event.clientX + 'px')\n\t\t\t\t\t\t})\n\t\t\t\t\t\tbody.on('mouseup', event => {\n\t\t\t\t\t\t\tthis.resizewidthbutton.style('right', this.rpad + this.rightheadw + 'px')\n\t\t\t\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t\t\t\t\t\tif (this.busy) {\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\tthis.zoomedin = false\n\t\t\t\t\t\t\tthis.pannedpx = undefined\n\t\t\t\t\t\t\t// the only place to set it to true\n\t\t\t\t\t\t\tthis.resized = true\n\n\t\t\t\t\t\t\tthis.width += event.clientX - x\n\n\t\t\t\t\t\t\tthis.block_coord_updated()\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (arg.butrowbottom) {\n\t\t\tbutrow = this.holder.append('div').style('margin-top', '5px')\n\t\t}\n\t\tif (arg.hidegenecontrol) {\n\t\t\tthis.hidegenecontrol = true\n\t\t\tbutrow.style('display', 'none')\n\t\t}\n\n\t\tif (this.legend) {\n\t\t\tconst div = this.holder.append('div').style('margin-top', '5px')\n\n\t\t\tlet shown = !arg.foldlegend\n\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.text('LEGEND')\n\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('color', this.legend.legendcolor)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (shown) {\n\t\t\t\t\t\tshown = false\n\t\t\t\t\t\tdisappear(div2)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tshown = true\n\t\t\t\t\t\tappear(div2)\n\t\t\t\t\t}\n\t\t\t\t})\n\n\t\t\tconst div2 = this.holder.append('div').style('border-top', 'solid 1px ' + this.legend.legendcolor)\n\t\t\t//.style('background-color', '#FCFBF7')\n\t\t\tif (arg.foldlegend) {\n\t\t\t\tdiv2.style('display', 'none')\n\t\t\t}\n\n\t\t\tthis.legend.holder = div2.append('table').style('border-spacing', '15px').style('border-collapse', 'separate')\n\n\t\t\tconst [tr1, td1] = Legend.legend_newrow(\n\t\t\t\tthis,\n\t\t\t\t//Allows user to set left-side group designation for classes\n\t\t\t\targ.mclassOverride ? arg.mclassOverride.className : 'CLASS'\n\t\t\t)\n\t\t\tthis.legend.tr_mclass = tr1.style('display', 'none')\n\t\t\tthis.legend.td_mclass = td1\n\t\t\tconst [tr2, td2] = Legend.legend_newrow(this, 'ORIGIN')\n\t\t\tthis.legend.tr_morigin = tr2.style('display', 'none')\n\t\t\tthis.legend.td_morigin = td2\n\n\t\t\tif (arg.legendimg) {\n\t\t\t\tconst [tr, td] = Legend.legend_newrow(this, arg.legendimg.name || '')\n\t\t\t\tthis.make_legend_img(arg.legendimg, td)\n\t\t\t}\n\t\t}\n\n\t\tif (arg.usegm) {\n\t\t\t// do this after legend is set\n\t\t\t// fills this.rglst[], this.startidx, this.stopidx\n\t\t\tthis.setgmmode(arg.gmmode || client.gmmode.genomic)\n\t\t}\n\n\t\t// rglst is set, can process ideogram\n\t\tif (this.ideogram) {\n\t\t\tif (this.ideogram.visible) this.updateIdeogram()\n\t\t\telse this.ideogram.div.style('display', 'none')\n\t\t}\n\n\t\tif (arg.nobox) {\n\t\t\t// no dogtag\n\t\t} else {\n\t\t\t// use dogtag\n\t\t\tbutrow\n\t\t\t\t.append('div')\n\t\t\t\t.html(arg.dogtag ? arg.dogtag : arg.chr)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '5px')\n\t\t\t\t.style('background-color', '#bbb')\n\t\t\t\t.style('color', 'white')\n\t\t}\n\t\tif (this.usegm) {\n\t\t\tthis.usegmtip = new Menu({ padding: 'none' })\n\t\t\t// name button\n\t\t\tthis.ctrl.namebutt = butrow\n\t\t\t\t.append('span')\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t.html(\n\t\t\t\t\t'<span data-testid=\"sja_block_usegm_name\" style=\"font-size:1.5em;font-weight:bold\">' +\n\t\t\t\t\t\tthis.usegm.name +\n\t\t\t\t\t\t'</span> ' +\n\t\t\t\t\t\tthis.usegm.isoform\n\t\t\t\t)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tevent.stopPropagation()\n\t\t\t\t\tthis.genemenu()\n\t\t\t\t})\n\t\t\tbutrow.append('span').html('&nbsp;&nbsp;&nbsp;')\n\n\t\t\tbutrow\n\t\t\t\t.append('div') // duplicated\n\t\t\t\t.text(this.genome.name)\n\t\t\t\t.attr('class', 'sjpp-active-tiny-button')\n\n\t\t\t// official dataset (legacy ds), only use in gm mode, won't show in plain browser\n\t\t\tthis.ctrl.dshandleholder = butrow.append('span')\n\t\t\tif (!arg.hide_dsHandles) {\n\t\t\t\t// can show ds handles\n\t\t\t\tif (this.genome.datasets) {\n\t\t\t\t\tfor (const n in this.genome.datasets) {\n\t\t\t\t\t\tif (this.genome.datasets[n].isMds) {\n\t\t\t\t\t\t\t// old ds, do not show mds here\n\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (this.genome.datasets[n].noHandleOnClient) continue\n\t\t\t\t\t\tthis.old_dshandle_new(n)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// custom data, legacy ds\n\t\t\t\tbutrow\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_opaque8 sjpp-plus-button')\n\t\t\t\t\t.text('+')\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\t\tthis.tip.clear().show(p.left - 150, p.top + p.height - 15)\n\t\t\t\t\t\timport('../mds3/customdata.inputui').then(q => q.default(this))\n\t\t\t\t\t})\n\t\t\t}\n\t\t\tbutrow.append('span').html('&nbsp;&nbsp;&nbsp;')\n\t\t}\n\n\t\tthis.coord = {\n\t\t\theight: 0\n\t\t}\n\t\tif (this.usegm) {\n\t\t\t// no input box\n\t\t} else {\n\t\t\tmakecoordinput(this, butrow)\n\n\t\t\tthis.coordwidthsays = butrow.append('span').style('padding', '0px 10px 0px 5px').style('font-size', '80%')\n\n\t\t\tbutrow\n\t\t\t\t.append('div') // duplicated\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.text(this.genome.name)\n\t\t\t\t.style('background', '#465f75')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('color', 'white')\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.style('border-radius', '4px')\n\t\t}\n\n\t\t/*\n\tmds handle always shown\n\tafter coord input\n\tmay configure not to show\n\t*/\n\t\tif (!arg.hide_dsHandles && this.genome.datasets) {\n\t\t\tconst lst = []\n\t\t\tfor (const n in this.genome.datasets) {\n\t\t\t\tif (this.genome.datasets[n].isMds && !this.genome.datasets[n].noHandleOnClient) {\n\t\t\t\t\tlst.push(n)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (lst.length) {\n\t\t\t\tthis.ctrl.mdsHandleHolder = butrow.append('span').style('margin-right', '10px')\n\t\t\t\tfor (const i of lst) this.mds_handle_make(i)\n\t\t\t}\n\t\t}\n\n\t\tthis.ctrl.zinbutt = butrow\n\t\t\t.append('button')\n\t\t\t.html('In')\n\t\t\t.on('click', () => this.zoomblock(2))\n\t\t\t.on('mouseover', () => this.zoombutton_mouseover(2, false, this.ctrl.zinbutt.node()))\n\t\t//.on('mouseout',()=>this.blocktip.hide())\n\t\tthis.ctrl.zobutt1 = butrow\n\t\t\t.append('button')\n\t\t\t.html('Out &times;2')\n\t\t\t.on('click', () => this.zoomblock(2, true))\n\t\t\t.on('mouseover', () => this.zoombutton_mouseover(2, true, this.ctrl.zobutt1.node()))\n\t\tthis.ctrl.zobutt2 = butrow\n\t\t\t.append('button')\n\t\t\t.html('&times;10')\n\t\t\t.attr('data-testid', 'sjpp-block-zoombtnx10')\n\t\t\t.on('click', () => this.zoomblock(10, true))\n\t\t\t.on('mouseover', () => this.zoombutton_mouseover(10, true, this.ctrl.zobutt2.node()))\n\t\tthis.ctrl.zobutt3 = butrow\n\t\t\t.append('button')\n\t\t\t.html('&times;50')\n\t\t\t.attr('data-testid', 'sjpp-block-zoombtnx50')\n\t\t\t.on('click', () => this.zoomblock(50, true))\n\t\t\t.on('mouseover', () => this.zoombutton_mouseover(50, true, this.ctrl.zobutt3.node()))\n\n\t\t/*\n\tthis.ctrl.revbutt=butrow.append('button')\n\t\t.html(this.coord.reverse ? 'Reverse &laquo;' : 'Forward &raquo;')\n\t\t.on('click',()=>this.reverseorient())\n\t\t*/\n\n\t\t{\n\t\t\tconst button = butrow.append('button').text('Tracks').style('margin-left', '10px')\n\t\t\tconst tip = new Menu({ padding: 'none' })\n\t\t\tbutton.on('click', event => {\n\t\t\t\t// remove past state for refreshing tk data\n\t\t\t\tthis.pannedpx = undefined\n\t\t\t\tthis.zoomedin = false\n\t\t\t\tthis.resized = false\n\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\timport('./block.tk.menu').then(q => {\n\t\t\t\t\tq.default(this, tip, p.left - 100, p.top + p.height - 15, button.node())\n\t\t\t\t})\n\t\t\t})\n\t\t}\n\n\t\t{\n\t\t\tconst moreBtn = butrow\n\t\t\t\t.append('button')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.text('More')\n\t\t\t\t.on('click', event => {\n\t\t\t\t\theaderTip.clear()\n\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\tthis.moremenu(headerTip)\n\t\t\t\t\t// must create menu contents first then show, so the height-placement will work\n\t\t\t\t\theaderTip.show2(p.left - 50, p.top + p.height - 15, { elem: moreBtn.node() })\n\t\t\t\t})\n\t\t}\n\n\t\tthis.gdcBamSliceDownloadBtn = butrow\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('display', 'none')\n\t\t\t.text('Download GDC BAM slice')\n\t\t\t.on('click', async () => {\n\t\t\t\tconst tks = this.tklst.filter(i => i.type == 'bam' && i.gdcFile)\n\t\t\t\tif (tks.length == 0) return\n\t\t\t\tif (tks.length == 1) {\n\t\t\t\t\tdownloadOneFile(tks[0], this.gdcBamSliceDownloadBtn)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\theaderTip.clear().showunder(this.gdcBamSliceDownloadBtn.node())\n\t\t\t\tfor (const t of tks) {\n\t\t\t\t\tconst button = headerTip.d\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.text(t.name)\n\t\t\t\t\t\t.style('display', 'block')\n\t\t\t\t\t\t.style('margin', '4px')\n\t\t\t\t\t\t.on('click', () => downloadOneFile(t, button))\n\t\t\t\t}\n\n\t\t\t\tasync function downloadOneFile(tk, button) {\n\t\t\t\t\tbutton.property('disabled', true)\n\n\t\t\t\t\t// old method of window.open() won't allow passing token via request header\n\t\t\t\t\t//const requestUrl = `tkbam?genome=${this.genome.name}&clientdownloadgdcslice=`\n\t\t\t\t\t//window.open(requestUrl, '_self', 'download')\n\n\t\t\t\t\t// FIXME the entire bam slice is cached in browser memory before downloading, which can be slow\n\t\t\t\t\t// will be nice to directly \"stream\" to a download file without caching\n\n\t\t\t\t\tconst headers = {\n\t\t\t\t\t\t'Content-Type': 'application/json',\n\t\t\t\t\t\tAccept: 'application/json'\n\t\t\t\t\t}\n\t\t\t\t\tif (tk.gdcToken) {\n\t\t\t\t\t\theaders['X-Auth-Token'] = tk.gdcToken\n\t\t\t\t\t}\n\t\t\t\t\tconst lst = []\n\t\t\t\t\tconst data = await dofetch3('tkbam', {\n\t\t\t\t\t\theaders,\n\t\t\t\t\t\tbody: {\n\t\t\t\t\t\t\tclientdownloadgdcslice: 1,\n\t\t\t\t\t\t\tgdcFileUUID: tk.gdcFile.uuid,\n\t\t\t\t\t\t\tgdcFilePosition: tk.gdcFile.position\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\n\t\t\t\t\tbutton.property('disabled', false)\n\n\t\t\t\t\tconst a = document.createElement('a')\n\t\t\t\t\ta.href = URL.createObjectURL(data)\n\t\t\t\t\ta.download = tk.aboutThisFile ? tk.aboutThisFile[0].v + '.bam' : 'gdc.bam'\n\t\t\t\t\ta.style.display = 'none'\n\t\t\t\t\tdocument.body.appendChild(a)\n\t\t\t\t\ta.click()\n\t\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\t}\n\t\t\t})\n\n\t\tthis.gbase = this.svg.append('g').attr('transform', 'translate(0,0)')\n\n\t\t// cloak that covers gbase with a rect to indicate loading and prevent user interaction\n\t\tthis.gCloak = this.svg.append('g').attr('transform', 'scale(0)')\n\t\tthis.gCloakRect = this.gCloak.append('rect').attr('fill', 'white')\n\t\tthis.gCloakWord = this.gCloak\n\t\t\t.append('text')\n\t\t\t.attr('id', 'loadinggCloak')\n\t\t\t.text('Loading ...')\n\t\t\t.attr('fill', common.defaultcolor)\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('font-weight', 'bold')\n\t\t\t.attr('font-size', '18px')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'middle')\n\n\t\tthis.pica = { g: this.svg.append('g') }\n\n\t\tthis.hlregion = {\n\t\t\tg: this.gbase.append('g'),\n\t\t\tlst: []\n\t\t}\n\n\t\tinit_cursorhlbar(this)\n\n\t\tthis.leftheadw = arg.leftheadw || 100\n\t\tthis.rightheadw = arg.rightheadw || 100\n\n\t\t// row - coordinate ruler\n\t\tthis.rulerheight = 20\n\t\tthis.rulerfontsize = 13\n\t\tthis.rulerticksize = 6\n\t\tthis.lpad = 3\n\t\tthis.rpad = 10\n\t\tthis.coordyp1 = 3 // top pad\n\t\tthis.coordyp2 = 3 // bottom pad\n\n\t\t// grand holder, to contain main coord ruler of both main tk and sub panels, so they pan independently\n\t\tthis.coord.g0 = this.gbase\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(' + (this.leftheadw + this.lpad) + ',' + (this.coordyp1 + this.rulerheight) + ')')\n\n\t\t// ruler for main track, pans along with them\n\t\tthis.coord.g = this.coord.g0.append('g')\n\n\t\t// main holder for subpanel rulers, each pans independently\n\t\tthis.coord.gcoordsubpanels = this.coord.g0.append('g')\n\n\t\tthis.coord.name = this.coord.g\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('x', -this.lpad + this.tkleftlabel_xshift)\n\t\t\t.attr('y', -this.rulerheight / 2)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('font-size', 13)\n\t\tif (this.hidegenecontrol) {\n\t\t\tthis.coord.name\n\t\t\t\t.text('Zoom out')\n\t\t\t\t.classed('sja_clbtext', true)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (this.busy) return\n\t\t\t\t\tif (this.nozoomout()) {\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tthis.zoomblock(2, true)\n\t\t\t\t})\n\t\t}\n\t\tthis.coord.axesg = this.coord.g.append('g')\n\t\tthis.coord.grab = this.coord.g\n\t\t\t.append('rect')\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', -this.coordyp1 - this.rulerheight)\n\t\t\t.attr('width', this.width)\n\t\t\t.on('mousedown', event => {\n\t\t\t\tthis.rulermousedown(event, this)\n\t\t\t\t\t.then(tmp => {\n\t\t\t\t\t\tconst [toofine, startpx, spanpx] = tmp\n\n\t\t\t\t\t\tif (this.toselecthlregion) {\n\t\t\t\t\t\t\tthis.busy = false\n\t\t\t\t\t\t\tdelete this.toselecthlregion\n\t\t\t\t\t\t\tconst [startidx, startpos] = this.pxoff2region(startpx)\n\t\t\t\t\t\t\tconst [stopidx, stoppos] = this.pxoff2region(startpx + spanpx)\n\t\t\t\t\t\t\tconst chr = this.rglst[startidx].chr\n\t\t\t\t\t\t\tif (chr == this.rglst[stopidx].chr) {\n\t\t\t\t\t\t\t\tthis.addhlregion(chr, Math.min(startpos, stoppos), Math.max(startpos, stoppos))\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\t// zoom in\n\t\t\t\t\t\tif (toofine) {\n\t\t\t\t\t\t\t// too fine won't zoom in\n\t\t\t\t\t\t\tthis.busy = false\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.zoomedin = true\n\t\t\t\t\t\tthis.zoom2px(startpx, startpx + spanpx)\n\t\t\t\t\t})\n\t\t\t\t\t.catch(e => {\n\t\t\t\t\t\tif (e == 'busy') return\n\t\t\t\t\t\tthis.error(e.message)\n\t\t\t\t\t\tconsole.log(e.stack)\n\t\t\t\t\t})\n\t\t\t})\n\n\t\t// sub panels\n\t\t// contain master instruction of each subpanel (chr/start/stop/width), to be propagated to .subpanels[] of each track\n\t\tthis.subpanels = []\n\t\tif (arg.subpanels) {\n\t\t\tthis.subpanels = arg.subpanels\n\t\t\tfor (const [idx, p] of this.subpanels.entries()) {\n\t\t\t\tp.exonsf = p.width / (p.stop - p.start)\n\t\t\t\tthis.init_coord_subpanel(p)\n\t\t\t}\n\t\t}\n\n\t\tthis.updateruler()\n\n\t\tif (arg.hlregions) {\n\t\t\tfor (const r of arg.hlregions) {\n\t\t\t\tthis.addhlregion(r.chr, r.start, r.stop, r.color)\n\t\t\t}\n\t\t}\n\n\t\tif (arg.tklst) {\n\t\t\tfor (const _tk of arg.tklst) {\n\t\t\t\t// validate input track!!!\n\n\t\t\t\tif (!_tk.type) {\n\t\t\t\t\tthis.error('missing type in a track')\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tlet pre_tk = _tk // for vcf track, the 'pre_tk' object will be replaced by dstk\n\n\t\t\t\tconst hidden = pre_tk.hidden\n\t\t\t\tdelete pre_tk.hidden\n\n\t\t\t\tif (pre_tk.type == 'vcf') {\n\t\t\t\t\t// convert vcf to dstk, this is duplicated in tk.menu\n\t\t\t\t\tconst [err, dstk] = vcf2dstk(pre_tk)\n\t\t\t\t\tif (err) {\n\t\t\t\t\t\tthis.error('VCF track error: ' + err)\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tpre_tk = dstk\n\t\t\t\t\tpre_tk.iscustom = _tk.iscustom\n\t\t\t\t}\n\n\t\t\t\tif (pre_tk.iscustom) {\n\t\t\t\t\t// should register\n\t\t\t\t\tif (!client.tkexists(pre_tk, this.genome.tracks)) {\n\t\t\t\t\t\t// this is a new custom track\n\t\t\t\t\t\tpre_tk.tkid = Math.random().toString() // important\n\t\t\t\t\t\tthis.genome.tracks.push(pre_tk)\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tif (!hidden) {\n\t\t\t\t\tthis.block_addtk_template(pre_tk)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (arg.nativetracks) {\n\t\t\t// add selected native tracks\n\n\t\t\tconst tklookup = new Map()\n\t\t\tif (this.genome.tracks) {\n\t\t\t\tfor (const t of this.genome.tracks) {\n\t\t\t\t\tif (t.iscustom) continue\n\t\t\t\t\ttklookup.set(t.name.toLowerCase(), t)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tlet lst = []\n\t\t\tif (Array.isArray(arg.nativetracks)) {\n\t\t\t\tfor (const nt of arg.nativetracks) {\n\t\t\t\t\tif (typeof nt == 'string') {\n\t\t\t\t\t\t// string for track name\n\t\t\t\t\t\tconst t2 = tklookup.get(nt.toLowerCase())\n\t\t\t\t\t\tif (t2) {\n\t\t\t\t\t\t\tlst.push(t2)\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// object with custom settings\n\t\t\t\t\t\tif (!nt.name) continue\n\t\t\t\t\t\tif (typeof nt.name != 'string') continue\n\t\t\t\t\t\tconst t2 = tklookup.get(nt.name.toLowerCase())\n\t\t\t\t\t\tif (t2) {\n\t\t\t\t\t\t\t// remember custom setting in registry object\n\t\t\t\t\t\t\tfor (const k in nt) {\n\t\t\t\t\t\t\t\tif (k == 'name') continue\n\t\t\t\t\t\t\t\tt2[k] = nt[k]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tlst.push(t2)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (typeof arg.nativetracks == 'string') {\n\t\t\t\tfor (const n of arg.nativetracks.split(',')) {\n\t\t\t\t\tconst t = tklookup.get(n.toLowerCase())\n\t\t\t\t\tif (t) {\n\t\t\t\t\t\tlst.push(t)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthis.error('invalid value for nativetracks')\n\t\t\t}\n\n\t\t\tfor (const t of lst) {\n\t\t\t\t// since arg.tklst[] may contain native track (gene), must check\n\t\t\t\tif (!client.tkexists(t, this.tklst)) {\n\t\t\t\t\tthis.block_addtk_template(t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t/* quick fix: \n\t\twhen there are bam tracks, these tracks usually are taller than a screen\n\t\tmaking it hard to compare to gene tracks lying on the bottom\n\t\tmove the native gene track to the top\n\t\tusually that is the only bedj track in the list\n\t\t*/\n\t\tif (this.tklst.find(i => i.type == client.tkt.bam)) {\n\t\t\tconst bedtkidx = this.tklst.findIndex(i => i.type == client.tkt.bedj)\n\t\t\tif (bedtkidx != -1) {\n\t\t\t\tconst t = this.tklst[bedtkidx]\n\t\t\t\tthis.tklst.splice(bedtkidx, 1)\n\t\t\t\tthis.tklst.unshift(t)\n\t\t\t}\n\t\t}\n\n\t\tthis.tk_load_all()\n\n\t\tif (arg.mset) {\n\t\t\t// not in use\n\t\t\t// precompiled sets of mutations\n\t\t\tfor (const set of arg.mset) {\n\t\t\t\tconst ds = {\n\t\t\t\t\tiscustom: true,\n\t\t\t\t\tmlst: set.mlst,\n\t\t\t\t\tlabel: set.name\n\t\t\t\t}\n\t\t\t\tthis.ownds[set.name] = ds\n\t\t\t\tconst tk = this.block_addtk_template({\n\t\t\t\t\ttype: client.tkt.ds,\n\t\t\t\t\tds: ds\n\t\t\t\t})\n\t\t\t\tblockds.dstkload(tk, this)\n\t\t\t}\n\t\t}\n\n\t\t/*** old official datasets ***/\n\t\tif (arg.datasetlst) {\n\t\t\tfor (const n of arg.datasetlst) {\n\t\t\t\tlet ds = null\n\t\t\t\tfor (const a in this.genome.datasets) {\n\t\t\t\t\tif (a.toUpperCase() == n.toUpperCase()) {\n\t\t\t\t\t\tds = this.genome.datasets[a]\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!ds) {\n\t\t\t\t\tthis.error('Invalid dataset to load: ' + n)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tif (ds.isMds3) {\n\t\t\t\t\t// extends the old \"dataset\" parameter to support mds3\n\t\t\t\t\tconst tk = this.block_addtk_template({ type: client.tkt.mds3, dslabel: n })\n\t\t\t\t\tthis.tk_load(tk)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst tk = this.block_addtk_template({ type: client.tkt.ds, ds })\n\t\t\t\tif (arg.hlaachange) {\n\t\t\t\t\ttk.hlaachange = arg.hlaachange\n\t\t\t\t}\n\t\t\t\tif (arg.hlvariants) {\n\t\t\t\t\ttk.hlvariants = arg.hlvariants\n\t\t\t\t}\n\t\t\t\ttk.legacyDsFilter = arg.legacyDsFilter // quick fix\n\t\t\t\tblockds.dstkload(tk, this)\n\t\t\t}\n\t\t}\n\n\t\t/*** new mds datasets ***/\n\n\t\tlet hasMdsDatasets = false\n\n\t\tif (arg.datasetqueries) {\n\t\t\tif (!Array.isArray(arg.datasetqueries)) {\n\t\t\t\tthis.error('datasetqueries should be array')\n\t\t\t} else {\n\t\t\t\targ.datasetqueries.forEach(q => {\n\t\t\t\t\tif (!q.dataset) return this.error('datasetqueries error: .dataset missing from a query')\n\t\t\t\t\tif (!q.querykey) return this.error('datasetqueries error: .querykey missing from a query')\n\t\t\t\t\tconst ds = this.genome.datasets[q.dataset]\n\t\t\t\t\tif (!ds) return this.error('invalid dataset name: ' + q.dataset)\n\t\t\t\t\tif (!ds.isMds) return this.error('query not supported in dataset: ' + q.dataset)\n\t\t\t\t\tthis.mds_load_query_bykey(ds, q)\n\n\t\t\t\t\thasMdsDatasets = true\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\t// help set block.busy off when there is no track to load\n\t\tthis.ifbusy()\n\n\t\tif (this.tklst.length == 0 && !hasMdsDatasets) {\n\t\t\t/* show this error when there's no tracks to be loaded\n\t\t\tsince the client-side dataset are async loaded, things from datasetqueries\n\t\t\tis not awaited (cannot do in Construtor)\n\t\t\tthus the mds track obj will not be added to this.tklst\n\t\t\tcausing the empty tklst array\n\t\t\t*/\n\t\t\tthis.error(\n\t\t\t\t'No tracks specified. If you don\\'t expect to see this, delete the \"block:true\" from runproteinpaint() argument.'\n\t\t\t)\n\t\t}\n\t}\n\t/****** end of constructor ***/\n\n\tasync make_legend_img(arg, div) {\n\t\t/*\n\t\tadd a legend showing a server-side image, either for a track or for this block\n\t\targ: {}\n\t\t.file: tp path to an image file\n\t\t.height: optional icon height\n\t\t*/\n\t\tconst data = await dofetch3('img?file=' + arg.file)\n\t\tif (data.error) {\n\t\t\tdiv.text(data.error)\n\t\t\treturn\n\t\t}\n\t\tlet fold = true\n\t\tconst img = div.append('img').attr('class', 'sja_clbb').attr('src', data.src).style('height', '80px')\n\t\timg.on('click', () => {\n\t\t\tif (fold) {\n\t\t\t\tfold = false\n\t\t\t\timg.transition().style('height', arg.height ? arg.height + 'px' : 'auto')\n\t\t\t} else {\n\t\t\t\tfold = true\n\t\t\t\timg.transition().style('height', '80px')\n\t\t\t}\n\t\t})\n\t}\n\n\tregioncumlen(ridx, notincludethisregion) {\n\t\t// region bp length up to the view start of a given region\n\t\tlet c = 0\n\t\tif (!notincludethisregion) {\n\t\t\tconst r = this.rglst[ridx]\n\t\t\tc = r.reverse ? r.bstop - r.stop : r.start - r.bstart\n\t\t}\n\t\tfor (let i = 0; i < ridx; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\t// FIXME include/exclude regulatory region?\n\t\t\t/*\n\t\tif(this.usegm && r.chr!=this.usegm.chr) {\n\t\t\tcontinue\n\t\t}\n\t\t*/\n\t\t\tc += r.bstop - r.bstart\n\t\t}\n\t\treturn c\n\t}\n\n\tblocksetw() {\n\t\t// call when any of the width has been udpated\n\n\t\tconst width =\n\t\t\tthis.leftheadw +\n\t\t\tthis.lpad +\n\t\t\tthis.width +\n\t\t\tthis.subpanels.reduce((i, j) => i + j.width + j.leftpad, 0) +\n\t\t\tthis.rpad +\n\t\t\tthis.rightheadw\n\n\t\tthis.svg.attr('width', width)\n\n\t\tthis.coord.gcoordsubpanels.transition().attr('transform', 'translate(' + this.width + ',0)')\n\t\tlet x = 0\n\t\tfor (const p of this.subpanels) {\n\t\t\t// coord ruler of each sub panel\n\t\t\tp.coord.g0.transition().attr('transform', 'translate(' + (x + p.leftpad) + ',0)') // shift the immobile ruler holder to correct position\n\t\t\tx += p.leftpad + p.width\n\t\t\tp.coord.grab.attr('width', p.width)\n\t\t\tp.subpanelbgrect.attr('width', p.width)\n\t\t}\n\n\t\tfor (const t of this.tklst) {\n\t\t\tif (t.hidden) continue\n\t\t\t// re position subpanel group holder for each track\n\t\t\tt.gtksubpanels.transition().attr('transform', 'translate(' + (this.leftheadw + this.lpad + this.width) + ',0)')\n\n\t\t\t// reposition each subpanel\n\t\t\tlet x = 0\n\t\t\tfor (const p of t.subpanels) {\n\t\t\t\tp.gtksubpanel.transition().attr('transform', 'translate(' + (x + p.leftpad) + ',0)')\n\t\t\t\tx += p.leftpad + p.width\n\t\t\t}\n\n\t\t\t// re position g right\n\t\t\tt.gright.transition().attr('transform', 'translate(' + (width - this.rightheadw) + ',0)')\n\t\t}\n\n\t\tif (this.resizewidthbutton) {\n\t\t\t// re position of drag-resize button\n\t\t\tthis.resizewidthbutton.style('right', this.rpad + this.rightheadw + 'px')\n\t\t}\n\t}\n\n\t/******* __ruler ****/\n\n\tupdateruler() {\n\t\t/*\n\tcall this when main block view range changes\n\tworks for genomic mode and gm modes\n\n\ton the block it's called coord not ruler\n\t*/\n\n\t\tthis.coord.g.attr('transform', 'translate(0,0)')\n\t\tthis.coord.grab.attr('width', this.width)\n\t\tthis.blocksetw()\n\n\t\tif (this.coord.input && this.startidx == this.stopidx) {\n\t\t\t// view range is inside single region\n\t\t\tconst r = this.rglst[this.startidx]\n\t\t\t// must show 1-based coord in <input>. this will allow to show exactly what user types in e.g. chr1:10000-20000 rather than 9999-19999\n\t\t\tthis.coord.input.property('value', `${r.chr}:${r.start + 1}-${r.stop + 1}`)\n\t\t\tthis.coordwidthsays.text(common.bplen(r.stop - r.start))\n\t\t}\n\n\t\t// reset view start/stop\n\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\tif (i != this.startidx) {\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tr.stop = r.bstop\n\t\t\t\t} else {\n\t\t\t\t\tr.start = r.bstart\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (i != this.stopidx) {\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tr.start = r.bstart\n\t\t\t\t} else {\n\t\t\t\t\tr.stop = r.bstop\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t/*\n\treset .exonsf, pixel per bp\n\texonlen will be used later\n\t*/\n\t\tlet exonlen = 0\n\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\texonlen += this.rglst[i].stop - this.rglst[i].start\n\t\t}\n\t\tthis.exonsf = (this.width - this.regionspace * (this.stopidx - this.startidx)) / exonlen\n\n\t\t// reset px width for regions in view range\n\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\tr.width = (r.stop - r.start) * this.exonsf\n\t\t}\n\n\t\tthis.update_ruler_height()\n\n\t\tthis.coord.grab.attr('height', this.coord.height)\n\t\tthis.coord.axesg.selectAll('*').remove()\n\n\t\tif (!this.gmmode || this.gmmode == client.gmmode.genomic) {\n\t\t\t/*\n\t\tin genomic mode\n\t\t*/\n\t\t\t{\n\t\t\t\tconst __g = this.coord.axesg.append('g').attr('transform', 'translate(0,0)')\n\t\t\t\tthis.region_makeruler(__g)\n\t\t\t}\n\t\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\t\tlet x = 0\n\t\t\t\tfor (let j = this.startidx; j < i; j++) {\n\t\t\t\t\tx += this.rglst[j].width + this.regionspace\n\t\t\t\t}\n\t\t\t\tconst r = this.rglst[i]\n\n\t\t\t\tif (r.stop - r.start <= r.width) {\n\t\t\t\t\tif (this.usegm && this.gmmode != client.gmmode.genomic) {\n\t\t\t\t\t\t// wont show sequence\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tconst __g = this.coord.axesg.append('g').attr('transform', 'translate(' + x + ',' + this.coordyp2 + ')')\n\t\t\t\t\tthis.getntsequence4ruler(r, __g)\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t/*\n\t\tnot in genomic mode\n\t\tstill a single ruler but for diferent coordinate (rna/protein)\n\t\t*/\n\t\t\tif (this.gmmode == client.gmmode.exononly || this.gmmode == client.gmmode.protein) {\n\t\t\t\t/*\n\t\t\tcontinuous scale\n\t\t\t*/\n\t\t\t\tconst rna = this.gmmode == client.gmmode.exononly\n\t\t\t\tif (!this.hidegenecontrol) {\n\t\t\t\t\tthis.coord.name.text(rna ? 'RNA bp len' : 'Protein length')\n\t\t\t\t}\n\t\t\t\tlet r = this.rglst[this.startidx]\n\t\t\t\tconst exoncumbp = this.regioncumlen(this.startidx)\n\t\t\t\tconst scale = scaleLinear()\n\t\t\t\t\t.domain(\n\t\t\t\t\t\trna\n\t\t\t\t\t\t\t? [exoncumbp, exoncumbp + exonlen]\n\t\t\t\t\t\t\t: [Math.floor(exoncumbp / 3) + 1, Math.floor((exoncumbp + exonlen) / 3) + 1]\n\t\t\t\t\t)\n\t\t\t\t\t.range([0, this.width])\n\t\t\t\tconst axis = axisTop().scale(scale).tickFormat(d3format('d'))\n\t\t\t\tconst __g = this.coord.axesg.append('g').attr('transform', 'translate(0,0)')\n\t\t\t\taxisstyle({\n\t\t\t\t\taxis: __g.call(axis),\n\t\t\t\t\tcolor: 'black',\n\t\t\t\t\tshowline: true\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\t/*\n\t\t\tjoined segments\n\t\t\t*/\n\t\t\t\tconst domain = [],\n\t\t\t\t\trange = []\n\t\t\t\tlet tickformat\n\t\t\t\tif (this.gmmode == client.gmmode.splicingrna) {\n\t\t\t\t\tif (!this.hidegenecontrol) {\n\t\t\t\t\t\tthis.coord.name.text('RNA bp len')\n\t\t\t\t\t}\n\t\t\t\t\tlet exonbp = this.regioncumlen(this.startidx)\n\t\t\t\t\tlet x = 0\n\t\t\t\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\t\t\t\tconst r = this.rglst[i]\n\t\t\t\t\t\tdomain.push(exonbp)\n\t\t\t\t\t\trange.push(x)\n\t\t\t\t\t\texonbp += r.stop - r.start\n\t\t\t\t\t\tdomain.push(exonbp)\n\t\t\t\t\t\trange.push(x + r.width)\n\t\t\t\t\t\tx += r.width + this.regionspace\n\t\t\t\t\t}\n\t\t\t\t\ttickformat = d3format(',d')\n\t\t\t\t} else if (this.gmmode == client.gmmode.gmsum) {\n\t\t\t\t\tif (!this.hidegenecontrol) {\n\t\t\t\t\t\tthis.coord.name.text('Genomic')\n\t\t\t\t\t}\n\t\t\t\t\tlet x = 0\n\t\t\t\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\t\t\t\tconst r = this.rglst[i]\n\t\t\t\t\t\tdomain.push(r.reverse ? r.stop : r.start)\n\t\t\t\t\t\trange.push(x)\n\t\t\t\t\t\tdomain.push(r.reverse ? r.start : r.stop)\n\t\t\t\t\t\trange.push(x + r.width)\n\t\t\t\t\t\tx += r.width + this.regionspace\n\t\t\t\t\t}\n\t\t\t\t\ttickformat = d3format(',d')\n\t\t\t\t} else {\n\t\t\t\t\tthis.error('unknown gmmode for making single ruler: ' + this.gmmode)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst scale = scaleLinear().domain(domain).range(range)\n\t\t\t\tconst axis = axisTop().scale(scale).tickFormat(tickformat)\n\t\t\t\tconst __g = this.coord.axesg.append('g').attr('transform', 'translate(0,0)')\n\t\t\t\taxisstyle({\n\t\t\t\t\taxis: __g.call(axis),\n\t\t\t\t\tcolor: 'black',\n\t\t\t\t\tshowline: true\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tconst noout = this.nozoomout()\n\t\tthis.ctrl.zobutt1.attr('disabled', noout ? 'true' : null)\n\t\tthis.ctrl.zobutt2.attr('disabled', noout ? 'true' : null)\n\t\tthis.ctrl.zobutt3.attr('disabled', noout ? 'true' : null)\n\t\tthis.ctrl.zinbutt.attr('disabled', this.exonsf >= ntpxwidth ? 1 : null)\n\t}\n\n\tupdate_ruler_height() {\n\t\t// set coord.height\n\t\tlet atbplevel = false // if main block or any sub panel is at bp level\n\t\tif (this.gmmode && this.gmmode != client.gmmode.genomic) {\n\t\t\t// showing protein, do not apply bplevel\n\t\t} else {\n\t\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\t\tconst r = this.rglst[i]\n\t\t\t\tif (r.stop - r.start <= r.width) atbplevel = true\n\t\t\t}\n\t\t}\n\t\tfor (const p of this.subpanels) {\n\t\t\tif (p.stop - p.start <= p.width) atbplevel = true\n\t\t}\n\n\t\tthis.coord.height = this.coordyp1 + this.rulerheight + this.coordyp2 + (atbplevel ? baseheight + 2 : 0)\n\t}\n\n\tasync getntsequence4ruler(r, g) {\n\t\tr.busy = true // assessed by ifbusy()\n\n\t\ttry {\n\t\t\tconst data = await dofetch3('ntseq', {\n\t\t\t\tmethod: 'POST',\n\t\t\t\tbody: JSON.stringify({\n\t\t\t\t\tgenome: this.genome.name,\n\t\t\t\t\tcoord: r.chr + ':' + (r.start + 1) + '-' + r.stop\n\t\t\t\t})\n\t\t\t})\n\t\t\tg.selectAll('*').remove()\n\t\t\tif (data.error) throw data.error\n\n\t\t\tconst basewidth = r.width / data.seq.length\n\t\t\t// tentative nt font size\n\t\t\tlet _fs = Math.min(this.rulerheight, basewidth / client.textlensf)\n\n\t\t\tif (_fs > 6) {\n\t\t\t\t// show nt\n\t\t\t\tfor (let i = 0; i < data.seq.length; i++) {\n\t\t\t\t\tlet nt = data.seq[r.reverse ? data.seq.length - 1 - i : i]\n\t\t\t\t\tif (r.reverse) {\n\t\t\t\t\t\tnt = common.basecompliment(nt)\n\t\t\t\t\t}\n\t\t\t\t\tg.append('text')\n\t\t\t\t\t\t.text(nt)\n\t\t\t\t\t\t.attr('font-family', 'Courier')\n\t\t\t\t\t\t.attr('font-size', _fs)\n\t\t\t\t\t\t.attr('dominant-baseline', 'hanging')\n\t\t\t\t\t\t.attr('x', basewidth * i + basewidth / 2) //+this.exonsf/2\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// no show nt\n\t\t\t\t_fs = 0\n\t\t\t}\n\t\t\tfor (let i = 0; i < data.seq.length; i++) {\n\t\t\t\tlet nt = data.seq[r.reverse ? data.seq.length - 1 - i : i]\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tnt = common.basecompliment(nt)\n\t\t\t\t}\n\t\t\t\tg.append('rect')\n\t\t\t\t\t.attr('x', i * basewidth)\n\t\t\t\t\t.attr('y', Math.min(baseheight - 2, _fs))\n\t\t\t\t\t.attr('width', basewidth)\n\t\t\t\t\t.attr('height', Math.max(2, baseheight - _fs))\n\t\t\t\t\t.attr('fill', common.basecolor[nt.toUpperCase()] || basecolorunknown)\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tg.append('text').text(e.message || e)\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t}\n\t\tr.busy = false\n\t\tthis.ifbusy()\n\t}\n\n\tnozoomout() {\n\t\tlet noout = false\n\t\tconst r1 = this.rglst[this.startidx],\n\t\t\tr2 = this.rglst[this.stopidx]\n\t\tif (this.startidx == 0 && this.stopidx == this.rglst.length - 1) {\n\t\t\tlet r1over = false,\n\t\t\t\tr2over = false\n\t\t\tconst r1 = this.rglst[this.startidx]\n\t\t\tif (r1.reverse ? r1.stop >= r1.bstop : r1.start <= r1.bstart) {\n\t\t\t\tconst r2 = this.rglst[this.stopidx]\n\t\t\t\tif (r2.reverse ? r2.start <= r2.bstart : r2.stop >= r2.bstop) {\n\t\t\t\t\tnoout = true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn noout\n\t}\n\n\tregion_makeruler(g) {\n\t\t/*\n\tgenomic only!\n\tassumed that the view range is in one continuous region\n\t*/\n\n\t\tif (this.usegm && this.gmmode != client.gmmode.genomic) return\n\t\tconst rulerg = g.append('g')\n\t\tif (!this.hidegenecontrol) {\n\t\t\tthis.coord.name.text('Genomic')\n\t\t}\n\t\t// genomic\n\t\t// but still can be multi-region so need to render ruler for each region\n\t\t// 0-based to 1-based\n\t\tconst domain = [],\n\t\t\trange = []\n\t\tlet x = 0\n\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\tconst r = this.rglst[i]\n\n\t\t\tif (r.reverse) {\n\t\t\t\tdomain.push(r.stop)\n\t\t\t\tdomain.push(r.start + 1) // this adjustment is needed for showing rulers for reversed and non-reversed regions\n\t\t\t} else {\n\t\t\t\tdomain.push(r.start + 1)\n\t\t\t\tdomain.push(r.stop)\n\t\t\t}\n\n\t\t\trange.push(x + this.exonsf / 2) // ADJUST shift half nt px width to right\n\n\t\t\trange.push(x + r.width - this.exonsf / 2) // ADJUST shift half nt px width to left: critical for ruler to appear good when in bp resolution\n\n\t\t\tx += r.width + this.exonsf / 2\n\t\t}\n\n\t\t// measure coordinate text width to decide how many ticks to use\n\t\tlet maxticknumber\n\t\t{\n\t\t\tconst pos = Math.max(this.rglst[this.startidx].stop, this.rglst[this.stopidx].stop)\n\t\t\tconst t = rulerg\n\t\t\t\t.append('text')\n\t\t\t\t.text(pos > 1000000 ? d3format('s')(pos) : d3format(',d')(pos))\n\t\t\t\t.attr('font-size', this.rulerfontsize)\n\t\t\tmaxticknumber = Math.floor(this.width / (t.node().getBBox().width + 60))\n\t\t\tt.remove()\n\t\t}\n\n\t\tconst r = this.rglst[this.startidx]\n\n\t\tconst scale = scaleLinear().domain(domain).range(range)\n\t\tconst axis = axisTop().scale(scale).tickSize(this.rulerticksize).ticks(maxticknumber)\n\n\t\tif (r.stop - r.start > 1000000) {\n\t\t\taxis.tickFormat(d3format('s'))\n\t\t} else {\n\t\t\taxis.tickFormat(d3format(',d'))\n\t\t}\n\t\taxisstyle({\n\t\t\taxis: rulerg.call(axis),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true,\n\t\t\tfontsize: this.rulerfontsize\n\t\t})\n\t}\n\n\trulermousedown(event, panel) {\n\t\t/*\n\tpane is either block, or a sub panel, will operate zoom-in on it\n\t*/\n\n\t\treturn new Promise((resolve, reject) => {\n\t\t\tif (panel.busy) reject('busy')\n\n\t\t\tpanel.busy = true\n\t\t\tpanel.pannedpx = undefined\n\t\t\tpanel.resized = false\n\n\t\t\tconst size = 1\n\n\t\t\tconst istoofine = w => {\n\t\t\t\treturn w / panel.exonsf < panel.width / ntpxwidth\n\t\t\t}\n\t\t\tconst color = istoofine(size) ? '#ccc' : '#ff6633'\n\t\t\tconst body = d3select(document.body)\n\n\t\t\tconst svg = body\n\t\t\t\t.append('svg')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('z-index', rulergrabzindex)\n\t\t\tconst rect = svg.append('rect').attr('fill', color).attr('fill-opacity', 0.2).attr('stroke', color)\n\t\t\tconst text0 = svg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('font-size', '18px')\n\t\t\t\t.attr('fill', 'none')\n\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t.attr('stroke-width', 3)\n\t\t\tconst text = svg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('font-size', 18)\n\t\t\t\t.attr('fill', 'black')\n\n\t\t\tconst printwidth = w => {\n\t\t\t\tif (w <= 0) {\n\t\t\t\t\ttext.text('')\n\t\t\t\t\ttext0.text('')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst bpc = Math.ceil(w / panel.exonsf)\n\t\t\t\tconst t = d3format('.2s')(panel.gmmode == client.gmmode.protein ? Math.ceil(bpc / 3) : bpc)\n\t\t\t\ttext0.text(t)\n\t\t\t\ttext.text(t)\n\t\t\t}\n\n\t\t\t// not rotated\n\t\t\tlet xleft, ytop, blockheight, x0\n\t\t\t// rotated\n\t\t\tlet r_xleft, r_ytop, y0\n\n\t\t\tif (panel.rotated) {\n\t\t\t\tconst tmp = panel.coord.g0.node().getBoundingClientRect()\n\t\t\t\tr_xleft = tmp.left\n\t\t\t\tr_ytop = event.target.getBoundingClientRect().top\n\t\t\t\tblockheight = this.totalheight()\n\t\t\t\ty0 = event.clientY\n\t\t\t} else {\n\t\t\t\txleft = event.target.getBoundingClientRect().left\n\t\t\t\tconst tmp = panel.coord.g0.node().getBoundingClientRect()\n\t\t\t\tytop = tmp.top\n\t\t\t\tblockheight = this.totalheight()\n\t\t\t\tx0 = event.clientX\n\t\t\t}\n\n\t\t\tif (panel.rotated) {\n\t\t\t\tsvg\n\t\t\t\t\t.attr('width', blockheight)\n\t\t\t\t\t.attr('height', size)\n\t\t\t\t\t.style('left', window.pageXOffset + r_xleft + 'px')\n\t\t\t\t\t.style('top', window.pageYOffset + y0 + 'px')\n\t\t\t\trect.attr('width', blockheight).attr('height', size)\n\t\t\t\ttext0.attr('y', 0).attr('x', blockheight / 2)\n\t\t\t\ttext.attr('y', 0).attr('x', blockheight / 2)\n\t\t\t} else {\n\t\t\t\tsvg\n\t\t\t\t\t.attr('width', size)\n\t\t\t\t\t.attr('height', blockheight)\n\t\t\t\t\t.style('left', window.pageXOffset + x0 + 'px')\n\t\t\t\t\t.style('top', window.pageYOffset + ytop + 'px')\n\t\t\t\trect.attr('width', size).attr('height', blockheight)\n\t\t\t\ttext0.attr('x', 0).attr('y', blockheight / 2)\n\t\t\t\ttext.attr('x', 0).attr('y', blockheight / 2)\n\t\t\t}\n\n\t\t\tbody\n\t\t\t\t.on('mousemove', event => {\n\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\tif (panel.rotated) {\n\t\t\t\t\t\tconst my = event.clientY\n\t\t\t\t\t\tlet h = 0\n\t\t\t\t\t\tif (my > y0) {\n\t\t\t\t\t\t\th = size + Math.min(r_ytop + panel.width, my) - y0\n\t\t\t\t\t\t} else if (my < y0) {\n\t\t\t\t\t\t\th = size + y0 - Math.max(r_ytop, my)\n\t\t\t\t\t\t\tsvg.style('top', window.pageYOffset + y0 + Math.max(r_ytop, my) - y0 + 'px')\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsvg.attr('height', h)\n\t\t\t\t\t\trect.attr('height', h)\n\t\t\t\t\t\tconst color = istoofine(h) ? '#ccc' : '#ff6633'\n\t\t\t\t\t\ttext0.attr('y', h / 2)\n\t\t\t\t\t\ttext.attr('y', h / 2)\n\t\t\t\t\t\trect.attr('fill', color).attr('stroke', color)\n\t\t\t\t\t\tprintwidth(h)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconst mx = event.clientX\n\t\t\t\t\t\tlet w = 0\n\t\t\t\t\t\tif (mx > x0) {\n\t\t\t\t\t\t\tw = size + Math.min(xleft + panel.width, mx) - x0\n\t\t\t\t\t\t} else if (mx < x0) {\n\t\t\t\t\t\t\tw = size + x0 - Math.max(xleft, mx)\n\t\t\t\t\t\t\tsvg.style('left', window.pageXOffset + x0 + Math.max(xleft, mx) - x0 + 'px')\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsvg.attr('width', w)\n\t\t\t\t\t\trect.attr('width', w)\n\t\t\t\t\t\tconst color = istoofine(w) ? '#ccc' : '#ff6633'\n\t\t\t\t\t\ttext0.attr('x', w / 2)\n\t\t\t\t\t\ttext.attr('x', w / 2)\n\t\t\t\t\t\trect.attr('fill', color).attr('stroke', color)\n\t\t\t\t\t\tprintwidth(w)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\t.on('mouseup', () => {\n\t\t\t\t\tlet startpx, // start and span in pixel, over the region to zoom into\n\t\t\t\t\t\tspanpx\n\n\t\t\t\t\tif (panel.rotated) {\n\t\t\t\t\t\tconst h = Number.parseInt(svg.attr('height'))\n\t\t\t\t\t\t/*\n\t\t\t\ttwo ways of rotation\n\t\t\t\tnose point up or down\n\t\t\t\tfor the moment it's pointing down only\n\t\t\t\tFIXME to support pointing up\n\t\t\t\t*/\n\t\t\t\t\t\tstartpx = panel.width - (h + Number.parseInt(svg.style('top')) - r_ytop - window.pageYOffset)\n\t\t\t\t\t\tspanpx = h\n\t\t\t\t\t} else {\n\t\t\t\t\t\tspanpx = Number.parseInt(svg.attr('width'))\n\t\t\t\t\t\tstartpx = Number.parseInt(svg.style('left')) - xleft - window.pageXOffset\n\t\t\t\t\t}\n\t\t\t\t\tsvg.remove()\n\t\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\n\t\t\t\t\tresolve([istoofine(spanpx), startpx, spanpx])\n\t\t\t\t})\n\t\t})\n\t}\n\n\t/******* __ruler ends ****/\n\n\thighlight_1basedcoordinate(s) {\n\t\tconst l = s.split(/[:-]/)\n\t\tif (l.length != 3) return\n\t\tconst start = Number.parseInt(l[1])\n\t\tconst stop = Number.parseInt(l[2])\n\t\tif (Number.isNaN(start) || Number.isNaN(stop)) {\n\t\t\treturn\n\t\t}\n\t\tthis.addhlregion(l[0], start - 1, stop - 1)\n\t}\n\n\taddhlregion(chr, start, stop, color) {\n\t\tconst t1 = this.seekcoord(chr, start)[0]\n\t\tif (!t1) {\n\t\t\treturn\n\t\t}\n\t\tconst t2 = this.seekcoord(chr, stop)[0]\n\t\tif (!t2) {\n\t\t\treturn\n\t\t}\n\n\t\tlet x1, x2\n\n\t\tif (t1.x > t2.x) {\n\t\t\t// region is reverse!!\n\t\t\tx1 = t2.x - this.exonsf / 2\n\t\t\tx2 = t1.x + this.exonsf / 2\n\t\t} else {\n\t\t\t// region is not reverse\n\t\t\tx1 = t1.x - this.exonsf / 2\n\t\t\tx2 = t2.x + this.exonsf / 2\n\t\t}\n\n\t\tconst hl = {\n\t\t\tchr: chr,\n\t\t\tstart: start,\n\t\t\tstop: stop,\n\t\t\tx: x1,\n\t\t\tcolor: color || hlregioncolor,\n\t\t\trect: this.hlregion.g\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', x1)\n\t\t\t\t.attr('y', 0)\n\t\t\t\t.attr('width', x2 - x1)\n\t\t\t\t.attr('fill', color || hlregioncolor)\n\t\t}\n\t\tthis.hlregion.lst.push(hl)\n\t\tthis.block_setheight()\n\t}\n\n\t/*\nreverseorient() {\n\tthis.coord.reverse=!this.coord.reverse\n\tthis.ctrl.revbutt.html(this.coord.reverse ? 'Reverse &laquo;' : 'Forward &raquo;')\n\tthis.block_coord_updated(false)\n}\n*/\n\n\tpxoff2region(px) {\n\t\t// genomic\n\t\tlet ridx = this.startidx\n\t\tlet r = this.rglst[ridx]\n\t\tif (px == 0) return [ridx, r.reverse ? r.stop : r.start]\n\t\t// starts from .startidx/begin\n\t\tconst px0 = px\n\t\tif (px > 0) {\n\t\t\t// to right\n\t\t\twhile (1) {\n\t\t\t\tif (ridx >= this.rglst.length) {\n\t\t\t\t\t//this.error('right seek error: '+px0)\n\t\t\t\t\tconst r = this.rglst[this.rglst.length - 1]\n\t\t\t\t\treturn [this.rglst.length - 1, r.reverse ? r.bstart : r.bstop]\n\t\t\t\t}\n\t\t\t\tconst r = this.rglst[ridx]\n\t\t\t\tlet availablepx\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tconst lookstart = ridx >= this.startidx && ridx <= this.stopidx ? r.stop : r.bstop\n\t\t\t\t\tavailablepx = (lookstart - r.bstart) * this.exonsf\n\t\t\t\t\tif (availablepx + this.regionspace >= px) {\n\t\t\t\t\t\treturn [ridx, lookstart - Math.floor(px / this.exonsf)]\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tconst lookstart = ridx >= this.startidx && ridx <= this.stopidx ? r.start : r.bstart\n\t\t\t\t\tavailablepx = (r.bstop - lookstart) * this.exonsf\n\t\t\t\t\tif (availablepx + this.regionspace >= px) {\n\t\t\t\t\t\treturn [ridx, lookstart + Math.floor(px / this.exonsf)]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tpx -= availablepx + this.regionspace\n\t\t\t\tridx++\n\t\t\t}\n\t\t}\n\t\t// to left\n\t\tpx = -px\n\t\t// first, chew .startidx\n\t\tr = this.rglst[this.startidx]\n\t\tif (r.reverse) {\n\t\t\tconst availablepx = (r.bstop - r.stop) * this.exonsf\n\t\t\tif (availablepx + this.regionspace >= px) {\n\t\t\t\treturn [ridx, r.stop + Math.floor(px / this.exonsf)]\n\t\t\t}\n\t\t} else {\n\t\t\tconst availablepx = (r.start - r.bstart) * this.exonsf\n\t\t\tif (availablepx + this.regionspace >= px) {\n\t\t\t\treturn [ridx, r.start - Math.floor(px / this.exonsf)]\n\t\t\t}\n\t\t}\n\t\t// keep chewing\n\t\tridx--\n\t\twhile (1) {\n\t\t\tif (ridx < 0) {\n\t\t\t\t//this.error('left seek error: '+px0)\n\t\t\t\tconst r = this.rglst[0]\n\t\t\t\treturn [0, r.reverse ? r.bstop : r.bstart]\n\t\t\t}\n\t\t\tconst r = this.rglst[ridx]\n\t\t\tconst availablepx = (r.bstop - r.bstart) * this.exonsf\n\t\t\tif (availablepx + this.regionspace >= px) {\n\t\t\t\tif (r.reverse) return [ridx, r.bstart + Math.floor(px / this.exonsf)]\n\t\t\t\treturn [ridx, r.bstop - Math.floor(px / this.exonsf)]\n\t\t\t}\n\t\t\tpx -= availablepx + this.regionspace\n\t\t\tridx--\n\t\t}\n\t}\n\n\tzoomblock(fold, zoomout) {\n\t\tif (this.busy) return\n\t\tthis.pannedpx = undefined\n\t\tthis.resized = false\n\t\tlet px1, px2\n\t\tif (zoomout) {\n\t\t\tthis.zoomedin = false\n\t\t\tconst span = Math.floor((this.width * (fold - 1)) / 2)\n\t\t\tpx1 = -span\n\t\t\tpx2 = this.width + span\n\t\t} else {\n\t\t\tthis.zoomedin = true\n\t\t\tconst span = Math.max((this.width / ntpxwidth) * this.exonsf, this.width / fold)\n\t\t\tpx1 = Math.floor(this.width / 2 - span / 2)\n\t\t\tpx2 = Math.floor(this.width / 2 + span / 2)\n\t\t}\n\t\tthis.zoom2px(px1, px2)\n\t}\n\n\tzoom2px(px1, px2) {\n\t\tconst [startidx, startpos] = this.pxoff2region(px1)\n\t\tconst [stopidx, stoppos] = this.pxoff2region(px2)\n\t\tthis.startidx = startidx\n\t\tthis.stopidx = stopidx\n\t\tconst r1 = this.rglst[startidx]\n\t\tif (r1.reverse) {\n\t\t\tr1.stop = startpos\n\t\t} else {\n\t\t\tr1.start = startpos\n\t\t}\n\t\tconst r2 = this.rglst[stopidx]\n\t\tif (r2.reverse) {\n\t\t\tr2.start = stoppos\n\t\t} else {\n\t\t\tr2.stop = stoppos\n\t\t}\n\t\tthis.block_coord_updated()\n\t}\n\n\tblock_coord_updated(panned) {\n\t\tthis.busy = true\n\t\tthis.updateruler()\n\t\tthis.tk_load_all()\n\t\tif (this.tklst.length == 0) {\n\t\t\tthis.busy = false\n\t\t}\n\n\t\t// reposition hl regions\n\t\tlet blockh = this.coord.height\n\t\tfor (const t of this.tklst) {\n\t\t\tif (t.hidden) continue\n\t\t\tblockh += t.height\n\t\t}\n\n\t\tfor (const hl of this.hlregion.lst) {\n\t\t\tconst hit1 = this.seekcoord(hl.chr, hl.start)[0]\n\t\t\tconst hit2 = this.seekcoord(hl.chr, hl.stop)[0]\n\t\t\tif (!hit1 || !hit2) {\n\t\t\t\thl.rect.attr('width', 0)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst startx = Math.min(hit1.x, hit2.x) - this.exonsf / 2\n\t\t\tconst stopx = Math.max(hit1.x, hit2.x) + this.exonsf / 2\n\t\t\tif (startx >= this.width || stopx <= 0) {\n\t\t\t\thl.rect.attr('width', 0)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\thl.x = startx\n\t\t\thl.rect\n\t\t\t\t.attr('x', Math.max(0, startx))\n\t\t\t\t.attr('width', Math.max(2, Math.min(this.width, stopx) - Math.max(0, startx)))\n\t\t\t\t.attr('height', blockh)\n\t\t}\n\t\tif (this.onCoordinateChange) {\n\t\t\tthis.onCoordinateChange(this.rglst)\n\t\t}\n\t}\n\n\tasync jump_1basedcoordinate(s) {\n\t\t/*\n\tif input is coord string, should be 1-based!!\n\talso supports gene name and rsname\n\t*/\n\t\tif (this.busy) return\n\t\tthis.zoomedin = false\n\t\tthis.pannedpx = undefined\n\t\tthis.resized = false\n\n\t\tif (typeof s == 'string') {\n\t\t\tconst pos = coord.string2pos(s, this.genome)\n\t\t\tif (pos) {\n\t\t\t\tthis.rglst = [\n\t\t\t\t\t{\n\t\t\t\t\t\tchr: pos.chr,\n\t\t\t\t\t\tbstart: 0,\n\t\t\t\t\t\tbstop: pos.chrlen,\n\t\t\t\t\t\tstart: Math.max(0, pos.start - 1),\n\t\t\t\t\t\tstop: pos.stop - 1,\n\t\t\t\t\t\treverse: this.showreverse\n\t\t\t\t\t}\n\t\t\t\t]\n\n\t\t\t\tif (pos.actualposition && pos.actualposition.len <= 40) {\n\t\t\t\t\tthis.addhlregion(\n\t\t\t\t\t\tpos.chr,\n\t\t\t\t\t\tpos.actualposition.position - 1,\n\t\t\t\t\t\tpos.actualposition.position - 1 + pos.actualposition.len - 1\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tthis.startidx = this.stopidx = 0\n\t\t\t\tthis.block_coord_updated()\n\t\t\t\treturn\n\t\t\t}\n\t\t} else if (typeof s == 'object' && s.chr && Number.isInteger(s.start)) {\n\t\t\t// quick fix to avoid calling string2pos and zoom out to 400bp\n\t\t\tconst _chr = this.genome.chrlookup[s.chr.toUpperCase()]\n\t\t\tif (_chr) {\n\t\t\t\tlet start = s.start,\n\t\t\t\t\tstop = Number.isInteger(s.stop) ? s.stop : s.start\n\t\t\t\tconst actualstart = start,\n\t\t\t\t\tactualstop = stop\n\t\t\t\tconst minspan = Math.ceil(this.width / ntpxwidth) //200\n\t\t\t\tif (stop - start < minspan) {\n\t\t\t\t\tconst h = Math.ceil(minspan / 2)\n\t\t\t\t\tconst m = Math.floor((start + stop) / 2)\n\t\t\t\t\tstart = m - h\n\t\t\t\t\tstop = m + h\n\t\t\t\t}\n\t\t\t\tthis.rglst = [\n\t\t\t\t\t{\n\t\t\t\t\t\tchr: _chr.name,\n\t\t\t\t\t\tbstart: 0,\n\t\t\t\t\t\tbstop: _chr.len,\n\t\t\t\t\t\tstart: start - 1,\n\t\t\t\t\t\tstop: stop - 1,\n\t\t\t\t\t\treverse: this.showreverse\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t\tthis.startidx = this.stopidx = 0\n\t\t\t\tif (actualstop - actualstart < 40) {\n\t\t\t\t\tthis.addhlregion(s.chr, actualstart - 1, actualstop - 1)\n\t\t\t\t}\n\t\t\t\tthis.block_coord_updated()\n\t\t\t\treturn\n\t\t\t} else {\n\t\t\t\tthis.error('Invalid chr: ' + s.chr)\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\t\t// try\n\t\tawait this.block_jump_gene(s)\n\t}\n\n\tasync block_jump_gene(s) {\n\t\ttry {\n\t\t\tconst data = await dofetch3('genelookup', {\n\t\t\t\tbody: { genome: this.genome.name, input: s, deep: 1 }\n\t\t\t})\n\t\t\tif (data.error) throw data.error\n\t\t\tif (!data.gmlst || data.gmlst.length == 0) {\n\t\t\t\t// no gene match\n\t\t\t\tif (this.genome.hasSNP) {\n\t\t\t\t\tif (s.toLowerCase().startsWith('rs')) {\n\t\t\t\t\t\t// looks like a snp\n\t\t\t\t\t\tthis.block_jump_snp(s)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.inputerr('Not a gene or SNP: ' + s)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tthis.inputerr('Unknown gene name: ' + s)\n\t\t\t\t}\n\t\t\t\treturn\n\t\t\t}\n\t\t\t// \"s\" matches with a gene name\n\n\t\t\t// quick fix: update valid gene name to pgv\n\t\t\tfor (const t of this.tklst) {\n\t\t\t\tif (t.type == client.tkt.pgv) {\n\t\t\t\t\tt.genename = s\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// aggregate loci for all isoforms from data.gmlst[]\n\t\t\tconst locs = client.gmlst2loci(data.gmlst)\n\n\t\t\tif (locs.length == 1) {\n\t\t\t\t// all isoforms are on the same locus\n\t\t\t\tconst r = locs[0]\n\t\t\t\tconst e = coord.invalidcoord(this.genome, r.chr, r.start, r.stop)\n\t\t\t\tif (e) {\n\t\t\t\t\tthis.inputerr('this should not happen: gene error: ' + e)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.rglst = [\n\t\t\t\t\t{\n\t\t\t\t\t\tchr: r.chr,\n\t\t\t\t\t\tbstart: 0,\n\t\t\t\t\t\tbstop: this.genome.chrlookup[r.chr.toUpperCase()].len,\n\t\t\t\t\t\tstart: r.start,\n\t\t\t\t\t\tstop: r.stop,\n\t\t\t\t\t\treverse: this.showreverse\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t\tthis.startidx = this.stopidx = 0\n\t\t\t\tthis.block_coord_updated()\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// isoforms are spread out on multiple locations\n\t\t\tthis.coord.inputtipshow()\n\t\t\tfor (const r of locs) {\n\t\t\t\tthis.coord.inputtip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.text(r.name + ' ' + r.chr + ':' + r.start + '-' + r.stop)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.coord.inputtip.hide()\n\t\t\t\t\t\tthis.rglst = [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tchr: r.chr,\n\t\t\t\t\t\t\t\tbstart: 0,\n\t\t\t\t\t\t\t\tbstop: this.genome.chrlookup[r.chr.toUpperCase()].len,\n\t\t\t\t\t\t\t\tstart: r.start,\n\t\t\t\t\t\t\t\tstop: r.stop,\n\t\t\t\t\t\t\t\treverse: this.showreverse\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t\tthis.startidx = this.stopidx = 0\n\t\t\t\t\t\tthis.block_coord_updated()\n\t\t\t\t\t})\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthis.inputerr(e.message || e)\n\t\t}\n\t}\n\n\tblock_jump_snp(s) {\n\t\tstring2snp(this.genome, s)\n\t\t\t.then(r => {\n\t\t\t\tconst span = Math.ceil(this.width / ntpxwidth)\n\t\t\t\tthis.rglst = [\n\t\t\t\t\t{\n\t\t\t\t\t\tchr: r.chr,\n\t\t\t\t\t\tbstart: 0,\n\t\t\t\t\t\tbstop: this.genome.chrlookup[r.chr.toUpperCase()].len,\n\t\t\t\t\t\tstart: Math.max(0, r.start - Math.ceil(span / 2)),\n\t\t\t\t\t\tstop: r.start + span,\n\t\t\t\t\t\treverse: this.showreverse\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t\tthis.startidx = this.stopidx = 0\n\t\t\t\tthis.addhlregion(r.chr, r.start, r.stop - 1)\n\t\t\t\tthis.block_coord_updated()\n\t\t\t})\n\t\t\t.catch(err => {\n\t\t\t\tthis.inputerr(s + ': not a gene or SNP')\n\t\t\t\tif (err.stack) console.log(err.stack)\n\t\t\t})\n\t}\n\n\tinputerr(msg) {\n\t\tthis.coord.inputtipshow()\n\t\tthis.coord.inputtip.d\n\t\t\t.append('div')\n\t\t\t// must not do .html(), msg is user-provided\n\t\t\t.text(msg)\n\t\t\t.style('border', 'solid 1px red')\n\t\t\t.style('padding', '10px 20px')\n\t}\n\n\tgenemenu() {\n\t\tfor (const tk of this.tklst) {\n\t\t\tif (tk.type == client.tkt.usegm) {\n\t\t\t\tif (tk.controller) {\n\t\t\t\t\t// hide gmtk controller\n\t\t\t\t\ttk.controller.paneoff()\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tconst gm = this.usegm\n\t\tif (!gm) {\n\t\t\tconsole.log('usegm missing!!')\n\t\t\treturn\n\t\t}\n\t\tthis.usegmtip.clear()\n\t\tconst menu = this.usegmtip.d\n\t\t// header\n\t\tconst sec1 = menu\n\t\t\t.append('div')\n\t\t\t.style('padding', '20px')\n\t\t\t.style('background-color', '#E6EEF5')\n\t\t\t.style('margin-bottom', '20px')\n\n\t\tconst description_div = sec1.append('div').style('width', '580px')\n\t\tif (!gm.description) {\n\t\t\tdescription_div.html(`${gm.name}: No description`)\n\t\t} else if (gm.description.length >= 120) {\n\t\t\t// Detect when the description is very long\n\t\t\tconst truncDescrip = gm.description.substring(0, 100)\n\t\t\tlet activeDesc = false\n\t\t\tdescription_div.html(`${gm.name}: <strong>${truncDescrip}</strong> ...`)\n\t\t\tconst a = sec1.append('a')\n\t\t\ta.text('Show More')\n\t\t\t\t// Add simple a tag. Should show and hide text on click\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tactiveDesc = !activeDesc\n\t\t\t\t\tdescription_div.html(\n\t\t\t\t\t\tactiveDesc == true\n\t\t\t\t\t\t\t? `${gm.name}: <strong>${gm.description}</strong>`\n\t\t\t\t\t\t\t: `${gm.name}: <strong>${truncDescrip}</strong> ...`\n\t\t\t\t\t)\n\t\t\t\t\ta.text(activeDesc == true ? 'Hide' : 'Show More')\n\t\t\t\t})\n\t\t} else {\n\t\t\tdescription_div.html(`${gm.name}: <strong>${gm.description}</strong>`)\n\t\t}\n\n\t\tconst p2 = sec1.append('div').style('margin-top', '10px')\n\n\t\tp2.append('span').text(gm.isoform).style('padding-right', '10px')\n\n\t\tp2.append('a')\n\t\t\t.attr('target', '_blank')\n\t\t\t.attr('href', 'https://www.ncbi.nlm.nih.gov/gene/?term=' + gm.isoform)\n\t\t\t.style('padding-right', '10px')\n\t\t\t.text('NCBI')\n\n\t\tp2.append('a')\n\t\t\t.attr('target', '_blank')\n\t\t\t.attr('href', 'https://genome.ucsc.edu/cgi-bin/hgTracks?db=' + this.genome.name + '&position=' + gm.isoform)\n\t\t\t.text('UCSC')\n\n\t\tp2.append('span')\n\t\t\t.style('padding-left', '30px')\n\t\t\t.html(\n\t\t\t\tgm.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\t(gm.start + 1) +\n\t\t\t\t\t'-' +\n\t\t\t\t\tgm.stop +\n\t\t\t\t\t'&nbsp;&nbsp;<span style=\"font-size:.7em\">' +\n\t\t\t\t\t(gm.strand == '+' ? 'FORWARD' : 'REVERSE') +\n\t\t\t\t\t'</span>' +\n\t\t\t\t\t'&nbsp;&nbsp;<span style=\"color:#555\">' +\n\t\t\t\t\tcommon.bplen(gm.stop - gm.start) +\n\t\t\t\t\t'</span>'\n\t\t\t)\n\t\tconst sec2 = menu.append('div').style('margin', '20px 30px 40px 30px')\n\t\tsec2\n\t\t\t.append('div')\n\t\t\t.text('Switch display')\n\t\t\t.style('font-size', '1.5em')\n\t\t\t.style('color', '#555')\n\t\t\t.style('margin-bottom', '20px')\n\t\tthis.showgmmode4switch(sec2, true)\n\t\t// sec 3\n\t\tif (this.allgm.length > 1) {\n\t\t\tconst sec3 = menu\n\t\t\t\t.append('div')\n\t\t\t\t//.style('background-color','#F5F5F0')\n\t\t\t\t.style('padding', '20px 30px 40px 30px')\n\t\t\tsec3\n\t\t\t\t.append('div')\n\t\t\t\t.style('color', '#555')\n\t\t\t\t.style('font-size', '1.5em')\n\t\t\t\t.style('margin-bottom', '20px')\n\t\t\t\t.text('Switch isoform')\n\t\t\tthis.showisoform4switch(sec3, true)\n\t\t}\n\t\tthis.usegmtip.showunder(this.ctrl.namebutt.node())\n\t}\n\n\told_dshandle_new(dsname) {\n\t\t// for old official dataset, and mds3\n\t\t// won't add handle for either children or custom datasets\n\t\tlet ds = this.genome.datasets[dsname]\n\t\tif (!ds) {\n\t\t\tds = this.ownds[dsname]\n\t\t}\n\t\tif (!ds) {\n\t\t\tthis.error('unknown dsname ' + dsname)\n\t\t\treturn\n\t\t}\n\t\tconst box = this.ctrl.dshandleholder.append('div').attr('class', 'sjpp-dshandleholder')\n\t\tconst says = box\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_opaque8 sjpp-dslabel')\n\t\t\t.text(ds.label)\n\t\t\t.on('click', async () => {\n\t\t\t\tthis.pannedpx = undefined // important!\n\t\t\t\tthis.resized = false\n\t\t\t\tlet tk = this.tklst.find(t => {\n\t\t\t\t\tif (ds.isMds3) {\n\t\t\t\t\t\tif (t.type == client.tkt.mds3 && t.mds && t.mds.label == ds.label) return t\n\t\t\t\t\t} else if (t.type == client.tkt.ds && t.ds && t.ds.label == ds.label) {\n\t\t\t\t\t\treturn t\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tif (tk) {\n\t\t\t\t\tif (tk.hidden) {\n\t\t\t\t\t\ttk.hidden = false\n\t\t\t\t\t\tthis.tk_load(tk)\n\t\t\t\t\t\t//says.style('background-color','#ddd').style('color','black')\n\t\t\t\t\t\tthis.setllabel() // must do it here, not called in tk_load\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.tk_hide(tk)\n\t\t\t\t\t\t//says.style('background-color','#999').style('color','white')\n\t\t\t\t\t}\n\t\t\t\t\tthis.tkchangeaffectlegend(tk)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (ds.busy) return\n\t\t\t\tif (ds.isMds3) {\n\t\t\t\t\ttk = this.block_addtk_template({ type: client.tkt.mds3, dslabel: ds.label })\n\t\t\t\t\tthis.tk_load(tk)\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\t// is legacy ds\n\t\t\t\tif (ds.legacyDsIsUninitiated) {\n\t\t\t\t\t/* only for legacy ds\n\t\t\t\t\tcan delete this step when migrated to mds3\n\t\t\t\t\t*/\n\t\t\t\t\tconst d = await dofetch3(`getDataset?genome=${this.genome.name}&dsname=${ds.label}`)\n\t\t\t\t\tif (d.error) throw 'invalid name'\n\t\t\t\t\tif (!d.ds) throw '.ds missing'\n\n\t\t\t\t\tObject.assign(ds, d.ds)\n\t\t\t\t\tconst _ = await import('./legacyDataset')\n\t\t\t\t\t_.validate_oldds(ds)\n\n\t\t\t\t\tdelete ds.legacyDsIsUninitiated\n\t\t\t\t}\n\n\t\t\t\ttk = this.block_addtk_template({ ds, type: client.tkt.ds })\n\t\t\t\tblockds.dstkload(tk, this)\n\t\t\t})\n\t\t\t.on('mouseover', event => {\n\t\t\t\tif (ds.iscustom) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!ds.dsinfo) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.blocktip\n\t\t\t\t\t.showunder(event.target)\n\t\t\t\t\t.clear()\n\t\t\t\t\t.d.append('div')\n\t\t\t\t\t.style('font-size', '80%')\n\t\t\t\t\t.style('padding', '10px')\n\t\t\t\t\t.style('color', '#858585')\n\t\t\t\t\t.attr('class', 'sja_clb')\n\t\t\t\t\t.text('ABOUT')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.blocktip.clear()\n\t\t\t\t\t\tclient.make_table_2col(this.blocktip.d, ds.dsinfo).style('padding', '10px')\n\t\t\t\t\t})\n\t\t\t})\n\t\tthis.ds2handle[dsname] = {\n\t\t\thandle: box,\n\t\t\thandlesays: says\n\t\t}\n\t}\n\n\tviewrangeabovelimit(span) {\n\t\tif (span == undefined) {\n\t\t\t// no upper limit was set\n\t\t\treturn false\n\t\t}\n\t\tlet len = 0\n\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\tlen += r.stop - r.start\n\t\t}\n\t\treturn len >= span\n\t}\n\n\tseekcoord(chr, pos) {\n\t\t/*\n\treturn px offset relative to view range start!!!\n\talso look at subpanels\n\n\tfind all hits\n\t*/\n\n\t\tpos += 0.5 // +.5 important!!!\n\n\t\tconst hits = []\n\t\tconst overgene = this.usegm && chr == this.usegm.chr && this.gmmode != client.gmmode.genomic\n\n\t\tfor (let i = 0; i < this.rglst.length; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\tif (r.chr != chr) continue\n\t\t\tif (pos >= r.bstart && pos < r.bstop) {\n\t\t\t\t// inside region\n\t\t\t\thits.push({\n\t\t\t\t\tridx: i,\n\t\t\t\t\tx:\n\t\t\t\t\t\t(this.regioncumlen(i, true) + (r.reverse ? r.bstop - pos : pos - r.bstart)) * this.exonsf +\n\t\t\t\t\t\ti * this.regionspace\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\t} else if (i > 0 && overgene) {\n\t\t\t\t// assuming that intron is always between regions\n\t\t\t\tconst r0 = this.rglst[i - 1]\n\t\t\t\tif (r0.chr != chr) continue\n\t\t\t\t// TODO need a way to exclude regulatory regions\n\t\t\t\t// assuming the same orientation of all exons\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tif (pos < r0.bstart && pos >= r.bstop) {\n\t\t\t\t\t\thits.push({\n\t\t\t\t\t\t\tridx: i,\n\t\t\t\t\t\t\tx: this.regioncumlen(i, true) * this.exonsf + i * this.regionspace - this.regionspace / 2\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} else {\n\t\t\t\t\tif (pos < r.bstart && pos >= r0.bstop) {\n\t\t\t\t\t\thits.push({\n\t\t\t\t\t\t\tridx: i,\n\t\t\t\t\t\t\tx: this.regioncumlen(i, true) * this.exonsf + i * this.regionspace - this.regionspace / 2\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}\n\t\t}\n\n\t\tif (hits.length == 0 && overgene) {\n\t\t\t// should be out of gene body range\n\t\t\t// cannot use just .usegm, maybe in gmsum\n\t\t\t// find out where gene body start/end in rglst\n\t\t\tlet startidx = null,\n\t\t\t\tstopidx = 0\n\t\t\tfor (let i = 0; i < this.rglst.length; i++) {\n\t\t\t\t// TODO exclude regulatory regions, appended regions\n\t\t\t\tif (startidx == null) {\n\t\t\t\t\tstartidx = i\n\t\t\t\t}\n\t\t\t\tstopidx = i\n\t\t\t}\n\t\t\tif (startidx == null) {\n\t\t\t\tconsole.error('seekcoord: null startidx')\n\t\t\t} else {\n\t\t\t\tconst r1 = this.rglst[startidx]\n\t\t\t\tconst r2 = this.rglst[stopidx]\n\t\t\t\tif (this.usegm.strand == '+') {\n\t\t\t\t\tif (pos < r1.bstart) {\n\t\t\t\t\t\thits.push({\n\t\t\t\t\t\t\tridx: startidx,\n\t\t\t\t\t\t\tx: this.regioncumlen(startidx, true) * this.exonsf + startidx * this.regionspace\n\t\t\t\t\t\t})\n\t\t\t\t\t} else if (pos >= r2.bstop) {\n\t\t\t\t\t\thits.push({\n\t\t\t\t\t\t\tridx: stopidx,\n\t\t\t\t\t\t\tx: this.exonsf * (this.regioncumlen(stopidx, true) + r2.bstop - r2.bstart) + stopidx * this.regionspace\n\t\t\t\t\t\t})\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconsole.error(chr + ':' + pos + ' not mapped to gene')\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tif (pos < r2.bstart) {\n\t\t\t\t\t\thits.push({\n\t\t\t\t\t\t\tridx: stopidx,\n\t\t\t\t\t\t\tx: this.exonsf * (this.regioncumlen(stopidx, true) + r2.bstop - r2.bstart) + stopidx * this.regionspace\n\t\t\t\t\t\t})\n\t\t\t\t\t} else if (pos >= r1.bstop) {\n\t\t\t\t\t\thits.push({\n\t\t\t\t\t\t\tridx: startidx,\n\t\t\t\t\t\t\tx: this.regioncumlen(startidx, true) * this.exonsf + startidx * this.regionspace\n\t\t\t\t\t\t})\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconsole.error(chr + ':' + pos + ' not mapped to gene')\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst reduct = this.regioncumlen(this.startidx) * this.exonsf + this.startidx * this.regionspace\n\t\tfor (const h of hits) {\n\t\t\th.x -= reduct\n\t\t}\n\n\t\tif (this.subpanels.length) {\n\t\t\t// also search sub panels\n\t\t\tlet x = this.width\n\t\t\tfor (const [idx, r] of this.subpanels.entries()) {\n\t\t\t\tx += r.leftpad\n\t\t\t\tif (chr == r.chr && pos >= r.start && pos <= r.stop) {\n\t\t\t\t\thits.push({\n\t\t\t\t\t\tsubpanelidx: idx,\n\t\t\t\t\t\tx: x + r.exonsf * (pos - r.start)\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tx += r.width\n\t\t\t}\n\t\t}\n\n\t\treturn hits\n\t}\n\n\t/*\nseekrange(chr,start,stop) {\n\t// not in use\n\tlet startpx=-1,\n\t\tstoppx=-1\n\tfor(let i=this.startidx; i<=this.stopidx; i++) {\n\t\tconst r=this.rglst[i]\n\t\tif(r.chr!=chr) continue\n\t\tconst start0=Math.max(start,r.start)\n\t\tconst stop0 =Math.min(stop,r.stop)\n\t\tif(start0 < stop0) {\n\t\t\tconst bp=this.regioncumlen(i)\n\t\t\tif(startpx==-1) {\n\t\t\t\tstartpx=(bp+(r.reverse ? r.stop-stop0 : start0-r.start))*this.exonsf+i*this.regionspace\n\t\t\t}\n\t\t\tstoppx=(bp+(r.reverse ? r.stop-start0 : stop0-r.start))*this.exonsf+i*this.regionspace\n\t\t}\n\t}\n\treturn [startpx,stoppx]\n}\n*/\n\n\t/** __tk__ **/\n\n\tsetllabel() {\n\t\t// from left labels of all tracks, derive .leftheadw\n\t\t// then set width of leftlabshade1/2 of all left labels\n\t\tlet w = 10\n\t\tfor (const tk of this.tklst) {\n\t\t\tif (tk.hidden) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tw = Math.max(w, 100, tk.leftLabelMaxwidth + 20)\n\t\t}\n\t\tthis.leftheadw = w\n\t\tthis.hlregion.g.transition().attr('transform', 'translate(' + (this.leftheadw + this.lpad) + ',0)')\n\t\tthis.coord.g0\n\t\t\t.transition()\n\t\t\t.attr('transform', 'translate(' + (this.leftheadw + this.lpad) + ',' + (this.coordyp1 + this.rulerheight) + ')')\n\n\t\tconst entirewidth =\n\t\t\tthis.leftheadw + this.lpad + this.width + this.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0) + this.rpad\n\n\t\tfor (const tk of this.tklst) {\n\t\t\ttk.gleft.transition().attr('transform', 'translate(' + this.leftheadw + ',0)')\n\t\t\ttk.gmiddle.transition().attr('transform', 'translate(' + (this.leftheadw + this.lpad) + ',0)')\n\t\t\ttk.gright.transition().attr('transform', 'translate(' + entirewidth + ',0)')\n\t\t}\n\t\tthis.blocksetw()\n\t}\n\n\ttk_remove(i) {\n\t\tconst oldt = this.tklst[i]\n\t\tif (oldt.type == client.tkt.ds && oldt.ds && oldt.ds.iscustom) {\n\t\t\t// is a custom dstk, as the child from a official dstk\n\t\t\tdelete this.genome.datasets[oldt.ds.label]\n\t\t\tconst ds = this.ownds[oldt.ds.label]\n\t\t\tif (ds) {\n\t\t\t\t// registered in this.ownds{}\n\t\t\t\tdelete this.ownds[ds.label]\n\t\t\t\tif (ds.parentname) {\n\t\t\t\t\t// decrement children count in parent ds handle\n\t\t\t\t\tconst parenthandle = this.ds2handle[ds.parentname]\n\t\t\t\t\tif (parenthandle && parenthandle.childicon) {\n\t\t\t\t\t\tconst count = Number.parseInt(parenthandle.childicon.text())\n\t\t\t\t\t\tif (count == 1) {\n\t\t\t\t\t\t\tparenthandle.childicon.remove()\n\t\t\t\t\t\t\tdelete parenthandle.childicon\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tparenthandle.childicon.text(count - 1)\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.tklst[i].g.remove()\n\t\tthis.tklst.splice(i, 1)\n\t\tthis.setllabel()\n\t\tthis.block_setheight()\n\t\tif (oldt.type == client.tkt.ds) {\n\t\t\tconst dshandle = this.ds2handle[oldt.name]\n\t\t\tif (dshandle) {\n\t\t\t\tdshandle.handlesays.style('background-color', 'white').style('color', 'black')\n\t\t\t}\n\t\t\tif (oldt.eplst) {\n\t\t\t\tfor (const ep of oldt.eplst) {\n\t\t\t\t\tif (ep.handle) {\n\t\t\t\t\t\tep.handle.remove()\n\t\t\t\t\t}\n\t\t\t\t\tif (ep.pane) {\n\t\t\t\t\t\tep.pane.pane.remove()\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (oldt.tr_legend) {\n\t\t\tdisappear(oldt.tr_legend, true)\n\t\t}\n\t\tif (this.onAddRemoveTk) this.onAddRemoveTk(oldt) // lack of 2nd arg for removing\n\t}\n\n\tdeletecustomdsbyname(dsname) {\n\t\t// this should not be in genome.datasets\n\t\tfor (let i = 0; i < this.tklst.length; i++) {\n\t\t\tconst t = this.tklst[i]\n\t\t\tif (t.type == client.tkt.ds && t.ds.label == dsname) {\n\t\t\t\tthis.tk_remove(i)\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t}\n\n\taddchilddsnoload(childds) {\n\t\tconst paname = childds.parentname\n\t\tconst parenthandle = this.ds2handle[paname]\n\t\tif (parenthandle) {\n\t\t\tconst d = parenthandle.childicon\n\t\t\tif (d) {\n\t\t\t\td.text(Number.parseInt(d.text()) + 1)\n\t\t\t} else {\n\t\t\t\t// create new icon\n\t\t\t\tparenthandle.childicon = parenthandle.handle\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('margin-left', '1px')\n\t\t\t\t\t.style('padding', '2px 5px')\n\t\t\t\t\t.style('background-color', '#ccc')\n\t\t\t\t\t.classed('sja_opaque8', true)\n\t\t\t\t\t.text(1)\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tconst div = this.tip.clear().showunder(event.target).d.append('div').style('padding', '20px')\n\t\t\t\t\t\tdiv\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.text('Click to remove')\n\t\t\t\t\t\t\t.style('font-size', '.9em')\n\t\t\t\t\t\t\t.style('color', '#858585')\n\t\t\t\t\t\t\t.style('margin-bottom', '10px')\n\t\t\t\t\t\tfor (const tk of this.tklst) {\n\t\t\t\t\t\t\tif (!tk.ds || tk.ds.parentname != paname) continue\n\t\t\t\t\t\t\tconst row = div.append('div').classed('sja_menuoption', true).text(tk.ds.label)\n\t\t\t\t\t\t\trow.on('click', () => {\n\t\t\t\t\t\t\t\trow.remove()\n\t\t\t\t\t\t\t\tthis.deletecustomdsbyname(tk.ds.label)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tthis.ownds[childds.label] = childds\n\t}\n\n\tblock_addtk_template(template) {\n\t\t/*\n\tthis: init attributes\n\tcalls: block_maketk() to make dom/svg\n\tdo not load tk yet\n\t*/\n\t\tconst tk = {\n\t\t\theight_main: 25,\n\t\t\theight: 30,\n\t\t\t// template.tkid will override\n\t\t\ttkid: Math.random().toString(),\n\t\t\ttoppad: 5,\n\t\t\tbottompad: 5,\n\t\t\tyoff: 0,\n\t\t\taxisfontsize: 12,\n\t\t\tbusy: false,\n\t\t\tleftLabelMaxwidth: 0,\n\t\t\trightheadw_tk: this.rightheadw,\n\t\t\tsubpanels: [] // to keep in sync with block.subpanels\n\t\t}\n\t\tfor (const k in template) {\n\t\t\ttk[k] = template[k]\n\t\t}\n\n\t\tswitch (template.type) {\n\t\t\tcase client.tkt.bampile:\n\t\t\t\tbampilefromtemplate(tk, template)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ds:\n\t\t\t\tif (!tk.ds) {\n\t\t\t\t\tthis.error('dstk template missing .ds')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!tk.ds.label) {\n\t\t\t\t\tthis.error('dstk template missing .ds.label')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.name = tk.ds.label\n\t\t\t\t/*\n\t\ttell blockds.load2tk to insert it into .tklst and then remove this trigger\n\t\tso subsequent data request won't do the .tklst insert\n\t\t*/\n\t\t\t\ttk.dsuninitiated = true\n\t\t\t\tbreak\n\t\t\tcase client.tkt.pgv:\n\t\t\t\tconst e1 = pgvfromtemplate(tk, template)\n\t\t\t\tif (e1) {\n\t\t\t\t\tthis.error(e1)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ld:\n\t\t\t\tconst e14 = ldfromtemplate(tk, template)\n\t\t\t\tif (e14) {\n\t\t\t\t\tthis.error(e14)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bam:\n\t\t\t\tconst e12 = bamfromtemplate(tk, template)\n\t\t\t\tif (e12) {\n\t\t\t\t\tthis.error(e12)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.usegm:\n\t\t\t\tgmtkfromtemplate(tk)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bedj:\n\t\t\t\tconst e2 = bedjfromtemplate(tk, template)\n\t\t\t\tif (e2) {\n\t\t\t\t\tthis.error(e2)\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.junction:\n\t\t\t\tconst e3 = junctionfromtemplate(tk, template)\n\t\t\t\tif (e3) {\n\t\t\t\t\tthis.error(e3)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t/*\n\tcase client.tkt.ai:\n\t\ttk.covermax=tk.readdepthcutoff\n\t\tdelete tk.readdepthcutoff\n\t\tconst h=Math.max(60,(document.body.clientHeight-200)/12)\n\t\ttk.rowheight=Math.ceil(h)\n\t\ttk.barheight=Math.ceil(h/2)\n\t\ttk.rowspace=5\n\t\ttk.uninit=true\n\t\tbreak\n\t*/\n\t\t\tcase client.tkt.aicheck:\n\t\t\t\taicheckfromtemplate(tk, template)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bigwig:\n\t\t\t\tbigwigfromtemplate(tk, template)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bigwigstranded:\n\t\t\t\tbigwigstrandedfromtemplate(tk, template)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bam:\n\t\t\t\ttk.stackheight = tk.stackheight || 10\n\t\t\t\ttk.barheight = tk.barheight || 80\n\t\t\t\ttk.fcolor = tk.fcolor || '#005EBD'\n\t\t\t\ttk.rcolor = tk.rcolor || '#D66B00'\n\t\t\t\ttk.mmcolor = tk.mmcolor || '#FF3D3D'\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdsjunction:\n\t\t\t\tconst e6 = mdsjunctionfromtemplate(tk, template)\n\t\t\t\tif (e6) {\n\t\t\t\t\tthis.error(e6)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdssvcnv:\n\t\t\t\tconst e7 = mdssvcnvfromtemplate(tk, template)\n\t\t\t\tif (e7) {\n\t\t\t\t\tthis.error(e7)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mds3:\n\t\t\t\tconst e13 = mds3_fromtemplate(tk, template)\n\t\t\t\tif (e13) {\n\t\t\t\t\tthis.error(e13)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bedgraphdot:\n\t\t\t\tconst e11 = bedgraphdot_fromtemplate(tk, template)\n\t\t\t\tif (e11) {\n\t\t\t\t\tthis.error(e11)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdsexpressionrank:\n\t\t\t\tconst e8 = mdsexpressionrankfromtemplate(tk, template, this)\n\t\t\t\tif (e8) {\n\t\t\t\t\tthis.error(e8)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.hicstraw:\n\t\t\t\tconst e4 = hicstrawfromtemplate(tk, template)\n\t\t\t\tif (e4) {\n\t\t\t\t\tthis.error(e4)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ase:\n\t\t\t\tconst e9 = asefromtemplate(tk, template)\n\t\t\t\tif (e9) {\n\t\t\t\t\tthis.error(e9)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tthis.error('addtk: unknown template tk type ' + template.type)\n\t\t}\n\n\t\t// upon breaking error, quit and do not add this track\n\t\tthis.tklst.push(tk)\n\n\t\tthis.block_maketk(tk)\n\t\tthis.blocksetw()\n\t\treturn tk\n\t}\n\n\tblock_maketk(tk) {\n\t\t// keep separate from addtk()\n\t\t// call each time to show a tk in .tklst\n\t\ttk.tktip = new Menu({ padding: '15px' })\n\t\ttk.tkconfigtip = new Menu({ padding: '15px' })\n\n\t\ttk.g = this.gbase.append('g').attr('data-testid', 'sja_sample_menu_opener').attr('transform', 'translate(0,0)')\n\t\t/*\n\torder of precedence:\n\tgtksubpanels < gmiddle < gleft and gright\n\tso that right-open axis in gleft can not be blocked by gmiddle\n\t*/\n\n\t\t/*\n\tholder for all subpanels\n\tmust not append to gmiddle, since gmiddle catches mousedown for panning the main panel, and subpanel must pan independently\n\t*/\n\t\ttk.gtksubpanels = tk.g.append('g')\n\n\t\ttk.gmiddle = tk.g.append('g').attr('transform', 'translate(' + (this.leftheadw + this.lpad) + ',0)')\n\n\t\ttk.tkbodybgrect = tk.gmiddle.append('rect').attr('fill', 'white').attr('fill-opacity', 0)\n\n\t\ttk.glider = tk.gmiddle.append('g').attr('transform', 'translate(0,0)').style('cursor', 'default')\n\n\t\ttk.gleft = tk.g.append('g').attr('transform', 'translate(' + this.leftheadw + ',0)')\n\t\ttk.gright = tk.g\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(' + (this.leftheadw + this.lpad + this.width + this.rpad) + ',0)')\n\n\t\ttk.tklabel = this.maketklefthandle(tk).attr('class', null).attr('font-weight', 'bold')\n\n\t\t// tk name may be available now or will be defined later\n\t\tif (tk.name) {\n\t\t\t// two conditions to show tooltip on hovering the label\n\t\t\t// 1. label truncated, hover to show full label\n\t\t\t// 2. list_description[{k,v}] provided:\n\t\t\t// a.hover to show table of details\n\t\t\t// b. click label to show and leave table of details\n\t\t\tconst labeltruncated = tk.name.length >= 25\n\t\t\tif (labeltruncated) {\n\t\t\t\t// to truncate name and also apply tooltip\n\t\t\t\ttk.tklabel.text(tk.name.substring(0, 20) + ' ...')\n\t\t\t} else {\n\t\t\t\t// no need to truncate label\n\t\t\t\ttk.tklabel.text(tk.name)\n\t\t\t}\n\t\t\tif (labeltruncated || tk.list_description) {\n\t\t\t\t// will show tooltip to display both info if available\n\n\t\t\t\t// detects if tooltip is in use or not\n\t\t\t\tlet tktip_active = false\n\t\t\t\ttk.tktip.onHide = () => {\n\t\t\t\t\ttktip_active = false\n\t\t\t\t}\n\t\t\t\ttk.tklabel.on('mouseover', event => {\n\t\t\t\t\t// Only fires if menu not active from click event\n\t\t\t\t\tif (tktip_active == true) return\n\t\t\t\t\tshowTkLabelTooltip(event, tk, labeltruncated)\n\t\t\t\t\ttktip_active = false\n\t\t\t\t})\n\t\t\t\ttk.tklabel.on('mouseout', () => {\n\t\t\t\t\tif (tktip_active == true) return\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t})\n\t\t\t\ttk.tklabel.on('click', event => {\n\t\t\t\t\ttktip_active = !tktip_active\n\t\t\t\t\tif (tktip_active == true) {\n\t\t\t\t\t\tshowTkLabelTooltip(event, tk, labeltruncated)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t\t// tklabel content is set. initiate leftLabelMaxwidth with <text> width\n\t\t\t// this width may be overwritten (only by larger width) in individual tk maker scripts (adding sublabels or change tk.name ...)\n\t\t\t// when it's overwritten, must call block.setllabel() to update ui\n\t\t\ttk.leftLabelMaxwidth = tk.tklabel.node().getBBox().width\n\t\t} else {\n\t\t\t// tk.name is not provided, e.g. mds2\n\t\t\t// its maketk will be responsible for filling the tklabel and setting tk.leftLabelMaxwidth\n\t\t\t// fault is that the tooltip cannot be provided in this case\n\t\t}\n\t\tfunction showTkLabelTooltip(event, tk, labeltruncated) {\n\t\t\ttk.tktip.clear().show(event.clientX, event.clientY - 30)\n\t\t\tif (labeltruncated) {\n\t\t\t\tconst d = tk.tktip.d.append('div').text(tk.name)\n\t\t\t\tif (tk.list_description) d.style('margin-bottom', '5px')\n\t\t\t}\n\t\t\tif (tk.list_description) {\n\t\t\t\tclient.make_table_2col(tk.tktip.d.append('div'), tk.list_description).style('margin', '0px')\n\t\t\t}\n\t\t}\n\n\t\ttk.pica = {\n\t\t\tg: tk.gmiddle.append('g')\n\t\t}\n\t\ttk.cloak = tk.gmiddle.append('g').attr('transform', 'scale(0)')\n\t\ttk.cloakbox = tk.cloak.append('rect').attr('fill', 'white').attr('fill-opacity', 0)\n\t\ttk.cloaktext = tk.cloak\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'loading_message')\n\t\t\t.text('Loading ...')\n\t\t\t.attr('fill', common.defaultcolor)\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('font-weight', 'bold')\n\t\t\t.attr('font-size', '18px')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\ttk.cloakline = tk.cloak.append('line').attr('stroke', common.defaultcolor).attr('stroke-width', '2px')\n\t\t// set default if missing from template\n\t\tswitch (tk.type) {\n\t\t\tcase client.tkt.bampile:\n\t\t\t\tbampilemaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ds:\n\t\t\t\tdsmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.pgv:\n\t\t\t\tpgvmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ld:\n\t\t\t\tldmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bam:\n\t\t\t\tbammaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.usegm:\n\t\t\t\tgmtkmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bedj:\n\t\t\t\tbedjmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.junction:\n\t\t\t\tjunctionmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.aicheck:\n\t\t\t\taicheckmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bigwig:\n\t\t\t\tbigwigmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bigwigstranded:\n\t\t\t\tbigwigstrandedmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdsjunction:\n\t\t\t\tmdsjunctionmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdssvcnv:\n\t\t\t\tmdssvcnvmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mds3:\n\t\t\t\tmds3_maketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bedgraphdot:\n\t\t\t\tbedgraphdot_maketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdsexpressionrank:\n\t\t\t\tmdsexpressionrankmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.hicstraw:\n\t\t\t\thicstrawmaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ase:\n\t\t\t\tasemaketk(tk, this)\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tthis.error('maketk: unknown template tk type ' + tk.type)\n\t\t}\n\t\tthis.setllabel()\n\n\t\t/*******    pan    *******/\n\n\t\ttk.gmiddle.on('mousedown', event => {\n\t\t\tif (this.busy) return\n\t\t\tif (event.which == 3) {\n\t\t\t\t// right click\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tthis.busy = true\n\t\t\tthis.resized = false\n\n\t\t\tevent.preventDefault()\n\t\t\tconst body = d3select(document.body)\n\n\t\t\tconst x0 = this.rotated ? event.clientY : event.clientX\n\n\t\t\tbody.on('mousemove', event => {\n\t\t\t\tconst xoff = (this.rotated ? event.clientY : event.clientX) - x0\n\t\t\t\tthis.panning(xoff)\n\t\t\t})\n\t\t\tbody.on('mouseup', event => {\n\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t\t\tconst xoff = (this.rotated ? event.clientY : event.clientX) - x0\n\t\t\t\tthis.pannedby(xoff)\n\t\t\t})\n\t\t})\n\n\t\t/******* drag up down *******/\n\n\t\ttk.gleft.on('mousedown', event => {\n\t\t\tevent.preventDefault()\n\t\t\tconst body = d3select(document.body)\n\t\t\tlet y0 = event.clientY\n\t\t\tbody.on('mousemove', event => {\n\t\t\t\tconst dy = event.clientY - y0\n\n\t\t\t\ttk.g.attr('transform', 'translate(0,' + (tk.yoff + dy) + ')')\n\n\t\t\t\tlet tkidx = 0\n\t\t\t\tfor (let i = 0; i < this.tklst.length; i++) {\n\t\t\t\t\tif (this.tklst[i].tkid == tk.tkid) {\n\t\t\t\t\t\ttkidx = i\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (dy < 0 && tkidx > 0) {\n\t\t\t\t\tlet t2idx = tkidx - 1,\n\t\t\t\t\t\tt2 = this.tklst[t2idx]\n\t\t\t\t\twhile (t2.hidden) {\n\t\t\t\t\t\tt2idx--\n\t\t\t\t\t\tif (t2idx < 0) {\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tt2 = this.tklst[t2idx]\n\t\t\t\t\t}\n\t\t\t\t\tif (!t2) {\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tif (-dy >= t2.height) {\n\t\t\t\t\t\t// swap\n\t\t\t\t\t\tthis.tklst[t2idx] = tk\n\t\t\t\t\t\tthis.tklst[tkidx] = t2\n\t\t\t\t\t\ttk.yoff = t2.yoff - t2.toppad + tk.toppad // important since tk/t2 may have different toppad, and yoff does not include toppad\n\t\t\t\t\t\tt2.yoff += tk.height\n\n\t\t\t\t\t\tt2.g.transition().attr('transform', 'translate(0,' + t2.yoff + ')')\n\n\t\t\t\t\t\ty0 = event.clientY\n\t\t\t\t\t\tif (tk.type == client.tkt.usegm && t2.type == client.tkt.ds && t2.aboveprotein) {\n\t\t\t\t\t\t\t// t2 go down\n\t\t\t\t\t\t\tblockds.skewer_flip(t2)\n\t\t\t\t\t\t} else if (t2.type == client.tkt.usegm && tk.type == client.tkt.ds && !tk.aboveprotein) {\n\t\t\t\t\t\t\t// tk go up\n\t\t\t\t\t\t\tblockds.skewer_flip(tk)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else if (dy > 0 && tkidx < this.tklst.length - 1) {\n\t\t\t\t\tlet t2idx = tkidx + 1,\n\t\t\t\t\t\tt2 = this.tklst[t2idx]\n\t\t\t\t\twhile (t2.hidden) {\n\t\t\t\t\t\tt2idx++\n\t\t\t\t\t\tif (t2idx >= this.tklst.length) {\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tt2 = this.tklst[t2idx]\n\t\t\t\t\t}\n\t\t\t\t\tif (!t2) {\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tif (dy >= t2.height) {\n\t\t\t\t\t\t// swap\n\t\t\t\t\t\tthis.tklst[t2idx] = tk\n\t\t\t\t\t\tthis.tklst[tkidx] = t2\n\t\t\t\t\t\tt2.yoff = tk.yoff - tk.toppad + t2.toppad\n\t\t\t\t\t\ttk.yoff += t2.height\n\n\t\t\t\t\t\tt2.g.transition().attr('transform', 'translate(0,' + t2.yoff + ')')\n\n\t\t\t\t\t\ty0 = event.clientY\n\t\t\t\t\t\tif (tk.type == client.tkt.usegm && t2.type == client.tkt.ds && !t2.aboveprotein) {\n\t\t\t\t\t\t\t// t2 go up\n\t\t\t\t\t\t\tblockds.skewer_flip(t2)\n\t\t\t\t\t\t} else if (t2.type == client.tkt.usegm && tk.type == client.tkt.ds && tk.aboveprotein) {\n\t\t\t\t\t\t\t// tk go down\n\t\t\t\t\t\t\tblockds.skewer_flip(tk)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t\tbody.on('mouseup', () => {\n\t\t\t\ttk.g.transition().attr('transform', 'translate(0,' + tk.yoff + ')')\n\n\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t\t})\n\t\t})\n\t}\n\n\tpanning(xoff) {\n\t\tif (this.showreverse) {\n\t\t\txoff *= -1\n\t\t}\n\n\t\tthis.coord.g.attr('transform', 'translate(' + xoff + ',0)')\n\n\t\tfor (const tk of this.tklst) {\n\t\t\ttk.glider.attr('transform', 'translate(' + xoff + ',0)')\n\n\t\t\tif (tk.type == client.tkt.pgv) {\n\t\t\t\t// need to shift some part of its member tracks\n\t\t\t\tfor (const t of tk.tracks) {\n\t\t\t\t\tt.immobileg.attr('transform', 'translate(' + -xoff + ',0)')\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tfor (const r of this.hlregion.lst) {\n\t\t\tr.rect.attr('x', r.x + xoff)\n\t\t}\n\t\tif (this.onpanning) {\n\t\t\tthis.onpanning(xoff)\n\t\t}\n\t}\n\n\tpannedby(xoff) {\n\t\tif (xoff == 0) {\n\t\t\tthis.busy = false\n\t\t\tthis.pannedpx = undefined\n\t\t\treturn\n\t\t}\n\n\t\tif (this.showreverse) {\n\t\t\txoff *= -1\n\t\t}\n\n\t\tlet back = false\n\t\tif (xoff < 0) {\n\t\t\tif (this.stopidx == this.rglst.length - 1) {\n\t\t\t\tconst r = this.rglst[this.stopidx]\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tif (r.start <= r.bstart) back = true\n\t\t\t\t} else {\n\t\t\t\t\tif (r.stop >= r.bstop) back = true\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\tif (this.startidx == 0) {\n\t\t\t\tconst r = this.rglst[0]\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tif (r.stop >= r.bstop) back = true\n\t\t\t\t} else {\n\t\t\t\t\tif (r.start <= r.bstart) back = true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (back) {\n\t\t\tthis.coord.g.transition().attr('transform', 'translate(0,0)')\n\t\t\tfor (const t of this.tklst) {\n\t\t\t\tt.glider.transition().attr('transform', 'translate(0,0)')\n\t\t\t}\n\t\t\tthis.busy = false\n\t\t\tthis.pannedpx = undefined\n\t\t\tfor (const r of this.hlregion.lst) {\n\t\t\t\tr.rect.transition().attr('x', r.x)\n\t\t\t}\n\t\t\tif (this.onpanning) {\n\t\t\t\tthis.onpanning(0)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\t\tthis.pannedpx = xoff\n\t\tthis.zoomedin = false\n\t\tthis.zoom2px(-xoff, this.width - xoff)\n\t}\n\n\ttk_hide(tk) {\n\t\ttk.hidden = true\n\t\ttk.g.remove()\n\t\tif (tk.eplst) {\n\t\t\t// ds tk that has epaint\n\t\t\tfor (const ep of tk.eplst) {\n\t\t\t\tif (ep.pane && ep.pane.pane && ep.pane.pane.style('display') != 'none') {\n\t\t\t\t\tep.epaintfold(this)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.setllabel()\n\t\tthis.block_setheight()\n\t\tif (tk.type == client.tkt.ds) {\n\t\t\tconst hd = this.ds2handle[tk.name]\n\t\t\tif (hd) {\n\t\t\t\thd.handlesays.style('background-color', '#999').style('color', 'white')\n\t\t\t}\n\t\t}\n\t\tif (tk.tr_legend) {\n\t\t\tdisappear(tk.tr_legend)\n\t\t}\n\t}\n\n\ttkchangeaffectlegend(tk) {\n\t\tif (!this.legend) return\n\t\t// tk has been turned shown/hidden\n\t\tif (tk.type == client.tkt.ds) {\n\t\t\t// mclass / morigin legend\n\t\t\tlet dsshown = false\n\t\t\tfor (const t of this.tklst) {\n\t\t\t\tif (!t.hidden && t.type == client.tkt.ds) {\n\t\t\t\t\tdsshown = true\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (dsshown) {\n\t\t\t\tthis.legend.tr_mclass.style('display', 'table-row')\n\t\t\t\tLegend.legend_mclass(this)\n\t\t\t\tthis.legend.tr_morigin.style('display', 'table-row')\n\t\t\t\tLegend.legend_morigin(this)\n\t\t\t} else {\n\t\t\t\tthis.legend.tr_mclass.style('display', 'none')\n\t\t\t\tthis.legend.tr_morigin.style('display', 'none')\n\t\t\t}\n\t\t}\n\t}\n\n\ttk_load_all() {\n\t\t/*\n\ttk_load of individual tk is sync and blocking in nature\n\te.g.\n\twhen zooming in, a junction track will be rendered all in sync, and will attempt to run splice event analysis via onloadalltk()\n\tbut the gene tk following the junction tk still hasn't been set busy flag\n\tso results in the onloadalltk to be run on stale gene tk data\n\tso must set busy flag to all tk first, then call tk_load\n\t*/\n\t\tfor (const t of this.tklst) {\n\t\t\tt.busy = true\n\t\t}\n\t\tfor (const t of this.tklst) {\n\t\t\tthis.tk_load(t)\n\t\t}\n\t}\n\n\ttk_load(tk) {\n\t\t/*\n\tcalled when track first created\n\tand when view range updated\n\tdetection of viewrangeupperlimit is handled in the loader of each track type, so that each track can respond to beyond-limit in their own way\n\t*/\n\n\t\tif (tk.hidden) {\n\t\t\tif (tk.g) {\n\t\t\t\ttk.g.remove()\n\t\t\t}\n\t\t\treturn\n\t\t}\n\t\t// in case this tk is brought back from hidden\n\t\tif (!tk.g.node().parentNode) {\n\t\t\tthis.gbase.node().appendChild(tk.g.node())\n\t\t}\n\t\tif (tk.tr_legend && tk.tr_legend.style('display') == 'none') {\n\t\t\tappear(tk.tr_legend, 'table-row')\n\t\t}\n\t\ttk.busy = true\n\t\tswitch (tk.type) {\n\t\t\tcase client.tkt.bampile:\n\t\t\t\tbampileload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.pgv:\n\t\t\t\tpgvload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ld:\n\t\t\t\tldload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bam:\n\t\t\t\tbamload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ds:\n\t\t\t\tconst hd = this.ds2handle[tk.name]\n\t\t\t\tif (hd) {\n\t\t\t\t\thd.handlesays.style('background-color', '#ddd').style('color', 'black')\n\t\t\t\t}\n\t\t\t\tif (\n\t\t\t\t\ttk.dsuninitiated ||\n\t\t\t\t\t!this.usegm ||\n\t\t\t\t\tthis.gmmode == client.gmmode.genomic ||\n\t\t\t\t\tthis.gmmodepast == client.gmmode.genomic\n\t\t\t\t) {\n\t\t\t\t\t// re-request data, only for range-queries, not for gene expression\n\t\t\t\t\tblockds.dstkload(tk, this)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tblockds.dstkrender(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.usegm:\n\t\t\t\tgmtkrender(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bigwig:\n\t\t\t\tbigwigload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.aicheck:\n\t\t\t\taicheckload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bigwigstranded:\n\t\t\t\tbigwigstrandedload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.junction:\n\t\t\t\tjunctionload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bam:\n\t\t\t\tthis.loadtk_bam(tk)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bedj:\n\t\t\t\tbedjload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdsjunction:\n\t\t\t\tmdsjunctionload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdssvcnv:\n\t\t\t\tmdssvcnvload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mds3:\n\t\t\t\tmds3_load(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.bedgraphdot:\n\t\t\t\tbedgraphdot_load(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.mdsexpressionrank:\n\t\t\t\tmdsexpressionrankload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.hicstraw:\n\t\t\t\thicstrawload(tk, this)\n\t\t\t\tbreak\n\t\t\tcase client.tkt.ase:\n\t\t\t\taseload(tk, this)\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tthis.error('tk_load: unknown tk type')\n\t\t}\n\t\tif (this.onAddRemoveTk) this.onAddRemoveTk(tk, true)\n\t}\n\n\tcloakOn() {\n\t\t// will cloak the entire svg\n\t\t// right now not called in block, but is called by external code on a block instance\n\t\tconst w = Number(this.svg.attr('width')),\n\t\t\th = Number(this.svg.attr('height'))\n\t\tthis.gCloak.attr('transform', 'scale(1)')\n\t\tthis.gCloakRect.attr('width', w).attr('height', h).transition().duration(600).attr('fill-opacity', 0.5)\n\t\tthis.gCloakWord\n\t\t\t.attr('x', w / 2)\n\t\t\t.attr('y', h / 2)\n\t\t\t.transition()\n\t\t\t.duration(600)\n\t\t\t.attr('fill-opacity', 1)\n\t}\n\tcloakOff() {\n\t\tthis.gCloak.attr('transform', 'scale(0)')\n\t}\n\n\ttkcloakon(tk) {\n\t\ttk.busy = true\n\t\tthis.busy = true\n\t\ttk.cloak.attr('transform', 'scale(1)')\n\t\ttk.cloakbox.attr('width', this.width).attr('height', tk.height).transition().duration(600).attr('fill-opacity', 0.5)\n\t\ttk.cloaktext\n\t\t\t.attr('x', this.width / 2)\n\t\t\t.attr('y', tk.height / 2)\n\t\t\t.transition()\n\t\t\t.duration(600)\n\t\t\t.attr('fill-opacity', 1)\n\t\ttk.cloakline.attr('y1', tk.height).attr('y2', tk.height).attr('x2', 0)\n\t\tif (tk.gerror) {\n\t\t\ttk.gerror.remove()\n\t\t}\n\t}\n\n\ttkcloakoff(tk, data) {\n\t\ttk.busy = false\n\t\tthis.ifbusy()\n\t\ttk.cloak.attr('transform', 'scale(0)')\n\t\ttk.cloakbox.attr('fill-opacity', 0).attr('height', 0) //This is a fix for issue #259. Set to 0. Otherwise Safari will not detect event.listeners for the first few track rows.\n\t\ttk.cloaktext.attr('fill-opacity', 0)\n\t\ttk.cloakline.attr('x2', 0)\n\t\ttk.glider.attr('transform', 'translate(0,0)')\n\n\t\tif (tk.gerror) {\n\t\t\t// must do this before tkerror\n\t\t\ttk.gerror.remove()\n\t\t}\n\n\t\tif (!data) {\n\t\t\tthis.tkerror(tk, 'Server error ...')\n\t\t} else if (data.error) {\n\t\t\tthis.tkerror(tk, data.error)\n\t\t}\n\t}\n\n\tifbusy() {\n\t\tlet quiet = true\n\t\tfor (const t of this.tklst) {\n\t\t\tif (!t.hidden && t.busy) quiet = false\n\t\t}\n\t\tfor (const r of this.rglst) {\n\t\t\tif (r.busy) quiet = false\n\t\t}\n\t\tif (quiet) {\n\t\t\tthis.busy = false\n\n\t\t\t// insert subpanels\n\t\t\tthis.add_subpanel()\n\n\t\t\t/*\n\t\tspecial actions only when it finishes loading all tracks\n\t\t*/\n\t\t\twhile (this.onloadalltk.length > 0) {\n\t\t\t\tconst task = this.onloadalltk.pop()\n\t\t\t\ttask()\n\t\t\t}\n\n\t\t\tif (this.onloadalltk_always) {\n\t\t\t\tthis.onloadalltk_always(this)\n\t\t\t}\n\t\t}\n\t}\n\n\ttkprogress(tk, percent) {\n\t\ttk.cloakline.attr('x2', this.width * percent)\n\t}\n\n\ttkerror(tk, msg, y) {\n\t\t// only works for main track, not subpanel\n\t\t// FIXME when printing new error old error register is overwritten!!\n\t\ttk.gerror = tk.glider\n\t\t\t.append('text')\n\t\t\t.text(msg.length > this.width / 10 ? msg.substring(0, this.width / 10 - 20) + '...' : msg)\n\t\t\t.attr('x', this.width / 2)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('y', y ? y : (tk.height_main - tk.toppad - tk.bottompad) / 2)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('font-size', '14px')\n\t}\n\n\tblock_setheight() {\n\t\t/*\n\teach track has height_main and heights from each subpanel\n\tset tk.height for each track\n\tthen set tk.yoff\n\t*/\n\t\tlet h = this.coord.height\n\n\t\tfor (const t of this.tklst) {\n\t\t\tif (t.hidden) continue\n\n\t\t\tt.yoff = h + t.toppad\n\t\t\tt.g.transition().attr('transform', 'translate(0,' + t.yoff + ')')\n\n\t\t\tif (!Number.isFinite(t.height_main)) {\n\t\t\t\t// should not happen\n\t\t\t\tif (this.debugmode) {\n\t\t\t\t\tconsole.log('block_setheight: invalid height_main for ' + t.name)\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// heights to be considered: subpanels, and main track\n\t\t\t{\n\t\t\t\tconst lst = t.subpanels.map(i => i.height)\n\t\t\t\tlst.push(t.height_main)\n\t\t\t\tt.height = Math.max(...lst)\n\t\t\t}\n\n\t\t\th += t.height\n\t\t\tt.tkbodybgrect.attr('width', this.width).attr('height', t.height)\n\n\t\t\tfor (const [i, p] of t.subpanels.entries()) {\n\t\t\t\tp.subpaneltkbgrect.attr('width', this.subpanels[i].width).attr('height', t.height)\n\t\t\t}\n\t\t}\n\n\t\tfor (const p of this.subpanels) {\n\t\t\tp.subpanelbgrect.attr('height', h)\n\t\t\tp.subpanelleftborder.attr('height', h)\n\t\t}\n\n\t\tthis.svg.transition().attr('height', h)\n\n\t\tfor (const r of this.hlregion.lst) {\n\t\t\tr.rect.attr('height', h)\n\t\t}\n\n\t\tif (this.onsetheight) {\n\t\t\tthis.onsetheight(h)\n\t\t}\n\t}\n\n\ttkarg_bedj(tk) {\n\t\tconst par = {\n\t\t\tname: tk.name,\n\t\t\tgenome: this.genome.name,\n\t\t\trglst: this.tkarg_rglst(),\n\t\t\tstackheight: tk.stackheight,\n\t\t\tstackspace: tk.stackspace,\n\t\t\tregionspace: this.regionspace,\n\t\t\twidth: this.width,\n\t\t\tdevicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1\n\t\t}\n\t\tif (tk.bedItems) {\n\t\t\tpar.bedItems = tk.bedItems\n\t\t} else if (tk.file) {\n\t\t\tpar.file = tk.file\n\t\t} else {\n\t\t\tpar.url = tk.url\n\t\t\tif (tk.indexURL) par.indexURL = tk.indexURL\n\t\t}\n\t\tif (tk.color) par.color = tk.color\n\t\tif (tk.categories) par.categories = tk.categories\n\t\tif (tk.translatecoding) par.translatecoding = 1\n\t\tif (tk.onerow) par.onerow = 1\n\t\tif (tk.usevalue) par.usevalue = tk.usevalue\n\t\tif (tk.bplengthUpperLimit) par.bplengthUpperLimit = tk.bplengthUpperLimit\n\t\tif (tk.hideItemNames) par.hideItemNames = tk.hideItemNames\n\t\tif (tk.filterByName) par.filterByName = tk.filterByName\n\t\tif (this.usegm && this.gmmode != client.gmmode.genomic) {\n\t\t\t// important, will render a gene in a single row across rglst\n\t\t\tpar.gmregion = this.tkarg_maygm(tk)[0]\n\t\t\tpar.isoform = this.usegm.isoform\n\t\t}\n\t\treturn par\n\t}\n\n\tbedj_tooltip(tk, data, panel) {\n\t\t// process data loaded from main tk and subpanel\n\t\t// TODO move this to bedj.js as this is type-specific logic\n\t\tlet tipnum = 0\n\t\tif (data.mapisoform) tipnum += data.mapisoform.length\n\t\tif (data.mapexon) tipnum += data.mapexon.length\n\t\tif (data.mapaa) tipnum += data.mapaa.length\n\n\t\tconst img = (panel || tk).img\n\n\t\tif (tipnum) {\n\t\t\timg\n\t\t\t\t.on('mousemove', event => {\n\t\t\t\t\tif (this.busy) return\n\t\t\t\t\tconst lst = []\n\t\t\t\t\tconst p = pointer(event, img.node())\n\t\t\t\t\tlet stacknumber\n\t\t\t\t\tif (data.mapisoform) {\n\t\t\t\t\t\tfor (const i of data.mapisoform) {\n\t\t\t\t\t\t\tconst y = (i.y - 1) * (tk.stackheight + tk.stackspace)\n\t\t\t\t\t\t\tif (i.x1 < p[0] && i.x2 > p[0] && y < p[1] && y + tk.stackheight > p[1]) {\n\t\t\t\t\t\t\t\tstacknumber = i.y\n\t\t\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t\t\ti.name +\n\t\t\t\t\t\t\t\t\t\t' <span style=\"font-size:.7em\">' +\n\t\t\t\t\t\t\t\t\t\ti.chr +\n\t\t\t\t\t\t\t\t\t\t':' +\n\t\t\t\t\t\t\t\t\t\t(i.start + 1) +\n\t\t\t\t\t\t\t\t\t\t'-' +\n\t\t\t\t\t\t\t\t\t\ti.stop +\n\t\t\t\t\t\t\t\t\t\t' ' +\n\t\t\t\t\t\t\t\t\t\tcommon.bplen(i.stop - i.start) +\n\t\t\t\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (data.mapexon) {\n\t\t\t\t\t\tfor (const i of data.mapexon) {\n\t\t\t\t\t\t\tconst y = (i.y - 1) * (tk.stackheight + tk.stackspace)\n\t\t\t\t\t\t\tif (i.x1 < p[0] && i.x2 > p[0] && y < p[1] && y + tk.stackheight > p[1]) {\n\t\t\t\t\t\t\t\tstacknumber = i.y\n\t\t\t\t\t\t\t\tlst.push(\n\t\t\t\t\t\t\t\t\ti.name +\n\t\t\t\t\t\t\t\t\t\t' <span style=\"font-size:.7em\">' +\n\t\t\t\t\t\t\t\t\t\ti.chr +\n\t\t\t\t\t\t\t\t\t\t':' +\n\t\t\t\t\t\t\t\t\t\t(i.start + 1) +\n\t\t\t\t\t\t\t\t\t\t'-' +\n\t\t\t\t\t\t\t\t\t\ti.stop +\n\t\t\t\t\t\t\t\t\t\t' ' +\n\t\t\t\t\t\t\t\t\t\tcommon.bplen(i.stop - i.start) +\n\t\t\t\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (data.mapaa) {\n\t\t\t\t\t\tfor (const i of data.mapaa) {\n\t\t\t\t\t\t\tconst y = (i.y - 1) * (tk.stackheight + tk.stackspace)\n\t\t\t\t\t\t\tif (i.x1 < p[0] && i.x2 > p[0] && y < p[1] && y + tk.stackheight > p[1]) {\n\t\t\t\t\t\t\t\tstacknumber = i.y\n\t\t\t\t\t\t\t\tlst.push(i.name)\n\t\t\t\t\t\t\t\t// break: a hack to resolve issue that sometimes two aa show at cursor position\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (lst.length) {\n\t\t\t\t\t\ttk.tktip.clear()\n\t\t\t\t\t\tfor (const i of lst) {\n\t\t\t\t\t\t\ttk.tktip.d.append('div').html(i)\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttk.tktip.show(\n\t\t\t\t\t\t\tevent.clientX,\n\t\t\t\t\t\t\timg.node().getBoundingClientRect().top + stacknumber * (tk.stackheight + tk.stackspace) - 10\n\t\t\t\t\t\t)\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\ttk.tktip.hide()\n\t\t\t\t})\n\n\t\t\t/*\n\t\tisoform is also for singular bed item\n\t\t*/\n\t\t\tif (data.mapisoform) {\n\t\t\t\t// has isoform, may enable clicking for different reasons\n\n\t\t\t\tif (tk.itemurl_appendname) {\n\t\t\t\t\t// append item name to url for clicking\n\t\t\t\t\timg.on('click', event => {\n\t\t\t\t\t\tconst p = pointer(event, img.node())\n\t\t\t\t\t\tfor (const i of data.mapisoform) {\n\t\t\t\t\t\t\tconst y = (i.y - 1) * (tk.stackheight + tk.stackspace)\n\t\t\t\t\t\t\tif (i.x1 < p[0] && i.x2 > p[0] && y < p[1] && y + tk.stackheight > p[1] && i.name) {\n\t\t\t\t\t\t\t\t// hit an item with name\n\t\t\t\t\t\t\t\twindow.open(tk.itemurl_appendname + i.name)\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t} else if (data.mapisoform.find(i => i.isoform)) {\n\t\t\t\t\t// has isoform name, enable clicking on a isoform to launch protein view\n\n\t\t\t\t\tif (tk.__isgene) {\n\t\t\t\t\t\t// this flag is true for native gene tracks\n\t\t\t\t\t\t// only allow this menu option for these tracks, and won't show it for custom gene tracks\n\n\t\t\t\t\t\tif (this.tklst.find(i => i.type == 'bam')) {\n\t\t\t\t\t\t\t// currently there's a bam tk showing in block; as it does not work for protein view yet, disable this option\n\t\t\t\t\t\t\t// this check can be deleted with a fix e.g. when bam tk is able to properly show pileup-only and no alignment over whole gene\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\timg.on('click', event => {\n\t\t\t\t\t\t\t\tconst p = pointer(event, img.node())\n\t\t\t\t\t\t\t\tfor (const i of data.mapisoform) {\n\t\t\t\t\t\t\t\t\tconst y = (i.y - 1) * (tk.stackheight + tk.stackspace)\n\t\t\t\t\t\t\t\t\tif (i.x1 < p[0] && i.x2 > p[0] && y < p[1] && y + tk.stackheight > p[1] && i.isoform) {\n\t\t\t\t\t\t\t\t\t\t// hit an isoform\n\t\t\t\t\t\t\t\t\t\ttk.tkconfigtip\n\t\t\t\t\t\t\t\t\t\t\t.clear()\n\t\t\t\t\t\t\t\t\t\t\t.show(event.clientX - 40, event.clientY)\n\t\t\t\t\t\t\t\t\t\t\t.d.append('div')\n\t\t\t\t\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t\t\t\t\t.text('Gene/protein view for ' + i.isoform)\n\t\t\t\t\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\t\t\t\t\ttk.tkconfigtip.hide()\n\t\t\t\t\t\t\t\t\t\t\t\tthis.to_proteinview(i.isoform, tk)\n\t\t\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t\t\treturn\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} else {\n\t\t\t\t\timg.on('click', null)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\timg.on('click', null)\n\t\t\t}\n\t\t} else {\n\t\t\timg.on('mouseover', null).on('click', null)\n\t\t}\n\t}\n\n\t/* show protein view for a given isoform\n\tand bring along current tracks\n\tif fromgenetk is provided, will skip this track\n\t*/\n\tto_proteinview(isoform, fromgenetk) {\n\t\t// when a mds3 tk is part of genomebrowser app in mass ui, this special folder exists; create sandbox into it to make it look nice that the new sandbox is on top of existing genomebrowser sandbox, rather than inside it which looks bad\n\t\tconst sandbox = newSandboxDiv(this.tklst.find(i => i.type == 'mds3')?.newChartHolder || this.holder0)\n\t\tsandbox.header.text(isoform)\n\t\tconst arg = {\n\t\t\tgenome: this.genome,\n\t\t\tdebugmode: this.debugmode,\n\t\t\tholder: sandbox.body,\n\t\t\ttklst: [],\n\t\t\tquery: isoform\n\t\t}\n\t\t// bring along current tracks\n\t\tfor (const tk of this.tklst) {\n\t\t\tif (fromgenetk && tk.tkid == fromgenetk.tkid) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (tk.type == common.tkt.mdsexpressionrank) {\n\t\t\t\t// somehow this track won't work (no need to fix)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (tk.type == 'mds3') {\n\t\t\t\targ.tklst.push(tk.duplicateTk())\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\targ.tklst.push(tk)\n\t\t\tconsole.log('tk used as-is')\n\t\t}\n\t\tblockinit(arg)\n\t}\n\n\ttkarg_rglst() {\n\t\t// per region/exon, should be used for bigwig and bedj\n\t\tconst lst = []\n\t\tfor (let i = this.startidx; i <= this.stopidx; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\tlst.push({\n\t\t\t\tchr: r.chr,\n\t\t\t\tstart: r.start,\n\t\t\t\tstop: r.stop,\n\t\t\t\twidth: r.width,\n\t\t\t\treverse: r.reverse\n\t\t\t})\n\t\t}\n\t\treturn lst\n\t}\n\n\ttkarg_maygm(tk) {\n\t\tif (!this.usegm || this.gmmode == client.gmmode.genomic) {\n\t\t\treturn this.tkarg_rglst()\n\t\t}\n\t\tconst r = this.rglst[this.startidx]\n\t\tconst reverse = r.reverse\n\t\tif (tk.type == client.tkt.ds || tk.mds) {\n\t\t\t/* use entire gm for:\n\t\t1. old official ds, vcf\n\t\t2. any track from mds\n\t\t*/\n\t\t\treturn [\n\t\t\t\t{\n\t\t\t\t\tchr: this.usegm.chr,\n\t\t\t\t\tstart: this.usegm.start,\n\t\t\t\t\tstop: this.usegm.stop,\n\t\t\t\t\twidth: this.width,\n\t\t\t\t\treverse: reverse\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\t// for bedj/junction\n\t\t// restrict by current view range\n\t\t// will include entire gm span in view range including hidden introns in exon mode\n\t\tlet min = Math.min(r.start, r.stop)\n\t\tlet max = Math.max(r.start, r.stop)\n\t\tfor (let i = this.startidx + 1; i <= this.stopidx; i++) {\n\t\t\tconst r = this.rglst[i]\n\t\t\tmin = Math.min(min, r.start, r.stop)\n\t\t\tmax = Math.max(max, r.start, r.stop)\n\t\t}\n\t\treturn [\n\t\t\t{\n\t\t\t\tchr: this.usegm.chr,\n\t\t\t\tstart: min,\n\t\t\t\tstop: max,\n\t\t\t\twidth: this.width,\n\t\t\t\treverse: reverse\n\t\t\t}\n\t\t]\n\t}\n\n\ttkarg_q(tk) {\n\t\t// bigwig track\n\t\tconst a = {\n\t\t\tjwt: this.jwt,\n\t\t\tgenome: this.genome.name,\n\t\t\tname: tk.name,\n\t\t\trglst: this.tkarg_rglst(),\n\t\t\tregionspace: this.regionspace,\n\t\t\twidth: this.width,\n\t\t\tfile: tk.file,\n\t\t\turl: tk.url,\n\t\t\tindexURL: tk.indexURL, // for bedgraph\n\t\t\tbarheight: tk.barheight,\n\t\t\tminv: tk.scale.min,\n\t\t\tmaxv: tk.scale.max,\n\t\t\tpercentile: tk.scale.percentile,\n\t\t\tautoscale: tk.scale.auto,\n\t\t\tpcolor: tk.pcolor,\n\t\t\tpcolor2: tk.pcolor2,\n\t\t\tncolor: tk.ncolor,\n\t\t\tncolor2: tk.ncolor2,\n\t\t\tdevicePixelRatio: window.devicePixelRatio > 1 ? window.devicePixelRatio : 1\n\t\t}\n\t\tif (tk.normalize && !tk.normalize.disable) {\n\t\t\ta.dividefactor = tk.normalize.dividefactor\n\t\t}\n\t\treturn a\n\t}\n\n\tmaketkconfighandle(tk) {\n\t\treturn tk.gright\n\t\t\t.append('text')\n\t\t\t.text('CONFIG')\n\t\t\t.attr('fill', '#555')\n\t\t\t.attr('font-size', this.labelfontsize)\n\t\t\t.attr('y', this.labelfontsize)\n\t\t\t.attr('class', 'sja_clbtext2')\n\t}\n\n\tmaketklefthandle(tk, y) {\n\t\treturn tk.gleft\n\t\t\t.append('text')\n\t\t\t.attr('font-size', this.labelfontsize)\n\t\t\t.attr('y', this.labelfontsize / 2 + (y || 0))\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('class', 'sja_clbtext2')\n\t\t\t.attr('fill', 'black')\n\t\t\t.attr('x', this.tkleftlabel_xshift)\n\t}\n\n\t/** __tk__ end **/\n\n\t/** __gm__ **/\n\n\tsetgmmode(mode, willupdate) {\n\t\tif (!mode) return this.error('setgmmode: no given mode')\n\t\tif (typeof mode != 'string') return this.error('setgmmode: mode value is not string')\n\t\tif (!this.usegm) return this.error('setgmmode: this.usegm missing')\n\n\t\tthis.rglst = []\n\t\tconst c = this.genome.chrlookup[this.usegm.chr.toUpperCase()]\n\t\tif (!c) {\n\t\t\tthis.error('invalid chr of usegm: ' + this.usegm.chr)\n\t\t\treturn true\n\t\t}\n\t\tif (this.gmmode == mode) {\n\t\t\treturn\n\t\t}\n\t\tif (this.gmmode) {\n\t\t\tthis.gmmodepast = this.gmmode\n\t\t}\n\t\tthis.gmmode = mode\n\t\tlet addgene = false\n\t\tswitch (this.gmmode) {\n\t\t\tcase client.gmmode.genomic:\n\t\t\t\tthis.rglst = [\n\t\t\t\t\t{\n\t\t\t\t\t\tchr: this.usegm.chr,\n\t\t\t\t\t\tbstart: 0,\n\t\t\t\t\t\tbstop: c.len,\n\t\t\t\t\t\tstart: this.usegm.start,\n\t\t\t\t\t\tstop: this.usegm.stop,\n\t\t\t\t\t\treverse: this.usegm.strand == '-'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t\tthis.regionspace = 0\n\t\t\t\taddgene = true\n\t\t\t\tbreak\n\t\t\tcase client.gmmode.splicingrna:\n\t\t\t\t// TODO allow padding bases\n\t\t\t\tfor (const e of this.usegm.exon) {\n\t\t\t\t\tthis.rglst.push({\n\t\t\t\t\t\tchr: this.usegm.chr,\n\t\t\t\t\t\tbstart: e[0],\n\t\t\t\t\t\tbstop: e[1],\n\t\t\t\t\t\tstart: e[0],\n\t\t\t\t\t\tstop: e[1],\n\t\t\t\t\t\treverse: this.usegm.strand == '-'\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tthis.regionspace = 10\n\t\t\t\tbreak\n\t\t\tcase client.gmmode.exononly:\n\t\t\t\tfor (const e of this.usegm.exon) {\n\t\t\t\t\tthis.rglst.push({\n\t\t\t\t\t\tchr: this.usegm.chr,\n\t\t\t\t\t\tbstart: e[0],\n\t\t\t\t\t\tbstop: e[1],\n\t\t\t\t\t\tstart: e[0],\n\t\t\t\t\t\tstop: e[1],\n\t\t\t\t\t\treverse: this.usegm.strand == '-'\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tthis.regionspace = 0\n\t\t\t\tbreak\n\t\t\tcase client.gmmode.protein:\n\t\t\t\tfor (const e of this.usegm.coding) {\n\t\t\t\t\tthis.rglst.push({\n\t\t\t\t\t\tchr: this.usegm.chr,\n\t\t\t\t\t\tbstart: e[0],\n\t\t\t\t\t\tbstop: e[1],\n\t\t\t\t\t\tstart: e[0],\n\t\t\t\t\t\tstop: e[1],\n\t\t\t\t\t\treverse: this.usegm.strand == '-'\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tthis.regionspace = 0\n\t\t\t\tbreak\n\t\t\tcase client.gmmode.gmsum:\n\t\t\t\tthis.rglst = allgm2sum(this.allgm)[0]\n\t\t\t\tthis.regionspace = 10\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tthis.error('setgmmode: unknown mode ' + this.gmmode)\n\t\t\t\tthis.gmmode = this.gmmodepast\n\t\t\t\treturn\n\t\t}\n\t\tthis.startidx = 0\n\t\tthis.stopidx = this.rglst.length - 1\n\t\tif (this.rglst.length > 1 && this.regionspace > 0) {\n\t\t\t// adjust width\n\t\t\tif (this.regionspace * (this.rglst.length - 1) > this.width * 0.3) {\n\t\t\t\tthis.regionspace = Math.max(2, (this.width * 0.3) / (this.rglst.length - 1))\n\t\t\t}\n\t\t\tconst inw = this.regionspace * (this.rglst.length - 1)\n\t\t\tconst exonlen = this.rglst.reduce((a, b) => a + b.stop - b.start, 0)\n\t\t\tthis.exonsf = (this.width - (inw > this.width * 0.4 ? 0 : inw)) / exonlen\n\t\t\tthis.width = exonlen * this.exonsf + inw\n\t\t}\n\n\t\tif (this.gbase) {\n\t\t\tlet hasgene = false\n\t\t\tfor (const tk of this.tklst) {\n\t\t\t\tif (tk.__isgene) hasgene = true\n\t\t\t}\n\t\t\tif (addgene) {\n\t\t\t\tif (!hasgene) {\n\t\t\t\t\t// add\n\t\t\t\t\tfor (const tk of this.genome.tracks) {\n\t\t\t\t\t\tif (tk.__isgene) {\n\t\t\t\t\t\t\tthis.block_addtk_template(tk)\n\t\t\t\t\t\t\t// by breaking, block will only add the first gene track, but not more than 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}\n\t\t\t} else {\n\t\t\t\tif (hasgene) {\n\t\t\t\t\t// remove\n\t\t\t\t\twhile (hasgene) {\n\t\t\t\t\t\tfor (let i = 0; i < this.tklst.length; i++) {\n\t\t\t\t\t\t\tif (this.tklst[i].__isgene) {\n\t\t\t\t\t\t\t\tthis.tk_remove(i)\n\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\thasgene = false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (willupdate) {\n\t\t\t\tdelete this.pannedpx\n\t\t\t\tthis.block_coord_updated()\n\t\t\t}\n\t\t} else {\n\t\t\t// gbase is missing\n\t\t\t// this is setting gmmode at init\n\t\t\t// somehow this will also prevent from adding default gene track\n\t\t}\n\t}\n\n\tshowgmmode4switch(holder, hideuponselect) {\n\t\tlet row1, row2, row3, row4, row5\n\n\t\tconst width = 400\n\n\t\tif (this.allowGenomeMode()) {\n\t\t\t// 1 - genomic\n\t\t\trow1 = holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '1px')\n\t\t\t\t.attr('class', this.gmmode == client.gmmode.genomic ? 'sja_inset_a' : 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.setgmmode(client.gmmode.genomic, true)\n\t\t\t\t\tif (hideuponselect) {\n\t\t\t\t\t\tthis.usegmtip.fadeout()\n\t\t\t\t\t} else {\n\t\t\t\t\t\trow1.attr('class', 'sja_inset_a')\n\t\t\t\t\t\tif (row2) row2.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row3) row3.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row4) row4.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row5) row5.attr('class', 'sja_menuoption')\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\tsketchGene(\n\t\t\t\trow1.append('div').style('vertical-align', 'middle').style('display', 'inline-block'),\n\t\t\t\tthis.usegm,\n\t\t\t\twidth,\n\t\t\t\t20,\n\t\t\t\tthis.usegm.start,\n\t\t\t\tthis.usegm.stop,\n\t\t\t\tcommon.exoncolor,\n\t\t\t\ttrue,\n\t\t\t\tthis.usegm.strand == '-'\n\t\t\t)\n\t\t\trow1.append('div').style('display', 'inline-block').style('padding', '13px').text(client.gmmode.genomic)\n\t\t}\n\n\t\t// 2 - splicing rna\n\t\tif (this.usegm.exon.length > 1) {\n\t\t\trow2 = holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '1px')\n\t\t\t\t.attr('class', this.gmmode == client.gmmode.splicingrna ? 'sja_inset_a' : 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.setgmmode(client.gmmode.splicingrna, true)\n\t\t\t\t\tif (hideuponselect) {\n\t\t\t\t\t\tthis.usegmtip.fadeout()\n\t\t\t\t\t} else {\n\t\t\t\t\t\trow2.attr('class', 'sja_inset_a')\n\t\t\t\t\t\tif (row1) row1.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row3) row3.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row4) row4.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row5) row5.attr('class', 'sja_menuoption')\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\tsketchSplicerna(\n\t\t\t\trow2.append('div').style('vertical-align', 'middle').style('display', 'inline-block').style('padding', '0px'),\n\t\t\t\tthis.usegm,\n\t\t\t\twidth,\n\t\t\t\tcommon.exoncolor\n\t\t\t)\n\t\t\trow2.append('div').style('display', 'inline-block').style('padding', '13px').text(client.gmmode.splicingrna)\n\t\t}\n\t\t// 3 - whole rna\n\t\trow3 = holder\n\t\t\t.append('div')\n\t\t\t.style('margin', '1px')\n\t\t\t.attr('class', this.gmmode == client.gmmode.exononly ? 'sja_inset_a' : 'sja_menuoption')\n\t\t\t.on('click', () => {\n\t\t\t\tif (hideuponselect) {\n\t\t\t\t\tthis.usegmtip.fadeout()\n\t\t\t\t} else {\n\t\t\t\t\trow3.attr('class', 'sja_inset_a')\n\t\t\t\t\tif (row1) row1.attr('class', 'sja_menuoption')\n\t\t\t\t\tif (row2) row2.attr('class', 'sja_menuoption')\n\t\t\t\t\tif (row4) row4.attr('class', 'sja_menuoption')\n\t\t\t\t\tif (row5) row5.attr('class', 'sja_menuoption')\n\t\t\t\t}\n\t\t\t\tthis.setgmmode(client.gmmode.exononly, true)\n\t\t\t})\n\t\tsketchRna(\n\t\t\trow3.append('div').style('vertical-align', 'middle').style('display', 'inline-block').style('padding', '0px'),\n\t\t\tthis.usegm,\n\t\t\twidth,\n\t\t\tcommon.exoncolor\n\t\t)\n\t\trow3\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '13px')\n\t\t\t.text(this.usegm.exon.length == 1 ? 'RNA' : client.gmmode.exononly)\n\t\t// 4 - protein\n\t\tif (this.usegm.coding) {\n\t\t\trow4 = holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '1px')\n\t\t\t\t.attr('class', this.gmmode == client.gmmode.protein ? 'sja_inset_a' : 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (hideuponselect) {\n\t\t\t\t\t\tthis.usegmtip.fadeout()\n\t\t\t\t\t} else {\n\t\t\t\t\t\trow4.attr('class', 'sja_inset_a')\n\t\t\t\t\t\tif (row1) row1.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row2) row2.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row3) row3.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row5) row5.attr('class', 'sja_menuoption')\n\t\t\t\t\t}\n\t\t\t\t\tthis.setgmmode(client.gmmode.protein, true)\n\t\t\t\t})\n\t\t\tsketchProtein2(\n\t\t\t\trow4.append('div').style('vertical-align', 'middle').style('display', 'inline-block').style('padding', '0px'),\n\t\t\t\tthis.usegm,\n\t\t\t\twidth\n\t\t\t)\n\t\t\trow4.append('div').style('display', 'inline-block').style('padding', '13px').text(client.gmmode.protein)\n\t\t}\n\t\tif (this.allgm.length > 1) {\n\t\t\trow5 = holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '1px')\n\t\t\t\t.attr('class', this.gmmode == client.gmmode.gmsum ? 'sja_inset_a' : 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (hideuponselect) {\n\t\t\t\t\t\tthis.usegmtip.fadeout()\n\t\t\t\t\t} else {\n\t\t\t\t\t\trow5.attr('class', 'sja_inset_a')\n\t\t\t\t\t\tif (row1) row1.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row2) row2.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row3) row3.attr('class', 'sja_menuoption')\n\t\t\t\t\t\tif (row4) row4.attr('class', 'sja_menuoption')\n\t\t\t\t\t}\n\t\t\t\t\tthis.setgmmode(client.gmmode.gmsum, true)\n\t\t\t\t})\n\t\t\trow5\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '13px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.text('Aggregation of ' + this.allgm.length + ' isoforms')\n\t\t}\n\t}\n\n\tallowGenomeMode() {\n\t\t/*\n\t\tallow some mds3 tk to disable genomic view mode, due to gdc ssm genomic range query is not working yet\n\t\t*/\n\t\tfor (const t of this.tklst) {\n\t\t\tif (t.type == 'mds3' && t.mds?.noGenomicMode4lollipopTk) return false\n\t\t}\n\t\treturn true\n\t}\n\n\tshowisoform4switch(holder, hideuponselect) {\n\t\t/*\n\t\tshowing gene in gmmode\n\t\tlist all isoforms to allow switching isoform\n\t\tnow delegates to the reusable isoformSelect component in dom/\n\t\t*/\n\t\tif (!this.allgm) {\n\t\t\tthis.error('this.allgm[] missing')\n\t\t\treturn\n\t\t}\n\t\tif (!this.usegm) {\n\t\t\tthis.error('this.usegm missing')\n\t\t\treturn\n\t\t}\n\n\t\tisoformSelect({\n\t\t\tholder,\n\t\t\tallgm: this.allgm,\n\t\t\tusegm: this.usegm,\n\t\t\tonSelect: async gm1 => {\n\t\t\t\tif (hideuponselect) {\n\t\t\t\t\tthis.usegmtip.fadeout()\n\t\t\t\t}\n\t\t\t\tthis.holder0.selectAll('*').remove()\n\n\t\t\t\t/*\n\t\t\t\tthis selected isoform may not have genomic sequence loaded\n\t\t\t\twhich is initially only loaded in block.init for bb.usegm\n\t\t\t\tnow may need to load it\n\t\t\t\t*/\n\t\t\t\tif (!gm1.genomicseq) {\n\t\t\t\t\tconst data = await dofetch3('ntseq', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: JSON.stringify({\n\t\t\t\t\t\t\tgenome: this.genome.name,\n\t\t\t\t\t\t\tcoord: gm1.chr + ':' + (gm1.start + 1) + '-' + gm1.stop\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t\tif (data.error) {\n\t\t\t\t\t\tthis.error(data.error)\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tgm1.genomicseq = data.seq\n\t\t\t\t\tgm1.aaseq = common.nt2aa(gm1)\n\t\t\t\t}\n\n\t\t\t\t// quick fix based on changes to mds3/maketk\n\t\t\t\tconst tklst = []\n\t\t\t\tfor (const t of this.tklst) {\n\t\t\t\t\tif (t.type == client.tkt.usegm) continue\n\t\t\t\t\tif (t.type == client.tkt.mds3) delete t.mds\n\t\t\t\t\ttklst.push(t)\n\t\t\t\t}\n\t\t\t\tnew Block({\n\t\t\t\t\tholder: this.holder0,\n\t\t\t\t\tgenome: this.genome,\n\t\t\t\t\thostURL: this.hostURL,\n\t\t\t\t\tnobox: true,\n\t\t\t\t\tgmstackheight: 37,\n\t\t\t\t\tusegm: gm1,\n\t\t\t\t\tallgm: this.allgm,\n\t\t\t\t\ttklst,\n\t\t\t\t\tgmmode: gm1.cdslen ? client.gmmode.protein : client.gmmode.exononly,\n\t\t\t\t\thidedatasetexpression: this.hidedatasetexpression,\n\t\t\t\t\thidegenecontrol: this.hidegenecontrol,\n\t\t\t\t\thidegenelegend: this.hidegenelegend,\n\t\t\t\t\tvariantPageCall_snv: this.variantPageCall_snv,\n\t\t\t\t\tsamplecart: this.samplecart,\n\t\t\t\t\tdebugmode: this.debugmode\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\t/** __gm__ ends **/\n\n\t/** __subpanel **/\n\n\tadd_subpanel() {\n\t\t/*\n\tcalled by:\n\t- in ifbusy(), when all tracks of the browser finish loading\n\t- when changing view range for one subpanel (by panning, zooming)\n\t*/\n\n\t\tif (this.subpanels.length == 0) {\n\t\t\tthis.clean_subpanel()\n\t\t\treturn\n\t\t}\n\t\tfor (let panelidx = 0; panelidx < this.subpanels.length; panelidx++) {\n\t\t\tconst panelrecord = this.subpanels[panelidx]\n\n\t\t\tfor (const tk of this.tklst) {\n\t\t\t\tif (tk.hidden) continue\n\n\t\t\t\tif (!tk.subpanels[panelidx]) {\n\t\t\t\t\t/*\n\t\t\t\tmust not closure the panelidx with each tk's subpanel\n\t\t\t\tsince panels from block.subpanels[] can be deleted and array index shifted\n\t\t\t\t*/\n\t\t\t\t\ttk.subpanels[panelidx] = this.new_tk_subpanel(tk, panelrecord)\n\t\t\t\t}\n\n\t\t\t\tconst thispanel = tk.subpanels[panelidx]\n\n\t\t\t\t// position this panel\n\t\t\t\t{\n\t\t\t\t\tlet x = panelrecord.leftpad\n\t\t\t\t\tfor (let i = 0; i < panelidx; i++) {\n\t\t\t\t\t\tx += this.subpanels[i].leftpad + this.subpanels[i].width\n\t\t\t\t\t}\n\t\t\t\t\tthispanel.gtksubpanel.transition().attr('transform', 'translate(' + x + ',0)')\n\t\t\t\t}\n\n\t\t\t\tif (\n\t\t\t\t\tthispanel.chr == panelrecord.chr &&\n\t\t\t\t\tthispanel.start == panelrecord.start &&\n\t\t\t\t\tthispanel.stop == panelrecord.stop &&\n\t\t\t\t\tthispanel.width == panelrecord.width\n\t\t\t\t) {\n\t\t\t\t\t// no need to update this panel\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\t// update this panel in this track\n\t\t\t\tthispanel.chr = panelrecord.chr\n\t\t\t\tthispanel.start = panelrecord.start\n\t\t\t\tthispanel.stop = panelrecord.stop\n\t\t\t\tthispanel.width = panelrecord.width\n\t\t\t\tthispanel.leftpad = panelrecord.leftpad\n\n\t\t\t\tthis.updateruler_subpanel(panelrecord)\n\n\t\t\t\tswitch (tk.type) {\n\t\t\t\t\tcase client.tkt.bam:\n\t\t\t\t\t\tbamload(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.bedj:\n\t\t\t\t\t\tbedjloadsubpanel(tk, this, thispanel)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.bigwig:\n\t\t\t\t\t\tbigwigloadsubpanel(tk, this, thispanel)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.bigwigstranded:\n\t\t\t\t\t\tbigwigstrandedloadsubpanel(tk, this, thispanel)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.hicstraw:\n\t\t\t\t\t\thicstrawload(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.ase:\n\t\t\t\t\t\taseload(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.mdsjunction:\n\t\t\t\t\t\tmdsjunctionload(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.mdssvcnv:\n\t\t\t\t\t\tmdssvcnvload(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.mds3:\n\t\t\t\t\t\tmds3_load(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.bedgraphdot:\n\t\t\t\t\t\tbedgraphdot_load(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.mdsexpressionrank:\n\t\t\t\t\t\tmdsexpressionrankload(tk, this)\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase client.tkt.aicheck:\n\t\t\t\t\t\taicheckloadsubpanel(tk, this, thispanel)\n\t\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.clean_subpanel()\n\t}\n\n\tnew_tk_subpanel(tk, panelrecord) {\n\t\t/*\n\tpanelrecord is from block.subpanels[]\n\tcreate an instance of it for this track\n\tokay to keep closure between paneltkinstance with panelrecord\n\t*/\n\n\t\t// panel instance in this track\n\t\t// do not assign chr/start so that it won't match and will trigger track loading\n\t\tconst obj = {\n\t\t\theight: 30 // default dummy height\n\t\t}\n\n\t\tobj.gtksubpanel = tk.gtksubpanels.append('g').on('mousedown', event => {\n\t\t\t// scrolling a sub panel\n\n\t\t\tevent.preventDefault()\n\t\t\tconst body = d3select(document.body)\n\t\t\tconst x = event.clientX\n\n\t\t\tbody\n\t\t\t\t.on('mousemove', event => {\n\t\t\t\t\tpanelrecord.coord.g.attr('transform', 'translate(' + (event.clientX - x) + ',0)')\n\n\t\t\t\t\tfor (const t2 of this.tklst) {\n\t\t\t\t\t\tif (t2.hidden) continue\n\t\t\t\t\t\tconst t2panel = t2.subpanels.find(\n\t\t\t\t\t\t\ti => i.chr == panelrecord.chr && i.start == panelrecord.start && i.stop == panelrecord.stop\n\t\t\t\t\t\t)\n\t\t\t\t\t\tif (t2panel) {\n\t\t\t\t\t\t\tt2panel.glider.attr('transform', 'translate(' + (event.clientX - x) + ',0)')\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tconsole.log(panelrecord.chr, panelrecord.start, panelrecord.stop)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\t.on('mouseup', event => {\n\t\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t\t\t\tconst xoff = event.clientX - x\n\t\t\t\t\tif (xoff == 0) return\n\t\t\t\t\t// set new view range\n\t\t\t\t\tconst bpspan = panelrecord.stop - panelrecord.start // bp span won't change when panning\n\t\t\t\t\tconst dist = Math.ceil((Math.abs(xoff) * bpspan) / panelrecord.width)\n\t\t\t\t\tlet shiftback = false\n\t\t\t\t\tif (xoff > 0) {\n\t\t\t\t\t\t// to left\n\t\t\t\t\t\tif (panelrecord.start <= 0) {\n\t\t\t\t\t\t\tshiftback = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (panelrecord.start < dist) {\n\t\t\t\t\t\t\t\tpanelrecord.start = 0\n\t\t\t\t\t\t\t\tpanelrecord.stop = dist\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tpanelrecord.start -= dist\n\t\t\t\t\t\t\t\tpanelrecord.stop -= dist\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// to right\n\t\t\t\t\t\tconst l = this.genome.chrlookup[panelrecord.chr.toUpperCase()].len\n\t\t\t\t\t\tif (panelrecord.stop >= l) {\n\t\t\t\t\t\t\tshiftback = true\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (panelrecord.stop + dist > l) {\n\t\t\t\t\t\t\t\tpanelrecord.stop = l\n\t\t\t\t\t\t\t\tpanelrecord.start = panelrecord.stop - bpspan\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tpanelrecord.start += dist\n\t\t\t\t\t\t\t\tpanelrecord.stop += dist\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (shiftback) {\n\t\t\t\t\t\tpanelrecord.coord.g.transition().attr('transform', 'translate(0,0)')\n\t\t\t\t\t\tfor (const t2 of this.tklst) {\n\t\t\t\t\t\t\tif (t2.hidden) continue\n\t\t\t\t\t\t\tconst t2panel = t2.subpanels.find(\n\t\t\t\t\t\t\t\ti => i.chr == panelrecord.chr && i.start == panelrecord.start && i.stop == panelrecord.stop\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\tif (t2panel) {\n\t\t\t\t\t\t\t\tt2panel.glider.transition().attr('transform', 'translate(0,0)')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\t// subpanel panned, reload tracks\n\t\t\t\t\t// for this, must cancel block pan memory so reloading some client-rendered tracks (junction) won't be affected\n\t\t\t\t\tdelete this.pannedpx\n\t\t\t\t\tthis.add_subpanel()\n\t\t\t\t})\n\t\t})\n\n\t\tobj.subpaneltkbgrect = obj.gtksubpanel.append('rect').attr('fill', 'white').attr('fill-opacity', 0)\n\n\t\tobj.glider = obj.gtksubpanel.append('g')\n\n\t\t// important!\n\n\t\tif (tk.type == client.tkt.bedj) {\n\t\t\tobj.img = obj.glider.append('image')\n\t\t} else if (tk.type == client.tkt.bigwig) {\n\t\t\tobj.img = obj.glider.append('image')\n\t\t} else if (tk.type == client.tkt.bigwigstranded) {\n\t\t\tobj.strand1 = {\n\t\t\t\timg: obj.glider.append('image')\n\t\t\t}\n\t\t\tobj.strand2 = {\n\t\t\t\timg: obj.glider.append('image')\n\t\t\t}\n\t\t} else if (tk.type == client.tkt.aicheck) {\n\t\t\tobj.img = obj.glider.append('image')\n\t\t}\n\n\t\tobj.cloak = obj.gtksubpanel.append('g').attr('transform', 'scale(0)')\n\t\tobj.cloakbox = obj.cloak.append('rect').attr('fill', 'white').attr('fill-opacity', 0)\n\t\tobj.cloaktext = obj.cloak\n\t\t\t.append('text')\n\t\t\t.attr('id', 'loadingCloak2')\n\t\t\t.text('Loading ...')\n\t\t\t.attr('fill', common.defaultcolor)\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('font-weight', 'bold')\n\t\t\t.attr('font-size', '18px')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'middle')\n\n\t\treturn obj\n\t}\n\n\tclean_subpanel() {\n\t\t// remove excess panels\n\t\tlet removed = false\n\t\tfor (const tk of this.tklst) {\n\t\t\tif (tk.hidden) continue\n\t\t\twhile (tk.subpanels.length > this.subpanels.length) {\n\t\t\t\tconst p = tk.subpanels.pop()\n\t\t\t\tp.gtksubpanel.remove()\n\t\t\t\tremoved = true\n\t\t\t}\n\t\t}\n\t\tif (removed) {\n\t\t\tthis.blocksetw()\n\t\t}\n\t}\n\n\ttkcloakon_subpanel(panel) {\n\t\tpanel.cloak.attr('transform', 'scale(1)')\n\t\tpanel.cloakbox\n\t\t\t.attr('width', panel.width)\n\t\t\t.attr('height', panel.height)\n\t\t\t.transition()\n\t\t\t.duration(600)\n\t\t\t.attr('fill-opacity', 0.5)\n\t\tpanel.cloaktext\n\t\t\t.attr('x', panel.width / 2)\n\t\t\t.attr('y', panel.height / 2)\n\t\t\t.transition()\n\t\t\t.duration(600)\n\t\t\t.attr('fill-opacity', 1)\n\t\tif (panel.gerror) {\n\t\t\tpanel.gerror.remove()\n\t\t}\n\t}\n\n\ttkcloakoff_subpanel(panel, data) {\n\t\tpanel.cloak.attr('transform', 'scale(0)')\n\t\tpanel.cloakbox.attr('fill-opacity', 0)\n\t\tpanel.cloaktext.attr('fill-opacity', 0)\n\t\tpanel.glider.attr('transform', 'translate(0,0)')\n\t\tif (!data) {\n\t\t\tthis.tkerror_subpanel(panel, 'Server error ...')\n\t\t} else if (data.error) {\n\t\t\tthis.tkerror_subpanel(panel, data.error)\n\t\t}\n\t}\n\n\ttkerror_subpanel(panel, msg) {\n\t\tpanel.gerror = panel.glider\n\t\t\t.append('text')\n\t\t\t.text(msg)\n\t\t\t.attr('x', panel.width / 2)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('y', panel.height / 2)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('font-size', '14px')\n\t}\n\n\tzoombutton_mouseover(fold, zoomout, button) {\n\t\t/* mouse over zoom button\n\tif there are subpanels, show button for subpanels to allow zoom that panel instead of main rglst\n\t*/\n\n\t\tif (this.subpanels.length == 0) return\n\t\t// has subpanels, show options for zooming subpanels\n\n\t\t{\n\t\t\tconst p = button.getBoundingClientRect()\n\t\t\tthis.blocktip\n\t\t\t\t.clear()\n\t\t\t\t.showunder(button)\n\t\t\t\t.d.style('top', null)\n\t\t\t\t.style('bottom', window.innerHeight - p.top - window.pageYOffset + 3 + 'px')\n\t\t}\n\n\t\tthis.blocktip.d\n\t\t\t.append('div')\n\t\t\t.html('ZOOM ' + (zoomout ? 'OUT' : 'IN') + ' ' + fold + ' FOLDS ON A SUB PANEL')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('color', '#858585')\n\t\t\t.style('margin', '5px')\n\n\t\tconst table = this.blocktip.d.append('table')\n\n\t\tfor (const [panelidx, panel] of this.subpanels.entries()) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.text(panel.chr + ':' + panel.start + '-' + panel.stop)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst mid = Math.ceil((panel.start + panel.stop) / 2)\n\t\t\t\t\tconst span = Math.ceil(\n\t\t\t\t\t\tMath.max((panel.stop - panel.start) * (zoomout ? fold : 1 / fold), panel.width / ntpxwidth)\n\t\t\t\t\t)\n\t\t\t\t\tconst chrlen = this.genome.chrlookup[panel.chr.toUpperCase()].len\n\n\t\t\t\t\t// buggy!\n\t\t\t\t\tif (mid < span / 2) {\n\t\t\t\t\t\tpanel.start = 0\n\t\t\t\t\t\tpanel.stop = span\n\t\t\t\t\t} else if (mid + span / 2 > chrlen) {\n\t\t\t\t\t\tpanel.stop = chrlen\n\t\t\t\t\t\tpanel.start = chrlen - span\n\t\t\t\t\t} else {\n\t\t\t\t\t\tpanel.start = mid - Math.ceil(span / 2)\n\t\t\t\t\t\tpanel.stop = panel.start + span\n\t\t\t\t\t}\n\n\t\t\t\t\tpanel.start = Math.max(0, panel.start)\n\t\t\t\t\tpanel.stop = Math.min(panel.stop, chrlen)\n\n\t\t\t\t\tpanel.exonsf = panel.width / (panel.stop - panel.start)\n\n\t\t\t\t\tthis.blocktip.hide()\n\t\t\t\t\tthis.add_subpanel()\n\t\t\t\t})\n\n\t\t\t/*\n\t\ttr.append('td')\n\t\t\t.text('DELETE')\n\t\t\t.attr('class','sja_clbtext')\n\t\t\t.style('font-size','.7em')\n\t\t\t.on('click',()=>{\n\t\t\t\tthis.blocktip.hide()\n\n\t\t\t\tconst _p = this.subpanels.splice(panelidx,1)[0]\n\t\t\t\t_p.coord.g0.remove()\n\n\t\t\t\t// remove instances of this panel from tracks\n\t\t\t\tfor(const t of this.tklst) {\n\t\t\t\t\tif(t.hidden) continue\n\t\t\t\t\tconst thispanel = t.subpanels.splice( panelidx, 1)[0]\n\t\t\t\t\tthispanel.gtksubpanel.remove()\n\t\t\t\t}\n\n\t\t\t\tthis.blocksetw()\n\t\t\t\tthis.block_setheight()\n\t\t\t})\n\t\t\t*/\n\t\t}\n\t}\n\n\tinit_coord_subpanel(panel) {\n\t\t/*\n\tinitialize subpanel\n\tan element from block.subpanels[]\n\t*/\n\t\tpanel.coord = {}\n\t\tpanel.coord.g0 = this.coord.gcoordsubpanels.append('g') // immobile\n\n\t\t// background box works for drag and move\n\t\tpanel.subpanelbgrect = panel.coord.g0.append('rect').attr('y', -this.coordyp1 - this.rulerheight)\n\t\tif (panel.background) {\n\t\t\tpanel.subpanelbgrect.attr('fill', panel.background)\n\t\t} else {\n\t\t\tpanel.subpanelbgrect.attr('fill', 'white').attr('fill-opacity', 0)\n\t\t}\n\n\t\tpanel.subpanelleftborder = panel.coord.g0\n\t\t\t.append('rect')\n\t\t\t.attr('y', -this.coordyp1 - this.rulerheight)\n\t\t\t.attr('x', -panel.leftpad)\n\t\t\t.attr('width', panel.leftpad)\n\t\tif (panel.leftborder) {\n\t\t\tpanel.subpanelleftborder.attr('fill', panel.leftborder)\n\t\t} else {\n\t\t\tpanel.subpanelleftborder.attr('fill', 'white').attr('fill-opacity', 0)\n\t\t}\n\n\t\tpanel.coord.g = panel.coord.g0.append('g') // scrolls\n\t\tpanel.coord.axesg = panel.coord.g.append('g')\n\t\tpanel.coord.grab = panel.coord.g\n\t\t\t.append('rect')\n\t\t\t.attr('fill', 'white')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.attr('y', -this.coordyp1 - this.rulerheight)\n\t\t\t.on('mousedown', event => {\n\t\t\t\tthis.rulermousedown(event, panel)\n\t\t\t\t\t.then(tmp => {\n\t\t\t\t\t\tpanel.busy = false\n\t\t\t\t\t\tconst [toofine, startpx, spanpx] = tmp\n\t\t\t\t\t\t/*\n\t\t\t\tif(panel.toselecthlregion) {\n\t\t\t\t\tthis.busy=false\n\t\t\t\t\tdelete this.toselecthlregion\n\t\t\t\t\tconst [startidx,startpos] = this.pxoff2region(startpx)\n\t\t\t\t\tconst [stopidx, stoppos] = this.pxoff2region(startpx+spanpx)\n\t\t\t\t\tconst chr=this.rglst[startidx].chr\n\t\t\t\t\tif(chr==this.rglst[stopidx].chr) {\n\t\t\t\t\t\tthis.addhlregion( chr, Math.min(startpos, stoppos), Math.max(startpos, stoppos) )\n\t\t\t\t\t}\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t*/\n\t\t\t\t\t\t// zoom in\n\t\t\t\t\t\tif (toofine) {\n\t\t\t\t\t\t\t// too fine won't zoom in\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t\tpanel.zoomedin = true\n\t\t\t\t\t\tpanel.start += Math.ceil(startpx / panel.exonsf)\n\t\t\t\t\t\tpanel.stop = panel.start + Math.ceil(spanpx / panel.exonsf)\n\t\t\t\t\t\tpanel.exonsf = panel.width / (panel.stop - panel.start)\n\n\t\t\t\t\t\t// must cancel block pan memory so reloading some client-rendered tracks (junction) won't be affected\n\t\t\t\t\t\tdelete this.pannedpx\n\t\t\t\t\t\tthis.add_subpanel()\n\t\t\t\t\t})\n\t\t\t\t\t.catch(e => {\n\t\t\t\t\t\tif (e == 'busy') return\n\t\t\t\t\t\tthis.error(e.message)\n\t\t\t\t\t\tconsole.log(e.stack)\n\t\t\t\t\t})\n\t\t\t})\n\t}\n\n\tupdateruler_subpanel(panel) {\n\t\t// panel is element from block.subpanels[]\n\n\t\tpanel.coord.g.attr('transform', 'translate(0,0)')\n\n\t\t// if at bplevel, will show nt seq\n\t\tpanel.coord.height =\n\t\t\tthis.coordyp1 + this.rulerheight + this.coordyp2 + (panel.stop - panel.start <= panel.width ? baseheight + 2 : 0)\n\t\tthis.update_ruler_height()\n\n\t\tpanel.coord.grab.attr('height', panel.coord.height)\n\t\tpanel.coord.axesg.selectAll('*').remove()\n\n\t\tconst pxpernt = panel.width / (panel.stop - panel.start) // # pixel per nt\n\n\t\t{\n\t\t\tconst rulerg = panel.coord.axesg.append('g')\n\t\t\t// 0-based to 1-based\n\t\t\tconst domain = [panel.start + 1, panel.stop + 1]\n\t\t\tconst range = [pxpernt / 2, panel.width - pxpernt / 2] // ADJUST shift half nt px width to right\n\n\t\t\t// measure coordinate text width to decide how many ticks to use\n\t\t\tlet maxticknumber\n\t\t\t{\n\t\t\t\tlet w\n\t\t\t\tconst pos = panel.stop\n\t\t\t\trulerg\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(pos > 1000000 ? d3format('s')(pos) : d3format(',d')(pos))\n\t\t\t\t\t.attr('font-size', this.rulerfontsize)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tw = this.getBBox().width\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t\tmaxticknumber = Math.floor(panel.width / (w + 60))\n\t\t\t}\n\n\t\t\tconst scale = scaleLinear().domain(domain).range(range)\n\t\t\tconst axis = axisTop().scale(scale).tickSize(this.rulerticksize).ticks(maxticknumber)\n\t\t\tif (panel.stop - panel.start > 1000000) {\n\t\t\t\taxis.tickFormat(d3format('s'))\n\t\t\t} else {\n\t\t\t\taxis.tickFormat(d3format(',d'))\n\t\t\t}\n\t\t\taxisstyle({\n\t\t\t\taxis: rulerg.call(axis),\n\t\t\t\tcolor: 'black',\n\t\t\t\tshowline: true,\n\t\t\t\tfontsize: this.rulerfontsize\n\t\t\t})\n\t\t}\n\n\t\tif (panel.stop - panel.start <= panel.width) {\n\t\t\t// get nt sequence\n\t\t\tconst seqg = panel.coord.axesg.append('g').attr('transform', 'translate(0,' + this.coordyp2 + ')')\n\t\t\tthis.getntsequence4ruler(panel, seqg)\n\t\t}\n\t}\n\n\t/** __subpanel ends **/\n\n\terror(m) {\n\t\tsayerror(this.errdiv, m)\n\t}\n\n\tmoremenu(tip) {\n\t\t// a row of buttons\n\t\t{\n\t\t\tconst row = tip.d.append('div').style('margin-bottom', '10px')\n\n\t\t\t// svg\n\t\t\trow\n\t\t\t\t.append('button')\n\t\t\t\t.text('Export SVG')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.hide()\n\t\t\t\t\timport('./block.svg').then(p => {\n\t\t\t\t\t\tp.default(this)\n\t\t\t\t\t})\n\t\t\t\t})\n\n\t\t\t// dna\n\t\t\trow\n\t\t\t\t.append('button')\n\t\t\t\t.text('Reference DNA sequence')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tmaygetdna(this, tip)\n\t\t\t\t})\n\n\t\t\t// ideogram\n\t\t\tif (this.genome.hasIdeogram) {\n\t\t\t\trow\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.text((this.ideogram.visible ? 'Hide' : 'Show') + ' ideogram')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.toggleIdeogram()\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\t// highlight region\n\t\t{\n\t\t\tconst div = tip.d\n\t\t\t\t.append('div')\n\t\t\t\t.style('border', 'solid 1px #eee')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.style('margin', '20px 0px 20px 0px')\n\t\t\tconst row = div.append('div')\n\t\t\trow.append('span').text('Highlight').style('opacity', 0.75).style('padding-right', '10px')\n\t\t\trow\n\t\t\t\t.append('button')\n\t\t\t\t.text('Select a region')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.clear()\n\t\t\t\t\ttip.d.append('div').html('&#9660; drag on the ruler')\n\t\t\t\t\ttip.d.transition().style('top', Number.parseInt(tip.d.style('top')) - 60 + 'px')\n\t\t\t\t\tthis.toselecthlregion = true\n\t\t\t\t})\n\t\t\trow\n\t\t\t\t.append('button')\n\t\t\t\t.text('Enter regions')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.clear()\n\t\t\t\t\tconst ta = tip.d.append('textarea').attr('rows', 5).attr('cols', 30)\n\t\t\t\t\tconst row = tip.d.append('div').style('margin-top', '3px')\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.text('Submit')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tconst str = ta.property('value').trim()\n\t\t\t\t\t\t\tif (!str) return\n\t\t\t\t\t\t\tfor (const line of str.split('\\n')) {\n\t\t\t\t\t\t\t\tconst l = line.split(' ')\n\t\t\t\t\t\t\t\tif (!l[0]) continue\n\t\t\t\t\t\t\t\tconst r = coord.string2pos(\n\t\t\t\t\t\t\t\t\tl[0],\n\t\t\t\t\t\t\t\t\tthis.genome,\n\t\t\t\t\t\t\t\t\ttrue // do not extend\n\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\tif (!r) continue\n\t\t\t\t\t\t\t\tthis.addhlregion(r.chr, r.start, r.stop, l[1] || hlregioncolor)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tthis.moremenu(tip.clear())\n\t\t\t\t\t\t})\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.text('Clear')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tta.property('value', '')\n\t\t\t\t\t\t})\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.html(\n\t\t\t\t\t\t\t'<ul><li>Limited to adding regions to the current chromosome</li><li>One row per region</li><li>Example row: \"chr1:123-456 #96FAF8\"</li><li>Color is optional, must be hex format</li><li>If provided, separate coordinate and color by space</ul>'\n\t\t\t\t\t\t)\n\t\t\t\t})\n\n\t\t\t// list for editing\n\t\t\tif (this.hlregion.lst.length) {\n\t\t\t\tconst div2 = div.append('div').style('margin-top', '10px')\n\t\t\t\tfor (const h of this.hlregion.lst) {\n\t\t\t\t\tconst row = div2.append('div')\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.html('&#10005;')\n\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tfor (let i = 0; i < this.hlregion.lst.length; i++) {\n\t\t\t\t\t\t\t\tconst h2 = this.hlregion.lst[i]\n\t\t\t\t\t\t\t\tif (h2.chr == h.chr && h2.start == h.start && h2.stop == h.stop) {\n\t\t\t\t\t\t\t\t\tthis.hlregion.lst.splice(i, 1)\n\t\t\t\t\t\t\t\t\th2.rect.remove()\n\t\t\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\trow.remove()\n\t\t\t\t\t\t})\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('color', '#858585')\n\t\t\t\t\t\t.html('&nbsp;&nbsp;' + h.chr + ':' + h.start + '-' + h.stop + '&nbsp;&nbsp;')\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('input')\n\t\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t\t.property('value', h.color)\n\t\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\t\th.color = event.target.value\n\t\t\t\t\t\t\th.rect.transition().attr('fill', h.color)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// experimental\n\t\tif (!JSON.parse(sessionStorage.getItem('optionalFeatures')).disableBlockExperimentFeatures) {\n\t\t\ttip.d\n\t\t\t\t.append('div')\n\t\t\t\t.text('EXPERIMENTAL')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('margin', '10px 0px 2px 0px')\n\t\t\t\t.style('opacity', 0.5)\n\t\t\ttip.d\n\t\t\t\t.append('button')\n\t\t\t\t.text('Customize mutation class color')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.clear()\n\t\t\t\t\tclient.mclasscolorchangeui(tip)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tinitIdeogram(arg) {\n\t\tconst vpad = 5\n\t\tthis.ideogram = {\n\t\t\twidth: 800,\n\t\t\theight: 20,\n\t\t\tvisible: arg.showIdeogram, // boolean, if ideogram is showing or not\n\t\t\tchr: null // current chr, to be set when rglst is available\n\t\t}\n\t\tthis.ideogram.div = this.holder\n\t\t\t.append('div') // place to show ideogram\n\t\t\t.style('position', 'relative')\n\t\t\t.style('width', this.ideogram.width + 'px')\n\t\t\t.style('margin', '5px')\n\n\t\tthis.ideogram.canvas = this.ideogram.div\n\t\t\t.append('canvas')\n\t\t\t.attr('width', this.ideogram.width)\n\t\t\t.attr('height', this.ideogram.height)\n\t\t\t.style('margin-top', vpad + 'px')\n\n\t\tthis.ideogram.ctx = this.ideogram.canvas.node().getContext('2d')\n\t\tthis.ideogram.blueBox = this.ideogram.div\n\t\t\t.append('div')\n\t\t\t.style('border', 'solid 1px blue')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('height', this.ideogram.height + vpad * 2 + 'px')\n\t\t\t.style('top', '0px')\n\t}\n\ttoggleIdeogram() {\n\t\tif (!this.ideogram) return\n\t\tthis.ideogram.visible = !this.ideogram.visible\n\t\tif (!this.ideogram.visible) {\n\t\t\tdisappear(this.ideogram.div)\n\t\t\treturn\n\t\t}\n\t\tappear(this.ideogram.div)\n\t\tthis.updateIdeogram()\n\t}\n\tasync updateIdeogram() {\n\t\tif (!this.ideogram) return\n\t\tconst currentChr = this.rglst[0].chr\n\t\tif (currentChr != this.ideogram.chr) await this.plotIdeogram(currentChr)\n\t\t// TODO move blueBox\n\t}\n\tasync plotIdeogram(chr) {\n\t\tif (!this.ideogram) return\n\t\ttry {\n\t\t\tif (!chr) throw 'unknonw chr to show ideogram'\n\t\t\tthis.ideogram.chr = chr\n\t\t\tconst data = await dofetch3('ideogram?genome=' + this.genome.name + '&chr=' + chr)\n\t\t\tif (data.error) throw data.error\n\t\t\tif (!Array.isArray(data)) throw 'data is not array'\n\t\t\tconsole.log(data)\n\t\t\t// TODO plot on canvas\n\t\t} catch (e) {\n\t\t\tthis.error(e.message || e)\n\t\t}\n\t}\n\n\tmds_handle_make(key) {\n\t\t// make handle for a mds dataset, also the click menu for that handle\n\t\tconst ds = this.genome.datasets[key]\n\t\tif (!ds) return\n\t\tconst d0 = this.ctrl.mdsHandleHolder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin-right', '2px')\n\t\t\t.style('border', 'solid 1px black')\n\t\tds.handle = {\n\t\t\tholder: d0\n\t\t}\n\t\tds.handle.labelButton = d0\n\t\t\t.append('div')\n\t\t\t.text(ds.label)\n\t\t\t.attr('class', 'sja_handle_green')\n\t\t\t.on('click', async event => {\n\t\t\t\tthis.blocktip.clear().showunder(event.target)\n\n\t\t\t\tif (ds.mdsIsUninitiated) {\n\t\t\t\t\tconst d = await dofetch3(`getDataset?genome=${this.genome.name}&dsname=${ds.label}`)\n\t\t\t\t\tif (d.error) throw d.error\n\t\t\t\t\tif (!d.ds) throw 'ds missing'\n\t\t\t\t\tObject.assign(ds, d.ds)\n\t\t\t\t\tdelete ds.mdsIsUninitiated\n\t\t\t\t}\n\n\t\t\t\tif (ds.queries) {\n\t\t\t\t\tconst table = this.blocktip.d.append('table')\n\t\t\t\t\t// one tk per tr\n\n\t\t\t\t\tfor (const querykey in ds.queries) {\n\t\t\t\t\t\tif (ds.queries[querykey].hideforthemoment) continue\n\n\t\t\t\t\t\tconst findtkindex = this.tklst.findIndex(t => t.mds && t.mds.label == key && t.querykey == querykey)\n\n\t\t\t\t\t\tconst tr = table.append('tr')\n\t\t\t\t\t\tconst td1 = tr.append('td')\n\t\t\t\t\t\tif (findtkindex != -1) {\n\t\t\t\t\t\t\ttd1.html('&nbsp;&nbsp;SHOWN').style('color', '#858585').style('font-size', '.8em')\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\ttr.append('td')\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.style('padding', '10px 15px')\n\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t.text(ds.queries[querykey].name)\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tthis.blocktip.hide()\n\t\t\t\t\t\t\t\tif (findtkindex != -1) {\n\t\t\t\t\t\t\t\t\t// shown, to drop\n\t\t\t\t\t\t\t\t\tthis.tk_remove(findtkindex)\n\t\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tthis.mds_load_query_bykey(ds, { querykey: querykey })\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (ds.about) {\n\t\t\t\t\tthis.blocktip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t\t.style('color', '#858585')\n\t\t\t\t\t\t.text('About this dataset')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tthis.blocktip.clear()\n\t\t\t\t\t\t\tclient.make_table_2col(this.blocktip.d, ds.about)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t}\n\n\tasync mds_load_query_bykey(ds, q) {\n\t\t/*\n\t\tofficial ds\n\t\tq comes from datasetqueries of embedding, with customizations\n\t\t*/\n\n\t\tif (ds.mdsIsUninitiated) {\n\t\t\tconst d = await dofetch3(`getDataset?genome=${this.genome.name}&dsname=${ds.label}`)\n\t\t\tif (d.error) throw d.error\n\t\t\tif (!d.ds) throw 'ds missing'\n\t\t\tObject.assign(ds, d.ds)\n\t\t\tdelete ds.mdsIsUninitiated\n\t\t}\n\n\t\tif (!ds.queries) return console.log('ds.queries{} missing')\n\t\tconst tk0 = ds.queries[q.querykey]\n\t\tif (!tk0) return console.log('querykey not found in ds.queries: ' + q.querykey)\n\n\t\tif (tk0.isgenenumeric) {\n\t\t\t// gene numeric values, show gene search box\n\t\t\t// TODO not doing anything yet\n\t\t\treturn\n\t\t}\n\n\t\tif (this.tklst.find(t => t.mds && t.mds.label == ds.label && t.querykey == q.querykey)) {\n\t\t\t// already shown\n\t\t\treturn\n\t\t}\n\n\t\tif (q.singlesample && q.getsampletrackquickfix) {\n\t\t\tconst data = await dofetch3('mdssvcnv', {\n\t\t\t\tmethod: 'POST',\n\t\t\t\tbody: JSON.stringify({\n\t\t\t\t\tgenome: this.genome.name,\n\t\t\t\t\tdslabel: ds.label,\n\t\t\t\t\tquerykey: q.querykey,\n\t\t\t\t\tgettrack4singlesample: q.singlesample.name\n\t\t\t\t})\n\t\t\t})\n\t\t\tif (data.error) throw data.error\n\t\t\tif (data.tracks) {\n\t\t\t\tfor (const t of data.tracks) {\n\t\t\t\t\tconst tk = this.block_addtk_template(t)\n\t\t\t\t\tthis.tk_load(tk)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tconst tk = this.block_addtk_template(tk0)\n\t\ttk.mds = ds\n\t\ttk.querykey = q.querykey\n\t\tif (q.singlesample) {\n\t\t\t// in sampleview, to show all cnvs, not just focal ones\n\t\t\ttk.bplengthUpperLimit = 0\n\t\t}\n\t\ttk.customization = q\n\n\t\tthis.tk_load(tk)\n\t}\n\n\ttotalheight() {\n\t\tlet h = this.coord.height\n\t\tfor (const t of this.tklst) {\n\t\t\tif (t.hidden) continue\n\t\t\th += t.height\n\t\t}\n\t\treturn h\n\t}\n\n\tnewblock(arg) {\n\t\tif (!arg.holder) return this.error('holder missing')\n\t\targ.genome = this.genome\n\t\targ.hostURL = this.hostURL\n\t\targ.jwt = this.jwt\n\t\targ.nobox = true\n\t\treturn new Block(arg)\n\t}\n\n\tturnOnTrack(arg) {\n\t\tconst lst = Array.isArray(arg) ? arg : [arg]\n\t\tconst toadd = []\n\t\tfor (const t of lst) {\n\t\t\t{\n\t\t\t\tconst [i, tt] = findtrack(this.tklst, t)\n\t\t\t\tif (tt) {\n\t\t\t\t\t// already shown\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst [i, f] = findtrack(this.genome.tracks, t)\n\t\t\tif (f) {\n\t\t\t\ttoadd.push(f)\n\t\t\t} else {\n\t\t\t\ttoadd.push(t)\n\t\t\t}\n\t\t}\n\t\tfor (const f of toadd) {\n\t\t\tdelete f.hidden\n\t\t\tconst t = this.block_addtk_template(f)\n\t\t\tthis.tk_load(t)\n\t\t}\n\t}\n\tturnOffTrack(arg) {\n\t\tconst lst = Array.isArray(arg) ? arg : [arg]\n\t\tfor (const t of lst) {\n\t\t\tconst [idx, f] = findtrack(this.tklst, t)\n\t\t\tif (idx != -1) this.tk_remove(idx)\n\t\t}\n\t}\n\n\tshowTrackByFile(files) {\n\t\tif (!Array.isArray(files)) {\n\t\t\tthis.error('showTrackByFile() argument must be array')\n\t\t\treturn\n\t\t}\n\t\tconst type2files = new Map()\n\t\tfor (const f of files) {\n\t\t\tif (!f.type) {\n\t\t\t\tthis.error('.type missing from a file')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!f.file) {\n\t\t\t\tthis.error('.file missing from a file')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!type2files.has(f.type)) type2files.set(f.type, new Set())\n\t\t\ttype2files.get(f.type).add(f.file)\n\t\t}\n\t\tconst toremove = this.tklst.filter(t => type2files.has(t.type) && !type2files.get(t.type).has(t.file))\n\t\tconst toadd = []\n\t\tfor (const [type, files] of type2files) {\n\t\t\tfor (const file of files) {\n\t\t\t\tconst gt = this.genome.tracks.find(t => t.type == type && t.file == file)\n\t\t\t\tif (gt && !this.tklst.find(t => t.type == type && t.file == file)) {\n\t\t\t\t\t// in genome.tracks but not tklst, to show\n\t\t\t\t\ttoadd.push(gt)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tfor (const f of toremove) {\n\t\t\tthis.tk_remove(this.tklst.findIndex(t => t.type == f.type && t.file == f.file))\n\t\t}\n\t\tfor (const f of toadd) {\n\t\t\tconst t = this.block_addtk_template(f)\n\t\t\tthis.tk_load(t)\n\t\t}\n\t}\n\n\t/*********** end of class:Block  ************/\n}\n\nfunction findtrack(lst, t) {\n\t// given track object t, find the identical one in lst[]\n\tfor (const [i, f] of lst.entries()) {\n\t\tif (f.type != t.type) continue\n\t\tif (t.type == client.tkt.junction) {\n\t\t\tif (t.file || t.url) {\n\t\t\t\t// t is a single-sample track\n\t\t\t\tif (f.tracks.length == 1) {\n\t\t\t\t\tif (f.tracks[0].file ? f.tracks[0].file == t.file : f.tracks[0].url == t.url) {\n\t\t\t\t\t\treturn [i, f]\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// a multi-sample track,\n\t\t\t\t}\n\t\t\t} else if (t.tracks) {\n\t\t\t\tif (t.tracks.length == 1 && f.tracks.length == 1) {\n\t\t\t\t\t// both single sample\n\t\t\t\t\tif (f.tracks[0].file ? f.tracks[0].file == t.tracks[0].file : f.tracks[0].url == t.tracks[0].url) {\n\t\t\t\t\t\treturn [i, f]\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// number of samples not matching\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// should throw exception\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\t\t// all other track types\n\t\tif (f.type == t.type && (f.file ? f.file == t.file : f.url == t.url)) {\n\t\t\treturn [i, f]\n\t\t}\n\t}\n\treturn [-1, null]\n}\n\nfunction getrulerunit(span, ticks) {\n\t// not in use\n\tconst u = []\n\tfor (let i = 0; i < 10; i++) {\n\t\tconst p = Math.pow(10, i)\n\t\tu.push(p)\n\t\tu.push(2 * p)\n\t\tu.push(5 * p)\n\t}\n\tfor (let j of u) {\n\t\tif (Math.floor(span / j) <= ticks) {\n\t\t\treturn j\n\t\t}\n\t}\n}\n\nfunction makecoordinput(bb, butrow) {\n\tbb.coord.inputtip = new Menu({\n\t\tpadding: '0px',\n\t\toffsetX: 0,\n\t\toffsetY: 0\n\t})\n\n\tbb.coord.input = butrow\n\t\t.append('input')\n\t\t.attr('type', 'text')\n\t\t.attr('size', 20)\n\t\t.style('margin-left', '10px')\n\t\t.style('padding-right', '20px')\n\t\t.attr('aria-label', 'Genome browser coordinates')\n\n\tbb.coord.inputtipshow = () => {\n\t\tbb.coord.inputtip.clear()\n\t\tconst p = bb.coord.input.node().getBoundingClientRect()\n\t\tbb.coord.inputtip.show(p.left, p.top + p.height + 5)\n\t}\n\n\tbb.coord.input\n\t\t.on('focus', event => {\n\t\t\tevent.target.select()\n\t\t})\n\t\t.on('keyup', event => {\n\t\t\tbb.zoomedin = false\n\t\t\tbb.pannedpx = undefined\n\t\t\tbb.resized = false\n\t\t\tconst input = event.target\n\t\t\tconst v = input.value.trim()\n\t\t\tif (v.length <= 1) {\n\t\t\t\tbb.coord.inputtip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (client.keyupEnter(event)) {\n\t\t\t\tbb.coord.inputtip.hide()\n\t\t\t\tinput.blur()\n\t\t\t\tbb.jump_1basedcoordinate(v)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (event.code == 'Escape') {\n\t\t\t\tbb.coord.inputtip.hide()\n\t\t\t\tif (bb.rglst.length == 1) {\n\t\t\t\t\tconst r = bb.rglst[0]\n\t\t\t\t\tinput.value = r.chr + ':' + (r.start + 1) + '-' + (r.stop + 1)\n\t\t\t\t}\n\t\t\t\tinput.blur()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (v.length > 6) return\n\t\t\tdebouncer()\n\t\t})\n\n\tasync function genesearch() {\n\t\t// gene name lookup\n\t\tconst v = bb.coord.input.property('value')\n\t\tif (!v) return\n\t\tbb.coord.inputtipshow()\n\t\ttry {\n\t\t\tconst data = await dofetch3('genelookup', {\n\t\t\t\tbody: { genome: bb.genome.name, input: v }\n\t\t\t})\n\t\t\tif (data.error) throw data.error\n\t\t\tif (!data.hits || data.hits.length == 0) return bb.coord.inputtip.hide()\n\t\t\tfor (const s of data.hits) {\n\t\t\t\tbb.coord.inputtip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.text(s)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tbb.coord.inputtip.hide()\n\t\t\t\t\t\tbb.block_jump_gene(s)\n\t\t\t\t\t})\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tbb.inputerr(e.message || e)\n\t\t}\n\t}\n\n\tconst debouncer = debounce(genesearch, 300)\n}\n\n// allgm2sum is now imported from #dom (dom/isoformSelect.ts)\n\nconst dnalenlimit = 100000\n\nasync function maygetdna(block, tip) {\n\ttip.clear()\n\tconst regions = []\n\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\tconst r = block.rglst[i]\n\t\tregions.push({\n\t\t\tchr: r.chr,\n\t\t\tstart: r.start,\n\t\t\tstop: r.stop\n\t\t})\n\t}\n\tconst totallen = regions.reduce((i, j) => i + j.stop - j.start, 0)\n\tif (totallen > dnalenlimit) {\n\t\ttip.d.append('div').text('Please zoom in under ' + common.bplen(dnalenlimit) + ' to get DNA sequence.')\n\t\treturn\n\t}\n\tconst lst = []\n\tfor (const r of regions) {\n\t\tconst coord = r.chr + ':' + (r.start + 1) + '-' + r.stop\n\t\tconst data = await dofetch3('ntseq', {\n\t\t\tmethod: 'POST',\n\t\t\tbody: JSON.stringify({ genome: block.genome.name, coord })\n\t\t})\n\t\tlst.push('>' + coord + '\\n' + data.seq)\n\t}\n\tclient.export_data(\n\t\t'Reference DNA from ' + block.genome.name,\n\t\t[{ text: lst.join('\\n') }],\n\t\t1,\n\t\t1,\n\t\t10,\n\t\t100,\n\t\ttip.d.style('left', '100px')\n\t)\n}\n\nfunction init_cursorhlbar(block) {\n\t// highlight bar under the cursor\n\t// default fill color is registered on block, as the bar can be changed by actions in certain tracks\n\t// eg hover over splice junction. this allows the style to be restored to the bar\n\tblock.cursorhlbarFillColor = '#FFFF99'\n\tblock.cursorhlbar = block.gbase.append('rect').attr('fill', block.cursorhlbarFillColor)\n\n\tblock.gbase\n\t\t.on('mousemove', event => {\n\t\t\t// pointer() accounts for whether block is rotated or not\n\t\t\tconst x = pointer(event, block.gbase.node())[0]\n\n\t\t\tlet xoffset = block.leftheadw + block.lpad\n\n\t\t\tif (x < xoffset) {\n\t\t\t\tblock.cursorhlbar.attr('width', 0)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// if cursor in main block or sub panels, light up bar\n\t\t\tlet barx, barw\n\n\t\t\tif (x < xoffset + block.width) {\n\t\t\t\t// in main block\n\t\t\t\tbarw = Math.max(2, block.exonsf)\n\t\t\t\tbarx = x\n\t\t\t\tif (block.exonsf >= 2) {\n\t\t\t\t\t// at bp level, highlight to a bp\n\t\t\t\t\tbarx -= (x - xoffset) % block.exonsf\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\txoffset += block.width\n\t\t\t\tfor (const panel of block.subpanels) {\n\t\t\t\t\txoffset += panel.leftpad\n\t\t\t\t\tif (x < xoffset + panel.leftpad) {\n\t\t\t\t\t\t// inside left padding, no show\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\tif (x < xoffset + panel.leftpad + panel.width) {\n\t\t\t\t\t\t// inside this panel\n\t\t\t\t\t\tbarw = Math.max(2, panel.exonsf)\n\t\t\t\t\t\tbarx = x\n\t\t\t\t\t\tif (panel.exonsf >= 2) {\n\t\t\t\t\t\t\tbarx -= (x - xoffset - panel.leftpad) % panel.exonsf\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\txoffset += panel.leftpad + panel.width\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (barx) {\n\t\t\t\tblock.cursorhlbar.attr('x', barx).attr('width', barw).attr('height', block.totalheight())\n\t\t\t}\n\t\t})\n\t\t.on('mouseout', () => {\n\t\t\tblock.cursorhlbar.attr('width', 0)\n\t\t})\n}\n", "export function bamfromtemplate(tk, template) {\n\tif (!template.file && !template.url && !template.gdcFile) return 'neither file or url given'\n\treturn null\n}\n\nexport function bammaketk(tk, block) {\n\ttk.uninitialized = true\n}\n\nexport function bamload(tk, block) {\n\timport('./block.tk.bam').then(_ => {\n\t\t_.loadTk(tk, block)\n\t})\n}\n", "export function pgvfromtemplate(tk, template) {\n\ttk._template = template\n}\n\nexport function pgvmaketk(tk, block) {\n\ttk.uninitiated = 1\n}\n\nexport function pgvload(tk, block) {\n\timport('./block.tk.pgv').then(p => {\n\t\tp.loadTk(tk, block)\n\t})\n}\n", "export function ldfromtemplate(tk, template) {\n\ttk._template = template\n}\n\nexport function ldmaketk(tk, block) {\n\ttk.uninitiated = 1\n}\n\nexport function ldload(tk, block) {\n\timport('./block.tk.ld').then(p => {\n\t\tp.loadTk(tk, block)\n\t})\n}\n", "export function junctionfromtemplate(tk, template) {\n\tif (!template.tracks) {\n\t\tif (template.file || template.url) {\n\t\t\t/*\n\t\t\tno .tracks[] but has .file/.url\n\t\t\told format of defining single track\n\t\t\tor for adding a member track by clicking a dot in beeswarm plot\n\t\t\t*/\n\t\t\ttemplate.tracks = [\n\t\t\t\t{\n\t\t\t\t\tfile: template.file,\n\t\t\t\t\turl: template.url,\n\t\t\t\t\tindexURL: template.indexURL\n\t\t\t\t}\n\t\t\t]\n\t\t\tdelete template.file\n\t\t\tdelete template.url\n\t\t\tdelete template.indexURL\n\t\t\tdelete tk.file\n\t\t\tdelete tk.url\n\t\t\tdelete tk.indexURL\n\t\t} else {\n\t\t\t// no tracks\n\t\t\treturn '.tracks[] missing from junction track template'\n\t\t}\n\t}\n\ttk.tracks = []\n\tfor (const t0 of template.tracks) {\n\t\tconst t1 = {}\n\t\tfor (const k in t0) {\n\t\t\tt1[k] = t0[k]\n\t\t}\n\t\ttk.tracks.push(t1)\n\t}\n\tif (tk.tracks.length == 0) {\n\t\treturn '.tracks[] has 0 length for junction track'\n\t}\n\n\t/*\n\tINITSETSIZE\n\taxisheight and other size remains undefined\n\tfor it needs to know if the track is single sample or multi-sample\n\tupon first time data load, it will be able to tell that and set size accordingly\n\t*/\n\n\tif (template.categories) {\n\t\ttk.categories = {}\n\t\tfor (const k in template.categories) {\n\t\t\tconst t = template.categories[k]\n\t\t\ttk.categories[k] = {\n\t\t\t\tcolor: t.color,\n\t\t\t\tlabel: t.label\n\t\t\t}\n\t\t}\n\t} else {\n\t\t// no category preconfig, if found .type from data, will create on the fly\n\t\ttk.nocatepreconfig = true\n\t}\n\treturn null\n}\n\nexport function junctionmaketk(tk, block) {\n\ttk.uninitialized = true\n}\n\nexport function junctionload(tk, block) {\n\timport('./block.tk.junction').then(_ => {\n\t\t_.junctionload(tk, block)\n\t})\n}\n", "import { scaleLinear } from 'd3-scale'\nimport { axisLeft, axisRight } from 'd3-axis'\nimport * as client from './client'\nimport { basecolor } from '#shared/common.js'\n\nexport function bampilefromtemplate(tk, template) {\n\tif (!tk.fineheight) {\n\t\ttk.fineheight = 200\n\t}\n\tif (!tk.allheight) {\n\t\ttk.allheight = 100\n\t}\n\tif (!tk.midpad) {\n\t\ttk.midpad = 15\n\t}\n\tif (!tk.fineymax) {\n\t\ttk.fineymax = 50\n\t}\n}\n\nexport function bampilemaketk(tk, block) {\n\ttk.img = tk.glider.append('image').on('click', event => {\n\t\tif (!tk.link) return\n\t\t// if tk.link is provided, will work\n\t\tif (block.exonsf < 1) return\n\t\tconst x = event.clientX - block.svg.node().getBoundingClientRect().left - block.leftheadw - block.lpad\n\t\tconst [ridx, pos] = block.pxoff2region(x)\n\t\tconst chr = block.rglst[ridx].chr\n\t\tconst link = tk.link.replace('__CHR__', chr).replace('__POS__', pos + 1)\n\t\twindow.open(link)\n\t})\n\n\ttk.allaxis = tk.gleft.append('g')\n\ttk.fineaxis = tk.gleft.append('g').attr('transform', 'translate(0,' + (tk.allheight + tk.midpad) + ')')\n\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', event => {\n\t\tconfigpanel(tk, block)\n\t})\n}\n\nexport function bampileload(tk, block) {\n\tblock.tkcloakon(tk)\n\tconst par = [\n\t\t'genome=' + block.genome.name,\n\t\t'fineheight=' + tk.fineheight,\n\t\t'allheight=' + tk.allheight,\n\t\t'midpad=' + tk.midpad,\n\t\t'fineymax=' + tk.fineymax,\n\t\t'regionspace=' + block.regionspace,\n\t\t'width=' + block.width,\n\t\t'rglst=' + JSON.stringify(block.tkarg_rglst())\n\t]\n\tif (tk.usegrade) par.push('usegrade=' + tk.usegrade)\n\tif (tk.file) par.push('file=' + tk.file)\n\telse par.push('url=' + tk.url)\n\tclient\n\t\t.dofetch2('tkbampile?' + par.join('&'))\n\t\t.then(data => {\n\t\t\tif (data.error) throw { message: data.error }\n\n\t\t\tif (data.allgrades) {\n\t\t\t\ttk.grades = data.allgrades\n\t\t\t\ttk.usegrade = data.usegrade\n\t\t\t\t// show controls\n\t\t\t}\n\t\t\ttk.img\n\t\t\t\t.attr('width', block.width)\n\t\t\t\t.attr('height', tk.allheight + tk.midpad + tk.fineheight)\n\t\t\t\t.attr('xlink:href', data.src)\n\t\t\ttk.allaxis.selectAll('*').remove()\n\t\t\tif (data.allmax) {\n\t\t\t\tconst scale = scaleLinear().domain([0, data.allmax]).range([tk.allheight, 0])\n\t\t\t\tclient.axisstyle({\n\t\t\t\t\taxis: tk.allaxis.call(axisRight().scale(scale).ticks(4)),\n\t\t\t\t\tcolor: 'black',\n\t\t\t\t\tshowline: true\n\t\t\t\t})\n\t\t\t}\n\t\t\tconst scale = scaleLinear().domain([0, tk.fineymax]).range([tk.fineheight, 0])\n\t\t\tclient.axisstyle({\n\t\t\t\taxis: tk.fineaxis.call(axisLeft().scale(scale)),\n\t\t\t\tcolor: 'black',\n\t\t\t\tshowline: true\n\t\t\t})\n\t\t})\n\t\t.catch(err => {\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t\treturn err.message\n\t\t})\n\t\t.then(errmsg => {\n\t\t\ttk.height_main = tk.toppad + tk.allheight + tk.midpad + tk.fineheight + tk.bottompad\n\t\t\tblock.tkcloakoff(tk, { error: errmsg })\n\t\t\tblock.block_setheight()\n\t\t})\n}\n\nfunction configpanel(tk, block) {\n\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\tconst holder = tk.tkconfigtip.d\n\n\tif (tk.grades) {\n\t\tconst table = holder.append('table').style('margin-bottom', '10px')\n\t\tfor (const g of tk.grades) {\n\t\t\tconst tr = table.append('tr')\n\t\t\ttr.append('td').html(g == tk.usegrade ? '&#10004;' : '')\n\t\t\ttr.append('td')\n\t\t\t\t.text(g)\n\t\t\t\t.classed('sja_menuoption', true)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\ttk.usegrade = g\n\t\t\t\t\tbampileload(tk, block)\n\t\t\t\t\ttk.tkconfigtip.hide()\n\t\t\t\t})\n\t\t}\n\t} else {\n\t\tholder.append('div').style('margin', '10px').text('No grades yet.')\n\t}\n\t// read depth cutoff\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '10px')\n\t\trow.append('div').text('Read depth cutoff:').style('font-size', '.8em')\n\t\tconst input = row\n\t\t\t.append('input')\n\t\t\t.attr('size', 5)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter') return\n\t\t\t\tconst s = event.target.value\n\t\t\t\tif (!s) return\n\t\t\t\tconst v = Number.parseInt(s)\n\t\t\t\tif (Number.isNaN(v)) return\n\t\t\t\tif (v <= 0) return\n\t\t\t\ttk.fineymax = v\n\t\t\t\tbampileload(tk, block)\n\t\t\t})\n\t\trow\n\t\t\t.append('button')\n\t\t\t.text('Set')\n\t\t\t.style('margin-left', '3px')\n\t\t\t.on('click', event => {\n\t\t\t\tconst s = input.property('value')\n\t\t\t\tif (!s) return\n\t\t\t\tconst v = Number.parseInt(s)\n\t\t\t\tif (Number.isNaN(v)) return\n\t\t\t\tif (v <= 0) return\n\t\t\t\ttk.fineymax = v\n\t\t\t\tbampileload(tk, block)\n\t\t\t})\n\t}\n\tfor (const nt in basecolor) {\n\t\tconst row = holder.append('div').style('margin-bottom', '3px')\n\t\trow\n\t\t\t.append('div')\n\t\t\t.style('width', '12px')\n\t\t\t.style('height', '12px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('background-color', basecolor[nt])\n\t\t\t.style('margin-right', '10px')\n\t\trow.append('span').text(nt)\n\t}\n}\n", "export function aicheckfromtemplate(tk,template) {\n\tif(!template.file && !template.url) return 'no file or url'\n\treturn null\n}\n\n\nexport function aicheckmaketk(tk,block) {\n\ttk.uninitialized=true\n}\n\n\nexport function aicheckload(tk,block) {\n\timport('./block.tk.aicheck').then(_=>{\n\t\t_.loadTk(tk,block)\n\t})\n}\nexport function aicheckloadsubpanel(tk,block,panel) {\n\timport('./block.tk.aicheck').then(_=>{\n\t\t_.loadTksubpanel(tk,block,panel)\n\t})\n}\n", "import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport * as client from './client'\nimport { defaultcolor } from '#shared/common.js'\nimport { format as d3format } from 'd3-format'\nimport { bigwigconfigpanel } from './block.tk.bigwig'\n\nexport function bigwigstrandedfromtemplate(tk, template) {\n\tif (template.strand1) {\n\t\tconst s = {}\n\t\tfor (const k in template.strand1) {\n\t\t\ts[k] = template.strand1[k]\n\t\t}\n\t\ts.scale = {}\n\t\tif (template.strand1.scale) {\n\t\t\tfor (const k in template.strand1.scale) {\n\t\t\t\ts.scale[k] = template.strand1.scale[k]\n\t\t\t}\n\t\t} else {\n\t\t\ts.scale.auto = 1\n\t\t}\n\t\ts.barheight = template.strand1.height || 50\n\t\tif (!s.ncolor) s.ncolor = '#BD005E'\n\t\tif (!s.ncolor2) s.ncolor2 = '#5E00BD'\n\t\tif (!s.pcolor) s.pcolor = '#005EBD'\n\t\tif (!s.pcolor2) s.pcolor2 = '#FA7D00'\n\n\t\tif (s.normalize) {\n\t\t} else {\n\t\t\t// disable by default\n\t\t\ts.normalize = {\n\t\t\t\tdividefactor: 1,\n\t\t\t\tdisable: 1\n\t\t\t}\n\t\t}\n\t\ttk.strand1 = s\n\n\t\tif (!tk.strand1.name) tk.strand1.name = 'Forward'\n\t}\n\tif (template.strand2) {\n\t\tconst s = {}\n\t\tfor (const k in template.strand2) {\n\t\t\ts[k] = template.strand2[k]\n\t\t}\n\t\ts.scale = {}\n\t\tif (template.strand2.scale) {\n\t\t\tfor (const k in template.strand2.scale) {\n\t\t\t\ts.scale[k] = template.strand2.scale[k]\n\t\t\t}\n\t\t} else {\n\t\t\ts.scale.auto = 1\n\t\t}\n\t\ts.barheight = template.strand2.height || 50\n\t\tif (!s.ncolor) s.ncolor = '#BD005E'\n\t\tif (!s.ncolor2) s.ncolor2 = '#5E00BD'\n\t\tif (!s.pcolor) s.pcolor = '#005EBD'\n\t\tif (!s.pcolor2) s.pcolor2 = '#FA7D00'\n\n\t\tif (s.normalize) {\n\t\t} else {\n\t\t\t// disable by default\n\t\t\ts.normalize = {\n\t\t\t\tdividefactor: 1,\n\t\t\t\tdisable: 1\n\t\t\t}\n\t\t}\n\t\ttk.strand2 = s\n\n\t\tif (!tk.strand2.name) tk.strand2.name = 'Reverse'\n\t}\n\n\ttk.height_main =\n\t\ttk.toppad + (tk.strand1 ? tk.strand1.barheight : 0) + (tk.strand2 ? tk.strand2.barheight : 0) + tk.bottompad\n}\n\nexport function bigwigstrandedmaketk(tk, block) {\n\tconst collectlabelw = []\n\n\ttk.tklabel\n\t\t.attr('y', 1) // tk label y position is fixed\n\t\t.each(function () {\n\t\t\tcollectlabelw.push(this.getBBox().width)\n\t\t})\n\n\ttk.labforward = block\n\t\t.maketklefthandle(tk)\n\t\t.text(tk.strand1.name)\n\t\t.each(function () {\n\t\t\tcollectlabelw.push(this.getBBox().width)\n\t\t})\n\ttk.labreverse = block\n\t\t.maketklefthandle(tk)\n\t\t.text(tk.strand2.name)\n\t\t.each(function () {\n\t\t\tcollectlabelw.push(this.getBBox().width)\n\t\t})\n\n\ttk.leftLabelMaxwidth = Math.max(...collectlabelw)\n\n\ttk.leftaxis = tk.gleft.append('g').attr('transform', 'translate(' + block.lpad + ',0)')\n\tif (tk.strand1) {\n\t\ttk.strand1.img = tk.glider.append('image')\n\t}\n\tif (tk.strand2) {\n\t\ttk.strand2.img = tk.glider.append('image')\n\t}\n\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\t\tconfigpanel(tk, block)\n\t})\n}\n\nexport function bigwigstrandedload(tk, block) {\n\tif (!tk.strand1) {\n\t\ttk.height_main = 50\n\t\tblock.tkcloakoff(tk, { error: tk.name + ': forward strand track missing' })\n\t\tblock.block_setheight()\n\t\treturn\n\t}\n\tif (!tk.strand2) {\n\t\ttk.height_main = 50\n\t\tblock.tkcloakoff(tk, { error: tk.name + ': reverse strand track missing' })\n\t\tblock.block_setheight()\n\t\treturn\n\t}\n\tblock.tkcloakon(tk)\n\n\ttk.strand1.img.attr('width', block.width).attr('height', tk.strand1.barheight)\n\ttk.strand2.img.attr('width', block.width).attr('height', tk.strand2.barheight).attr('y', tk.strand1.barheight)\n\n\t// load strand1\n\n\tconst par1 = block.tkarg_q(tk.strand1)\n\tpar1.name = tk.name + ' forward strand'\n\n\tclient\n\t\t.dofetch('tkbigwig', par1)\n\t\t.then(data => {\n\t\t\tif (data.error) throw 'forward strand error: ' + data.error\n\n\t\t\ttk.strand1.img.attr('xlink:href', data.src)\n\t\t\tif (block.pannedpx != undefined) {\n\t\t\t\t// offset panned distance\n\t\t\t\ttk.strand1.img.attr('x', -block.pannedpx)\n\t\t\t}\n\t\t\tif (data.minv != undefined) {\n\t\t\t\ttk.strand1.scale.min = data.minv\n\t\t\t}\n\t\t\tif (data.maxv != undefined) {\n\t\t\t\ttk.strand1.scale.max = data.maxv\n\t\t\t}\n\t\t\ttk.strand1.nodata = data.nodata\n\n\t\t\t// load strand2\n\n\t\t\tconst par2 = block.tkarg_q(tk.strand2)\n\t\t\tpar2.name = tk.name + ' reverse strand'\n\n\t\t\treturn client.dofetch('tkbigwig', par2).then(data => {\n\t\t\t\tif (data.error) throw 'reverse strand error: ' + data.error\n\t\t\t\ttk.strand2.img.attr('xlink:href', data.src)\n\t\t\t\tif (data.minv != undefined) {\n\t\t\t\t\ttk.strand2.scale.min = data.minv\n\t\t\t\t}\n\t\t\t\tif (data.maxv != undefined) {\n\t\t\t\t\ttk.strand2.scale.max = data.maxv\n\t\t\t\t}\n\t\t\t\ttk.strand2.nodata = data.nodata\n\t\t\t})\n\t\t})\n\t\t.then(() => {\n\t\t\ttk.strand1.img.attr('x', 0) // shift back\n\t\t\tblock.tkcloakoff(tk, {})\n\t\t\ttk.leftaxis.selectAll('*').remove()\n\n\t\t\tconst minvalue = tk.strand2.nodata ? 0 : tk.strand2.scale.min\n\t\t\tconst maxvalue = tk.strand1.nodata ? 0 : tk.strand1.scale.max\n\n\t\t\tconst scale = scaleLinear()\n\t\t\t\t.domain([minvalue, 0, maxvalue])\n\t\t\t\t.range([tk.strand1.barheight + tk.strand2.barheight, tk.strand1.barheight, 0])\n\n\t\t\tlet formatstr = 'r'\n\t\t\tif (tk.integer4axis) {\n\t\t\t\t// show integer\n\t\t\t\tformatstr = 'd'\n\t\t\t}\n\n\t\t\tconst axis = d3axis.axisRight().scale(scale).tickFormat(d3format(formatstr)).tickValues([minvalue, 0, maxvalue])\n\n\t\t\tclient.axisstyle({\n\t\t\t\taxis: tk.leftaxis.call(axis),\n\t\t\t\tcolor: 'black',\n\t\t\t\tshowline: true\n\t\t\t})\n\t\t\ttk.height_main = tk.toppad + tk.strand1.barheight + tk.strand2.barheight + tk.bottompad\n\t\t\ttk.labforward.transition().attr('y', tk.strand1.barheight / 2)\n\t\t\ttk.labreverse.transition().attr('y', tk.strand1.barheight + tk.strand2.barheight / 2)\n\t\t\tblock.block_setheight()\n\n\t\t\tfor (const panel of tk.subpanels) {\n\t\t\t\tbigwigstrandedloadsubpanel(tk, block, panel)\n\t\t\t}\n\t\t})\n\t\t.catch(err => {\n\t\t\ttk.strand1.img.attr('x', 0) // shift back\n\t\t\ttk.height_main = 50\n\t\t\tblock.tkcloakoff(tk, { error: typeof err == 'string' ? err : err.message })\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t\tblock.block_setheight()\n\t\t})\n}\n\nexport function bigwigstrandedloadsubpanel(tk, block, panel) {\n\tblock.tkcloakon_subpanel(panel)\n\n\tpanel.strand1.img.attr('width', panel.width).attr('height', tk.strand1.barheight)\n\tpanel.strand2.img.attr('width', panel.width).attr('height', tk.strand2.barheight).attr('y', tk.strand1.barheight)\n\n\tconst par1 = block.tkarg_q(tk.strand1)\n\tpar1.width = panel.width\n\tpar1.rglst = [\n\t\t{\n\t\t\tchr: panel.chr,\n\t\t\tstart: panel.start,\n\t\t\tstop: panel.stop,\n\t\t\twidth: panel.width\n\t\t}\n\t]\n\tpar1.maxv = tk.strand1.scale.max\n\tpar1.minv = tk.strand1.scale.min\n\tdelete par1.autoscale\n\tdelete par1.percentile\n\n\tclient\n\t\t.dofetch('tkbigwig', par1)\n\t\t.then(data => {\n\t\t\tif (data.error) throw data.error\n\t\t\tpanel.strand1.img.attr('xlink:href', data.src)\n\n\t\t\tconst par2 = block.tkarg_q(tk.strand2)\n\t\t\tpar2.width = panel.width\n\t\t\tpar2.rglst = [\n\t\t\t\t{\n\t\t\t\t\tchr: panel.chr,\n\t\t\t\t\tstart: panel.start,\n\t\t\t\t\tstop: panel.stop,\n\t\t\t\t\twidth: panel.width\n\t\t\t\t}\n\t\t\t]\n\t\t\tpar2.maxv = tk.strand2.scale.max\n\t\t\tpar2.minv = tk.strand2.scale.min\n\t\t\tdelete par2.autoscale\n\t\t\tdelete par2.percentile\n\n\t\t\treturn client.dofetch('tkbigwig', par2).then(data => {\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tpanel.strand2.img.attr('xlink:href', data.src)\n\t\t\t})\n\t\t})\n\t\t.catch(obj => {\n\t\t\tif (obj.stack) {\n\t\t\t\t// error\n\t\t\t\tconsole.log(obj.stack)\n\t\t\t}\n\t\t\treturn typeof obj == 'string' ? obj : obj.message\n\t\t})\n\t\t.then(errtext => {\n\t\t\tblock.tkcloakoff_subpanel(panel, { error: errtext })\n\t\t})\n}\n\nfunction configpanel(tk, block) {\n\tconst holder = tk.tkconfigtip.d\n\t{\n\t\tconst div = client.labelbox({\n\t\t\tholder: holder,\n\t\t\tmargin: '0px 0px 15px 0px',\n\t\t\tlabel: tk.strand1.name\n\t\t})\n\t\tconst obj = bigwigconfigpanel(tk.strand1, block, div, () => bigwigstrandedload(tk, block))\n\t\tobj.ncolor.row.remove()\n\t\tobj.dotplot.row.remove()\n\t\tif (obj.ncolor2.row) {\n\t\t\tobj.ncolor2.row.remove()\n\t\t}\n\t\tobj.pcolor.lab.text('Color')\n\t\tif (obj.pcolor2.lab) {\n\t\t\tobj.pcolor2.lab.text('Beyond threshold')\n\t\t}\n\t}\n\t{\n\t\tconst div = client.labelbox({\n\t\t\tholder: holder,\n\t\t\tlabel: tk.strand2.name\n\t\t})\n\t\tconst obj = bigwigconfigpanel(tk.strand2, block, div, () => bigwigstrandedload(tk, block))\n\t\tobj.pcolor.row.remove()\n\t\tobj.dotplot.row.remove()\n\t\tif (obj.pcolor2.row) {\n\t\t\tobj.pcolor2.row.remove()\n\t\t}\n\t\tobj.ncolor.lab.text('Color')\n\t\tif (obj.ncolor2.lab) {\n\t\t\tobj.ncolor2.lab.text('Beyong threshold')\n\t\t}\n\t}\n}\n", "import { dofetch3 } from '#common/dofetch'\nimport { bplen, gmmode } from '#shared/common.js'\nimport { legend_newrow } from './block.legend'\nimport { make_one_checkbox } from '#dom'\n\n/*\ntk {\n\t_td_legend\n\n\tcategories{}\n\t\tkey: category key\n\t\tvalue: {color,label}\n\t\tpredefined by gencode tk\n\n\tmainRegionCategory2count{}\n\t\tkey: category key\n\t\tvalue: integer\n\t\treturned from server for main region\n\n\tsubpanels[]\n\t\t.category2count{}\n\t\t\treturned from server for each panel\n}\n\nbedj can only be loaded from POST but not GET\nthe rglst parameter is generated by tkarg_bedj()\nwhich under the protein mode of a big gene, will generate very long parameter string\nand cause url too long error\n\nsolution is for tkarg_bedj or related function to use following parameter:\n{genetrack:'refgene', isoform:'NM_xxx',start:123,stop:456,width:800}\n\nthen the backend needs to recreate rglst[]. all the GET handlers need to do this\n\nthis hardcodes the rglst building logic with backend gene tracks and not extendable to arbitrary rglst from client\n\n*** may not worth the trouble ***\n*/\n\nexport function bedjfromtemplate(tk, template) {\n\ttk.stackheight = template.stackheight || 12\n\ttk.stackspace = template.stackspace || 1\n\ttk.color = tk.color || '#2c9c96'\n\n\tif (template.usevalue) {\n\t\tif (!template.usevalue.key) {\n\t\t\treturn '.usevalue.key missing'\n\t\t}\n\t\ttk.usevalue = {}\n\t\tfor (const k in template.usevalue) {\n\t\t\ttk.usevalue[k] = template.usevalue[k]\n\t\t}\n\t}\n\t/*\n\tsince bedj tk is always loaded via ajax from server\n\twon't break if set it busy here\n\tthis is important for junction tracks\n\tsince somehow some junction tk will finish loading so fast (e.g. with built-in data)\n\tand the gene bedj track hasn't been loaded yet...\n\tthe splice event finder won't run since no gene data loaded!!!\n\t*** this is legacy!! remove once new junction track replaced old TODO\n\t*/\n\ttk.busy = true\n\treturn null\n}\n\nexport function bedjmaketk(tk, block) {\n\ttk.img = tk.glider.append('image')\n\n\tif (tk.categories && block.legend && block.legend.holder) {\n\t\t// has categories, block supports legend, show entry\n\t\tconst [tr, td] = legend_newrow(block, tk.name)\n\t\ttk.tr_legend = tr\n\t\ttk._td_legend = td // private to bedj tk, hardcoded to only show category2count\n\t}\n\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\tconfigpanel(tk, block)\n\t})\n}\n\nexport function bedjload(tk, block) {\n\tif (block.viewrangeabovelimit(tk.viewrangeupperlimit)) {\n\t\tblock.tkcloakoff(tk, { error: tk.name + ': zoom in under ' + bplen(tk.viewrangeupperlimit) + ' to view data' })\n\t\ttk.height_main = 30\n\t\ttk.img.attr('width', 1).attr('height', 1)\n\t\tblock.block_setheight()\n\t\treturn\n\t}\n\n\tblock.tkcloakon(tk)\n\tconst arg = block.tkarg_bedj(tk)\n\tif (tk.__isgene) {\n\t\t// is native gene track\n\t\tif (!block.gmmode || block.gmmode == gmmode.genomic) {\n\t\t\t/*\n\t\t\tnot in gene-view\n\t\t\twill provide the flag to server to request gene model data for client use:\n\t\t\t- junction\n\t\t\t*/\n\t\t\targ.__isgene = true\n\t\t}\n\t}\n\n\tdofetch3('tkbedj', { method: 'POST', body: JSON.stringify(arg) }) // to add serverdata\n\t\t.then(data => {\n\t\t\tif (tk.__isgene) {\n\t\t\t\t/*\n\t\t\t\tmay receive gene data\n\t\t\t\t!! gene data must be appended prior to tkcloakoff()\n\t\t\t\twhich calls block.ifbusy(), and will trigger the gene data-based tk-specific actions\n\t\t\t\twhich cannot run if tk.gmdata[] is not updated\n\t\t\t\t*/\n\t\t\t\tif (data.returngmdata) {\n\t\t\t\t\ttk.gmdata = data.returngmdata\n\t\t\t\t} else {\n\t\t\t\t\t// TODO tell if there is too many genes or no gene\n\t\t\t\t\tdelete tk.gmdata\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (data.error) throw { message: data.error }\n\n\t\t\t// always clear data from last query; data from subpanel query will be appended to it to generate legend\n\t\t\ttk.mainRegionCategory2count = data.category2count\n\n\t\t\ttk.img.attr('width', block.width).attr('height', data.height).attr('xlink:href', data.src)\n\n\t\t\ttk.height_main = tk.toppad + data.height + tk.bottompad\n\t\t\treturn data\n\t\t})\n\t\t.catch(err => {\n\t\t\ttk.height_main = 30\n\t\t\tif (err.stack) {\n\t\t\t\tconsole.log(err.stack)\n\t\t\t}\n\t\t\treturn { error: err.message }\n\t\t})\n\t\t.then(data => {\n\t\t\tmayShowCategoryLegend(tk)\n\t\t\tblock.tkcloakoff(tk, data)\n\t\t\tblock.block_setheight()\n\t\t\tblock.bedj_tooltip(tk, data)\n\t\t})\n}\n\nfunction mayShowCategoryLegend(tk) {\n\ttk._td_legend?.selectAll('*').remove()\n\tif (!tk.categories) return // simple fix to require this setting, may fix to support custom tk\n\tconst categories = []\n\t{\n\t\tconst c2c = {} // accumulate category2count data from both main region and all sub panels\n\t\tconst lst = [tk.mainRegionCategory2count]\n\t\tif (tk.subpanels) {\n\t\t\tfor (const p of tk.subpanels) lst.push(p.category2count)\n\t\t}\n\t\tfor (const m of lst) {\n\t\t\tif (!m) continue\n\t\t\tfor (const key in m) {\n\t\t\t\tif (!c2c[key]) c2c[key] = 0\n\t\t\t\tc2c[key] += m[key]\n\t\t\t}\n\t\t}\n\t\tfor (const k in c2c) categories.push([k, c2c[k]])\n\t\tcategories.sort((a, b) => b[1] - a[1])\n\t}\n\tfor (const [key, count] of categories) {\n\t\tconst d = tk._td_legend.append('div').style('display', 'inline-block').style('white-space', 'nowrap')\n\t\td.append('span')\n\t\t\t.style('background', tk.categories[key]?.color || 'black')\n\t\t\t.style('padding', '1px 3px')\n\t\t\t.style('color', 'white')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text(count)\n\t\td.append('span')\n\t\t\t.style('color', tk.categories[key]?.color || 'black')\n\t\t\t.text(tk.categories[key]?.label || key)\n\t\t\t.style('margin', '0px 20px 0px 5px')\n\t}\n}\n\nexport function bedjloadsubpanel(tk, block, panel) {\n\tif (tk.viewrangeupperlimit && tk.viewrangeupperlimit >= panel.stop - panel.start) {\n\t\tpanel.height = 30\n\t\tpanel.img.attr('width', 1).attr('height', 1)\n\t\tblock.block_setheight()\n\t\treturn\n\t}\n\n\tconst arg = block.tkarg_bedj(tk)\n\targ.width = panel.width\n\targ.rglst = [\n\t\t{\n\t\t\tchr: panel.chr,\n\t\t\tstart: panel.start,\n\t\t\tstop: panel.stop,\n\t\t\twidth: panel.width\n\t\t}\n\t]\n\n\tif (tk.__isgene) {\n\t\t// is native gene track\n\t\tif (!block.gmmode || block.gmmode == gmmode.genomic) {\n\t\t\t/*\n\t\t\tnot in gene-view\n\t\t\twill provide the flag to server to request gene model data for client use:\n\t\t\t- junction\n\t\t\t*/\n\t\t\targ.__isgene = true\n\t\t}\n\t}\n\n\tblock.tkcloakon_subpanel(panel)\n\n\tdofetch3('tkbedj', { method: 'POST', body: JSON.stringify(arg) })\n\t\t.then(data => {\n\t\t\tif (tk.__isgene) {\n\t\t\t\t/*\n\t\t\tmay receive gene data\n\t\t\t!! gene data must be appended prior to tkcloakoff()\n\t\t\twhich calls block.ifbusy(), and will trigger the gene data-based tk-specific actions\n\t\t\twhich cannot run if tk.gmdata[] is not updated\n\t\t\t*/\n\t\t\t\tif (data.returngmdata) {\n\t\t\t\t\tpanel.gmdata = data.returngmdata\n\t\t\t\t} else {\n\t\t\t\t\tdelete panel.gmdata\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (data.error) throw { message: data.error }\n\n\t\t\tpanel.img.attr('width', panel.width).attr('height', data.height).attr('xlink:href', data.src)\n\n\t\t\tpanel.height = data.height + tk.toppad + tk.bottompad\n\n\t\t\t// register updated data on this panel\n\t\t\tpanel.category2count = data.category2count\n\n\t\t\treturn data\n\t\t})\n\t\t.catch(err => {\n\t\t\tpanel.height = 30\n\t\t\tif (err.stack) {\n\t\t\t\tconsole.log(err.stack)\n\t\t\t}\n\t\t\treturn { error: err.message }\n\t\t})\n\t\t.then(data => {\n\t\t\tmayShowCategoryLegend(tk) // rerenders legend with updated data\n\t\t\tblock.tkcloakoff_subpanel(panel, data)\n\t\t\tblock.block_setheight()\n\t\t\tblock.bedj_tooltip(tk, data, panel)\n\t\t})\n}\n\nfunction configpanel(tk, block) {\n\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\tconst holder = tk.tkconfigtip.d\n\n\t// height\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '10px')\n\t\trow.append('span').html('Item height&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', tk.stackheight)\n\t\t\t.style('width', '50px')\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tconst s = event.target.value\n\t\t\t\tif (s == '') return\n\t\t\t\tconst v = Number.parseInt(s)\n\t\t\t\tif (Number.isNaN(v) || v <= 0) {\n\t\t\t\t\talert('please use positive integer for height')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.stackheight = v\n\t\t\t\tbedjload(tk, block)\n\t\t\t})\n\t}\n\tif (!tk.categories) {\n\t\t// color\n\t\tconst row = holder.append('div').style('margin-bottom', '10px')\n\t\trow.append('span').html('Color&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.property('value', tk.color)\n\t\t\t.attr('type', 'color')\n\t\t\t.on('change', event => {\n\t\t\t\ttk.color = event.target.value\n\t\t\t\tbedjload(tk, block)\n\t\t\t})\n\t}\n\t{\n\t\t// hide names\n\t\tconst row = holder.append('div').style('margin-bottom', '10px')\n\t\tmake_one_checkbox({\n\t\t\tholder: row,\n\t\t\tlabeltext: 'Hide item names',\n\t\t\tchecked: tk.hideItemNames,\n\t\t\tcallback: () => {\n\t\t\t\ttk.hideItemNames = !tk.hideItemNames\n\t\t\t\tbedjload(tk, block)\n\t\t\t}\n\t\t})\n\t}\n\t{\n\t\t// filter items\n\t\tconst row = holder.append('div').style('margin-bottom', '10px')\n\t\tmake_one_checkbox({\n\t\t\tholder: row,\n\t\t\tlabeltext: 'Show items by names',\n\t\t\tchecked: tk.filterByName ? true : false,\n\t\t\tcallback: () => {\n\t\t\t\tif (div.style('display') == 'none') {\n\t\t\t\t\t// show ui\n\t\t\t\t\tdiv.style('display', 'block')\n\t\t\t\t} else {\n\t\t\t\t\t// hide ui, also disable filtering\n\t\t\t\t\tdiv.style('display', 'none')\n\t\t\t\t\tdelete tk.filterByName\n\t\t\t\t\tbedjload(tk, block)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\tconst div = holder\n\t\t\t.append('div')\n\t\t\t.style('margin', '0px 0px 10px 25px')\n\t\t\t.style('display', tk.filterByName ? 'block' : 'none')\n\t\tconst ta = div.append('textarea').property('rows', 4)\n\t\tif (tk.filterByName) ta.property('value', tk.filterByName)\n\t\tta.property('placeholder', 'One name per row. Case sensitive. Use isoform names for gene track.')\n\t\tdiv\n\t\t\t.append('button')\n\t\t\t.style('display', 'block')\n\t\t\t.text('Submit')\n\t\t\t.on('click', () => {\n\t\t\t\tconst v = ta.property('value').trim()\n\t\t\t\tif (!v) return\n\t\t\t\ttk.filterByName = v\n\t\t\t\tbedjload(tk, block)\n\t\t\t})\n\t}\n}\n", "import * as client from './client'\nimport { table2col } from '#dom'\nimport { scaleLinear } from 'd3-scale'\nimport { axisBottom } from 'd3-axis'\nimport { format as d3format } from 'd3-format'\nimport { select as d3select } from 'd3-selection'\nimport * as coord from './coord'\nimport { legend_newrow } from './block.legend'\nimport { basecompliment, default_text_color } from '#shared/common.js'\nimport { rgb } from 'd3-color'\n\n/*\nthe \"gene model\" track, showing in one of four modes:\n- genomic\n- splicing RNA\n- exon only\n- protein\n- aggregated isoforms\n\n\n\n********************** EXPORTED\n\ngmtkfromtemplate()\ngmtkmaketk()\ngmtkrender()\n\n\n\n********************** INTERNAL\n\nconfigpanel()\nconfigpanel_gmsum()\nrender1gm()\ndomainlegend()\n\n\nTODO make adaptor and split from block bundle\n\n*/\n\nconst linecolor = 'black'\n\nconst exonboundaryclass = 'exonboundaryclass'\n\nexport function gmtkfromtemplate(tk) {\n\ttk.stackheight = tk.stackheight0 = tk.stackheight || 30\n\ttk.stackspace = 5\n\tif (!tk.noncodingcolor) {\n\t\ttk.noncodingcolor = '#ccc'\n\t}\n}\n\nexport function gmtkmaketk(tk, block) {\n\ttk.tklabel.text(block.usegm.name)\n\ttk.isoformlabel = block.maketklefthandle(tk, 13).attr('class', null).text(block.usegm.isoform)\n\tdomainlegend(tk, block)\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\tconfigpanel(tk, block)\n\t})\n}\n\nfunction configpanel(tk, block) {\n\t// config panel for gm track\n\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\tconst holder = tk.tkconfigtip.d\n\n\tconst table = holder.append('table')\n\n\t// display mode\n\tconst tr1 = table.append('tr')\n\ttr1.append('td').text(block.gmmode)\n\ttr1\n\t\t.append('td')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.text('switch display mode')\n\t\t.on('click', () => {\n\t\t\ttable.remove()\n\t\t\tblock.showgmmode4switch(holder)\n\t\t})\n\n\t// change isoform\n\tconst tr2 = table.append('tr')\n\tif (block.allgm.length > 1) {\n\t\ttr2.append('td').text(block.usegm.isoform)\n\t\ttr2\n\t\t\t.append('td')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.text('switch isoform')\n\t\t\t.on('click', () => {\n\t\t\t\ttable.remove()\n\t\t\t\tblock.showisoform4switch(holder)\n\t\t\t})\n\t}\n\tif (block.gmmode == client.gmmode.gmsum) {\n\t\t// in gmsum mode, customize isoform\n\t\tconst tr3 = table.append('tr')\n\t\tlet usecount = 0\n\t\tfor (const m of block.allgm) {\n\t\t\tif (!m.hidden) usecount++\n\t\t}\n\t\ttr3\n\t\t\t.append('td')\n\t\t\t.text(\n\t\t\t\tusecount == block.allgm.length\n\t\t\t\t\t? 'Showing all ' + usecount + ' isoforms'\n\t\t\t\t\t: 'Showing ' + usecount + ' of ' + block.allgm.length + ' isoforms'\n\t\t\t)\n\t\ttr3\n\t\t\t.append('td')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.text('show/hide isoforms')\n\t\t\t.on('click', () => {\n\t\t\t\ttable.remove()\n\t\t\t\tconfigpanel_gmsum(block, holder)\n\t\t\t})\n\t\ttable\n\t\t\t.append('tr')\n\t\t\t.append('td')\n\t\t\t.attr('colspan', 2)\n\t\t\t.style('padding-top', '15px')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.html('To rearrange isoforms, drag and move<br>isoform names on the left of the track.')\n\t}\n\n\tif (\n\t\tblock.usegm.exon.length > 1 &&\n\t\t(block.gmmode == client.gmmode.protein || block.gmmode == client.gmmode.exononly)\n\t) {\n\t\t// show/hide exon boundary lines\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').text('Exon boundary')\n\t\ttr.append('td')\n\t\t\t.append('button')\n\t\t\t.text(tk.exonboundaryhide ? 'show lines' : 'hide lines')\n\t\t\t.on('click', event => {\n\t\t\t\ttk.exonboundaryhide = !tk.exonboundaryhide\n\t\t\t\tevent.target.innerHTML = tk.exonboundaryhide ? 'show lines' : 'hide lines'\n\t\t\t\tblock.usegm.__tkg.selectAll('.' + exonboundaryclass).attr('stroke-opacity', tk.exonboundaryhide ? 0 : 1)\n\t\t\t})\n\t}\n\tif (block.gmmode == client.gmmode.protein || block.gmmode == client.gmmode.exononly) {\n\t\tconst tr = table.append('tr')\n\t\tconst label = tr.append('td').attr('colspan', 2).append('label')\n\t\tlabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.property('checked', tk.noCodonNumberInsideBox)\n\t\t\t.on('change', () => {\n\t\t\t\ttk.noCodonNumberInsideBox = !tk.noCodonNumberInsideBox\n\t\t\t\tgmtkrender(tk, block)\n\t\t\t})\n\t\tlabel.append('span').style('margin-left', '10px').text('Hide codon numbers')\n\t}\n}\n\nfunction configpanel_gmsum(block, holder) {\n\t// group isoforms by gene track name\n\tconst genetkset = new Map()\n\tfor (const g of block.allgm) {\n\t\tif (!g.trackname) {\n\t\t\tclient.sayerror(holder, '.trackname missing for ' + g.isoform)\n\t\t\tcontinue\n\t\t}\n\t\tif (!genetkset.has(g.trackname)) {\n\t\t\tgenetkset.set(g.trackname, new Map())\n\t\t}\n\t\tgenetkset.get(g.trackname).set(g, { hidden: g.hidden })\n\t}\n\tif (genetkset.size == 0) {\n\t\tclient.sayerror(holder, 'no gene track names!')\n\t\treturn\n\t}\n\tfor (const [genetkname, isoformset] of genetkset) {\n\t\tconst row = holder.append('div').style('margin', '5px')\n\t\t// if all isoforms of this track are hidden\n\t\tconst id = Math.random()\n\t\tconst tkcheckbox = row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.attr('id', id)\n\t\t\t.on('change', () => {\n\t\t\t\tfor (const obj of isoformset.values()) {\n\t\t\t\t\tobj.checkbox.node().checked = tkcheckbox.node().checked\n\t\t\t\t}\n\t\t\t})\n\t\tlet allhidden = true\n\t\tfor (const obj of isoformset.values()) {\n\t\t\tif (!obj.hidden) {\n\t\t\t\tallhidden = false\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!allhidden) {\n\t\t\ttkcheckbox.property('checked', true)\n\t\t}\n\t\trow\n\t\t\t.append('label')\n\t\t\t.html('&nbsp;&nbsp;' + genetkname)\n\t\t\t.attr('for', id)\n\t\t\t.attr('class', 'sja_clbtext')\n\t\tfor (const [isoform, obj] of isoformset) {\n\t\t\tconst row = holder.append('div').style('margin', '3px 5px 3px 30px')\n\t\t\tconst id = Math.random()\n\t\t\tobj.checkbox = row.append('input').attr('type', 'checkbox').attr('id', id)\n\t\t\tif (!obj.hidden) {\n\t\t\t\tobj.checkbox.property('checked', true)\n\t\t\t}\n\t\t\trow\n\t\t\t\t.append('label')\n\t\t\t\t.html(\n\t\t\t\t\t'&nbsp;&nbsp;' +\n\t\t\t\t\t\tisoform.isoform +\n\t\t\t\t\t\t' <span style=\"color:#858585\">' +\n\t\t\t\t\t\t(isoform.cdslen ? Math.ceil(isoform.cdslen / 3) + ' AA' : 'noncoding') +\n\t\t\t\t\t\t'</span>'\n\t\t\t\t)\n\t\t\t\t.attr('for', id)\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t}\n\t}\n\tholder\n\t\t.append('button')\n\t\t.style('display', 'block')\n\t\t.style('margin-top', '5px')\n\t\t.text('Apply changes')\n\t\t.on('click', () => {\n\t\t\tlet usecount = 0\n\t\t\tconst isoform2hide = new Set()\n\t\t\tfor (const isoformset of genetkset.values()) {\n\t\t\t\tfor (const [isoform, obj] of isoformset) {\n\t\t\t\t\tconst show = obj.checkbox.node().checked\n\t\t\t\t\tif (show) {\n\t\t\t\t\t\tusecount++\n\t\t\t\t\t} else {\n\t\t\t\t\t\tisoform2hide.add(isoform)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (usecount <= 1) {\n\t\t\t\twindow.alert('Must select at least two isoforms')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tfor (const gm of block.allgm) {\n\t\t\t\tgm.hidden = isoform2hide.has(gm)\n\t\t\t}\n\t\t\tdelete block.gmmode\n\t\t\tblock.setgmmode(client.gmmode.gmsum, true)\n\t\t})\n}\n\nexport function gmtkrender(tk, block) {\n\ttk.busy = false\n\tblock.ifbusy()\n\ttk.glider.attr('transform', 'translate(0,0)').selectAll('*').remove()\n\tif (!block.gmmode) {\n\t\tblock.tkerror(tk, 'running usegm track but gmmode not set')\n\t\treturn\n\t}\n\n\tconst collectlabw = []\n\n\tif (block.gmmode == client.gmmode.gmsum) {\n\t\ttk.tklabel.text('')\n\t\ttk.isoformlabel.text('')\n\t\ttk.isoformnames = []\n\t\tconst h = tk.stackheight * 0.7\n\n\t\tlet y = 0\n\t\tfor (const gm of block.allgm) {\n\t\t\tif (gm.hidden) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tgm.__tkg = tk.glider.append('g').attr('transform', 'translate(0,' + y + ')')\n\t\t\tgm.__tky = y\n\t\t\trender1gm(gm, h, tk, block)\n\t\t\tconst thislab = gm.__tkg\n\t\t\t\t.append('text')\n\t\t\t\t.text(gm.isoform)\n\t\t\t\t.attr('y', h / 2)\n\t\t\t\t.attr('x', -12)\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t.attr('fill', 'black')\n\t\t\t\t.attr('font-size', block.labelfontsize)\n\t\t\t\t.each(function () {\n\t\t\t\t\tcollectlabw.push(this.getBBox().width)\n\t\t\t\t})\n\t\t\t\t.on('mousedown', event => {\n\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\tevent.stopPropagation()\n\t\t\t\t\tmoveisoform(gm, block, event.clientY, h + tk.stackspace)\n\t\t\t\t})\n\t\t\ttk.isoformnames.push(thislab)\n\t\t\ty += h + tk.stackspace\n\t\t}\n\t\ttk.height_main = y + tk.bottompad\n\t} else {\n\t\ttk.isoformnames = null\n\t\tblock.usegm.__tkg = tk.glider.append('g')\n\t\trender1gm(block.usegm, tk.stackheight, tk, block)\n\t\ttk.height_main = tk.toppad + tk.stackheight + tk.bottompad\n\t\ttk.tklabel.text(block.usegm.name).each(function () {\n\t\t\tcollectlabw.push(this.getBBox().width)\n\t\t})\n\t\ttk.isoformlabel.text(block.usegm.isoform).each(function () {\n\t\t\tcollectlabw.push(this.getBBox().width)\n\t\t})\n\t}\n\ttk.leftLabelMaxwidth = Math.max(...collectlabw)\n\tblock.block_setheight()\n\tblock.setllabel()\n}\n\nfunction render1gm(gm, h, tk, block) {\n\t/*\ngm:\nh: coding exon height, reduced for noncoding exons\ntk:\nblock:\n*/\n\n\t// overall container\n\tconst tkg = gm.__tkg\n\n\t// thickness reduction for noncoding exons\n\tconst thinpad = Math.floor(h / 5)\n\n\t// 1 - get onscreen start/stop for gm in view range\n\n\t// left side of visible part of gm\n\tlet start = null\n\tlet x = 0 // cumulate\n\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\tconst r = block.rglst[i]\n\t\tif (r.chr != gm.chr) {\n\t\t\tx += r.width + block.regionspace\n\t\t\tcontinue\n\t\t}\n\t\tconst a = Math.max(r.start, gm.start),\n\t\t\tb = Math.min(r.stop, gm.stop)\n\t\tif (a < b) {\n\t\t\t// left side of visible part is valid\n\t\t\tstart = x + (r.reverse ? r.stop - b : a - r.start) * block.exonsf\n\t\t\tbreak\n\t\t}\n\t\tx += r.width + block.regionspace\n\t}\n\tif (start == null) {\n\t\ttkg\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('fill', linecolor)\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('font-size', Math.min(15, h))\n\t\t\t.attr('x', block.width / 2)\n\t\t\t.attr('y', h / 2)\n\t\t\t.text(gm.name + ' ' + gm.isoform + ' is not in view range')\n\t\treturn\n\t}\n\t// right side of visible part of gm\n\tlet stop = null\n\tx = 0\n\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\tconst r = block.rglst[i]\n\t\tif (r.chr != gm.chr) {\n\t\t\tx += r.width + block.regionspace\n\t\t\tcontinue\n\t\t}\n\t\tconst a = Math.max(r.start, gm.start),\n\t\t\tb = Math.min(r.stop, gm.stop)\n\t\tif (a < b) {\n\t\t\tstop = x + (r.reverse ? r.stop - a : b - r.start) * block.exonsf\n\t\t\t// don't break here keep looking till end of rglst to find max stop\n\t\t}\n\t\tx += r.width + block.regionspace\n\t}\n\tif (stop == null) {\n\t\tconsole.log('should not happen: stop position not found')\n\t\ttkg\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('font-size', Math.min(15, h))\n\t\t\t.attr('x', block.width / 2)\n\t\t\t.attr('y', h / 2)\n\t\t\t.text(gm.name + ' not in view range')\n\t\treturn\n\t}\n\n\t// 2 - backdrop horizontal line from start to end\n\tconst startinvr = start\n\tconst stopinvr = stop\n\ttkg\n\t\t.append('line')\n\t\t.attr('x1', startinvr)\n\t\t.attr('y1', h / 2)\n\t\t.attr('x2', stopinvr)\n\t\t.attr('y2', h / 2)\n\t\t.attr('stroke', linecolor)\n\t\t.attr('shape-rendering', 'crispEdges')\n\n\t// collect all exonic boxes, for showing kicker\n\tconst eboxes = []\n\n\t// 3 - thin box for noncoding exon\n\t//     collect them for printing nt letters later\n\tconst thinlst = []\n\n\tif (block.gmmode != client.gmmode.protein) {\n\t\tif (gm.utr5) {\n\t\t\tthinlst.push(...gm.utr5)\n\t\t}\n\t\tif (gm.utr3) {\n\t\t\tthinlst.push(...gm.utr3)\n\t\t}\n\t\tif (gm.exon && !gm.coding) {\n\t\t\t// this is a noncoding gene\n\t\t\tthinlst.push(...gm.exon)\n\t\t}\n\t\tfor (const e of thinlst) {\n\t\t\tx = 0\n\t\t\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\t\t\tconst r = block.rglst[i]\n\t\t\t\tif (r.chr != gm.chr) {\n\t\t\t\t\tx += r.width + block.regionspace\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst start = Math.max(r.start, e[0]),\n\t\t\t\t\tstop = Math.min(r.stop, e[1])\n\t\t\t\tif (start >= stop) {\n\t\t\t\t\tx += r.width + block.regionspace\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst b = tkg\n\t\t\t\t\t.append('rect')\n\t\t\t\t\t.attr('x', x + (r.reverse ? r.stop - stop : start - r.start) * block.exonsf)\n\t\t\t\t\t.attr('y', thinpad)\n\t\t\t\t\t.attr('width', Math.max(1, (stop - start) * block.exonsf))\n\t\t\t\t\t.attr('height', h - thinpad * 2)\n\t\t\t\t\t.attr('fill', tk.noncodingcolor)\n\t\t\t\teboxes.push({ b: b, r: r, start: start, stop: stop })\n\t\t\t}\n\t\t}\n\t}\n\n\t// 4 - thick box coding and domain\n\tif (gm.pdomains) {\n\t\tgm.pdomains.sort((a, b) => b.stop - b.start - (a.stop - a.start))\n\t}\n\t// for drawing protein box if in view range\n\tlet viewcodingstartpx = null,\n\t\tviewcodingstart = null, // genomic coord\n\t\tviewcodingstoppx = null,\n\t\tviewcodingstop = null\n\tif (gm.coding) {\n\t\tfor (let ei = 0; ei < gm.coding.length; ei++) {\n\t\t\tconst e = gm.coding[ei]\n\t\t\tx = 0\n\t\t\tfor (let ri = block.startidx; ri <= block.stopidx; ri++) {\n\t\t\t\tconst r = block.rglst[ri]\n\t\t\t\tif (r.chr != gm.chr) {\n\t\t\t\t\tx += r.width + block.regionspace\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst start = Math.max(r.start, e[0]),\n\t\t\t\t\tstop = Math.min(r.stop, e[1])\n\t\t\t\tif (start >= stop) {\n\t\t\t\t\tx += r.width + block.regionspace\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\t// will draw a thick box\n\t\t\t\tconst boxstart = x + (r.reverse ? r.stop - stop : start - r.start) * block.exonsf\n\t\t\t\tconst boxwidth = Math.max(1, (stop - start) * block.exonsf)\n\t\t\t\tif (viewcodingstartpx == null) {\n\t\t\t\t\tviewcodingstartpx = boxstart\n\t\t\t\t\tviewcodingstart = start\n\t\t\t\t\tviewcodingstop = stop\n\t\t\t\t} else {\n\t\t\t\t\tviewcodingstart = Math.min(start, viewcodingstart)\n\t\t\t\t\tviewcodingstop = Math.max(stop, viewcodingstop)\n\t\t\t\t}\n\t\t\t\tviewcodingstoppx = boxstart + boxwidth\n\t\t\t\t// white bg\n\t\t\t\tconst b = tkg.append('rect').attr('x', boxstart).attr('width', boxwidth).attr('height', h).attr('fill', 'white')\n\t\t\t\teboxes.push({ b: b, r: r, start: start, stop: stop })\n\t\t\t\t// domain?\n\t\t\t\tif (gm.pdomains) {\n\t\t\t\t\tlet exoncdsstart = 0\n\t\t\t\t\tfor (let j = 0; j < ei; j++) {\n\t\t\t\t\t\texoncdsstart += gm.coding[j][1] - gm.coding[j][0]\n\t\t\t\t\t}\n\t\t\t\t\tconst cdsstart = exoncdsstart + (r.reverse ? e[1] - stop : start - e[0])\n\t\t\t\t\tconst cdsstop = exoncdsstart + (r.reverse ? e[1] - start : stop - e[0])\n\t\t\t\t\tfor (const domain of gm.pdomains) {\n\t\t\t\t\t\tif (domain.name + domain.description in gm.domain_hidden) {\n\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t}\n\t\t\t\t\t\tconst dstart = Math.max(cdsstart, (domain.start - 1) * 3)\n\t\t\t\t\t\tconst dstop = Math.min(cdsstop, domain.stop * 3)\n\t\t\t\t\t\tif (dstart < dstop) {\n\t\t\t\t\t\t\ttkg\n\t\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t\t// FIXME assumed that the rglst can only be in 5'-3' order!!!\n\t\t\t\t\t\t\t\t.attr('x', boxstart + (dstart - cdsstart) * block.exonsf)\n\t\t\t\t\t\t\t\t.attr('width', Math.max(1, (dstop - dstart) * block.exonsf))\n\t\t\t\t\t\t\t\t.attr('height', h)\n\t\t\t\t\t\t\t\t.attr('fill', domain.color)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (block.gmmode != client.gmmode.protein && block.gmmode != client.gmmode.exononly) {\n\t\t\t\t\t// enclosing box for each coding exon\n\t\t\t\t\tif (start == e[0]) {\n\t\t\t\t\t\tconst _x = boxstart + (r.reverse ? boxwidth : 0)\n\t\t\t\t\t\ttkg.append('line').attr('x1', _x).attr('x2', _x).attr('y2', h).attr('stroke', linecolor)\n\t\t\t\t\t}\n\t\t\t\t\tif (stop == e[1]) {\n\t\t\t\t\t\tconst _x = boxstart + (r.reverse ? 0 : boxwidth)\n\t\t\t\t\t\ttkg.append('line').attr('x1', _x).attr('x2', _x).attr('y2', h).attr('stroke', linecolor)\n\t\t\t\t\t}\n\t\t\t\t\ttkg\n\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t.attr('x1', boxstart)\n\t\t\t\t\t\t.attr('x2', boxstart + boxwidth)\n\t\t\t\t\t\t.attr('stroke', linecolor)\n\t\t\t\t\ttkg\n\t\t\t\t\t\t.append('line')\n\t\t\t\t\t\t.attr('x1', boxstart)\n\t\t\t\t\t\t.attr('x2', boxstart + boxwidth)\n\t\t\t\t\t\t.attr('y1', h)\n\t\t\t\t\t\t.attr('y2', h)\n\t\t\t\t\t\t.attr('stroke', linecolor)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// 5 - enclosing box of entire coding region\n\tif (block.gmmode == client.gmmode.exononly || block.gmmode == client.gmmode.protein) {\n\t\tif (viewcodingstartpx != null && viewcodingstoppx != null) {\n\t\t\ttkg.append('line').attr('x1', viewcodingstartpx).attr('x2', viewcodingstoppx).attr('stroke', linecolor)\n\t\t\ttkg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('x1', viewcodingstartpx)\n\t\t\t\t.attr('x2', viewcodingstoppx)\n\t\t\t\t.attr('y1', h)\n\t\t\t\t.attr('y2', h)\n\t\t\t\t.attr('stroke', linecolor)\n\t\t\t// FIXME association of codingstart and px is not clear\n\t\t\tconst reverse = gm.strand == '-'\n\t\t\tif (viewcodingstart == gm.codingstart) {\n\t\t\t\ttkg\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('x1', reverse ? viewcodingstoppx : viewcodingstartpx)\n\t\t\t\t\t.attr('x2', reverse ? viewcodingstoppx : viewcodingstartpx)\n\t\t\t\t\t.attr('y2', h)\n\t\t\t\t\t.attr('stroke', linecolor)\n\t\t\t}\n\t\t\tif (viewcodingstop == gm.codingstop) {\n\t\t\t\ttkg\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.attr('x1', reverse ? viewcodingstartpx : viewcodingstoppx)\n\t\t\t\t\t.attr('x2', reverse ? viewcodingstartpx : viewcodingstoppx)\n\t\t\t\t\t.attr('y2', h)\n\t\t\t\t\t.attr('stroke', linecolor)\n\t\t\t}\n\t\t}\n\t\t// exon boundary\n\t\tfor (let i = block.startidx; i < block.stopidx; i++) {\n\t\t\tconst r = block.rglst[i]\n\t\t\tif (r.chr != gm.chr) continue\n\t\t\tx = 0\n\t\t\tfor (let j = block.startidx; j < i; j++) {\n\t\t\t\tx += block.rglst[j].width + block.regionspace\n\t\t\t}\n\t\t\tlet thin = true\n\t\t\tif (gm.coding) {\n\t\t\t\tif (r.reverse) {\n\t\t\t\t\tthin = r.start <= gm.codingstart || r.start >= gm.codingstop\n\t\t\t\t} else {\n\t\t\t\t\tthin = r.stop <= gm.codingstart || r.stop >= gm.codingstop\n\t\t\t\t}\n\t\t\t}\n\t\t\ttkg\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', exonboundaryclass)\n\t\t\t\t.attr('x1', x + r.width + block.regionspace / 2)\n\t\t\t\t.attr('x2', x + r.width + block.regionspace / 2)\n\t\t\t\t.attr('y1', thin ? thinpad : 0)\n\t\t\t\t.attr('y2', h - (thin ? thinpad : 0))\n\t\t\t\t.attr('stroke', linecolor)\n\t\t\t\t.attr('stroke-dasharray', '4,2')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t.attr('stroke-opacity', tk.exonboundaryhide ? 0 : 1)\n\t\t}\n\t}\n\n\tconst showntseq = block.exonsf >= 6\n\n\t// 6 -  aa sequence and position\n\tif (\n\t\tgm.coding &&\n\t\t(block.gmmode == client.gmmode.protein ||\n\t\t\tblock.gmmode == client.gmmode.exononly ||\n\t\t\tblock.gmmode == client.gmmode.splicingrna)\n\t) {\n\t\t// is protein\n\t\tconst showaaseq = block.exonsf >= 2\n\t\tconst rowh = (h - 2) / 3\n\t\t// show aa\n\t\tlet utr5len\n\t\tif (block.gmmode == client.gmmode.protein) {\n\t\t\t// not using utr\n\t\t\tutr5len = 0\n\t\t} else {\n\t\t\tutr5len = gm.utr5 ? gm.utr5.reduce((a, b) => a + b[1] - b[0], 0) : 0\n\t\t}\n\n\t\tconst aadomain = [],\n\t\t\taarange = []\n\t\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\t\tconst r = block.rglst[i]\n\t\t\tif (r.chr != gm.chr) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tx = 0\n\t\t\tfor (let j = block.startidx; j < i; j++) {\n\t\t\t\tx += block.rglst[j].width + block.regionspace\n\t\t\t}\n\t\t\tconst rstartexonbp = block.regioncumlen(i)\n\t\t\tconst rstopexonbp = rstartexonbp + r.stop - r.start\n\t\t\tif (rstartexonbp >= utr5len + gm.cdslen || rstopexonbp <= utr5len) {\n\t\t\t\t// not in block region\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tlet cdsstart, pxstart\n\t\t\tif (rstartexonbp < utr5len) {\n\t\t\t\tcdsstart = 0\n\t\t\t\tpxstart = (utr5len - rstartexonbp) * block.exonsf\n\t\t\t} else {\n\t\t\t\tcdsstart = rstartexonbp - utr5len\n\t\t\t\tpxstart = 0\n\t\t\t}\n\n\t\t\t/* TRICKY!!!\n\t\t\toffset value is usually 0\n\t\t\tif startCodonFrame is specified, will set non-0 value\n\t\t\tfor modifying nt array index below while iterating through whose nt that will be translated\n\t\t\tthis is because gm.cdseq (CDS sequence) contains extra nts associated with startCodonFrame\n\t\t\t*/\n\t\t\tconst codonNtOffset = gm.startCodonFrame ? 3 - gm.startCodonFrame : 0\n\n\t\t\tconst cdsstop = Math.min(gm.cdslen, rstopexonbp - utr5len)\n\n\t\t\t/*\n\t\tFIXME\n\t\tdomain/range of the aa position scale is imprecise\n\t\t*/\n\t\t\taadomain.push(1 + Math.floor(cdsstart / 3))\n\t\t\taarange.push(x + pxstart + block.exonsf * (cdsstart % 3 == 0 ? 1.5 : cdsstart % 3 == 1 ? 0.5 : -0.5))\n\t\t\taadomain.push(1 + Math.floor(cdsstop / 3))\n\t\t\taarange.push(x + pxstart + (cdsstop - cdsstart) * block.exonsf)\n\t\t\tif (showntseq) {\n\t\t\t\t// must not include cdsstop\n\t\t\t\tfor (let j = cdsstart; j < cdsstop; j++) {\n\t\t\t\t\t// shade over a codon\n\n\t\t\t\t\tconst j2 = j - codonNtOffset // modified index\n\n\t\t\t\t\tif (Math.floor(j2 / 3) % 2 == 0) {\n\t\t\t\t\t\ttkg\n\t\t\t\t\t\t\t.append('rect')\n\t\t\t\t\t\t\t.attr('x', x + pxstart + (j - cdsstart) * block.exonsf)\n\t\t\t\t\t\t\t.attr('width', block.exonsf)\n\t\t\t\t\t\t\t.attr('height', rowh * 2)\n\t\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t\t.attr('fill-opacity', 0.1)\n\t\t\t\t\t}\n\t\t\t\t\ttkg\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(gm.cdseq[j]) // do not use j2 here\n\t\t\t\t\t\t.attr('font-size', rowh)\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t.attr('x', x + pxstart + (j - cdsstart + 0.5) * block.exonsf)\n\t\t\t\t\t\t.attr('y', 2 + rowh / 2)\n\t\t\t\t\t\t.attr('font-family', 'Courier') // no override; customary to show nucleotide/aa in this font\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (cdsstart % 3 == 2) {\n\t\t\t\t// trim one bp\n\t\t\t\tcdsstart++\n\t\t\t\tpxstart += block.exonsf\n\t\t\t}\n\t\t\tif (showaaseq) {\n\t\t\t\t// must not include cdsstop\n\t\t\t\tfor (let j = cdsstart; j < cdsstop; j++) {\n\t\t\t\t\tconst j2 = j - codonNtOffset // modified index\n\n\t\t\t\t\tif (j2 % 3 != 1) {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\ttkg\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(gm.aaseq[Math.floor(j2 / 3)])\n\t\t\t\t\t\t.attr('font-size', rowh)\n\t\t\t\t\t\t.attr('font-weight', 'bold')\n\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t.attr('dominant-baseline', showntseq ? 'central' : 'auto')\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('x', x + pxstart + (j - cdsstart + 0.5) * block.exonsf) // do not use j2 here\n\t\t\t\t\t\t.attr('y', h / 2)\n\t\t\t\t\t\t.attr('font-family', 'Courier') // no override; customary to show nucleotide/aa in this font\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (aadomain.length && !tk.noCodonNumberInsideBox) {\n\t\t\tconst scale = scaleLinear().domain(aadomain).range(aarange)\n\t\t\tclient.axisstyle({\n\t\t\t\taxis: tkg\n\t\t\t\t\t.append('g')\n\t\t\t\t\t.attr('transform', 'translate(0,' + (showaaseq ? (showntseq ? rowh * 2 : h / 2) : h / 2) + ')')\n\t\t\t\t\t.call(axisBottom().scale(scale).tickSize(0).tickFormat(d3format('d'))),\n\t\t\t\tcolor: 'black',\n\t\t\t\tshowline: false,\n\t\t\t\tfontsize: rowh\n\t\t\t})\n\t\t}\n\t}\n\n\t// 7 - nt sequence in noncoding exons\n\tif (showntseq && gm.genomicseq) {\n\t\tconst rowh = (h - 2) / 3\n\t\tfor (const e of thinlst) {\n\t\t\tx = 0\n\t\t\tfor (let i = block.startidx; i <= block.stopidx; i++) {\n\t\t\t\tconst r = block.rglst[i]\n\t\t\t\tif (r.chr != gm.chr) {\n\t\t\t\t\tx += r.width + block.regionspace\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tconst start = Math.max(r.start, e[0]),\n\t\t\t\t\tstop = Math.min(r.stop, e[1])\n\t\t\t\tif (start >= stop) {\n\t\t\t\t\tx += r.width + block.regionspace\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tfor (let j = start; j < stop; j++) {\n\t\t\t\t\tlet nt = gm.genomicseq[j - gm.start]\n\t\t\t\t\tif (r.reverse) {\n\t\t\t\t\t\tnt = basecompliment(nt)\n\t\t\t\t\t}\n\t\t\t\t\ttkg\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text(nt)\n\t\t\t\t\t\t.attr('font-size', rowh)\n\t\t\t\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('fill', 'black')\n\t\t\t\t\t\t.attr('font-family', 'Courier') // no override; customary to show nucleotide/aa in this font\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'x',\n\t\t\t\t\t\t\tx +\n\t\t\t\t\t\t\t\t(r.reverse\n\t\t\t\t\t\t\t\t\t? (r.stop - stop) * block.exonsf + (stop - start) * block.exonsf - (j - start + 0.5) * block.exonsf\n\t\t\t\t\t\t\t\t\t: (start - r.start) * block.exonsf + (j - start + 0.5) * block.exonsf)\n\t\t\t\t\t\t)\n\t\t\t\t\t\t.attr('y', h / 2)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// 8 - invisible cover for tooltipping\n\tfor (const e of eboxes) {\n\t\ttkg\n\t\t\t.append('rect')\n\t\t\t.attr('x', e.b.attr('x'))\n\t\t\t.attr('y', e.b.attr('y'))\n\t\t\t.attr('width', e.b.attr('width'))\n\t\t\t.attr('height', e.b.attr('height'))\n\t\t\t.attr('fill', '#858585')\n\t\t\t.attr('fill-opacity', 0)\n\t\t\t.on('mouseover', event => event.target.setAttribute('fill-opacity', 0.2))\n\t\t\t.on('mousemove', event => coord2legend(tk, event, e.r, e.start, e.stop, gm, block, h))\n\t\t\t.on('mouseout', event => {\n\t\t\t\tevent.target.setAttribute('fill-opacity', 0)\n\t\t\t\ttk.tktip.hide()\n\t\t\t})\n\t}\n}\n\nfunction moveisoform(gm, block, y0, height) {\n\tconst body = d3select(document.body)\n\tbody.on('mousemove', event => {\n\t\tconst dy = event.clientY - y0\n\t\tgm.__tkg.attr('transform', 'translate(0,' + (gm.__tky + dy) + ')')\n\t\tlet gmidx = 0\n\t\tfor (let i = 0; i < block.allgm.length; i++) {\n\t\t\tif (block.allgm[i].isoform == gm.isoform) {\n\t\t\t\tgmidx = i\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (dy < 0 && gmidx > 0) {\n\t\t\tlet t2idx = gmidx - 1,\n\t\t\t\tt2 = block.allgm[t2idx]\n\t\t\twhile (t2.hidden) {\n\t\t\t\tt2idx--\n\t\t\t\tif (t2idx < 0) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tt2 = block.allgm[t2idx]\n\t\t\t}\n\t\t\tif (!t2) {\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (-dy >= height) {\n\t\t\t\tblock.allgm[t2idx] = gm\n\t\t\t\tblock.allgm[gmidx] = t2\n\t\t\t\tgm.__tky = t2.__tky\n\t\t\t\tt2.__tky += height\n\t\t\t\tt2.__tkg.transition().attr('transform', 'translate(0,' + t2.__tky + ')')\n\t\t\t\ty0 = event.clientY\n\t\t\t}\n\t\t} else if (dy > 0 && gmidx < block.allgm.length - 1) {\n\t\t\tlet t2idx = gmidx + 1,\n\t\t\t\tt2 = block.allgm[t2idx]\n\t\t\twhile (t2.hidden) {\n\t\t\t\tt2idx++\n\t\t\t\tif (t2idx >= block.allgm.length) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tt2 = block.allgm[t2idx]\n\t\t\t}\n\t\t\tif (!t2) {\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (dy >= height) {\n\t\t\t\t// swap\n\t\t\t\tblock.allgm[t2idx] = gm\n\t\t\t\tblock.allgm[gmidx] = t2\n\t\t\t\tt2.__tky = gm.__tky\n\t\t\t\tgm.__tky += height\n\t\t\t\tt2.__tkg.transition().attr('transform', 'translate(0,' + t2.__tky + ')')\n\t\t\t\ty0 = event.clientY\n\t\t\t}\n\t\t}\n\t})\n\tbody.on('mouseup', () => {\n\t\tgm.__tkg.transition().attr('transform', 'translate(0,' + gm.__tky + ')')\n\t\tbody.on('mousemove', null).on('mouseup', null)\n\t})\n}\n\nfunction coord2legend(tk, event, r, start, stop, gm, block, h) {\n\ttk.tktip.clear()\n\tconst table = table2col({ holder: tk.tktip.d, margin: '0px' })\n\tconst a = event.target.getBoundingClientRect()\n\tconst x = event.clientX - a.left\n\n\tlet pos\n\t/*\n\tpos is 0-based!\n\tfor reverse, must use stop minus ceil\n\tfor forward, must use start plus floor\n\t*/\n\tif (r.reverse) {\n\t\tpos = stop - Math.ceil(x / block.exonsf)\n\t} else {\n\t\tpos = start + Math.floor(x / block.exonsf)\n\t}\n\n\tconst p = coord.genomic2gm(pos, gm)\n\tif (p.atexon) table.addRow('Exon', p.atexon)\n\n\tif (p.atutr5) table.addRow(\"5' UTR\", p.atutr5.off + ' bp')\n\telse if (p.atutr3) table.addRow(\"3' UTR\", p.atutr3.off + ' bp')\n\telse if (p.aapos) table.addRow('AA', p.aapos + ' aa')\n\n\tif (p.rnapos) table.addRow('RNA', p.rnapos + ' bp')\n\ttable.addRow(gm.chr, pos + 1)\n\tif (p.aapos && gm.pdomains) {\n\t\ttable.table.style('margin-bottom', '5px')\n\t\tfor (const d of gm.pdomains) {\n\t\t\tif (d.name + d.description in gm.domain_hidden) continue\n\t\t\tif (d.start <= p.aapos && d.stop >= p.aapos) {\n\t\t\t\tconst row = tk.tktip.d.append('div')\n\t\t\t\trow.append('span').style('background-color', d.color).html('&nbsp;&nbsp;')\n\t\t\t\trow.append('span').html('&nbsp;' + d.name)\n\t\t\t\tif (d.description) {\n\t\t\t\t\trow\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t\t.html('&nbsp;' + (d.description.length > 30 ? d.description.substring(0, 20) + ' ...' : d.description))\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\ttk.tktip.show(event.clientX, gm.__tkg.node().getBoundingClientRect().top + h - 10)\n}\n\n//////////////// render domain legend ///////////////\n\n// all link types. makelink() arg is element returned by getdomaintypes()\nconst domainLinks = [\n\t{\n\t\tkey: 'CDD',\n\t\tmakelink: domaintype => `https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=${domaintype.CDD}`\n\t},\n\t{\n\t\tkey: 'Pfam',\n\t\tmakelink: domaintype => `https://www.ebi.ac.uk/interpro/entry/pfam/PF${domaintype.Pfam.substr(4)}`\n\t},\n\t{\n\t\tkey: 'SMART',\n\t\tmakelink: domaintype =>\n\t\t\t`https://smart.embl.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=${domaintype.SMART.substr(5)}`\n\t},\n\t{\n\t\tkey: 'COG',\n\t\tmakelink: domaintype => `https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=${domaintype.COG}`\n\t},\n\t{\n\t\tkey: 'PRK',\n\t\tmakelink: domaintype => `https://www.ncbi.nlm.nih.gov/proteinclusters?term=${domaintype.PRK}`\n\t},\n\t{\n\t\tkey: 'pmid', // may support comma-joined ids\n\t\tmakelink: domaintype => `https://pubmed.ncbi.nlm.nih.gov/${domaintype.pmid}/`,\n\t\ttxt: domaintype => `PubMed ${domaintype.pmid}`\n\t},\n\t{\n\t\tkey: 'url',\n\t\tmakelink: domaintype => domaintype.url,\n\t\ttxt: () => 'Reference'\n\t}\n]\nasync function domainlegend(tk, block) {\n\tif (!block.legend || !block.legend.holder) {\n\t\t// block not support legend\n\t\treturn\n\t}\n\tif (!block.usegm) {\n\t\t// no gm in use?\n\t\treturn\n\t}\n\tif (!tk.tr_legend) {\n\t\tconst [tr, td] = legend_newrow(block, 'PROTEIN')\n\t\ttk.tr_legend = tr\n\t\ttk.td_legend = td\n\t}\n\ttk.td_legend.selectAll('*').remove()\n\n\t// get unique list of domain types from current gm (note that it may not cover all domains from all gm which could be minor issue)\n\t// any customizations to the domains (visibility and color), apply to all gm\n\tconst domainTypes = client.getdomaintypes(block.usegm)\n\n\tconst menuOptions = [\n\t\t{\n\t\t\tlabel: 'Hide',\n\t\t\thide: d => block.usegm.domain_hidden[d.key],\n\t\t\tcallback: d => {\n\t\t\t\tfor (const m of block.allgm) {\n\t\t\t\t\tm.domain_hidden[d.key] = 1\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Show',\n\t\t\thide: d => !block.usegm.domain_hidden[d.key],\n\t\t\tcallback: d => {\n\t\t\t\tfor (const m of block.allgm) {\n\t\t\t\t\tdelete m.domain_hidden[d.key]\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Show All',\n\t\t\thide: () => !Object.keys(block.usegm.domain_hidden).length,\n\t\t\tcallback: () => {\n\t\t\t\tfor (const m of block.allgm) {\n\t\t\t\t\tm.domain_hidden = {}\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Show only',\n\t\t\thide: () => Object.keys(block.usegm.domain_hidden).length == domainTypes.length - 1,\n\t\t\tcallback: d => {\n\t\t\t\tfor (const m of block.allgm) {\n\t\t\t\t\tdelete m.domain_hidden[d.key]\n\t\t\t\t\tfor (const c of domainTypes) {\n\t\t\t\t\t\tif (c.key != d.key) m.domain_hidden[c.key] = 1\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t]\n\n\tconst legendRows = tk.td_legend\n\t\t.selectAll('div')\n\t\t.data(domainTypes)\n\t\t.enter()\n\t\t.append('div')\n\t\t.classed('sjpp-domain-legend-item', true)\n\t\t.style('margin', block.legend.vpad + ' 0px 8px 0px')\n\n\tlegendRows.append('span').style('padding', '5px 0px').style('margin-right', '10px')\n\n\t//sja_clb class adds the background color hover effect\n\tconst clickableRow = legendRows.append('span').classed('sja_clb', true)\n\n\t//Color box\n\tconst colorbox = clickableRow\n\t\t.append('span')\n\t\t.style('background-color', d => d.fill)\n\t\t.html('&nbsp;&nbsp;&nbsp;')\n\t\t.style('margin-right', '10px')\n\n\t//Domain name\n\tconst name = clickableRow\n\t\t.append('span')\n\t\t.text(d => d.name)\n\t\t.style('text-decoration', d => (block.usegm.domain_hidden[d.key] ? 'line-through' : 'none'))\n\t\t.style('color', default_text_color)\n\t\t.style('margin-right', '10px')\n\n\t//Domain description\n\tconst description = clickableRow\n\t\t.append('span')\n\t\t.text(d => d.description)\n\t\t.style('text-decoration', d => (block.usegm.domain_hidden[d.key] ? 'line-through' : 'none'))\n\t\t.style('color', default_text_color)\n\t\t.style('font-size', '.7em')\n\t\t.style('margin-right', '10px')\n\n\tclickableRow.on('click', async (event, domaintype) => {\n\t\tblock.tip.clear().showunder(event.target)\n\n\t\t//Dynamically add options from the array above\n\t\tawait block.tip.d\n\t\t\t.selectAll('div')\n\t\t\t.data(menuOptions.filter(o => !o.hide(domaintype)))\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.style('border-radius', '0px')\n\t\t\t.classed('sja_menuoption', true)\n\t\t\t.text(o => o.label)\n\t\t\t.on('click', (event, option) => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\toption.callback(domaintype)\n\t\t\t\tupdateItems()\n\n\t\t\t\t// Destroy menu and re-render the visualization\n\t\t\t\tblock.tip.hide()\n\t\t\t\tgmtkrender(tk, block)\n\t\t\t})\n\n\t\t// Add color picker seperately to accommodate rendering needs\n\t\tif (!block.usegm.domain_hidden[domaintype.key]) {\n\t\t\tblock.tip.d\n\t\t\t\t.append('div')\n\t\t\t\t.text('Color: ')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', domaintype.fill)\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.on('change', event => {\n\t\t\t\t\tdomaintype.fill = event.target.value\n\t\t\t\t\tfor (const p of block.allgm) {\n\t\t\t\t\t\t// a gm may have more than 1 domain instances of this type. thus use .filter() to find all of them but not .find() to find only 1st one\n\t\t\t\t\t\tp.pdomains\n\t\t\t\t\t\t\t.filter(pd => pd.name + pd.description == domaintype.key)\n\t\t\t\t\t\t\t.forEach(i => (i.color = event.target.value))\n\t\t\t\t\t}\n\t\t\t\t\tupdateItems()\n\t\t\t\t\t// Same as above\n\t\t\t\t\tblock.tip.hide()\n\t\t\t\t\tgmtkrender(tk, block)\n\t\t\t\t})\n\t\t}\n\t})\n\t/* Add links dynamically to the row from the array above\n\t\tin a separate span. The hover effect will not apply to \n\t\tthis span. */\n\tlegendRows.append('span').each(function (domaintype) {\n\t\tconst holder = d3select(this)\n\t\tfor (const link of domainLinks) {\n\t\t\tif (domaintype[link.key]) {\n\t\t\t\tholder\n\t\t\t\t\t.append('a')\n\t\t\t\t\t.attr('href', link.makelink(domaintype))\n\t\t\t\t\t.attr('target', '_blank')\n\t\t\t\t\t.text(link.txt ? link.txt(domaintype) : link.key)\n\t\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t\t.style('padding-right', '10px')\n\t\t\t}\n\t\t}\n\t})\n\n\t//Updates the styling of the domain legend items based on the current hidden domains\n\tconst updateItems = () => {\n\t\tconst isHidden = domaintype => block.usegm.domain_hidden && block.usegm.domain_hidden[domaintype.key]\n\t\tcolorbox.style('background-color', d => (isHidden(d) ? 'transparent' : d.fill))\n\t\tname.style('text-decoration', d => (isHidden(d) ? 'line-through' : 'none'))\n\t\tdescription.style('text-decoration', d => (isHidden(d) ? 'line-through' : 'none'))\n\t}\n\n\tif (block.usegm.coding && block.usegm.coding.length > 0) {\n\t\t// custom domain ui, only for coding gene\n\t\tlet displayUI = false\n\n\t\tconst addProteinBtn = tk.td_legend.append('div').style('margin-top', '10px')\n\n\t\tconst proteinDomainUI = tk.td_legend.append('div').style('display', 'none')\n\t\tcustomdomainmakeui(block, tk, proteinDomainUI)\n\n\t\tconst btn = addProteinBtn\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.classed('sja_menuoption', true)\n\t\t\t.style('font-size', '.8em')\n\t\t\t.html(displayUI ? '&#9650; Add protein domain' : '&#9660; add protein domain')\n\t\t\t.on('click', () => {\n\t\t\t\tdisplayUI = !displayUI\n\t\t\t\tproteinDomainUI.style('display', displayUI ? 'block' : 'none')\n\t\t\t\tbtn.html(displayUI ? '&#9650; add protein domain' : '&#9660; add protein domain')\n\t\t\t})\n\t}\n}\n\nlet idIncrement = 0\nfunction getId() {\n\treturn `sjpp-customdomainui-${idIncrement++}`\n}\n\nfunction customdomainmakeui(block, tk, proteinDomainUI) {\n\tconst wrapper = proteinDomainUI.style('padding', '20px')\n\tconst textAreaId = getId()\n\t//header\n\twrapper\n\t\t.append('label')\n\t\t.attr('for', textAreaId)\n\t\t.html(`Add domains for ${block.usegm.name} <span style=\"font-size:.8em\">${block.usegm.isoform}</span>`)\n\tconst lst = client.getdomaintypes(block.usegm)\n\n\tconst customd = []\n\tfor (const d of lst) {\n\t\tif (d.iscustom) customd.push(d)\n\t}\n\tif (customd.length > 0) {\n\t\tconst div = wrapper.append('div').style('margin', '20px 0px')\n\t\tdiv.append('div').text('Click to remove a domain').style('font-size', '.8em').style('margin-bottom', '5px')\n\t\tfor (const i of customd) {\n\t\t\tconst row = div.append('div').classed('sja_menuoption', true)\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('background-color', i.fill)\n\t\t\t\t.style('border', 'solid 1px ' + i.stroke)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.style('padding', '1px 2px')\n\t\t\t\t.html('&nbsp;')\n\t\t\trow.append('div').style('display', 'inline-block').text(i.name)\n\t\t\trow.on('click', () => {\n\t\t\t\trow.remove()\n\t\t\t\tconst lst2 = []\n\t\t\t\tfor (const d of block.usegm.pdomains) {\n\t\t\t\t\tif (d.iscustom && d.name == i.name) continue\n\t\t\t\t\tlst2.push(d)\n\t\t\t\t}\n\t\t\t\tblock.usegm.pdomains = lst2\n\t\t\t\tgmtkrender(tk, block)\n\t\t\t\tdomainlegend(tk, block)\n\t\t\t})\n\t\t}\n\t}\n\twrapper\n\t\t.append('p')\n\t\t.style('font-size', '.9em')\n\t\t.html('<span style=\"font-size:.8em;color:#000\">EXAMPLE</span>&nbsp;&nbsp;domain_name ; 100 200 ; red')\n\tconst ta = wrapper.append('textarea').attr('id', textAreaId).attr('rows', 5).attr('cols', 30)\n\tconst row1 = wrapper.append('div').style('margin-top', '5px')\n\tconst select = row1.append('select')\n\tselect.append('option').text('Codon position')\n\tselect.append('option').text('mRNA position')\n\tselect.append('option').text('Genomic position')\n\trow1\n\t\t.append('button')\n\t\t.text('Submit')\n\t\t.style('margin-left', '5px')\n\t\t.on('click', () => {\n\t\t\tconst v = ta.property('value')\n\t\t\tif (v == '') return\n\t\t\terrdiv.style('display', 'none')\n\t\t\tconst lines = v.trim().split('\\n')\n\t\t\tfor (const line of lines) {\n\t\t\t\tconst l = line.split(';')\n\t\t\t\tif (l.length != 3) return err('invalid line: ' + line)\n\t\t\t\tconst t = l[1].trim().split(' ')\n\t\t\t\tif (t.length != 2) return err('position requires start and stop: ' + line)\n\t\t\t\tconst a = Number.parseInt(t[0])\n\t\t\t\tconst b = Number.parseInt(t[1])\n\t\t\t\tif (Number.isNaN(a) || Number.isNaN(b)) return err('invalid position value: ' + line)\n\t\t\t\tlet start, stop\n\t\t\t\tswitch (select.node().selectedIndex) {\n\t\t\t\t\tcase 0:\n\t\t\t\t\t\tstart = a\n\t\t\t\t\t\tstop = b\n\t\t\t\t\t\tbreak\n\t\t\t\t\tcase 1:\n\t\t\t\t\t\tlet x = coord.rna2gmcoord(a, block.usegm)\n\t\t\t\t\t\tif (x == null) return err('cannot map RNA position ' + a + ' to gene model')\n\t\t\t\t\t\tstart = coord.genomic2gm(x, block.usegm).aapos\n\t\t\t\t\t\tx = coord.rna2gmcoord(b, block.usegm)\n\t\t\t\t\t\tif (x == null) return err('cannot map RNA position ' + b + ' to gene model')\n\t\t\t\t\t\tstop = coord.genomic2gm(x, block.usegm).aapos\n\t\t\t\t\t\tbreak\n\t\t\t\t\tdefault:\n\t\t\t\t\t\tconst a1 = coord.genomic2gm(a, block.usegm).aapos\n\t\t\t\t\t\tconst a2 = coord.genomic2gm(b, block.usegm).aapos\n\t\t\t\t\t\tstart = Math.min(a1, a2)\n\t\t\t\t\t\tstop = Math.max(a1, a2)\n\t\t\t\t}\n\n\t\t\t\t//Fix for users entering colors in different formats (i.e. red, rgb(255,0,0), etc.)\n\t\t\t\t//Color picker only accepts hex code for value\n\t\t\t\tconst color = l[2].trim().startsWith('#') ? l[2].trim() : rgb(l[2].trim()).formatHex()\n\t\t\t\tblock.usegm.pdomains.push({\n\t\t\t\t\tiscustom: true,\n\t\t\t\t\tname: l[0].trim(),\n\t\t\t\t\tcolor,\n\t\t\t\t\tstart: start,\n\t\t\t\t\tstop: stop\n\t\t\t\t})\n\t\t\t}\n\t\t\tproteinDomainUI.style('display', 'none')\n\t\t\tgmtkrender(tk, block)\n\t\t\tdomainlegend(tk, block)\n\t\t\t//customdomainmakeui(block, tk, pane)\n\t\t})\n\trow1\n\t\t.append('button')\n\t\t.text('Clear')\n\t\t.style('margin-left', '5px')\n\t\t.on('click', () => ta.property('value', ''))\n\tconst errdiv = wrapper.append('div').style('margin-top', '10px').style('display', 'none')\n\tconst err = m => {\n\t\terrdiv.style('display', 'block')\n\t\tclient.sayerror(errdiv, m)\n\t}\n\twrapper\n\t\t.append('div')\n\t\t.style('color', '#000')\n\t\t.style('margin-top', '20px')\n\t\t.html(\n\t\t\t`One protein domain per line.<br>\nEach line has three fields joined by semicolon:\n<ol>\n  <li>Name, text with space, no semicolon.</li>\n  <li>Range, two integers joined by space.</li>\n  <li>Color, e.g. red, #FF0000, rgb(255,0,0).</li>\n</ol>`\n\t\t)\n}\n", "export function hicstrawfromtemplate(tk: any, template: any) {\n\tif (tk.textdata) {\n\t\tif (!tk.textdata.raw) return '.textdata.raw missing'\n\t\tif (typeof tk.textdata.raw != 'string') return '.textdata.raw should be string'\n\t\tdelete template.enzyme\n\t} else if (tk.bedfile || tk.bedurl) {\n\t\t// bed file\n\t} else {\n\t\t// by hic straw file\n\t\tif (!template.file && !template.url)\n\t\t\treturn 'none of the data sources available: text data, bedj file, or juicebox file'\n\t}\n\tif (template.domainoverlay) {\n\t\tif (!template.domainoverlay.file && !template.domainoverlay.url) return 'file or url missing for domainoverlay'\n\t\ttk.domainoverlay = {}\n\t\tfor (const k in template.domainoverlay) {\n\t\t\ttk.domainoverlay[k] = template.domainoverlay[k]\n\t\t}\n\t}\n\t// the \"hic\" object to work with ../tracks/hic/app.ts\n\ttk.hic = {\n\t\tenzyme: template.enzyme\n\t}\n\tdelete tk.enzyme\n\treturn null\n}\n\nexport function hicstrawmaketk(tk: any) {\n\ttk.uninitialized = true\n}\n\nexport function hicstrawload(tk: any, block: any) {\n\timport('./block.tk.hicstraw.ts').then(module => {\n\t\tmodule.loadTk(tk, block)\n\t})\n}\n", "export function asefromtemplate ( tk, template ) {\n\tif( !template.samplename ) return 'samplename missing'\n\tif( !template.rnabamfile ) {\n\t\tif( !template.rnabamurl ) return 'neither file or url given for rnabam'\n\t}\n\tif( !template.vcffile ) {\n\t\tif( !template.vcfurl ) return 'neither file or url given for vcf'\n\t}\n\treturn null\n}\n\n\nexport function asemaketk(tk,block) {\n\ttk.uninitialized=true\n}\n\n\nexport function aseload(tk,block) {\n\timport('./block.tk.ase').then(_=>{\n\t\t_.loadTk(tk,block)\n\t})\n}\n", "/*\n\nonly one source of data: loaded from server\n\n*/\n\n// duplicated stuff from dataset/pediatric.js\nconst valuePerSample = {\n\tkey: 'percentage',\n\tlabel: 'Percentage',\n\tcutoffValueLst: [\n\t\t{ side: '>', value: 5, label: '>5%' },\n\t\t{ side: '>', value: 10, label: '>10%' },\n\t\t{ side: '>', value: 20, label: '>20%' },\n\t\t{ side: '>', value: 30, label: '>30%' },\n\t\t{ side: '>', value: 40, label: '>40%' }\n\t]\n}\n\nexport function mdsjunctionfromtemplate(tk, template) {\n\tif (template.axisheight) {\n\t\tconst v = Number.parseInt(template.axisheight)\n\t\tif (Number.isNaN(v)) return 'invalid value for axisheight'\n\t\ttk.axisheight = v\n\t} else {\n\t\ttk.axisheight = 200\n\t}\n\tif (template.legheight) {\n\t\tconst v = Number.parseInt(template.legheight)\n\t\tif (Number.isNaN(v)) return 'invalid value for legheight'\n\t\ttk.legheight = v\n\t} else {\n\t\ttk.legheight = 50\n\t}\n\tif (template.neckheight) {\n\t\tconst v = Number.parseInt(template.neckheight)\n\t\tif (Number.isNaN(v)) return 'invalid value for neckheight'\n\t\ttk.neckheight = v\n\t} else {\n\t\ttk.neckheight = 50\n\t}\n\ttk.height_main = tk.toppad + tk.axisheight + tk.legheight + tk.neckheight + tk.bottompad\n\ttk.yscaleUseLog = template.yscaleUseLog != undefined ? template.yscaleUseLog : true\n\tif (tk.iscustom) {\n\t\t// custom mdsjunction\n\t\ttk.mds = {}\n\n\t\tif (template.infoFilter) {\n\t\t\tif (!template.infoFilter.lst) return '.lst missing from infoFilter'\n\t\t\ttk.infoFilter = { lst: [] }\n\t\t\tfor (const i of template.infoFilter.lst) {\n\t\t\t\tif (!i.key) return '.key missing from an item of .infoFilter.lst'\n\t\t\t\tif (!i.label) i.label = i.key\n\t\t\t\tif (!i.categories) return '.categories missing from an item of .infoFilter.lst'\n\t\t\t\tconst o = {\n\t\t\t\t\tkey: i.key,\n\t\t\t\t\tlabel: i.label,\n\t\t\t\t\tcategories: {},\n\t\t\t\t\thiddenCategories: {}\n\t\t\t\t}\n\t\t\t\tfor (const k in i.categories) {\n\t\t\t\t\to.categories[k] = i.categories[k]\n\t\t\t\t}\n\t\t\t\tif (i.hiddenCategories) {\n\t\t\t\t\tfor (const k in i.hiddenCategories) {\n\t\t\t\t\t\to.hiddenCategories[k] = 1\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\ttk.infoFilter.lst.push(o)\n\t\t\t}\n\t\t} else {\n\t\t\t// no infoFilter from custom tk, use the hardcoded one given that the junction annotation will be done by pp script\n\t\t\ttk.infoFilter = {\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'type',\n\t\t\t\t\t\tlabel: 'Type',\n\t\t\t\t\t\tcategories: {\n\t\t\t\t\t\t\tcanonical: {\n\t\t\t\t\t\t\t\tlabel: 'Canonical',\n\t\t\t\t\t\t\t\tcolor: '#0C72A8'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\texonskip: {\n\t\t\t\t\t\t\t\tlabel: 'Exon skipping',\n\t\t\t\t\t\t\t\tcolor: '#D14747',\n\t\t\t\t\t\t\t\tvaluePerSample: valuePerSample\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\texonaltuse: {\n\t\t\t\t\t\t\t\tlabel: 'Exon alternative usage',\n\t\t\t\t\t\t\t\tcolor: '#E69525',\n\t\t\t\t\t\t\t\tvaluePerSample: valuePerSample\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\ta5ss: {\n\t\t\t\t\t\t\t\tlabel: \"Alternative 5' splice site\",\n\t\t\t\t\t\t\t\tcolor: '#476CD1',\n\t\t\t\t\t\t\t\tvaluePerSample: valuePerSample\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\ta3ss: {\n\t\t\t\t\t\t\t\tlabel: \"Alternative 3' splice site\",\n\t\t\t\t\t\t\t\tcolor: '#47B582',\n\t\t\t\t\t\t\t\tvaluePerSample: valuePerSample\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tUnannotated: {\n\t\t\t\t\t\t\t\tlabel: 'Not annotated',\n\t\t\t\t\t\t\t\tcolor: '#787854'\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\thiddenCategories: {\n\t\t\t\t\t\t\t// in custom track, show all junctions by default\n\t\t\t\t\t\t\t//Unannotated: 1\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\t}\n\treturn null\n}\n\nexport function mdsjunctionmaketk(tk, block) {\n\ttk.leftaxis = tk.gleft.append('g')\n\ttk.tktip.d.style('padding', '8px')\n\ttk.subTracks = [] // as a parent track, collect subtracks (subtrack won't have this)\n\ttk.uninitialized = true\n\t// everything to be made in mdsjunction.render, since handles and config will rerender the track\n}\n\nexport function mdsjunctionload(tk, block) {\n\timport('./block.mds.junction').then(module => {\n\t\tmodule.loadTk(tk, block)\n\t})\n}\n", "export function mdssvcnvfromtemplate(tk,template) {\n\tif(tk.file || tk.url) {\n\t\t// svcnv file is now optional\n\t\ttk.iscustom=true\n\t}\n\tif(template.singlesample) {\n\t\tif(!template.singlesample.name) return 'singlesample.name missing'\n\t\ttk.singlesample = template.singlesample\n\t}\n\tif(template.checkexpressionrank) {\n\t\tif(tk.iscustom) {\n\t\t\tif(!template.checkexpressionrank.file && !template.checkexpressionrank.url) return 'file/url missing for checkexpressionrank in custom track'\n\t\t}\n\t\ttk.checkexpressionrank = {}\n\t\tfor(const k in template.checkexpressionrank) {\n\t\t\ttk.checkexpressionrank[k] = template.checkexpressionrank[k]\n\t\t}\n\t}\n\tif( template.checkrnabam ) {\n\t\tif( !template.checkrnabam.samples) return 'samples{} missing from checkrnabam'\n\t\t// will check against a custom vcf\n\t\ttk.iscustom = true\n\t}\n\n\ttk.gaincolor= template.gaincolor || '#D6683C'\n\ttk.losscolor= template.losscolor || '#67a9cf'\n\ttk.lohcolor= template.lohcolor || '#545454'\n\treturn null\n}\n\n\n\nexport function mdssvcnvmaketk(tk,block) {\n\ttk.uninitialized=true\n}\n\n\n\nexport function mdssvcnvload(tk,block) {\n\timport('./block.mds.svcnv').then(module=>{\n\t\tmodule.loadTk(tk,block)\n\t})\n}\n", "export function mdsexpressionrankfromtemplate(tk, template, block) {\n\treturn null\n}\n\nexport function mdsexpressionrankmaketk(tk, block) {\n\ttk.uninitialized = true\n}\n\nexport function mdsexpressionrankload(tk, block) {\n\timport('./block.mds.expressionrank').then(module => {\n\t\tmodule.loadTk(tk, block)\n\t})\n}\n", "export function mds3_fromtemplate(tk, template) {\n\treturn null\n}\n\nexport function mds3_maketk(tk, block) {\n\ttk.uninitialized = true\n}\n\nexport function mds3_load(tk, block) {\n\timport('./tk').then(_ => {\n\t\t_.loadTk(tk, block)\n\t})\n}\n", "export function bedgraphdot_fromtemplate(tk,template) {\n\treturn null\n}\n\n\n\nexport function bedgraphdot_maketk(tk,block) {\n\ttk.uninitialized=true\n}\n\n\n\nexport function bedgraphdot_load(tk,block) {\n\timport('./block.tk.bedgraphdot').then(_=>{\n\t\t_.loadTk(tk,block)\n\t})\n}\n", "import { select as d3select } from 'd3-selection'\nimport {\n\titemtable,\n\truntimeattr_sv,\n\truntimeattr_itd,\n\truntimeattr_del,\n\truntimeattr_trunc,\n\truntimeattr_snvindel\n} from './block.ds.itemtable'\nimport * as client from './client'\nimport * as common from '#shared/common.js'\nimport may_sunburst from './block.sunburst'\nimport { stratinput } from '#shared/tree.js'\nimport { stratify } from 'd3-hierarchy'\nimport * as blockds from './block.ds'\nimport { legend_newrow } from './block.legend'\nimport { dstkrender } from './block.ds'\n\n/*\ncreate tk labels\nlegend that belongs to this tk, contains options\n\n************************ EXPORTED\n\ndsmaketk()\n\n\n\n************************ INTERNAL\n\nlabel_mcount_fillpane()\nlabel_strat_fillpane()\n\nmlstfilter() \n\nctrlui_populationfrequency\nctrlui_vcfinfofilter\nctrlui_sampleattribute\n\n\n*/\n\nconst hotcolor = '#FFE5E5'\n\nexport default function dsmaketk(tk, block) {\n\t/*\n\tmake:\n\tsvg holders\n\tleft labels and controllers, and menu\n\tlegend\n\n\t*/\n\n\ttk.labyspace = 5 // must kept with tk: will be used by ds.numericmode\n\n\ttk.leftaxis = tk.gleft.append('g')\n\n\tif (!tk.itemlabelname) {\n\t\ttk.itemlabelname = 'mutation'\n\t}\n\n\tlet laby = tk.labyspace + block.labelfontsize\n\n\t// controller - # mutations\n\tconst thistip = new client.Menu({ padding: 'none' })\n\ttk.label_mcount = block.maketklefthandle(tk, laby).on('click', () => {\n\t\tlabel_mcount_fillpane(tk, block, tk.label_mcount, thistip)\n\t})\n\n\tlaby += tk.labyspace + block.labelfontsize\n\n\t// assume that stratify directives are available at time of making tk\n\tif (tk.ds.stratify) {\n\t\ttk.label_stratify = []\n\t\tconst thistip = new client.Menu()\n\t\tfor (const s of tk.ds.stratify) {\n\t\t\tconst strat = JSON.parse(JSON.stringify(s))\n\t\t\ttk.label_stratify.push(strat)\n\n\t\t\tstrat.svglabel = block.maketklefthandle(tk, laby).on('click', () => {\n\t\t\t\tlabel_strat_fillpane(tk, block, strat, thistip)\n\t\t\t})\n\n\t\t\tlaby += tk.labyspace + block.labelfontsize\n\t\t}\n\t}\n\n\tif (tk.ds.iscustom) {\n\t\t// close button for all custom, no matter if official.children or not\n\t\t// register the label, when making svg will hide this label\n\t\ttk.label_close = block\n\t\t\t.maketklefthandle(tk, laby)\n\t\t\t.text('Close')\n\t\t\t.on('mousedown', event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tevent.preventDefault()\n\t\t\t})\n\t\t\t.on('click', () => {\n\t\t\t\tblock.deletecustomdsbyname(tk.ds.label)\n\t\t\t})\n\t\tlaby += tk.labyspace + block.labelfontsize\n\t}\n\n\tblock.setllabel(tk)\n\n\t// attributes from official ds, move to tk level\n\tif (tk.ds.vcfinfofilter) {\n\t\ttk.vcfinfofilter = tk.ds.vcfinfofilter\n\t}\n\tif (tk.ds.info2table) {\n\t\ttk.info2table = tk.ds.info2table\n\t}\n\tif (tk.ds.info2singletable) {\n\t\ttk.info2singletable = tk.ds.info2singletable\n\t}\n\tif (tk.ds.itemlabelname) {\n\t\ttk.itemlabelname = tk.ds.itemlabelname\n\t}\n\tif (tk.ds.url4variant) {\n\t\ttk.url4variant = tk.ds.url4variant\n\t}\n\n\tif (block.legend && block.legend.holder) {\n\t\t/*\n\t\tmay make legend given following conditions\n\t\t*/\n\n\t\tlet showlegend = false\n\t\tif (tk.populationfrequencyfilter) {\n\t\t\tshowlegend = true\n\t\t}\n\t\tif (tk.vcfinfofilter) {\n\t\t\tshowlegend = true\n\t\t}\n\t\tif (tk.ds.cohort && tk.ds.cohort.sampleattribute) {\n\t\t\tshowlegend = true\n\t\t}\n\n\t\tif (showlegend) {\n\t\t\tconst [tr, td] = legend_newrow(block, tk.name)\n\t\t\ttk.tr_legend = tr\n\t\t\ttk.td_legend = td\n\n\t\t\tif (tk.vcfinfofilter) {\n\t\t\t\tconst err = ctrlui_vcfinfofilter(tk, block)\n\t\t\t\tif (err) {\n\t\t\t\t\tdelete tk.vcfinfofilter\n\t\t\t\t\tblock.error(tk.name + ': ' + err)\n\t\t\t\t}\n\t\t\t\tconst row = td.append('div').style('margin', '10px').style('display', 'none')\n\t\t\t\ttk.genotype2color = {\n\t\t\t\t\trr: '#ccc',\n\t\t\t\t\tra: 'blue',\n\t\t\t\t\taa: 'red',\n\t\t\t\t\tlegend: row\n\t\t\t\t}\n\t\t\t\trow.append('span').text('Genotype').style('color', '#858585')\n\t\t\t\tlet s = row.append('span').style('padding-left', '10px')\n\t\t\t\ts.append('div').style('display', 'inline-block').style('background', tk.genotype2color.rr).html('&nbsp;&nbsp;')\n\t\t\t\ts.append('span').html('&nbsp;Ref/Ref')\n\t\t\t\ts = row.append('span').style('padding-left', '10px')\n\t\t\t\ts.append('div').style('display', 'inline-block').style('background', tk.genotype2color.ra).html('&nbsp;&nbsp;')\n\t\t\t\ts.append('span').html('&nbsp;Ref/Alt')\n\t\t\t\ts = row.append('span').style('padding-left', '10px')\n\t\t\t\ts.append('div').style('display', 'inline-block').style('background', tk.genotype2color.aa).html('&nbsp;&nbsp;')\n\t\t\t\ts.append('span').html('&nbsp;Alt/Alt')\n\t\t\t}\n\n\t\t\tif (tk.populationfrequencyfilter) {\n\t\t\t\tconst err = ctrlui_populationfrequency(tk, block)\n\t\t\t\tif (err) {\n\t\t\t\t\tdelete tk.populationfrequencyfilter\n\t\t\t\t\tblock.error(tk.name + ': ' + err)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (tk.ds.cohort && tk.ds.cohort.sampleattribute) {\n\t\t\t\tconst err = ctrlui_sampleattribute(tk, block)\n\t\t\t\tif (err) {\n\t\t\t\t\tdelete tk.ds.cohort.sampleattribute\n\t\t\t\t\tblock.error(tk.name + ': ' + err)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction mlstfilter(tk, block) {\n\tconst lst = []\n\tfor (const m of tk.mlst) {\n\t\tif (block.legend) {\n\t\t\tif (block.legend.mclasses.has(m.class) && block.legend.mclasses.get(m.class).hidden) continue\n\t\t\tif (block.legend.morigins.has(m.origin) && block.legend.morigins.get(m.origin).hidden) continue\n\t\t}\n\t\tlst.push(m)\n\t}\n\treturn lst\n}\n\nfunction downloadmlst(tk, block) {\n\tconst mlst = mlstfilter(tk, block)\n\tconst exported = []\n\tif (tk.ds.id2vcf) {\n\t\t// is vcf file(s)\n\t\tconst txt = []\n\t\tfor (const vcfid in tk.ds.id2vcf) {\n\t\t\tconst lst2 = []\n\t\t\tfor (const m of mlst) {\n\t\t\t\tif (m.vcfid == vcfid) lst2.push(m)\n\t\t\t}\n\t\t\tif (lst2.length == 0) continue\n\t\t\tconst vcf = tk.ds.id2vcf[vcfid]\n\t\t\ttxt.push('CHROM\\tPOS\\tREF\\tALT\\tINFO-locus\\tINFO-altAllele\\tclass\\tname')\n\t\t\tfor (const m of lst2) {\n\t\t\t\tconst info = []\n\t\t\t\tif (m.info) {\n\t\t\t\t\tfor (const k in m.info) info.push(k + '=' + m.info[k])\n\t\t\t\t}\n\t\t\t\tconst altinfo = []\n\t\t\t\tif (m.altinfo) {\n\t\t\t\t\tfor (const k in m.altinfo) altinfo.push(k + '=' + m.altinfo[k])\n\t\t\t\t}\n\t\t\t\ttxt.push(\n\t\t\t\t\t`${m.chr}\\t${m.pos}\\t${m.ref}\\t${m.alt}\\t${info.join(';')}\\t${altinfo.join(';')}\\t${\n\t\t\t\t\t\tcommon.mclass[m.class].label\n\t\t\t\t\t}\\t${m.mname}`\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t\texported.push({ text: txt.join('\\n') })\n\t} else {\n\t\t// regular ds\n\t\tconst dt2lst = new Map()\n\t\tfor (const m of mlst) {\n\t\t\tif (!dt2lst.has(m.dt)) {\n\t\t\t\tdt2lst.set(m.dt, [])\n\t\t\t}\n\t\t\tdt2lst.get(m.dt).push(m)\n\t\t}\n\t\tfor (const [dt, mlst2] of dt2lst) {\n\t\t\tlet atlst = null\n\t\t\tswitch (dt) {\n\t\t\t\tcase common.dtsnvindel:\n\t\t\t\t\tif (!tk.snvindelattr) {\n\t\t\t\t\t\truntimeattr_snvindel(tk, mlst2)\n\t\t\t\t\t}\n\t\t\t\t\tatlst = tk.snvindelattr\n\t\t\t\t\tbreak\n\t\t\t\tcase common.dtsv:\n\t\t\t\tcase common.dtfusionrna:\n\t\t\t\t\tif (!tk.svattr) {\n\t\t\t\t\t\truntimeattr_sv(tk, mlst2)\n\t\t\t\t\t}\n\t\t\t\t\tatlst = tk.svattr\n\t\t\t\t\tbreak\n\t\t\t\tcase common.dtitd:\n\t\t\t\t\tif (!tk.itdattr) {\n\t\t\t\t\t\truntimeattr_itd(tk, mlst2)\n\t\t\t\t\t}\n\t\t\t\t\tatlst = tk.itdattr\n\t\t\t\t\tbreak\n\t\t\t\tcase common.dtnloss:\n\t\t\t\tcase common.dtcloss:\n\t\t\t\t\tif (!tk.truncattr) {\n\t\t\t\t\t\truntimeattr_trunc(tk, mlst2)\n\t\t\t\t\t}\n\t\t\t\t\tatlst = tk.truncattr\n\t\t\t\t\tbreak\n\t\t\t\tcase common.dtdel:\n\t\t\t\t\tif (!tk.delattr) {\n\t\t\t\t\t\truntimeattr_del(tk, mlst2)\n\t\t\t\t\t}\n\t\t\t\t\tatlst = tk.delattr\n\t\t\t\t\tbreak\n\t\t\t\tcase common.dtcnv:\n\t\t\t\t\tbreak\n\t\t\t}\n\t\t\tif (!atlst) {\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst head = []\n\t\t\tfor (const a of atlst) {\n\t\t\t\tif (a.lst) {\n\t\t\t\t\tfor (const b of a.lst) {\n\t\t\t\t\t\tif (b.ismaf) {\n\t\t\t\t\t\t\thead.push(b.label + ' mutant allele fraction')\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\thead.push(b.label)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tif (a.ismaf) {\n\t\t\t\t\t\thead.push(a.label + ' mutant allele fraction')\n\t\t\t\t\t} else {\n\t\t\t\t\t\thead.push(a.label)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst content = [head.join('\\t')]\n\t\t\tfor (const m of mlst2) {\n\t\t\t\tconst lst = []\n\t\t\t\tfor (const a of atlst) {\n\t\t\t\t\tif (a.lst) {\n\t\t\t\t\t\tfor (const b of a.lst) {\n\t\t\t\t\t\t\tif (b.ismaf) {\n\t\t\t\t\t\t\t\tconst v = b.get(m)\n\t\t\t\t\t\t\t\tif (v && Number.isFinite(v.f)) {\n\t\t\t\t\t\t\t\t\tlst.push(v.f.toFixed(2))\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\tlst.push('n/a')\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\tlst.push(b.get(m))\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (a.ismaf) {\n\t\t\t\t\t\t\tconst v = a.get(m)\n\t\t\t\t\t\t\tif (v && Number.isFinite(v.f)) {\n\t\t\t\t\t\t\t\tlst.push(v.f.toFixed(2))\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tlst.push('n/a')\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tlst.push(a.get(m))\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontent.push(lst.join('\\t'))\n\t\t\t}\n\t\t\texported.push({\n\t\t\t\tlabel: common.dt2label[dt],\n\t\t\t\ttext: content.join('\\n')\n\t\t\t})\n\t\t}\n\t}\n\tclient.export_data(tk.ds.label, exported)\n}\n\nfunction getmlstattrnames(tk) {\n\tconst skip = new Set([\n\t\t'__x',\n\t\t'isrim1',\n\t\t'isrim2',\n\t\t'aapos',\n\t\t'alt',\n\t\t'chr',\n\t\t'class',\n\t\t'dt',\n\t\t'isoform',\n\t\t'mname',\n\t\t'origin',\n\t\t'pos',\n\t\t'ref',\n\t\t'rnapos',\n\t\t'rnaposition',\n\t\t'gene',\n\t\t'rnaduplength',\n\t\t'rnadellength'\n\t])\n\tif (tk.ds.cohort && tk.ds.cohort.levels) {\n\t\tfor (const l of tk.ds.cohort.levels) {\n\t\t\tskip.add(l.k)\n\t\t\tif (l.full) {\n\t\t\t\tskip.add(l.full)\n\t\t\t}\n\t\t}\n\t}\n\tconst attrnames = new Set()\n\tfor (const m of tk.mlst) {\n\t\tfor (const k in m) {\n\t\t\tif (skip.has(k)) continue\n\t\t\tconst v = m[k]\n\t\t\tif (typeof v == 'object') {\n\t\t\t\t// skip things like maf_dna, fusion.pairlst, truncation.partner, itd.a, itd.b\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tattrnames.add(k)\n\t\t}\n\t}\n\tconst low2name = new Map() // tidy for identify\n\tfor (const i of attrnames) {\n\t\tlow2name.set(i.toLowerCase(), i)\n\t}\n\tconst lst = []\n\t// try to put sample name as the first of list to show as default\n\tif (low2name.has('sample')) lst.push(low2name.get('sample'))\n\tif (low2name.has('samplename')) lst.push(low2name.get('samplename'))\n\tif (low2name.has('patient')) lst.push(low2name.get('patient'))\n\tif (low2name.has('patientname')) lst.push(low2name.get('patientname'))\n\tif (low2name.has('sampletype')) lst.push(low2name.get('sampletype'))\n\tif (low2name.has('person')) lst.push(low2name.get('person'))\n\tif (low2name.has('individual')) lst.push(low2name.get('individual'))\n\tfor (const [i, j] of low2name) {\n\t\tif (lst.indexOf(j) == -1) {\n\t\t\tlst.push(j)\n\t\t}\n\t}\n\treturn lst\n}\n\nfunction mlststratifyui(tk, holder, block) {\n\tconst div = holder.append('div').style('margin', '20px')\n\n\tconst row1 = div.append('div').style('margin-bottom', '5px')\n\trow1.append('span').style('font-size', '.7em').html('Stratify by&nbsp;&nbsp;')\n\tconst attrnames = getmlstattrnames(tk)\n\tconst select = row1.append('select').on('change', () => {\n\t\tconst sn = select.node()\n\t\tconst k = sn.options[sn.selectedIndex].innerHTML\n\t\tfreestratify(k, tk, block, resultdiv)\n\t})\n\n\tconst resultdiv = div.append('div')\n\tfor (const attrname of attrnames) {\n\t\tselect.append('option').text(attrname)\n\t}\n\tif (attrnames[0]) {\n\t\tfreestratify(attrnames[0], tk, block, resultdiv)\n\t}\n}\n\nfunction freestratify(key, tk, block, div) {\n\tconst map = new Map()\n\tfor (const m of tk.mlst) {\n\t\tlet v = m[key]\n\t\tif (v == undefined) {\n\t\t\tcontinue\n\t\t}\n\t\tif (typeof v == 'boolean') {\n\t\t\tif (v) {\n\t\t\t\tv = 'true'\n\t\t\t} else {\n\t\t\t\tv = 'false'\n\t\t\t}\n\t\t}\n\t\tif (map.has(v)) {\n\t\t\tmap.get(v).push(m)\n\t\t} else {\n\t\t\tmap.set(v, [m])\n\t\t}\n\t}\n\tconst resultlst = [...map]\n\tresultlst.sort((a, b) => b[1].length - a[1].length)\n\n\tdiv.selectAll('*').remove()\n\tif (map.size > 10) {\n\t\tdiv.style('height', '200px').style('overflow-y', 'scroll').style('resize', 'vertical').style('padding', '5px')\n\t}\n\tconst table = div\n\t\t.append('table')\n\t\t.style('border-spacing', '1px')\n\t\t.style('border-collapse', 'separate')\n\t\t.style('font-size', '.8em')\n\n\tfor (const [v, mlst] of resultlst) {\n\t\tconst tr = table.append('tr')\n\t\t// td 1\n\t\ttr.append('td').text(mlst.length).style('text-align', 'right')\n\t\t// td 2\n\t\tconst td = tr.append('td').classed('sja_menuoption', true)\n\t\ttd.text(v)\n\t\ttd.on('click', () => {\n\t\t\tconst thisdsname = tk.ds.label + ' - ' + key + ' - ' + v\n\t\t\tif (block.ownds[thisdsname]) {\n\t\t\t\tblock.deletecustomdsbyname(thisdsname)\n\t\t\t} else {\n\t\t\t\t// create child tk\n\t\t\t\tconst _ds = {\n\t\t\t\t\tlabel: thisdsname,\n\t\t\t\t\tbulkdata: {},\n\t\t\t\t\tparentname: tk.ds.label,\n\t\t\t\t\tiscustom: true,\n\t\t\t\t\tsampleselectable: tk.ds.sampleselectable\n\t\t\t\t}\n\t\t\t\t_ds.bulkdata[block.usegm.name.toUpperCase()] = mlst\n\t\t\t\tblock.addchilddsnoload(_ds)\n\t\t\t\tconst childtk = block.block_addtk_template({ type: client.tkt.ds, ds: _ds })\n\t\t\t\tblockds.dstkload(childtk, block)\n\t\t\t}\n\t\t})\n\t\t// td 3\n\t\tconst td3 = tr.append('td')\n\t\tsummarizemclass(mlst, td3)\n\t}\n}\n\nfunction summarizemclass(mlst, holder) {\n\tconst map = new Map()\n\tfor (const m of mlst) {\n\t\tif (map.has(m.class)) {\n\t\t\tmap.set(m.class, map.get(m.class) + 1)\n\t\t} else {\n\t\t\tmap.set(m.class, 1)\n\t\t}\n\t}\n\tconst lst = [...map]\n\tlst.sort((a, b) => b[1] - a[1])\n\tfor (const c of lst) {\n\t\tholder\n\t\t\t.append('span')\n\t\t\t.html(c[1] == 1 ? '&nbsp;' : c[1])\n\t\t\t.style('background-color', common.mclass[c[0]].color)\n\t\t\t.classed('sja_mcdot', true)\n\t}\n}\n\nfunction label_mcount_fillpane(tk, block, handle, tip) {\n\ttip.clear()\n\tconst holder = tip.d\n\n\tif (!tk.mlst) {\n\t\tconsole.error('.mlst missing for ' + tk.name)\n\t\treturn\n\t}\n\tif (tk.mlst.length == 0) {\n\t\t// when mlst is empty this controller should not be clickable\n\t\treturn\n\t}\n\n\t// 1. free stratify\n\tif (tk.ds.id2vcf) {\n\t\t// TODO support vcf meta for stratifying\n\t} else {\n\t\tif (tk.mlst.length < 1000) {\n\t\t\t// too many\n\t\t\tmlststratifyui(tk, holder, block)\n\t\t} else {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Stratify ' + tk.mlst.length + ' variants')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tholder.selectAll('*').remove()\n\t\t\t\t\tmlststratifyui(tk, holder, block)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tif (block.samplecart && tk.ds && tk.ds.sampleselectable) {\n\t\t// select sample API\n\t\t// allow samples to be selected\n\t\tconst sampleset = new Set()\n\t\tfor (const m of tk.mlst) {\n\t\t\tif (m.sample) {\n\t\t\t\t// FIXME hardcoded sample attribute\n\t\t\t\tsampleset.add(m.sample)\n\t\t\t}\n\t\t}\n\n\t\tblock.samplecart.setBtns({\n\t\t\tsamplelst: [...sampleset],\n\t\t\tid: block.usegm ? block.usegm.name : '',\n\t\t\tbasket: 'Gene Mutation',\n\t\t\tcontainer: holder.append('div')\n\t\t})\n\t}\n\n\tif (tk.numericmode) {\n\t} else {\n\t\t// not in numeric mode\n\t\t// 2. expand / fold skewers\n\t\tlet hasshown = false\n\t\tfor (const i of tk.data) {\n\t\t\tif (i.showmode == 1) {\n\t\t\t\thasshown = true\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (hasshown) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Fold')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.hide()\n\t\t\t\t\tblockds.fold_glyph(tk.data, tk)\n\t\t\t\t})\n\t\t} else {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.text('Expand')\n\t\t\t\t.classed('sja_menuoption', true)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ttip.hide()\n\t\t\t\t\tblockds.settle_glyph(tk, block)\n\t\t\t\t})\n\t\t}\n\t}\n\n\t// 3. sunburst\n\tif (tk.ds.cohort) {\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.text('To sunburst')\n\t\t\t.classed('sja_menuoption', true)\n\t\t\t.on('click', async () => {\n\t\t\t\ttip.hide()\n\t\t\t\tconst mlst = mlstfilter(tk, block)\n\t\t\t\tawait may_sunburst(mlst.length, mlst, 100, tk.height_main / 2, tk, block)\n\t\t\t})\n\t}\n\t// 4.\n\tholder\n\t\t.append('div')\n\t\t.text('To table')\n\t\t.classed('sja_menuoption', true)\n\t\t.on('click', () => {\n\t\t\tconst p = holder.node().getBoundingClientRect()\n\t\t\ttip.hide()\n\t\t\tconst mlst = mlstfilter(tk, block)\n\t\t\titemtable({\n\t\t\t\tmlst: mlst,\n\t\t\t\tpane: true,\n\t\t\t\tx: p.left,\n\t\t\t\ty: p.top,\n\t\t\t\ttk: tk,\n\t\t\t\tblock: block\n\t\t\t})\n\t\t})\n\t// 5.\n\tholder\n\t\t.append('div')\n\t\t.text('Download')\n\t\t.classed('sja_menuoption', true)\n\t\t.on('click', () => {\n\t\t\ttip.hide()\n\t\t\tdownloadmlst(tk, block)\n\t\t})\n\ttip.showunder(handle.node())\n}\n\nfunction label_strat_fillpane(tk, block, strat, tip) {\n\ttip.clear()\n\n\t// compute stratification on client\n\n\tconst mlst = mlstfilter(tk, block)\n\n\tlet levels = []\n\tif (strat.bycohort) {\n\t\tif (!tk.ds || !tk.ds.cohort || !tk.ds.cohort.levels) {\n\t\t\tconsole.error('some part is missing: tk.ds.cohort.levels')\n\t\t\treturn\n\t\t}\n\t\tlevels = tk.ds.cohort.levels\n\t} else {\n\t\tif (strat.attr1) {\n\t\t\tlevels.push({ label: strat.attr1.label, k: strat.attr1.k })\n\t\t}\n\t\tif (strat.attr2) {\n\t\t\tlevels.push({ label: strat.attr2.label, k: strat.attr2.k })\n\t\t}\n\t\tif (strat.attr3) {\n\t\t\tlevels.push({ label: strat.attr3.label, k: strat.attr3.k })\n\t\t}\n\t}\n\tconst root = stratify()(stratinput(mlst, levels))\n\troot.sum(i => i.value)\n\tconst table = tip.d.append('table')\n\tconst tr = table.append('tr').style('font-size', '.9em').style('color', '#858585')\n\ttr.append('td').text(strat.label.toUpperCase())\n\tif (strat.bycohort && tk.ds.cohort.root) {\n\t\ttr.append('td').text('% TUMOR')\n\t}\n\ttr.append('td')\n\ttr.append('td').text('MUTATIONS')\n\troot.eachBefore(n => {\n\t\tif (!n.parent) return\n\t\tconst thisdsname = tk.ds.label + ' - ' + n.data.name\n\t\tconst tr = table.append('tr').classed('sja_clb', true)\n\t\tif (block.ownds[thisdsname]) {\n\t\t\ttr.style('background-color', hotcolor)\n\t\t}\n\t\t// td1\n\t\ttr.append('td')\n\t\t\t.style('padding-left', (n.depth - 1) * 15 + 'px')\n\t\t\t.html(\n\t\t\t\tn.data.name + (n.data.full ? '&nbsp;<span style=\"font-size:.7em;color:#858585\">' + n.data.full + '</span>' : '')\n\t\t\t)\n\t\t// td2\n\t\tif (strat.bycohort && tk.ds.cohort.root) {\n\t\t\tconst td2 = tr.append('td')\n\t\t\tlet cohortsize = 0\n\t\t\ttk.ds.cohort.root.each(i => {\n\t\t\t\tif (i.id == n.id) {\n\t\t\t\t\tcohortsize = i.value\n\t\t\t\t}\n\t\t\t})\n\t\t\tif (cohortsize == 0) {\n\t\t\t\ttd2.text('not found').style('font-size', '.7em')\n\t\t\t} else {\n\t\t\t\tclient.fillbar(\n\t\t\t\t\ttd2,\n\t\t\t\t\t{ f: n.value / cohortsize, v1: n.value, v2: cohortsize },\n\t\t\t\t\t{ fillbg: tk.ds.cohort.fbarbg, fill: tk.ds.cohort.fbarfg }\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t\t// td3\n\t\ttr.append('td').style('text-align', 'right').style('font-size', '.8em').text(n.value)\n\t\t// td4\n\t\tconst td4 = tr.append('td')\n\t\tsummarizemclass(n.data.lst, td4)\n\t\ttr.on('click', () => {\n\t\t\tif (block.ownds[thisdsname]) {\n\t\t\t\tblock.deletecustomdsbyname(thisdsname)\n\t\t\t\ttr.style('background-color', 'transparent')\n\t\t\t} else {\n\t\t\t\ttr.style('background-color', hotcolor)\n\t\t\t\t// create child tk\n\t\t\t\tconst _ds = {\n\t\t\t\t\tlabel: thisdsname,\n\t\t\t\t\tbulkdata: {},\n\t\t\t\t\tparentname: tk.ds.label,\n\t\t\t\t\tiscustom: true,\n\t\t\t\t\tsampleselectable: tk.ds.sampleselectable\n\t\t\t\t}\n\t\t\t\t_ds.bulkdata[block.usegm.name.toUpperCase()] = n.data.lst\n\t\t\t\tblock.addchilddsnoload(_ds)\n\t\t\t\tconst childtk = block.block_addtk_template({ type: client.tkt.ds, ds: _ds })\n\t\t\t\tblockds.dstkload(childtk, block)\n\t\t\t}\n\t\t})\n\t})\n\ttip.showunder(strat.svglabel.node())\n}\n\nfunction ctrlui_vcfinfofilter(tk, block) {\n\t/*\n\tfrom m.info or m.altinfo, of a vcf track\n\tin legend, each term shown in one row\n\tterm name clickable to select and apply to the track\n\n\tcategorical:\n\t\thas the .categories{} attribute\n\t\tif autocategory is set, .categories{} will be dynamically filled with color roster each time data is loaded\n\n\tnumerical:\n\t\tdoes not have .categories{}\n\n\tcontents for each term to be filled up at runtime\n\t*/\n\n\tconst err = common.validate_vcfinfofilter(tk.vcfinfofilter)\n\tif (err) return err\n\n\tconst obj = tk.vcfinfofilter\n\n\tobj.tip = new client.Menu({ padding: '0px' })\n\n\tif (obj.setidx4mclass != undefined) {\n\t\t// given setidx4mclass\n\t\tif (!Number.isInteger(obj.setidx4mclass)) return '.setidx4mclass value should be array index (non-negative integer)'\n\t\tconst set = obj.lst[obj.setidx4mclass]\n\t\tif (!set) return '.setidx4mclass value out of bound'\n\t\tif (!set.autocategory) {\n\t\t\tif (!set.categories) return '.setidx4mclass does not point to a categorical set'\n\t\t}\n\t}\n\n\tif (obj.setidx4numeric != undefined) {\n\t\t// given setidx4mclass\n\t\tif (!Number.isInteger(obj.setidx4numeric))\n\t\t\treturn '.setidx4numeric value should be array index (non-negative integer)'\n\t\tconst set = obj.lst[obj.setidx4numeric]\n\t\tif (!set) return '.setidx4numeric value out of bound'\n\t\tif (set.categories) return '.setidx4numeric does not point to a numeric set'\n\t}\n\n\t// validated\n\n\tobj.holder = tk.td_legend.append('table').style('border-spacing', '5px')\n\n\t// display holder for each set\n\tfor (let i = 0; i < obj.lst.length; i++) {\n\t\tconst set = obj.lst[i]\n\n\t\tconst row = obj.holder.append('tr')\n\n\t\tset.namebutton = row\n\t\t\t.append('td')\n\t\t\t.text(set.name)\n\t\t\t.attr('class', 'sja_clb')\n\t\t\t.style('text-align', 'right')\n\t\t\t.on('click', () => {\n\t\t\t\tlet usethisset = true\n\t\t\t\tif (set.categories) {\n\t\t\t\t\t// wash out categorical sets, leave out numeric sets\n\t\t\t\t\tfor (const s2 of obj.lst) {\n\t\t\t\t\t\tif (s2.categories) {\n\t\t\t\t\t\t\ts2.namebutton.style('background-color', null).style('border-bottom', null)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (i == obj.setidx4mclass) {\n\t\t\t\t\t\tdelete obj.setidx4mclass\n\t\t\t\t\t\tusethisset = false\n\t\t\t\t\t} else {\n\t\t\t\t\t\tobj.setidx4mclass = i\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// wash out numeric sets, leave out categorical sets\n\t\t\t\t\tfor (const s2 of obj.lst) {\n\t\t\t\t\t\tif (!s2.categories) {\n\t\t\t\t\t\t\ts2.namebutton.style('background-color', null).style('border-bottom', null)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (i == obj.setidx4numeric) {\n\t\t\t\t\t\tdelete obj.setidx4numeric\n\t\t\t\t\t\tusethisset = false\n\t\t\t\t\t} else {\n\t\t\t\t\t\tobj.setidx4numeric = i\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (usethisset) {\n\t\t\t\t\tset.namebutton.style('background-color', '#f1f1f1').style('border-bottom', 'solid 2px #ccc')\n\t\t\t\t}\n\t\t\t\tdstkrender(tk, block)\n\t\t\t})\n\n\t\tif (i == obj.setidx4mclass || i == obj.setidx4numeric) {\n\t\t\tset.namebutton.style('background-color', '#f1f1f1').style('border-bottom', 'solid 2px #ccc')\n\t\t}\n\t\t// for on-the-fly fill\n\t\tset.holder = row.append('td')\n\t}\n\treturn null\n}\n\nfunction ctrlui_populationfrequency(tk, block) {\n\t/*\n\tfilter variants by population frequency\n\tfor multi-sample vcf\n\tlegend filled on the fly\n\t*/\n\n\tif (!tk.populationfrequencyfilter.lst) return '.lst[] missing for .populationfrequencyfilter'\n\n\t// swap lst\n\tconst lst = []\n\tfor (const v of tk.populationfrequencyfilter.lst) {\n\t\tif (typeof v == 'number') {\n\t\t\tlst.push({ value: v })\n\t\t\tcontinue\n\t\t}\n\t\tif (v.value == undefined || typeof v.value != 'number') {\n\t\t\treturn '.populationfrequencyfilter.lst[].value is not a number'\n\t\t}\n\t\tlst.push({ value: v.value })\n\t}\n\ttk.populationfrequencyfilter.lst = lst\n\n\tconst div = tk.td_legend.append('div')\n\tif (tk.populationfrequencyfilter.name) {\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.text(tk.populationfrequencyfilter.name)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', '#858585')\n\t\t\t.style('margin-right', '10px')\n\t}\n\ttk.populationfrequencyfilter.holder = div.append('div').style('display', 'inline-block')\n}\n\nfunction ctrlui_sampleattribute(tk, block) {\n\t/*\n\tfor multi-sample vcf, filter variants by sample annotation\n\tlegend filled on the fly\n\tchallenge for variant-cohort composite track\n\t*/\n\n\tconst smat = tk.ds.cohort.sampleattribute\n\tif (!smat.lst) return '.lst[] missing for .cohort.sampleattribute'\n\tconst div = tk.td_legend.append('div')\n\tsmat.holder = div\n\tsmat.tip = new client.Menu({ padding: '0px' })\n}\n"],
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+}