@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/tk-4E3XJ7CO.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../j2/legend.js", "../j2/render.js", "../j2/makeTk.js", "../j2/tk.js"],
+  "sourcesContent": ["import { legend_newrow } from '#src/block.legend'\nimport { Menu } from '#dom'\nimport { JTypes } from '#shared'\nimport { printCategory } from '../mds3/legend'\n\n/*\n */\n\nexport function initLegend(tk, block) {\n\t// run only once, called by makeTk\n\tif (!block.legend) return // block has no legend. could be due to hidegenelegend flag\n\tif (!tk.legend) tk.legend = {}\n\ttk.legend.tip = new Menu({ padding: '0px' })\n\n\tconst [tr, td, td0] = legend_newrow(block, tk.dslabel)\n\ttk.legend.headTd = td0 // for updating tk name in legend when filterObj updates\n\n\ttk.tr_legend = tr // to be compatible with block.tk_remove()\n\n\tconst table = td.append('table').style('border-spacing', '5px').style('border-collapse', 'separate')\n\n\ttk.legend.table = table\n\tcreate_type(tk, block)\n}\nexport function updateLegend(data, tk, block) {\n\tif (!tk.legend) {\n\t\t// if using invalid dslabel, upon initiating initLegend() will not be called\n\t\t//and tk.legend may not be created\n\t\treturn\n\t}\n\tupdate_type(tk)\n}\nfunction create_type(tk, block) {\n\tif (!tk.legend.type) tk.legend.type = {}\n\tif (!tk.legend.type.hiddenvalues) tk.legend.type.hiddenvalues = new Set()\n\n\tif (tk.hiddentypes) {\n\t\t// some types to be hidden by default according to ds\n\t\tfor (const c of tk.hiddentypes.split(',')) tk.legend.type.hiddenvalues.add(c)\n\t\tdelete tk.hiddentypes\n\t}\n\n\ttk.legend.type.row = tk.legend.table.append('tr')\n\n\ttk.legend.type.row\n\t\t.append('td')\n\t\t.attr('data-testid', 'sjpp-j2-legend-row-type')\n\t\t.style('text-align', 'right')\n\t\t.style('opacity', 0.7)\n\t\t.text('Type')\n\n\ttk.legend.type.holder = tk.legend.type.row.append('td')\n}\nfunction update_type(tk) {\n\tif (tk.hardcodeCnvOnly) return // legend is permanently hidden, no need to update\n\tconst type2count = new Map() // k: type, v: count\n\tfor (const j of tk.data) {\n\t\tfor (const t of j.types) {\n\t\t\ttype2count.set(t, 1 + (type2count.get(t) || 0))\n\t\t}\n\t}\n\n\ttk.legend.type.holder.selectAll('*').remove()\n\n\tfor (const [t, c] of [...type2count].sort((i, j) => j[1] - i[1])) {\n\t\t// { k, count }\n\t\tprintCategory({\n\t\t\tholder: tk.legend.type.holder,\n\t\t\tkey: t,\n\t\t\tlabel: JTypes[t].name,\n\t\t\tcolor: JTypes[t].color,\n\t\t\tcount: c,\n\t\t\ttestid: 'sjpp-j2-legend-row-type-item',\n\t\t\tclick: event => {\n\t\t\t\tconst opts = [\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Hide',\n\t\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\t\ttk.legend.type.hiddenvalues.add(t)\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Show only',\n\t\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\t\tfor (const t2 of type2count.keys()) {\n\t\t\t\t\t\t\t\ttk.legend.type.hiddenvalues.add(t2)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\ttk.legend.type.hiddenvalues.delete(t)\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Show all',\n\t\t\t\t\t\tisVisible: () => tk.legend.type.hiddenvalues.size,\n\t\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\t\ttk.legend.type.hiddenvalues.clear()\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t\ttk.legend.tip.clear().showunder(event.target)\n\t\t\t\tfor (const o of opts) {\n\t\t\t\t\tif (o.isVisible && o.isVisible() == false) continue\n\t\t\t\t\ttk.legend.tip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.attr('data-testid', `sjpp-legend-option-${o.label.toLowerCase().replace(/\\s/g, '-')}`)\n\t\t\t\t\t\t.style('border-radius', '0px')\n\t\t\t\t\t\t.text(o.label)\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\to.callback()\n\t\t\t\t\t\t\ttk.legend.tip.hide()\n\t\t\t\t\t\t\ttk.load()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\t// hidden ones\n\tfor (const c of tk.legend.type.hiddenvalues) {\n\t\tlet loading = false\n\n\t\ttk.legend.type.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.attr('class', 'sja_clb')\n\t\t\t.style('text-decoration', 'line-through')\n\t\t\t.style('opacity', 0.7)\n\t\t\t.text(JTypes[c].name)\n\t\t\t.on('click', async event => {\n\t\t\t\tif (loading) return\n\t\t\t\tloading = true\n\t\t\t\ttk.legend.type.hiddenvalues.delete(c)\n\t\t\t\tevent.target.innerHTML = 'Updating...'\n\t\t\t\tawait tk.load()\n\t\t\t})\n\t}\n}\n", "import { scaleLinear, scaleLog, scaleOrdinal } from 'd3-scale'\nimport { select as d3select } from 'd3-selection'\nimport { axisRight } from 'd3-axis'\nimport * as d3force from 'd3-force'\nimport { axisstyle, table2col } from '#dom'\nimport { bplen, IN_frame, JTypes, JT_canonical, JT_exonskip, JT_exonaltuse, JT_a5ss, JT_a3ss } from '#shared/common.js'\nimport { getParameter } from './tk'\nimport { dofetch3 } from '#common/dofetch'\nimport { TermTypes } from '#types'\nimport { makeJunctionCustomTerm } from '#termdb/handlers/junction.customTerm'\n\n/*\n */\n\nconst minfontsize = 12\nconst lineopacity = 0.5\nconst discopacity = 0.5\nconst cohortLegendDotColor = '#858585' // '#EBBD5B' // also for sample percentage bar foreground color\nconst notAnnotatedLabel = 'Unannotated'\nconst junctionNoSpliceeventLabel = 'None'\nconst labyspace = 5\n\nconst hardcode_infoKey_type = 'type' // currently the only infoFilter key\nconst hardcode_infoValue_canonical = 'canonical'\n\n/////////////  __render begins\n\nexport function renderTk(data, tk, block) {\n\tif (data) {\n\t\t// server returned fresh data\n\t\tif (data.junctions?.length == 0) {\n\t\t\ttk.data = []\n\t\t\ttk.leftlabels?.doms?.jug?.text('0 junctions')\n\t\t\treturn\n\t\t}\n\t\tif (!Number.isFinite(data.maxReadCount)) throw new Error('data.maxReadCount is not number')\n\t\trawdata2track(data.junctions, tk, block)\n\t\t// tk.data[] set\n\t} else {\n\t\t// this is called from config menu. server data is already parsed at tk.data[]\n\t}\n\n\ttk.leftlabels.doms.jug.text(`${tk.data.length} junction${tk.data.length > 1 ? 's' : ''}`)\n\n\tconst viewpxwidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0)\n\n\tsetColor(tk)\n\n\ttk.sections.jug.g.selectAll('*').remove()\n\n\t// do not clear leftaxis, leave it to transition\n\n\t// all graphs go in here\n\tconst mg = tk.sections.jug.g\n\n\ttk.data.sort((a, b) => {\n\t\treturn a._x - b._x\n\t})\n\n\t/* disc radius, determined by sample count for each junction\n\twill show >1 sample count in disc\n\tTODO may show piechart for sample stratification\n\tso need to slightly increase disc radius to fit these\n*/\n\tconst maxsamplecount = tk.data.reduce((max, j) => Math.max(max, j.sampleCount), 0)\n\t{\n\t\tconst radius = 5\n\t\tlet mrd = 0 // max radius\n\t\tconst w = Math.pow(radius, 2) * Math.PI // unit area\n\t\tif (maxsamplecount <= 10) {\n\t\t\tmrd = w * maxsamplecount * 0.9\n\t\t} else if (maxsamplecount <= 100) {\n\t\t\tmrd = w * 10\n\t\t} else if (maxsamplecount <= 1000) {\n\t\t\tmrd = w * 14\n\t\t} else {\n\t\t\tmrd = w * 20\n\t\t}\n\t\tconst sf_discradius = scaleLinear()\n\t\t\t.domain([\n\t\t\t\t1,\n\t\t\t\tmaxsamplecount * 0.5 + 0.1,\n\t\t\t\tmaxsamplecount * 0.6 + 0.1,\n\t\t\t\tmaxsamplecount * 0.7 + 0.1,\n\t\t\t\tmaxsamplecount * 0.8 + 0.1,\n\t\t\t\tmaxsamplecount\n\t\t\t])\n\t\t\t.range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd])\n\t\tlet maxradius = 0\n\t\tfor (const j of tk.data) {\n\t\t\tj.radius = Math.sqrt(sf_discradius(j.sampleCount) / Math.PI)\n\t\t\tif (j.sampleCount > 1) {\n\t\t\t\t// more than 1 sample, to show #sample in disc, so to adjust disc radius\n\t\t\t\tmg.append('text')\n\t\t\t\t\t.attr('font-family', 'Arial')\n\t\t\t\t\t.attr('font-size', Math.max(minfontsize, j.radius))\n\t\t\t\t\t.text(j.sampleCount)\n\t\t\t\t\t.each(function () {\n\t\t\t\t\t\tconst b = this.getBBox()\n\t\t\t\t\t\tconst newrad = Math.sqrt(Math.pow(b.width, 2) + Math.pow(b.height, 2)) / 2\n\t\t\t\t\t\tj.radius = Math.max(j.radius, newrad)\n\t\t\t\t\t})\n\t\t\t\t\t.remove()\n\t\t\t}\n\t\t\tj.rimwidth = j.rimcount ? Math.max(2, j.radius / 6) : 0\n\t\t\tj.radius2 = j.radius + j.rimwidth + (j.rimwidth > 0 ? 1 : 0)\n\t\t\tmaxradius = Math.max(maxradius, j.radius2)\n\t\t}\n\t\ttk.maxradius = maxradius\n\t}\n\n\t// y position, by median read count for each junction\n\tconst maxmedian = tk.data.reduce((c, j) => Math.max(c, j.medianReadCount), 0)\n\n\t/*\n\tessential to use data.maxReadCount as yscale max\n\tthis may leave some white space above the disks (median positioned)\n\tbut will allow the hover boxplot to fully show\n\t*/\n\ttk.sections.jug.yscale = (tk.yscaleUseLog ? scaleLog() : scaleLinear())\n\t\t.domain([tk.readcountCutoff || 1, data.maxReadCount])\n\t\t.range([tk.sections.jug.axisheight, 0])\n\n\t// fill axis-y for those junction without previous axisy\n\tfor (const j of tk.data) {\n\t\tif (j.axisy == undefined) {\n\t\t\tj.axisy = tk.sections.jug.axisheight - tk.sections.jug.yscale(j.medianReadCount)\n\t\t}\n\t}\n\n\t// set y position, also pad height for lower discs\n\t// all vertical heights set\n\ttk.sections.jug.height = tk.sections.jug.axisheight + tk.sections.jug.neckheight + tk.sections.jug.legheight\n\n\t// svg\n\tmg.attr('transform', `translate(0,${tk.sections.jug.height})`)\n\n\t{\n\t\t// top line\n\t\tconst topy = -tk.sections.jug.legheight - tk.sections.jug.neckheight - tk.sections.jug.axisheight\n\t\tmg.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('y1', topy)\n\t\t\t.attr('y2', topy)\n\t\t\t.attr('x2', viewpxwidth)\n\t\t\t.attr('stroke', '#858585')\n\t\t\t.attr('stroke-opacity', 0.2)\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t// bottom line\n\t\tmg.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('y1', topy + tk.sections.jug.axisheight)\n\t\t\t.attr('y2', topy + tk.sections.jug.axisheight)\n\t\t\t.attr('x2', viewpxwidth)\n\t\t\t.attr('stroke', '#858585')\n\t\t\t.attr('stroke-opacity', 0.2)\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\tlet v = 10\n\t\twhile (v <= data.maxReadCount) {\n\t\t\t// order of magnitude line\n\t\t\tmg.append('line')\n\t\t\t\t.attr('x1', 0)\n\t\t\t\t.attr('y1', topy + tk.sections.jug.yscale(v))\n\t\t\t\t.attr('y2', topy + tk.sections.jug.yscale(v))\n\t\t\t\t.attr('x2', viewpxwidth)\n\t\t\t\t.attr('stroke', '#858585')\n\t\t\t\t.attr('stroke-opacity', 0.2)\n\t\t\t\t.attr('stroke-dasharray', '4,4')\n\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\tv *= 10\n\t\t}\n\t}\n\n\tconst jug = mg\n\t\t.selectAll()\n\t\t.data(tk.data)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('class', 'sja_jug')\n\t\t.attr('transform', d => set_jug(d))\n\t\t.each(function (j) {\n\t\t\tj.jugg = this\n\t\t})\n\n\t// leg 1\n\t// leg y1/y2 are constant\n\tjug\n\t\t.append('line')\n\t\t.attr('stroke', d => d.color)\n\t\t.attr('x1', d => set_leg_x1(d))\n\t\t.attr('y2', -tk.sections.jug.legheight)\n\t\t.attr('stroke-opacity', lineopacity)\n\t\t.attr('class', 'sja_jug_leg1')\n\t\t.each(function (d) {\n\t\t\td.leg1 = this\n\t\t})\n\n\t// leg 2\n\tjug\n\t\t.append('line')\n\t\t.attr('stroke', d => d.color)\n\t\t.attr('x2', d => set_leg_x2(d))\n\t\t.attr('y1', -tk.sections.jug.legheight)\n\t\t.attr('stroke-opacity', lineopacity)\n\t\t.attr('class', 'sja_jug_leg2')\n\t\t.each(function (d) {\n\t\t\td.leg2 = this\n\t\t})\n\n\t// jug2\n\tconst jug2 = jug\n\t\t.append('g')\n\t\t.attr('class', 'sja_jug_jug2')\n\t\t.attr('transform', d => set_jug2(d, tk))\n\n\t// stem - jug2\n\t// stem may transit to reflect change in yscale / read count\n\tjug2\n\t\t.append('line')\n\t\t.attr('stroke', d => d.color)\n\t\t.attr('class', 'sja_jug_stem')\n\t\t.attr('stroke-dasharray', '2,2')\n\t\t.attr('shape-rendering', 'crispEdges')\n\t\t.attr('y1', d => d.radius)\n\t\t.attr('y2', d => {\n\t\t\t// use previous value\n\t\t\treturn tk.sections.jug.neckheight + d.axisy\n\t\t})\n\t\t.attr('stroke-opacity', lineopacity)\n\t\t.each(function (d) {\n\t\t\td.stem = this\n\t\t})\n\n\t// disc\n\tjug2\n\t\t.append('circle')\n\t\t.each(function (d) {\n\t\t\td.disc = this\n\t\t})\n\t\t.attr('r', d => d.radius)\n\t\t.attr('fill', d => d.color)\n\t\t.attr('stroke', 'white')\n\t\t.attr('fill-opacity', discopacity)\n\n\t// text in disc\n\tjug2\n\t\t.filter(d => d.sampleCount > 1)\n\t\t.append('text')\n\t\t.text(d => d.sampleCount)\n\t\t.attr('font-size', d => Math.max(minfontsize, d.radius))\n\t\t.attr('class', 'sja_jug_discnum')\n\t\t.attr('fill', 'white')\n\t\t.attr('font-family', 'Arial')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('dominant-baseline', 'central')\n\n\t/*\n\tarcs, not in use\n\nvar arcfunc=d3.svg.arc()\n\t.innerRadius(function(d){return d.radius+1})\n\t.outerRadius(function(d){return d.radius+1+d.rimwidth})\n\t.startAngle(0)\n\t.endAngle(function(d){return Math.PI*2*d.rimcount/d.data.length})\njug2.filter(function(d){return d.rimwidth>0})\n\t.append('path')\n\t.attr('d',arcfunc)\n\t.attr('fill',function(d){return d.color})\n\t.attr('fill-opacity',function(d){return set_rim(d)})\n\t.attr('class','sja_jug_rim')\n*/\n\n\t// kick\n\tjug2\n\t\t.append('circle')\n\t\t.attr('r', d => d.radius)\n\t\t.attr('stroke', d => d.color)\n\t\t//.attr('class','sja_aa_disckick')\n\t\t.attr('fill', 'white')\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('stroke-opacity', 0)\n\t\t.on('mouseover', (event, d) => {\n\t\t\t// stop default trigger for block.cursorhlbar\n\t\t\tevent.stopPropagation()\n\t\t\td3select(d.disc).attr('fill-opacity', 0.8)\n\t\t\td3select(d.stem).attr('stroke-opacity', 1)\n\t\t\td3select(d.leg1).attr('stroke-opacity', 1)\n\t\t\td3select(d.leg2).attr('stroke-opacity', 1)\n\n\t\t\tmouseoverSpanBackground(d, tk, block, viewpxwidth)\n\t\t\tmouseoverBoxplot(d, tk)\n\n\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\ttk.hovertip.clear().show(p.left + p.width, p.top - 50)\n\t\t\tshowOneJunction(d, tk, tk.hovertip.d, block)\n\t\t})\n\t\t.on('mouseout', (event, d) => {\n\t\t\ttk.hovertip.hide()\n\t\t\ttk.pica.g.selectAll('*').remove()\n\t\t\tblock.cursorhlbar.attr('fill', block.cursorhlbarFillColor) // restore\n\t\t\td3select(d.disc).attr('fill-opacity', discopacity)\n\t\t\td3select(d.stem).attr('stroke-opacity', lineopacity)\n\t\t\td3select(d.leg1).attr('stroke-opacity', lineopacity)\n\t\t\td3select(d.leg2).attr('stroke-opacity', lineopacity)\n\t\t})\n\t\t.on('mousedown', event => {\n\t\t\tevent.stopPropagation()\n\t\t})\n\t\t.on('mousemove', event => {\n\t\t\tevent.stopPropagation()\n\t\t})\n\t\t.on('click', (event, d) => {\n\t\t\ttk.hovertip.hide()\n\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\ttk.itemtip.clear().show(p.left + p.width, p.top - 50)\n\t\t\tshowOneJunction(d, tk, tk.itemtip.d.append('div'), block, true)\n\t\t})\n\n\tdoForceLayout(tk, block, viewpxwidth).then(() => {\n\t\t// done layout\n\t\tset_all(tk)\n\t\taxisstyle({\n\t\t\taxis: tk.sections.jug.axis.transition().call(\n\t\t\t\taxisRight()\n\t\t\t\t\t.scale(tk.sections.jug.yscale)\n\t\t\t\t\t.ticks(Math.floor(tk.sections.jug.axisheight / 20), '.0f')\n\t\t\t),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t})\n}\n\nfunction rawdata2track(raw, tk, block) {\n\t/*\n\trun only once, to parse new junctions to tk.data\n\ta junction could be following:\n\t\tsplicing:\n\t\t\ton same chromosome, j.start - j.stop\n\t\tsv:\n\t\t\tbreak ends: j.chr - j.start, j.sv.mate.chr - j.sv.mate.start\n\t*/\n\n\tconst viewpxwidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0)\n\n\tconst junctions = []\n\tfor (const j of raw) {\n\t\tif (j.sv && j.chr == j.sv.mate.chr) {\n\t\t\t// same-chr sv, may need to swap start/stop\n\t\t\tif (j.start > j.sv.mate.start) {\n\t\t\t\tconst p = j.start\n\t\t\t\tj.start = j.stop = j.sv.mate.start\n\t\t\t\tj.sv.mate.start = j.sv.mate.stop = p\n\t\t\t\tconst q = j.strand\n\t\t\t\tj.strand = j.sv.mate.strand\n\t\t\t\tj.sv.mate.strand = q\n\t\t\t}\n\t\t}\n\n\t\tconst e = j2block(j, block, viewpxwidth)\n\t\tif (e) {\n\t\t\tconsole.log(\n\t\t\t\t'junction not in view range: ' +\n\t\t\t\t\tj.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\tj.start +\n\t\t\t\t\t'-' +\n\t\t\t\t\t(j.sv ? j.sv.mate.chr + ':' + j.sv.mate.start : j.stop)\n\t\t\t)\n\t\t\tcontinue\n\t\t}\n\t\tjunctions.push(j)\n\t}\n\tif (tk.data) {\n\t\t/*\n\t\tthere has been old junctions, reserve old settings for transitioning on both X and Y\n\t\t*/\n\t\tconst map = new Map()\n\t\ttk.data.forEach(j => map.set(j.chr + '.' + j.start + '.' + j.stop + '.' + j.strand, j))\n\n\t\tconst pannedpx = Number.isInteger(block.pannedpx) ? block.pannedpx : 0\n\t\tfor (const i of junctions) {\n\t\t\tconst j = map.get(i.chr + '.' + i.start + '.' + i.stop + '.' + i.strand)\n\t\t\tif (j) {\n\t\t\t\ti.x = j.x + pannedpx\n\t\t\t\ti.axisy = j.axisy\n\t\t\t}\n\t\t}\n\t}\n\tif (junctions.length == 0) {\n\t\treturn 'no junctions in view range'\n\t}\n\ttk.data = junctions\n}\n\nfunction j2block(j, block, viewpxwidth) {\n\tlet starthit\n\tlet stophit\n\t{\n\t\tconst l = block.seekcoord(j.chr, j.start)\n\t\tfor (const hit of l) {\n\t\t\tif (hit.ridx != undefined && block.subpanels) {\n\t\t\t\t// hit in rglst and also has subpanels:\n\t\t\t\tif (hit.x < 0 || hit.x > block.width) {\n\t\t\t\t\t// hit position is actually out of block range, do not use it\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\t\t\tstarthit = hit\n\t\t}\n\t}\n\n\t{\n\t\tconst l = block.seekcoord(j.sv ? j.sv.mate.chr : j.chr, j.sv ? j.sv.mate.start : j.stop)\n\t\tfor (const hit of l) {\n\t\t\tif (hit.ridx != undefined && block.subpanels) {\n\t\t\t\tif (hit.x < 0 || hit.x > block.width) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\t\t\tstophit = hit\n\t\t}\n\t}\n\n\tif (starthit) {\n\t\tif (!stophit) {\n\t\t\tstophit = starthit // stop not mapped, use start\n\t\t}\n\t} else {\n\t\tif (stophit) {\n\t\t\tstarthit = stophit\n\t\t} else {\n\t\t\treturn true\n\t\t}\n\t}\n\n\tlet startout = starthit.x < 0 || starthit.x > viewpxwidth\n\tlet stopout = stophit.x < 0 || stophit.x > viewpxwidth\n\tif (startout && stopout) {\n\t\t// both start/stop are out of view range, drop\n\t\treturn true\n\t}\n\n\tj.x0 = starthit.x\n\tj.x1 = stophit.x\n\tj.x = (j.x0 + j.x1) / 2 // adjusted by force layout\n\tj._x = j.x // constant\n\treturn false\n}\n\nfunction setColor(tk) {\n\tfor (const j of tk.data) {\n\t\t// remove prior color, as color may be reassigned by switching infoFilter and then calling renderTk()\n\t\tdelete j.color\n\t\tj.color = JTypes[j.types[0]]?.color\n\t\tif (j.color == undefined) throw new Error('unknown j.type')\n\t}\n}\n\nfunction set_jug(d) {\n\treturn 'translate(' + d.x + ',0)'\n}\nfunction set_leg_x1(d) {\n\treturn d.x0 - d.x\n}\nfunction set_leg_x2(d) {\n\treturn d.x1 - d.x\n}\nfunction set_stem_y2(d, tk) {\n\treturn tk.sections.jug.neckheight + tk.sections.jug.axisheight - tk.sections.jug.yscale(d.medianReadCount)\n}\nfunction set_jug2(d, tk) {\n\treturn 'translate(0,-' + (tk.sections.jug.legheight + tk.sections.jug.neckheight + d.axisy) + ')'\n}\n\nfunction set_all(tk) {\n\t// must update axisy to current value\n\tconst mg = tk.sections.jug\n\ttk.data.forEach(j => (j.axisy = mg.axisheight - mg.yscale(j.medianReadCount)))\n\n\tconst dur = 500\n\tmg.g\n\t\t.selectAll('.sja_jug_leg1')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('y2', -mg.legheight)\n\t\t.attr('x1', d => set_leg_x1(d))\n\tmg.g\n\t\t.selectAll('.sja_jug_leg2')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('y1', -mg.legheight)\n\t\t.attr('x2', d => set_leg_x2(d))\n\tmg.g\n\t\t.selectAll('.sja_jug_jug2')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => set_jug2(d, tk))\n\t/*\n\tmg.g.selectAll('.sja_jug_rim')\n\t\t.transition().duration(dur)\n\t\t.attr('fill-opacity',(d)=> set_rim(d))\n\t\t*/\n\tmg.g\n\t\t.selectAll('.sja_jug')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('transform', d => set_jug(d))\n\tmg.g\n\t\t.selectAll('.sja_jug_stem')\n\t\t.transition()\n\t\t.duration(dur)\n\t\t.attr('y2', d => mg.neckheight + d.axisy)\n}\n\nfunction doForceLayout(tk, block, viewpxwidth) {\n\t// may return promise\n\tconst nodes = [] // nodes in simulation\n\tlet sumdiscwidth = 0 // sum of disc width, for comparing with view range width\n\ttk.data.map(j => {\n\t\tlet tox // ideal x\n\t\tif (j.x0 < 0) {\n\t\t\t// left foot out of range\n\t\t\ttox = j.x1 - j.radius2 * 2\n\t\t} else if (j.x1 > viewpxwidth) {\n\t\t\t// right foot out\n\t\t\ttox = j.x0 + j.radius2 * 2\n\t\t} else {\n\t\t\ttox = j._x\n\t\t}\n\t\tnodes.push({\n\t\t\tjunction: j,\n\t\t\ttox: tox,\n\t\t\tx: tox,\n\t\t\ty: tk.sections.jug.axisheight - tk.sections.jug.yscale(j.medianReadCount)\n\t\t})\n\t\tsumdiscwidth += j.radius2 * 2\n\t})\n\n\t// must sort nodes, must apply index by ascending order!!\n\tnodes.sort((i, j) => i.tox - j.tox)\n\tnodes.forEach((n, i) => (n.index = i))\n\n\tconst collidestrength = sumdiscwidth <= viewpxwidth ? 1 : viewpxwidth / sumdiscwidth\n\n\treturn new Promise((resolve, reject) => {\n\t\td3force\n\t\t\t.forceSimulation(nodes)\n\t\t\t.force(\n\t\t\t\t'y',\n\t\t\t\td3force\n\t\t\t\t\t.forceY(d => {\n\t\t\t\t\t\treturn tk.sections.jug.axisheight - tk.sections.jug.yscale(d.junction.medianReadCount)\n\t\t\t\t\t})\n\t\t\t\t\t.strength(1)\n\t\t\t)\n\t\t\t.force('x', d3force.forceX(d => d.tox).strength(0.1))\n\t\t\t.force(\n\t\t\t\t'collide',\n\t\t\t\td3force\n\t\t\t\t\t.forceCollide(d => {\n\t\t\t\t\t\treturn d.junction.radius2 + 2\n\t\t\t\t\t})\n\t\t\t\t\t.strength(collidestrength)\n\t\t\t)\n\t\t\t.alphaMin(0.5)\n\t\t\t.on('end', () => {\n\t\t\t\tnodes.forEach(n => {\n\t\t\t\t\tn.junction.x = n.x\n\t\t\t\t})\n\t\t\t\tresolve()\n\t\t\t})\n\t})\n}\n\nfunction mouseoverSpanBackground(j, tk, block, viewpxwidth) {\n\t/*\n\tin genome mode, j.x0 is on left, j.x1 is on right\n\tin gm mode of reverse strand gene, j.x1 is on left, j.x0 is on right\n\t*/\n\n\tlet xleft = Math.min(j.x0, j.x1)\n\tlet xright = Math.max(j.x0, j.x1)\n\n\tif (block.usegm && block.usegm.strand == '-') {\n\t\txleft = j.x1\n\t\txright = j.x0\n\t}\n\n\tif (xleft >= 0 && xright <= viewpxwidth) {\n\t\t// two feet within view range\n\t\tblock.cursorhlbar\n\t\t\t.attr('x', block.leftheadw + block.lpad + xleft)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('width', xright - xleft)\n\t\t\t.attr('height', block.totalheight())\n\t\t\t.attr('fill', 'url(#' + tk.gradient4spanBackground.mid.id + ')')\n\t\treturn\n\t}\n\n\t// one foot is out of view range\n\n\tconst boxwidth = 50\n\n\tif (xleft >= 0) {\n\t\tblock.cursorhlbar\n\t\t\t.attr('x', block.leftheadw + block.lpad + xleft)\n\t\t\t.attr('fill', 'url(#' + tk.gradient4spanBackground.left.id + ')')\n\t} else {\n\t\tblock.cursorhlbar\n\t\t\t.attr('x', block.leftheadw + block.lpad + xright - boxwidth)\n\t\t\t.attr('fill', 'url(#' + tk.gradient4spanBackground.right.id + ')')\n\t}\n\tblock.cursorhlbar.attr('y', 0).attr('width', boxwidth).attr('height', block.totalheight())\n}\n\nfunction mouseoverBoxplot(j, tk) {\n\t// mouse over disc show boxplot for read count\n\tif (!j.readcountBoxplot) return\n\tconst color = 'black'\n\tconst p5 = tk.sections.jug.yscale(j.readcountBoxplot[0])\n\tconst p25 = tk.sections.jug.yscale(j.readcountBoxplot[1])\n\tconst p50 = tk.sections.jug.yscale(j.readcountBoxplot[2])\n\tconst p75 = tk.sections.jug.yscale(j.readcountBoxplot[3])\n\tconst p95 = tk.sections.jug.yscale(j.readcountBoxplot[4])\n\tconst w = 10\n\ttk.pica.g.selectAll('*').remove()\n\ttk.pica.g.attr('transform', 'translate(' + j.x + ',' + p50 + ')')\n\tconst g = tk.pica.g.append('g').attr('transform', 'translate(' + (-5 - w - j.radius2) + ',0)')\n\t// v line\n\tg.append('line')\n\t\t.attr('x1', w / 2)\n\t\t.attr('x2', w / 2)\n\t\t.attr('y1', p95 - p50)\n\t\t.attr('y2', p5 - p50)\n\t\t.attr('stroke', color)\n\t\t.attr('shape-rendering', 'crispEdges')\n\tg.append('line')\n\t\t.attr('x1', 0)\n\t\t.attr('x2', w)\n\t\t.attr('y1', p5 - p50)\n\t\t.attr('y2', p5 - p50)\n\t\t.attr('stroke', color)\n\t\t.attr('shape-rendering', 'crispEdges')\n\tg.append('line')\n\t\t.attr('x1', 0)\n\t\t.attr('x2', w)\n\t\t.attr('y1', p95 - p50)\n\t\t.attr('y2', p95 - p50)\n\t\t.attr('stroke', color)\n\t\t.attr('shape-rendering', 'crispEdges')\n\tg.append('rect')\n\t\t.attr('y', p75 - p50)\n\t\t.attr('width', w)\n\t\t.attr('height', p25 - p75)\n\t\t.attr('stroke', color)\n\t\t.attr('fill', 'white')\n\t\t.attr('shape-rendering', 'crispEdges')\n\t// median\n\tif (p25 - p75 > 3) {\n\t\tg.append('line').attr('x2', w).attr('stroke', color).attr('shape-rendering', 'crispEdges')\n\t}\n}\n\n/////////////  __render ENDS\n\n/************* __eventdiagram\n\nexon skip or a5ss events, junctionB has a number of samples passing current filter from which median read count is generated on previous view-range request\nto illustrate canonical junctionAlst, the same set of samples from junctionB should be used to find out median read count for each of them\nthus the query\n*/\n\nfunction showOneJunction(j, tk, holder, block, isClickMenu = false) {\n\tconst table = table2col({ holder, margin: '0px' })\n\t{\n\t\tconst [t1, t2] = table.addRow()\n\t\tt1.text('Junction')\n\t\tconst div = t2.append('div')\n\t\tif (!j.sv || j.chr == j.sv.mate.chr) {\n\t\t\t// same chr\n\t\t\tdiv.html(\n\t\t\t\tbplen(Math.abs(j.start - (j.sv ? j.sv.mate.start : j.stop))) +\n\t\t\t\t\t' <span style=\"font-size:.8em;\">' +\n\t\t\t\t\tj.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\t(j.start + 1) +\n\t\t\t\t\t'-' +\n\t\t\t\t\t((j.sv ? j.sv.mate.start : j.stop) + 1) +\n\t\t\t\t\t'</span>'\n\t\t\t)\n\t\t} else {\n\t\t\t// inter-chr sv\n\t\t\tdiv.html(\n\t\t\t\t'<span style=\"font-size:.8em;\">' +\n\t\t\t\t\tj.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\t(j.start + 1) +\n\t\t\t\t\t'-' +\n\t\t\t\t\tj.sv.mate.chr +\n\t\t\t\t\t':' +\n\t\t\t\t\t(j.sv.mate.start + 1) +\n\t\t\t\t\t'</span>'\n\t\t\t)\n\t\t}\n\t\t// print all types in 2nd row\n\t\tconst d2 = t2.append('div')\n\t\td2.append('span') // strand\n\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t.style('padding', '1px 5px')\n\t\t\t.style('background-color', '#555')\n\t\t\t.style('margin-right', '5px')\n\t\t\t.text(j.strand)\n\t\tif (j.info.site) {\n\t\t\td2.append('span') // strand\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.text(j.info.site)\n\t\t}\n\t\tfor (const t of j.types) {\n\t\t\td2.append('span')\n\t\t\t\t.attr('class', 'sja_mcdot')\n\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t.style('background-color', JTypes[t]?.color || 'black')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.text(JTypes[t]?.name || '?')\n\t\t}\n\t}\n\tconst [t1, t2] = table.addRow()\n\tif (j.sampleCount == 1) {\n\t\tt1.text('Sample')\n\t\tconst sndiv = t2.append('div')\n\t\tsndiv.text(j.sampleName || 'single sample')\n\t\tt2.append('div').html(j.medianReadCount + ' <span style=\"font-size:.7em\">read count</span>')\n\t} else {\n\t\tt1.text('Samples')\n\t\tt2.append('div').html(`${j.sampleCount} <span style=\"font-size:.7em\">samples</span>\n\t\t\t<br>${j.medianReadCount} <span style=\"font-size:.7em\">median read count</span>`)\n\t}\n\n\tif (isClickMenu && tk.massApp) {\n\t\tconst [, buttonCell] = table.addRow()\n\t\tbuttonCell\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-junction-details')\n\t\t\t.text('Details')\n\t\t\t.on('click', async () => {\n\t\t\t\ttk.itemtip.hide()\n\t\t\t\tawait tk.massApp.dispatch({\n\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\t\tterm: { term: makeJunctionTerm(j), q: { mode: 'continuous' } }\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\t\tbuttonCell\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-junction-select')\n\t\t\t.text('Select')\n\t\t\t.on('click', async event => {\n\t\t\t\tawait addJunctionCustomTerm(tk, [makeJunctionTerm(j)], event.currentTarget, msgDiv)\n\t\t\t})\n\t\tconst msgDiv = buttonCell.append('div').style('font-size', '.7em')\n\t}\n\n\tconst type2elst = new Map() // k: event.type, v: list of events of that type\n\tfor (const e of j.info?.events || []) {\n\t\tif (!type2elst.has(e.type)) type2elst.set(e.type, [])\n\t\ttype2elst.get(e.type).push(e)\n\t}\n\n\tfor (const [type, elst] of type2elst) {\n\t\tlistAllEvents(elst, table, j, tk, block, isClickMenu)\n\t}\n\n\tif (type2elst.size == 0) {\n\t\t// no events. it's either canonical or not annotated, show free diagram\n\t\tconst [t1, t2] = table.addRow()\n\t\tt1.text('Diagram')\n\t\tshowJunctionDiagram(j, tk, t2)\n\t}\n}\n\nexport function makeJunctionTerm(j) {\n\tconst position = `${j.chr}:${j.start + 1}-${j.stop + 1}`\n\treturn {\n\t\ttype: TermTypes.JUNCTION,\n\t\tid: `${j.chr}:${j.start}-${j.stop}:${j.strand}`,\n\t\tname: j.name || `${position} (${j.strand})`,\n\t\tchr: j.chr,\n\t\tstart: j.start,\n\t\tstop: j.stop,\n\t\tstrand: j.strand,\n\t\tinfo: j.info || {}\n\t}\n}\n\nfunction showJunctionDiagram(j, tk, holder) {\n\t/* a junction with no known event, show diagram with respect to either end mapping to gene\n\there just use first isoform\n\tTODO allow choosing an isoform/event\n\tif start/stop are on same gene, render using one function\n\tif no different genes, show with another  function\n\t*/\n\tif (typeof j.info != 'object' || Object.keys(j.info).length == 0) {\n\t\t// either missing j.info, or is empty object\n\t\treturn\n\t}\n\n\tconst leftgenes = new Map()\n\tif (j.info.exonleft) j.info.exonleft.forEach(i => leftgenes.set(i.isoform, { gene: i.gene, strand: i.strand }))\n\tif (j.info.exonleftin) j.info.exonleftin.forEach(i => leftgenes.set(i.isoform, { gene: i.gene, strand: i.strand }))\n\tif (j.info.intronleft) j.info.intronleft.forEach(i => leftgenes.set(i.isoform, { gene: i.gene, strand: i.strand }))\n\n\tconst rightgenes = new Map()\n\tif (j.info.exonright) j.info.exonright.forEach(i => rightgenes.set(i.isoform, { gene: i.gene, strand: i.strand }))\n\tif (j.info.exonrightin) j.info.exonrightin.forEach(i => rightgenes.set(i.isoform, { gene: i.gene, strand: i.strand }))\n\tif (j.info.intronright) j.info.intronright.forEach(i => rightgenes.set(i.isoform, { gene: i.gene, strand: i.strand }))\n\n\tlet isoform // the one with both start/stop in it\n\tlet strand\n\n\tif (leftgenes.size) {\n\t\tif (rightgenes.size) {\n\t\t\t// start/stop both in genes\n\t\t\tfor (const [n, a] of leftgenes) {\n\t\t\t\tif (rightgenes.has(n)) {\n\t\t\t\t\tisoform = n\n\t\t\t\t\tstrand = a.strand\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\t// stop not in a gene, use start\n\t\t\tconst a = [...leftgenes][0]\n\t\t\tisoform = a[0]\n\t\t\tstrand = a[1].strand\n\t\t}\n\t} else if (rightgenes.size) {\n\t\t// start not in a gene, use stop\n\t\tconst a = [...rightgenes][0]\n\t\tisoform = a[0]\n\t\tstrand = a[1].strand\n\t}\n\n\tif (isoform) {\n\t\tif (strand != '+' && strand != '-') {\n\t\t\tholder.text('unknown strand for ' + isoform)\n\t\t\treturn\n\t\t}\n\t\timport('../src/spliceevent.noeventdiagram').then(p => {\n\t\t\tp.samegene({\n\t\t\t\tisoform: isoform,\n\t\t\t\treverse: strand == '-',\n\t\t\t\tongene: j.info,\n\t\t\t\tholder: holder\n\t\t\t})\n\t\t})\n\t\treturn\n\t}\n\n\t// here start/stop are on different genes\n\timport('../src/spliceevent.noeventdiagram').then(p => {\n\t\tp.differentgenes({\n\t\t\tongene: j.info,\n\t\t\tholder: holder\n\t\t})\n\t})\n}\n\nfunction showEventdiagram_a53ss(j, e, tk, holder, block, isClickMenu) {\n\t// a5ss, a3ss\n\tconst e2 = {\n\t\tjunctionB: {\n\t\t\tstart: j.start,\n\t\t\tstop: j.stop,\n\t\t\tstrand: j.strand,\n\t\t\tv: j.medianReadCount\n\t\t},\n\t\ta5ss: e.type == JT_a5ss,\n\t\ta3ss: e.type == JT_a3ss,\n\t\taltinintron: e.altinintron,\n\t\taltinexon: e.altinexon,\n\t\tframe: e.frame,\n\t\texon5idx: e.exon5idx,\n\t\tstrand: e.strand,\n\t\tsitedist: e.sitedist\n\t}\n\tconst otherJs = []\n\tif (e.junctionA) {\n\t\te2.junctionA = { start: e.junctionA.start, stop: e.junctionA.stop, strand: e.junctionA.strand, v: '...' }\n\t\tconst aj = structuredClone(e.junctionA)\n\t\taj.name = `E${e.exon5idx + 1}-E${e.exon5idx + 1 + 1}`\n\t\totherJs.push(aj)\n\t}\n\n\tif (isClickMenu) {\n\t\tmayGroupSelect(tk, block, j, otherJs, `${e.gene} ${e.isoform} E${e.exon5idx + 1} ${e.type}`, holder)\n\t}\n\n\timport('../src/spliceevent.a53ss.diagram').then(p => {\n\t\tconst text = p.default({\n\t\t\tevent: e2,\n\t\t\tholder: holder\n\t\t})\n\t\tif (!text) return\n\t\tsetTimeout(() => {\n\t\t\tif (text.node().getBoundingClientRect().top == 0) return\n\t\t\tconst strandA = e.junctionA.strand\n\t\t\tfetchReadcount4junctionAbyjunctionBsamples(\n\t\t\t\ttk,\n\t\t\t\tblock,\n\t\t\t\tj,\n\t\t\t\tnew Map([[e.junctionA.start + '.' + e.junctionA.stop + '.' + strandA, text]]),\n\t\t\t\t[[e.junctionA.start, e.junctionA.stop, strandA]]\n\t\t\t)\n\t\t}, 1000)\n\t})\n}\n\nfunction showEventdiagram_skipalt_fetchreadcount(j, e, tk, holder, block, isClickMenu) {\n\t/*\n\tj is the junctionB of this event\n\tevent is as from j.info.spliceEvent, either skip or alt\n\t*/\n\tconst e2 = {\n\t\tgm: {\n\t\t\t// confirm if can delete\n\t\t\tname: e.gene,\n\t\t\tisoform: e.isoform\n\t\t},\n\t\tjunctionB: {\n\t\t\tdata: [{ v: j.medianReadCount }]\n\t\t},\n\t\tskippedexon: e.skippedexon,\n\t\tisskipexon: e.type == JT_exonskip,\n\t\tisaltexon: e.type == JT_exonaltuse,\n\t\tframe: e.frame,\n\t\tjunctionAlst: [],\n\t\tcolor: '#99004d'\n\t}\n\n\tconst otherJs = []\n\n\t/* e.skippedexon[] is an array of one or more 0-based exon index, in 5'->3' order of the isoform\n\tconvert to 1-based exon number of the first and last skipped exon, for naming junctions by the pair of\n\texons they join, e.g. exon 3 skipping gives \"E2-E4\" for junction B, and \"E2-E3\"/\"E3-E4\" for junction A\n\t*/\n\tconst firstSkipped = Math.min(...e.skippedexon) + 1\n\tconst lastSkipped = Math.max(...e.skippedexon) + 1\n\n\tif (e.junctionAlst) {\n\t\t/* the canonical junctions skipped by junction B, ordered 5'->3' and with missing ones kept as null,\n\t\tthus array index tells which pair of exons a junction joins:\n\t\tidx0 joins E(firstSkipped-1) and E(firstSkipped), and the last one joins E(lastSkipped) and E(lastSkipped+1)\n\t\t*/\n\t\tfor (const [i, jA] of e.junctionAlst.entries()) {\n\t\t\tif (jA) {\n\t\t\t\tconst aj = structuredClone(jA)\n\t\t\t\taj.name = `E${firstSkipped - 1 + i}-E${firstSkipped + i}`\n\t\t\t\totherJs.push(aj)\n\t\t\t\tjA.data = [{ v: '...' }]\n\t\t\t\te2.junctionAlst.push(jA)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// this canonical junction is missing from data; must keep the slot as the diagram indexes\n\t\t\t// junctionAlst[] by exon position and draws a dashed junction for a null\n\t\t\te2.junctionAlst.push(null)\n\t\t}\n\t}\n\tif (e.up1junction) {\n\t\t// junction upstream of the first skipped exon\n\t\tconst uj = structuredClone(e.up1junction)\n\t\tuj.name = `E${firstSkipped - 2}-E${firstSkipped - 1}`\n\t\totherJs.push(uj)\n\t\te.up1junction.data = [{ v: '...' }] // needed for read count fetching in diagram\n\t\te2.up1junction = e.up1junction\n\t}\n\tif (e.down1junction) {\n\t\t// junction downstream of the last skipped exon\n\t\tconst dj = structuredClone(e.down1junction)\n\t\tdj.name = `E${lastSkipped + 1}-E${lastSkipped + 2}`\n\t\totherJs.push(dj)\n\t\te.down1junction.data = [{ v: '...' }]\n\t\te2.down1junction = e.down1junction\n\t}\n\n\tif (isClickMenu) {\n\t\tconst jc = structuredClone({\n\t\t\t// duplicate j.info{} just in case\n\t\t\tchr: j.chr,\n\t\t\tstart: j.start,\n\t\t\tstop: j.stop,\n\t\t\tstrand: j.strand,\n\t\t\tinfo: j.info\n\t\t})\n\t\t// junction B joins the exons flanking the skipped ones\n\t\tjc.name = `E${firstSkipped - 1}-E${lastSkipped + 1}`\n\t\tmayGroupSelect(\n\t\t\ttk,\n\t\t\tblock,\n\t\t\tjc,\n\t\t\totherJs,\n\t\t\t`${e.gene} ${e.isoform} ${e.skippedexon.map(i => 'E' + (i + 1)).join(',')} ${e.type}`,\n\t\t\tholder\n\t\t)\n\t}\n\n\timport('../src/spliceevent.exonskip.diagram').then(p => {\n\t\tconst [junction2readcounttext, junctionlst] = p.default({\n\t\t\tevent: e2,\n\t\t\tholder: holder,\n\t\t\tnophrase: true\n\t\t})\n\t\tsetTimeout(() => {\n\t\t\t// if the diagram already disappears, don't make query\n\t\t\tfor (const [k, text] of junction2readcounttext) {\n\t\t\t\tif (text.node().getBoundingClientRect().top == 0) {\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t}\n\t\t\tfetchReadcount4junctionAbyjunctionBsamples(tk, block, j, junction2readcounttext, junctionlst)\n\t\t}, 1000)\n\t})\n}\n\n/*\nmainJ:\n\tthe one with event and already has j.info\notherJs[]:\n\tarray of auxiliary junctions from the mainJ event and lacks .chr, .info\ngrouplabel:\n\thuman readable label of the event\n*/\nfunction mayGroupSelect(tk, block, mainJ, otherJs, eventlabel, holder) {\n\tif (!tk.massApp) return\n\n\t// assuming otherJs are all canonical junctions!\n\tfor (const j of otherJs) {\n\t\tj.chr = mainJ.chr\n\t\tj.info = {\n\t\t\ttype: JT_canonical\n\t\t}\n\t}\n\n\tholder\n\t\t.append('button')\n\t\t.attr('data-testid', 'sjpp-junction-select')\n\t\t.text(`Select ${otherJs.length + 1} junctions`)\n\t\t.on('click', async event => {\n\t\t\tawait addJunctionCustomTerm(\n\t\t\t\ttk,\n\t\t\t\t[makeJunctionTerm(mainJ), ...otherJs.map(makeJunctionTerm)],\n\t\t\t\tevent.currentTarget,\n\t\t\t\tmsgDiv,\n\t\t\t\teventlabel\n\t\t\t)\n\t\t})\n\tconst msgDiv = holder.append('div').style('font-size', '.7em')\n}\n\nasync function addJunctionCustomTerm(tk, junctions, button, msgDiv, eventlabel) {\n\tawait tk.massApp.dispatch({\n\t\ttype: 'add_customTerm',\n\t\tobj: makeJunctionCustomTerm(junctions, eventlabel)\n\t})\n\tbutton.remove()\n\tmsgDiv.text(\n\t\teventlabel\n\t\t\t? `${junctions.length} junctions can now be found through variable selection under ${eventlabel}.`\n\t\t\t: 'This junction can now be found through variable selection.'\n\t)\n}\n\nfunction listAllEvents(lst, table, j, tk, block, isClickMenu) {\n\tif (lst.length == 1) {\n\t\tconst [t1, t2] = table.addRow()\n\t\tconst e = lst[0]\n\t\tt1.append('div').text(e.gene)\n\t\tt1.append('div').text(e.isoform).style('font-size', '.8em')\n\t\tif (e.type == JT_exonskip || e.type == JT_exonaltuse) {\n\t\t\tshowEventdiagram_skipalt_fetchreadcount(j, e, tk, t2, block, isClickMenu)\n\t\t} else if (e.type == JT_a5ss || e.type == JT_a3ss) {\n\t\t\tshowEventdiagram_a53ss(j, e, tk, t2, block, isClickMenu)\n\t\t}\n\t\treturn\n\t}\n\n\t// multiple events\n\t// for events on different isoform that may be showing identical events, group them\n\tconst map = new Map() // k: stringified event less isoform, v: isoform\n\tfor (const e of lst) {\n\t\tconst f = structuredClone(e)\n\t\tconst v = e.isoform\n\t\tdelete f.isoform\n\t\tconst key = JSON.stringify(f)\n\t\tif (map.has(key)) map.get(key).push(e.isoform)\n\t\telse map.set(key, [e.isoform])\n\t}\n\tfor (const [key, isolst] of map) {\n\t\tconst eo = JSON.parse(key)\n\n\t\teo.isoform = isolst[0] // hack! add back so it can get printed as eventlabel in mayGroupSelect()\n\n\t\tconst [t1, t2] = table.addRow()\n\t\tt1.append('div').text(eo.gene)\n\t\t{\n\t\t\tconst s = isolst.length >= 5 ? 0.7 : 0.8\n\t\t\tfor (const i of isolst)\n\t\t\t\tt1.append('div')\n\t\t\t\t\t.text(i)\n\t\t\t\t\t.style('font-size', s + 'em')\n\t\t}\n\t\tif (eo.type == JT_exonskip || eo.type == JT_exonaltuse) {\n\t\t\tshowEventdiagram_skipalt_fetchreadcount(j, eo, tk, t2, block, isClickMenu)\n\t\t} else if (eo.type == JT_a5ss || eo.type == JT_a3ss) {\n\t\t\tshowEventdiagram_a53ss(j, eo, tk, t2, block, isClickMenu)\n\t\t}\n\t}\n}\n\n/*\nquery server to get median read count for display for these junctions\nover the same group of sample\n\njB: junction B\njAlst: [ [start,stop] ]\njunction2readcounttext: svg text for printing median read count for each A junction\n*/\nasync function fetchReadcount4junctionAbyjunctionBsamples(tk, block, jB, junction2readcounttext, jAlst) {\n\tconst [body, headers] = getParameter(tk, block)\n\tdelete body.rglst\n\tdelete body.hiddenTypes\n\tbody.junctionB = { chr: jB.chr, start: jB.start, stop: jB.stop, strand: jB.strand }\n\tbody.junctionAposlst = jAlst\n\ttry {\n\t\tconst data = await dofetch3('termdb/junctions/AbyB', { body, headers })\n\t\tif (data.error) throw new Error(data.error)\n\t\tif (!Array.isArray(data.lst)) throw new Error('.lst[] missing')\n\t\tfor (const j of data.lst) {\n\t\t\t/*\n\t\t\t.start\n\t\t\t.stop\n\t\t\t.v\n\t\t\t*/\n\t\t\tconst key = j.start + '.' + j.stop + '.' + j.strand\n\t\t\tif (junction2readcounttext.has(key)) {\n\t\t\t\tjunction2readcounttext.get(key).text(j.v)\n\t\t\t}\n\t\t}\n\t} catch (e) {\n\t\tconsole.error(e.message || e)\n\t}\n}\n\n/////////////// __eventdiagram ENDS\n\nasync function queryOneJunction(j, tk, block, holder) {}\n\nfunction get_list_cells(table) {\n\treturn [\n\t\ttable\n\t\t\t.append('div')\n\t\t\t.style('width', '100%')\n\t\t\t.style('padding', '5px 20px 5px 0px')\n\t\t\t.style('border-bottom', 'solid 1px #ededed'),\n\t\ttable\n\t\t\t.append('div')\n\t\t\t.style('width', '100%')\n\t\t\t.style('border-bottom', 'solid 1px #ededed')\n\t\t\t.style('padding', '5px 20px 5px 0px')\n\t]\n}\n", "import { Menu } from '#dom'\nimport { initLegend, updateLegend } from './legend'\nimport { loadTk } from './tk'\nimport { renderTk } from './render'\nimport { getFilterName } from '../mds3/filterName'\nimport { fillTermWrapper } from '#termsetting'\nimport { rehydrateFilter } from '../filter/rehydrateFilter'\nimport { makelabel } from '../mds3/leftlabel'\n\n/*\n */\n\nexport async function makeTk(tk, block) {\n\t// run just once to initiate a track by adding in essential attributes to tk object\n\n\t// validate default values\n\tif ('yscaleUseLog' in tk) {\n\t\tif (typeof tk.yscaleUseLog != 'boolean') throw new Error('tk.yscaleUseLog not boolean')\n\t} else {\n\t\ttk.yscaleUseLog = true\n\t}\n\tif (tk.hiddentypes) {\n\t\t// comma joined type strings to be hidden by default. the property will be assessed by legend and removed\n\t\tif (typeof tk.hiddentypes != 'string') throw new Error('tk.hiddentypes not string')\n\t}\n\tif (tk.readcountCutoff) {\n\t\tif (!Number.isInteger(tk.readcountCutoff) || tk.readcountCutoff < 0)\n\t\t\tthrow new Error('tk.readcountCutoff is not positive integer')\n\t} else {\n\t\ttk.readcountCutoff = 0\n\t}\n\n\t// make color gradients\n\t{\n\t\tconst pale = '#FFFEAB'\n\t\tconst dark = '#F7F69E'\n\t\tconst id1 = Math.random().toString()\n\t\tconst id2 = Math.random().toString()\n\t\tconst id3 = Math.random().toString()\n\t\tconst defs = tk.gleft.append('defs')\n\t\tconst left = defs.append('linearGradient').attr('id', id1)\n\t\tleft.append('stop').attr('offset', 0).attr('stop-color', dark)\n\t\tleft.append('stop').attr('offset', 1).attr('stop-color', 'white')\n\t\tconst mid = defs.append('linearGradient').attr('id', id2)\n\t\tmid.append('stop').attr('offset', 0).attr('stop-color', pale)\n\t\tmid.append('stop').attr('offset', 0.5).attr('stop-color', 'white')\n\t\tmid.append('stop').attr('offset', 1).attr('stop-color', pale)\n\t\tconst right = defs.append('linearGradient').attr('id', id3)\n\t\tright.append('stop').attr('offset', 0).attr('stop-color', 'white')\n\t\tright.append('stop').attr('offset', 1).attr('stop-color', dark)\n\n\t\ttk.gradient4spanBackground = {\n\t\t\tleft: { id: id1, gradient: left },\n\t\t\tmid: { id: id2, gradient: mid },\n\t\t\tright: { id: id3, gradient: right }\n\t\t}\n\t}\n\n\ttk.leftlabels = {\n\t\t// all labels are rendered here, except track label\n\t\tg: tk.gleft.append('g').attr('transform', 'translate(0,17)'),\n\t\tdoms: {},\n\t\t// keys: label name, value: label dom\n\t\t// to avoid having to delete all labels upon tk rendering\n\t\tlaby: 0, // cumulative height, 0 for no labels\n\t\txoff: 0,\n\t\tmaxwidth: 0 // set default 0 in case track runs into err, can still render tk\n\t}\n\ttk.leftlabels.doms.jug = makelabel(tk, block, 0)\n\n\t{\n\t\tconst g = tk.glider.append('g')\n\t\ttk.sections = {\n\t\t\t// sections from top to bottom.\n\t\t\tjug: {\n\t\t\t\theight: 0, // total height of the jug section\n\t\t\t\tg: g.append('g'),\n\t\t\t\taxis: g.append('g')\n\t\t\t}\n\t\t}\n\t}\n\tsetH(tk, 'axisheight', 200)\n\tsetH(tk, 'legheight', 50)\n\tsetH(tk, 'neckheight', 50)\n\n\ttk._finish = loadTk_finish_closure(tk, block)\n\n\ttk.hovertip = new Menu() // show contents here on hovering an item and avoid reusing itemtip\n\ttk.itemtip = new Menu() // show contents on clicking an item\n\ttk.menutip = new Menu({ padding: '' }) // to show menu options without margin\n\n\ttk.load = _load(tk, block) // shorthand\n\n\tawait initTermdb(tk, block)\n\n\tif (tk.filter) await Promise.all(rehydrateFilter(tk.filter, tk.vocabApi))\n\n\ttk.tklabel.text(tk.dslabel || tk.name)\n\n\ttk.clear = () => {\n\t\t// called in loadTk, when uninitialized is true\n\t\ttk.sections.jug.g.selectAll('*').remove()\n\t}\n\n\t// config\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\tconfigPanel(tk, block)\n\t})\n\n\tinitLegend(tk, block)\n}\n\nfunction setH(tk, prop, v) {\n\t// custom value is defined at tk.prop. it's moved to tk.sections.jug.prop\n\tconst customv = tk[prop]\n\tif (customv != undefined) {\n\t\tif (!Number.isFinite(customv) || customv <= 0) throw new Error('invalid tk.' + prop)\n\t\ttk.sections.jug[prop] = customv\n\t\tdelete tk[prop]\n\t\treturn\n\t}\n\ttk.sections.jug[prop] = v // no custom value. use default\n}\n\nfunction loadTk_finish_closure(tk, block) {\n\t// call this when tk finish rendering\n\treturn data => {\n\t\t// update legend name in case filter has changed\n\t\t// tk.legend{} is missing if tk is not initiated (wrong ds name)\n\t\ttk.legend?.headTd.text(tk.dslabel + (tk.filter ? ' - ' + getFilterName(tk.filter) : ''))\n\n\t\tif (data) {\n\t\t\t// centralized place on indicating if tk has error or simply no data\n\t\t\t// only do this when server return data is present. data may not be supplied e.g when switching skewer mode\n\n\t\t\tif (data.error) {\n\t\t\t\t// has error e.g. server snafu. set skewer height to show error msg later\n\t\t\t\ttk.sections.jug.height = 40\n\t\t\t} else {\n\t\t\t\t// no error. detect if has data or not\n\t\t\t\tif (data.junctions?.length == 0) {\n\t\t\t\t\ttk.sections.jug.g.selectAll('*').remove()\n\t\t\t\t\ttk.sections.jug.axis.selectAll('*').remove()\n\t\t\t\t\ttk.sections.jug.g.transition().attr('transform', 'translate(0,0)')\n\t\t\t\t\ttk.sections.jug.g\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.text('No splice junctions')\n\t\t\t\t\t\t.attr('y', 25)\n\t\t\t\t\t\t.attr('x', block.width / 2)\n\t\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t\t.attr('dominant-baseline', 'center')\n\t\t\t\t\ttk.sections.jug.height = 40\n\t\t\t\t}\n\t\t\t\tif (data.alert) {\n\t\t\t\t\tconsole.log('TODO print this alert in tk', data.alert)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// derive tk height\n\t\ttk.height_main = tk.sections.jug.height + tk.toppad + tk.bottompad\n\n\t\tif (data) {\n\t\t\tupdateLegend(data, tk, block)\n\t\t}\n\n\t\t;(tk.leftLabelMaxwidth = tk.leftlabels.maxwidth + tk.leftlabels.xoff),\n\t\t\tblock.tkcloakoff(tk, { error: data ? data.error : null })\n\t\tblock.block_setheight()\n\t\tblock.setllabel()\n\n\t\ttk.callbackOnRender?.(tk, block) // run if present\n\t}\n}\n\nasync function initTermdb(tk, block) {\n\tif (!tk.dslabel) {\n\t\t// later support custom vocab\n\t\tthrow new Error('tk.dslabel missing')\n\t}\n\tif (!tk.vocabApi) {\n\t\tconst arg = {\n\t\t\tvocab: {\n\t\t\t\tgenome: block.genome.name,\n\t\t\t\tdslabel: tk.dslabel\n\t\t\t}\n\t\t}\n\t\tconst _ = await import('#termdb/vocabulary')\n\t\ttk.vocabApi = _.vocabInit(arg)\n\n\t\tif (!tk.vocabApi.app) {\n\t\t\t// see notes in mds3/makeTk\n\t\t\ttk.vocabApi.app = { opts: { genome: block.genome } }\n\t\t}\n\t}\n\tif (!tk.termdbConfig) {\n\t\ttk.termdbConfig = await tk.vocabApi.getTermdbConfig()\n\t}\n\tif (!tk.termdbConfig.queries?.junction) throw new Error('queries.junction missing')\n}\n\nfunction _load(tk, block) {\n\treturn async () => {\n\t\treturn await loadTk(tk, block)\n\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// read count cutoff\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').html('Read count cutoff&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.property('value', tk.readcountCutoff || 0)\n\t\t\t.attr('type', 'number')\n\t\t\t.style('width', '50px')\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tlet v = Number(event.target.value)\n\t\t\t\tif (!v || v < 0) {\n\t\t\t\t\t// set to zero to cancel\n\t\t\t\t\tv = 0\n\t\t\t\t}\n\t\t\t\tif (v == 0) {\n\t\t\t\t\tif (tk.readcountCutoff) {\n\t\t\t\t\t\t// cutoff has been set, cancel and refetch data\n\t\t\t\t\t\ttk.readcountCutoff = 0\n\t\t\t\t\t\tloadTk(tk, block, true)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// cutoff has not been set, do nothing\n\t\t\t\t\t}\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// set cutoff\n\t\t\t\tif (tk.readcountCutoff) {\n\t\t\t\t\t// cutoff has been set\n\t\t\t\t\tif (tk.readcountCutoff == v) {\n\t\t\t\t\t\t// same as current cutoff, do nothing\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// set new cutoff\n\t\t\t\t\t\ttk.readcountCutoff = v\n\t\t\t\t\t\tloadTk(tk, block, true)\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// cutoff has not been set\n\t\t\t\t\ttk.readcountCutoff = v\n\t\t\t\t\tloadTk(tk, block, true)\n\t\t\t\t}\n\t\t\t})\n\t\trow\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('color', '#858585')\n\t\t\t.text('For a junction, samples with read count lower than cutoff will not be shown.')\n\t}\n\n\t// height\n\t{\n\t\tconst k = tk.sections.jug\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').text('Track height')\n\t\trow\n\t\t\t.append('button')\n\t\t\t.html('&nbsp;&nbsp;+&nbsp;&nbsp;')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.on('click', () => {\n\t\t\t\tk.axisheight += 30\n\t\t\t\tk.legheight = k.axisheight / 4\n\t\t\t\trenderTk(null, tk, block)\n\t\t\t\tblock.block_setheight()\n\t\t\t})\n\t\trow\n\t\t\t.append('button')\n\t\t\t.html('&nbsp;&nbsp;-&nbsp;&nbsp;')\n\t\t\t.style('margin-left', '5px')\n\t\t\t.on('click', () => {\n\t\t\t\tif (k.axisheight <= 90) return\n\t\t\t\tk.axisheight -= 30\n\t\t\t\tk.legheight = k.axisheight / 4\n\t\t\t\trenderTk(null, tk, block)\n\t\t\t\tblock.block_setheight()\n\t\t\t})\n\t}\n\n\t// log scale\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '1px')\n\t\tconst id = Math.random()\n\t\tconst input = row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'checkbox')\n\t\t\t.style('margin-right', '10px')\n\t\t\t.attr('id', id)\n\t\t\t.on('change', () => {\n\t\t\t\ttk.yscaleUseLog = !tk.yscaleUseLog\n\t\t\t\trenderTk(null, tk, block)\n\t\t\t})\n\t\tif (tk.yscaleUseLog) {\n\t\t\tinput.property('checked', 1)\n\t\t}\n\t\trow.append('label').text('Use log10 for Y scale read count').attr('for', id)\n\t}\n}\n", "import { dofetch3 } from '#common/dofetch'\nimport { makeTk } from './makeTk'\nimport { renderTk } from './render'\nimport { rangequery_rglst } from '../mds3/tk'\n//import { make_leftlabels } from './leftlabel'\n\n/*\nexport type Tk = {\n\tdslabel:string\n\ttermdbConfig: any\n\tvocabApi: any\n\tmaxReadCount: number\n\t/ in flight list of junctions, with rendering x/y coordinates \n\tdata?: Junction[]\n}\nexport type Junction = {\n\tchr: string\n\tstart: number\n\tstop: number\n\tstrand: string\n\tsampleCount: number\n\tmedianReadCount: number\n\tsv?: object\n\tx0?: number\n\tx1?: number\n\tx?: number\n\t_x?: number\n\taxisy?: number\n}\n*/\n\nexport async function loadTk(tk, block) {\n\tblock.tkcloakon(tk)\n\tblock.block_setheight()\n\n\ttry {\n\t\tif (tk.uninitialized) {\n\t\t\tawait makeTk(tk, block)\n\t\t\tdelete tk.uninitialized\n\t\t}\n\n\t\tconst data = await getTkData(tk, block)\n\n\t\t// render each possible track type. if indeed rendered, return sub track height\n\n\t\t// left labels and skewer at same row, whichever taller\n\t\trenderTk(data, tk, block)\n\n\t\t// must render tk first, then left labels\n\t\t//await make_leftlabels(data, tk, block)\n\n\t\t// done tk rendering, adjust height\n\t\ttk._finish(data)\n\t} catch (e) {\n\t\tif (tk.clear) tk.clear() // if the error is thrown upon initiating the track, clear() function may not have been added\n\t\tif (tk._finish) tk._finish({ error: e.message || e })\n\t\tif (e.stack) console.log(e.stack)\n\t}\n}\n\nexport function getParameter(tk, block) {\n\t// to get data for current view range\n\n\tconst par = {\n\t\tgenome: block.genome.name,\n\t\tdslabel: tk.dslabel,\n\t\tfilter0: tk.filter0,\n\t\tfilter: tk.filter,\n\t\treadcountCutoff: tk.readcountCutoff\n\t}\n\n\tconst headers = { 'Content-Type': 'application/json', Accept: 'application/json' }\n\n\trangequery_rglst(tk, block, par)\n\n\tif (tk.legend?.type?.hiddenvalues?.size) par.hiddenTypes = [...tk.legend.type.hiddenvalues].join(',')\n\n\treturn [par, headers]\n}\n\n/*\nabstract various data sources\n\nreturned data{}:\n\n.skewer[]\n\tlist of data points to show as skewer plot\n.mclass2variantcount[]\n\tmclass breakdown of skewer[]\n*/\nasync function getTkData(tk, block) {\n\tlet data\n\tif (tk.custom_data) {\n\t\t// has custom data on client side, no need to request from server\n\t\tdata = await dataFromCustomData(tk, block)\n\t} else {\n\t\t// request data from server, either official or custom sources\n\t\tconst [body, headers] = getParameter(tk, block)\n\t\tdata = await dofetch3('termdb/junctions', { body, headers })\n\t}\n\tif (data.error) throw new Error(data.error)\n\treturn data\n}\n\nasync function dataFromCustomData(tk, block) {\n\tconst data = []\n\t// todo\n\treturn data\n}\n"],
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+}