@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-4FQYRDZS.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../dom/svgSeriesTips.js", "../dom/renderAtRisk.js", "../dom/renderPvalueTable.js"],
+  "sourcesContent": ["import { Menu } from '#dom/menu'\nimport { pointer } from 'd3-selection'\n\n/*\n\tWill create a multi-series tooltip that follows\n \tthe cursor with a moving vertical line\n \tover a chart's plot area\n\n\tArguments:\n\tline \trequired, \n\t\t\t\ta d3-wrapped svg.line element, to be used as the moving vertical line\n\t\t\t\t\n\t\t\t\t!!! NOTE: this line must be immediately under the rect element to avoid\n\t\t\t\tflickering and other undesired behavior !!!\n\n\t\t\t\tthis line must already be styled with stroke, etc\n\t\t\t\tonly the line's visibility and positions will be modified on mouseOver()\n\t\t\t\tthe length will also be adjusted in the returned API's update() method\n\t\n\trect \trequired, \n\t\t\t\ta d3-wrapped svg.rect element, which covers the plot area\n\t      in order to capture mouse events for this tooltip\n\t      !!! will be styled with fill: 'transparent' !!!\n\n\t_tip  optional,\n\t\t\t\ta client.Menu instance\n\n\tReturns\n\tan API object (see the specs at the end of this function)\n*/\nexport function getSeriesTip(line, rect, _tip = null) {\n\tconst tip = _tip || new Menu({ padding: '5px' })\n\tline.style('display', 'none')\n\n\tconst rectNode = rect.style('fill', 'transparent').node()\n\n\tfunction mouseOver(event) {\n\t\tconst m = pointer(event, rectNode)\n\t\tconst mx = m[0]\n\t\tconst xVal = +opts.xScale.invert(mx).toFixed(opts.decimals)\n\t\tconst x = opts.xScale(xVal) /* + 0.5*/ // do not add a small float value here; otherwise, the line will not match up with the data\n\n\t\tline.style('display', '').attr('stroke', '#aaa').attr('stroke-dasharray', 4).attr('x1', x).attr('x2', x)\n\n\t\tconst seriesHtmls = []\n\t\tfor (const series of opts.serieses) {\n\t\t\tconst data = series.data\n\t\t\tconst data_x = data.map(d => d.x)\n\t\t\tif (xVal >= Math.min(...data_x) && xVal <= Math.max(...data_x)) {\n\t\t\t\t// xVal is within range of the series\n\t\t\t\t// determine max timepoint that is less than or\n\t\t\t\t// equal to xVal\n\t\t\t\tconst max = Math.max(...data_x.filter(x => x <= xVal))\n\t\t\t\t// store html of this timepoint\n\t\t\t\tconst timepoint = data.find(d => d.x == max)\n\t\t\t\tif (timepoint) seriesHtmls.push(timepoint.html)\n\t\t\t}\n\t\t}\n\n\t\tif (seriesHtmls.length) {\n\t\t\ttip\n\t\t\t\t.show(event.clientX, event.clientY)\n\t\t\t\t.d.html(`<span>${opts.xTitleLabel}: ${xVal}</span><br>` + seriesHtmls.map(d => d).join(opts.separator))\n\t\t} else {\n\t\t\ttip.hide()\n\t\t}\n\t}\n\n\trect\n\t\t.on('mouseover', mouseOver)\n\t\t.on('mousemove', mouseOver)\n\t\t.on('mouseout', () => {\n\t\t\tline.style('display', 'none')\n\t\t\ttip.hide()\n\t\t})\n\n\tconst opts = {\n\t\tseparator: '<br>',\n\t\tdecimals: 1\n\t}\n\n\t/*\n\t\tThe API object for this tooltip is returned below\n\t*/\n\treturn {\n\t\t/*\n\t\t\tWill update the length of the vertical line\n\t\t\tand reassign optional data values\n\n\t\t\t!!! MUST call api.update() before the expected mouseover event,\n\t\t\tso that the line will have the proper length and the mouse\n\t\t\tposition could be computed with .xScale !!! \n\n\t\t\t_opts{}\n\t\t\t.xScale\t\t\t\t\trequired\n\t\t\t\t\t\t\t\t\t\tthe d3-scale object that was used for the rect dimensions\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t.xTitleLabel\t\t\trequired\n\t\t\t\t\t\t\t\t\t\ttitle of x-axis\n\t\t\t\t\t\t\t\t\t\twill be used as label of x-value in tooltip\n\n\t\t\t.serieses[{data}] \t\trequired\n\t\t\t\t\t\t\t\t\t\tarray of series objects, assumed to be visibly rendered\n\t\t\t\t\t\t\t\n\t\t\t\t.data[{x, html}]\trequired\n\t\t\t\t\t\t\t\t\t\tarray of data objects\n\t\t\t\t\t\t\t\t\t\tthe series data that is currently rendered in the chart\n\t\t\t\t\t\n\t\t\t\t\t.x \t\t\t\trequired, float\n\t\t\t\t\t\t\t\t\t\tthe datapoint's actual, unscaled x value\n\t\t\t\t\t\n\t\t\t\t\t.html   \t\trequired, string\n\t\t\t\t\t\t\t\t\t\tthe HTML to display in the tooltip if this datapoint's \n\t\t\t\t\t\t\t\t\t\tx value matched the vertical line's position\n\n\t\t\t.separator\t\t\t\toptional, string\n\t\t\t\t\t\t\t\t\t\tthe html to be used to join the series html strings when displayed in the tooltip\n\n\t\t\t.decimals\t\t\t\toptional, number\n\t\t\t\t\t\t\t\t\t\tnumber of decimal places of the datapoint's x-value\n\t\t\t\t\t\t\t\t\t\twill control the precision of the vertical line\n\t\t*/\n\t\tupdate(_opts = {}) {\n\t\t\tObject.assign(opts, _opts)\n\t\t\tconst x = rect.attr('x')\n\t\t\tconst y = rect.attr('y')\n\t\t\tline\n\t\t\t\t.attr('x1', x)\n\t\t\t\t.attr('x2', x)\n\t\t\t\t.attr('y1', y)\n\t\t\t\t.attr('y2', rect.attr('height') - y)\n\t\t},\n\n\t\t/*\n\t\t\tdetroy to help minimize memory leaks\n\t\t\tfrom elements and event handlers not being garbage collected\n\t\t\tbecause of non-deactivated references\n\t\t*/\n\t\tdestroy() {\n\t\t\trect.on('mouseover', null).on('mousemove', null).on('mouseout', null)\n\t\t}\n\t}\n}\n", "import { select } from 'd3-selection'\n\n/*\nrender at-risk counts at x-axis tick values\n\nused by survival plot and cuminc plot\n\ninput parameter:\n{\n    g: selection\n    s: {} self.settings\n    chart: {} chart object\n    order: [] array of series ids to specify series order\n    term2toColor: {} map term2 values to colors\n}\n*/\n\nexport function renderAtRiskG({ g, s, chart, order, term2toColor, onSerieClick }) {\n\t// {seriesId: string, seriesLabel: string, counts: [number, number, number][]}[]\n\tconst atRiskGroups = []\n\n\t// do not compute at-risk counts of tick values that are\n\t// smaller than the first timepoint of the chart\n\t// e.g. if all curves start at 5 years, we do not want\n\t// to compute at-risk counts at tick value 0\n\tconst xTickValues = chart.xTickValues.filter(xTick => xTick >= chart.xMin)\n\n\t// compute at-risk counts of filtered tick values\n\tfor (const series of chart.visibleSerieses) {\n\t\tconst counts = []\n\t\tlet i = 0,\n\t\t\td = series.data[0],\n\t\t\tprev = d, // prev = \"previous\" data point\n\t\t\tnCensored = 0\n\n\t\t// for each x-axis tick value, find and use the data that applies\n\t\tfor (const time of xTickValues) {\n\t\t\twhile (d && d.x < time) {\n\t\t\t\tnCensored += d.ncensor\n\t\t\t\tprev = d\n\t\t\t\ti++\n\t\t\t\td = series.data[i]\n\t\t\t}\n\n\t\t\t// prev will become last timepoint before tick value\n\t\t\t// for example, if tick value is 10 and timepoint A is at time 8.5, timepoint B is at time 9.2, timepoint C is at 9.8, and timepoint D is at time 10.2, then prev will be set to the timepoint C\n\t\t\t// the at-risk count at tick value 10 will then be the nrisk at prev minus any events/censored exits that occurred at prev\n\n\t\t\tif (d && d.x === time) {\n\t\t\t\t// iterated timepoint is equal to tick value\n\t\t\t\t// can use nrisk of timepoint as the nrisk of tick value\n\t\t\t\tcounts.push([time, d.nrisk, nCensored])\n\t\t\t} else {\n\t\t\t\t// iterated timepoint does not equal tick value\n\t\t\t\t// use the nrisk of prev minus any events/censored exits\n\t\t\t\t// at prev as the nrisk of tick value\n\t\t\t\tcounts.push([time, prev.nrisk - prev.nevent - prev.ncensor, nCensored])\n\t\t\t}\n\t\t}\n\t\tconst { seriesId, seriesLabel } = series\n\t\tatRiskGroups.push({ seriesId, seriesLabel, counts })\n\t}\n\n\tconst y = s.svgh - s.svgPadding.top - s.svgPadding.bottom + 60 // make y-offset option???\n\t// fully rerender, later may reuse previously rendered elements\n\t// g.selectAll('*').remove()\n\n\tconst seriesOrder = order || chart.serieses.map(s => s.seriesId)\n\n\tg.selectAll('.sjpp-atrisk-title').remove()\n\tif (s.atRiskVisible) {\n\t\t// at-risk counts are visible\n\t\t// sort the data\n\t\tatRiskGroups.sort((a, b) => seriesOrder.indexOf(a.seriesId) - seriesOrder.indexOf(b.seriesId))\n\t\t// render the title\n\t\t// add a y offset to title if there is no series id\n\t\tconst addYoffset = chart.serieses.length == 1 && !chart.serieses[0].seriesId\n\t\tconst titleg = g\n\t\t\t.append('text')\n\t\t\t.attr('class', 'sjpp-atrisk-title')\n\t\t\t.attr('transform', `translate(${s.atRiskLabelOffset}, ${addYoffset ? 2 * s.axisTitleFontSize : 0})`)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t\t.attr('cursor', chart.serieses.length == 1 ? 'pointer' : 'default')\n\t\t\t.text('Number at risk')\n\t\t\t.on('click', chart.serieses.length == 1 ? e => onSerieClick({ seriesId: '' }, e.clientX, e.clientY) : null)\n\t\tif (term2toColor['']) titleg.style('fill', s.defaultColor)\n\t\ttitleg\n\t\t\t.append('tspan')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', s.axisTitleFontSize - 4)\n\t\t\t.text('(# censored)')\n\t} else {\n\t\t// at-risk counts are not visible\n\t\t// empty the data\n\t\tatRiskGroups.length = 0\n\t}\n\n\t// render at-risk counts\n\tconst sg = g\n\t\t.attr('transform', `translate(0,${y})`)\n\t\t.selectAll(':scope > g')\n\t\t.data(atRiskGroups, s => s.seriesLabel || s.seriesId)\n\n\tsg.exit().remove()\n\n\tsg.each(function (atRiskGroup, i) {\n\t\tconst { seriesId, seriesLabel, counts } = atRiskGroup\n\t\tconst y = (i + 1) * (2 * s.axisTitleFontSize)\n\t\tconst g = select(this)\n\t\t\t.attr('transform', `translate(0,${y})`)\n\t\t\t.attr('fill', term2toColor[''] ? s.defaultColor : term2toColor[seriesId].adjusted) // TODO: attached series color to the data of 'sg'\n\n\t\tlet legendText = g.select(':scope>text')\n\t\tif (!legendText.size()) legendText = g.append('text')\n\t\tlegendText.text(seriesId && seriesId !== '*' ? seriesLabel || seriesId : '')\n\n\t\tlet ticksG = g.select(':scope>g')\n\t\tif (!ticksG.size()) ticksG = g.append('g')\n\n\t\trenderAtRiskTick(ticksG, chart, xTickValues, s, atRiskGroup)\n\t})\n\n\tsg.enter()\n\t\t.append('g')\n\t\t.each(function (atRiskGroup, i) {\n\t\t\tconst { seriesId, seriesLabel, counts } = atRiskGroup\n\t\t\tconst y = (i + 1) * (2 * s.axisTitleFontSize)\n\t\t\tconst g = select(this)\n\t\t\t\t.attr('transform', `translate(0,${y})`)\n\t\t\t\t.attr('fill', term2toColor[''] ? s.defaultColor : term2toColor[seriesId].adjusted)\n\t\t\t\t.on('click', e => onSerieClick({ seriesId }, e.clientX, e.clientY))\n\n\t\t\tg.append('text')\n\t\t\t\t.attr('data-testid', 'sjpp-atrisk-seriesId')\n\t\t\t\t.attr('transform', `translate(${s.atRiskLabelOffset}, 0)`)\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t\t\t.attr('cursor', 'pointer')\n\t\t\t\t.datum({ seriesId })\n\t\t\t\t.text(seriesId && seriesId !== '*' ? seriesLabel || seriesId : '')\n\n\t\t\trenderAtRiskTick(g.append('g'), chart, xTickValues, s, atRiskGroup)\n\t\t})\n}\n\nfunction renderAtRiskTick(g, chart, xTickValues, s, atRiskGroup) {\n\tconst { seriesId, counts } = atRiskGroup\n\tconst reversed = counts.slice().reverse()\n\tconst data = xTickValues.map(tickVal => {\n\t\tif (tickVal === 0) return { seriesId, tickVal, atRisk: counts[0][1], nCensored: counts[0][2] }\n\t\tconst d = reversed.find(d => d[0] <= tickVal)\n\t\treturn { seriesId, tickVal, atRisk: d[1], nCensored: d[2] }\n\t})\n\n\tconst text = g.selectAll('text').data(data)\n\ttext.exit().remove()\n\ttext\n\t\t.attr('transform', d => `translate(${chart.xScale(d.tickVal)},0)`)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t.attr('cursor', 'pointer')\n\t\t.each(renderAtRiskLabel)\n\ttext\n\t\t.enter()\n\t\t.append('text')\n\t\t.attr('transform', d => `translate(${chart.xScale(d.tickVal)},0)`)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${s.axisTitleFontSize - 4}px`)\n\t\t.attr('cursor', 'pointer')\n\t\t.each(renderAtRiskLabel)\n\n\tfunction renderAtRiskLabel(d) {\n\t\tconst tspans = select(this)\n\t\t\t.selectAll('tspan')\n\t\t\t.data([d.atRisk, `(${d.nCensored})`])\n\n\t\ttspans.exit().remove()\n\n\t\ttspans.attr('y', (d, i) => (i === 0 ? 0 : i * (s.axisTitleFontSize - 4))).text(d => d)\n\n\t\ttspans\n\t\t\t.enter()\n\t\t\t.append('tspan')\n\t\t\t.attr('x', 0)\n\t\t\t.attr('y', (d, i) => (i === 0 ? 0 : i * (s.axisTitleFontSize - 4)))\n\t\t\t.text(d => d)\n\t}\n}\n", "import { select } from 'd3-selection'\n\n/*\nrender a table of p-values\n\nused by survival plot and cuminc plot\n\ninput parameter:\n{\n\ttitle: 'str' value specified by user,\n\ttitleTestid: overrides default testid\n    holder: holder div,\n    plot: plot type ('survial' or 'cuminc'),\n    tests: [] chart tests,\n    s: {} self.settings,\n    bins: [] self.refs.bins,\n    tip: self.app.tip,\n    setActiveMenu: callback for setting self.activeMenu,\n    updateHiddenPvalues: callback for updating s.hiddenPvalues\n}\n*/\n\nexport function renderPvalues({\n\ttitle,\n\ttitleTestid = undefined,\n\tholder,\n\tplot,\n\ttests,\n\ts,\n\tbins,\n\ttip,\n\tsetActiveMenu,\n\tupdateHiddenPvalues\n}) {\n\tlet fontSize\n\n\tif (s.axisTitleFontSize) {\n\t\tfontSize = s.axisTitleFontSize - 2\n\t} else fontSize = 15\n\tconst maxPvalsToShow = 10\n\n\tholder.selectAll('*').remove()\n\n\t// title div\n\tif (!plot) {\n\t\tthrow `plot type '${plot}' not recognized`\n\t}\n\n\tholder\n\t\t.append('div')\n\t\t.style('padding-bottom', '5px')\n\t\t.style('font-size', fontSize + 'px')\n\t\t.style('font-weight', 'bold')\n\t\t.attr('data-testid', titleTestid || 'sjpp-pvalueTable-title')\n\t\t.text(title)\n\n\t// table div\n\t// need separate divs for title and table\n\t// to support table scrolling\n\tconst tablediv = holder.append('div').style('border', '1px solid #ccc')\n\tif ((plot == 'violin' && tests.pvalues.length > maxPvalsToShow) || tests.length > maxPvalsToShow) {\n\t\ttablediv.style('overflow', 'auto').style('height', '220px')\n\t}\n\t// in survival plot, individual tests can be hidden by s.hiddenPvalues\n\t// in cuminc plot, s.hiddenPvalues is not defined\n\tconst visibleTests = s.hiddenPvalues\n\t\t? tests.filter(t => !s.hiddenPvalues.find(p => p.series1.id === t.series1.id && p.series2.id === t.series2.id))\n\t\t: tests\n\n\tif (plot == 'violin' ? visibleTests.pvalues.length : visibleTests.length) {\n\t\tconst binOrder = bins && bins.length > 0 ? bins.map(b => b.label) : null\n\t\tif (binOrder) {\n\t\t\t// series are numeric bins\n\t\t\t// the tests of these series should be sorted as follows\n\n\t\t\t// within each test, series 1 should have a smaller bin\n\t\t\t// value than series 2\n\t\t\tfor (const test of visibleTests) {\n\t\t\t\tconst orderedSeries = [test.series1.id, test.series2.id].sort(\n\t\t\t\t\t(a, b) => binOrder.indexOf(a) - binOrder.indexOf(b)\n\t\t\t\t)\n\t\t\t\tif (test.series2.id == orderedSeries[0]) {\n\t\t\t\t\ttest.series1_new = test.series2\n\t\t\t\t\ttest.series2_new = test.series1\n\t\t\t\t\ttest.series1 = test.series1_new\n\t\t\t\t\ttest.series2 = test.series2_new\n\t\t\t\t\tdelete test.series1_new\n\t\t\t\t\tdelete test.series2_new\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// then sort tests first by series1 then by series2\n\t\t\tvisibleTests.sort(\n\t\t\t\t(a, b) =>\n\t\t\t\t\tbinOrder.indexOf(a.series1.id) - binOrder.indexOf(b.series1.id) ||\n\t\t\t\t\tbinOrder.indexOf(a.series2.id) - binOrder.indexOf(b.series2.id)\n\t\t\t)\n\t\t}\n\n\t\t// table\n\t\tconst table = tablediv.append('table').style('width', '100%')\n\n\t\t// table header\n\t\ttable\n\t\t\t.append('thead')\n\t\t\t.append('tr')\n\t\t\t.selectAll('td')\n\t\t\t.data(['Group 1', 'Group 2', 'P-value'])\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.style('padding', '1px 8px 1px 2px')\n\t\t\t.style('color', '#555')\n\t\t\t.style('position', 'sticky')\n\t\t\t.style('top', '0px')\n\t\t\t.style('background', 'white')\n\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t.text(column => column)\n\n\t\t// table rows\n\t\tconst tbody = table.append('tbody')\n\n\t\tconst tr = tbody\n\t\t\t.selectAll('tr')\n\t\t\t.data(plot == 'violin' ? visibleTests.pvalues : visibleTests)\n\t\t\t.enter()\n\t\t\t.append('tr')\n\t\t\t.attr('class', `pp-${plot}-chartLegends-pvalue`)\n\n\t\tif (plot == 'survival') {\n\t\t\ttr.on('click', (event, t) => {\n\t\t\t\tconst hiddenPvalues = s.hiddenPvalues.slice()\n\t\t\t\thiddenPvalues.push(t)\n\t\t\t\tupdateHiddenPvalues(hiddenPvalues)\n\t\t\t})\n\t\t}\n\n\t\t// table cells\n\t\ttr.selectAll('td')\n\t\t\t.data(d => [d.series1, d.series2, d.pvalue])\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.attr('aria-label', plot ? 'Click to hide a p-value' : '')\n\t\t\t.style('color', plot == 'violin' ? 'black' : d => d.color)\n\t\t\t.style('padding', '1px 8px 1px 2px')\n\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t.style('cursor', plot == 'survival' ? 'pointer' : 'auto')\n\t\t\t.text(d => (plot == 'violin' ? d : d.text))\n\n\t\t// footnote div\n\t\tif (plot == 'cuminc') {\n\t\t\tif (visibleTests.find(test => test.permutation)) {\n\t\t\t\tholder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('margin-top', '10px')\n\t\t\t\t\t.style('font-size', fontSize - 2 + 'px')\n\t\t\t\t\t.text(\"*computed by permutation of Gray's test statistic\")\n\t\t\t}\n\t\t}\n\t}\n\n\tif (plot == 'survival') {\n\t\t// features specific to survival plot\n\t\tconst hiddenTests = tests.filter(t =>\n\t\t\ts.hiddenPvalues.find(p => p.series1.id === t.series1.id && p.series2.id === t.series2.id)\n\t\t)\n\t\tif (hiddenTests.length) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.style('color', '#aaa')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.html(`<span style='color:#aaa; font-weight:400'><span>Hidden tests (${hiddenTests.length})</span>`)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\ttip.clear()\n\t\t\t\t\tconst divs = tip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.selectAll('div')\n\t\t\t\t\t\t.data(hiddenTests)\n\t\t\t\t\t\t.enter()\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.each(function (d) {\n\t\t\t\t\t\t\tsetActiveMenu(true)\n\t\t\t\t\t\t\tconst div = select(this)\n\t\t\t\t\t\t\tdiv.append('input').attr('type', 'checkbox').style('margin-right', '5px')\n\t\t\t\t\t\t\tdiv.append('span').html(`${d.series1.id} vs ${d.series2.id}`)\n\t\t\t\t\t\t})\n\n\t\t\t\t\ttip.d\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.html('Show checked test(s)')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tconst hiddenPvalues = []\n\t\t\t\t\t\t\tdivs\n\t\t\t\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\t\t\t\treturn !select(this.firstChild).property('checked')\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t.each(d => hiddenPvalues.push(d))\n\t\t\t\t\t\t\tupdateHiddenPvalues(hiddenPvalues)\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t})\n\n\t\t\t\t\ttip.show(event.clientX, event.clientY)\n\t\t\t\t})\n\t\t}\n\n\t\t//footnote: pvalue is still computed with all survival data when Survival Time Visualized is set\n\t\tif (s.maxTimeToEvent && visibleTests.length) {\n\t\t\tholder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-top', '10px')\n\t\t\t\t.style('font-size', fontSize - 2 + 'px')\n\t\t\t\t.text((visibleTests.length > 1 ? 'p-values are' : 'p-value is') + ' computed with all survival data')\n\t\t}\n\t}\n}\n"],
+  "mappings": ";;;;;;;;;AA8BO,SAAS,aAAa,MAAM,MAAM,OAAO,MAAM;AACrD,QAAM,MAAM,QAAQ,IAAI,KAAK,EAAE,SAAS,MAAM,CAAC;AAC/C,OAAK,MAAM,WAAW,MAAM;AAE5B,QAAM,WAAW,KAAK,MAAM,QAAQ,aAAa,EAAE,KAAK;AAExD,WAAS,UAAU,OAAO;AACzB,UAAM,IAAI,gBAAQ,OAAO,QAAQ;AACjC,UAAM,KAAK,EAAE,CAAC;AACd,UAAM,OAAO,CAAC,KAAK,OAAO,OAAO,EAAE,EAAE,QAAQ,KAAK,QAAQ;AAC1D,UAAM,IAAI,KAAK,OAAO,IAAI;AAE1B,SAAK,MAAM,WAAW,EAAE,EAAE,KAAK,UAAU,MAAM,EAAE,KAAK,oBAAoB,CAAC,EAAE,KAAK,MAAM,CAAC,EAAE,KAAK,MAAM,CAAC;AAEvG,UAAM,cAAc,CAAC;AACrB,eAAW,UAAU,KAAK,UAAU;AACnC,YAAM,OAAO,OAAO;AACpB,YAAM,SAAS,KAAK,IAAI,OAAK,EAAE,CAAC;AAChC,UAAI,QAAQ,KAAK,IAAI,GAAG,MAAM,KAAK,QAAQ,KAAK,IAAI,GAAG,MAAM,GAAG;AAI/D,cAAM,MAAM,KAAK,IAAI,GAAG,OAAO,OAAO,CAAAA,OAAKA,MAAK,IAAI,CAAC;AAErD,cAAM,YAAY,KAAK,KAAK,OAAK,EAAE,KAAK,GAAG;AAC3C,YAAI,UAAW,aAAY,KAAK,UAAU,IAAI;AAAA,MAC/C;AAAA,IACD;AAEA,QAAI,YAAY,QAAQ;AACvB,UACE,KAAK,MAAM,SAAS,MAAM,OAAO,EACjC,EAAE,KAAK,SAAS,KAAK,WAAW,KAAK,IAAI,gBAAgB,YAAY,IAAI,OAAK,CAAC,EAAE,KAAK,KAAK,SAAS,CAAC;AAAA,IACxG,OAAO;AACN,UAAI,KAAK;AAAA,IACV;AAAA,EACD;AAEA,OACE,GAAG,aAAa,SAAS,EACzB,GAAG,aAAa,SAAS,EACzB,GAAG,YAAY,MAAM;AACrB,SAAK,MAAM,WAAW,MAAM;AAC5B,QAAI,KAAK;AAAA,EACV,CAAC;AAEF,QAAM,OAAO;AAAA,IACZ,WAAW;AAAA,IACX,UAAU;AAAA,EACX;AAKA,SAAO;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,IAsCN,OAAO,QAAQ,CAAC,GAAG;AAClB,aAAO,OAAO,MAAM,KAAK;AACzB,YAAM,IAAI,KAAK,KAAK,GAAG;AACvB,YAAM,IAAI,KAAK,KAAK,GAAG;AACvB,WACE,KAAK,MAAM,CAAC,EACZ,KAAK,MAAM,CAAC,EACZ,KAAK,MAAM,CAAC,EACZ,KAAK,MAAM,KAAK,KAAK,QAAQ,IAAI,CAAC;AAAA,IACrC;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,IAOA,UAAU;AACT,WAAK,GAAG,aAAa,IAAI,EAAE,GAAG,aAAa,IAAI,EAAE,GAAG,YAAY,IAAI;AAAA,IACrE;AAAA,EACD;AACD;;;AC7HO,SAAS,cAAc,EAAE,GAAG,GAAG,OAAO,OAAO,cAAc,aAAa,GAAG;AAEjF,QAAM,eAAe,CAAC;AAMtB,QAAM,cAAc,MAAM,YAAY,OAAO,WAAS,SAAS,MAAM,IAAI;AAGzE,aAAW,UAAU,MAAM,iBAAiB;AAC3C,UAAM,SAAS,CAAC;AAChB,QAAI,IAAI,GACP,IAAI,OAAO,KAAK,CAAC,GACjB,OAAO,GACP,YAAY;AAGb,eAAW,QAAQ,aAAa;AAC/B,aAAO,KAAK,EAAE,IAAI,MAAM;AACvB,qBAAa,EAAE;AACf,eAAO;AACP;AACA,YAAI,OAAO,KAAK,CAAC;AAAA,MAClB;AAMA,UAAI,KAAK,EAAE,MAAM,MAAM;AAGtB,eAAO,KAAK,CAAC,MAAM,EAAE,OAAO,SAAS,CAAC;AAAA,MACvC,OAAO;AAIN,eAAO,KAAK,CAAC,MAAM,KAAK,QAAQ,KAAK,SAAS,KAAK,SAAS,SAAS,CAAC;AAAA,MACvE;AAAA,IACD;AACA,UAAM,EAAE,UAAU,YAAY,IAAI;AAClC,iBAAa,KAAK,EAAE,UAAU,aAAa,OAAO,CAAC;AAAA,EACpD;AAEA,QAAM,IAAI,EAAE,OAAO,EAAE,WAAW,MAAM,EAAE,WAAW,SAAS;AAI5D,QAAM,cAAc,SAAS,MAAM,SAAS,IAAI,CAAAC,OAAKA,GAAE,QAAQ;AAE/D,IAAE,UAAU,oBAAoB,EAAE,OAAO;AACzC,MAAI,EAAE,eAAe;AAGpB,iBAAa,KAAK,CAAC,GAAG,MAAM,YAAY,QAAQ,EAAE,QAAQ,IAAI,YAAY,QAAQ,EAAE,QAAQ,CAAC;AAG7F,UAAM,aAAa,MAAM,SAAS,UAAU,KAAK,CAAC,MAAM,SAAS,CAAC,EAAE;AACpE,UAAM,SAAS,EACb,OAAO,MAAM,EACb,KAAK,SAAS,mBAAmB,EACjC,KAAK,aAAa,aAAa,EAAE,iBAAiB,KAAK,aAAa,IAAI,EAAE,oBAAoB,CAAC,GAAG,EAClG,KAAK,eAAe,KAAK,EACzB,KAAK,aAAa,GAAG,EAAE,oBAAoB,CAAC,IAAI,EAChD,KAAK,UAAU,MAAM,SAAS,UAAU,IAAI,YAAY,SAAS,EACjE,KAAK,gBAAgB,EACrB,GAAG,SAAS,MAAM,SAAS,UAAU,IAAI,OAAK,aAAa,EAAE,UAAU,GAAG,GAAG,EAAE,SAAS,EAAE,OAAO,IAAI,IAAI;AAC3G,QAAI,aAAa,EAAE,EAAG,QAAO,MAAM,QAAQ,EAAE,YAAY;AACzD,WACE,OAAO,OAAO,EACd,KAAK,KAAK,CAAC,EACX,KAAK,KAAK,EAAE,oBAAoB,CAAC,EACjC,KAAK,cAAc;AAAA,EACtB,OAAO;AAGN,iBAAa,SAAS;AAAA,EACvB;AAGA,QAAM,KAAK,EACT,KAAK,aAAa,eAAe,CAAC,GAAG,EACrC,UAAU,YAAY,EACtB,KAAK,cAAc,CAAAA,OAAKA,GAAE,eAAeA,GAAE,QAAQ;AAErD,KAAG,KAAK,EAAE,OAAO;AAEjB,KAAG,KAAK,SAAU,aAAa,GAAG;AACjC,UAAM,EAAE,UAAU,aAAa,OAAO,IAAI;AAC1C,UAAMC,MAAK,IAAI,MAAM,IAAI,EAAE;AAC3B,UAAMC,KAAI,eAAO,IAAI,EACnB,KAAK,aAAa,eAAeD,EAAC,GAAG,EACrC,KAAK,QAAQ,aAAa,EAAE,IAAI,EAAE,eAAe,aAAa,QAAQ,EAAE,QAAQ;AAElF,QAAI,aAAaC,GAAE,OAAO,aAAa;AACvC,QAAI,CAAC,WAAW,KAAK,EAAG,cAAaA,GAAE,OAAO,MAAM;AACpD,eAAW,KAAK,YAAY,aAAa,MAAM,eAAe,WAAW,EAAE;AAE3E,QAAI,SAASA,GAAE,OAAO,UAAU;AAChC,QAAI,CAAC,OAAO,KAAK,EAAG,UAASA,GAAE,OAAO,GAAG;AAEzC,qBAAiB,QAAQ,OAAO,aAAa,GAAG,WAAW;AAAA,EAC5D,CAAC;AAED,KAAG,MAAM,EACP,OAAO,GAAG,EACV,KAAK,SAAU,aAAa,GAAG;AAC/B,UAAM,EAAE,UAAU,aAAa,OAAO,IAAI;AAC1C,UAAMD,MAAK,IAAI,MAAM,IAAI,EAAE;AAC3B,UAAMC,KAAI,eAAO,IAAI,EACnB,KAAK,aAAa,eAAeD,EAAC,GAAG,EACrC,KAAK,QAAQ,aAAa,EAAE,IAAI,EAAE,eAAe,aAAa,QAAQ,EAAE,QAAQ,EAChF,GAAG,SAAS,OAAK,aAAa,EAAE,SAAS,GAAG,EAAE,SAAS,EAAE,OAAO,CAAC;AAEnE,IAAAC,GAAE,OAAO,MAAM,EACb,KAAK,eAAe,sBAAsB,EAC1C,KAAK,aAAa,aAAa,EAAE,iBAAiB,MAAM,EACxD,KAAK,eAAe,KAAK,EACzB,KAAK,aAAa,GAAG,EAAE,oBAAoB,CAAC,IAAI,EAChD,KAAK,UAAU,SAAS,EACxB,MAAM,EAAE,SAAS,CAAC,EAClB,KAAK,YAAY,aAAa,MAAM,eAAe,WAAW,EAAE;AAElE,qBAAiBA,GAAE,OAAO,GAAG,GAAG,OAAO,aAAa,GAAG,WAAW;AAAA,EACnE,CAAC;AACH;AAEA,SAAS,iBAAiB,GAAG,OAAO,aAAa,GAAG,aAAa;AAChE,QAAM,EAAE,UAAU,OAAO,IAAI;AAC7B,QAAM,WAAW,OAAO,MAAM,EAAE,QAAQ;AACxC,QAAM,OAAO,YAAY,IAAI,aAAW;AACvC,QAAI,YAAY,EAAG,QAAO,EAAE,UAAU,SAAS,QAAQ,OAAO,CAAC,EAAE,CAAC,GAAG,WAAW,OAAO,CAAC,EAAE,CAAC,EAAE;AAC7F,UAAM,IAAI,SAAS,KAAK,CAAAC,OAAKA,GAAE,CAAC,KAAK,OAAO;AAC5C,WAAO,EAAE,UAAU,SAAS,QAAQ,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE;AAAA,EAC3D,CAAC;AAED,QAAM,OAAO,EAAE,UAAU,MAAM,EAAE,KAAK,IAAI;AAC1C,OAAK,KAAK,EAAE,OAAO;AACnB,OACE,KAAK,aAAa,OAAK,aAAa,MAAM,OAAO,EAAE,OAAO,CAAC,KAAK,EAChE,KAAK,eAAe,QAAQ,EAC5B,KAAK,aAAa,GAAG,EAAE,oBAAoB,CAAC,IAAI,EAChD,KAAK,UAAU,SAAS,EACxB,KAAK,iBAAiB;AACxB,OACE,MAAM,EACN,OAAO,MAAM,EACb,KAAK,aAAa,OAAK,aAAa,MAAM,OAAO,EAAE,OAAO,CAAC,KAAK,EAChE,KAAK,eAAe,QAAQ,EAC5B,KAAK,aAAa,GAAG,EAAE,oBAAoB,CAAC,IAAI,EAChD,KAAK,UAAU,SAAS,EACxB,KAAK,iBAAiB;AAExB,WAAS,kBAAkB,GAAG;AAC7B,UAAM,SAAS,eAAO,IAAI,EACxB,UAAU,OAAO,EACjB,KAAK,CAAC,EAAE,QAAQ,IAAI,EAAE,SAAS,GAAG,CAAC;AAErC,WAAO,KAAK,EAAE,OAAO;AAErB,WAAO,KAAK,KAAK,CAACA,IAAG,MAAO,MAAM,IAAI,IAAI,KAAK,EAAE,oBAAoB,EAAG,EAAE,KAAK,CAAAA,OAAKA,EAAC;AAErF,WACE,MAAM,EACN,OAAO,OAAO,EACd,KAAK,KAAK,CAAC,EACX,KAAK,KAAK,CAACA,IAAG,MAAO,MAAM,IAAI,IAAI,KAAK,EAAE,oBAAoB,EAAG,EACjE,KAAK,CAAAA,OAAKA,EAAC;AAAA,EACd;AACD;;;ACtKO,SAAS,cAAc;AAAA,EAC7B;AAAA,EACA,cAAc;AAAA,EACd;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACD,GAAG;AACF,MAAI;AAEJ,MAAI,EAAE,mBAAmB;AACxB,eAAW,EAAE,oBAAoB;AAAA,EAClC,MAAO,YAAW;AAClB,QAAM,iBAAiB;AAEvB,SAAO,UAAU,GAAG,EAAE,OAAO;AAG7B,MAAI,CAAC,MAAM;AACV,UAAM,cAAc,IAAI;AAAA,EACzB;AAEA,SACE,OAAO,KAAK,EACZ,MAAM,kBAAkB,KAAK,EAC7B,MAAM,aAAa,WAAW,IAAI,EAClC,MAAM,eAAe,MAAM,EAC3B,KAAK,eAAe,eAAe,wBAAwB,EAC3D,KAAK,KAAK;AAKZ,QAAM,WAAW,OAAO,OAAO,KAAK,EAAE,MAAM,UAAU,gBAAgB;AACtE,MAAK,QAAQ,YAAY,MAAM,QAAQ,SAAS,kBAAmB,MAAM,SAAS,gBAAgB;AACjG,aAAS,MAAM,YAAY,MAAM,EAAE,MAAM,UAAU,OAAO;AAAA,EAC3D;AAGA,QAAM,eAAe,EAAE,gBACpB,MAAM,OAAO,OAAK,CAAC,EAAE,cAAc,KAAK,OAAK,EAAE,QAAQ,OAAO,EAAE,QAAQ,MAAM,EAAE,QAAQ,OAAO,EAAE,QAAQ,EAAE,CAAC,IAC5G;AAEH,MAAI,QAAQ,WAAW,aAAa,QAAQ,SAAS,aAAa,QAAQ;AACzE,UAAM,WAAW,QAAQ,KAAK,SAAS,IAAI,KAAK,IAAI,OAAK,EAAE,KAAK,IAAI;AACpE,QAAI,UAAU;AAMb,iBAAW,QAAQ,cAAc;AAChC,cAAM,gBAAgB,CAAC,KAAK,QAAQ,IAAI,KAAK,QAAQ,EAAE,EAAE;AAAA,UACxD,CAAC,GAAG,MAAM,SAAS,QAAQ,CAAC,IAAI,SAAS,QAAQ,CAAC;AAAA,QACnD;AACA,YAAI,KAAK,QAAQ,MAAM,cAAc,CAAC,GAAG;AACxC,eAAK,cAAc,KAAK;AACxB,eAAK,cAAc,KAAK;AACxB,eAAK,UAAU,KAAK;AACpB,eAAK,UAAU,KAAK;AACpB,iBAAO,KAAK;AACZ,iBAAO,KAAK;AAAA,QACb;AAAA,MACD;AAGA,mBAAa;AAAA,QACZ,CAAC,GAAG,MACH,SAAS,QAAQ,EAAE,QAAQ,EAAE,IAAI,SAAS,QAAQ,EAAE,QAAQ,EAAE,KAC9D,SAAS,QAAQ,EAAE,QAAQ,EAAE,IAAI,SAAS,QAAQ,EAAE,QAAQ,EAAE;AAAA,MAChE;AAAA,IACD;AAGA,UAAM,QAAQ,SAAS,OAAO,OAAO,EAAE,MAAM,SAAS,MAAM;AAG5D,UACE,OAAO,OAAO,EACd,OAAO,IAAI,EACX,UAAU,IAAI,EACd,KAAK,CAAC,WAAW,WAAW,SAAS,CAAC,EACtC,MAAM,EACN,OAAO,IAAI,EACX,MAAM,WAAW,iBAAiB,EAClC,MAAM,SAAS,MAAM,EACrB,MAAM,YAAY,QAAQ,EAC1B,MAAM,OAAO,KAAK,EAClB,MAAM,cAAc,OAAO,EAC3B,MAAM,aAAa,WAAW,IAAI,EAClC,KAAK,YAAU,MAAM;AAGvB,UAAM,QAAQ,MAAM,OAAO,OAAO;AAElC,UAAM,KAAK,MACT,UAAU,IAAI,EACd,KAAK,QAAQ,WAAW,aAAa,UAAU,YAAY,EAC3D,MAAM,EACN,OAAO,IAAI,EACX,KAAK,SAAS,MAAM,IAAI,sBAAsB;AAEhD,QAAI,QAAQ,YAAY;AACvB,SAAG,GAAG,SAAS,CAAC,OAAO,MAAM;AAC5B,cAAM,gBAAgB,EAAE,cAAc,MAAM;AAC5C,sBAAc,KAAK,CAAC;AACpB,4BAAoB,aAAa;AAAA,MAClC,CAAC;AAAA,IACF;AAGA,OAAG,UAAU,IAAI,EACf,KAAK,OAAK,CAAC,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,CAAC,EAC1C,MAAM,EACN,OAAO,IAAI,EACX,KAAK,cAAc,OAAO,4BAA4B,EAAE,EACxD,MAAM,SAAS,QAAQ,WAAW,UAAU,OAAK,EAAE,KAAK,EACxD,MAAM,WAAW,iBAAiB,EAClC,MAAM,aAAa,WAAW,IAAI,EAClC,MAAM,UAAU,QAAQ,aAAa,YAAY,MAAM,EACvD,KAAK,OAAM,QAAQ,WAAW,IAAI,EAAE,IAAK;AAG3C,QAAI,QAAQ,UAAU;AACrB,UAAI,aAAa,KAAK,UAAQ,KAAK,WAAW,GAAG;AAChD,eACE,OAAO,KAAK,EACZ,MAAM,cAAc,MAAM,EAC1B,MAAM,aAAa,WAAW,IAAI,IAAI,EACtC,KAAK,mDAAmD;AAAA,MAC3D;AAAA,IACD;AAAA,EACD;AAEA,MAAI,QAAQ,YAAY;AAEvB,UAAM,cAAc,MAAM;AAAA,MAAO,OAChC,EAAE,cAAc,KAAK,OAAK,EAAE,QAAQ,OAAO,EAAE,QAAQ,MAAM,EAAE,QAAQ,OAAO,EAAE,QAAQ,EAAE;AAAA,IACzF;AACA,QAAI,YAAY,QAAQ;AACvB,aACE,OAAO,KAAK,EACZ,MAAM,SAAS,MAAM,EACrB,MAAM,UAAU,SAAS,EACzB,KAAK,iEAAiE,YAAY,MAAM,UAAU,EAClG,GAAG,SAAS,WAAS;AACrB,YAAI,MAAM;AACV,cAAM,OAAO,IAAI,EACf,OAAO,KAAK,EACZ,UAAU,KAAK,EACf,KAAK,WAAW,EAChB,MAAM,EACN,OAAO,KAAK,EACZ,KAAK,SAAU,GAAG;AAClB,wBAAc,IAAI;AAClB,gBAAM,MAAM,eAAO,IAAI;AACvB,cAAI,OAAO,OAAO,EAAE,KAAK,QAAQ,UAAU,EAAE,MAAM,gBAAgB,KAAK;AACxE,cAAI,OAAO,MAAM,EAAE,KAAK,GAAG,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAAE;AAAA,QAC7D,CAAC;AAEF,YAAI,EACF,OAAO,QAAQ,EACf,KAAK,sBAAsB,EAC3B,GAAG,SAAS,MAAM;AAClB,gBAAM,gBAAgB,CAAC;AACvB,eACE,OAAO,WAAY;AACnB,mBAAO,CAAC,eAAO,KAAK,UAAU,EAAE,SAAS,SAAS;AAAA,UACnD,CAAC,EACA,KAAK,OAAK,cAAc,KAAK,CAAC,CAAC;AACjC,8BAAoB,aAAa;AACjC,cAAI,KAAK;AAAA,QACV,CAAC;AAEF,YAAI,KAAK,MAAM,SAAS,MAAM,OAAO;AAAA,MACtC,CAAC;AAAA,IACH;AAGA,QAAI,EAAE,kBAAkB,aAAa,QAAQ;AAC5C,aACE,OAAO,KAAK,EACZ,MAAM,cAAc,MAAM,EAC1B,MAAM,aAAa,WAAW,IAAI,IAAI,EACtC,MAAM,aAAa,SAAS,IAAI,iBAAiB,gBAAgB,kCAAkC;AAAA,IACtG;AAAA,EACD;AACD;",
+  "names": ["x", "s", "y", "g", "d"]
+}

package/dist/chunk-4HZN6PMU.js

@@ -0,0 +1,129 @@
+import {
+  keyupEnter
+} from "./chunk-TKW5TW4Z.js";
+
+// src/block.mds.svcnv.share.js
+function rnabamtk_initparam(c) {
+  if (!c.dna_mintotalreads) c.dna_mintotalreads = 8;
+  if (!c.rna_mintotalreads) c.rna_mintotalreads = 8;
+  if (!c.hetsnp_minbaf) c.hetsnp_minbaf = 0.3;
+  if (!c.hetsnp_maxbaf) c.hetsnp_maxbaf = 0.7;
+  if (c.rnapileup_q == void 0) c.rnapileup_q = 0;
+  if (!c.rnapileup_Q) c.rnapileup_Q = 13;
+  if (!c.binompvaluecutoff) c.binompvaluecutoff = 0.05;
+  if (!c.clientcolor_snpinuse) c.clientcolor_snpinuse = "blue";
+  if (!c.clientcolor_markernotinuse) c.clientcolor_markernotinuse = "#bbb";
+}
+function configPanel_rnabam(tk, block, loadTk) {
+  const c = tk.checkrnabam;
+  if (!c) return;
+  tk.tkconfigtip.d.append("hr");
+  const d = tk.tkconfigtip.d.append("div").style("margin", "15px 0px");
+  d.append("div").style("opacity", 0.5).style("font-size", ".9em").text("Finding heterozygous SNPs in DNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("DNA minimum total read count ");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.dna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.dna_mintotalreads == v) {
+        return;
+      }
+      c.dna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.");
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_minbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_minbaf == v) {
+        return;
+      }
+      c.hetsnp_minbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("span").style("opacity", ".5").style("font-size", ".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_maxbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_maxbaf == v) {
+        return;
+      }
+      c.hetsnp_maxbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.");
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Counting alleles in RNA-seq BAM file");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip alignments with mapQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v < 0) return;
+      if (c.rnapileup_q == v) {
+        return;
+      }
+      c.rnapileup_q = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_Q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rnapileup_Q == v) {
+        return;
+      }
+      c.rnapileup_Q = v;
+      loadTk(tk, block);
+    });
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("P-value cutoff&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.binompvaluecutoff).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0 || v >= 1) return;
+      if (c.binompvaluecutoff == v) {
+        return;
+      }
+      c.binompvaluecutoff = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("RNA minimum total read count&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rna_mintotalreads == v) {
+        return;
+      }
+      c.rna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.");
+  }
+}
+
+export {
+  rnabamtk_initparam,
+  configPanel_rnabam
+};
+//# sourceMappingURL=chunk-4HZN6PMU.js.map

package/dist/chunk-4KRGCOTL.js

@@ -0,0 +1,479 @@
+import {
+  rehydrateFilter
+} from "./chunk-SKMFMGCD.js";
+import {
+  findParent,
+  getFilter,
+  getFilterItemByTag,
+  getSamplelstTW
+} from "./chunk-TKW5TW4Z.js";
+import {
+  importPlot
+} from "./chunk-3SHZTAGF.js";
+import {
+  StoreApi,
+  StoreBase
+} from "./chunk-M3J4MINX.js";
+import {
+  CustomError
+} from "./chunk-JNITUVXP.js";
+
+// mass/store.ts
+var idPrefix = "_MASS_AUTOID_" + Math.random().toString().slice(-6);
+var id = 0;
+var usedPlotIds = /* @__PURE__ */ new Set();
+function getId() {
+  return idPrefix + "_" + id++;
+}
+var navHeaderModes = /* @__PURE__ */ new Set([
+  "with_tabs",
+  // default, shows tabs cohort/charts/filter etc
+  "hidden",
+  // no header
+  "search_only",
+  // ?
+  "hide_search",
+  // ?
+  "with_cohortHtmlSelect",
+  // only show cohort toggle as <select>
+  "only_buttons"
+]);
+var defaultState = {
+  nav: {
+    header_mode: "with_tabs",
+    activeTab: 0
+    // -1 for no active tab and all closed
+  },
+  // will be ignored if there is no dataset termdb.selectCohort
+  // or value will be set to match a filter node that has been tagged
+  // as 'cohortfilter' in state.termfilter.filter
+  activeCohort: 0,
+  search: { isVisible: true },
+  plots: [],
+  termfilter: {
+    filter: {
+      type: "tvslst",
+      in: true,
+      join: "",
+      lst: []
+    }
+  },
+  reuse: {
+    customTermQ: {
+      byId: {},
+      // non-dictionary terms do not have a term.id,
+      // save by term.type + name?
+      byName: {}
+    }
+  },
+  groups: [],
+  // element: {name=str, filter={}}, to show in Groups tab
+  customTerms: [],
+  // element: {name=str, term={}}, able to attach more attr to object if needed
+  autoSave: true
+};
+var MassStore = class extends StoreBase {
+  constructor(opts, api) {
+    super(opts);
+    // expected class-specific props
+    this.defaultState = defaultState;
+    this.plotAdjusters = /* @__PURE__ */ new WeakMap();
+    this.app = opts.app;
+    this.api = api;
+    this.type = "store";
+    let savedState = {};
+    try {
+      const key = window.navigator.webdriver && window["SJPP_E2E_STORAGE_STATES_KEY"];
+      const savedStateStr = key && window.localStorage.getItem("SJPP_E2E_STORAGE_STATES") || "{}";
+      savedState = JSON.parse(savedStateStr)[key]?.state || {};
+    } catch (_) {
+      savedState = {};
+    }
+    this.state = this.copyMerge(this.toJson(defaultState), opts.state, savedState);
+    this.prevGeneratedId = 0;
+  }
+  static {
+    this.type = "store";
+  }
+  validateOpts(opts) {
+    const s = opts.state;
+    if (s.vocab.dslabel) {
+      if (!s.vocab.genome) throw ".state[.vocab].genome missing";
+    } else {
+      if (!Array.isArray(s.vocab.terms)) throw "vocab.terms must be an array of objects";
+    }
+    return opts;
+  }
+  validateState() {
+    if (!navHeaderModes.has(this.state.nav.header_mode)) throw "invalid state.nav.header_mode";
+  }
+  async init() {
+    try {
+      this.state.termdbConfig = await this.app.vocabApi.getTermdbConfig();
+      await this.setTermfilter();
+      await this.rehydrateGroups();
+      await this.app.vocabApi.main({
+        termfilter: JSON.parse(JSON.stringify(this.state.termfilter)),
+        termdbConfig: this.state.termdbConfig
+      });
+      const invalidPlots = [];
+      for (const [i, savedPlot] of this.state.plots.entries()) {
+        let plot;
+        try {
+          const _ = await importPlot(savedPlot.chartType);
+          plot = await _.getPlotConfig(savedPlot, this.app, this.state.activeCohort);
+        } catch (e) {
+          this.app.printError(e);
+          console.error(`getPlotConfig() failed: ${e}`);
+        }
+        if (!plot) {
+          invalidPlots.push(i);
+          continue;
+        }
+        this.state.plots[i] = plot;
+        if (!("id" in plot)) plot.id = `_AUTOID_${id++}_${i}`;
+        if (plot.mayAdjustConfig) {
+          plot.mayAdjustConfig(plot);
+          this.plotAdjusters.set(plot, plot.mayAdjustConfig);
+          delete plot.mayAdjustConfig;
+        }
+      }
+      if (invalidPlots.length) {
+        for (const i of invalidPlots) {
+          this.state.plots.splice(i, 1);
+        }
+      }
+    } catch (e) {
+      console.log("store.init() error", e);
+      throw e;
+    }
+  }
+  setId(item) {
+    item.$id = this.prevGeneratedId++;
+    if (item.$lst) {
+      for (const subitem of item.$lst) {
+        this.setId(subitem);
+      }
+    }
+  }
+  async setTermfilter() {
+    let filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, "filterUiRoot");
+    if (!filterUiRoot) {
+      this.state.termfilter.filter.tag = "filterUiRoot";
+      filterUiRoot = this.state.termfilter.filter;
+    }
+    await Promise.all(rehydrateFilter(this.state.termfilter.filter, this.app.vocabApi));
+    if (!this.state.termdbConfig.selectCohort) {
+      this.state.activeCohort = -1;
+      if (this.state.activeTab === 0) this.state.activeTab = 1;
+      if (this.state.nav.header_mode === "with_cohortHtmlSelect") {
+        console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);
+        this.state.nav.header_mode = "search_only";
+      }
+    } else {
+      let cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
+      if (!cohortFilter) {
+        cohortFilter = {
+          tag: "cohortFilter",
+          type: "tvs",
+          tvs: {
+            term: JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),
+            values: this.state.activeCohort == -1 ? [] : this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((key) => {
+              return { key, label: key };
+            })
+          }
+        };
+        this.state.termfilter.filter = {
+          type: "tvslst",
+          in: true,
+          join: "and",
+          lst: [cohortFilter, filterUiRoot]
+        };
+      } else {
+        const sorter = (a, b) => a < b ? -1 : 1;
+        cohortFilter.tvs.values.sort((a, b) => a.key < b.key ? -1 : 1);
+        const keysStr = JSON.stringify(cohortFilter.tvs.values.map((v) => v.key).sort(sorter));
+        const i = this.state.termdbConfig.selectCohort.values.findIndex(
+          (v) => keysStr == JSON.stringify(v.keys.sort(sorter))
+        );
+        if (this.state.activeCohort !== -1 && this.state.activeCohort !== 0 && i !== this.state.activeCohort) {
+          console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch");
+        }
+        this.state.activeCohort = i;
+      }
+    }
+  }
+  async rehydrateGroups() {
+    const lst = [];
+    for (const g of this.state.groups) {
+      lst.push(...rehydrateFilter(g.filter, this.app.vocabApi));
+    }
+    await Promise.all(lst);
+  }
+};
+MassStore.prototype.actions = {
+  // Type '{ app_refresh(this: MassStore, action?: {}): Promise<void>; tab_set(action: any): void; cohort_set(action: any): void; plot_prep(action: any): Promise<void>; ... 13 more ...; delete_group({ name }: { ...; }): void; }' is not assignable to type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.
+  // Object literal may only specify known properties, and 'app_refresh' does not exist in type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.
+  async app_refresh(action) {
+    this.state = this.copyMerge(this.toJson(this.state), action.state || {});
+    const subactionPlotIds = /* @__PURE__ */ new Set();
+    const promises = [];
+    if (action.subactions) {
+      for (const a of action.subactions) {
+        promises.push(this.actions[a.type].call(this, a));
+        if (a.type.startsWith("plot_")) subactionPlotIds.add(a.id);
+      }
+    }
+    await Promise.all(promises);
+    for (const plot of this.state.plots) {
+      const mayAdjustConfig = this.plotAdjusters.get(plot);
+      if (mayAdjustConfig && !subactionPlotIds.has(plot.id)) {
+        mayAdjustConfig(plot, action.config);
+      }
+    }
+  },
+  tab_set(action) {
+    this.state.nav.activeTab = action.activeTab;
+  },
+  cohort_set(action) {
+    this.state.activeCohort = action.activeCohort;
+    const cohort = this.state.termdbConfig.selectCohort.values[action.activeCohort];
+    const cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
+    if (!cohortFilter) throw `No item tagged with 'cohortFilter'`;
+    cohortFilter.tvs.values = cohort.keys.map((key) => {
+      return { key, label: key };
+    });
+  },
+  // dispatch "plot_prep" action to produce a 'initiating' UI of this plot, for user to fill in additional details to launch the plot
+  // example: table, scatterplot which requires user to select two terms
+  async plot_prep(action) {
+    if (usedPlotIds.has(action.id)) delete action.id;
+    const plot = {
+      // rx.getComponents() relies on parsing dot-separated key names that breaks if a key has a dot,
+      // the plot.id value should be assumed to be auto-generated and to not have any non-rx usage expectations
+      id: "id" in action && !action.id.includes(".") ? action.id : getId()
+    };
+    usedPlotIds.add(plot.id);
+    if (!action.config) throw ".config{} missing for plot_prep";
+    if (action.config.chartType && Object.keys(action.config).length == 1) {
+      const _ = await importPlot(action.config.chartType);
+      const config = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
+      action.config = Object.assign(config, action.config);
+    }
+    Object.assign(plot, action.config);
+    this.state.plots.push(plot);
+  },
+  async plot_create(action) {
+    if (usedPlotIds.has(action.id)) delete action.id;
+    const _ = await importPlot(action.config.chartType);
+    const plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
+    if (!("id" in action) || action.id.includes(".")) action.id = getId();
+    plot.id = action.id;
+    usedPlotIds.add(plot.id);
+    if (plot.mayAdjustConfig) {
+      plot.mayAdjustConfig(plot);
+      this.plotAdjusters.set(plot, plot.mayAdjustConfig);
+      delete plot.mayAdjustConfig;
+    }
+    this.state.plots.push(plot);
+    if (plot.sections) {
+      for (const section of plot.sections) {
+        for (const p of section.plots) {
+          p.parentId = plot.id;
+          if (!p.id) p.id = getId();
+          const _2 = await importPlot(p.chartType);
+          const config = await _2.getPlotConfig(p, this.app, this.state.activeCohort);
+          this.state.plots.push(config);
+        }
+      }
+    }
+  },
+  plot_edit(action) {
+    const plot = this.state.plots.find((p) => p.id === action.id);
+    if (!plot) {
+      throw new CustomError(`missing plot config for id='${action.id}' in store.plot_edit()`, {
+        name: "MISSING_PLOT_CONFIG",
+        level: "warn"
+      });
+    }
+    this.copyMerge(plot, action.config, action.opts ? action.opts : {});
+    const mayAdjustConfig = this.plotAdjusters.get(plot);
+    if (mayAdjustConfig) mayAdjustConfig(plot, action.config);
+    if (action.config && "cutoff" in action.config) {
+      plot.cutoff = action.config.cutoff;
+    } else {
+      delete plot.cutoff;
+    }
+    if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
+  },
+  plot_delete(action) {
+    const i = this.state.plots.findIndex((p) => p.id === action.id);
+    if (i !== -1) {
+      this.state.plots.splice(i, 1);
+      const plot = this.state.plots[i];
+      if (!action.parentId && plot?.parentId) action.parentId = plot.parentId;
+    }
+  },
+  plot_nestedEdits(action) {
+    const plot = this.state.plots.find((p) => p.id === action.id);
+    if (!plot) {
+      throw new CustomError(`missing plot config for id='${action.id}' in store.plot_edit_nested`, {
+        name: "MISSING_PLOT_CONFIG",
+        level: "warn"
+      });
+    }
+    for (const edit of action.edits) {
+      const lastKey = edit.nestedKeys.pop();
+      const obj = edit.nestedKeys.reduce((obj2, key) => obj2[key], plot);
+      obj[lastKey] = edit.value;
+    }
+    if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
+  },
+  // TODO: delete this action? does not seem to be used
+  async plot_splice(action) {
+    for (const a of action.subactions) {
+      await this.actions[a.type].call(this, a);
+    }
+  },
+  filter_replace(action) {
+    if ("filter0" in action) {
+      this.state.termfilter.filter0 = action.filter0;
+      return;
+    }
+    const replacementFilter = action.filter ? action.filter : { type: "tvslst", join: "", in: 1, lst: [] };
+    if (!action.filter.tag) {
+      this.state.termfilter.filter = replacementFilter;
+    } else {
+      const filter = getFilterItemByTag(this.state.termfilter.filter, action.filter.tag);
+      if (!filter) throw `cannot replace missing filter with tag '${action.filter.tag}'`;
+      const parent = findParent(this.state.termfilter.filter, filter.$id);
+      if (parent == filter) {
+        this.state.termfilter.filter = replacementFilter;
+      } else {
+        const i = parent.lst.indexOf(filter);
+        parent.lst[i] = replacementFilter;
+      }
+    }
+    if (this.app.opts.app?.onFilterChange) this.app.opts.app.onFilterChange(this.state.plots);
+  },
+  cache_termq({ termId, q }) {
+    if (!termId) throw `missing termId for caching custom term.q`;
+    if (!q?.reuseId) throw `missing or empty tw.q.reuseId as cache identifier for term='${termId}'`;
+    const cache = this.state.reuse.customTermQ.byId;
+    if (!cache[termId]) cache[termId] = {};
+    cache[termId][q.reuseId] = q;
+    for (const plot of this.state.plots) {
+      if (!(plot.chartType in getTwsByChartType)) continue;
+      const twlst = getTwsByChartType[plot.chartType](plot);
+      for (const tw of twlst) {
+        if (tw?.q?.reuseId === q.reuseId) tw.q = q;
+      }
+    }
+  },
+  uncache_termq({ term, q }) {
+    if (!term.id) throw `missing term.id for uncaching custom term.q`;
+    if (!q.reuseId) throw `missing qname as uncache identifier for term.id='${term.id}'`;
+    const cache = this.state.reuse.customTermQ.byId[term.id];
+    if (!cache) throw `missing term.q cache for term.id='${term.id}`;
+    if (!(q.reuseId in cache)) console.warn(`q.reuseId='${q.cacheid}' not cached for term.id='${term.id}'`);
+    else {
+      delete cache[q.reuseId];
+      for (const plot of this.state.plots) {
+        if (!(plot.chartType in getTwsByChartType)) continue;
+        const twlst = getTwsByChartType[plot.chartType](plot);
+        for (const tw of twlst) {
+          if (tw.q.reuseId === q.reuseId) {
+            delete tw.q.reuseId;
+            delete tw.q.name;
+          }
+        }
+      }
+    }
+  },
+  add_customTerm(action) {
+    const i = action.obj.id ? this.state.customTerms.findIndex((term) => term.id === action.obj.id) : -1;
+    if (i === -1) this.state.customTerms.push(action.obj);
+    else this.state.customTerms[i] = action.obj;
+  },
+  delete_customTerm({ id: id2, name }) {
+    const i = this.state.customTerms.findIndex((term) => id2 ? term.id === id2 : term.name == name);
+    if (i != -1) this.state.customTerms.splice(i, 1);
+  },
+  add_group(action) {
+    if (this.state.nav.header_mode != "hidden") {
+      const group = action.obj;
+      const name = `Group ${this.state.groups.length + 1}`;
+      const samplelstTW = getSamplelstTW([group]);
+      const appGroup = {
+        name,
+        filter: getFilter(samplelstTW),
+        plotId: group.plotId
+      };
+      this.state.groups.push(appGroup);
+      this.state.nav.activeTab = 1;
+    } else if ("plotId" in action.obj) {
+      const plot = this.state.plots.find((p) => p.id == action.obj.plotId);
+      if (plot.groups) {
+        action.obj.index = plot.groups.length;
+        action.obj.name = `Group ${plot.groups.length + 1}`;
+        plot.groups.push(action.obj);
+      }
+    }
+  },
+  rename_group(action) {
+    const index = action.index;
+    const newName = action.newName;
+    if (this.state.nav.header_mode != "hidden") {
+      this.state.groups[index].name = newName;
+    } else {
+      for (const plot of this.state.plots) {
+        if (plot?.groups) {
+          plot.groups[index].name = newName;
+        }
+      }
+    }
+  },
+  change_color_group(action) {
+    const index = action.index;
+    const newColor = action.newColor;
+    if (this.state.nav.header_mode != "hidden") {
+      this.state.groups[index].color = newColor;
+    } else {
+      for (const plot of this.state.plots) {
+        if (plot?.groups) {
+          plot.groups[index].color = newColor;
+        }
+      }
+    }
+  },
+  delete_group({ name }) {
+    if (this.state.nav.header_mode != "hidden") {
+      const i = this.state.groups.findIndex((i2) => i2.name == name);
+      if (i != -1) this.state.groups.splice(i, 1);
+    } else {
+      for (const plot of this.state.plots) {
+        if (plot?.groups) {
+          const j = plot.groups.findIndex((j2) => j2.name == name);
+          if (j != -1) plot.groups.splice(j, 1);
+        }
+      }
+    }
+  }
+};
+var getNestedChartSeriesDataTws = (plot) => [plot.term0, plot.term, plot.term2].filter((d) => !!d);
+var getTwsByChartType = {
+  summary: getNestedChartSeriesDataTws,
+  survival: getNestedChartSeriesDataTws,
+  cuminc: getNestedChartSeriesDataTws,
+  regression: (plot) => [plot.outcome, ...plot.independent].filter((d) => !!d),
+  matrix: (plot) => plot.termgroups.reduce((arr, grp) => {
+    arr.push(...grp.lst);
+    return arr;
+  }, [])
+};
+var storeInit = StoreApi.getInitFxn(MassStore);
+
+export {
+  storeInit
+};
+//# sourceMappingURL=chunk-4KRGCOTL.js.map