@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/chunk-SYPSS3JQ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../filter/tvs.numeric.js"],
-  "sourcesContent": ["import { select } from 'd3-selection'\nimport { scaleLinear } from 'd3'\nimport { addBrushes, addNewBrush } from './tvs.density'\nimport { NumericRangeInput } from '#dom/numericRangeInput'\nimport { convertUnits, getValueConversionFactor } from '#shared/helpers.js'\nimport { violinRenderer } from '../dom/violinRenderer'\nimport { niceNumLabels } from '../dom/niceNumLabels.ts'\n\n/*\n********************** EXPORTED\nhandler:\n\t// internal functions as part of handler\n\tterm_name_gen()\n\tget_pill_label()\n\t\tformat_val_text()\n\tgetSelectRemovePos()\n\tfillMenu()\n\tsetTvsDefaults()\n\n********************** INTERNAL\naddRangeTableNoDensity() // for terms without desnity table, show brushes but without density_plot on blank svg\naddRangeTable() // add table for existing ranges or start with empty_range with brush in center \nenterRange() // add row for each range, for existing readonly and for new or edit, show inputs\nmakeRangeButtons() // add buttons for  Apply / DELETE \nmergeOverlapRanges() // when Apply is pressed, check if ranges are overlapping, if so, merge them\nshowCheckList_numeric() // so checklist of uncomputable values\nvalidateNumericTvs() // validate tvs before sending it to callback\n\n*/\n\nexport const handler = {\n\ttype: 'numeric',\n\tterm_name_gen,\n\tget_pill_label,\n\tgetSelectRemovePos,\n\tfillMenu,\n\tsetTvsDefaults\n}\n\nfunction term_name_gen(d) {\n\tconst name = d.term.name\n\treturn name.length < 26 ? name : '<label title=\"' + name + '\">' + name.substring(0, 24) + '...' + '</label>'\n}\n\nfunction get_pill_label(tvs) {\n\tif (tvs.ranges.length == 1) {\n\t\tconst v = tvs.ranges[0]\n\t\tif ('value' in v) {\n\t\t\t// category\n\t\t\tif (v.label) return { txt: v.label }\n\t\t\tif (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)\n\t\t\t\treturn { txt: tvs.term.values[v.value].label }\n\t\t\tconsole.error(`key \"${v.value}\" not found in values{} of ${tvs.term.name}`)\n\t\t\treturn { txt: v.value }\n\t\t}\n\t\t// numeric range\n\t\treturn { txt: format_val_text(v, tvs.term) }\n\t}\n\t// multiple\n\treturn { txt: tvs.ranges.length + ' intervals' }\n}\n\nexport function format_val_text(range, term) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;font-size:1em; vertical-align:top\">x</span>'\n\tif (range.startunbounded && range.stopunbounded) {\n\t\tconst inf = (sign = '') =>\n\t\t\t`<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`\n\t\tconst lt = `<span style='vertical-align: top; font-size: 0.9em'>&lt;</span>`\n\t\treturn `<span>${inf('\uFE63')} ${lt} ${x} ${lt} ${inf('\uFE62')}</span>`\n\t}\n\n\t/* logic about value converting:\n\tif term.valueConversion is present, will convert e.g. from day to years. this takes higher priority\n\telse, if range is one-sided, return as is\n\telse, apply nice method to adjust digits. this requires a start-stop range\n\t*/\n\n\tconst vc = term.valueConversion\n\n\tif (range.startunbounded)\n\t\treturn `${x} ${range.stopinclusive ? '&le;' : '&lt;'} ${\n\t\t\tvc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop\n\t\t}`\n\n\tif (range.stopunbounded)\n\t\treturn `${x} ${range.startinclusive ? '&ge;' : '&gt;'} ${\n\t\t\tvc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start\n\t\t}`\n\n\t// range is not unbounded and can apply nice method if there's no vc\n\n\tlet startName, stopName\n\tif (vc) {\n\t\tstartName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t\tstopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t} else {\n\t\t//Rms excessive number of decimals\n\t\t;[startName, stopName] = niceNumLabels([range.start, range.stop])\n\t}\n\n\treturn `${startName} \n\t\t\t${range.startinclusive ? '&le;' : '&lt;'}\n\t\t\t${x}\n\t\t\t${range.stopinclusive ? '&le;' : '&lt;'}\n\t\t\t${stopName}`\n}\n\nfunction getSelectRemovePos(j, tvs) {\n\treturn j - tvs.ranges.slice(0, j).filter(a => a.start || a.stop).length\n}\n\nasync function fillMenu(self, div, tvs) {\n\t//numerical range div\n\tconst num_parent_div = div.append('div')\n\tself.num_obj = {}\n\n\tself.num_obj.num_div = num_parent_div\n\t\t.append('div')\n\t\t.attr('class', 'num_div')\n\t\t.style('padding', '5px')\n\t\t.style('color', '#000')\n\n\tself.num_obj.plot_size = {\n\t\twidth: 450,\n\t\theight: 100,\n\t\txpad: 10,\n\t\typad: 20,\n\t\tradius: 8\n\t}\n\n\tif (typeof self.opts.vocabApi.getViolinBox == 'function') {\n\t\ttry {\n\t\t\tconst data = await self.opts.vocabApi.getViolinBox(\n\t\t\t\t{\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\ttw: { term: tvs.term, q: { mode: 'continuous' } },\n\t\t\t\t\t// must supply this filter and override state filter in function, so the density plot will not be limited to range defined by current numeric tvs but will show whole range\n\t\t\t\t\tfilter: self.filter,\n\t\t\t\t\tsvgw: self.num_obj.plot_size.width,\n\t\t\t\t\tradius: self.num_obj.plot_size.radius\n\t\t\t\t},\n\t\t\t\tself.opts.getCategoriesArguments\n\t\t\t)\n\t\t\tif (data.error) throw data.error\n\t\t\tif (data.max === null && data.min === null) {\n\t\t\t\tthrow `No data available under current filter conditions.`\n\t\t\t}\n\t\t\tself.num_obj.density_data = data\n\t\t} catch (err) {\n\t\t\tthrow err\n\t\t}\n\t} else {\n\t\t// frontend vocab lacks this method, return no density data so ui will not show the plot\n\t\t// if the method is added to front vocab, the method must check if sample data is available for the front vocab;\n\t\t// if no sample data then return no density.\n\t\t// such is the case for INFO terms used for variant filtering\n\t\tself.num_obj.density_data = {}\n\t}\n\n\tif (self.num_obj.density_data.error) throw self.num_obj.density_data.error\n\n\tif (!self.num_obj.density_data.charts?.['']?.plots?.[0]?.density?.bins) {\n\t\t// no density data for this term (e.g. bcf numeric info field in a custom filter)\n\t\taddRangeTableNoDensity(self, tvs)\n\t\treturn\n\t}\n\n\tself.vr = new violinRenderer({\n\t\tholder: self.num_obj.num_div,\n\t\trd: self.num_obj.density_data,\n\t\twidth: self.num_obj.plot_size.width,\n\t\tradius: self.num_obj.plot_size.radius,\n\t\theight: self.num_obj.plot_size.height,\n\t\t// axis ticks are labeled in the term's user-facing unit, e.g. years and not days\n\t\tscaleFactor: getValueConversionFactor(tvs.term)\n\t})\n\tself.vr.render()\n\tself.num_obj.svg = self.vr.svg\n\n\tself.num_obj.range_table = self.num_obj.num_div\n\t\t.append('table')\n\t\t.style('table-layout', 'fixed')\n\t\t.style('border-collapse', 'collapse')\n\n\tconst ranges = []\n\n\tfor (const [index, range] of tvs.ranges.entries()) {\n\t\trange.index = index\n\t\tranges.push(range)\n\t}\n\t// add brush_g for tvs brushes\n\tself.num_obj.brush_g = self.vr.brushG.attr('class', 'brush_g')\n\n\tself.num_obj.xscale = self.vr.axisScale\n\n\tself.num_obj.ranges = ranges\n\tself.num_obj.brushes = []\n\taddBrushes(self)\n\taddRangeTable(self)\n\t// const add_range_btn = self.num_obj.num_div\n\t// \t.append('div')\n\t// \t.style('width', '100px')\n\t// \t.attr('class', 'add_range_btn sja_menuoption')\n\t// \t.style('border-radius', '13px')\n\t// \t.style('padding', '7px 6px')\n\t// \t.style('margin', '5px')\n\t// \t.style('margin-left', '20px')\n\t// \t.style('text-align', 'center')\n\t// \t.style('font-size', '.8em')\n\t// \t.text('Add a Range')\n\t// \t.on('click', () => {\n\t// \t\tconst callback = () => addRangeTable(self)\n\t// \t\taddNewBrush(self, ranges.length ? 'end' : 'center', callback)\n\t// \t})\n\n\tif (!ranges.length) {\n\t\tconst callback = () => addRangeTable(self)\n\t\taddNewBrush(self, 'center', callback)\n\t}\n\n\tself.num_obj.brushes.forEach(brush => brush.init())\n\tawait showCheckList_numeric(self, tvs, div)\n}\n\nfunction setTvsDefaults(tvs) {\n\tif (!tvs.ranges) tvs.ranges = []\n}\n\nfunction addRangeTableNoDensity(self, tvs) {\n\tconst termrange = tvs.term.range || {}\n\tconst range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange\n\trange.min = 'min' in tvs.term ? tvs.term.min : null\n\trange.max = 'max' in tvs.term ? tvs.term.max : null\n\tconst num_div = self.num_obj.num_div\n\tnum_div.selectAll('*').remove()\n\n\tconst brush = {}\n\tconst holder = num_div.append('div').style('padding-left', '5px')\n\tconst rangeRow = holder\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('column-gap', '5px')\n\tconst rangeLabel = rangeRow.append('span')\n\tbrush.equation_div = rangeRow.append('div')\n\tbrush.rangeInput = new NumericRangeInput(brush.equation_div, range, () => {}, {\n\t\twidth: '125px',\n\t\tscaleFactor: getValueConversionFactor(tvs.term)\n\t})\n\n\t// for maf filter tvs, the term's mode determines which metric is filtered\n\tconst mafFilterMode = self.opts.isMafFilter ? tvs.term.mafFilterMode || 'maf' : null\n\tif (mafFilterMode == 'maf') {\n\t\t// maf filter tvs\n\t\t// render maf range input and min allelic depth input\n\t\trangeLabel.text('MAF Range (0-1)')\n\t\tconst depthRow = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('column-gap', '5px')\n\t\t\t.style('margin-top', '5px')\n\t\tdepthRow.append('span').text('Minimum Total Depth')\n\t\tbrush.depthInput = depthRow\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 1)\n\t\t\t.attr('step', 1)\n\t\t\t.style('width', '125px')\n\t\t\t.property('value', tvs.minAllelicDepth)\n\t\tbrush.apply_btn = addApplyButton(holder.append('div').style('margin-top', '10px'))\n\t} else if (mafFilterMode == 'totalDepth' || mafFilterMode == 'altDepth') {\n\t\t// allelic depth filter tvs; render an integer range input\n\t\trangeLabel.text(mafFilterMode == 'totalDepth' ? 'Total Depth' : 'Alt Allele Depth')\n\t\tbrush.apply_btn = addApplyButton(rangeRow)\n\t} else {\n\t\t// tvs is not part of maf filter\n\t\t// render range input\n\t\trangeLabel.text('Range')\n\t\tbrush.apply_btn = addApplyButton(rangeRow)\n\t}\n\n\tfunction addApplyButton(holder) {\n\t\treturn holder.append('button').text('Apply').on('click', clickApply)\n\t}\n\n\tfunction clickApply() {\n\t\tconst r = brush.rangeInput.getRange()\n\t\tif (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {\n\t\t\twindow.alert('Invalid range.')\n\t\t\treturn\n\t\t}\n\t\tconst new_tvs = { term: tvs.term, ranges: [r] }\n\t\tif (brush.depthInput) {\n\t\t\tconst minAllelicDepth = Number(brush.depthInput.property('value'))\n\t\t\tif (!Number.isFinite(minAllelicDepth)) {\n\t\t\t\twindow.alert('Minimum allelic depth must be a numeric value.')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tnew_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1)\n\t\t}\n\t\tself.dom.tip.hide()\n\t\tself.opts.callback(new_tvs)\n\t}\n}\n\nfunction addRangeTable(self) {\n\tconst brushes = self.num_obj.brushes\n\n\tconst range_divs = self.num_obj.range_table.selectAll('.range_div').data(brushes) //, d => brushes.indexOf(d))\n\n\trange_divs.exit().each(function () {\n\t\tselect(this).style('opacity', 1).transition().duration(100).style('opacity', 0).remove()\n\t})\n\n\trange_divs\n\t\t.enter()\n\t\t.append('tr')\n\t\t.attr('class', 'range_div')\n\t\t.style('white-space', 'nowrap')\n\t\t.style('padding', '2px')\n\t\t.transition()\n\t\t.duration(200)\n\t\t.each(function (brush, i) {\n\t\t\tenterRange(self, this, brush, i)\n\t\t})\n}\n\nfunction enterRange(self, tr, brush, i) {\n\tif (!brush.range_tr) brush.range_tr = select(tr)\n\tconst range_tr = brush.range_tr\n\tconst xscale = self.num_obj.xscale\n\n\trange_tr\n\t\t.append('td')\n\t\t.style('margin-left', '10px')\n\t\t.style('padding', '3px 10px')\n\t\t.style('font-size', '.9em')\n\t\t.text('Range ' + (i + 1) + ': ')\n\n\tbrush.equation_td = range_tr.append('td').style('width', '150px')\n\t// brush.range stays in the unit the term's values are stored in; only the <input> text is converted\n\tbrush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply, {\n\t\tscaleFactor: getValueConversionFactor(self.tvs.term)\n\t})\n\n\tmakeRangeButtons(self, brush)\n\t// note for empty range\n\tif (i == 0) {\n\t\tself.num_obj.range_table\n\t\t\t.append('tr')\n\t\t\t.attr('class', 'note_tr')\n\t\t\t.append('td')\n\t\t\t.attr('colspan', '3')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('margin-left', '20px')\n\t\t\t.style('font-style', 'italic')\n\t\t\t.style('color', '#888')\n\t\t\t.html('Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged.')\n\t}\n\n\t// A note showing there is also the option to type values to select range\n\tif (i == 0) {\n\t\tself.num_obj.range_table\n\t\t\t.append('tr')\n\t\t\t.attr('class', 'note_tr')\n\t\t\t.append('td')\n\t\t\t.attr('colspan', '3')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('margin-left', '20px')\n\t\t\t.style('font-style', 'italic')\n\t\t\t.style('color', '#888')\n\t\t\t.html(\n\t\t\t\t`Option 2: Type in values to select a range.${\n\t\t\t\t\tself.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.toUnit}.` : ''\n\t\t\t\t}`\n\t\t\t)\n\t}\n\n\tasync function apply(new_range) {\n\t\ttry {\n\t\t\tbrush.range = new_range\n\t\t\tconst minvalue = self.num_obj.density_data.min\n\t\t\tconst maxvalue = self.num_obj.density_data.max\n\n\t\t\tconst start =\n\t\t\t\tnew_range.value != undefined ? new_range.value : new_range.start != undefined ? new_range.start : minvalue\n\t\t\tconst stop =\n\t\t\t\tnew_range.value != undefined ? new_range.value : new_range.stop != undefined ? new_range.stop : maxvalue\n\t\t\tbrush.elem.call(brush.d3brush).call(brush.d3brush.move, [start, stop].map(xscale))\n\t\t} catch (e) {\n\t\t\twindow.alert(e)\n\t\t}\n\t}\n\n\tfunction makeRangeButtons(self, brush) {\n\t\tconst buttons_td = brush.range_tr.append('td')\n\t\tconst range = brush.range\n\n\t\t//'Apply' button\n\t\tbrush.apply_btn = buttons_td\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.text('Apply')\n\t\t\t.on('click', async () => {\n\t\t\t\tself.dom.tip.hide()\n\t\t\t\tconst new_range = brush.rangeInput.parseRange()\n\t\t\t\tconst new_tvs = JSON.parse(JSON.stringify(self.tvs))\n\t\t\t\tdelete new_tvs.groupset_label\n\t\t\t\t// merge overlapping ranges\n\t\t\t\tif (self.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self, new_range)\n\t\t\t\telse new_tvs.ranges[range.index] = new_range\n\t\t\t\ttry {\n\t\t\t\t\tvalidateNumericTvs(new_tvs)\n\t\t\t\t\tself.opts.callback(new_tvs)\n\t\t\t\t} catch (ex) {\n\t\t\t\t\talert(ex)\n\t\t\t\t}\n\t\t\t})\n\n\t\t//'Delete' button\n\t\tbuttons_td\n\t\t\t.append('button')\n\t\t\t.attr('class', 'sja_filter_tag_btn sjpp_delete_btn')\n\t\t\t.style('display', self.num_obj.ranges.length > 1 ? 'inline-block' : 'none')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('text-transform', 'uppercase')\n\t\t\t.text('Delete')\n\t\t\t.on('click', async () => {\n\t\t\t\tconst new_tvs = JSON.parse(JSON.stringify(self.tvs))\n\t\t\t\tnew_tvs.ranges.splice(range.index, 1)\n\t\t\t\tself.num_obj.ranges.pop()\n\t\t\t\tself.num_obj.brushes.pop()\n\t\t\t\tself.num_obj.num_div.select('.note_tr').remove()\n\t\t\t\taddBrushes(self)\n\t\t\t\taddRangeTable(self)\n\t\t\t\tif (new_tvs.ranges.length) self.opts.callback(new_tvs) //Remove the filter if no ranges\n\t\t\t})\n\t}\n}\n\nfunction mergeOverlapRanges(self, new_range) {\n\tlet ranges = JSON.parse(JSON.stringify(self.tvs.ranges))\n\tlet merged_flag = false\n\tfor (const [i, range] of ranges.entries()) {\n\t\t// skip unannotated categories and same range edits\n\t\tif (!range.value && new_range.index != i) {\n\t\t\tif (new_range.start <= range.start && new_range.stop >= range.stop) {\n\t\t\t\t// if new range is covering any existing range\n\t\t\t\trange.start = new_range.start\n\t\t\t\trange.stop = new_range.stop\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.start <= range.stop && new_range.stop >= range.stop) {\n\t\t\t\t// if overlapping only at start of new range\n\t\t\t\trange.stop = new_range.stop\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.stop >= range.start && new_range.start <= range.start) {\n\t\t\t\t// if overlapping only at end of new range\n\t\t\t\trange.start = new_range.start\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.start >= range.start && new_range.stop <= range.stop) {\n\t\t\t\t//new_range is covered by existing range\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.startunbounded) {\n\t\t\t\tif (new_range.stop > range.stop) {\n\t\t\t\t\t// if new_range is startunbounded and covering existing range\n\t\t\t\t\trange.stop = new_range.stop\n\t\t\t\t}\n\t\t\t\tdelete range.start\n\t\t\t\trange.startunbounded = true\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.stopunbounded) {\n\t\t\t\tif (new_range.start < range.start) {\n\t\t\t\t\t// if new_range is stopunbounded and covering existing range\n\t\t\t\t\trange.start = new_range.start\n\t\t\t\t}\n\t\t\t\tdelete range.stop\n\t\t\t\trange.stopunbounded = true\n\t\t\t\tmerged_flag = true\n\t\t\t}\n\t\t}\n\t}\n\n\tif (merged_flag) {\n\t\t// if overlapped and existing range merged then remove existing merged range\n\t\tif (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1)\n\t} else {\n\t\t//if not overlapped then add to ranges[]\n\t\tranges = JSON.parse(JSON.stringify(self.tvs.ranges))\n\t\tif (new_range.index) ranges[new_range.index] = new_range\n\t\telse ranges.push(new_range)\n\t}\n\treturn ranges\n}\n\nasync function showCheckList_numeric(self, tvs, div) {\n\tif (!tvs.term.values) {\n\t\t// no special categories available for this term\n\t\treturn\n\t}\n\t// numerical checkbox for unannotated cats\n\tconst values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter)\n\tconst unannotated_cats = []\n\tconst lst = values?.lst || values\n\tfor (const cat of lst) {\n\t\tconst key = 'key' in cat ? 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-  "names": ["holder", "self", "brush"]
-}

package/dist/chunk-TSI4W6XO.js

@@ -1,98 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-QJ3HYZH3.js";
-import {
-  require_debounce
-} from "./chunk-KV4W2ACA.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  dofetch,
-  dofetch3
-} from "./chunk-VMRO6DMC.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// src/gene.js
-var import_debounce = __toESM(require_debounce(), 1);
-var tip;
-function gene_searchbox(p) {
-  if (!tip) {
-    tip = new Menu({ padding: "" });
-    tip.d.style("z-index", 1e3);
-  }
-  const input = p.div.append("input").attr("placeholder", "Search gene").style("width", p.width || "100px");
-  const printdiv = p.resultdiv || (p.tip ? p.tip.d : tip.d);
-  function fold() {
-    if (p.resultdiv) {
-      p.resultdiv.selectAll("*").remove();
-    } else if (p.tip) {
-      p.tip.hide();
-    } else {
-      tip.hide();
-    }
-  }
-  input.on("keyup", (event) => {
-    const str = event.target.value;
-    if (str.length <= 1) {
-      fold();
-      return;
-    }
-    if (keyupEnter(event)) {
-      const hitgene = printdiv.select(".sja_menuoption");
-      if (hitgene.size() > 0) {
-        p.callback(hitgene.text());
-        fold();
-      }
-      return;
-    }
-    debouncer();
-  });
-  input.node().focus();
-  function genesearch() {
-    dofetch("genelookup", { genome: p.genome, input: input.property("value") }).then((data) => {
-      if (data.error) throw data.error;
-      if (!data.hits) throw ".hits[] missing";
-      if (p.resultdiv) {
-        p.resultdiv.selectAll("*").remove();
-      } else if (p.tip) {
-        p.tip.clear().showunder(input.node());
-      } else {
-        tip.clear().showunder(input.node());
-      }
-      for (const name of data.hits) {
-        printdiv.append("div").attr("class", "sja_menuoption").text(name).on("click", () => {
-          p.callback(name);
-          fold();
-        });
-      }
-    }).catch((err) => {
-      printdiv.append("div").text(err.message || err);
-      if (err.stack) console.log(err.stack);
-    });
-  }
-  const debouncer = (0, import_debounce.debounce)(genesearch, 300);
-}
-function findgenemodel_bysymbol(genome, str) {
-  return dofetch3("genelookup", {
-    body: {
-      deep: 1,
-      input: str,
-      genome
-    }
-  }).then((data) => {
-    if (data.error) throw data.error;
-    if (!data.gmlst || data.gmlst.length == 0) return null;
-    return data.gmlst;
-  }).catch((e) => {
-    throw e;
-  });
-}
-
-export {
-  gene_searchbox,
-  findgenemodel_bysymbol
-};
-//# sourceMappingURL=chunk-TSI4W6XO.js.map

package/dist/chunk-TXIQ5PHR.js

@@ -1,468 +0,0 @@
-import {
-  getDefaultScatterSettings
-} from "./chunk-WXX2YD4Q.js";
-import {
-  getDefaultViolinSettings
-} from "./chunk-KAY2ODXX.js";
-import {
-  getDefaultBoxplotSettings
-} from "./chunk-HKSRIEWJ.js";
-import {
-  PlotBase,
-  Tabs,
-  defaultUiLabels,
-  fillTermWrapper,
-  filterRxCompInit,
-  getCurrentCohortChartTypes,
-  getDefaultBarSettings,
-  getDefaultFractionBins,
-  getT0T2defaultQ
-} from "./chunk-QJ3HYZH3.js";
-import {
-  importPlot
-} from "./chunk-DMWOK4DS.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  isNumericTw
-} from "./chunk-GMRIEUBW.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-
-// plots/summary.ts
-var SummaryPlot = class _SummaryPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    // expected class-specific props
-    this.chartsByType = {};
-    this.configTermKeys = ["term", "term0", "term2"];
-    this.type = _SummaryPlot.type;
-    this.dom = this.getDom(opts);
-    this.tabsData = this.getTabsData();
-    this.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true });
-    this.components = {
-      plots: {}
-    };
-  }
-  static {
-    this.type = "summary";
-  }
-  preApiFreeze(api) {
-    api.getError = () => {
-      return this.error;
-    };
-  }
-  getDom(opts) {
-    const holder = opts.holder;
-    holder.header.style("padding", 0);
-    const paneTitleDiv = holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px");
-    return {
-      tip: new Menu({ padding: "0px" }),
-      holder,
-      body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-      // will hold no data notice or the page title in multichart views
-      errdiv: holder.body.append("div").attr("class", "sja_errorbar").style("display", "none").style("padding", "5px"),
-      loading: holder.body.append("div").style("display", "none").style("padding", "5px").html("Loading ..."),
-      // dom.viz will hold the rendered view
-      viz: holder.body.append("div"),
-      plotDivs: {},
-      paneTitleDiv,
-      paneTitleText: paneTitleDiv.append("div").classed("sjpp-term-header", true).style("display", "inline-block").style("vertical-align", "sub"),
-      chartToggles: paneTitleDiv.append("div").style("display", "inline-block").style("margin-left", "10px"),
-      localRecoverDiv: paneTitleDiv.append("div").style("display", "inline-block"),
-      filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9)
-    };
-  }
-  getTabsData() {
-    const callback = (event, tab) => this.tabClickCallback(event, tab);
-    return [
-      {
-        childType: "barchart",
-        label: "Barchart",
-        isVisible: () => true,
-        disabled: () => false,
-        getConfig: async () => {
-          if (!this.config) return;
-          const config = { id: this.id, childType: "barchart" };
-          const { term, term2 } = this.config || {};
-          if (term) {
-            const mode = isNumericTw(term) ? "discrete" : term?.q.mode || "discrete";
-            config.term = await this.getWrappedTermCopy(term, mode);
-          }
-          if (term2) {
-            const mode = isNumericTw(term2) ? "discrete" : term2.q.mode || "discrete";
-            config.term2 = await this.getWrappedTermCopy(term2, mode);
-          }
-          return config;
-        },
-        active: true,
-        callback
-      },
-      {
-        childType: "violin",
-        label: "Violin",
-        disabled: () => false,
-        isVisible: () => isNumericTw(this.config?.term) || isNumericTw(this.config?.term2),
-        getConfig: async () => {
-          const term = this.config?.term;
-          const term2 = this.config.term2;
-          let _term, _term2;
-          this.violinContTerm = isNumericTw(term) ? "term" : "term2";
-          if (this.violinContTerm && this.violinContTerm === "term" || term.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          } else if (this.violinContTerm && this.violinContTerm === "term2" || term2?.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else if (term2?.q?.mode == "discrete") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          }
-          const config = { childType: "violin", term: _term, term2: _term2 };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "boxplot",
-        label: "Boxplot",
-        disabled: () => false,
-        isVisible: () => isNumericTw(this.config?.term) || isNumericTw(this.config?.term2),
-        getConfig: async () => {
-          const _term = this.config?.term;
-          const _term2 = this.config.term2;
-          let termMode = "continuous", term2Mode = "discrete";
-          this.boxContTerm = isNumericTw(_term) ? "term" : "term2";
-          if (this.boxContTerm && this.boxContTerm === "term" || _term.q?.mode == "continuous") {
-            termMode = "continuous";
-            term2Mode = "discrete";
-            this.boxContTerm = "term";
-          } else if (this.boxContTerm && this.boxContTerm === "term2" || _term2?.q?.mode == "continuous") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          } else if (_term2?.q?.mode == "discrete") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          }
-          const term = await this.getWrappedTermCopy(_term, termMode);
-          const term2 = await this.getWrappedTermCopy(_term2, term2Mode);
-          const config = {
-            childType: "boxplot",
-            term,
-            term2
-          };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "sampleScatter",
-        label: "Scatter",
-        disabled: () => false,
-        isVisible: () => isScatterToggleVisible(this.app.getState(), this.config?.term, this.config?.term2),
-        getConfig: async () => {
-          const _term = await this.getWrappedTermCopy(this.config?.term, "continuous");
-          const _term2 = await this.getWrappedTermCopy(this.config?.term2, "continuous");
-          const config = {
-            childType: "sampleScatter",
-            term: _term,
-            term2: _term2,
-            groups: [],
-            term0: this.config.term0
-          };
-          return config;
-        },
-        active: false,
-        callback
-      }
-    ];
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.initUi(this.opts, config);
-    if (config?.hidePlotFilter) return;
-    this.components.filter = await filterRxCompInit({
-      app: this.app,
-      vocabApi: this.app.vocabApi,
-      parentId: this.id,
-      holder: this.dom.filterDiv,
-      hideLabel: true,
-      emptyLabel: "+Add new filter",
-      callback: (filter) => {
-        this.app.dispatch({
-          id: this.id,
-          type: "plot_edit",
-          config: { filter }
-        });
-      }
-    });
-  }
-  reactsTo(action) {
-    if (action.type.startsWith("plot_")) {
-      if (action.type.startsWith("plot_")) {
-        return action.id === this.id || action.id == this.parentId;
-      }
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    return false;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    delete this.error;
-    this.dom.errdiv.style("display", "none").html("");
-    this.dom.loading.style("display", "");
-    this.config = await this.getMutableConfig();
-    this.maySetSandboxHeader();
-    if (!this.components.plots[this.config.childType]) {
-      await this.setComponent(this.config);
-    }
-    this.dom.loading.style("display", "none");
-    this.render();
-    const activeTabIndex = this.tabsData.findIndex((tab) => tab.childType == this.config.childType);
-    this.chartToggles.update(activeTabIndex);
-    const numVisTabs = this.tabsData.filter((d) => d.isVisible()).length;
-    if (numVisTabs > 1) this.dom.chartToggles.style("display", "inline-block");
-    else this.dom.chartToggles.style("display", "none");
-  }
-  maySetSandboxHeader() {
-    const { term, term2, headerText, assayCohortTitle } = this.config;
-    const mainTerm = term.getTitleText?.() || term.term.name;
-    const _headerPretext = headerText ? `${headerText} ` : "";
-    const _headerSuffix = assayCohortTitle ? ` (${assayCohortTitle})` : "";
-    const titleBase = mainTerm + _headerSuffix;
-    if (term2?.type) {
-      this.dom.paneTitleText.html(`${_headerPretext}${term2.getTitleText?.() || term2.term.name} vs ${titleBase}`);
-    } else {
-      this.dom.paneTitleText.html(`${_headerPretext}${titleBase}`);
-    }
-  }
-  async setComponent(config) {
-    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
-    this.dom.plotDivs[config.childType] = this.dom.viz.append("div");
-    const componentOpts = {
-      app: this.app,
-      holder: this.dom.plotDivs[config.childType],
-      id: this.id,
-      parent: this.api
-    };
-    if (config.parentId) componentOpts.parentId = config.parentId;
-    this.components.plots[config.childType] = await _.componentInit(componentOpts);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-  initUi(opts, config) {
-    this.dom.paneTitleText.html(config.term.term.name);
-    this.chartToggles.main();
-  }
-  async tabClickCallback(event, tab) {
-    if (!tab || !tab.getConfig) return;
-    let config;
-    try {
-      this.dom.viz.style("display", "none");
-      this.dom.loading.style("display", "");
-      config = await tab.getConfig();
-      this.dom.loading.style("display", "none");
-      this.dom.viz.style("display", "");
-      if (config)
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config
-        });
-    } catch (e) {
-      this.dom.loading.style("display", "none");
-      this.error = e;
-      this.dom.errdiv.style("display", "").html(`Error: ${e.message || e.error || e}`);
-    }
-  }
-  async getWrappedTermCopy(term, mode) {
-    if (!term) return;
-    const tw = structuredClone(term);
-    tw.q.mode = mode;
-    if (tw.type === "TermCollectionTWFraction") {
-      if (mode === "discrete" && tw.q.type !== "regular-bin" && tw.q.type !== "custom-bin") {
-        tw.q = {
-          mode: "discrete",
-          type: "custom-bin",
-          lst: getDefaultFractionBins(),
-          denominators: tw.q.denominators,
-          numerators: tw.q.numerators
-        };
-      } else if (mode === "continuous") {
-        tw.q = {
-          mode: "continuous",
-          denominators: tw.q.denominators,
-          numerators: tw.q.numerators
-        };
-      }
-    }
-    await fillTermWrapper(tw, this.app.vocabApi);
-    return tw;
-  }
-  render() {
-    for (const childType of Object.keys(this.components.plots)) {
-      const chart = this.components.plots[childType];
-      if (chart.type != this.config.childType) {
-        this.dom.plotDivs[chart.type].style("display", "none");
-      }
-    }
-    this.dom.plotDivs[this.config.childType].style("display", "");
-  }
-  getChartImages() {
-    const chart = this.components.plots[this.config.childType];
-    if (chart?.getChartImages) {
-      return chart.getChartImages();
-    }
-    return null;
-  }
-};
-var summaryInit = getCompInit(SummaryPlot);
-var componentInit = summaryInit;
-async function getPlotConfig(opts, app) {
-  try {
-    await app.opts?.getPlotConfig_mutateSummary?.(opts);
-    if (!opts.term) throw new Error("summary getPlotConfig: opts.term{} missing");
-    opts.term = await fillTermWrapper(
-      opts.term,
-      app.vocabApi,
-      opts.term.q || { geneVariant: { type: "predefined-groupset" } }
-    );
-    if (opts.term2)
-      opts.term2 = await fillTermWrapper(
-        opts.term2,
-        app.vocabApi,
-        opts.term2.bins || opts.term2.q ? void 0 : getT0T2defaultQ()
-      );
-    if (opts.term0)
-      opts.term0 = await fillTermWrapper(
-        opts.term0,
-        app.vocabApi,
-        opts.term0.bins || opts.term0.q ? void 0 : getT0T2defaultQ()
-      );
-    if (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi);
-    if (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi);
-    if (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi);
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    throw new Error(`${e} [summary getPlotConfig()]`);
-  }
-  const config = {
-    chartType: "summary",
-    childType: "barchart",
-    term: opts.term,
-    groups: [],
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    //Allow hiding the plot filter when appropriate (e.g. single cell summary plots)
-    hidePlotFilter: opts.hidePlotFilter || false,
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      common: {
-        use_logscale: false,
-        // flag for y-axis scale type, 0=linear, 1=log
-        use_percentage: false
-        // Move to barchart settings
-        // barheight: 300, // maximum bar length
-        // barwidth: 20, // bar thickness
-        // barspace: 2 // space between two bars
-      },
-      barchart: getDefaultBarSettings(app),
-      violin: getDefaultViolinSettings(app),
-      boxplot: getDefaultBoxplotSettings(app),
-      sampleScatter: getDefaultScatterSettings(opts)
-    },
-    mayAdjustConfig(config2, edits = {}) {
-      return mayAdjustConfig(config2, opts, edits);
-    }
-  };
-  if (config.term.term.type == "geneVariant") config.settings.barchart.colorBars = true;
-  copyMerge(config, opts);
-  Object.assign(config.controlLabels, app.vocabApi.termdbConfig.uiLabels || {});
-  return config;
-}
-function isScatterToggleVisible(appState, term, term2) {
-  const isSupportedChart = getCurrentCohortChartTypes(appState).includes("dynamicScatter");
-  return isSupportedChart && isNumericTw(term) && isNumericTw(term2);
-}
-var discreteByContinuousPlots = /* @__PURE__ */ new Set(["violin", "boxplot"]);
-function mayAdjustConfig(config, opts, edits = {}) {
-  if (edits.childType) {
-    if (config.childType != edits.childType) throw `action.config.childType was not applied in mass store.plot_edit()`;
-    return;
-  }
-  if (config.term?.q?.mode == "continuous" && config.term2?.q?.mode == "continuous") {
-    config.childType = "sampleScatter";
-  } else if (config.term?.term?.type == "termCollection" && config.term?.type !== "TermCollectionTWFraction") {
-    if (config.term.term.memberType == "categorical") {
-      config.childType = "barchart";
-    } else if (config.term.term.memberType == "numeric") {
-      if (config.childType) {
-        if (config.childType == "barchart") {
-          config.childType = "violin";
-        } else {
-        }
-      } else {
-        config.childType = "violin";
-      }
-    } else {
-      throw new Error("config.term.term.memberType not categorical or numeric");
-    }
-  } else if (config.term?.q?.mode == "continuous" || config.term2?.q?.mode == "continuous") {
-    if (!discreteByContinuousPlots.has(config.childType)) {
-      if (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {
-        console.warn(
-          `ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`
-        );
-        config.childType = "violin";
-      } else {
-        config.childType = opts.childType || "violin";
-      }
-    }
-  } else {
-    config.childType = "barchart";
-  }
-}
-
-export {
-  summaryInit,
-  componentInit,
-  getPlotConfig,
-  isScatterToggleVisible,
-  mayAdjustConfig
-};
-//# sourceMappingURL=chunk-TXIQ5PHR.js.map