@sjcrh/proteinpaint-client 2.170.13 → 2.170.16

package/dist/chunk-VC3CXZ4O.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 } 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.getViolinPlotData == 'function') {\n\t\ttry {\n\t\t\tconst data = await self.opts.vocabApi.getViolinPlotData(\n\t\t\t\t{\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) throw `no available data`\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})\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\t// addRangeTable(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\tconst num_div = self.num_obj.num_div\n\tnum_div.selectAll('*').remove()\n\tnum_div.append('div').style('padding', '5px').style('font-weight', 600).html(tvs.term.name)\n\n\tconst brush = {}\n\tconst table = num_div.append('table')\n\tconst tr = table.append('tr')\n\ttr.append('td').html('Range')\n\tbrush.equation_td = tr.append('td')\n\n\trange.min = 'min' in tvs.term ? tvs.term.min : null\n\trange.max = 'max' in tvs.term ? tvs.term.max : null\n\tbrush.rangeInput = new NumericRangeInput(brush.equation_td, range, applyRange)\n\n\tbrush.apply_btn = tr\n\t\t.append('td')\n\t\t.attr('class', 'sja_filter_tag_btn sjpp_apply_btn')\n\t\t.style('border-radius', '13px')\n\t\t.style('margin', '5px')\n\t\t.style('margin-left', '10px')\n\t\t.style('text-align', 'center')\n\t\t.style('font-size', '.8em')\n\t\t.style('text-transform', 'uppercase')\n\t\t.text('apply')\n\t\t.on('click', async () => {\n\t\t\tbrush.rangeInput.parseRange()\n\t\t})\n\n\tfunction applyRange() {\n\t\tself.dom.tip.hide()\n\t\tself.opts.callback({ term: tvs.term, ranges: [brush.rangeInput.getRange()] })\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.append('td')\n\t\t.style('display', 'inline-block')\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\tbrush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply)\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.fromUnit}.` : ''\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('td')\n\t\t\t.attr('class', 'sja_filter_tag_btn sjpp_apply_btn')\n\t\t\t.style('border-radius', '13px')\n\t\t\t.style('margin', '5px')\n\t\t\t.style('margin-left', '10px')\n\t\t\t// .style('padding', '5px 12px')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('text-transform', 'uppercase')\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('td')\n\t\t\t.attr('class', 'sja_filter_tag_btn sjpp_delete_btn')\n\t\t\t.style('border-radius', '13px')\n\t\t\t.style('display', self.num_obj.ranges.length > 1 ? 'inline-block' : 'none')\n\t\t\t.style('margin', '5px')\n\t\t\t.style('margin-left', '10px')\n\t\t\t// .style('padding', '5px 12px')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('font-size', '.8em')\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 ? cat.key : cat.value\n\t\tif (!('key' in cat)) cat.key = key\n\t\tif (!('value' in cat)) cat.value = key\n\t\tif (key in tvs.term.values) {\n\t\t\tcat.label = tvs.term.values[key].label\n\t\t\tunannotated_cats.push(cat)\n\t\t}\n\t}\n\n\tconst sortedVals = unannotated_cats.sort((a, b) => {\n\t\treturn b.samplecount - a.samplecount\n\t})\n\n\t// other categories div\t(only appear if unannotated categories present)\n\tconst unanno_div = div.append('div').style('padding', '5px').style('color', '#000')\n\n\t// 'Apply' button\n\tconst callback = indexes => {\n\t\t//update term values by ckeckbox values\n\t\ttry {\n\t\t\tconst new_tvs = JSON.parse(JSON.stringify(tvs))\n\t\t\tdelete new_tvs.groupset_label\n\t\t\tnew_tvs.ranges = [\n\t\t\t\t...new_tvs.ranges.filter(r => !('value' in r)),\n\t\t\t\t...indexes.map(i => ({ value: sortedVals[i].value, label: sortedVals[i].label }))\n\t\t\t]\n\t\t\tself.dom.tip.hide()\n\t\t\tif (new_tvs.ranges.length == 0) throw 'select at least one range or category'\n\t\t\t//callback only if tvs is changed\n\t\t\tif (JSON.parse(JSON.stringify(tvs) != new_tvs)) {\n\t\t\t\ttry {\n\t\t\t\t\tvalidateNumericTvs(new_tvs)\n\t\t\t\t} catch (e) {\n\t\t\t\t\twindow.alert(e)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tself.opts.callback(new_tvs)\n\t\t\t}\n\t\t} catch (e) {\n\t\t\twindow.alert(e)\n\t\t}\n\t}\n\n\tconst values_table = self.makeValueTable(unanno_div, tvs, sortedVals, callback).node()\n}\n\nfunction validateNumericTvs(tvs) {\n\tif (!tvs.term) throw 'tvs.term is not defined'\n\tif (!tvs.ranges) throw `.values[] missing for a term ${tvs.term.name}`\n\tif (!Array.isArray(tvs.ranges)) throw `.values[] is not an array for a term ${tvs.term.name}`\n\tif (!tvs.ranges.length) throw `no categories selected for ${tvs.term.name}`\n\tfor (const range of tvs.ranges) {\n\t\tif (range.value != undefined) {\n\t\t\t// a special category, not a value from numerical range\n\t\t\tif (!range.label) throw `.label missing for special category for a term ${tvs.term.name}`\n\t\t} else {\n\t\t\t// a regular range\n\t\t\tif (range.startunbounded) {\n\t\t\t\tif (range.stopunbounded) throw `both start & stop are unbounded for a term ${tvs.term.name}`\n\t\t\t\tif (!Number.isFinite(range.stop)) throw `.stop undefined when start is unbounded for a term ${tvs.term.name}`\n\t\t\t} else if (range.stopunbounded) {\n\t\t\t\tif (!Number.isFinite(range.start)) throw `.start undefined when stop is unbounded for a term ${tvs.term.name}`\n\t\t\t} else {\n\t\t\t\tif (!Number.isFinite(range.start))\n\t\t\t\t\tthrow `.start undefined when start is not unbounded for a term ${tvs.term.name}`\n\t\t\t\tif (!Number.isFinite(range.stop)) throw `.stop undefined when stop is not unbounded for a term ${tvs.term.name}`\n\t\t\t\tif (range.start >= range.stop) throw `.start is not lower than stop for a term ${tvs.term.name}`\n\t\t\t}\n\t\t}\n\t}\n}\n"],
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-  "names": ["self", "brush"]
-}

package/dist/chunk-VCZZ6N2C.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/violin.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge } from '../rx'\nimport { controlsInit, term0_term2_defaultQ, renderTerm1Label } from './controls'\nimport setViolinRenderer from './violin.renderer'\n//import htmlLegend from '../dom/html.legend'\nimport { htmlLegend, Menu } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\nimport { setInteractivity } from './violin.interactivity'\nimport { plotColor } from '#shared/common.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\n\n/*\nwhen opts.mode = 'minimal', a minimal violin plot will be rendered that will have a single term and minimal features (i.e. no controls, legend, labels, brushing, transitions, etc.)\n\nTODO default to unit=log if term enables\n*/\n\nclass ViolinPlot extends PlotBase {\n\tstatic type = 'violin'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = 'violin'\n\t}\n\n\tasync init(appState) {\n\t\tconst controls = this.opts.holder.append('div').attr('class', 'sjpp-plot-controls').style('display', 'inline-block')\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\n\t\tconst holder = this.opts.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', this.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t.style('padding-left', this.opts.mode != 'minimal' ? '20px' : '0px')\n\t\t\t.attr('id', 'sjpp-vp-holder')\n\n\t\tthis.dom = {\n\t\t\thovertip: new Menu({ padding: '3px' }), // separate tips for hover & click on violin labels to avoid interfering\n\t\t\tclicktip: new Menu({ padding: '0px' }),\n\t\t\tsampletabletip: new Menu({ padding: '3px' }), // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..\n\t\t\theader: this.opts.header,\n\t\t\tcontrols,\n\t\t\tbanner: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.style('font-size', '16px'),\n\t\t\tloadingDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', this.opts.mode != 'minimal' ? 'inline-block' : 'none')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.text('Loading ...'),\n\t\t\tviolinDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-vp-violinDiv')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('flex-direction', 'row')\n\t\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t\t.style('max-width', '100vw'),\n\t\t\tlegendDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sjpp-vp-legend', true)\n\t\t\t\t.style('margin-left', '-15px')\n\t\t\t\t.style('padding-top', '20px')\n\t\t}\n\n\t\tsetViolinRenderer(this)\n\t\tsetInteractivity(this)\n\n\t\tif (this.opts.mode != 'minimal') {\n\t\t\tthis.legendRenderer = htmlLegend(this.dom.legendDiv, {\n\t\t\t\tsettings: {\n\t\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t\t},\n\t\t\t\thandlers: {}\n\t\t\t})\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t\treturn true\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\n\t\tapi.getChartImages = () => this.getChartImages()\n\t}\n\n\tasync setControls() {\n\t\t// do not replace this.components.controls on every re-render,\n\t\t// that could lead to missing control.state if there are errors\n\t\t// with config.terms filling, etc. Better to set getDisplayStyle()\n\t\t// option for an input that doesn't have to be rendered for a given\n\t\t// term/term2/term0 combination.\n\t\tif (this.components.controls) return\n\t\tthis.dom.controls.selectAll('*').remove()\n\t\tconst controlLabels = this.state.config.controlLabels\n\t\tif (!controlLabels) throw 'controls labels not found'\n\t\tthis.components = {}\n\t\tif (this.opts.mode == 'minimal') return\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term' },\n\t\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tmenuOptions: 'edit'\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term2',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term2' },\n\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term0',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term0' },\n\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Orientation',\n\t\t\t\ttitle: 'Orientation of the chart',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orientation',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Data symbol',\n\t\t\t\ttitle: 'Symbol type',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'datasymbol',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Ticks', value: 'rug' },\n\t\t\t\t\t{ label: 'Circles', value: 'bean' },\n\t\t\t\t\t{ label: 'Off', value: 'none' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Scale',\n\t\t\t\ttitle: 'Axis scale',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'unit',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Linear', value: 'abs' },\n\t\t\t\t\t{ label: 'Log10', value: 'log' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Order by',\n\t\t\t\ttitle: 'Order violin plots by parameters',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orderByMedian',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Default', value: false },\n\t\t\t\t\t{ label: 'Median', value: true }\n\t\t\t\t],\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\tlet style = 'none'\n\t\t\t\t\tconst charts = this.data?.charts || {}\n\t\t\t\t\tfor (const k of Object.keys(charts)) {\n\t\t\t\t\t\tconst chart = charts[k]\n\t\t\t\t\t\tif (chart?.plots.length > 1) style = ''\n\t\t\t\t\t}\n\t\t\t\t\treturn style\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Symbol size',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'radius',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 30,\n\t\t\t\tmin: 4\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Bins',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'ticks',\n\t\t\t\ttitle: 'Number of bins used to build the plot',\n\t\t\t\tmin: 1,\n\t\t\t\tmax: 50\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot length',\n\t\t\t\ttitle: 'Length of the plot',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 1000,\n\t\t\t\tmin: 200,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot thickness',\n\t\t\t\ttitle: 'If not specified, the plot thickness is calculated based on the number of categories',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'plotThickness',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 200,\n\t\t\t\tmin: 20,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot padding',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'rowSpace',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 20,\n\t\t\t\tmin: 0,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median length',\n\t\t\t\ttitle: 'Length of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianLength',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 50,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median color',\n\t\t\t\ttitle: 'color of median',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median thickness',\n\t\t\t\ttitle: 'Width of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianThickness',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 10,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 100\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Default violin color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show stats',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showStats',\n\t\t\t\tboxLabel: 'Yes'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show association tests',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showAssociationTests',\n\t\t\t\tboxLabel: 'Yes',\n\t\t\t\tgetDisplayStyle: plot => (plot.term2 ? 'table-row' : 'none')\n\t\t\t}\n\t\t]\n\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.controls,\n\t\t\tinputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.violin', this.download)\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermfilter,\n\t\t\tconfig,\n\t\t\tdisplaySampleIds: appState.termdbConfig.displaySampleIds,\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken()\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config)\n\t\tthis.settings = this.config.settings.violin\n\t\tawait this.setControls()\n\n\t\tif (this.config.chartType != this.type && this.config.childType != this.type) return\n\t\tif (this.dom.header)\n\t\t\tthis.dom.header.html(\n\t\t\t\tthis.config.term.term.name + ` <span style=\"opacity:.6;font-size:1em;margin-left:10px;\">Violin Plot</span>`\n\t\t\t)\n\n\t\t//Fix for rm'ing error message when plot re-renders\n\t\t//Leave in main() so the message doesn't linger whilst\n\t\t//the plot is rendering\n\t\tconst existingMsg = this.dom.banner.style('display', 'none').select('span')\n\t\tif (!existingMsg.empty()) existingMsg.remove()\n\n\t\tconst args = this.validateArgs()\n\t\tlet data\n\t\ttry {\n\t\t\tthis.toggleLoadingDiv()\n\t\t\tdata = await this.app.vocabApi.getViolinPlotData(args, null, this.api.getAbortSignal())\n\t\t} catch (e) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthrow e\n\t\t}\n\n\t\tthis.data = data\n\t\tif (this.data.error) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthrow this.data.error\n\t\t}\n\t\targs.tw.q.descrStats = this.data.descrStats\n\n\t\tthis.toggleLoadingDiv(this.opts.mode == 'minimal' ? 'none' : '')\n\t\tsetTimeout(\n\t\t\t() => {\n\t\t\t\tthis.render()\n\t\t\t},\n\t\t\tthis.opts.mode == 'minimal' ? 0 : 500\n\t\t)\n\t\tthis.toggleLoadingDiv('none')\n\t}\n\n\tvalidateArgs() {\n\t\tconst { term, term2, term0, settings } = this.config\n\t\tconst s = this.settings\n\t\tconst arg = {\n\t\t\tsvgw: s.svgw,\n\t\t\torientation: s.orientation,\n\t\t\tdevicePixelRatio: window.devicePixelRatio,\n\t\t\tdatasymbol: s.datasymbol,\n\t\t\tradius: s.radius,\n\t\t\taxisHeight: s.axisHeight,\n\t\t\trightMargin: s.rightMargin,\n\t\t\tunit: s.unit,\n\t\t\tticks: s.ticks,\n\t\t\torderByMedian: s.orderByMedian,\n\t\t\tfilter: this.state.termfilter.filter\n\t\t}\n\n\t\tif (this.opts.mode == 'minimal') {\n\t\t\targ.tw = term\n\t\t\t// assume a single term for minimal plot\n\t\t\tif (term2 || term0) throw 'only a single term allowed for minimal plot'\n\t\t\tif (term.q.mode == 'spline') {\n\t\t\t\t/** FIXME bad design; should not modify setting or even plot state in runtime, \n\t\t\t\tinstead supply this in constructor arg and generalize it beyond spline\n\t\t\t\t// term may be cubic spline from regression analysis\n\t\t\t\t// render knot values as vertical lines on the plot\n\t\t\t\t*/\n\t\t\t\ts.lines = term.q.knots.map(x => Number(x.value))\n\t\t\t} else {\n\t\t\t\ts.lines = []\n\t\t\t}\n\t\t\tif (term.q.scale) {\n\t\t\t\t// term may be scaled from regression analysis\n\t\t\t\t// scale the data on the server-side\n\t\t\t\targ.scale = term.q.scale\n\t\t\t}\n\t\t} else if (isNumericTerm(term.term) && term.q.mode === 'continuous') {\n\t\t\targ.tw = term\n\t\t\tif (term2) arg.overlayTw = term2\n\t\t} else if (isNumericTerm(term2?.term) && term2.q.mode === 'continuous') {\n\t\t\targ.tw = term2\n\t\t\targ.overlayTw = term\n\t\t} else {\n\t\t\tthrow 'both term1 and term2 are not numeric/continuous'\n\t\t}\n\n\t\tif (term0) arg.divideTw = term0\n\t\treturn arg\n\t}\n}\n\nexport const violinInit = getCompInit(ViolinPlot)\nexport const componentInit = violinInit\n\nexport function getDefaultViolinSettings(app, overrides = {}) {\n\tconst defaults = {\n\t\torientation: 'horizontal',\n\t\trowlabelw: 250,\n\t\tbrushRange: null, //object with start and end if there is a brush selection\n\t\tsvgw: 500, // span length of a plot/svg, not including margin\n\t\tdatasymbol: 'rug',\n\t\tradius: 10,\n\t\taxisHeight: 60,\n\t\trightMargin: 50,\n\t\tlines: [],\n\t\tunit: 'abs', // abs: absolute scale, log: log scale\n\t\trowSpace: 10,\n\t\tmedianLength: 7,\n\t\tmedianColor: '#FF0000',\n\t\tmedianThickness: 3,\n\t\tticks: 15,\n\t\tdefaultColor: plotColor,\n\t\tmethod: 0,\n\t\torderByMedian: false,\n\t\tshowStats: true,\n\t\tshowAssociationTests: true\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'violin getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tthrow `${e} [violin getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\t// common: {\n\t\t\t// \tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t// \tuse_percentage: false,\n\t\t\t// \tbarheight: 300, // maximum bar length\n\t\t\t// \tbarwidth: 20, // bar thickness\n\t\t\t// \tbarspace: 2 // space between two bars\n\t\t\t// },\n\t\t\tviolin: getDefaultViolinSettings(app)\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n"],
-  "mappings": 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package/dist/importPlot-LCTQOZHQ.js

@@ -1,8 +0,0 @@
-import {
-  importPlot
-} from "./chunk-BUQ7S2O2.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  importPlot
-};
-//# sourceMappingURL=importPlot-LCTQOZHQ.js.map