@sjcrh/proteinpaint-client 2.170.13 → 2.170.16

package/dist/{chunk-VMVBUU63.js → chunk-PDD65V7Q.js}

@@ -3,7 +3,7 @@ import {
   fillTermWrapper,
   table2col,
   termsettingInit
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 
 // plots/summarizeMutationDiagnosis.ts
 async function makeChartBtnMenu(holder, chartsInstance) {
@@ -97,4 +97,4 @@ export {
   makeChartBtnMenu,
   launchPlot
 };
-//# sourceMappingURL=chunk-VMVBUU63.js.map
+//# sourceMappingURL=chunk-PDD65V7Q.js.map

package/dist/{chunk-MW5SFVPY.js → chunk-PYXTLYHY.js}

@@ -1,10 +1,10 @@
 import {
   renderTable
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   clusterMethodLst,
   distanceMethodLst
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   NUMERIC_DICTIONARY_TERM,
   TermTypes
@@ -479,4 +479,4 @@ export {
   setClusteringBtn,
   hierCluster_interactivity_exports
 };
-//# sourceMappingURL=chunk-MW5SFVPY.js.map
+//# sourceMappingURL=chunk-PYXTLYHY.js.map

package/dist/{chunk-BJANTR6U.js → chunk-Q3XAAYDT.js}

@@ -1,9 +1,9 @@
 import {
   legend_newrow
-} from "./chunk-FYJDO2WJ.js";
+} from "./chunk-EAZI7WHA.js";
 import {
   showLDlegend
-} from "./chunk-PWNZL5IJ.js";
+} from "./chunk-RKNGKVSF.js";
 import {
   rehydrateFilter
 } from "./chunk-SKMFMGCD.js";
@@ -26,7 +26,7 @@ import {
   shapes,
   table2col,
   to_textfile
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   genomic2gm
 } from "./chunk-HJ6L54YS.js";
@@ -38,7 +38,7 @@ import {
   guessSsmid,
   ssmIdFieldsSeparator,
   summarize_mclass
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   bplen,
   dt2label,
@@ -421,7 +421,7 @@ async function makeSvgraph(m, div, block) {
     await getGm(svpair.a, block, m.pairlst[0].a.name);
     await getGm(svpair.b, block, m.pairlst[0].b.name);
     wait.remove();
-    const _ = await import("./svgraph-EV7XM3VZ.js");
+    const _ = await import("./svgraph-2IJMZU2M.js");
     _.default({
       pairlst: [svpair],
       genome: block.genome,
@@ -543,7 +543,7 @@ async function displaySampleTable(samples, args) {
         callback: async (event2, i) => {
           const sandbox = newSandboxDiv(args.tk.newChartHolder || args.block.holder0);
           sandbox.header.text(samples[i].sample_id);
-          await (await import("./plot.ssgq-LIEYVBR6.js")).plotSingleSampleGenomeQuantification(
+          await (await import("./plot.ssgq-K5WT5SRR.js")).plotSingleSampleGenomeQuantification(
             args.tk.mds,
             args.tk.mds.label,
             k,
@@ -680,7 +680,7 @@ function printSampleName(sample, tk, div, block, thisMutation) {
       extraRow.append("button").text(k).on("click", async () => {
         const sandbox = newSandboxDiv(tk.newChartHolder || block.holder0);
         sandbox.header.text(sample.sample_id);
-        await (await import("./plot.ssgq-LIEYVBR6.js")).plotSingleSampleGenomeQuantification(
+        await (await import("./plot.ssgq-K5WT5SRR.js")).plotSingleSampleGenomeQuantification(
           tk.mds,
           tk.mds.label,
           k,
@@ -711,7 +711,7 @@ async function createDiscoInSandbox(tk, block, sample, thisMutation) {
   sandbox.header.text(headerTexts.join(""));
   try {
     ;
-    (await import("./plot.disco-BOW777AK.js")).default(
+    (await import("./plot.disco-DY6FSDYY.js")).default(
       tk.mds.termdbConfig,
       tk.mds.label,
       sample,
@@ -1006,7 +1006,7 @@ async function click2sunburst(d, tk, block, tippos) {
       arg.chartlabel = d.mlst.reduce((i, j) => j.occurrence > i.occurrence ? j : i).mname + " etc";
     }
   }
-  const _ = await import("./sunburst-DRZZYAUH.js");
+  const _ = await import("./sunburst-Z5XCA3RM.js");
   _.default(arg);
 }
 function dataGood4sunburst(data) {
@@ -1824,7 +1824,7 @@ async function make_leftlabels(data, tk, block) {
     laby += labyspace + block.labelfontsize;
   }
   if ("sampleTotalNumber" in data || tk.leftlabels.doms.samples) {
-    const _ = await import("./leftlabel.sample-SUXEIOQ2.js");
+    const _ = await import("./leftlabel.sample-XBOIEYD7.js");
     _.makeSampleLabel(data, tk, block, laby);
     laby += labyspace + block.labelfontsize;
     if (tk.filterObj) {
@@ -4106,7 +4106,7 @@ async function mayInitTermdb(tk, block) {
     } else {
       throw "do not know how to init vocab";
     }
-    const _ = await import("./vocabulary-PJOKSM2P.js");
+    const _ = await import("./vocabulary-NLMHEXMG.js");
     tdb.vocabApi = _.vocabInit(arg);
     if (!tdb.vocabApi.app) {
       tdb.vocabApi.app = { opts: { genome: block.genome } };
@@ -4941,4 +4941,4 @@ export {
   loadTk,
   rangequery_rglst
 };
-//# sourceMappingURL=chunk-BJANTR6U.js.map
+//# sourceMappingURL=chunk-Q3XAAYDT.js.map

package/dist/{chunk-VC3CXZ4O.js → chunk-QIW4W25A.js}

@@ -9,7 +9,7 @@ import {
 import {
   addBrushes,
   addNewBrush
-} from "./chunk-JJ5EP2O5.js";
+} from "./chunk-YNBNNKZT.js";
 import {
   select_default
 } from "./chunk-NDWTN4U5.js";
@@ -127,6 +127,7 @@ async function fillMenu(self, div, tvs) {
   self.num_obj.ranges = ranges;
   self.num_obj.brushes = [];
   addBrushes(self);
+  addRangeTable(self);
   if (!ranges.length) {
     const callback = () => addRangeTable(self);
     addNewBrush(self, "center", callback);
@@ -342,4 +343,4 @@ export {
   handler,
   format_val_text
 };
-//# sourceMappingURL=chunk-VC3CXZ4O.js.map
+//# sourceMappingURL=chunk-QIW4W25A.js.map

package/dist/chunk-QIW4W25A.js.map

@@ -0,0 +1,7 @@
+{
+  "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\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\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-VCZQJQIS.js → chunk-QWMTKXKY.js}

@@ -12,16 +12,16 @@ import {
   renderTable,
   sayerror,
   to_textfile
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   importPlot
-} from "./chunk-BUQ7S2O2.js";
+} from "./chunk-OY63PKHC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
 import {
   dofetch3
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   icons
 } from "./chunk-CY52TN75.js";
@@ -1138,4 +1138,4 @@ export {
   getId,
   navInit
 };
-//# sourceMappingURL=chunk-VCZQJQIS.js.map
+//# sourceMappingURL=chunk-QWMTKXKY.js.map

package/dist/{chunk-7QW52A66.js → chunk-QWNTXJ7F.js}

@@ -4,7 +4,7 @@ import {
 import {
   defaultUiLabels,
   fillTermWrapper
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   isDictionaryType
 } from "./chunk-YJWWWCJ6.js";
@@ -274,4 +274,4 @@ export {
   getPlotConfig,
   setComputedConfig
 };
-//# sourceMappingURL=chunk-7QW52A66.js.map
+//# sourceMappingURL=chunk-QWNTXJ7F.js.map

package/dist/{chunk-GYJW2AB2.js → chunk-RF5NZEPS.js}

@@ -11,7 +11,7 @@ import {
   svgScroll,
   to_svg,
   zoom
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
@@ -1219,7 +1219,7 @@ var MatrixControls = class {
     }
   }
   async addDictMenu(app, parent, holder = void 0) {
-    const termdb = await import("./app-WTWHDUA6.js");
+    const termdb = await import("./app-2RFP3X67.js");
     termdb.appInit({
       holder: holder || app.tip.d,
       vocabApi: this.parent.app.vocabApi,
@@ -1410,4 +1410,4 @@ var MatrixControls = class {
 export {
   MatrixControls
 };
-//# sourceMappingURL=chunk-GYJW2AB2.js.map
+//# sourceMappingURL=chunk-RF5NZEPS.js.map

package/dist/{chunk-J24OUE4D.js → chunk-RK2DFKN7.js}

@@ -5,10 +5,10 @@ import {
   disappear2 as disappear,
   makeNumericAxisConfig,
   rgb2hex
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   dofetch3
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   axisLeft
 } from "./chunk-LOZEKOES.js";
@@ -294,4 +294,4 @@ export {
   bigwigloadsubpanel,
   bigwigconfigpanel
 };
-//# sourceMappingURL=chunk-J24OUE4D.js.map
+//# sourceMappingURL=chunk-RK2DFKN7.js.map

package/dist/{chunk-PWNZL5IJ.js → chunk-RKNGKVSF.js}

@@ -5,7 +5,7 @@ import {
   first_genetrack_tolist,
   makeSsmLink,
   sayerror
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
@@ -254,7 +254,7 @@ function setRenderers(self) {
       "Cumulative incidence test:"
       /*, 'p-value = ' + result.cuminc.pvalue*/
     );
-    const _ = await import("./cuminc-SJMGX2HP.js");
+    const _ = await import("./cuminc-QTH3B2OM.js");
     const plotter = new _.Cuminc({
       holder,
       config: {
@@ -1106,7 +1106,7 @@ async function createGenomebrowser(self, input, resultLst) {
       overrideTw.q.chr = chr;
       overrideTw.q.start = start;
       overrideTw.q.stop = stop;
-      const _2 = await import("./snplocus-BQZ72QBQ.js");
+      const _2 = await import("./snplocus-KVUQ3I35.js");
       await _2.fillTW(overrideTw, self.app.vocabApi);
       self.hasUnsubmittedEdits_nullify_singleuse = true;
       input.pill.runCallback(overrideTw);
@@ -1143,7 +1143,7 @@ async function createGenomebrowser(self, input, resultLst) {
     }
   });
   first_genetrack_tolist(self.parent.genomeObj, arg.tklst);
-  const _ = await import("./block-WCLO3QIC.js");
+  const _ = await import("./block-TJKTLTZ6.js");
   return new _.Block(arg);
 }
 async function updateMds3Tk(self, input, resultLst) {
@@ -1272,4 +1272,4 @@ export {
   RegressionResults,
   showLDlegend
 };
-//# sourceMappingURL=chunk-PWNZL5IJ.js.map
+//# sourceMappingURL=chunk-RKNGKVSF.js.map

package/dist/{chunk-SV6N2HNL.js → chunk-RNYFQ6H3.js}

@@ -1,9 +1,9 @@
 import {
   getPlotConfig
-} from "./chunk-7QW52A66.js";
+} from "./chunk-QWNTXJ7F.js";
 import {
   fillTermWrapper
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   TermTypes,
   numericTypes
@@ -92,4 +92,4 @@ function canTermBeInHierGrp(grpType, twType) {
 export {
   getPlotConfig2 as getPlotConfig
 };
-//# sourceMappingURL=chunk-SV6N2HNL.js.map
+//# sourceMappingURL=chunk-RNYFQ6H3.js.map

package/dist/{chunk-MTHJNV5B.js → chunk-S3L6HE2R.js}

@@ -1,6 +1,6 @@
 import {
   VolcanoModel
-} from "./chunk-PHHTY45N.js";
+} from "./chunk-JUIPKB3J.js";
 import {
   PlotBase,
   axisstyle,
@@ -9,13 +9,13 @@ import {
   getDefaultVolcanoSettings,
   renderTable,
   table2col
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
 import {
   dofetch3
-} from "./chunk-TMFHJD3G.js";
+} from "./chunk-XKXTJHA7.js";
 import {
   copyMerge,
   getCompInit
@@ -625,4 +625,4 @@ export {
   componentInit,
   makeChartBtnMenu
 };
-//# sourceMappingURL=chunk-MTHJNV5B.js.map
+//# sourceMappingURL=chunk-S3L6HE2R.js.map

package/dist/{chunk-KRAEDA33.js → chunk-TFSJW2FL.js}

@@ -6,10 +6,10 @@ import {
   getFilter,
   getFilterItemByTag,
   getSamplelstTW
-} from "./chunk-Y6OL4KUS.js";
+} from "./chunk-PAIFJRXC.js";
 import {
   importPlot
-} from "./chunk-BUQ7S2O2.js";
+} from "./chunk-OY63PKHC.js";
 import {
   StoreApi,
   StoreBase
@@ -459,4 +459,4 @@ var storeInit = StoreApi.getInitFxn(MassStore);
 export {
   storeInit
 };
-//# sourceMappingURL=chunk-KRAEDA33.js.map
+//# sourceMappingURL=chunk-TFSJW2FL.js.map