@sjcrh/proteinpaint-client 2.172.0 → 2.174.0

package/dist/{2dmaf-XQ6GVICJ.js → 2dmaf-64NPOYZM.js}

@@ -8,13 +8,13 @@ import {
   renderSandboxFormDiv,
   sayerror,
   to_svg
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
-import "./chunk-TR6EV3FG.js";
+import "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import {
   mclass,
@@ -1365,4 +1365,4 @@ export {
   d2mafparseinput,
   d2mafui
 };
-//# sourceMappingURL=2dmaf-XQ6GVICJ.js.map
+//# sourceMappingURL=2dmaf-64NPOYZM.js.map

package/dist/{AIProjectAdmin-XTDPXBBF.js → AIProjectAdmin-ICSCBVVP.js}

@@ -7,14 +7,14 @@ import {
   getNormalRoot,
   renderTable,
   sayerror
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import "./chunk-QSSTMH7C.js";
 import {
   dofetch2,
   dofetch3
-} from "./chunk-TR6EV3FG.js";
+} from "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import {
   getColors
@@ -330,7 +330,7 @@ var AIProjectAdminInteractions = class {
       );
       images = response.images;
     }
-    const wsiViewer = await import("./plot.wsi-JJVGRFRG.js");
+    const wsiViewer = await import("./plot.wsi-FH6MUUI2.js");
     wsiViewer.default(this.dslabel, holder, { name: this.genome }, null, config.settings.project.id, images, true);
   }
   async appDispatchEdit(settings, config = {}) {
@@ -824,4 +824,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=AIProjectAdmin-XTDPXBBF.js.map
+//# sourceMappingURL=AIProjectAdmin-ICSCBVVP.js.map

package/dist/{AppHeader-ZHL24RTE.js → AppHeader-MLNU46N4.js}

@@ -1,20 +1,20 @@
 import {
   makeButton,
   openSandbox
-} from "./chunk-UVLNSOJV.js";
+} from "./chunk-WFRQCWN3.js";
 import {
   get_tklst
-} from "./chunk-J4WQB4VB.js";
-import "./chunk-BPCMPZFS.js";
-import "./chunk-O34KTQTH.js";
+} from "./chunk-IFLJ4O7L.js";
+import "./chunk-THU7RQMK.js";
+import "./chunk-X4DVXWSS.js";
 import {
   block_init_default
-} from "./chunk-EOAWPFLW.js";
+} from "./chunk-3JBRSSUK.js";
 import "./chunk-MKAF2BHB.js";
 import {
   urlmap_default
 } from "./chunk-RS3G3HE7.js";
-import "./chunk-RDMXKGKH.js";
+import "./chunk-MAVYGIVC.js";
 import "./chunk-PRZWSBMA.js";
 import {
   InputSearch,
@@ -22,15 +22,15 @@ import {
   newSandboxDiv,
   sayerror,
   throwMsgWithFilePathAndFnName
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import {
   string2pos
 } from "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import "./chunk-QSSTMH7C.js";
 import {
   dofetch3
-} from "./chunk-TR6EV3FG.js";
+} from "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import {
   defaultcolor
@@ -215,7 +215,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-ELGRFRYZ.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-EEETZJSA.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -801,7 +801,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-ELGRFRYZ.js").then((b) => new b.Block(par));
+      import("./block-EEETZJSA.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -814,4 +814,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-ZHL24RTE.js.map
+//# sourceMappingURL=AppHeader-MLNU46N4.js.map

package/dist/{BoxPlot-GRY2GOVY.js → BoxPlot-GVYESXN3.js}

@@ -17,13 +17,13 @@ import {
   renderTable,
   renderTerm1Label,
   term0_term2_defaultQ
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
-import "./chunk-TR6EV3FG.js";
+import "./chunk-3HPIIGQW.js";
 import {
   isNumericTerm
 } from "./chunk-3JH6BKPD.js";
@@ -452,15 +452,23 @@ var BoxPlotInteractions = class {
     const state = this.app.getState();
     const plotConfig = this.getPlotConfig();
     const config = structuredClone(plotConfig);
-    config.bins = this.getResData().bins;
+    const bins = this.getResData().bins;
     const start = this.getResData().absMin;
-    const stop = this.getResData().absMax;
+    const end = this.getResData().absMax;
     const contTerm = config.term.q.mode == "continuous" ? config.term : config.term2;
-    if (config.term != contTerm) {
-      config.term2 = config.term;
-      config.term = contTerm;
-    }
-    const sampleList = new ListSamples(this.app, state.termfilter, config, plot, start, stop);
+    const term = config.term != contTerm ? contTerm : config.term;
+    const term2 = config.term != contTerm ? config.term : config.term2;
+    const sampleList = new ListSamples({
+      app: this.app,
+      termfilter: state.termfilter,
+      term,
+      term2,
+      term0: config.term0,
+      plot,
+      bins,
+      start,
+      end
+    });
     return sampleList;
   }
   /** Option from box plot label to show the samples in a table within the tooltip. */
@@ -975,7 +983,7 @@ var TdbBoxplot = class _TdbBoxplot extends PlotBase {
     const holder = opts.holder.classed("sjpp-boxplot-main", true);
     const controls = opts.controls ? holder : holder.append("div");
     const div = holder.append("div");
-    const errorDiv = div.append("div").attr("class", "sjpp-boxplot-error").style("opacity", 0.75);
+    const errorDiv = div.append("div").attr("class", "sjpp-boxplot-error");
     const loading = div.append("div").style("padding", "24px").text("Loading ...");
     const chartsDiv = div.append("div").attr("class", "sjpp-boxplot-charts").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw");
     this.dom = {
@@ -999,7 +1007,7 @@ var TdbBoxplot = class _TdbBoxplot extends PlotBase {
       this.app,
       this.opts,
       () => {
-        return this.data.charts;
+        return this.data?.charts || [];
       },
       this.useDefaultSettings
     );
@@ -1068,6 +1076,7 @@ var TdbBoxplot = class _TdbBoxplot extends PlotBase {
       if (!data.charts || !Object.keys(data.charts).length) {
         this.interactions.clearDom();
         this.dom.error.style("padding", "20px 20px 20px 60px").text("No visible box plot data to render");
+        this.toggleLoadingDiv("none");
         return;
       }
       this.data = data;
@@ -1165,4 +1174,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=BoxPlot-GRY2GOVY.js.map
+//# sourceMappingURL=BoxPlot-GVYESXN3.js.map

package/dist/BoxPlot-GVYESXN3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/boxplot/model/Model.ts", "../plots/boxplot/viewModel/LegendDataMapper.ts", "../plots/boxplot/viewModel/ChartsDataMapper.ts", "../plots/boxplot/viewModel/ViewModel.ts", "../plots/boxplot/interactions/BoxPlotInteractions.ts", "../plots/boxplot/view/LegendRender.ts", "../plots/boxplot/view/BoxPlotToolTips.ts", "../plots/boxplot/view/BoxPlotLabelMenu.ts", "../plots/boxplot/view/AssociationTableRender.ts", "../plots/boxplot/view/ChartRender.ts", "../plots/boxplot/view/View.ts", "../plots/boxplot/BoxPlotControlInputs.ts", "../plots/boxplot/BoxPlot.ts"],
+  "sourcesContent": ["import type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { BoxPlotConfig } from '../BoxPlotTypes'\nimport type { TdbBoxplot } from '../BoxPlot.ts'\nimport type { BoxPlotResponse } from '#types'\nimport { isNumericTerm } from '#shared/terms.js'\nimport type { BoxPlotSettings } from '../Settings.ts'\n\n/**\n * Requests data for the boxplots.\n * Add more methods for formating the request opts and api requests.\n */\nexport class Model {\n\tboxplot: TdbBoxplot\n\tconfig: BoxPlotConfig\n\tstate: MassState\n\tapp: MassAppApi\n\tsettings: BoxPlotSettings\n\n\tconstructor(boxplot: TdbBoxplot, config: BoxPlotConfig) {\n\t\tthis.boxplot = boxplot\n\t\tthis.config = config\n\t\tthis.state = boxplot.state\n\t\tthis.app = boxplot.app\n\t\tthis.settings = config.settings.boxplot\n\t}\n\n\tasync getData() {\n\t\tconst boxPlotDataArgs = this.setRequestOpts()\n\t\tconst data: BoxPlotResponse = await this.app.vocabApi.getBoxPlotData(\n\t\t\tboxPlotDataArgs,\n\t\t\tthis.boxplot.api.getAbortSignal()\n\t\t)\n\t\treturn data\n\t}\n\n\tsetRequestOpts() {\n\t\tconst opts: { [index: string]: any } = {\n\t\t\ttw: this.getContinousTerm(),\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0: this.state.termfilter.filter0,\n\t\t\torderByMedian: this.settings.orderByMedian,\n\t\t\tisLogScale: this.settings.isLogScale,\n\t\t\tremoveOutliers: this.settings.removeOutliers,\n\t\t\tshowAssocTests: this.settings.showAssocTests\n\t\t}\n\t\tif (this.config.term2)\n\t\t\topts.overlayTw = this.getContinousTerm() == this.config.term ? this.config.term2 : this.config.term\n\n\t\tif (this.config.term0) opts.divideTw = this.config.term0\n\n\t\treturn opts\n\t}\n\n\tgetContinousTerm() {\n\t\tif (!this.config?.term2) return this.config.term\n\t\treturn isNumericTerm(this.config.term.term) && this.config.term.q.mode == 'continuous'\n\t\t\t? this.config.term\n\t\t\t: this.config.term2\n\t}\n}\n", "import type { LegendData, LegendItemEntry, BoxPlotConfig } from '../BoxPlotTypes'\nimport type { BoxPlotChartEntry, DescrStats } from '#types'\n\n/** Combines the overall .descrStats{} response with 1) the\n * uncomputable and/or hidden term values; and 2) any\n * previously hidden plots. Formats the result for the\n * View -> LegendRender. */\nexport class LegendDataMapper {\n\tlegendData: LegendData = []\n\tconfig: BoxPlotConfig\n\n\tconstructor(config: BoxPlotConfig) {\n\t\tthis.config = config\n\n\t\tconst isTerm2 = config?.term2\n\t\tconst isTerm0 = config?.term0\n\n\t\tif (config.term.q?.descrStats) {\n\t\t\tthis.legendData.push({\n\t\t\t\tlabel: `Descriptive Statistics${isTerm2 ? `: ${config.term.term.name}` : ''}`,\n\t\t\t\titems: this.setDescrStatItems(config.term.q.descrStats)\n\t\t\t})\n\t\t}\n\t\tif (isTerm2 && isTerm2.q?.descrStats && !isTerm0) {\n\t\t\tthis.legendData.push({\n\t\t\t\tlabel: `Descriptive Statistics: ${config.term2.term.name}`,\n\t\t\t\titems: this.setDescrStatItems(isTerm2.q.descrStats)\n\t\t\t})\n\t\t}\n\t}\n\n\tmap(charts: { [index: string]: BoxPlotChartEntry }, uncomputableValues: { label: string; value: number }[]) {\n\t\tconst hiddenPlots = this.getHiddenPlots(charts)\n\n\t\tif (this.config.term.term?.values) {\n\t\t\tconst term1Label = this.config.term2 ? this.config.term.term.name : 'Other categories'\n\t\t\tconst term1Data = this.setHiddenCategoryItems(this.config.term, term1Label, hiddenPlots, uncomputableValues || [])\n\t\t\tif (term1Data) this.legendData.push(term1Data)\n\t\t}\n\n\t\tif (this.config.term2?.term?.values) {\n\t\t\tconst term2Data = this.setHiddenCategoryItems(\n\t\t\t\tthis.config.term2,\n\t\t\t\tthis.config.term2.term.name,\n\t\t\t\thiddenPlots,\n\t\t\t\tuncomputableValues || []\n\t\t\t)\n\t\t\tif (term2Data) this.legendData.push(term2Data)\n\t\t}\n\n\t\treturn this.legendData\n\t}\n\n\tgetHiddenPlots(charts: { [index: string]: BoxPlotChartEntry }) {\n\t\tconst hiddenPlots = Object.values(charts)\n\t\t\t.reduce((plotMap: Map<string, any>, chart: any) => {\n\t\t\t\tfor (const p of chart.plots ?? []) {\n\t\t\t\t\tif (!p.isHidden || plotMap.has(p.key)) continue\n\n\t\t\t\t\tplotMap.set(p.key, {\n\t\t\t\t\t\tkey: p.key,\n\t\t\t\t\t\ttext: p.key,\n\t\t\t\t\t\tisHidden: true,\n\t\t\t\t\t\tisPlot: true\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\treturn plotMap\n\t\t\t}, new Map<string, any>())\n\t\t\t.values()\n\t\treturn Array.from(hiddenPlots)\n\t}\n\n\tsetDescrStatItems(stats: DescrStats) {\n\t\treturn Object.values(stats).map(s => ({\n\t\t\tkey: s.key,\n\t\t\ttext: `${s.label}: ${s.value}`,\n\t\t\tisHidden: false,\n\t\t\tisPlot: false\n\t\t}))\n\t}\n\n\tsetHiddenCategoryItems(\n\t\ttw: any,\n\t\tlabel: string,\n\t\thiddenPlots: LegendItemEntry[],\n\t\tuncomputableValues?: { label: string; value: number }[]\n\t) {\n\t\tconst termData: { label: string; items: LegendItemEntry[] } = { label, items: [] }\n\n\t\tif (hiddenPlots.length) {\n\t\t\tfor (const key of Object.keys(tw.q.hiddenValues || {})) {\n\t\t\t\tconst plot = hiddenPlots.find(p => p.key === key)\n\t\t\t\tif (plot) termData.items.push(plot)\n\t\t\t}\n\t\t}\n\t\tif (uncomputableValues && uncomputableValues.length) {\n\t\t\tfor (const v of Object.values((tw.term.values || {}) as { label: string }[])) {\n\t\t\t\tconst uncomputableItem = uncomputableValues.find(u => u.label === v.label)\n\t\t\t\tif (uncomputableItem) {\n\t\t\t\t\ttermData.items.push({\n\t\t\t\t\t\tkey: uncomputableItem.label,\n\t\t\t\t\t\ttext: `${uncomputableItem.label}, n=${uncomputableItem.value}`,\n\t\t\t\t\t\tisHidden: true,\n\t\t\t\t\t\tisPlot: false\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn termData.items.length ? termData : null\n\t}\n}\n", "import { format } from 'd3-format'\nimport { decimalPlacesUntilFirstNonZero } from '#shared/roundValue.js'\nimport { rgb } from 'd3-color'\nimport type { BoxPlotChartEntry } from '#types'\nimport type { BoxPlotSettings } from '../Settings'\nimport type { BoxPlotConfig } from '../BoxPlotTypes'\n\n/** Formats the .charts{} response data for rendering\n * in the View -> ChartRender. */\nexport class ChartsDataMapper {\n\t/** Top padding for the svg */\n\t#topPad = 20\n\t/** Bottom padding for the svg */\n\t#bottomPad = 25\n\t/** Horizontal, or right and left padding */\n\t#horizPad = 120\n\t/** For outliers, set a radius rather than using the default. */\n\t#outRadius = 5\n\t/** Offset applied when divide by term is present\n\t * Creates space for the subtitle*/\n\t#divideByOffset = 20\n\n\t/** Max value from server response */\n\tabsMax: number\n\t/** Min value from server response */\n\tabsMin: number\n\t/** Array of charts from server response */\n\tcharts: BoxPlotChartEntry[]\n\t/** Range is 20 - 50 */\n\trowHeight: number\n\t/** Range is 10 - 20 */\n\trowSpace: number\n\t/** Settings from the user or default */\n\tsettings: any\n\t/** Total length of the labels. May reflect height or width depending on orientation */\n\ttotalLabelSize: number\n\t/** Total size (ie. thickness) of each box plot. May reflect height or width depending on orientation */\n\ttotalBoxSize: number\n\n\tconstructor(data: any, settings: any, maxLabelLgth: number, useDefaultSettings: boolean) {\n\t\tthis.validateInputData(data)\n\n\t\tthis.absMin = data.absMin\n\t\tthis.absMax = data.absMax\n\t\tthis.charts = Object.values(data.charts)\n\t\tthis.settings = settings\n\n\t\t/** As requested, adjust the size of each plot based\n\t\t * on the number of boxplots. Manages rendering very large svgs.\n\t\t * When the user sets the height or space, use those values\n\t\t * for all further rendering. */\n\t\tif (useDefaultSettings) {\n\t\t\tconst { rowHeight, rowSpace } = this.getRowSettings(this.charts)\n\t\t\tthis.rowHeight = rowHeight\n\t\t\tthis.rowSpace = rowSpace\n\t\t} else {\n\t\t\tthis.rowHeight = settings.rowHeight\n\t\t\tthis.rowSpace = settings.rowSpace\n\t\t}\n\n\t\tthis.totalLabelSize = maxLabelLgth + settings.labelPad\n\t\tthis.totalBoxSize = this.rowHeight + this.rowSpace\n\t}\n\n\t/** Same checks are in the server route */\n\tvalidateInputData(data: any) {\n\t\tif (!data) throw new Error('No data provided to ChartDataMapper')\n\t\tif (!data.charts) throw new Error('No charts data provided to ChartDataMapper')\n\t\tif (!Array.isArray(data.charts) && typeof data.charts !== 'object')\n\t\t\tthrow new Error('Invalid charts data provided to ChartDataMapper')\n\t\tif (data.absMin === undefined || data.absMax === undefined)\n\t\t\tthrow new Error('Missing absMin or absMax in data provided to ChartDataMapper')\n\t}\n\n\t/** Set the row settings based on all plots */\n\tgetRowSettings(charts: BoxPlotChartEntry[]) {\n\t\tlet totalNumPlots = 0\n\t\tfor (const chart of charts) {\n\t\t\ttotalNumPlots = totalNumPlots + chart.plots.filter(p => !p.isHidden).length\n\t\t}\n\t\tconst isLargePlotCount = totalNumPlots > 20\n\t\tconst rowHeight = totalNumPlots > 10 ? (isLargePlotCount ? 20 : 35) : 50\n\t\tconst rowSpace = totalNumPlots > 10 ? (isLargePlotCount ? 10 : 12) : 15\n\n\t\treturn { rowHeight, rowSpace }\n\t}\n\n\tmap(config: BoxPlotConfig) {\n\t\tconst chartData = {}\n\t\tfor (const chart of this.charts) {\n\t\t\t/** Increasing padding to space out the boxplots and determine position */\n\t\t\tlet incrPad = 40\n\n\t\t\tconst plotDim = this.setPlotDimensions(chart, config, this.settings, incrPad)\n\t\t\t//Include extra space for the subtitle\n\t\t\tif (config?.term0) incrPad += this.#divideByOffset\n\t\t\t//20 for the axis offset (above), 10 more for the first boxplot\n\t\t\tincrPad += 30\n\n\t\t\tchartData[chart.chartId] = {\n\t\t\t\tplotDim: plotDim,\n\t\t\t\tplots: this.setPlotData(chart, config, this.settings, incrPad),\n\t\t\t\twilcoxon: chart?.wilcoxon || null\n\t\t\t}\n\t\t}\n\t\treturn chartData\n\t}\n\n\tsetPlotDimensions(chart: BoxPlotChartEntry, config: any, settings: BoxPlotSettings, incrPad: number) {\n\t\tconst svg = this.setSvgDimensions(settings, chart, incrPad, config)\n\t\tconst plotCenter = this.totalLabelSize + settings.plotLength / 2\n\t\tconst plotDim = {\n\t\t\t//Add 1 to the max is big enough so the upper line to boxplot isn't cutoff\n\t\t\tdomain: [this.absMin, this.absMax <= 1 ? this.absMax : this.absMax + 1],\n\t\t\trange: [0, settings.plotLength],\n\t\t\tsvg,\n\t\t\tsubtitle: this.setSubtitleDimensions(\n\t\t\t\tconfig,\n\t\t\t\tsettings,\n\t\t\t\tsvg.height,\n\t\t\t\tchart.chartId,\n\t\t\t\tchart.sampleCount,\n\t\t\t\tplotCenter,\n\t\t\t\tincrPad\n\t\t\t),\n\t\t\ttitle: this.setTitleDimensions(config, settings, svg.height, plotCenter, incrPad),\n\t\t\taxis: {\n\t\t\t\tx: settings.isVertical ? this.#horizPad / 2 + incrPad + this.#topPad : this.totalLabelSize,\n\t\t\t\ty: this.#topPad + (settings.isVertical ? settings.labelPad : incrPad + 20),\n\t\t\t\tvalues: (ticks: number[]) => {\n\t\t\t\t\tif (settings.isLogScale) return this.filterTickValues(ticks)\n\t\t\t\t\treturn ticks\n\t\t\t\t},\n\t\t\t\tformat: (d: number) => {\n\t\t\t\t\tif (settings.isLogScale) {\n\t\t\t\t\t\tif (Number.isInteger(d)) return format('.0f')(d)\n\t\t\t\t\t\tconst dec = decimalPlacesUntilFirstNonZero(d)\n\t\t\t\t\t\tif (dec > 1) return format(`.${dec + 1}f`)(d)\n\t\t\t\t\t\treturn format('.2f')(d)\n\t\t\t\t\t}\n\t\t\t\t\treturn d.toString()\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (config?.term0) {\n\t\t\tif (settings.isVertical) plotDim.axis.x += this.#divideByOffset\n\t\t\telse plotDim.axis.y += this.#divideByOffset\n\t\t}\n\n\t\treturn plotDim\n\t}\n\n\tsetSvgDimensions(\n\t\tsettings: BoxPlotSettings,\n\t\tchart: BoxPlotChartEntry,\n\t\tincrPad: number,\n\t\tconfig: any\n\t): { width: number; height: number } {\n\t\tlet plotsSpace =\n\t\t\tchart.plots.filter(p => !p.isHidden).length * this.totalBoxSize + this.#topPad + this.#bottomPad + incrPad\n\t\tif (config?.term0) plotsSpace += this.#divideByOffset + incrPad\n\n\t\tconst length = settings.plotLength + this.totalLabelSize + this.#horizPad / 2\n\t\treturn {\n\t\t\twidth: settings.isVertical ? plotsSpace + this.#horizPad : length,\n\t\t\theight: settings.isVertical ? length : plotsSpace\n\t\t}\n\t}\n\n\tsetSubtitleDimensions(\n\t\tconfig: any,\n\t\tsettings: BoxPlotSettings,\n\t\theight: number,\n\t\tchartId: string,\n\t\tsampleCount: number,\n\t\tplotCenter: number,\n\t\tincrPad: number\n\t): { x: number | null; y: number | null; text: string | null } {\n\t\tconst dim: { x: number | null; y: number | null; text: string | null } = {\n\t\t\tx: null,\n\t\t\ty: null,\n\t\t\ttext: null\n\t\t}\n\t\tif (config.term0) {\n\t\t\tdim.x = settings.isVertical ? this.#horizPad / 2 : plotCenter\n\t\t\tdim.y = settings.isVertical ? height - plotCenter - this.#horizPad / 2 : this.#topPad + incrPad / 2\n\t\t\tdim.text = `${getChartSubtitle(config, chartId)} (n=${sampleCount})`\n\t\t}\n\t\treturn dim\n\t}\n\n\tsetTitleDimensions(config: any, settings: BoxPlotSettings, height: number, plotCenter: number, incrPad: number) {\n\t\tconst dim = {\n\t\t\tx: settings.isVertical ? this.#horizPad / 2 : plotCenter,\n\t\t\ty: settings.isVertical ? height - plotCenter - this.#horizPad / 2 : this.#topPad + incrPad / 2,\n\t\t\ttext: config.term.q.mode == 'continuous' ? config.term.term.name : config.term2.term.name\n\t\t}\n\t\tif (config?.term0) {\n\t\t\tif (settings.isVertical) dim.x += this.#divideByOffset + 10\n\t\t\telse dim.y += this.#divideByOffset + 10\n\t\t}\n\t\treturn dim\n\t}\n\n\tfilterTickValues(ticks: number[]) {\n\t\tif (!ticks || ticks.length == 0) {\n\t\t\tthrow new Error('No ticks provided to filterTickValues')\n\t\t}\n\t\tconst significantLessThanOne = ticks.filter(t => t < 1).length / ticks.length\n\t\tconst range = ticks[ticks.length - 1] - ticks[0]\n\t\tconst spread = range > 1000 ? 4 : range > 100 ? 3 : 2\n\t\tconst formattedTicks = ticks.filter((t, i) => {\n\t\t\tif (t === 0 || (i == ticks.length - 1 && i % spread !== 0)) return t\n\t\t\telse if (t <= 1 && significantLessThanOne > 0.5) {\n\t\t\t\t/** Scales with a significant number of values under 1\n\t\t\t\t * require more space. Show every fifth value if under 1 */\n\t\t\t\tif (i % 5 === 0) return t\n\t\t\t} else if (i % spread === 0) return t\n\t\t})\n\t\treturn formattedTicks\n\t}\n\n\tsetPlotData(chart: any, config: any, settings: BoxPlotSettings, incrPad: number) {\n\t\tconst plots = structuredClone(chart.plots.filter(p => !p.isHidden))\n\t\tfor (const plot of plots) {\n\t\t\t/** Set rendering properties for the plot */\n\n\t\t\t//Set the color for all plots\n\t\t\tlet color\n\t\t\tconst term2 = config.term2\n\t\t\tif (term2) {\n\t\t\t\tif (term2.q.type == 'predefined-groupset' || term2.q.type == 'custom-groupset') {\n\t\t\t\t\tconst groupset =\n\t\t\t\t\t\tterm2.q.type == 'predefined-groupset'\n\t\t\t\t\t\t\t? term2.term.groupsetting.lst[term2.q.predefined_groupset_idx]\n\t\t\t\t\t\t\t: term2.q.customset\n\t\t\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\t\t\tconst group = groupset.groups.find(g => g.name == plot.seriesId)\n\t\t\t\t\tif (group?.color) color = group.color\n\t\t\t\t} else {\n\t\t\t\t\tcolor = term2.term.values?.[plot.seriesId]?.color\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!color) color = settings.color\n\n\t\t\tif (!plot.color) plot.color = color\n\t\t\t//Brighten the colors in dark mode for better visibility\n\t\t\tif (settings.displayMode == 'dark') plot.color = rgb(plot.color).brighter(0.75)\n\t\t\tif (plot.boxplot.out.length) {\n\t\t\t\tconst maxOut = plot.boxplot.out.reduce((a: { value: number }, b: { value: number }) =>\n\t\t\t\t\tMath.max(a.value, b.value)\n\t\t\t\t)\n\t\t\t\tif (maxOut && maxOut.value > chart.absMax) chart.absMax = maxOut.value\n\t\t\t\tplot.boxplot.radius = this.#outRadius\n\t\t\t}\n\t\t\tplot.boxplot.rectFill =\n\t\t\t\tsettings.displayMode == 'dark' ? 'black' : settings.displayMode == 'filled' ? color : 'white'\n\t\t\tplot.x = settings.isVertical ? this.#horizPad / 2 + incrPad : this.totalLabelSize\n\t\t\tplot.y = this.#topPad + (settings.isVertical ? settings.plotLength + settings.labelPad : incrPad)\n\t\t\tincrPad += this.totalBoxSize\n\n\t\t\t//Use for data requests in interactions\n\t\t\tplot.chartId = chart.chartId || ' '\n\t\t}\n\t\treturn plots\n\t}\n}\n\nexport function getChartSubtitle(config: any, chartId: string): string {\n\tif (!config.term0) return chartId\n\treturn config.term0.term.values && chartId in config.term0.term.values\n\t\t? config.term0.term.values[chartId].label\n\t\t: chartId\n}\n", "import type { BoxPlotSettings } from '../Settings'\nimport type { ViewData, BoxPlotConfig } from '../BoxPlotTypes'\nimport { LegendDataMapper } from './LegendDataMapper'\nimport { ChartsDataMapper } from './ChartsDataMapper'\n\nexport class ViewModel {\n\tviewData: ViewData\n\trowHeight: number\n\trowSpace: number\n\n\tconstructor(\n\t\tconfig: BoxPlotConfig,\n\t\tdata: any,\n\t\tsettings: BoxPlotSettings,\n\t\tmaxLabelLgth: number,\n\t\tuseDefaultSettings: boolean\n\t) {\n\t\tconst chartsMapper = new ChartsDataMapper(data, settings, maxLabelLgth, useDefaultSettings)\n\t\tconst legendMapper = new LegendDataMapper(config)\n\n\t\tconst charts = chartsMapper.map(config)\n\n\t\tthis.rowHeight = chartsMapper.rowHeight\n\t\tthis.rowSpace = chartsMapper.rowSpace\n\n\t\tthis.viewData = {\n\t\t\tbackgroundColor: settings.displayMode == 'dark' ? 'black' : 'white',\n\t\t\ttextColor: settings.displayMode == 'dark' ? 'white' : 'black',\n\t\t\tcharts,\n\t\t\tlegend: legendMapper.map(data.charts, data.uncomputableValues || [])\n\t\t}\n\t}\n}\n", "import type { BoxPlotDom, LegendItemEntry, BoxPlotConfig } from '../BoxPlotTypes'\nimport type { MassAppApi } from '#mass/types/mass'\nimport type { RenderedPlot } from '../view/RenderedPlot'\nimport { ListSamples } from '#dom/summary/ListSamples'\nimport { filterJoin, getFilterItemByTag } from '#filter'\n\nexport class BoxPlotInteractions {\n\tapp: MassAppApi\n\tdom: BoxPlotDom\n\tid: string\n\tgetResData: () => any\n\n\tconstructor(app: MassAppApi, dom: BoxPlotDom, id: string, getResData: () => any) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.id = id\n\t\tthis.getResData = getResData\n\t}\n\n\thelp() {\n\t\t//May add more options in the future\n\t\twindow.open('https://github.com/stjude/proteinpaint/wiki/Box-plot')\n\t}\n\n\t/** Option to add a global filter from the box plot label menu. */\n\taddFilter(plot: any) {\n\t\tconst state = this.app.getState()\n\t\tconst sampleList = this.initListSamples(plot)\n\t\tconst filterUiRoot = getFilterItemByTag(state.termfilter.filter, 'filterUiRoot')\n\t\tconst filter = filterJoin([filterUiRoot, sampleList.tvslst])\n\t\tfilter.tag = 'filterUiRoot'\n\t\tthis.app.dispatch({\n\t\t\ttype: 'filter_replace',\n\t\t\tfilter\n\t\t})\n\t}\n\n\t/** Option to hide a plot from the box plot label menu. */\n\thidePlot(plot: RenderedPlot) {\n\t\tconst plotConfig = this.getPlotConfig()\n\t\t//Don't try to modify a frozen object\n\t\tconst config = structuredClone(plotConfig)\n\t\tconst contTerm = config.term.q.mode == 'continuous' ? 'term2' : 'term'\n\t\tif (!config[contTerm].q.hiddenValues) config[contTerm].q.hiddenValues = {}\n\t\tconfig[contTerm].q.hiddenValues[plot.key] = 1\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: config\n\t\t})\n\t}\n\n\t/** Trigger when clicking on a hidden plot in the legend */\n\tunhidePlot(item: LegendItemEntry) {\n\t\tconst plotConfig = this.getPlotConfig()\n\t\tconst config = structuredClone(plotConfig)\n\t\tconst contTerm = config.term.q.mode == 'continuous' ? 'term2' : 'term'\n\t\tdelete config[contTerm].q.hiddenValues[item.key]\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig\n\t\t})\n\t}\n\n\tinitListSamples(plot: any) {\n\t\tconst state = this.app.getState()\n\t\tconst plotConfig = this.getPlotConfig()\n\t\tconst config = structuredClone(plotConfig)\n\t\tconst bins = this.getResData().bins\n\t\t/** Some continuous terms require a range but no\n\t\t * bins are calculated for the response. Passing\n\t\t * the absolute min/max solves this issue. */\n\t\tconst start = this.getResData().absMin\n\t\tconst end = this.getResData().absMax\n\t\t//The continuous term is always used as the tw\n\t\t//Need to update here to match the server req and res\n\t\tconst contTerm = config.term.q.mode == 'continuous' ? config.term : config.term2\n\t\tconst term = config.term != contTerm ? contTerm : config.term\n\t\tconst term2 = config.term != contTerm ? config.term : config.term2\n\t\tconst sampleList = new ListSamples({\n\t\t\tapp: this.app,\n\t\t\ttermfilter: state.termfilter,\n\t\t\tterm,\n\t\t\tterm2,\n\t\t\tterm0: config.term0,\n\t\t\tplot,\n\t\t\tbins,\n\t\t\tstart,\n\t\t\tend\n\t\t})\n\t\treturn sampleList\n\t}\n\n\t/** Option from box plot label to show the samples in a table within the tooltip. */\n\tasync listSamples(plot: any) {\n\t\tconst sampleList = this.initListSamples(plot)\n\t\tconst data = await sampleList.getData()\n\t\tconst [rows, columns] = sampleList.setTableData(data)\n\t\treturn [rows, columns]\n\t}\n\n\t/** Callback for color picker in plot(s) label menu */\n\tupdatePlotColor(plot: RenderedPlot, color: string) {\n\t\tif (!plot.seriesId) return\n\t\tconst plotConfig = this.getPlotConfig()\n\t\tconst config = structuredClone(plotConfig)\n\t\tconfig.term2.term.values[plot.seriesId].color = color\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig\n\t\t})\n\t}\n\n\tgetPlotConfig() {\n\t\treturn this.app.getState().plots.find((p: BoxPlotConfig) => p.id === this.id)\n\t}\n\n\tclearDom() {\n\t\tthis.dom.error.style('padding', '').text('')\n\t\tthis.dom.charts.selectAll('*').remove()\n\t\tthis.dom.legend.selectAll('*').remove()\n\t}\n}\n", "import type { LegendData, LegendItemEntry } from '../BoxPlotTypes'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\nimport type { Div } from '../../../types/d3'\n\n/** Handles rendering legend items formatted\n * in the LegendDataMapper. */\nexport class LegendRenderer {\n\tinteractions: BoxPlotInteractions\n\ttextColor: string\n\tconstructor(legendDiv: Div, legendData: LegendData, interactions: BoxPlotInteractions, textColor: string) {\n\t\tthis.interactions = interactions\n\t\tthis.textColor = textColor\n\t\tthis.renderLegend(legendDiv, legendData)\n\t}\n\n\trenderLegend(legendDiv: Div, legendData: LegendData) {\n\t\tlegendDiv.attr('id', 'sjpp-boxplot-legend')\n\t\tfor (const section of legendData) {\n\t\t\t// increased opacity, previously 0.5, to address Section 508 contrast issue\n\t\t\tlegendDiv.append('div').style('opacity', '0.75').style('color', this.textColor).text(section.label)\n\t\t\tconst sectionDiv = legendDiv.append('div').style('padding-left', '10px')\n\t\t\tfor (const item of section.items) {\n\t\t\t\tthis.addItem(item, sectionDiv)\n\t\t\t}\n\t\t}\n\t}\n\n\taddItem(item: LegendItemEntry, sectionDiv: Div) {\n\t\tconst legendItem = sectionDiv.append('div')\n\t\tif (item.isPlot) {\n\t\t\tlegendItem\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin-right', '3px')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('vertical-align', 'middle')\n\t\t\t\t.html(`<svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"${this.textColor}\" class=\"bi bi-arrow-counterclockwise\" viewBox=\"0 0 16 16\" style=\"vertical-align: middle; display: block; margin: auto;\">\n                <path stroke=\"#000\" stroke-width=\"0.25\" fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z\"/>\n                <path d=\"M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z\"/>\n                </svg>`)\n\t\t}\n\t\tlegendItem\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', this.textColor)\n\t\t\t.style('text-decoration', item.isHidden ? 'line-through' : '')\n\t\t\t.text(item.text)\n\n\t\tif (item.isPlot) {\n\t\t\t//Do not apply to uncomputable values, only items with plot data\n\t\t\tlegendItem.attr('aria-label', `Click to unhide plot`).on('click', () => {\n\t\t\t\tthis.interactions.unhidePlot(item)\n\t\t\t})\n\t\t}\n\t}\n}\n", "import type { Menu, RenderedBoxPlot } from '#dom'\nimport type { SvgG } from 'types/d3'\nimport type { RenderedPlot } from './RenderedPlot'\nimport { select } from 'd3-selection'\n\nexport class BoxPlotToolTips {\n\tboxplot: RenderedBoxPlot\n\tg: SvgG\n\tplot: RenderedPlot\n\tisVertical: boolean\n\ttip: Menu\n\treadonly tablePadding = '3px'\n\tconstructor(plot: any, g: SvgG, tip: Menu, isVertical: boolean) {\n\t\tthis.plot = plot\n\t\tthis.g = g\n\t\tthis.boxplot = plot.boxplot\n\t\tthis.isVertical = isVertical\n\t\tthis.tip = tip\n\n\t\tthis.addLabelTooltip()\n\t\t// this.addLineToolTips()\n\t\tthis.addOutliersTooltip()\n\t}\n\n\t//Add rendering preferences here to maintain styles\n\t//across all tooltip instances\n\taddText(text: string) {\n\t\tthis.tip.d.append('div').text(text)\n\t}\n\n\taddLabelTooltip() {\n\t\tif (Object.keys(this.plot.descrStats).length < 2) return\n\t\tthis.boxplot.labelG.on('mouseover', (event: MouseEvent) => {\n\t\t\tthis.tip.clear()\n\t\t\tif (this.isVertical) this.tip.show(event.clientX, event.clientY)\n\t\t\telse this.tip.showunder(this.boxplot.labelG.node())\n\t\t\tconst table = this.tip.d.append('table').attr('class', 'sja_simpletable')\n\t\t\ttable\n\t\t\t\t.append('tr')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.append('td')\n\t\t\t\t.attr('colspan', 2)\n\t\t\t\t.style('padding', this.tablePadding)\n\t\t\t\t.text(this.plot.key)\n\t\t\tfor (const stat of Object.values(this.plot.descrStats)) {\n\t\t\t\tconst row = table.append('tr')\n\t\t\t\trow.append('td').style('padding', this.tablePadding).style('opacity', 0.5).text(stat.label)\n\t\t\t\trow\n\t\t\t\t\t.append('td')\n\t\t\t\t\t.style('padding', this.tablePadding)\n\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t.style('opacity', stat.value === null || stat.value === undefined ? 0.5 : 1)\n\t\t\t\t\t.text(stat.value ?? 'N/A')\n\t\t\t}\n\t\t})\n\t\tthis.boxplot.labelG.on('mouseout', () => {\n\t\t\tthis.tip.hide()\n\t\t})\n\t}\n\n\t// addLineToolTips() {\n\t// \tconst addToolTips = (elem, text: string) => {\n\t// \t\tconst elemBBox = elem.node().getBBox()\n\t// \t\t//Add an expanded area for the tooltip\n\t// \t\t//Easier for user to hover over\n\t// \t\tthis.g\n\t// \t\t\t.append('rect')\n\t// \t\t\t.attr('x', elemBBox.x - 10)\n\t// \t\t\t.attr('y', elemBBox.y - 10)\n\t// \t\t\t.attr('width', elemBBox.width + 20)\n\t// \t\t\t.attr('height', elemBBox.height + 20)\n\t// \t\t\t.attr('fill', 'transparent')\n\t// \t\t\t.style('pointer-events', 'all')\n\t// \t\t\t.on('mouseover', () => {\n\t// \t\t\t\tthis.tip.clear().showunder(elem.node())\n\t// \t\t\t\tthis.addText(text)\n\t// \t\t\t})\n\t// \t\t\t.on('mouseout', () => {\n\t// \t\t\t\tthis.tip.hide()\n\t// \t\t\t})\n\t// \t}\n\n\t// \tif (this.boxplot.linep50) {\n\t// \t\tconst median = this.plot.descrStats.find((d: any) => d.id == 'median')\n\t// \t\tif (!median) throw `Missing median value for ${this.plot.key}`\n\t// \t\taddToolTips(this.boxplot.linep50, `Median: ${median.value}`)\n\t// \t}\n\t// \tif (this.boxplot.linew1) {\n\t// \t\taddToolTips(this.boxplot.linew1, `${this.boxplot.w1}`)\n\t// \t}\n\t// \tif (this.boxplot.linew2) {\n\t// \t\taddToolTips(this.boxplot.linew2, `${this.boxplot.w2}`)\n\t// \t}\n\t// }\n\n\taddOutliersTooltip() {\n\t\tthis.g\n\t\t\t.selectAll('circle')\n\t\t\t.data(this.boxplot.out)\n\t\t\t.each((d: any, i, nodes) => {\n\t\t\t\tconst circle = select(nodes[i])\n\t\t\t\tcircle.on('mouseover', () => {\n\t\t\t\t\tthis.tip.clear().showunder(circle.node())\n\t\t\t\t\tthis.addText(d.value)\n\t\t\t\t})\n\t\t\t\tcircle.on('mouseout', () => {\n\t\t\t\t\tthis.tip.hide()\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n", "import type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\nimport type { RenderedPlot } from './RenderedPlot'\nimport { renderTable, type Menu } from '#dom'\nimport { rgb } from 'd3-color'\n\n/** Menu is available when more than one boxplot is rendered. */\nexport class BoxPlotLabelMenu {\n\tconstructor(\n\t\tplot: RenderedPlot,\n\t\tapp: MassAppApi,\n\t\tinteractions: BoxPlotInteractions,\n\t\ttip: Menu,\n\t\tisVertical: boolean\n\t\t/*chart: any*/\n\t) {\n\t\tconst options = [\n\t\t\t{\n\t\t\t\ttext: `Add filter: ${plot.key}`,\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: () => interactions.addFilter(plot)\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: `Hide ${plot.key}`,\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: () => interactions.hidePlot(plot)\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: `List samples`,\n\t\t\t\tisVisible: (state: MassState) => state.termdbConfig.displaySampleIds && app.vocabApi.hasVerifiedToken(),\n\t\t\t\tcallback: async (event: MouseEvent) => {\n\t\t\t\t\tif (isVertical) tip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\telse tip.clear().showunder(plot.boxplot.labelG.node())\n\t\t\t\t\tconst [rows, columns] = await interactions.listSamples(plot)\n\n\t\t\t\t\tconst tableDiv = tip.d.append('div')\n\t\t\t\t\trenderTable({\n\t\t\t\t\t\trows: rows as any,\n\t\t\t\t\t\tcolumns: columns as any,\n\t\t\t\t\t\tdiv: tableDiv,\n\t\t\t\t\t\tmaxHeight: '35vh',\n\t\t\t\t\t\tresize: true,\n\t\t\t\t\t\tshowLines: true,\n\t\t\t\t\t\tdataTestId: 'sjpp-listsampletable'\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t\tplot.boxplot.labelG.on('click', (event: MouseEvent) => {\n\t\t\ttip.clear()\n\t\t\tif (isVertical) tip.show(event.clientX, event.clientY)\n\t\t\telse tip.showunder(plot.boxplot.labelG.node())\n\t\t\tconst state = app.getState()\n\t\t\tfor (const opt of options) {\n\t\t\t\t//Adds all the menu options before the color picker\n\t\t\t\tif (!opt.isVisible(state)) continue\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.classed('sja_menuoption', true)\n\t\t\t\t\t.text(opt.text)\n\t\t\t\t\t.on('click', (event: MouseEvent) => {\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\topt.callback(event)\n\t\t\t\t\t})\n\t\t\t}\n\t\t\tif (plot.color) {\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.text('Color:')\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.property('value', rgb(plot.color).formatHex())\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tinteractions.updatePlotColor(plot, event.target.value)\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n}\n", "import { renderTable } from '#dom'\n\n/** If wilcoxon test results are available, render the association table */\nexport class AssociationTableRender {\n\tconstructor(div, data) {\n\t\tconst wrapper = div.style('vertical-align', 'top').style('margin-top', '30px')\n\n\t\t//Title div\n\t\twrapper\n\t\t\t.append('div')\n\t\t\t.text(\"Group comparisons (Wilcoxon's rank sum test)\")\n\t\t\t.style('font-weight', '600')\n\t\t\t.style('text-align', 'center')\n\n\t\tconst tableDiv = wrapper.append('div').style('margin-top', '5px')\n\t\trenderTable({\n\t\t\tdiv: tableDiv,\n\t\t\tcolumns: [{ label: 'Group 1' }, { label: 'Group 2' }, { label: 'P-Value' }],\n\t\t\trows: data\n\t\t})\n\t}\n}\n", "import { drawBoxplot, Menu } from '#dom'\nimport { scaleLinear, scaleLog, type ScaleLinear } from 'd3-scale'\nimport { axisstyle } from '#src/client'\nimport { axisTop, axisLeft } from 'd3-axis'\nimport type { PlotDimensions, FormattedBoxPlotChartsEntry } from '../BoxPlotTypes'\nimport type { BoxPlotSettings } from '../Settings'\nimport type { RenderedPlot } from './RenderedPlot'\nimport { BoxPlotToolTips } from './BoxPlotToolTips'\nimport { BoxPlotLabelMenu } from './BoxPlotLabelMenu'\nimport { AssociationTableRender } from './AssociationTableRender'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\n\n/** Handles the rendering for charts individually.\n * Data is formatted in ChartsDataMapper.*/\nexport class ChartRender {\n\tapp: any\n\tinteractions: BoxPlotInteractions\n\ttextColor: string\n\n\tconstructor(\n\t\tdom: any,\n\t\tsettings: BoxPlotSettings,\n\t\tapp: any,\n\t\tinteractions: BoxPlotInteractions,\n\t\tchart: FormattedBoxPlotChartsEntry,\n\t\tbackgroundColor: string,\n\t\ttextColor: string\n\t) {\n\t\tthis.app = app\n\t\tthis.interactions = interactions\n\t\tthis.textColor = textColor\n\n\t\tconst plotDim = chart.plotDim\n\n\t\tdom.svg\n\t\t\t.transition()\n\t\t\t.attr('width', plotDim.svg.width)\n\t\t\t.attr('height', plotDim.svg.height)\n\t\t\t//Fix for white background when downloading dark mode image.\n\t\t\t.style('fill', backgroundColor)\n\n\t\tconst setScaleFunc = settings.isLogScale ? scaleLog().base(10) : scaleLinear()\n\t\tconst scale = setScaleFunc.domain(plotDim.domain).range(plotDim.range)\n\n\t\tthis.renderTitles(plotDim, dom, settings)\n\t\tthis.renderBoxPlots(dom, chart, scale, settings)\n\t\tthis.renderAxis(plotDim, dom, scale, settings)\n\n\t\tif (chart.wilcoxon && dom.assocTableDiv) {\n\t\t\t//add text and background color to the association table div\n\t\t\t//for display mode\n\t\t\tnew AssociationTableRender(dom.assocTableDiv, chart.wilcoxon)\n\t\t}\n\t}\n\n\trenderTitles(plotDim: PlotDimensions, dom: any, settings: BoxPlotSettings) {\n\t\t//Title of the plot\n\t\tconst transformStr = `translate(${plotDim.title.x}, ${plotDim.title.y})${settings.isVertical ? `,rotate(-90)` : ''}`\n\t\tdom.title\n\t\t\t.attr('class', 'sjpp-boxplot-title')\n\t\t\t.style('font-weight', 600)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('transform', transformStr)\n\t\t\t.attr('fill', this.textColor)\n\t\t\t.text(plotDim.title.text.length > 80 ? plotDim.title.text.slice(0, 80) + '...' : plotDim.title.text)\n\n\t\t/** If divide by term applied, show the value above\n\t\t * the chart with sample count */\n\t\tif (plotDim.subtitle.text) {\n\t\t\tconst subTransformStr = `translate(${plotDim.subtitle.x}, ${plotDim.subtitle.y})${\n\t\t\t\tsettings.isVertical ? `,rotate(-90)` : ''\n\t\t\t}`\n\t\t\tdom.subtitle\n\t\t\t\t.attr('class', 'sjpp-boxplot-subtitle')\n\t\t\t\t.style('font-size', '1.1em')\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('transform', subTransformStr)\n\t\t\t\t.attr('fill', this.textColor)\n\t\t\t\t.text(plotDim.subtitle.text.length > 80 ? plotDim.subtitle.text.slice(0, 80) + '...' : plotDim.subtitle.text)\n\t\t}\n\t}\n\n\trenderAxis(plotDim: PlotDimensions, dom: any, scale: ScaleLinear<number, number, never>, settings: BoxPlotSettings) {\n\t\t//Fix for the axis rendering min -> max when the plot is vertical\n\t\t/** draw_boxplot renders the boxplot from min-max but the scale\n\t\t * renders the axis from max - min. Render the box plots, then change\n\t\t * the scale vector to match. */\n\t\tif (settings.isVertical) scale.range([scale.range()[1], scale.range()[0]])\n\t\tconst ticks = scale.ticks()\n\t\tconst tickValues = plotDim.axis.values(ticks)\n\t\tdom.axis\n\t\t\t.attr('class', 'sjpp-boxplot-axis')\n\t\t\t.attr('transform', `translate(${plotDim.axis.x}, ${plotDim.axis.y})`)\n\t\t\t.transition()\n\t\t\t.call(\n\t\t\t\tsettings.isVertical\n\t\t\t\t\t? axisLeft(scale)\n\t\t\t\t\t\t\t.tickValues(tickValues)\n\t\t\t\t\t\t\t.tickFormat(d => plotDim.axis.format(d as number))\n\t\t\t\t\t\t\t.tickPadding(8)\n\t\t\t\t\t: axisTop(scale)\n\t\t\t\t\t\t\t.tickValues(tickValues)\n\t\t\t\t\t\t\t.tickFormat(d => plotDim.axis.format(d as number))\n\t\t\t)\n\n\t\taxisstyle({\n\t\t\taxis: dom.axis,\n\t\t\tshowline: true,\n\t\t\tfontsize: 12,\n\t\t\tcolor: this.textColor\n\t\t})\n\t}\n\n\trenderBoxPlots(\n\t\tdom: any,\n\t\tchart: FormattedBoxPlotChartsEntry,\n\t\tscale: ScaleLinear<number, number, never>,\n\t\tsettings: BoxPlotSettings\n\t) {\n\t\t/** Draw boxplots, incrementing by the total row height */\n\t\tfor (const plot of chart.plots) {\n\t\t\tconst g = dom.boxplots.append('g').attr('class', 'sjpp-boxplot-plot').attr('padding', '5px')\n\t\t\tdrawBoxplot({\n\t\t\t\tbp: plot.boxplot,\n\t\t\t\tg,\n\t\t\t\tcolor: settings.displayMode == 'filled' ? 'black' : plot.color,\n\t\t\t\tscale: scale,\n\t\t\t\trowheight: settings.rowHeight,\n\t\t\t\tlabpad: settings.labelPad,\n\t\t\t\tlabColor: this.textColor\n\t\t\t})\n\n\t\t\tconst transformStr = `translate(${plot.x}, ${plot.y})${settings.isVertical ? `, rotate(-90)` : ''}`\n\t\t\tg.attr('transform', transformStr)\n\n\t\t\tif (settings.isVertical) {\n\t\t\t\t//Rotate the text slightly in veritcal orientation\n\t\t\t\tg.select('text').attr('transform', 'rotate(45)')\n\t\t\t}\n\n\t\t\tnew BoxPlotToolTips(plot, g, dom.tip, settings.isVertical)\n\t\t\tif (chart.plots.length > 1) {\n\t\t\t\t//Do not try to use the same tip for the menu as the tooltips.\n\t\t\t\t//When the boxplots are rendered close together, the menu\n\t\t\t\t//disappears to show the tooltip for the next boxplot.\n\t\t\t\t//The user can't make a selection in time.\n\t\t\t\tconst labelMenuTip = new Menu({ padding: '' })\n\t\t\t\tnew BoxPlotLabelMenu(\n\t\t\t\t\tplot as unknown as RenderedPlot,\n\t\t\t\t\tthis.app,\n\t\t\t\t\tthis.interactions,\n\t\t\t\t\tlabelMenuTip,\n\t\t\t\t\tsettings.isVertical\n\t\t\t\t\t/*chart*/\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n}\n", "import type { BoxPlotSettings } from '../Settings'\nimport type { ViewData, FormattedBoxPlotChartsEntry } from '../BoxPlotTypes'\nimport type { MassAppApi } from '#mass/types/mass'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\nimport { LegendRenderer } from './LegendRender'\nimport { ChartRender } from './ChartRender'\n\n/** Handles rendering each chart and the legend */\nexport class View {\n\tapp: MassAppApi\n\tdom: any\n\tinteractions: BoxPlotInteractions\n\tsettings: BoxPlotSettings\n\tconstructor(\n\t\tviewData: ViewData,\n\t\tsettings: BoxPlotSettings,\n\t\tdom: any,\n\t\tapp: MassAppApi,\n\t\tinteractions: BoxPlotInteractions\n\t) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.interactions = interactions\n\t\tthis.settings = settings\n\t\tif (!viewData || !viewData.charts) return\n\n\t\tdom.div.style('background-color', viewData.backgroundColor)\n\n\t\tfor (const chart of Object.values(viewData.charts) as FormattedBoxPlotChartsEntry[]) {\n\t\t\tconst chartWrapper = dom.charts.append('div').attr('class', 'sjpp-boxplot-chart-wrapper')\n\n\t\t\tconst svg = chartWrapper.append('svg').attr('class', 'sjpp-boxplot-svg')\n\n\t\t\t/** Enables downloading the chart image for\n\t\t\t * DownloadMenu after rendering. */\n\t\t\tchart['svg'] = svg\n\n\t\t\tconst chartDom: any = {\n\t\t\t\tsvg,\n\t\t\t\ttip: dom.tip\n\t\t\t}\n\t\t\tif (chart.plotDim.subtitle.text) {\n\t\t\t\tchartDom.subtitle = svg.append('text')\n\t\t\t}\n\t\t\tchartDom.title = svg.append('text')\n\t\t\tchartDom.axis = svg.append('g')\n\t\t\tchartDom.boxplots = svg.append('g').attr('class', 'sjpp-boxplot-boxplots')\n\n\t\t\tif (chart.wilcoxon) {\n\t\t\t\tchartDom.assocTableDiv = chartWrapper\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sjpp-boxplot-wilcoxon')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t}\n\n\t\t\tnew ChartRender(\n\t\t\t\tchartDom,\n\t\t\t\tthis.settings,\n\t\t\t\tthis.app,\n\t\t\t\tthis.interactions,\n\t\t\t\tchart,\n\t\t\t\tviewData.backgroundColor,\n\t\t\t\tviewData.textColor\n\t\t\t)\n\t\t}\n\n\t\tnew LegendRenderer(dom.legend, viewData.legend, interactions, viewData.textColor)\n\t}\n}\n", "import { term0_term2_defaultQ, renderTerm1Label } from '../controls'\n\nexport function setBoxPlotControlInputs(state: any, app: any, opts: any, getCharts: any, useDefaultSettings: boolean) {\n\tconst controlLabels = state.config.controlLabels\n\tif (!controlLabels) throw new Error('controls labels not found')\n\n\tconst inputs: { [index: string]: any }[] = [\n\t\t{\n\t\t\ttype: 'term',\n\t\t\tconfigKey: 'term',\n\t\t\tchartType: 'boxplot',\n\t\t\tusecase: { target: 'boxplot', detail: 'term' },\n\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\tvocabApi: app.vocabApi,\n\t\t\tmenuOptions: 'edit'\n\t\t},\n\t\t{\n\t\t\ttype: 'term',\n\t\t\tconfigKey: 'term2',\n\t\t\tchartType: 'boxplot',\n\t\t\tusecase: { target: 'boxplot', detail: 'term2' },\n\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\tlabel: controlLabels.term2.label,\n\t\t\tvocabApi: app.vocabApi,\n\t\t\tnumericEditMenuVersion: opts.numericEditMenuVersion || ['continuous', 'discrete'],\n\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t},\n\t\t{\n\t\t\ttype: 'term',\n\t\t\tconfigKey: 'term0',\n\t\t\tchartType: 'boxplot',\n\t\t\tusecase: { target: 'boxplot', detail: 'term0' },\n\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\tlabel: controlLabels.term0.label,\n\t\t\tvocabApi: app.vocabApi,\n\t\t\tnumericEditMenuVersion: opts.numericEditMenuVersion || ['continuous', 'discrete'],\n\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t},\n\t\t{\n\t\t\tlabel: 'Order by',\n\t\t\ttitle: 'Order box plots by parameters',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'orderByMedian',\n\t\t\toptions: [\n\t\t\t\t{ label: 'Default', value: false },\n\t\t\t\t{ label: 'Median values', value: true }\n\t\t\t],\n\t\t\tgetDisplayStyle: () => {\n\t\t\t\tconst charts = getCharts()\n\t\t\t\tlet style = 'none'\n\t\t\t\tfor (const k of Object.keys(charts)) {\n\t\t\t\t\tconst chart = charts[k]\n\t\t\t\t\tif (chart.plots.length > 1) style = ''\n\t\t\t\t}\n\t\t\t\treturn style\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Scale',\n\t\t\ttitle: 'Change the axis scale',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'isLogScale',\n\t\t\toptions: [\n\t\t\t\t{ label: 'Linear', value: false },\n\t\t\t\t{ label: 'Log10', value: true }\n\t\t\t]\n\t\t},\n\t\t{\n\t\t\tlabel: 'Orientation',\n\t\t\ttitle: 'Change the orientation of the box plots',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'isVertical',\n\t\t\toptions: [\n\t\t\t\t{ label: 'Horizontal', value: false },\n\t\t\t\t{ label: 'Vertical', value: true }\n\t\t\t]\n\t\t},\n\t\t{\n\t\t\tlabel: 'Plot length',\n\t\t\ttitle: 'Set the plot length of the entire plot in pixels, >=200',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'plotLength',\n\t\t\tdebounceInterval: 500,\n\t\t\tmin: 200,\n\t\t\tstep: 10\n\t\t},\n\t\t{\n\t\t\tlabel: 'Box size',\n\t\t\ttitle: 'Set the box size or thickness in pixels of each box plot between 20 and 50',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'rowHeight',\n\t\t\tstep: 1,\n\t\t\tmax: 50,\n\t\t\tmin: 20,\n\t\t\tdebounceInterval: 500,\n\t\t\tprocessInput: (val: number) => {\n\t\t\t\t/**TODO: This is a hack. */\n\t\t\t\tif (useDefaultSettings == true) useDefaultSettings = false\n\t\t\t\treturn val\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Plots padding',\n\t\t\ttitle: 'Set the space between each box plot. Number must be between 10 and 20',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'rowSpace',\n\t\t\tstep: 1,\n\t\t\tmax: 20,\n\t\t\tmin: 10,\n\t\t\tdebounceInterval: 500,\n\t\t\tprocessInput: (val: number) => {\n\t\t\t\t/**TODO: This is a hack. */\n\t\t\t\tif (useDefaultSettings == true) useDefaultSettings = false\n\t\t\t\treturn val\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Default color',\n\t\t\ttype: 'color',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'color',\n\t\t\tgetDisplayStyle: () => {\n\t\t\t\tconst charts = getCharts()\n\t\t\t\tlet style = ''\n\t\t\t\tfor (const k of Object.keys(charts)) {\n\t\t\t\t\tconst chart = charts[k]\n\t\t\t\t\tif (chart.plots.length > 1) style = 'none'\n\t\t\t\t}\n\t\t\t\treturn style\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Display mode',\n\t\t\ttitle: 'Apply a dark theme to the plot',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'displayMode',\n\t\t\toptions: [\n\t\t\t\t{ label: 'Default', value: 'default' },\n\t\t\t\t{ label: 'Filled', value: 'filled' },\n\t\t\t\t{ label: 'Dark mode', value: 'dark' }\n\t\t\t]\n\t\t},\n\t\t{\n\t\t\tlabel: 'Show association tests',\n\t\t\tboxLabel: '',\n\t\t\ttype: 'checkbox',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'showAssocTests',\n\t\t\ttitle: `Show association tests next to the box plots.`,\n\t\t\tgetDisplayStyle: plot => {\n\t\t\t\treturn plot?.term2 ? '' : 'none'\n\t\t\t}\n\t\t}\n\t]\n\n\tif (state.termdbConfig?.boxplots?.removeOutliers) {\n\t\tinputs.push({\n\t\t\tlabel: 'Remove outliers',\n\t\t\tboxLabel: '',\n\t\t\ttype: 'checkbox',\n\t\t\tchartType: 'boxplot',\n\t\t\tsettingsKey: 'removeOutliers',\n\t\t\ttitle: `Option to remove outliers from the analysis`\n\t\t})\n\t}\n\n\treturn inputs\n}\n", "import { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.ts'\nimport { fillTermWrapper } from '#termsetting'\nimport { getCombinedTermFilter } from '#filter'\nimport { controlsInit } from '#plots/controls.js'\nimport { Menu, getMaxLabelWidth, DownloadMenu } from '#dom'\nimport type { Elem } from '../../types/d3'\nimport type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { TdbBoxPlotOpts, BoxPlotDom, BoxPlotConfigOpts } from './BoxPlotTypes'\nimport { Model } from './model/Model'\nimport { ViewModel } from './viewModel/ViewModel'\nimport { getChartSubtitle } from './viewModel/ChartsDataMapper'\nimport { BoxPlotInteractions } from './interactions/BoxPlotInteractions'\nimport { View } from './view/View'\nimport { getDefaultBoxplotSettings } from './defaults'\nimport { setBoxPlotControlInputs } from './BoxPlotControlInputs'\n\nexport class TdbBoxplot extends PlotBase implements RxComponent {\n\tstatic type = 'boxplot'\n\ttype: string\n\tcomponents: { controls: any }\n\tdom: BoxPlotDom\n\tdata: any\n\tinteractions?: BoxPlotInteractions\n\tprivate useDefaultSettings = true\n\tparentId?: string\n\tapi: any\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\n\tconstructor(opts: TdbBoxPlotOpts, api: MassAppApi) {\n\t\tsuper(opts)\n\t\tthis.opts = opts\n\t\tthis.api = api\n\t\tthis.type = TdbBoxplot.type\n\t\tthis.components = {\n\t\t\tcontrols: {}\n\t\t}\n\n\t\tconst holder = opts.holder.classed('sjpp-boxplot-main', true)\n\t\tconst controls = opts.controls ? holder : holder.append('div')\n\t\tconst div = holder.append('div')\n\t\tconst errorDiv = div.append('div').attr('class', 'sjpp-boxplot-error') //.style('opacity', 0.75)\n\t\tconst loading = div.append('div').style('padding', '24px').text('Loading ...')\n\t\tconst chartsDiv = div\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-boxplot-charts')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-direction', 'row')\n\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t.style('max-width', '100vw')\n\t\tthis.dom = {\n\t\t\tcontrols: controls as Elem,\n\t\t\tdiv,\n\t\t\terror: errorDiv,\n\t\t\tloading,\n\t\t\tcharts: chartsDiv,\n\t\t\tlegend: div.append('div').attr('class', 'sjpp-boxplot-legend').style('margin-top', '25px'),\n\t\t\ttip: new Menu()\n\t\t}\n\t\tif (opts.header) this.dom.header = opts.header.html('Box plot')\n\t}\n\n\tasync setControls() {\n\t\tconst state = this.getState(this.app.getState())\n\t\tconst inputs = setBoxPlotControlInputs(\n\t\t\tstate,\n\t\t\tthis.app,\n\t\t\tthis.opts,\n\t\t\t() => {\n\t\t\t\treturn this.data?.charts || []\n\t\t\t},\n\t\t\tthis.useDefaultSettings\n\t\t)\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.style('display', 'inline-block'),\n\t\t\tinputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.boxplot', event => {\n\t\t\tthis.download(event)\n\t\t})\n\t\tthis.components.controls.on('helpClick.boxplot', () => {\n\t\t\tthis.interactions!.help()\n\t\t})\n\n\t\tif (state.vocab.dslabel.toLowerCase() == 'gdc') {\n\t\t\t//Remove for now. May add gdc specific user guide\n\t\t\t//in interactions.help later.\n\t\t\tthis.dom.controls.select('div[aria-label=\"Documentation\"]').remove()\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\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: any) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\ttermfilter,\n\t\t\tvocab: appState.vocab,\n\t\t\tconfig: Object.assign({}, config, {\n\t\t\t\tsettings: {\n\t\t\t\t\tboxplot: config.settings.boxplot\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tasync init() {\n\t\tthis.dom.div.style('display', 'inline-block').style('margin-left', '20px')\n\t\tthis.interactions = new BoxPlotInteractions(this.app, this.dom, this.id, () => {\n\t\t\treturn this.data\n\t\t})\n\t\tawait this.setControls()\n\t}\n\n\tasync main() {\n\t\tconst c = this.state.config\n\t\tif (c.childType != this.type && c.chartType != this.type) return\n\t\tif (!this.interactions) throw new Error('Interactions not initialized [box plot main()]')\n\n\t\tthis.toggleLoadingDiv()\n\t\tconst config = await this.getMutableConfig()\n\t\tconst settings = config.settings.boxplot\n\t\tconst model = new Model(this, config)\n\n\t\ttry {\n\t\t\tconst data = await model.getData()\n\t\t\tconfig.term.q.descrStats = data.descrStats\n\t\t\tconfig.bins = data.bins\n\n\t\t\tif (data.error) throw new Error(data.error)\n\t\t\tif (!data.charts || !Object.keys(data.charts).length) {\n\t\t\t\tthis.interactions.clearDom()\n\t\t\t\tthis.dom.error.style('padding', '20px 20px 20px 60px').text('No visible box plot data to render')\n\t\t\t\tthis.toggleLoadingDiv('none')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.data = data\n\t\t} catch (e: any) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t\tif (e instanceof Error) console.error(e.message || e)\n\t\t\tthrow new Error(e)\n\t\t}\n\n\t\tthis.interactions.clearDom()\n\n\t\t/** The space needed for the labels must be calculated\n\t\t * before calculating the plot dimensions in the view model. */\n\t\tconst labels: string[] = Object.values(this.data.charts).reduce((labels: string[], chart: any) => {\n\t\t\tconst chartLabels = chart.plots.filter(p => !p.isHidden).map(p => p.boxplot.label)\n\t\t\tlabels.push(...chartLabels)\n\t\t\treturn labels\n\t\t}, [])\n\t\tconst tempsvg = this.dom.charts.append('svg')\n\t\tconst maxLabelLgth = getMaxLabelWidth(tempsvg.append('g'), labels)\n\t\ttempsvg.remove()\n\n\t\tconst viewModel = new ViewModel(config, this.data, settings, maxLabelLgth, this.useDefaultSettings)\n\t\tif (!viewModel.viewData) throw new Error('No viewData from ViewModel')\n\n\t\tif (\n\t\t\t(viewModel.rowSpace !== settings.rowSpace || viewModel.rowHeight !== settings.rowHeight) &&\n\t\t\tthis.useDefaultSettings == true\n\t\t) {\n\t\t\t/** TODO: Get rid of this work around\n\t\t\t *\n\t\t\t * If the row height or space changed during data processing,\n\t\t\t * save the new settings without calling app.dispatch.\n\t\t\t * Will show updated value in the controls. */\n\t\t\tsettings.rowSpace = viewModel.rowSpace\n\t\t\tsettings.rowHeight = viewModel.rowHeight\n\n\t\t\tthis.app.save({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tboxplot: {\n\t\t\t\t\t\t\trowSpace: viewModel.rowSpace,\n\t\t\t\t\t\t\trowHeight: viewModel.rowHeight\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\tthis.toggleLoadingDiv('none')\n\t\tnew View(viewModel.viewData, settings, this.dom, this.app, this.interactions)\n\t\t/** Enables downloading the chart images for DownloadMenu after rendering. */\n\t\tthis.data.charts = viewModel.viewData.charts\n\t}\n\n\tgetChartImages() {\n\t\tconst chartImages: any[] = []\n\t\tconst charts: any[] = this.data.charts\n\t\tfor (const [key, chart] of Object.entries(charts)) {\n\t\t\tconst svg: any = chart.svg\n\t\t\tconst title = getChartSubtitle(this.state.config, key)\n\t\t\tconst name = `${this.state.config.term.term.name}  ${title}`\n\t\t\tchartImages.push({ name, svg })\n\t\t}\n\t\treturn chartImages\n\t}\n\n\tdownload(event) {\n\t\tif (!this.state) return\n\t\tconst name2svg = this.getChartImages()\n\t\tconst dm = new DownloadMenu(name2svg, this.state.config.term.term.name)\n\t\tdm.show(event.clientX, event.clientY, event.target)\n\t}\n\n\ttoggleLoadingDiv(display = '') {\n\t\tif (display != 'none') {\n\t\t\tthis.dom.loading.style('opacity', 0).style('display', display).transition().duration(3000).style('opacity', 1)\n\t\t} else {\n\t\t\tthis.dom.loading.style('display', display)\n\t\t}\n\t}\n}\n\nexport const boxplotInit = getCompInit(TdbBoxplot)\nexport const componentInit = boxplotInit\n\nexport async function getPlotConfig(opts: BoxPlotConfigOpts, app: MassAppApi) {\n\tif (!opts.term) throw new Error('opts.term{} missing')\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tconsole.error(new Error(`${e} [boxplot getPlotConfig()]`))\n\t\tthrow new Error(`boxplot getPlotConfig() failed`)\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,\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\tboxplot: getDefaultBoxplotSettings(app, opts.overrides || {})\n\t\t}\n\t}\n\n\treturn copyMerge(config, opts)\n}\n"],
+  "mappings": 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+  "names": ["event", "labels"]
+}

package/dist/{CorrelationVolcano-I5G5GPOX.js → CorrelationVolcano-REQRYH2M.js}

@@ -8,13 +8,13 @@ import {
   fillTwLst,
   table2col,
   to_svg
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
-import "./chunk-TR6EV3FG.js";
+import "./chunk-3HPIIGQW.js";
 import {
   termType2label
 } from "./chunk-3JH6BKPD.js";
@@ -611,4 +611,4 @@ export {
   getDefaultCorrVolcanoSettings,
   getPlotConfig
 };
-//# sourceMappingURL=CorrelationVolcano-I5G5GPOX.js.map
+//# sourceMappingURL=CorrelationVolcano-REQRYH2M.js.map

package/dist/{DifferentialAnalysis-NXTJPOCM.js → DifferentialAnalysis-KGQROTZI.js}

@@ -1,21 +1,21 @@
 import {
   getDefaultGseaSettings
-} from "./chunk-GB76RKBG.js";
-import "./chunk-TKNO4Y2X.js";
+} from "./chunk-TPEG3F7N.js";
+import "./chunk-DNF2UA2R.js";
 import {
   PlotBase,
   Tabs,
   getDefaultVolcanoSettings,
   validateVolcanoSettings
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
 import {
   importPlot
-} from "./chunk-VEGMCJKQ.js";
+} from "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
-import "./chunk-TR6EV3FG.js";
+import "./chunk-3HPIIGQW.js";
 import {
   TermTypes,
   termType2label
@@ -230,4 +230,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=DifferentialAnalysis-NXTJPOCM.js.map
+//# sourceMappingURL=DifferentialAnalysis-KGQROTZI.js.map

package/dist/{Disco-MJ752FL2.js → Disco-OX7SZIWS.js}

@@ -5,15 +5,15 @@ import {
   renderTable,
   svgLegend,
   table2col
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
 import {
   dofetch3
-} from "./chunk-TR6EV3FG.js";
+} from "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import {
   bplen,
@@ -179,7 +179,7 @@ async function makeSvgraph(fusion, div, genome) {
   await getGm(svpair.a, genome.name, fusion.source.gene);
   await getGm(svpair.b, genome.name, fusion.target.gene);
   wait.remove();
-  const _ = await import("./svgraph-Y75ERQ6I.js");
+  const _ = await import("./svgraph-2BRH2IAX.js");
   _.default({
     pairlst: [svpair],
     genome,
@@ -278,7 +278,7 @@ var DiscoInteractions = class {
           }
         ]
       };
-      const _ = await import("./block.init-PLDXJDKU.js");
+      const _ = await import("./block.init-DIAKC2UR.js");
       await _.default(arg);
     };
     this.colorScaleNumericInputsCallback = async (obj) => {
@@ -3124,4 +3124,4 @@ export {
   discoInit,
   getPlotConfig
 };
-//# sourceMappingURL=Disco-MJ752FL2.js.map
+//# sourceMappingURL=Disco-OX7SZIWS.js.map

package/dist/{Disco.UI-5TXOVQI5.js → Disco.UI-NLKF3CLE.js}

@@ -1,6 +1,6 @@
 import {
   launch
-} from "./chunk-QEHDMXH3.js";
+} from "./chunk-662BKGG2.js";
 import {
   makeBtn,
   makeFileUpload,
@@ -9,19 +9,19 @@ import {
   makeResetBtn,
   makeTextAreaInput
 } from "./chunk-CUSG5PZE.js";
-import "./chunk-4JDI7ALX.js";
-import "./chunk-3AJTDJYW.js";
+import "./chunk-HVNP7GNR.js";
+import "./chunk-XVRPUSH2.js";
 import "./chunk-SKMFMGCD.js";
 import "./chunk-WWVHAWV4.js";
 import {
   Tabs,
   appear,
   sayerror
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import "./chunk-QSSTMH7C.js";
-import "./chunk-TR6EV3FG.js";
+import "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
@@ -236,4 +236,4 @@ function backButton(holder, genomes) {
 export {
   init_discoplotUI
 };
-//# sourceMappingURL=Disco.UI-5TXOVQI5.js.map
+//# sourceMappingURL=Disco.UI-NLKF3CLE.js.map

package/dist/{GB-UCD5AARN.js → GB-MZKRHE66.js}

@@ -10,15 +10,15 @@ import {
   make_one_checkbox,
   renderTable,
   sayerror
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
 import {
   dofetch3
-} from "./chunk-TR6EV3FG.js";
+} from "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import "./chunk-6RC5V24O.js";
 import "./chunk-IQIXGTQV.js";
@@ -891,7 +891,7 @@ var View = class {
     if (this.state.config.blockIsProteinMode) {
       if (!this.state.config.geneSearchResult.geneSymbol) throw "blockIsProteinMode=true but geneSymbol missing";
       arg.query = this.state.config.geneSearchResult.geneSymbol;
-      const _2 = await import("./block.init-PLDXJDKU.js");
+      const _2 = await import("./block.init-DIAKC2UR.js");
       await _2.default(arg);
       this.blockInstance = arg.__blockInstance;
       this.opts.header.text(arg.query);
@@ -902,7 +902,7 @@ var View = class {
     arg.start = this.state.config.geneSearchResult.start;
     arg.stop = this.state.config.geneSearchResult.stop;
     first_genetrack_tolist(this.opts.genome, arg.tklst);
-    const _ = await import("./block-ELGRFRYZ.js");
+    const _ = await import("./block-EEETZJSA.js");
     this.blockInstance = new _.Block(arg);
   }
 };
@@ -1098,4 +1098,4 @@ export {
   getPlotConfig,
   makeChartBtnMenu
 };
-//# sourceMappingURL=GB-UCD5AARN.js.map
+//# sourceMappingURL=GB-MZKRHE66.js.map

package/dist/{HicApp-TGI7FCZB.js → HicApp-V7AAKLW5.js}

@@ -1,9 +1,9 @@
 import {
   blocklazyload
-} from "./chunk-JTGW7ANC.js";
+} from "./chunk-5WK3YO6E.js";
 import {
   hicParseFile
-} from "./chunk-IAMFJMMC.js";
+} from "./chunk-ZTBG2CWD.js";
 import {
   ColorScale,
   axisstyle,
@@ -12,15 +12,15 @@ import {
   newpane,
   showErrorsWithCounter,
   tkt
-} from "./chunk-ZZPYB24S.js";
+} from "./chunk-OEWCFZ5K.js";
 import "./chunk-HJ6L54YS.js";
-import "./chunk-VEGMCJKQ.js";
+import "./chunk-WOVWZWSL.js";
 import {
   Menu
 } from "./chunk-QSSTMH7C.js";
 import {
   dofetch3
-} from "./chunk-TR6EV3FG.js";
+} from "./chunk-3HPIIGQW.js";
 import "./chunk-3JH6BKPD.js";
 import {
   bplen
@@ -2219,4 +2219,4 @@ var hicInit = getAppInit(HicApp);
 export {
   hicInit
 };
-//# sourceMappingURL=HicApp-TGI7FCZB.js.map
+//# sourceMappingURL=HicApp-V7AAKLW5.js.map