@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/chunk-QMXCK4Y5.js

@@ -1,203 +0,0 @@
-import {
-  tkt
-} from "./chunk-WY2PGUVX.js";
-import {
-  stratinput
-} from "./chunk-PF4DSFDR.js";
-import {
-  stratify_default
-} from "./chunk-VQZ2Z5YU.js";
-
-// src/vcf.tkconvert.js
-function vcf2dstk(arg) {
-  const ds = {
-    id2vcf: {},
-    label: arg.name || "Unnamed VCF file"
-  };
-  let vcfobj;
-  if (arg.file) {
-    const id = Math.random().toString();
-    vcfobj = {
-      file: arg.file,
-      indexURL: arg.indexURL,
-      vcfid: id
-    };
-    ds.id2vcf[id] = vcfobj;
-  } else if (arg.url) {
-    const id = Math.random().toString();
-    vcfobj = {
-      url: arg.url,
-      indexURL: arg.indexURL,
-      vcfid: id
-    };
-    ds.id2vcf[id] = vcfobj;
-  } else {
-    return ["no .file or .url"];
-  }
-  vcfobj.headernotloaded = true;
-  if (arg.samplenamemap) {
-    vcfobj.samplenamemap = arg.samplenamemap;
-  }
-  if (arg.variant2img) {
-    if (!arg.variant2img.path) return [".path missing from .variant2img{}"];
-  }
-  const tk = {
-    type: tkt.ds,
-    // to be loaded by loadvcftk() as a custom track, rather than "/dsdata" for official ds
-    isvcf: true,
-    name: ds.label,
-    ds,
-    populationfrequencyfilter: arg.populationfrequencyfilter,
-    vcfinfofilter: arg.vcfinfofilter,
-    itemlabelname: arg.itemlabelname,
-    viewrangeupperlimit: arg.viewrangeupperlimit,
-    variant2img: arg.variant2img,
-    axisheight: arg.axisheight
-  };
-  if (arg.url4variant) {
-    const err = check_url4variant(arg.url4variant);
-    if (err) return [".url4variant error: " + err];
-    tk.url4variant = arg.url4variant;
-  }
-  if (arg.button4variant) {
-    const err = check_button4variant(arg.button4variant);
-    if (err) return [".button4variant error: " + err];
-    tk.button4variant = arg.button4variant;
-  }
-  if (arg.sampleannotation) {
-    const sn = arg.sampleannotation;
-    if (!sn.annotation) return [".annotation{} missing from .sampleannotation"];
-    if (sn.levels) {
-      if (!Array.isArray(sn.levels)) return [".sampleannotation.levels should be array"];
-      const lst = [];
-      for (const sample in sn.annotation) {
-        const o = { sample_name: sample };
-        for (const k in sn.annotation[sample]) {
-          o[k] = sn.annotation[sample][k];
-        }
-        lst.push(o);
-      }
-      const nodes = stratinput(lst, sn.levels);
-      sn.root = stratify_default()(nodes);
-      sn.root.sum((i) => i.value);
-    }
-    if (sn.variantsunburst) {
-      if (!sn.levels) return [".levels missing when .variantsunburst is on from .sampleannotation"];
-    }
-    tk.ds.cohort = sn;
-  }
-  if (arg.vcfcohorttrack) {
-    if (!arg.vcfcohorttrack.file && !arg.vcfcohorttrack.url) return ["no .file or .url provided from .vcfcohorttrack"];
-    tk.ds.vcfcohorttrack = arg.vcfcohorttrack;
-  }
-  if (arg.germline2dvafplot) {
-    if (!arg.germline2dvafplot.individualkey) return [".individualkey missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.sampletypekey) return [".sampletypekey missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.xsampletype) return [".xsampletype missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.yleftsampletype) return [".yleftsampletype missing from germline2dvafplot"];
-    if (arg.germline2dvafplot.yrightsampletype) {
-      if (arg.germline2dvafplot.yrightsampletype == arg.germline2dvafplot.yleftsampletype)
-        return [".yrightsampletype should not be same as yleftsampletype"];
-    }
-    tk.ds.germline2dvafplot = arg.germline2dvafplot;
-  }
-  if (arg.vaf2coverageplot) {
-    if (arg.vaf2coverageplot.categorykey) {
-      if (!arg.vaf2coverageplot.categories)
-        return [".categories missing when .categorykey is in use for .vaf2coverageplot"];
-    }
-    tk.ds.vaf2coverageplot = arg.vaf2coverageplot;
-  }
-  if (arg.genotype2boxplot) {
-    if (arg.genotype2boxplot.boxplotvaluekey) {
-    } else if (arg.genotype2boxplot.sampleannotationkey) {
-      if (!tk.ds.cohort) return ["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];
-      if (!tk.ds.cohort.annotation)
-        return ["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];
-      let found = false;
-      for (const k in tk.ds.cohort.annotation) {
-        if (arg.genotype2boxplot.sampleannotationkey in tk.ds.cohort.annotation[k]) {
-          found = true;
-          break;
-        }
-      }
-      if (!found) return [arg.genotype2boxplot.sampleannotationkey + " not found in any sample annotation"];
-    } else {
-      return ["incomplete instruction for genotype2boxplot"];
-    }
-    tk.ds.genotype2boxplot = arg.genotype2boxplot;
-  }
-  if (arg.discardsymbolicallele) {
-    tk.ds.discardsymbolicallele = true;
-  }
-  if (arg.samplebynumericvalue) {
-    if (!arg.samplebynumericvalue.attrkey) return ["attrkey missing from samplebynumericvalue"];
-    if (!tk.ds.cohort) return ["sampleannotation missing when using samplebynumericvalue"];
-    if (!tk.ds.cohort.annotation) return ["sampleannotation.annotation missing when using samplebynumericvalue"];
-    let found = false;
-    for (const k in tk.ds.cohort.annotation) {
-      if (Number.isFinite(tk.ds.cohort.annotation[k][arg.samplebynumericvalue.attrkey])) {
-        found = true;
-        break;
-      }
-    }
-    if (!found) return ["samplebynumericvalue.attrkey not found in any sample annotation"];
-    tk.ds.samplebynumericvalue = arg.samplebynumericvalue;
-  }
-  {
-    const g = arg.genotypebynumericvalue;
-    if (g) {
-      if (!g.refref) return [tk.name + ": refref missing from genotypebynumericvalue"];
-      if (!g.refalt) return [tk.name + ": refalt missing from genotypebynumericvalue"];
-      if (!g.altalt) return [tk.name + ": altalt missing from genotypebynumericvalue"];
-      if (!g.refref.infokey) return [tk.name + ": refref.infokey missing from genotypebynumericvalue"];
-      if (!g.refalt.infokey) return [tk.name + ": refalt.infokey missing from genotypebynumericvalue"];
-      if (!g.altalt.infokey) return [tk.name + ": altalt.infokey missing from genotypebynumericvalue"];
-      if (g.refref.genotypeCountInfokey || g.refalt.genotypeCountInfokey || g.altalt.genotypeCountInfokey) {
-        if (!g.refref.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refref{}"];
-        if (!g.refalt.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refalt{}"];
-        if (!g.altalt.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.altalt{}"];
-      }
-      tk.ds.genotypebynumericvalue = g;
-    }
-  }
-  if (arg.pointdown) {
-    tk.aboveprotein = false;
-  }
-  if (arg.dstk_novcferror) {
-    tk.dstk_novcferror = true;
-  }
-  return [null, tk];
-}
-function check_url4variant(lst) {
-  if (!Array.isArray(lst)) return "value is not an array";
-  for (const item of lst) {
-    if (!item.makeurl) {
-      return ".makeurl missing";
-    }
-    if (typeof item.makeurl != "function") {
-      return ".makeurl must be a function";
-    }
-  }
-  return false;
-}
-function check_button4variant(lst) {
-  if (!Array.isArray(lst)) return "value is not an array";
-  for (const item of lst) {
-    if (!item.makebutton) {
-      return ".makebutton missing";
-    }
-    if (typeof item.makebutton != "function") {
-      return ".makebutton must be a function";
-    }
-  }
-  return false;
-}
-
-export {
-  vcf2dstk
-};
-//# sourceMappingURL=chunk-QMXCK4Y5.js.map

package/dist/chunk-ROJ3LJLE.js

@@ -1,448 +0,0 @@
-import {
-  setViolinRenderer
-} from "./chunk-W5X6C7LY.js";
-import {
-  setInteractivity
-} from "./chunk-25XCVML7.js";
-import {
-  PlotBase,
-  controlsInit,
-  defaultUiLabels,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  getSingleCellSpecialCase,
-  htmlLegend,
-  renderTerm1Label,
-  term0_term2_defaultQ
-} from "./chunk-WY2PGUVX.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  isNumericTerm
-} from "./chunk-NNFAUP2I.js";
-import {
-  plotColor
-} from "./chunk-7KRS7L4U.js";
-
-// plots/violin.js
-var ViolinPlot = class _ViolinPlot extends PlotBase {
-  static type = "violin";
-  constructor(opts) {
-    super(opts);
-    this.type = _ViolinPlot.type;
-  }
-  async init(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    const holder = this.opts.holder.append("div").attr("id", "sjpp-vp-holder");
-    const { controls, errdiv, loadingDiv, banner, renderedData, charts, legendDiv } = this.getStandardDomLayout(
-      holder,
-      this.opts
-    );
-    this.dom = {
-      hovertip: new Menu({ padding: "3px" }),
-      // separate tips for hover & click on violin labels to avoid interfering
-      clicktip: new Menu({ padding: "0px" }),
-      sampletabletip: new Menu({ padding: "3px" }),
-      // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..
-      header: this.opts.header,
-      controls: controls.attr("class", "sjpp-plot-controls").style("display", "inline-block"),
-      banner: banner.attr("data-testid", "sjpp-violin-banner"),
-      errdiv,
-      loadingDiv: loadingDiv.attr("data-testid", "sjpp-violin-loading-div").style("display", this.opts.mode != "minimal" ? "inline-block" : "none"),
-      renderedData,
-      violinDiv: charts.append("div").attr("class", "sjpp-vp-violinDiv").attr("data-testid", "sjpp-violin-div").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
-      legendDiv: legendDiv.classed("sjpp-vp-legend", true).attr("data-testid", "sjpp-violin-legend").style("margin-left", "-15px").style("padding-top", "20px")
-    };
-    setViolinRenderer(this);
-    setInteractivity(this);
-    if (this.opts.mode != "minimal") {
-      this.legendRenderer = htmlLegend(this.dom.legendDiv, {
-        settings: {
-          legendOrientation: "vertical"
-        },
-        handlers: {}
-      });
-    }
-  }
-  reactsTo(action) {
-    if (action.type.startsWith("plot_")) {
-      return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
-    }
-    return true;
-  }
-  preApiFreeze(api) {
-    api.download = this.download;
-    api.getChartImages = () => this.getChartImages();
-  }
-  async setControls() {
-    if (this.components.controls) return;
-    this.dom.controls.selectAll("*").remove();
-    const controlLabels = this.state.config.controlLabels;
-    if (!controlLabels) throw "controls labels not found";
-    this.components = {};
-    if (this.opts.mode == "minimal") return;
-    const specialCase = getSingleCellSpecialCase(this.config);
-    const inputs = [
-      {
-        type: "term",
-        configKey: "term",
-        chartType: "violin",
-        usecase: { target: "violin", detail: "term" },
-        label: controlLabels.term1?.label || renderTerm1Label,
-        vocabApi: this.app.vocabApi,
-        menuOptions: "edit"
-      },
-      {
-        type: "term",
-        configKey: "term2",
-        chartType: "violin",
-        usecase: { target: "violin", detail: "term2", specialCase },
-        title: controlLabels.term2.title || controlLabels.term2.label,
-        label: controlLabels.term2.label,
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: this.opts.numericEditMenuVersion,
-        defaultQ4fillTW: term0_term2_defaultQ,
-        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
-      },
-      {
-        type: "term",
-        configKey: "term0",
-        chartType: "violin",
-        usecase: { target: "violin", detail: "term0", specialCase },
-        title: controlLabels.term0.title || controlLabels.term0.label,
-        label: controlLabels.term0.label,
-        vocabApi: this.app.vocabApi,
-        // by default, do not allow continuous mode for divide-by term, since
-        // it will create a separate violin-overlay group per unique float or integer value
-        // and there will nonsensical tens/hundreds of these charts based on the cohort size
-        numericEditMenuVersion: this.opts.numericEditMenuVersion || ["discrete"],
-        defaultQ4fillTW: term0_term2_defaultQ,
-        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
-      },
-      {
-        label: "Orientation",
-        title: "Orientation of the chart",
-        type: "radio",
-        chartType: "violin",
-        settingsKey: "orientation",
-        options: [
-          { label: "Vertical", value: "vertical" },
-          { label: "Horizontal", value: "horizontal" }
-        ]
-      },
-      {
-        label: "Data symbol",
-        title: "Symbol type",
-        type: "radio",
-        chartType: "violin",
-        settingsKey: "datasymbol",
-        options: [
-          { label: "Ticks", value: "rug" },
-          { label: "Circles", value: "bean" },
-          { label: "Off", value: "none" }
-        ]
-      },
-      {
-        label: "Scale",
-        title: "Axis scale",
-        type: "radio",
-        chartType: "violin",
-        settingsKey: "isLogScale",
-        options: [
-          { label: "Linear", value: false },
-          { label: "Log10", value: true }
-        ]
-      },
-      {
-        label: "Order by",
-        title: "Order violin plots by parameters",
-        type: "radio",
-        chartType: "violin",
-        settingsKey: "orderByMedian",
-        options: [
-          { label: "Default", value: false },
-          { label: "Median", value: true }
-        ],
-        getDisplayStyle: () => {
-          let style = "none";
-          const charts = this.data?.charts || {};
-          for (const k of Object.keys(charts)) {
-            const chart = charts[k];
-            if (chart?.plots.length > 1) style = "";
-          }
-          return style;
-        }
-      },
-      {
-        label: "Symbol size",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "radius",
-        step: 1,
-        max: 30,
-        min: 4
-      },
-      {
-        label: "Bins",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "ticks",
-        title: "Number of bins used to build the plot",
-        min: 1,
-        max: 50
-      },
-      {
-        label: "Plot length",
-        title: "Length of the plot",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "svgw",
-        step: 10,
-        max: 1e3,
-        min: 200,
-        debounceInterval: 1e3
-      },
-      {
-        label: "Plot thickness",
-        title: "If not specified, the plot thickness is calculated based on the number of categories",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "plotThickness",
-        step: 10,
-        max: 200,
-        min: 20,
-        debounceInterval: 1e3
-      },
-      {
-        label: "Plot padding",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "rowSpace",
-        step: 1,
-        max: 20,
-        min: 0,
-        debounceInterval: 1e3
-      },
-      {
-        label: "Median length",
-        title: "Length of median",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "medianLength",
-        step: 1,
-        max: 50,
-        min: 3,
-        debounceInterval: 1e3
-      },
-      {
-        label: "Median color",
-        title: "color of median",
-        type: "color",
-        chartType: "violin",
-        settingsKey: "medianColor"
-      },
-      {
-        label: "Median thickness",
-        title: "Width of median",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "medianThickness",
-        step: 1,
-        max: 10,
-        min: 3,
-        debounceInterval: 100
-      },
-      {
-        label: "Default violin color",
-        type: "color",
-        chartType: "violin",
-        settingsKey: "defaultColor"
-      },
-      {
-        label: "Show stats",
-        type: "checkbox",
-        chartType: "violin",
-        settingsKey: "showStats",
-        boxLabel: "Yes"
-      },
-      {
-        label: "Show association tests",
-        type: "checkbox",
-        chartType: "violin",
-        settingsKey: "showAssociationTests",
-        boxLabel: "Yes",
-        getDisplayStyle: (plot) => plot.term2 ? "table-row" : "none"
-      }
-    ];
-    this.components.controls = await controlsInit({
-      app: this.app,
-      id: this.id,
-      holder: this.dom.controls,
-      inputs
-    });
-    this.components.controls.on("downloadClick.violin", this.download);
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      termfilter,
-      config,
-      displaySampleIds: appState.termdbConfig.displaySampleIds,
-      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken()
-    };
-  }
-  async main() {
-    this.config = structuredClone(this.state.config);
-    this.settings = this.config.settings.violin;
-    await this.setControls();
-    if (this.config.chartType != this.type && this.config.childType != this.type) return;
-    if (this.dom.header)
-      this.dom.header.html(
-        this.config.term.term.name + ` <span style="opacity:.6;font-size:1em;margin-left:10px;">Violin Plot</span>`
-      );
-    const existingMsg = this.dom.banner.style("display", "none").select("span");
-    if (!existingMsg.empty()) existingMsg.remove();
-    const args = this.validateArgs();
-    let data;
-    try {
-      this.toggleLoadingDiv("block", "block");
-      data = await this.app.vocabApi.getViolinBox(args, null, this.api.getAbortSignal());
-    } catch (e) {
-      this.toggleLoadingDiv("none", "none");
-      if (this.app.isAbortError(e)) return;
-      throw e;
-    }
-    this.data = data;
-    if (this.data.error) {
-      this.toggleLoadingDiv("none", "none");
-      throw this.data.error;
-    }
-    args.tw.q.descrStats = this.data.descrStats;
-    setTimeout(
-      () => {
-        this.render();
-        this.toggleLoadingDiv("none");
-      },
-      this.opts.mode == "minimal" ? 0 : 500
-    );
-  }
-  validateArgs() {
-    const { term, term2, term0, settings } = this.config;
-    const s = this.settings;
-    const arg = {
-      plotType: "violin",
-      svgw: s.svgw,
-      orientation: s.orientation,
-      devicePixelRatio: window.devicePixelRatio,
-      datasymbol: s.datasymbol,
-      radius: s.radius,
-      axisHeight: s.axisHeight,
-      rightMargin: s.rightMargin,
-      isLogScale: s.isLogScale,
-      ticks: s.ticks,
-      orderByMedian: s.orderByMedian,
-      filter: this.state.termfilter.filter
-    };
-    if (this.opts.mode == "minimal") {
-      arg.tw = term;
-      if (term2 || term0) throw "only a single term allowed for minimal plot";
-      if (term.q.mode == "spline") {
-        s.lines = term.q.knots.map((x) => Number(x.value));
-      } else {
-        s.lines = [];
-      }
-      if (term.q.scale) {
-        arg.scale = term.q.scale;
-      }
-    } else if (term.term?.type === "termCollection" && term.term?.memberType === "numeric") {
-      arg.tw = term;
-    } else if (isNumericTerm(term.term) && term.q.mode === "continuous") {
-      arg.tw = term;
-      if (term2) arg.overlayTw = term2;
-    } else if (isNumericTerm(term2?.term) && term2.q.mode === "continuous") {
-      arg.tw = term2;
-      arg.overlayTw = term;
-    } else {
-      throw "both term1 and term2 are not numeric/continuous";
-    }
-    if (term0) arg.divideTw = term0;
-    return arg;
-  }
-};
-var violinInit = getCompInit(ViolinPlot);
-var componentInit = violinInit;
-function getDefaultViolinSettings(app, overrides = {}) {
-  const defaults = {
-    orientation: "horizontal",
-    rowlabelw: 250,
-    brushRange: null,
-    //object with start and end if there is a brush selection
-    svgw: 500,
-    // span length of a plot/svg, not including margin
-    datasymbol: "rug",
-    radius: 10,
-    axisHeight: 60,
-    rightMargin: 50,
-    lines: [],
-    isLogScale: false,
-    // false: linear scale, true: log scale
-    rowSpace: 10,
-    medianLength: 7,
-    medianColor: "#FF0000",
-    medianThickness: 3,
-    ticks: 15,
-    defaultColor: plotColor,
-    method: 0,
-    orderByMedian: false,
-    showStats: true,
-    showAssociationTests: true
-  };
-  return Object.assign(defaults, overrides);
-}
-async function getPlotConfig(opts, app) {
-  if (!opts.term) throw "violin getPlotConfig: opts.term{} missing";
-  try {
-    await fillTermWrapper(opts.term, app.vocabApi);
-    if (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi);
-    if (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi);
-  } catch (e) {
-    throw `${e} [violin getPlotConfig()]`;
-  }
-  const config = {
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    settings: {
-      controls: {
-        term2: null,
-        // the previous overlay value may be displayed as a convenience for toggling
-        term0: null
-      },
-      // common: {
-      // 	use_logscale: false, // flag for y-axis scale type, 0=linear, 1=log
-      // 	use_percentage: false,
-      // 	barheight: 300, // maximum bar length
-      // 	barwidth: 20, // bar thickness
-      // 	barspace: 2 // space between two bars
-      // },
-      violin: getDefaultViolinSettings(app)
-    }
-  };
-  return copyMerge(config, opts);
-}
-
-export {
-  violinInit,
-  componentInit,
-  getDefaultViolinSettings,
-  getPlotConfig
-};
-//# sourceMappingURL=chunk-ROJ3LJLE.js.map