@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/chunk-L3PMRBTA.js

@@ -1,422 +0,0 @@
-import {
-  setViolinRenderer
-} from "./chunk-RCVZ4L7K.js";
-import {
-  setInteractivity
-} from "./chunk-F3FTQWTA.js";
-import {
-  PlotBase,
-  defaultUiLabels
-} from "./chunk-I2GCD26Y.js";
-import {
-  controlsInit,
-  renderTerm1Label,
-  term0_term2_defaultQ
-} from "./chunk-CZTC4MTE.js";
-import {
-  fillTermWrapper,
-  getCombinedTermFilter,
-  htmlLegend
-} from "./chunk-UT6W4ZZL.js";
-import {
-  isNumericTerm
-} from "./chunk-RYRCMHYR.js";
-import {
-  plotColor
-} from "./chunk-ECKWM4HB.js";
-import {
-  Menu
-} from "./chunk-NXOWHUR4.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-FYTZCTJC.js";
-
-// plots/violin.js
-var ViolinPlot = class extends PlotBase {
-  static type = "violin";
-  constructor(opts) {
-    super(opts);
-    this.type = "violin";
-  }
-  async init(appState) {
-    const controls = this.opts.holder.append("div").attr("class", "sjpp-plot-controls").style("display", "inline-block");
-    const config = appState.plots.find((p) => p.id === this.id);
-    const holder = this.opts.holder.append("div").style("display", "inline-block").style("padding", this.opts.mode != "minimal" ? "5px" : "0px").style("padding-left", this.opts.mode != "minimal" ? "20px" : "0px").attr("id", "sjpp-vp-holder");
-    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,
-      loadingDiv: this.opts.holder.append("div").style("display", this.opts.mode != "minimal" ? "inline-block" : "none").style("padding", "24px").text("Loading ..."),
-      controls,
-      banner: holder.append("div").style("display", "none").style("text-align", "center").style("padding", "24px").style("font-size", "16px").style("color", "#aaa"),
-      violinDiv: holder.append("div").attr("class", "sjpp-vp-violinDiv").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
-      legendDiv: holder.append("div").classed("sjpp-vp-legend", true).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() {
-    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 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" },
-        title: controlLabels.term2.title || controlLabels.term2.label,
-        label: controlLabels.term2.label,
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: this.opts.numericEditMenuVersion,
-        defaultQ4fillTW: term0_term2_defaultQ
-      },
-      {
-        type: "term",
-        configKey: "term0",
-        chartType: "violin",
-        usecase: { target: "violin", detail: "term0" },
-        title: controlLabels.term0.title || controlLabels.term0.label,
-        label: controlLabels.term0.label,
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: this.opts.numericEditMenuVersion,
-        defaultQ4fillTW: term0_term2_defaultQ
-      },
-      {
-        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: "unit",
-        options: [
-          { label: "Linear", value: "abs" },
-          { label: "Log10", value: "log" }
-        ]
-      },
-      {
-        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";
-          for (const k of Object.keys(this.data.charts)) {
-            const chart = this.data.charts[k];
-            if (chart.plots.length > 1) style = "";
-          }
-          return style;
-        }
-      },
-      {
-        label: "Symbol size",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "radius",
-        step: 1,
-        max: 10,
-        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: 15,
-        min: 3,
-        debounceInterval: 1e3
-      },
-      {
-        label: "Median thickness",
-        title: "Width of median",
-        type: "number",
-        chartType: "violin",
-        settingsKey: "medianThickness",
-        step: 1,
-        max: 10,
-        min: 3,
-        debounceInterval: 100
-      },
-      {
-        label: "Default color",
-        type: "color",
-        chartType: "violin",
-        settingsKey: "defaultColor"
-      },
-      {
-        label: "Show stats",
-        type: "checkbox",
-        chartType: "violin",
-        settingsKey: "showStats",
-        boxLabel: "Yes"
-      }
-    ];
-    if (this.config.term2)
-      inputs.push({
-        label: "Show association tests",
-        type: "checkbox",
-        chartType: "violin",
-        settingsKey: "showAssociationTests",
-        boxLabel: "Yes"
-      });
-    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 args = this.validateArgs();
-    let data;
-    try {
-      data = await this.app.vocabApi.getViolinPlotData(args, null, this.api.getAbortSignal());
-    } catch (e) {
-      if (this.app.isAbortError(e)) return;
-      throw e;
-    }
-    this.data = data;
-    if (this.data.error) throw this.data.error;
-    args.tw.q.descrStats = this.data.descrStats;
-    this.toggleLoadingDiv(this.opts.mode == "minimal" ? "none" : "");
-    setTimeout(
-      () => {
-        this.render();
-      },
-      this.opts.mode == "minimal" ? 0 : 500
-    );
-    this.toggleLoadingDiv("none");
-  }
-  validateArgs() {
-    const { term, term2, term0, settings } = this.config;
-    const s = this.settings;
-    const arg = {
-      svgw: s.svgw,
-      orientation: s.orientation,
-      devicePixelRatio: window.devicePixelRatio,
-      datasymbol: s.datasymbol,
-      radius: s.radius,
-      axisHeight: s.axisHeight,
-      rightMargin: s.rightMargin,
-      unit: s.unit,
-      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 (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: [],
-    unit: "abs",
-    // abs: absolute scale, log: log scale
-    rowSpace: 10,
-    medianLength: 7,
-    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 = {
-    id: opts.term.term.id,
-    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-L3PMRBTA.js.map

package/dist/chunk-M7QVMSRW.js

@@ -1,293 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-UT6W4ZZL.js";
-import {
-  dofetch3
-} from "./chunk-5TDKRZN5.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-ECKWM4HB.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-B7WMYLPO.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-5YJ4U4BV.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-B7WMYLPO.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-M7QVMSRW.js.map