@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/chunk-EM6KUVI5.js

@@ -1,194 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-Y3SDMRDX.js";
-import {
-  isDictionaryType
-} from "./chunk-4Y5W26UF.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.data.js
-var matrix_data_exports = {};
-__export(matrix_data_exports, {
-  applyLegendValueFilter: () => applyLegendValueFilter,
-  getMatrixRequestOpts: () => getMatrixRequestOpts,
-  mayRequireToken: () => mayRequireToken,
-  setData: () => setData
-});
-function mayRequireToken(tokenMessage = "") {
-  const message = tokenMessage || this.state.tokenVerificationMessage;
-  if (!message && this.state.hasVerifiedToken) {
-    this.dom.errdiv.style("display", "none").html();
-    this.dom.controls.style("display", this.opts.controls ? "inline-block" : "");
-    this.dom.svg.style("display", "");
-    return false;
-  } else {
-    this.dom.errdiv.style("display", "").html(message || "Requires login");
-    this.dom.controls.style("display", "none");
-    this.dom.svg.style("display", "none");
-    return true;
-  }
-}
-function getMatrixRequestOpts(state, config) {
-  const terms = [];
-  const termgroups = this.chartType == "hierCluster" ? config.termgroups.filter((grp) => grp.type != "hierCluster") : config.termgroups;
-  for (const grp of termgroups) {
-    terms.push(...getNormalizedTwLstCopy(grp.lst));
-  }
-  if (config.divideBy) terms.push(normalizeTwForRequest(structuredClone(config.divideBy)));
-  const opts = {
-    terms,
-    filter: state.filter,
-    filter0: state.filter0,
-    maxGenes: state.config.settings.matrix.maxGenes,
-    /*********** quick fix
-    when the flag is true, set artificially large number to ensure all genes are sent in one query
-    this avoids changing getAnnotatedSampleData()
-    additional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX
-    */
-    termsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1e3 : 1
-  };
-  if (this.chartType == "hierCluster") {
-    opts.isHierCluster = 1;
-  }
-  return opts;
-}
-function getNormalizedTwLstCopy(twlst) {
-  const lst = [];
-  for (const tw of twlst) {
-    if (tw.type && tw.constructor.name != "Object") lst.push(tw);
-    else lst.push(normalizeTwForRequest(tw));
-  }
-  lst.forEach(normalizeTwForRequest);
-  lst.sort(sortTwLst);
-  return lst;
-}
-function normalizeTwForRequest(_tw) {
-  const tw = structuredClone(_tw);
-  if (!tw?.term) return;
-  delete tw.term.category2samplecount;
-  if (isDictionaryType(tw.term.type) && tw.term.type !== "samplelst") delete tw.term.values;
-  return tw;
-}
-function sortTwLst(twa, twb) {
-  const a = twa?.$id || twa.term?.id || twa?.term?.name;
-  const b = twb?.$id || twb.term?.id || twb?.term?.name;
-  return a < b ? -1 : 1;
-}
-async function setData(_data) {
-  const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state, this.config);
-  this.numTerms = opts.terms.length;
-  opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
-  opts.signal = this.api.getAbortSignal();
-  const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
-  this.data = data;
-  this.origData = structuredClone(this.data);
-  this.sampleIdMap = {};
-  for (const d of this.data.lst) {
-    this.sampleIdMap[d.sample] = d._ref_.label;
-  }
-}
-function applyLegendValueFilter() {
-  const self = this;
-  if (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return;
-  for (const grpFilter of self.config.legendGrpFilter.lst) {
-    if (grpFilter.dt) {
-      const filteredOutCats = /* @__PURE__ */ new Set();
-      for (const oneSampleData of self.origData.lst) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values) {
-            const newValues = [];
-            for (const v of annoForOneTerm.values) {
-              if (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {
-                newValues.push(v);
-              } else {
-                filteredOutCats.add(v.class);
-              }
-            }
-            annoForOneTerm.values = newValues;
-          }
-        }
-      }
-      grpFilter.filteredOutCats = [...filteredOutCats];
-      for (const oneSampleData of Object.values(self.origData.samples)) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values)
-            annoForOneTerm.values = annoForOneTerm.values.filter(
-              (v) => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))
-            );
-        }
-      }
-    }
-  }
-  const geneVariant$ids = Object.values(self.data.refs.byTermId).filter((v) => v.term?.type == "geneVariant").map((v) => v.$id);
-  const data = { samples: {}, lst: [], refs: self.data.refs };
-  const onlyHardFilter = structuredClone(self.config.legendValueFilter);
-  onlyHardFilter.lst = onlyHardFilter.lst.filter(
-    (l) => !l.tvs.legendFilterType || l.tvs.legendFilterType !== "geneVariant_soft"
-  );
-  for (const row of self.origData.lst) {
-    const include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids);
-    if (include || self.chartType == "hierCluster") {
-      data.samples[row.sample] = row;
-      data.lst.push(row);
-    }
-  }
-  for (const valFilter of self.config.legendValueFilter.lst) {
-    if (valFilter.tvs.legendFilterType !== "geneVariant_soft") continue;
-    const tvsV = valFilter.tvs.values[0];
-    const filteredOutCats = /* @__PURE__ */ new Set();
-    for (const oneSampleData of data.lst) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values) {
-          const newValues = [];
-          for (const v of annoForOneTerm.values) {
-            if (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {
-              newValues.push(v);
-            } else {
-              filteredOutCats.add(v.class);
-            }
-          }
-          annoForOneTerm.values = newValues;
-        }
-      }
-    }
-    valFilter.filteredOutCats = [...filteredOutCats];
-    for (const oneSampleData of Object.values(data.samples)) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values)
-          annoForOneTerm.values = annoForOneTerm.values.filter(
-            (v) => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))
-          );
-      }
-    }
-  }
-  if (self.chartType !== "hierCluster" && geneVariant$ids.length && self.app.vocabApi.termdbConfig?.matrix?.removeEmptySamples)
-    remove_empty_sample(data, geneVariant$ids);
-  self.data = data;
-}
-function remove_empty_sample(data) {
-  for (const oneSampleData of data.lst) {
-    let removeSample = true;
-    for (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {
-      if (!annoForOneTerm.values) continue;
-      const annoType = data.refs.byTermId[key].term.type;
-      if (annoType != "geneVariant") continue;
-      if (annoForOneTerm.values.length) removeSample = false;
-    }
-    if (removeSample) {
-      data.lst = data.lst.filter((dl) => dl.sample !== oneSampleData.sample);
-      delete data.samples[parseInt(oneSampleData.sample)];
-    }
-  }
-  return data;
-}
-
-export {
-  mayRequireToken,
-  getMatrixRequestOpts,
-  setData,
-  applyLegendValueFilter,
-  matrix_data_exports
-};
-//# sourceMappingURL=chunk-EM6KUVI5.js.map

package/dist/chunk-F4GYWCRF.js

@@ -1,302 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  bwSetting,
-  disappear2 as disappear,
-  makeNumericAxisConfig,
-  rgb2hex
-} from "./chunk-CSAS3PVJ.js";
-import {
-  dofetch3
-} from "./chunk-VTHZGUSZ.js";
-import {
-  axisLeft
-} from "./chunk-Z2ZITHT4.js";
-import {
-  format,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// src/block.tk.bigwig.js
-function bigwigfromtemplate(tk, template) {
-  tk.scale = {};
-  if (template.scale) {
-    for (const k in template.scale) {
-      tk.scale[k] = template.scale[k];
-    }
-  } else {
-    tk.scale.auto = 1;
-  }
-  if (tk.normalize) {
-  } else {
-    tk.normalize = {
-      dividefactor: 1,
-      disable: 1
-    };
-  }
-  tk.barheight = template.height || 50;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  if (!tk.ncolor) tk.ncolor = "#BD005E";
-  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
-  if (!tk.pcolor) tk.pcolor = "#005EBD";
-  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
-}
-function bigwigmaketk(tk, block) {
-  tk.img = tk.glider.append("image");
-  tk.tklabel.attr("y", tk.barheight / 2);
-  tk.leftaxis = tk.gleft.append("g");
-  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
-    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
-  });
-}
-async function bigwigload(tk, block) {
-  block.tkcloakon(tk);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
-  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  tk.img.attr("width", block.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    let data;
-    if (tk.imgData) {
-      data = tk.imgData;
-    } else {
-      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    }
-    if (data.error) throw data.error;
-    if (!data.src) throw "data.src missing";
-    tk.tklabel.transition().attr("y", tk.barheight / 2);
-    tk.img.attr("xlink:href", data.src);
-    if (data.minv != void 0) {
-      tk.scale.min = data.minv;
-    }
-    if (data.maxv != void 0) {
-      tk.scale.max = data.maxv;
-    }
-    tk.leftaxis.selectAll("*").remove();
-    if (data.nodata) {
-      throw "No data in view range";
-    }
-    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
-    const axis = axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max]);
-    if (tk.integer4axis) {
-      axis.tickFormat(format("d"));
-    }
-    axisstyle({
-      axis: tk.leftaxis.call(axis),
-      color: "black",
-      showline: true
-    });
-  } catch (err) {
-    tk.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff(tk, { error: errtext });
-    block.block_setheight();
-    for (const panel of tk.subpanels) {
-      bigwigloadsubpanel(tk, block, panel);
-    }
-  }
-}
-async function bigwigloadsubpanel(tk, block, panel) {
-  block.tkcloakon_subpanel(panel);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) {
-    par.dotplotfactor = tk.dotplotfactor;
-  }
-  par.width = panel.width;
-  par.rglst = [
-    {
-      chr: panel.chr,
-      start: panel.start,
-      stop: panel.stop,
-      width: panel.width
-    }
-  ];
-  delete par.percentile;
-  delete par.autoscale;
-  panel.img.attr("width", panel.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    if (tk.imgData) throw "subpanel not supported by imgData yet";
-    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    if (data.error) throw data.error;
-    panel.img.attr("xlink:href", data.src);
-  } catch (err) {
-    panel.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff_subpanel(panel, { error: errtext });
-  }
-}
-function bigwigconfigpanel(tk, block, holder, loader) {
-  const config = {
-    pcolor: {},
-    ncolor: {},
-    pcolor2: {},
-    ncolor2: {},
-    // .row
-    // .lab
-    dotplot: {},
-    // .row
-    dividefactor: {}
-  };
-  {
-    const row = holder.append("div").style("margin-bottom", "15px");
-    row.append("span").html("Height  ");
-    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
-      if (event.code != "Enter") return;
-      const s = event.target.value;
-      if (s == "") return;
-      const v = Number.parseInt(s);
-      if (Number.isNaN(v) || v <= 1) {
-        alert("track height must be positive integer");
-        return;
-      }
-      tk.barheight = v;
-      loader(bwSetting.height);
-    });
-  }
-  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
-  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
-    tk.pcolor = event.target.value;
-    loader(bwSetting.pcolor);
-  });
-  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
-  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
-    tk.ncolor = event.target.value;
-    loader(bwSetting.ncolor);
-  });
-  if (!tk.scale.auto) {
-    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
-    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
-      tk.pcolor2 = event.target.value;
-      loader(bwSetting.pcolor2);
-    });
-    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
-    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
-      tk.ncolor2 = event.target.value;
-      loader(bwSetting.ncolor2);
-    });
-  }
-  {
-    const setting = {};
-    if (tk.scale.auto) {
-      setting.auto = 1;
-    } else if (tk.scale.percentile) {
-      setting.percentile = tk.scale.percentile;
-    } else {
-      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
-    }
-    makeNumericAxisConfig({
-      holder: holder.append("div").style("margin-bottom", "15px"),
-      setting,
-      callback: (s) => {
-        if (s.auto) {
-          tk.scale.auto = 1;
-          loader(bwSetting.autoscale);
-          return;
-        }
-        if (s.fixed) {
-          delete tk.scale.auto;
-          delete tk.scale.percentile;
-          tk.scale.max = s.fixed.max;
-          tk.scale.min = s.fixed.min;
-          loader(bwSetting.fixedscale);
-          return;
-        }
-        delete tk.scale.auto;
-        tk.scale.percentile = s.percentile;
-        loader(bwSetting.percentilescale);
-      }
-    });
-  }
-  {
-    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
-    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
-    const s = config.dotplot.row.append("select").on("change", (event) => {
-      const i = event.target.selectedIndex;
-      if (i == 0) {
-        delete tk.dotplotfactor;
-      } else {
-        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
-      }
-      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
-    });
-    let o = s.append("option").text("no");
-    if (!tk.dotplotfactor) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("5");
-    if (tk.dotplotfactor == 5) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("10");
-    if (tk.dotplotfactor == 10) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("15");
-    if (tk.dotplotfactor == 15) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("20");
-    if (tk.dotplotfactor == 20) {
-      o.property("selected", 1);
-    }
-  }
-  config.dividefactor.row = holder.append("div");
-  {
-    const id = Math.random().toString();
-    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
-    if (!tk.normalize.disable) {
-      input.property("checked", 1);
-    }
-    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
-    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
-    folder.append("span").html("Divide raw value by&nbsp;");
-    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      const v = event.target.value;
-      if (v <= 0) {
-        return;
-      }
-      tk.normalize.dividefactor = v;
-      loader(bwSetting.usedividefactor);
-    });
-    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
-    input.on("change", (event) => {
-      if (event.target.checked) {
-        appear(folder);
-        delete tk.normalize.disable;
-        factorinput.property("value", tk.normalize.dividefactor);
-        loader(bwSetting.usedividefactor);
-        return;
-      }
-      disappear(folder);
-      tk.normalize.disable = 1;
-      loader(bwSetting.nodividefactor);
-    });
-  }
-  return config;
-}
-
-export {
-  bigwigfromtemplate,
-  bigwigmaketk,
-  bigwigload,
-  bigwigloadsubpanel,
-  bigwigconfigpanel
-};
-//# sourceMappingURL=chunk-F4GYWCRF.js.map

package/dist/chunk-FJ3JD7B3.js

@@ -1,59 +0,0 @@
-import {
-  plotColor
-} from "./chunk-UYKJOBRO.js";
-
-// plots/scatter/settings/defaults.ts
-function getDefaultScatterSettings(opts = {}) {
-  const overrides = opts?.overrides || {};
-  const defaults = {
-    size: 0.8,
-    minShapeSize: 0.5,
-    maxShapeSize: 4,
-    scaleDotOrder: "Ascending",
-    refSize: 0.8,
-    svgw: 600,
-    svgh: 600,
-    svgd: 600,
-    axisTitleFontSize: 16,
-    showAxes: true,
-    showRef: true,
-    opacity: 0.6,
-    defaultColor: plotColor,
-    regression: "None",
-    fov: 50,
-    threeSize: 5e-3,
-    threeFOV: 70,
-    maxSvgSamplesCutoff: 2e4,
-    // if a cohort is larger than this, switch from svg to webgl/canvas rendering
-    //ColorScale settings
-    colorScaleMode: "auto",
-    colorScalePercentile: 95,
-    colorScaleMinFixed: null,
-    colorScaleMaxFixed: null,
-    noExpColor: "#F5F5F5",
-    // light gray, for dots with no gene expression value
-    expColor: "#ff000d",
-    // default color for the maximum gene expression value
-    //3D Plot settings
-    showContour: false,
-    colorContours: false,
-    contourBandwidth: 30,
-    contourThresholds: 10,
-    duration: 500,
-    useGlobalMinMax: true,
-    saveZoomTransform: false,
-    // Axis scale settings
-    minXScale: null,
-    maxXScale: null,
-    minYScale: null,
-    maxYScale: null,
-    itemLabel: opts?.singleCellPlot ? "Cell" : "Sample",
-    maxTooltipRows: 5
-  };
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultScatterSettings
-};
-//# sourceMappingURL=chunk-FJ3JD7B3.js.map

package/dist/chunk-FW3ME75U.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-CSAS3PVJ.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-
-// termdb/handlers/snp.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: opts.holder,
-      searchOnly: "snp",
-      allowVariant: true,
-      callback: () => this.selectSnp(geneSearch)
-    });
-  }
-  async selectSnp(geneSearch) {
-    const { chr, ref, alt, fromWhat } = geneSearch;
-    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
-    let start, stop;
-    if (!geneSearch.start && !geneSearch.stop) {
-      if (geneSearch.pos) {
-        start = geneSearch.pos - 1;
-        stop = geneSearch.pos;
-      } else {
-        throw "missing coordinate of snp";
-      }
-    } else {
-      start = geneSearch.start;
-      stop = geneSearch.stop;
-    }
-    const term = {
-      id: fromWhat,
-      chr,
-      start,
-      stop,
-      name: fromWhat,
-      ref,
-      alt: typeof alt == "string" ? [alt] : alt,
-      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
-      type: "snp"
-    };
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-FW3ME75U.js.map