@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/chunk-WHI6466S.js

@@ -1,146 +0,0 @@
-import {
-  violinRenderer
-} from "./chunk-DD4R5P6W.js";
-import {
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import {
-  drag_default
-} from "./chunk-KYBIQBXE.js";
-import {
-  pointer_default,
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// termsetting/handlers/NumericDensity.ts
-var NumericDensity = class {
-  constructor(opts) {
-    this.dom = {};
-    // WeakMap allows deletion of value when the object/DOM key is deleted,
-    // so better for avoiding memory leak
-    this.vrByDiv = /* @__PURE__ */ new WeakMap();
-    this.ranges = [];
-    this.no_density_data = false;
-    this.brushes = [];
-    this.plot_size = {
-      width: 500,
-      height: 100,
-      xpad: 10,
-      ypad: 20,
-      radius: 8
-    };
-    this.opts = opts;
-    this.termsetting = opts.termsetting;
-    this.tw = opts.termsetting.tw;
-  }
-  async setData() {
-    const self = this.termsetting;
-    const d = await self.vocabApi.getViolinBox(
-      {
-        plotType: "violin",
-        tw: { term: self.term, q: self.q },
-        svgw: this.plot_size.width,
-        radius: this.plot_size.radius,
-        filter: self.filter
-      },
-      self.opts.getBodyParams?.()
-    );
-    if (d.error) throw d;
-    this.density_data = d;
-    return this.density_data;
-  }
-  async showViolin(div, boundaryOpts) {
-    await this.setData();
-    if (!this.vrByDiv.has(div)) {
-      div.style("padding", "5px").selectAll("*").remove();
-      const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
-      const densityDiv = div.append("div");
-      loadingDiv.remove();
-      const vr = new violinRenderer({
-        holder: densityDiv,
-        rd: this.density_data,
-        width: this.plot_size.width,
-        height: this.plot_size.height,
-        radius: this.plot_size.radius
-      });
-      this.vrByDiv.set(div, vr);
-    }
-    this.vr = this.vrByDiv.get(div);
-    this.dom.svg = this.vr.svg;
-    this.vr.render();
-    if (boundaryOpts) await this.setBinLines(boundaryOpts);
-    return this.density_data;
-  }
-  async setBinLines(boundaryOpts) {
-    if (this.density_data.max == this.density_data.min) {
-      this.handleNoDensity();
-    } else {
-      if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
-      this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
-      const maxvalue = this.density_data.max;
-      const minvalue = this.density_data.min;
-      this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
-      this.ranges = [];
-      this.brushes = [];
-      this.renderBinLines(boundaryOpts);
-    }
-  }
-  handleNoDensity() {
-    this.no_density_data = true;
-    this.ranges = [];
-    this.brushes = [];
-  }
-  renderBinLines(boundaryOpts) {
-    const { density_data, plot_size, tw, xscale } = this;
-    if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
-    const scaledMinX = Math.round(this.xscale(density_data.min));
-    const scaledMaxX = Math.round(this.xscale(density_data.max));
-    const lines = [];
-    for (const [index, v] of boundaryOpts.values.entries()) {
-      lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
-    }
-    const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
-    const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
-    const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
-    this.dom.binsize_g.selectAll("line").remove();
-    this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
-      if (d.isDraggable) select_default(this).style("stroke-width", 3);
-    }).on("mouseout", function() {
-      select_default(this).style("stroke-width", 1);
-    }).each(function(d) {
-      if (d.isDraggable) select_default(this).call(dragger);
-    });
-    const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
-    function onDrag(event, _d) {
-      const draggedX = pointer_default(event, this)[0];
-      if (draggedX <= scaledMinX || draggedX >= scaledMaxX) return;
-      const d = _d;
-      d.draggedX = draggedX;
-      select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
-      const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
-      const xOffset = d.draggedX - d.scaledX;
-      if (xOffset) {
-        for (const elem of lineElems) {
-          const c = elem.__data__;
-          if (c.movesWithLineIndex !== d.index) continue;
-          c.draggedX = c.scaledX + xOffset;
-          select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
-        }
-        const inverted = xscale.invert(d.draggedX);
-        const value = tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3);
-        boundaryOpts.callback(d, Number(value));
-      }
-    }
-  }
-  destroy() {
-    for (const [k, v] of Object.entries(this.dom)) {
-      delete this.dom[k];
-      if (typeof v.remove == "function") v.remove();
-    }
-  }
-};
-
-export {
-  NumericDensity
-};
-//# sourceMappingURL=chunk-WHI6466S.js.map

package/dist/chunk-WSDUD52Y.js

@@ -1,55 +0,0 @@
-import {
-  colorinframe
-} from "./chunk-SA7APTJR.js";
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-4UWS5Y3N.js";
-
-// src/spliceevent.phrase.js
-function spliceevent_phrase_default(evt) {
-  const htmls = [];
-  if (evt.isaltexon || evt.isskipexon) {
-    const exonstart = Math.min(...evt.skippedexon);
-    const exonstop = Math.max(...evt.skippedexon);
-    htmls.push(
-      '<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
-    );
-    if (evt.isaltexon) {
-      htmls.push(
-        "<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
-      );
-    } else {
-      htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
-    }
-    if (evt.junctionB.data) {
-      htmls.push(
-        "<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
-      );
-    }
-    htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
-    if (evt.framenocheck) {
-      if (evt.utr3) {
-        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
-      } else if (evt.utr5) {
-        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
-      }
-    } else if (evt.frame == IN_frame) {
-      htmls.push(
-        '<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
-      );
-    } else if (evt.frame == OUT_frame) {
-      htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
-    } else {
-      htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
-    }
-  } else {
-    return "unknown event type!!";
-  }
-  return htmls.join(" ");
-}
-
-export {
-  spliceevent_phrase_default
-};
-//# sourceMappingURL=chunk-WSDUD52Y.js.map

package/dist/chunk-XAVNZNXQ.js

@@ -1,95 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-BWGU5NJS.js";
-import {
-  fillTermWrapper
-} from "./chunk-SA7APTJR.js";
-import {
-  copyMerge
-} from "./chunk-M3J4MINX.js";
-import {
-  TermTypes,
-  numericTypes
-} from "./chunk-NOEAT6CX.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const hierClusterSubTypeOverrides = app.vocabApi.termdbConfig[`${config.dataType}Cluster`] || {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    hierClusterSubTypeOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType == TermTypes.GENE_EXPRESSION || config.dataType == TermTypes.METABOLITE_INTENSITY || config.dataType == TermTypes.PROTEOME_ABUNDANCE || config.dataType == TermTypes.SSGSEA) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (grpType == "numericDictTerm") {
-    if (twType == "float" || twType == "integer") return true;
-  }
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-XAVNZNXQ.js.map

package/dist/chunk-XMLURPEP.js

@@ -1,194 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-YZK37YCC.js";
-import {
-  isDictionaryType
-} from "./chunk-NOEAT6CX.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.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.vocab?.dslabel == "GDC")
-    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-XMLURPEP.js.map