@sjcrh/proteinpaint-client 2.224.1 → 2.224.2

package/dist/chunk-MNN6NFZK.js

@@ -1,203 +0,0 @@
-import {
-  tkt
-} from "./chunk-3YQYWX4M.js";
-import {
-  stratinput
-} from "./chunk-PF4DSFDR.js";
-import {
-  stratify_default
-} from "./chunk-4OLM3KSB.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-MNN6NFZK.js.map

package/dist/chunk-N4ULQIGJ.js

@@ -1,379 +0,0 @@
-import {
-  SPANSELECTOR,
-  renderLabelSpans,
-  trackLabelSpanData
-} from "./chunk-C2MCQZWH.js";
-import {
-  fillTermWrapper,
-  termsettingInit
-} from "./chunk-3YQYWX4M.js";
-import {
-  isNumericTerm
-} from "./chunk-JHLF2ZC2.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// plots/matrix/matrix.renderers.js
-function setRenderers(self) {
-  self.render = function() {
-    const s = self.settings.matrix;
-    const l = self.layout;
-    const d = self.dimensions;
-    const duration = self.dom.svg.attr("width") ? s.duration : 0;
-    self.dom.clipRect.attr("x", d.xOffset - 1).attr("y", 0).attr("width", d.mainw + 3).attr("height", d.mainh + 500);
-    self.renderSerieses(s, l, d, duration);
-    self.renderLabels(s, l, d, duration);
-    self.renderDivideByLabel(s, l, d, duration);
-    self.dom.colBeam.attr("width", d.dx).attr("height", d.mainh).style("stroke", s.beamStroke);
-    self.dom.rowBeam.attr("width", d.zoomedMainW).attr("height", s.rowh).style("stroke", s.beamStroke);
-  };
-  self.renderSerieses = function(s, l, d, duration) {
-    if (self.prevUseCanvas != s.useCanvas) {
-      self.dom.seriesesG.selectAll("g").remove();
-    }
-    if (s.useCanvas) {
-      const _g = self.dom.seriesesG.selectAll("g");
-      const g = (
-        /*(_g.size() && _g) ||*/
-        self.dom.seriesesG.append("g").datum(this.serieses)
-      );
-      self.renderCanvas(this.serieses, g, d, s, _g, duration);
-    } else {
-      self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
-      const sg = self.dom.seriesesG.selectAll(".sjpp-mass-series-g").data(this.serieses, (series) => series.tw.$id);
-      sg.exit().remove();
-      sg.each(self.renderSeries);
-      sg.enter().append("g").attr("class", "sjpp-mass-series-g").attr("data-testid", (d2) => `sjpp-mass-series-g-${d2.tw.term.name}`).style("opacity", 1e-3).each(self.renderSeries);
-      self.mouseout();
-    }
-    self.prevUseCanvas = s.useCanvas;
-  };
-  self.renderSeries = async function(series) {
-    const s = self.settings.matrix;
-    const d = self.dimensions;
-    const g = select_default(this);
-    const duration = g.attr("transform") ? s.duration : 0;
-    g.attr("transform", `translate(${series.x},${series.y})`).style("opacity", 1);
-    const last = series.cells[series.cells.length - 1];
-    const height = series.y + last?.y + s.rowh;
-    const rects = g.selectAll("rect").data(series.cells, (cell) => cell.sample + ";;" + cell.tw.$id + ";;" + cell.valueIndex);
-    rects.exit().remove();
-    rects.each(self.renderCell);
-    rects.enter().append("rect").each(self.renderCell);
-  };
-  self.renderCanvas = async function(serieses, g, d, s, _g, duration) {
-    const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
-    g.selectAll("*").remove();
-    const width = d.imgW;
-    const height = self.dimensions.mainh;
-    const canvas = window.OffscreenCanvas ? new OffscreenCanvas(width * pxr, height * pxr) : (
-      // TODO: no need to support older browser versions???
-      self.dom.holder.append("canvas").attr("width", pxr * width).attr("height", pxr * height).style("opacity", 0).node()
-    );
-    const ctx = canvas.getContext("2d");
-    ctx.imageSmoothingEnabled = false;
-    ctx.imageSmoothingQuality = "high";
-    ctx.scale(pxr, pxr);
-    for (const series of serieses) {
-      for (const cell of series.cells) {
-        self.renderCellWithCanvas(ctx, cell, series, s, d, series.y);
-      }
-    }
-    if (window.OffscreenCanvas) {
-      const reader = new FileReader();
-      reader.addEventListener(
-        "load",
-        () => {
-          _g?.remove();
-          self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
-          g.selectAll("image").remove();
-          g.append("image").attr("xlink:href", reader.result).attr("x", d.xMin).attr("width", width).attr("height", height);
-        },
-        false
-      );
-      const blob = await canvas.convertToBlob({ quality: 1 });
-      const dataURL = reader.readAsDataURL(blob);
-    } else {
-      _g?.remove();
-      self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
-      const dataURL = canvas.toDataURL();
-      const ratio = window.devicePixelRatio * window.devicePixelRatio;
-      g.append("image").attr("width", width).attr("height", height).attr("xlink:href", dataURL);
-      if (!window.OffscreenCanvas) canvas.remove();
-    }
-    self.mouseout();
-  };
-  self.renderCellWithCanvas = function(ctx, cell, series, s, d, _y) {
-    if (!cell.fill)
-      cell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell);
-    const x = cell.x ? cell.x - d.xMin : 0;
-    const y = _y ? _y + cell.y : cell.y || 0;
-    const width = s.useMinPixelWidth ? Math.max(cell.width || d.colw, d.pxw) : cell.width || d.colw;
-    const height = "height" in cell ? cell.height : s.rowh;
-    ctx.fillStyle = cell.fill;
-    ctx.fillRect(x, y, width, height);
-    const borderWidth = Math.min(width, height) * 0.1;
-    if (cell.border) {
-      ctx.lineWidth = borderWidth;
-      ctx.strokeStyle = "white";
-      ctx.strokeRect(x, y, width, height);
-    }
-  };
-  self.renderCell = function(cell) {
-    if (!cell.fill)
-      cell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell);
-    const s = self.settings.matrix;
-    const rect = select_default(this).attr("x", cell.x || 0).attr("y", cell.y || 0).attr("width", cell.width || self.dimensions.colw).attr("height", "height" in cell ? Math.max(0, cell.height) : s.rowh).attr("shape-rendering", "crispEdges").attr("fill", cell.fill);
-    if (cell.border) {
-      rect.attr("stroke", "white").attr("stroke-width", 0.8);
-    }
-  };
-  self.renderLabels = function(s, l, d, duration) {
-    const relatedSamplesByAncestorId = /* @__PURE__ */ new Map();
-    for (const direction of ["top", "btm", "left", "right"]) {
-      let renderLabel2 = function(lab) {
-        const g = select_default(this);
-        g.attr("transform", side.attr.labelGTransform);
-        if (!g.select(":scope>text").size()) g.append("text");
-        const showContAxis = !side.isGroup && lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous";
-        const labelText = side.label(lab);
-        const text = g.select(":scope>text").attr("fill", "#000").attr("data-testid", `sjpp-matrix-label-${direction}`).style("display", side.display || "");
-        let continuousBarHAdjust;
-        const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-        const twSettingsBarH = twSpecificSettings[lab.tw?.$id]?.contBarH;
-        if (twSettingsBarH && s.barh) continuousBarHAdjust = (twSettingsBarH - s.barh) * 0.5;
-        text.attr(
-          "display",
-          lab.grp?.type === "hierCluster" && s.clusterRowh < 6 ? "none" : side.attr.fontSize < 6 || labelText === "configure" ? "none" : ""
-        ).attr("font-size", lab.grp?.type === "hierCluster" ? Math.max(4, s.clusterRowh - 4) : side.attr.fontSize).attr("text-anchor", side.attr.labelAnchor).attr(
-          "transform",
-          side.attr.labelTransform + (continuousBarHAdjust ? ` translate(0,${continuousBarHAdjust})` : "")
-        ).attr("cursor", "pointer").attr(side.attr.textpos.coord, side.attr.textpos.factor * (showContAxis ? 30 : 0));
-        if (!Array.isArray(labelText)) {
-          text.text(labelText);
-          text.attr(
-            "y",
-            lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous" ? 10 : lab.grp?.type === "hierCluster" ? 0.1 * s.clusterRowh : 0
-          );
-          if (lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous") text.attr("x", -20);
-        } else {
-          text.text("");
-          const tspan = text.selectAll("tspan").data(labelText);
-          tspan.enter().append("tspan").attr("class", getTspanCls2).attr("dx", getTspanDx2).attr("font-size", getTspanFontSize2).text(getTspanText2);
-        }
-        text.on("mouseover", labelText === "configure" ? () => text.attr("opacity", 0.5) : null).on("mouseout", labelText === "configure" ? () => text.attr("opacity", 0) : null);
-        const hasAxis = g.select(".sjpp-matrix-cell-axis").size() && true;
-        if (showContAxis && labelText) {
-          if (!hasAxis) {
-            g.append("g").attr("class", "sjpp-matrix-cell-axis").attr("shape-rendering", "crispEdges");
-          }
-          const axisg = g.select(".sjpp-matrix-cell-axis");
-          axisg.selectAll("*").remove();
-          const domain = [lab.counts.maxval, lab.counts.minval];
-          if (s.transpose) domain.reverse();
-          const twSpecificSettings2 = self.config.settings.matrix.twSpecificSettings;
-          const twSettings = twSpecificSettings2[lab.tw.$id];
-          const x = !s.transpose ? 0 : twSettings.contBarGap - 1 - lab.labelOffset;
-          const y = !s.transpose ? twSettings.contBarGap - 1 - lab.labelOffset : 0;
-          axisg.attr("shape-rendering", "crispEdges").attr("transform", `translate(${x},${y})`).call(side.attr.axisFxn(lab.scales.full.domain(lab.scales.tickValues)).tickValues(lab.scales.tickValues));
-        } else if (hasAxis) {
-          g.select(".sjpp-matrix-cell-axis").remove();
-        }
-        if (self.config.chartType == "matrix" && s.sortBySampleAncestry && side.prefix == "sample")
-          trackLabelSpanData(lab, side, direction, text, relatedSamplesByAncestorId);
-      }, getTspanCls2 = function(d2) {
-        return d2.cls;
-      }, getTspanDx2 = function(d2) {
-        return d2.dx;
-      }, getTspanFontSize2 = function(d2) {
-        return d2.fontSize || side.attr.fontSize;
-      }, getTspanText2 = function(d2) {
-        return d2.text;
-      };
-      var renderLabel = renderLabel2, getTspanCls = getTspanCls2, getTspanDx = getTspanDx2, getTspanFontSize = getTspanFontSize2, getTspanText = getTspanText2;
-      const side = l[direction];
-      side.box.style("display", side.display || "").attr("transform", side.attr.boxTransform);
-      const labels = side.box.selectAll(".sjpp-matrix-label").data(side.data, side.key);
-      labels.exit().remove();
-      labels.each(renderLabel2);
-      labels.enter().append("g").attr("class", "sjpp-matrix-label").each(renderLabel2);
-      side.box.selectAll(SPANSELECTOR).remove();
-      if (self.config.chartType == "matrix" && s.sortBySampleAncestry && side.prefix == "sample")
-        renderLabelSpans(relatedSamplesByAncestorId, side, d);
-    }
-  };
-  self.colLabelGTransform = (lab, grpIndex) => {
-    const s = self.settings.matrix;
-    const d = self.dimensions;
-    lab.labelOffset = 0.8 * d.colw;
-    const x = lab.grpIndex * s.colgspace + lab.totalIndex * d.dx + lab.labelOffset + lab.totalHtAdjustments;
-    const y = 0;
-    return `translate(${x + d.seriesXoffset},${y})`;
-  };
-  self.colGrpLabelGTransform = (lab, grpIndex) => {
-    const s = self.settings.matrix;
-    const d = self.dimensions;
-    const len = (lab.processedLst || lab.grp.lst).length;
-    const x = lab.grpIndex * s.colgspace + lab.prevGrpTotalIndex * d.dx + len * d.dx / 2 + s.grpLabelFontSize / 2 + lab.totalHtAdjustments;
-    return `translate(${x + d.seriesXoffset},0)`;
-  };
-  self.rowLabelGTransform = (lab, grpIndex) => {
-    const s = self.settings.matrix;
-    const d = self.dimensions;
-    const x = 0;
-    lab.labelOffset = 0.7 * (lab.grp.type == "hierCluster" ? s.clusterRowh : s.rowh);
-    const y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + lab.labelOffset + lab.totalHtAdjustments;
-    return `translate(${x},${y})`;
-  };
-  self.rowGrpLabelGTransform = (lab, grpIndex) => {
-    const s = self.settings.matrix;
-    const d = self.dimensions;
-    const len = (lab.processedLst || lab.grp.lst).length;
-    const x = lab.tw?.q?.mode == "continuous" ? 20 : 0;
-    const y = lab.grpIndex * s.rowgspace + lab.prevGrpTotalIndex * d.dy + len * d.dy / 2 + s.grpLabelFontSize / 2 + lab.totalHtAdjustments;
-    return `translate(${x},${y})`;
-  };
-  self.rowAxisGTransform = (lab, grpIndex) => {
-    const s = self.settings.matrix;
-    const d = self.dimensions;
-    const x = 0;
-    const y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + 0.7 * s.rowh + lab.totalHtAdjustments;
-    return `translate(${x},${y})`;
-  };
-  self.renderDivideByLabel = async (s, l, d) => {
-    self.dom.mainG.selectAll(".sjpp-matrix-divide-by-label").remove();
-    if (!self.config.divideBy) return;
-    const name = self.config.divideBy?.term.name || "";
-    const text = name.length <= s.rowlabelmaxchars ? name : name.slice(0, s.rowlabelmaxchars) + "\u2026";
-    const sides = !s.transpose ? [l.left, l.right] : [l.top, l.bottom];
-    const box = sides.find((d2) => !d2.isGroup)?.box;
-    const y = (s.collabelpos == "top" ? d.mainh + s.collabelmaxchars : -s.collabelmaxchars) + 8;
-    const anchor = s.rowlabelpos == "left" ? "end" : "start";
-    const cl = s.controlLabels;
-    const gNote = box.append("g").attr("class", "sjpp-matrix-divide-by-label").attr("transform", `translate(0, ${y})`);
-    gNote.append("text").attr("text-anchor", anchor).attr("font-style", "italic").attr("y", -20).text(`${cl.Samples} grouped by`);
-    const g = box.datum({ tw: self.config.divideBy }).append("g").attr("class", "sjpp-matrix-divide-by-label").attr("transform", `translate(0, ${y})`).on("click", (event, d2) => {
-      pill.showMenu(event, textElem.node());
-    });
-    const textElem = g.append("text").attr("text-anchor", anchor).attr("font-weight", 600).text(text);
-    g.append("title").text(`${cl.Samples} are grouped by this gene or variable. Click to edit.`);
-    const customMenuOptions = [];
-    const tvsKey = isNumericTerm(self.config.divideBy.term) ? "ranges" : "values";
-    if (self.config.legendValueFilter.lst?.find(
-      (l2) => l2.legendGrpName == self.config.divideBy.term.id || l2.legendGrpName == self.config.divideBy.term.name
-    )?.tvs[tvsKey]?.length) {
-      customMenuOptions.push({ label: `Show filtered ${cl.samples}`, callback: self.showDeletedSampleGroups });
-    }
-    const pill = await termsettingInit({
-      menuOptions: "{edit,replace,remove}",
-      //numericEditMenuVersion: opts.numericEditMenuVersion,
-      customMenuOptions,
-      //custom menu options other than menuOptions
-      vocabApi: self.app.vocabApi,
-      vocab: self.state.vocab,
-      //activeCohort: opts.state?.activeCohort,
-      holder: g,
-      debug: self.opts.debug,
-      usecase: { target: "matrix" },
-      getBodyParams: () => {
-        const currentGeneNames = self.termOrder.filter((t) => t.tw.term.type === "geneVariant").map(
-          (t) => t.tw.term.chr ? `${t.tw.term.chr}:${t.tw.term.start}-${t.tw.term.stop}` : t.tw.term.gene || t.tw.term.name
-        );
-        if (currentGeneNames.length) return { currentGeneNames };
-        return {};
-      },
-      callback: async (tw) => {
-        if (self.dom.loadingDiv && self.dom.svg) {
-          self.dom.loadingDiv.selectAll("*").remove();
-          self.dom.loadingDiv.html("").style("display", "").style("position", "relative").style("left", "45%");
-          self.dom.loadingDiv.html("Processing data ...");
-          self.dom.svg.style("opacity", 0.1).style("pointer-events", "none");
-        }
-        if (tw && !tw.q) throw "data.q{} missing from pill callback";
-        if (tw?.term && isNumericTerm(tw.term)) {
-          tw.q = { ...tw.q, mode: "discrete" };
-        }
-        if (tw) await fillTermWrapper(tw, self.app.vocabApi);
-        await pill.main(tw ? tw : { term: null, q: null });
-        box.datum({ tw });
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            divideBy: tw,
-            legendValueFilter: self.mayRemoveTvsEntry(self.config.divideBy)
-          }
-        });
-      }
-    });
-    const arg = {
-      term: self.config.divideBy.term,
-      q: self.config.divideBy.q
-    };
-    if (self.config.divideBy.$id) arg.$id = self.config.divideBy.$id;
-    pill.main(arg);
-  };
-  self.adjustSvgDimensions = async function(prevTranspose) {
-    const s = self.settings.matrix;
-    const hc = self.settings.hierCluster || {};
-    const l = self.layout;
-    const hcHeight = !hc.yDendrogramHeight ? 0 : hc.yDendrogramHeight + (l.top.display === "none" ? 0 : 10);
-    const hcWidth = hc.xDendrogramHeight || 0;
-    const d = self.dimensions;
-    const duration = self.dom.svg.attr("width") ? s.duration : 0;
-    await sleep(prevTranspose == s.transpose ? duration : s.duration);
-    const topBox = l.top.box.node().getBBox();
-    const btmBox = l.btm.box.node().getBBox();
-    const leftBox = l.left.box.node().getBBox();
-    const rtBox = l.right.box.node().getBBox();
-    const legendBox = self.dom.legendG.node().getBBox();
-    const seriesBox = self.dom.seriesesG.node().getBBox();
-    d.extraWidth = leftBox.width + rtBox.width + s.margin.left + s.margin.right + s.rowlabelgap * 2;
-    d.extraHeight = topBox.height + btmBox.height + s.margin.top + s.margin.bottom + s.collabelgap * 2;
-    d.svgw = d.mainw + d.extraWidth + hcWidth;
-    d.svgh = d.mainh + d.extraHeight + legendBox.height + 20 + s.scrollHeight + hcHeight;
-    self.dom.svg.attr("width", d.svgw).attr("height", d.svgh);
-    let maxLabelWidth = self.type == "hierCluster" ? 0 : leftBox.width, maxLabelNumChars = 0;
-    if (hc.xDendrogramHeight) {
-      self.dom.termLabelG.selectAll(".sjpp-matrix-label").each(function(d2) {
-        if (d2.grp.type !== "hierCluster") return;
-        const box = this.getBBox();
-        if (box.width > maxLabelWidth) {
-          maxLabelWidth = box.width;
-          maxLabelNumChars = d2.label.length;
-        }
-      });
-    }
-    const x = -l.left.offset + hcWidth + maxLabelWidth;
-    const xAdjust = !hc.xDendrogramHeight ? 0 : Math.max(leftBox.width - (hc.xDendrogramHeight + maxLabelWidth), 0);
-    const y = (l.top.display == "none" ? 0 : topBox.height) - l.top.offset + hcHeight;
-    self.dom.mainG.attr("transform", `translate(${x + xAdjust},${y})`);
-    self.dom.clipRect.attr("y", -y).attr("height", d.mainh + 500 + y);
-    const legendX = d.xOffset + (s.transpose ? 20 : 0);
-    const legendY = d.yOffset + d.mainh + s.collabelgap + (l.btm.display == "none" ? 0 : btmBox.height) + 20;
-    self.dom.legendG.attr("transform", `translate(${legendX},${legendY})`);
-    if (hc.xDendrogramHeight) {
-      const dendroX = maxLabelWidth + xAdjust - l.left.offset + d.xOffset - d.dx / 2;
-      self.dom.hcClipRect.attr("x", dendroX + hcWidth + d.dx / 2).attr("y", 0).attr("width", d.mainw + 3).attr("height", d.mainh + hc.yDendrogramHeight + 500);
-      self.topDendroX = dendroX + d.seriesXoffset;
-      self.dom.topDendrogram.attr("transform", `translate(${self.topDendroX}, 0)`);
-      const y2 = l.top.display == "none" ? 0 : topBox.height + s.collabelgap;
-      self.dom.leftDendrogram.attr("transform", `translate(${dendroX - maxLabelWidth - 10}, ${y2})`);
-    }
-  };
-}
-function getRectFill(d) {
-  if (d.fill) return d.fill;
-  const cls = d.class || Array.isArray(d.values) && d.values[0].class;
-  if (!cls) console.log;
-  return cls ? mclass[cls].color : "#555";
-}
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-export {
-  setRenderers
-};
-//# sourceMappingURL=chunk-N4ULQIGJ.js.map

package/dist/chunk-NX5IB4IY.js

@@ -1,37 +0,0 @@
-import {
-  DMR_SCAN_ELEMENT_TYPE
-} from "./chunk-WJLRU5OF.js";
-
-// plots/gsea/settings/defaults.ts
-function isDmrScanRanking(opts) {
-  return opts?.elementType === DMR_SCAN_ELEMENT_TYPE || opts?.gsea_params?.daRequest?.element_type === DMR_SCAN_ELEMENT_TYPE;
-}
-function getDefaultGseaSettings(overrides = {}, opts = {}) {
-  const defaults = {
-    fdr_cutoff: 0.05,
-    num_permutations: 1e3,
-    top_genesets: 40,
-    pathway: opts?.gsea_params?.pathway ?? void 0,
-    geneset_name: null,
-    min_gene_set_size_cutoff: 0,
-    /* 500 only for a DMR scan's gene-body ranking, where blitzgsea's null fit is unstable above it.
-    The server enforces that ceiling on the library before the fit (genesetEnrichment.ts); this
-    default only keeps the table's own size filter consistent with it, and daRequest may not be
-    known yet when defaults are first built. Every other caller keeps 20,000, because lowering it
-    for them would silently drop large GO and Reactome sets from analyses that have always shown
-    them. */
-    max_gene_set_size_cutoff: isDmrScanRanking(opts) ? 500 : 2e4,
-    filter_non_coding_genes: true,
-    fdr_or_top: "top",
-    gsea_method: "blitzgsea"
-  };
-  if (JSON.parse(sessionStorage.getItem("optionalFeatures") || "{}")?.gsea_test) {
-    defaults.gsea_method = "cerno";
-  }
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultGseaSettings
-};
-//# sourceMappingURL=chunk-NX5IB4IY.js.map