@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-TPVHGI7Q.js

@@ -0,0 +1,368 @@
+import {
+  fillTermWrapper,
+  termsettingInit
+} from "./chunk-K6OVOHIZ.js";
+import {
+  isNumericTerm
+} from "./chunk-X6VTVZY7.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.$id);
+      sg.exit().remove();
+      sg.each(self.renderSeries);
+      sg.enter().append("g").attr("class", "sjpp-mass-series-g").style("opacity", 1e-3).each(self.renderSeries);
+      self.mouseout();
+    }
+    self.prevUseCanvas = s.useCanvas;
+  };
+  self.renderSeries = async function(series) {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const g = select_default(this);
+    const duration = g.attr("transform") ? s.duration : 0;
+    g.attr("transform", `translate(${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) {
+    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");
+        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},${y})`).call(side.attr.axisFxn(lab.scales.full.domain(lab.scales.tickValues)).tickValues(lab.scales.tickValues));
+        } else if (hasAxis) {
+          g.select(".sjpp-matrix-cell-axis").remove();
+        }
+      }, getTspanCls2 = function(d2) {
+        return d2.cls;
+      }, getTspanDx2 = function(d2) {
+        return d2.dx;
+      }, getTspanFontSize2 = function(d2) {
+        return d2.fontSize || side.attr.fontSize;
+      }, getTspanText2 = function(d2) {
+        return d2.text;
+      };
+      var renderLabel = renderLabel2, getTspanCls = getTspanCls2, getTspanDx = getTspanDx2, getTspanFontSize = getTspanFontSize2, getTspanText = getTspanText2;
+      const side = l[direction];
+      side.box.style("display", side.display || "").attr("transform", side.attr.boxTransform);
+      const labels = side.box.selectAll(".sjpp-matrix-label").data(side.data, side.key);
+      labels.exit().remove();
+      labels.each(renderLabel2);
+      labels.enter().append("g").attr("class", "sjpp-matrix-label").each(renderLabel2);
+    }
+  };
+  self.colLabelGTransform = (lab, grpIndex) => {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    lab.labelOffset = 0.8 * d.colw;
+    const x = lab.grpIndex * s.colgspace + lab.totalIndex * d.dx + lab.labelOffset + lab.totalHtAdjustments;
+    const y = 0;
+    return `translate(${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-TPVHGI7Q.js.map

package/dist/chunk-TRQUMV4T.js

@@ -0,0 +1,254 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getTermSorter
+} from "./chunk-UO7MD3XA.js";
+import {
+  sample_match_termvaluesetting
+} from "./chunk-4WF3XDQP.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel
+} from "./chunk-GEQUQ3GG.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.groups.js
+var matrix_groups_exports = {};
+__export(matrix_groups_exports, {
+  classifyValues: () => classifyValues,
+  getSampleGroups: () => getSampleGroups,
+  getSampleOrder: () => getSampleOrder,
+  getTermOrder: () => getTermOrder,
+  stackSiblingCellsByClass: () => stackSiblingCellsByClass
+});
+function getTermOrder(data) {
+  const s = this.settings.matrix;
+  this.termSorter = getTermSorter(this, s);
+  const termOrder = [];
+  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
+  this.mclassSorter = getMclassSorter(this);
+  for (const [grpIndex, grp] of this.termGroups.entries()) {
+    const lst = [];
+    for (const [index, tw] of grp.lst.entries()) {
+      const counts = { samples: 0, hits: 0 };
+      const countedSamples = /* @__PURE__ */ new Set();
+      for (const sd of data.lst) {
+        if (countedSamples.has(sd.sample)) continue;
+        countedSamples.add(sd.sample);
+        const anno = sd[tw.$id];
+        if (anno) {
+          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
+          anno.filteredValues = filteredValues;
+          anno.countedValues = countedValues;
+          anno.renderedValues = renderedValues;
+          if (anno.countedValues?.length) {
+            const v = tw.term.values?.[anno.value];
+            if (v?.uncountable) continue;
+            counts.samples += 1;
+            counts.hits += anno.countedValues.length;
+            if (tw.q?.mode == "continuous") {
+              const v2 = anno.value;
+              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
+              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
+            }
+          }
+        }
+      }
+      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
+      if (grp.type == "hierCluster") numClusterTerms++;
+    }
+    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
+    const processedLst = lst.filter((t) => {
+      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
+      if (!grp.settings) return true;
+      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
+    }).sort(termSorter);
+    if (!processedLst.length) continue;
+    for (const [index, t] of processedLst.entries()) {
+      const { tw, counts } = t;
+      const ref = data.refs.byTermId[t.tw.$id] || {};
+      termOrder.push({
+        grp,
+        grpIndex,
+        visibleGrpIndex,
+        tw,
+        index,
+        // rendered index
+        lstIndex: t.index,
+        // as-listed index, before applying term filters
+        processedLst,
+        prevGrpTotalIndex: totalIndex,
+        totalIndex: totalIndex + index,
+        ref,
+        allCounts: counts
+        // note: term label will be assigned after sample counts are known
+        // label: t.tw.label || t.tw.term.name,
+      });
+    }
+    totalIndex += processedLst.length;
+    visibleGrpIndex += 1;
+  }
+  this.numTerms = termOrder.length;
+  this.numClusterTerms = numClusterTerms;
+  return termOrder;
+}
+function getSampleGroups(data) {
+  const s = this.settings.matrix;
+  const defaultSampleGrp = {
+    id: this.config.divideBy?.$id,
+    name: this.config.divideBy ? "Not annotated" : "",
+    lst: []
+  };
+  const sampleGroups = /* @__PURE__ */ new Map();
+  const term = this.config.divideBy?.term || {};
+  const $id = this.config.divideBy?.$id || "-";
+  const exclude = this.config.divideBy?.exclude || [];
+  const values = term.values || {};
+  const ref = data.refs.byTermId[$id] || {};
+  for (const row of data.lst) {
+    if ($id in row) {
+      const key = row[$id].key;
+      const name = key in values && values[key].label ? values[key].label : key;
+      if (!sampleGroups.has(key)) {
+        const grp = {
+          name: `${name}`,
+          // convert to a string
+          id: key,
+          lst: [],
+          tw: this.config.divideBy,
+          legendGroups: {},
+          isExcluded: exclude.includes(key)
+        };
+        if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
+        else delete grp.order;
+        sampleGroups.set(key, grp);
+      }
+      sampleGroups.get(key).lst.push(row);
+    } else {
+      defaultSampleGrp.lst.push(row);
+    }
+  }
+  const sampleGrpsArr = [...sampleGroups.values()];
+  const n = sampleGroups.size;
+  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
+    const l = s.controlLabels;
+    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
+  }
+  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
+    sampleGroups.set(void 0, defaultSampleGrp);
+    sampleGrpsArr.push(...sampleGroups.values());
+  }
+  this.asListedSampleOrder = [];
+  for (const grp of sampleGrpsArr) {
+    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
+  }
+  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
+  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
+    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
+  });
+  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
+  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
+  const dataFilter = (d) => allowedSamples.includes(d);
+  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
+  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
+  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
+  for (const grp of sampleGrpsArr) {
+    grp.lst = grp.lst.filter(dataFilter);
+    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
+    grp.lst.sort(grpLstSampleSorter);
+  }
+  const sampleGrpSorter = getSampleGroupSorter(this);
+  return sampleGrpsArr.sort(sampleGrpSorter);
+}
+function getSampleOrder(data) {
+  const s = this.settings.matrix;
+  this.visibleSampleGrps = /* @__PURE__ */ new Set();
+  const sampleOrder = [];
+  let total = 0, numHiddenGrps = 0;
+  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
+    if (!grp.lst.length) continue;
+    if (grp.isExcluded) numHiddenGrps++;
+    let processedLst = grp.lst;
+    for (const [index, row] of processedLst.entries()) {
+      sampleOrder.push({
+        grp,
+        grpIndex: grpIndex - numHiddenGrps,
+        // : this.sampleGroups.length,
+        row,
+        index,
+        prevGrpTotalIndex: total,
+        totalIndex: total + index,
+        totalHtAdjustments: 0,
+        // may be required when transposed???
+        grpTotals: { htAdjustment: 0 },
+        // may be required when transposed???
+        processedLst
+      });
+    }
+    if (!grp.isExcluded) total += processedLst.length;
+    this.visibleSampleGrps.add(grp);
+  }
+  this.unfilteredSampleOrder = sampleOrder;
+  return sampleOrder.filter((so) => !so.grp.isExcluded);
+}
+function classifyValues(anno, tw, grp, s, sample) {
+  const values = "value" in anno ? [anno.value] : anno.values;
+  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
+  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
+  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
+    throw `unknown matrix value filter type='${isSpecific.type}'`;
+  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
+  const renderedValues = [];
+  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
+    filteredValues.sort(this.mclassSorter);
+    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
+    else {
+      const sortedFilteredValues = [];
+      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
+        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
+        if (v) renderedValues.push(v);
+        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
+        sortedFilteredValues.push(...oneDtV);
+      }
+      filteredValues = sortedFilteredValues;
+    }
+  } else {
+    renderedValues.push(...filteredValues);
+  }
+  return {
+    filteredValues,
+    countedValues: filteredValues.filter((v) => {
+      if (tw.term.type == "geneVariant") {
+        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
+          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
+          if (!groupset) throw "groupset not found";
+          const group = groupset.groups[0];
+          if (v != group.name) return false;
+        } else {
+          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
+            return false;
+        }
+      }
+      return true;
+    }),
+    renderedValues
+  };
+}
+function stackSiblingCellsByClass(a, b) {
+  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
+}
+
+export {
+  getTermOrder,
+  getSampleGroups,
+  getSampleOrder,
+  classifyValues,
+  stackSiblingCellsByClass,
+  matrix_groups_exports
+};
+//# sourceMappingURL=chunk-TRQUMV4T.js.map