@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/chunk-DZDK64XY.js

@@ -1,516 +0,0 @@
-import {
-  colorDelta,
-  getInterpolatedDomainRange,
-  removeOutliers
-} from "./chunk-PEKCVKJK.js";
-import {
-  variantFilterLabel
-} from "./chunk-MHWYRNGA.js";
-import {
-  Blues_default,
-  Reds_default,
-  axisBottom,
-  axisLeft,
-  axisRight,
-  axisTop,
-  dtcnv
-} from "./chunk-WJLRU5OF.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.layout.js
-var matrix_layout_exports = {};
-__export(matrix_layout_exports, {
-  getMaxGrpLabelWidth: () => getMaxGrpLabelWidth,
-  setAutoDimensions: () => setAutoDimensions,
-  setLabelsAndScales: () => setLabelsAndScales,
-  setLayout: () => setLayout
-});
-var MINCOLWSPACED = 7;
-function setAutoDimensions(xOffset) {
-  const m = this.state.config.settings.matrix;
-  if (!this.autoDimensions) this.autoDimensions = /* @__PURE__ */ new Set();
-  if (!m.colw) this.autoDimensions.add("colw");
-  else this.autoDimensions.delete("colw");
-  if (!m.rowh) this.autoDimensions.add("rowh");
-  else this.autoDimensions.delete("rowh");
-  const s = this.settings.matrix;
-  this.computedSettings = {
-    useCanvas: this.sampleOrder.length > m.svgCanvasSwitch
-  };
-  if (s.availContentWidth) {
-    this.availContentWidth = s.availContentWidth;
-  } else {
-    let boundingWidth = this.dom.contentNode.getBoundingClientRect().width;
-    if (boundingWidth < 600) {
-      boundingWidth = window.document.body.clientWidth;
-    }
-    const maxGrpLabelWidth = this.getMaxGrpLabelWidth();
-    const padding = Math.max(65, maxGrpLabelWidth);
-    const hcw = this.state.config.settings.hierCluster?.xDendrogramHeight || 0;
-    this.availContentWidth = boundingWidth - padding - s.margin.right - xOffset - hcw;
-  }
-  let colwSpaced, colwNoSpace;
-  if (this.autoDimensions.has("colw")) {
-    const totalColgspace = s.colgspace * Math.max(0, this.visibleSampleGrps.size - 1);
-    const tentativeGaps = this.sampleOrder.length * s.colspace + totalColgspace;
-    const spacedColw = (this.availContentWidth - tentativeGaps) / this.sampleOrder.length;
-    const constrainedMINCOLWSPACED = Math.max(s.colwMin, Math.min(MINCOLWSPACED, s.colwMax));
-    colwSpaced = Math.max(constrainedMINCOLWSPACED, Math.min(spacedColw, s.colwMax));
-    const noSpacedColw = (this.availContentWidth - totalColgspace) / this.sampleOrder.length;
-    colwNoSpace = Math.max(s.colwMin, Math.min(noSpacedColw, s.colwMax));
-    this.computedSettings.colw = colwSpaced <= MINCOLWSPACED ? colwNoSpace : colwSpaced;
-    this.computedSettings.zoomMin = s.colwMin / this.computedSettings.colw;
-    this.computedSettings.zoomMax = s.colwMax / this.computedSettings.colw;
-  } else {
-    colwSpaced = m.colw;
-    colNoSpace = m.colw;
-    this.computedSettings.colw = m.colw;
-    this.computedSettings.zoomMin = s.colwMin / m.colw;
-    this.computedSettings.zoomMax = s.colwMax / m.colw;
-  }
-  const { colw } = this.computedSettings;
-  this.computedSettings.colspace = colw === colwNoSpace && colwSpaced < colwNoSpace || colw * s.zoomLevel < MINCOLWSPACED ? 0 : s.colspace;
-  const hch = this.state.config.settings.hierCluster?.yDendrogramHeight || 0;
-  const availHeight = s.availContentHeight || screen.availHeight - hch;
-  this.computedSettings.clusterRowh = Math.min(
-    s.rowhMax,
-    Math.max(s.rowhMin, Math.floor(availHeight / this.numClusterTerms))
-  );
-  copyMerge(this.settings.matrix, this.computedSettings);
-}
-function getMaxGrpLabelWidth() {
-  const s = this.settings.matrix;
-  const g = this.dom.svg.append("g").attr("opacity", 0.01);
-  let maxWidth = 0;
-  for (const grp of this.termGroups) {
-    const grpLabel = !grp.name ? "" : grp.name.length <= s.termGrpLabelMaxChars ? grp.name : grp.name.slice(0, s.termGrpLabelMaxChars) + "\u2026";
-    const text = g.append("text").text(grpLabel).attr("font-size", 12);
-    const box = text.node().getBBox();
-    if (maxWidth < box.width) maxWidth = box.width;
-  }
-  g.remove();
-  return maxWidth;
-}
-function setLabelsAndScales() {
-  const s = this.settings.matrix;
-  this.cnvValues = [];
-  const ht = s.transpose ? s.colw : s.rowh;
-  const grpTotals = {};
-  const processedLabels = { sampleGrpByName: {}, termGrpByName: {} };
-  let totalHtAdjustments = 0;
-  for (const t of this.termOrder) {
-    const countedSamples = /* @__PURE__ */ new Set();
-    t.counts = { samples: 0, hits: 0 };
-    const renderedContinuousVs = [];
-    let hasMixedValues = false;
-    if (t.tw.term.type == "termCollection") {
-      t.counts.minval = 0;
-      t.counts.maxval = 0;
-    }
-    t.counts.subGroupCounts = {};
-    for (const group of this.sampleGroups) {
-      t.counts.subGroupCounts[group.name] = {
-        samplesTotal: 0,
-        // number of counted (not Blank or WT) samples
-        classes: {}
-        // number of each class
-      };
-      if (t.tw.term.type == "geneVariant") {
-        t.counts.subGroupCounts[group.name].samplesNotTested = 0;
-      }
-    }
-    if (!processedLabels.termGrpByName[t.grp.name || ""]) {
-      const name = t.grp.name || "";
-      t.grp.label = name.length <= s.termGrpLabelMaxChars ? name : name.slice(0, s.termGrpLabelMaxChars) + "\u2026";
-      processedLabels.termGrpByName[name] = t.grp.label;
-    }
-    for (const sample of this.sampleOrder) {
-      if (countedSamples.has(sample.row.sample)) continue;
-      const name = sample.grp.name || "";
-      if (!(name in processedLabels.sampleGrpByName)) {
-        sample.grp.label = name.length <= s.sampleGrpLabelMaxChars ? name : name.slice(0, s.sampleGrpLabelMaxChars) + "\u2026";
-        if (this.config.divideBy) sample.grp.label += ` (${sample.grp.lst.length})`;
-        processedLabels.sampleGrpByName[name] = sample.grp.label;
-      }
-      const sampleName = sample.row._ref_.label || "";
-      sample.label = sampleName.length <= s.collabelmaxchars ? sampleName : sampleName.slice(0, s.collabelmaxchars) + "\u2026";
-      const anno = sample.row[t.tw.$id];
-      if (!anno) continue;
-      if (t.tw.term.type == "termCollection" && anno.hasMixedValues) {
-        hasMixedValues = true;
-      }
-      if (t.tw.term.type == "termCollection" && anno.values) {
-        for (const val of anno.values) {
-          const pct = val.value;
-          if (pct > 0) {
-            const cumSum = val.pre_val_sum + pct;
-            if (!("maxval" in t.counts) || t.counts.maxval < cumSum) {
-              t.counts.maxval = cumSum;
-            }
-          } else if (pct < 0) {
-            const cumSum = val.pre_val_sum + pct;
-            if (!("minval" in t.counts) || t.counts.minval > cumSum) {
-              t.counts.minval = cumSum;
-            }
-          }
-        }
-      }
-      const { filteredValues, countedValues, renderedValues } = this.classifyValues(
-        anno,
-        t.tw,
-        t.grp,
-        this.settings.matrix,
-        sample.row
-      );
-      anno.filteredValues = filteredValues;
-      anno.countedValues = countedValues;
-      anno.renderedValues = renderedValues;
-      if (anno.countedValues?.length) {
-        t.counts.samples += 1;
-        t.counts.hits += anno.countedValues.length;
-        if (t.tw.q?.mode == "continuous") {
-          const v = anno.value;
-          if (!t.tw.term.values?.[v]?.uncomputable) {
-            if (!("minval" in t.counts) || t.counts.minval > v) t.counts.minval = v;
-            if (!("maxval" in t.counts) || t.counts.maxval < v) t.counts.maxval = v;
-          }
-        }
-        if (t.tw.term.type == "geneVariant" && anno.values) {
-          for (const val of anno.values) {
-            if (val.dt == dtcnv && "value" in val && !s.ignoreCnvValues) {
-              const v = val.value;
-              this.cnvValues.push(v);
-            }
-          }
-        }
-      }
-      if (t.tw.q?.mode == "continuous" && renderedValues?.length && t.grp.type != "hierCluster") {
-        renderedContinuousVs.push(
-          t.tw.term.valueConversion ? t.tw.term.valueConversion.scaleFactor * (renderedValues[0].value || renderedValues[0]) : renderedValues[0].value || renderedValues[0]
-        );
-      }
-      const subGroup = t.counts.subGroupCounts?.[sample.grp.name];
-      const countedValuesNoSkip = anno.filteredValues.filter((v) => {
-        if (t.tw.term.type == "geneVariant") {
-          if (v.class == "WT" || v.class == "Blank") return false;
-        }
-        return true;
-      });
-      if (countedValuesNoSkip.length) {
-        if (t.tw.term.type == "geneVariant") {
-          let sampleCounted = false;
-          for (const countedValue of countedValuesNoSkip) {
-            if (s.geneVariantCountSamplesSkipMclass.includes(countedValue.class)) {
-              if (!subGroup.notTestedClasses) subGroup.notTestedClasses = {};
-              if (!(countedValue.class in subGroup.notTestedClasses)) subGroup.notTestedClasses[countedValue.class] = 1;
-              else subGroup.notTestedClasses[countedValue.class] += 1;
-            } else if (!(countedValue.class in subGroup.classes)) {
-              if (!sampleCounted) {
-                subGroup.samplesTotal += 1;
-                sampleCounted = true;
-              }
-              subGroup.classes[countedValue.class] = 1;
-            } else {
-              if (!sampleCounted) {
-                subGroup.samplesTotal += 1;
-                sampleCounted = true;
-              }
-              subGroup.classes[countedValue.class] += 1;
-            }
-          }
-        } else {
-          subGroup.samplesTotal += 1;
-          for (const countedValue of countedValuesNoSkip) {
-            if (!(countedValue in subGroup.classes)) subGroup.classes[countedValue] = 1;
-            else subGroup.classes[countedValue] += 1;
-          }
-        }
-      }
-      if (anno.filteredValues?.length && t.tw.term.type == "geneVariant") {
-        const notTested = anno.filteredValues.every((v) => v.class == "Blank");
-        if (notTested) {
-          subGroup.samplesNotTested += 1;
-        }
-      }
-    }
-    if (t.tw.label) {
-      t.label = t.tw.label;
-    } else if (t.grp.type == "hierCluster") {
-      t.label = t.tw.term.gene || t.tw.term.name;
-    } else if (t.tw.q?.variantFilter) {
-      const selected = variantFilterLabel(t.tw.q.variantFilter, this.mclass);
-      t.label = selected ? `${t.tw.term.name} ${selected}` : t.tw.term.name;
-    } else {
-      t.label = t.tw.term.name;
-    }
-    if (t.label.length > s.rowlabelmaxchars) t.label = t.label.slice(0, s.rowlabelmaxchars - 1) + "\u2026";
-    const termGroupName = this.config?.settings.hierCluster?.termGroupName;
-    if (s.samplecount4gene && t.tw.term.type.startsWith("gene") && (!termGroupName || t.grp.name !== termGroupName)) {
-      const count = s.samplecount4gene === "abs" ? t.counts.samples : (100 * t.counts.samples / this.sampleOrder.length).toFixed(1) + "%";
-      t.label = `${t.label} (${count})`;
-    }
-    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
-    if (!twSpecificSettings[t.tw.$id]) twSpecificSettings[t.tw.$id] = {};
-    const twSettings = twSpecificSettings[t.tw.$id];
-    if (t.grp.type !== "hierCluster" && t.tw.q?.mode == "continuous") {
-      const vc = t.tw.term.valueConversion;
-      if (vc) {
-        t.counts.minval *= vc.scaleFactor;
-        t.counts.maxval *= vc.scaleFactor;
-      }
-      if (renderedContinuousVs.length && t.tw.q.convert2ZScore) {
-        const mean = renderedContinuousVs.reduce((acc, val) => acc + val, 0) / renderedContinuousVs.length;
-        const std = Math.sqrt(
-          renderedContinuousVs.reduce((acc, val) => acc + Math.pow(val - mean, 2), 0) / renderedContinuousVs.length
-        );
-        t.mean = mean;
-        t.std = std;
-        t.counts.minval = (t.counts.minval - mean) / std;
-        t.counts.maxval = (t.counts.maxval - mean) / std;
-      }
-      if (!twSettings.contBarH) twSettings.contBarH = t.tw.term.type == "termCollection" ? 150 : s.barh;
-      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-      const barh = twSettings.contBarH;
-      if (t.tw.term.type == "termCollection") {
-        if (!("minval" in t.counts)) t.counts.minval = 0;
-        if (!("maxval" in t.counts)) t.counts.maxval = 0;
-      }
-      const absMin = Math.abs(t.counts.minval);
-      const rangeSpansZero = t.counts.minval < 0 && t.counts.maxval > 0;
-      const ratio = t.counts.minval >= 0 ? 1 : t.counts.maxval / (absMin + t.counts.maxval);
-      t.counts.posMaxHt = ratio * barh;
-      const tickValues = [t.counts.maxval, t.counts.minval];
-      t.scales = {
-        tickValues,
-        full: linear().domain(tickValues).range([1, barh])
-      };
-      if (t.counts.maxval >= 0) {
-        const domainMin = rangeSpansZero ? 0 : t.counts.minval;
-        t.scales.pos = linear().domain([domainMin, t.counts.maxval]).range([1, t.counts.posMaxHt]);
-      }
-      if (t.counts.minval < 0) {
-        const domainMax = rangeSpansZero ? 0 : t.counts.maxval;
-        t.scales.neg = linear().domain([domainMax, t.counts.minval]).range([1, barh - t.counts.posMaxHt]);
-      }
-    }
-    t.totalHtAdjustments = totalHtAdjustments;
-    t.rowHt = t.grp.type == "hierCluster" ? s.clusterRowh : twSettings.contBarH && t.tw.q?.mode == "continuous" ? twSettings.contBarH + 2 * twSettings.contBarGap : ht;
-    const adjustment = t.rowHt - ht - (t.grp.type == "hierCluster" ? s.rowspace : 0);
-    totalHtAdjustments += adjustment;
-    t.cumulativeAdjustment = totalHtAdjustments;
-    if (!(t.visibleGrpIndex in grpTotals)) grpTotals[t.visibleGrpIndex] = { htAdjustment: 0 };
-    grpTotals[t.visibleGrpIndex].htAdjustment += adjustment;
-    t.grpTotals = grpTotals[t.visibleGrpIndex];
-  }
-  let cnvLegendDomainRange;
-  if (this.cnvValues.length) {
-    if (s.cnvValues.cutoffMode == "fixed") {
-      this.cnvValues = this.cnvValues.filter((v) => v >= s.cnvValues.min && v <= s.cnvValues.max).sort((a, b) => a - b);
-      if (this.cnvValues[0] != s.cnvValues.min) this.cnvValues.unshift(s.cnvValues.min);
-      if (this.cnvValues[this.cnvValues.length - 1] != s.cnvValues.max) this.cnvValues.push(s.cnvValues.max);
-    } else if (s.cnvValues.cutoffMode == "percentile" || s.cnvValues.cutoffMode == "auto") {
-      let maxPercentile = s.cnvValues.cutoffMode == "auto" ? s.cnvValues.defaultPercentile : s.cnvValues.percentile;
-      maxPercentile = maxPercentile / 100;
-      const minPercentile = roundValueAuto(1 - maxPercentile);
-      this.cnvValues = removeOutliers(this.cnvValues, { minPercentile, maxPercentile, baseValue: 0 });
-    } else throw new Error(`Invalid cnvValues cutoffMode: ${s.cnvValues.cutoffMode}`);
-    const minLoss = this.cnvValues[0] <= 0 ? this.cnvValues[0] : void 0;
-    const maxGain = this.cnvValues[this.cnvValues.length - 1] >= 0 ? this.cnvValues[this.cnvValues.length - 1] : void 0;
-    let maxLoss, minGain, absMax;
-    for (const n of this.cnvValues) {
-      if (n < 0) maxLoss = n;
-      if (!minGain && n > 0) {
-        minGain = n;
-        break;
-      }
-    }
-    for (const t of this.termOrder) {
-      if (t.tw.term.type == "geneVariant") {
-        if (!cnvLegendDomainRange) {
-          const loss0color = Blues_default(0);
-          const gain0color = Reds_default(0);
-          const colorDiff = colorDelta(loss0color, gain0color);
-          if (minLoss !== void 0 && maxGain !== void 0 && colorDiff > 25)
-            console.warn(
-              `CNV loss and gain do not have the same middle color for value=0'${loss0color}' vs '${gain0color}', color difference=${colorDiff}`
-            );
-          absMax = minLoss !== void 0 && maxGain !== void 0 ? Math.max(Math.abs(minLoss), maxGain) : minLoss !== void 0 ? Math.abs(minLoss) : maxGain;
-          cnvLegendDomainRange = getInterpolatedDomainRange({
-            absMin: 0,
-            absMax,
-            totalNumSteps: 10,
-            negInterpolator: minLoss !== void 0 && Blues_default,
-            posInterpolator: maxGain !== void 0 && Reds_default,
-            // force this middleColor to white, knowing that interpolateBlues and interpolateReds,
-            // as hardcoded above and below, share similar white colors for their minimum abs values
-            middleColor: "white"
-          });
-        }
-        t.scales = {
-          loss: Blues_default,
-          gain: Reds_default,
-          maxLoss,
-          maxGain,
-          minLoss,
-          minGain,
-          absMax,
-          legend: cnvLegendDomainRange
-        };
-      }
-    }
-  }
-}
-function setLayout() {
-  const s = this.settings.matrix;
-  const [col, row] = !s.transpose ? ["sample", "term"] : ["term", "sample"];
-  const [_t_, _b_] = s.collabelpos == "top" ? ["", "Grp"] : ["Grp", ""];
-  const [_l_, _r_] = s.rowlabelpos == "left" ? ["", "Grp"] : ["Grp", ""];
-  const top = col + _t_;
-  const btm = col + _b_;
-  const left = row + _l_;
-  const right = row + _r_;
-  this.samples = this.sampleOrder;
-  this.sampleGrps = this.sampleOrder.filter((s2) => s2.index === 0);
-  this.terms = this.termOrder;
-  this.termGrps = this.termOrder.filter((t) => t.index === 0);
-  const layout = {};
-  const sides = { top, btm, left, right };
-  for (const direction in sides) {
-    const d = sides[direction];
-    const Direction = direction[0].toUpperCase() + direction.slice(1);
-    layout[direction] = {
-      prefix: d,
-      data: this[`${d}s`],
-      offset: s[`${d}LabelOffset`],
-      box: this.dom[`${d}LabelG`],
-      key: this[`${d}Key`],
-      label: this[`${d}Label`],
-      render: this[`render${Direction}Label`],
-      isGroup: sides[direction].includes("Grp")
-    };
-  }
-  const yOffset = layout.top.offset + s.margin.top + s.scrollHeight;
-  const xOffset = layout.left.offset + s.margin.left;
-  this.setAutoDimensions(xOffset);
-  this.setLabelsAndScales();
-  const colw = Math.max(s.colwMin, Math.min(s.colwMax, s.colw * s.zoomLevel));
-  const dx = colw + s.colspace;
-  const nx = this[`${col}s`].length;
-  const dy = s.rowh + s.rowspace;
-  const ny = this[`${row}s`].length;
-  const mainwByColDimensions = nx * (colw + s.colspace) + this[`${col}Grps`].length * s.colgspace + (this[`${col}s`].slice(-1)[0]?.totalHtAdjustments || 0);
-  const mainw = Math.min(mainwByColDimensions, this.availContentWidth);
-  const lastRow = this[`${row}s`].slice(-1)[0];
-  const mainh = ny * dy + (this[`${row}Grps`].length - 1) * s.rowgspace + (lastRow?.cumulativeAdjustment || 0);
-  const colLabelFontSize = Math.min(
-    Math.max(colw + s.colspace - 2 * s.collabelpad - s.colspace, s.minLabelFontSize),
-    s.maxLabelFontSize
-  );
-  const topFontSize = _t_ == "Grp" ? s.grpLabelFontSize : colLabelFontSize;
-  layout.top.attr = {
-    boxTransform: `translate(${xOffset}, ${yOffset - s.collabelgap})`,
-    adjustBoxTransform: (dx2) => layout.top.box.attr("transform", `translate(${xOffset + dx2}, ${yOffset - s.collabelgap})`),
-    labelTransform: "rotate(-90)",
-    labelAnchor: "start",
-    labelGY: 0,
-    labelGTransform: this[`col${_t_}LabelGTransform`],
-    fontSize: topFontSize,
-    textpos: { coord: "y", factor: -1 },
-    axisFxn: axisTop
-  };
-  if (layout.top.prefix == "sample")
-    layout.top.display = s.sampleLabelsToggle !== "hide" && colw >= s.minLabelFontSize ? "" : "none";
-  const btmFontSize = _b_ == "Grp" ? s.grpLabelFontSize : colLabelFontSize;
-  layout.btm.attr = {
-    boxTransform: `translate(${xOffset}, ${yOffset + mainh + s.collabelgap})`,
-    adjustBoxTransform: (dx2) => layout.btm.box.attr("transform", `translate(${xOffset + dx2}, ${yOffset + mainh + s.collabelgap})`),
-    labelTransform: "rotate(-90)",
-    labelAnchor: "end",
-    labelGY: 0,
-    labelGTransform: this[`col${_b_}LabelGTransform`],
-    fontSize: btmFontSize,
-    textpos: { coord: "y", factor: 1 },
-    axisFxn: axisBottom
-  };
-  if (layout.btm.prefix == "sample")
-    layout.btm.display = s.sampleLabelsToggle !== "hide" && colw >= s.minLabelFontSize ? "" : "none";
-  const leftFontSize = _l_ == "Grp" ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad - s.rowspace, s.minLabelFontSize);
-  layout.left.attr = {
-    boxTransform: `translate(${xOffset - s.rowlabelgap}, ${yOffset})`,
-    labelTransform: "",
-    labelAnchor: "end",
-    labelGX: 0,
-    labelGTransform: this[`row${_l_}LabelGTransform`],
-    fontSize: leftFontSize,
-    textpos: { coord: "x", factor: -1 },
-    axisFxn: axisLeft
-  };
-  const rtFontSize = _r_ == "Grp" ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad, s.minLabelFontSize);
-  layout.right.attr = {
-    boxTransform: `translate(${xOffset + mainw + s.rowlabelgap}, ${yOffset})`,
-    labelTransform: "",
-    labelAnchor: "start",
-    labelGX: 0,
-    labelGTransform: this[`row${_r_}LabelGTransform`],
-    fontSize: rtFontSize,
-    textpos: { coord: "x", factor: 1 },
-    axisFxn: axisRight
-  };
-  this.dom.sampleLabelsPG.attr("clip-path", s.transpose ? "" : `url(#${this.seriesClipId})`);
-  this.dom.termLabelsPG.attr("clip-path", s.transpose ? `url(#${this.seriesClipId})` : "");
-  this.layout = layout;
-  if (!s.zoomCenterPct) {
-    s.zoomCenterPct = 0.5;
-    s.zoomIndex = Math.round(s.zoomCenterPct * mainw / dx);
-    s.zoomGrpIndex = this.sampleOrder[s.zoomIndex]?.grpIndex || 0;
-  }
-  const zoomCenter = s.zoomCenterPct * mainw;
-  const centerCellX = s.zoomIndex * dx + s.zoomGrpIndex * s.colgspace;
-  const zoomedMainW = Math.max(0, nx * dx + (this[`${col}Grps`].length - 1) * s.colgspace);
-  const seriesXoffset = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : Math.max(zoomCenter - centerCellX, mainw - zoomedMainW);
-  const imgW = (s.imgWMax > zoomedMainW ? zoomedMainW : s.imgWMax) - 1e-7;
-  const halfImgW = 0.5 * imgW;
-  const unwantedRightOvershoot = Math.max(0, centerCellX + halfImgW - zoomedMainW);
-  const imgLeftMin = Math.max(0, centerCellX - Math.min(halfImgW, imgW) - unwantedRightOvershoot);
-  const xMin = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : imgLeftMin;
-  const xMax = imgW + xMin;
-  this.dimensions = {
-    xMin,
-    xMax,
-    dx,
-    dy,
-    xOffset,
-    yOffset,
-    mainw,
-    mainh,
-    colw,
-    zoomedMainW,
-    seriesXoffset: seriesXoffset > 0 ? 0 : seriesXoffset,
-    maxMainW: Math.max(mainwByColDimensions, this.availContentWidth),
-    imgW,
-    // recompute the resolvable "pixel width", in case the pixel ratio changes
-    // when moving the browser window to a different monitor,
-    // will be used to sharpen canvas shapes that are smaller than this pixel width
-    pxw: 1 / window.devicePixelRatio
-  };
-}
-
-export {
-  setAutoDimensions,
-  getMaxGrpLabelWidth,
-  setLabelsAndScales,
-  setLayout,
-  matrix_layout_exports
-};
-//# sourceMappingURL=chunk-DZDK64XY.js.map

package/dist/chunk-E6C2EWHU.js

@@ -1,176 +0,0 @@
-import {
-  appInit
-} from "./chunk-VHC4FDEJ.js";
-import {
-  showErrorsWithCounter
-} from "./chunk-PEKCVKJK.js";
-import {
-  mclass
-} from "./chunk-WJLRU5OF.js";
-
-// plots/disco/launch.adhoc.ts
-async function launch(arg, genomeObj, holder) {
-  const [mlst, errors] = await getMlst(arg);
-  if (errors?.length) {
-    return showErrorsWithCounter(errors, holder);
-  }
-  const opts = {
-    holder,
-    vocabApi: {
-      // api is required by plot.app.js, so create a mock one for the adhoc data
-      vocab: { terms: [] },
-      main: () => {
-        return;
-      },
-      getTermdbConfig: () => {
-        return {};
-      }
-    },
-    state: {
-      args: {
-        data: mlst,
-        genome: genomeObj
-      },
-      plots: [
-        {
-          chartType: "Disco",
-          subfolder: "disco",
-          extension: "ts",
-          /** NOTE: Users should only override the settings in the default
-           * settings.Disco:{}, not the entire settings:{} object.*/
-          overrides: { Disco: arg?.settings || {} }
-        }
-      ]
-    }
-  };
-  const plotAppApi = await appInit(opts);
-  return plotAppApi;
-}
-async function getMlst(arg) {
-  if (Array.isArray(arg.mlst)) {
-    return [arg.mlst, null];
-  }
-  const mlst = [];
-  const errors = [];
-  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
-  if (arg.svText) parseSvText(arg.svText, mlst, errors);
-  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
-  return [mlst, errors];
-}
-function parseSnvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (![5, 7, 9].includes(l.length)) {
-      errors.push("snv input not equal to 5, 7, or 9 columns");
-      continue;
-    }
-    let m;
-    try {
-      m = {
-        dt: 1,
-        chr: l[0],
-        position: Number(l[1]),
-        gene: l[2],
-        mname: l[3],
-        class: validateMutation(l[4], errors)
-      };
-      const vafs = parseOptionalVafs(l, errors);
-      if (vafs.length) m.vafs = vafs;
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function parseOptionalVafs(line, errors) {
-  const vafs = [];
-  const addVaf = (id, totalIndex, altIndex) => {
-    if (line.length <= altIndex) return;
-    const totalCount = Number(line[totalIndex]);
-    const altCount = Number(line[altIndex]);
-    if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
-      errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
-      return;
-    }
-    vafs.push({ id, totalCount, altCount });
-  };
-  addVaf("DNA", 5, 6);
-  addVaf("RNA", 7, 8);
-  return vafs;
-}
-function parseSvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (l.length < 4 || l.length > 6) {
-      errors.push("sv input not equal to 4 or 6 columns");
-      continue;
-    }
-    let m;
-    try {
-      const length = l.length;
-      if (length == 4) {
-        m = {
-          dt: 2,
-          chrA: l[0],
-          posA: Number(l[1]),
-          chrB: l[2],
-          posB: Number(l[3])
-        };
-      } else {
-        m = {
-          dt: 2,
-          chrA: l[0],
-          posA: Number(l[1]),
-          geneA: l[2],
-          chrB: l[3],
-          posB: Number(l[4]),
-          geneB: l[5]
-        };
-      }
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function parseCnvText(text, mlst, errors) {
-  for (const line of text.trim().split("\n")) {
-    const l = line.trim().split("	");
-    if (l.length != 4) {
-      errors.push("cnv input not equal to 4 columns");
-      continue;
-    }
-    let m;
-    try {
-      m = {
-        dt: 4,
-        chr: l[0],
-        start: Number(l[1]),
-        stop: Number(l[2]),
-        value: Number(l[3])
-      };
-    } catch (e) {
-      errors.push(e);
-      continue;
-    }
-    mlst.push(m);
-  }
-}
-function validateMutation(mutation, errors) {
-  const mut2check = mutation.toLowerCase();
-  const foundMutation = Object.values(mclass).find(
-    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
-  );
-  if (foundMutation) {
-    return foundMutation.key;
-  } else {
-    errors.push(`Invalid mutation class: ${mutation}`);
-  }
-}
-
-export {
-  launch
-};
-//# sourceMappingURL=chunk-E6C2EWHU.js.map