@sjcrh/proteinpaint-client 2.209.0 → 2.210.0

package/dist/chunk-6FG6JFZP.js

@@ -1,339 +0,0 @@
-import {
-  matchesGvQueryEntry
-} from "./chunk-3XBG5HIV.js";
-import {
-  mclass
-} from "./chunk-SB36AUG7.js";
-
-// ../shared/utils/dist/src/termCollection.js
-function validateTermCollectionTerm(term) {
-  if (!Array.isArray(term?.termlst) || !term.termlst.length)
-    throw new Error("termCollection requires nonempty term.termlst[]");
-  const memberIds = /* @__PURE__ */ new Set();
-  const types = /* @__PURE__ */ new Set();
-  for (const t of term.termlst) {
-    if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
-    if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
-    if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
-    memberIds.add(t.id);
-    types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
-  }
-  if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
-  return memberIds;
-}
-function validateFractionMembers(numerators, denominators, memberIds) {
-  if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
-  if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
-  if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
-  if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
-  for (const id of denominators) {
-    if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
-    if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
-  }
-  for (const id of numerators) {
-    if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
-    if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
-  }
-}
-var FRACTION_TW_TYPE = "TermCollectionTWFraction";
-function isFractionTw(tw) {
-  return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
-}
-function getFractionTvsTerm(tw) {
-  if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
-  const term = structuredClone(tw.term);
-  const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
-  const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
-  const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
-  validateFractionMembers(numerators, denominators, memberIds);
-  term.numerators = numerators;
-  term.denominators = denominators;
-  return term;
-}
-function validateTermCollectionFraction(q, term) {
-  const memberIds = validateTermCollectionTerm(term);
-  validateFractionMembers(q?.numerators, q?.denominators, memberIds);
-  if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
-    throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
-}
-
-// ../shared/utils/dist/src/filter.js
-function getFilteredSamples(sampleAnno, filter) {
-  setDatasetAnnotations(filter);
-  const samples = /* @__PURE__ */ new Set();
-  for (const anno of sampleAnno) {
-    if (samples.has(anno.sample)) continue;
-    const data = anno.s || anno.data;
-    if (data && sample_match_termvaluesetting(data, filter)) {
-      samples.add(anno.sample);
-    }
-  }
-  return samples;
-}
-function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
-  const lst = filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if ("type" in item && item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item, _term, sample)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const itemCopy = JSON.parse(JSON.stringify(item));
-      const t = itemCopy.tvs;
-      if (_term && t.term) {
-        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
-          numberofmatchedterms++;
-          continue;
-        }
-      }
-      let samplevalue;
-      if (_term && !t.term) {
-        if (t.term$type && t.term$type !== _term.type) {
-          numberofmatchedterms++;
-          continue;
-        }
-        t.term = _term;
-        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
-      } else if (sample && t.term.$id) {
-        samplevalue = sample[t.term.$id].value;
-      } else {
-        samplevalue = t.term.id in row ? row[t.term.id] : row;
-      }
-      setDatasetAnnotations(itemCopy);
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) continue;
-        thistermmatch = t.valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float") {
-        if (samplevalue === void 0) continue;
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "geneVariant") {
-        const svalues = samplevalue.values || [samplevalue];
-        for (const sv of svalues) {
-          thistermmatch = t.values.find(
-            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
-          ) && true;
-          if (thistermmatch) break;
-        }
-      } else {
-        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or") {
-      if (numberofmatchedterms && filter.in) return true;
-      if (!numberofmatchedterms && !filter.in) return true;
-    }
-  }
-  if (!("in" in filter)) filter.in = true;
-  return filter.in == (numberofmatchedterms == lst.length);
-}
-function setDatasetAnnotations(item, ds = null) {
-  if (item.type == "tvslst") {
-    for (const subitem of item.lst) {
-      setDatasetAnnotations(subitem, ds);
-    }
-  } else {
-    if (ds && typeof ds.setAnnoByTermId == "function") {
-      ds.setAnnoByTermId(item.tvs.term.id);
-    }
-    if (item.tvs.term.type == "categorical") {
-      const tvsAny = item.tvs;
-      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
-    }
-  }
-}
-function getPrecomputedKey(q) {
-  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
-  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
-  return precomputedKey;
-}
-function getWrappedTvslst(lst = [], join = "", $id = null) {
-  const filter = {
-    type: "tvslst",
-    in: true,
-    join,
-    lst
-  };
-  if ($id !== null) filter.$id = $id;
-  return filter;
-}
-function getTvsDenominators(term) {
-  if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
-  return (term?.termlst || []).map((t) => t.id);
-}
-function validateTermCollectionTvs(term) {
-  const memberIds = validateTermCollectionTerm(term);
-  if (!term.numerators) return;
-  validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
-}
-
-// ../shared/utils/dist/src/geneVariantFilter.js
-var statusClasses = /* @__PURE__ */ new Set(["WT", "Blank"]);
-function unsupported(what) {
-  return `tw.q.variantFilter does not support ${what}, which qualifies a sample rather than an individual variant. Use a groupset (q.type='custom-groupset') for a sample-level filter.`;
-}
-function validateVariantFilter(filter, term) {
-  if (!filter) return;
-  if (filter.type != "tvslst") throw `tw.q.variantFilter.type must be 'tvslst'`;
-  if (!Array.isArray(filter.lst) || !filter.lst.length) throw "tw.q.variantFilter.lst[] is empty";
-  if (filter.lst.length > 1 && filter.join != "and" && filter.join != "or")
-    throw `tw.q.variantFilter.join must be 'and' or 'or' when lst[] has more than one item`;
-  const dts = term?.childTerms?.length ? new Set(term.childTerms.map((t) => t.dt)) : null;
-  for (const item of filter.lst) {
-    if (item.type == "tvslst") {
-      validateVariantFilter(item, term);
-      continue;
-    }
-    if (item.type != "tvs") throw `unexpected tw.q.variantFilter item.type='${item.type}'`;
-    const tvs = item.tvs;
-    if (!tvs) throw "missing tvs of a tw.q.variantFilter item";
-    if (!Number.isInteger(tvs.term?.dt)) throw "tw.q.variantFilter tvs.term must be a dt term, with an integer .dt";
-    if (dts && !dts.has(tvs.term.dt))
-      throw `tw.q.variantFilter tvs.term.dt=${tvs.term.dt} is not a dt of term '${term.name}'`;
-    if (!Array.isArray(tvs.values) || !tvs.values.length) throw "tw.q.variantFilter tvs.values[] is empty";
-    for (const v of tvs.values) {
-      if (!v.key) throw "a tw.q.variantFilter tvs.values[] entry is missing .key";
-      if (statusClasses.has(v.key))
-        throw `tw.q.variantFilter cannot select the '${v.key}' class, which is a testing status and not a variant`;
-      if (v.partnerBreakpointRange) throw unsupported("partnerBreakpointRange");
-    }
-    if (tvs.genotype && tvs.genotype != "variant") throw unsupported(`genotype='${tvs.genotype}'`);
-    if (tvs.mcount && tvs.mcount != "any") throw unsupported(`mcount='${tvs.mcount}'`);
-    if (tvs.mafFilter) throw unsupported("mafFilter");
-    if (tvs.continuousCnv) throw unsupported("continuousCnv");
-    if (tvs.selfBreakpointRange) throw unsupported("selfBreakpointRange");
-  }
-}
-function getFilterScope(filter, scope = /* @__PURE__ */ new Set()) {
-  for (const item of filter.lst) {
-    if (item.type == "tvslst") getFilterScope(item, scope);
-    else scope.add(`${item.tvs.term.dt}:${item.tvs.term.origin || "*"}`);
-  }
-  return scope;
-}
-function isInScope(v, scope) {
-  return scope.has(`${v.dt}:*`) || scope.has(`${v.dt}:${v.origin || ""}`);
-}
-function matchTvs(v, tvs) {
-  let match = false;
-  if (v.dt == tvs.term.dt && (!tvs.term.origin || v.origin == tvs.term.origin)) {
-    match = tvs.values.some((e) => e.key == v.class && (!e.mname || e.mname == v.mname && matchesGvQueryEntry(e, v)));
-  }
-  return tvs.isnot ? !match : match;
-}
-function matchFilter(v, filter) {
-  const lst = filter.type == "tvslst" ? filter.lst : [filter];
-  let numMatched = 0;
-  for (const item of lst) {
-    const matched = item.type == "tvslst" ? matchFilter(v, item) : matchTvs(v, item.tvs);
-    if (matched) numMatched++;
-    if (filter.join == "or" && numMatched) break;
-  }
-  const pass = filter.join == "or" ? numMatched > 0 : numMatched == lst.length;
-  return filter.in === false ? !pass : pass;
-}
-function filterVariantValues(values, filter) {
-  if (!filter || !values) return values;
-  const scope = getFilterScope(filter);
-  const kept = [];
-  const annotated = /* @__PURE__ */ new Set();
-  const dropped = /* @__PURE__ */ new Map();
-  for (const v of values) {
-    if (!isInScope(v, scope)) continue;
-    const key = `${v.dt}:${v.origin || ""}`;
-    if (statusClasses.has(v.class) || matchFilter(v, filter)) {
-      kept.push(v);
-      annotated.add(key);
-    } else if (!dropped.has(key)) {
-      dropped.set(key, v);
-    }
-  }
-  for (const [key, v] of dropped) {
-    if (annotated.has(key)) continue;
-    const wt = { dt: v.dt, class: "WT", label: mclass.WT.label };
-    if (v.gene) wt.gene = v.gene;
-    if (v.origin) wt.origin = v.origin;
-    kept.push(wt);
-  }
-  return kept;
-}
-function variantFilterLabel(filter, mclassOverride, maxItems = 3) {
-  if (!filter) return "";
-  const entries = [];
-  collect(filter, false);
-  function collect(f, negated) {
-    const flipped = f.in === false ? !negated : negated;
-    for (const item of f.lst) {
-      if (item.type == "tvslst") collect(item, flipped);
-      else if (flipped === !!item.tvs.isnot) entries.push(...item.tvs.values);
-    }
-  }
-  if (!entries.length) return "";
-  const classes = mclass;
-  const names = [
-    ...new Set(entries.map((e) => e.mname || mclassOverride?.[e.key]?.label || classes[e.key]?.label || e.key))
-  ];
-  return names.length > maxItems ? `${names.slice(0, maxItems).join("/")}\u2026` : names.join("/");
-}
-
-export {
-  isFractionTw,
-  getFractionTvsTerm,
-  validateTermCollectionFraction,
-  getFilteredSamples,
-  sample_match_termvaluesetting,
-  getWrappedTvslst,
-  getTvsDenominators,
-  validateTermCollectionTvs,
-  validateVariantFilter,
-  filterVariantValues,
-  variantFilterLabel
-};
-//# sourceMappingURL=chunk-6FG6JFZP.js.map

package/dist/chunk-6G45AUSV.js

@@ -1,237 +0,0 @@
-import {
-  DataPointInteractions,
-  axisstyle,
-  createLollipopFromGene,
-  drawHoverShapes,
-  showResultsTable,
-  table2col,
-  to_svg
-} from "./chunk-C3HEDQPT.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  icons
-} from "./chunk-6RRZRISL.js";
-import {
-  axisLeft
-} from "./chunk-Z2ZITHT4.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// plots/manhattan/manhattan.ts
-var manhattanLayoutDefaults = {
-  plotWidth: 1e3,
-  plotHeight: 400,
-  pngDotRadius: 2,
-  yAxisX: 70,
-  yAxisY: 40,
-  yAxisSpace: 20,
-  xAxisLabelPad: 30,
-  yAxisPad: 5,
-  axisColor: "#545454",
-  showYAxisLine: true,
-  fontSize: 12,
-  showLegend: true,
-  legendItemWidth: 80,
-  legendDotRadius: 3,
-  legendRightOffset: 15,
-  legendTextOffset: 12,
-  legendVerticalOffset: 4,
-  legendFontSize: 12,
-  showInteractiveDots: true,
-  interactiveDotRadius: 2,
-  interactiveDotStrokeWidth: 1,
-  showDownload: true,
-  interactiveDotsCap: 5e3,
-  maxTooltipGenes: 5
-};
-function plotManhattan(div, data, settings, app, custom = {}) {
-  const handle = { points: [], highlight: () => {
-  } };
-  settings = {
-    ...settings
-  };
-  let interactivePoints = data.plotData.points;
-  if (data.plotData.points.length > settings.interactiveDotsCap) {
-    interactivePoints = data.plotData.points.sort((a, b) => Math.abs(b.y) - Math.abs(a.y)).slice(0, settings.interactiveDotsCap);
-  }
-  const signed = data.plotData.y_min < 0;
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
-  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
-  const yPad = data.plotData.y_pad ?? settings.pngDotRadius;
-  const yAxisLow = signed ? data.plotData.y_min + yPad : 0;
-  const yAxisScale = linear().domain([yAxisLow, data.plotData.y_max - yPad]).range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)]);
-  const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
-  axisG.call(
-    axisLeft(yAxisScale).tickSizeOuter(0)
-    // removes top/bottom cap lines for clean look
-  );
-  axisstyle({
-    axis: axisG,
-    color: settings.axisColor,
-    fontsize: settings.fontSize + 2,
-    showline: settings.showYAxisLine
-  });
-  svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text((custom.yAxisLabel ?? "-log\u2081\u2080(q-value)") + (data.plotData.has_capped_points ? " [capped]" : ""));
-  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
-  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
-  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
-    const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
-    const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
-    const linkedLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    handle.points = interactivePoints;
-    handle.highlight = (dots) => drawHoverShapes(
-      linkedLayer,
-      dots.map((d) => ({
-        path: circlePath(settings.pngDotRadius + 2),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        stroke: "black",
-        strokeWidth: 2
-      }))
-    );
-    const grin2Hover = (d, container) => {
-      const table = table2col({ holder: container.append("div"), margin: "10px" });
-      table.addRow("Gene", d.gene);
-      table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
-      const [t1, t2] = table.addRow();
-      t1.text("Type");
-      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-      table.addRow("Q-value", d.q_value.toPrecision(3));
-      table.addRow("Subject count", d.nsubj);
-    };
-    const grin2Table = (dots) => ({
-      columns: [
-        { label: "Gene" },
-        { label: "Position" },
-        { label: "Type" },
-        { label: "Q-value", sortable: true },
-        { label: "Subject count", sortable: true }
-      ],
-      rows: dots.map((d) => [
-        { value: d.gene },
-        { value: `${d.chrom}:${d.start}-${d.end}` },
-        {
-          html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
-        },
-        { value: d.q_value.toPrecision(3) },
-        { value: d.nsubj }
-      ])
-    });
-    const interactions = new DataPointInteractions({
-      cover,
-      hoverLayer,
-      hoverTip: geneTip,
-      points: interactivePoints,
-      getX: (d) => d.pixel_x,
-      getY: (d) => d.pixel_y,
-      hitRadius: settings.pngDotRadius + 3,
-      toHoverSpec: (d) => ({
-        path: circlePath(settings.pngDotRadius),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        fill: "none",
-        stroke: "black",
-        strokeWidth: settings.interactiveDotStrokeWidth
-      }),
-      maxTooltipRows: settings.maxTooltipGenes,
-      onHover: custom.onHover,
-      itemNoun: custom.itemNoun ?? "gene",
-      renderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,
-      buildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,
-      // A caller with actions gets the module's standard click flow: an action menu for one
-      // dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.
-      ...custom.getActions ? {
-        getActions: custom.getActions,
-        renderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,
-        getRowKey: custom.getRowKey
-      } : {
-        // Manhattan single-click goes straight to a lollipop launch — no menu.
-        // Release hover-suppression immediately so the cursor's next move re-engages.
-        onSingleClick: (d, _event, ctx) => {
-          ctx.dismiss();
-          if (app && d.gene) createLollipopFromGene(d.gene, app);
-        },
-        // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
-        // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
-        // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
-        // Content is built BEFORE show2 so Menu can measure the populated rect for
-        // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
-        // and extends off the right edge of the viewport.
-        onMultiClick: (dots, event, ctx) => {
-          if (!app) {
-            ctx.dismiss();
-            return;
-          }
-          ctx.clickMenu.clear();
-          const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
-          showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
-          ctx.clickMenu.show2(event.clientX, event.clientY);
-        }
-      }
-    });
-    interactions.attach();
-  }
-  if (data.plotData.chrom_data) {
-    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
-    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
-    });
-  }
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr("y", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text("Chromosomes");
-  const title = svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text(custom.title ?? "Manhattan Plot");
-  const titleWidth = title.node().getBBox?.().width || 100;
-  if (settings.showDownload) {
-    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + titleWidth + 8}px`);
-    icons["download"](downloadDiv, {
-      width: 16,
-      height: 16,
-      title: "Download Manhattan plot",
-      handler: () => {
-        const svgNode = svg.node();
-        const clone = svgNode.cloneNode(true);
-        const bbox = svgNode.getBBox();
-        clone.setAttribute("width", bbox.width.toString());
-        clone.setAttribute("height", bbox.height.toString());
-        clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
-        to_svg(clone, `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`, {
-          apply_dom_styles: true
-        });
-      }
-    });
-  }
-  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type).filter(Boolean))];
-  const legendData = custom.legend?.map((l) => ({ type: l.label, color: l.color, hollow: l.hollow })) ?? mutationTypes.map((type) => {
-    const point = data.plotData.points.find((p) => p.type === type);
-    return {
-      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
-      color: point?.color
-    };
-  });
-  if (settings.showLegend && legendData.length > 0) {
-    const legendY = settings.yAxisY / 2;
-    const totalWidth = legendData.length * settings.legendItemWidth;
-    const legendX = settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) - totalWidth - settings.legendRightOffset;
-    legendData.forEach((item, i) => {
-      const x = legendX + i * settings.legendItemWidth;
-      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.hollow ? "none" : item.color).attr("stroke", item.hollow ? item.color : "none");
-      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
-    });
-  }
-  return handle;
-}
-
-export {
-  manhattanLayoutDefaults,
-  plotManhattan
-};
-//# sourceMappingURL=chunk-6G45AUSV.js.map

package/dist/chunk-6LDKSKYQ.js

@@ -1,70 +0,0 @@
-import {
-  junctionCustomTermSource
-} from "./chunk-JTANDSTD.js";
-import {
-  mayRenderFractionSelection
-} from "./chunk-C3HEDQPT.js";
-
-// termdb/handlers/junction.ts
-var SearchHandler = class {
-  async init(opts) {
-    if (!opts?.holder) throw new Error("opts.holder is required");
-    if (typeof opts.callback != "function") throw new Error("opts.callback is required");
-    const entries = getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms);
-    render(opts, entries);
-  }
-};
-function getJunctionCustomTerms(customTerms) {
-  if (!Array.isArray(customTerms)) return [];
-  return customTerms.filter((term) => term?.source === junctionCustomTermSource && term.tw?.term);
-}
-function render(opts, entries) {
-  const holder = opts.holder;
-  holder.selectAll("*").remove();
-  const div = holder.append("div").style("padding", "10px 0px");
-  if (!entries.length) {
-    div.append("div").text("Junctions selected from genome browser will be shown here.");
-    return;
-  }
-  const listDiv = div.append("div");
-  const fractionDiv = div.append("div");
-  for (const entry of entries) {
-    if (entry.eventlabel) renderJunctionEvent(listDiv, fractionDiv, entry, opts);
-    else renderJunction(listDiv, entry, opts);
-  }
-  listDiv.append("div").style("font-size", ".7em").style("margin-top", "10px").style("opacity", 0.7).text("Select additional junctions from genome browser.");
-}
-function renderJunction(holder, entry, opts) {
-  const choice = holder.append("div");
-  choice.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.tw.term.name).on("click", () => opts.callback(entry.tw.term));
-  addDeleteButton(choice, entry, opts);
-}
-function renderJunctionEvent(holder, fractionDiv, entry, opts) {
-  const eventHolder = holder.append("div");
-  const pillRow = eventHolder.append("div");
-  pillRow.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.eventlabel).on("click", () => selectJunctionEvent(holder, fractionDiv, entry, opts));
-  addDeleteButton(pillRow, entry, opts);
-  eventHolder.append("div").style("margin-left", "10px").style("font-size", ".7em").selectAll("div").data(entry.tw.term.termlst, (term) => term.id).enter().append("div").text((term) => term.name);
-}
-function selectJunctionEvent(listDiv, fractionDiv, entry, opts) {
-  const isStaged = mayRenderFractionSelection({
-    term: entry.tw.term,
-    selectionMode: opts.termCollectionSelectionMode,
-    listDiv,
-    fractionDiv,
-    callback: (tw) => opts.callback(tw)
-  });
-  if (!isStaged) opts.callback(entry.tw.term);
-}
-function addDeleteButton(holder, entry, opts) {
-  holder.append("button").attr("data-testid", "sjpp-junction-delete").style("margin-left", "4px").attr("aria-label", `Delete ${entry.name}`).text("\xD7").on("click", async () => {
-    await opts.app.vocabApi.deleteCustomTermById(entry.id);
-    render(opts, getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms));
-  });
-}
-
-export {
-  SearchHandler,
-  getJunctionCustomTerms
-};
-//# sourceMappingURL=chunk-6LDKSKYQ.js.map