@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/chunk-PQDYA3ZQ.js

@@ -0,0 +1,274 @@
+import {
+  termType2label
+} from "./chunk-CFYWQJ7F.js";
+import {
+  TermTypes
+} from "./chunk-2N345NXD.js";
+import {
+  __export
+} from "./chunk-HS5PO5ZQ.js";
+
+// plots/matrix/hierCluster.renderers.js
+var hierCluster_renderers_exports = {};
+__export(hierCluster_renderers_exports, {
+  maySetSandboxHeader: () => maySetSandboxHeader,
+  plotDendrogramHclust: () => plotDendrogramHclust,
+  renderImage: () => renderImage
+});
+function maySetSandboxHeader(appState) {
+  if (!this.dom.header) return;
+  const dataType = this.config.dataType;
+  const headerText = this.config?.headerText ? `${this.config.headerText} ` : "";
+  let title;
+  if (this.config.preBuiltPlotTitle) {
+    title = this.config.preBuiltPlotTitle;
+  } else if (this.config.appName) {
+    title = `${headerText}${this.config.appName} Clustering`;
+  } else if (dataType == TermTypes.PROTEOME_ABUNDANCE) {
+    title = this.config.assayCohortTitle ? `Protein Abundance Clustering (${this.config.assayCohortTitle})` : "Protein Abundance Clustering";
+  } else {
+    title = `${headerText}${termType2label(dataType)} Clustering`;
+  }
+  this.dom.header.text(title);
+}
+function plotDendrogramHclust(plotOnly) {
+  const d = this.dimensions;
+  const s = this.config.settings.matrix;
+  const xOffset = d.seriesXoffset;
+  const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
+  const obj = this.hierClusterData.clustering;
+  const row = obj.row;
+  const col = obj.col;
+  const rowHeight = this.settings.matrix.clusterRowh, { xDendrogramHeight, yDendrogramHeight } = this.settings.hierCluster, colWidth = this.dimensions.dx;
+  if (plotOnly !== "left") {
+    if (!this.settings.hierCluster.clusterSamples) {
+      this.dom.topDendrogram.selectAll("*").remove();
+    } else {
+      const height2px = getHclustHeightScalefactor(col.height, yDendrogramHeight);
+      const height = yDendrogramHeight + 1e-7;
+      const width = Math.min(colWidth * col.inputOrder.length, s.imgWMax);
+      if (width <= 0 || height <= 0) {
+        console.warn(
+          "Skipping top dendrogram render: invalid dimensions.",
+          "This may indicate a zoom feedback loop issue.",
+          {
+            width,
+            height,
+            colWidth,
+            sampleCount: col.inputOrder.length,
+            yDendrogramHeight
+          }
+        );
+        this.dom.topDendrogram.selectAll("*").remove();
+        return;
+      }
+      const canvas = new OffscreenCanvas(width * pxr, height * pxr);
+      const ctx = canvas.getContext("2d");
+      ctx.scale(pxr, pxr);
+      ctx.translate(-d.xMin, 0);
+      ctx.imageSmoothingEnabled = false;
+      ctx.imageSmoothingQuality = "high";
+      ctx.strokeStyle = "black";
+      const mergedClusters = /* @__PURE__ */ new Map();
+      for (const [clusterid0, pair] of col.merge.entries()) {
+        const clusterid = clusterid0 + 1;
+        const children = [];
+        const childrenClusters = [];
+        let x1, x2, y1, y2;
+        if (pair.n1 < 0) {
+          const [name, columnNumber] = getLeafNumber(pair.n1, col.inputOrder, col.order);
+          x1 = colWidth * (columnNumber + 0.5);
+          y1 = yDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n1);
+          x1 = c.x;
+          y1 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n1);
+        }
+        if (pair.n2 < 0) {
+          const [name, columnNumber] = getLeafNumber(pair.n2, col.inputOrder, col.order);
+          x2 = colWidth * (columnNumber + 0.5);
+          y2 = yDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n2);
+          x2 = c.x;
+          y2 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n2);
+        }
+        const clusterY = yDendrogramHeight - col.height[clusterid0].height * height2px;
+        const highlight = this.clickedClusterIds?.includes(clusterid);
+        ctx.strokeStyle = highlight ? "red" : "black";
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(x1, clusterY);
+        ctx.lineTo(x2, clusterY);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+        ctx.closePath();
+        mergedClusters.set(clusterid, {
+          x: (x1 + x2) / 2,
+          y: clusterY,
+          children,
+          childrenClusters,
+          clusterPosition: {
+            x1,
+            x2,
+            y1,
+            y2,
+            clusterY
+          }
+        });
+      }
+      this.renderImage(
+        this.api,
+        this.dom.topDendrogram,
+        canvas,
+        width,
+        height,
+        xDendrogramHeight + 0.5 * colWidth + d.xMin,
+        s.margin.top + s.scrollHeight
+      );
+      col.mergedClusters = mergedClusters;
+    }
+  }
+  if (plotOnly !== "top") {
+    if (!this.settings.hierCluster.clusterRows) {
+      this.dom.leftDendrogram.selectAll("*").remove();
+    } else {
+      const height2px = getHclustHeightScalefactor(row.height, xDendrogramHeight);
+      const width = xDendrogramHeight + 1e-7;
+      const height = rowHeight * row.inputOrder.length;
+      const canvasWidthPx = Number.isFinite(width) && Number.isFinite(pxr) ? Math.max(0, Math.floor(width * pxr)) : 0;
+      const canvasHeightPx = Number.isFinite(height) && Number.isFinite(pxr) ? Math.max(0, Math.floor(height * pxr)) : 0;
+      if (!Number.isFinite(width) || !Number.isFinite(height) || !Number.isFinite(pxr) || width <= 0 || height <= 0 || pxr <= 0 || canvasWidthPx < 1 || canvasHeightPx < 1) {
+        console.warn(
+          "Skipping left dendrogram render: invalid dimensions.",
+          "This may indicate a zoom feedback loop issue.",
+          {
+            width,
+            height,
+            pxr,
+            canvasWidthPx,
+            canvasHeightPx,
+            rowHeight,
+            termCount: row.inputOrder.length,
+            xDendrogramHeight
+          }
+        );
+        this.dom.leftDendrogram.selectAll("*").remove();
+        return;
+      }
+      const canvas = new OffscreenCanvas(canvasWidthPx, canvasHeightPx);
+      const ctx = canvas.getContext("2d");
+      ctx.scale(pxr, pxr);
+      ctx.imageSmoothingEnabled = false;
+      ctx.imageSmoothingQuality = "high";
+      ctx.strokeStyle = "black";
+      const mergedClusters = /* @__PURE__ */ new Map();
+      for (const [clusterid0, pair] of row.merge.entries()) {
+        const clusterid = clusterid0 + 1;
+        const children = [];
+        const childrenClusters = [];
+        let x1, x2, y1, y2;
+        if (pair.n1 < 0) {
+          const [name, rowNumber] = getLeafNumber(pair.n1, row.inputOrder, row.order);
+          y1 = rowHeight * (rowNumber + 0.5);
+          x1 = xDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n1);
+          x1 = c.x;
+          y1 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n1);
+        }
+        if (pair.n2 < 0) {
+          const [name, rowNumber] = getLeafNumber(pair.n2, row.inputOrder, row.order);
+          y2 = rowHeight * (rowNumber + 0.5);
+          x2 = xDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n2);
+          x2 = c.x;
+          y2 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n2);
+        }
+        const clusterX = xDendrogramHeight - row.height[clusterid0].height * height2px;
+        const highlight = this.clickedLeftClusterIds?.includes(clusterid);
+        ctx.strokeStyle = highlight ? "red" : "black";
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(clusterX, y1);
+        ctx.lineTo(clusterX, y2);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+        ctx.closePath();
+        mergedClusters.set(clusterid, {
+          x: clusterX,
+          y: (y1 + y2) / 2,
+          children,
+          childrenClusters,
+          clusterPosition: {
+            x1,
+            x2,
+            y1,
+            y2,
+            clusterX
+          }
+        });
+      }
+      const t = this.termOrder.find((t2) => t2.grp.type == "hierCluster" || t2.grp.name == this.hcTermGroup.name);
+      const y = (
+        // t.labelOffset is commented out because it is already handled in adjustSvgDimensions
+        t.grpIndex * s.rowgspace + t.prevGrpTotalIndex * s.rowh + t.totalHtAdjustments + s.margin.top + s.scrollHeight + // left dendrogram image must be lower than the top dendrogram image height
+        yDendrogramHeight
+      );
+      this.renderImage(this.api, this.dom.leftDendrogram, canvas, width, height, 0, y);
+      row.mergedClusters = mergedClusters;
+    }
+  }
+}
+async function renderImage(componentApi, g, canvas, width, height, x, y) {
+  const sequenceId = componentApi.getSequenceId();
+  const reader = new FileReader();
+  reader.addEventListener(
+    "load",
+    () => {
+      if (componentApi.isStaleSequenceId(sequenceId)) return;
+      g.selectAll("*").remove();
+      g.append("image").attr("x", x + 0.033).attr("y", y + 0.033).attr("xlink:href", reader.result).attr("width", width).attr("height", height);
+    },
+    false
+  );
+  const blob = await canvas.convertToBlob({ quality: 1 });
+  reader.readAsDataURL(blob);
+}
+function getHclustHeightScalefactor(lst, ph) {
+  let max = lst[0].height;
+  for (const h of lst) max = Math.max(max, h.height);
+  return ph / max;
+}
+function getLeafNumber(minus, inputOrder, order) {
+  const name = inputOrder[-minus - 1];
+  if (!name) throw "minus not in inputOrder";
+  const i = order.findIndex((j) => j.name == name);
+  if (i == -1) throw "name not found in hc$order";
+  return [name, i];
+}
+
+export {
+  maySetSandboxHeader,
+  plotDendrogramHclust,
+  renderImage,
+  hierCluster_renderers_exports
+};
+//# sourceMappingURL=chunk-PQDYA3ZQ.js.map

package/dist/chunk-PVJ6IIFA.js

@@ -0,0 +1,176 @@
+import {
+  appInit
+} from "./chunk-R6O3FLKW.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-YBXQBSFY.js";
+import {
+  mclass
+} from "./chunk-2N345NXD.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-PVJ6IIFA.js.map

package/dist/chunk-QGG5MTIL.js

@@ -0,0 +1,161 @@
+import {
+  NumericDensity
+} from "./chunk-6CV3YVJD.js";
+import {
+  HandlerBase,
+  Tabs
+} from "./chunk-YBXQBSFY.js";
+import {
+  getTermLabelSuffix
+} from "./chunk-CFYWQJ7F.js";
+
+// termsetting/handlers/NumericHandler.ts
+var NumericHandler = class extends HandlerBase {
+  constructor(opts) {
+    super(opts);
+    this.tabs = [];
+    this.handlerByMode = {};
+    this.dom = {};
+    this.opts = opts;
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+    this.tabs = this.setTabData();
+    this.density = new NumericDensity(opts);
+  }
+  getPillStatus() {
+    this.tw = this.termsetting.tw;
+    const status = this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
+    if (this.tw.term.type == "geneExpression") status.text += getTermLabelSuffix(this.tw.term);
+    return status;
+  }
+  setTabData() {
+    const self = this.termsetting;
+    const tabs = [];
+    const callback = async (event, tabData) => {
+      if (event) event.stopPropagation();
+      try {
+        await this.setEditHandler(tabData);
+        await this.editHandler.showEditMenu(tabData.contentHolder);
+      } catch (e) {
+        this.dom.errdiv.style("display", "").text(e);
+      }
+    };
+    const numTabs = self.opts.numericEditMenuVersion.length;
+    if (self.opts.numericEditMenuVersion.includes("continuous")) {
+      tabs.push({
+        mode: "continuous",
+        label: self.term.type == "survival" ? "Time to Event" : "Continuous",
+        callback,
+        active: this.tw.q.mode === "continuous" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("discrete")) {
+      tabs.push({
+        mode: "discrete",
+        label: self.term.type == "survival" ? "Exit code" : "Discrete",
+        callback,
+        active: this.tw.q.mode === "discrete" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("spline")) {
+      tabs.push({
+        mode: "spline",
+        label: "Cubic spline",
+        callback,
+        active: this.tw.q.mode === "spline" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("binary")) {
+      tabs.push({
+        mode: "binary",
+        label: "Binary",
+        callback,
+        active: this.tw.q.mode === "binary" || numTabs === 1
+      });
+    }
+    return tabs;
+  }
+  async setEditHandler(tabData) {
+    if (!this.handlerByMode[tabData.mode]) {
+      switch (tabData.mode) {
+        case "continuous": {
+          const { NumContEditor } = await import("./NumContEditor-YPSYWU2A.js");
+          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
+          break;
+        }
+        case "discrete": {
+          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-BLQ5DEB7.js");
+          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
+          break;
+        }
+        case "binary": {
+          const { NumBinaryEditor } = await import("./NumBinaryEditor-SEC2NDGG.js");
+          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
+          break;
+        }
+        case "spline": {
+          const { NumSplineEditor } = await import("./NumSplineEditor-LO3ZR3T3.js");
+          this.handlerByMode.spline = new NumSplineEditor(this.opts, this);
+          break;
+        }
+        default:
+          throw `unexpected numeric tabData.mode='${tabData.mode}'`;
+          break;
+      }
+    }
+    this.editHandler = this.handlerByMode[tabData.mode];
+  }
+  async showEditMenu(div) {
+    try {
+      this.showLoading(div);
+      this.dom.errdiv = div.append("div").attr("class", "sja_errorbar").style("display", "none");
+      this.tw = this.termsetting.tw;
+      const self = this.tw;
+      for (const t of this.tabs) {
+        t.active = this.tabs.length === 1 || self.q.mode == t.mode || t.mode == "continuous" && !self.q.mode;
+      }
+      this.density_data = await this.density.setData();
+      await this.setEditHandler(this.tabs.find((t) => t.active));
+      this.dom.editDiv = div.append("div").attr("data-testid", "sjpp-num-ts-edit-div");
+      this.dom.btnDiv = div.append("div").style("margin", "0px 0px 5px 5px");
+      this.renderButtons(this.dom.btnDiv);
+      if (this.tabs.length > 1) {
+        this.dom.topBar = this.dom.editDiv.append("div").attr("data-testid", "sja-ts-numeric-edit-top-bar").style("padding", "10px");
+        this.dom.topBar.append("span").html("Use as ");
+        new Tabs({
+          holder: this.dom.topBar.append("div").style("display", "inline-block"),
+          contentHolder: this.dom.editDiv.append("div"),
+          noTopContentStyle: true,
+          tabs: this.tabs
+        }).main();
+      } else {
+        await this.editHandler.showEditMenu(this.dom.editDiv);
+      }
+      this.dom.loadingDiv.style("display", "none");
+    } catch (e) {
+      this.hideLoading();
+      this.dom.errdiv.style("display", "").text(typeof e == "object" ? e.message || e.error || e : e);
+    }
+  }
+  renderButtons(btnDiv) {
+    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_apply").html("Apply").on("click", () => {
+      this.termsetting.q = this.editHandler.getEditedQ();
+      this.termsetting.dom.tip.hide();
+      this.termsetting.api.runCallback();
+    });
+    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_reset").html("Reset").on("click", () => {
+      this.editHandler.undoEdits();
+    });
+  }
+  destroy() {
+    for (const s of Object.values(this.dom)) {
+      if (typeof s.remove == "function") s.remove();
+    }
+    this.density.destroy();
+  }
+};
+
+export {
+  NumericHandler
+};
+//# sourceMappingURL=chunk-QGG5MTIL.js.map

package/dist/chunk-QGG5MTIL.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumericHandler.ts"],
+  "sourcesContent": ["import { HandlerBase } from '../HandlerBase.ts'\nimport type { Handler } from '../index.ts'\nimport type { NumRegularBin, NumCustomBins, NumCont, NumSpline } from '#tw'\nimport { Tabs } from '#dom'\nimport { NumericDensity } from './NumericDensity.ts'\nimport type { NumContEditor } from './NumContEditor'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor'\nimport type { NumBinaryEditor } from './NumBinaryEditor'\nimport type { NumSplineEditor } from './NumSplineEditor'\nimport { getTermLabelSuffix } from '#shared/terms.js'\n\ntype NumericTabCallback = (event: PointerEvent, tab: TabData) => void\n\ntype TabData = {\n\tmode: 'continuous' | 'discrete' | 'binary' | 'spline'\n\tlabel: string\n\tcallback: NumericTabCallback\n\tcontentHolder?: any //\n\tactive?: boolean\n}\n\n/*\n\tNumericHandler \n\t- NumericDensity\n\t- NumericDiscrete\n\t\t - NumRegularBinEditor\n\t\t - NumCustomBinEditor\n*/\n\ntype EditHandler = NumContEditor | NumDiscreteEditor | NumBinaryEditor | NumSplineEditor\n\nexport class NumericHandler extends HandlerBase implements Handler {\n\topts: any // TODO\n\ttw: NumRegularBin | NumCustomBins | NumCont | NumSpline\n\ttabs: TabData[] = []\n\thandlerByMode: {\n\t\t[twType: string]: EditHandler\n\t} = {}\n\teditHandler!: EditHandler\n\ttoggleBtns!: Tabs\n\n\tdom: {\n\t\t[name: string]: any\n\t} = {}\n\n\tdensity: NumericDensity\n\tdensity_data!: any\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.opts = opts\n\t\tthis.termsetting = opts.termsetting\n\t\tthis.tw = opts.termsetting.tw\n\t\tthis.tabs = this.setTabData()\n\t\tthis.density = new NumericDensity(opts)\n\t}\n\n\tgetPillStatus() {\n\t\tthis.tw = this.termsetting.tw as NumRegularBin | NumCustomBins | NumCont | NumSpline // TODO: do not force type\n\t\tconst status = this.tw.getStatus(this.termsetting.usecase, this.termsetting.data)\n\t\t// other term types with sample types name them in term.name, see getTermLabelSuffix()\n\t\tif (this.tw.term.type == 'geneExpression') status.text += getTermLabelSuffix(this.tw.term)\n\t\treturn status\n\t}\n\n\tsetTabData() {\n\t\tconst self = this.termsetting\n\t\tconst tabs: TabData[] = []\n\t\tconst callback = async (event, tabData) => {\n\t\t\tif (event) event.stopPropagation()\n\t\t\ttry {\n\t\t\t\tawait this.setEditHandler(tabData)\n\t\t\t\t//this.dom.editDiv.selectAll('*').remove()\n\t\t\t\tawait this.editHandler.showEditMenu(tabData.contentHolder) //this.dom.editDiv)\n\t\t\t} catch (e) {\n\t\t\t\tthis.dom.errdiv.style('display', '').text(e)\n\t\t\t}\n\t\t}\n\n\t\tconst numTabs = self.opts.numericEditMenuVersion.length\n\t\tif (self.opts.numericEditMenuVersion.includes('continuous')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'continuous',\n\t\t\t\tlabel: self.term.type == 'survival' ? 'Time to Event' : 'Continuous',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'continuous' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\tif (self.opts.numericEditMenuVersion.includes('discrete')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'discrete',\n\t\t\t\tlabel: self.term.type == 'survival' ? 'Exit code' : 'Discrete',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'discrete' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\tif (self.opts.numericEditMenuVersion.includes('spline')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'spline',\n\t\t\t\tlabel: 'Cubic spline',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'spline' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\tif (self.opts.numericEditMenuVersion.includes('binary')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'binary',\n\t\t\t\tlabel: 'Binary',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'binary' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\treturn tabs\n\t}\n\n\tasync setEditHandler(tabData) {\n\t\tif (!this.handlerByMode[tabData.mode]) {\n\t\t\tswitch (tabData.mode) {\n\t\t\t\tcase 'continuous': {\n\t\t\t\t\tconst { NumContEditor } = await import('./NumContEditor.ts')\n\t\t\t\t\tthis.handlerByMode.continuous = new NumContEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcase 'discrete': {\n\t\t\t\t\tconst { NumDiscreteEditor } = await import('./NumDiscreteEditor.ts')\n\t\t\t\t\tthis.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcase 'binary': {\n\t\t\t\t\tconst { NumBinaryEditor } = await import('./NumBinaryEditor.ts')\n\t\t\t\t\tthis.handlerByMode.binary = new NumBinaryEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcase 'spline': {\n\t\t\t\t\tconst { NumSplineEditor } = await import('./NumSplineEditor.ts')\n\t\t\t\t\tthis.handlerByMode.spline = new NumSplineEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tdefault:\n\t\t\t\t\tthrow `unexpected numeric tabData.mode='${tabData.mode}'`\n\t\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tthis.editHandler = this.handlerByMode[tabData.mode]\n\t}\n\n\tasync showEditMenu(div) {\n\t\ttry {\n\t\t\tthis.showLoading(div)\n\t\t\tthis.dom.errdiv = div.append('div').attr('class', 'sja_errorbar').style('display', 'none')\n\t\t\tthis.tw = this.termsetting.tw as NumRegularBin | NumCustomBins | NumCont | NumSpline // TODO: do not force type\n\n\t\t\tconst self = this.tw\n\t\t\tfor (const t of this.tabs) {\n\t\t\t\tt.active = this.tabs.length === 1 || self.q.mode == t.mode || (t.mode == 'continuous' && !self.q.mode)\n\t\t\t}\n\n\t\t\tthis.density_data = await this.density.setData()\n\t\t\tawait this.setEditHandler(this.tabs.find(t => t.active))\n\t\t\tthis.dom.editDiv = div.append('div').attr('data-testid', 'sjpp-num-ts-edit-div')\n\t\t\tthis.dom.btnDiv = div.append('div').style('margin', '0px 0px 5px 5px')\n\t\t\tthis.renderButtons(this.dom.btnDiv)\n\n\t\t\tif (this.tabs.length > 1) {\n\t\t\t\tthis.dom.topBar = this.dom.editDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('data-testid', 'sja-ts-numeric-edit-top-bar')\n\t\t\t\t\t.style('padding', '10px')\n\t\t\t\tthis.dom.topBar.append('span').html('Use as ')\n\t\t\t\tnew Tabs({\n\t\t\t\t\tholder: this.dom.topBar.append('div').style('display', 'inline-block'),\n\t\t\t\t\tcontentHolder: this.dom.editDiv.append('div'),\n\t\t\t\t\tnoTopContentStyle: true,\n\t\t\t\t\ttabs: this.tabs\n\t\t\t\t}).main()\n\t\t\t} else {\n\t\t\t\tawait this.editHandler.showEditMenu(this.dom.editDiv)\n\t\t\t}\n\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t} catch (e: any) {\n\t\t\tthis.hideLoading()\n\t\t\tthis.dom.errdiv.style('display', '').text(typeof e == 'object' ? e.message || e.error || e : e)\n\t\t}\n\t}\n\n\trenderButtons(btnDiv) {\n\t\tbtnDiv\n\t\t\t.append('button')\n\t\t\t.style('margin', '5px')\n\t\t\t.attr('data-testId', 'sjpp_numeric_edit_apply')\n\t\t\t.html('Apply')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.termsetting.q = this.editHandler.getEditedQ()\n\t\t\t\tthis.termsetting.dom.tip.hide()\n\t\t\t\tthis.termsetting.api.runCallback()\n\t\t\t})\n\n\t\tbtnDiv\n\t\t\t.append('button')\n\t\t\t.style('margin', '5px')\n\t\t\t.attr('data-testId', 'sjpp_numeric_edit_reset')\n\t\t\t.html('Reset')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.editHandler.undoEdits()\n\t\t\t})\n\t}\n\n\tdestroy() {\n\t\tfor (const s of Object.values(this.dom)) {\n\t\t\tif (typeof s.remove == 'function') s.remove()\n\t\t}\n\t\tthis.density.destroy()\n\t}\n}\n"],
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+}