@sjcrh/proteinpaint-client 2.221.0 → 2.223.0

package/dist/chunk-GKLDVEAQ.js

@@ -0,0 +1,194 @@
+import {
+  violinRenderer
+} from "./chunk-JP4IU7DO.js";
+import {
+  getValueConversionFactor
+} from "./chunk-W5J3LTYS.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import {
+  drag_default
+} from "./chunk-5R63Q5KH.js";
+import {
+  pointer_default,
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// termsetting/handlers/NumericDensity.ts
+var NumericDensity = class {
+  constructor(opts) {
+    this.dom = {};
+    // WeakMap allows deletion of value when the object/DOM key is deleted,
+    // so better for avoiding memory leak
+    this.vrByDiv = /* @__PURE__ */ new WeakMap();
+    this.ranges = [];
+    this.no_density_data = false;
+    this.brushes = [];
+    this.plot_size = {
+      width: 500,
+      height: 100,
+      xpad: 10,
+      ypad: 20,
+      radius: 8
+    };
+    this.opts = opts;
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+  }
+  /* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in
+  	the term's user-facing unit; density_data is in the unit the values are stored in. only the two
+  	getters below cross that line, to put the plot's endpoints in the same unit as those values.
+  
+  	they multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown
+  	in an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown
+  	digit, and collapses the domain outright when the converted range is smaller than that (a stored
+  	range of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose
+  	axis this plot's lines overlay and which scales its own domain unrounded */
+  get scaleFactor() {
+    return getValueConversionFactor(this.tw.term);
+  }
+  get displayMin() {
+    return this.density_data.min * this.scaleFactor;
+  }
+  get displayMax() {
+    return this.density_data.max * this.scaleFactor;
+  }
+  async setData() {
+    const self = this.termsetting;
+    const d = await self.vocabApi.getViolinBox(
+      {
+        plotType: "violin",
+        tw: { type: self.tw.type, term: self.term, q: self.q },
+        svgw: this.plot_size.width,
+        radius: this.plot_size.radius,
+        filter: self.filter
+      },
+      self.opts.getBodyParams?.()
+    );
+    if (d.error) throw d;
+    this.density_data = d;
+    return this.density_data;
+  }
+  async showViolin(div, boundaryOpts) {
+    await this.setData();
+    if (!this.vrByDiv.has(div)) {
+      div.style("padding", "5px").selectAll("*").remove();
+      const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
+      const densityDiv = div.append("div");
+      loadingDiv.remove();
+      const vr = new violinRenderer({
+        holder: densityDiv,
+        rd: this.density_data,
+        width: this.plot_size.width,
+        height: this.plot_size.height,
+        radius: this.plot_size.radius,
+        // axis ticks are labeled in the term's user-facing unit, e.g. years and not days
+        scaleFactor: this.scaleFactor
+      });
+      this.vrByDiv.set(div, vr);
+    }
+    this.vr = this.vrByDiv.get(div);
+    this.dom.svg = this.vr.svg;
+    this.vr.render();
+    if (boundaryOpts) await this.setBinLines(boundaryOpts);
+    return this.density_data;
+  }
+  async setBinLines(boundaryOpts) {
+    if (this.density_data.max == this.density_data.min) {
+      this.handleNoDensity();
+    } else {
+      if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
+      this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
+      const maxvalue = this.displayMax;
+      const minvalue = this.displayMin;
+      this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
+      this.ranges = [];
+      this.brushes = [];
+      this.renderBinLines(boundaryOpts);
+    }
+  }
+  handleNoDensity() {
+    this.no_density_data = true;
+    this.ranges = [];
+    this.brushes = [];
+  }
+  renderBinLines(boundaryOpts) {
+    const { plot_size, tw, xscale, scaleFactor } = this;
+    if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
+    const scaledMinX = Math.round(this.xscale(this.displayMin));
+    const scaledMaxX = Math.round(this.xscale(this.displayMax));
+    const lines = [];
+    for (const [index, v] of boundaryOpts.values.entries()) {
+      lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
+    }
+    const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
+    const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
+    const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
+    this.dom.binsize_g.selectAll("line").remove();
+    this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
+      if (d.isDraggable) select_default(this).style("stroke-width", 3);
+    }).on("mouseout", function() {
+      select_default(this).style("stroke-width", 1);
+    }).each(function(d) {
+      if (d.isDraggable) select_default(this).call(dragger);
+    });
+    const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
+    function toBoundaryValue(x) {
+      const inverted = xscale.invert(x);
+      return Number(
+        scaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3)
+      );
+    }
+    function toLineValue(line) {
+      return line.draggedX === void 0 ? line.x : toBoundaryValue(line.draggedX);
+    }
+    function getNeighbors(d) {
+      const x = d.draggedX ?? d.scaledX;
+      let lower, upper;
+      for (const line of lines) {
+        if (line.index === d.index || !line.isDraggable) continue;
+        const lineX = line.draggedX ?? line.scaledX;
+        if (lineX <= x) {
+          if (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line;
+        } else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line;
+      }
+      return [lower, upper];
+    }
+    function onDrag(event, _d) {
+      const d = _d;
+      const [lower, upper] = getNeighbors(d);
+      const lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX);
+      const upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX);
+      if (upperX - lowerX < 2) return;
+      const draggedX = Math.min(Math.max(pointer_default(event, this)[0], lowerX + 1), upperX - 1);
+      const value = toBoundaryValue(draggedX);
+      if (lower && value === toLineValue(lower)) return;
+      if (upper && value === toLineValue(upper)) return;
+      d.draggedX = draggedX;
+      select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
+      const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
+      const xOffset = d.draggedX - d.scaledX;
+      if (xOffset) {
+        for (const elem of lineElems) {
+          const c = elem.__data__;
+          if (c.movesWithLineIndex !== d.index) continue;
+          c.draggedX = c.scaledX + xOffset;
+          select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
+        }
+        boundaryOpts.callback(d, value);
+      }
+    }
+  }
+  destroy() {
+    for (const [k, v] of Object.entries(this.dom)) {
+      delete this.dom[k];
+      if (typeof v.remove == "function") v.remove();
+    }
+  }
+};
+
+export {
+  NumericDensity
+};
+//# sourceMappingURL=chunk-GKLDVEAQ.js.map

package/dist/chunk-GLGFZPWM.js

@@ -0,0 +1,103 @@
+import {
+  SearchHandler,
+  fillTermWrapper,
+  table2col,
+  termsettingInit
+} from "./chunk-JP4IU7DO.js";
+
+// plots/summarizeMutationDiagnosis.ts
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let dictTw;
+  {
+    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
+    if (!t) throw "defaultTw4correlationPlot missing";
+    dictTw = structuredClone(t);
+    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+  }
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "0px 10px 10px 10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Mutation Variable");
+    const searchDiv = td2.append("div");
+    const geneSearchInst = new SearchHandler();
+    geneSearchInst.init({
+      holder: searchDiv,
+      app: chartsInstance.app,
+      // required to supply "opts.app.vocabApi" for the search ui
+      genomeObj: chartsInstance.app.opts.genome,
+      msg: "Hit ENTER to launch plot.",
+      /* the geneTw below is used as it comes, so a grouping the user built for this gene
+      elsewhere can be offered here, see keepsQ in client/termdb/TermTypeSearch.ts */
+      keepsQ: true,
+      callback: async (geneTw) => {
+        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
+        launchPlot({
+          tw1: dictTw,
+          tw2: geneTw,
+          chartsInstance,
+          holder
+        });
+      }
+    });
+    searchDiv.style("padding", "0px 0px 5px 0px");
+  }
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Compare Mutations Against");
+    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
+    const pill = await termsettingInit({
+      menuOptions: "{edit,replace}",
+      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
+      target="filter" works for gdc since in gdc ds it is overriding filter to dict
+      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
+      maybe this is okay for non-gdc ds as the default dictTw is meaningful
+      */
+      usecase: { target: "filter" },
+      vocabApi: chartsInstance.app.vocabApi,
+      holder: pillDiv,
+      callback: async (tw) => {
+        waitDiv.text("LOADING ...");
+        try {
+          await pill.main(tw);
+          dictTw = tw;
+          waitDiv.text("Click to edit/replace the variable before searching gene.");
+        } catch (e) {
+          waitDiv.text("Error: " + (e.message || e));
+        }
+      }
+    });
+    try {
+      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+      await pill.main(dictTw);
+      waitDiv.text("Click to edit/replace the variable before searching gene.");
+    } catch (e) {
+      waitDiv.text("Error: " + (e.message || e));
+    }
+  }
+}
+function launchPlot({ tw1, tw2, chartsInstance, holder }) {
+  const chart = {
+    config: {
+      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
+      // TODO define sandbox header with gene+term name
+      term: tw1,
+      term2: tw2
+    }
+  };
+  chartsInstance.plotCreate(chart);
+  holder.selectAll("*").remove();
+  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
+  setTimeout(() => {
+    holder.style("display", "none");
+  }, 1e3);
+}
+
+export {
+  makeChartBtnMenu,
+  launchPlot
+};
+//# sourceMappingURL=chunk-GLGFZPWM.js.map

package/dist/chunk-HKXQA27S.js

@@ -0,0 +1,305 @@
+import {
+  appear2 as appear,
+  axisstyle,
+  bwSetting,
+  disappear2 as disappear,
+  makeNumericAxisConfig,
+  rgb2hex
+} from "./chunk-JP4IU7DO.js";
+import {
+  dofetch3
+} from "./chunk-4TJO2DGU.js";
+import {
+  axisLeft
+} from "./chunk-WJLRU5OF.js";
+import {
+  format,
+  linear
+} from "./chunk-4OLM3KSB.js";
+
+// src/block.tk.bigwig.js
+function bigwigfromtemplate(tk, template) {
+  tk.scale = {};
+  if (template.scale) {
+    for (const k in template.scale) {
+      tk.scale[k] = template.scale[k];
+    }
+  } else {
+    tk.scale.auto = 1;
+  }
+  if (tk.normalize) {
+  } else {
+    tk.normalize = {
+      dividefactor: 1,
+      disable: 1
+    };
+  }
+  tk.barheight = template.height || 50;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  if (!tk.ncolor) tk.ncolor = "#BD005E";
+  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
+  if (!tk.pcolor) tk.pcolor = "#005EBD";
+  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
+}
+function bigwigmaketk(tk, block) {
+  tk.img = tk.glider.append("image");
+  tk.tklabel.attr("y", tk.barheight / 2);
+  tk.leftaxis = tk.gleft.append("g");
+  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
+    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
+  });
+}
+async function bigwigload(tk, block) {
+  block.tkcloakon(tk);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
+  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  tk.img.attr("width", block.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    let data;
+    if (tk.imgData) {
+      data = tk.imgData;
+    } else {
+      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    }
+    if (data.error) throw data.error;
+    if (!data.src) throw "data.src missing";
+    tk.img.attr("xlink:href", data.src);
+    if (data.minv != void 0) {
+      tk.scale.min = data.minv;
+    }
+    if (data.maxv != void 0) {
+      tk.scale.max = data.maxv;
+    }
+    const sameMinMax = tk.scale.min == tk.scale.max;
+    tk.tklabel.transition().attr("y", !data.nodata && sameMinMax ? block.labelfontsize / 2 : tk.barheight / 2);
+    tk.leftaxis.selectAll("*").remove();
+    if (data.nodata) {
+      throw "No data in view range";
+    }
+    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
+    const axis = axisLeft().scale(scale).tickValues(sameMinMax ? [tk.scale.min] : [tk.scale.min, tk.scale.max]);
+    if (tk.integer4axis) {
+      axis.tickFormat(format("d"));
+    } else if (sameMinMax) {
+      axis.tickFormat(format("~g"));
+    }
+    axisstyle({
+      axis: tk.leftaxis.call(axis),
+      color: "black",
+      showline: true
+    });
+  } catch (err) {
+    tk.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff(tk, { error: errtext });
+    block.block_setheight();
+    for (const panel of tk.subpanels) {
+      bigwigloadsubpanel(tk, block, panel);
+    }
+  }
+}
+async function bigwigloadsubpanel(tk, block, panel) {
+  block.tkcloakon_subpanel(panel);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) {
+    par.dotplotfactor = tk.dotplotfactor;
+  }
+  par.width = panel.width;
+  par.rglst = [
+    {
+      chr: panel.chr,
+      start: panel.start,
+      stop: panel.stop,
+      width: panel.width
+    }
+  ];
+  delete par.percentile;
+  delete par.autoscale;
+  panel.img.attr("width", panel.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    if (tk.imgData) throw "subpanel not supported by imgData yet";
+    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    if (data.error) throw data.error;
+    panel.img.attr("xlink:href", data.src);
+  } catch (err) {
+    panel.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff_subpanel(panel, { error: errtext });
+  }
+}
+function bigwigconfigpanel(tk, block, holder, loader) {
+  const config = {
+    pcolor: {},
+    ncolor: {},
+    pcolor2: {},
+    ncolor2: {},
+    // .row
+    // .lab
+    dotplot: {},
+    // .row
+    dividefactor: {}
+  };
+  {
+    const row = holder.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Height  ");
+    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
+      if (event.code != "Enter") return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseInt(s);
+      if (Number.isNaN(v) || v <= 1) {
+        alert("track height must be positive integer");
+        return;
+      }
+      tk.barheight = v;
+      loader(bwSetting.height);
+    });
+  }
+  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
+  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
+    tk.pcolor = event.target.value;
+    loader(bwSetting.pcolor);
+  });
+  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
+  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
+    tk.ncolor = event.target.value;
+    loader(bwSetting.ncolor);
+  });
+  if (!tk.scale.auto) {
+    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
+    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
+      tk.pcolor2 = event.target.value;
+      loader(bwSetting.pcolor2);
+    });
+    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
+    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
+      tk.ncolor2 = event.target.value;
+      loader(bwSetting.ncolor2);
+    });
+  }
+  {
+    const setting = {};
+    if (tk.scale.auto) {
+      setting.auto = 1;
+    } else if (tk.scale.percentile) {
+      setting.percentile = tk.scale.percentile;
+    } else {
+      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
+    }
+    makeNumericAxisConfig({
+      holder: holder.append("div").style("margin-bottom", "15px"),
+      setting,
+      callback: (s) => {
+        if (s.auto) {
+          tk.scale.auto = 1;
+          loader(bwSetting.autoscale);
+          return;
+        }
+        if (s.fixed) {
+          delete tk.scale.auto;
+          delete tk.scale.percentile;
+          tk.scale.max = s.fixed.max;
+          tk.scale.min = s.fixed.min;
+          loader(bwSetting.fixedscale);
+          return;
+        }
+        delete tk.scale.auto;
+        tk.scale.percentile = s.percentile;
+        loader(bwSetting.percentilescale);
+      }
+    });
+  }
+  {
+    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
+    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
+    const s = config.dotplot.row.append("select").on("change", (event) => {
+      const i = event.target.selectedIndex;
+      if (i == 0) {
+        delete tk.dotplotfactor;
+      } else {
+        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
+      }
+      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
+    });
+    let o = s.append("option").text("no");
+    if (!tk.dotplotfactor) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("5");
+    if (tk.dotplotfactor == 5) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("10");
+    if (tk.dotplotfactor == 10) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("15");
+    if (tk.dotplotfactor == 15) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("20");
+    if (tk.dotplotfactor == 20) {
+      o.property("selected", 1);
+    }
+  }
+  config.dividefactor.row = holder.append("div");
+  {
+    const id = Math.random().toString();
+    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
+    if (!tk.normalize.disable) {
+      input.property("checked", 1);
+    }
+    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
+    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
+    folder.append("span").html("Divide raw value by&nbsp;");
+    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      const v = event.target.value;
+      if (v <= 0) {
+        return;
+      }
+      tk.normalize.dividefactor = v;
+      loader(bwSetting.usedividefactor);
+    });
+    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
+    input.on("change", (event) => {
+      if (event.target.checked) {
+        appear(folder);
+        delete tk.normalize.disable;
+        factorinput.property("value", tk.normalize.dividefactor);
+        loader(bwSetting.usedividefactor);
+        return;
+      }
+      disappear(folder);
+      tk.normalize.disable = 1;
+      loader(bwSetting.nodividefactor);
+    });
+  }
+  return config;
+}
+
+export {
+  bigwigfromtemplate,
+  bigwigmaketk,
+  bigwigload,
+  bigwigloadsubpanel,
+  bigwigconfigpanel
+};
+//# sourceMappingURL=chunk-HKXQA27S.js.map

package/dist/chunk-HKXQA27S.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/block.tk.bigwig.js"],
+  "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport * as client from './client'\nimport { dofetch3 } from '#common/dofetch'\nimport { format as d3format } from 'd3-format'\nimport { makeNumericAxisConfig } from '#dom/numericAxis'\n\n/*\nFIXME\nbigwigloadsubpanel should return promise and be tracked\n*/\n\nexport function bigwigfromtemplate(tk, template) {\n\ttk.scale = {}\n\tif (template.scale) {\n\t\tfor (const k in template.scale) {\n\t\t\ttk.scale[k] = template.scale[k]\n\t\t}\n\t} else {\n\t\ttk.scale.auto = 1\n\t}\n\n\tif (tk.normalize) {\n\t} else {\n\t\t// disable by default\n\t\ttk.normalize = {\n\t\t\tdividefactor: 1,\n\t\t\tdisable: 1\n\t\t}\n\t}\n\ttk.barheight = template.height || 50\n\ttk.height_main = tk.toppad + tk.barheight + tk.bottompad\n\tif (!tk.ncolor) tk.ncolor = '#BD005E'\n\tif (!tk.ncolor2) tk.ncolor2 = '#5E00BD'\n\tif (!tk.pcolor) tk.pcolor = '#005EBD'\n\tif (!tk.pcolor2) tk.pcolor2 = '#FA7D00'\n}\n\nexport function bigwigmaketk(tk, block) {\n\ttk.img = tk.glider.append('image')\n\ttk.tklabel.attr('y', tk.barheight / 2)\n\n\ttk.leftaxis = tk.gleft.append('g')\n\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\t\tbigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block))\n\t})\n}\n\nexport async function bigwigload(tk, block) {\n\t/*\n\tcalled by change view range\n\tor updating any rendering style, e.g. height\n\t*/\n\tblock.tkcloakon(tk)\n\tconst par = block.tkarg_q(tk)\n\tif (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor\n\tif (tk.bgcolor) par.bgcolor = tk.bgcolor // bg colors for loci with a valid numerical value, useful when low values are cared about e.g. in dna methylation beta value\n\n\ttk.height_main = tk.toppad + tk.barheight + tk.bottompad\n\ttk.img.attr('width', block.width).attr('height', tk.barheight)\n\n\tlet errtext\n\ttry {\n\t\tlet data\n\t\tif (tk.imgData) {\n\t\t\tdata = tk.imgData // premade data; same structure as below\n\t\t} else {\n\t\t\tdata = await dofetch3('tkbigwig', { method: 'POST', body: JSON.stringify(par) })\n\t\t}\n\t\tif (data.error) throw data.error\n\t\tif (!data.src) throw 'data.src missing'\n\n\t\ttk.img.attr('xlink:href', data.src)\n\n\t\tif (data.minv != undefined) {\n\t\t\ttk.scale.min = data.minv\n\t\t}\n\t\tif (data.maxv != undefined) {\n\t\t\ttk.scale.max = data.maxv\n\t\t}\n\n\t\t// when min=max, the axis has a sole tick in the middle\n\t\tconst sameMinMax = tk.scale.min == tk.scale.max\n\n\t\t// in case height changed\n\t\t// with a sole tick in the middle, move the label up to not overlap with it\n\t\ttk.tklabel.transition().attr('y', !data.nodata && sameMinMax ? block.labelfontsize / 2 : tk.barheight / 2)\n\n\t\ttk.leftaxis.selectAll('*').remove()\n\n\t\tif (data.nodata) {\n\t\t\tthrow 'No data in view range'\n\t\t\t// won't update axis\n\t\t}\n\n\t\t// update axis\n\t\tconst scale = scaleLinear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0])\n\n\t\tconst axis = d3axis\n\t\t\t.axisLeft()\n\t\t\t.scale(scale)\n\t\t\t.tickValues(sameMinMax ? [tk.scale.min] : [tk.scale.min, tk.scale.max])\n\n\t\tif (tk.integer4axis) {\n\t\t\taxis.tickFormat(d3format('d'))\n\t\t} else if (sameMinMax) {\n\t\t\t// the default format of a zero-span scale shows 0 as 0.000000\n\t\t\taxis.tickFormat(d3format('~g'))\n\t\t}\n\n\t\tclient.axisstyle({\n\t\t\taxis: tk.leftaxis.call(axis),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t} catch (err) {\n\t\ttk.img.attr('width', 0).attr('height', 0)\n\t\tif (err.stack) {\n\t\t\t// error\n\t\t\tconsole.log(err.stack)\n\t\t}\n\t\terrtext = typeof err == 'string' ? err : err.message\n\t} finally {\n\t\tblock.tkcloakoff(tk, { error: errtext })\n\t\tblock.block_setheight()\n\n\t\t// also load subpanels whenever main panel updates\n\t\tfor (const panel of tk.subpanels) {\n\t\t\tbigwigloadsubpanel(tk, block, panel)\n\t\t}\n\t}\n}\n\nexport async function bigwigloadsubpanel(tk, block, panel) {\n\tblock.tkcloakon_subpanel(panel)\n\tconst par = block.tkarg_q(tk)\n\tif (tk.dotplotfactor) {\n\t\tpar.dotplotfactor = tk.dotplotfactor\n\t}\n\tpar.width = panel.width\n\tpar.rglst = [\n\t\t{\n\t\t\tchr: panel.chr,\n\t\t\tstart: panel.start,\n\t\t\tstop: panel.stop,\n\t\t\twidth: panel.width\n\t\t}\n\t]\n\tdelete par.percentile\n\tdelete par.autoscale\n\n\tpanel.img.attr('width', panel.width).attr('height', tk.barheight)\n\n\tlet errtext\n\ttry {\n\t\tif (tk.imgData) throw 'subpanel not supported by imgData yet'\n\t\tconst data = await dofetch3('tkbigwig', { method: 'POST', body: JSON.stringify(par) })\n\t\tif (data.error) throw data.error\n\t\tpanel.img.attr('xlink:href', data.src)\n\t} catch (err) {\n\t\tpanel.img.attr('width', 0).attr('height', 0)\n\t\tif (err.stack) {\n\t\t\t// error\n\t\t\tconsole.log(err.stack)\n\t\t}\n\t\terrtext = typeof err == 'string' ? err : err.message\n\t} finally {\n\t\tblock.tkcloakoff_subpanel(panel, { error: errtext })\n\t}\n}\n\nexport function bigwigconfigpanel(tk, block, holder, loader) {\n\t// provide hooks to each component, so that caller can choose to hide certain ones\n\tconst config = {\n\t\tpcolor: {},\n\t\tncolor: {},\n\t\tpcolor2: {},\n\t\tncolor2: {},\n\t\t// .row\n\t\t// .lab\n\n\t\tdotplot: {},\n\t\t// .row\n\n\t\tdividefactor: {}\n\t}\n\n\t// height\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').html('Height&nbsp;&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('size', 5)\n\t\t\t.property('value', tk.barheight)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter') return\n\t\t\t\tconst s = event.target.value\n\t\t\t\tif (s == '') return\n\t\t\t\tconst v = Number.parseInt(s)\n\t\t\t\tif (Number.isNaN(v) || v <= 1) {\n\t\t\t\t\talert('track height must be positive integer')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.barheight = v\n\t\t\t\tloader(client.bwSetting.height)\n\t\t\t})\n\t}\n\n\t// pcolor\n\tconfig.pcolor.row = holder.append('div').style('margin-bottom', '15px')\n\tconfig.pcolor.lab = config.pcolor.row.append('span').text('Positive value color').style('padding-right', '10px')\n\tconfig.pcolor.row\n\t\t.append('input')\n\t\t.attr('type', 'color')\n\t\t.property('value', client.rgb2hex(tk.pcolor))\n\t\t.on('change', event => {\n\t\t\ttk.pcolor = event.target.value\n\t\t\tloader(client.bwSetting.pcolor)\n\t\t})\n\n\t// ncolor\n\tconfig.ncolor.row = holder.append('div').style('margin-bottom', '15px')\n\tconfig.ncolor.lab = config.ncolor.row.append('span').text('Negative value color').style('padding-right', '10px')\n\tconfig.ncolor.row\n\t\t.append('input')\n\t\t.attr('type', 'color')\n\t\t.property('value', client.rgb2hex(tk.ncolor))\n\t\t.on('change', event => {\n\t\t\ttk.ncolor = event.target.value\n\t\t\tloader(client.bwSetting.ncolor)\n\t\t})\n\n\tif (!tk.scale.auto) {\n\t\t// pcolor2\n\t\tconfig.pcolor2.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.pcolor2.lab = config.pcolor2.row.append('span').html('&ge;Max color').style('padding-right', '10px')\n\t\tconfig.pcolor2.row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', client.rgb2hex(tk.pcolor2))\n\t\t\t.on('change', event => {\n\t\t\t\ttk.pcolor2 = event.target.value\n\t\t\t\tloader(client.bwSetting.pcolor2)\n\t\t\t})\n\t\t// ncolor2\n\t\tconfig.ncolor2.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.ncolor2.lab = config.ncolor2.row.append('span').html('&le;Min color').style('padding-right', '10px')\n\t\tconfig.ncolor2.row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', client.rgb2hex(tk.ncolor2))\n\t\t\t.on('change', event => {\n\t\t\t\ttk.ncolor2 = event.target.value\n\t\t\t\tloader(client.bwSetting.ncolor2)\n\t\t\t})\n\t}\n\n\t// y-scale\n\t{\n\t\tconst setting = {}\n\t\tif (tk.scale.auto) {\n\t\t\tsetting.auto = 1\n\t\t} else if (tk.scale.percentile) {\n\t\t\tsetting.percentile = tk.scale.percentile\n\t\t} else {\n\t\t\tsetting.fixed = { min: tk.scale.min, max: tk.scale.max }\n\t\t}\n\t\tmakeNumericAxisConfig({\n\t\t\tholder: holder.append('div').style('margin-bottom', '15px'),\n\t\t\tsetting,\n\t\t\tcallback: s => {\n\t\t\t\tif (s.auto) {\n\t\t\t\t\ttk.scale.auto = 1\n\t\t\t\t\tloader(client.bwSetting.autoscale)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (s.fixed) {\n\t\t\t\t\tdelete tk.scale.auto\n\t\t\t\t\tdelete tk.scale.percentile\n\t\t\t\t\ttk.scale.max = s.fixed.max\n\t\t\t\t\ttk.scale.min = s.fixed.min\n\t\t\t\t\tloader(client.bwSetting.fixedscale)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tdelete tk.scale.auto\n\t\t\t\ttk.scale.percentile = s.percentile\n\t\t\t\tloader(client.bwSetting.percentilescale)\n\t\t\t}\n\t\t})\n\t}\n\n\t// dot plot\n\t{\n\t\tconfig.dotplot.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.dotplot.row.append('span').html('Dot plot&nbsp;&nbsp;')\n\t\tconst s = config.dotplot.row.append('select').on('change', event => {\n\t\t\tconst i = event.target.selectedIndex\n\t\t\tif (i == 0) {\n\t\t\t\tdelete tk.dotplotfactor\n\t\t\t} else {\n\t\t\t\ttk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML)\n\t\t\t}\n\t\t\tloader(i == 0 ? client.bwSetting.nodotplot : client.bwSetting.usedotplot)\n\t\t})\n\t\tlet o = s.append('option').text('no')\n\t\tif (!tk.dotplotfactor) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('5')\n\t\tif (tk.dotplotfactor == 5) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('10')\n\t\tif (tk.dotplotfactor == 10) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('15')\n\t\tif (tk.dotplotfactor == 15) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('20')\n\t\tif (tk.dotplotfactor == 20) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t}\n\n\t// normalization using a divide-by factor\n\tconfig.dividefactor.row = holder.append('div')\n\t//.style('margin-bottom','15px')\n\t{\n\t\tconst id = Math.random().toString()\n\t\tconst input = config.dividefactor.row.append('input').attr('type', 'checkbox').attr('id', id)\n\t\tif (!tk.normalize.disable) {\n\t\t\tinput.property('checked', 1)\n\t\t}\n\t\tconfig.dividefactor.row.append('label').html('&nbsp;Apply normalization').attr('for', id)\n\n\t\tconst folder = config.dividefactor.row\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px 10px 0px 20px')\n\t\t\t.style('display', tk.normalize.disable ? 'none' : 'block')\n\t\tfolder.append('span').html('Divide raw value by&nbsp;')\n\t\tconst factorinput = folder\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('width', '60px')\n\t\t\t.property('value', tk.normalize.dividefactor)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tconst v = event.target.value\n\t\t\t\tif (v <= 0) {\n\t\t\t\t\t// don't allow\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.normalize.dividefactor = v\n\t\t\t\tloader(client.bwSetting.usedividefactor)\n\t\t\t})\n\t\tfolder.append('div').text('Enter a value above zero').style('font-size', '.7em').style('color', '#858585')\n\t\tinput.on('change', event => {\n\t\t\tif (event.target.checked) {\n\t\t\t\tclient.appear(folder)\n\t\t\t\tdelete tk.normalize.disable\n\t\t\t\tfactorinput.property('value', tk.normalize.dividefactor)\n\t\t\t\tloader(client.bwSetting.usedividefactor)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tclient.disappear(folder)\n\t\t\ttk.normalize.disable = 1\n\t\t\tloader(client.bwSetting.nodividefactor)\n\t\t})\n\t}\n\treturn config\n}\n"],
+  "mappings": 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+}