@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/Disco.UI-MQ7WZQOP.js

@@ -0,0 +1,239 @@
+import {
+  launch
+} from "./chunk-FCQPQD7Z.js";
+import {
+  makeBtn,
+  makeFileUpload,
+  makeGenomeDropDown,
+  makePrompt,
+  makeResetBtn,
+  makeTextAreaInput
+} from "./chunk-5EBRF6Z7.js";
+import "./chunk-7E37WMAX.js";
+import "./chunk-2E3AJFOA.js";
+import "./chunk-4E2F26CC.js";
+import "./chunk-7NVFEGCE.js";
+import {
+  Tabs,
+  appear,
+  sayerror
+} from "./chunk-CXCAQOFB.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-ILAYJZBC.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/disco/Disco.UI.ts
+function init_discoplotUI(holder, genomes, debugmode) {
+  const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
+    "font-family",
+    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
+  ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true).classed("sjpp-disco-ui", true);
+  const obj = {
+    data: []
+  };
+  makePrompt(wrapper, "Select Genome").style("font-size", "1.15em").style("padding", "10px 0px").style("color", "#003366");
+  genomeSelection(wrapper, genomes, obj);
+  makePrompt(wrapper, "Provide Data").style("font-size", "1.15em").style("padding", "10px 0px 5px 0px").style("color", "#003366");
+  wrapper.append("div").style("opacity", 0.75).style("padding", "10px 10px 15px 20px").style("width", "65vw").style("line-height", "1.5em").html(
+    '<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>'
+  );
+  const dataTypeTabs_div = wrapper.append("div").style("margin-left", "2vw");
+  makeDataTypeTabs(dataTypeTabs_div, obj);
+  const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("padding", "15px 0px");
+  submitButton(controlBtns_div, obj, genomes, wrapper, holder);
+  makeResetBtn(controlBtns_div, obj, ".disco_input");
+  if (debugmode) window["doms"] = obj;
+  return obj;
+}
+function genomeSelection(div, genomes, obj) {
+  const genome_div = div.append("div").style("margin-left", "40px");
+  const g = makeGenomeDropDown(genome_div, genomes).style("border", "1px solid rgb(138, 177, 212)");
+  obj.genome = g.node();
+}
+function makeDataTypeTabs(dataTypeTabs_div, obj) {
+  const tabs = [
+    {
+      label: "SNV Indel",
+      active: true,
+      callback: async (event, dataTypeTab) => {
+        dataTypeTab.key = "snv";
+        const listHTML = `<ol>
+					<li>chr</li>
+					<li>position</li>
+					<li>gene</li>
+					<li>aachange</li>
+					<li>class</li>
+					<li>DNA total reads (optional)</li>
+					<li>DNA alt reads (optional)</li>
+					<li>RNA total reads (optional)</li>
+					<li>RNA alt reads (optional)</li></ol>
+					<p>Example:</p>
+<pre style="margin-left: 10px;">
+chr1	226252135	H3F3A	K28M	M	100	25	80	16
+chr2	98765432	TestGene	TestMutation	F
+</pre>`;
+        mainTabCallback(dataTypeTab, obj, listHTML);
+      }
+    },
+    {
+      label: "SV",
+      active: false,
+      callback: async (event, dataTypeTab) => {
+        dataTypeTab.key = "sv";
+        const listHTML = `<ol>
+					<li>chrA</li>
+					<li>posA</li>
+					<li>geneA (optional)</li>
+					<li>chrB</li>
+					<li>posB</li>
+					<li>geneB (optional)</li>
+				</ol>
+				<p>Example (with genes):</p>
+<pre style="margin-left: 10px;">
+chr6	3067605	MDC1	chr12	61521661	KMT2D
+</pre>
+				<p>Example (without genes):</p>
+<pre style="margin-left: 10px;">
+chr6	3067605	chr12	61521661
+</pre>`;
+        mainTabCallback(dataTypeTab, obj, listHTML);
+      }
+    },
+    {
+      label: "CNV",
+      active: false,
+      callback: async (event, dataTypeTab) => {
+        dataTypeTab.key = "cnv";
+        const listHTML = `<ol>
+				<li>chr</li>
+				<li>start</li>
+				<li>stop</li>
+				<li>value</li>
+				</ol>
+				<p>Example:</p>
+<pre style="margin-left: 10px;">
+chr1	1	100000000	0.5
+chr1	100000000	200000000	-0.5
+</pre>`;
+        mainTabCallback(dataTypeTab, obj, listHTML);
+      }
+    }
+  ];
+  new Tabs({ holder: dataTypeTabs_div, tabs, tabsPosition: "vertical", linePosition: "right" }).main();
+}
+function mainTabCallback(dataTypeTab, obj, listHTML) {
+  dataTypeTab.contentHolder.style("border", "none").style("display", "block").style("padding-left", "30px");
+  makeDataInputTabs(dataTypeTab, obj);
+  dataTypeTab.contentHolder.append("div").style("padding", "15px 0px 0px 10px").style("opacity", 0.75).text(`Provide ${dataTypeTab.label} data in tab delimited format with the following columns:`).append("span").html(listHTML);
+  delete dataTypeTab.callback;
+}
+function makeDataInputTabs(dataTypeTab, obj) {
+  const width = 95;
+  const tabs = [
+    // //TODO: implement file upload and file path input once launch.adhoc is ready
+    {
+      label: "Select File",
+      active: true,
+      width,
+      callback: async (event, tab) => {
+        const key = dataTypeTab.key;
+        tab.contentHolder.style("border", "none").style("display", "block");
+        appear(tab.contentHolder);
+        tab.contentHolder.append("div").style("padding", "0px 0px 5px 15px").style("opacity", 0.65).text(`Select a local file`);
+        makeFileUpload2(tab, obj, key);
+        delete tab.callback;
+      }
+    },
+    // {
+    // 	label: 'File Path',
+    // 	active: false,
+    // 	width,
+    // 	callback: async (tab: Tab) => {
+    // 		const key = dataTypeTab.key
+    // 		tab.contentHolder.style('border', 'none').style('display', 'block')
+    // 		appear(tab.contentHolder)
+    // 		tab.contentHolder
+    // 			.append('div')
+    // 			.html(`<p style="margin-left: 10px; opacity: 0.65;">Provide a URL file path.</p>`)
+    // 		uiutils.makePrompt(tab.contentHolder, 'URL')
+    // 		makeTextEntryFilePathInput(tab.contentHolder, obj, key)
+    // 		delete tab.callback
+    // 	}
+    // },
+    {
+      label: "Paste Data",
+      active: false,
+      width,
+      callback: async (event, tab) => {
+        const key = dataTypeTab.key;
+        tab.contentHolder.style("border", "none").style("display", "block");
+        appear(tab.contentHolder);
+        makeCopyPasteInput(tab, obj, key);
+        delete tab.callback;
+      }
+    }
+  ];
+  new Tabs({ holder: dataTypeTab.contentHolder, tabs }).main();
+}
+function makeFileUpload2(tab, obj, key) {
+  const upload_div = tab.contentHolder.append("div").style("display", "inline-block");
+  const upload = makeFileUpload(upload_div).classed("disco_input", true);
+  upload.on("change", (event) => {
+    const file = event.target.files[0];
+    const reader = new FileReader();
+    reader.onload = (event2) => {
+      obj.data[key + "Text"] = event2.target.result;
+    };
+    reader.readAsText(file, "utf8");
+  });
+}
+function makeCopyPasteInput(tab, obj, key) {
+  const paste_div = tab.contentHolder.append("div").style("display", "block");
+  const paste = makeTextAreaInput({ div: paste_div, cols: 50 }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("disco_input", true).on("keyup", async () => {
+    obj.data[key + "Text"] = paste.property("value").trim();
+  });
+}
+function submitButton(div, obj, genomes, wrapper, holder) {
+  const submit = makeBtn({ div, text: "Create Disco Plot" });
+  const errorMessage_div = div.append("div");
+  submit.style("margin-right", "10px").style("font-size", "16px").classed("sjpp-ui-submitBtn", true).attr("type", "submit").on("click", () => {
+    if (!obj.data || obj.data == void 0) {
+      const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
+      sayerror(sayerrorDiv, "Please provide data");
+      setTimeout(() => sayerrorDiv.remove(), 2e3);
+    } else {
+      const genomeObj = genomes[obj.genome.options[obj.genome.selectedIndex].text];
+      wrapper.remove();
+      launch(obj.data, genomeObj, holder);
+      backButton(holder, genomes);
+    }
+  });
+}
+function backButton(holder, genomes) {
+  holder.append("button").html("&#171; Back").on("click", () => {
+    holder.selectAll("*").remove();
+    init_discoplotUI(holder, genomes, false);
+  });
+}
+export {
+  init_discoplotUI
+};
+//# sourceMappingURL=Disco.UI-MQ7WZQOP.js.map

package/dist/DmrPlot-MKAKFUJR.js

@@ -0,0 +1,366 @@
+import {
+  DmrViewModel,
+  getDefaultDMRSettings
+} from "./chunk-DYX6B6RN.js";
+import {
+  PlotBase,
+  startElapsedTimer,
+  table2col
+} from "./chunk-CXCAQOFB.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-ILAYJZBC.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch3,
+  formatElapsedTime
+} from "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/dmr/model/DmrModel.ts
+var DmrModel = class {
+  constructor(config, vocab) {
+    this.config = config;
+    this.vocab = vocab;
+  }
+  async fetchDmr(chr, start, stop, signal) {
+    const { group1, group2, settings } = this.config;
+    const { genome, dslabel } = this.vocab;
+    return dofetch3("termdb/dmr", {
+      signal,
+      body: {
+        genome,
+        dslabel,
+        chr,
+        start,
+        stop,
+        group1,
+        group2,
+        lambda: settings.dmr.lambda,
+        C: settings.dmr.C,
+        fdr_cutoff: settings.dmr.fdr_cutoff,
+        group1Name: this.config.group1Name,
+        group2Name: this.config.group2Name,
+        blockWidth: settings.dmr.blockWidth,
+        devicePixelRatio: typeof window !== "undefined" ? window.devicePixelRatio : 1,
+        maxLoessRegion: settings.dmr.maxLoessRegion,
+        colors: settings.dmr.colors,
+        scanChromosomes: this.config.scanChromosomes,
+        backgroundCorrection: this.config.backgroundCorrection,
+        minCpgs: this.config.minCpgs,
+        yAxis: this.config.yAxis,
+        filter0: this.config.filter0
+      }
+    });
+  }
+};
+
+// plots/dmr/view/DmrView.ts
+var DmrView = class {
+  constructor(dom) {
+    this.dom = dom;
+  }
+  async renderBlock(viewData, genomeObj, settings, chr, start, stop, onCoordinateChange) {
+    const { Block } = await import("./block-QKO2PO4A.js");
+    return new Block({
+      holder: this.dom.holder,
+      genome: genomeObj,
+      chr,
+      start,
+      stop,
+      tklst: viewData.tklst,
+      nobox: true,
+      width: settings.blockWidth,
+      onCoordinateChange
+    });
+  }
+  updateTracks(viewData, blockInstance) {
+    for (const tk of blockInstance.tklst) {
+      const updated = viewData.tklst.find((t) => t.name === tk.name);
+      if (!updated) continue;
+      if (tk.type === "bedj" && updated.bedItems) {
+        tk.bedItems = updated.bedItems;
+        blockInstance.tk_load(tk);
+      } else if (tk.type === "bigwig" && updated.imgData) {
+        tk.imgData = updated.imgData;
+        blockInstance.tk_load(tk);
+      }
+    }
+  }
+  updateLegend(blockInstance, legendRows) {
+    if (!blockInstance?.legend?.holder) return;
+    const labels = ["Per-CpG Means", "DMR", "Sig. CpGs"];
+    blockInstance.legend.holder.selectAll("tr").filter((_d, i, nodes) => {
+      const td = nodes[i].querySelector("td");
+      return td && labels.includes(td.textContent);
+    }).remove();
+    this.renderLegend(blockInstance, legendRows);
+  }
+  renderLegend(blockInstance, legendRows) {
+    if (!blockInstance?.legend?.holder) return;
+    const { legendcolor, vpad } = blockInstance.legend;
+    for (const row of legendRows) {
+      const tr = blockInstance.legend.holder.append("tr");
+      tr.append("td").text(row.label).attr("style", `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`);
+      const td = tr.append("td");
+      for (const entry of row.items) {
+        const item = td.append("div").attr("style", `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`);
+        if (entry.style === "shaded") {
+          item.append("div").attr(
+            "style",
+            `display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`
+          );
+        } else if (entry.style === "dashed") {
+          item.append("div").attr(
+            "style",
+            `display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`
+          );
+        } else {
+          item.append("div").attr(
+            "style",
+            `display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`
+          );
+        }
+        item.append("div").attr("style", "display:inline-block;color:#555;font-size:.8em").text(entry.text);
+      }
+    }
+  }
+  renderDiagnostics(diagnostic, dmrs, fdr_cutoff) {
+    const panel = this.dom.diagnosticPanel;
+    panel.selectAll("*").remove();
+    panel.style("display", "block");
+    const { probes } = diagnostic;
+    const toggle = panel.append("div").attr("style", "cursor:default;font-size:12px;color:#888;padding:2px 0");
+    const statsContent = panel.append("div").style("display", "none");
+    let expanded = false;
+    toggle.text("+ Diagnostic details").on("click", () => {
+      expanded = !expanded;
+      toggle.text((expanded ? "\u2212 " : "+ ") + "Diagnostic details");
+      statsContent.style("display", expanded ? "block" : "none");
+    });
+    const spacings = diagnostic.probe_spacings;
+    const medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0;
+    const maxGap = spacings.length ? Math.max(...spacings) : 0;
+    const gapsOver1kb = spacings.filter((s) => s > 1e3).length;
+    const density = probes.positions.length > 1 ? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1e3) : 0;
+    const sigFdrCount = probes.sig.filter(Boolean).length;
+    const minDeltaBeta = 0.05;
+    const sigDualCount = probes.sig.filter((s, i) => {
+      if (!s) return false;
+      const m1 = probes.mean_group1[i];
+      const m2 = probes.mean_group2[i];
+      if (m1 == null || m2 == null) return false;
+      return Math.abs(m2 - m1) >= minDeltaBeta;
+    }).length;
+    const t = table2col({ holder: statsContent, disableScroll: true });
+    for (const [k, v] of [
+      ["Probes in region", String(probes.positions.length)],
+      ["FDR significant", `${sigFdrCount} (FDR < ${fdr_cutoff})`],
+      ["FDR + effect size", `${sigDualCount} (FDR < ${fdr_cutoff} & |\u0394\u03B2| \u2265 ${minDeltaBeta})`],
+      ["Probe density", `${density.toFixed(1)} probes/kb`],
+      ["Median spacing", `${medianSpacing.toFixed(0)} bp`],
+      ["Max gap", `${maxGap.toFixed(0)} bp`],
+      ["Gaps > 1kb", String(gapsOver1kb)],
+      ["DMRs called", String(dmrs.length)],
+      ...diagnostic.total_probes_analyzed ? [["Probes analyzed (genome-wide)", diagnostic.total_probes_analyzed.toLocaleString()]] : [],
+      ...diagnostic.elapsed_ms != null ? [["Analysis time", formatElapsedTime(diagnostic.elapsed_ms)]] : [],
+      ...diagnostic.peak_memory_mb != null ? [["Peak memory", `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : []
+    ]) {
+      t.addRow(k, v);
+    }
+  }
+  showOverlay() {
+    this.dom.loadingOverlay.style("display", "");
+  }
+  hideOverlay() {
+    this.dom.loadingOverlay.style("display", "none");
+  }
+  clearDiagnostics() {
+    this.dom.diagnosticPanel.selectAll("*").remove();
+    this.dom.diagnosticPanel.style("display", "none");
+  }
+  /** The view model's notes, one line each, under the plot */
+  showNotes(notes) {
+    this.dom.note.selectAll("*").remove();
+    for (const text of notes)
+      this.dom.note.append("div").attr("class", "sjpp-dmr-note").style("color", "#666").style("font-size", ".85em").style("padding", "4px 0").style("max-width", "900px").text(text);
+  }
+};
+
+// plots/dmr/DmrPlot.ts
+var LOADING_TEXT = "Running DMR analysis\u2026 A comparison not yet cached first runs DMRcate over the whole genome, which can take minutes.";
+var DmrPlot = class _DmrPlot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _DmrPlot.type;
+    this.blockInstance = null;
+    this.analyzedRegion = null;
+    /** counts the requests that showed the loading text; see showLoading() */
+    this.loadingRequest = 0;
+    const wrapper = opts.holder.append("div").style("position", "relative");
+    const loadingOverlay = wrapper.append("div").attr("class", "sjpp-spinner").style("display", "none").style("position", "absolute").style("z-index", "10").style("background-color", "rgba(255,255,255,0.65)");
+    this.dom = {
+      header: opts?.header,
+      holder: wrapper.append("div"),
+      loadingOverlay,
+      error: opts.holder.append("div"),
+      note: opts.holder.append("div"),
+      loading: opts.holder.append("div").style("display", "none"),
+      diagnosticPanel: opts.holder.append("div").style("display", "none")
+    };
+    this.view = new DmrView(this.dom);
+  }
+  static {
+    this.type = "dmr";
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw new Error(`No plot with id='${this.id}' found`);
+    return { config };
+  }
+  async init(appState) {
+    const { config } = this.getState(appState);
+    validateConfig(config);
+    if (this.dom.header) this.dom.header.text(config.headerText || "DMR Analysis");
+    this.genomeObj = this.app.opts.genome;
+    this.model = new DmrModel(config, this.app.vocabApi.vocab);
+  }
+  async main() {
+    const config = this.state.config;
+    this.model = new DmrModel(config, this.app.vocabApi.vocab);
+    const c = config.coordinateOverride;
+    if (!c) return;
+    const pad = config.settings.dmr.pad;
+    const chr = c.chr;
+    const start = Math.max(0, Number(c.start) - pad);
+    const stop = Number(c.stop) + pad;
+    const a = this.analyzedRegion;
+    const coordsChanged = a && (chr !== a.chr || start !== a.start || stop !== a.stop);
+    if (a && coordsChanged) {
+      this.view.showOverlay();
+      const hideLoading = this.showLoading();
+      try {
+        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
+        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
+        if ("error" in dmrResult) throw new Error(dmrResult.error);
+        this.analyzedRegion = { chr, start, stop };
+        const blkRegion = this.blockInstance?.rglst?.[0];
+        const viewStart = blkRegion?.start ?? start;
+        const viewStop = blkRegion?.stop ?? stop;
+        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop);
+        this.view.updateTracks(vm.viewData, this.blockInstance);
+        this.view.updateLegend(this.blockInstance, vm.viewData.legendRows);
+        this.view.showNotes(vm.viewData.notes);
+        this.view.clearDiagnostics();
+        if (vm.viewData.diagnostic)
+          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
+      } catch (e) {
+        if (this.app.isAbortError(e)) return;
+        this.view.hideOverlay();
+        throw e;
+      } finally {
+        hideLoading();
+      }
+      this.view.hideOverlay();
+    } else {
+      this.dom.holder.selectAll("*").remove();
+      const hideLoading = this.showLoading();
+      this.blockInstance = null;
+      try {
+        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
+        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
+        if ("error" in dmrResult) throw new Error(dmrResult.error);
+        this.analyzedRegion = { chr, start, stop };
+        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop);
+        this.blockInstance = await this.view.renderBlock(
+          vm.viewData,
+          this.genomeObj,
+          config.settings.dmr,
+          chr,
+          start,
+          stop,
+          (rglst) => this.onBlockCoordinateChange(rglst)
+        );
+        this.view.renderLegend(this.blockInstance, vm.viewData.legendRows);
+        this.view.showNotes(vm.viewData.notes);
+        if (vm.viewData.diagnostic)
+          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
+      } catch (e) {
+        if (this.app.isAbortError(e)) return;
+        throw e;
+      } finally {
+        hideLoading();
+      }
+    }
+  }
+  /** Shows the loading text with its elapsed timer. The returned cleanup stops this request's timer and hides the text
+   * only when no newer request has shown it since: an aborted request ending late must not hide a newer one's. */
+  showLoading() {
+    const request = ++this.loadingRequest;
+    this.dom.loading.style("display", "block");
+    const stopTimer = startElapsedTimer(this.dom.loading, LOADING_TEXT);
+    return () => {
+      stopTimer();
+      if (request == this.loadingRequest) this.dom.loading.style("display", "none");
+    };
+  }
+  onBlockCoordinateChange(rglst) {
+    if (!this.analyzedRegion || !rglst.length) return;
+    const r = rglst[0];
+    if (r.start >= r.stop || r.start < 0) return;
+    const a = this.analyzedRegion;
+    if (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return;
+    this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }
+    });
+  }
+};
+var componentInit = getCompInit(DmrPlot);
+function getPlotConfig(opts, app) {
+  validateConfig(opts);
+  const config = {
+    settings: {
+      // app is passed through so the defaults can tell a CpG-level dataset from an
+      // element-level one; opts alone does not carry termdbConfig
+      dmr: getDefaultDMRSettings({ ...opts, app })
+    }
+  };
+  return copyMerge(config, opts);
+}
+function validateConfig(opts) {
+  if (!opts.coordinateOverride) throw new Error("coordinateOverride (chr/start/stop) is required for DMR plot");
+  if (!opts.group1) throw new Error("group1 is required for DMR plot");
+  if (!opts.group2) throw new Error("group2 is required for DMR plot");
+}
+function checkRegionSize(span, maxRegionSize) {
+  if (span > maxRegionSize) {
+    const mbLimit = (maxRegionSize / 1e6).toFixed(0);
+    const mbSpan = (span / 1e6).toFixed(1);
+    throw new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`);
+  }
+}
+export {
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DmrPlot-MKAKFUJR.js.map